[med-svn] [lamarc] 05/07: New upstream version 2.1.10.1+dfsg
Andreas Tille
tille at debian.org
Thu Jan 4 20:52:59 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository lamarc.
commit 0f706980d6c88a6fa55a2d63a2ca1834aa880bc4
Author: Andreas Tille <tille at debian.org>
Date: Thu Jan 4 21:32:48 2018 +0100
New upstream version 2.1.10.1+dfsg
---
CONTENTS | 71 +
COPYING | 57 +
HISTORY | 97 +
INSTALL | 2 +
MAINTAINER.README | 179 +
Makefile.am | 22 +-
Makefile.in | 10162 +++++++++++++++++++
README | 61 +
aclocal.m4 | 1188 +++
config/{conf.h.in => conf.h} | 70 +-
config/conf.h.in | 5 +-
config/config.guess | 1447 +++
config/config.sub | 1555 +++
config/depcomp | 520 +
config/dynacounter.bash | 138 +
config/install-sh | 316 +
config/missing | 360 +
configure | 7765 ++++++++++++++
configure.ac | 4 +-
depcomp | 520 +
doc/html/changes.html | 15 +-
doc/html/compiling.html | 6 +-
doc/html/converter_cmd.html | 6 +-
doc/html/genetic_map.html | 6 +-
doc/html/index.html | 4 +-
doc/html/mapping.html | 4 +-
doc/html/menu.html | 11 +-
doc/html/panels.html | 8 +-
doc/pipeline.txt | 235 +
doc/wx-osx-notes.txt | 52 +
firstLinuxBuild.sh | 4 +
install-sh | 316 +
makedebug.sh | 26 +
makegcov.sh | 14 +
makeopt.sh | 17 +
missing | 360 +
projects/macos/MacOSPrefix.h | 37 +
projects/macos/MacOSPrefixDebug.h | 68 +
projects/macos/carb.r | 18 +
projects/macos/lam_conv make | Bin 0 -> 85969 bytes
projects/macos/lamarc make | Bin 0 -> 94970 bytes
projects/macos/make_mwerks.pl | 171 +
projects/macos/mwerks_xml_template | 1261 +++
projects/win32/README | 2 +
projects/win32/gui_lam_conv.vcproj | 324 +
projects/win32/lam_conv.vcproj | 183 +
projects/win32/lamarc.vcproj | 433 +
projects/win32/make_vcproj.pl | 174 +
projects/win32/vcproj_template | 126 +
scripts/buildDmg.sh | 134 +
scripts/pyParallel/README | 19 +
scripts/pyParallel/combine_regions.py | 191 +
scripts/pyParallel/combine_replicates.py | 164 +
scripts/pyParallel/divide_data.py | 108 +
scripts/pyParallel/parallelCommon.py | 239 +
.../binutils-2.15.91-20040904-1-src.tar.gz | Bin 0 -> 14507299 bytes
.../xmingw32/gcc-core-3.4.2-20040916-1-src.tar.gz | Bin 0 -> 14096017 bytes
.../xmingw32/gcc-g++-3.4.2-20040916-1-src.tar.gz | Bin 0 -> 3607955 bytes
.../xmingw32/gcc-g77-3.4.2-20040916-1-src.tar.gz | Bin 0 -> 1200272 bytes
scripts/xmingw32/mingw-runtime-3.7.tar.gz | Bin 0 -> 343841 bytes
scripts/xmingw32/w32api-3.2.tar.gz | Bin 0 -> 1530078 bytes
scripts/xmingw32/xmingw32.bat.in | 59 +
scripts/xmingw32/xmingw32.mak | 285 +
scripts/xmingw32/xmingw32.sh.in | 53 +
src/BUGS | 453 -
src/bayeslike/bayesanalyzer_1d.cpp | 22 +-
src/bayeslike/bayesanalyzer_1d.h | 22 +-
src/bayeslike/bayescurve.cpp | 22 +-
src/bayeslike/bayescurve.h | 22 +-
src/bayeslike/bayesparamlike_1d.cpp | 22 +-
src/bayeslike/bayesparamlike_1d.h | 22 +-
src/control/chainmanager.cpp | 22 +-
src/control/chainmanager.h | 22 +-
src/control/chainout.cpp | 22 +-
src/control/chainout.h | 22 +-
src/control/chainpack.cpp | 22 +-
src/control/chainpack.h | 22 +-
src/control/chainparam.cpp | 22 +-
src/control/chainparam.h | 22 +-
src/control/constants.cpp | 22 +-
src/control/constants.h | 22 +-
src/control/definitions.h | 22 +-
src/control/dynatracer.cpp | 26 +-
src/control/dynatracer.h | 26 +-
src/control/errhandling.cpp | 22 +-
src/control/errhandling.h | 22 +-
src/control/lamarc.cpp | 28 +-
src/control/lamarc.h | 22 +-
src/control/regiongammainfo.cpp | 22 +-
src/control/regiongammainfo.h | 22 +-
src/control/registry.cpp | 22 +-
src/control/registry.h | 22 +-
src/control/sumfilehandler.cpp | 28 +-
src/control/sumfilehandler.h | 22 +-
src/control/types.h | 24 +-
src/control/userparam.cpp | 22 +-
src/control/userparam.h | 22 +-
src/control/xmlsum_strings.cpp | 22 +-
src/control/xmlsum_strings.h | 22 +-
src/convErr/gc_cmdfile_err.cpp | 22 +-
src/convErr/gc_cmdfile_err.h | 22 +-
src/convErr/gc_data_missing_err.cpp | 22 +-
src/convErr/gc_data_missing_err.h | 22 +-
src/convErr/gc_errhandling.cpp | 22 +-
src/convErr/gc_errhandling.h | 22 +-
src/convErr/gc_individual_err.cpp | 22 +-
src/convErr/gc_individual_err.h | 22 +-
src/convErr/gc_infile_err.cpp | 22 +-
src/convErr/gc_infile_err.h | 22 +-
src/convErr/gc_locus_err.cpp | 22 +-
src/convErr/gc_locus_err.h | 22 +-
src/convErr/gc_map_err.cpp | 22 +-
src/convErr/gc_map_err.h | 22 +-
src/convErr/gc_phase_err.cpp | 22 +-
src/convErr/gc_phase_err.h | 22 +-
src/convErr/gc_structures_err.cpp | 24 +-
src/convErr/gc_structures_err.h | 22 +-
src/convErr/gc_trait_err.cpp | 22 +-
src/convErr/gc_trait_err.h | 22 +-
src/convModel/cmdfileschema.cpp | 22 +-
src/convModel/cmdfileschema.h | 22 +-
src/convModel/gc_creation_info.cpp | 22 +-
src/convModel/gc_creation_info.h | 22 +-
src/convModel/gc_datastore.cpp | 22 +-
src/convModel/gc_datastore.h | 22 +-
src/convModel/gc_datastore_export.cpp | 22 +-
src/convModel/gc_datastore_files.cpp | 22 +-
src/convModel/gc_datastore_readcmd.cpp | 22 +-
src/convModel/gc_datastore_writebatch.cpp | 22 +-
src/convModel/gc_default.cpp | 22 +-
src/convModel/gc_default.h | 22 +-
src/convModel/gc_dictionary.cpp | 22 +-
src/convModel/gc_dictionary.h | 22 +-
src/convModel/gc_exportable.cpp | 22 +-
src/convModel/gc_exportable.h | 22 +-
src/convModel/gc_file.cpp | 22 +-
src/convModel/gc_file.h | 22 +-
src/convModel/gc_file_info.cpp | 22 +-
src/convModel/gc_file_info.h | 22 +-
src/convModel/gc_id_set.cpp | 22 +-
src/convModel/gc_id_set.h | 22 +-
src/convModel/gc_individual.cpp | 22 +-
src/convModel/gc_individual.h | 22 +-
src/convModel/gc_mapfile.cpp | 22 +-
src/convModel/gc_mapfile.h | 22 +-
src/convModel/gc_migration.cpp | 22 +-
src/convModel/gc_migration.h | 22 +-
src/convModel/gc_panel.cpp | 22 +-
src/convModel/gc_panel.h | 22 +-
src/convModel/gc_parent.cpp | 22 +-
src/convModel/gc_parent.h | 22 +-
src/convModel/gc_phase.cpp | 22 +-
src/convModel/gc_phase.h | 22 +-
src/convModel/gc_phase_info.cpp | 22 +-
src/convModel/gc_phase_info.h | 22 +-
src/convModel/gc_phenotype.cpp | 22 +-
src/convModel/gc_phenotype.h | 22 +-
src/convModel/gc_set_util.cpp | 22 +-
src/convModel/gc_set_util.h | 22 +-
src/convModel/gc_structure_maps.cpp | 26 +-
src/convModel/gc_structure_maps.h | 22 +-
src/convModel/gc_structures.cpp | 58 +-
src/convModel/gc_structures.h | 36 +-
src/convModel/gc_trait.cpp | 22 +-
src/convModel/gc_trait.h | 22 +-
src/convModel/gc_trait_allele.cpp | 22 +-
src/convModel/gc_trait_allele.h | 22 +-
src/convModel/gc_types.cpp | 22 +-
src/convModel/gc_types.h | 22 +-
src/convParse/gc_genotype_resolution.cpp | 22 +-
src/convParse/gc_genotype_resolution.h | 22 +-
src/convParse/gc_loci_match.cpp | 22 +-
src/convParse/gc_loci_match.h | 22 +-
src/convParse/gc_locus.cpp | 22 +-
src/convParse/gc_locus.h | 22 +-
src/convParse/gc_migrate.cpp | 22 +-
src/convParse/gc_migrate.h | 22 +-
src/convParse/gc_parse.cpp | 22 +-
src/convParse/gc_parse.h | 22 +-
src/convParse/gc_parse_block.cpp | 22 +-
src/convParse/gc_parse_block.h | 22 +-
src/convParse/gc_parse_locus.cpp | 22 +-
src/convParse/gc_parse_locus.h | 22 +-
src/convParse/gc_parse_pop.cpp | 22 +-
src/convParse/gc_parse_pop.h | 22 +-
src/convParse/gc_parse_sample.cpp | 22 +-
src/convParse/gc_parse_sample.h | 22 +-
src/convParse/gc_parser.cpp | 22 +-
src/convParse/gc_parser.h | 22 +-
src/convParse/gc_phylip.cpp | 22 +-
src/convParse/gc_phylip.h | 22 +-
src/convParse/gc_pop_match.cpp | 22 +-
src/convParse/gc_pop_match.h | 22 +-
src/convParse/gc_population.cpp | 22 +-
src/convParse/gc_population.h | 22 +-
src/convParse/gc_region.cpp | 22 +-
src/convParse/gc_region.h | 22 +-
src/convParse/gc_sequential_data.cpp | 22 +-
src/convParse/gc_sequential_data.h | 22 +-
src/convParse/tixml_util.cpp | 22 +-
src/convParse/tixml_util.h | 22 +-
src/convStrings/cnv_strings.cpp | 22 +-
src/convStrings/cnv_strings.h | 22 +-
src/convStrings/gc_strings.h | 22 +-
src/convStrings/gc_strings_cmdfile.cpp | 22 +-
src/convStrings/gc_strings_cmdfile.h | 22 +-
src/convStrings/gc_strings_creation.cpp | 22 +-
src/convStrings/gc_strings_creation.h | 22 +-
src/convStrings/gc_strings_data.cpp | 22 +-
src/convStrings/gc_strings_data.h | 22 +-
src/convStrings/gc_strings_err.cpp | 22 +-
src/convStrings/gc_strings_individual.cpp | 22 +-
src/convStrings/gc_strings_individual.h | 22 +-
src/convStrings/gc_strings_infile.cpp | 22 +-
src/convStrings/gc_strings_infile.h | 22 +-
src/convStrings/gc_strings_io.cpp | 22 +-
src/convStrings/gc_strings_io.h | 22 +-
src/convStrings/gc_strings_locus.cpp | 22 +-
src/convStrings/gc_strings_locus.h | 22 +-
src/convStrings/gc_strings_map.cpp | 22 +-
src/convStrings/gc_strings_map.h | 22 +-
src/convStrings/gc_strings_mig.cpp | 22 +-
src/convStrings/gc_strings_mig.h | 22 +-
src/convStrings/gc_strings_parse.cpp | 22 +-
src/convStrings/gc_strings_parse.h | 22 +-
src/convStrings/gc_strings_parse_locus.cpp | 22 +-
src/convStrings/gc_strings_parse_locus.h | 22 +-
src/convStrings/gc_strings_phase.cpp | 22 +-
src/convStrings/gc_strings_phase.h | 22 +-
src/convStrings/gc_strings_pop.cpp | 22 +-
src/convStrings/gc_strings_pop.h | 22 +-
src/convStrings/gc_strings_region.cpp | 22 +-
src/convStrings/gc_strings_region.h | 22 +-
src/convStrings/gc_strings_str_a_m.cpp | 24 +-
src/convStrings/gc_strings_str_n_z.cpp | 22 +-
src/convStrings/gc_strings_structures.cpp | 22 +-
src/convStrings/gc_strings_structures.h | 22 +-
src/convStrings/gc_strings_trait.cpp | 22 +-
src/convStrings/gc_strings_trait.h | 22 +-
src/convUtil/gc_file_util.cpp | 22 +-
src/convUtil/gc_file_util.h | 22 +-
src/conversion/ConverterIf.cpp | 25 +-
src/conversion/ConverterUI.cpp | 25 +-
src/conversion/ConverterUIMain.cpp | 25 +-
src/conversion/Converter_ConverterIf.h | 25 +-
src/conversion/Converter_ConverterUI.h | 25 +-
src/conversion/Converter_DataSourceException.h | 25 +-
src/conversion/Converter_DataSourceIf.h | 25 +-
src/conversion/Converter_HapConverter.h | 25 +-
src/conversion/Converter_IndividualDS.h | 25 +-
src/conversion/Converter_LamarcDS.h | 25 +-
src/conversion/Converter_MigrateConverter.h | 25 +-
src/conversion/Converter_ModelDS.h | 25 +-
src/conversion/Converter_ParserUtil.h | 25 +-
src/conversion/Converter_PhylipConverter.h | 25 +-
src/conversion/Converter_PopulationDS.h | 25 +-
src/conversion/Converter_RegionDS.h | 25 +-
src/conversion/Converter_Sequence.h | 25 +-
src/conversion/Converter_SpaceConverter.h | 25 +-
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src/conversion/Converter_UserFileUtil.h | 25 +-
src/conversion/Converter_XmlParserUtil.h | 25 +-
src/conversion/Converter_types.h | 25 +-
src/conversion/DataSourceException.cpp | 22 +-
src/conversion/DataSourceIf.cpp | 25 +-
src/conversion/HapConverter.cpp | 25 +-
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src/conversion/ParserUtil.cpp | 25 +-
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src/guiconv/gc_locitab.cpp | 22 +-
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src/guiconv/gc_locus_dialogs.cpp | 22 +-
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src/guiconv/gc_logic.cpp | 22 +-
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src/lamarcmenus/traitmodelmenu.cpp | 22 +-
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src/menu/newmenuitems.h | 26 +-
src/menu/setmenuitem.cpp | 22 +-
src/menu/setmenuitem.h | 28 +-
src/menu/togglemenuitem.cpp | 22 +-
src/menu/togglemenuitem.h | 22 +-
src/menu/twodtable.cpp | 24 +-
src/menu/twodtable.h | 22 +-
src/postlike/analyzer.cpp | 22 +-
src/postlike/analyzer.h | 22 +-
src/postlike/derivatives.cpp | 22 +-
src/postlike/likelihood.cpp | 22 +-
src/postlike/likelihood.h | 22 +-
src/postlike/maximizer.cpp | 24 +-
src/postlike/maximizer.h | 22 +-
src/postlike/maximizer_strings.cpp | 22 +-
src/postlike/maximizer_strings.h | 22 +-
src/postlike/plforces.cpp | 22 +-
src/postlike/plforces.h | 56 +-
src/postlike/plotstat.cpp | 22 +-
src/postlike/plotstat.h | 22 +-
src/postlike/profile.cpp | 22 +-
src/report/curvefiles.cpp | 22 +-
src/report/curvefiles.h | 22 +-
src/report/outputfile.cpp | 22 +-
src/report/outputfile.h | 22 +-
src/report/reportpage.cpp | 22 +-
src/report/reportpage.h | 26 +-
src/report/runreport.cpp | 22 +-
src/report/runreport.h | 22 +-
src/report/spreadsheet.cpp | 22 +-
src/report/spreadsheet.h | 22 +-
src/report/xml_report.cpp | 22 +-
src/report/xml_report.h | 22 +-
src/tools/mathx.cpp | 25 +-
src/tools/mathx.h | 22 +-
src/tools/random.cpp | 22 +-
src/tools/random.h | 22 +-
src/tools/rangex.cpp | 22 +-
src/tools/rangex.h | 22 +-
src/tools/stringx.cpp | 23 +-
src/tools/stringx.h | 22 +-
src/tools/timex.cpp | 22 +-
src/tools/timex.h | 22 +-
src/tools/tools.h | 22 +-
src/tools/vector_constants.cpp | 22 +-
src/tools/vector_constants.h | 27 +-
src/tools/vectorx.cpp | 22 +-
src/tools/vectorx.h | 22 +-
src/tree/argtree.cpp | 30 +-
src/tree/argtree.h | 22 +-
src/tree/arranger.cpp | 22 +-
src/tree/arranger.h | 28 +-
src/tree/arranger_types.cpp | 22 +-
src/tree/arranger_types.h | 22 +-
src/tree/arrangervec.cpp | 24 +-
src/tree/arrangervec.h | 22 +-
src/tree/branch.cpp | 22 +-
src/tree/branch.h | 30 +-
src/tree/branchbuffer.cpp | 22 +-
src/tree/branchbuffer.h | 22 +-
src/tree/branchtag.cpp | 22 +-
src/tree/branchtag.h | 22 +-
src/tree/chain.cpp | 22 +-
src/tree/chain.h | 22 +-
src/tree/chainstate.cpp | 22 +-
src/tree/chainstate.h | 22 +-
src/tree/collector.cpp | 24 +-
src/tree/collector.h | 26 +-
src/tree/collmanager.cpp | 22 +-
src/tree/collmanager.h | 22 +-
src/tree/fc_status.cpp | 26 +-
src/tree/fc_status.h | 26 +-
src/tree/individual.cpp | 22 +-
src/tree/individual.h | 22 +-
src/tree/intervaldata.cpp | 22 +-
src/tree/intervaldata.h | 22 +-
src/tree/newick.h | 24 +-
src/tree/parameter.cpp | 22 +-
src/tree/parameter.h | 22 +-
src/tree/partition.cpp | 22 +-
src/tree/partition.h | 22 +-
src/tree/prior.cpp | 41 +-
src/tree/prior.h | 22 +-
src/tree/range.cpp | 22 +-
src/tree/range.h | 32 +-
src/tree/rectree.cpp | 22 +-
src/tree/sticksum.h | 28 +-
src/tree/summary.cpp | 22 +-
src/tree/summary.h | 26 +-
src/tree/tempident.cpp | 22 +-
src/tree/tempident.h | 22 +-
src/tree/timelist.cpp | 22 +-
src/tree/timelist.h | 22 +-
src/tree/tree.cpp | 24 +-
src/tree/tree.h | 26 +-
src/tree/treesum.cpp | 22 +-
src/tree/treesum.h | 20 +-
src/ui_interface/chainparam_interface.cpp | 27 +-
src/ui_interface/chainparam_interface.h | 27 +-
src/ui_interface/constraint_interface.cpp | 27 +-
src/ui_interface/constraint_interface.h | 27 +-
src/ui_interface/data_interface.cpp | 27 +-
src/ui_interface/data_interface.h | 27 +-
src/ui_interface/datamodel_interface.cpp | 27 +-
src/ui_interface/datamodel_interface.h | 27 +-
src/ui_interface/force_interface.cpp | 27 +-
src/ui_interface/force_interface.h | 27 +-
src/ui_interface/front_end_warnings.cpp | 22 +-
src/ui_interface/front_end_warnings.h | 27 +-
src/ui_interface/prior_interface.cpp | 27 +-
src/ui_interface/prior_interface.h | 27 +-
src/ui_interface/profile_interface.cpp | 27 +-
src/ui_interface/profile_interface.h | 27 +-
src/ui_interface/setget.h | 87 +-
src/ui_interface/setgetmachine.cpp | 27 +-
src/ui_interface/setgetmachine.h | 22 +-
src/ui_interface/traitmodel_interface.cpp | 27 +-
src/ui_interface/traitmodel_interface.h | 27 +-
src/ui_interface/ui_constants.cpp | 27 +-
src/ui_interface/ui_constants.h | 27 +-
src/ui_interface/ui_id.cpp | 27 +-
src/ui_interface/ui_id.h | 27 +-
src/ui_interface/ui_interface.cpp | 27 +-
src/ui_interface/ui_interface.h | 27 +-
src/ui_interface/ui_regid.cpp | 27 +-
src/ui_interface/ui_regid.h | 27 +-
src/ui_interface/ui_strings.cpp | 22 +-
src/ui_interface/ui_strings.h | 27 +-
src/ui_interface/ui_warnings.cpp | 22 +-
src/ui_interface/ui_warnings.h | 27 +-
src/ui_interface/userparam_interface.cpp | 27 +-
src/ui_interface/userparam_interface.h | 27 +-
src/ui_util/undoredochain.cpp | 27 +-
src/ui_util/undoredochain.h | 27 +-
src/ui_vars/report_strings.cpp | 22 +-
src/ui_vars/report_strings.h | 22 +-
src/ui_vars/ui_vars.cpp | 27 +-
src/ui_vars/ui_vars.h | 27 +-
src/ui_vars/ui_vars_chainparams.cpp | 27 +-
src/ui_vars/ui_vars_chainparams.h | 27 +-
src/ui_vars/ui_vars_component.cpp | 27 +-
src/ui_vars/ui_vars_component.h | 27 +-
src/ui_vars/ui_vars_datamodel.cpp | 27 +-
src/ui_vars/ui_vars_datamodel.h | 27 +-
src/ui_vars/ui_vars_datapackplus.cpp | 22 +-
src/ui_vars/ui_vars_datapackplus.h | 27 +-
src/ui_vars/ui_vars_forces.cpp | 27 +-
src/ui_vars/ui_vars_forces.h | 27 +-
src/ui_vars/ui_vars_prior.cpp | 27 +-
src/ui_vars/ui_vars_prior.h | 27 +-
src/ui_vars/ui_vars_traitmodels.cpp | 27 +-
src/ui_vars/ui_vars_traitmodels.h | 27 +-
src/ui_vars/ui_vars_userparams.cpp | 27 +-
src/ui_vars/ui_vars_userparams.h | 27 +-
src/xml/lamarc_input_schema.h | 22 +-
src/xml/lamarcschema.cpp | 22 +-
src/xml/parsetreeschema.cpp | 22 +-
src/xml/parsetreeschema.h | 22 +-
src/xml/parsetreetodata.cpp | 22 +-
src/xml/parsetreetodata.h | 22 +-
src/xml/parsetreetosettings.cpp | 22 +-
src/xml/parsetreetosettings.h | 22 +-
src/xml/parsetreewalker.cpp | 22 +-
src/xml/parsetreewalker.h | 22 +-
src/xml/tixml_base.cpp | 23 +-
src/xml/tixml_base.h | 22 +-
src/xml/toxml.cpp | 22 +-
src/xml/toxml.h | 22 +-
src/xml/xml.cpp | 22 +-
src/xml/xml.h | 22 +-
src/xml/xml_strings.cpp | 22 +-
src/xml/xml_strings.h | 22 +-
tools/README | 2 +
tools/apache-forrest-0.7.tar.gz | Bin 0 -> 21917527 bytes
website/apacheInput/skinconf.xml | 446 +
website/apacheInput/xdocs/documentation/index.xml | 15 +
website/apacheInput/xdocs/download/index.xml | 15 +
website/apacheInput/xdocs/images/icon.png | Bin 0 -> 696 bytes
website/apacheInput/xdocs/images/lamarc.gif | Bin 0 -> 1359 bytes
website/apacheInput/xdocs/index.xml | 55 +
website/apacheInput/xdocs/more/index.xml | 26 +
.../xdocs/publications/beerli-felsenstein-2001.pdf | Bin 0 -> 137971 bytes
.../xdocs/publications/evolution2000-pb-mkk.pdf | 1340 +++
.../xdocs/publications/fluctuate1.1.pdf | Bin 0 -> 1914419 bytes
.../apacheInput/xdocs/publications/g_explain.pdf | Bin 0 -> 39859 bytes
.../apacheInput/xdocs/publications/genetics763.pdf | Bin 0 -> 210247 bytes
website/apacheInput/xdocs/publications/index.xml | 75 +
.../xdocs/publications/metro-hastings.pdf | Bin 0 -> 2579896 bytes
website/apacheInput/xdocs/site.xml | 59 +
website/apacheInput/xdocs/tabs.xml | 42 +
662 files changed, 41963 insertions(+), 3877 deletions(-)
diff --git a/CONTENTS b/CONTENTS
new file mode 100644
index 0000000..947679f
--- /dev/null
+++ b/CONTENTS
@@ -0,0 +1,71 @@
+
+Contents of this distribution
+
+==============================================
+Files with information about this distribution
+==============================================
+CONTENTS -- this file
+COPYING -- license info for Lamarc and third party tools we
+ distribute
+HISTORY -- major Lamarc project versions/milestones
+INSTALL -- a pointer to doc/html/compiling.html (installation
+ instructions)
+README -- overview of Lamarc project and distributions available
+
+======================================
+Files used or created by the autotools
+======================================
+Makefile.am -- Automake makefile for the entire project
+Makefile.in -- generated from Makefile.am by automake,
+aclocal.m4 -- aclocal generates this
+configure.ac -- autoconf generates configure from this
+configure -- generates Makefile from Makefile.in
+
+config/ -- helper scripts and files used or generated by ./configure
+ including conf.h
+
+depcomp -- belongs in config/ directory but awaiting autotools bugfix
+install-sh -- belongs in config/ directory but awaiting autotools bugfix
+missing -- belongs in config/ directory but awaiting autotools bugfix
+
+=============================
+Lamarc Code and Documentation
+=============================
+doc/ -- documentation directory
+doc/html -- HTML documentation
+doc/licenses/ -- complete text of licences for all software in this distribution
+doc/testfiles -- program test files
+resources/ -- icons and packaging support
+src/bayeslike -- code specific to doing Bayesian search
+src/control -- the main control routines of LAMARC
+src/convErr -- error handling for converter gui
+src/conversion -- legacy file conversion program
+src/convModel -- gui-free parts of data storage for converter gui
+src/convParse -- parsing related structures for converter gui
+src/convStrings -- error messages and dialog strings for converter gui
+src/convUtil -- utility methods for converter gui
+src/datalike -- routines dealing with data and data likelihoods
+src/force -- code for different evolutionary forces (e.g. migration)
+src/guiconv -- gui-involved parts of converter gui
+src/guiutil -- gui stuff thought to be generally useful
+src/lamarcmenus -- lamarc-specific menus
+src/menu -- general-purpose menu routines
+src/postlike -- posterior-likelihood computation and display routines
+src/report -- output reporting
+src/tools -- utility routines (string handling, random numbers, etc.)
+src/tree -- phylogenetic trees and rearrangement
+src/ui_interface -- non-menu parts of lamarc's UI
+src/ui_util -- utilities used by UI (e.g. undo/redo machinery)
+src/ui_vars -- storage of settings data during user input
+src/xml -- input data handling in XML
+
+================================================================
+Third-party tools -- see COPYING file for licenses and more info
+================================================================
+boost/ -- highly useful C++ library collection
+tinyxml/ -- bare-bones xml parser
+wxWidgets/ -- multi-platform GUI library
+wxWidgetsLamarc/ -- (may be empty) Lamarc patches to wxWidgets library
+
+
+$Id: CONTENTS,v 1.5 2007/09/17 20:39:53 lpsmith Exp $
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..40f4eff
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,57 @@
+========================================================================
+
+Code, documentation, libraries, and executables included with this
+distribution are subject to various licenses.
+
+Without the availablilty of other open source projects to draw
+upon, producing Lamarc would be much less satisfying and much
+more difficult. We are greatful to the authors of the software
+projects we have used. Their licenses, and ours are available in
+the subdirectory ./doc/licenses as summarized below.
+
+========================================================================
+
+* the lamarc project, including code, documentation, examples, and images
+ located under ./doc/html ./doc/testfiles ./resources ./scripts ./src
+ is licensed under the Apache License, Version 2.0
+ see ./doc/licenses/lamarc.txt
+
+* MS windows executables were produced using a cross-compiling tool
+ chain that makes use of the MinGW tools. These executables probably
+ contain the mingw w32api library which
+ is licensed under the mingw license,
+ available at ./doc/licenses/mingw.txt
+ See http://www.mingw.org for more info
+
+* the boost library
+ located under ./boost
+ is licensed under the boost license
+ available at ./doc/licenses/boost.txt
+ See http://www.boost.org
+
+* tinyxml,
+ located under ./tinyxml
+ is licensed under the zlib license,
+ available at ./doc/licenses/zlib.txt
+ See http://www.grinninglizard.com/tinyxml/
+ and http://sourceforge.net/projects/tinyxml
+
+* wxWidgets code (which may include wxWidgets-produced patches),
+ located under ./wxWidgets
+ is licenced under the wxWindows license,
+ available in doc/licenses/wx.txt
+ This license refers to the GNU GPL and GNU L-GPL licenses
+ which are available in ./doc/licenses/gpl.txt and ./doc/licenses/lgpl.txt
+ See http://www.wxwidgets.org for more info
+
+* wxWidgets documentation
+ located under ./wxWidgets
+ is licenced under the wxWindows Documentation license,
+ available in doc/licenses/wxdoc.txt
+ See http://www.wxwidgets.org for more info
+
+* wxWidgets patches created by the lamarc team,
+ located under ./wxWidgetsLamarc
+ are intended to be contributed to the wxWidgets project and are
+ licenced under the wxWindows license,
+ available in doc/licenses/wx.txt
diff --git a/HISTORY b/HISTORY
new file mode 100644
index 0000000..d0eb12c
--- /dev/null
+++ b/HISTORY
@@ -0,0 +1,97 @@
+History of Lamarc -- the program
+--------------------------------
+2013
+Nov 14 Lamarc-2.1.9: This is a bug fix release
+ * FIXED MULTIPLE BUGS IN DIVERGENCE. Results
+ from release 2.1.8 with divergence turned on
+ should be re-run.
+ * DIVERGENCE PRIORS can be set from menu
+ * INVARIANT LOCI no longer cause crashes as in 2.1.8
+
+2012
+May 29 Lamarc-2.1.8: This is a bug fix and new feature release
+ * FIXED BUG in MIGRATION
+ * FIXED BUG in negative GROWTH cases
+ * FASTER convergence in LIKELIHOOD cases
+ * NEW FEATURE -- panels
+ * NEW FEATURE -- divergence
+
+2011
+January 21 Lamarc-2.1.6: This is a bug fix release, with the
+ following changes:
+ * FIXED data likelihood bug that appears only
+ in cases with RECOMBINATION turned on. Results
+ obtained from releases 2.1.2 through 2.1.5
+ with the recombination force turned on should
+ be re-run.
+ * FIXED calculation of invariant data term for
+ SNP data modeled with a per-base error rate
+ * UPDATED random number generator to use the
+ Boost library, and added guards against
+ returning values of exactly 0 or 1 for
+ double values
+
+2009
+December 21 Lamarc-2.1.5: This release includes a beta test version
+ of "data uncertainty", csv output formats for
+ curvefile and profile data (to make them easier
+ to read with R or Excel), and supplemental XML output
+ file "report.xml" to make it easier to automate
+ reading lamarc output.
+
+2009
+July 17 Lamarc-2.1.4: This release brings the code base up to
+ compilability with g++ 4.3.3. Additionally, minor user
+ experience bugs are fixed. This was used at the
+ Woods Hole Molecular Evolution Conference but
+ not distributed via the Lamarc web site
+
+2008
+July 14 Lamarc-2.1.3: This release fixes a bug introduced into
+ the code used to guess haplotype resolution. Analyses
+ using this feature in LAMARC versions 2.1.2 and 2.1.2b
+ should be re-run. Additional improvements include:
+ * Tracer output now renders step counts as integers
+ instead of reals.
+ * Mapping output now writable to its own file.
+ * Upgraded default wxWidgets installation to 2.8.8.
+
+2007
+October 9 Lamarc-2.1.2b: Minor fixes to 2.1.2 affecting user
+ experience only
+
+2007
+October 4 Lamarc-2.1.2: Recombination now does not attempt to
+ insert recombination events that have no effect on
+ present-day data.
+
+2007
+July Lamarc-2.1.1: Bug fixes
+
+2007
+May Lamarc-2.1: full support for trait mapping, multi-locus data.
+ New GUI for lam_conv; batch modes for lamarc and lam_conv.
+
+2006
+July 24 Lamarc-2.0.3_Woods_Hole_Beta: Bug fixes, preliminary
+ support for trait mapping, multi-locus data.
+
+2005
+August 26 Lamarc-2.0.2: bug-fix replication, Bayesian multi-region,
+ and multi-region effective popsize, version numbers in xml,
+ Bayesian summary file reading
+2005
+June 1 Lamarc-2.0: Bayes, constraints, models, replicates, max.
+
+2004
+June 25 Lamarc-1.2.2: bug-fix of growth, improved maximization
+
+2004
+June 1 Lamarc-1.2.1: added growth, adaptive heating
+
+2002
+June 25 Lamarc-1.1: added microsatellites, SNPs, genotypic data
+
+2001
+December 10 Lamarc-1.0: first (alpha) version of lamarc.
+
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 0000000..fba44d9
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,2 @@
+
+This file has been superceded by doc/html/compiling.html
diff --git a/MAINTAINER.README b/MAINTAINER.README
new file mode 100644
index 0000000..92097be
--- /dev/null
+++ b/MAINTAINER.README
@@ -0,0 +1,179 @@
+********************************************************
+********************************************************
+NOTES ON BUILDING AND MAINTAINING LAMARC USING AUTOTOOLS
+********************************************************
+********************************************************
+
+With each new CVS checkout of the lamarc package, and
+with each update to the files Makefile.am or configure.ac,
+developers should use the autotools to generate the
+configure script and an up-to-date Makefile.
+
+Maintaners need recent versions of automake and autoconf.
+I used automake 1.8.3 and autoconf 2.59. These are
+readily available from
+ http://www.gnu.org/software/autoconf/
+ http://www.gnu.org/software/automake/
+If you don't have root permission, you can install these
+in a directory tree you call <sandbox> by invoking the
+autoconf and automake ./configure scripts like this:
+ ./configure --prefix=<sandbox>
+and putting <sandbox>/bin on your path. You will need
+to install autoconf before automake.
+
+Our code now relies on the wxWidgets (a.k.a. wxWindows)
+library. We include a gzip'd tar file of a release of
+wxWindows 2.6.3 in the lamarc/wxWidgets directory
+To unpack the archive and build the wxWidgets library, the
+easiest thing to do is execute the following steps
+from this directory:
+ cvs co lamarc
+ cd lamarc
+ mkdir debug
+ cd debug
+ ../configure --enable-debug --enable-buildwx
+ make
+
+If you make changes to Makefile.am (such as adding or removing source
+files) you'll need to do
+ cd <lamarc top dir>
+ aclocal
+ autoconf
+ automake
+ cd debug
+ ../configure --enable-debug
+ make
+
+The Lamarc version number is set only in configure.ac
+
+Our users build distributions that are created by us
+using the "dist" target and should not be required
+to follow the maintainer building instructions
+above. They need to be supported to do only:
+ mkdir release
+ cd release
+ ../configure --enable-buildwx
+ make
+
+===========================
+Building a universal binary
+===========================
+
+(1) check out the lamarc source on a linux box and build the
+distribution. The "--disable-gui and --disable-batch are to
+keep the configure script from requiring wxWidgets, which is
+not needed for building a distribution
+ cvs co lamarc
+ cd lamarc
+ mkdir dist
+ cd dist
+ ../configure --disable-gui --disable-batch
+ make dist
+
+(2) copy the resulting distribution lamarc-<version_number>.tar.gz
+to a modern mac
+
+(3) on the mac, unpack the distribution and build
+ tar xfvz lamarc-<version_number>.tar.gz
+ cd lamarc-<version_number>
+ mkdir debug
+ cd debug
+ ../configure --enable-buildwx --enable-universal_binary --disable-dependency-tracking --enable-debug
+ make
+
+the "--disable-dependency-tracking" should be automatic with the
+"--enable-universal_binary", but I haven't done that yet.
+
+==============================
+Additional configuration files
+==============================
+
+Several settings can also be changed using a copy of the local_build.h
+file. The default lives in ./config . Read the comments in the default
+version for more information
+ ./config/local_build.h
+
+Additionally, the local_build.h file includes information on how to
+use Lamarc's tracing abilities. See local_build.h plus these files
+for more information:
+ ./src/control/dynatracer.h
+ ./src/control/dynatracer.cpp
+
+
+
+================
+Updating Tinyxml
+================
+
+When updating to a new version of tinyxml (or any other
+third-party software) please use the "cvs import" command.
+This is how I did it for tinyxml:
+
+ got the latest tinyxml src distribution
+ untar'd it
+ cd into top level directory ("tinyxml")
+ cvs import lamarc/tinyxml tinyxml v_2_2_1
+
+As of this writing (7/28/2004) there are two versions of
+the scripts "missing", "install-sh", and "depcomp" under
+this directory and under the config subdirectory. This is
+due to a bug in autoconf. Eventually they should only need
+to be in the config subdirectory
+
+==========================================================
+How we used to compile lamarc under codewarrior on the Mac
+(Probably doesn't work anymore)
+==========================================================
+
+ started up codewarrior
+
+ New > Mac OS C++ Stationery
+ folder macos,
+ project "lamarc_proj"
+ C++ console carbon (Under Mac OS Carbon > Standard Console)
+
+ Under "Targets" tab on "lamarc_proj"
+ Removed Debug target (control-click, choose "clear")
+
+ Under "Files" tab on "lamarc_proj"
+ removed HelloWorld.cp (control-click, choose "clear")
+ dragged src directory, removed converter
+ dragged tinyxml directory, removed tinystr.*, xmltest.cpp
+ dragged config directory
+ dragged resources/lamarc.icns
+
+ in Settings Menu (File > Carbon C++ Console Final Settings)
+
+ Target > Target Settings
+ renamed target name to LAMARCTARGET
+ save project entries using relative paths
+
+ Target > Access Paths
+ always search user paths
+ added projects/macos to search paths (to pick up MacOSPrefix.h)
+ added resources to search paths (to pick up lamarc.icns)
+ (To add, click in User paths box and then click "Add")
+
+ Target > PPC Target
+
+ Creator LMRK
+ File name "lamarc-mac"
+ Prefered Heap 100 Meg
+ Min Heap 10 Meg
+ Stack 1 Meg
+
+ Language Settings > C/C++ Language
+
+ Prefix File: MacOSPrefix.h
+
+ Language Settings > C/C++ Warnings
+
+ turned off: unused vars, unused args, hidden virtual,
+ inconsistent use of struct/class
+
+ Linker > Mac OS Packager
+
+ turned on Use Mac OS Packager
+ create alias to Classic executable
+
+*********************************************************************
diff --git a/Makefile.am b/Makefile.am
index 4b19939..723986f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,5 +1,7 @@
## Process this file with automake to produce Makefile.in
+AUTOMAKE_OPTIONS = subdir-objects
+
lamarc_srcdir=$(top_srcdir)/src
SUFFIXES = .rc
@@ -33,6 +35,7 @@ endif
if LAMARC_APP_OSX
bin_PROGRAMS += lamarc.app
+AM_CXXFLAGS += -mmacosx-version-min=10.7
if CONVERTER
if GUI
bin_PROGRAMS += lam_conv.app
@@ -71,7 +74,10 @@ LDADD =
noinst_LIBRARIES = libtinyxml.a
-libtinyxml_a_CXXFLAGS = -DTIXML_USE_STL
+libtinyxml_a_CXXFLAGS = -DTIXML_USE_STL
+if LAMARC_APP_OSX
+ libtinyxml_a_CXXFLAGS += -mmacosx-version-min=10.7
+endif
libtinyxml_a_SOURCES = \
tinyxml/tinyxml.h \
@@ -942,7 +948,12 @@ lam_conv_SOURCES = \
$(lam_conv_core) \
$(lam_conv_resources)
-lam_conv_LDADD = @WX_LIBS@ -lX11 libtinyxml.a
+lam_conv_LDADD = @WX_LIBS@
+if LAMARC_APP_OSX
+ lam_conv_LDADD += libtinyxml.a
+else
+ lam_conv_LDADD += -lX11 libtinyxml.a
+endif
EXTRA_lam_conv_SOURCES = $(tinyxml_suite) $(lam_conv_icons)
@@ -961,7 +972,7 @@ batch_lam_conv_testable = \
batch_lam_conv_SOURCES = \
$(batch_lam_conv_testable)
-batch_lam_conv_LDADD = @WX_LIBS@ -lX11 libtinyxml.a
+batch_lam_conv_LDADD = lam_conv_LDADD
EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)
@@ -970,7 +981,7 @@ EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)
## ############################################################
lam_conv_app_SOURCES=
-lam_conv.app: lam_conv
+lam_conv.app$(EXEEXT): lam_conv
@rm -rf lam_conv.app
$(MACDEVTOOLS)/Rez -d __DARWIN__ -t APPL Carbon.r -o lam_conv
$(MACDEVTOOLS)/SetFile -a C lam_conv
@@ -988,7 +999,7 @@ lam_conv.app: lam_conv
lamarc_app_SOURCES=
-lamarc.app: lamarc
+lamarc.app$(EXEEXT): lamarc
@rm -rf lamarc.app
$(MACDEVTOOLS)/Rez -d __DARWIN__ -t APPL Carbon.r -o lamarc
$(MACDEVTOOLS)/SetFile -a C lamarc
@@ -1049,7 +1060,6 @@ html_DATA = \
doc/html/genotype.html \
doc/html/glossary.html \
doc/html/growthmenu.html \
- doc/html/forces.html \
doc/html/index.html \
doc/html/insumfile.2reg3rep.html \
doc/html/insumfile.2reg3rep.xml \
diff --git a/Makefile.in b/Makefile.in
new file mode 100644
index 0000000..f5e3b61
--- /dev/null
+++ b/Makefile.in
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+# @configure_input@
+
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
+
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+
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+ fi; \
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+ at LAMARC_APP_OSX_TRUE@am__append_5 = lamarc.app
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+ at LAMARC_APP_MSW_TRUE@am__append_10 = resources/lam_conv_rc.rc
+ at LAMARC_APP_MSW_TRUE@am__append_11 = resources/lam_conv_rc.rc
+ at NODATA_TRUE@am__append_12 = -DSTATIONARIES -DNOPROGRESSBAR
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+# no other flags if user set
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+ at UNIVB_TRUE@am__append_25 = -arch ppc -arch i386
+ at ARRCHECK_TRUE@am__append_26 = -DHAPARRANGERTEST
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+ at LAMARC_APP_OSX_TRUE@am__EXEEXT_3 = lamarc.app$(EXEEXT)
+ at CONVERTER_TRUE@@GUI_TRUE@@LAMARC_APP_OSX_TRUE at am__EXEEXT_4 = lam_conv.app$(EXEEXT)
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+ src/convModel/gc_panel.h src/convModel/gc_panel.cpp \
+ src/convModel/gc_parent.h src/convModel/gc_parent.cpp \
+ src/convModel/gc_phase.h src/convModel/gc_phase.cpp \
+ src/convModel/gc_phase_info.h src/convModel/gc_phase_info.cpp \
+ src/convModel/gc_phenotype.h src/convModel/gc_phenotype.cpp \
+ src/convModel/gc_set_util.h src/convModel/gc_set_util.cpp \
+ src/convModel/gc_structure_maps.h \
+ src/convModel/gc_structure_maps.cpp \
+ src/convModel/gc_structures.h src/convModel/gc_structures.cpp \
+ src/convModel/gc_trait.h src/convModel/gc_trait.cpp \
+ src/convModel/gc_trait_allele.h \
+ src/convModel/gc_trait_allele.cpp src/convModel/gc_types.h \
+ src/convModel/gc_types.cpp src/guiconv/gc_quantum.h \
+ src/guiconv/gc_quantum.cpp \
+ src/convParse/gc_genotype_resolution.h \
+ src/convParse/gc_genotype_resolution.cpp \
+ src/convModel/gc_creation_info.h \
+ src/convModel/gc_creation_info.cpp \
+ src/convModel/gc_individual.h src/convModel/gc_individual.cpp \
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+ src/convParse/gc_migrate.h src/convParse/gc_migrate.cpp \
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+ src/convParse/gc_pop_match.cpp src/convParse/gc_population.h \
+ src/convParse/gc_population.cpp src/convParse/gc_region.h \
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+ src/ui_interface/ui_constants.cpp src/ui_interface/ui_id.h \
+ src/ui_interface/ui_id.cpp src/ui_interface/ui_strings.h \
+ src/ui_interface/ui_strings.cpp src/convStrings/cnv_strings.h \
+ src/convStrings/cnv_strings.cpp src/convStrings/gc_strings.h \
+ src/convStrings/gc_strings_cmdfile.h \
+ src/convStrings/gc_strings_cmdfile.cpp \
+ src/convStrings/gc_strings_creation.h \
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+ src/convStrings/gc_strings_data.h \
+ src/convStrings/gc_strings_data.cpp \
+ src/convStrings/gc_strings_err.cpp \
+ src/convStrings/gc_strings_individual.h \
+ src/convStrings/gc_strings_individual.cpp \
+ src/convStrings/gc_strings_infile.h \
+ src/convStrings/gc_strings_infile.cpp \
+ src/convStrings/gc_strings_io.h \
+ src/convStrings/gc_strings_io.cpp \
+ src/convStrings/gc_strings_locus.h \
+ src/convStrings/gc_strings_locus.cpp \
+ src/convStrings/gc_strings_map.h \
+ src/convStrings/gc_strings_map.cpp \
+ src/convStrings/gc_strings_mig.h \
+ src/convStrings/gc_strings_mig.cpp \
+ src/convStrings/gc_strings_parse.h \
+ src/convStrings/gc_strings_parse.cpp \
+ src/convStrings/gc_strings_parse_locus.h \
+ src/convStrings/gc_strings_parse_locus.cpp \
+ src/convStrings/gc_strings_phase.h \
+ src/convStrings/gc_strings_phase.cpp \
+ src/convStrings/gc_strings_pop.h \
+ src/convStrings/gc_strings_pop.cpp \
+ src/convStrings/gc_strings_region.h \
+ src/convStrings/gc_strings_region.cpp \
+ src/convStrings/gc_strings_str_a_m.cpp \
+ src/convStrings/gc_strings_str_n_z.cpp \
+ src/convStrings/gc_strings_structures.h \
+ src/convStrings/gc_strings_structures.cpp \
+ src/convStrings/gc_strings_trait.h \
+ src/convStrings/gc_strings_trait.cpp \
+ src/convUtil/gc_file_util.h src/convUtil/gc_file_util.cpp \
+ src/guiutil/gc_clickpanel.h src/guiutil/gc_clickpanel.cpp \
+ src/guiutil/gc_gridpanel.h src/guiutil/gc_gridpanel.cpp \
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+ src/guiconv/gc_color.cpp src/guiconv/gc_data_display.h \
+ src/guiconv/gc_data_display.cpp src/guiconv/gc_dialog.h \
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+ src/guiconv/gc_event_publisher.cpp \
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+ src/guiconv/gc_file_list.h src/guiconv/gc_file_list.cpp \
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+ src/guiconv/gc_logic.cpp src/guiconv/gc_matrix_display.h \
+ src/guiconv/gc_matrix_display.cpp src/guiconv/gc_menu_actors.h \
+ src/guiconv/gc_menu_actors.cpp \
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+ src/guiconv/gc_migtab.cpp src/guiconv/gc_panel_dialogs.h \
+ src/guiconv/gc_panel_dialogs.cpp \
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+ src/guiconv/gc_parent_dialogs.cpp \
+ src/guiconv/gc_population_dialogs.h \
+ src/guiconv/gc_population_dialogs.cpp \
+ src/guiconv/gc_region_dialogs.h \
+ src/guiconv/gc_region_dialogs.cpp \
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+ src/convErr/lam_conv-gc_data_missing_err.$(OBJEXT) \
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+ src/xml/lam_conv-tixml_base.$(OBJEXT) \
+ src/xml/lam_conv-xml.$(OBJEXT) \
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+ src/convStrings/lam_conv-gc_strings_mig.$(OBJEXT) \
+ src/convStrings/lam_conv-gc_strings_parse.$(OBJEXT) \
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+ src/convStrings/lam_conv-gc_strings_region.$(OBJEXT) \
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+ src/convStrings/lam_conv-gc_strings_trait.$(OBJEXT)
+am__objects_16 = src/convUtil/lam_conv-gc_file_util.$(OBJEXT)
+am__objects_17 = src/guiutil/lam_conv-gc_clickpanel.$(OBJEXT) \
+ src/guiutil/lam_conv-gc_gridpanel.$(OBJEXT) \
+ src/guiutil/lam_conv-gc_text_ctrl.$(OBJEXT) \
+ src/guiutil/lam_conv-gc_validators.$(OBJEXT)
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+ src/guiconv/lam_conv-gc_color.$(OBJEXT) \
+ src/guiconv/lam_conv-gc_data_display.$(OBJEXT) \
+ src/guiconv/lam_conv-gc_dialog.$(OBJEXT) \
+ src/guiconv/lam_conv-gc_event_publisher.$(OBJEXT) \
+ src/guiconv/lam_conv-gc_file_dialogs.$(OBJEXT) \
+ src/guiconv/lam_conv-gc_file_list.$(OBJEXT) \
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+ src/guiconv/lam_conv-gc_layout.$(OBJEXT) \
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+ src/guiconv/lam_conv-gc_parent_dialogs.$(OBJEXT) \
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+ src/guiconv/lam_conv-gc_trait_dialogs.$(OBJEXT) \
+ src/guiconv/lam_conv-guiconverter.$(OBJEXT)
+am__objects_19 = $(am__objects_17) $(am__objects_18)
+ at LAMARC_APP_MSW_TRUE@am__objects_20 = resources/lam_conv_rc.$(OBJEXT)
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+am_lam_conv_OBJECTS = $(am__objects_10) $(am__objects_11) \
+ $(am__objects_14) $(am__objects_15) $(am__objects_16) \
+ $(am__objects_19) $(am__objects_21)
+lam_conv_OBJECTS = $(am_lam_conv_OBJECTS)
+ at LAMARC_APP_OSX_FALSE@am__DEPENDENCIES_1 = libtinyxml.a
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+lam_conv_LINK = $(CXXLD) $(lam_conv_CXXFLAGS) $(CXXFLAGS) \
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+ src/lamarcmenus/coalmenus.cpp \
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+ src/lamarcmenus/constraintmenus.cpp \
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+ src/lamarcmenus/datafilenamedialog.cpp \
+ src/lamarcmenus/datamodelmenu.h \
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+ src/lamarcmenus/divmenus.h src/lamarcmenus/divmigmenus.cpp \
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+ src/lamarcmenus/forcesmenus.h src/lamarcmenus/growthmenus.cpp \
+ src/lamarcmenus/growthmenus.h \
+ src/lamarcmenus/lamarc_strings.cpp \
+ src/lamarcmenus/lamarc_strings.h \
+ src/lamarcmenus/lamarcheaderdialog.cpp \
+ src/lamarcmenus/lamarcheaderdialog.h \
+ src/lamarcmenus/lamarcmenu.cpp src/lamarcmenus/lamarcmenu.h \
+ src/lamarcmenus/lamarcmenuitems.cpp \
+ src/lamarcmenus/lamarcmenuitems.h \
+ src/lamarcmenus/logselectmenus.cpp \
+ src/lamarcmenus/logselectmenus.h src/lamarcmenus/migmenus.cpp \
+ src/lamarcmenus/migmenus.h \
+ src/lamarcmenus/nomenufilereaddialog.cpp \
+ src/lamarcmenus/nomenufilereaddialog.h \
+ src/lamarcmenus/outfilemenus.cpp \
+ src/lamarcmenus/outfilemenus.h \
+ src/lamarcmenus/overviewmenus.cpp \
+ src/lamarcmenus/overviewmenus.h \
+ src/lamarcmenus/popsizemenu.cpp src/lamarcmenus/popsizemenu.h \
+ src/lamarcmenus/priormenus.cpp src/lamarcmenus/priormenus.h \
+ src/lamarcmenus/profilemenus.cpp \
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+ src/lamarcmenus/recmenus.h \
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+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target = @target@
+target_alias = @target_alias@
+target_cpu = @target_cpu@
+target_os = @target_os@
+target_vendor = @target_vendor@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = subdir-objects
+lamarc_srcdir = $(top_srcdir)/src
+SUFFIXES = .rc
+AM_CXXFLAGS = -D at LAMARC_CODE_OSTYPE@ $(am__append_1) $(am__append_6) \
+ $(am__append_12) $(am__append_13) $(am__append_14) \
+ $(am__append_15) $(am__append_16) $(am__append_18) \
+ $(am__append_20) $(am__append_21) $(am__append_22) \
+ $(am__append_23) $(am__append_24) $(am__append_25) \
+ $(am__append_26)
+AM_CFLAGS =
+AM_LDFLAGS = $(am__append_2)
+optflags = -O3 -funroll-loops
+debugflags = -ggdb
+LDADD = $(am__append_17) $(am__append_19)
+noinst_LIBRARIES = libtinyxml.a
+libtinyxml_a_CXXFLAGS = -DTIXML_USE_STL $(am__append_8)
+libtinyxml_a_SOURCES = \
+ tinyxml/tinyxml.h \
+ tinyxml/tinyxml.cpp \
+ tinyxml/tinyxmlerror.cpp \
+ tinyxml/tinyxmlparser.cpp \
+ tinyxml/tinystr.h \
+ tinyxml/tinystr.cpp
+
+lamarc_includes = \
+ -I $(builddir)/config \
+ -I $(top_srcdir)/config \
+ -I $(lamarc_srcdir)/bayeslike \
+ -I $(lamarc_srcdir)/control \
+ -I $(lamarc_srcdir)/conversion \
+ -I $(lamarc_srcdir)/convErr \
+ -I $(lamarc_srcdir)/convModel \
+ -I $(lamarc_srcdir)/convParse \
+ -I $(lamarc_srcdir)/convStrings \
+ -I $(lamarc_srcdir)/convUtil \
+ -I $(lamarc_srcdir)/datalike \
+ -I $(lamarc_srcdir)/force \
+ -I $(lamarc_srcdir)/guiconv \
+ -I $(lamarc_srcdir)/guiutil \
+ -I $(lamarc_srcdir)/lamarcmenus \
+ -I $(lamarc_srcdir)/menu \
+ -I $(lamarc_srcdir)/postlike \
+ -I $(lamarc_srcdir)/report \
+ -I $(lamarc_srcdir)/tools \
+ -I $(lamarc_srcdir)/tree \
+ -I $(lamarc_srcdir)/ui_interface \
+ -I $(lamarc_srcdir)/ui_util \
+ -I $(lamarc_srcdir)/ui_vars \
+ -I $(lamarc_srcdir)/xml \
+ -I $(top_srcdir)/boost \
+ -I $(top_srcdir)/resources \
+ -I $(top_srcdir)/tinyxml
+
+lamarc_resources = $(am__append_9)
+lam_conv_resources = $(am__append_10)
+batch_lam_conv_resources = $(am__append_11)
+lamarc_CXXFLAGS = $(AM_CXXFLAGS) -Wall -Wextra -Wno-unused $(lamarc_includes) -DTIXML_USE_STL
+old_lam_conv_CXXFLAGS = $(AM_CXXFLAGS) $(lamarc_includes)
+lam_conv_CXXFLAGS = $(AM_CXXFLAGS) -Wall -Wextra -Wno-unused $(lamarc_includes) @WX_CXXFLAGS@ -DTIXML_USE_STL
+batch_lam_conv_CXXFLAGS = $(AM_CXXFLAGS) -Wall -Wextra -Wno-unused $(lamarc_includes) @WX_CXXFLAGS@ -DTIXML_USE_STL
+MACDEVTOOLS = /Developer/Tools
+scripts_to_dist = install-sh
+py_parallel = scripts/pyParallel/README \
+ scripts/pyParallel/divide_data.py \
+ scripts/pyParallel/combine_regions.py \
+ scripts/pyParallel/combine_replicates.py \
+ scripts/pyParallel/parallelCommon.py
+
+lam_conv_icons = resources/lam_conv_rc.rc \
+ resources/lam_conv.ico \
+ resources/lam_conv.icns \
+ resources/empty16.bmp \
+ resources/excl16.bmp \
+ resources/giraffe32.bmp
+
+lamarc_icons = resources/lamarc_rc.rc \
+ resources/lamarc.ico \
+ resources/lamarc.icns
+
+EXTRA_lamarc_SOURCES = $(lamarc_icons) \
+ config/local_build.h
+
+bayeslike_sources = \
+ src/bayeslike/bayesanalyzer_1d.h \
+ src/bayeslike/bayesanalyzer_1d.cpp \
+ src/bayeslike/bayescurve.h \
+ src/bayeslike/bayescurve.cpp \
+ src/bayeslike/bayesparamlike_1d.h \
+ src/bayeslike/bayesparamlike_1d.cpp
+
+control_sources = \
+ src/control/chainmanager.h \
+ src/control/chainmanager.cpp \
+ src/control/chainout.h \
+ src/control/chainout.cpp \
+ src/control/chainpack.h \
+ src/control/chainpack.cpp \
+ src/control/chainparam.h \
+ src/control/chainparam.cpp \
+ src/control/constants.h \
+ src/control/constants.cpp \
+ src/control/defaults.h \
+ src/control/defaults.cpp \
+ src/control/definitions.h \
+ src/control/dynatracer.cpp \
+ src/control/dynatracer.h \
+ src/control/errhandling.h \
+ src/control/errhandling.cpp \
+ src/control/lamarc.h \
+ src/control/lamarc.cpp \
+ src/control/regiongammainfo.h \
+ src/control/regiongammainfo.cpp \
+ src/control/registry.h \
+ src/control/registry.cpp \
+ src/control/sumfilehandler.h \
+ src/control/sumfilehandler.cpp \
+ src/control/types.h \
+ src/control/userparam.h \
+ src/control/userparam.cpp \
+ src/control/xmlsum_strings.h \
+ src/control/xmlsum_strings.cpp
+
+datalike_sources = \
+ src/datalike/calculators.h \
+ src/datalike/calculators.cpp \
+ src/datalike/datapack.h \
+ src/datalike/datapack.cpp \
+ src/datalike/datatype.h \
+ src/datalike/datatype.cpp \
+ src/datalike/dlcalc.h \
+ src/datalike/dlcalc.cpp \
+ src/datalike/dlcell.h \
+ src/datalike/dlcell.cpp \
+ src/datalike/cellmanager.h \
+ src/datalike/cellmanager.cpp \
+ src/datalike/dlmodel.h \
+ src/datalike/dlmodel.cpp \
+ src/datalike/funcMax.h \
+ src/datalike/funcMax.cpp \
+ src/datalike/haplotypes.h \
+ src/datalike/haplotypes.cpp \
+ src/datalike/locus.h \
+ src/datalike/locus.cpp \
+ src/datalike/locuscell.h \
+ src/datalike/locuscell.cpp \
+ src/datalike/phenotypes.h \
+ src/datalike/phenotypes.cpp \
+ src/datalike/region.h \
+ src/datalike/region.cpp \
+ src/datalike/tipdata.h \
+ src/datalike/tipdata.cpp
+
+force_sources = \
+ src/force/epoch.h \
+ src/force/epoch.cpp \
+ src/force/event.h \
+ src/force/event.cpp \
+ src/force/force.h \
+ src/force/force.cpp \
+ src/force/forceparam.h \
+ src/force/forceparam.cpp \
+ src/force/forcesummary.h \
+ src/force/forcesummary.cpp \
+ src/force/priorreport.h \
+ src/force/priorreport.cpp \
+ src/force/timemanager.h \
+ src/force/timemanager.cpp \
+ src/force/stair.h \
+ src/force/stair.cpp \
+ src/force/paramstat.h \
+ src/force/paramstat.cpp
+
+lamarcmenus_sources = \
+ src/lamarcmenus/coalmenus.h \
+ src/lamarcmenus/coalmenus.cpp \
+ src/lamarcmenus/constraintmenus.h \
+ src/lamarcmenus/constraintmenus.cpp \
+ src/lamarcmenus/datafilenamedialog.h \
+ src/lamarcmenus/datafilenamedialog.cpp \
+ src/lamarcmenus/datamodelmenu.h \
+ src/lamarcmenus/datamodelmenu.cpp \
+ src/lamarcmenus/diseasemenus.cpp \
+ src/lamarcmenus/diseasemenus.h \
+ src/lamarcmenus/divmenus.cpp \
+ src/lamarcmenus/divmenus.h \
+ src/lamarcmenus/divmigmenus.cpp \
+ src/lamarcmenus/divmigmenus.h \
+ src/lamarcmenus/forcesmenus.cpp \
+ src/lamarcmenus/forcesmenus.h \
+ src/lamarcmenus/growthmenus.cpp \
+ src/lamarcmenus/growthmenus.h \
+ src/lamarcmenus/lamarc_strings.cpp \
+ src/lamarcmenus/lamarc_strings.h \
+ src/lamarcmenus/lamarcheaderdialog.cpp \
+ src/lamarcmenus/lamarcheaderdialog.h \
+ src/lamarcmenus/lamarcmenu.cpp \
+ src/lamarcmenus/lamarcmenu.h \
+ src/lamarcmenus/lamarcmenuitems.cpp \
+ src/lamarcmenus/lamarcmenuitems.h \
+ src/lamarcmenus/logselectmenus.cpp \
+ src/lamarcmenus/logselectmenus.h \
+ src/lamarcmenus/migmenus.cpp \
+ src/lamarcmenus/migmenus.h \
+ src/lamarcmenus/nomenufilereaddialog.cpp \
+ src/lamarcmenus/nomenufilereaddialog.h \
+ src/lamarcmenus/outfilemenus.cpp \
+ src/lamarcmenus/outfilemenus.h \
+ src/lamarcmenus/overviewmenus.cpp \
+ src/lamarcmenus/overviewmenus.h \
+ src/lamarcmenus/popsizemenu.cpp \
+ src/lamarcmenus/popsizemenu.h \
+ src/lamarcmenus/priormenus.cpp \
+ src/lamarcmenus/priormenus.h \
+ src/lamarcmenus/profilemenus.cpp \
+ src/lamarcmenus/profilemenus.h \
+ src/lamarcmenus/recmenus.cpp \
+ src/lamarcmenus/recmenus.h \
+ src/lamarcmenus/regiongammamenus.cpp \
+ src/lamarcmenus/regiongammamenus.h \
+ src/lamarcmenus/traitmodelmenu.cpp \
+ src/lamarcmenus/traitmodelmenu.h \
+ src/lamarcmenus/treesummenus.cpp \
+ src/lamarcmenus/treesummenus.h
+
+menu_sources = \
+ src/menu/dialog.h \
+ src/menu/dialog.cpp \
+ src/menu/dialognoinput.h \
+ src/menu/dialognoinput.cpp \
+ src/menu/dialogrepeat.h \
+ src/menu/dialogrepeat.cpp \
+ src/menu/display.h \
+ src/menu/display.cpp \
+ src/menu/matrixitem.h \
+ src/menu/matrixitem.cpp \
+ src/menu/menu_strings.h \
+ src/menu/menu_strings.cpp \
+ src/menu/menudefs.h \
+ src/menu/menuerror.h \
+ src/menu/menuinteraction.h \
+ src/menu/menuinteraction.cpp \
+ src/menu/menuitem.h \
+ src/menu/menuitem.cpp \
+ src/menu/menutypedefs.h \
+ src/menu/newmenu.h \
+ src/menu/newmenu.cpp \
+ src/menu/newmenuitems.h \
+ src/menu/newmenuitems.cpp \
+ src/menu/setmenuitem.h \
+ src/menu/setmenuitem.cpp \
+ src/menu/togglemenuitem.h \
+ src/menu/togglemenuitem.cpp \
+ src/menu/twodtable.h \
+ src/menu/twodtable.cpp
+
+postlike_sources = \
+ src/postlike/analyzer.h \
+ src/postlike/analyzer.cpp \
+ src/postlike/derivatives.cpp \
+ src/postlike/likelihood.h \
+ src/postlike/likelihood.cpp \
+ src/postlike/maximizer.h \
+ src/postlike/maximizer.cpp \
+ src/postlike/maximizer_strings.h \
+ src/postlike/maximizer_strings.cpp \
+ src/postlike/plforces.h \
+ src/postlike/plforces.cpp \
+ src/postlike/plotstat.h \
+ src/postlike/plotstat.cpp \
+ src/postlike/profile.cpp
+
+report_sources = \
+ src/report/curvefiles.h \
+ src/report/curvefiles.cpp \
+ src/report/outputfile.h \
+ src/report/outputfile.cpp \
+ src/report/reportpage.h \
+ src/report/reportpage.cpp \
+ src/report/runreport.h \
+ src/report/runreport.cpp \
+ src/report/spreadsheet.h \
+ src/report/spreadsheet.cpp \
+ src/report/xml_report.h \
+ src/report/xml_report.cpp
+
+tools_sources = \
+ src/tools/mathx.h \
+ src/tools/mathx.cpp \
+ src/tools/random.h \
+ src/tools/random.cpp \
+ src/tools/rangex.h \
+ src/tools/rangex.cpp \
+ src/tools/stringx.h \
+ src/tools/stringx.cpp \
+ src/tools/timex.h \
+ src/tools/timex.cpp \
+ src/tools/tools.h \
+ src/tools/vector_constants.h \
+ src/tools/vector_constants.cpp \
+ src/tools/vectorx.h \
+ src/tools/vectorx.cpp
+
+tree_sources = \
+ src/tree/argtree.h \
+ src/tree/argtree.cpp \
+ src/tree/arranger.h \
+ src/tree/arranger.cpp \
+ src/tree/arranger_types.h \
+ src/tree/arranger_types.cpp \
+ src/tree/arrangervec.h \
+ src/tree/arrangervec.cpp \
+ src/tree/branch.h \
+ src/tree/branch.cpp \
+ src/tree/branchbuffer.h \
+ src/tree/branchbuffer.cpp \
+ src/tree/branchtag.h \
+ src/tree/branchtag.cpp \
+ src/tree/chain.h \
+ src/tree/chain.cpp \
+ src/tree/chainstate.h \
+ src/tree/chainstate.cpp \
+ src/tree/collector.h \
+ src/tree/collector.cpp \
+ src/tree/collmanager.h \
+ src/tree/collmanager.cpp \
+ src/tree/fc_status.h \
+ src/tree/fc_status.cpp \
+ src/tree/individual.h \
+ src/tree/individual.cpp \
+ src/tree/intervaldata.h \
+ src/tree/intervaldata.cpp \
+ src/tree/newick.h \
+ src/tree/newick.cpp \
+ src/tree/parameter.h \
+ src/tree/parameter.cpp \
+ src/tree/partition.h \
+ src/tree/partition.cpp \
+ src/tree/prior.h \
+ src/tree/prior.cpp \
+ src/tree/range.h \
+ src/tree/range.cpp \
+ src/tree/rectree.cpp \
+ src/tree/summary.h \
+ src/tree/summary.cpp \
+ src/tree/tempident.h \
+ src/tree/tempident.cpp \
+ src/tree/timelist.h \
+ src/tree/timelist.cpp \
+ src/tree/tree.h \
+ src/tree/tree.cpp \
+ src/tree/treesum.h \
+ src/tree/treesum.cpp
+
+ui_interface_sources = \
+ src/ui_interface/chainparam_interface.cpp \
+ src/ui_interface/chainparam_interface.h \
+ src/ui_interface/constraint_interface.cpp \
+ src/ui_interface/constraint_interface.h \
+ src/ui_interface/data_interface.cpp \
+ src/ui_interface/data_interface.h \
+ src/ui_interface/datamodel_interface.cpp \
+ src/ui_interface/datamodel_interface.h \
+ src/ui_interface/force_interface.cpp \
+ src/ui_interface/force_interface.h \
+ src/ui_interface/front_end_warnings.cpp \
+ src/ui_interface/front_end_warnings.h \
+ src/ui_interface/prior_interface.cpp \
+ src/ui_interface/prior_interface.h \
+ src/ui_interface/profile_interface.cpp \
+ src/ui_interface/profile_interface.h \
+ src/ui_interface/setget.h \
+ src/ui_interface/setgetmachine.cpp \
+ src/ui_interface/setgetmachine.h \
+ src/ui_interface/traitmodel_interface.cpp \
+ src/ui_interface/traitmodel_interface.h \
+ src/ui_interface/ui_constants.cpp \
+ src/ui_interface/ui_constants.h \
+ src/ui_interface/ui_id.cpp \
+ src/ui_interface/ui_id.h \
+ src/ui_interface/ui_interface.cpp \
+ src/ui_interface/ui_interface.h \
+ src/ui_interface/ui_regid.cpp \
+ src/ui_interface/ui_regid.h \
+ src/ui_interface/ui_strings.cpp \
+ src/ui_interface/ui_strings.h \
+ src/ui_interface/ui_warnings.h \
+ src/ui_interface/ui_warnings.cpp \
+ src/ui_interface/userparam_interface.cpp \
+ src/ui_interface/userparam_interface.h
+
+ui_util_sources = \
+ src/ui_util/undoredochain.h \
+ src/ui_util/undoredochain.cpp
+
+ui_vars_sources = \
+ src/ui_vars/report_strings.h \
+ src/ui_vars/report_strings.cpp \
+ src/ui_vars/ui_vars.h \
+ src/ui_vars/ui_vars.cpp \
+ src/ui_vars/ui_vars_chainparams.h \
+ src/ui_vars/ui_vars_chainparams.cpp \
+ src/ui_vars/ui_vars_component.h \
+ src/ui_vars/ui_vars_component.cpp \
+ src/ui_vars/ui_vars_datamodel.h \
+ src/ui_vars/ui_vars_datamodel.cpp \
+ src/ui_vars/ui_vars_datapackplus.cpp \
+ src/ui_vars/ui_vars_datapackplus.h \
+ src/ui_vars/ui_vars_forces.cpp \
+ src/ui_vars/ui_vars_forces.h \
+ src/ui_vars/ui_vars_prior.cpp \
+ src/ui_vars/ui_vars_prior.h \
+ src/ui_vars/ui_vars_traitmodels.cpp \
+ src/ui_vars/ui_vars_traitmodels.h \
+ src/ui_vars/ui_vars_userparams.cpp \
+ src/ui_vars/ui_vars_userparams.h
+
+xml_core_sources = \
+ src/xml/parsetreeschema.h \
+ src/xml/parsetreeschema.cpp \
+ src/xml/tixml_base.h \
+ src/xml/tixml_base.cpp \
+ src/xml/xml.h \
+ src/xml/xml.cpp \
+ src/xml/xml_strings.h \
+ src/xml/xml_strings.cpp
+
+xml_support_sources = \
+ src/control/constants.h \
+ src/control/constants.cpp \
+ src/control/defaults.h \
+ src/control/defaults.cpp \
+ src/tools/stringx.h \
+ src/tools/stringx.cpp \
+ src/force/paramstat.h \
+ src/force/paramstat.cpp \
+ src/ui_interface/ui_constants.h \
+ src/ui_interface/ui_constants.cpp \
+ src/ui_interface/ui_id.h \
+ src/ui_interface/ui_id.cpp \
+ src/ui_interface/ui_strings.h \
+ src/ui_interface/ui_strings.cpp
+
+xml_sources = \
+ src/xml/lamarcschema.cpp \
+ src/xml/parsetreetodata.h \
+ src/xml/parsetreetodata.cpp \
+ src/xml/parsetreetosettings.h \
+ src/xml/parsetreetosettings.cpp \
+ src/xml/parsetreewalker.h \
+ src/xml/parsetreewalker.cpp \
+ src/xml/toxml.h \
+ src/xml/toxml.cpp \
+ $(xml_core_sources)
+
+tinyxml_sources = \
+ tinyxml/tinyxml.h \
+ tinyxml/tinyxml.cpp \
+ tinyxml/tinyxmlerror.cpp \
+ tinyxml/tinyxmlparser.cpp \
+ tinyxml/tinystr.h \
+ tinyxml/tinystr.cpp
+
+config_sources = \
+ config/conf.h
+
+lamarcgcov_sources = $(bayeslike_sources) \
+ $(control_sources) \
+ $(datalike_sources) \
+ $(force_sources) \
+ $(lamarcmenus_sources) \
+ $(menu_sources) \
+ $(postlike_sources) \
+ $(report_sources) \
+ $(tools_sources) \
+ $(tree_sources) \
+ $(ui_interface_sources) \
+ $(ui_util_sources) \
+ $(ui_vars_sources) \
+ $(xml_sources)
+
+lamarc_SOURCES = $(lamarcgcov_sources) \
+ $(lamarc_resources) \
+ $(config_sources)
+
+lamarc_LDADD = libtinyxml.a
+old_lam_conv_core = \
+ src/conversion/ConverterIf.cpp \
+ src/conversion/Converter_ConverterIf.h \
+ src/conversion/Converter_ConverterUI.h \
+ src/conversion/Converter_DataSourceException.h \
+ src/conversion/Converter_DataSourceIf.h \
+ src/conversion/Converter_HapConverter.h \
+ src/conversion/Converter_IndividualDS.h \
+ src/conversion/Converter_LamarcDS.h \
+ src/conversion/Converter_MigrateConverter.h \
+ src/conversion/Converter_ModelDS.h \
+ src/conversion/Converter_ParserUtil.h \
+ src/conversion/Converter_PhylipConverter.h \
+ src/conversion/Converter_PopulationDS.h \
+ src/conversion/Converter_RegionDS.h \
+ src/conversion/Converter_Sequence.h \
+ src/conversion/Converter_SpaceConverter.h \
+ src/conversion/Converter_SpacingDS.h \
+ src/conversion/Converter_UserFileUtil.h \
+ src/conversion/Converter_XmlParserUtil.h \
+ src/conversion/Converter_types.h \
+ src/conversion/ConverterUI.cpp \
+ src/conversion/DataSourceException.cpp \
+ src/conversion/DataSourceIf.cpp \
+ src/conversion/HapConverter.cpp \
+ src/conversion/IndividualDS.cpp \
+ src/conversion/LamarcDS.cpp \
+ src/conversion/MigrateConverter.cpp \
+ src/conversion/ModelDS.cpp \
+ src/conversion/ParserUtil.cpp \
+ src/conversion/PhylipConverter.cpp \
+ src/conversion/PopulationDS.cpp \
+ src/conversion/RegionDS.cpp \
+ src/conversion/Sequence.cpp \
+ src/conversion/SpaceConverter.cpp \
+ src/conversion/SpacingDS.cpp \
+ src/conversion/UserFileUtil.cpp \
+ src/conversion/XmlParserUtil.cpp \
+ src/conversion/nomenuglobals.h \
+ src/conversion/nomenuglobals.cpp \
+ src/control/constants.h \
+ src/control/constants.cpp \
+ src/control/defaults.h \
+ src/control/defaults.cpp \
+ src/control/errhandling.h \
+ src/control/errhandling.cpp \
+ src/tools/random.h \
+ src/tools/random.cpp \
+ src/tools/stringx.h \
+ src/tools/stringx.cpp \
+ src/ui_interface/ui_constants.h \
+ src/ui_interface/ui_constants.cpp \
+ src/ui_interface/ui_id.h \
+ src/ui_interface/ui_id.cpp \
+ src/ui_interface/ui_strings.h \
+ src/ui_interface/ui_strings.cpp \
+ src/xml/xml_strings.h \
+ src/xml/xml_strings.cpp
+
+old_lam_conv_SOURCES = $(old_lam_conv_core) \
+ $(old_lam_conv_resources) \
+ src/conversion/ConverterUIMain.cpp
+
+EXTRA_old_lam_conv_SOURCES = $(old_lam_conv_icons)
+converter_err_sources = \
+ src/control/errhandling.h \
+ src/control/errhandling.cpp \
+ src/convErr/gc_errhandling.h \
+ src/convErr/gc_errhandling.cpp \
+ \
+ src/convErr/gc_cmdfile_err.h \
+ src/convErr/gc_cmdfile_err.cpp \
+ src/convErr/gc_data_missing_err.h \
+ src/convErr/gc_data_missing_err.cpp \
+ src/convErr/gc_individual_err.h \
+ src/convErr/gc_individual_err.cpp \
+ src/convErr/gc_infile_err.h \
+ src/convErr/gc_infile_err.cpp \
+ src/convErr/gc_locus_err.h \
+ src/convErr/gc_locus_err.cpp \
+ src/convErr/gc_map_err.h \
+ src/convErr/gc_map_err.cpp \
+ src/convErr/gc_phase_err.h \
+ src/convErr/gc_phase_err.cpp \
+ src/convErr/gc_structures_err.h \
+ src/convErr/gc_structures_err.cpp \
+ src/convErr/gc_trait_err.h \
+ src/convErr/gc_trait_err.cpp
+
+converter_model_sources = \
+ src/guiconv/gc_cmdline.h \
+ src/guiconv/gc_cmdline.cpp \
+ src/guiconv/gc_data.h \
+ src/guiconv/gc_data.cpp \
+ src/convModel/gc_dictionary.h \
+ src/convModel/gc_dictionary.cpp \
+ src/ui_interface/front_end_warnings.cpp \
+ src/ui_interface/front_end_warnings.h \
+ src/convModel/cmdfileschema.h \
+ src/convModel/cmdfileschema.cpp \
+ src/convModel/gc_datastore.h \
+ src/convModel/gc_datastore.cpp \
+ src/convModel/gc_datastore_export.cpp \
+ src/convModel/gc_datastore_files.cpp \
+ src/convModel/gc_datastore_readcmd.cpp \
+ src/convModel/gc_datastore_writebatch.cpp \
+ src/convModel/gc_default.h \
+ src/convModel/gc_default.cpp \
+ src/convModel/gc_exportable.h \
+ src/convModel/gc_exportable.cpp \
+ src/convModel/gc_file.h \
+ src/convModel/gc_file.cpp \
+ src/convModel/gc_file_info.h \
+ src/convModel/gc_file_info.cpp \
+ src/convModel/gc_migration.h \
+ src/convModel/gc_migration.cpp \
+ src/convModel/gc_panel.h \
+ src/convModel/gc_panel.cpp \
+ src/convModel/gc_parent.h \
+ src/convModel/gc_parent.cpp \
+ src/convModel/gc_phase.h \
+ src/convModel/gc_phase.cpp \
+ src/convModel/gc_phase_info.h \
+ src/convModel/gc_phase_info.cpp \
+ src/convModel/gc_phenotype.h \
+ src/convModel/gc_phenotype.cpp \
+ src/convModel/gc_set_util.h \
+ src/convModel/gc_set_util.cpp \
+ src/convModel/gc_structure_maps.h \
+ src/convModel/gc_structure_maps.cpp \
+ src/convModel/gc_structures.h \
+ src/convModel/gc_structures.cpp \
+ src/convModel/gc_trait.h \
+ src/convModel/gc_trait.cpp \
+ src/convModel/gc_trait_allele.h \
+ src/convModel/gc_trait_allele.cpp \
+ src/convModel/gc_types.h \
+ src/convModel/gc_types.cpp \
+ src/guiconv/gc_quantum.h \
+ src/guiconv/gc_quantum.cpp
+
+converter_parse_sources = \
+ src/convParse/gc_genotype_resolution.h \
+ src/convParse/gc_genotype_resolution.cpp \
+ src/convModel/gc_creation_info.h \
+ src/convModel/gc_creation_info.cpp \
+ src/convModel/gc_individual.h \
+ src/convModel/gc_individual.cpp \
+ src/convParse/gc_loci_match.h \
+ src/convParse/gc_loci_match.cpp \
+ src/convParse/gc_locus.h \
+ src/convParse/gc_locus.cpp \
+ src/convParse/gc_migrate.h \
+ src/convParse/gc_migrate.cpp \
+ src/convParse/gc_parse.h \
+ src/convParse/gc_parse.cpp \
+ src/convParse/gc_parse_block.h \
+ src/convParse/gc_parse_block.cpp \
+ src/convParse/gc_parse_locus.h \
+ src/convParse/gc_parse_locus.cpp \
+ src/convParse/gc_parse_pop.h \
+ src/convParse/gc_parse_pop.cpp \
+ src/convParse/gc_parse_sample.h \
+ src/convParse/gc_parse_sample.cpp \
+ src/convParse/gc_parser.h \
+ src/convParse/gc_parser.cpp \
+ src/convParse/gc_phylip.h \
+ src/convParse/gc_phylip.cpp \
+ src/convParse/gc_pop_match.h \
+ src/convParse/gc_pop_match.cpp \
+ src/convParse/gc_population.h \
+ src/convParse/gc_population.cpp \
+ src/convParse/gc_region.h \
+ src/convParse/gc_region.cpp \
+ src/convParse/gc_sequential_data.h \
+ src/convParse/gc_sequential_data.cpp \
+ src/convParse/tixml_util.h \
+ src/convParse/tixml_util.cpp \
+ $(xml_core_sources) \
+ $(xml_support_sources)
+
+converter_string_sources = \
+ src/convStrings/cnv_strings.h \
+ src/convStrings/cnv_strings.cpp \
+ src/convStrings/gc_strings.h \
+ src/convStrings/gc_strings_cmdfile.h \
+ src/convStrings/gc_strings_cmdfile.cpp \
+ src/convStrings/gc_strings_creation.h \
+ src/convStrings/gc_strings_creation.cpp \
+ src/convStrings/gc_strings_data.h \
+ src/convStrings/gc_strings_data.cpp \
+ src/convStrings/gc_strings_err.cpp \
+ src/convStrings/gc_strings_individual.h \
+ src/convStrings/gc_strings_individual.cpp \
+ src/convStrings/gc_strings_infile.h \
+ src/convStrings/gc_strings_infile.cpp \
+ src/convStrings/gc_strings_io.h \
+ src/convStrings/gc_strings_io.cpp \
+ src/convStrings/gc_strings_locus.h \
+ src/convStrings/gc_strings_locus.cpp \
+ src/convStrings/gc_strings_map.h \
+ src/convStrings/gc_strings_map.cpp \
+ src/convStrings/gc_strings_mig.h \
+ src/convStrings/gc_strings_mig.cpp \
+ src/convStrings/gc_strings_parse.h \
+ src/convStrings/gc_strings_parse.cpp \
+ src/convStrings/gc_strings_parse_locus.h \
+ src/convStrings/gc_strings_parse_locus.cpp \
+ src/convStrings/gc_strings_phase.h \
+ src/convStrings/gc_strings_phase.cpp \
+ src/convStrings/gc_strings_pop.h \
+ src/convStrings/gc_strings_pop.cpp \
+ src/convStrings/gc_strings_region.h \
+ src/convStrings/gc_strings_region.cpp \
+ src/convStrings/gc_strings_str_a_m.cpp \
+ src/convStrings/gc_strings_str_n_z.cpp \
+ src/convStrings/gc_strings_structures.h \
+ src/convStrings/gc_strings_structures.cpp \
+ src/convStrings/gc_strings_trait.h \
+ src/convStrings/gc_strings_trait.cpp
+
+converter_util_sources = \
+ src/convUtil/gc_file_util.h \
+ src/convUtil/gc_file_util.cpp
+
+gui_util_sources = \
+ src/guiutil/gc_clickpanel.h \
+ src/guiutil/gc_clickpanel.cpp \
+ src/guiutil/gc_gridpanel.h \
+ src/guiutil/gc_gridpanel.cpp \
+ src/guiutil/gc_text_ctrl.h \
+ src/guiutil/gc_text_ctrl.cpp \
+ src/guiutil/gc_validators.h \
+ src/guiutil/gc_validators.cpp
+
+old_gui_conv_sources = \
+ src/guiconv/gc_export_dialogs.h \
+ src/guiconv/gc_export_dialogs.cpp \
+ src/guiconv/gc_unit_dialogs.h \
+ src/guiconv/gc_unit_dialogs.cpp
+
+gui_conv_sources = \
+ resources/empty16.xpm \
+ resources/excl16.xpm \
+ resources/giraffe32.xpm \
+ src/guiconv/gc_assigntab.h \
+ src/guiconv/gc_assigntab.cpp \
+ src/guiconv/gc_block_dialogs.h \
+ src/guiconv/gc_block_dialogs.cpp \
+ src/guiconv/gc_color.h \
+ src/guiconv/gc_color.cpp \
+ src/guiconv/gc_data_display.h \
+ src/guiconv/gc_data_display.cpp \
+ src/guiconv/gc_dialog.h \
+ src/guiconv/gc_dialog.cpp \
+ src/guiconv/gc_event_ids.h \
+ src/guiconv/gc_event_publisher.h \
+ src/guiconv/gc_event_publisher.cpp \
+ src/guiconv/gc_file_dialogs.h \
+ src/guiconv/gc_file_dialogs.cpp \
+ src/guiconv/gc_file_list.h \
+ src/guiconv/gc_file_list.cpp \
+ src/guiconv/gc_frame.h \
+ src/guiconv/gc_frame.cpp \
+ src/guiconv/gc_layout.h \
+ src/guiconv/gc_layout.cpp \
+ src/guiconv/gc_locus_dialogs.h \
+ src/guiconv/gc_locus_dialogs.cpp \
+ src/guiconv/gc_logic.h \
+ src/guiconv/gc_logic.cpp \
+ src/guiconv/gc_matrix_display.h \
+ src/guiconv/gc_matrix_display.cpp \
+ src/guiconv/gc_menu_actors.h \
+ src/guiconv/gc_menu_actors.cpp \
+ src/guiconv/gc_migration_dialogs.h \
+ src/guiconv/gc_migration_dialogs.cpp \
+ src/guiconv/gc_migtab.h \
+ src/guiconv/gc_migtab.cpp \
+ src/guiconv/gc_panel_dialogs.h \
+ src/guiconv/gc_panel_dialogs.cpp \
+ src/guiconv/gc_parent_dialogs.h \
+ src/guiconv/gc_parent_dialogs.cpp \
+ src/guiconv/gc_population_dialogs.h \
+ src/guiconv/gc_population_dialogs.cpp \
+ src/guiconv/gc_region_dialogs.h \
+ src/guiconv/gc_region_dialogs.cpp \
+ src/guiconv/gc_trait_dialogs.h \
+ src/guiconv/gc_trait_dialogs.cpp \
+ src/guiconv/guiconverter.h \
+ src/guiconv/guiconverter.cpp
+
+lam_conv_core = \
+ $(gui_util_sources) \
+ $(gui_conv_sources)
+
+lam_conv_SOURCES = \
+ $(converter_err_sources) \
+ $(converter_model_sources) \
+ $(converter_parse_sources) \
+ $(converter_string_sources) \
+ $(converter_util_sources) \
+ $(lam_conv_core) \
+ $(lam_conv_resources)
+
+lam_conv_LDADD = @WX_LIBS@ $(am__append_27) $(am__append_28)
+EXTRA_lam_conv_SOURCES = $(tinyxml_suite) $(lam_conv_icons)
+batch_lam_conv_core = \
+ src/guiconv/batchconverter.h \
+ src/guiconv/batchconverter.cpp
+
+batch_lam_conv_testable = \
+ $(batch_lam_conv_core) \
+ $(converter_err_sources) \
+ $(converter_model_sources) \
+ $(converter_parse_sources) \
+ $(converter_string_sources) \
+ $(converter_util_sources)
+
+batch_lam_conv_SOURCES = \
+ $(batch_lam_conv_testable)
+
+batch_lam_conv_LDADD = lam_conv_LDADD
+EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)
+lam_conv_app_SOURCES =
+lamarc_app_SOURCES =
+html_DATA = \
+ doc/html/bayes.html \
+ doc/html/bayes_howto.html \
+ doc/html/changes.html \
+ doc/html/comparing_curvefiles.sxc \
+ doc/html/comparing_curvefiles.xls \
+ doc/html/compiling.html \
+ doc/html/converter.html \
+ doc/html/converter_cmd.html \
+ doc/html/curve-smoothing.html \
+ doc/html/data_models.html \
+ doc/html/data_required.html \
+ doc/html/divergence.html \
+ doc/html/forces.html \
+ doc/html/gamma.html \
+ doc/html/genetic_map.html \
+ doc/html/genotype.html \
+ doc/html/glossary.html \
+ doc/html/growthmenu.html \
+ doc/html/forces.html \
+ doc/html/index.html \
+ doc/html/insumfile.2reg3rep.html \
+ doc/html/insumfile.2reg3rep.xml \
+ doc/html/insumfile.3rep.html \
+ doc/html/insumfile.3rep.xml \
+ doc/html/limitations.html \
+ doc/html/mapping.html \
+ doc/html/menu.html \
+ doc/html/messages.html \
+ doc/html/migration_matrix.html \
+ doc/html/output.html \
+ doc/html/outsumfile.2reg3rep.html \
+ doc/html/outsumfile.2reg3rep.xml \
+ doc/html/outsumfile.3rep.html \
+ doc/html/outsumfile.3rep.xml \
+ doc/html/overview.html \
+ doc/html/panels.html \
+ doc/html/parallel.html \
+ doc/html/parameters.html \
+ doc/html/regions.html \
+ doc/html/search.html \
+ doc/html/tracer.html \
+ doc/html/troubleshooting.html \
+ doc/html/tutorial.html \
+ doc/html/tutorial2.html \
+ doc/html/upcoming.html \
+ doc/html/viral_data.html \
+ doc/html/xmlinput.html
+
+htmlimgdir = $(prefix)/html/lamarc/images
+htmlimg_DATA = \
+ doc/html/images/LamarcAnalysisScreen.png \
+ doc/html/images/LamarcDataScreen.png \
+ doc/html/images/LamarcIOScreen.png \
+ doc/html/images/LamarcMainScreen.png \
+ doc/html/images/LamarcOverviewScreen.png \
+ doc/html/images/LamarcSearchScreen.png \
+ doc/html/images/browser-gtk.gif \
+ doc/html/images/correlated1.gif \
+ doc/html/images/correlated2.gif \
+ doc/html/images/gui_lam_conv.gif \
+ doc/html/images/lam_conv.gif \
+ doc/html/images/lamarc.gif \
+ doc/html/images/loci-gtk.png \
+ doc/html/images/loci2-gtk.png \
+ doc/html/images/partitions-gtk.png \
+ doc/html/images/partitions2-gtk.png \
+ doc/html/images/populations-gtk.png \
+ doc/html/images/startup-gtk.png \
+ doc/html/images/tracer_trend.png \
+ doc/html/images/uncorrelated.gif \
+ doc/html/images/variably_correlated.gif
+
+htmlbconvdir = $(prefix)/html/lamarc/batch_converter
+htmlbconv_DATA = \
+ doc/html/batch_converter/README.txt \
+ doc/html/batch_converter/chrom1_lamarc.html \
+ doc/html/batch_converter/chrom1_lamarc.xml \
+ doc/html/batch_converter/chrom1.mig \
+ doc/html/batch_converter/chrom2_lamarc.xml \
+ doc/html/batch_converter/chrom2.mig \
+ doc/html/batch_converter/chrom3_lamarc.xml \
+ doc/html/batch_converter/chrom3_phase_cmd.xml \
+ doc/html/batch_converter/chrom3microsat.mig \
+ doc/html/batch_converter/chrom3snp.mig \
+ doc/html/batch_converter/exported-lamarc-input.xml \
+ doc/html/batch_converter/sample-conv-cmd.html \
+ doc/html/batch_converter/sample-conv-cmd.xml
+
+htmlbconvimgdir = $(prefix)/html/lamarc/batch_converter/images
+htmlbconvimg_DATA = \
+ doc/html/batch_converter/images/CombinedPanels.png \
+ doc/html/batch_converter/images/DataFilesTab.png \
+ doc/html/batch_converter/images/DataPartitionsMigTab.png \
+ doc/html/batch_converter/images/DebugLogTab.png \
+ doc/html/batch_converter/images/DivergeOff.png \
+ doc/html/batch_converter/images/DivMigMatrixTab.png \
+ doc/html/batch_converter/images/EditMigration.png \
+ doc/html/batch_converter/images/EditPanelCorrection.png \
+ doc/html/batch_converter/images/FirstParent.png \
+ doc/html/batch_converter/images/FirstParent2Children.png \
+ doc/html/batch_converter/images/FullParentsImage.png \
+ doc/html/batch_converter/images/InterumParentImage.png \
+ doc/html/batch_converter/images/MigrationOnlyMatrixTab.png \
+ doc/html/batch_converter/images/PanelCorrectionOn.png \
+ doc/html/batch_converter/images/SecondParent.png \
+ doc/html/batch_converter/images/lam_conv_chrom1_export_file_selection.png \
+ doc/html/batch_converter/images/lam_conv_chrom1_export_warn_1.png \
+ doc/html/batch_converter/images/lam_conv_chrom1_input.png \
+ doc/html/batch_converter/images/lam_conv_chrom1_segment_panel.png \
+ doc/html/batch_converter/images/lam_conv_chrom2_segment1.png \
+ doc/html/batch_converter/images/lam_conv_chrom3_error_map_position.png \
+ doc/html/batch_converter/images/lam_conv_chrom3_error_phase_file_needed.png \
+ doc/html/batch_converter/images/lam_conv_chrom3_input.png \
+ doc/html/batch_converter/images/lam_conv_chrom3_region_panel.png \
+ doc/html/batch_converter/images/lam_conv_chrom3_region_table.png \
+ doc/html/batch_converter/images/lam_conv_chrom3_segment_snp.png \
+ doc/html/batch_converter/images/lam_conv_export_file_mac_minimal.png \
+ doc/html/batch_converter/images/lam_conv_export_file_mac_expanded.png
+
+htmltraitdir = $(prefix)/html/lamarc/trait_mapping
+htmltrait_DATA = \
+ doc/html/trait_mapping/README.txt \
+ doc/html/trait_mapping/lamarc-trait-input.html \
+ doc/html/trait_mapping/lamarc-trait-input.xml \
+ doc/html/trait_mapping/mapfile_funny-nose.txt \
+ doc/html/trait_mapping/outfile.txt \
+ doc/html/trait_mapping/traitCmd.html \
+ doc/html/trait_mapping/traitCmd.xml \
+ doc/html/trait_mapping/traitCmd.xml.txt \
+ doc/html/trait_mapping/traitData.mig
+
+license_info = \
+ COPYING \
+ doc/licenses/boost.txt \
+ doc/licenses/gpl.txt \
+ doc/licenses/lamarc.txt \
+ doc/licenses/lgpl.txt \
+ doc/licenses/wx.txt \
+ doc/licenses/wxdoc.txt \
+ doc/licenses/zlib.txt
+
+wx_curr = \
+ wxWidgets/wxWidgets-2.8.12.tar.gz
+
+wx_stuff = \
+ wxWidgets/wxWidgets-2.8.10.tar.gz \
+ wxWidgets/wxWidgets-2.8.8.tar.gz \
+ $(wx_curr)
+
+EXTRA_DIST = \
+ Makefile.am \
+ configure.ac \
+ boost \
+ tinyxml \
+ $(license_info) \
+ $(wx_curr) \
+ $(scripts_to_dist) \
+ scripts/pyParallel \
+ $(html_DATA) $(htmlimg_DATA) $(htmlbconv_DATA)\
+ $(htmlbconvimg_DATA) \
+ $(htmltrait_DATA) \
+ doc/testfiles/sample_infile.xml \
+ doc/testfiles/sample_outfile.txt \
+ doc/testfiles/sample_outsumfile.xml \
+ CONTENTS \
+ HISTORY \
+ INSTALL \
+ README \
+ $(top_srcdir)/resources/Info.plist.in \
+ $(top_srcdir)/resources/lamarc.command
+
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .rc .cpp .o .obj
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+ @:
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+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
+ $(am__cd) $(top_srcdir) && \
+ $(AUTOMAKE) --foreign Makefile
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+ ($(am__cd) $(top_srcdir) && $(AUTOHEADER))
+ rm -f config/stamp-h1
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+
+distclean-hdr:
+ -rm -f config/conf.h config/stamp-h1
+
+clean-noinstLIBRARIES:
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+ sed -e 'p;s,.*/,,;n;h' \
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+ $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
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+ END { for (d in files) print "f", d, files[d] }' | \
+ while read type dir files; do \
+ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
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+ } \
+ ; done
+
+uninstall-binPROGRAMS:
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+ test -n "$$list" || exit 0; \
+ echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+ cd "$(DESTDIR)$(bindir)" && rm -f $$files
+
+clean-binPROGRAMS:
+ -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
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+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
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+ uninstall-htmlbconvDATA uninstall-htmlbconvimgDATA \
+ uninstall-htmlimgDATA uninstall-htmltraitDATA
+
+.PRECIOUS: Makefile
+
+
+.rc.o:
+ @LAMARC_HOST_PREFIX at windres -i $< -o $@ -I $(top_srcdir)/resources
+
+lamarc_rc.o : $(top_srcdir)/resources/lamarc_rc.rc
+ @LAMARC_HOST_PREFIX at windres -i $< -o $@ -I $(top_srcdir)/resources
+
+lam_conv_rc.o : $(top_srcdir)/resources/lam_conv_rc.rc
+ @LAMARC_HOST_PREFIX at windres -i $< -o $@ -I $(top_srcdir)/resources
+
+lam_conv.app$(EXEEXT): lam_conv
+ @rm -rf lam_conv.app
+ $(MACDEVTOOLS)/Rez -d __DARWIN__ -t APPL Carbon.r -o lam_conv
+ $(MACDEVTOOLS)/SetFile -a C lam_conv
+ -mkdir -p lam_conv.app/Contents/MacOS
+ -mkdir -p lam_conv.app/Contents/Resources
+ sed -e "s/IDENTIFIER/lam_conv/" \
+ -e "s/COMMAND/lam_conv/" \
+ -e "s/EXECUTABLE/lam_conv/" \
+ -e "s/ICONNAME/lam_conv/" \
+ -e "s/VERSION/@VERSION@/" \
+ $(top_srcdir)/resources/Info.plist.in > lam_conv.app/Contents/Info.plist
+ echo -n "APPL????" >lam_conv.app/Contents/PkgInfo
+ cp -f lam_conv lam_conv.app/Contents/MacOS/lam_conv
+ cp -f $(top_srcdir)/resources/lam_conv.icns lam_conv.app/Contents/Resources/lam_conv.icns
+
+lamarc.app$(EXEEXT): lamarc
+ @rm -rf lamarc.app
+ $(MACDEVTOOLS)/Rez -d __DARWIN__ -t APPL Carbon.r -o lamarc
+ $(MACDEVTOOLS)/SetFile -a C lamarc
+ -mkdir -p lamarc.app/Contents/MacOS
+ -mkdir -p lamarc.app/Contents/Resources
+ sed -e "s/IDENTIFIER/lamarc/" \
+ -e "s/COMMAND/lamarc.command/" \
+ -e "s/EXECUTABLE/lamarc/" \
+ -e "s/ICONNAME/lamarc/" \
+ -e "s/VERSION/@VERSION@/" \
+ $(top_srcdir)/resources/Info.plist.in > lamarc.app/Contents/Info.plist
+ cp -f $(top_srcdir)/resources/lamarc.command lamarc.app/Contents/MacOS/lamarc.command
+ chmod ug+x lamarc.app/Contents/MacOS/lamarc.command
+ echo -n "APPL????" >lamarc.app/Contents/PkgInfo
+ ln -f lamarc lamarc.app/Contents/MacOS/lamarc
+ cp -f $(top_srcdir)/resources/lamarc.icns lamarc.app/Contents/Resources/lamarc.icns
+
+# these used to be in EXTRA_DIST, but it's broken and not testable
+# should I decide to fix it
+# $(vcprojdir)/batch_lam_conv.vcproj
+# $(vcprojdir)/lam_conv.vcproj
+# $(vcprojdir)/lamarc.vcproj
+
+dist-hook:
+ rm -rf `find $(distdir)/boost -name CVS`
+ rm -rf `find $(distdir)/tinyxml -name CVS`
+
+filelist :
+ echo $(lamarcgcov_sources)
+
+batchfilelist :
+ echo $(batch_lam_conv_testable)
+
+guifilelist :
+ echo $(lam_conv_core)
+
+resourcelist :
+ echo $(lamarc_resources)
+
+.PHONY : filelist resourcelist
+
+webskeleton :
+ tar xfvz $(top_srcdir)/tools/apache-forrest-0.7.tar.gz
+ rm -f -r webBuildDir
+ mkdir webBuildDir
+ cd webBuildDir ; \
+ ../apache-forrest-0.7/bin/forrest seed
+ cp $(top_srcdir)/website/apacheInput/skinconf.xml webBuildDir/src/documentation
+ rm -f -r webBuildDir/src/documentation/content
+ mkdir webBuildDir/src/documentation/content
+ cp -r $(top_srcdir)/website/apacheInput/xdocs webBuildDir/src/documentation/content/
+ cd webBuildDir ; \
+ ../apache-forrest-0.7/bin/forrest
+ cd webBuildDir/build ; \
+ mv site lamarc ; \
+ tar cfvz ../../lamarcweb-$(VERSION).tar.gz lamarc
+
+all-local:
+ @echo "-----------------------------------------------------"
+ @echo "Lamarc $(VERSION)"
+ @echo "Please read the documentation in ./doc/html/"
+ @echo "This Makefile will produce executables lam_conv and lamarc"
+ @echo ""
+ @echo "If you have problems, please send us an email including "
+ @echo " any compile warnings, error messages, and information"
+ @echo " on other issues you may have to lamarc at gs.washington.edu"
+ @echo "[Mary Kuhner, Jon Yamato, Peter Beerli]"
+ @echo "----------------------------------------------------"
+
+ at CONVERTER_TRUE@@GUI_TRUE at batch_lam_conv:
+ at CONVERTER_TRUE@@GUI_TRUE@ @echo "-----------------------------------------------------"
+ at CONVERTER_TRUE@@GUI_TRUE@ @echo "batch_lam_conv cannot be compiled because you have"
+ at CONVERTER_TRUE@@GUI_TRUE@ @echo "configured with --enable-gui"
+ at CONVERTER_TRUE@@GUI_TRUE@ @echo "-----------------------------------------------------"
+
+ at CONVERTER_TRUE@@GUI_FALSE at lam_conv:
+ at CONVERTER_TRUE@@GUI_FALSE@ @echo "-----------------------------------------------------"
+ at CONVERTER_TRUE@@GUI_FALSE@ @echo "lam_conv cannot be compiled because you have"
+ at CONVERTER_TRUE@@GUI_FALSE@ @echo "configured with --disable-gui"
+ at CONVERTER_TRUE@@GUI_FALSE@ @echo "-----------------------------------------------------"
+
+ at CONVERTER_FALSE@batch_lam_conv:
+ at CONVERTER_FALSE@ @echo "-----------------------------------------------------"
+ at CONVERTER_FALSE@ @echo "batch_lam_conv cannot be compiled because you have"
+ at CONVERTER_FALSE@ @echo "configured with --disable-converter"
+ at CONVERTER_FALSE@ @echo "-----------------------------------------------------"
+
+ at CONVERTER_FALSE@lam_conv:
+ at CONVERTER_FALSE@ @echo "-----------------------------------------------------"
+ at CONVERTER_FALSE@ @echo "lam_conv cannot be compiled because you have"
+ at CONVERTER_FALSE@ @echo "configured with --disable-converter"
+ at CONVERTER_FALSE@ @echo "-----------------------------------------------------"
+
+distclean-local:
+ rm -f $(vcprojdir)/*.vcproj projects/macos/*.xml
+
+clean-local:
+ rm -f *.gcov *.gcno *.gcda
+ rm -f -r *.app
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/README b/README
new file mode 100644
index 0000000..93e8c8c
--- /dev/null
+++ b/README
@@ -0,0 +1,61 @@
+Lamarc 2.1.10
+Sep 3 2014
+===============
+
+A program to estimate population parameters from genetic data. All
+parameters are estimated jointly. Currently the program allows estimation
+of population sizes, recombination rate, migration rates, growth
+rates, and population divergence times, and can estimate the location of
+a trait allele.
+
+This version is a bug fix update to version 2.1.8 (May 2012). It
+fixes severe bugs in estimation of divergence times and of migration
+in the presence of divergence; runs inferring those parameters should
+be re-done. The bugs did not exist prior to 2.1.8 as divergence was
+not released before that.
+
+DOCUMENTATION & GETTING HELP
+============================
+
+Extensive documentation is available in the doc/ subdirectory of
+your lamarc distribution. You will likely wish to begin with
+the HTML documentation available in doc/html/index.html .
+
+Careful reading of the documentation will be necessary to obtain
+a high quality lamarc analysis of your data. As the program user,
+you will need to make decisions such as
+ * which evolutionary forces to model,
+ * which mutational model to assume for your data, and
+ * how long to run the program.
+Please note that there may be specific documentation sections
+relevant to your particular data type, such as viral data, or
+phase unresolved data.
+
+The most up-to-date information on Lamarc is available at the project
+website http://evolution.gs.washington.edu/lamarc/
+
+If, after reading the relevant documentation, you still have questions,
+please email the lamarc developers at:
+
+ lamarc at uw.edu
+
+BINARY DISTRIBUTIONS:
+=====================
+If you have downloaded a binary distribution (executables) you are all
+set and the programs "lamarc" and "lam_conv" are in the same directory
+as this README.
+
+Linux users--you may recieve a cryptic sounding error message concerning
+"libstdc++.so.6" or something similar. In order to run lamarc you
+will need to either get the lamarc source distribution and compile
+it on your computer, or you will need to install some variant of
+version 6 of the standard c++ shared library. Debian users with
+"apt" installed can use "apt-get install libstdc++6" to get the needed
+library.
+
+SOURCE DISTRIBUTIONS:
+=====================
+If you have downloaded the source and have a *UNIX* system (LINUX,
+BSD, MACOSX, SOLARIS, TRU64, etc) see doc/html/compiling.html for
+directions to build "lamarc" and "lam_conv".
+
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+AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
+# We need awk for the "check" target (and possibly the TAP driver). The
+# system "awk" is bad on some platforms.
+AC_REQUIRE([AC_PROG_AWK])dnl
+AC_REQUIRE([AC_PROG_MAKE_SET])dnl
+AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+_AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
+ [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])],
+ [_AM_PROG_TAR([v7])])])
+_AM_IF_OPTION([no-dependencies],,
+[AC_PROVIDE_IFELSE([AC_PROG_CC],
+ [_AM_DEPENDENCIES([CC])],
+ [m4_define([AC_PROG_CC],
+ m4_defn([AC_PROG_CC])[_AM_DEPENDENCIES([CC])])])dnl
+AC_PROVIDE_IFELSE([AC_PROG_CXX],
+ [_AM_DEPENDENCIES([CXX])],
+ [m4_define([AC_PROG_CXX],
+ m4_defn([AC_PROG_CXX])[_AM_DEPENDENCIES([CXX])])])dnl
+AC_PROVIDE_IFELSE([AC_PROG_OBJC],
+ [_AM_DEPENDENCIES([OBJC])],
+ [m4_define([AC_PROG_OBJC],
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+AC_PROVIDE_IFELSE([AC_PROG_OBJCXX],
+ [_AM_DEPENDENCIES([OBJCXX])],
+ [m4_define([AC_PROG_OBJCXX],
+ m4_defn([AC_PROG_OBJCXX])[_AM_DEPENDENCIES([OBJCXX])])])dnl
+])
+AC_REQUIRE([AM_SILENT_RULES])dnl
+dnl The testsuite driver may need to know about EXEEXT, so add the
+dnl 'am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This
+dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
+AC_CONFIG_COMMANDS_PRE(dnl
+[m4_provide_if([_AM_COMPILER_EXEEXT],
+ [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
+
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
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+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
+ fi
+fi
+dnl The trailing newline in this macro's definition is deliberate, for
+dnl backward compatibility and to allow trailing 'dnl'-style comments
+dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
+])
+
+dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
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+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# AM_PROG_INSTALL_SH
+# ------------------
+# Define $install_sh.
+AC_DEFUN([AM_PROG_INSTALL_SH],
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+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+AC_SUBST([install_sh])])
+
+# Copyright (C) 2003-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# Check whether the underlying file-system supports filenames
+# with a leading dot. For instance MS-DOS doesn't.
+AC_DEFUN([AM_SET_LEADING_DOT],
+[rm -rf .tst 2>/dev/null
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+rmdir .tst 2>/dev/null
+AC_SUBST([am__leading_dot])])
+
+# Add --enable-maintainer-mode option to configure. -*- Autoconf -*-
+# From Jim Meyering
+
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_MAINTAINER_MODE([DEFAULT-MODE])
+# ----------------------------------
+# Control maintainer-specific portions of Makefiles.
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+# can override the default with the --enable/--disable switch.
+AC_DEFUN([AM_MAINTAINER_MODE],
+[m4_case(m4_default([$1], [disable]),
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+ m4_warn([syntax], [unexpected argument to AM@&t at _MAINTAINER_MODE: $1])])
+AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])
+ dnl maintainer-mode's default is 'disable' unless 'enable' is passed
+ AC_ARG_ENABLE([maintainer-mode],
+ [AS_HELP_STRING([--]am_maintainer_other[-maintainer-mode],
+ am_maintainer_other[ make rules and dependencies not useful
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+ AC_SUBST([MAINT])dnl
+]
+)
+
+# Check to see how 'make' treats includes. -*- Autoconf -*-
+
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_MAKE_INCLUDE()
+# -----------------
+# Check to see how make treats includes.
+AC_DEFUN([AM_MAKE_INCLUDE],
+[am_make=${MAKE-make}
+cat > confinc << 'END'
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+ @echo this is the am__doit target
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+# If we don't find an include directive, just comment out the code.
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+am__include="#"
+am__quote=
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+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
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+ case `$am_make -s -f confmf 2> /dev/null` in #(
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+ _am_result=BSD
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+AC_SUBST([am__include])
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+rm -f confinc confmf
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+
+# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
+
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+#
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+# with or without modifications, as long as this notice is preserved.
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+# AM_MISSING_PROG(NAME, PROGRAM)
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+AC_SUBST($1)])
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+# AM_MISSING_HAS_RUN
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+# Use eval to expand $SHELL
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+ am_missing_run="$MISSING "
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+ am_missing_run=
+ AC_MSG_WARN(['missing' script is too old or missing])
+fi
+])
+
+# Helper functions for option handling. -*- Autoconf -*-
+
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
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+# with or without modifications, as long as this notice is preserved.
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+# _AM_MANGLE_OPTION(NAME)
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+# _AM_SET_OPTIONS(OPTIONS)
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+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
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+# with or without modifications, as long as this notice is preserved.
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+# _AM_PROG_CC_C_O
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+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
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+
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+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
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+# Copyright (C) 2009-2014 Free Software Foundation, Inc.
+#
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+# with or without modifications, as long as this notice is preserved.
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+# AM_SILENT_RULES([DEFAULT])
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+dnl A few 'make' implementations (e.g., NonStop OS and NextStep)
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+dnl See automake bug#9928 and bug#10237.
+am_make=${MAKE-make}
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+_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
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+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
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+
+# AM_PROG_INSTALL_STRIP
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+# Copyright (C) 2006-2014 Free Software Foundation, Inc.
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+# _AM_SUBST_NOTMAKE(VARIABLE)
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+# Check how to create a tarball. -*- Autoconf -*-
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+# _AM_PROG_TAR(FORMAT)
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+m4_if([$1], [v7],
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+ [ustar],
+ [# The POSIX 1988 'ustar' format is defined with fixed-size fields.
+ # There is notably a 21 bits limit for the UID and the GID. In fact,
+ # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
+ # and bug#13588).
+ am_max_uid=2097151 # 2^21 - 1
+ am_max_gid=$am_max_uid
+ # The $UID and $GID variables are not portable, so we need to resort
+ # to the POSIX-mandated id(1) utility. Errors in the 'id' calls
+ # below are definitely unexpected, so allow the users to see them
+ # (that is, avoid stderr redirection).
+ am_uid=`id -u || echo unknown`
+ am_gid=`id -g || echo unknown`
+ AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
+ if test $am_uid -le $am_max_uid; then
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ _am_tools=none
+ fi
+ AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
+ if test $am_gid -le $am_max_gid; then
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ _am_tools=none
+ fi],
+
+ [pax],
+ [],
+
+ [m4_fatal([Unknown tar format])])
+
+ AC_MSG_CHECKING([how to create a $1 tar archive])
+
+ # Go ahead even if we have the value already cached. We do so because we
+ # need to set the values for the 'am__tar' and 'am__untar' variables.
+ _am_tools=${am_cv_prog_tar_$1-$_am_tools}
+
+ for _am_tool in $_am_tools; do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar; do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
+
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
+
+ # tar/untar a dummy directory, and stop if the command works.
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ AM_RUN_LOG([cat conftest.dir/file])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+ done
+ rm -rf conftest.dir
+
+ AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+ AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+
+AC_SUBST([am__tar])
+AC_SUBST([am__untar])
+]) # _AM_PROG_TAR
+
diff --git a/config/conf.h.in b/config/conf.h
similarity index 67%
copy from config/conf.h.in
copy to config/conf.h
index ea1e6d5..957314a 100644
--- a/config/conf.h.in
+++ b/config/conf.h
@@ -1,103 +1,101 @@
+/* config/conf.h. Generated from conf.h.in by configure. */
/* config/conf.h.in. Generated from configure.ac by autoheader. */
/* Define to 1 if you have the <float.h> header file. */
-#undef HAVE_FLOAT_H
+#define HAVE_FLOAT_H 1
/* Define to 1 if you have the `getcwd' function. */
-#undef HAVE_GETCWD
+#define HAVE_GETCWD 1
/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
+#define HAVE_INTTYPES_H 1
/* Define to 1 if you have the <limits.h> header file. */
-#undef HAVE_LIMITS_H
+#define HAVE_LIMITS_H 1
/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
+#define HAVE_MEMORY_H 1
/* Define to 1 if you have the `pow' function. */
-#undef HAVE_POW
+/* #undef HAVE_POW */
/* Define to 1 if you have the `sqrt' function. */
-#undef HAVE_SQRT
+/* #undef HAVE_SQRT */
/* Define to 1 if stdbool.h conforms to C99. */
-#undef HAVE_STDBOOL_H
+#define HAVE_STDBOOL_H 1
/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
+#define HAVE_STDINT_H 1
/* Define to 1 if you have the <stdlib.h> header file. */
-#undef HAVE_STDLIB_H
+#define HAVE_STDLIB_H 1
/* Define to 1 if you have the `strchr' function. */
-#undef HAVE_STRCHR
+#define HAVE_STRCHR 1
/* Define to 1 if you have the `strftime' function. */
-#undef HAVE_STRFTIME
+#define HAVE_STRFTIME 1
/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
+#define HAVE_STRINGS_H 1
/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
+#define HAVE_STRING_H 1
/* Define to 1 if you have the `strpbrk' function. */
-#undef HAVE_STRPBRK
+#define HAVE_STRPBRK 1
/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
+#define HAVE_SYS_STAT_H 1
/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
+#define HAVE_SYS_TYPES_H 1
/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
+#define HAVE_UNISTD_H 1
/* Define to 1 if the system has the type `_Bool'. */
-#undef HAVE__BOOL
+#define HAVE__BOOL 1
/* Name of package */
-#undef PACKAGE
+#define PACKAGE "lamarc"
/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
+#define PACKAGE_BUGREPORT "lamarc at u.washington.edu"
/* Define to the full name of this package. */
-#undef PACKAGE_NAME
+#define PACKAGE_NAME "lamarc"
/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
+#define PACKAGE_STRING "lamarc 2.1.10"
/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
+#define PACKAGE_TARNAME "lamarc"
/* Define to the version of this package. */
-#undef PACKAGE_VERSION
+#define PACKAGE_VERSION "2.1.10"
/* The release date of the program */
-#undef RELEASE_DATE
+#define RELEASE_DATE "14 Nov 2013"
/* Define to 1 if you have the ANSI C header files. */
-#undef STDC_HEADERS
+#define STDC_HEADERS 1
/* Define to 1 if your <sys/time.h> declares `struct tm'. */
-#undef TM_IN_SYS_TIME
+/* #undef TM_IN_SYS_TIME */
/* Version number of package */
-#undef VERSION
+#define VERSION "2.1.10"
/* Define to empty if `const' does not conform to ANSI C. */
-#undef const
+/* #undef const */
/* Define to `__inline__' or `__inline' if that's what the C compiler
calls it, or to nothing if 'inline' is not supported under any name. */
#ifndef __cplusplus
-#undef inline
+/* #undef inline */
#endif
-/* Define to `unsigned int' if <sys/types.h> does not define. */
-#undef size_t
+/* Define to `unsigned' if <sys/types.h> does not define. */
+/* #undef size_t */
diff --git a/config/conf.h.in b/config/conf.h.in
index ea1e6d5..c3bcbd5 100644
--- a/config/conf.h.in
+++ b/config/conf.h.in
@@ -72,9 +72,6 @@
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
-
/* Define to the version of this package. */
#undef PACKAGE_VERSION
@@ -99,5 +96,5 @@
#undef inline
#endif
-/* Define to `unsigned int' if <sys/types.h> does not define. */
+/* Define to `unsigned' if <sys/types.h> does not define. */
#undef size_t
diff --git a/config/config.guess b/config/config.guess
new file mode 100755
index 0000000..7d0185e
--- /dev/null
+++ b/config/config.guess
@@ -0,0 +1,1447 @@
+#! /bin/sh
+# Attempt to guess a canonical system name.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004 Free Software Foundation, Inc.
+
+timestamp='2004-09-07'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Per Bothner <per at bothner.com>.
+# Please send patches to <config-patches at gnu.org>. Submit a context
+# diff and a properly formatted ChangeLog entry.
+#
+# This script attempts to guess a canonical system name similar to
+# config.sub. If it succeeds, it prints the system name on stdout, and
+# exits with 0. Otherwise, it exits with 1.
+#
+# The plan is that this can be called by configure scripts if you
+# don't specify an explicit build system type.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION]
+
+Output the configuration name of the system \`$me' is run on.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.guess ($timestamp)
+
+Originally written by Per Bothner.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004
+Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit 0 ;;
+ --version | -v )
+ echo "$version" ; exit 0 ;;
+ --help | --h* | -h )
+ echo "$usage"; exit 0 ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help" >&2
+ exit 1 ;;
+ * )
+ break ;;
+ esac
+done
+
+if test $# != 0; then
+ echo "$me: too many arguments$help" >&2
+ exit 1
+fi
+
+trap 'exit 1' 1 2 15
+
+# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
+# compiler to aid in system detection is discouraged as it requires
+# temporary files to be created and, as you can see below, it is a
+# headache to deal with in a portable fashion.
+
+# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
+# use `HOST_CC' if defined, but it is deprecated.
+
+# Portable tmp directory creation inspired by the Autoconf team.
+
+set_cc_for_build='
+trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
+trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
+: ${TMPDIR=/tmp} ;
+ { tmp=`(umask 077 && mktemp -d -q "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
+ { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
+ { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
+dummy=$tmp/dummy ;
+tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
+case $CC_FOR_BUILD,$HOST_CC,$CC in
+ ,,) echo "int x;" > $dummy.c ;
+ for c in cc gcc c89 c99 ; do
+ if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
+ CC_FOR_BUILD="$c"; break ;
+ fi ;
+ done ;
+ if test x"$CC_FOR_BUILD" = x ; then
+ CC_FOR_BUILD=no_compiler_found ;
+ fi
+ ;;
+ ,,*) CC_FOR_BUILD=$CC ;;
+ ,*,*) CC_FOR_BUILD=$HOST_CC ;;
+esac ;'
+
+# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
+# (ghazi at noc.rutgers.edu 1994-08-24)
+if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
+ PATH=$PATH:/.attbin ; export PATH
+fi
+
+UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
+UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
+UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
+UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+
+# Note: order is significant - the case branches are not exclusive.
+
+case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
+ *:NetBSD:*:*)
+ # NetBSD (nbsd) targets should (where applicable) match one or
+ # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
+ # switched to ELF, *-*-netbsd* would select the old
+ # object file format. This provides both forward
+ # compatibility and a consistent mechanism for selecting the
+ # object file format.
+ #
+ # Note: NetBSD doesn't particularly care about the vendor
+ # portion of the name. We always set it to "unknown".
+ sysctl="sysctl -n hw.machine_arch"
+ UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
+ /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
+ case "${UNAME_MACHINE_ARCH}" in
+ armeb) machine=armeb-unknown ;;
+ arm*) machine=arm-unknown ;;
+ sh3el) machine=shl-unknown ;;
+ sh3eb) machine=sh-unknown ;;
+ *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
+ esac
+ # The Operating System including object format, if it has switched
+ # to ELF recently, or will in the future.
+ case "${UNAME_MACHINE_ARCH}" in
+ arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ eval $set_cc_for_build
+ if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep __ELF__ >/dev/null
+ then
+ # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
+ # Return netbsd for either. FIX?
+ os=netbsd
+ else
+ os=netbsdelf
+ fi
+ ;;
+ *)
+ os=netbsd
+ ;;
+ esac
+ # The OS release
+ # Debian GNU/NetBSD machines have a different userland, and
+ # thus, need a distinct triplet. However, they do not need
+ # kernel version information, so it can be replaced with a
+ # suitable tag, in the style of linux-gnu.
+ case "${UNAME_VERSION}" in
+ Debian*)
+ release='-gnu'
+ ;;
+ *)
+ release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+ ;;
+ esac
+ # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
+ # contains redundant information, the shorter form:
+ # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
+ echo "${machine}-${os}${release}"
+ exit 0 ;;
+ amd64:OpenBSD:*:*)
+ echo x86_64-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ amiga:OpenBSD:*:*)
+ echo m68k-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ cats:OpenBSD:*:*)
+ echo arm-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ hp300:OpenBSD:*:*)
+ echo m68k-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ luna88k:OpenBSD:*:*)
+ echo m88k-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ mac68k:OpenBSD:*:*)
+ echo m68k-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ macppc:OpenBSD:*:*)
+ echo powerpc-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ mvme68k:OpenBSD:*:*)
+ echo m68k-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ mvme88k:OpenBSD:*:*)
+ echo m88k-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ mvmeppc:OpenBSD:*:*)
+ echo powerpc-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ sgi:OpenBSD:*:*)
+ echo mips64-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ sun3:OpenBSD:*:*)
+ echo m68k-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ *:OpenBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-openbsd${UNAME_RELEASE}
+ exit 0 ;;
+ *:ekkoBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+ exit 0 ;;
+ macppc:MirBSD:*:*)
+ echo powerppc-unknown-mirbsd${UNAME_RELEASE}
+ exit 0 ;;
+ *:MirBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+ exit 0 ;;
+ alpha:OSF1:*:*)
+ case $UNAME_RELEASE in
+ *4.0)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+ ;;
+ *5.*)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ ;;
+ esac
+ # According to Compaq, /usr/sbin/psrinfo has been available on
+ # OSF/1 and Tru64 systems produced since 1995. I hope that
+ # covers most systems running today. This code pipes the CPU
+ # types through head -n 1, so we only detect the type of CPU 0.
+ ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
+ case "$ALPHA_CPU_TYPE" in
+ "EV4 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "EV4.5 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "LCA4 (21066/21068)")
+ UNAME_MACHINE="alpha" ;;
+ "EV5 (21164)")
+ UNAME_MACHINE="alphaev5" ;;
+ "EV5.6 (21164A)")
+ UNAME_MACHINE="alphaev56" ;;
+ "EV5.6 (21164PC)")
+ UNAME_MACHINE="alphapca56" ;;
+ "EV5.7 (21164PC)")
+ UNAME_MACHINE="alphapca57" ;;
+ "EV6 (21264)")
+ UNAME_MACHINE="alphaev6" ;;
+ "EV6.7 (21264A)")
+ UNAME_MACHINE="alphaev67" ;;
+ "EV6.8CB (21264C)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8AL (21264B)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8CX (21264D)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.9A (21264/EV69A)")
+ UNAME_MACHINE="alphaev69" ;;
+ "EV7 (21364)")
+ UNAME_MACHINE="alphaev7" ;;
+ "EV7.9 (21364A)")
+ UNAME_MACHINE="alphaev79" ;;
+ esac
+ # A Pn.n version is a patched version.
+ # A Vn.n version is a released version.
+ # A Tn.n version is a released field test version.
+ # A Xn.n version is an unreleased experimental baselevel.
+ # 1.2 uses "1.2" for uname -r.
+ echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ exit 0 ;;
+ Alpha\ *:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # Should we change UNAME_MACHINE based on the output of uname instead
+ # of the specific Alpha model?
+ echo alpha-pc-interix
+ exit 0 ;;
+ 21064:Windows_NT:50:3)
+ echo alpha-dec-winnt3.5
+ exit 0 ;;
+ Amiga*:UNIX_System_V:4.0:*)
+ echo m68k-unknown-sysv4
+ exit 0;;
+ *:[Aa]miga[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-amigaos
+ exit 0 ;;
+ *:[Mm]orph[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-morphos
+ exit 0 ;;
+ *:OS/390:*:*)
+ echo i370-ibm-openedition
+ exit 0 ;;
+ *:OS400:*:*)
+ echo powerpc-ibm-os400
+ exit 0 ;;
+ arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
+ echo arm-acorn-riscix${UNAME_RELEASE}
+ exit 0;;
+ SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
+ echo hppa1.1-hitachi-hiuxmpp
+ exit 0;;
+ Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
+ # akee at wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
+ if test "`(/bin/universe) 2>/dev/null`" = att ; then
+ echo pyramid-pyramid-sysv3
+ else
+ echo pyramid-pyramid-bsd
+ fi
+ exit 0 ;;
+ NILE*:*:*:dcosx)
+ echo pyramid-pyramid-svr4
+ exit 0 ;;
+ DRS?6000:unix:4.0:6*)
+ echo sparc-icl-nx6
+ exit 0 ;;
+ DRS?6000:UNIX_SV:4.2*:7*)
+ case `/usr/bin/uname -p` in
+ sparc) echo sparc-icl-nx7 && exit 0 ;;
+ esac ;;
+ sun4H:SunOS:5.*:*)
+ echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit 0 ;;
+ sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
+ echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit 0 ;;
+ i86pc:SunOS:5.*:*)
+ echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit 0 ;;
+ sun4*:SunOS:6*:*)
+ # According to config.sub, this is the proper way to canonicalize
+ # SunOS6. Hard to guess exactly what SunOS6 will be like, but
+ # it's likely to be more like Solaris than SunOS4.
+ echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit 0 ;;
+ sun4*:SunOS:*:*)
+ case "`/usr/bin/arch -k`" in
+ Series*|S4*)
+ UNAME_RELEASE=`uname -v`
+ ;;
+ esac
+ # Japanese Language versions have a version number like `4.1.3-JL'.
+ echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
+ exit 0 ;;
+ sun3*:SunOS:*:*)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ exit 0 ;;
+ sun*:*:4.2BSD:*)
+ UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+ test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+ case "`/bin/arch`" in
+ sun3)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ ;;
+ sun4)
+ echo sparc-sun-sunos${UNAME_RELEASE}
+ ;;
+ esac
+ exit 0 ;;
+ aushp:SunOS:*:*)
+ echo sparc-auspex-sunos${UNAME_RELEASE}
+ exit 0 ;;
+ # The situation for MiNT is a little confusing. The machine name
+ # can be virtually everything (everything which is not
+ # "atarist" or "atariste" at least should have a processor
+ # > m68000). The system name ranges from "MiNT" over "FreeMiNT"
+ # to the lowercase version "mint" (or "freemint"). Finally
+ # the system name "TOS" denotes a system which is actually not
+ # MiNT. But MiNT is downward compatible to TOS, so this should
+ # be no problem.
+ atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit 0 ;;
+ atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit 0 ;;
+ *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit 0 ;;
+ milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
+ echo m68k-milan-mint${UNAME_RELEASE}
+ exit 0 ;;
+ hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
+ echo m68k-hades-mint${UNAME_RELEASE}
+ exit 0 ;;
+ *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
+ echo m68k-unknown-mint${UNAME_RELEASE}
+ exit 0 ;;
+ m68k:machten:*:*)
+ echo m68k-apple-machten${UNAME_RELEASE}
+ exit 0 ;;
+ powerpc:machten:*:*)
+ echo powerpc-apple-machten${UNAME_RELEASE}
+ exit 0 ;;
+ RISC*:Mach:*:*)
+ echo mips-dec-mach_bsd4.3
+ exit 0 ;;
+ RISC*:ULTRIX:*:*)
+ echo mips-dec-ultrix${UNAME_RELEASE}
+ exit 0 ;;
+ VAX*:ULTRIX*:*:*)
+ echo vax-dec-ultrix${UNAME_RELEASE}
+ exit 0 ;;
+ 2020:CLIX:*:* | 2430:CLIX:*:*)
+ echo clipper-intergraph-clix${UNAME_RELEASE}
+ exit 0 ;;
+ mips:*:*:UMIPS | mips:*:*:RISCos)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+#ifdef __cplusplus
+#include <stdio.h> /* for printf() prototype */
+ int main (int argc, char *argv[]) {
+#else
+ int main (argc, argv) int argc; char *argv[]; {
+#endif
+ #if defined (host_mips) && defined (MIPSEB)
+ #if defined (SYSTYPE_SYSV)
+ printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_SVR4)
+ printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+ printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+ #endif
+ #endif
+ exit (-1);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c \
+ && $dummy `echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` \
+ && exit 0
+ echo mips-mips-riscos${UNAME_RELEASE}
+ exit 0 ;;
+ Motorola:PowerMAX_OS:*:*)
+ echo powerpc-motorola-powermax
+ exit 0 ;;
+ Motorola:*:4.3:PL8-*)
+ echo powerpc-harris-powermax
+ exit 0 ;;
+ Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
+ echo powerpc-harris-powermax
+ exit 0 ;;
+ Night_Hawk:Power_UNIX:*:*)
+ echo powerpc-harris-powerunix
+ exit 0 ;;
+ m88k:CX/UX:7*:*)
+ echo m88k-harris-cxux7
+ exit 0 ;;
+ m88k:*:4*:R4*)
+ echo m88k-motorola-sysv4
+ exit 0 ;;
+ m88k:*:3*:R3*)
+ echo m88k-motorola-sysv3
+ exit 0 ;;
+ AViiON:dgux:*:*)
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
+ then
+ if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
+ [ ${TARGET_BINARY_INTERFACE}x = x ]
+ then
+ echo m88k-dg-dgux${UNAME_RELEASE}
+ else
+ echo m88k-dg-dguxbcs${UNAME_RELEASE}
+ fi
+ else
+ echo i586-dg-dgux${UNAME_RELEASE}
+ fi
+ exit 0 ;;
+ M88*:DolphinOS:*:*) # DolphinOS (SVR3)
+ echo m88k-dolphin-sysv3
+ exit 0 ;;
+ M88*:*:R3*:*)
+ # Delta 88k system running SVR3
+ echo m88k-motorola-sysv3
+ exit 0 ;;
+ XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
+ echo m88k-tektronix-sysv3
+ exit 0 ;;
+ Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
+ echo m68k-tektronix-bsd
+ exit 0 ;;
+ *:IRIX*:*:*)
+ echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
+ exit 0 ;;
+ ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+ echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
+ exit 0 ;; # Note that: echo "'`uname -s`'" gives 'AIX '
+ i*86:AIX:*:*)
+ echo i386-ibm-aix
+ exit 0 ;;
+ ia64:AIX:*:*)
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
+ exit 0 ;;
+ *:AIX:2:3)
+ if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <sys/systemcfg.h>
+
+ main()
+ {
+ if (!__power_pc())
+ exit(1);
+ puts("powerpc-ibm-aix3.2.5");
+ exit(0);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c && $dummy && exit 0
+ echo rs6000-ibm-aix3.2.5
+ elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
+ echo rs6000-ibm-aix3.2.4
+ else
+ echo rs6000-ibm-aix3.2
+ fi
+ exit 0 ;;
+ *:AIX:*:[45])
+ IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
+ if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
+ IBM_ARCH=rs6000
+ else
+ IBM_ARCH=powerpc
+ fi
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${IBM_ARCH}-ibm-aix${IBM_REV}
+ exit 0 ;;
+ *:AIX:*:*)
+ echo rs6000-ibm-aix
+ exit 0 ;;
+ ibmrt:4.4BSD:*|romp-ibm:BSD:*)
+ echo romp-ibm-bsd4.4
+ exit 0 ;;
+ ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
+ echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to
+ exit 0 ;; # report: romp-ibm BSD 4.3
+ *:BOSX:*:*)
+ echo rs6000-bull-bosx
+ exit 0 ;;
+ DPX/2?00:B.O.S.:*:*)
+ echo m68k-bull-sysv3
+ exit 0 ;;
+ 9000/[34]??:4.3bsd:1.*:*)
+ echo m68k-hp-bsd
+ exit 0 ;;
+ hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
+ echo m68k-hp-bsd4.4
+ exit 0 ;;
+ 9000/[34678]??:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ case "${UNAME_MACHINE}" in
+ 9000/31? ) HP_ARCH=m68000 ;;
+ 9000/[34]?? ) HP_ARCH=m68k ;;
+ 9000/[678][0-9][0-9])
+ if [ -x /usr/bin/getconf ]; then
+ sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case "${sc_cpu_version}" in
+ 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case "${sc_kernel_bits}" in
+ 32) HP_ARCH="hppa2.0n" ;;
+ 64) HP_ARCH="hppa2.0w" ;;
+ '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
+ esac ;;
+ esac
+ fi
+ if [ "${HP_ARCH}" = "" ]; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
+
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
+
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
+EOF
+ (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ test -z "$HP_ARCH" && HP_ARCH=hppa
+ fi ;;
+ esac
+ if [ ${HP_ARCH} = "hppa2.0w" ]
+ then
+ # avoid double evaluation of $set_cc_for_build
+ test -n "$CC_FOR_BUILD" || eval $set_cc_for_build
+ if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E -) | grep __LP64__ >/dev/null
+ then
+ HP_ARCH="hppa2.0w"
+ else
+ HP_ARCH="hppa64"
+ fi
+ fi
+ echo ${HP_ARCH}-hp-hpux${HPUX_REV}
+ exit 0 ;;
+ ia64:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ echo ia64-hp-hpux${HPUX_REV}
+ exit 0 ;;
+ 3050*:HI-UX:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <unistd.h>
+ int
+ main ()
+ {
+ long cpu = sysconf (_SC_CPU_VERSION);
+ /* The order matters, because CPU_IS_HP_MC68K erroneously returns
+ true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
+ results, however. */
+ if (CPU_IS_PA_RISC (cpu))
+ {
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
+ default: puts ("hppa-hitachi-hiuxwe2"); break;
+ }
+ }
+ else if (CPU_IS_HP_MC68K (cpu))
+ puts ("m68k-hitachi-hiuxwe2");
+ else puts ("unknown-hitachi-hiuxwe2");
+ exit (0);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c && $dummy && exit 0
+ echo unknown-hitachi-hiuxwe2
+ exit 0 ;;
+ 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
+ echo hppa1.1-hp-bsd
+ exit 0 ;;
+ 9000/8??:4.3bsd:*:*)
+ echo hppa1.0-hp-bsd
+ exit 0 ;;
+ *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
+ echo hppa1.0-hp-mpeix
+ exit 0 ;;
+ hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
+ echo hppa1.1-hp-osf
+ exit 0 ;;
+ hp8??:OSF1:*:*)
+ echo hppa1.0-hp-osf
+ exit 0 ;;
+ i*86:OSF1:*:*)
+ if [ -x /usr/sbin/sysversion ] ; then
+ echo ${UNAME_MACHINE}-unknown-osf1mk
+ else
+ echo ${UNAME_MACHINE}-unknown-osf1
+ fi
+ exit 0 ;;
+ parisc*:Lites*:*:*)
+ echo hppa1.1-hp-lites
+ exit 0 ;;
+ C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
+ echo c1-convex-bsd
+ exit 0 ;;
+ C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit 0 ;;
+ C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
+ echo c34-convex-bsd
+ exit 0 ;;
+ C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
+ echo c38-convex-bsd
+ exit 0 ;;
+ C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
+ echo c4-convex-bsd
+ exit 0 ;;
+ CRAY*Y-MP:*:*:*)
+ echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit 0 ;;
+ CRAY*[A-Z]90:*:*:*)
+ echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
+ -e 's/\.[^.]*$/.X/'
+ exit 0 ;;
+ CRAY*TS:*:*:*)
+ echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit 0 ;;
+ CRAY*T3E:*:*:*)
+ echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit 0 ;;
+ CRAY*SV1:*:*:*)
+ echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit 0 ;;
+ *:UNICOS/mp:*:*)
+ echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit 0 ;;
+ F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
+ FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit 0 ;;
+ 5000:UNIX_System_V:4.*:*)
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+ echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit 0 ;;
+ i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
+ echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
+ exit 0 ;;
+ sparc*:BSD/OS:*:*)
+ echo sparc-unknown-bsdi${UNAME_RELEASE}
+ exit 0 ;;
+ *:BSD/OS:*:*)
+ echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+ exit 0 ;;
+ *:FreeBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ exit 0 ;;
+ i*:CYGWIN*:*)
+ echo ${UNAME_MACHINE}-pc-cygwin
+ exit 0 ;;
+ i*:MINGW*:*)
+ echo ${UNAME_MACHINE}-pc-mingw32
+ exit 0 ;;
+ i*:PW*:*)
+ echo ${UNAME_MACHINE}-pc-pw32
+ exit 0 ;;
+ x86:Interix*:[34]*)
+ echo i586-pc-interix${UNAME_RELEASE}|sed -e 's/\..*//'
+ exit 0 ;;
+ [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
+ echo i${UNAME_MACHINE}-pc-mks
+ exit 0 ;;
+ i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
+ # UNAME_MACHINE based on the output of uname instead of i386?
+ echo i586-pc-interix
+ exit 0 ;;
+ i*:UWIN*:*)
+ echo ${UNAME_MACHINE}-pc-uwin
+ exit 0 ;;
+ p*:CYGWIN*:*)
+ echo powerpcle-unknown-cygwin
+ exit 0 ;;
+ prep*:SunOS:5.*:*)
+ echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit 0 ;;
+ *:GNU:*:*)
+ # the GNU system
+ echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ exit 0 ;;
+ *:GNU/*:*:*)
+ # other systems with GNU libc and userland
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+ exit 0 ;;
+ i*86:Minix:*:*)
+ echo ${UNAME_MACHINE}-pc-minix
+ exit 0 ;;
+ arm*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit 0 ;;
+ cris:Linux:*:*)
+ echo cris-axis-linux-gnu
+ exit 0 ;;
+ crisv32:Linux:*:*)
+ echo crisv32-axis-linux-gnu
+ exit 0 ;;
+ frv:Linux:*:*)
+ echo frv-unknown-linux-gnu
+ exit 0 ;;
+ ia64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit 0 ;;
+ m32r*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit 0 ;;
+ m68*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit 0 ;;
+ mips:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef mips
+ #undef mipsel
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=mipsel
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=mips
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=`
+ test x"${CPU}" != x && echo "${CPU}-unknown-linux-gnu" && exit 0
+ ;;
+ mips64:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef mips64
+ #undef mips64el
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=mips64el
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=mips64
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=`
+ test x"${CPU}" != x && echo "${CPU}-unknown-linux-gnu" && exit 0
+ ;;
+ ppc:Linux:*:*)
+ echo powerpc-unknown-linux-gnu
+ exit 0 ;;
+ ppc64:Linux:*:*)
+ echo powerpc64-unknown-linux-gnu
+ exit 0 ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
+ if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ exit 0 ;;
+ parisc:Linux:*:* | hppa:Linux:*:*)
+ # Look for CPU level
+ case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
+ PA7*) echo hppa1.1-unknown-linux-gnu ;;
+ PA8*) echo hppa2.0-unknown-linux-gnu ;;
+ *) echo hppa-unknown-linux-gnu ;;
+ esac
+ exit 0 ;;
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ echo hppa64-unknown-linux-gnu
+ exit 0 ;;
+ s390:Linux:*:* | s390x:Linux:*:*)
+ echo ${UNAME_MACHINE}-ibm-linux
+ exit 0 ;;
+ sh64*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit 0 ;;
+ sh*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit 0 ;;
+ sparc:Linux:*:* | sparc64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit 0 ;;
+ x86_64:Linux:*:*)
+ echo x86_64-unknown-linux-gnu
+ exit 0 ;;
+ i*86:Linux:*:*)
+ # The BFD linker knows what the default object file format is, so
+ # first see if it will tell us. cd to the root directory to prevent
+ # problems with other programs or directories called `ld' in the path.
+ # Set LC_ALL=C to ensure ld outputs messages in English.
+ ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
+ | sed -ne '/supported targets:/!d
+ s/[ ][ ]*/ /g
+ s/.*supported targets: *//
+ s/ .*//
+ p'`
+ case "$ld_supported_targets" in
+ elf32-i386)
+ TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu"
+ ;;
+ a.out-i386-linux)
+ echo "${UNAME_MACHINE}-pc-linux-gnuaout"
+ exit 0 ;;
+ coff-i386)
+ echo "${UNAME_MACHINE}-pc-linux-gnucoff"
+ exit 0 ;;
+ "")
+ # Either a pre-BFD a.out linker (linux-gnuoldld) or
+ # one that does not give us useful --help.
+ echo "${UNAME_MACHINE}-pc-linux-gnuoldld"
+ exit 0 ;;
+ esac
+ # Determine whether the default compiler is a.out or elf
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <features.h>
+ #ifdef __ELF__
+ # ifdef __GLIBC__
+ # if __GLIBC__ >= 2
+ LIBC=gnu
+ # else
+ LIBC=gnulibc1
+ # endif
+ # else
+ LIBC=gnulibc1
+ # endif
+ #else
+ #ifdef __INTEL_COMPILER
+ LIBC=gnu
+ #else
+ LIBC=gnuaout
+ #endif
+ #endif
+ #ifdef __dietlibc__
+ LIBC=dietlibc
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=`
+ test x"${LIBC}" != x && echo "${UNAME_MACHINE}-pc-linux-${LIBC}" && exit 0
+ test x"${TENTATIVE}" != x && echo "${TENTATIVE}" && exit 0
+ ;;
+ i*86:DYNIX/ptx:4*:*)
+ # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
+ # earlier versions are messed up and put the nodename in both
+ # sysname and nodename.
+ echo i386-sequent-sysv4
+ exit 0 ;;
+ i*86:UNIX_SV:4.2MP:2.*)
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
+ # I just have to hope. -- rms.
+ # Use sysv4.2uw... so that sysv4* matches it.
+ echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+ exit 0 ;;
+ i*86:OS/2:*:*)
+ # If we were able to find `uname', then EMX Unix compatibility
+ # is probably installed.
+ echo ${UNAME_MACHINE}-pc-os2-emx
+ exit 0 ;;
+ i*86:XTS-300:*:STOP)
+ echo ${UNAME_MACHINE}-unknown-stop
+ exit 0 ;;
+ i*86:atheos:*:*)
+ echo ${UNAME_MACHINE}-unknown-atheos
+ exit 0 ;;
+ i*86:syllable:*:*)
+ echo ${UNAME_MACHINE}-pc-syllable
+ exit 0 ;;
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
+ echo i386-unknown-lynxos${UNAME_RELEASE}
+ exit 0 ;;
+ i*86:*DOS:*:*)
+ echo ${UNAME_MACHINE}-pc-msdosdjgpp
+ exit 0 ;;
+ i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
+ UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
+ if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
+ echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
+ else
+ echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
+ fi
+ exit 0 ;;
+ i*86:*:5:[78]*)
+ case `/bin/uname -X | grep "^Machine"` in
+ *486*) UNAME_MACHINE=i486 ;;
+ *Pentium) UNAME_MACHINE=i586 ;;
+ *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
+ esac
+ echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+ exit 0 ;;
+ i*86:*:3.2:*)
+ if test -f /usr/options/cb.name; then
+ UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
+ echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
+ elif /bin/uname -X 2>/dev/null >/dev/null ; then
+ UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
+ (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
+ (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
+ && UNAME_MACHINE=i586
+ (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
+ && UNAME_MACHINE=i686
+ (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
+ && UNAME_MACHINE=i686
+ echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
+ else
+ echo ${UNAME_MACHINE}-pc-sysv32
+ fi
+ exit 0 ;;
+ pc:*:*:*)
+ # Left here for compatibility:
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i386.
+ echo i386-pc-msdosdjgpp
+ exit 0 ;;
+ Intel:Mach:3*:*)
+ echo i386-pc-mach3
+ exit 0 ;;
+ paragon:*:*:*)
+ echo i860-intel-osf1
+ exit 0 ;;
+ i860:*:4.*:*) # i860-SVR4
+ if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
+ echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
+ else # Add other i860-SVR4 vendors below as they are discovered.
+ echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4
+ fi
+ exit 0 ;;
+ mini*:CTIX:SYS*5:*)
+ # "miniframe"
+ echo m68010-convergent-sysv
+ exit 0 ;;
+ mc68k:UNIX:SYSTEM5:3.51m)
+ echo m68k-convergent-sysv
+ exit 0 ;;
+ M680?0:D-NIX:5.3:*)
+ echo m68k-diab-dnix
+ exit 0 ;;
+ M68*:*:R3V[5678]*:*)
+ test -r /sysV68 && echo 'm68k-motorola-sysv' && exit 0 ;;
+ 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
+ OS_REL=''
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && echo i486-ncr-sysv4.3${OS_REL} && exit 0
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && echo i586-ncr-sysv4.3${OS_REL} && exit 0 ;;
+ 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && echo i486-ncr-sysv4 && exit 0 ;;
+ m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
+ echo m68k-unknown-lynxos${UNAME_RELEASE}
+ exit 0 ;;
+ mc68030:UNIX_System_V:4.*:*)
+ echo m68k-atari-sysv4
+ exit 0 ;;
+ TSUNAMI:LynxOS:2.*:*)
+ echo sparc-unknown-lynxos${UNAME_RELEASE}
+ exit 0 ;;
+ rs6000:LynxOS:2.*:*)
+ echo rs6000-unknown-lynxos${UNAME_RELEASE}
+ exit 0 ;;
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
+ echo powerpc-unknown-lynxos${UNAME_RELEASE}
+ exit 0 ;;
+ SM[BE]S:UNIX_SV:*:*)
+ echo mips-dde-sysv${UNAME_RELEASE}
+ exit 0 ;;
+ RM*:ReliantUNIX-*:*:*)
+ echo mips-sni-sysv4
+ exit 0 ;;
+ RM*:SINIX-*:*:*)
+ echo mips-sni-sysv4
+ exit 0 ;;
+ *:SINIX-*:*:*)
+ if uname -p 2>/dev/null >/dev/null ; then
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ echo ${UNAME_MACHINE}-sni-sysv4
+ else
+ echo ns32k-sni-sysv
+ fi
+ exit 0 ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel at ccMail.Census.GOV>
+ echo i586-unisys-sysv4
+ exit 0 ;;
+ *:UNIX_System_V:4*:FTX*)
+ # From Gerald Hewes <hewes at openmarket.com>.
+ # How about differentiating between stratus architectures? -djm
+ echo hppa1.1-stratus-sysv4
+ exit 0 ;;
+ *:*:*:FTX*)
+ # From seanf at swdc.stratus.com.
+ echo i860-stratus-sysv4
+ exit 0 ;;
+ *:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo hppa1.1-stratus-vos
+ exit 0 ;;
+ mc68*:A/UX:*:*)
+ echo m68k-apple-aux${UNAME_RELEASE}
+ exit 0 ;;
+ news*:NEWS-OS:6*:*)
+ echo mips-sony-newsos6
+ exit 0 ;;
+ R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
+ if [ -d /usr/nec ]; then
+ echo mips-nec-sysv${UNAME_RELEASE}
+ else
+ echo mips-unknown-sysv${UNAME_RELEASE}
+ fi
+ exit 0 ;;
+ BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
+ echo powerpc-be-beos
+ exit 0 ;;
+ BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
+ echo powerpc-apple-beos
+ exit 0 ;;
+ BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
+ echo i586-pc-beos
+ exit 0 ;;
+ SX-4:SUPER-UX:*:*)
+ echo sx4-nec-superux${UNAME_RELEASE}
+ exit 0 ;;
+ SX-5:SUPER-UX:*:*)
+ echo sx5-nec-superux${UNAME_RELEASE}
+ exit 0 ;;
+ SX-6:SUPER-UX:*:*)
+ echo sx6-nec-superux${UNAME_RELEASE}
+ exit 0 ;;
+ Power*:Rhapsody:*:*)
+ echo powerpc-apple-rhapsody${UNAME_RELEASE}
+ exit 0 ;;
+ *:Rhapsody:*:*)
+ echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+ exit 0 ;;
+ *:Darwin:*:*)
+ UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
+ case $UNAME_PROCESSOR in
+ *86) UNAME_PROCESSOR=i686 ;;
+ unknown) UNAME_PROCESSOR=powerpc ;;
+ esac
+ echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
+ exit 0 ;;
+ *:procnto*:*:* | *:QNX:[0123456789]*:*)
+ UNAME_PROCESSOR=`uname -p`
+ if test "$UNAME_PROCESSOR" = "x86"; then
+ UNAME_PROCESSOR=i386
+ UNAME_MACHINE=pc
+ fi
+ echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
+ exit 0 ;;
+ *:QNX:*:4*)
+ echo i386-pc-qnx
+ exit 0 ;;
+ NSR-?:NONSTOP_KERNEL:*:*)
+ echo nsr-tandem-nsk${UNAME_RELEASE}
+ exit 0 ;;
+ *:NonStop-UX:*:*)
+ echo mips-compaq-nonstopux
+ exit 0 ;;
+ BS2000:POSIX*:*:*)
+ echo bs2000-siemens-sysv
+ exit 0 ;;
+ DS/*:UNIX_System_V:*:*)
+ echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
+ exit 0 ;;
+ *:Plan9:*:*)
+ # "uname -m" is not consistent, so use $cputype instead. 386
+ # is converted to i386 for consistency with other x86
+ # operating systems.
+ if test "$cputype" = "386"; then
+ UNAME_MACHINE=i386
+ else
+ UNAME_MACHINE="$cputype"
+ fi
+ echo ${UNAME_MACHINE}-unknown-plan9
+ exit 0 ;;
+ *:TOPS-10:*:*)
+ echo pdp10-unknown-tops10
+ exit 0 ;;
+ *:TENEX:*:*)
+ echo pdp10-unknown-tenex
+ exit 0 ;;
+ KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
+ echo pdp10-dec-tops20
+ exit 0 ;;
+ XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
+ echo pdp10-xkl-tops20
+ exit 0 ;;
+ *:TOPS-20:*:*)
+ echo pdp10-unknown-tops20
+ exit 0 ;;
+ *:ITS:*:*)
+ echo pdp10-unknown-its
+ exit 0 ;;
+ SEI:*:*:SEIUX)
+ echo mips-sei-seiux${UNAME_RELEASE}
+ exit 0 ;;
+ *:DragonFly:*:*)
+ echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ exit 0 ;;
+ *:*VMS:*:*)
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ case "${UNAME_MACHINE}" in
+ A*) echo alpha-dec-vms && exit 0 ;;
+ I*) echo ia64-dec-vms && exit 0 ;;
+ V*) echo vax-dec-vms && exit 0 ;;
+ esac
+esac
+
+#echo '(No uname command or uname output not recognized.)' 1>&2
+#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
+
+eval $set_cc_for_build
+cat >$dummy.c <<EOF
+#ifdef _SEQUENT_
+# include <sys/types.h>
+# include <sys/utsname.h>
+#endif
+main ()
+{
+#if defined (sony)
+#if defined (MIPSEB)
+ /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
+ I don't know.... */
+ printf ("mips-sony-bsd\n"); exit (0);
+#else
+#include <sys/param.h>
+ printf ("m68k-sony-newsos%s\n",
+#ifdef NEWSOS4
+ "4"
+#else
+ ""
+#endif
+ ); exit (0);
+#endif
+#endif
+
+#if defined (__arm) && defined (__acorn) && defined (__unix)
+ printf ("arm-acorn-riscix"); exit (0);
+#endif
+
+#if defined (hp300) && !defined (hpux)
+ printf ("m68k-hp-bsd\n"); exit (0);
+#endif
+
+#if defined (NeXT)
+#if !defined (__ARCHITECTURE__)
+#define __ARCHITECTURE__ "m68k"
+#endif
+ int version;
+ version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
+ if (version < 4)
+ printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
+ else
+ printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
+ exit (0);
+#endif
+
+#if defined (MULTIMAX) || defined (n16)
+#if defined (UMAXV)
+ printf ("ns32k-encore-sysv\n"); exit (0);
+#else
+#if defined (CMU)
+ printf ("ns32k-encore-mach\n"); exit (0);
+#else
+ printf ("ns32k-encore-bsd\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (__386BSD__)
+ printf ("i386-pc-bsd\n"); exit (0);
+#endif
+
+#if defined (sequent)
+#if defined (i386)
+ printf ("i386-sequent-dynix\n"); exit (0);
+#endif
+#if defined (ns32000)
+ printf ("ns32k-sequent-dynix\n"); exit (0);
+#endif
+#endif
+
+#if defined (_SEQUENT_)
+ struct utsname un;
+
+ uname(&un);
+
+ if (strncmp(un.version, "V2", 2) == 0) {
+ printf ("i386-sequent-ptx2\n"); exit (0);
+ }
+ if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
+ printf ("i386-sequent-ptx1\n"); exit (0);
+ }
+ printf ("i386-sequent-ptx\n"); exit (0);
+
+#endif
+
+#if defined (vax)
+# if !defined (ultrix)
+# include <sys/param.h>
+# if defined (BSD)
+# if BSD == 43
+ printf ("vax-dec-bsd4.3\n"); exit (0);
+# else
+# if BSD == 199006
+ printf ("vax-dec-bsd4.3reno\n"); exit (0);
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# endif
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# else
+ printf ("vax-dec-ultrix\n"); exit (0);
+# endif
+#endif
+
+#if defined (alliant) && defined (i860)
+ printf ("i860-alliant-bsd\n"); exit (0);
+#endif
+
+ exit (1);
+}
+EOF
+
+$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && $dummy && exit 0
+
+# Apollos put the system type in the environment.
+
+test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit 0; }
+
+# Convex versions that predate uname can use getsysinfo(1)
+
+if [ -x /usr/convex/getsysinfo ]
+then
+ case `getsysinfo -f cpu_type` in
+ c1*)
+ echo c1-convex-bsd
+ exit 0 ;;
+ c2*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit 0 ;;
+ c34*)
+ echo c34-convex-bsd
+ exit 0 ;;
+ c38*)
+ echo c38-convex-bsd
+ exit 0 ;;
+ c4*)
+ echo c4-convex-bsd
+ exit 0 ;;
+ esac
+fi
+
+cat >&2 <<EOF
+$0: unable to guess system type
+
+This script, last modified $timestamp, has failed to recognize
+the operating system you are using. It is advised that you
+download the most up to date version of the config scripts from
+
+ ftp://ftp.gnu.org/pub/gnu/config/
+
+If the version you run ($0) is already up to date, please
+send the following data and any information you think might be
+pertinent to <config-patches at gnu.org> in order to provide the needed
+information to handle your system.
+
+config.guess timestamp = $timestamp
+
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
+
+hostinfo = `(hostinfo) 2>/dev/null`
+/bin/universe = `(/bin/universe) 2>/dev/null`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
+/bin/arch = `(/bin/arch) 2>/dev/null`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
+
+UNAME_MACHINE = ${UNAME_MACHINE}
+UNAME_RELEASE = ${UNAME_RELEASE}
+UNAME_SYSTEM = ${UNAME_SYSTEM}
+UNAME_VERSION = ${UNAME_VERSION}
+EOF
+
+exit 1
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/config/config.sub b/config/config.sub
new file mode 100755
index 0000000..edb6b66
--- /dev/null
+++ b/config/config.sub
@@ -0,0 +1,1555 @@
+#! /bin/sh
+# Configuration validation subroutine script.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004 Free Software Foundation, Inc.
+
+timestamp='2004-08-29'
+
+# This file is (in principle) common to ALL GNU software.
+# The presence of a machine in this file suggests that SOME GNU software
+# can handle that machine. It does not imply ALL GNU software can.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330,
+# Boston, MA 02111-1307, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Please send patches to <config-patches at gnu.org>. Submit a context
+# diff and a properly formatted ChangeLog entry.
+#
+# Configuration subroutine to validate and canonicalize a configuration type.
+# Supply the specified configuration type as an argument.
+# If it is invalid, we print an error message on stderr and exit with code 1.
+# Otherwise, we print the canonical config type on stdout and succeed.
+
+# This file is supposed to be the same for all GNU packages
+# and recognize all the CPU types, system types and aliases
+# that are meaningful with *any* GNU software.
+# Each package is responsible for reporting which valid configurations
+# it does not support. The user should be able to distinguish
+# a failure to support a valid configuration from a meaningless
+# configuration.
+
+# The goal of this file is to map all the various variations of a given
+# machine specification into a single specification in the form:
+# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
+# It is wrong to echo any other type of specification.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION] CPU-MFR-OPSYS
+ $0 [OPTION] ALIAS
+
+Canonicalize a configuration name.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.sub ($timestamp)
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004
+Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit 0 ;;
+ --version | -v )
+ echo "$version" ; exit 0 ;;
+ --help | --h* | -h )
+ echo "$usage"; exit 0 ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help"
+ exit 1 ;;
+
+ *local*)
+ # First pass through any local machine types.
+ echo $1
+ exit 0;;
+
+ * )
+ break ;;
+ esac
+done
+
+case $# in
+ 0) echo "$me: missing argument$help" >&2
+ exit 1;;
+ 1) ;;
+ *) echo "$me: too many arguments$help" >&2
+ exit 1;;
+esac
+
+# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
+# Here we must recognize all the valid KERNEL-OS combinations.
+maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+case $maybe_os in
+ nto-qnx* | linux-gnu* | linux-dietlibc | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | \
+ kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | storm-chaos* | os2-emx* | rtmk-nova*)
+ os=-$maybe_os
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+ ;;
+ *)
+ basic_machine=`echo $1 | sed 's/-[^-]*$//'`
+ if [ $basic_machine != $1 ]
+ then os=`echo $1 | sed 's/.*-/-/'`
+ else os=; fi
+ ;;
+esac
+
+### Let's recognize common machines as not being operating systems so
+### that things like config.sub decstation-3100 work. We also
+### recognize some manufacturers as not being operating systems, so we
+### can provide default operating systems below.
+case $os in
+ -sun*os*)
+ # Prevent following clause from handling this invalid input.
+ ;;
+ -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
+ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
+ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
+ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
+ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
+ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
+ -apple | -axis | -knuth | -cray)
+ os=
+ basic_machine=$1
+ ;;
+ -sim | -cisco | -oki | -wec | -winbond)
+ os=
+ basic_machine=$1
+ ;;
+ -scout)
+ ;;
+ -wrs)
+ os=-vxworks
+ basic_machine=$1
+ ;;
+ -chorusos*)
+ os=-chorusos
+ basic_machine=$1
+ ;;
+ -chorusrdb)
+ os=-chorusrdb
+ basic_machine=$1
+ ;;
+ -hiux*)
+ os=-hiuxwe2
+ ;;
+ -sco5)
+ os=-sco3.2v5
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco4)
+ os=-sco3.2v4
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2.[4-9]*)
+ os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2v[4-9]*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco*)
+ os=-sco3.2v2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -udk*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -isc)
+ os=-isc2.2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -clix*)
+ basic_machine=clipper-intergraph
+ ;;
+ -isc*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -lynx*)
+ os=-lynxos
+ ;;
+ -ptx*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
+ ;;
+ -windowsnt*)
+ os=`echo $os | sed -e 's/windowsnt/winnt/'`
+ ;;
+ -psos*)
+ os=-psos
+ ;;
+ -mint | -mint[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+esac
+
+# Decode aliases for certain CPU-COMPANY combinations.
+case $basic_machine in
+ # Recognize the basic CPU types without company name.
+ # Some are omitted here because they have special meanings below.
+ 1750a | 580 \
+ | a29k \
+ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
+ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
+ | am33_2.0 \
+ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr \
+ | c4x | clipper \
+ | d10v | d30v | dlx | dsp16xx \
+ | fr30 | frv \
+ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+ | i370 | i860 | i960 | ia64 \
+ | ip2k | iq2000 \
+ | m32r | m32rle | m68000 | m68k | m88k | mcore \
+ | mips | mipsbe | mipseb | mipsel | mipsle \
+ | mips16 \
+ | mips64 | mips64el \
+ | mips64vr | mips64vrel \
+ | mips64orion | mips64orionel \
+ | mips64vr4100 | mips64vr4100el \
+ | mips64vr4300 | mips64vr4300el \
+ | mips64vr5000 | mips64vr5000el \
+ | mipsisa32 | mipsisa32el \
+ | mipsisa32r2 | mipsisa32r2el \
+ | mipsisa64 | mipsisa64el \
+ | mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64sb1 | mipsisa64sb1el \
+ | mipsisa64sr71k | mipsisa64sr71kel \
+ | mipstx39 | mipstx39el \
+ | mn10200 | mn10300 \
+ | msp430 \
+ | ns16k | ns32k \
+ | openrisc | or32 \
+ | pdp10 | pdp11 | pj | pjl \
+ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
+ | pyramid \
+ | sh | sh[1234] | sh[23]e | sh[34]eb | shbe | shle | sh[1234]le | sh3ele \
+ | sh64 | sh64le \
+ | sparc | sparc64 | sparc86x | sparclet | sparclite | sparcv8 | sparcv9 | sparcv9b \
+ | strongarm \
+ | tahoe | thumb | tic4x | tic80 | tron \
+ | v850 | v850e \
+ | we32k \
+ | x86 | xscale | xstormy16 | xtensa \
+ | z8k)
+ basic_machine=$basic_machine-unknown
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12)
+ # Motorola 68HC11/12.
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
+ ;;
+
+ # We use `pc' rather than `unknown'
+ # because (1) that's what they normally are, and
+ # (2) the word "unknown" tends to confuse beginning users.
+ i*86 | x86_64)
+ basic_machine=$basic_machine-pc
+ ;;
+ # Object if more than one company name word.
+ *-*-*)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+ # Recognize the basic CPU types with company name.
+ 580-* \
+ | a29k-* \
+ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
+ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
+ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \
+ | avr-* \
+ | bs2000-* \
+ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
+ | clipper-* | craynv-* | cydra-* \
+ | d10v-* | d30v-* | dlx-* \
+ | elxsi-* \
+ | f30[01]-* | f700-* | fr30-* | frv-* | fx80-* \
+ | h8300-* | h8500-* \
+ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+ | i*86-* | i860-* | i960-* | ia64-* \
+ | ip2k-* | iq2000-* \
+ | m32r-* | m32rle-* \
+ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
+ | m88110-* | m88k-* | mcore-* \
+ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
+ | mips16-* \
+ | mips64-* | mips64el-* \
+ | mips64vr-* | mips64vrel-* \
+ | mips64orion-* | mips64orionel-* \
+ | mips64vr4100-* | mips64vr4100el-* \
+ | mips64vr4300-* | mips64vr4300el-* \
+ | mips64vr5000-* | mips64vr5000el-* \
+ | mipsisa32-* | mipsisa32el-* \
+ | mipsisa32r2-* | mipsisa32r2el-* \
+ | mipsisa64-* | mipsisa64el-* \
+ | mipsisa64r2-* | mipsisa64r2el-* \
+ | mipsisa64sb1-* | mipsisa64sb1el-* \
+ | mipsisa64sr71k-* | mipsisa64sr71kel-* \
+ | mipstx39-* | mipstx39el-* \
+ | mmix-* \
+ | msp430-* \
+ | none-* | np1-* | ns16k-* | ns32k-* \
+ | orion-* \
+ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
+ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
+ | pyramid-* \
+ | romp-* | rs6000-* \
+ | sh-* | sh[1234]-* | sh[23]e-* | sh[34]eb-* | shbe-* \
+ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
+ | sparc-* | sparc64-* | sparc86x-* | sparclet-* | sparclite-* \
+ | sparcv8-* | sparcv9-* | sparcv9b-* | strongarm-* | sv1-* | sx?-* \
+ | tahoe-* | thumb-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tron-* \
+ | v850-* | v850e-* | vax-* \
+ | we32k-* \
+ | x86-* | x86_64-* | xps100-* | xscale-* | xstormy16-* \
+ | xtensa-* \
+ | ymp-* \
+ | z8k-*)
+ ;;
+ # Recognize the various machine names and aliases which stand
+ # for a CPU type and a company and sometimes even an OS.
+ 386bsd)
+ basic_machine=i386-unknown
+ os=-bsd
+ ;;
+ 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
+ basic_machine=m68000-att
+ ;;
+ 3b*)
+ basic_machine=we32k-att
+ ;;
+ a29khif)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ abacus)
+ basic_machine=abacus-unknown
+ ;;
+ adobe68k)
+ basic_machine=m68010-adobe
+ os=-scout
+ ;;
+ alliant | fx80)
+ basic_machine=fx80-alliant
+ ;;
+ altos | altos3068)
+ basic_machine=m68k-altos
+ ;;
+ am29k)
+ basic_machine=a29k-none
+ os=-bsd
+ ;;
+ amd64)
+ basic_machine=x86_64-pc
+ ;;
+ amd64-*)
+ basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ amdahl)
+ basic_machine=580-amdahl
+ os=-sysv
+ ;;
+ amiga | amiga-*)
+ basic_machine=m68k-unknown
+ ;;
+ amigaos | amigados)
+ basic_machine=m68k-unknown
+ os=-amigaos
+ ;;
+ amigaunix | amix)
+ basic_machine=m68k-unknown
+ os=-sysv4
+ ;;
+ apollo68)
+ basic_machine=m68k-apollo
+ os=-sysv
+ ;;
+ apollo68bsd)
+ basic_machine=m68k-apollo
+ os=-bsd
+ ;;
+ aux)
+ basic_machine=m68k-apple
+ os=-aux
+ ;;
+ balance)
+ basic_machine=ns32k-sequent
+ os=-dynix
+ ;;
+ c90)
+ basic_machine=c90-cray
+ os=-unicos
+ ;;
+ convex-c1)
+ basic_machine=c1-convex
+ os=-bsd
+ ;;
+ convex-c2)
+ basic_machine=c2-convex
+ os=-bsd
+ ;;
+ convex-c32)
+ basic_machine=c32-convex
+ os=-bsd
+ ;;
+ convex-c34)
+ basic_machine=c34-convex
+ os=-bsd
+ ;;
+ convex-c38)
+ basic_machine=c38-convex
+ os=-bsd
+ ;;
+ cray | j90)
+ basic_machine=j90-cray
+ os=-unicos
+ ;;
+ craynv)
+ basic_machine=craynv-cray
+ os=-unicosmp
+ ;;
+ cr16c)
+ basic_machine=cr16c-unknown
+ os=-elf
+ ;;
+ crds | unos)
+ basic_machine=m68k-crds
+ ;;
+ crisv32 | crisv32-* | etraxfs*)
+ basic_machine=crisv32-axis
+ ;;
+ cris | cris-* | etrax*)
+ basic_machine=cris-axis
+ ;;
+ crx)
+ basic_machine=crx-unknown
+ os=-elf
+ ;;
+ da30 | da30-*)
+ basic_machine=m68k-da30
+ ;;
+ decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
+ basic_machine=mips-dec
+ ;;
+ decsystem10* | dec10*)
+ basic_machine=pdp10-dec
+ os=-tops10
+ ;;
+ decsystem20* | dec20*)
+ basic_machine=pdp10-dec
+ os=-tops20
+ ;;
+ delta | 3300 | motorola-3300 | motorola-delta \
+ | 3300-motorola | delta-motorola)
+ basic_machine=m68k-motorola
+ ;;
+ delta88)
+ basic_machine=m88k-motorola
+ os=-sysv3
+ ;;
+ dpx20 | dpx20-*)
+ basic_machine=rs6000-bull
+ os=-bosx
+ ;;
+ dpx2* | dpx2*-bull)
+ basic_machine=m68k-bull
+ os=-sysv3
+ ;;
+ ebmon29k)
+ basic_machine=a29k-amd
+ os=-ebmon
+ ;;
+ elxsi)
+ basic_machine=elxsi-elxsi
+ os=-bsd
+ ;;
+ encore | umax | mmax)
+ basic_machine=ns32k-encore
+ ;;
+ es1800 | OSE68k | ose68k | ose | OSE)
+ basic_machine=m68k-ericsson
+ os=-ose
+ ;;
+ fx2800)
+ basic_machine=i860-alliant
+ ;;
+ genix)
+ basic_machine=ns32k-ns
+ ;;
+ gmicro)
+ basic_machine=tron-gmicro
+ os=-sysv
+ ;;
+ go32)
+ basic_machine=i386-pc
+ os=-go32
+ ;;
+ h3050r* | hiux*)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ h8300hms)
+ basic_machine=h8300-hitachi
+ os=-hms
+ ;;
+ h8300xray)
+ basic_machine=h8300-hitachi
+ os=-xray
+ ;;
+ h8500hms)
+ basic_machine=h8500-hitachi
+ os=-hms
+ ;;
+ harris)
+ basic_machine=m88k-harris
+ os=-sysv3
+ ;;
+ hp300-*)
+ basic_machine=m68k-hp
+ ;;
+ hp300bsd)
+ basic_machine=m68k-hp
+ os=-bsd
+ ;;
+ hp300hpux)
+ basic_machine=m68k-hp
+ os=-hpux
+ ;;
+ hp3k9[0-9][0-9] | hp9[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k2[0-9][0-9] | hp9k31[0-9])
+ basic_machine=m68000-hp
+ ;;
+ hp9k3[2-9][0-9])
+ basic_machine=m68k-hp
+ ;;
+ hp9k6[0-9][0-9] | hp6[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k7[0-79][0-9] | hp7[0-79][0-9])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k78[0-9] | hp78[0-9])
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][13679] | hp8[0-9][13679])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][0-9] | hp8[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hppa-next)
+ os=-nextstep3
+ ;;
+ hppaosf)
+ basic_machine=hppa1.1-hp
+ os=-osf
+ ;;
+ hppro)
+ basic_machine=hppa1.1-hp
+ os=-proelf
+ ;;
+ i370-ibm* | ibm*)
+ basic_machine=i370-ibm
+ ;;
+# I'm not sure what "Sysv32" means. Should this be sysv3.2?
+ i*86v32)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv32
+ ;;
+ i*86v4*)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv4
+ ;;
+ i*86v)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv
+ ;;
+ i*86sol2)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-solaris2
+ ;;
+ i386mach)
+ basic_machine=i386-mach
+ os=-mach
+ ;;
+ i386-vsta | vsta)
+ basic_machine=i386-unknown
+ os=-vsta
+ ;;
+ iris | iris4d)
+ basic_machine=mips-sgi
+ case $os in
+ -irix*)
+ ;;
+ *)
+ os=-irix4
+ ;;
+ esac
+ ;;
+ isi68 | isi)
+ basic_machine=m68k-isi
+ os=-sysv
+ ;;
+ m88k-omron*)
+ basic_machine=m88k-omron
+ ;;
+ magnum | m3230)
+ basic_machine=mips-mips
+ os=-sysv
+ ;;
+ merlin)
+ basic_machine=ns32k-utek
+ os=-sysv
+ ;;
+ mingw32)
+ basic_machine=i386-pc
+ os=-mingw32
+ ;;
+ miniframe)
+ basic_machine=m68000-convergent
+ ;;
+ *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+ mips3*-*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
+ ;;
+ mips3*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
+ ;;
+ monitor)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ morphos)
+ basic_machine=powerpc-unknown
+ os=-morphos
+ ;;
+ msdos)
+ basic_machine=i386-pc
+ os=-msdos
+ ;;
+ mvs)
+ basic_machine=i370-ibm
+ os=-mvs
+ ;;
+ ncr3000)
+ basic_machine=i486-ncr
+ os=-sysv4
+ ;;
+ netbsd386)
+ basic_machine=i386-unknown
+ os=-netbsd
+ ;;
+ netwinder)
+ basic_machine=armv4l-rebel
+ os=-linux
+ ;;
+ news | news700 | news800 | news900)
+ basic_machine=m68k-sony
+ os=-newsos
+ ;;
+ news1000)
+ basic_machine=m68030-sony
+ os=-newsos
+ ;;
+ news-3600 | risc-news)
+ basic_machine=mips-sony
+ os=-newsos
+ ;;
+ necv70)
+ basic_machine=v70-nec
+ os=-sysv
+ ;;
+ next | m*-next )
+ basic_machine=m68k-next
+ case $os in
+ -nextstep* )
+ ;;
+ -ns2*)
+ os=-nextstep2
+ ;;
+ *)
+ os=-nextstep3
+ ;;
+ esac
+ ;;
+ nh3000)
+ basic_machine=m68k-harris
+ os=-cxux
+ ;;
+ nh[45]000)
+ basic_machine=m88k-harris
+ os=-cxux
+ ;;
+ nindy960)
+ basic_machine=i960-intel
+ os=-nindy
+ ;;
+ mon960)
+ basic_machine=i960-intel
+ os=-mon960
+ ;;
+ nonstopux)
+ basic_machine=mips-compaq
+ os=-nonstopux
+ ;;
+ np1)
+ basic_machine=np1-gould
+ ;;
+ nsr-tandem)
+ basic_machine=nsr-tandem
+ ;;
+ op50n-* | op60c-*)
+ basic_machine=hppa1.1-oki
+ os=-proelf
+ ;;
+ or32 | or32-*)
+ basic_machine=or32-unknown
+ os=-coff
+ ;;
+ os400)
+ basic_machine=powerpc-ibm
+ os=-os400
+ ;;
+ OSE68000 | ose68000)
+ basic_machine=m68000-ericsson
+ os=-ose
+ ;;
+ os68k)
+ basic_machine=m68k-none
+ os=-os68k
+ ;;
+ pa-hitachi)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ paragon)
+ basic_machine=i860-intel
+ os=-osf
+ ;;
+ pbd)
+ basic_machine=sparc-tti
+ ;;
+ pbb)
+ basic_machine=m68k-tti
+ ;;
+ pc532 | pc532-*)
+ basic_machine=ns32k-pc532
+ ;;
+ pentium | p5 | k5 | k6 | nexgen | viac3)
+ basic_machine=i586-pc
+ ;;
+ pentiumpro | p6 | 6x86 | athlon | athlon_*)
+ basic_machine=i686-pc
+ ;;
+ pentiumii | pentium2 | pentiumiii | pentium3)
+ basic_machine=i686-pc
+ ;;
+ pentium4)
+ basic_machine=i786-pc
+ ;;
+ pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
+ basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumpro-* | p6-* | 6x86-* | athlon-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium4-*)
+ basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pn)
+ basic_machine=pn-gould
+ ;;
+ power) basic_machine=power-ibm
+ ;;
+ ppc) basic_machine=powerpc-unknown
+ ;;
+ ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppcle | powerpclittle | ppc-le | powerpc-little)
+ basic_machine=powerpcle-unknown
+ ;;
+ ppcle-* | powerpclittle-*)
+ basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64) basic_machine=powerpc64-unknown
+ ;;
+ ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+ basic_machine=powerpc64le-unknown
+ ;;
+ ppc64le-* | powerpc64little-*)
+ basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ps2)
+ basic_machine=i386-ibm
+ ;;
+ pw32)
+ basic_machine=i586-unknown
+ os=-pw32
+ ;;
+ rom68k)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ rm[46]00)
+ basic_machine=mips-siemens
+ ;;
+ rtpc | rtpc-*)
+ basic_machine=romp-ibm
+ ;;
+ s390 | s390-*)
+ basic_machine=s390-ibm
+ ;;
+ s390x | s390x-*)
+ basic_machine=s390x-ibm
+ ;;
+ sa29200)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ sb1)
+ basic_machine=mipsisa64sb1-unknown
+ ;;
+ sb1el)
+ basic_machine=mipsisa64sb1el-unknown
+ ;;
+ sei)
+ basic_machine=mips-sei
+ os=-seiux
+ ;;
+ sequent)
+ basic_machine=i386-sequent
+ ;;
+ sh)
+ basic_machine=sh-hitachi
+ os=-hms
+ ;;
+ sh64)
+ basic_machine=sh64-unknown
+ ;;
+ sparclite-wrs | simso-wrs)
+ basic_machine=sparclite-wrs
+ os=-vxworks
+ ;;
+ sps7)
+ basic_machine=m68k-bull
+ os=-sysv2
+ ;;
+ spur)
+ basic_machine=spur-unknown
+ ;;
+ st2000)
+ basic_machine=m68k-tandem
+ ;;
+ stratus)
+ basic_machine=i860-stratus
+ os=-sysv4
+ ;;
+ sun2)
+ basic_machine=m68000-sun
+ ;;
+ sun2os3)
+ basic_machine=m68000-sun
+ os=-sunos3
+ ;;
+ sun2os4)
+ basic_machine=m68000-sun
+ os=-sunos4
+ ;;
+ sun3os3)
+ basic_machine=m68k-sun
+ os=-sunos3
+ ;;
+ sun3os4)
+ basic_machine=m68k-sun
+ os=-sunos4
+ ;;
+ sun4os3)
+ basic_machine=sparc-sun
+ os=-sunos3
+ ;;
+ sun4os4)
+ basic_machine=sparc-sun
+ os=-sunos4
+ ;;
+ sun4sol2)
+ basic_machine=sparc-sun
+ os=-solaris2
+ ;;
+ sun3 | sun3-*)
+ basic_machine=m68k-sun
+ ;;
+ sun4)
+ basic_machine=sparc-sun
+ ;;
+ sun386 | sun386i | roadrunner)
+ basic_machine=i386-sun
+ ;;
+ sv1)
+ basic_machine=sv1-cray
+ os=-unicos
+ ;;
+ symmetry)
+ basic_machine=i386-sequent
+ os=-dynix
+ ;;
+ t3e)
+ basic_machine=alphaev5-cray
+ os=-unicos
+ ;;
+ t90)
+ basic_machine=t90-cray
+ os=-unicos
+ ;;
+ tic54x | c54x*)
+ basic_machine=tic54x-unknown
+ os=-coff
+ ;;
+ tic55x | c55x*)
+ basic_machine=tic55x-unknown
+ os=-coff
+ ;;
+ tic6x | c6x*)
+ basic_machine=tic6x-unknown
+ os=-coff
+ ;;
+ tx39)
+ basic_machine=mipstx39-unknown
+ ;;
+ tx39el)
+ basic_machine=mipstx39el-unknown
+ ;;
+ toad1)
+ basic_machine=pdp10-xkl
+ os=-tops20
+ ;;
+ tower | tower-32)
+ basic_machine=m68k-ncr
+ ;;
+ tpf)
+ basic_machine=s390x-ibm
+ os=-tpf
+ ;;
+ udi29k)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ ultra3)
+ basic_machine=a29k-nyu
+ os=-sym1
+ ;;
+ v810 | necv810)
+ basic_machine=v810-nec
+ os=-none
+ ;;
+ vaxv)
+ basic_machine=vax-dec
+ os=-sysv
+ ;;
+ vms)
+ basic_machine=vax-dec
+ os=-vms
+ ;;
+ vpp*|vx|vx-*)
+ basic_machine=f301-fujitsu
+ ;;
+ vxworks960)
+ basic_machine=i960-wrs
+ os=-vxworks
+ ;;
+ vxworks68)
+ basic_machine=m68k-wrs
+ os=-vxworks
+ ;;
+ vxworks29k)
+ basic_machine=a29k-wrs
+ os=-vxworks
+ ;;
+ w65*)
+ basic_machine=w65-wdc
+ os=-none
+ ;;
+ w89k-*)
+ basic_machine=hppa1.1-winbond
+ os=-proelf
+ ;;
+ xps | xps100)
+ basic_machine=xps100-honeywell
+ ;;
+ ymp)
+ basic_machine=ymp-cray
+ os=-unicos
+ ;;
+ z8k-*-coff)
+ basic_machine=z8k-unknown
+ os=-sim
+ ;;
+ none)
+ basic_machine=none-none
+ os=-none
+ ;;
+
+# Here we handle the default manufacturer of certain CPU types. It is in
+# some cases the only manufacturer, in others, it is the most popular.
+ w89k)
+ basic_machine=hppa1.1-winbond
+ ;;
+ op50n)
+ basic_machine=hppa1.1-oki
+ ;;
+ op60c)
+ basic_machine=hppa1.1-oki
+ ;;
+ romp)
+ basic_machine=romp-ibm
+ ;;
+ mmix)
+ basic_machine=mmix-knuth
+ ;;
+ rs6000)
+ basic_machine=rs6000-ibm
+ ;;
+ vax)
+ basic_machine=vax-dec
+ ;;
+ pdp10)
+ # there are many clones, so DEC is not a safe bet
+ basic_machine=pdp10-unknown
+ ;;
+ pdp11)
+ basic_machine=pdp11-dec
+ ;;
+ we32k)
+ basic_machine=we32k-att
+ ;;
+ sh3 | sh4 | sh[34]eb | sh[1234]le | sh[23]ele)
+ basic_machine=sh-unknown
+ ;;
+ sh64)
+ basic_machine=sh64-unknown
+ ;;
+ sparc | sparcv8 | sparcv9 | sparcv9b)
+ basic_machine=sparc-sun
+ ;;
+ cydra)
+ basic_machine=cydra-cydrome
+ ;;
+ orion)
+ basic_machine=orion-highlevel
+ ;;
+ orion105)
+ basic_machine=clipper-highlevel
+ ;;
+ mac | mpw | mac-mpw)
+ basic_machine=m68k-apple
+ ;;
+ pmac | pmac-mpw)
+ basic_machine=powerpc-apple
+ ;;
+ *-unknown)
+ # Make sure to match an already-canonicalized machine name.
+ ;;
+ *)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+
+# Here we canonicalize certain aliases for manufacturers.
+case $basic_machine in
+ *-digital*)
+ basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
+ ;;
+ *-commodore*)
+ basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
+ ;;
+ *)
+ ;;
+esac
+
+# Decode manufacturer-specific aliases for certain operating systems.
+
+if [ x"$os" != x"" ]
+then
+case $os in
+ # First match some system type aliases
+ # that might get confused with valid system types.
+ # -solaris* is a basic system type, with this one exception.
+ -solaris1 | -solaris1.*)
+ os=`echo $os | sed -e 's|solaris1|sunos4|'`
+ ;;
+ -solaris)
+ os=-solaris2
+ ;;
+ -svr4*)
+ os=-sysv4
+ ;;
+ -unixware*)
+ os=-sysv4.2uw
+ ;;
+ -gnu/linux*)
+ os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
+ ;;
+ # First accept the basic system types.
+ # The portable systems comes first.
+ # Each alternative MUST END IN A *, to match a version number.
+ # -sysv* is not here because it comes later, after sysvr4.
+ -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
+ | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
+ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
+ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
+ | -aos* \
+ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
+ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
+ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* | -openbsd* \
+ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
+ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
+ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
+ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
+ | -chorusos* | -chorusrdb* \
+ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+ | -mingw32* | -linux-gnu* | -linux-uclibc* | -uxpv* | -beos* | -mpeix* | -udk* \
+ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
+ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
+ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
+ | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
+ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
+ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly*)
+ # Remember, each alternative MUST END IN *, to match a version number.
+ ;;
+ -qnx*)
+ case $basic_machine in
+ x86-* | i*86-*)
+ ;;
+ *)
+ os=-nto$os
+ ;;
+ esac
+ ;;
+ -nto-qnx*)
+ ;;
+ -nto*)
+ os=`echo $os | sed -e 's|nto|nto-qnx|'`
+ ;;
+ -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
+ | -windows* | -osx | -abug | -netware* | -os9* | -beos* \
+ | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
+ ;;
+ -mac*)
+ os=`echo $os | sed -e 's|mac|macos|'`
+ ;;
+ -linux-dietlibc)
+ os=-linux-dietlibc
+ ;;
+ -linux*)
+ os=`echo $os | sed -e 's|linux|linux-gnu|'`
+ ;;
+ -sunos5*)
+ os=`echo $os | sed -e 's|sunos5|solaris2|'`
+ ;;
+ -sunos6*)
+ os=`echo $os | sed -e 's|sunos6|solaris3|'`
+ ;;
+ -opened*)
+ os=-openedition
+ ;;
+ -os400*)
+ os=-os400
+ ;;
+ -wince*)
+ os=-wince
+ ;;
+ -osfrose*)
+ os=-osfrose
+ ;;
+ -osf*)
+ os=-osf
+ ;;
+ -utek*)
+ os=-bsd
+ ;;
+ -dynix*)
+ os=-bsd
+ ;;
+ -acis*)
+ os=-aos
+ ;;
+ -atheos*)
+ os=-atheos
+ ;;
+ -syllable*)
+ os=-syllable
+ ;;
+ -386bsd)
+ os=-bsd
+ ;;
+ -ctix* | -uts*)
+ os=-sysv
+ ;;
+ -nova*)
+ os=-rtmk-nova
+ ;;
+ -ns2 )
+ os=-nextstep2
+ ;;
+ -nsk*)
+ os=-nsk
+ ;;
+ # Preserve the version number of sinix5.
+ -sinix5.*)
+ os=`echo $os | sed -e 's|sinix|sysv|'`
+ ;;
+ -sinix*)
+ os=-sysv4
+ ;;
+ -tpf*)
+ os=-tpf
+ ;;
+ -triton*)
+ os=-sysv3
+ ;;
+ -oss*)
+ os=-sysv3
+ ;;
+ -svr4)
+ os=-sysv4
+ ;;
+ -svr3)
+ os=-sysv3
+ ;;
+ -sysvr4)
+ os=-sysv4
+ ;;
+ # This must come after -sysvr4.
+ -sysv*)
+ ;;
+ -ose*)
+ os=-ose
+ ;;
+ -es1800*)
+ os=-ose
+ ;;
+ -xenix)
+ os=-xenix
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ os=-mint
+ ;;
+ -aros*)
+ os=-aros
+ ;;
+ -kaos*)
+ os=-kaos
+ ;;
+ -none)
+ ;;
+ *)
+ # Get rid of the `-' at the beginning of $os.
+ os=`echo $os | sed 's/[^-]*-//'`
+ echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+else
+
+# Here we handle the default operating systems that come with various machines.
+# The value should be what the vendor currently ships out the door with their
+# machine or put another way, the most popular os provided with the machine.
+
+# Note that if you're going to try to match "-MANUFACTURER" here (say,
+# "-sun"), then you have to tell the case statement up towards the top
+# that MANUFACTURER isn't an operating system. Otherwise, code above
+# will signal an error saying that MANUFACTURER isn't an operating
+# system, and we'll never get to this point.
+
+case $basic_machine in
+ *-acorn)
+ os=-riscix1.2
+ ;;
+ arm*-rebel)
+ os=-linux
+ ;;
+ arm*-semi)
+ os=-aout
+ ;;
+ c4x-* | tic4x-*)
+ os=-coff
+ ;;
+ # This must come before the *-dec entry.
+ pdp10-*)
+ os=-tops20
+ ;;
+ pdp11-*)
+ os=-none
+ ;;
+ *-dec | vax-*)
+ os=-ultrix4.2
+ ;;
+ m68*-apollo)
+ os=-domain
+ ;;
+ i386-sun)
+ os=-sunos4.0.2
+ ;;
+ m68000-sun)
+ os=-sunos3
+ # This also exists in the configure program, but was not the
+ # default.
+ # os=-sunos4
+ ;;
+ m68*-cisco)
+ os=-aout
+ ;;
+ mips*-cisco)
+ os=-elf
+ ;;
+ mips*-*)
+ os=-elf
+ ;;
+ or32-*)
+ os=-coff
+ ;;
+ *-tti) # must be before sparc entry or we get the wrong os.
+ os=-sysv3
+ ;;
+ sparc-* | *-sun)
+ os=-sunos4.1.1
+ ;;
+ *-be)
+ os=-beos
+ ;;
+ *-ibm)
+ os=-aix
+ ;;
+ *-knuth)
+ os=-mmixware
+ ;;
+ *-wec)
+ os=-proelf
+ ;;
+ *-winbond)
+ os=-proelf
+ ;;
+ *-oki)
+ os=-proelf
+ ;;
+ *-hp)
+ os=-hpux
+ ;;
+ *-hitachi)
+ os=-hiux
+ ;;
+ i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
+ os=-sysv
+ ;;
+ *-cbm)
+ os=-amigaos
+ ;;
+ *-dg)
+ os=-dgux
+ ;;
+ *-dolphin)
+ os=-sysv3
+ ;;
+ m68k-ccur)
+ os=-rtu
+ ;;
+ m88k-omron*)
+ os=-luna
+ ;;
+ *-next )
+ os=-nextstep
+ ;;
+ *-sequent)
+ os=-ptx
+ ;;
+ *-crds)
+ os=-unos
+ ;;
+ *-ns)
+ os=-genix
+ ;;
+ i370-*)
+ os=-mvs
+ ;;
+ *-next)
+ os=-nextstep3
+ ;;
+ *-gould)
+ os=-sysv
+ ;;
+ *-highlevel)
+ os=-bsd
+ ;;
+ *-encore)
+ os=-bsd
+ ;;
+ *-sgi)
+ os=-irix
+ ;;
+ *-siemens)
+ os=-sysv4
+ ;;
+ *-masscomp)
+ os=-rtu
+ ;;
+ f30[01]-fujitsu | f700-fujitsu)
+ os=-uxpv
+ ;;
+ *-rom68k)
+ os=-coff
+ ;;
+ *-*bug)
+ os=-coff
+ ;;
+ *-apple)
+ os=-macos
+ ;;
+ *-atari*)
+ os=-mint
+ ;;
+ *)
+ os=-none
+ ;;
+esac
+fi
+
+# Here we handle the case where we know the os, and the CPU type, but not the
+# manufacturer. We pick the logical manufacturer.
+vendor=unknown
+case $basic_machine in
+ *-unknown)
+ case $os in
+ -riscix*)
+ vendor=acorn
+ ;;
+ -sunos*)
+ vendor=sun
+ ;;
+ -aix*)
+ vendor=ibm
+ ;;
+ -beos*)
+ vendor=be
+ ;;
+ -hpux*)
+ vendor=hp
+ ;;
+ -mpeix*)
+ vendor=hp
+ ;;
+ -hiux*)
+ vendor=hitachi
+ ;;
+ -unos*)
+ vendor=crds
+ ;;
+ -dgux*)
+ vendor=dg
+ ;;
+ -luna*)
+ vendor=omron
+ ;;
+ -genix*)
+ vendor=ns
+ ;;
+ -mvs* | -opened*)
+ vendor=ibm
+ ;;
+ -os400*)
+ vendor=ibm
+ ;;
+ -ptx*)
+ vendor=sequent
+ ;;
+ -tpf*)
+ vendor=ibm
+ ;;
+ -vxsim* | -vxworks* | -windiss*)
+ vendor=wrs
+ ;;
+ -aux*)
+ vendor=apple
+ ;;
+ -hms*)
+ vendor=hitachi
+ ;;
+ -mpw* | -macos*)
+ vendor=apple
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ vendor=atari
+ ;;
+ -vos*)
+ vendor=stratus
+ ;;
+ esac
+ basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
+ ;;
+esac
+
+echo $basic_machine$os
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/config/depcomp b/config/depcomp
new file mode 100755
index 0000000..9e5522d
--- /dev/null
+++ b/config/depcomp
@@ -0,0 +1,520 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2003-11-08.23
+
+# Copyright (C) 1999, 2000, 2003 Free Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
+
+case $1 in
+ '')
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+ depmode Dependency tracking mode.
+ source Source file read by `PROGRAMS ARGS'.
+ object Object file output by `PROGRAMS ARGS'.
+ depfile Dependency file to output.
+ tmpdepfile Temporary file to use when outputing dependencies.
+ libtool Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit 0
+ ;;
+ -v | --v*)
+ echo "depcomp $scriptversion"
+ exit 0
+ ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+ echo "depcomp: Variables source, object and depmode must be set" 1>&2
+ exit 1
+fi
+# `libtool' can also be set to `yes' or `no'.
+
+if test -z "$depfile"; then
+ base=`echo "$object" | sed -e 's,^.*/,,' -e 's,\.\([^.]*\)$,.P\1,'`
+ dir=`echo "$object" | sed 's,/.*$,/,'`
+ if test "$dir" = "$object"; then
+ dir=
+ fi
+ # FIXME: should be _deps on DOS.
+ depfile="$dir.deps/$base"
+fi
+
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags. We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write. Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+ # HP compiler uses -M and no extra arg.
+ gccflag=-M
+ depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want. Yay! Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff. Hmm.
+ "$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ mv "$tmpdepfile" "$depfile"
+ ;;
+
+gcc)
+## There are various ways to get dependency output from gcc. Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+## up in a subdir. Having to rename by hand is ugly.
+## (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+## -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+## than renaming).
+ if test -z "$gccflag"; then
+ gccflag=-MD,
+ fi
+ "$@" -Wp,"$gccflag$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+ sed -e 's/^[^:]*: / /' \
+ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header). We avoid this by adding
+## dummy dependencies for each header file. Too bad gcc doesn't do
+## this for us directly.
+ tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'. On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+sgi)
+ if test "$libtool" = yes; then
+ "$@" "-Wp,-MDupdate,$tmpdepfile"
+ else
+ "$@" -MDupdate "$tmpdepfile"
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+
+ if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
+ echo "$object : \\" > "$depfile"
+
+ # Clip off the initial element (the dependent). Don't try to be
+ # clever and replace this with sed code, as IRIX sed won't handle
+ # lines with more than a fixed number of characters (4096 in
+ # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
+ # the IRIX cc adds comments like `#:fec' to the end of the
+ # dependency line.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+ tr '
+' ' ' >> $depfile
+ echo >> $depfile
+
+ # The second pass generates a dummy entry for each header file.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> $depfile
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+aix)
+ # The C for AIX Compiler uses -M and outputs the dependencies
+ # in a .u file. In older versions, this file always lives in the
+ # current directory. Also, the AIX compiler puts `$object:' at the
+ # start of each line; $object doesn't have directory information.
+ # Version 6 uses the directory in both cases.
+ stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
+ tmpdepfile="$stripped.u"
+ if test "$libtool" = yes; then
+ "$@" -Wc,-M
+ else
+ "$@" -M
+ fi
+ stat=$?
+
+ if test -f "$tmpdepfile"; then :
+ else
+ stripped=`echo "$stripped" | sed 's,^.*/,,'`
+ tmpdepfile="$stripped.u"
+ fi
+
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+
+ if test -f "$tmpdepfile"; then
+ outname="$stripped.o"
+ # Each line is of the form `foo.o: dependent.h'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
+ sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+icc)
+ # Intel's C compiler understands `-MD -MF file'. However on
+ # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+ # ICC 7.0 will fill foo.d with something like
+ # foo.o: sub/foo.c
+ # foo.o: sub/foo.h
+ # which is wrong. We want:
+ # sub/foo.o: sub/foo.c
+ # sub/foo.o: sub/foo.h
+ # sub/foo.c:
+ # sub/foo.h:
+ # ICC 7.1 will output
+ # foo.o: sub/foo.c sub/foo.h
+ # and will wrap long lines using \ :
+ # foo.o: sub/foo.c ... \
+ # sub/foo.h ... \
+ # ...
+
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ # Each line is of the form `foo.o: dependent.h',
+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+ sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+tru64)
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in `foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+ if test "$libtool" = yes; then
+ tmpdepfile1="$dir.libs/$base.lo.d"
+ tmpdepfile2="$dir.libs/$base.d"
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1="$dir$base.o.d"
+ tmpdepfile2="$dir$base.d"
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2"
+ exit $stat
+ fi
+
+ if test -f "$tmpdepfile1"; then
+ tmpdepfile="$tmpdepfile1"
+ else
+ tmpdepfile="$tmpdepfile2"
+ fi
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+#nosideeffect)
+ # This comment above is used by automake to tell side-effect
+ # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout, regardless of -o.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test $1 != '--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ test -z "$dashmflag" && dashmflag=-M
+ # Require at least two characters before searching for `:'
+ # in the target name. This is to cope with DOS-style filenames:
+ # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+ "$@" $dashmflag |
+ sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+dashXmstdout)
+ # This case only exists to satisfy depend.m4. It is never actually
+ # run, as this mode is specially recognized in the preamble.
+ exit 1
+ ;;
+
+makedepend)
+ "$@" || exit $?
+ # Remove any Libtool call
+ if test "$libtool" = yes; then
+ while test $1 != '--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+ # X makedepend
+ shift
+ cleared=no
+ for arg in "$@"; do
+ case $cleared in
+ no)
+ set ""; shift
+ cleared=yes ;;
+ esac
+ case "$arg" in
+ -D*|-I*)
+ set fnord "$@" "$arg"; shift ;;
+ # Strip any option that makedepend may not understand. Remove
+ # the object too, otherwise makedepend will parse it as a source file.
+ -*|$object)
+ ;;
+ *)
+ set fnord "$@" "$arg"; shift ;;
+ esac
+ done
+ obj_suffix="`echo $object | sed 's/^.*\././'`"
+ touch "$tmpdepfile"
+ ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile" "$tmpdepfile".bak
+ ;;
+
+cpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test $1 != '--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ "$@" -E |
+ sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+ sed '$ s: \\$::' > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ cat < "$tmpdepfile" >> "$depfile"
+ sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvisualcpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout, regardless of -o,
+ # because we must use -o when running libtool.
+ "$@" || exit $?
+ IFS=" "
+ for arg
+ do
+ case "$arg" in
+ "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+ set fnord "$@"
+ shift
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
+ esac
+ done
+ "$@" -E |
+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ echo " " >> "$depfile"
+ . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+none)
+ exec "$@"
+ ;;
+
+*)
+ echo "Unknown depmode $depmode" 1>&2
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/config/dynacounter.bash b/config/dynacounter.bash
new file mode 100644
index 0000000..3df0c72
--- /dev/null
+++ b/config/dynacounter.bash
@@ -0,0 +1,138 @@
+#!/bin/bash
+# $Id: dynacounter.bash,v 1.6 2012/06/30 01:32:25 bobgian Exp $
+
+# config/dynacounter.bash in toplevel LAMARC directory
+# Shell FUNCTION definition, not shell SCRIPT.
+
+#-----------------------------------------------------------------------------------------------------------------------
+#
+# Builds count for DYNACOUNTER_START.
+# Run this in the top-level LAMARC directory (ie, "~/lamarc").
+# Takes no arguments.
+#
+# This BASH function scans all LAMARC source files ("./src/*/*.cpp") in the current toplevel directory,
+# counts calls to "StartDynameter()", and builds a list of values for DYNACOUNTER_START. It then writes
+# a file called "dynacount.h" (in the "config" subdirectory of the current directory) which defines
+# DYNACOUNTER_START as a function of DYNAMETER_FILE_INDEX. Each file using the Dynameter machinery
+# must include the following lines (indented portion, not the initial comment character):
+#
+# // Must include this file BEFORE testing DYNAMETER_LEVEL (either explicitly below or implicitly
+# // inside file "dynatracer.h"), because this file establishes the definition (or not) of that symbol.
+# #include "local_build.h"
+# //
+# #ifdef DYNAMETER_LEVEL // If the Dynameter is enabled,
+# #define DYNAMETER_FILE_INDEX 0 // this symbol is defined uniquely in each ".cpp" file
+# #include "dynacount.h" // and used in this file (hence order is important).
+# #endif // DYNAMETER_LEVEL
+# //
+# // If Dynameter calls are included (whether or not they are enabled by defining DYNAMETER_LEVEL),
+# // this file must be included. It defines calls to StartDynameter() as macros that expand either into
+# // code (if enabled) or into whitespace (if disabled). Also, if the Dynameter is enabled, this file
+# // depends on some definitions in "dynacount.h" (and thus must included AFTER it).
+# #include "dynatracer.h"
+#
+# The compile-time constant DYNAMETER_FILE_INDEX identifies the file (the value should be set sequentially
+# starting from zero for the first Dynameter-using file and incrementing by one for each of the rest).
+# That is, the value here will be different for each source file. The other lines can appear verbatim.
+#
+# The file "dynacount.h" (written by this function) maps that index into the appropriate value of the
+# compile-time constant DYNACOUNTER_START, which defines the value of the index used by the first invocation
+# in that file of the macro StartDynameter(). For each invocation after the first, the index value passed
+# as an argument to that macro in incremented automatically by the pre-defined macro __COUNTER__ (which starts
+# at zero and increments with each usage in a given file). This guarantees that each call to StartDynameter()
+# system-wide gets its own unique index value, despite separate compilation of multiple source files.
+#
+# This function also keeps track of the maximum index value ever used (ie, the max count of all calls to
+# StartDynameter() over all LAMARC source files processed by a run of this function) and writes the accumulated
+# value as the definition of the constant DYNAMETER_ARRAYSIZE, which is used to dimension the array holding all
+# the tracing and metering information. This constant is used by "dynatracer.h", which is why THIS file must
+# be included before THAT file.
+#
+# If source file editing ever leads to a change in the number of calls to StartDynameter(), systemwide,
+# then make sure that the lines above are present in each file where needed, including a new value for the
+# symbol DYNAMETER_FILE_INDEX for any files with freshly-added calls to StartDynameter(). Then run this
+# function BEFORE recompiling the sources to make sure that the appropriate constants are defined with their
+# newly-updated values during that compilation.
+#
+#-----------------------------------------------------------------------------------------------------------------------
+
+function dynacounter()
+{
+ local dir file line startcounter flag
+ local index_file=${PWD}/config/dynacount.h
+ let startcounter=0
+
+ if [[ ! -f ${PWD}/config/dynacounter.bash ]] || [[ ! -f ${PWD}/config/local_build.h ]] ; then
+ echo
+ echo "Run this in the toplevel LAMARC directory (the one containing \"config\" and \"src\" as subdirectories)."
+ return 1
+ fi
+
+ if [[ -f ${PWD}/config/dynacount.h ]] ; then
+ echo
+ echo "Deleting old file: \"${PWD}/config/dynacount.h\""
+ /bin/rm -v ${PWD}/config/dynacount.h
+ fi
+
+ echo
+ echo "Writing index file: \"${index_file}\""
+
+ echo "// ${index_file}" > ${index_file}
+ echo "// Automatically-generated index map for Dynameter." >> ${index_file}
+ echo >> ${index_file}
+ echo "#ifndef DYNACOUNT_H" >> ${index_file}
+ echo "#define DYNACOUNT_H" >> ${index_file}
+ echo >> ${index_file}
+
+ # If DYNAMETER_FILE_INDEX is not defined when "dynacount.h" is included, then DYNACOUNTER_START
+ # will not get defined either. However, "dynacount.h" may still be needed even if DYNACOUNTER_START
+ # is not, because "dynacount.h" also defines DYNAMETER_ARRAYSIZE. For example, "dynameter.h"
+ # requires DYNAMETER_ARRAYSIZE be defined but not DYNACOUNTER_START. And "dynameter.h" requires
+ # the correct value for DYNAMETER_ARRAYSIZE, so it needs the result of this function's count, even
+ # though it does NOT need the intermediate results conveyed by DYNACOUNTER_START.
+ #
+ # The file "dynacount.h" provides a multi-way SWITCH statement, a compile-time sequence of
+ # "#elif ( DYNAMETER_FILE_INDEX == XXX )" branches (where XXX is an incrementing integer sequence).
+ # This next line provides the first line of that sequence, so that all the rest can start with "#elif"
+ # rather than having to use a special case for the first value processed.
+ #
+ echo "#ifndef DYNAMETER_FILE_INDEX" >> ${index_file}
+
+ echo
+ for dir in ${PWD}/src/* ; do
+ if [[ -d ${dir} ]] ; then
+ for file in ${dir}/*.cpp ; do
+ # Note that some of these will "count" even if commented out (ie, the ones NOT preceeded by "^[<>] "). In this case, a disabled
+ # call to "StartDynameter()" will result in incrementage of the count whether the call is used or not. Wasteful, but not harmful.
+ flag=NIL
+ echo -n "File: \"${file}\", Starting index: ${startcounter}"
+ for line in $( /bin/grep -e "StartDynameter();" -e "DYNAMETER_FILE_INDEX" ${file} ) ; do
+ if [[ ${line} = DYNAMETER_FILE_INDEX ]] ; then
+ flag=T
+ elif [[ ${flag} = T ]] ; then
+ echo "#elif ( DYNAMETER_FILE_INDEX == ${line} )" >> ${index_file}
+ echo " #define DYNACOUNTER_START ${startcounter}" >> ${index_file}
+ flag=NIL
+ elif [[ ${line} = "StartDynameter();" ]] ; then
+ let startcounter=$(( startcounter + 1 ))
+ fi
+ done
+ echo ", Ending index: ${startcounter}"
+ done
+ fi
+ done
+
+ echo "#endif" >> ${index_file}
+
+ echo >> ${index_file}
+ echo "#define DYNAMETER_ARRAYSIZE ${startcounter}" >> ${index_file}
+
+ echo >> ${index_file}
+ echo "#endif // DYNACOUNT_H" >> ${index_file}
+ echo >> ${index_file}
+ echo "//____________________________________________________________________________________" >> ${index_file}
+
+ return 0
+}
+
+#_______________________________________________________________________________________________________________________
diff --git a/config/install-sh b/config/install-sh
new file mode 100755
index 0000000..77bc381
--- /dev/null
+++ b/config/install-sh
@@ -0,0 +1,316 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2004-02-15.20
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch. It can only install one file at a time, a restriction
+# shared with many OS's install programs.
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit="${DOITPROG-}"
+
+# put in absolute paths if you don't have them in your path; or use env. vars.
+
+mvprog="${MVPROG-mv}"
+cpprog="${CPPROG-cp}"
+chmodprog="${CHMODPROG-chmod}"
+chownprog="${CHOWNPROG-chown}"
+chgrpprog="${CHGRPPROG-chgrp}"
+stripprog="${STRIPPROG-strip}"
+rmprog="${RMPROG-rm}"
+mkdirprog="${MKDIRPROG-mkdir}"
+
+transformbasename=
+transform_arg=
+instcmd="$mvprog"
+chmodcmd="$chmodprog 0755"
+chowncmd=
+chgrpcmd=
+stripcmd=
+rmcmd="$rmprog -f"
+mvcmd="$mvprog"
+src=
+dst=
+dir_arg=
+
+usage="Usage: $0 [OPTION]... SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 -d DIRECTORIES...
+
+In the first form, install SRCFILE to DSTFILE, removing SRCFILE by default.
+In the second, create the directory path DIR.
+
+Options:
+-b=TRANSFORMBASENAME
+-c copy source (using $cpprog) instead of moving (using $mvprog).
+-d create directories instead of installing files.
+-g GROUP $chgrp installed files to GROUP.
+-m MODE $chmod installed files to MODE.
+-o USER $chown installed files to USER.
+-s strip installed files (using $stripprog).
+-t=TRANSFORM
+--help display this help and exit.
+--version display version info and exit.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG
+"
+
+while test -n "$1"; do
+ case $1 in
+ -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
+ shift
+ continue;;
+
+ -c) instcmd=$cpprog
+ shift
+ continue;;
+
+ -d) dir_arg=true
+ shift
+ continue;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift
+ shift
+ continue;;
+
+ --help) echo "$usage"; exit 0;;
+
+ -m) chmodcmd="$chmodprog $2"
+ shift
+ shift
+ continue;;
+
+ -o) chowncmd="$chownprog $2"
+ shift
+ shift
+ continue;;
+
+ -s) stripcmd=$stripprog
+ shift
+ continue;;
+
+ -t=*) transformarg=`echo $1 | sed 's/-t=//'`
+ shift
+ continue;;
+
+ --version) echo "$0 $scriptversion"; exit 0;;
+
+ *) # When -d is used, all remaining arguments are directories to create.
+ test -n "$dir_arg" && break
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dstarg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dstarg"
+ shift # fnord
+ fi
+ shift # arg
+ dstarg=$arg
+ done
+ break;;
+ esac
+done
+
+if test -z "$1"; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+for src
+do
+ # Protect names starting with `-'.
+ case $src in
+ -*) src=./$src ;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ src=
+
+ if test -d "$dst"; then
+ instcmd=:
+ chmodcmd=
+ else
+ instcmd=$mkdirprog
+ fi
+ else
+ # Waiting for this to be detected by the "$instcmd $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dstarg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+
+ dst=$dstarg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst ;;
+ esac
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ dst=$dst/`basename "$src"`
+ fi
+ fi
+
+ # This sed command emulates the dirname command.
+ dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
+
+ # Make sure that the destination directory exists.
+
+ # Skip lots of stat calls in the usual case.
+ if test ! -d "$dstdir"; then
+ defaultIFS='
+ '
+ IFS="${IFS-$defaultIFS}"
+
+ oIFS=$IFS
+ # Some sh's can't handle IFS=/ for some reason.
+ IFS='%'
+ set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
+ IFS=$oIFS
+
+ pathcomp=
+
+ while test $# -ne 0 ; do
+ pathcomp=$pathcomp$1
+ shift
+ if test ! -d "$pathcomp"; then
+ $mkdirprog "$pathcomp" || lasterr=$?
+ # mkdir can fail with a `File exist' error in case several
+ # install-sh are creating the directory concurrently. This
+ # is OK.
+ test ! -d "$pathcomp" && { (exit ${lasterr-1}); exit; }
+ fi
+ pathcomp=$pathcomp/
+ done
+ fi
+
+ if test -n "$dir_arg"; then
+ $doit $instcmd "$dst" \
+ && { test -z "$chowncmd" || $doit $chowncmd "$dst"; } \
+ && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } \
+ && { test -z "$stripcmd" || $doit $stripcmd "$dst"; } \
+ && { test -z "$chmodcmd" || $doit $chmodcmd "$dst"; }
+
+ else
+ # If we're going to rename the final executable, determine the name now.
+ if test -z "$transformarg"; then
+ dstfile=`basename "$dst"`
+ else
+ dstfile=`basename "$dst" $transformbasename \
+ | sed $transformarg`$transformbasename
+ fi
+
+ # don't allow the sed command to completely eliminate the filename.
+ test -z "$dstfile" && dstfile=`basename "$dst"`
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'status=$?; rm -f "$dsttmp" "$rmtmp" && exit $status' 0
+ trap '(exit $?); exit' 1 2 13 15
+
+ # Move or copy the file name to the temp name
+ $doit $instcmd "$src" "$dsttmp" &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $instcmd $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } \
+ && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } \
+ && { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } \
+ && { test -z "$chmodcmd" || $doit $chmodcmd "$dsttmp"; } &&
+
+ # Now remove or move aside any old file at destination location. We
+ # try this two ways since rm can't unlink itself on some systems and
+ # the destination file might be busy for other reasons. In this case,
+ # the final cleanup might fail but the new file should still install
+ # successfully.
+ {
+ if test -f "$dstdir/$dstfile"; then
+ $doit $rmcmd -f "$dstdir/$dstfile" 2>/dev/null \
+ || $doit $mvcmd -f "$dstdir/$dstfile" "$rmtmp" 2>/dev/null \
+ || {
+ echo "$0: cannot unlink or rename $dstdir/$dstfile" >&2
+ (exit 1); exit
+ }
+ else
+ :
+ fi
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dstdir/$dstfile"
+ fi || { (exit 1); exit; }
+done
+
+# The final little trick to "correctly" pass the exit status to the exit trap.
+{
+ (exit 0); exit
+}
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/config/missing b/config/missing
new file mode 100755
index 0000000..e7ef83a
--- /dev/null
+++ b/config/missing
@@ -0,0 +1,360 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2003-09-02.23
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003
+# Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case "$1" in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case "$1" in
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Send bug reports to <bug-automake at gnu.org>."
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+ aclocal*)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case "$f" in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n 's/.*--output[ =]*\([^ ]*\).*/\1/p'`
+ test -z "$file" && file=`echo "$*" | sed -n 's/.*-o[ ]*\([^ ]*\).*/\1/p'`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison|yacc)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if [ $# -ne 1 ]; then
+ eval LASTARG="\${$#}"
+ case "$LASTARG" in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if [ ! -f y.tab.h ]; then
+ echo >y.tab.h
+ fi
+ if [ ! -f y.tab.c ]; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex|flex)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if [ $# -ne 1 ]; then
+ eval LASTARG="\${$#}"
+ case "$LASTARG" in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if [ ! -f lex.yy.c ]; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+ if test -z "$file"; then
+ file=`echo "$*" | sed -n 's/.*--output=\([^ ]*\).*/\1/p'`
+ fi
+ if [ -f "$file" ]; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit 1
+ fi
+ ;;
+
+ makeinfo)
+ if test -z "$run" && (makeinfo --version) > /dev/null 2>&1; then
+ # We have makeinfo, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+ if test -z "$file"; then
+ file=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $file`
+ fi
+ touch $file
+ ;;
+
+ tar)
+ shift
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ fi
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case "$firstarg" in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case "$firstarg" in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/configure b/configure
new file mode 100755
index 0000000..bde570f
--- /dev/null
+++ b/configure
@@ -0,0 +1,7765 @@
+#! /bin/sh
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.69 for lamarc 2.1.10.
+#
+# Report bugs to <lamarc at u.washington.edu>.
+#
+#
+# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
+#
+#
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+# Use a proper internal environment variable to ensure we don't fall
+ # into an infinite loop, continuously re-executing ourselves.
+ if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then
+ _as_can_reexec=no; export _as_can_reexec;
+ # We cannot yet assume a decent shell, so we have to provide a
+# neutralization value for shells without unset; and this also
+# works around shells that cannot unset nonexistent variables.
+# Preserve -v and -x to the replacement shell.
+BASH_ENV=/dev/null
+ENV=/dev/null
+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+case $- in # ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+esac
+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
+# Admittedly, this is quite paranoid, since all the known shells bail
+# out after a failed `exec'.
+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
+as_fn_exit 255
+ fi
+ # We don't want this to propagate to other subprocesses.
+ { _as_can_reexec=; unset _as_can_reexec;}
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
+
+exitcode=0
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
+
+else
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1
+test -x / || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
+test \$(( 1 + 1 )) = 2 || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
+else
+ as_have_required=no
+fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
+
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ as_found=:
+ case $as_dir in #(
+ /*)
+ for as_base in sh bash ksh sh5; do
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
+ done;;
+ esac
+ as_found=false
+done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
+IFS=$as_save_IFS
+
+
+ if test "x$CONFIG_SHELL" != x; then :
+ export CONFIG_SHELL
+ # We cannot yet assume a decent shell, so we have to provide a
+# neutralization value for shells without unset; and this also
+# works around shells that cannot unset nonexistent variables.
+# Preserve -v and -x to the replacement shell.
+BASH_ENV=/dev/null
+ENV=/dev/null
+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+case $- in # ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+esac
+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
+# Admittedly, this is quite paranoid, since all the known shells bail
+# out after a failed `exec'.
+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
+exit 255
+fi
+
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug-autoconf at gnu.org and
+$0: lamarc at u.washington.edu about your system, including
+$0: any error possibly output before this message. Then
+$0: install a modern shell, or manually run the script
+$0: under such a shell if you do have one."
+ fi
+ exit 1
+fi
+fi
+fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
+
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+ test -f "$1" && test -x "$1"
+} # as_fn_executable_p
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+
+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+
+ # If we had to re-execute with $CONFIG_SHELL, we're ensured to have
+ # already done that, so ensure we don't try to do so again and fall
+ # in an infinite loop. This has already happened in practice.
+ _as_can_reexec=no; export _as_can_reexec
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -pR'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -pR'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -pR'
+ fi
+else
+ as_ln_s='cp -pR'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+test -n "$DJDIR" || exec 7<&0 </dev/null
+exec 6>&1
+
+# Name of the host.
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_clean_files=
+ac_config_libobj_dir=.
+LIBOBJS=
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+
+# Identity of this package.
+PACKAGE_NAME='lamarc'
+PACKAGE_TARNAME='lamarc'
+PACKAGE_VERSION='2.1.10'
+PACKAGE_STRING='lamarc 2.1.10'
+PACKAGE_BUGREPORT='lamarc at u.washington.edu'
+PACKAGE_URL=''
+
+ac_unique_file="src/control/lamarc.cpp"
+# Factoring default headers for most tests.
+ac_includes_default="\
+#include <stdio.h>
+#ifdef HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#ifdef HAVE_SYS_STAT_H
+# include <sys/stat.h>
+#endif
+#ifdef STDC_HEADERS
+# include <stdlib.h>
+# include <stddef.h>
+#else
+# ifdef HAVE_STDLIB_H
+# include <stdlib.h>
+# endif
+#endif
+#ifdef HAVE_STRING_H
+# if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+# include <memory.h>
+# endif
+# include <string.h>
+#endif
+#ifdef HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#ifdef HAVE_INTTYPES_H
+# include <inttypes.h>
+#endif
+#ifdef HAVE_STDINT_H
+# include <stdint.h>
+#endif
+#ifdef HAVE_UNISTD_H
+# include <unistd.h>
+#endif"
+
+ac_subst_vars='am__EXEEXT_FALSE
+am__EXEEXT_TRUE
+LTLIBOBJS
+USERCXXFLAGS_FALSE
+USERCXXFLAGS_TRUE
+UNIVB_FALSE
+UNIVB_TRUE
+TREETRACK_FALSE
+TREETRACK_TRUE
+PROFILE_FALSE
+PROFILE_TRUE
+NOPROGRESS_FALSE
+NOPROGRESS_TRUE
+NODATA_FALSE
+NODATA_TRUE
+JSIM_FALSE
+JSIM_TRUE
+GUI_FALSE
+GUI_TRUE
+GCOV_FALSE
+GCOV_TRUE
+EFENCE_FALSE
+EFENCE_TRUE
+DMALLOC_FALSE
+DMALLOC_TRUE
+DENOVO_FALSE
+DENOVO_TRUE
+DEBUG_FALSE
+DEBUG_TRUE
+CONVERTER_FALSE
+CONVERTER_TRUE
+ARRCHECK_FALSE
+ARRCHECK_TRUE
+LIBOBJS
+EGREP
+GREP
+CPP
+am__fastdepCC_FALSE
+am__fastdepCC_TRUE
+CCDEPMODE
+ac_ct_CC
+CFLAGS
+CC
+RANLIB
+am__fastdepCXX_FALSE
+am__fastdepCXX_TRUE
+CXXDEPMODE
+am__nodep
+AMDEPBACKSLASH
+AMDEP_FALSE
+AMDEP_TRUE
+am__quote
+am__include
+DEPDIR
+OBJEXT
+EXEEXT
+ac_ct_CXX
+CPPFLAGS
+LDFLAGS
+CXXFLAGS
+CXX
+WX_LIBS
+WX_CXXFLAGS
+WXCONFIG2
+LAMARC_APP_MSW_FALSE
+LAMARC_APP_MSW_TRUE
+LAMARC_APP_OSX_FALSE
+LAMARC_APP_OSX_TRUE
+LAMARC_HOST_PREFIX
+LAMARC_CODE_OSTYPE
+AM_BACKSLASH
+AM_DEFAULT_VERBOSITY
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+AM_V
+am__untar
+am__tar
+AMTAR
+am__leading_dot
+SET_MAKE
+AWK
+mkdir_p
+MKDIR_P
+INSTALL_STRIP_PROGRAM
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+install_sh
+MAKEINFO
+AUTOHEADER
+AUTOMAKE
+AUTOCONF
+ACLOCAL
+VERSION
+PACKAGE
+CYGPATH_W
+am__isrc
+INSTALL_DATA
+INSTALL_SCRIPT
+INSTALL_PROGRAM
+target_os
+target_vendor
+target_cpu
+target
+host_os
+host_vendor
+host_cpu
+host
+build_os
+build_vendor
+build_cpu
+build
+MAINT
+MAINTAINER_MODE_FALSE
+MAINTAINER_MODE_TRUE
+target_alias
+host_alias
+build_alias
+LIBS
+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
+oldincludedir
+includedir
+runstatedir
+localstatedir
+sharedstatedir
+sysconfdir
+datadir
+datarootdir
+libexecdir
+sbindir
+bindir
+program_transform_name
+prefix
+exec_prefix
+PACKAGE_URL
+PACKAGE_BUGREPORT
+PACKAGE_STRING
+PACKAGE_VERSION
+PACKAGE_TARNAME
+PACKAGE_NAME
+PATH_SEPARATOR
+SHELL'
+ac_subst_files=''
+ac_user_opts='
+enable_option_checking
+enable_maintainer_mode
+enable_silent_rules
+enable_arrcheck
+enable_buildwx
+enable_converter
+enable_data
+enable_denovo
+enable_debug
+enable_dmalloc
+enable_efence
+enable_gcov
+enable_gui
+enable_jsim
+enable_profile
+enable_progress
+enable_shared
+enable_treetrack
+enable_universal_binary
+with_wx_config
+enable_dependency_tracking
+'
+ ac_precious_vars='build_alias
+host_alias
+target_alias
+CXX
+CXXFLAGS
+LDFLAGS
+LIBS
+CPPFLAGS
+CCC
+CC
+CFLAGS
+CPP'
+
+
+# Initialize some variables set by options.
+ac_init_help=
+ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+cache_file=/dev/null
+exec_prefix=NONE
+no_create=
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+# (The list follows the same order as the GNU Coding Standards.)
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datarootdir='${prefix}/share'
+datadir='${datarootdir}'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+runstatedir='${localstatedir}/run'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+infodir='${datarootdir}/info'
+htmldir='${docdir}'
+dvidir='${docdir}'
+pdfdir='${docdir}'
+psdir='${docdir}'
+libdir='${exec_prefix}/lib'
+localedir='${datarootdir}/locale'
+mandir='${datarootdir}/man'
+
+ac_prev=
+ac_dashdash=
+for ac_option
+do
+ # If the previous option needs an argument, assign it.
+ if test -n "$ac_prev"; then
+ eval $ac_prev=\$ac_option
+ ac_prev=
+ continue
+ fi
+
+ case $ac_option in
+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *=) ac_optarg= ;;
+ *) ac_optarg=yes ;;
+ esac
+
+ # Accept the important Cygnus configure options, so we can diagnose typos.
+
+ case $ac_dashdash$ac_option in
+ --)
+ ac_dashdash=yes ;;
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir=$ac_optarg ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build_alias ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build_alias=$ac_optarg ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=*)
+ datadir=$ac_optarg ;;
+
+ -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
+ | --dataroo | --dataro | --datar)
+ ac_prev=datarootdir ;;
+ -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
+ | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
+ datarootdir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
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+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
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+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
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+ -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
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+
+ -host | --host | --hos | --ho)
+ ac_prev=host_alias ;;
+ -host=* | --host=* | --hos=* | --ho=*)
+ host_alias=$ac_optarg ;;
+
+ -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht)
+ ac_prev=htmldir ;;
+ -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \
+ | --ht=*)
+ htmldir=$ac_optarg ;;
+
+ -includedir | --includedir | --includedi | --included | --include \
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+ ac_prev=includedir ;;
+ -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
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+ includedir=$ac_optarg ;;
+
+ -infodir | --infodir | --infodi | --infod | --info | --inf)
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+ -libdir | --libdir | --libdi | --libd)
+ ac_prev=libdir ;;
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+
+ -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
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+ libexecdir=$ac_optarg ;;
+
+ -localedir | --localedir | --localedi | --localed | --locale)
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+ localedir=$ac_optarg ;;
+
+ -localstatedir | --localstatedir | --localstatedi | --localstated \
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+ ac_prev=localstatedir ;;
+ -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
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+ localstatedir=$ac_optarg ;;
+
+ -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
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+ -nfp | --nfp | --nf)
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+
+ -no-recursion | --no-recursion | --no-recursio | --no-recursi \
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+ no_recursion=yes ;;
+
+ -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
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+ ac_prev=oldincludedir ;;
+ -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
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+ oldincludedir=$ac_optarg ;;
+
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+ prefix=$ac_optarg ;;
+
+ -program-prefix | --program-prefix | --program-prefi | --program-pref \
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+ program_prefix=$ac_optarg ;;
+
+ -program-suffix | --program-suffix | --program-suffi | --program-suff \
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+ -program-suffix=* | --program-suffix=* | --program-suffi=* \
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+ program_suffix=$ac_optarg ;;
+
+ -program-transform-name | --program-transform-name \
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+ program_transform_name=$ac_optarg ;;
+
+ -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd)
+ ac_prev=pdfdir ;;
+ -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*)
+ pdfdir=$ac_optarg ;;
+
+ -psdir | --psdir | --psdi | --psd | --ps)
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+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
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+ -runstatedir | --runstatedir | --runstatedi | --runstated \
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+ ac_prev=runstatedir ;;
+ -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
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+ runstatedir=$ac_optarg ;;
+
+ -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
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+ -sharedstatedir | --sharedstatedir | --sharedstatedi \
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+ ac_prev=sharedstatedir ;;
+ -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
+ | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
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+ sharedstatedir=$ac_optarg ;;
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+ srcdir=$ac_optarg ;;
+
+ -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
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+ ac_prev=sysconfdir ;;
+ -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
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+ sysconfdir=$ac_optarg ;;
+
+ -target | --target | --targe | --targ | --tar | --ta | --t)
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+ -version | --version | --versio | --versi | --vers | -V)
+ ac_init_version=: ;;
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+ -with-* | --with-*)
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+ ac_unrecognized_sep=', ';;
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+ -without-* | --without-*)
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+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
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+"with_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval with_$ac_useropt=no ;;
+
+ --x)
+ # Obsolete; use --with-x.
+ with_x=yes ;;
+
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+ x_includes=$ac_optarg ;;
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+ ac_prev=x_libraries ;;
+ -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
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+ x_libraries=$ac_optarg ;;
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+Try \`$0 --help' for more information"
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+
+ *)
+ # FIXME: should be removed in autoconf 3.0.
+ $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2
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+ ;;
+
+ esac
+done
+
+if test -n "$ac_prev"; then
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+ esac
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+
+# Check all directory arguments for consistency.
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+do
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+ # Remove trailing slashes.
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+ eval $ac_var=\$ac_val;;
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+ NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
+ esac
+ as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
+done
+
+# There might be people who depend on the old broken behavior: `$host'
+# used to hold the argument of --host etc.
+# FIXME: To remove some day.
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+host=$host_alias
+target=$target_alias
+
+# FIXME: To remove some day.
+if test "x$host_alias" != x; then
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+ elif test "x$build_alias" != "x$host_alias"; then
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+
+ac_tool_prefix=
+test -n "$host_alias" && ac_tool_prefix=$host_alias-
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+
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+test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
+ as_fn_error $? "pwd does not report name of working directory"
+
+
+# Find the source files, if location was not specified.
+if test -z "$srcdir"; then
+ ac_srcdir_defaulted=yes
+ # Try the directory containing this script, then the parent directory.
+ ac_confdir=`$as_dirname -- "$as_myself" ||
+$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
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+ /^X\(\/\).*/{
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+ fi
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+ ac_srcdir_defaulted=no
+fi
+if test ! -r "$srcdir/$ac_unique_file"; then
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+ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
+ac_abs_confdir=`(
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+ pwd)`
+# When building in place, set srcdir=.
+if test "$ac_abs_confdir" = "$ac_pwd"; then
+ srcdir=.
+fi
+# Remove unnecessary trailing slashes from srcdir.
+# Double slashes in file names in object file debugging info
+# mess up M-x gdb in Emacs.
+case $srcdir in
+*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
+esac
+for ac_var in $ac_precious_vars; do
+ eval ac_env_${ac_var}_set=\${${ac_var}+set}
+ eval ac_env_${ac_var}_value=\$${ac_var}
+ eval ac_cv_env_${ac_var}_set=\${${ac_var}+set}
+ eval ac_cv_env_${ac_var}_value=\$${ac_var}
+done
+
+#
+# Report the --help message.
+#
+if test "$ac_init_help" = "long"; then
+ # Omit some internal or obsolete options to make the list less imposing.
+ # This message is too long to be a string in the A/UX 3.1 sh.
+ cat <<_ACEOF
+\`configure' configures lamarc 2.1.10 to adapt to many kinds of systems.
+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE. See below for descriptions of some of the useful variables.
+
+Defaults for the options are specified in brackets.
+
+Configuration:
+ -h, --help display this help and exit
+ --help=short display options specific to this package
+ --help=recursive display the short help of all the included packages
+ -V, --version display version information and exit
+ -q, --quiet, --silent do not print \`checking ...' messages
+ --cache-file=FILE cache test results in FILE [disabled]
+ -C, --config-cache alias for \`--cache-file=config.cache'
+ -n, --no-create do not create output files
+ --srcdir=DIR find the sources in DIR [configure dir or \`..']
+
+Installation directories:
+ --prefix=PREFIX install architecture-independent files in PREFIX
+ [$ac_default_prefix]
+ --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
+ [PREFIX]
+
+By default, \`make install' will install all the files in
+\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
+an installation prefix other than \`$ac_default_prefix' using \`--prefix',
+for instance \`--prefix=\$HOME'.
+
+For better control, use the options below.
+
+Fine tuning of the installation directories:
+ --bindir=DIR user executables [EPREFIX/bin]
+ --sbindir=DIR system admin executables [EPREFIX/sbin]
+ --libexecdir=DIR program executables [EPREFIX/libexec]
+ --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
+ --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
+ --localstatedir=DIR modifiable single-machine data [PREFIX/var]
+ --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run]
+ --libdir=DIR object code libraries [EPREFIX/lib]
+ --includedir=DIR C header files [PREFIX/include]
+ --oldincludedir=DIR C header files for non-gcc [/usr/include]
+ --datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
+ --datadir=DIR read-only architecture-independent data [DATAROOTDIR]
+ --infodir=DIR info documentation [DATAROOTDIR/info]
+ --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
+ --mandir=DIR man documentation [DATAROOTDIR/man]
+ --docdir=DIR documentation root [DATAROOTDIR/doc/lamarc]
+ --htmldir=DIR html documentation [DOCDIR]
+ --dvidir=DIR dvi documentation [DOCDIR]
+ --pdfdir=DIR pdf documentation [DOCDIR]
+ --psdir=DIR ps documentation [DOCDIR]
+_ACEOF
+
+ cat <<\_ACEOF
+
+Program names:
+ --program-prefix=PREFIX prepend PREFIX to installed program names
+ --program-suffix=SUFFIX append SUFFIX to installed program names
+ --program-transform-name=PROGRAM run sed PROGRAM on installed program names
+
+System types:
+ --build=BUILD configure for building on BUILD [guessed]
+ --host=HOST cross-compile to build programs to run on HOST [BUILD]
+ --target=TARGET configure for building compilers for TARGET [HOST]
+_ACEOF
+fi
+
+if test -n "$ac_init_help"; then
+ case $ac_init_help in
+ short | recursive ) echo "Configuration of lamarc 2.1.10:";;
+ esac
+ cat <<\_ACEOF
+
+Optional Features:
+ --disable-option-checking ignore unrecognized --enable/--with options
+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --enable-maintainer-mode
+ enable make rules and dependencies not useful (and
+ sometimes confusing) to the casual installer
+ --enable-silent-rules less verbose build output (undo: "make V=1")
+ --disable-silent-rules verbose build output (undo: "make V=0")
+ --enable-arrcheck LAMARC: produce output to check arrangers
+ --enable-buildwx LAMARC: do a local build the wxWidgets library
+ --disable-converter LAMARC: don't build data conversion program(s)
+ --disable-data LAMARC: ignore data file
+ --enable-denovo LAMARC: all trees generated de-novo
+ --enable-debug Compile with debug flags
+ --enable-dmalloc LAMARC: Link with dmalloc library
+ --enable-efence LAMARC: Link with electric fence
+ --enable-gcov LAMARC: Compile with gcov flags
+ --disable-gui LAMARC: don't create lam_conv with graphic UI capability
+ --enable-jsim LAMARC: Compile with Jon's simulation flags
+ --enable-profile LAMARC: compile with profiling flags
+ --disable-progress LAMARC: turn off progress bar
+ --disable-shared LAMARC: don't use shared libs
+ --enable-treetrack LAMARC: track datalikelihoods of sampled trees
+ --enable-universal_binary LAMARC: build universal binary
+ --enable-dependency-tracking
+ do not reject slow dependency extractors
+ --disable-dependency-tracking
+ speeds up one-time build
+
+Optional Packages:
+ --with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
+ --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
+ --with-wx-config=FILE LAMARC: use existing wxWindows installation
+
+Some influential environment variables:
+ CXX C++ compiler command
+ CXXFLAGS C++ compiler flags
+ LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
+ nonstandard directory <lib dir>
+ LIBS libraries to pass to the linker, e.g. -l<library>
+ CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
+ you have headers in a nonstandard directory <include dir>
+ CC C compiler command
+ CFLAGS C compiler flags
+ CPP C preprocessor
+
+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
+
+Report bugs to <lamarc at u.washington.edu>.
+_ACEOF
+ac_status=$?
+fi
+
+if test "$ac_init_help" = "recursive"; then
+ # If there are subdirs, report their specific --help.
+ for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+ test -d "$ac_dir" ||
+ { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
+ continue
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+ cd "$ac_dir" || { ac_status=$?; continue; }
+ # Check for guested configure.
+ if test -f "$ac_srcdir/configure.gnu"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure.gnu" --help=recursive
+ elif test -f "$ac_srcdir/configure"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure" --help=recursive
+ else
+ $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+ fi || ac_status=$?
+ cd "$ac_pwd" || { ac_status=$?; break; }
+ done
+fi
+
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+ cat <<\_ACEOF
+lamarc configure 2.1.10
+generated by GNU Autoconf 2.69
+
+Copyright (C) 2012 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+ exit
+fi
+
+## ------------------------ ##
+## Autoconf initialization. ##
+## ------------------------ ##
+
+# ac_fn_cxx_try_compile LINENO
+# ----------------------------
+# Try to compile conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_compile
+
+# ac_fn_c_try_compile LINENO
+# --------------------------
+# Try to compile conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_compile
+
+# ac_fn_c_try_cpp LINENO
+# ----------------------
+# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_cpp ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } > conftest.i && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_cpp
+
+# ac_fn_c_try_run LINENO
+# ----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
+# that executables *can* be run.
+ac_fn_c_try_run ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=$ac_status
+fi
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_run
+
+# ac_fn_c_check_header_mongrel LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
+# Tests whether HEADER exists, giving a warning if it cannot be compiled using
+# the include files in INCLUDES and setting the cache variable VAR
+# accordingly.
+ac_fn_c_check_header_mongrel ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if eval \${$3+:} false; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+ $as_echo_n "(cached) " >&6
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
+$as_echo_n "checking $2 usability... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_header_compiler=yes
+else
+ ac_header_compiler=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
+$as_echo_n "checking $2 presence... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <$2>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ ac_header_preproc=yes
+else
+ ac_header_preproc=no
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in #((
+ yes:no: )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+( $as_echo "## -------------------------------------- ##
+## Report this to lamarc at u.washington.edu ##
+## -------------------------------------- ##"
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=\$ac_header_compiler"
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+fi
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_c_check_header_mongrel
+
+# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
+# Tests whether HEADER exists and can be compiled using the include files in
+# INCLUDES, setting the cache variable VAR accordingly.
+ac_fn_c_check_header_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_c_check_header_compile
+
+# ac_fn_c_check_type LINENO TYPE VAR INCLUDES
+# -------------------------------------------
+# Tests whether TYPE exists after having included INCLUDES, setting cache
+# variable VAR accordingly.
+ac_fn_c_check_type ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=no"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+int
+main ()
+{
+if (sizeof ($2))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+int
+main ()
+{
+if (sizeof (($2)))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ eval "$3=yes"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_c_check_type
+
+# ac_fn_c_try_link LINENO
+# -----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_link ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext conftest$ac_exeext
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ test -x conftest$ac_exeext
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+ # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+ # interfere with the next link command; also delete a directory that is
+ # left behind by Apple's compiler. We do this before executing the actions.
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_link
+
+# ac_fn_c_check_func LINENO FUNC VAR
+# ----------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_c_check_func ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $2 (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_c_check_func
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by lamarc $as_me 2.1.10, which was
+generated by GNU Autoconf 2.69. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ $as_echo "PATH: $as_dir"
+ done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *\'*)
+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+ 2)
+ as_fn_append ac_configure_args1 " '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
+ ;;
+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ as_fn_append ac_configure_args " '$ac_arg'"
+ ;;
+ esac
+ done
+done
+{ ac_configure_args0=; unset ac_configure_args0;}
+{ ac_configure_args1=; unset ac_configure_args1;}
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ $as_echo "## ---------------- ##
+## Cache variables. ##
+## ---------------- ##"
+ echo
+ # The following way of writing the cache mishandles newlines in values,
+(
+ for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+ (set) 2>&1 |
+ case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ sed -n \
+ "s/'\''/'\''\\\\'\'''\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
+ ;; #(
+ *)
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+)
+ echo
+
+ $as_echo "## ----------------- ##
+## Output variables. ##
+## ----------------- ##"
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ $as_echo "## ------------------- ##
+## File substitutions. ##
+## ------------------- ##"
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ $as_echo "## ----------- ##
+## confdefs.h. ##
+## ----------- ##"
+ echo
+ cat confdefs.h
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ $as_echo "$as_me: caught signal $ac_signal"
+ $as_echo "$as_me: exit $exit_status"
+ } >&5
+ rm -f core *.core core.conftest.* &&
+ rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
+ exit $exit_status
+' 0
+for ac_signal in 1 2 13 15; do
+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -f -r conftest* confdefs.h
+
+$as_echo "/* confdefs.h */" > confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_VERSION "$PACKAGE_VERSION"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_URL "$PACKAGE_URL"
+_ACEOF
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer an explicitly selected file to automatically selected ones.
+ac_site_file1=NONE
+ac_site_file2=NONE
+if test -n "$CONFIG_SITE"; then
+ # We do not want a PATH search for config.site.
+ case $CONFIG_SITE in #((
+ -*) ac_site_file1=./$CONFIG_SITE;;
+ */*) ac_site_file1=$CONFIG_SITE;;
+ *) ac_site_file1=./$CONFIG_SITE;;
+ esac
+elif test "x$prefix" != xNONE; then
+ ac_site_file1=$prefix/share/config.site
+ ac_site_file2=$prefix/etc/config.site
+else
+ ac_site_file1=$ac_default_prefix/share/config.site
+ ac_site_file2=$ac_default_prefix/etc/config.site
+fi
+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
+do
+ test "x$ac_site_file" = xNONE && continue
+ if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+$as_echo "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file" \
+ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special files
+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+$as_echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+$as_echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to enable maintainer-specific portions of Makefiles" >&5
+$as_echo_n "checking whether to enable maintainer-specific portions of Makefiles... " >&6; }
+ # Check whether --enable-maintainer-mode was given.
+if test "${enable_maintainer_mode+set}" = set; then :
+ enableval=$enable_maintainer_mode; USE_MAINTAINER_MODE=$enableval
+else
+ USE_MAINTAINER_MODE=no
+fi
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $USE_MAINTAINER_MODE" >&5
+$as_echo "$USE_MAINTAINER_MODE" >&6; }
+ if test $USE_MAINTAINER_MODE = yes; then
+ MAINTAINER_MODE_TRUE=
+ MAINTAINER_MODE_FALSE='#'
+else
+ MAINTAINER_MODE_TRUE='#'
+ MAINTAINER_MODE_FALSE=
+fi
+
+ MAINT=$MAINTAINER_MODE_TRUE
+
+
+ac_aux_dir=
+for ac_dir in config "$srcdir"/config; do
+ if test -f "$ac_dir/install-sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f "$ac_dir/shtool"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in config \"$srcdir\"/config" "$LINENO" 5
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+
+
+$as_echo "#define RELEASE_DATE \"14 Nov 2013\"" >>confdefs.h
+
+
+wxRequiredMajorVersion=2
+wxRequiredMinorVersion=8
+wxRequiredPatchVersion=3
+wxVersionRequired=${wxRequiredMajorVersion}.${wxRequiredMinorVersion}.${wxRequiredPatchVersion}
+
+wxProvidedMajorVersion=2
+wxProvidedMinorVersion=8
+wxProvidedPatchVersion=12
+wxVersionProvided=${wxProvidedMajorVersion}.${wxProvidedMinorVersion}.${wxProvidedPatchVersion}
+
+# setting up OS and CPU variables
+# Make sure we can run config.sub.
+$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
+ as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
+$as_echo_n "checking build system type... " >&6; }
+if ${ac_cv_build+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_build_alias=$build_alias
+test "x$ac_build_alias" = x &&
+ ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
+test "x$ac_build_alias" = x &&
+ as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
+ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
+$as_echo "$ac_cv_build" >&6; }
+case $ac_cv_build in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5;;
+esac
+build=$ac_cv_build
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_build
+shift
+build_cpu=$1
+build_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+build_os=$*
+IFS=$ac_save_IFS
+case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
+$as_echo_n "checking host system type... " >&6; }
+if ${ac_cv_host+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "x$host_alias" = x; then
+ ac_cv_host=$ac_cv_build
+else
+ ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
+$as_echo "$ac_cv_host" >&6; }
+case $ac_cv_host in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5;;
+esac
+host=$ac_cv_host
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_host
+shift
+host_cpu=$1
+host_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+host_os=$*
+IFS=$ac_save_IFS
+case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5
+$as_echo_n "checking target system type... " >&6; }
+if ${ac_cv_target+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "x$target_alias" = x; then
+ ac_cv_target=$ac_cv_host
+else
+ ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5
+$as_echo "$ac_cv_target" >&6; }
+case $ac_cv_target in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5;;
+esac
+target=$ac_cv_target
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_target
+shift
+target_cpu=$1
+target_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+target_os=$*
+IFS=$ac_save_IFS
+case $target_os in *\ *) target_os=`echo "$target_os" | sed 's/ /-/g'`;; esac
+
+
+# The aliases save the names the user supplied, while $host etc.
+# will get canonicalized.
+test -n "$target_alias" &&
+ test "$program_prefix$program_suffix$program_transform_name" = \
+ NONENONEs,x,x, &&
+ program_prefix=${target_alias}-
+
+am__api_version='1.15'
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if ${ac_cv_path_install+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in #((
+ ./ | .// | /[cC]/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+ done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5;;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error $? "unsafe srcdir value: '$srcdir'" "$LINENO" 5;;
+esac
+
+# Do 'set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ am_has_slept=no
+ for am_try in 1 2; do
+ echo "timestamp, slept: $am_has_slept" > conftest.file
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
+ alias in your environment" "$LINENO" 5
+ fi
+ if test "$2" = conftest.file || test $am_try -eq 2; then
+ break
+ fi
+ # Just in case.
+ sleep 1
+ am_has_slept=yes
+ done
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ as_fn_error $? "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+# If we didn't sleep, we still need to ensure time stamps of config.status and
+# generated files are strictly newer.
+am_sleep_pid=
+if grep 'slept: no' conftest.file >/dev/null 2>&1; then
+ ( sleep 1 ) &
+ am_sleep_pid=$!
+fi
+
+rm -f conftest.file
+
+test "$program_prefix" != NONE &&
+ program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.
+# By default was `s,x,x', remove it if useless.
+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# Expand $ac_aux_dir to an absolute path.
+am_aux_dir=`cd "$ac_aux_dir" && pwd`
+
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --is-lightweight"; then
+ am_missing_run="$MISSING "
+else
+ am_missing_run=
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
+fi
+
+if test x"${install_sh+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using 'strip' when the user
+# run "make install-strip". However 'strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the 'STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_STRIP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if ${ac_cv_path_mkdir+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in mkdir gmkdir; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext" || continue
+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
+ 'mkdir (GNU coreutils) '* | \
+ 'mkdir (coreutils) '* | \
+ 'mkdir (fileutils) '4.1*)
+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
+ break 3;;
+ esac
+ done
+ done
+ done
+IFS=$as_save_IFS
+
+fi
+
+ test -d ./--version && rmdir ./--version
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ MKDIR_P="$ac_cv_path_mkdir -p"
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for MKDIR_P within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ MKDIR_P="$ac_install_sh -d"
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_AWK+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+# Check whether --enable-silent-rules was given.
+if test "${enable_silent_rules+set}" = set; then :
+ enableval=$enable_silent_rules;
+fi
+
+case $enable_silent_rules in # (((
+ yes) AM_DEFAULT_VERBOSITY=0;;
+ no) AM_DEFAULT_VERBOSITY=1;;
+ *) AM_DEFAULT_VERBOSITY=1;;
+esac
+am_make=${MAKE-make}
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5
+$as_echo_n "checking whether $am_make supports nested variables... " >&6; }
+if ${am_cv_make_support_nested_variables+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if $as_echo 'TRUE=$(BAR$(V))
+BAR0=false
+BAR1=true
+V=1
+am__doit:
+ @$(TRUE)
+.PHONY: am__doit' | $am_make -f - >/dev/null 2>&1; then
+ am_cv_make_support_nested_variables=yes
+else
+ am_cv_make_support_nested_variables=no
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_make_support_nested_variables" >&5
+$as_echo "$am_cv_make_support_nested_variables" >&6; }
+if test $am_cv_make_support_nested_variables = yes; then
+ AM_V='$(V)'
+ AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
+else
+ AM_V=$AM_DEFAULT_VERBOSITY
+ AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
+fi
+AM_BACKSLASH='\'
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='lamarc'
+ VERSION='2.1.10'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+# For better backward compatibility. To be removed once Automake 1.9.x
+# dies out for good. For more background, see:
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+mkdir_p='$(MKDIR_P)'
+
+# We need awk for the "check" target (and possibly the TAP driver). The
+# system "awk" is bad on some platforms.
+# Always define AMTAR for backward compatibility. Yes, it's still used
+# in the wild :-( We should find a proper way to deprecate it ...
+AMTAR='$${TAR-tar}'
+
+
+# We'll loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar pax cpio none'
+
+am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+
+
+
+
+
+
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
+ fi
+fi
+
+
+ac_config_headers="$ac_config_headers config/conf.h"
+
+
+# define conditionals/arguments ***************************
+
+
+
+# use --disable-data for generating stationaries
+# Check whether --enable-arrcheck was given.
+if test "${enable_arrcheck+set}" = set; then :
+ enableval=$enable_arrcheck; lamARRCHECK=$enableval
+else
+ lamARRCHECK=no
+fi
+
+# Check whether --enable-buildwx was given.
+if test "${enable_buildwx+set}" = set; then :
+ enableval=$enable_buildwx; lamBUILDWX=$enableval
+else
+ lamBUILDWX=no
+fi
+
+# Check whether --enable-converter was given.
+if test "${enable_converter+set}" = set; then :
+ enableval=$enable_converter; lamCONV=$enableval
+else
+ lamCONV=yes
+fi
+
+# Check whether --enable-data was given.
+if test "${enable_data+set}" = set; then :
+ enableval=$enable_data; lamDATA_READ=$enableval
+else
+ lamDATA_READ=yes
+fi
+
+# Check whether --enable-denovo was given.
+if test "${enable_denovo+set}" = set; then :
+ enableval=$enable_denovo; lamDENOVO=$enableval
+else
+ lamDENOVO=no
+fi
+
+# Check whether --enable-debug was given.
+if test "${enable_debug+set}" = set; then :
+ enableval=$enable_debug; lamDEBUG=$enableval
+else
+ lamDEBUG=no
+fi
+
+# Check whether --enable-dmalloc was given.
+if test "${enable_dmalloc+set}" = set; then :
+ enableval=$enable_dmalloc; lamDMALLOC=$enableval
+else
+ lamDMALLOC=no
+fi
+
+# Check whether --enable-efence was given.
+if test "${enable_efence+set}" = set; then :
+ enableval=$enable_efence; lamEFENCE=$enableval
+else
+ lamEFENCE=no
+fi
+
+# Check whether --enable-gcov was given.
+if test "${enable_gcov+set}" = set; then :
+ enableval=$enable_gcov; lamGCOV=$enableval
+else
+ lamGCOV=no
+fi
+
+# Check whether --enable-gui was given.
+if test "${enable_gui+set}" = set; then :
+ enableval=$enable_gui; lamGUI=$enableval
+else
+ lamGUI=yes
+fi
+
+# Check whether --enable-jsim was given.
+if test "${enable_jsim+set}" = set; then :
+ enableval=$enable_jsim; lamJSIM=$enableval
+else
+ lamJSIM=no
+fi
+
+# Check whether --enable-profile was given.
+if test "${enable_profile+set}" = set; then :
+ enableval=$enable_profile; lamPROFILE=$enableval
+else
+ lamPROFILE=no
+fi
+
+# Check whether --enable-progress was given.
+if test "${enable_progress+set}" = set; then :
+ enableval=$enable_progress; lamPROGRESS=$enableval
+else
+ lamPROGRESS=yes
+fi
+
+# Check whether --enable-shared was given.
+if test "${enable_shared+set}" = set; then :
+ enableval=$enable_shared; lamSHARED=$enableval
+else
+ lamSHARED=no
+fi
+
+# Check whether --enable-treetrack was given.
+if test "${enable_treetrack+set}" = set; then :
+ enableval=$enable_treetrack; lamTREETRACK=$enableval
+else
+ lamTREETRACK=no
+fi
+
+# Check whether --enable-universal_binary was given.
+if test "${enable_universal_binary+set}" = set; then :
+ enableval=$enable_universal_binary; lamUNIVB=$enableval
+else
+ lamUNIVB=no
+fi
+
+
+# Check whether --with-wx-config was given.
+if test "${with_wx_config+set}" = set; then :
+ withval=$with_wx_config; lamWX_CONFIG=$withval
+fi
+
+
+
+# check that we either have info on GUI toolkit and OS, or get it and complain
+
+case "$target_os" in
+ darwin*)
+ if test "X${lamCONV}" = "Xyes" ; then
+ if test "X${lamGUI}" = "Xyes" ; then
+ if test "X${GUI_TOOLKIT}" = "X" ; then
+ GUI_TOOLKIT=osx_cocoa
+ fi
+ fi
+ fi
+ if test "X${LAMARC_CODE_OSTYPE}" = "X" ; then
+ LAMARC_CODE_OSTYPE=LAMARC_COMPILE_MACOSX
+ fi
+ ;;
+ freebsd*|linux*)
+ if test "X${lamCONV}" = "Xyes" ; then
+ if test "X${lamGUI}" = "Xyes" ; then
+ if test "X${GUI_TOOLKIT}" = "X" ; then
+ GUI_TOOLKIT=gtk2
+ fi
+ fi
+ fi
+ if test "X${LAMARC_CODE_OSTYPE}" = "X" ; then
+ LAMARC_CODE_OSTYPE=LAMARC_COMPILE_LINUX
+ fi
+ ;;
+ *mingw32*)
+ if test "X${lamCONV}" = "Xyes" ; then
+ if test "X${lamGUI}" = "Xyes" ; then
+ if test "X${GUI_TOOLKIT}" = "X" ; then
+ GUI_TOOLKIT=msw
+ fi
+ fi
+ fi
+ if test "X${LAMARC_CODE_OSTYPE}" = "X" ; then
+ LAMARC_CODE_OSTYPE=LAMARC_COMPILE_MSWINDOWS
+ fi
+ ;;
+ *)
+ if test "X${LAMARC_CODE_OSTYPE}" = "X" ; then
+ GUI_TOOLKIT=osx_cocoa
+ LAMARC_CODE_OSTYPE=LAMARC_COMPILE_MACOSX
+ echo "*************************************************************"
+ echo "DO NOT CHECK THIS config.ac in, it has GUI_TOOLKIT and"
+ echo "LAMARC_CODE_OSTYPE hardwired for 10.7 mac"
+ echo "*************************************************************"
+ fi
+ ;;
+esac
+
+if test "X${LAMARC_CODE_OSTYPE}" = "X" ; then
+ echo "An internal error occured. We thought it was impossible not"
+ echo "to have LAMARC_CODE_OSTYPE set. Please notify the lamarc"
+ echo "team at lamarc at u.washington.edu and try setting the environment"
+ echo "variable LAMARC_CODE_OSTYPE as described in the \"Compiling"
+ echo "Lamarc\" portion of the documentation."
+ as_fn_error $? "cannot proceed without LAMARC_CODE_OSTYPE" "$LINENO" 5
+fi
+
+if test "X${lamCONV}" = "Xyes" ; then
+ if test "X${lamGUI}" = "Xyes" ; then
+ if test "X${GUI_TOOLKIT}" = "X" ; then
+ echo "*************************************************************"
+ echo "You have enabled compilation of the converter GUI but the"
+ echo "configure script was not able to guess the correct GUI"
+ echo "toolkit to use. See the section entitled Compiling"
+ echo "Lamarc in the Lamarc documentation for more information."
+ echo "*************************************************************"
+ as_fn_error $? "cannot proceed without GUI_TOOLKIT" "$LINENO" 5
+ fi
+ else
+ if test "X${GUI_TOOLKIT}" != "X" ; then
+ if test "X${GUI_TOOLKIT}" != "Xbase" ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: changing GUI_TOOLKIT ${GUI_TOOLKIT} to base because GUI is disabled" >&5
+$as_echo "$as_me: WARNING: changing GUI_TOOLKIT ${GUI_TOOLKIT} to base because GUI is disabled" >&2;}
+ fi
+ fi
+ GUI_TOOLKIT=base
+ fi
+fi
+
+
+
+if test "X${host_alias}" = "X" ; then
+ LAMARC_HOST_PREFIX=""
+else
+ LAMARC_HOST_PREFIX="${host_alias}-"
+fi
+
+# conditionals used in Makefile.am to specify different
+# resources and/or compilation products for different
+# platforms
+ if test $LAMARC_CODE_OSTYPE = LAMARC_COMPILE_MACOSX; then
+ LAMARC_APP_OSX_TRUE=
+ LAMARC_APP_OSX_FALSE='#'
+else
+ LAMARC_APP_OSX_TRUE='#'
+ LAMARC_APP_OSX_FALSE=
+fi
+
+ if test $LAMARC_CODE_OSTYPE = LAMARC_COMPILE_MSWINDOWS; then
+ LAMARC_APP_MSW_TRUE=
+ LAMARC_APP_MSW_FALSE='#'
+else
+ LAMARC_APP_MSW_TRUE='#'
+ LAMARC_APP_MSW_FALSE=
+fi
+
+
+# now a few functions for checking the wxWidgets stuff
+
+build_wx()
+{
+ echo "*******************************************"
+ echo "* starting wxWidgets build *"
+ echo "*******************************************"
+
+ # build wx options
+ if test "X${lamGUI}" = "Xyes" ; then
+ guiOption="--with-${GUI_TOOLKIT}"
+ else
+ guiOption="--disable-gui"
+ fi
+
+ sharedOption="--disable-shared"
+
+ debugOption="--disable-debug"
+ if test "X${lamDEBUG}" = "Xyes" ; then
+ debugOption="--enable-debug"
+ fi
+
+ crossOptions=
+ if test "$host_os" != "$build_os" ; then
+ crossOptions="--disable-threads --host=${host_alias}"
+ fi
+
+ # this is not optimal -- but it is the easiest way to solve
+ # the problem that builtin tiff is needed for debian, yet
+ # we compile releases on red hat
+ tiffOptions=
+ if test "$LAMARC_CODE_OSTYPE" = "LAMARC_COMPILE_LINUX" ; then
+ tiffOptions="--with-libtiff=builtin"
+ fi
+
+ universalBinaryOptions=
+ if test "X${lamUNIVB}" = "Xyes" ; then
+ universalBinaryOptions="--enable-universal_binary --disable-dependency-tracking"
+ fi
+
+
+ wxConfigOptions="${guiOption} ${sharedOption} ${debugOption} ${crossOptions} ${tiffOptions} ${universalBinaryOptions}"
+
+ thisDir=`pwd`;
+ configScriptDir=`dirname $0`
+ topOfPackage=`(cd $configScriptDir 2> /dev/null && pwd ;)`
+ wxTarFile=${topOfPackage}/wxWidgets/wxWidgets-${wxVersionProvided}.tar.gz
+ wxUnpackedDir=wxWidgets-${wxVersionProvided}
+
+ # unpack tar file
+ if test ! -d ${wxUnpackedDir} ; then
+ echo "untar-ing wxWidgets distribution ${wxTarFile}"
+ tar xfvz ${wxTarFile}
+ else
+ echo "${wxUnpackedDir} already exists. Skipping main un-tar step"
+ fi
+
+ if test ! -d ${wxUnpackedDir} ; then
+ as_fn_error $? "Unsuccessful trying to un-tar ${wxTarFile}" "$LINENO" 5
+ else
+ cd ${wxUnpackedDir}
+ fi
+
+ # untar patches over tar file
+ for file in ${topOfPackage}/wxWidgets/wxWidgets-${wxVersionProvided}-Patch*.tar.gz
+ do
+ tar xfvz ${file}
+ done
+
+ # build wxWidgets
+ ./configure ${wxConfigOptions}
+ make
+ cd ${thisDir}
+ RETURN_STRING=${thisDir}/${wxUnpackedDir}/wx-config
+}
+
+get_wx_config_script()
+{
+ if test "X${lamWX_CONFIG}" = "Xyes" ; then
+ # whoops, user used --with-wx-config without an argument
+ # let's assume it is going to be on their path
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: no argument given to --with-wx-config" >&5
+$as_echo "$as_me: WARNING: no argument given to --with-wx-config" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Assuming \"wx-config\" is on your \$PATH" >&5
+$as_echo "$as_me: WARNING: Assuming \"wx-config\" is on your \$PATH" >&2;}
+ WXCONFIG="wx-config"
+ else
+ if test "X${lamWX_CONFIG}" = "X" ; then
+ # whoops, user didn't give --with-wx-config
+ # let's assume wx-config is going to be on their path
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: No option --with-wx-config given" >&5
+$as_echo "$as_me: WARNING: No option --with-wx-config given" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Assuming \"wx-config\" is on your \$PATH" >&5
+$as_echo "$as_me: WARNING: Assuming \"wx-config\" is on your \$PATH" >&2;}
+ WXCONFIG="wx-config"
+ else
+ # take the value of wx-config script the user gave us
+ WXCONFIG=$lamWX_CONFIG
+ fi
+ fi
+
+ # Extract the first word of "$WXCONFIG", so it can be a program name with args.
+set dummy $WXCONFIG; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_path_WXCONFIG2+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $WXCONFIG2 in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_WXCONFIG2="$WXCONFIG2" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_path_WXCONFIG2="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ test -z "$ac_cv_path_WXCONFIG2" && ac_cv_path_WXCONFIG2=""""
+ ;;
+esac
+fi
+WXCONFIG2=$ac_cv_path_WXCONFIG2
+if test -n "$WXCONFIG2"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $WXCONFIG2" >&5
+$as_echo "$WXCONFIG2" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ if test "X${WXCONFIG2}" = "X" ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Failure of above check for $WXCONFIG might have been a bug" >&5
+$as_echo "$as_me: WARNING: Failure of above check for $WXCONFIG might have been a bug" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Searching for it using AC CHECK FILE macro" >&5
+$as_echo "$as_me: WARNING: Searching for it using AC CHECK FILE macro" >&2;}
+ as_ac_File=`$as_echo "ac_cv_file_$WXCONFIG" | $as_tr_sh`
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $WXCONFIG" >&5
+$as_echo_n "checking for $WXCONFIG... " >&6; }
+if eval \${$as_ac_File+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ test "$cross_compiling" = yes &&
+ as_fn_error $? "cannot check for file existence when cross compiling" "$LINENO" 5
+if test -r "$WXCONFIG"; then
+ eval "$as_ac_File=yes"
+else
+ eval "$as_ac_File=no"
+fi
+fi
+eval ac_res=\$$as_ac_File
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if eval test \"x\$"$as_ac_File"\" = x"yes"; then :
+ WXCONFIG2=$WXCONFIG
+else
+ WXCONFIG2=""
+fi
+
+ fi
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking wxWidgets version" >&5
+$as_echo_n "checking wxWidgets version... " >&6; }
+ if test "X${WXCONFIG2}" = "X" ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5
+$as_echo "not found" >&6; }
+ wxVersion=""
+ else
+ if wxVersion=`$WXCONFIG2 --version`; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $wxVersion" >&5
+$as_echo "$wxVersion" >&6; }
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5
+$as_echo "not found" >&6; }
+ fi
+ fi
+
+ whatIsWxProb=""
+ isVersionBad=""
+ if test "X${wxVersion}" = "X" ; then
+ whatIsWxProb="Could not find wxWidgets config script"
+ isVersionBad="yes"
+ else
+ whatIsWxProb="Your wxWidgets version is ${wxVersion}"
+ wxVersionMajor=`echo ${wxVersion} | awk -F. '{ print $1 }' - `
+ wxVersionMinor=`echo ${wxVersion} | awk -F. '{ print $2 }' - `
+ wxVersionPatch=`echo ${wxVersion} | awk -F. '{ print $3 }' - `
+
+ if test "$wxVersionMajor" -lt "$wxRequiredMajorVersion" ; then
+ isVersionBad="yes"
+ else
+ if test "$wxVersionMajor" -eq "$wxRequiredMajorVersion" ; then
+ if test "$wxVersionMinor" -lt "$wxRequiredMinorVersion" ; then
+ isVersionBad="yes"
+ else
+ if test "$wxVersionMinor" -eq "$wxRequiredMinorVersion" ; then
+ if test "$wxVersionPatch" -lt "$wxRequiredPatchVersion" ; then
+ isVersionBad="yes"
+ fi
+ fi
+ fi
+ fi
+ fi
+ fi
+
+ if test "${isVersionBad}" ; then
+ echo "*******************************************"
+ echo "wxWidgets version ${wxVersionRequired} or greater is required"
+ echo "to build lamarc data converters, but the configure script"
+ echo "found version ${wxVersion}."
+ echo ""
+ echo "If you don't want to install your own version of wxWidgets,"
+ echo "you can try using the configure switch --enable-buildwx"
+ echo ""
+ echo "See the section entitled Compiling Lamarc in the"
+ echo "Lamarc documentation for more information."
+ echo "*******************************************"
+ as_fn_error $? "needed wxWidgets version ${wxVersionRequired} or greater" "$LINENO" 5
+ fi
+
+ RETURN_STRING=${WXCONFIG2}
+}
+
+
+if test "X${lamBUILDWX}" = "Xyes" ; then
+ if test "X${lamWX_CONFIG}" != "X" ; then
+ as_fn_error $? "configure switches --with-wx-config and --enable-buildwx mutually exclusive" "$LINENO" 5
+ fi
+ build_wx
+ lamWX_CONFIG=${RETURN_STRING}
+fi
+
+
+
+WXCONFIG3=""
+if test "X${lamCONV}" = "Xyes" ; then
+ get_wx_config_script
+ WXCONFIG3=${RETURN_STRING}
+ if test "$host_os" != "$build_os" ; then
+ WXCONFIG3="${WXCONFIG3} --host=${host_alias}"
+ fi
+
+ if test "X${lamDEBUG}" = "Xyes" ; then
+ WXCONFIG3="${WXCONFIG3} --debug=yes"
+ else
+ WXCONFIG3="${WXCONFIG3} --debug=no"
+ fi
+
+ # we may have many toolkits installed so specify
+ # if we are GUI-less GUI_TOOLKIT should already have
+ # been set to "base"
+ WXCONFIG3="${WXCONFIG3} --toolkit=${GUI_TOOLKIT}"
+
+ # check that the wx-config we found will provide us anything
+ wxListResult=`${WXCONFIG3} --list`
+ wxOK=`echo ${wxListResult} | awk '{ if (/will be used/) {print 1} ; if (/Specification best match/) {print 1} }' - `
+ if test "X${wxOK}" != "X1" ; then
+ echo "*************************************************************"
+ echo " Lamarc configure script failed because it could not find the "
+ echo " correct wxWidgets library. You might check your path, the "
+ echo " value of variable GUI_TOOLKIT, or try adding the configure"
+ echo " option --enable-build_wx . For more details see the section"
+ echo " entitled \"Compiling Lamarc\" in the lamarc documentation."
+ echo ""
+ echo " Here is error message from wx-config, in case that helps:"
+ echo ""
+ echo " " ${wxListResult}
+ echo ""
+ echo "*************************************************************"
+ as_fn_error $? "cannot proceed without suitable wxWidgets library" "$LINENO" 5
+ fi
+
+
+WX_CXXFLAGS=`$WXCONFIG3 --cxxflags`
+
+WX_LIBS=`$WXCONFIG3 --libs`
+
+fi
+
+# Checks for programs. -- tests and setting of cxxflags are to
+# keep AC_PROG_CXX from setting unfortunate default values
+if test -n "${CXXFLAGS}"; then
+ user_set_cxxflags=yes
+fi
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CXX+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CXX+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler works" >&5
+$as_echo_n "checking whether the C++ compiler works... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
+ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"
+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { { ac_try="$ac_link_default"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile. We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ then :; else
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ fi
+ # We set ac_cv_exeext here because the later test for it is not
+ # safe: cross compilers may not add the suffix if given an `-o'
+ # argument, so we may need to know it at that point already.
+ # Even if this section looks crufty: it has the advantage of
+ # actually working.
+ break;;
+ * )
+ break;;
+ esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+ ac_file=''
+fi
+if test -z "$ac_file"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error 77 "C++ compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler default output file name" >&5
+$as_echo_n "checking for C++ compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
+ac_exeext=$ac_cv_exeext
+
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
+$as_echo_n "checking for suffix of executables... " >&6; }
+if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+rm -f conftest conftest$ac_cv_exeext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C++ compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+$as_echo_n "checking for suffix of object files... " >&6; }
+if ${ac_cv_objext+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ for ac_file in conftest.o conftest.obj conftest.*; do
+ test -f "$ac_file" || continue;
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+$as_echo "$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if ${ac_cv_cxx_compiler_gnu+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if ${ac_cv_prog_cxx_g+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+else
+ CXXFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+DEPDIR="${am__leading_dot}deps"
+
+ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo this is the am__doit target
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+$as_echo_n "checking for style of include used by $am_make... " >&6; }
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# Ignore all kinds of additional output from 'make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+$as_echo "$_am_result" >&6; }
+rm -f confinc confmf
+
+# Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then :
+ enableval=$enable_dependency_tracking;
+fi
+
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+ am__nodep='_no'
+fi
+ if test "x$enable_dependency_tracking" != xno; then
+ AMDEP_TRUE=
+ AMDEP_FALSE='#'
+else
+ AMDEP_TRUE='#'
+ AMDEP_FALSE=
+fi
+
+
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if ${am_cv_CXX_dependencies_compiler_type+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named 'D' -- because '-MD' means "put the output
+ # in D".
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+ # Solaris 10 /bin/sh.
+ echo '/* dummy */' > sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with '-c' and '-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle '-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs.
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # After this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested.
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvc7 | msvc7msys | msvisualcpp | msvcmsys)
+ # This compiler won't grok '-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+if test X$user_set_cxxflags != Xyes; then
+ CXXFLAGS=" "
+fi
+
+# so we can build tinyxml as a library
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_RANLIB+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$RANLIB"; then
+ ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+RANLIB=$ac_cv_prog_RANLIB
+if test -n "$RANLIB"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5
+$as_echo "$RANLIB" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_RANLIB"; then
+ ac_ct_RANLIB=$RANLIB
+ # Extract the first word of "ranlib", so it can be a program name with args.
+set dummy ranlib; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_RANLIB+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_RANLIB"; then
+ ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_RANLIB="ranlib"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
+if test -n "$ac_ct_RANLIB"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5
+$as_echo "$ac_ct_RANLIB" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_RANLIB" = x; then
+ RANLIB=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ RANLIB=$ac_ct_RANLIB
+ fi
+else
+ RANLIB="$ac_cv_prog_RANLIB"
+fi
+
+
+# Checks for libraries.
+
+# Checks for header files.
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if ${ac_cv_c_compiler_gnu+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if ${ac_cv_prog_cc_g+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+else
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if ${ac_cv_prog_cc_c89+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+struct stat;
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
+$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
+if ${am_cv_prog_cc_c_o+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ # Make sure it works both with $CC and with simple cc.
+ # Following AC_PROG_CC_C_O, we do the test twice because some
+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
+ ($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
+$as_echo "$am_cv_prog_cc_c_o" >&6; }
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if ${am_cv_CC_dependencies_compiler_type+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named 'D' -- because '-MD' means "put the output
+ # in D".
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+ # Solaris 10 /bin/sh.
+ echo '/* dummy */' > sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with '-c' and '-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle '-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs.
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # After this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested.
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvc7 | msvc7msys | msvisualcpp | msvcmsys)
+ # This compiler won't grok '-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5
+$as_echo_n "checking how to run the C preprocessor... " >&6; }
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+ CPP=
+fi
+if test -z "$CPP"; then
+ if ${ac_cv_prog_CPP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CPP needs to be expanded
+ for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+ break
+fi
+
+ done
+ ac_cv_prog_CPP=$CPP
+
+fi
+ CPP=$ac_cv_prog_CPP
+else
+ ac_cv_prog_CPP=$CPP
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5
+$as_echo "$CPP" >&6; }
+ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details" "$LINENO" 5; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
+$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
+if ${ac_cv_path_GREP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$GREP"; then
+ ac_path_GREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in grep ggrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
+ as_fn_executable_p "$ac_path_GREP" || continue
+# Check for GNU ac_path_GREP and select it if it is found.
+ # Check for GNU $ac_path_GREP
+case `"$ac_path_GREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'GREP' >> "conftest.nl"
+ "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_GREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_GREP="$ac_path_GREP"
+ ac_path_GREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_GREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_GREP"; then
+ as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_GREP=$GREP
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
+$as_echo "$ac_cv_path_GREP" >&6; }
+ GREP="$ac_cv_path_GREP"
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
+$as_echo_n "checking for egrep... " >&6; }
+if ${ac_cv_path_EGREP+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
+ then ac_cv_path_EGREP="$GREP -E"
+ else
+ if test -z "$EGREP"; then
+ ac_path_EGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in egrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
+ as_fn_executable_p "$ac_path_EGREP" || continue
+# Check for GNU ac_path_EGREP and select it if it is found.
+ # Check for GNU $ac_path_EGREP
+case `"$ac_path_EGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'EGREP' >> "conftest.nl"
+ "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_EGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_EGREP="$ac_path_EGREP"
+ ac_path_EGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_EGREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_EGREP"; then
+ as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_EGREP=$EGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
+$as_echo "$ac_cv_path_EGREP" >&6; }
+ EGREP="$ac_cv_path_EGREP"
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
+$as_echo_n "checking for ANSI C header files... " >&6; }
+if ${ac_cv_header_stdc+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_header_stdc=yes
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "memchr" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "free" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+ if test "$cross_compiling" = yes; then :
+ :
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+ (('a' <= (c) && (c) <= 'i') \
+ || ('j' <= (c) && (c) <= 'r') \
+ || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+ int i;
+ for (i = 0; i < 256; i++)
+ if (XOR (islower (i), ISLOWER (i))
+ || toupper (i) != TOUPPER (i))
+ return 2;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
+$as_echo "$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+$as_echo "#define STDC_HEADERS 1" >>confdefs.h
+
+fi
+
+# On IRIX 5.3, sys/types and inttypes.h are conflicting.
+for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
+ inttypes.h stdint.h unistd.h
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
+"
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+for ac_header in float.h limits.h stdlib.h string.h unistd.h
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+# Checks for typedefs, structures, and compiler characteristics.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for stdbool.h that conforms to C99" >&5
+$as_echo_n "checking for stdbool.h that conforms to C99... " >&6; }
+if ${ac_cv_header_stdbool_h+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+ #include <stdbool.h>
+ #ifndef bool
+ "error: bool is not defined"
+ #endif
+ #ifndef false
+ "error: false is not defined"
+ #endif
+ #if false
+ "error: false is not 0"
+ #endif
+ #ifndef true
+ "error: true is not defined"
+ #endif
+ #if true != 1
+ "error: true is not 1"
+ #endif
+ #ifndef __bool_true_false_are_defined
+ "error: __bool_true_false_are_defined is not defined"
+ #endif
+
+ struct s { _Bool s: 1; _Bool t; } s;
+
+ char a[true == 1 ? 1 : -1];
+ char b[false == 0 ? 1 : -1];
+ char c[__bool_true_false_are_defined == 1 ? 1 : -1];
+ char d[(bool) 0.5 == true ? 1 : -1];
+ /* See body of main program for 'e'. */
+ char f[(_Bool) 0.0 == false ? 1 : -1];
+ char g[true];
+ char h[sizeof (_Bool)];
+ char i[sizeof s.t];
+ enum { j = false, k = true, l = false * true, m = true * 256 };
+ /* The following fails for
+ HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */
+ _Bool n[m];
+ char o[sizeof n == m * sizeof n[0] ? 1 : -1];
+ char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1];
+ /* Catch a bug in an HP-UX C compiler. See
+ http://gcc.gnu.org/ml/gcc-patches/2003-12/msg02303.html
+ http://lists.gnu.org/archive/html/bug-coreutils/2005-11/msg00161.html
+ */
+ _Bool q = true;
+ _Bool *pq = &q;
+
+int
+main ()
+{
+
+ bool e = &s;
+ *pq |= q;
+ *pq |= ! q;
+ /* Refer to every declared value, to avoid compiler optimizations. */
+ return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
+ + !m + !n + !o + !p + !q + !pq);
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_header_stdbool_h=yes
+else
+ ac_cv_header_stdbool_h=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdbool_h" >&5
+$as_echo "$ac_cv_header_stdbool_h" >&6; }
+ ac_fn_c_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
+if test "x$ac_cv_type__Bool" = xyes; then :
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE__BOOL 1
+_ACEOF
+
+
+fi
+
+
+if test $ac_cv_header_stdbool_h = yes; then
+
+$as_echo "#define HAVE_STDBOOL_H 1" >>confdefs.h
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5
+$as_echo_n "checking for an ANSI C-conforming const... " >&6; }
+if ${ac_cv_c_const+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+#ifndef __cplusplus
+ /* Ultrix mips cc rejects this sort of thing. */
+ typedef int charset[2];
+ const charset cs = { 0, 0 };
+ /* SunOS 4.1.1 cc rejects this. */
+ char const *const *pcpcc;
+ char **ppc;
+ /* NEC SVR4.0.2 mips cc rejects this. */
+ struct point {int x, y;};
+ static struct point const zero = {0,0};
+ /* AIX XL C 1.02.0.0 rejects this.
+ It does not let you subtract one const X* pointer from another in
+ an arm of an if-expression whose if-part is not a constant
+ expression */
+ const char *g = "string";
+ pcpcc = &g + (g ? g-g : 0);
+ /* HPUX 7.0 cc rejects these. */
+ ++pcpcc;
+ ppc = (char**) pcpcc;
+ pcpcc = (char const *const *) ppc;
+ { /* SCO 3.2v4 cc rejects this sort of thing. */
+ char tx;
+ char *t = &tx;
+ char const *s = 0 ? (char *) 0 : (char const *) 0;
+
+ *t++ = 0;
+ if (s) return 0;
+ }
+ { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */
+ int x[] = {25, 17};
+ const int *foo = &x[0];
+ ++foo;
+ }
+ { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */
+ typedef const int *iptr;
+ iptr p = 0;
+ ++p;
+ }
+ { /* AIX XL C 1.02.0.0 rejects this sort of thing, saying
+ "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */
+ struct s { int j; const int *ap[3]; } bx;
+ struct s *b = &bx; b->j = 5;
+ }
+ { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */
+ const int foo = 10;
+ if (!foo) return 0;
+ }
+ return !cs[0] && !zero.x;
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_c_const=yes
+else
+ ac_cv_c_const=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5
+$as_echo "$ac_cv_c_const" >&6; }
+if test $ac_cv_c_const = no; then
+
+$as_echo "#define const /**/" >>confdefs.h
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
+$as_echo_n "checking for inline... " >&6; }
+if ${ac_cv_c_inline+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_c_inline=no
+for ac_kw in inline __inline__ __inline; do
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifndef __cplusplus
+typedef int foo_t;
+static $ac_kw foo_t static_foo () {return 0; }
+$ac_kw foo_t foo () {return 0; }
+#endif
+
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_c_inline=$ac_kw
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ test "$ac_cv_c_inline" != no && break
+done
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
+$as_echo "$ac_cv_c_inline" >&6; }
+
+case $ac_cv_c_inline in
+ inline | yes) ;;
+ *)
+ case $ac_cv_c_inline in
+ no) ac_val=;;
+ *) ac_val=$ac_cv_c_inline;;
+ esac
+ cat >>confdefs.h <<_ACEOF
+#ifndef __cplusplus
+#define inline $ac_val
+#endif
+_ACEOF
+ ;;
+esac
+
+ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default"
+if test "x$ac_cv_type_size_t" = xyes; then :
+
+else
+
+cat >>confdefs.h <<_ACEOF
+#define size_t unsigned int
+_ACEOF
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether struct tm is in sys/time.h or time.h" >&5
+$as_echo_n "checking whether struct tm is in sys/time.h or time.h... " >&6; }
+if ${ac_cv_struct_tm+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <sys/types.h>
+#include <time.h>
+
+int
+main ()
+{
+struct tm tm;
+ int *p = &tm.tm_sec;
+ return !p;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_struct_tm=time.h
+else
+ ac_cv_struct_tm=sys/time.h
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_struct_tm" >&5
+$as_echo "$ac_cv_struct_tm" >&6; }
+if test $ac_cv_struct_tm = sys/time.h; then
+
+$as_echo "#define TM_IN_SYS_TIME 1" >>confdefs.h
+
+fi
+
+
+# Checks for library functions.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for error_at_line" >&5
+$as_echo_n "checking for error_at_line... " >&6; }
+if ${ac_cv_lib_error_at_line+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <error.h>
+int
+main ()
+{
+error_at_line (0, 0, "", 0, "an error occurred");
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_error_at_line=yes
+else
+ ac_cv_lib_error_at_line=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_error_at_line" >&5
+$as_echo "$ac_cv_lib_error_at_line" >&6; }
+if test $ac_cv_lib_error_at_line = no; then
+ case " $LIBOBJS " in
+ *" error.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS error.$ac_objext"
+ ;;
+esac
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for working memcmp" >&5
+$as_echo_n "checking for working memcmp... " >&6; }
+if ${ac_cv_func_memcmp_working+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ ac_cv_func_memcmp_working=no
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+
+ /* Some versions of memcmp are not 8-bit clean. */
+ char c0 = '\100', c1 = '\200', c2 = '\201';
+ if (memcmp(&c0, &c2, 1) >= 0 || memcmp(&c1, &c2, 1) >= 0)
+ return 1;
+
+ /* The Next x86 OpenStep bug shows up only when comparing 16 bytes
+ or more and with at least one buffer not starting on a 4-byte boundary.
+ William Lewis provided this test program. */
+ {
+ char foo[21];
+ char bar[21];
+ int i;
+ for (i = 0; i < 4; i++)
+ {
+ char *a = foo + i;
+ char *b = bar + i;
+ strcpy (a, "--------01111111");
+ strcpy (b, "--------10000000");
+ if (memcmp (a, b, 16) >= 0)
+ return 1;
+ }
+ return 0;
+ }
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+ ac_cv_func_memcmp_working=yes
+else
+ ac_cv_func_memcmp_working=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_memcmp_working" >&5
+$as_echo "$ac_cv_func_memcmp_working" >&6; }
+test $ac_cv_func_memcmp_working = no && case " $LIBOBJS " in
+ *" memcmp.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS memcmp.$ac_objext"
+ ;;
+esac
+
+
+for ac_func in strftime
+do :
+ ac_fn_c_check_func "$LINENO" "strftime" "ac_cv_func_strftime"
+if test "x$ac_cv_func_strftime" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_STRFTIME 1
+_ACEOF
+
+else
+ # strftime is in -lintl on SCO UNIX.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for strftime in -lintl" >&5
+$as_echo_n "checking for strftime in -lintl... " >&6; }
+if ${ac_cv_lib_intl_strftime+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lintl $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char strftime ();
+int
+main ()
+{
+return strftime ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_intl_strftime=yes
+else
+ ac_cv_lib_intl_strftime=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_intl_strftime" >&5
+$as_echo "$ac_cv_lib_intl_strftime" >&6; }
+if test "x$ac_cv_lib_intl_strftime" = xyes; then :
+ $as_echo "#define HAVE_STRFTIME 1" >>confdefs.h
+
+LIBS="-lintl $LIBS"
+fi
+
+fi
+done
+
+for ac_func in getcwd pow sqrt strchr strpbrk
+do :
+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+ if test x$lamARRCHECK = xyes; then
+ ARRCHECK_TRUE=
+ ARRCHECK_FALSE='#'
+else
+ ARRCHECK_TRUE='#'
+ ARRCHECK_FALSE=
+fi
+
+ if test x$lamCONV = xyes; then
+ CONVERTER_TRUE=
+ CONVERTER_FALSE='#'
+else
+ CONVERTER_TRUE='#'
+ CONVERTER_FALSE=
+fi
+
+ if test x$lamDEBUG = xyes; then
+ DEBUG_TRUE=
+ DEBUG_FALSE='#'
+else
+ DEBUG_TRUE='#'
+ DEBUG_FALSE=
+fi
+
+ if test x$lamDENOVO = xyes; then
+ DENOVO_TRUE=
+ DENOVO_FALSE='#'
+else
+ DENOVO_TRUE='#'
+ DENOVO_FALSE=
+fi
+
+ if test x$lamDMALLOC = xyes; then
+ DMALLOC_TRUE=
+ DMALLOC_FALSE='#'
+else
+ DMALLOC_TRUE='#'
+ DMALLOC_FALSE=
+fi
+
+ if test x$lamEFENCE = xyes; then
+ EFENCE_TRUE=
+ EFENCE_FALSE='#'
+else
+ EFENCE_TRUE='#'
+ EFENCE_FALSE=
+fi
+
+ if test x$lamGCOV = xyes; then
+ GCOV_TRUE=
+ GCOV_FALSE='#'
+else
+ GCOV_TRUE='#'
+ GCOV_FALSE=
+fi
+
+ if test x$lamGUI = xyes; then
+ GUI_TRUE=
+ GUI_FALSE='#'
+else
+ GUI_TRUE='#'
+ GUI_FALSE=
+fi
+
+ if test x$lamJSIM = xyes; then
+ JSIM_TRUE=
+ JSIM_FALSE='#'
+else
+ JSIM_TRUE='#'
+ JSIM_FALSE=
+fi
+
+ if test x$lamDATA_READ != xyes; then
+ NODATA_TRUE=
+ NODATA_FALSE='#'
+else
+ NODATA_TRUE='#'
+ NODATA_FALSE=
+fi
+
+ if test x$lamPROGRESS != xyes; then
+ NOPROGRESS_TRUE=
+ NOPROGRESS_FALSE='#'
+else
+ NOPROGRESS_TRUE='#'
+ NOPROGRESS_FALSE=
+fi
+
+ if test x$lamPROFILE = xyes; then
+ PROFILE_TRUE=
+ PROFILE_FALSE='#'
+else
+ PROFILE_TRUE='#'
+ PROFILE_FALSE=
+fi
+
+ if test x$lamTREETRACK = xyes; then
+ TREETRACK_TRUE=
+ TREETRACK_FALSE='#'
+else
+ TREETRACK_TRUE='#'
+ TREETRACK_FALSE=
+fi
+
+ if test x$lamUNIVB = xyes; then
+ UNIVB_TRUE=
+ UNIVB_FALSE='#'
+else
+ UNIVB_TRUE='#'
+ UNIVB_FALSE=
+fi
+
+ if test x$user_set_cxxflags = xyes; then
+ USERCXXFLAGS_TRUE=
+ USERCXXFLAGS_FALSE='#'
+else
+ USERCXXFLAGS_TRUE='#'
+ USERCXXFLAGS_FALSE=
+fi
+
+
+ac_config_files="$ac_config_files Makefile"
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ if test "x$cache_file" != "x/dev/null"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ if test ! -f "$cache_file" || test -h "$cache_file"; then
+ cat confcache >"$cache_file"
+ else
+ case $cache_file in #(
+ */* | ?:*)
+ mv -f confcache "$cache_file"$$ &&
+ mv -f "$cache_file"$$ "$cache_file" ;; #(
+ *)
+ mv -f confcache "$cache_file" ;;
+ esac
+ fi
+ fi
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+DEFS=-DHAVE_CONFIG_H
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+if test -z "${MAINTAINER_MODE_TRUE}" && test -z "${MAINTAINER_MODE_FALSE}"; then
+ as_fn_error $? "conditional \"MAINTAINER_MODE\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking that generated files are newer than configure" >&5
+$as_echo_n "checking that generated files are newer than configure... " >&6; }
+ if test -n "$am_sleep_pid"; then
+ # Hide warnings about reused PIDs.
+ wait $am_sleep_pid 2>/dev/null
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: done" >&5
+$as_echo "done" >&6; }
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
+if test -z "${LAMARC_APP_OSX_TRUE}" && test -z "${LAMARC_APP_OSX_FALSE}"; then
+ as_fn_error $? "conditional \"LAMARC_APP_OSX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${LAMARC_APP_MSW_TRUE}" && test -z "${LAMARC_APP_MSW_FALSE}"; then
+ as_fn_error $? "conditional \"LAMARC_APP_MSW\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ as_fn_error $? "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${ARRCHECK_TRUE}" && test -z "${ARRCHECK_FALSE}"; then
+ as_fn_error $? "conditional \"ARRCHECK\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${CONVERTER_TRUE}" && test -z "${CONVERTER_FALSE}"; then
+ as_fn_error $? "conditional \"CONVERTER\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${DEBUG_TRUE}" && test -z "${DEBUG_FALSE}"; then
+ as_fn_error $? "conditional \"DEBUG\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${DENOVO_TRUE}" && test -z "${DENOVO_FALSE}"; then
+ as_fn_error $? "conditional \"DENOVO\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${DMALLOC_TRUE}" && test -z "${DMALLOC_FALSE}"; then
+ as_fn_error $? "conditional \"DMALLOC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${EFENCE_TRUE}" && test -z "${EFENCE_FALSE}"; then
+ as_fn_error $? "conditional \"EFENCE\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${GCOV_TRUE}" && test -z "${GCOV_FALSE}"; then
+ as_fn_error $? "conditional \"GCOV\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${GUI_TRUE}" && test -z "${GUI_FALSE}"; then
+ as_fn_error $? "conditional \"GUI\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${JSIM_TRUE}" && test -z "${JSIM_FALSE}"; then
+ as_fn_error $? "conditional \"JSIM\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${NODATA_TRUE}" && test -z "${NODATA_FALSE}"; then
+ as_fn_error $? "conditional \"NODATA\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${NOPROGRESS_TRUE}" && test -z "${NOPROGRESS_FALSE}"; then
+ as_fn_error $? "conditional \"NOPROGRESS\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${PROFILE_TRUE}" && test -z "${PROFILE_FALSE}"; then
+ as_fn_error $? "conditional \"PROFILE\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${TREETRACK_TRUE}" && test -z "${TREETRACK_FALSE}"; then
+ as_fn_error $? "conditional \"TREETRACK\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${UNIVB_TRUE}" && test -z "${UNIVB_FALSE}"; then
+ as_fn_error $? "conditional \"UNIVB\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${USERCXXFLAGS_TRUE}" && test -z "${USERCXXFLAGS_FALSE}"; then
+ as_fn_error $? "conditional \"USERCXXFLAGS\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+
+: "${CONFIG_STATUS=./config.status}"
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -pR'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -pR'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -pR'
+ fi
+else
+ as_ln_s='cp -pR'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+ test -f "$1" && test -x "$1"
+} # as_fn_executable_p
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by lamarc $as_me 2.1.10, which was
+generated by GNU Autoconf 2.69. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+case $ac_config_headers in *"
+"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
+esac
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_headers="$ac_config_headers"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+ --header=FILE[:TEMPLATE]
+ instantiate the configuration header FILE
+
+Configuration files:
+$config_files
+
+Configuration headers:
+$config_headers
+
+Configuration commands:
+$config_commands
+
+Report bugs to <lamarc at u.washington.edu>."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
+ac_cs_version="\\
+lamarc config.status 2.1.10
+configured by $0, generated by GNU Autoconf 2.69,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2012 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --header | --heade | --head | --hea )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ as_fn_append CONFIG_HEADERS " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h)
+ # Conflict between --help and --header
+ as_fn_error $? "ambiguous option: \`$1'
+Try \`$0 --help' for more information.";;
+ --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "config/conf.h") CONFIG_HEADERS="$CONFIG_HEADERS config/conf.h" ;;
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp= ac_tmp=
+ trap 'exit_status=$?
+ : "${ac_tmp:=$tmp}"
+ { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+ac_tmp=$tmp
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
+_ACEOF
+
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+
+ print line
+}
+
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+# Set up the scripts for CONFIG_HEADERS section.
+# No need to generate them if there are no CONFIG_HEADERS.
+# This happens for instance with `./config.status Makefile'.
+if test -n "$CONFIG_HEADERS"; then
+cat >"$ac_tmp/defines.awk" <<\_ACAWK ||
+BEGIN {
+_ACEOF
+
+# Transform confdefs.h into an awk script `defines.awk', embedded as
+# here-document in config.status, that substitutes the proper values into
+# config.h.in to produce config.h.
+
+# Create a delimiter string that does not exist in confdefs.h, to ease
+# handling of long lines.
+ac_delim='%!_!# '
+for ac_last_try in false false :; do
+ ac_tt=`sed -n "/$ac_delim/p" confdefs.h`
+ if test -z "$ac_tt"; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+
+# For the awk script, D is an array of macro values keyed by name,
+# likewise P contains macro parameters if any. Preserve backslash
+# newline sequences.
+
+ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
+sed -n '
+s/.\{148\}/&'"$ac_delim"'/g
+t rset
+:rset
+s/^[ ]*#[ ]*define[ ][ ]*/ /
+t def
+d
+:def
+s/\\$//
+t bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3"/p
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2"/p
+d
+:bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3\\\\\\n"\\/p
+t cont
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
+t cont
+d
+:cont
+n
+s/.\{148\}/&'"$ac_delim"'/g
+t clear
+:clear
+s/\\$//
+t bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/"/p
+d
+:bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
+b cont
+' <confdefs.h | sed '
+s/'"$ac_delim"'/"\\\
+"/g' >>$CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ for (key in D) D_is_set[key] = 1
+ FS = ""
+}
+/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
+ line = \$ 0
+ split(line, arg, " ")
+ if (arg[1] == "#") {
+ defundef = arg[2]
+ mac1 = arg[3]
+ } else {
+ defundef = substr(arg[1], 2)
+ mac1 = arg[2]
+ }
+ split(mac1, mac2, "(") #)
+ macro = mac2[1]
+ prefix = substr(line, 1, index(line, defundef) - 1)
+ if (D_is_set[macro]) {
+ # Preserve the white space surrounding the "#".
+ print prefix "define", macro P[macro] D[macro]
+ next
+ } else {
+ # Replace #undef with comments. This is necessary, for example,
+ # in the case of _POSIX_SOURCE, which is predefined and required
+ # on some systems where configure will not decide to define it.
+ if (defundef == "undef") {
+ print "/*", prefix defundef, macro, "*/"
+ next
+ }
+ }
+}
+{ print }
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
+fi # test -n "$CONFIG_HEADERS"
+
+
+eval set X " :F $CONFIG_FILES :H $CONFIG_HEADERS :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$ac_tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$ac_tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+ esac
+ ac_MKDIR_P=$MKDIR_P
+ case $MKDIR_P in
+ [\\/$]* | ?:[\\/]* ) ;;
+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
+ esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+s&@MKDIR_P@&$ac_MKDIR_P&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
+ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
+ "$ac_tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&5
+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$ac_tmp/stdin"
+ case $ac_file in
+ -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
+ *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
+ esac \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+ :H)
+ #
+ # CONFIG_HEADER
+ #
+ if test x"$ac_file" != x-; then
+ {
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs"
+ } >"$ac_tmp/config.h" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ if diff "$ac_file" "$ac_tmp/config.h" >/dev/null 2>&1; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
+$as_echo "$as_me: $ac_file is unchanged" >&6;}
+ else
+ rm -f "$ac_file"
+ mv "$ac_tmp/config.h" "$ac_file" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ fi
+ else
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \
+ || as_fn_error $? "could not create -" "$LINENO" 5
+ fi
+# Compute "$ac_file"'s index in $config_headers.
+_am_arg="$ac_file"
+_am_stamp_count=1
+for _am_header in $config_headers :; do
+ case $_am_header in
+ $_am_arg | $_am_arg:* )
+ break ;;
+ * )
+ _am_stamp_count=`expr $_am_stamp_count + 1` ;;
+ esac
+done
+echo "timestamp for $_am_arg" >`$as_dirname -- "$_am_arg" ||
+$as_expr X"$_am_arg" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$_am_arg" : 'X\(//\)[^/]' \| \
+ X"$_am_arg" : 'X\(//\)$' \| \
+ X"$_am_arg" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$_am_arg" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`/stamp-h$_am_stamp_count
+ ;;
+
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+$as_echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+ esac
+
+
+ case $ac_file$ac_mode in
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Older Autoconf quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named 'Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`$as_dirname -- "$mf" ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running 'make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "$am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+ ;;
+
+ esac
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
+
+echo "*************************************************************"
+echo " Settings for lamarc build. For information on how to change"
+echo " try executing \"configure --help\" and reading the lamarc"
+echo " documentation section entitled \"Compiling Lamarc\"."
+echo "*************************************************************"
+echo ""
+echo "Options that are almost always on:"
+echo " Compile lam_conv, the lamarc data converter? ${lamCONV}"
+if test "X${lamCONV}" = "Xyes" ; then
+echo " Compile lam_conv as a GUI? ${lamGUI}"
+else
+echo " Compile lam_conv as a GUI? --"
+fi
+echo " Compile LAMARC to read data? ${lamDATA_READ}"
+echo " Compile LAMARC to display progress bar? ${lamPROGRESS}"
+echo "Options that are almost always off:"
+echo " Compile LAMARC to check arrangers? ${lamARRCHECK}"
+echo " Compile LAMARC to generate all trees denovo? ${lamDENOVO}"
+echo " Compile LAMARC to use dmalloc? ${lamDMALLOC}"
+echo " Compile LAMARC to use electric fence? ${lamEFENCE}"
+echo " Compile LAMARC to use gcov? ${lamGCOV}"
+echo " Compile LAMARC to use Jon's simulation code? ${lamJSIM}"
+echo " Compile LAMARC to generate profile data? ${lamPROFILE}"
+echo " Track data likelihoods of sampled trees? ${lamTREETRACK}"
+echo " Attempt to compile universal binary (MAC)? ${lamUNIVB}"
+echo ""
+echo "Commonly toggled configure options:"
+echo " Compile LAMARC in debug mode? ${lamDEBUG}"
+echo ""
+if test "X${lamCONV}" = "Xyes" ; then
+echo "wxWidgets version ${wxVersion}"
+else
+echo "wxWidgets version --"
+fi
+if test "X${lamCONV}" = "Xyes" ; then
+echo "gui toolkit ${GUI_TOOLKIT}"
+else
+echo "gui toolkit --"
+fi
+echo "LAMARC_CODE_OSTYPE ${LAMARC_CODE_OSTYPE}"
+echo "*************************************************************"
+
+case "${LAMARC_CODE_OSTYPE}" in
+ LAMARC_COMPILE_MACOSX)
+ ;;
+ LAMARC_COMPILE_LINUX)
+ ;;
+ LAMARC_COMPILE_MSWINDOWS)
+ ;;
+ *)
+ echo "The lamarc compile script either failed to recognize"
+ echo "${LAMARC_CODE_OSTYPE} as a legal value for "
+ echo "LAMARC_CODE_OSTYPE. It is likely that you will have"
+ echo "trouble compiling lamarc."
+ echo ""
+ echo "We recommend that you see the section entitled \"Compiling"
+ echo "Lamarc\" in the lamarc documentation for alternative solutions."
+ echo "*************************************************************"
+ ;;
+esac
+
+if test "X${lamCONV}" = "Xyes" ; then
+ case "${GUI_TOOLKIT}" in
+ gtk2)
+ ;;
+ mac)
+ ;;
+ msw)
+ ;;
+ base)
+ ;;
+ *)
+ echo "The lamarc compile script did not recognize your GUI toolkit,"
+ echo "\"$GUI_TOOLKIT\", as one we have tested. It is very likely"
+ echo "that the lamarc file converter, lam_conv, will not work."
+ echo ""
+ echo "We recommend that you see the section entitled \"Compiling"
+ echo "Lamarc\" in the lamarc documentation for alternative solutions."
+ echo "*************************************************************"
+ ;;
+ esac
+fi
+
+
+if test "X$user_set_cxxflags" = "Xyes"; then
+ echo "************************************************************* "
+ echo "You have set your own value of CXXFLAGS. Did you remember to"
+ echo "use a matching argument of --enable-debug or --disable-debug?"
+ echo "If not, you may have trouble running the programs. "
+ echo "************************************************************* "
+fi
+
+echo "Configure script finished successfully."
diff --git a/configure.ac b/configure.ac
index 29de069..b4f8113 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,11 +2,11 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
-AC_INIT(lamarc, 2.1.8, lamarc at u.washington.edu, lamarc)
+AC_INIT(lamarc, 2.1.10, lamarc at u.washington.edu, lamarc)
AM_MAINTAINER_MODE
AC_CONFIG_AUX_DIR([config])
-AC_DEFINE(RELEASE_DATE, ["29 May 2012"], [The release date of the program])
+AC_DEFINE(RELEASE_DATE, ["14 Nov 2013"], [The release date of the program])
wxRequiredMajorVersion=2
wxRequiredMinorVersion=8
diff --git a/depcomp b/depcomp
new file mode 100755
index 0000000..9e5522d
--- /dev/null
+++ b/depcomp
@@ -0,0 +1,520 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2003-11-08.23
+
+# Copyright (C) 1999, 2000, 2003 Free Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
+
+case $1 in
+ '')
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+ depmode Dependency tracking mode.
+ source Source file read by `PROGRAMS ARGS'.
+ object Object file output by `PROGRAMS ARGS'.
+ depfile Dependency file to output.
+ tmpdepfile Temporary file to use when outputing dependencies.
+ libtool Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit 0
+ ;;
+ -v | --v*)
+ echo "depcomp $scriptversion"
+ exit 0
+ ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+ echo "depcomp: Variables source, object and depmode must be set" 1>&2
+ exit 1
+fi
+# `libtool' can also be set to `yes' or `no'.
+
+if test -z "$depfile"; then
+ base=`echo "$object" | sed -e 's,^.*/,,' -e 's,\.\([^.]*\)$,.P\1,'`
+ dir=`echo "$object" | sed 's,/.*$,/,'`
+ if test "$dir" = "$object"; then
+ dir=
+ fi
+ # FIXME: should be _deps on DOS.
+ depfile="$dir.deps/$base"
+fi
+
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags. We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write. Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+ # HP compiler uses -M and no extra arg.
+ gccflag=-M
+ depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want. Yay! Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff. Hmm.
+ "$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ mv "$tmpdepfile" "$depfile"
+ ;;
+
+gcc)
+## There are various ways to get dependency output from gcc. Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+## up in a subdir. Having to rename by hand is ugly.
+## (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+## -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+## than renaming).
+ if test -z "$gccflag"; then
+ gccflag=-MD,
+ fi
+ "$@" -Wp,"$gccflag$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+ sed -e 's/^[^:]*: / /' \
+ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header). We avoid this by adding
+## dummy dependencies for each header file. Too bad gcc doesn't do
+## this for us directly.
+ tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'. On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+sgi)
+ if test "$libtool" = yes; then
+ "$@" "-Wp,-MDupdate,$tmpdepfile"
+ else
+ "$@" -MDupdate "$tmpdepfile"
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+
+ if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
+ echo "$object : \\" > "$depfile"
+
+ # Clip off the initial element (the dependent). Don't try to be
+ # clever and replace this with sed code, as IRIX sed won't handle
+ # lines with more than a fixed number of characters (4096 in
+ # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
+ # the IRIX cc adds comments like `#:fec' to the end of the
+ # dependency line.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+ tr '
+' ' ' >> $depfile
+ echo >> $depfile
+
+ # The second pass generates a dummy entry for each header file.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> $depfile
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+aix)
+ # The C for AIX Compiler uses -M and outputs the dependencies
+ # in a .u file. In older versions, this file always lives in the
+ # current directory. Also, the AIX compiler puts `$object:' at the
+ # start of each line; $object doesn't have directory information.
+ # Version 6 uses the directory in both cases.
+ stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
+ tmpdepfile="$stripped.u"
+ if test "$libtool" = yes; then
+ "$@" -Wc,-M
+ else
+ "$@" -M
+ fi
+ stat=$?
+
+ if test -f "$tmpdepfile"; then :
+ else
+ stripped=`echo "$stripped" | sed 's,^.*/,,'`
+ tmpdepfile="$stripped.u"
+ fi
+
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+
+ if test -f "$tmpdepfile"; then
+ outname="$stripped.o"
+ # Each line is of the form `foo.o: dependent.h'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
+ sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+icc)
+ # Intel's C compiler understands `-MD -MF file'. However on
+ # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+ # ICC 7.0 will fill foo.d with something like
+ # foo.o: sub/foo.c
+ # foo.o: sub/foo.h
+ # which is wrong. We want:
+ # sub/foo.o: sub/foo.c
+ # sub/foo.o: sub/foo.h
+ # sub/foo.c:
+ # sub/foo.h:
+ # ICC 7.1 will output
+ # foo.o: sub/foo.c sub/foo.h
+ # and will wrap long lines using \ :
+ # foo.o: sub/foo.c ... \
+ # sub/foo.h ... \
+ # ...
+
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ # Each line is of the form `foo.o: dependent.h',
+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+ sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+tru64)
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in `foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+ if test "$libtool" = yes; then
+ tmpdepfile1="$dir.libs/$base.lo.d"
+ tmpdepfile2="$dir.libs/$base.d"
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1="$dir$base.o.d"
+ tmpdepfile2="$dir$base.d"
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2"
+ exit $stat
+ fi
+
+ if test -f "$tmpdepfile1"; then
+ tmpdepfile="$tmpdepfile1"
+ else
+ tmpdepfile="$tmpdepfile2"
+ fi
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+#nosideeffect)
+ # This comment above is used by automake to tell side-effect
+ # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout, regardless of -o.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test $1 != '--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ test -z "$dashmflag" && dashmflag=-M
+ # Require at least two characters before searching for `:'
+ # in the target name. This is to cope with DOS-style filenames:
+ # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+ "$@" $dashmflag |
+ sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+dashXmstdout)
+ # This case only exists to satisfy depend.m4. It is never actually
+ # run, as this mode is specially recognized in the preamble.
+ exit 1
+ ;;
+
+makedepend)
+ "$@" || exit $?
+ # Remove any Libtool call
+ if test "$libtool" = yes; then
+ while test $1 != '--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+ # X makedepend
+ shift
+ cleared=no
+ for arg in "$@"; do
+ case $cleared in
+ no)
+ set ""; shift
+ cleared=yes ;;
+ esac
+ case "$arg" in
+ -D*|-I*)
+ set fnord "$@" "$arg"; shift ;;
+ # Strip any option that makedepend may not understand. Remove
+ # the object too, otherwise makedepend will parse it as a source file.
+ -*|$object)
+ ;;
+ *)
+ set fnord "$@" "$arg"; shift ;;
+ esac
+ done
+ obj_suffix="`echo $object | sed 's/^.*\././'`"
+ touch "$tmpdepfile"
+ ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile" "$tmpdepfile".bak
+ ;;
+
+cpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test $1 != '--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ "$@" -E |
+ sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+ sed '$ s: \\$::' > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ cat < "$tmpdepfile" >> "$depfile"
+ sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvisualcpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout, regardless of -o,
+ # because we must use -o when running libtool.
+ "$@" || exit $?
+ IFS=" "
+ for arg
+ do
+ case "$arg" in
+ "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+ set fnord "$@"
+ shift
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
+ esac
+ done
+ "$@" -E |
+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ echo " " >> "$depfile"
+ . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+none)
+ exec "$@"
+ ;;
+
+*)
+ echo "Unknown depmode $depmode" 1>&2
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/doc/html/changes.html b/doc/html/changes.html
index 34ca455..66118f4 100644
--- a/doc/html/changes.html
+++ b/doc/html/changes.html
@@ -20,6 +20,19 @@ rate, effective population size, recombination rate, maximum likelihood -->
<P>(<A HREF="overview.html">Previous</A> | <A HREF="index.html">Contents</A>
| <A HREF="upcoming.html">Next</A>)</P>
+<H2> Changes between LAMARC version 2.1.9 and 2.1.8 </h2>
+
+<p><b>BUG FIX: corrected major divergence bugs.</b> Attempts
+to infer epoch times produced markedly wrong results. All runs
+inferring epoch times should be re-run.
+</p>
+
+<p><b>BUG FIX: spurious migration blocks in single population
+converter runs.</b> The lam_conv file converter no longer creates
+dysfunctional migration-enabled lamarc XML files when there is only
+one population in the input data.
+</p>
+
<H2> Changes between LAMARC version 2.1.8 and 2.1.6 </h2>
<p><b>BUG FIX: corrected major migration bug</b>
@@ -491,7 +504,7 @@ to deal with a much wider array of input data.</P>
| <A HREF="upcoming.html">Next</A>)</P>
<!--
-//$Id: changes.html,v 1.52 2012/05/25 23:28:10 ewalkup Exp $
+//$Id: changes.html,v 1.53 2013/11/08 23:09:53 mkkuhner Exp $
-->
</BODY>
</HTML>
diff --git a/doc/html/compiling.html b/doc/html/compiling.html
index bcf5cd2..708e131 100644
--- a/doc/html/compiling.html
+++ b/doc/html/compiling.html
@@ -1,5 +1,5 @@
<!-- header fragment for html documentation -->
-<!--$Id: compiling.html,v 1.36 2012/05/25 23:28:10 ewalkup Exp $ -->
+<!--$Id: compiling.html,v 1.37 2013/11/08 23:09:53 mkkuhner Exp $ -->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<HTML>
<HEAD>
@@ -163,8 +163,8 @@ to compile in. This will keep your object files
from cluttering up a listing of the top level of the distribution.
<pre>
- tar xfvz lamarc-2.1.8-src.tar.gz
- cd lamarc-2.1.8
+ tar xfvz lamarc-2.1.9-src.tar.gz
+ cd lamarc-2.1.9
mkdir release
cd release
</pre>
diff --git a/doc/html/converter_cmd.html b/doc/html/converter_cmd.html
index 1fb6031..9761410 100644
--- a/doc/html/converter_cmd.html
+++ b/doc/html/converter_cmd.html
@@ -300,7 +300,7 @@ of the documentation
<td>dna</td><td colspan=2>DNA data</td></tr>
<tr><td>snp</td><td colspan=2>SNP data</td></tr>
<tr><td>kallele</td><td colspan=2>k-allele data</td></tr>
- <tr><td>microsat</td><td colspan=2>microsattelite data</td></tr>
+ <tr><td>microsat</td><td colspan=2>microsatellite data</td></tr>
<tr><td rowspan=2><em>marker-proximity</em></td>
<td>linked</td><td colspan=2>individual data markers likely to be inherited together</td></tr>
<tr><td>unlinked</td><td colspan=2>individual data markers are independently inherited</td></tr>
@@ -378,7 +378,7 @@ regions, segments, and populations.
<td>dna</td><td colspan=2>DNA data</td></tr>
<tr><td>snp</td><td colspan=2>SNP data</td></tr>
<tr><td>kallele</td><td colspan=2>k-allele data</td></tr>
- <tr><td>microsat</td><td colspan=2>microsattelite data</td></tr>
+ <tr><td>microsat</td><td colspan=2>microsatellite data</td></tr>
<tr><td rowspan=2><em>format</em></td>
<td>migrate</td><td colspan=2>input file is a migrate file</td></tr>
<tr><td>phylip</td><td colspan=2>input file is a phylip file</td></tr>
@@ -558,7 +558,7 @@ the second chromosome has SNP data with markers at positions 13, 19, 35, 77,
| <A HREF="xmlinput.html">Next</A>)</P>
<!--
-//$Id: converter_cmd.html,v 1.18 2012/05/14 19:55:38 ewalkup Exp $
+//$Id: converter_cmd.html,v 1.19 2016/04/19 21:01:32 lpsmith Exp $
-->
</BODY>
</HTML>
diff --git a/doc/html/genetic_map.html b/doc/html/genetic_map.html
index effb8bd..65bbbcb 100644
--- a/doc/html/genetic_map.html
+++ b/doc/html/genetic_map.html
@@ -102,7 +102,7 @@ of spacings.
However, a set of SNPs count as a 'coherent segment' --
while we don't know what the sequence is between the
SNPs, we do know that it doesn't vary.
-Linked microsattelite data is similar -- the number of microsat
+Linked microsatellite data is similar -- the number of microsat
repeats and their relative locations are relevant, not the sequences
between them.
</p>
@@ -351,7 +351,7 @@ in this error:
<img src="batch_converter/images/lam_conv_chrom3_error_map_position.png" alt="xxx"/>
<p>
-The problem is that we don't know how close together the microsattelite and
+The problem is that we don't know how close together the microsatellite and
the SNP are. To solve this problem you'll need to edit fields on the
segment panels for each coherent segment.
</p>
@@ -379,7 +379,7 @@ You should now be able to write the Lamarc file.
| <A HREF="migration_matrix.html">Next</A>)</P>
<!--
-//$Id: genetic_map.html,v 1.12 2011/12/09 17:14:03 jmcgill Exp $
+//$Id: genetic_map.html,v 1.13 2016/04/19 21:01:32 lpsmith Exp $
-->
</BODY>
</HTML>
diff --git a/doc/html/index.html b/doc/html/index.html
index d3fbf56..0ff55ec 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -31,7 +31,7 @@ University.</P>
<UL>
<H3>General:</H3>
<LI> <A HREF="overview.html">Overview</A></LI>
-<LI> <A HREF="changes.html">Changes in Version 2.1.8</A></LI>
+<LI> <A HREF="changes.html">Changes in Version 2.1.9</A></LI>
<LI> <A HREF="upcoming.html">Plans for the Future</A></LI>
<LI> <A HREF="troubleshooting.html">Frequently Asked Questions</A></LI>
<LI> <A HREF="messages.html">Error and Warning Messages</A></LI>
@@ -90,7 +90,7 @@ University of Washington, Box 355065,
Seattle, WA 98195-5065, USA. Phone: (206) 543-8751, Fax: (206) 543-0754</ADDRESS>
<!--
-//$Id: index.html,v 1.50 2012/05/25 23:28:10 ewalkup Exp $
+//$Id: index.html,v 1.51 2013/11/08 23:09:53 mkkuhner Exp $
-->
</BODY>
</HTML>
diff --git a/doc/html/mapping.html b/doc/html/mapping.html
index 96c7dd4..7f7e320 100644
--- a/doc/html/mapping.html
+++ b/doc/html/mapping.html
@@ -257,7 +257,7 @@ tag.
<p>This indicates that the samples "s0" and "s1" belong
to the same individual and that that individual displays the
"broken" phenotype. (If your individuals are named in your data
-input file but do not have sample names, as in migrate-format microsattelite
+input file but do not have sample names, as in migrate-format microsatellite
data, you do not need to provide extra sample names here.)</P>
<p>
@@ -458,7 +458,7 @@ better visualize your results.</p>
<A HREF="compiling.html">Next</A>)</P>
<!--
-//$Id: mapping.html,v 1.22 2011/06/23 21:00:36 jmcgill Exp $
+//$Id: mapping.html,v 1.23 2016/04/19 21:01:32 lpsmith Exp $
-->
</BODY>
</HTML>
diff --git a/doc/html/menu.html b/doc/html/menu.html
index a27fd20..1750555 100644
--- a/doc/html/menu.html
+++ b/doc/html/menu.html
@@ -609,7 +609,8 @@ force </A></H4>
<p>
The only value that can be edited in Divergence is
Epoch Boundary Time (scaled by the mutation rate) of each Divergence event. You can
-set starting values, priors, etc. for these as usual. However, if you wish
+set starting values and priors for these as usual. There are no
+constraints available for these parameters. If you wish
to redefine the Ancestor/Descendent relationships you need to either return to the <A HREF="converter.html">file converter</A> or edit the input file XML.
</p>
@@ -628,7 +629,7 @@ for starting values are not available for cases with divergence.
<H4> Options common to all Force submenus </H4>
<P> Three options are available on all Forces submenus (except
-for Trait mapping), and they all behave
+for Trait mapping and Divergence), and they all behave
in the same fashion. Constraints allow you to hold parameters constant or
constrain them to be equal to other parameters. Profiling affects the
reported support intervals around the estimates (and can affect how long it
@@ -662,7 +663,9 @@ values to zero).</P>
<P> In general, a LAMARC run with constraints will be somewhat faster than
one without, since fewer parameters have to be estimated. This can be
particularly helpful for complex systems where you already have some
-information, and are interested in estimating just a few parameters. </P>
+information, and are interested in estimating just a few parameters.
+Unfortunately, constraints are not available at this time for the
+Epoch Boundary Time parameters.</P>
<P> Select 'C' to go to the Constraints sub-menu for any force. To change
the constraint on a particular parameter, enter that parameter's menu index
@@ -1173,7 +1176,7 @@ to change the displayed settings. </P>
HREF="index.html">Contents</A> | <A HREF="regions.html">Next</A>)</P>
<!--
-//$Id: menu.html,v 1.51 2013/11/07 22:46:06 mkkuhner Exp $
+//$Id: menu.html,v 1.52 2013/11/08 23:09:53 mkkuhner Exp $
-->
</BODY>
</HTML>
diff --git a/doc/html/panels.html b/doc/html/panels.html
index 1ab11bf..b5b71b7 100644
--- a/doc/html/panels.html
+++ b/doc/html/panels.html
@@ -108,9 +108,9 @@ results are highly dependent on having accurate panel size information. Therefor
<b>Do Not Estimate The Count!</b> You cannot perform an accurate coalescent
analysis on your data.</p>
<li><p>If your panel SNPs are limited to positions which met a Minor Allele Frequency
-(MAF) cutoff, your panel size must be adjusted to compensate for this effect. Please
-email us at <A HREF="mailto:lamarc at u.washington.edu">lamarc at u.washington.edu</A>
-for help with this calculation.
+(MAF) cutoff, your panel size must be adjusted to compensate for this effect. The
+procedure is described in McGill, Walkup and Kuhner, Genetics 193(4): 1185-1196
+(2013). We are happy to help with this correction on email request.
</p>
</ul>
@@ -157,7 +157,7 @@ for an example.
<A HREF="converter_cmd.html">Next</A>)</P>
<!--
-//$Id: panels.html,v 1.7 2012/05/29 18:59:45 ewalkup Exp $
+//$Id: panels.html,v 1.8 2014/09/08 21:05:23 mkkuhner Exp $
-->
</BODY>
</HTML>
diff --git a/doc/pipeline.txt b/doc/pipeline.txt
new file mode 100644
index 0000000..80a909a
--- /dev/null
+++ b/doc/pipeline.txt
@@ -0,0 +1,235 @@
+//$Id: pipeline.txt,v 1.5 2016/04/20 23:58:27 lpsmith Exp $
+
+Instructions for compiling lamarc and lam_conv for all major
+platforms, tested December 2013, revised September 2014.
+
+******
+On Linux (tested on two Ubuntu 64-bit machines):
+
+cvs checkout of lamarc
+cd into lamarc
+make a directory buildwxopt for wxWidgets build
+cd into buildwxopt
+configure using the following:
+../configure --enable-buildwx
+(this defaults to 2.8.12)
+go back up to lamarc
+make a directory opt for lamarc build
+cd into opt
+build lamarc and lam_conv using the following configuration:
+../configure --with-wx-config=../buildwxopt/wxWidgets-2.8.12/wx-config --no-create --no-recursion
+make
+
+This creates executables lamarc and lam_conv. Put them in a directory whose name
+is the release name (e.g. lamarc-2.1.9-Linux-i686-gtk). Tar that directory
+using tar cvzf to produce a gzipped tar file which will by default end in .tgz.
+Put that on the web site in /felsenstein/www/html/downloads. Make the linux
+entry in lamarc_downloads.html point to it. Note: doing tar followed by
+gzip and renaming the result to .tgz is NOT equivalent!
+
+Note 9/2014: We had to add -lX11 to the Makefile to make this compile
+on recent gcc. Unfortunately this does not work for any other platform
+(including Windows cross-compiles on Linux) and has to be edited out again
+before trying those compiles. We'll try to make it conditional but have
+not yet succeeded.
+
+(What did not work: The Sanity scripts that are supposed to do this
+automatically.)
+
+******
+
+On MacOSX:
+
+As of 4/2016, we successfully compiled wxWidgets again, after having
+lost that ability. Yay! See wx-osx-notes.txt for compiling that.
+
+If gcc and/or cvs are missing, they may be available through the XCode
+Tools (install XCode Command Line Tools). If you want a version of
+XCode for your current OS, but that OS is not the latest, you can still
+get the older versions, but you'll have to sign in as a Mac developer to
+get them. See https://developer.apple.com/xcode/download/, and scroll
+down to 'additional tools'. Not only do you need to install XCode, but
+you'll also need to install the 'Command Line Tools' to get the full
+package of what we need for lamarc.
+
+To install CVS, the simplest method I found was to install 'brew', and
+using that to install CVS. Once 'brew' was up and running:
+
+ brew install cvs
+
+worked like a charm.
+
+On kolmogorov:
+
+Makefile.am has been modified to automatically set the macosx minimum
+version to 10.7, so 'configure' no longer needs to do this. It does
+mean that Makefile.am will need to be updated in the future if this
+minimum version changes.
+
+It is possible to use the flags '--disable-unicode' and
+'--disable-shared', but it is unclear why they were being used in the
+first place. Lamarc and lam_conv seem to work OK without them. Ditto
+'--with-osx-cocoa' and '--with-macosx-sdk'. As of right now, this will
+work:
+
+cvs checkout of lamarc
+cd into lamarc
+make directory opt
+cd into opt
+ export WX_INSTALL=/Users/lpsmith/wxWidgets-3.1.0
+ ../configure --with-wx-config=${WX_INSTALL}/opt/wx-config
+ make
+
+If things go wrong, try adding in some of the older options that seem to
+used to be required:
+
+ export WX_INSTALL=/Users/lpsmith/wxWidgets-3.1.0
+ ../configure --disable-unicode --disable-shared \
+ --with-osx_cocoa \
+ --with-macosx-version-min=10.7 \
+ --with-macosx-sdk=/Developer/SDKs/MacOSX10.7.sdk \
+ --with-wx-config=${WX_INSTALL}/opt/wx-config
+
+(It should no longer be necessary to edit out '-lX11' from the generated
+Makefile; this is now handled in Makefile.am)
+
+This produces an apparently useless lamarc and lam_conv, plus
+lamarc.app and lam_conv.app directories which are what you actually
+want.
+
+Put lamarc.app and lam_conv.app into a directory named for the
+release, such as lamarc-2.1.9. (Don't add suffix "-osx" as the
+script does this automatically.)
+
+Remove any directories named "build" before running this script.
+Run the script buildDmg.sh (it can be found in lamarc/scripts/):
+
+buildDmg.sh <name of directory with the .apps in it>
+
+This will create a "build" directory containing a .dmg file.
+Transfer this .dmg to a DIFFERENT Mac and test both clickability
+and command-line runnability (use "open" to run on command
+line). Be sure to test lam_conv as it is the more vulnerable
+of the two, and always use a different Mac than the one you
+compiled on.
+
+(What did not work:
+
+any attempts to make universal binaries
+)
+
+******
+
+On MSW:
+
+We installed mingw32 on griffiths.gs using instructions on its
+web site. Hopefully this doesn't need to be done again.
+
+make a clean cvs checkout of lamarc on griffiths
+
+** make wxwidgets
+NOTE: If you previously did a 32 bit install be sure to do
+ALL OF THIS again. Also, if you are using a pre-existing directory
+you must do "make distclean" before proceeding. "make clean" is
+not enough. This applies to both wxWidgets and Lamarc.
+
+cd to ~mkkuhner/src/wxWidgets/wxWidgets-3.0.0
+make a directory msw-64
+ export HOST_TYPE=x86_64-w64-mingw32
+ export WX_INSTALL_LOC=$HOME/wx-libs
+
+ ../configure --disable-shared --with-libtiff=builtin \
+ --host=$HOST_TYPE \
+ --prefix=$WX_INSTALL_LOC
+ make
+ make install
+
+** make lamarc
+cd back to lamarc
+make a directory msw
+cd into msw
+ ../configure --host=$HOST_TYPE \
+ --with-wx-config=$WX_INSTALL_LOC/wxMSW/bin/wx-config
+edit Makefile to remove two references to -lX11
+ make
+
+this will create lamarc.exe and lam_conv.exe
+put them into a directory whose name is the version name, such as
+lamarc-2.1.9-Windows.
+tar this directory using tar -cvf (don't compress it)
+transfer this file to a Windows machine; put it on the Desktop
+right-click on it and select 7-zip > extract files
+change "location to extract" to the Desktop (otherwise you get a spurious
+ level of indirection)
+right click on the resulting folder (not the tar file!)
+choose 7-zip > add to archive and make a .zip file
+
+(What did not work: trying to compile any version of wxWidgets on
+our Windows box either with mingw or cygwin; cross-compiling on lamarc.gs--
+probably due to wrong "modules" commands.)
+
+***
+
+On MSW for 32-bit target:
+
+NOTE: If you previously did a 64 bit install be sure to do
+ALL OF THIS again. Also, if you are using a pre-existing directory
+you must do "make distclean" before proceeding. "make clean" is
+not enough. This applies to both wxWidgets and Lamarc.
+
+make a clean cvs checkout of lamarc on griffiths
+
+make wxwidgets:
+
+cd into ~mkkuhner/src/wxWidgets/wxWidgets-3.0.0
+make a directory msw-32
+cd into it
+export HOST_TYPE=i686-w64-mingw32
+(yes, w64 even for 32-bit builds)
+export WX_INSTALL_LOC=$HOME/wx-libs32
+
+ ../configure --disable-shared --with-libtiff=builtin \
+ --host=$HOST_TYPE \
+ --prefix=$WX_INSTALL_LOC
+ make
+ make install
+
+cd back to lamarc
+make a directory msw
+cd into msw
+ ../configure --host=$HOST_TYPE \
+ --with-wx-config=$WX_INSTALL_LOC/bin/wx-config
+edit Makefile to remove two references to -lX11
+ make
+
+this will create lamarc.exe and lam_conv.exe
+put them into a directory whose name is the version name, such as
+lamarc-2.1.9-Win32.
+tar this directory using tar -cvf (don't compress it)
+transfer this file to a Windows machine; put it on the Desktop
+right-click on it and select 7-zip > extract files
+change "location to extract" to the Desktop (otherwise you get a spurious
+ level of indirection)
+right click on the resulting folder (not the tar file!)
+choose 7-zip > add to archive and make a .zip file
+
+WARNING: I don't see why this recipe would produce a 32-bit compile,
+and I don't have a 32-bit machine to test it on, so it must be
+regarded with suspicion!
+
+(What did not work: trying to compile any version of wxWidgets on
+our Windows box either with mingw or cygwin; cross-compiling on lamarc.gs--
+probably due to wrong "modules" commands.)
+
+***
+
+Everywhere:
+
+Transfer the files to evolution.gs.washington.edu (to get them off
+the Windows machine, try Dropbox).
+
+The Lamarc web pages are at:
+/felsenstein/www/html/lamarc/
+
+You will need to edit index.html to describe the new release, and
+lamarc_download.html to point to the new executables.
diff --git a/doc/wx-osx-notes.txt b/doc/wx-osx-notes.txt
index cf479c2..366d142 100644
--- a/doc/wx-osx-notes.txt
+++ b/doc/wx-osx-notes.txt
@@ -1,3 +1,55 @@
+UPDATE, 4/19/2016, Lucian Smith
+
+Based on the most recent behavior of wxwidgets on the mac, it looks like the Mac operating system
+itself is a moving target, enough so that it seems like only the most recent version of wxwidgets will
+work on it. As a result, we recommend that you get the most recent version of wxwidgets, compile it
+for the mac, and then use that, every time a new version of lam_conv for the mac is needed.
+
+Here's what worked in April of 2016 for OSX 10.10:
+
+* Fetched version 3.1.0 from wxwidgets.org
+* untarr'ed to wxWidgets-3.1.0/
+* cd wxWidgets-3.1.0/
+* mkdir build
+* cd build
+* ../configure --disable-shared --with-cocoa --with-macosx-version-min=10.7
+* make
+
+To make sure things worked, you can then:
+* cd samples/minimal/
+* make
+* open minimal.app
+
+(see https://forums.wxwidgets.org/viewtopic.php?t=41965)
+
+Then when you configure lamarc, point it to the newly-built wx-config:
+
+* cd lamarc/build/
+* ../configure --with-wx-config=../../wxWidgets-3.1.0/build/wx-config
+
+And that will hopefully work!
+
+If wxwidgets stops supporting 10.7, you'll need to update to 10.8 or whatever, and then make a
+corresponding change to Makefile.am: wherever you see '-mmacosx-version-min=10.7', change that to
+10.8. It might also be necessary to change how tinyxml is linked: when I added that line when
+compiling it, this caused X11 to no longer be used, and it couldn't be found--this explains the lines
+in Makefile.am:
+
+lam_conv_LDADD = @WX_LIBS@
+if LAMARC_APP_OSX
+ lam_conv_LDADD += libtinyxml.a
+else
+ lam_conv_LDADD += -lX11 libtinyxml.a
+endif
+
+So, if X11 starts being used again, re-add it to the osx-specific line.
+
+
+
+
+
+ORIGINAL TEXT, from 2012 (Elizabeth Walkup):
+
This file is supposed to live here:
malecot.gs.washington.edu:/Users/Shared/wxWidgets/wx-osx-notes.txt
diff --git a/firstLinuxBuild.sh b/firstLinuxBuild.sh
new file mode 100755
index 0000000..f22309d
--- /dev/null
+++ b/firstLinuxBuild.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+scriptdir=`dirname $0`
+exec ${scriptdir}/scripts/build.sh --autotools --x11 --enable-debug
diff --git a/install-sh b/install-sh
new file mode 100755
index 0000000..77bc381
--- /dev/null
+++ b/install-sh
@@ -0,0 +1,316 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2004-02-15.20
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch. It can only install one file at a time, a restriction
+# shared with many OS's install programs.
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit="${DOITPROG-}"
+
+# put in absolute paths if you don't have them in your path; or use env. vars.
+
+mvprog="${MVPROG-mv}"
+cpprog="${CPPROG-cp}"
+chmodprog="${CHMODPROG-chmod}"
+chownprog="${CHOWNPROG-chown}"
+chgrpprog="${CHGRPPROG-chgrp}"
+stripprog="${STRIPPROG-strip}"
+rmprog="${RMPROG-rm}"
+mkdirprog="${MKDIRPROG-mkdir}"
+
+transformbasename=
+transform_arg=
+instcmd="$mvprog"
+chmodcmd="$chmodprog 0755"
+chowncmd=
+chgrpcmd=
+stripcmd=
+rmcmd="$rmprog -f"
+mvcmd="$mvprog"
+src=
+dst=
+dir_arg=
+
+usage="Usage: $0 [OPTION]... SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 -d DIRECTORIES...
+
+In the first form, install SRCFILE to DSTFILE, removing SRCFILE by default.
+In the second, create the directory path DIR.
+
+Options:
+-b=TRANSFORMBASENAME
+-c copy source (using $cpprog) instead of moving (using $mvprog).
+-d create directories instead of installing files.
+-g GROUP $chgrp installed files to GROUP.
+-m MODE $chmod installed files to MODE.
+-o USER $chown installed files to USER.
+-s strip installed files (using $stripprog).
+-t=TRANSFORM
+--help display this help and exit.
+--version display version info and exit.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG
+"
+
+while test -n "$1"; do
+ case $1 in
+ -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
+ shift
+ continue;;
+
+ -c) instcmd=$cpprog
+ shift
+ continue;;
+
+ -d) dir_arg=true
+ shift
+ continue;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift
+ shift
+ continue;;
+
+ --help) echo "$usage"; exit 0;;
+
+ -m) chmodcmd="$chmodprog $2"
+ shift
+ shift
+ continue;;
+
+ -o) chowncmd="$chownprog $2"
+ shift
+ shift
+ continue;;
+
+ -s) stripcmd=$stripprog
+ shift
+ continue;;
+
+ -t=*) transformarg=`echo $1 | sed 's/-t=//'`
+ shift
+ continue;;
+
+ --version) echo "$0 $scriptversion"; exit 0;;
+
+ *) # When -d is used, all remaining arguments are directories to create.
+ test -n "$dir_arg" && break
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dstarg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dstarg"
+ shift # fnord
+ fi
+ shift # arg
+ dstarg=$arg
+ done
+ break;;
+ esac
+done
+
+if test -z "$1"; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+for src
+do
+ # Protect names starting with `-'.
+ case $src in
+ -*) src=./$src ;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ src=
+
+ if test -d "$dst"; then
+ instcmd=:
+ chmodcmd=
+ else
+ instcmd=$mkdirprog
+ fi
+ else
+ # Waiting for this to be detected by the "$instcmd $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dstarg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+
+ dst=$dstarg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst ;;
+ esac
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ dst=$dst/`basename "$src"`
+ fi
+ fi
+
+ # This sed command emulates the dirname command.
+ dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
+
+ # Make sure that the destination directory exists.
+
+ # Skip lots of stat calls in the usual case.
+ if test ! -d "$dstdir"; then
+ defaultIFS='
+ '
+ IFS="${IFS-$defaultIFS}"
+
+ oIFS=$IFS
+ # Some sh's can't handle IFS=/ for some reason.
+ IFS='%'
+ set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
+ IFS=$oIFS
+
+ pathcomp=
+
+ while test $# -ne 0 ; do
+ pathcomp=$pathcomp$1
+ shift
+ if test ! -d "$pathcomp"; then
+ $mkdirprog "$pathcomp" || lasterr=$?
+ # mkdir can fail with a `File exist' error in case several
+ # install-sh are creating the directory concurrently. This
+ # is OK.
+ test ! -d "$pathcomp" && { (exit ${lasterr-1}); exit; }
+ fi
+ pathcomp=$pathcomp/
+ done
+ fi
+
+ if test -n "$dir_arg"; then
+ $doit $instcmd "$dst" \
+ && { test -z "$chowncmd" || $doit $chowncmd "$dst"; } \
+ && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } \
+ && { test -z "$stripcmd" || $doit $stripcmd "$dst"; } \
+ && { test -z "$chmodcmd" || $doit $chmodcmd "$dst"; }
+
+ else
+ # If we're going to rename the final executable, determine the name now.
+ if test -z "$transformarg"; then
+ dstfile=`basename "$dst"`
+ else
+ dstfile=`basename "$dst" $transformbasename \
+ | sed $transformarg`$transformbasename
+ fi
+
+ # don't allow the sed command to completely eliminate the filename.
+ test -z "$dstfile" && dstfile=`basename "$dst"`
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'status=$?; rm -f "$dsttmp" "$rmtmp" && exit $status' 0
+ trap '(exit $?); exit' 1 2 13 15
+
+ # Move or copy the file name to the temp name
+ $doit $instcmd "$src" "$dsttmp" &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $instcmd $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } \
+ && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } \
+ && { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } \
+ && { test -z "$chmodcmd" || $doit $chmodcmd "$dsttmp"; } &&
+
+ # Now remove or move aside any old file at destination location. We
+ # try this two ways since rm can't unlink itself on some systems and
+ # the destination file might be busy for other reasons. In this case,
+ # the final cleanup might fail but the new file should still install
+ # successfully.
+ {
+ if test -f "$dstdir/$dstfile"; then
+ $doit $rmcmd -f "$dstdir/$dstfile" 2>/dev/null \
+ || $doit $mvcmd -f "$dstdir/$dstfile" "$rmtmp" 2>/dev/null \
+ || {
+ echo "$0: cannot unlink or rename $dstdir/$dstfile" >&2
+ (exit 1); exit
+ }
+ else
+ :
+ fi
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dstdir/$dstfile"
+ fi || { (exit 1); exit; }
+done
+
+# The final little trick to "correctly" pass the exit status to the exit trap.
+{
+ (exit 0); exit
+}
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/makedebug.sh b/makedebug.sh
new file mode 100755
index 0000000..f3978ab
--- /dev/null
+++ b/makedebug.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#This script requires that you have 'wx-config' in your path somewhere. For
+# example, if you're on darwin and want to use sanity's version, you can
+# put ~sanity/wxLibs/bin/ in your path.
+#
+# Also note that if your makefiles are not working, you may need to start
+# from scratch, with:
+#
+# aclocal
+# autoconf
+# automake
+#
+# (in this directory) before running this script.
+
+if [ ! -r debug/Makefile ]; then
+ mkdir -p debug
+ cd debug
+ ../configure --enable-debug --enable-gui
+ cd ..
+fi
+cd debug
+make lamarc && cp -f lamarc .. && echo 'lamarc updated to the debug version.'
+make lam_conv && cp -f lam_conv .. && echo 'lam_conv updated to the debug version.'
+make old_lam_conv && cp -f old_lam_conv .. && echo 'old_lam_conv updated to the debug version.'
+
diff --git a/makegcov.sh b/makegcov.sh
new file mode 100755
index 0000000..fcf660f
--- /dev/null
+++ b/makegcov.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+#This script requires that you have 'wx-config' in your path somewhere. For
+# example, if you're on darwin and want to use sanity's version, you can
+# put ~sanity/wxLibs/bin/ in your path.
+
+if [ ! -r gcov/Makefile ]; then
+ mkdir -p gcov
+ cd gcov
+ ../configure --enable-debug --enable-gcov --enable-gui
+ cd ..
+fi
+cd gcov
+make && echo 'Executables updated in the gcov directory--cd gcov to run.'
diff --git a/makeopt.sh b/makeopt.sh
new file mode 100755
index 0000000..d6928f9
--- /dev/null
+++ b/makeopt.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+#This script requires that you have 'wx-config' in your path somewhere. For
+# example, if you're on darwin and want to use sanity's version, you can
+# put ~sanity/wxLibs/bin/ in your path.
+
+if [ ! -r opt/Makefile ]; then
+ mkdir -p opt
+ cd opt
+ ../configure --enable-gui
+ cd ..
+fi
+cd opt
+make lamarc && cp -f lamarc .. && echo 'lamarc updated to the optimized version.'
+make lam_conv && cp -f lam_conv .. && echo 'lam_conv updated to the optimized version.'
+make old_lam_conv && cp -f old_lam_conv .. && echo 'old_lam_conv updated to the optimized version.'
+
diff --git a/missing b/missing
new file mode 100755
index 0000000..e7ef83a
--- /dev/null
+++ b/missing
@@ -0,0 +1,360 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2003-09-02.23
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003
+# Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case "$1" in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case "$1" in
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Send bug reports to <bug-automake at gnu.org>."
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+ aclocal*)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case "$f" in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n 's/.*--output[ =]*\([^ ]*\).*/\1/p'`
+ test -z "$file" && file=`echo "$*" | sed -n 's/.*-o[ ]*\([^ ]*\).*/\1/p'`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison|yacc)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if [ $# -ne 1 ]; then
+ eval LASTARG="\${$#}"
+ case "$LASTARG" in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if [ ! -f y.tab.h ]; then
+ echo >y.tab.h
+ fi
+ if [ ! -f y.tab.c ]; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex|flex)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if [ $# -ne 1 ]; then
+ eval LASTARG="\${$#}"
+ case "$LASTARG" in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if [ ! -f lex.yy.c ]; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+ if test -z "$file"; then
+ file=`echo "$*" | sed -n 's/.*--output=\([^ ]*\).*/\1/p'`
+ fi
+ if [ -f "$file" ]; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit 1
+ fi
+ ;;
+
+ makeinfo)
+ if test -z "$run" && (makeinfo --version) > /dev/null 2>&1; then
+ # We have makeinfo, but it failed.
+ exit 1
+ fi
+
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+ if test -z "$file"; then
+ file=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $file`
+ fi
+ touch $file
+ ;;
+
+ tar)
+ shift
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ fi
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case "$firstarg" in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case "$firstarg" in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/projects/macos/MacOSPrefix.h b/projects/macos/MacOSPrefix.h
new file mode 100644
index 0000000..d8c66a0
--- /dev/null
+++ b/projects/macos/MacOSPrefix.h
@@ -0,0 +1,37 @@
+
+
+/*
+ * MacOSPrefix.h (c) 2000 Zero-Knowledge Systems, Inc.
+ *
+ * $Id: MacOSPrefix.h,v 1.2 2004/08/04 21:57:41 lpsmith Exp $
+ *
+ * General-purpose CodeWarrior prefix file, for release builds
+ *
+ */
+
+#define TIXML_USE_STL
+
+#define NDEBUG 1
+#undef _DEBUG
+
+#if !defined(Rez)
+# define FREEDOM_PRODUCTION_BUILD "FREEDOM BUILD ("__DATE__", "__TIME__")"
+#endif
+
+#if defined(__MWERKS__) && !defined(Rez)
+ /* CodeWarrior */
+# if __POWERPC__
+ /* PowerPC compiler */
+# pragma traceback off
+# elif __MC68K__
+ /* Motorola 680x0 compiler */
+# pragma macsbug off
+# endif
+#endif
+
+/* we want the <stdint.h> macros, even with C++ */
+#define __STDC_LIMIT_MACROS 1
+
+/* strip out patented stuff in OpenSSL */
+#define NO_IDEA
+#define NO_RC5
diff --git a/projects/macos/MacOSPrefixDebug.h b/projects/macos/MacOSPrefixDebug.h
new file mode 100644
index 0000000..d390358
--- /dev/null
+++ b/projects/macos/MacOSPrefixDebug.h
@@ -0,0 +1,68 @@
+
+
+
+
+/*
+
+ * MacOSPrefix.h (c) 2000 Zero-Knowledge Systems, Inc.
+
+ *
+
+ * $Id: MacOSPrefixDebug.h,v 1.2 2004/08/04 21:57:41 lpsmith Exp $
+
+ *
+
+ * General-purpose CodeWarrior prefix file, for release builds
+
+ *
+
+ */
+
+
+
+#define TIXML_USE_STL
+
+
+
+#if !defined(Rez)
+
+# define FREEDOM_PRODUCTION_BUILD "FREEDOM BUILD ("__DATE__", "__TIME__")"
+
+#endif
+
+
+
+#if defined(__MWERKS__) && !defined(Rez)
+
+ /* CodeWarrior */
+
+# if __POWERPC__
+
+ /* PowerPC compiler */
+
+# pragma traceback off
+
+# elif __MC68K__
+
+ /* Motorola 680x0 compiler */
+
+# pragma macsbug off
+
+# endif
+
+#endif
+
+
+
+/* we want the <stdint.h> macros, even with C++ */
+
+#define __STDC_LIMIT_MACROS 1
+
+
+
+/* strip out patented stuff in OpenSSL */
+
+#define NO_IDEA
+
+#define NO_RC5
+
diff --git a/projects/macos/carb.r b/projects/macos/carb.r
new file mode 100644
index 0000000..a0f51c0
--- /dev/null
+++ b/projects/macos/carb.r
@@ -0,0 +1,18 @@
+/*
+ * Permit this Carbon application to launch on OS X
+ *
+ * Copyright � 1997-2002 Metrowerks Corporation. All Rights Reserved.
+ *
+ * Questions and comments to:
+ * <mailto:support at metrowerks.com>
+ * <http://www.metrowerks.com/>
+ */
+
+
+/*----------------------------carb � Carbon on OS X launch information --------------------------*/
+type 'carb' {
+};
+
+
+resource 'carb'(0) {
+};
\ No newline at end of file
diff --git a/projects/macos/lam_conv make b/projects/macos/lam_conv make
new file mode 100644
index 0000000..97f4a7e
Binary files /dev/null and b/projects/macos/lam_conv make differ
diff --git a/projects/macos/lamarc make b/projects/macos/lamarc make
new file mode 100644
index 0000000..b97d154
Binary files /dev/null and b/projects/macos/lamarc make differ
diff --git a/projects/macos/make_mwerks.pl b/projects/macos/make_mwerks.pl
new file mode 100755
index 0000000..aaec6ee
--- /dev/null
+++ b/projects/macos/make_mwerks.pl
@@ -0,0 +1,171 @@
+#!/usr/bin/perl
+
+## constant strings, not expected to change
+$templateFile = "projects/macos/mwerks_xml_template";
+$fromXmlToTop = "../../";
+$cr = "\n";
+
+$matchesHeaderFiles = "\\\.h\$";
+$matchesSourceFiles = "\\\.cpp\$";
+$matchesResourceFiles = "\\\.ico\$";
+
+## prints out one user search path
+sub makeSearchPath
+{
+ my($localPath) = @_;
+
+ my($path) = $fromXmlToTop.$localPath;
+
+ printf " <SETTING>$cr";
+ printf " <SETTING><NAME>SearchPath</NAME>$cr";
+ printf " <SETTING><NAME>Path</NAME><VALUE>$path</VALUE></SETTING>$cr";
+ printf " <SETTING><NAME>PathFormat</NAME><VALUE>Unix</VALUE></SETTING>$cr";
+ printf " <SETTING><NAME>PathRoot</NAME><VALUE>Project</VALUE></SETTING>$cr";
+ printf " </SETTING>$cr";
+ printf " <SETTING><NAME>Recursive</NAME><VALUE>true</VALUE></SETTING>$cr";
+ printf " <SETTING><NAME>FrameworkPath</NAME><VALUE>false</VALUE></SETTING>$cr";
+ printf " <SETTING><NAME>HostFlags</NAME><VALUE>All</VALUE></SETTING>$cr";
+ printf " </SETTING>$cr";
+
+}
+
+
+## prints out one file name when within a list of sources
+sub makeFileEntry
+{
+ my($fileName) = @_;
+
+ my(@exploded) = split /\// , $fileName;
+
+ my($fname) = pop @exploded;
+ my($fpath) = $fromXmlToTop . (join ('/', at exploded));
+
+
+ printf " <FILE>$cr";
+ printf " <PATHTYPE>Name</PATHTYPE>$cr";
+ printf " <PATH>$fname</PATH>$cr";
+ printf " <PATHFORMAT>Unix</PATHFORMAT>$cr";
+ printf " </FILE>$cr";
+}
+
+sub makeGroupEntry
+{
+ my($fileName) = @_;
+
+ my(@exploded) = split /\// , $fileName;
+
+ my($fname) = pop @exploded;
+ my($fpath) = $fromXmlToTop . (join ('/', at exploded));
+
+ printf " <FILEREF>$cr";
+ printf " <TARGETNAME>$lamarcTargetName</TARGETNAME>$cr";
+ printf " <PATHTYPE>Name</PATHTYPE>$cr";
+ printf " <PATH>$fname</PATH>$cr";
+ printf " <PATHFORMAT>Unix</PATHFORMAT>$cr";
+ printf " </FILEREF>$cr";
+}
+
+
+## gonna slurp a bunch of file names into these
+ at headers = ();
+ at sources = ();
+ at resources = ();
+ at includeDirs = ();
+
+########################################################
+## first argument is the project name, it could be lamarc
+## or lam_conv, for example
+$projectName = shift;
+
+$lamarcTargetName = $projectName."-mac";
+
+########################################################
+## divide up remaining arguments into files and include
+## path items
+$nextIsInclude = ""; ## true when we just saw -I
+foreach $item (@ARGV)
+{
+
+ if($nextIsInclude)
+ {
+ push @includeDirs, $item ;
+ $nextIsInclude = "";
+ }
+ elsif ($item =~ /$matchesHeaderFiles/)
+ {
+ push @headers, $item ;
+ }
+ elsif ($item =~ /$matchesSourceFiles/)
+ {
+ push @sources, $item ;
+ }
+ elsif ($item =~ /$matchesResourceFiles/)
+ {
+ push @resources, $item ;
+ }
+ elsif ($item =~ /^-I$/)
+ {
+ $nextIsInclude = "yes";
+ }
+}
+
+open(TEMPLATEFILE,$templateFile); ## modify content of this file
+
+$inFiles = $inFilter = $filterType = "";
+while(<TEMPLATEFILE>)
+{
+
+ ## #################################################
+ ## in this section, producing output
+ ## #################################################
+
+ s/LAMARCTARGETNAME/$lamarcTargetName/g;
+
+ if($_ =~ /LAMARC: SEARCHPATHS/)
+ {
+ printf;
+ foreach $item (@includeDirs)
+ {
+ makeSearchPath($item);
+ }
+ }
+ elsif($_ =~ /LAMARC: FILELIST/)
+ {
+ printf;
+ foreach $item (@headers)
+ {
+ makeFileEntry($item);
+ }
+ foreach $item (@sources)
+ {
+ makeFileEntry($item);
+ }
+ foreach $item (@resources)
+ {
+ makeFileEntry($item);
+ }
+ }
+ elsif($_ =~ /LAMARC: GROUPLIST/)
+ {
+ printf;
+ foreach $item (@headers)
+ {
+ makeGroupEntry($item);
+ }
+ foreach $item (@sources)
+ {
+ makeGroupEntry($item);
+ }
+ foreach $item (@resources)
+ {
+ makeGroupEntry($item);
+ }
+ }
+ else
+ {
+ printf;
+ }
+}
+close(TEMPLATEFILE);
+
+
diff --git a/projects/macos/mwerks_xml_template b/projects/macos/mwerks_xml_template
new file mode 100644
index 0000000..4844ab1
--- /dev/null
+++ b/projects/macos/mwerks_xml_template
@@ -0,0 +1,1261 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
+<?codewarrior exportversion="1.0.1" ideversion="5.0" ?>
+
+<!DOCTYPE PROJECT [
+<!ELEMENT PROJECT (TARGETLIST, TARGETORDER, GROUPLIST, DESIGNLIST?)>
+<!ELEMENT TARGETLIST (TARGET+)>
+<!ELEMENT TARGET (NAME, SETTINGLIST, FILELIST?, LINKORDER?, SEGMENTLIST?, OVERLAYGROUPLIST?, SUBTARGETLIST?, SUBPROJECTLIST?, FRAMEWORKLIST?)>
+<!ELEMENT NAME (#PCDATA)>
+<!ELEMENT USERSOURCETREETYPE (#PCDATA)>
+<!ELEMENT PATH (#PCDATA)>
+<!ELEMENT FILELIST (FILE*)>
+<!ELEMENT FILE (PATHTYPE, PATHROOT?, ACCESSPATH?, PATH, PATHFORMAT?, ROOTFILEREF?, FILEKIND?, FILEFLAGS?)>
+<!ELEMENT PATHTYPE (#PCDATA)>
+<!ELEMENT PATHROOT (#PCDATA)>
+<!ELEMENT ACCESSPATH (#PCDATA)>
+<!ELEMENT PATHFORMAT (#PCDATA)>
+<!ELEMENT ROOTFILEREF (PATHTYPE, PATHROOT?, ACCESSPATH?, PATH, PATHFORMAT?)>
+<!ELEMENT FILEKIND (#PCDATA)>
+<!ELEMENT FILEFLAGS (#PCDATA)>
+<!ELEMENT FILEREF (TARGETNAME?, PATHTYPE, PATHROOT?, ACCESSPATH?, PATH, PATHFORMAT?)>
+<!ELEMENT TARGETNAME (#PCDATA)>
+<!ELEMENT SETTINGLIST ((SETTING|PANELDATA)+)>
+<!ELEMENT SETTING (NAME?, (VALUE|(SETTING+)))>
+<!ELEMENT PANELDATA (NAME, VALUE)>
+<!ELEMENT VALUE (#PCDATA)>
+<!ELEMENT LINKORDER (FILEREF*)>
+<!ELEMENT SEGMENTLIST (SEGMENT+)>
+<!ELEMENT SEGMENT (NAME, ATTRIBUTES?, FILEREF*)>
+<!ELEMENT ATTRIBUTES (#PCDATA)>
+<!ELEMENT OVERLAYGROUPLIST (OVERLAYGROUP+)>
+<!ELEMENT OVERLAYGROUP (NAME, BASEADDRESS, OVERLAY*)>
+<!ELEMENT BASEADDRESS (#PCDATA)>
+<!ELEMENT OVERLAY (NAME, FILEREF*)>
+<!ELEMENT SUBTARGETLIST (SUBTARGET+)>
+<!ELEMENT SUBTARGET (TARGETNAME, ATTRIBUTES?, FILEREF?)>
+<!ELEMENT SUBPROJECTLIST (SUBPROJECT+)>
+<!ELEMENT SUBPROJECT (FILEREF, SUBPROJECTTARGETLIST)>
+<!ELEMENT SUBPROJECTTARGETLIST (SUBPROJECTTARGET*)>
+<!ELEMENT SUBPROJECTTARGET (TARGETNAME, ATTRIBUTES?, FILEREF?)>
+<!ELEMENT FRAMEWORKLIST (FRAMEWORK+)>
+<!ELEMENT FRAMEWORK (FILEREF, LIBRARYFILE?, VERSION?)>
+<!ELEMENT LIBRARYFILE (FILEREF)>
+<!ELEMENT VERSION (#PCDATA)>
+<!ELEMENT TARGETORDER (ORDEREDTARGET|ORDEREDDESIGN)*>
+<!ELEMENT ORDEREDTARGET (NAME)>
+<!ELEMENT ORDEREDDESIGN (NAME, ORDEREDTARGET+)>
+<!ELEMENT GROUPLIST (GROUP|FILEREF)*>
+<!ELEMENT GROUP (NAME, (GROUP|FILEREF)*)>
+<!ELEMENT DESIGNLIST (DESIGN+)>
+<!ELEMENT DESIGN (NAME, DESIGNDATA)>
+<!ELEMENT DESIGNDATA (#PCDATA)>
+]>
+
+<PROJECT>
+ <TARGETLIST>
+ <TARGET>
+ <NAME>LAMARCTARGETNAME</NAME>
+ <SETTINGLIST>
+
+ <!-- Settings for "Source Trees" panel -->
+ <SETTING><NAME>UserSourceTrees</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "Access Paths" panel -->
+ <SETTING><NAME>AlwaysSearchUserPaths</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>InterpretDOSAndUnixPaths</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>RequireFrameworkStyleIncludes</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>UserSearchPaths</NAME>
+ <SETTING>
+ <SETTING><NAME>SearchPath</NAME>
+ <SETTING><NAME>Path</NAME><VALUE>..</VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>Unix</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Project</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>Recursive</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>FrameworkPath</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>HostFlags</NAME><VALUE>All</VALUE></SETTING>
+ </SETTING>
+ <!-- LAMARC: SEARCHPATHS -->
+ </SETTING>
+ <SETTING><NAME>SystemSearchPaths</NAME>
+ <SETTING>
+ <SETTING><NAME>SearchPath</NAME>
+ <SETTING><NAME>Path</NAME><VALUE>:MSL:</VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>MacOS</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>CodeWarrior</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>Recursive</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>FrameworkPath</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>HostFlags</NAME><VALUE>All</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>SearchPath</NAME>
+ <SETTING><NAME>Path</NAME><VALUE>:MacOS Support:</VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>MacOS</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>CodeWarrior</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>Recursive</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>FrameworkPath</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>HostFlags</NAME><VALUE>All</VALUE></SETTING>
+ </SETTING>
+ </SETTING>
+
+ <!-- Settings for "Debugger Runtime" panel -->
+ <SETTING><NAME>MWRuntimeSettings_WorkingDirectory</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWRuntimeSettings_CommandLine</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWRuntimeSettings_HostApplication</NAME>
+ <SETTING><NAME>Path</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>Generic</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Absolute</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>MWRuntimeSettings_EnvVars</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "Target Settings" panel -->
+ <SETTING><NAME>Linker</NAME><VALUE>MacOS PPC Linker</VALUE></SETTING>
+ <SETTING><NAME>PreLinker</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>PostLinker</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Targetname</NAME><VALUE>LAMARCTARGETNAME</VALUE></SETTING>
+ <SETTING><NAME>OutputDirectory</NAME>
+ <SETTING><NAME>Path</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>Unix</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Project</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>SaveEntriesUsingRelativePaths</NAME><VALUE>true</VALUE></SETTING>
+
+ <!-- Settings for "File Mappings" panel -->
+ <SETTING><NAME>FileMappings</NAME>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>APPL</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>Appl</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>MMLB</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Lib Import PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Balloon Help</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>MPLF</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Lib Import PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Balloon Help</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>MWCD</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>RSRC</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.arr</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.axp</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.bh</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Balloon Help</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.c</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.c++</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.cc</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.cp</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.cpp</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.exp</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.h</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.h++</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.hpp</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.m</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.mm</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.pch</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.pch++</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.pchm</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>MW C/C++ PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>C/C++</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.plc</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Property List Compiler</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Property List</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.ploc</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Property List Compiler</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Property List</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.r</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Rez</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Rez</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.s</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>PPCAsm</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Balloon Help</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>TEXT</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.wke</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>XCOF</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>XCOFF Import PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Balloon Help</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>docu</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>rsrc</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>shlb</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>PEF Import PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Balloon Help</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileType</NAME><VALUE>stub</VALUE></SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>PEF Import PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Balloon Help</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.doc</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.gif</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Copy To Package</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.icns</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Copy To Package</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.jpg</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Copy To Package</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.nib</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Copy To Package</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.o</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>XCOFF Import PPC</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE>Balloon Help</VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.plist</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Copy To Package</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.ppob</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.rsrc</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>false</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.strings</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Copy To Package</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ <SETTING>
+ <SETTING><NAME>FileExtension</NAME><VALUE>.tiff</VALUE></SETTING>
+ <SETTING><NAME>Compiler</NAME><VALUE>Copy To Package</VALUE></SETTING>
+ <SETTING><NAME>EditLanguage</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>Precompile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Launchable</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>ResourceFile</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>IgnoredByMake</NAME><VALUE>true</VALUE></SETTING>
+ </SETTING>
+ </SETTING>
+
+ <!-- Settings for "Build Extras" panel -->
+ <SETTING><NAME>CacheModDates</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>DumpBrowserInfo</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>CacheSubprojects</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>UseThirdPartyDebugger</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>BrowserGenerator</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>DebuggerAppPath</NAME>
+ <SETTING><NAME>Path</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>Generic</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Absolute</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>DebuggerCmdLineArgs</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>DebuggerWorkingDir</NAME>
+ <SETTING><NAME>Path</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>Generic</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Absolute</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>CodeCompletionPrefixFileName</NAME><VALUE>MacHeaders.c</VALUE></SETTING>
+ <SETTING><NAME>CodeCompletionMacroFileName</NAME><VALUE>MacOS_Carbon_C++_Macros.h</VALUE></SETTING>
+
+ <!-- Settings for "Debugger Target" panel -->
+ <SETTING><NAME>ConsoleEncoding</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>LogSystemMessages</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>AutoTargetDLLs</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>StopAtWatchpoints</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>PauseWhileRunning</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>PauseInterval</NAME><VALUE>5</VALUE></SETTING>
+ <SETTING><NAME>PauseUIFlags</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>AltExePath</NAME>
+ <SETTING><NAME>Path</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>Generic</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Absolute</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>StopAtTempBPOnLaunch</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>CacheSymbolics</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>TempBPFunctionName</NAME><VALUE>main</VALUE></SETTING>
+ <SETTING><NAME>TempBPType</NAME><VALUE>0</VALUE></SETTING>
+
+ <!-- Settings for "Remote Debug" panel -->
+ <SETTING><NAME>Enabled</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ConnectionName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>DownloadPath</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>LaunchRemoteApp</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>RemoteAppPath</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>CoreID</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>JTAGClockSpeed</NAME><VALUE>8000</VALUE></SETTING>
+ <SETTING><NAME>IsMultiCore</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>OSDownload</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>UseGlobalOSDownload</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>OSDownloadConnectionName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>OSDownloadPath</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>AltDownload</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>AltDownloadConnectionName</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "Auto-target" panel -->
+ <SETTING><NAME>OtherExecutables</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "Custom Keywords" panel -->
+ <SETTING><NAME>CustomColor1</NAME>
+ <SETTING><NAME>Red</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>Green</NAME><VALUE>32767</VALUE></SETTING>
+ <SETTING><NAME>Blue</NAME><VALUE>0</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>CustomColor2</NAME>
+ <SETTING><NAME>Red</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>Green</NAME><VALUE>32767</VALUE></SETTING>
+ <SETTING><NAME>Blue</NAME><VALUE>0</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>CustomColor3</NAME>
+ <SETTING><NAME>Red</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>Green</NAME><VALUE>32767</VALUE></SETTING>
+ <SETTING><NAME>Blue</NAME><VALUE>0</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>CustomColor4</NAME>
+ <SETTING><NAME>Red</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>Green</NAME><VALUE>32767</VALUE></SETTING>
+ <SETTING><NAME>Blue</NAME><VALUE>0</VALUE></SETTING>
+ </SETTING>
+
+ <!-- Settings for "C/C++ Compiler" panel -->
+ <SETTING><NAME>MWFrontEnd_C_cplusplus</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_checkprotos</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_arm</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_trigraphs</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_onlystdkeywords</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_enumsalwaysint</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_mpwpointerstyle</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_prefixname</NAME><VALUE>MacOSPrefix.h</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_ansistrict</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_mpwcnewline</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_wchar_type</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_enableexceptions</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_dontreusestrings</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_poolstrings</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_dontinline</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_useRTTI</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_multibyteaware</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_unsignedchars</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_autoinline</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_booltruefalse</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_inlinelevel</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_ecplusplus</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_objective_c</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_defer_codegen</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_templateparser</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_c99</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFrontEnd_C_bottomupinline</NAME><VALUE>1</VALUE></SETTING>
+
+ <!-- Settings for "C/C++ Warnings" panel -->
+ <SETTING><NAME>MWWarning_C_warn_illpragma</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_emptydecl</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_possunwant</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_unusedvar</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_unusedarg</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_extracomma</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_pedantic</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warningerrors</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_hidevirtual</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_implicitconv</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_notinlined</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWWarning_C_warn_structclass</NAME><VALUE>0</VALUE></SETTING>
+
+ <!-- Settings for "FTP Panel" panel -->
+ <SETTING><NAME>MWFTP_Post_hostName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_username</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_password</NAME><VALUE>0ÿÄ@Eø`"²|</VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_remoteDir</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_ftp_PathVersion</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_ftp_PathType</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_ftp_PathFormat</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_ftp_tree</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_uploadDir</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_ftp_port</NAME><VALUE>21</VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_SendBin</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWFTP_Post_ShouldLog</NAME><VALUE>1</VALUE></SETTING>
+
+ <!-- Settings for "Java Command Line" panel -->
+ <SETTING><NAME>MWCommandLine_Java_clsName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWCommandLine_Java_args</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "PJavaDebugging" panel -->
+ <SETTING><NAME>MWVJavaDebugging_Protocol</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWVJavaDebugging_JDKVersion</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWVJavaDebugging_TimeOut</NAME><VALUE>25</VALUE></SETTING>
+ <SETTING><NAME>MWVJavaDebugging_SupportSlowDevices</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWVJavaDebugging_UseRemoteLaunchAgent</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWVJavaDebugging_LaunchVMasServer</NAME><VALUE>false</VALUE></SETTING>
+
+ <!-- Settings for "Java Language" panel -->
+ <SETTING><NAME>MWJava_Language_optimize</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_warnDeprecated</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_emitMap</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_strictFileNames</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_strictFileHierarchy</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_1_1_Compatible</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_emitHeaders</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_headerType</NAME><VALUE>JNINativeHeaders</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_packageFilter</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_genComments</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_genHeaders</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_enableAsserts</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Language_targetVM</NAME><VALUE>1.1</VALUE></SETTING>
+
+ <!-- Settings for "Java Manifest-JAD Setting Info" panel -->
+ <SETTING><NAME>Manifest-JAD Attributes</NAME>
+ <SETTING>
+ <SETTING><NAME>Attribute</NAME><VALUE>Main-Class</VALUE></SETTING>
+ <SETTING><NAME>Value</NAME><VALUE>Auto-Generated</VALUE></SETTING>
+ </SETTING>
+ </SETTING>
+
+ <!-- Settings for "Java MRJAppBuilder" panel -->
+ <SETTING><NAME>MWJava_MRJAppBuilder_outFile</NAME><VALUE>MRJApplication</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_merge</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_quitMenu</NAME><VALUE>true</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_grow</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdoutType</NAME><VALUE>Console</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stderrType</NAME><VALUE>Console</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdinType</NAME><VALUE>Console</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_appIconPVersion</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_appIconPType</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_appIconPFormat</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_appIconPTree</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_appIconFile</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_splashScreenPVersion</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_splashScreenPType</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_splashScreenPFormat</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_splashScreenPTree</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_splashScreenPICTFile</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_aboutName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdoutPVersion</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdoutPType</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdoutPFormat</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdoutPTree</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdoutFile</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdoutAppend</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stderrPType</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stderrPFormat</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stderrPTree</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stderrFile</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stderrAppend</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdinPType</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdinPFormat</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdinPTree</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_MRJAppBuilder_stdinFile</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "Java Output" panel -->
+ <SETTING><NAME>MWJava_Output_outputtype</NAME><VALUE>JarFile</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_outfile</NAME><VALUE>JavaClasses.jar</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_ftype</NAME><VALUE>1514754080</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_fcreator</NAME><VALUE>1297570384</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_compress</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_genManifest</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_trunctype</NAME><VALUE>Front</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_deleteClasses</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_consoleApp</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_preverify</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_genJad</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Output_obfuscate</NAME><VALUE>0</VALUE></SETTING>
+
+ <!-- Settings for "Java Project" panel -->
+ <SETTING><NAME>MWJava_Proj_projtype</NAME><VALUE>Applet</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_mainClassName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_HTMLAppCreator</NAME><VALUE>1463898714</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_HTMLAppName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_PathVersion</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_PathType</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_PathFormat</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_tree</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_HTMLAppWin32Name</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_compress</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_simulator</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_useVM</NAME><VALUE>\000\000mrj225</VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_vmarguments</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_vmName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJava_Proj_simPropFile</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "JavaDoc Project" panel -->
+ <SETTING><NAME>MWJavaDoc_Proj_Version</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_Deprecated</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_Author</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_Index</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_Tree</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_SunResolveToSame</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_Shortnames</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_Folder</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_GenerateAPILinks</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_scope</NAME><VALUE>Public</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_fcreator</NAME><VALUE>1297303877</VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_encodingName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_decodingName</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWJavaDoc_Proj_javaPackagePath</NAME><VALUE>http://java.sun.com/products/jdk/1.1/docs/api/</VALUE></SETTING>
+
+ <!-- Settings for "MacOS Merge Panel" panel -->
+ <SETTING><NAME>MWMerge_MacOS_projectType</NAME><VALUE>Application</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_outputName</NAME><VALUE>Merge Out</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_outputCreator</NAME><VALUE>????</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_outputType</NAME><VALUE>APPL</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_suppressWarning</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_copyFragments</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_copyResources</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_flattenResource</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_flatFileName</NAME><VALUE>a.rsrc</VALUE></SETTING>
+ <SETTING><NAME>MWMerge_MacOS_flatFileOutputPath</NAME>
+ <SETTING><NAME>Path</NAME><VALUE>:</VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>MacOS</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Project</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>MWMerge_MacOS_skipResources</NAME>
+ <SETTING><VALUE>DLGX</VALUE></SETTING>
+ <SETTING><VALUE>ckid</VALUE></SETTING>
+ <SETTING><VALUE>Proj</VALUE></SETTING>
+ <SETTING><VALUE>WSPC</VALUE></SETTING>
+ </SETTING>
+
+ <!-- Settings for "Output Flags" panel -->
+ <SETTING><NAME>FileLocked</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>ResourcesMapIsReadOnly</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>PrinterDriverIsMultiFinderCompatible</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Invisible</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>HasBundle</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>NameLocked</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Stationery</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>HasCustomIcon</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Shared</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>HasBeenInited</NAME><VALUE>false</VALUE></SETTING>
+ <SETTING><NAME>Label</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>Comments</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "Packager Panel" panel -->
+ <SETTING><NAME>MWMacOSPackager_UsePackager</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWMacOSPackager_FolderToPackage</NAME>
+ <SETTING><NAME>Path</NAME><VALUE>:</VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>MacOS</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Project</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>MWMacOSPackager_CreateClassicAlias</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWMacOSPackager_ClassicAliasMethod</NAME><VALUE>UseTargetOutput</VALUE></SETTING>
+ <SETTING><NAME>MWMacOSPackager_ClassicAliasPath</NAME>
+ <SETTING><NAME>Path</NAME><VALUE>:</VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>MacOS</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Project</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>MWMacOSPackager_CreatePkgInfo</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWMacOSPackager_PkgCreatorType</NAME><VALUE>????</VALUE></SETTING>
+ <SETTING><NAME>MWMacOSPackager_PkgFileType</NAME><VALUE>APPL</VALUE></SETTING>
+
+ <!-- Settings for "PPC CodeGen" panel -->
+ <SETTING><NAME>MWCodeGen_PPC_structalignment</NAME><VALUE>PPC_mw</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_tracebacktables</NAME><VALUE>None</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_processor</NAME><VALUE>Generic</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_function_align</NAME><VALUE>4</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_tocdata</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_largetoc</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_profiler</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_vectortocdata</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_poolconst</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_peephole</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_readonlystrings</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_linkerpoolsstrings</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_volatileasm</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_schedule</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_altivec</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_altivec_move_block</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_strictIEEEfp</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_fpcontract</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_genfsel</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_PPC_orderedfpcmp</NAME><VALUE>0</VALUE></SETTING>
+
+ <!-- Settings for "PPC CodeGen Mach-O" panel -->
+ <SETTING><NAME>MWCodeGen_MachO_structalignment</NAME><VALUE>PPC_mw</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_profiler_enum</NAME><VALUE>Off</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_processor</NAME><VALUE>Generic</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_function_align</NAME><VALUE>4</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_common</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_peephole</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_readonlystrings</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_linkerpoolsstrings</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_volatileasm</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_schedule</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_altivec</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_vecmove</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_fp_ieee_strict</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_fpcontract</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_genfsel</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWCodeGen_MachO_fp_cmps_ordered</NAME><VALUE>0</VALUE></SETTING>
+
+ <!-- Settings for "PPC Disassembler" panel -->
+ <SETTING><NAME>MWDisassembler_PPC_showcode</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWDisassembler_PPC_extended</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWDisassembler_PPC_mix</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWDisassembler_PPC_nohex</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWDisassembler_PPC_showdata</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWDisassembler_PPC_showexceptions</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWDisassembler_PPC_showsym</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWDisassembler_PPC_shownames</NAME><VALUE>1</VALUE></SETTING>
+
+ <!-- Settings for "PPC Global Optimizer" panel -->
+ <SETTING><NAME>GlobalOptimizer_PPC_optimizationlevel</NAME><VALUE>Level4</VALUE></SETTING>
+ <SETTING><NAME>GlobalOptimizer_PPC_optfor</NAME><VALUE>Speed</VALUE></SETTING>
+
+ <!-- Settings for "PPC Linker" panel -->
+ <SETTING><NAME>MWLinker_PPC_linksym</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_symfullpath</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_linkmap</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_nolinkwarnings</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_dontdeadstripinitcode</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_permitmultdefs</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_linkmode</NAME><VALUE>Fast</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_initname</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_mainname</NAME><VALUE>__start</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_PPC_termname</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "PPC Mac OS X Linker" panel -->
+ <SETTING><NAME>MWLinker_MacOSX_linksym</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_symfullpath</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_nolinkwarnings</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_linkmap</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_dontdeadstripinitcode</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_permitmultdefs</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_use_objectivec_semantics</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_strip_debug_symbols</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_split_segs</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_report_msl_overloads</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_objects_follow_linkorder</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_linkmode</NAME><VALUE>Fast</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_exports</NAME><VALUE>ReferencedGlobals</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_sortcode</NAME><VALUE>None</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MacOSX_mainname</NAME><VALUE>start</VALUE></SETTING>
+
+ <!-- Settings for "PPC Mac OS X Project" panel -->
+ <SETTING><NAME>MWProject_MacOSX_type</NAME><VALUE>Executable</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_outfile</NAME><VALUE>LAMARCTARGETNAME</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_filecreator</NAME><VALUE>????</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_filetype</NAME><VALUE>APPL</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_vmaddress</NAME><VALUE>4096</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_usedefaultvmaddr</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_flatrsrc</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_flatrsrcfilename</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_flatrsrcoutputdir</NAME>
+ <SETTING><NAME>Path</NAME><VALUE>:</VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>MacOS</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Project</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>MWProject_MacOSX_installpath</NAME><VALUE>./</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_dont_prebind</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_flat_namespace</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_frameworkversion</NAME><VALUE>A</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_currentversion</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MacOSX_flat_oldimpversion</NAME><VALUE>0</VALUE></SETTING>
+
+ <!-- Settings for "PPC Mach-O Linker" panel -->
+ <SETTING><NAME>MWLinker_MachO_exports</NAME><VALUE>None</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_mainname</NAME><VALUE>start</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_currentversion</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_compatibleversion</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_symfullpath</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_supresswarnings</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_multisymerror</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_prebind</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_deadstrip</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_objectivecsemantics</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_whichfileloaded</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_whyfileloaded</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_readonlyrelocs</NAME><VALUE>Errors</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_undefinedsymbols</NAME><VALUE>Errors</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_twolevelnamespace</NAME><VALUE>1</VALUE></SETTING>
+ <SETTING><NAME>MWLinker_MachO_stripdebugsymbols</NAME><VALUE>0</VALUE></SETTING>
+
+ <!-- Settings for "PPC Mach-O Target" panel -->
+ <SETTING><NAME>MWProject_MachO_type</NAME><VALUE>Bundle</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MachO_outfile</NAME><VALUE>a.out</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MachO_filecreator</NAME><VALUE>????</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MachO_filetype</NAME><VALUE>MBND</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MachO_vmaddress</NAME><VALUE>4096</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MachO_flatrsrc</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MachO_flatrsrcfilename</NAME><VALUE>a.rsrc</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MachO_flatrsrcoutputdir</NAME>
+ <SETTING><NAME>Path</NAME><VALUE>:</VALUE></SETTING>
+ <SETTING><NAME>PathFormat</NAME><VALUE>MacOS</VALUE></SETTING>
+ <SETTING><NAME>PathRoot</NAME><VALUE>Project</VALUE></SETTING>
+ </SETTING>
+ <SETTING><NAME>MWProject_MachO_installpath</NAME><VALUE>./</VALUE></SETTING>
+ <SETTING><NAME>MWProject_MachO_frameworkversion</NAME><VALUE></VALUE></SETTING>
+
+ <!-- Settings for "PPC PEF" panel -->
+ <SETTING><NAME>MWPEF_exports</NAME><VALUE>None</VALUE></SETTING>
+ <SETTING><NAME>MWPEF_libfolder</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWPEF_sortcode</NAME><VALUE>None</VALUE></SETTING>
+ <SETTING><NAME>MWPEF_expandbss</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWPEF_sharedata</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWPEF_olddefversion</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWPEF_oldimpversion</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWPEF_currentversion</NAME><VALUE>0</VALUE></SETTING>
+ <SETTING><NAME>MWPEF_fragmentname</NAME><VALUE></VALUE></SETTING>
+ <SETTING><NAME>MWPEF_collapsereloads</NAME><VALUE>1</VALUE></SETTING>
+
+ <!-- Settings for "PPC Project" panel -->
+ <SETTING><NAME>MWProject_PPC_type</NAME><VALUE>Application</VALUE></SETTING>
+ <SETTING><NAME>MWProject_PPC_outfile</NAME><VALUE>lamarc</VALUE></SETTING>
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diff --git a/projects/win32/README b/projects/win32/README
new file mode 100644
index 0000000..a2ff74f
--- /dev/null
+++ b/projects/win32/README
@@ -0,0 +1,2 @@
+Compiling on VC++ requires us to set the heap size
+ infile.snowgoose fails in final chain at 164759 when heap is size 20 Meg
diff --git a/projects/win32/gui_lam_conv.vcproj b/projects/win32/gui_lam_conv.vcproj
new file mode 100644
index 0000000..5fca296
--- /dev/null
+++ b/projects/win32/gui_lam_conv.vcproj
@@ -0,0 +1,324 @@
+<?xml version="1.0" encoding = "Windows-1252"?>
+<VisualStudioProject
+ ProjectType="Visual C++"
+ Version="7.00"
+ Name="gui_lam_conv"
+ Keyword="Win32Proj">
+ <Platforms>
+ <Platform
+ Name="Win32"/>
+ </Platforms>
+ <Configurations>
+ <Configuration
+ Name="Release|Win32"
+ OutputDirectory="Release"
+ IntermediateDirectory="Release"
+ ConfigurationType="1"
+ CharacterSet="2">
+ <Tool
+ Name="VCCLCompilerTool"
+ Optimization="2"
+ InlineFunctionExpansion="1"
+ OmitFramePointers="TRUE"
+ AdditionalIncludeDirectories=""$(ProjectDir)\..\..\.\config";"$(ProjectDir)\..\..\src\bayeslike";"$(ProjectDir)\..\..\src\control";"$(ProjectDir)\..\..\src\conversion";"$(ProjectDir)\..\..\src\convErr";"$(ProjectDir)\..\..\src\convModel";"$(ProjectDir)\..\..\src\convParse";"$(ProjectDir)\..\..\src\convStrings";"$(ProjectDir)\..\..\src\convUtil";"$(ProjectDir)\..\..\src\datalike";" [...]
+ PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE;WINDOWS_COMPILE;TIXML_USE_STL"
+ StringPooling="TRUE"
+ RuntimeLibrary="4"
+ EnableFunctionLevelLinking="TRUE"
+ RuntimeTypeInfo="TRUE"
+ UsePrecompiledHeader="0"
+ WarningLevel="0"
+ Detect64BitPortabilityProblems="TRUE"
+ DebugInformationFormat="3"/>
+ <Tool
+ Name="VCCustomBuildTool"/>
+ <Tool
+ Name="VCLinkerTool"
+ OutputFile="$(ProjectDir)\..\..\\gui_lam_conv.exe"
+ LinkIncremental="0"
+ GenerateDebugInformation="TRUE"
+ SubSystem="1"
+ HeapReserveSize="100000000"
+ OptimizeReferences="2"
+ EnableCOMDATFolding="2"
+ TargetMachine="1"/>
+ <Tool
+ Name="VCMIDLTool"/>
+ <Tool
+ Name="VCPostBuildEventTool"/>
+ <Tool
+ Name="VCPreBuildEventTool"/>
+ <Tool
+ Name="VCPreLinkEventTool"/>
+ <Tool
+ Name="VCResourceCompilerTool"/>
+ <Tool
+ Name="VCWebServiceProxyGeneratorTool"/>
+ <Tool
+ Name="VCWebDeploymentTool"/>
+ </Configuration>
+ <Configuration
+ Name="Debug|Win32"
+ OutputDirectory="Debug"
+ IntermediateDirectory="Debug"
+ ConfigurationType="1"
+ CharacterSet="2">
+ <Tool
+ Name="VCCLCompilerTool"
+ Optimization="0"
+ OptimizeForWindowsApplication="TRUE"
+ AdditionalIncludeDirectories=""$(ProjectDir)\..\..\.\config";"$(ProjectDir)\..\..\src\bayeslike";"$(ProjectDir)\..\..\src\control";"$(ProjectDir)\..\..\src\conversion";"$(ProjectDir)\..\..\src\convErr";"$(ProjectDir)\..\..\src\convModel";"$(ProjectDir)\..\..\src\convParse";"$(ProjectDir)\..\..\src\convStrings";"$(ProjectDir)\..\..\src\convUtil";"$(ProjectDir)\..\..\src\datalike";" [...]
+ PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE;WINDOWS_COMPILE;TIXML_USE_STL"
+ MinimalRebuild="TRUE"
+ BasicRuntimeChecks="3"
+ RuntimeLibrary="5"
+ RuntimeTypeInfo="TRUE"
+ UsePrecompiledHeader="0"
+ WarningLevel="0"
+ Detect64BitPortabilityProblems="TRUE"
+ DebugInformationFormat="4"/>
+ <Tool
+ Name="VCCustomBuildTool"/>
+ <Tool
+ Name="VCLinkerTool"
+ OutputFile="$(ProjectDir)\..\..\\gui_lam_conv.exe"
+ LinkIncremental="2"
+ GenerateDebugInformation="TRUE"
+ ProgramDatabaseFile="$(OutDir)/gui_lam_conv.pdb"
+ SubSystem="1"
+ HeapReserveSize="100000000"
+ TargetMachine="1"/>
+ <Tool
+ Name="VCMIDLTool"/>
+ <Tool
+ Name="VCPostBuildEventTool"/>
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+ Name="VCPreBuildEventTool"/>
+ <Tool
+ Name="VCPreLinkEventTool"/>
+ <Tool
+ Name="VCResourceCompilerTool"/>
+ <Tool
+ Name="VCWebServiceProxyGeneratorTool"/>
+ <Tool
+ Name="VCWebDeploymentTool"/>
+ </Configuration>
+ </Configurations>
+ <Files>
+ <Filter
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new file mode 100644
index 0000000..6f3521f
--- /dev/null
+++ b/projects/win32/lam_conv.vcproj
@@ -0,0 +1,183 @@
+<?xml version="1.0" encoding = "Windows-1252"?>
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new file mode 100644
index 0000000..6dd1837
--- /dev/null
+++ b/projects/win32/lamarc.vcproj
@@ -0,0 +1,433 @@
+<?xml version="1.0" encoding = "Windows-1252"?>
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+ PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE;WINDOWS_COMPILE;TIXML_USE_STL"
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+ PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE;WINDOWS_COMPILE;TIXML_USE_STL"
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+ <File RelativePath="..\..\src\lamarcmenus\treesummenus.cpp"/>
+ <File RelativePath="..\..\src\menu\dialog.cpp"/>
+ <File RelativePath="..\..\src\menu\dialognoinput.cpp"/>
+ <File RelativePath="..\..\src\menu\dialogrepeat.cpp"/>
+ <File RelativePath="..\..\src\menu\display.cpp"/>
+ <File RelativePath="..\..\src\menu\matrixitem.cpp"/>
+ <File RelativePath="..\..\src\menu\menu_strings.cpp"/>
+ <File RelativePath="..\..\src\menu\menuinteraction.cpp"/>
+ <File RelativePath="..\..\src\menu\menuitem.cpp"/>
+ <File RelativePath="..\..\src\menu\newmenu.cpp"/>
+ <File RelativePath="..\..\src\menu\newmenuitems.cpp"/>
+ <File RelativePath="..\..\src\menu\setmenuitem.cpp"/>
+ <File RelativePath="..\..\src\menu\togglemenuitem.cpp"/>
+ <File RelativePath="..\..\src\menu\twodtable.cpp"/>
+ <File RelativePath="..\..\src\postlike\analyzer.cpp"/>
+ <File RelativePath="..\..\src\postlike\derivatives.cpp"/>
+ <File RelativePath="..\..\src\postlike\likelihood.cpp"/>
+ <File RelativePath="..\..\src\postlike\maximizer.cpp"/>
+ <File RelativePath="..\..\src\postlike\maximizer_strings.cpp"/>
+ <File RelativePath="..\..\src\postlike\plforces.cpp"/>
+ <File RelativePath="..\..\src\postlike\plotstat.cpp"/>
+ <File RelativePath="..\..\src\postlike\profile.cpp"/>
+ <File RelativePath="..\..\src\report\outputfile.cpp"/>
+ <File RelativePath="..\..\src\report\reportpage.cpp"/>
+ <File RelativePath="..\..\src\report\runreport.cpp"/>
+ <File RelativePath="..\..\src\tools\mathx.cpp"/>
+ <File RelativePath="..\..\src\tools\random.cpp"/>
+ <File RelativePath="..\..\src\tools\rangex.cpp"/>
+ <File RelativePath="..\..\src\tools\stringx.cpp"/>
+ <File RelativePath="..\..\src\tools\timex.cpp"/>
+ <File RelativePath="..\..\src\tools\vector_constants.cpp"/>
+ <File RelativePath="..\..\src\tools\vectorx.cpp"/>
+ <File RelativePath="..\..\src\tree\arranger.cpp"/>
+ <File RelativePath="..\..\src\tree\arranger_types.cpp"/>
+ <File RelativePath="..\..\src\tree\arrangervec.cpp"/>
+ <File RelativePath="..\..\src\tree\branch.cpp"/>
+ <File RelativePath="..\..\src\tree\branchbuffer.cpp"/>
+ <File RelativePath="..\..\src\tree\branchtag.cpp"/>
+ <File RelativePath="..\..\src\tree\chain.cpp"/>
+ <File RelativePath="..\..\src\tree\chainstate.cpp"/>
+ <File RelativePath="..\..\src\tree\collector.cpp"/>
+ <File RelativePath="..\..\src\tree\collmanager.cpp"/>
+ <File RelativePath="..\..\src\tree\individual.cpp"/>
+ <File RelativePath="..\..\src\tree\intervaldata.cpp"/>
+ <File RelativePath="..\..\src\tree\newick.cpp"/>
+ <File RelativePath="..\..\src\tree\parameter.cpp"/>
+ <File RelativePath="..\..\src\tree\partition.cpp"/>
+ <File RelativePath="..\..\src\tree\prior.cpp"/>
+ <File RelativePath="..\..\src\tree\range.cpp"/>
+ <File RelativePath="..\..\src\tree\rectree.cpp"/>
+ <File RelativePath="..\..\src\tree\summary.cpp"/>
+ <File RelativePath="..\..\src\tree\tempident.cpp"/>
+ <File RelativePath="..\..\src\tree\timelist.cpp"/>
+ <File RelativePath="..\..\src\tree\tree.cpp"/>
+ <File RelativePath="..\..\src\tree\treesum.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\chainparam_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\constraint_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\data_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\datamodel_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\force_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\front_end_warnings.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\prior_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\profile_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\setgetmachine.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\traitmodel_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\ui_constants.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\ui_id.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\ui_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\ui_regid.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\ui_strings.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\ui_warnings.cpp"/>
+ <File RelativePath="..\..\src\ui_interface\userparam_interface.cpp"/>
+ <File RelativePath="..\..\src\ui_util\undoredochain.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\report_strings.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_chainparams.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_component.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_datamodel.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_datapackplus.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_forces.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_prior.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_traitmodels.cpp"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_userparams.cpp"/>
+ <File RelativePath="..\..\src\xml\lamarcschema.cpp"/>
+ <File RelativePath="..\..\src\xml\parsetreetodata.cpp"/>
+ <File RelativePath="..\..\src\xml\parsetreetosettings.cpp"/>
+ <File RelativePath="..\..\src\xml\parsetreewalker.cpp"/>
+ <File RelativePath="..\..\src\xml\toxml.cpp"/>
+ <File RelativePath="..\..\src\xml\parsetreeschema.cpp"/>
+ <File RelativePath="..\..\src\xml\xml.cpp"/>
+ <File RelativePath="..\..\src\xml\xml_strings.cpp"/>
+ <File RelativePath="..\..\tinyxml\tinyxml.cpp"/>
+ <File RelativePath="..\..\tinyxml\tinyxmlerror.cpp"/>
+ <File RelativePath="..\..\tinyxml\tinyxmlparser.cpp"/>
+ <File RelativePath="..\..\tinyxml\tinystr.cpp"/>
+ </Filter>
+ <Filter
+ Name="Header Files"
+ Filter="h;hpp;hxx;hm;inl;inc">
+ <File RelativePath="..\..\src\bayeslike\bayesanalyzer_1d.h"/>
+ <File RelativePath="..\..\src\bayeslike\bayescurve.h"/>
+ <File RelativePath="..\..\src\bayeslike\bayesparamlike_1d.h"/>
+ <File RelativePath="..\..\src\control\chainmanager.h"/>
+ <File RelativePath="..\..\src\control\chainout.h"/>
+ <File RelativePath="..\..\src\control\chainpack.h"/>
+ <File RelativePath="..\..\src\control\chainparam.h"/>
+ <File RelativePath="..\..\src\control\constants.h"/>
+ <File RelativePath="..\..\src\control\defaults.h"/>
+ <File RelativePath="..\..\src\control\definitions.h"/>
+ <File RelativePath="..\..\src\control\errhandling.h"/>
+ <File RelativePath="..\..\src\control\lamarc.h"/>
+ <File RelativePath="..\..\src\control\regiongammainfo.h"/>
+ <File RelativePath="..\..\src\control\registry.h"/>
+ <File RelativePath="..\..\src\control\sumfilehandler.h"/>
+ <File RelativePath="..\..\src\control\types.h"/>
+ <File RelativePath="..\..\src\control\userparam.h"/>
+ <File RelativePath="..\..\src\control\xmlsum_strings.h"/>
+ <File RelativePath="..\..\src\datalike\calculators.h"/>
+ <File RelativePath="..\..\src\datalike\datapack.h"/>
+ <File RelativePath="..\..\src\datalike\datatype.h"/>
+ <File RelativePath="..\..\src\datalike\dlcalc.h"/>
+ <File RelativePath="..\..\src\datalike\dlcell.h"/>
+ <File RelativePath="..\..\src\datalike\cellmanager.h"/>
+ <File RelativePath="..\..\src\datalike\dlmodel.h"/>
+ <File RelativePath="..\..\src\datalike\funcMax.h"/>
+ <File RelativePath="..\..\src\datalike\haplotypes.h"/>
+ <File RelativePath="..\..\src\datalike\locus.h"/>
+ <File RelativePath="..\..\src\datalike\locuscell.h"/>
+ <File RelativePath="..\..\src\datalike\phenotypes.h"/>
+ <File RelativePath="..\..\src\datalike\region.h"/>
+ <File RelativePath="..\..\src\datalike\tipdata.h"/>
+ <File RelativePath="..\..\src\force\event.h"/>
+ <File RelativePath="..\..\src\force\force.h"/>
+ <File RelativePath="..\..\src\force\forceparam.h"/>
+ <File RelativePath="..\..\src\force\forcesummary.h"/>
+ <File RelativePath="..\..\src\force\priorreport.h"/>
+ <File RelativePath="..\..\src\force\timesize.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\coalmenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\constraintmenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\datafilenamedialog.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\datamodelmenu.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\diseasemenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\forcesmenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\growthmenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\lamarc_strings.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\lamarcheaderdialog.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\lamarcmenu.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\lamarcmenuitems.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\logselectmenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\migmenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\nomenufilereaddialog.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\outfilemenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\overviewmenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\popsizemenu.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\priormenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\profilemenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\recmenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\regiongammamenus.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\traitmodelmenu.h"/>
+ <File RelativePath="..\..\src\lamarcmenus\treesummenus.h"/>
+ <File RelativePath="..\..\src\menu\dialog.h"/>
+ <File RelativePath="..\..\src\menu\dialognoinput.h"/>
+ <File RelativePath="..\..\src\menu\dialogrepeat.h"/>
+ <File RelativePath="..\..\src\menu\display.h"/>
+ <File RelativePath="..\..\src\menu\matrixitem.h"/>
+ <File RelativePath="..\..\src\menu\menu_strings.h"/>
+ <File RelativePath="..\..\src\menu\menudefs.h"/>
+ <File RelativePath="..\..\src\menu\menuerror.h"/>
+ <File RelativePath="..\..\src\menu\menuinteraction.h"/>
+ <File RelativePath="..\..\src\menu\menuitem.h"/>
+ <File RelativePath="..\..\src\menu\menutypedefs.h"/>
+ <File RelativePath="..\..\src\menu\newmenu.h"/>
+ <File RelativePath="..\..\src\menu\newmenuitems.h"/>
+ <File RelativePath="..\..\src\menu\setmenuitem.h"/>
+ <File RelativePath="..\..\src\menu\togglemenuitem.h"/>
+ <File RelativePath="..\..\src\menu\twodtable.h"/>
+ <File RelativePath="..\..\src\postlike\analyzer.h"/>
+ <File RelativePath="..\..\src\postlike\likelihood.h"/>
+ <File RelativePath="..\..\src\postlike\maximizer.h"/>
+ <File RelativePath="..\..\src\postlike\maximizer_strings.h"/>
+ <File RelativePath="..\..\src\postlike\plforces.h"/>
+ <File RelativePath="..\..\src\postlike\plotstat.h"/>
+ <File RelativePath="..\..\src\report\outputfile.h"/>
+ <File RelativePath="..\..\src\report\reportpage.h"/>
+ <File RelativePath="..\..\src\report\runreport.h"/>
+ <File RelativePath="..\..\src\tools\mathx.h"/>
+ <File RelativePath="..\..\src\tools\random.h"/>
+ <File RelativePath="..\..\src\tools\rangex.h"/>
+ <File RelativePath="..\..\src\tools\stringx.h"/>
+ <File RelativePath="..\..\src\tools\timex.h"/>
+ <File RelativePath="..\..\src\tools\tools.h"/>
+ <File RelativePath="..\..\src\tools\vector_constants.h"/>
+ <File RelativePath="..\..\src\tools\vectorx.h"/>
+ <File RelativePath="..\..\src\tree\arranger.h"/>
+ <File RelativePath="..\..\src\tree\arranger_types.h"/>
+ <File RelativePath="..\..\src\tree\arrangervec.h"/>
+ <File RelativePath="..\..\src\tree\branch.h"/>
+ <File RelativePath="..\..\src\tree\branchbuffer.h"/>
+ <File RelativePath="..\..\src\tree\branchtag.h"/>
+ <File RelativePath="..\..\src\tree\chain.h"/>
+ <File RelativePath="..\..\src\tree\chainstate.h"/>
+ <File RelativePath="..\..\src\tree\collector.h"/>
+ <File RelativePath="..\..\src\tree\collmanager.h"/>
+ <File RelativePath="..\..\src\tree\individual.h"/>
+ <File RelativePath="..\..\src\tree\intervaldata.h"/>
+ <File RelativePath="..\..\src\tree\newick.h"/>
+ <File RelativePath="..\..\src\tree\parameter.h"/>
+ <File RelativePath="..\..\src\tree\partition.h"/>
+ <File RelativePath="..\..\src\tree\prior.h"/>
+ <File RelativePath="..\..\src\tree\range.h"/>
+ <File RelativePath="..\..\src\tree\summary.h"/>
+ <File RelativePath="..\..\src\tree\tempident.h"/>
+ <File RelativePath="..\..\src\tree\timelist.h"/>
+ <File RelativePath="..\..\src\tree\tree.h"/>
+ <File RelativePath="..\..\src\tree\treesum.h"/>
+ <File RelativePath="..\..\src\ui_interface\chainparam_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\constraint_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\data_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\datamodel_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\force_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\front_end_warnings.h"/>
+ <File RelativePath="..\..\src\ui_interface\prior_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\profile_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\setget.h"/>
+ <File RelativePath="..\..\src\ui_interface\setgetmachine.h"/>
+ <File RelativePath="..\..\src\ui_interface\traitmodel_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\ui_constants.h"/>
+ <File RelativePath="..\..\src\ui_interface\ui_id.h"/>
+ <File RelativePath="..\..\src\ui_interface\ui_interface.h"/>
+ <File RelativePath="..\..\src\ui_interface\ui_regid.h"/>
+ <File RelativePath="..\..\src\ui_interface\ui_strings.h"/>
+ <File RelativePath="..\..\src\ui_interface\ui_warnings.h"/>
+ <File RelativePath="..\..\src\ui_interface\userparam_interface.h"/>
+ <File RelativePath="..\..\src\ui_util\undoredochain.h"/>
+ <File RelativePath="..\..\src\ui_vars\report_strings.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_chainparams.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_component.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_datamodel.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_datapackplus.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_forces.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_prior.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_traitmodels.h"/>
+ <File RelativePath="..\..\src\ui_vars\ui_vars_userparams.h"/>
+ <File RelativePath="..\..\src\xml\parsetreetodata.h"/>
+ <File RelativePath="..\..\src\xml\parsetreetosettings.h"/>
+ <File RelativePath="..\..\src\xml\parsetreewalker.h"/>
+ <File RelativePath="..\..\src\xml\toxml.h"/>
+ <File RelativePath="..\..\src\xml\parsetreeschema.h"/>
+ <File RelativePath="..\..\src\xml\xml.h"/>
+ <File RelativePath="..\..\src\xml\xml_strings.h"/>
+ <File RelativePath="..\..\tinyxml\tinyxml.h"/>
+ <File RelativePath="..\..\tinyxml\tinystr.h"/>
+ <File RelativePath="..\..\config\conf.h"/>
+ </Filter>
+ <Filter
+ Name="Resource Files"
+ Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+ <File RelativePath="..\..\resources\lamarc_rc.rc"/>
+ <File RelativePath="..\..\resources\lamarc.ico"/>
+ </Filter>
+ </Files>
+ <Globals>
+ </Globals>
+</VisualStudioProject>
diff --git a/projects/win32/make_vcproj.pl b/projects/win32/make_vcproj.pl
new file mode 100755
index 0000000..cab408b
--- /dev/null
+++ b/projects/win32/make_vcproj.pl
@@ -0,0 +1,174 @@
+#!/usr/bin/perl
+
+use File::Basename;
+
+## prints out one file name when within a list of sources
+sub printOneFileToHandle
+{
+ my($fileName) = @_;
+
+ ## printf "\t\t\t<File\r\n";
+ ## printf "\t\t\t\tRelativePath=\"$fromVcprojToTop$fileName\">\r\n";
+ ## printf "\t\t\t</File>\r\n";
+ printf "\t\t\t<File RelativePath=\"$fromVcprojToTop$fileName\"/>\r\n";
+}
+
+## constant strings, not expected to change
+$templateFile = dirname($0)."/vcproj_template";
+$fromVcprojToTop = "..\\..\\";
+$fromVcprojToInclude = "..\\";
+
+$matchesHeaderFiles = "\\\.h\$";
+$matchesSourceFiles = "\\\.cpp\$";
+$matchesResourceFiles = "\\\.rc\$|\\\.ico\$";
+
+$heapSize = "100000000";
+$execPath = "\$(ProjectDir)\\$fromVcprojToTop";
+
+$originalProjectName = "PROJECTNAME";
+$originalHeapSize = "HEAPSIZE";
+$originalExecName = "EXECNAME";
+
+
+## gonna slurp a bunch of file names into these
+ at headers = ();
+ at sources = ();
+ at resources = ();
+ at includeDirs = ();
+
+########################################################
+## first argument is the project name, it could be lamarc
+## or lam_conv, for example
+$projectName = shift;
+
+########################################################
+## divide up remaining arguments into files and include
+## path items
+$nextIsInclude = ""; ## true when we just saw -I
+foreach $item (@ARGV)
+{
+ $item =~ s/\//\\/g;
+
+ if($nextIsInclude)
+ {
+ push @includeDirs, $item ;
+ $nextIsInclude = "";
+ }
+ elsif ($item =~ /$matchesHeaderFiles/)
+ {
+ push @headers, $item ;
+ }
+ elsif ($item =~ /$matchesSourceFiles/)
+ {
+ push @sources, $item ;
+ }
+ elsif ($item =~ /$matchesResourceFiles/)
+ {
+ push @resources, $item ;
+ }
+ elsif ($item =~ /^-I$/)
+ {
+ $nextIsInclude = "yes";
+ }
+}
+
+open(TEMPLATEFILE,$templateFile); ## modify content of this file
+
+$inFiles = $inFilter = $filterType = "";
+while(<TEMPLATEFILE>)
+{
+ ## #################################################
+ ## replacing project name, etc
+ ## #################################################
+ $_ =~ s/$originalProjectName/$projectName/g;
+ $_ =~ s/$originalHeapSize/$heapSize/g;
+ $_ =~ s/$originalExecName/$execPath\\$projectName\.exe/g;
+
+ ## #################################################
+ ## in this section, setting state but not outputting
+ ## #################################################
+ if($_ =~ /<Files>/)
+ {
+ $inFiles = "yes";
+ }
+ if ($_ =~ /<\/Files>/)
+ {
+ $inFiles = "";
+ }
+ if($_ =~ /<Filter/)
+ {
+ $inFilter = "yes";
+ }
+ if ($_ =~ /<\/Filter>/)
+ {
+ $inFilter = "";
+ }
+ if($_ =~ /Name=\"Header Files\"/)
+ {
+ $filterType = "h";
+ }
+ if($_ =~ /Name=\"Source Files\"/)
+ {
+ $filterType = "cpp";
+ }
+ if($_ =~ /Name=\"Resource Files\"/)
+ {
+ $filterType = "rc";
+ }
+
+
+ ## #################################################
+ ## in this section, producing output
+ ## #################################################
+ if($_ =~ /AdditionalIncludeDirectories/)
+ {
+ printf "\t\t\t\tAdditionalIncludeDirectories=\"";
+ foreach $item (@includeDirs)
+ {
+ if ($item =~ /\\config$/) {
+ printf ""\$(ProjectDir)\\$fromVcprojToTop$item";";
+ } else {
+ printf ""\$(ProjectDir)\\$fromVcprojToInclude$item";";
+ }
+ }
+ printf "\"\r\n";
+ }
+ elsif($_ =~ /<File\/>/)
+ {
+ ## dump out file names based on fiter type
+ if($inFiles && $inFilter)
+ {
+ if($filterType eq "h")
+ {
+ foreach $item (@headers)
+ {
+ printOneFileToHandle($item);
+ }
+ }
+ if($filterType eq "cpp")
+ {
+ foreach $item (@sources)
+ {
+ printOneFileToHandle($item);
+ }
+ }
+ if($filterType eq "rc")
+ {
+ foreach $item (@resources)
+ {
+ printOneFileToHandle($item);
+ }
+ }
+ }
+ else
+ {
+ }
+ }
+ else
+ {
+ printf $_;
+ }
+}
+close(TEMPLATEFILE);
+
+
diff --git a/projects/win32/vcproj_template b/projects/win32/vcproj_template
new file mode 100644
index 0000000..c48771a
--- /dev/null
+++ b/projects/win32/vcproj_template
@@ -0,0 +1,126 @@
+<?xml version="1.0" encoding = "Windows-1252"?>
+<VisualStudioProject
+ ProjectType="Visual C++"
+ Version="7.00"
+ Name="PROJECTNAME"
+ Keyword="Win32Proj">
+ <Platforms>
+ <Platform
+ Name="Win32"/>
+ </Platforms>
+ <Configurations>
+ <Configuration
+ Name="Release|Win32"
+ OutputDirectory="Release"
+ IntermediateDirectory="Release"
+ ConfigurationType="1"
+ CharacterSet="2">
+ <Tool
+ Name="VCCLCompilerTool"
+ Optimization="2"
+ InlineFunctionExpansion="1"
+ OmitFramePointers="TRUE"
+ AdditionalIncludeDirectories=""
+ PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE;WINDOWS_COMPILE;TIXML_USE_STL"
+ StringPooling="TRUE"
+ RuntimeLibrary="4"
+ EnableFunctionLevelLinking="TRUE"
+ RuntimeTypeInfo="TRUE"
+ UsePrecompiledHeader="0"
+ WarningLevel="0"
+ Detect64BitPortabilityProblems="TRUE"
+ DebugInformationFormat="3"/>
+ <Tool
+ Name="VCCustomBuildTool"/>
+ <Tool
+ Name="VCLinkerTool"
+ OutputFile="EXECNAME"
+ LinkIncremental="0"
+ GenerateDebugInformation="TRUE"
+ SubSystem="1"
+ HeapReserveSize="HEAPSIZE"
+ OptimizeReferences="2"
+ EnableCOMDATFolding="2"
+ TargetMachine="1"/>
+ <Tool
+ Name="VCMIDLTool"/>
+ <Tool
+ Name="VCPostBuildEventTool"/>
+ <Tool
+ Name="VCPreBuildEventTool"/>
+ <Tool
+ Name="VCPreLinkEventTool"/>
+ <Tool
+ Name="VCResourceCompilerTool"/>
+ <Tool
+ Name="VCWebServiceProxyGeneratorTool"/>
+ <Tool
+ Name="VCWebDeploymentTool"/>
+ </Configuration>
+ <Configuration
+ Name="Debug|Win32"
+ OutputDirectory="Debug"
+ IntermediateDirectory="Debug"
+ ConfigurationType="1"
+ CharacterSet="2">
+ <Tool
+ Name="VCCLCompilerTool"
+ Optimization="0"
+ OptimizeForWindowsApplication="TRUE"
+ AdditionalIncludeDirectories=""
+ PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE;WINDOWS_COMPILE;TIXML_USE_STL"
+ MinimalRebuild="TRUE"
+ BasicRuntimeChecks="3"
+ RuntimeLibrary="5"
+ RuntimeTypeInfo="TRUE"
+ UsePrecompiledHeader="0"
+ WarningLevel="0"
+ Detect64BitPortabilityProblems="TRUE"
+ DebugInformationFormat="4"/>
+ <Tool
+ Name="VCCustomBuildTool"/>
+ <Tool
+ Name="VCLinkerTool"
+ OutputFile="EXECNAME"
+ LinkIncremental="2"
+ GenerateDebugInformation="TRUE"
+ ProgramDatabaseFile="$(OutDir)/PROJECTNAME.pdb"
+ SubSystem="1"
+ HeapReserveSize="HEAPSIZE"
+ TargetMachine="1"/>
+ <Tool
+ Name="VCMIDLTool"/>
+ <Tool
+ Name="VCPostBuildEventTool"/>
+ <Tool
+ Name="VCPreBuildEventTool"/>
+ <Tool
+ Name="VCPreLinkEventTool"/>
+ <Tool
+ Name="VCResourceCompilerTool"/>
+ <Tool
+ Name="VCWebServiceProxyGeneratorTool"/>
+ <Tool
+ Name="VCWebDeploymentTool"/>
+ </Configuration>
+ </Configurations>
+ <Files>
+ <Filter
+ Name="Source Files"
+ Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm">
+ <File/>
+ </Filter>
+ <Filter
+ Name="Header Files"
+ Filter="h;hpp;hxx;hm;inl;inc">
+ <File/>
+ </Filter>
+ <Filter
+ Name="Resource Files"
+ Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+ <File/>
+ </Filter>
+ </Files>
+ <Globals>
+ </Globals>
+</VisualStudioProject>
diff --git a/scripts/buildDmg.sh b/scripts/buildDmg.sh
new file mode 100755
index 0000000..dadb045
--- /dev/null
+++ b/scripts/buildDmg.sh
@@ -0,0 +1,134 @@
+#!/bin/sh
+
+usage () {
+cat << buildDmgUsageInfo
+*****************************************************************
+USAGE: buildDmg <topdir> [<builddir>]
+
+ <topdir> full path to the directory to package
+ <builddir> directory to do the build in
+*****************************************************************
+buildDmgUsageInfo
+}
+
+doCommand () {
+ if [ -z "$1" ]
+ then
+ echo "INTERNAL ERROR: no arg to doCommand"
+ exit 2
+ else
+ echo "COMMAND: $1"
+ $1
+ fi
+}
+
+#
+localbuild="build"
+
+# find out where we've started
+invokedir=`pwd`
+
+###################################################################
+# required first argument -- full path to package directory
+packagetop=$1
+if test X$packagetop = "X" ; then
+ echo "ERROR: missing required first argument."
+ usage
+ exit 1
+fi
+if [ ! -e ${packagetop} ] ; then
+ echo "ERROR: couldn't find package directory "${packagetop}\""
+ usage
+ exit 1
+fi
+if [ ! -d ${packagetop} ] ; then
+ echo "ERROR: "${packagetop}\" not a directory"
+ usage
+ exit 1
+fi
+fullPathPackageTop=`(cd ${packagetop} 2> /dev/null && pwd ;)`
+
+###################################################################
+# optional second argument, place to build the .dmg
+# if not given, make in current directory and report
+#
+# $2 is where to do the build
+if test X$2 = "X" ; then
+ builddir=${invokedir}/${localbuild}
+else
+ builddir=$2
+fi
+if [ ! -e ${builddir} ] ; then
+ if ! mkdir ${builddir} 2> /dev/null
+ then
+ echo "ERROR: couldn't create ${builddir}"
+ usage
+ exit 2
+ fi
+fi
+if [ ! -d ${builddir} ] ; then
+ echo "ERROR: <builddir> \"$builddir\" missing or not a directory"
+ usage
+ exit 2
+fi
+fullPathBuildDir=`(cd ${builddir} 2> /dev/null && pwd ;)`
+
+###################################################################
+# Now we have full path names ${fullPathPackageTop} and
+# ${fullPathBuildDir}
+#
+# We have to extract the last part of ${fullPathPackageTop} to
+# get the current package name
+packageName=`basename ${fullPathPackageTop}`
+imageName=${packageName}-osx
+volumeName=${packageName}-vol
+
+## debugging stuff
+echo "full path to package : ${fullPathPackageTop}"
+echo "full path to build : ${fullPathBuildDir}"
+echo "package name : ${packageName}"
+echo "image name : ${imageName}"
+echo "volume name : ${volumeName}"
+
+## ewfix -- get real value
+imageSize=45
+
+###################################################################
+# ready to rumble!
+
+cd ${fullPathBuildDir}
+
+# remove old dmg if it exists
+rm -f ${imageName}.dmg
+
+# make the blank image
+hdiutil create ${imageName}.dmg -size ${imageSize}m -fs HFS+ -volname ${volumeName}
+
+# mount the image and store the device name into dev_handle
+hfsLoc=`hdid ${imageName}.dmg | grep Apple_HFS | perl -e '\$_=<>; /^\\/dev\\/(disk.)/; print \$1'`
+
+echo "HFS LOC:${hfsLoc}"
+
+# copy the software onto the disk
+# remove the trailing ${packageName} if you don't want a level
+# of indirection (in form of a folder) between the open volume
+# and the various executables and documents
+ditto -rsrcFork ${fullPathPackageTop} /Volumes/${volumeName}/${packageName}
+
+# unmount the volume
+hdiutil detach ${hfsLoc}
+
+# compress the image
+hdiutil convert ${imageName}.dmg -format UDZO -o ${imageName}.udzo.dmg
+
+# remove the uncompressed image
+rm -f ${imageName}.dmg
+
+# move the compressed image to take its place
+mv ${imageName}.udzo.dmg ${imageName}.dmg
+
+# flatten -- ensure resource forks (if any) aren't lost when we copy
+# this over to a linux system
+hdiutil flatten ${imageName}.dmg
+
+exit 0
diff --git a/scripts/pyParallel/README b/scripts/pyParallel/README
new file mode 100644
index 0000000..6d5ade8
--- /dev/null
+++ b/scripts/pyParallel/README
@@ -0,0 +1,19 @@
+This is pyParallel, a set of experimental Python scripts for automating "poor
+man's parallelization" in LAMARC.
+
+These scripts are minimally tested. If you run into trouble, please send email
+to lamarc at u.washington.edu and we will work with you to solve the problem.
+
+Begin by creating a LAMARC infile containing data for all your regions and with
+the replicates value set as high as you want.
+
+Put the infile in an empty directory, and run the first python script,
+divide_data.py from that directory. The script requires arguments, but
+just run it without them and it will tell you what it needs.
+
+After you successfully run divide_data.py, the progarm will tell you
+where to run several LAMARC instances and also tell you which Python
+script to run next.
+
+For help, refer first to the "Parallelizing LAMARC" page (parallel.html) in
+your copy of the LAMARC documentation
diff --git a/scripts/pyParallel/combine_regions.py b/scripts/pyParallel/combine_regions.py
new file mode 100644
index 0000000..a3f03ec
--- /dev/null
+++ b/scripts/pyParallel/combine_regions.py
@@ -0,0 +1,191 @@
+####################################################################
+# combine_regions.py
+# used to combine lamarc runs from regions (which may include
+# multiple replicates) into a single region file with insumfiles
+# for "poor man's parallelization"
+####################################################################
+
+# system imports
+import re
+import os.path
+import sys
+from xml.dom.minidom import parse, Document
+
+import parallelCommon
+
+
+file_reg_pattern = re.compile('reg(.*)')
+number_pattern = re.compile('\s*(\d+)\s+(\d+)\s+(\d+)')
+reg_rep_pattern = re.compile('\s*(\d+)\s+(\d+)')
+
+t_number_pattern = re.compile('(\s*<number>\s*)(\d+)(\s+\d+\s+\d+\s*</number>\s*)')
+t_reg_rep_pattern = re.compile('(\s*<reg_rep>\s*)(\d+)(\s+\d+\s*</reg_rep>\s*)')
+t_top_tag_pattern = re.compile('.*XML.summary.file.*')
+
+# each file assumes it is for the only region
+# and so has region numbers of zero. Here we
+# replace those zeroes in the <number> and <reg_rep> tags
+def replaceRegionNumbers(myElem,regNum):
+ if regNum < 0:
+ print "Bad region number, %s, to replaceRegionNumbers\n" , regNum
+ exit(2)
+
+ for numberTag in myElem.getElementsByTagName("number"):
+ for child in numberTag.childNodes:
+ if child.nodeType == child.TEXT_NODE:
+ m = number_pattern.match(child.data)
+ if m:
+ child.data = " %s %s %s " % (regNum,m.group(2),m.group(3))
+
+ for regRepTag in myElem.getElementsByTagName("reg_rep"):
+ for child in regRepTag.childNodes:
+ if child.nodeType == child.TEXT_NODE:
+ m = reg_rep_pattern.match(child.data)
+ if m:
+ child.data = " %s %s " % (regNum,m.group(2))
+
+# combine outsumfiles for single regions into a single insumfile.
+#
+# lamdir == top level directory containing subdirectories for runs
+# rundir == where to write the sumfile
+# regionList == list of strings like "reg0" and "reg1"
+def combineSumfilesRegion(lamdir,rundir,regionList):
+
+ parallelCommon.sumfileCombineWarn(rundir)
+
+ # write output file
+ sumfile = os.path.join(rundir,'insumfile_final.xml')
+ outf = open(sumfile,'w')
+ outf.write("<XML-summary-file>\n")
+
+ for suffix in regionList:
+ # get reg and rep number form suffix
+ m = file_reg_pattern.match(suffix)
+ regNum = ""
+ if m:
+ regNum = m.group(1)
+
+ # find file and parse it in
+ sumdir = os.path.join(lamdir,'reg%s' % regNum)
+ oneRep = os.path.join(sumdir,'outsumfile_%s.xml' % suffix)
+ print "processing %s" % oneRep
+ sys.stdout.flush()
+
+
+ # append to existing file, changing region numbers as necessary
+ for line in open(oneRep):
+
+ # throw away outermost tags
+ m = t_top_tag_pattern.match(line)
+ if m:
+ continue
+
+ # replace region number in <number> tag and continue
+ m = t_number_pattern.match(line)
+ if m:
+ outf.write("%s%s%s\n" % (m.group(1),regNum,m.group(3)))
+ continue
+
+ # replace region number in <reg_rep> tag and continue
+ m = t_reg_rep_pattern.match(line)
+ if m:
+ outf.write("%s%s%s\n" % (m.group(1),regNum,m.group(3)))
+ continue
+
+ # not a special case
+ outf.write("%s\n" % line)
+
+
+ outf.write("</XML-summary-file>\n")
+ outf.close()
+
+def combineSumfilesRegion__OLD(lamdir,rundir,regionList):
+
+ parallelCommon.sumfileCombineWarn(rundir)
+
+ # create output dom
+ sumDoc = Document()
+ topElem = sumDoc.createElement("XML-summary-file")
+ sumDoc.appendChild(topElem)
+
+
+ for suffix in regionList:
+ # get reg and rep number form suffix
+ m = file_reg_pattern.match(suffix)
+ regNum = ""
+ if m:
+ regNum = m.group(1)
+
+ # find file and parse it in
+ sumdir = os.path.join(lamdir,'reg%s' % regNum)
+ oneRep = os.path.join(sumdir,'outsumfile_%s.xml' % suffix)
+ inf = open(oneRep,'r')
+ oneDom = parse(inf)
+ inf.close()
+ localTop = parallelCommon.getFirstTag(oneDom,"XML-summary-file")
+
+ # add to output xml structure
+ childNodeList = localTop.childNodes
+ for myNode in childNodeList:
+ myNewNode = sumDoc.importNode(myNode,True)
+ topElem.appendChild(myNewNode)
+ if myNewNode.nodeType == myNewNode.ELEMENT_NODE:
+ replaceRegionNumbers(myNewNode,regNum)
+
+
+ # write output file
+ sumfile = os.path.join(rundir,'insumfile_final.xml')
+ outf = open(sumfile,'w')
+ sumDoc.writexml(outf)
+ outf.close()
+ parallelCommon.stripXmlInfo(sumfile)
+
+# input options
+[lamarcfile,lamdir,pydir] = parallelCommon.getOptionsAndVerify(False)
+parallelCommon.describeThisScript("combine_regions","combine all regions and replicates",lamarcfile,lamdir)
+
+inlamarc = open(lamarcfile,'r')
+lamDom = parse(inlamarc)
+inlamarc.close()
+
+# add comment to identify outfile as generated by this script
+lamarcTag = parallelCommon.getFirstTag(lamDom,"lamarc")
+commentNode = lamDom.createComment("Created by combine_regions.py")
+lamarcTag.insertBefore(commentNode,lamarcTag.firstChild)
+
+
+# EWFIX.REMOVE
+# find replicate number -- do not change it
+#chainsTag = parallelCommon.getFirstTag(lamarcTag,"chains")
+#replicatesTag = parallelCommon.getFirstTag(chainsTag,"replicates")
+#originalReplicateCount = 1
+#if replicatesTag:
+# originalReplicateCount = parallelCommon.getLongVal(replicatesTag)
+
+# find format tag
+formatTag = parallelCommon.getFirstTag(lamarcTag,"format")
+
+# divide up regions
+dataElem = parallelCommon.getSingleTag(lamarcTag,"data")
+regionElems = dataElem.getElementsByTagName("region")
+
+infileList = []
+
+# output each region file
+regionList = []
+for regCount in range(regionElems.length):
+ idString = 'reg%d' % regCount
+ regionList.append(idString)
+
+parallelCommon.fixFormatTag(lamDom,formatTag,"final",True)
+rundir = os.path.join(lamdir,'final')
+os.makedirs(rundir)
+regFile = os.path.join(rundir,'infile_final.xml')
+outf = open(regFile,'w')
+lamDom.writexml(outf)
+outf.close()
+
+combineSumfilesRegion(lamdir,rundir,regionList)
+
+# output instructions: files to run, next program to run
+parallelCommon.nextStep(lamdir,[regFile],True)
diff --git a/scripts/pyParallel/combine_replicates.py b/scripts/pyParallel/combine_replicates.py
new file mode 100644
index 0000000..cdbb5d7
--- /dev/null
+++ b/scripts/pyParallel/combine_replicates.py
@@ -0,0 +1,164 @@
+####################################################################
+# combine_replicates.py
+# used to combine lamarc runs from multiple replicates into a
+# single region file with insumfiles for "poor man's parallelization"
+####################################################################
+
+# system imports
+import getopt
+import random
+import re
+import sys
+import os.path
+from xml.dom.minidom import parse, Document
+
+import parallelCommon
+
+
+file_reg_rep_pattern = re.compile('reg(.*)_rep(.*)')
+number_pattern = re.compile('\s*(\d+)\s+(\d+)\s+(\d+)')
+reg_rep_pattern = re.compile('\s*(\d+)\s+(\d+)')
+
+# each file assumes it is for the only region and only replicate
+# and so has region and replicate numbers of zero. Here we
+# replace those zeroes in the <number> and <reg_rep> tags
+def replaceReplicateNumbers(myElem,repNum):
+ if repNum < 0:
+ print "bad replicate number, %s , to replaceReplicateNumbers\n" , repNum
+ exit(2)
+
+ for numberTag in myElem.getElementsByTagName("number"):
+ for child in numberTag.childNodes:
+ if child.nodeType == child.TEXT_NODE:
+ m = number_pattern.match(child.data)
+ if m:
+ child.data = " %s %s %s " % (m.group(1),repNum,m.group(3))
+
+ for regRepTag in myElem.getElementsByTagName("reg_rep"):
+ for child in regRepTag.childNodes:
+ if child.nodeType == child.TEXT_NODE:
+ m = reg_rep_pattern.match(child.data)
+ if m:
+ child.data = " %s %s " % (m.group(1),repNum)
+
+# combine outsumfiles for multiple replicates over a single region
+# into a single insumfile.
+# argument "regString" will usually be something like "reg2", but
+# can be "final" for a multiple replicate run over a single region
+def combineSumfiles(lamdir,regString,regRepList):
+
+ parallelCommon.sumfileCombineWarn(regString)
+
+ # create output dom
+ sumDoc = Document()
+ topElem = sumDoc.createElement("XML-summary-file")
+ sumDoc.appendChild(topElem)
+
+ for suffix in regRepList:
+ # get reg and rep number form suffix
+ m = file_reg_rep_pattern.match(suffix)
+ regNum = ""
+ repNum = ""
+ if m:
+ regNum = m.group(1)
+ repNum = m.group(2)
+
+ # find file and parse it in
+ outsumdir = os.path.join(lamdir,'%s' % suffix)
+ oneRep = os.path.join(outsumdir,'outsumfile_%s.xml' % suffix)
+ inf = open(oneRep,'r')
+ oneDom = parse(inf)
+ inf.close()
+ localTop = parallelCommon.getFirstTag(oneDom,"XML-summary-file")
+
+ # add to output xml structure
+ childNodeList = localTop.childNodes
+ for myNode in childNodeList:
+ myNewNode = sumDoc.importNode(myNode,True)
+ topElem.appendChild(myNewNode)
+ if myNewNode.nodeType == myNewNode.ELEMENT_NODE:
+ replaceReplicateNumbers(myNewNode,repNum)
+
+
+ # write output file
+ insumdir = os.path.join(lamdir,'%s' % regString)
+ sumfile = os.path.join(insumdir,'insumfile_%s.xml' % regString)
+ outf = open(sumfile,'w')
+ sumDoc.writexml(outf)
+ outf.close()
+ parallelCommon.stripXmlInfo(sumfile)
+
+
+# input options
+[lamarcfile,lamdir,pydir] = parallelCommon.getOptionsAndVerify(False)
+parallelCommon.describeThisScript("combine_replicates.py","combine replicate runs for each region",lamarcfile,lamdir)
+
+inlamarc = open(lamarcfile,'r')
+lamDom = parse(inlamarc)
+inlamarc.close()
+
+# add comment to identify outfile as generated by this script
+lamarcTag = parallelCommon.getFirstTag(lamDom,"lamarc")
+commentNode = lamDom.createComment("Created by combine_replicates.py")
+lamarcTag.insertBefore(commentNode,lamarcTag.firstChild)
+
+# divide up regions
+dataElem = parallelCommon.getSingleTag(lamarcTag,"data")
+regionElems = dataElem.getElementsByTagName("region")
+singleRegion = len(regionElems) == 1
+
+# turn off profiling -- we only do it at the end
+if not singleRegion:
+ parallelCommon.turnProfilesOff(lamDom,lamarcTag)
+
+# find replicate number -- do not change it
+chainsTag = parallelCommon.getFirstTag(lamarcTag,"chains")
+replicatesTag = parallelCommon.getFirstTag(chainsTag,"replicates")
+originalReplicateCount = 1
+if replicatesTag:
+ originalReplicateCount = parallelCommon.getLongVal(replicatesTag)
+
+# find format tag
+formatTag = parallelCommon.getFirstTag(lamarcTag,"format")
+
+# disconnect regions from dom
+for region in regionElems:
+ dataElem.removeChild(region)
+
+infileList = []
+
+# output each region file
+regCount = 0
+for region in regionElems:
+ dataElem.appendChild(region)
+ repList = []
+ for repCount in range(originalReplicateCount):
+ idString = 'reg%d_rep%d' % (regCount,repCount)
+ repList.append(idString)
+
+ regString = 'reg%d' % regCount
+ if singleRegion:
+ regString = "final"
+
+ parallelCommon.fixFormatTag(lamDom,formatTag,regString,True)
+
+ runDir = os.path.join(lamdir,'%s' % regString)
+ if not os.path.exists(runDir):
+ os.makedirs(runDir)
+ regFile = os.path.join(runDir,'infile_%s.xml' % regString)
+ outf = open(regFile,'w')
+ lamDom.writexml(outf)
+ outf.close()
+ infileList.append(regFile)
+
+ combineSumfiles(lamdir,regString,repList)
+
+ dataElem.removeChild(region)
+ regCount = regCount + 1
+ # unlink region
+
+
+# output instructions: files to run, next program to run
+parallelCommon.nextStep(lamdir,infileList,singleRegion)
+if not singleRegion:
+ parallelCommon.finalStep(pydir,"combine_regions.py",lamarcfile,lamdir)
diff --git a/scripts/pyParallel/divide_data.py b/scripts/pyParallel/divide_data.py
new file mode 100644
index 0000000..c8b1f69
--- /dev/null
+++ b/scripts/pyParallel/divide_data.py
@@ -0,0 +1,108 @@
+####################################################################
+# divide_data.py
+# used to do first break-apart of lamarc data into pieces for
+# "poor man's parallelization"
+####################################################################
+# system imports
+import os.path
+import sys
+from xml.dom.minidom import parse, Document
+
+# imports
+import parallelCommon
+
+
+# input options
+[lamarcfile,lamdir,pydir] = parallelCommon.getOptionsAndVerify(True)
+
+parallelCommon.describeThisScript("divide_data.py","divide regions and replicates",lamarcfile,lamdir)
+
+inlamarc = open(lamarcfile,'r')
+lamDom = parse(inlamarc)
+inlamarc.close()
+
+# find replicate count.
+lamarcTag = parallelCommon.getFirstTag(lamDom,"lamarc")
+chainsTag = parallelCommon.getFirstTag(lamarcTag,"chains")
+replicatesTag = parallelCommon.getFirstTag(chainsTag,"replicates")
+originalReplicateCount = 1
+if replicatesTag:
+ originalReplicateCount = parallelCommon.getLongVal(replicatesTag)
+
+# find region count
+dataElem = parallelCommon.getSingleTag(lamarcTag,"data")
+regionElems = dataElem.getElementsByTagName("region")
+regionCount = len(regionElems)
+
+# bail if regions and replicates are both singletons
+if ( regionCount == 1) and (originalReplicateCount == 1):
+ print "ERROR: lamarc input file %s has only one region" % lamarcfile
+ print " and only one replicate. It cannot be broken down any further"
+ sys.exit(2)
+
+
+# add comment to identify outfile as generated by this script
+commentNode = lamDom.createComment("Created by divide_data.py")
+lamarcTag.insertBefore(commentNode,lamarcTag.firstChild)
+
+# write out full copy using writexml. we do this so we can compare
+# the original input file content in the same formatting we're using
+# to generate the sub-files
+lamcopy = os.path.join(lamdir,"infile_copy.xml")
+outf = open(lamcopy,'w')
+lamDom.writexml(outf)
+outf.close()
+
+# don't do profiles until very last run
+parallelCommon.turnProfilesOff(lamDom,lamarcTag)
+
+
+# change replicate number to 1 if it exists
+if replicatesTag:
+ parallelCommon.setVal(replicatesTag,"1")
+
+# find format tag
+formatTag = parallelCommon.getFirstTag(lamarcTag,"format")
+
+# disconnect regions from dom -- we'll be putting them back
+# in later one at a time
+for region in regionElems:
+ dataElem.removeChild(region)
+
+# will store names of single region/single replicate lamarc files
+infileList = []
+
+# output each region file
+regCount = 0
+for region in regionElems:
+ dataElem.appendChild(region)
+ for repCount in range(originalReplicateCount):
+ idString = 'reg%d_rep%d' % (regCount,repCount)
+ if (originalReplicateCount == 1):
+ idString = 'reg%d' % regCount
+
+ parallelCommon.fixFormatTag(lamDom,formatTag,idString,False)
+
+ runDir = os.path.join(lamdir,'%s' % idString)
+ if not os.path.exists(runDir):
+ os.makedirs(runDir)
+ regFile = os.path.join(runDir,'infile_%s.xml' % idString)
+ outf = open(regFile,'w')
+ lamDom.writexml(outf)
+ outf.close()
+ infileList.append(regFile)
+
+ # remove the region tag so next file output doesn't include it
+ dataElem.removeChild(region)
+
+ regCount = regCount + 1
+
+ # EWFIX -- unlink region to save memory ??
+
+
+# output instructions: files to run, next program to run
+parallelCommon.nextStep(lamdir,infileList,False)
+if(originalReplicateCount == 1):
+ parallelCommon.finalStep(pydir,"combine_regions.py",lamarcfile,lamdir)
+else:
+ parallelCommon.finalStep(pydir,"combine_replicates.py",lamarcfile,lamdir)
diff --git a/scripts/pyParallel/parallelCommon.py b/scripts/pyParallel/parallelCommon.py
new file mode 100644
index 0000000..b2af2d9
--- /dev/null
+++ b/scripts/pyParallel/parallelCommon.py
@@ -0,0 +1,239 @@
+####################################################################
+# parallelCommon.py
+# routines used by: divide_data.py
+# combine_replicates.py
+# combine_regions.py
+####################################################################
+# system imports
+import fileinput
+import getopt
+import random
+import re
+import sys
+import os.path
+from xml.dom.minidom import parse, Document
+
+seedlim = 1000000
+
+
+# share
+def usage():
+ print '''Usage:
+ --lamarcfile REQUIRED <path to lamarc infile to fragment>
+ --outdir REQUIRED <path to output directory>
+'''
+
+
+# share
+def getOptionsAndVerify(barfIfOutdirExists):
+ lamarcfile = None
+ outdir = None
+
+ try:
+ opts, args = getopt.getopt(sys.argv[1:],"hl:o:",["help","lamarcfile=","outdir="])
+ except getopt.GetoptError, err:
+ usage()
+ sys.exit(2)
+
+ for o, a in opts:
+ if o in ("-h","--help"):
+ usage()
+ sys.exit()
+ elif o in ("-l", "--lamarcfile"):
+ lamarcfile = a
+ elif o in ("-o", "--outdir"):
+ outdir = a
+ else:
+ assert False, "unhandled option"
+
+ # lamarc input file and output directory both must exist
+ if lamarcfile == None or outdir == None:
+ usage()
+ sys.exit()
+
+ # make sure lamarcfile exists and is a file
+ if not os.path.isfile(lamarcfile):
+ print "%s doesn't exist or isn't a file. exiting" % lamarcfile
+ sys.exit(1)
+
+ # make sure outdir is a new, empty directory
+ if os.path.exists(outdir):
+ if barfIfOutdirExists:
+ print "directory %s already exists. exiting" % outdir
+ sys.exit(1)
+ else:
+ os.makedirs(outdir)
+
+ return (lamarcfile,outdir,os.getcwd())
+
+
+# gets first sub-tag named "tagname" of element "domElem"
+def getFirstTag(domElem,tagname):
+ elems = domElem.getElementsByTagName(tagname)
+ for elem in elems:
+ return elem
+ return None
+
+# gets only sub-tag named "tagname" of element "domElem"
+# EWFIX -- not actually doing any error checking
+def getSingleTag(elem,tagname):
+ return getFirstTag(elem,tagname)
+
+# gets the long value embedded in a tag
+def getLongVal(elem):
+ for child in elem.childNodes:
+ # EWFIX -- should check only one
+ if child.nodeType == child.TEXT_NODE:
+ return long(child.data)
+ return None
+
+
+# replaces data in the first text child node of "elem" with "strData"
+def setVal(elem,strData):
+ for child in elem.childNodes:
+ # EWFIX -- should check only one
+ if child.nodeType == child.TEXT_NODE:
+ child.data = strData
+ return
+
+# when creates or replaces child tag "childTagName" of parent element
+# "parentTag" with text of value "newValue"
+def replaceOrSet(domTop,parentTag,childTagName,newValue):
+
+ childTag = getSingleTag(parentTag,childTagName)
+ if childTag:
+ setVal(childTag,newValue)
+ else:
+ childTag = domTop.createElement(childTagName)
+ parentTag.appendChild(childTag)
+ parentTag.appendChild(domTop.createTextNode("\n"))
+ childTag.appendChild(domTop.createTextNode(newValue))
+
+
+# change the name (or set if not present) of all input and outputs specified
+# in the format tag to have an infix of "idStr"
+#
+# also sets seed to an appropriate random value
+#
+# input "useIn" when true, controls input summary file reading
+def fixFormatTag(domTop,fmtTag,idStr,useIn):
+ replaceOrSet(domTop,fmtTag,"seed", "%d" % (random.randint(0,seedlim)*4+1))
+ replaceOrSet(domTop,fmtTag,"results-file", "outfile_%s.txt" % idStr)
+ if useIn:
+ replaceOrSet(domTop,fmtTag,"use-in-summary", "true")
+ replaceOrSet(domTop,fmtTag,"in-summary-file", "insumfile_%s.xml" % idStr)
+ else:
+ replaceOrSet(domTop,fmtTag,"use-in-summary", "false")
+ replaceOrSet(domTop,fmtTag,"use-out-summary", "true")
+ replaceOrSet(domTop,fmtTag,"out-summary-file", "outsumfile_%s.xml" % idStr)
+ replaceOrSet(domTop,fmtTag,"curvefile-prefix", "curve_%s.xml" % idStr)
+ replaceOrSet(domTop,fmtTag,"tracefile-prefix", "trace_%s.xml" % idStr)
+ replaceOrSet(domTop,fmtTag,"newicktreefile-prefix", "newick_%s.xml" % idStr)
+ replaceOrSet(domTop,fmtTag,"out-xml-file", "menusettings_%s.xml" % idStr)
+ replaceOrSet(domTop,fmtTag,"xml-report-file", "report_%s.xml" % idStr)
+
+
+#
+#profilePattern = re.compile('\s*(\S+)\s+(.*)')
+#def replaceEachProfile(profileText):
+# if not profileText:
+# return
+# remainingText = profileText
+# outText = ""
+# m = profilePattern.match(remainingText)
+# while m:
+# outText = "%s %s" % ( outText, "none")
+# remainingText = m.group(2)
+# m = profilePattern.match(remainingText)
+# return outText
+
+# get population count from a top level lamarc XML document
+def getPopCount(lamDom):
+ dataTag = getSingleTag(lamDom,"data")
+ regionTag = getFirstTag(dataTag,"region")
+ return len(regionTag.getElementsByTagName("population"))
+
+# makes a string containing the word "none" "numProfiles" times
+# spaces are between each occurence and before the first and after
+# the last
+def makeProfilesString(numProfiles):
+ outstr = ""
+ for i in range(numProfiles):
+ outstr = "%s none" % outstr
+ outstr = "%s " % outstr
+ return outstr
+
+# turn off the profile for a given force
+def turnOneProfileOff(domTop,forcesTag,forceName,numProfiles):
+ thisForce = getSingleTag(forcesTag,forceName)
+ if thisForce:
+ newProfilesString = makeProfilesString(numProfiles)
+ replaceOrSet(domTop,thisForce,"profiles",newProfilesString)
+
+
+# turn off all profiles -- we use this because we don't want to
+# do any profiling until the last run of lamarc on the brought-together
+# data
+def turnProfilesOff(domTop,lamTag):
+ popCount = getPopCount(domTop)
+ tag = getSingleTag(lamTag,"forces")
+ turnOneProfileOff(domTop,tag,"coalescence",popCount)
+ turnOneProfileOff(domTop,tag,"migration",popCount*popCount)
+ turnOneProfileOff(domTop,tag,"growth",popCount)
+ turnOneProfileOff(domTop,tag,"recombination",1)
+
+
+# python outputs XML with an initial tag <?xml version="1.0" ?>
+# even though this is perfectly correct, the lamarc sum file reading
+# routines cannot handle it. This is a kludge to work around that
+linePattern = re.compile('(.*)<\?.*\?>(.*)')
+def stripXmlInfo(filename):
+ firstLine = True
+ for line in fileinput.input(filename,inplace=1):
+ if firstLine:
+ m = linePattern.match(line)
+ if m:
+ line = "%s%s" % (m.group(1),m.group(2))
+ firstLine = False
+ print line # prints line to file via fileinput inplace option
+ else:
+ line.rstrip()
+ print line , # prints line to file via fileinput inplace option
+
+def sumfileCombineWarn(where):
+ print "Combining sumfiles in %s. This can take a while..." % where
+
+def dividerLine():
+ print "****************************************************"
+
+def describeThisScript(scriptName,purpose,lamfile,lamdir):
+ dividerLine()
+ print "running python script: %s" % scriptName
+ print "purpose: %s" % purpose
+ print "arguments: -l %s" % lamfile
+ print " -o %s" % lamdir
+
+def nextStep(lamdir,filelist,nextIsLast):
+ dividerLine()
+
+ print "next step: run lamarc on",
+ if not nextIsLast:
+ print "each of:",
+ print
+
+ for fileName in filelist:
+ print " %s" % fileName
+ print " if you are running on a different machine, copy"
+ print " all files in each of the above directories there"
+ if not nextIsLast:
+ print " and copy all files generated by the run back to"
+ print " the same directory"
+ print
+
+def finalStep(pydir,pyscript,lamfile,lamdir):
+ print "then: change back to this directory"
+ print " (%s)" % pydir
+ print " and run python script %s with arguments" % pyscript
+ print " -l %s" % lamfile
+ print " -o %s" % lamdir
+ dividerLine()
diff --git a/scripts/xmingw32/binutils-2.15.91-20040904-1-src.tar.gz b/scripts/xmingw32/binutils-2.15.91-20040904-1-src.tar.gz
new file mode 100644
index 0000000..d05a5af
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diff --git a/scripts/xmingw32/gcc-core-3.4.2-20040916-1-src.tar.gz b/scripts/xmingw32/gcc-core-3.4.2-20040916-1-src.tar.gz
new file mode 100644
index 0000000..6e6a24f
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diff --git a/scripts/xmingw32/gcc-g++-3.4.2-20040916-1-src.tar.gz b/scripts/xmingw32/gcc-g++-3.4.2-20040916-1-src.tar.gz
new file mode 100644
index 0000000..0609aa8
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diff --git a/scripts/xmingw32/gcc-g77-3.4.2-20040916-1-src.tar.gz b/scripts/xmingw32/gcc-g77-3.4.2-20040916-1-src.tar.gz
new file mode 100644
index 0000000..a8e7994
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diff --git a/scripts/xmingw32/mingw-runtime-3.7.tar.gz b/scripts/xmingw32/mingw-runtime-3.7.tar.gz
new file mode 100644
index 0000000..d1fd1ee
Binary files /dev/null and b/scripts/xmingw32/mingw-runtime-3.7.tar.gz differ
diff --git a/scripts/xmingw32/w32api-3.2.tar.gz b/scripts/xmingw32/w32api-3.2.tar.gz
new file mode 100644
index 0000000..18b9a71
Binary files /dev/null and b/scripts/xmingw32/w32api-3.2.tar.gz differ
diff --git a/scripts/xmingw32/xmingw32.bat.in b/scripts/xmingw32/xmingw32.bat.in
new file mode 100644
index 0000000..018db2a
--- /dev/null
+++ b/scripts/xmingw32/xmingw32.bat.in
@@ -0,0 +1,59 @@
+ at echo off
+rem xmingw32.bat
+rem
+rem A batch file that defines several variables to use with a MinGW
+rem cross compiler under the cygwin enviroment.
+rem
+rem Copyright (C) 2002 Jos� Fonseca
+rem
+rem This program is free software; you can redistribute it and/or
+rem modify it under the terms of the GNU General Public License
+rem as published by the Free Software Foundation; either version 2
+rem of the License, or (at your option) any later version.
+rem
+rem This program is distributed in the hope that it will be useful,
+rem but WITHOUT ANY WARRANTY; without even the implied warranty of
+rem MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+rem GNU General Public License, http://www.gnu.org/copyleft/gpl.html
+rem for more details.
+rem
+rem Jos� Fonseca <j_r_fonseca at yahoo.co.uk>
+rem
+rem Copy to the cygwin installation dir (usually C:\cygwin) and run:
+rem xmingw32.bat
+rem
+
+C:
+chdir \cygwin\bin
+
+set PATH=@prefix@/bin;$PATH
+
+set C_INCLUDE_PATH=@prefix@/usr/include:@prefix@/usr/local/include
+set CPLUS_INCLUDE_PATH=@prefix@/usr/include:@prefix@/usr/local/include
+set LIBRARY_PATH=@prefix@/usr/lib:@prefix@/usr/local/lib
+
+set AS=@target at -as
+set AR=@target at -ar
+set CC=@target at -gcc
+set CFLAGS=-O2
+set CPP=%CC% -E
+set CXX=@target at -g++
+set CXXFLAGS=%CFLAGS%
+set DLLTOOL=@target at -dlltool
+set LD=@target at -ld
+set NM=@target at -nm
+set RANLIB=@target at -ranlib
+
+set AS_FOR_BUILD=as
+set AR_FOR_BUILD=ar
+set CC_FOR_BUILD=gcc
+set CFLAGS_FOR_BUILD=-O2
+set CPP_FOR_BUILD=%CC_FOR_BUILD% -E
+set CXX_FOR_BUILD=g++
+set CXXFLAGS_FOR_BUILD=%CFLAGS_FOR_BUILD%
+set DLLTOOL_FOR_BUILD=dlltool
+set LD_FOR_BUILD=ld
+set NM_FOR_BUILD=nm
+set RANLIB_FOR_BUILD=ranlib
+
+bash --login -i
diff --git a/scripts/xmingw32/xmingw32.mak b/scripts/xmingw32/xmingw32.mak
new file mode 100644
index 0000000..a8b46ec
--- /dev/null
+++ b/scripts/xmingw32/xmingw32.mak
@@ -0,0 +1,285 @@
+#!/usr/bin/make -f
+#
+# Description:
+#
+# A makefile that automates the process of building a MinGW cross compiler.
+#
+# Usage:
+#
+# make -f xmingw32.mak all test
+#
+# or simply
+#
+# ./xmingw32.mak all test
+#
+# License:
+#
+# Copyright (C) 2003 Jos\x{00E9} Fonseca
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License, http://www.gnu.org/copyleft/gpl.html
+# for more details.
+#
+# Author:
+#
+# Jos\x{00E9} Fonseca
+#
+# Changelog:
+#
+# * Wed, 15 Sep 2004 14:46:48 +0100
+# - Updated to the latest versions (binutils-2.15.90-20040222-1,
+# gcc-3.3.3-20040217-1, mingw-runtime-3.3 and w32api-2.5).
+#
+# * Mon, 23 Jun 2003 11:57:39 +0100
+# - Updated to the latest versions (binutils-2.13.90-20030111-1,
+# gcc-3.2.3-20030504-1, mingw-runtime-3.0 and w32api-2.3).
+# - Use of patches instead of hard-coded sed commands.
+# - Automatic detection of the installation directory.
+# - Small reorganization.
+#
+# * before
+# - lost in time...
+
+
+# Target definition
+
+TARGET = mingw32
+
+
+# Versions defintions
+
+BINUTILS_VERSION = 2.15.91-20040904-1
+GCC_VERSION = 3.4.2-20040916-1
+MINGW_RUNTIME_VERSION = 3.7
+W32API_VERSION = 3.2
+
+
+# Installation directory
+
+ifeq ($(shell whoami),root)
+PREFIX=/usr/local/xmingw32
+else
+PREFIX=$(HOME)/local/xmingw32
+endif
+
+
+# Choose one of the SourceForge mirrors.
+
+#BASE_URL = ftp://ftp.sf.net/pub/sourceforge/mingw/
+BASE_URL = http://telia.dl.sourceforge.net/sourceforge/mingw/
+#BASE_URL = http://unc.dl.sourceforge.net/sourceforge/mingw/
+#BASE_URL = http://belnet.dl.sourceforge.net/sourceforge/mingw/
+
+
+# Some shortcut variables
+#
+# NOTE: The upstream packaging is not very consistent so often these have to be
+# tweaked for each specific version.
+
+BINUTILS_TARBALL = binutils-$(BINUTILS_VERSION)-src.tar.gz
+#GCC_TARBALL = gcc-$(GCC_VERSION)-src.tar.gz
+GCC_TARBALL = gcc-core-$(GCC_VERSION)-src.tar.gz gcc-g++-$(GCC_VERSION)-src.tar.gz gcc-g77-$(GCC_VERSION)-src.tar.gz
+MINGW_RUNTIME_TARBALL = mingw-runtime-$(MINGW_RUNTIME_VERSION).tar.gz
+W32API_TARBALL = w32api-$(W32API_VERSION).tar.gz
+
+BINUTILS_PATCH = binutils-$(BINUTILS_VERSION).patch
+GCC_PATCH = gcc-$(GCC_VERSION).patch
+
+BINUTILS_DIR = binutils-$(BINUTILS_VERSION)#-src
+GCC_DIR = gcc-$(GCC_VERSION)
+
+
+# Configure flags
+#
+# NOTE: Some of these flags require certain versions. See the upstream
+# gcc-*-build.sh scripts for more information.
+
+CONFIGURE_FLAGS = \
+ --target=$(TARGET) \
+ --prefix=$(PREFIX)
+
+BINUTILS_CONFIGURE_FLAGS = \
+ $(CONFIGURE_FLAGS)
+
+GCC_CONFIGURE_FLAGS = \
+ $(CONFIGURE_FLAGS) \
+ --enable-languages=c,c++,f77 \
+ --disable-nls \
+ --disable-shared \
+ --enable-sjlj-exceptions \
+ --enable-threads \
+ --disable-win32-registry
+
+
+# Build flags
+
+CFLAGS = -O2
+LDFLAGS = -s
+DEBUG_FLAGS = -g0
+
+export CFLAGS LDFLAGS DEBUG_FLAGS
+
+
+# Set the path environment variable
+
+PATH := $(PREFIX)/bin:$(PATH)
+
+export PATH
+
+
+# Default target
+
+all: download binutils mingw-runtime w32api gcc scripts
+
+.PHONY: all
+
+
+# Download the tarballs
+
+WGET = wget
+WGET_FLAGS = --passive-ftp
+
+SOURCES = \
+ $(BINUTILS_TARBALL) \
+ $(GCC_TARBALL) \
+ $(MINGW_RUNTIME_TARBALL) \
+ $(W32API_TARBALL)
+
+download: $(SOURCES)
+
+$(SOURCES):
+ $(WGET) $(WGET_FLAGS) $(BASE_URL)$@
+
+.PHONY: download
+
+
+# Create the installation directories
+
+$(PREFIX):
+ mkdir -p $@
+
+$(PREFIX)/$(TARGET):
+ mkdir -p $@
+
+
+# Unpack, patch, build and install the binutils
+
+$(BINUTILS_DIR): $(BINUTILS_TARBALL)
+ gzip -dc $(BINUTILS_TARBALL) | tar xf -
+ [ -f $(BINUTILS_PATCH) ] && patch -p0 -i $(BINUTILS_PATCH) || true
+ touch $@
+
+$(BINUTILS_DIR)/Makefile: $(BINUTILS_DIR)
+ cd $(BINUTILS_DIR) && \
+ ./configure $(BINUTILS_CONFIGURE_FLAGS) > ../binutils-configure.log 2>&1
+
+binutils: .binutils-stamp
+
+.binutils-stamp: $(BINUTILS_DIR)/Makefile $(PREFIX)
+ cd $(BINUTILS_DIR) && \
+ make > ../binutils-build.log 2>&1
+ cd $(BINUTILS_DIR) && \
+ make install > ../binutils-install.log 2>&1
+ touch $@
+
+.PHONY: binutils
+
+
+# Install the MinGW C runtime headers and libraries
+
+mingw-runtime: .mingw-runtime-stamp
+
+.mingw-runtime-stamp: $(RUNTIME_TARBALL) $(PREFIX)/$(TARGET)
+ gzip -dc $(MINGW_RUNTIME_TARBALL) | tar xf - -C $(PREFIX)/$(TARGET) > mingw-runtime-install.log 2>&1
+ touch $@
+
+.PHONY: mingw-runtime
+
+
+# Install the MinGW Win32 API headers and libraries
+
+w32api: .w32api-stamp
+
+.w32api-stamp: $(W32API_TARBALL) $(PREFIX)/$(TARGET)
+ gzip -dc $(W32API_TARBALL) | tar xf - -C $(PREFIX)/$(TARGET) > w32api-install.log 2>&1
+ touch $@
+
+.PHONY: w32api
+
+
+# Unpack, patch, build and install the gcc
+
+$(GCC_DIR): $(GCC_TARBALL)
+ $(foreach TARBALL,$(GCC_TARBALL), gzip -dc $(TARBALL) | tar xf - ;)
+ [ -f $(GCC_PATCH) ] && patch -p0 -i $(GCC_PATCH) || true
+ touch $@
+
+$(GCC_DIR)/Makefile: $(GCC_DIR)
+ cd $(GCC_DIR) && \
+ ./configure $(GCC_CONFIGURE_FLAGS) > ../gcc-configure.log 2>&1
+
+gcc: .gcc-stamp
+
+.gcc-stamp: .binutils-stamp .mingw-runtime-stamp .w32api-stamp $(GCC_DIR)/Makefile $(PREFIX)
+ #cd $(GCC_DIR)/gcc && \
+ make installdirs > ../gcc-build.log 2>&1
+ cd $(GCC_DIR) && \
+ make >> ../gcc-build.log 2>&1
+ cd $(GCC_DIR) && \
+ make install > ../gcc-install.log 2>&1
+ touch $@
+
+.PHONY: gcc
+
+
+# Creates scripts to facilitate the use of the cross compiler toolchain
+
+scripts: xmingw32.sh xmingw32.bat
+
+xmingw32.sh: xmingw32.sh.in
+ sed -e s%@target@%$(TARGET)%g -e s%@prefix@%$(PREFIX)%g $< > $@
+
+xmingw32.bat: xmingw32.bat.in
+ sed -e s%@target@%$(TARGET)%g -e s%@prefix@%$(PREFIX)%g $< > $@
+
+.PHONY: scripts
+
+
+# A small test case
+
+test: test1.exe test2.exe
+
+test1.exe: hello.c
+ $(TARGET)-gcc -o $@ $<
+
+test2.exe: hello.cxx
+ $(TARGET)-g++ -o $@ $<
+
+.PHONY: test
+
+
+# Cleans the build trees
+
+clean:
+ rm -f .*-stamp
+ rm -f *.log
+ rm -rf $(BINUTILS_DIR) $(GCC_DIR)
+ rm -f xmingw32.sh xmingw32.bat
+ rm -f test*.exe
+
+.PHONY: clean
+
+
+# Uninstall the cross compiler (Use with care)
+
+uninstall:
+ rm -rf $(PREFIX)
+
+.PHONY: uninstall
diff --git a/scripts/xmingw32/xmingw32.sh.in b/scripts/xmingw32/xmingw32.sh.in
new file mode 100644
index 0000000..4a5d824
--- /dev/null
+++ b/scripts/xmingw32/xmingw32.sh.in
@@ -0,0 +1,53 @@
+# xmingw32.sh
+#
+# A shell script that defines several variables to use with a MinGW
+# cross compiler.
+#
+# Copyright (C) 2002 Jos� Fonseca
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License, http://www.gnu.org/copyleft/gpl.html
+# for more details.
+#
+# Jos� Fonseca <j_r_fonseca at yahoo.co.uk>
+#
+# Example,
+# source xmingw32.sh
+#
+
+export PATH=@prefix@/bin:$PATH
+
+export C_INCLUDE_PATH=@prefix@/usr/include:@prefix@/usr/local/include
+export CPLUS_INCLUDE_PATH=@prefix@/usr/include:@prefix@/usr/local/include
+export LIBRARY_PATH=@prefix@/usr/lib:@prefix@/usr/local/lib
+
+export AS=@target at -as
+export AR=@target at -ar
+export CC=@target at -gcc
+export CFLAGS=-O2
+export "CPP=$CC -E"
+export CXX=@target at -g++
+export CXXFLAGS=$CFLAGS
+export DLLTOOL=@target at -dlltool
+export LD=@target at -ld
+export NM=@target at -nm
+export RANLIB=@target at -ranlib
+
+export AS_FOR_BUILD=as
+export AR_FOR_BUILD=ar
+export CC_FOR_BUILD=gcc
+export CFLAGS_FOR_BUILD=-O2
+export "CPP_FOR_BUILD=$CC_FOR_BUILD -E"
+export CXX_FOR_BUILD=g++
+export CXXFLAGS_FOR_BUILD=$CFLAGS
+export DLLTOOL_FOR_BUILD=dlltool
+export LD_FOR_BUILD=ld
+export NM_FOR_BUILD=nm
+export RANLIB_FOR_BUILD=ranlib
diff --git a/src/BUGS b/src/BUGS
deleted file mode 100644
index 0750b61..0000000
--- a/src/BUGS
+++ /dev/null
@@ -1,453 +0,0 @@
-//$Id: BUGS,v 1.84 2005/03/11 20:59:55 mkkuhner Exp $
-
-//*********************************************************************
-Bugs needing resolution
-//*********************************************************************
-
-Deferred--multiple loci
-to Bugzilla 2005/03/10
-2003/04/28 Multiple loci do not work in the ReportPage; they are
- still hardcoded to locus 0. (Among other problems--2003/07/15)
-
-Deferred
-2003/07/11 Items commented out or cryptic in release 2.0: multiple
- loci, disease, tree summaries, tree reading and writing.
-
-to Bugzilla 2005/03/10
-PartialFix--Jon, program now throws a Data Error when IsReal/IsInteger encounter
- an empty string to parse.
-2003/12/01 since stringx.cpp::FindToken() requires a digit after a decimal
- point in reading a number; numbers of the form "2." cause the
- program to hang as ProduceDoubleOrBarf() fails due to problems with
- IsReal not handling an empty input string well...
-
-to Bugzilla 2005/03/10
-Deferred--multiple loci
-2004/02/12 map_position tag missing from XML documentation, and the
- section where it goes needs to be rewritten for multiple
- locus compliance.
-
-to Bugzilla 2005/03/10
-2004/03/09 In the converter, if you have 2+ datablocks and assign them
- all to the same region and population, the code just loops
- and asks for reassignment--a warning message would be good,
- at the very least. JAY
-
-to Bugzilla 2005/03/10
-2004/06/11 The signal handling code (in lamarc.cpp and chainmanager.cpp)
- needs to be checked on other OSes--the signal 'SIGXFSZ' is
- supposedly 'non-standard'. Possibly a check in 'configure'?
- --LS
-
- (This is definitely broken in Windows -- ewalkup 2004/06/14)
-
-2004/06/14 We need to do the following things to make sure our releases
- are higher quality:
- * document exact steps to creating a release, including
- how to get clean CVS checkout
- * have a standard test case suite to run through release
- candidates
- * institute a beta testing plan
- ewalkup
-
-to Bugzilla 2005/03/10
-Deferred
-2004/04/22 For recombination, and possibly migration and disease, it
- would be good to have correct handling of parameter=0 for
- confidence limit testing, and we don't. Mary
-
-to Bugzilla 2005/03/10
-Deferred
-2004/04/28 If DLCalculator::Calculate happens to be called on a tree which
- doesn't need recalculation, it seg-faults due to failing to
- set the DLCell variables. This doesn't happen in normal
- execution but is still ugly. Mary
-
-to Bugzilla 2005/03/10
-2004/08/06 outfile gives you the name of your infile relative to
- the directory you ran lamarc in, not the directory the
- outfile is written in. ewalkup
-
-to Bugzilla 2005/03/10
-Deferred
-2004/12/17 WARNING: The way that PlForces now handles starttime will
- fail badly if (a) we implement sequential sampling and
- (b) one genetic region lacks samples from the topmost
- time point.
-
-//*********************************************************************
-Bugs fixed for release 2.0
-//*********************************************************************
-
-Fixed--Lucian 2005/03/08
-2002/06/26 The XML reader reads a global data model and uses it to
- set unspecified regional data models, but then abandons
- it. This both leaks a little memory and means that the menu
- cannot know what this global model was.
-
-PartialFix--ewalkup
-2003/05/20 global datamodel menus are crocked when multiple regions
- have differing datamodels!
-
-PartialFix--Lucian and others (tree reading and writing)
-2003/07/11 Items commented out or cryptic in release 1.2: multiple
- loci, 2-allele model, disease, tree summaries, tree reading
- and writing.
-
-Accepted as-is Mary 2005/03/08
-2004/02/06 Brownian DataModel always doesn't normalize [ShouldNormalize()
- hard set to return false]. Is this really correct behaviour?
-
---Fixed LS 3/4/2005
-2004/05/21 Neither menu nor XML protects against asking for a Bayesian
- analysis with no BayesArranger, which will crash. Mary
-
-
-Eliminated--Not in current code base
-2004/01/15 Windows .NET compile on Wang Yi's machine (at least) complains
- about protected function pointers in Menu class. We "fixed"
- it temporarily by making them public, but does this still
- happen in 1.2, and if so why?
-
-//*********************************************************************
-Bugs fixed for release 1.2.3
-//*********************************************************************
-
-Declared Resolved--Lucian et al; 9/13/2004 (The 2 diseases problem can
-be solved by using a clever mix of constraints and setting things to zero)
-2002/11/22 The code is riddled through with the assumption that each
- force object is unique, so for example, there are never
- 2 disease force objects in existance. One of the main
- enforcers of this assumption is
- ForceSummary::GetForceByTag().
-
-//*********************************************************************
-Bugs fixed for release 1.2
-//*********************************************************************
-
-DECLARED UNFIXABLE--Mary 2003/07/11
-2002/01/18 Converter -- phylip file conversion -- if longer sequences
- are present than claimed in header, the reader will SILENTLY mangle
- sequences and names.
-
-Fixed--Jon 2003/07/11
-2002/06/20 Brownian and Stepwise output reports are butt-ugly when no
- categories are in use.
-
-FIXED--Jon 2004/02/11
-2002/07/19 The program dies with just "abort" showing to the user if
- the forces specify multiple populations and the data has
- only 1 population in it. This may only apply to forces
- specified in the xml input file.
- Partially fixed 09/23/02 -- now taps in to the xml-reading
- message error handling but doesn't give a good error
- message -- see force/force.cpp:Force::SetMethods
-
-Jon note: Partial fix--due to xml schema now we get an "unknown" element
- error 2003/08/03
-2002/06/21 Xml complains about mismatched tags when in fact the problem
- is tags at the wrong scoping level (<start-value> tags
- at the same level as a forcename tag).
-
-FIXED--Mary 2003/07/14
-2002/07/22 The program seems to run with duplicate site locations,
- i.e. same site number assigned to more than one base.
-
-FIXED--Mary 2003/05/30, 2003/07/14
-2002/07/23 Adaptive heating is present in the program but completely
- undocumented. (Now it's documented, but I wonder
- whether changing temperature with every swap is wise.
- Have sent a query to Peter.)
-
-FIXED--Jon 2003/07/14
-2002/07/23 The xmlreader throws if it encouters an empty force.
- Though even an invalid xml entry will suffice to avoid
- the throw.
-
-KLUDGED--Jon 2002/10/21 -- defaults now set for COAL, MIG, DISEASE
-2002/08/12 a multi-population infile with unspecified migration force
- (but specified theta and recombination) fails to set any
- migration starting values into ForceSummary::startParameters.
- This lead to an infinite loop in starting tree generation!
- addenda: 2002/10/21--it looks like if some but not all
- forces are specified, no default force is created for the
- unspecified in the xml file forces.
-
-Fixed--Mary 2002/08/21
-2002/08/20 I strongly suspect that if haplotyping is turned on in the
- XML and not the menu, and auto-pairing of haplotypes is
- supposed to happen, it won't happen correctly due to lack
- of a necessary call to DataPack::EvaluatePairing.
-
-FIXED--Jon 2002/08/27
-2002/08/27 Converter, when passed an interleaved phylip file spits out
- datablocks with only the first line of interleaved sequence
- on them.
-
-FIXED--Jon 2002/09/05
-2002/09/03 Microsats, loci position vector fails to get to
- Region::CreateTree(), other parts of Region::loci may
- also be wrong.
-
-FIXED--Jon 2002/09/04
-2002/09/03 MULTI-TEMPERATURE NOW FAILS, tip nodes parents are dead
- nodes in highest temperature tree!
-
-FIXED--Mary 2003/07/14
-2002/09/27 the html docs for the xmlinput does not address how to set
- an F84 model to do base frequencies calculated from the data.
-
-Fixed--Chia-Chi 11/14/03
-2002/10/28 Converter--if multiple sequences are present in Phylip
- format with the same phylip-truncated name, the converter
- will silently drop them from the analysis!
-
-FIXED--Jon 2002/10/10
-2002/10/10 the multicategory SNP case crashes in datalikelihood
- calculation due to uninitialized member "catcells" if
- there are no markers in the first subtree.
-
-Fixed--Jon--2003/02/21
-2003/02/06 Something expects there will be a profile
-
-FIXED--various--2003/07/11
-2003/02/21 Need to redo how static const strings are defined! Example
- in ui_interface/ui_strings.h and .cpp.
-
-FIXED--Mary--or rather it was a hallucination--2003/04/21
-2003/04/21 Handling of newly active sites in rectree.Migrate and
- rectree.DiseaseMutation suspected of being erroneous.
-
-Fixed--Jon--2003/05/02--added new make target nomenulamarc.
-2003/05/02 some users want a no-menu option for running in background.
-
-Fixed--ewalkup 10/14/03
-2003/05/20 in the menu, datamodel menus, the ncategories, probcats, and
- catrates are all set independently. They should check for
- mutual self-consistency at some point! Currently, they
- lead to a failed validity check if inconsistent.
-
-FIXED--Mary and Jon 2003/07/15
-2003/07/15 Loci need to be constrained to be non-overlapping, probably in
- Region::IsValid.
-
-Fixed--Mary 2003/07/30
-2003/07/15 Due to use of 'new' without 'delete' the menu leaks like a
- sieve. Use boost::shared_ptr here. [NB I used auto_ptr
- instead.]
-
-FIXED--Wang Yi 2004/04/05
-2003/07/15 The model claiming to be K-Allele is really 2-Allele,
- but changing its name is not very good because the data
- reading part really is K-Allele. Wang Yi is working on a
- genuine K-Allele model.
-
-Checked and found to be correct--Jon 2004/02/12
-2003/07/15 Handling of SNP positions in multi-locus code is probably wrong;
- we believe that they are assigned site numbers (in xml reading)
- relative to the offset of their locus but not its map position,
- leading to locus-specific positions that are then misused as
- regional positions in data likelihood code.
-
-FIXED--Jon 2003/07/24
-2003/07/22 Cannot set Adaptive/Static temperature regime via xml!
-
-Apparently not true--Mary 10/15/03
-2003/09/22 multi-cats set in menu are not initialized correctly!
- see dlmodel.cpp::Initialize()/Finalize()
-
-FIXED--Jon 2004/02/05
-2003/10/09 For DNA data, if number of markers (in XML) is inconsistent with
- sequence length, error checking doesn't catch this and the
- program eventually crashes in a cryptic way. (It doesn't work
- to just put in a check, because the number of sites
- is set to FLAGLONG unless there is explicit spacing data.)
-
-Fixed--Eric 11/14/03
-2003/11/3 The "threshhold" of maximum distance between microsatellite
- alleles should be set adaptively, not hardwired. This is
- set in the constructor of StepwiseModel.
-
-`Fixed--Lucian 2003/11/25 (no manpage; 'converter' now 'lam_conv')
-2003/11/20 'make install' fails to install the nonexistent manpage (oddly
- enough), and does not copy over the 'converter' program (which
- probably needs a new name).
-
-Fixed--Mary 2003/12/01
-2003/07/15 The inability of most arrangers to do DeNovoTree is ugly.
-
-FIXED--Mary 2003/12/09
-2003/12/09 Both adaptive and non-adaptive heating success reports have
- always, it turns out, reported complete nonsense.
-
-Fixed--we just deleted the file entirely.
-2003/12/22 The file "conversion/LamarcParser.cpp" is not ever actually
- compiled or incorporated into the converter. Is was created
- by Peter--did it ever work? Should we work on including it?
- -LS
-
-FIXED--Jon 2004/02/11
-2002/07/19 The program dies with just "abort" showing to the user if
- the forces specify multiple populations and the data has
- only 1 population in it. This may only apply to forces
- specified in the xml input file.
- Partially fixed 09/23/02 -- now taps in to the xml-reading
- message error handling but doesn't give a good error
- message -- see force/force.cpp:Force::SetMethods
-
-Checked and found to be correct--Jon 2004/02/12
-2003/07/15 Handling of SNP positions in multi-locus code is probably wrong;
- we believe that they are assigned site numbers (in xml reading)
- relative to the offset of their locus but not its map position,
- leading to locus-specific positions that are then misused as
- regional positions in data likelihood code.
-
-FIXED--mainly Eric 2004/5
-2003/07/15 A lot of PDEBUG in the postlike code that need to be addressed.
- (And some plain old DEBUG.)
-
-FIXED--mainly Eric
-2003/07/24 Worrisome comment in maximizer.h suggests growth may not work....?
-
-Irrelevant with removal of xerces
-2003/09/11 cryptic segfault after xerces schema catch output.
-
-Irrelevant with removal of Xerces
-2003/10/19 build from clean on darwin for fonzi at darwin failed to correctly
- find the xerces library on run--kludged by putting xerces-lib
- in /usr/lib, but need to find out why library not found!
-
-FIXED--Jon 2004/02/05
-2003/10/09 For DNA data, if number of markers (in XML) is inconsistent with
- sequence length, error checking doesn't catch this and the
- program eventually crashes in a cryptic way. (It doesn't work
- to just put in a check, because the number of sites
- is set to FLAGLONG unless there is explicit spacing data.)
-
-FIXED--Eric 2003/5
-2003/11/4 The behavior of the maximizer when a posterior likelihood
- overflows is bad.
-
-FIXED--Mary 2003/12/09
-2003/12/09 Both adaptive and non-adaptive heating success reports have
- always, it turns out, reported complete nonsense.
-
-FIXED--Lucian 2004/5
-2004/02/24 In the menu, if the profile types are changed (from
- 'percentile' to 'fixed'), and then a new force is added (i.e.
- growth), the new force will be listed as 'percentile', not
- 'fixed'. While we might allow this in the future, Peter's
- code comments say we cannot do both fixed and percentile
- profiling at once. --LS
-
-//*********************************************************************
-Bugs fixed for release 1.1
-//*********************************************************************
-
-FIXED--Mary 2002/02/13
-2002/02/13 Specifying output file name in the xml causes a "space"
- to be pre-pended to the file name (e.g. "outfile" becomes " outfile").
-
-FIXED--ewalkup 2002/05/31
-2002/01/29 A legal xml file with an extra </lamarc> tag after all the
- data causes the program to crash mysteriously in parsing without any
- error messages.
-
-FIXED--ewalkup 2002/05/31
-2001/12/17 If the user types a wrong filename in the menu,
- subsequent messages still display a default filename, but this
- default is actually not available.
-
-FIXED--Mary 2002/06/14
-2001/12/17 The acceptance rate information for individual arrangers
- is repeatedly overwritten (at the end of each swap interval) when
- heating is in effect.
-
-FIXED--ewalkup 2002/05/31
-2002/01/02 xml.cpp uses tests against -1 when it would be appropriate
- to use tests against string::npos. This is not necessarily portable
- though it happens to work on both our compilers at the moment.
-
-FIXED--ewalkup 2002/06/06
-2002/01/21 Menu entry to turn normalization on/off seems to be
- missing.
-
-FIXED--ewalkup 2002/06/03
-2002/01/21 There is no way to make an xml file that turns recombination
- off; only on.
-
-FIXED--Mary 2002/02/20
-2002/02/20 Converter loses last base of each sequence.
-
-FIXED--Mary 2002/03/04
-2002/03/01 Converter is wildly incorrect in cases with multiple
- populations (wrong method in <migration> tag, wrong number of entries in
- <coalescence> tag).
-
-FIXED--Mary 2002/03/04
-2002/03/01 XML error messages needed for the results of the
- above error (wrong methods, wrong number of populations, etc.)
-
-FIXED--Mary and Jon and Peter 2002/06/21
-2002/03/19 Default values in converter and program are too low.
-
-DECLARED A FEATURE--Mary and Jon 2002/05/21
-2002/04/12 XML reader is happy with SNP data and no positional info.
-
-FIXED--Mary 2002/05/21 (actually a while ago)
-2002/05/06 XML file shouldn't require a datamodel present.
-
-FIXED--Mary 2002/05/21
-2002/05/09 One-legged coalescence in stepwise model is handled wrong.
-
-FIXED--Mary 2002/05/21
-2002/05/20 In cases with migration and no recombination, serious problems with
- handling one-legged coalescence at the base of the tree. This bug
- WAS PRESENT in release 1.0.
-
-FIXED--ewalkup 2002/06/07
-2002/05/21 Lamarc seg-faults if there is no genetic data in the XML file.
-
-FIXED--Jon 2002/05/31
-2002/05/31 Attempts to print current settings of microsat data models in
- menu seg-fault.
-
-FIXED--ewalkup 2002/06/04
-2002/05/31 Lamarc menu shows some formating problems (possible bogus
- rec-rate entry) in case of ONLY coalescence force active.
-
-FIXED--ewalkup 2002/06/17
-2002/06/14 Immediate program crash if the "xml input file" is not XML.
-
-FIXED--Jon 2002/06/17
-2002/06/14 Converter, reading Migrate file, finds two populations with no
- name; the second overwrites the first
-
-FIXED--Jon 2002/06/17
-2002/06/14 There appears to be no way in the menu to call FST for Theta,
- even though the code apparently exists; Watterson is always called
- instead (but it's invalid on microsat data!)
-
-FIXED--Mary 2002/06/18
-2002/06/18 FST for Theta gives negative values habitually (it would be
- expected to do so occasionally but not all the time).
-
-FIXED--Mary 2002/06/21
-2002/06/20 Output report only reports on "Watterson" for Theta, even
- when the method used was actually FST.
-
-FIXED--Mary and Jon 2002/06/24
-2002/06/24 Rate categories cannot be set in menu for Brownian or Stepwise
- models (though the documentation claims we offer them)
-
-FIXED--ewalkup and Mary 2002/06/24
-2002/05/30 recombination start value gets not set when recombination
- is not specified in the xml file.
-
-FIXED -- xml schema now gives "unknown element" error
- Jon note: 2003/08/03
-2002/09/23 bogus tags are now rejected with a "mismatched tags" error
- message, is there no "unknown tag" error message.
- Note from ewalkup: this is best solved using a DTD
- for the XML.
-
diff --git a/src/bayeslike/bayesanalyzer_1d.cpp b/src/bayeslike/bayesanalyzer_1d.cpp
index 7546b1c..c34214a 100644
--- a/src/bayeslike/bayesanalyzer_1d.cpp
+++ b/src/bayeslike/bayesanalyzer_1d.cpp
@@ -1,13 +1,25 @@
-// $Id: bayesanalyzer_1d.cpp,v 1.39 2012/06/30 01:32:39 bobgian Exp $
+// $Id: bayesanalyzer_1d.cpp,v 1.40 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2004 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Devised May 2004 by Lucian Smith
// Uses data from a CollectionManager to do a bayesian analysis.
diff --git a/src/bayeslike/bayesanalyzer_1d.h b/src/bayeslike/bayesanalyzer_1d.h
index 1d2473d..f7fbba6 100644
--- a/src/bayeslike/bayesanalyzer_1d.h
+++ b/src/bayeslike/bayesanalyzer_1d.h
@@ -1,13 +1,25 @@
-// $Id: bayesanalyzer_1d.h,v 1.19 2012/06/30 01:32:39 bobgian Exp $
+// $Id: bayesanalyzer_1d.h,v 1.20 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2004 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*
The Bayesian analyzer holds vectors of 'BayesParamlike's, which are front
ends, of a sort, for BayesCurves. As the collection manager sends the
diff --git a/src/bayeslike/bayescurve.cpp b/src/bayeslike/bayescurve.cpp
index 676dc1c..4c9e4d2 100644
--- a/src/bayeslike/bayescurve.cpp
+++ b/src/bayeslike/bayescurve.cpp
@@ -1,13 +1,25 @@
-// $Id: bayescurve.cpp,v 1.22 2012/06/30 01:32:39 bobgian Exp $
+// $Id: bayescurve.cpp,v 1.23 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2004 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*
A bayes curve is a probability density function, aka a curve whose area
under its curve is 1.0
diff --git a/src/bayeslike/bayescurve.h b/src/bayeslike/bayescurve.h
index 5d59852..4605142 100644
--- a/src/bayeslike/bayescurve.h
+++ b/src/bayeslike/bayescurve.h
@@ -1,13 +1,25 @@
-// $Id: bayescurve.h,v 1.11 2011/03/07 06:08:39 bobgian Exp $
+// $Id: bayescurve.h,v 1.12 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2004 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*
A bayes curve is a probability density function, aka a curve whose area
under its curve is 1.0
diff --git a/src/bayeslike/bayesparamlike_1d.cpp b/src/bayeslike/bayesparamlike_1d.cpp
index fa21e70..8eebcb4 100644
--- a/src/bayeslike/bayesparamlike_1d.cpp
+++ b/src/bayeslike/bayesparamlike_1d.cpp
@@ -1,13 +1,25 @@
-// $Id: bayesparamlike_1d.cpp,v 1.20 2012/06/30 01:32:39 bobgian Exp $
+// $Id: bayesparamlike_1d.cpp,v 1.21 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2004 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cmath>
#include <utility>
diff --git a/src/bayeslike/bayesparamlike_1d.h b/src/bayeslike/bayesparamlike_1d.h
index 78fe22c..49cc258 100644
--- a/src/bayeslike/bayesparamlike_1d.h
+++ b/src/bayeslike/bayesparamlike_1d.h
@@ -1,13 +1,25 @@
-// $Id: bayesparamlike_1d.h,v 1.10 2011/03/07 06:08:39 bobgian Exp $
+// $Id: bayesparamlike_1d.h,v 1.11 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2004 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef BAYES_PARAMLIKE_1D_H
#define BAYES_PARAMLIKE_1D_H
diff --git a/src/control/chainmanager.cpp b/src/control/chainmanager.cpp
index f436408..24f9876 100644
--- a/src/control/chainmanager.cpp
+++ b/src/control/chainmanager.cpp
@@ -1,13 +1,25 @@
-// $Id: chainmanager.cpp,v 1.217 2013/10/25 17:00:52 mkkuhner Exp $
+// $Id: chainmanager.cpp,v 1.218 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cstdlib>
#include <iostream>
diff --git a/src/control/chainmanager.h b/src/control/chainmanager.h
index af4989c..435e9c6 100644
--- a/src/control/chainmanager.h
+++ b/src/control/chainmanager.h
@@ -1,13 +1,25 @@
-// $Id: chainmanager.h,v 1.54 2012/06/30 01:32:39 bobgian Exp $
+// $Id: chainmanager.h,v 1.55 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// The ChainManager is one of the big persistent objects in Lamarc. It
// is expected to exist from the end of the intial factory phase til
// after the last output report is displayed to the user.
diff --git a/src/control/chainout.cpp b/src/control/chainout.cpp
index 7fdd770..4f2f535 100644
--- a/src/control/chainout.cpp
+++ b/src/control/chainout.cpp
@@ -1,13 +1,25 @@
-// $Id: chainout.cpp,v 1.13 2011/02/20 04:13:59 bobgian Exp $
+// $Id: chainout.cpp,v 1.14 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include "chainout.h"
#ifdef DMALLOC_FUNC_CHECK
diff --git a/src/control/chainout.h b/src/control/chainout.h
index 1baefee..ec52893 100644
--- a/src/control/chainout.h
+++ b/src/control/chainout.h
@@ -1,13 +1,25 @@
-// $Id: chainout.h,v 1.17 2011/04/23 02:02:48 bobgian Exp $
+// $Id: chainout.h,v 1.18 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/********************************************************************
Class ChainOut contains summary information about the results of
a chain, such as the acceptance rate, parameter estimates, and
diff --git a/src/control/chainpack.cpp b/src/control/chainpack.cpp
index 8f4b968..f2bef51 100644
--- a/src/control/chainpack.cpp
+++ b/src/control/chainpack.cpp
@@ -1,13 +1,25 @@
-// $Id: chainpack.cpp,v 1.35 2012/06/30 01:32:39 bobgian Exp $
+// $Id: chainpack.cpp,v 1.36 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cstdlib>
#include <iostream>
diff --git a/src/control/chainpack.h b/src/control/chainpack.h
index fbb4b78..1aacfb6 100644
--- a/src/control/chainpack.h
+++ b/src/control/chainpack.h
@@ -1,13 +1,25 @@
-// $Id: chainpack.h,v 1.25 2012/06/30 01:32:39 bobgian Exp $
+// $Id: chainpack.h,v 1.26 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef CHAINPACK_H
#define CHAINPACK_H
diff --git a/src/control/chainparam.cpp b/src/control/chainparam.cpp
index 31f61aa..67dd187 100644
--- a/src/control/chainparam.cpp
+++ b/src/control/chainparam.cpp
@@ -1,13 +1,25 @@
-// $Id: chainparam.cpp,v 1.42 2013/06/03 17:23:13 jyamato Exp $
+// $Id: chainparam.cpp,v 1.43 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <numeric> // for std::accumulate in ChainParameters::GetNAllChains()
diff --git a/src/control/chainparam.h b/src/control/chainparam.h
index b8edb6a..65e7d78 100644
--- a/src/control/chainparam.h
+++ b/src/control/chainparam.h
@@ -1,13 +1,25 @@
-// $Id: chainparam.h,v 1.35 2012/06/30 01:32:39 bobgian Exp $
+// $Id: chainparam.h,v 1.36 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/********************************************************************
ChainParameters is a collection class used for internal communication
throughout Lamarc.
diff --git a/src/control/constants.cpp b/src/control/constants.cpp
index 877794a..55f5279 100644
--- a/src/control/constants.cpp
+++ b/src/control/constants.cpp
@@ -1,13 +1,25 @@
-// $Id: constants.cpp,v 1.28 2013/10/25 17:00:52 mkkuhner Exp $
+// $Id: constants.cpp,v 1.29 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
diff --git a/src/control/constants.h b/src/control/constants.h
index 309cd55..f966ab9 100644
--- a/src/control/constants.h
+++ b/src/control/constants.h
@@ -1,13 +1,25 @@
-// $Id: constants.h,v 1.108 2013/10/25 17:00:52 mkkuhner Exp $
+// $Id: constants.h,v 1.109 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef CONSTANTS_H
#define CONSTANTS_H
diff --git a/src/control/definitions.h b/src/control/definitions.h
index d22d31f..18c0ae8 100644
--- a/src/control/definitions.h
+++ b/src/control/definitions.h
@@ -1,13 +1,25 @@
-// $Id: definitions.h,v 1.21 2011/04/23 02:02:48 bobgian Exp $
+// $Id: definitions.h,v 1.22 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DEFINITIONS_H
#define DEFINITIONS_H
diff --git a/src/control/dynatracer.cpp b/src/control/dynatracer.cpp
index 754d9b2..768e25e 100644
--- a/src/control/dynatracer.cpp
+++ b/src/control/dynatracer.cpp
@@ -1,12 +1,24 @@
-// $Id: dynatracer.cpp,v 1.11 2012/06/30 01:32:39 bobgian Exp $
+// $Id: dynatracer.cpp,v 1.12 2018/01/03 21:32:54 mkkuhner Exp $
/*
- * Copyright 2009-2010 Bob Giansiracusa, Mary Kuhner, Jon Yamato, and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Bob Giansiracusa, Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
// The name of this file should be changed to "dynameter.cpp", but CVS makes that *so* difficult ...
diff --git a/src/control/dynatracer.h b/src/control/dynatracer.h
index b890bab..6790938 100644
--- a/src/control/dynatracer.h
+++ b/src/control/dynatracer.h
@@ -1,12 +1,24 @@
-// $Id: dynatracer.h,v 1.11 2012/06/30 01:32:39 bobgian Exp $
+// $Id: dynatracer.h,v 1.12 2018/01/03 21:32:54 mkkuhner Exp $
/*
- * Copyright 2009-2012 Bob Giansiracusa, Mary Kuhner, Jon Yamato, and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Bob Giansiracusa, Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
// The name of this file should be changed to "dynameter.h", but CVS makes that *so* difficult ...
#ifndef DYNATRACER_H
diff --git a/src/control/errhandling.cpp b/src/control/errhandling.cpp
index e2b397d..20e5e0b 100644
--- a/src/control/errhandling.cpp
+++ b/src/control/errhandling.cpp
@@ -1,13 +1,25 @@
-// $Id: errhandling.cpp,v 1.6 2012/06/30 01:32:39 bobgian Exp $
+// $Id: errhandling.cpp,v 1.7 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include "errhandling.h"
//------------------------------------------------------------------------------------
diff --git a/src/control/errhandling.h b/src/control/errhandling.h
index 37f53dc..6e3feac 100644
--- a/src/control/errhandling.h
+++ b/src/control/errhandling.h
@@ -1,13 +1,25 @@
-// $Id: errhandling.h,v 1.24 2011/03/07 06:08:47 bobgian Exp $
+// $Id: errhandling.h,v 1.25 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/**************************************************************
This file contains all exception classes defined for this
program. For all of these exceptions, the public function
diff --git a/src/control/lamarc.cpp b/src/control/lamarc.cpp
index db077a5..303ef57 100644
--- a/src/control/lamarc.cpp
+++ b/src/control/lamarc.cpp
@@ -1,12 +1,24 @@
-// $Id: lamarc.cpp,v 1.163 2013/11/07 22:56:31 jyamato Exp $
+// $Id: lamarc.cpp,v 1.165 2018/01/03 21:32:54 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <iostream>
@@ -796,7 +808,7 @@ void GetCloseConfirmation()
#if defined(LAMARC_COMPILE_LINUX) || defined(LAMARC_COMPILE_MACOSX)
-void CatchFileTooBigSignal(int signal)
+void CatchFileTooBigSignal(int)
{
//The kernel has sent a signal that the file size limit has been exceeded.
//We're going to assume that this was for the summary file writing, since
diff --git a/src/control/lamarc.h b/src/control/lamarc.h
index bdd8a6d..3150527 100644
--- a/src/control/lamarc.h
+++ b/src/control/lamarc.h
@@ -1,13 +1,25 @@
-// $Id: lamarc.h,v 1.25 2012/06/30 01:32:39 bobgian Exp $
+// $Id: lamarc.h,v 1.26 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/***************************************************************
This file (not a class at this time) contains the main driver
routines for LAMARC. It does the following:
diff --git a/src/control/regiongammainfo.cpp b/src/control/regiongammainfo.cpp
index 3d31850..b2db903 100644
--- a/src/control/regiongammainfo.cpp
+++ b/src/control/regiongammainfo.cpp
@@ -1,13 +1,25 @@
-// $Id: regiongammainfo.cpp,v 1.8 2011/03/07 06:08:47 bobgian Exp $
+// $Id: regiongammainfo.cpp,v 1.9 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, Eric Rynes and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, Eric Rynes and Joseph Felsenstein */
+
+
#include <cassert>
#include "regiongammainfo.h"
diff --git a/src/control/regiongammainfo.h b/src/control/regiongammainfo.h
index 203ec51..a44abb8 100644
--- a/src/control/regiongammainfo.h
+++ b/src/control/regiongammainfo.h
@@ -1,13 +1,25 @@
-// $Id: regiongammainfo.h,v 1.10 2011/03/08 19:21:53 bobgian Exp $
+// $Id: regiongammainfo.h,v 1.11 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef REGIONGAMMAINFO_H
#define REGIONGAMMAINFO_H
diff --git a/src/control/registry.cpp b/src/control/registry.cpp
index 9c3c5c7..d365872 100644
--- a/src/control/registry.cpp
+++ b/src/control/registry.cpp
@@ -1,13 +1,25 @@
-// $Id: registry.cpp,v 1.103 2013/10/17 21:36:15 mkkuhner Exp $
+// $Id: registry.cpp,v 1.104 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
diff --git a/src/control/registry.h b/src/control/registry.h
index 51368c0..245fdb8 100644
--- a/src/control/registry.h
+++ b/src/control/registry.h
@@ -1,13 +1,25 @@
-// $Id: registry.h,v 1.37 2012/06/30 01:32:39 bobgian Exp $
+// $Id: registry.h,v 1.38 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef REGISTRY_H
#define REGISTRY_H
diff --git a/src/control/sumfilehandler.cpp b/src/control/sumfilehandler.cpp
index bf01716..8540ffc 100644
--- a/src/control/sumfilehandler.cpp
+++ b/src/control/sumfilehandler.cpp
@@ -1,13 +1,25 @@
-// $Id: sumfilehandler.cpp,v 1.20 2013/11/07 22:46:06 mkkuhner Exp $
+// $Id: sumfilehandler.cpp,v 1.22 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <iostream>
#include "sumfilehandler.h"
@@ -187,7 +199,7 @@ void SumFileHandler::ReadInReplicateSummary(ChainPack& chainpack)
} // ReadInReplicateSummary
-void SumFileHandler::ReadInEndRegion(ChainPack& chainpack)
+void SumFileHandler::ReadInEndRegion(ChainPack&)
{
//This tag is only present when there is no Replicate Summary information.
string tag;
@@ -672,7 +684,7 @@ void SumFileHandler::WriteRegionSummary(ForceParameters& fp, double maxlike)
} // WriteRegionSummary
//Write summary info if more than one replicate is summarized.
-void SumFileHandler::WriteReplicateSummary( ForceParameters& fp, double maxlike, const ChainPack& chainpack)
+void SumFileHandler::WriteReplicateSummary( ForceParameters& fp, double maxlike, const ChainPack&)
{
if ( m_sumout.is_open() )
{
@@ -724,7 +736,7 @@ void SumFileHandler::WriteWhatWasRead(bool recoversumfile,
long int recover_chain,
bool recover_redochain,
bool recover_redomaximization,
- long int nregions,
+ long int, //nregions, but it was unused.
long int nreplicates,
const ChainPack& chainpack,
const CollectionManager& collectionmanager)
diff --git a/src/control/sumfilehandler.h b/src/control/sumfilehandler.h
index 8b405a8..908dfec 100644
--- a/src/control/sumfilehandler.h
+++ b/src/control/sumfilehandler.h
@@ -1,13 +1,25 @@
-// $Id: sumfilehandler.h,v 1.7 2011/03/07 06:08:47 bobgian Exp $
+// $Id: sumfilehandler.h,v 1.8 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2005 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// The Sumfile Handler is here to handle reading and writing of summary files.
// Earlier versions of the functions here can be found in chainmanager directly,
// since it was pulled out of there due to this sort of thing taking up too
diff --git a/src/control/types.h b/src/control/types.h
index 89c7909..5a60ff0 100644
--- a/src/control/types.h
+++ b/src/control/types.h
@@ -1,13 +1,25 @@
-// $Id: types.h,v 1.24 2012/06/30 01:32:39 bobgian Exp $
+// $Id: types.h,v 1.26 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TYPES_H
#define TYPES_H
@@ -23,7 +35,7 @@ class Branch;
class DataType;
class DataModel;
class Cell;
-class triplet;
+struct triplet;
class DLCalculator;
typedef boost::shared_ptr<Cell> Cell_ptr;
diff --git a/src/control/userparam.cpp b/src/control/userparam.cpp
index 65c4697..823a02f 100644
--- a/src/control/userparam.cpp
+++ b/src/control/userparam.cpp
@@ -1,13 +1,25 @@
-// $Id: userparam.cpp,v 1.51 2012/07/10 21:24:25 jmcgill Exp $
+// $Id: userparam.cpp,v 1.52 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <iostream>
#include <fstream>
diff --git a/src/control/userparam.h b/src/control/userparam.h
index 657a87b..2395a00 100644
--- a/src/control/userparam.h
+++ b/src/control/userparam.h
@@ -1,13 +1,25 @@
-// $Id: userparam.h,v 1.42 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: userparam.h,v 1.43 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/********************************************************************
UserParameters is a collection class used for internal communication
throughout Lamarc.
diff --git a/src/control/xmlsum_strings.cpp b/src/control/xmlsum_strings.cpp
index b5140ba..793a2ef 100644
--- a/src/control/xmlsum_strings.cpp
+++ b/src/control/xmlsum_strings.cpp
@@ -1,13 +1,25 @@
-// $Id: xmlsum_strings.cpp,v 1.20 2013/11/07 22:46:06 mkkuhner Exp $
+// $Id: xmlsum_strings.cpp,v 1.21 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
// strings assigned here should be defined in constants.h as
// public static const string xmlsum::members of class xmlsum
diff --git a/src/control/xmlsum_strings.h b/src/control/xmlsum_strings.h
index baacadc..b88519d 100644
--- a/src/control/xmlsum_strings.h
+++ b/src/control/xmlsum_strings.h
@@ -1,13 +1,25 @@
-// $Id: xmlsum_strings.h,v 1.21 2013/11/07 22:46:06 mkkuhner Exp $
+// $Id: xmlsum_strings.h,v 1.22 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef XMLSUMSTRINGS_H
#define XMLSUMSTRINGS_H
diff --git a/src/convErr/gc_cmdfile_err.cpp b/src/convErr/gc_cmdfile_err.cpp
index 54eb819..4d79d23 100644
--- a/src/convErr/gc_cmdfile_err.cpp
+++ b/src/convErr/gc_cmdfile_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_cmdfile_err.cpp,v 1.7 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_cmdfile_err.cpp,v 1.8 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_cmdfile_err.h"
#include "gc_strings_cmdfile.h"
diff --git a/src/convErr/gc_cmdfile_err.h b/src/convErr/gc_cmdfile_err.h
index 06715bc..eb3072a 100644
--- a/src/convErr/gc_cmdfile_err.h
+++ b/src/convErr/gc_cmdfile_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_cmdfile_err.h,v 1.8 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_cmdfile_err.h,v 1.9 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_CMDFILE_ERR
#define GC_CMDFILE_ERR
diff --git a/src/convErr/gc_data_missing_err.cpp b/src/convErr/gc_data_missing_err.cpp
index b88ed27..f1ec119 100644
--- a/src/convErr/gc_data_missing_err.cpp
+++ b/src/convErr/gc_data_missing_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_data_missing_err.cpp,v 1.4 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_data_missing_err.cpp,v 1.5 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_data_missing_err.h"
#include "gc_strings_data.h"
diff --git a/src/convErr/gc_data_missing_err.h b/src/convErr/gc_data_missing_err.h
index 06b9162..301b1e5 100644
--- a/src/convErr/gc_data_missing_err.h
+++ b/src/convErr/gc_data_missing_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_data_missing_err.h,v 1.5 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_data_missing_err.h,v 1.6 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_DATA_MISSING_ERR
#define GC_DATA_MISSING_ERR
diff --git a/src/convErr/gc_errhandling.cpp b/src/convErr/gc_errhandling.cpp
index 0a1dda6..283c48a 100644
--- a/src/convErr/gc_errhandling.cpp
+++ b/src/convErr/gc_errhandling.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_errhandling.cpp,v 1.13 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_errhandling.cpp,v 1.14 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_errhandling.h"
diff --git a/src/convErr/gc_errhandling.h b/src/convErr/gc_errhandling.h
index 0bc01b5..019bfba 100644
--- a/src/convErr/gc_errhandling.h
+++ b/src/convErr/gc_errhandling.h
@@ -1,13 +1,25 @@
-// $Id: gc_errhandling.h,v 1.11 2011/03/07 06:08:47 bobgian Exp $
+// $Id: gc_errhandling.h,v 1.12 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef GC_ERRHANDLING_H
#define GC_ERRHANDLING_H
diff --git a/src/convErr/gc_individual_err.cpp b/src/convErr/gc_individual_err.cpp
index 2ffeaea..83422f7 100644
--- a/src/convErr/gc_individual_err.cpp
+++ b/src/convErr/gc_individual_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_individual_err.cpp,v 1.6 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_individual_err.cpp,v 1.7 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_individual.h"
#include "gc_individual_err.h"
#include "gc_strings_individual.h"
diff --git a/src/convErr/gc_individual_err.h b/src/convErr/gc_individual_err.h
index cd95696..f0f1765 100644
--- a/src/convErr/gc_individual_err.h
+++ b/src/convErr/gc_individual_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_individual_err.h,v 1.7 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_individual_err.h,v 1.8 2018/01/03 21:32:54 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_INDIVIDUAL_ERR
#define GC_INDIVIDUAL_ERR
diff --git a/src/convErr/gc_infile_err.cpp b/src/convErr/gc_infile_err.cpp
index 0ea7b53..d199efa 100644
--- a/src/convErr/gc_infile_err.cpp
+++ b/src/convErr/gc_infile_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_infile_err.cpp,v 1.12 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_infile_err.cpp,v 1.13 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_data.h"
#include "gc_infile_err.h"
#include "gc_strings_infile.h"
diff --git a/src/convErr/gc_infile_err.h b/src/convErr/gc_infile_err.h
index 943f5e6..40bed35 100644
--- a/src/convErr/gc_infile_err.h
+++ b/src/convErr/gc_infile_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_infile_err.h,v 1.13 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_infile_err.h,v 1.14 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_INFILE_ERR
#define GC_INFILE_ERR
diff --git a/src/convErr/gc_locus_err.cpp b/src/convErr/gc_locus_err.cpp
index e75ce8e..b11c79e 100644
--- a/src/convErr/gc_locus_err.cpp
+++ b/src/convErr/gc_locus_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_locus_err.cpp,v 1.16 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_locus_err.cpp,v 1.17 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_data.h"
#include "gc_locus_err.h"
#include "gc_strings_locus.h"
diff --git a/src/convErr/gc_locus_err.h b/src/convErr/gc_locus_err.h
index 3ebab4c..9d50a44 100644
--- a/src/convErr/gc_locus_err.h
+++ b/src/convErr/gc_locus_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_locus_err.h,v 1.15 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_locus_err.h,v 1.16 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_LOCUS_ERR_H
#define GC_LOCUS_ERR_H
diff --git a/src/convErr/gc_map_err.cpp b/src/convErr/gc_map_err.cpp
index d8af44f..f594906 100644
--- a/src/convErr/gc_map_err.cpp
+++ b/src/convErr/gc_map_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_map_err.cpp,v 1.5 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_map_err.cpp,v 1.6 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_map_err.h"
#include "gc_strings_map.h"
diff --git a/src/convErr/gc_map_err.h b/src/convErr/gc_map_err.h
index 23121b0..ecff8b7 100644
--- a/src/convErr/gc_map_err.h
+++ b/src/convErr/gc_map_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_map_err.h,v 1.6 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_map_err.h,v 1.7 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_MAP_ERR
#define GC_MAP_ERR
diff --git a/src/convErr/gc_phase_err.cpp b/src/convErr/gc_phase_err.cpp
index 0d912ed..5c50f6a 100644
--- a/src/convErr/gc_phase_err.cpp
+++ b/src/convErr/gc_phase_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_phase_err.cpp,v 1.11 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_phase_err.cpp,v 1.12 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_phase_err.h"
#include "gc_phase_info.h"
#include "gc_strings_phase.h"
diff --git a/src/convErr/gc_phase_err.h b/src/convErr/gc_phase_err.h
index 217910a..8ba11fb 100644
--- a/src/convErr/gc_phase_err.h
+++ b/src/convErr/gc_phase_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_phase_err.h,v 1.11 2011/03/08 19:21:59 bobgian Exp $
+// $Id: gc_phase_err.h,v 1.12 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PHASE_ERR_H
#define GC_PHASE_ERR_H
diff --git a/src/convErr/gc_structures_err.cpp b/src/convErr/gc_structures_err.cpp
index 5ab000e..ac1885d 100644
--- a/src/convErr/gc_structures_err.cpp
+++ b/src/convErr/gc_structures_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_structures_err.cpp,v 1.12 2011/12/01 22:32:42 jmcgill Exp $
+// $Id: gc_structures_err.cpp,v 1.14 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_structures_err.h"
#include "gc_strings.h" // EWFIX.P4 refactor out
#include "gc_strings_structures.h"
@@ -73,7 +85,7 @@ missing_migration::missing_migration(const wxString & migrationName) throw()
{
}
-missing_migration::missing_migration(const wxString & fromName, const wxString & toName) throw()
+missing_migration::missing_migration(const wxString & toName, const wxString & fromName) throw()
: gc_structures_err(wxString::Format(gcerr_structures::migrationNotDefined, fromName.c_str(), toName.c_str()))
{
}
diff --git a/src/convErr/gc_structures_err.h b/src/convErr/gc_structures_err.h
index a79ba36..d8c0da5 100644
--- a/src/convErr/gc_structures_err.h
+++ b/src/convErr/gc_structures_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_structures_err.h,v 1.11 2011/12/01 22:32:42 jmcgill Exp $
+// $Id: gc_structures_err.h,v 1.12 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef GC_STRUCTURES_ERR_H
#define GC_STRUCTURES_ERR_H
diff --git a/src/convErr/gc_trait_err.cpp b/src/convErr/gc_trait_err.cpp
index 4eab2f6..0337d63 100644
--- a/src/convErr/gc_trait_err.cpp
+++ b/src/convErr/gc_trait_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_trait_err.cpp,v 1.9 2012/06/30 01:32:39 bobgian Exp $
+// $Id: gc_trait_err.cpp,v 1.10 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_trait_err.h"
#include "gc_strings_trait.h"
diff --git a/src/convErr/gc_trait_err.h b/src/convErr/gc_trait_err.h
index 408cd4d..d2ecbfe 100644
--- a/src/convErr/gc_trait_err.h
+++ b/src/convErr/gc_trait_err.h
@@ -1,13 +1,25 @@
-// $Id: gc_trait_err.h,v 1.9 2011/06/22 18:22:22 jmcgill Exp $
+// $Id: gc_trait_err.h,v 1.10 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_TRAIT_ERR
#define GC_TRAIT_ERR
diff --git a/src/convModel/cmdfileschema.cpp b/src/convModel/cmdfileschema.cpp
index b5929c4..3e1a65f 100644
--- a/src/convModel/cmdfileschema.cpp
+++ b/src/convModel/cmdfileschema.cpp
@@ -1,13 +1,25 @@
-// $Id: cmdfileschema.cpp,v 1.23 2012/06/30 01:32:39 bobgian Exp $
+// $Id: cmdfileschema.cpp,v 1.24 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <iostream>
#include "cmdfileschema.h"
diff --git a/src/convModel/cmdfileschema.h b/src/convModel/cmdfileschema.h
index 586289e..95ff37f 100644
--- a/src/convModel/cmdfileschema.h
+++ b/src/convModel/cmdfileschema.h
@@ -1,13 +1,25 @@
-// $Id: cmdfileschema.h,v 1.4 2011/03/07 06:08:47 bobgian Exp $
+// $Id: cmdfileschema.h,v 1.5 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef CMDFILESCHEMA_H
#define CMDFILESCHEMA_H
diff --git a/src/convModel/gc_creation_info.cpp b/src/convModel/gc_creation_info.cpp
index 7da031a..c83707b 100644
--- a/src/convModel/gc_creation_info.cpp
+++ b/src/convModel/gc_creation_info.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_creation_info.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_creation_info.cpp,v 1.4 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "wx/string.h"
diff --git a/src/convModel/gc_creation_info.h b/src/convModel/gc_creation_info.h
index 3eef6ed..b93393e 100644
--- a/src/convModel/gc_creation_info.h
+++ b/src/convModel/gc_creation_info.h
@@ -1,13 +1,25 @@
-// $Id: gc_creation_info.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_creation_info.h,v 1.5 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_CREATION_INFO_H
#define GC_CREATION_INFO_H
diff --git a/src/convModel/gc_datastore.cpp b/src/convModel/gc_datastore.cpp
index db2ddcd..cd42e18 100644
--- a/src/convModel/gc_datastore.cpp
+++ b/src/convModel/gc_datastore.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_datastore.cpp,v 1.104 2012/06/30 01:32:39 bobgian Exp $
+// $Id: gc_datastore.cpp,v 1.105 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "cmdfileschema.h"
diff --git a/src/convModel/gc_datastore.h b/src/convModel/gc_datastore.h
index 487a01c..410d06e 100644
--- a/src/convModel/gc_datastore.h
+++ b/src/convModel/gc_datastore.h
@@ -1,13 +1,25 @@
-// $Id: gc_datastore.h,v 1.99 2012/06/30 01:32:39 bobgian Exp $
+// $Id: gc_datastore.h,v 1.100 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_DATASTORE_H
#define GC_DATASTORE_H
diff --git a/src/convModel/gc_datastore_export.cpp b/src/convModel/gc_datastore_export.cpp
index 38d598f..e8275d9 100644
--- a/src/convModel/gc_datastore_export.cpp
+++ b/src/convModel/gc_datastore_export.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_datastore_export.cpp,v 1.80 2013/11/07 22:46:06 mkkuhner Exp $
+// $Id: gc_datastore_export.cpp,v 1.81 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_data.h"
diff --git a/src/convModel/gc_datastore_files.cpp b/src/convModel/gc_datastore_files.cpp
index bdfc7a5..8c6976d 100644
--- a/src/convModel/gc_datastore_files.cpp
+++ b/src/convModel/gc_datastore_files.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_datastore_files.cpp,v 1.36 2011/06/22 18:22:22 jmcgill Exp $
+// $Id: gc_datastore_files.cpp,v 1.37 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_creation_info.h"
diff --git a/src/convModel/gc_datastore_readcmd.cpp b/src/convModel/gc_datastore_readcmd.cpp
index 94026d3..41972d8 100644
--- a/src/convModel/gc_datastore_readcmd.cpp
+++ b/src/convModel/gc_datastore_readcmd.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_datastore_readcmd.cpp,v 1.67 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_datastore_readcmd.cpp,v 1.68 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "errhandling.h" // for unrecognized_tag_error // EWFIX.P4 -- factor out xml errors
diff --git a/src/convModel/gc_datastore_writebatch.cpp b/src/convModel/gc_datastore_writebatch.cpp
index e7afe04..c1de352 100644
--- a/src/convModel/gc_datastore_writebatch.cpp
+++ b/src/convModel/gc_datastore_writebatch.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_datastore_writebatch.cpp,v 1.10 2011/06/22 18:22:22 jmcgill Exp $
+// $Id: gc_datastore_writebatch.cpp,v 1.11 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "cnv_strings.h"
diff --git a/src/convModel/gc_default.cpp b/src/convModel/gc_default.cpp
index bd88746..cfd77e5 100644
--- a/src/convModel/gc_default.cpp
+++ b/src/convModel/gc_default.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_default.cpp,v 1.12 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_default.cpp,v 1.13 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_default.h"
#include "wx/string.h"
diff --git a/src/convModel/gc_default.h b/src/convModel/gc_default.h
index 5d6fde2..d436d79 100644
--- a/src/convModel/gc_default.h
+++ b/src/convModel/gc_default.h
@@ -1,13 +1,25 @@
-// $Id: gc_default.h,v 1.12 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_default.h,v 1.13 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_DEFAULT_H
#define GC_DEFAULT_H
diff --git a/src/convModel/gc_dictionary.cpp b/src/convModel/gc_dictionary.cpp
index 84aae4c..2ca672a 100644
--- a/src/convModel/gc_dictionary.cpp
+++ b/src/convModel/gc_dictionary.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_dictionary.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_dictionary.cpp,v 1.4 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_dictionary.h"
diff --git a/src/convModel/gc_dictionary.h b/src/convModel/gc_dictionary.h
index 1873f66..cde015c 100644
--- a/src/convModel/gc_dictionary.h
+++ b/src/convModel/gc_dictionary.h
@@ -1,13 +1,25 @@
-// $Id: gc_dictionary.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_dictionary.h,v 1.5 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_DICTIONARY_H
#define GC_DICTIONARY_H
diff --git a/src/convModel/gc_exportable.cpp b/src/convModel/gc_exportable.cpp
index b214fa6..a9a8825 100644
--- a/src/convModel/gc_exportable.cpp
+++ b/src/convModel/gc_exportable.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_exportable.cpp,v 1.7 2011/06/22 18:22:22 jmcgill Exp $
+// $Id: gc_exportable.cpp,v 1.8 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_errhandling.h"
#include "gc_exportable.h"
#include "gc_individual.h"
diff --git a/src/convModel/gc_exportable.h b/src/convModel/gc_exportable.h
index 02d6b37..2b27764 100644
--- a/src/convModel/gc_exportable.h
+++ b/src/convModel/gc_exportable.h
@@ -1,13 +1,25 @@
-// $Id: gc_exportable.h,v 1.7 2011/06/22 18:22:22 jmcgill Exp $
+// $Id: gc_exportable.h,v 1.8 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_EXPORTABLE_H
#define GC_EXPORTABLE_H
diff --git a/src/convModel/gc_file.cpp b/src/convModel/gc_file.cpp
index 7d6fa36..2f2ed99 100644
--- a/src/convModel/gc_file.cpp
+++ b/src/convModel/gc_file.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_file.cpp,v 1.38 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_file.cpp,v 1.39 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "Converter_LamarcDS.h"
diff --git a/src/convModel/gc_file.h b/src/convModel/gc_file.h
index 5bbd196..eca9ebc 100644
--- a/src/convModel/gc_file.h
+++ b/src/convModel/gc_file.h
@@ -1,13 +1,25 @@
-// $Id: gc_file.h,v 1.36 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_file.h,v 1.37 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_FILE_H
#define GC_FILE_H
diff --git a/src/convModel/gc_file_info.cpp b/src/convModel/gc_file_info.cpp
index 3adeea0..072d0ad 100644
--- a/src/convModel/gc_file_info.cpp
+++ b/src/convModel/gc_file_info.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_file_info.cpp,v 1.5 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_file_info.cpp,v 1.6 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_default.h"
diff --git a/src/convModel/gc_file_info.h b/src/convModel/gc_file_info.h
index ba25bf4..1aee34b 100644
--- a/src/convModel/gc_file_info.h
+++ b/src/convModel/gc_file_info.h
@@ -1,13 +1,25 @@
-// $Id: gc_file_info.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_file_info.h,v 1.5 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_FILE_INFO_H
#define GC_FILE_INFO_H
diff --git a/src/convModel/gc_id_set.cpp b/src/convModel/gc_id_set.cpp
index 1a584d1..9f463a7 100644
--- a/src/convModel/gc_id_set.cpp
+++ b/src/convModel/gc_id_set.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_id_set.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_id_set.cpp,v 1.4 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_id_set.h"
wxString
diff --git a/src/convModel/gc_id_set.h b/src/convModel/gc_id_set.h
index 5a35b6a..f99f1dc 100644
--- a/src/convModel/gc_id_set.h
+++ b/src/convModel/gc_id_set.h
@@ -1,13 +1,25 @@
-// $Id: gc_id_set.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_id_set.h,v 1.5 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_ID_SET_H
#define GC_ID_SET_H
diff --git a/src/convModel/gc_individual.cpp b/src/convModel/gc_individual.cpp
index 2537e10..b99d0b1 100644
--- a/src/convModel/gc_individual.cpp
+++ b/src/convModel/gc_individual.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_individual.cpp,v 1.18 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_individual.cpp,v 1.19 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_errhandling.h"
diff --git a/src/convModel/gc_individual.h b/src/convModel/gc_individual.h
index aff8b38..6758098 100644
--- a/src/convModel/gc_individual.h
+++ b/src/convModel/gc_individual.h
@@ -1,13 +1,25 @@
-// $Id: gc_individual.h,v 1.13 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_individual.h,v 1.14 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_INDIVIDUAL_H
#define GC_INDIVIDUAL_H
diff --git a/src/convModel/gc_mapfile.cpp b/src/convModel/gc_mapfile.cpp
index f16ec03..778f382 100644
--- a/src/convModel/gc_mapfile.cpp
+++ b/src/convModel/gc_mapfile.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_mapfile.cpp,v 1.11 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_mapfile.cpp,v 1.12 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#if 0 // Potentially DEAD CODE (bobgian, Feb 2010)
#include "gc_data.h"
diff --git a/src/convModel/gc_mapfile.h b/src/convModel/gc_mapfile.h
index 211362b..f6058cf 100644
--- a/src/convModel/gc_mapfile.h
+++ b/src/convModel/gc_mapfile.h
@@ -1,13 +1,25 @@
-// $Id: gc_mapfile.h,v 1.11 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_mapfile.h,v 1.12 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_MAPFILE_H
#define GC_MAPFILE_H
diff --git a/src/convModel/gc_migration.cpp b/src/convModel/gc_migration.cpp
index 0a66ad3..565ae07 100644
--- a/src/convModel/gc_migration.cpp
+++ b/src/convModel/gc_migration.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_migration.cpp,v 1.4 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_migration.cpp,v 1.5 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_creation_info.h" // JRM this doing anything?
diff --git a/src/convModel/gc_migration.h b/src/convModel/gc_migration.h
index c082f9e..cf7b4ab 100644
--- a/src/convModel/gc_migration.h
+++ b/src/convModel/gc_migration.h
@@ -1,13 +1,25 @@
-// $Id: gc_migration.h,v 1.4 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_migration.h,v 1.5 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_MIGRATION_H
#define GC_MIGRATION_H
diff --git a/src/convModel/gc_panel.cpp b/src/convModel/gc_panel.cpp
index 19fb6d9..66ed164 100644
--- a/src/convModel/gc_panel.cpp
+++ b/src/convModel/gc_panel.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_panel.cpp,v 1.2 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_panel.cpp,v 1.3 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_creation_info.h" // JRM this doing anything?
diff --git a/src/convModel/gc_panel.h b/src/convModel/gc_panel.h
index 79b68a7..8fcacb5 100644
--- a/src/convModel/gc_panel.h
+++ b/src/convModel/gc_panel.h
@@ -1,13 +1,25 @@
-// $Id: gc_panel.h,v 1.2 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_panel.h,v 1.3 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PANEL_H
#define GC_PANEL_H
diff --git a/src/convModel/gc_parent.cpp b/src/convModel/gc_parent.cpp
index 3a37e02..72c6331 100644
--- a/src/convModel/gc_parent.cpp
+++ b/src/convModel/gc_parent.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_parent.cpp,v 1.3 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_parent.cpp,v 1.4 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_creation_info.h" // JRM this doing anything?
diff --git a/src/convModel/gc_parent.h b/src/convModel/gc_parent.h
index abac7f4..c9468e9 100644
--- a/src/convModel/gc_parent.h
+++ b/src/convModel/gc_parent.h
@@ -1,13 +1,25 @@
-// $Id: gc_parent.h,v 1.3 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_parent.h,v 1.4 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PARENT_H
#define GC_PARENT_H
diff --git a/src/convModel/gc_phase.cpp b/src/convModel/gc_phase.cpp
index 64374d8..b9c5961 100644
--- a/src/convModel/gc_phase.cpp
+++ b/src/convModel/gc_phase.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_phase.cpp,v 1.9 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_phase.cpp,v 1.10 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_locus.h"
diff --git a/src/convModel/gc_phase.h b/src/convModel/gc_phase.h
index cd1067f..51eaa51 100644
--- a/src/convModel/gc_phase.h
+++ b/src/convModel/gc_phase.h
@@ -1,13 +1,25 @@
-// $Id: gc_phase.h,v 1.10 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_phase.h,v 1.11 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PHASE_H
#define GC_PHASE_H
diff --git a/src/convModel/gc_phase_info.cpp b/src/convModel/gc_phase_info.cpp
index 6fab35d..c74dd77 100644
--- a/src/convModel/gc_phase_info.cpp
+++ b/src/convModel/gc_phase_info.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_phase_info.cpp,v 1.13 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_phase_info.cpp,v 1.14 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_data.h"
diff --git a/src/convModel/gc_phase_info.h b/src/convModel/gc_phase_info.h
index 055a4e4..3258fa6 100644
--- a/src/convModel/gc_phase_info.h
+++ b/src/convModel/gc_phase_info.h
@@ -1,13 +1,25 @@
-// $Id: gc_phase_info.h,v 1.12 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_phase_info.h,v 1.13 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PHASE_INFO
#define GC_PHASE_INFO
diff --git a/src/convModel/gc_phenotype.cpp b/src/convModel/gc_phenotype.cpp
index e49e35b..6d44020 100644
--- a/src/convModel/gc_phenotype.cpp
+++ b/src/convModel/gc_phenotype.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_phenotype.cpp,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_phenotype.cpp,v 1.7 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_default.h"
diff --git a/src/convModel/gc_phenotype.h b/src/convModel/gc_phenotype.h
index 4283629..ab03375 100644
--- a/src/convModel/gc_phenotype.h
+++ b/src/convModel/gc_phenotype.h
@@ -1,13 +1,25 @@
-// $Id: gc_phenotype.h,v 1.6 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_phenotype.h,v 1.7 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PHENOTYPE_H
#define GC_PHENOTYPE_H
diff --git a/src/convModel/gc_set_util.cpp b/src/convModel/gc_set_util.cpp
index 480491b..b2be805 100644
--- a/src/convModel/gc_set_util.cpp
+++ b/src/convModel/gc_set_util.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_set_util.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_set_util.cpp,v 1.4 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_set_util.h"
#include "wx/log.h"
diff --git a/src/convModel/gc_set_util.h b/src/convModel/gc_set_util.h
index 04e0884..2355bae 100644
--- a/src/convModel/gc_set_util.h
+++ b/src/convModel/gc_set_util.h
@@ -1,13 +1,25 @@
-// $Id: gc_set_util.h,v 1.5 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_set_util.h,v 1.6 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_SET_UTIL_H
#define GC_SET_UTIL_H
diff --git a/src/convModel/gc_structure_maps.cpp b/src/convModel/gc_structure_maps.cpp
index 3a826aa..ae74c9f 100644
--- a/src/convModel/gc_structure_maps.cpp
+++ b/src/convModel/gc_structure_maps.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_structure_maps.cpp,v 1.18 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_structure_maps.cpp,v 1.20 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_data.h"
#include "gc_default.h"
#include "gc_region.h"
@@ -341,8 +353,8 @@ gcMigrationPair::gcMigrationPair()
{
}
-gcMigrationPair::gcMigrationPair(size_t fromId, size_t toId)
- : std::pair<size_t,size_t>(fromId,toId)
+gcMigrationPair::gcMigrationPair(size_t toId, size_t fromId)
+ : std::pair<size_t,size_t>(toId,fromId)
{
}
diff --git a/src/convModel/gc_structure_maps.h b/src/convModel/gc_structure_maps.h
index 1f799e0..f38d377 100644
--- a/src/convModel/gc_structure_maps.h
+++ b/src/convModel/gc_structure_maps.h
@@ -1,13 +1,25 @@
-// $Id: gc_structure_maps.h,v 1.15 2011/12/01 22:32:42 jmcgill Exp $
+// $Id: gc_structure_maps.h,v 1.16 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRUCTURE_MAPS_H
#define GC_STRUCTURE_MAPS_H
diff --git a/src/convModel/gc_structures.cpp b/src/convModel/gc_structures.cpp
index 036c354..1d3b76a 100644
--- a/src/convModel/gc_structures.cpp
+++ b/src/convModel/gc_structures.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_structures.cpp,v 1.66 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_structures.cpp,v 1.68 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_creation_info.h"
@@ -1065,31 +1077,29 @@ GCStructures::MakeParent(wxString name)
}
gcMigration &
-GCStructures::MakeMigration(bool blessed, size_t fromId, size_t toId )
+GCStructures::MakeMigration(bool blessed, size_t toId, size_t fromId )
{
gcMigration newMigration;
newMigration.m_blessed = true;
- newMigration.m_hasFrom = true;
- newMigration.m_fromId = fromId;
- newMigration.m_hasTo = true;
- newMigration.m_toId = toId;
+ newMigration.SetToId(toId);
+ newMigration.SetFromId(fromId);
newMigration.m_startValue = 50.0;
newMigration.m_method = migmethod_USER;
newMigration.m_profile = migprofile_NONE;
newMigration.m_constraint = migconstraint_UNCONSTRAINED;
- newMigration.SetName(wxString::Format(_T("cell%i:%i "), (int)fromId, (int)toId)); //JMDBG
+ newMigration.SetName(wxString::Format(_T("cell%i:%i "), (int)toId, (int)fromId)); //JMDBG
- wxLogVerbose("****MakeMigration from: %i to: %i", (int)fromId, (int)toId ); // JMDBG
+ wxLogVerbose("****MakeMigration into: %i from: %i", (int)toId, (int)fromId ); // JMDBG
size_t newId = newMigration.GetId();
- gcMigrationPair fromToPair = gcMigrationPair(fromId, toId);
+ gcMigrationPair toFromPair = gcMigrationPair(toId, fromId);
// don't do any setting after this step --
// it won't propagate
- m_migrations[fromToPair] = newMigration;
- return m_migrations[fromToPair];
+ m_migrations[toFromPair] = newMigration;
+ return m_migrations[toFromPair];
}
gcTraitInfo &
@@ -1336,9 +1346,9 @@ GCStructures::GetMigration(size_t id) const
}
bool
-GCStructures::HasMigration(size_t fromId, size_t toId) const
+GCStructures::HasMigration(size_t toId, size_t fromId) const
{
- gcMigrationPair p(fromId, toId);
+ gcMigrationPair p(toId, fromId);
gcMigrationMap::const_iterator iter = m_migrations.find(p);
if(iter != m_migrations.end())
{
@@ -1348,9 +1358,9 @@ GCStructures::HasMigration(size_t fromId, size_t toId) const
}
gcMigration &
-GCStructures::GetMigration(size_t fromId, size_t toId)
+GCStructures::GetMigration(size_t toId, size_t fromId)
{
- gcMigrationPair p(fromId, toId);
+ gcMigrationPair p(toId, fromId);
gcMigrationMap::iterator iter = m_migrations.find(p);
if(iter != m_migrations.end())
{
@@ -1390,13 +1400,13 @@ GCStructures::GetMigration(size_t fromId, size_t toId)
toName = wxString("Bad to ID:%s", toId);
}
}
- throw missing_migration(fromName, toName);
+ throw missing_migration(toName, fromName);
}
const gcMigration &
-GCStructures::GetMigration(size_t fromId, size_t toId) const
+GCStructures::GetMigration(size_t toId, size_t fromId) const
{
- gcMigrationPair p(fromId, toId);
+ gcMigrationPair p(toId, fromId);
gcMigrationMap::const_iterator iter = m_migrations.find(p);
if(iter != m_migrations.end())
{
@@ -2245,9 +2255,9 @@ GCStructures::RemoveLocus(gcLocus & locus)
}
void
-GCStructures::RemoveMigration(size_t fromId, size_t toId)
+GCStructures::RemoveMigration(size_t toId, size_t fromId)
{
- gcMigrationPair p(fromId, toId);
+ gcMigrationPair p(toId, fromId);
gcMigrationMap::iterator masterIter = m_migrations.find(p);
m_migrations.erase(masterIter);
}
diff --git a/src/convModel/gc_structures.h b/src/convModel/gc_structures.h
index 328acc9..ce8aad1 100644
--- a/src/convModel/gc_structures.h
+++ b/src/convModel/gc_structures.h
@@ -1,13 +1,25 @@
-// $Id: gc_structures.h,v 1.38 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_structures.h,v 1.40 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRUCTURES_H
#define GC_STRUCTURES_H
@@ -174,7 +186,7 @@ class GCStructures
const gcPanel & GetPanel(size_t regionId, size_t popId) const;
const gcParent & GetParent(size_t id) const;
const gcMigration & GetMigration(size_t id) const;
- const gcMigration & GetMigration(size_t fromId, size_t toId) const;
+ const gcMigration & GetMigration(size_t toId, size_t fromId) const;
gcTraitAllele & GetAllele(gcTraitInfo&,wxString name);
gcTraitAllele & GetAllele(wxString name);
@@ -188,7 +200,7 @@ class GCStructures
gcPanel & GetPanel(size_t regionId, size_t popId);
gcParent & GetParent(wxString name);
gcMigration & GetMigration(wxString name);
- gcMigration & GetMigration(size_t fromId, size_t toId);
+ gcMigration & GetMigration(size_t toId, size_t fromId);
const gcTraitAllele & GetAllele(wxString name) const;
const gcRegion & GetRegion(wxString name) const;
@@ -202,7 +214,7 @@ class GCStructures
bool HasParents() const;
bool HasPanel(size_t regionId, size_t popId) const;
bool HasBlock(size_t locusId, size_t popId) const;
- bool HasMigration(size_t fromId, size_t toId) const;
+ bool HasMigration(size_t toId, size_t fromId) const;
const GCPopMatcher & GetPopMatcher(const GCFile&) const;
const GCLocusMatcher & GetLocusMatcher(const GCFile&) const;
@@ -240,11 +252,11 @@ class GCStructures
gcPhenotype & MakePhenotype(wxString name=wxEmptyString);
gcPopulation & MakePop(wxString name=wxEmptyString, bool blessed=false);
gcTraitInfo & MakeTrait(wxString name);
- gcPanel & MakePanel(wxString name, bool blessed, size_t m_regionId, size_t m_popId);
+ gcPanel & MakePanel(wxString name, bool blessed, size_t regionId, size_t popId);
gcParent & MakeParent(wxString name);
- gcMigration & MakeMigration(bool blessed, size_t m_fromId, size_t m_toId);
+ gcMigration & MakeMigration(bool blessed, size_t toId, size_t fromId);
- gcPanel & CreatePanel(size_t m_regionId, size_t m_popId);
+ gcPanel & CreatePanel(size_t regionId, size_t popId);
void Rename(GCQuantum & object, wxString newName);
@@ -272,7 +284,7 @@ class GCStructures
void RemovePanel(size_t regionId, size_t popId);
void RemoveParent(size_t parentId);
void RemoveParents();
- void RemoveMigration(size_t fromId, size_t toId);
+ void RemoveMigration(size_t toId, size_t fromId);
bool GetFileSelection(size_t fileId) const;
void SetFileSelection(size_t fileId, bool selected);
diff --git a/src/convModel/gc_trait.cpp b/src/convModel/gc_trait.cpp
index 9656d54..531158d 100644
--- a/src/convModel/gc_trait.cpp
+++ b/src/convModel/gc_trait.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_trait.cpp,v 1.12 2011/06/22 18:22:22 jmcgill Exp $
+// $Id: gc_trait.cpp,v 1.13 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_default.h"
diff --git a/src/convModel/gc_trait.h b/src/convModel/gc_trait.h
index f215dfc..a33fec4 100644
--- a/src/convModel/gc_trait.h
+++ b/src/convModel/gc_trait.h
@@ -1,13 +1,25 @@
-// $Id: gc_trait.h,v 1.12 2011/06/22 18:22:22 jmcgill Exp $
+// $Id: gc_trait.h,v 1.13 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_TRAIT_H
#define GC_TRAIT_H
diff --git a/src/convModel/gc_trait_allele.cpp b/src/convModel/gc_trait_allele.cpp
index 8f7615f..9d6764d 100644
--- a/src/convModel/gc_trait_allele.cpp
+++ b/src/convModel/gc_trait_allele.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_trait_allele.cpp,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_trait_allele.cpp,v 1.5 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_default.h"
diff --git a/src/convModel/gc_trait_allele.h b/src/convModel/gc_trait_allele.h
index 43121c0..6077f2c 100644
--- a/src/convModel/gc_trait_allele.h
+++ b/src/convModel/gc_trait_allele.h
@@ -1,13 +1,25 @@
-// $Id: gc_trait_allele.h,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_trait_allele.h,v 1.6 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_TRAIT_ALLELE_H
#define GC_TRAIT_ALLELE_H
diff --git a/src/convModel/gc_types.cpp b/src/convModel/gc_types.cpp
index 5f2a567..58ad9b6 100644
--- a/src/convModel/gc_types.cpp
+++ b/src/convModel/gc_types.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_types.cpp,v 1.9 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_types.cpp,v 1.10 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_types.h"
gcGeneralDataType::gcGeneralDataType()
diff --git a/src/convModel/gc_types.h b/src/convModel/gc_types.h
index cce6881..fa5bf06 100644
--- a/src/convModel/gc_types.h
+++ b/src/convModel/gc_types.h
@@ -1,13 +1,25 @@
-// $Id: gc_types.h,v 1.30 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_types.h,v 1.31 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_TYPES_H
#define GC_TYPES_H
diff --git a/src/convParse/gc_genotype_resolution.cpp b/src/convParse/gc_genotype_resolution.cpp
index e909b29..c37dbed 100644
--- a/src/convParse/gc_genotype_resolution.cpp
+++ b/src/convParse/gc_genotype_resolution.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_genotype_resolution.cpp,v 1.9 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_genotype_resolution.cpp,v 1.10 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_genotype_resolution.h"
#include "gc_strings.h"
#include "gc_trait_err.h"
diff --git a/src/convParse/gc_genotype_resolution.h b/src/convParse/gc_genotype_resolution.h
index d2858ef..4220dc3 100644
--- a/src/convParse/gc_genotype_resolution.h
+++ b/src/convParse/gc_genotype_resolution.h
@@ -1,13 +1,25 @@
-// $Id: gc_genotype_resolution.h,v 1.8 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_genotype_resolution.h,v 1.9 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_GENOTYPE_RESOLUTION_H
#define GC_GENOTYPE_RESOLUTION_H
diff --git a/src/convParse/gc_loci_match.cpp b/src/convParse/gc_loci_match.cpp
index 1db5936..60c469a 100644
--- a/src/convParse/gc_loci_match.cpp
+++ b/src/convParse/gc_loci_match.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_loci_match.cpp,v 1.16 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_loci_match.cpp,v 1.17 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_datastore.h"
diff --git a/src/convParse/gc_loci_match.h b/src/convParse/gc_loci_match.h
index c9e1cfe..2d0f039 100644
--- a/src/convParse/gc_loci_match.h
+++ b/src/convParse/gc_loci_match.h
@@ -1,13 +1,25 @@
-// $Id: gc_loci_match.h,v 1.11 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_loci_match.h,v 1.12 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_LOCI_MATCH_H
#define GC_LOCI_MATCH_H
diff --git a/src/convParse/gc_locus.cpp b/src/convParse/gc_locus.cpp
index 25335df..f7c21ad 100644
--- a/src/convParse/gc_locus.cpp
+++ b/src/convParse/gc_locus.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_locus.cpp,v 1.35 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_locus.cpp,v 1.36 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_creation_info.h"
diff --git a/src/convParse/gc_locus.h b/src/convParse/gc_locus.h
index 0f16247..fb1d24b 100644
--- a/src/convParse/gc_locus.h
+++ b/src/convParse/gc_locus.h
@@ -1,13 +1,25 @@
-// $Id: gc_locus.h,v 1.21 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_locus.h,v 1.22 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_LOCUS_H
#define GC_LOCUS_H
diff --git a/src/convParse/gc_migrate.cpp b/src/convParse/gc_migrate.cpp
index b0d268f..d88677a 100644
--- a/src/convParse/gc_migrate.cpp
+++ b/src/convParse/gc_migrate.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_migrate.cpp,v 1.33 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_migrate.cpp,v 1.34 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_data.h"
diff --git a/src/convParse/gc_migrate.h b/src/convParse/gc_migrate.h
index 548e820..159aa63 100644
--- a/src/convParse/gc_migrate.h
+++ b/src/convParse/gc_migrate.h
@@ -1,13 +1,25 @@
-// $Id: gc_migrate.h,v 1.17 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_migrate.h,v 1.18 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_MIGRATE_H
#define GC_MIGRATE_H
diff --git a/src/convParse/gc_parse.cpp b/src/convParse/gc_parse.cpp
index e17428b..a419864 100644
--- a/src/convParse/gc_parse.cpp
+++ b/src/convParse/gc_parse.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_parse.cpp,v 1.23 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_parse.cpp,v 1.24 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_data.h"
diff --git a/src/convParse/gc_parse.h b/src/convParse/gc_parse.h
index ceecbaf..18b64e9 100644
--- a/src/convParse/gc_parse.h
+++ b/src/convParse/gc_parse.h
@@ -1,13 +1,25 @@
-// $Id: gc_parse.h,v 1.17 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_parse.h,v 1.18 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PARSE_H
#define GC_PARSE_H
diff --git a/src/convParse/gc_parse_block.cpp b/src/convParse/gc_parse_block.cpp
index 3742dc6..237d218 100644
--- a/src/convParse/gc_parse_block.cpp
+++ b/src/convParse/gc_parse_block.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_parse_block.cpp,v 1.8 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_parse_block.cpp,v 1.9 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_default.h"
diff --git a/src/convParse/gc_parse_block.h b/src/convParse/gc_parse_block.h
index 57a70be..c805aba 100644
--- a/src/convParse/gc_parse_block.h
+++ b/src/convParse/gc_parse_block.h
@@ -1,13 +1,25 @@
-// $Id: gc_parse_block.h,v 1.10 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_parse_block.h,v 1.11 2018/01/03 21:32:55 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PARSE_BLOCK_H
#define GC_PARSE_BLOCK_H
diff --git a/src/convParse/gc_parse_locus.cpp b/src/convParse/gc_parse_locus.cpp
index 2be66a4..5232bf8 100644
--- a/src/convParse/gc_parse_locus.cpp
+++ b/src/convParse/gc_parse_locus.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_parse_locus.cpp,v 1.13 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_parse_locus.cpp,v 1.14 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_default.h"
diff --git a/src/convParse/gc_parse_locus.h b/src/convParse/gc_parse_locus.h
index 235aeac..c48f7f7 100644
--- a/src/convParse/gc_parse_locus.h
+++ b/src/convParse/gc_parse_locus.h
@@ -1,13 +1,25 @@
-// $Id: gc_parse_locus.h,v 1.13 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_parse_locus.h,v 1.14 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PARSE_LOCUS_H
#define GC_PARSE_LOCUS_H
diff --git a/src/convParse/gc_parse_pop.cpp b/src/convParse/gc_parse_pop.cpp
index 343a018..adbd939 100644
--- a/src/convParse/gc_parse_pop.cpp
+++ b/src/convParse/gc_parse_pop.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_parse_pop.cpp,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_parse_pop.cpp,v 1.6 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_default.h"
diff --git a/src/convParse/gc_parse_pop.h b/src/convParse/gc_parse_pop.h
index 2f779b7..96f27eb 100644
--- a/src/convParse/gc_parse_pop.h
+++ b/src/convParse/gc_parse_pop.h
@@ -1,13 +1,25 @@
-// $Id: gc_parse_pop.h,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_parse_pop.h,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PARSE_POP_H
#define GC_PARSE_POP_H
diff --git a/src/convParse/gc_parse_sample.cpp b/src/convParse/gc_parse_sample.cpp
index 1fa5cb3..b56c8df 100644
--- a/src/convParse/gc_parse_sample.cpp
+++ b/src/convParse/gc_parse_sample.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_parse_sample.cpp,v 1.13 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_parse_sample.cpp,v 1.14 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_errhandling.h"
diff --git a/src/convParse/gc_parse_sample.h b/src/convParse/gc_parse_sample.h
index d0a7647..baccce7 100644
--- a/src/convParse/gc_parse_sample.h
+++ b/src/convParse/gc_parse_sample.h
@@ -1,13 +1,25 @@
-// $Id: gc_parse_sample.h,v 1.9 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_parse_sample.h,v 1.10 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PARSE_SAMPLE_H
#define GC_PARSE_SAMPLE_H
diff --git a/src/convParse/gc_parser.cpp b/src/convParse/gc_parser.cpp
index 26c2c3d..47cdad1 100644
--- a/src/convParse/gc_parser.cpp
+++ b/src/convParse/gc_parser.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_parser.cpp,v 1.28 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_parser.cpp,v 1.29 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "cnv_strings.h"
diff --git a/src/convParse/gc_parser.h b/src/convParse/gc_parser.h
index 902610d..78c830e 100644
--- a/src/convParse/gc_parser.h
+++ b/src/convParse/gc_parser.h
@@ -1,13 +1,25 @@
-// $Id: gc_parser.h,v 1.14 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_parser.h,v 1.15 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PARSER_H
#define GC_PARSER_H
diff --git a/src/convParse/gc_phylip.cpp b/src/convParse/gc_phylip.cpp
index e6cb27e..d21a865 100644
--- a/src/convParse/gc_phylip.cpp
+++ b/src/convParse/gc_phylip.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_phylip.cpp,v 1.29 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_phylip.cpp,v 1.30 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_errhandling.h"
diff --git a/src/convParse/gc_phylip.h b/src/convParse/gc_phylip.h
index 30bfe9c..b46fe2a 100644
--- a/src/convParse/gc_phylip.h
+++ b/src/convParse/gc_phylip.h
@@ -1,13 +1,25 @@
-// $Id: gc_phylip.h,v 1.16 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_phylip.h,v 1.17 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PHYLIP_H
#define GC_PHYLIP_H
diff --git a/src/convParse/gc_pop_match.cpp b/src/convParse/gc_pop_match.cpp
index 94c45c3..480c246 100644
--- a/src/convParse/gc_pop_match.cpp
+++ b/src/convParse/gc_pop_match.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_pop_match.cpp,v 1.19 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_pop_match.cpp,v 1.20 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_errhandling.h"
diff --git a/src/convParse/gc_pop_match.h b/src/convParse/gc_pop_match.h
index 5b54030..bb8ab19 100644
--- a/src/convParse/gc_pop_match.h
+++ b/src/convParse/gc_pop_match.h
@@ -1,13 +1,25 @@
-// $Id: gc_pop_match.h,v 1.10 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_pop_match.h,v 1.11 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_POP_MATCH_H
#define GC_POP_MATCH_H
diff --git a/src/convParse/gc_population.cpp b/src/convParse/gc_population.cpp
index 51ec7f9..2f2545c 100644
--- a/src/convParse/gc_population.cpp
+++ b/src/convParse/gc_population.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_population.cpp,v 1.13 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_population.cpp,v 1.14 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_population.h"
#include "gc_default.h"
#include "gc_strings.h"
diff --git a/src/convParse/gc_population.h b/src/convParse/gc_population.h
index 08f7a19..0603b8f 100644
--- a/src/convParse/gc_population.h
+++ b/src/convParse/gc_population.h
@@ -1,13 +1,25 @@
-// $Id: gc_population.h,v 1.15 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_population.h,v 1.16 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_POPULATION_H
#define GC_POPULATION_H
diff --git a/src/convParse/gc_region.cpp b/src/convParse/gc_region.cpp
index f8bed61..da4fb2f 100644
--- a/src/convParse/gc_region.cpp
+++ b/src/convParse/gc_region.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_region.cpp,v 1.18 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_region.cpp,v 1.19 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_errhandling.h"
#include "gc_locus.h"
#include "gc_region.h"
diff --git a/src/convParse/gc_region.h b/src/convParse/gc_region.h
index 7038ec5..82877dd 100644
--- a/src/convParse/gc_region.h
+++ b/src/convParse/gc_region.h
@@ -1,13 +1,25 @@
-// $Id: gc_region.h,v 1.15 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_region.h,v 1.16 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_REGION_H
#define GC_REGION_H
diff --git a/src/convParse/gc_sequential_data.cpp b/src/convParse/gc_sequential_data.cpp
index 53840de..592b27a 100644
--- a/src/convParse/gc_sequential_data.cpp
+++ b/src/convParse/gc_sequential_data.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_sequential_data.cpp,v 1.25 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_sequential_data.cpp,v 1.26 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_errhandling.h" // EWFIX.P4 -- can this be taken out
diff --git a/src/convParse/gc_sequential_data.h b/src/convParse/gc_sequential_data.h
index ca67c7e..e58b7c8 100644
--- a/src/convParse/gc_sequential_data.h
+++ b/src/convParse/gc_sequential_data.h
@@ -1,13 +1,25 @@
-// $Id: gc_sequential_data.h,v 1.16 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_sequential_data.h,v 1.17 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_SEQUENTIAL_DATA_H
#define GC_SEQUENTIAL_DATA_H
diff --git a/src/convParse/tixml_util.cpp b/src/convParse/tixml_util.cpp
index 3837f43..330bb67 100644
--- a/src/convParse/tixml_util.cpp
+++ b/src/convParse/tixml_util.cpp
@@ -1,13 +1,25 @@
-// $Id: tixml_util.cpp,v 1.10 2012/06/30 01:32:40 bobgian Exp $
+// $Id: tixml_util.cpp,v 1.11 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "errhandling.h"
diff --git a/src/convParse/tixml_util.h b/src/convParse/tixml_util.h
index 458ba77..55d8870 100644
--- a/src/convParse/tixml_util.h
+++ b/src/convParse/tixml_util.h
@@ -1,13 +1,25 @@
-// $Id: tixml_util.h,v 1.9 2012/06/30 01:32:40 bobgian Exp $
+// $Id: tixml_util.h,v 1.10 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef TIXML_UTIL_H
#define TIXML_UTIL_H
diff --git a/src/convStrings/cnv_strings.cpp b/src/convStrings/cnv_strings.cpp
index cf29109..80fdc6a 100644
--- a/src/convStrings/cnv_strings.cpp
+++ b/src/convStrings/cnv_strings.cpp
@@ -1,13 +1,25 @@
-// $Id: cnv_strings.cpp,v 1.19 2012/02/17 22:02:34 jmcgill Exp $
+// $Id: cnv_strings.cpp,v 1.20 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "cnv_strings.h"
#include "wx/intl.h"
diff --git a/src/convStrings/cnv_strings.h b/src/convStrings/cnv_strings.h
index b2049e1..c999778 100644
--- a/src/convStrings/cnv_strings.h
+++ b/src/convStrings/cnv_strings.h
@@ -1,13 +1,25 @@
-// $Id: cnv_strings.h,v 1.18 2012/02/17 22:02:34 jmcgill Exp $
+// $Id: cnv_strings.h,v 1.19 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef CNV_STR_H
#define CNV_STR_H
diff --git a/src/convStrings/gc_strings.h b/src/convStrings/gc_strings.h
index cb51232..03016be 100644
--- a/src/convStrings/gc_strings.h
+++ b/src/convStrings/gc_strings.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings.h,v 1.44 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_strings.h,v 1.45 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_H
#define GC_STRINGS_H
diff --git a/src/convStrings/gc_strings_cmdfile.cpp b/src/convStrings/gc_strings_cmdfile.cpp
index 84fa635..3d1e9da 100644
--- a/src/convStrings/gc_strings_cmdfile.cpp
+++ b/src/convStrings/gc_strings_cmdfile.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_cmdfile.cpp,v 1.12 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_cmdfile.cpp,v 1.13 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_cmdfile.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_cmdfile.h b/src/convStrings/gc_strings_cmdfile.h
index 03afc2c..20defd6 100644
--- a/src/convStrings/gc_strings_cmdfile.h
+++ b/src/convStrings/gc_strings_cmdfile.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_cmdfile.h,v 1.10 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_cmdfile.h,v 1.11 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_CMDFILE_H
#define GC_STRINGS_CMDFILE_H
diff --git a/src/convStrings/gc_strings_creation.cpp b/src/convStrings/gc_strings_creation.cpp
index b297fac..12d6fd5 100644
--- a/src/convStrings/gc_strings_creation.cpp
+++ b/src/convStrings/gc_strings_creation.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_creation.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_creation.cpp,v 1.4 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_creation.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_creation.h b/src/convStrings/gc_strings_creation.h
index a049ab4..e62b24c 100644
--- a/src/convStrings/gc_strings_creation.h
+++ b/src/convStrings/gc_strings_creation.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_creation.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_creation.h,v 1.5 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_CREATION_H
#define GC_STRINGS_CREATION_H
diff --git a/src/convStrings/gc_strings_data.cpp b/src/convStrings/gc_strings_data.cpp
index 2073bba..18b5ad9 100644
--- a/src/convStrings/gc_strings_data.cpp
+++ b/src/convStrings/gc_strings_data.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_data.cpp,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_data.cpp,v 1.6 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_data.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_data.h b/src/convStrings/gc_strings_data.h
index a744699..1de45be 100644
--- a/src/convStrings/gc_strings_data.h
+++ b/src/convStrings/gc_strings_data.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_data.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_data.h,v 1.5 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_DATA_H
#define GC_STRINGS_DATA_H
diff --git a/src/convStrings/gc_strings_err.cpp b/src/convStrings/gc_strings_err.cpp
index fd9233a..bba2220 100644
--- a/src/convStrings/gc_strings_err.cpp
+++ b/src/convStrings/gc_strings_err.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_err.cpp,v 1.8 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_strings_err.cpp,v 1.9 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_individual.cpp b/src/convStrings/gc_strings_individual.cpp
index a1582c8..2a5853b 100644
--- a/src/convStrings/gc_strings_individual.cpp
+++ b/src/convStrings/gc_strings_individual.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_individual.cpp,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_individual.cpp,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_individual.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_individual.h b/src/convStrings/gc_strings_individual.h
index a7daf8f..51eeb7e 100644
--- a/src/convStrings/gc_strings_individual.h
+++ b/src/convStrings/gc_strings_individual.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_individual.h,v 1.6 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_strings_individual.h,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_INDIVIDUAL_H
#define GC_STRINGS_INDIVIDUAL_H
diff --git a/src/convStrings/gc_strings_infile.cpp b/src/convStrings/gc_strings_infile.cpp
index d280123..a8536f2 100644
--- a/src/convStrings/gc_strings_infile.cpp
+++ b/src/convStrings/gc_strings_infile.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_infile.cpp,v 1.16 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_infile.cpp,v 1.17 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_infile.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_infile.h b/src/convStrings/gc_strings_infile.h
index 83f12b8..d6288bb 100644
--- a/src/convStrings/gc_strings_infile.h
+++ b/src/convStrings/gc_strings_infile.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_infile.h,v 1.14 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_infile.h,v 1.15 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_INFILE_H
#define GC_STRINGS_INFILE_H
diff --git a/src/convStrings/gc_strings_io.cpp b/src/convStrings/gc_strings_io.cpp
index 680894e..0040dc3 100644
--- a/src/convStrings/gc_strings_io.cpp
+++ b/src/convStrings/gc_strings_io.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_io.cpp,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_io.cpp,v 1.6 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_io.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_io.h b/src/convStrings/gc_strings_io.h
index 13fa190..269ff50 100644
--- a/src/convStrings/gc_strings_io.h
+++ b/src/convStrings/gc_strings_io.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_io.h,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_io.h,v 1.6 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_IO_H
#define GC_STRINGS_IO_H
diff --git a/src/convStrings/gc_strings_locus.cpp b/src/convStrings/gc_strings_locus.cpp
index 31cc20f..680a820 100644
--- a/src/convStrings/gc_strings_locus.cpp
+++ b/src/convStrings/gc_strings_locus.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_locus.cpp,v 1.15 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_locus.cpp,v 1.16 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_locus.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_locus.h b/src/convStrings/gc_strings_locus.h
index 3c4ebb0..5edf1e6 100644
--- a/src/convStrings/gc_strings_locus.h
+++ b/src/convStrings/gc_strings_locus.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_locus.h,v 1.14 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_locus.h,v 1.15 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_LOCUS_H
#define GC_STRINGS_LOCUS_H
diff --git a/src/convStrings/gc_strings_map.cpp b/src/convStrings/gc_strings_map.cpp
index 7970509..08c77fc 100644
--- a/src/convStrings/gc_strings_map.cpp
+++ b/src/convStrings/gc_strings_map.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_map.cpp,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_map.cpp,v 1.6 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_map.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_map.h b/src/convStrings/gc_strings_map.h
index c3b6afa..dd19213 100644
--- a/src/convStrings/gc_strings_map.h
+++ b/src/convStrings/gc_strings_map.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_map.h,v 1.6 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_strings_map.h,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_MAP_H
#define GC_STRINGS_MAP_H
diff --git a/src/convStrings/gc_strings_mig.cpp b/src/convStrings/gc_strings_mig.cpp
index 17884cb..56cd205 100644
--- a/src/convStrings/gc_strings_mig.cpp
+++ b/src/convStrings/gc_strings_mig.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_mig.cpp,v 1.2 2011/12/30 22:50:10 jmcgill Exp $
+// $Id: gc_strings_mig.cpp,v 1.3 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_mig.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_mig.h b/src/convStrings/gc_strings_mig.h
index 1f13f5d..5c60004 100644
--- a/src/convStrings/gc_strings_mig.h
+++ b/src/convStrings/gc_strings_mig.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_mig.h,v 1.2 2011/12/30 22:50:10 jmcgill Exp $
+// $Id: gc_strings_mig.h,v 1.3 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_MIG_H
#define GC_STRINGS_MIG_H
diff --git a/src/convStrings/gc_strings_parse.cpp b/src/convStrings/gc_strings_parse.cpp
index 71c3a4c..3d7afca 100644
--- a/src/convStrings/gc_strings_parse.cpp
+++ b/src/convStrings/gc_strings_parse.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_parse.cpp,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_parse.cpp,v 1.6 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_parse.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_parse.h b/src/convStrings/gc_strings_parse.h
index 8cd625e..95c63be 100644
--- a/src/convStrings/gc_strings_parse.h
+++ b/src/convStrings/gc_strings_parse.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_parse.h,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_parse.h,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_PARSE_H
#define GC_STRINGS_PARSE_H
diff --git a/src/convStrings/gc_strings_parse_locus.cpp b/src/convStrings/gc_strings_parse_locus.cpp
index 06314e2..27050b2 100644
--- a/src/convStrings/gc_strings_parse_locus.cpp
+++ b/src/convStrings/gc_strings_parse_locus.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_parse_locus.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_parse_locus.cpp,v 1.4 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_parse_locus.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_parse_locus.h b/src/convStrings/gc_strings_parse_locus.h
index 3bd14b3..2555816 100644
--- a/src/convStrings/gc_strings_parse_locus.h
+++ b/src/convStrings/gc_strings_parse_locus.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_parse_locus.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_parse_locus.h,v 1.5 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_PARSE_LOCUS_H
#define GC_STRINGS_PARSE_LOCUS_H
diff --git a/src/convStrings/gc_strings_phase.cpp b/src/convStrings/gc_strings_phase.cpp
index 0f25c64..1314dbe 100644
--- a/src/convStrings/gc_strings_phase.cpp
+++ b/src/convStrings/gc_strings_phase.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_phase.cpp,v 1.11 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_phase.cpp,v 1.12 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_phase.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_phase.h b/src/convStrings/gc_strings_phase.h
index 675f2ac..bbfa8bc 100644
--- a/src/convStrings/gc_strings_phase.h
+++ b/src/convStrings/gc_strings_phase.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_phase.h,v 1.12 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_phase.h,v 1.13 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_PHASE_H
#define GC_STRINGS_PHASE_H
diff --git a/src/convStrings/gc_strings_pop.cpp b/src/convStrings/gc_strings_pop.cpp
index 921ffbe..deb8795 100644
--- a/src/convStrings/gc_strings_pop.cpp
+++ b/src/convStrings/gc_strings_pop.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_pop.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_pop.cpp,v 1.4 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_pop.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_pop.h b/src/convStrings/gc_strings_pop.h
index 1b7c74c..fcc24dc 100644
--- a/src/convStrings/gc_strings_pop.h
+++ b/src/convStrings/gc_strings_pop.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_pop.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_pop.h,v 1.5 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_POP_H
#define GC_STRINGS_POP_H
diff --git a/src/convStrings/gc_strings_region.cpp b/src/convStrings/gc_strings_region.cpp
index a1964b7..6ef4ea8 100644
--- a/src/convStrings/gc_strings_region.cpp
+++ b/src/convStrings/gc_strings_region.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_region.cpp,v 1.9 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_region.cpp,v 1.10 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_region.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_region.h b/src/convStrings/gc_strings_region.h
index 0ae1929..e15fd95 100644
--- a/src/convStrings/gc_strings_region.h
+++ b/src/convStrings/gc_strings_region.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_region.h,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_region.h,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_REGION_H
#define GC_STRINGS_REGION_H
diff --git a/src/convStrings/gc_strings_str_a_m.cpp b/src/convStrings/gc_strings_str_a_m.cpp
index b064360..1f43be9 100644
--- a/src/convStrings/gc_strings_str_a_m.cpp
+++ b/src/convStrings/gc_strings_str_a_m.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_str_a_m.cpp,v 1.8 2011/12/01 22:32:42 jmcgill Exp $
+// $Id: gc_strings_str_a_m.cpp,v 1.10 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings.h"
#include "wx/intl.h"
@@ -94,7 +106,7 @@ const wxString gcstr::editCancel = wxTRANSLATE("Cancel");
const wxString gcstr::editDelete = wxTRANSLATE("Delete");
const wxString gcstr::editFileSettings = wxTRANSLATE("Edit/Review Settings for file \"%s\"");
const wxString gcstr::editLocus = wxTRANSLATE("Edit segment \"%s\"");
-const wxString gcstr::editMigration = wxTRANSLATE("Edit mig from \"%s\" to \"%s\"");
+const wxString gcstr::editMigration = wxTRANSLATE("Edit migration into \"%s\" from \"%s\"");
const wxString gcstr::editOK = wxTRANSLATE("OK");
const wxString gcstr::editParseBlock = wxTRANSLATE("Edit parsed data properties");
const wxString gcstr::editPanel = wxTRANSLATE("Edit panel \"%s\"");
diff --git a/src/convStrings/gc_strings_str_n_z.cpp b/src/convStrings/gc_strings_str_n_z.cpp
index 3e8f9ff..96f06a7 100644
--- a/src/convStrings/gc_strings_str_n_z.cpp
+++ b/src/convStrings/gc_strings_str_n_z.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_str_n_z.cpp,v 1.7 2012/02/15 18:13:41 jmcgill Exp $
+// $Id: gc_strings_str_n_z.cpp,v 1.8 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_structures.cpp b/src/convStrings/gc_strings_structures.cpp
index 7f3e3e8..8323097 100644
--- a/src/convStrings/gc_strings_structures.cpp
+++ b/src/convStrings/gc_strings_structures.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_structures.cpp,v 1.14 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_strings_structures.cpp,v 1.15 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_structures.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_structures.h b/src/convStrings/gc_strings_structures.h
index d5aefc8..37138e2 100644
--- a/src/convStrings/gc_strings_structures.h
+++ b/src/convStrings/gc_strings_structures.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_structures.h,v 1.11 2012/06/30 01:32:40 bobgian Exp $
+// $Id: gc_strings_structures.h,v 1.12 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_STRUCTURES_H
#define GC_STRINGS_STRUCTURES_H
diff --git a/src/convStrings/gc_strings_trait.cpp b/src/convStrings/gc_strings_trait.cpp
index 06eccd1..241db90 100644
--- a/src/convStrings/gc_strings_trait.cpp
+++ b/src/convStrings/gc_strings_trait.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_strings_trait.cpp,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_trait.cpp,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings_trait.h"
#include "wx/intl.h"
diff --git a/src/convStrings/gc_strings_trait.h b/src/convStrings/gc_strings_trait.h
index a67e1ea..34ecc12 100644
--- a/src/convStrings/gc_strings_trait.h
+++ b/src/convStrings/gc_strings_trait.h
@@ -1,13 +1,25 @@
-// $Id: gc_strings_trait.h,v 1.7 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_strings_trait.h,v 1.8 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_STRINGS_TRAIT_H
#define GC_STRINGS_TRAIT_H
diff --git a/src/convUtil/gc_file_util.cpp b/src/convUtil/gc_file_util.cpp
index 3c8a6b0..1df16ad 100644
--- a/src/convUtil/gc_file_util.cpp
+++ b/src/convUtil/gc_file_util.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_file_util.cpp,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_file_util.cpp,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_errhandling.h"
diff --git a/src/convUtil/gc_file_util.h b/src/convUtil/gc_file_util.h
index 851dfbf..255d41e 100644
--- a/src/convUtil/gc_file_util.h
+++ b/src/convUtil/gc_file_util.h
@@ -1,13 +1,25 @@
-// $Id: gc_file_util.h,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_file_util.h,v 1.7 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_FILE_UTIL_H
#define GC_FILE_UTIL_H
diff --git a/src/conversion/ConverterIf.cpp b/src/conversion/ConverterIf.cpp
index 5ba0b47..76236a1 100644
--- a/src/conversion/ConverterIf.cpp
+++ b/src/conversion/ConverterIf.cpp
@@ -1,14 +1,27 @@
-// $Id: ConverterIf.cpp,v 1.17 2012/06/30 01:32:40 bobgian Exp $
+// $Id: ConverterIf.cpp,v 1.18 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <iostream>
#include <sstream>
#include <ctype.h>
diff --git a/src/conversion/ConverterUI.cpp b/src/conversion/ConverterUI.cpp
index 92a2778..c739f22 100644
--- a/src/conversion/ConverterUI.cpp
+++ b/src/conversion/ConverterUI.cpp
@@ -1,14 +1,27 @@
-// $Id: ConverterUI.cpp,v 1.80 2011/03/07 06:08:48 bobgian Exp $
+// $Id: ConverterUI.cpp,v 1.81 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// This file contains the UI and the main() function for the converter program
// extensive revisions to allow UI and filereading to interact.
diff --git a/src/conversion/ConverterUIMain.cpp b/src/conversion/ConverterUIMain.cpp
index 72964f5..90a354b 100644
--- a/src/conversion/ConverterUIMain.cpp
+++ b/src/conversion/ConverterUIMain.cpp
@@ -1,14 +1,27 @@
-// $Id: ConverterUIMain.cpp,v 1.12 2012/06/30 01:32:40 bobgian Exp $
+// $Id: ConverterUIMain.cpp,v 1.13 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// This file contains the UI and the main() function for the converter program
// extensive revisions to allow UI and filereading to interact.
diff --git a/src/conversion/Converter_ConverterIf.h b/src/conversion/Converter_ConverterIf.h
index 473606e..1e6edea 100644
--- a/src/conversion/Converter_ConverterIf.h
+++ b/src/conversion/Converter_ConverterIf.h
@@ -1,14 +1,27 @@
-// $Id: Converter_ConverterIf.h,v 1.16 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_ConverterIf.h,v 1.17 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#ifndef Converter_ConverterIf_H
#define Converter_ConverterIf_H
diff --git a/src/conversion/Converter_ConverterUI.h b/src/conversion/Converter_ConverterUI.h
index 0dd5fdd..b798a6a 100644
--- a/src/conversion/Converter_ConverterUI.h
+++ b/src/conversion/Converter_ConverterUI.h
@@ -1,14 +1,27 @@
-// $Id: Converter_ConverterUI.h,v 1.24 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_ConverterUI.h,v 1.25 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#ifndef CONVERTER_UI_H
#define CONVERTER_UI_H
diff --git a/src/conversion/Converter_DataSourceException.h b/src/conversion/Converter_DataSourceException.h
index 58b5b22..b5e14f7 100644
--- a/src/conversion/Converter_DataSourceException.h
+++ b/src/conversion/Converter_DataSourceException.h
@@ -1,14 +1,27 @@
-// $Id: Converter_DataSourceException.h,v 1.11 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_DataSourceException.h,v 1.12 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#ifndef Converter_DataSourceException_H
#define Converter_DataSourceException_H
diff --git a/src/conversion/Converter_DataSourceIf.h b/src/conversion/Converter_DataSourceIf.h
index fd2f3f1..2b2b5f5 100644
--- a/src/conversion/Converter_DataSourceIf.h
+++ b/src/conversion/Converter_DataSourceIf.h
@@ -1,14 +1,27 @@
-// $Id: Converter_DataSourceIf.h,v 1.8 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_DataSourceIf.h,v 1.9 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#ifndef Converter_DataSourceIf_H
#define Converter_DataSourceIf_H
diff --git a/src/conversion/Converter_HapConverter.h b/src/conversion/Converter_HapConverter.h
index 96061bd..5354a3f 100644
--- a/src/conversion/Converter_HapConverter.h
+++ b/src/conversion/Converter_HapConverter.h
@@ -1,14 +1,27 @@
-// $Id: Converter_HapConverter.h,v 1.12 2012/06/30 01:32:41 bobgian Exp $
+// $Id: Converter_HapConverter.h,v 1.13 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// HapConverter reads the info from a prepared Converter-Haplotype
// format file and uses it to rearrange the innards of a RegionDS.
// Specifically, may consolidate multiple former individuals into a
diff --git a/src/conversion/Converter_IndividualDS.h b/src/conversion/Converter_IndividualDS.h
index bfdaf41..b6f3a3a 100644
--- a/src/conversion/Converter_IndividualDS.h
+++ b/src/conversion/Converter_IndividualDS.h
@@ -1,14 +1,27 @@
-// $Id: Converter_IndividualDS.h,v 1.14 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_IndividualDS.h,v 1.15 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// IndividualDS is a representation of the data for any individual.
// Each individual owns a name, and a sequence'.
// Theres no validation on individual, however, there is on sequence, so if you
diff --git a/src/conversion/Converter_LamarcDS.h b/src/conversion/Converter_LamarcDS.h
index 7f56640..01ebf4f 100644
--- a/src/conversion/Converter_LamarcDS.h
+++ b/src/conversion/Converter_LamarcDS.h
@@ -1,14 +1,27 @@
-// $Id: Converter_LamarcDS.h,v 1.22 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_LamarcDS.h,v 1.23 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// LamarcDS is a representation of the found seen in a Lamarc Datafile
// Each lamarcDS has the following information.
// Most of it is currently default.
diff --git a/src/conversion/Converter_MigrateConverter.h b/src/conversion/Converter_MigrateConverter.h
index 0124b96..a900fb1 100644
--- a/src/conversion/Converter_MigrateConverter.h
+++ b/src/conversion/Converter_MigrateConverter.h
@@ -1,14 +1,27 @@
-// $Id: Converter_MigrateConverter.h,v 1.16 2012/06/30 01:32:41 bobgian Exp $
+// $Id: Converter_MigrateConverter.h,v 1.17 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// Migrate Converter will take an old style migrate file, and create a lamarcDS out of it.
// Note that this can throw pretty much any ConverterBaseError.
// Anytime this is used, one should catch and handle these errors.
diff --git a/src/conversion/Converter_ModelDS.h b/src/conversion/Converter_ModelDS.h
index 643c260..f627f84 100644
--- a/src/conversion/Converter_ModelDS.h
+++ b/src/conversion/Converter_ModelDS.h
@@ -1,14 +1,27 @@
-// $Id: Converter_ModelDS.h,v 1.7 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_ModelDS.h,v 1.8 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// ModelDS is a representation of the data on any one model.
// Each model owns the following.
// A set of Base Freqs. These are four two digit frequencies that total 100. I guess.
diff --git a/src/conversion/Converter_ParserUtil.h b/src/conversion/Converter_ParserUtil.h
index 3bacda0..a465ca7 100644
--- a/src/conversion/Converter_ParserUtil.h
+++ b/src/conversion/Converter_ParserUtil.h
@@ -1,14 +1,27 @@
-// $Id: Converter_ParserUtil.h,v 1.9 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_ParserUtil.h,v 1.10 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#ifndef Converter_ParserUtil_H
#define Converter_ParserUtil_H
diff --git a/src/conversion/Converter_PhylipConverter.h b/src/conversion/Converter_PhylipConverter.h
index 3db9b18..1e07ee7 100644
--- a/src/conversion/Converter_PhylipConverter.h
+++ b/src/conversion/Converter_PhylipConverter.h
@@ -1,14 +1,27 @@
-// $Id: Converter_PhylipConverter.h,v 1.14 2012/06/30 01:32:41 bobgian Exp $
+// $Id: Converter_PhylipConverter.h,v 1.15 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// Phylip Converter will take an old style phylip file, and create a lamarcDS out of it.
// Note that this can throw pretty much any ConverterBaseError.
// Anytime this is used, one should catch and handle these errors.
diff --git a/src/conversion/Converter_PopulationDS.h b/src/conversion/Converter_PopulationDS.h
index 4ed5a9b..624996d 100644
--- a/src/conversion/Converter_PopulationDS.h
+++ b/src/conversion/Converter_PopulationDS.h
@@ -1,14 +1,27 @@
-// $Id: Converter_PopulationDS.h,v 1.14 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_PopulationDS.h,v 1.15 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// PopulationDS is a representation of the data on any one population.
// Each population owns a name, and a number of IndividualDS'.
// Validation is done whenever a new Individual is added. Population makes sure that
diff --git a/src/conversion/Converter_RegionDS.h b/src/conversion/Converter_RegionDS.h
index d628091..0dce084 100644
--- a/src/conversion/Converter_RegionDS.h
+++ b/src/conversion/Converter_RegionDS.h
@@ -1,14 +1,27 @@
-// $Id: Converter_RegionDS.h,v 1.19 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_RegionDS.h,v 1.20 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// RegionDS is a representation of the data on any one region.
// Each region owns the following.
// A Model
diff --git a/src/conversion/Converter_Sequence.h b/src/conversion/Converter_Sequence.h
index c6ffdd6..4c3b8e1 100644
--- a/src/conversion/Converter_Sequence.h
+++ b/src/conversion/Converter_Sequence.h
@@ -1,14 +1,27 @@
-// $Id: Converter_Sequence.h,v 1.17 2012/06/30 01:32:41 bobgian Exp $
+// $Id: Converter_Sequence.h,v 1.18 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// Sequence is a representation of a Nucleotide sequence of any length.
// Each Sequence owns a string that represents the DNA sequence.
// Validation is done on the DNA sequence upon construction. If any
diff --git a/src/conversion/Converter_SpaceConverter.h b/src/conversion/Converter_SpaceConverter.h
index 59ef363..acc7328 100644
--- a/src/conversion/Converter_SpaceConverter.h
+++ b/src/conversion/Converter_SpaceConverter.h
@@ -1,14 +1,27 @@
-// $Id: Converter_SpaceConverter.h,v 1.9 2012/06/30 01:32:41 bobgian Exp $
+// $Id: Converter_SpaceConverter.h,v 1.10 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// SpaceConverter reads the info from a prepared Converter-Haplotype
// format file and modifies the regions of a LamarcDS.
diff --git a/src/conversion/Converter_SpacingDS.h b/src/conversion/Converter_SpacingDS.h
index 92672ac..5b5c327 100644
--- a/src/conversion/Converter_SpacingDS.h
+++ b/src/conversion/Converter_SpacingDS.h
@@ -1,14 +1,27 @@
-// $Id: Converter_SpacingDS.h,v 1.11 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_SpacingDS.h,v 1.12 2018/01/03 21:32:56 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// SpacingDS is a representation of the spacing information for a
// region's genetic data.
//
diff --git a/src/conversion/Converter_UserFileUtil.h b/src/conversion/Converter_UserFileUtil.h
index 143207a..5a8d8f9 100644
--- a/src/conversion/Converter_UserFileUtil.h
+++ b/src/conversion/Converter_UserFileUtil.h
@@ -1,14 +1,27 @@
-// $Id: Converter_UserFileUtil.h,v 1.6 2011/03/07 06:08:48 bobgian Exp $
+// $Id: Converter_UserFileUtil.h,v 1.7 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// This file contains some useful file i/o functions for use with
// the user interface.
diff --git a/src/conversion/Converter_XmlParserUtil.h b/src/conversion/Converter_XmlParserUtil.h
index c3a349e..ba821f6 100644
--- a/src/conversion/Converter_XmlParserUtil.h
+++ b/src/conversion/Converter_XmlParserUtil.h
@@ -1,14 +1,27 @@
-// $Id: Converter_XmlParserUtil.h,v 1.7 2012/06/30 01:32:41 bobgian Exp $
+// $Id: Converter_XmlParserUtil.h,v 1.8 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#ifndef Converter_XmlParserUtil_H
#define Converter_XmlParserUtil_H
diff --git a/src/conversion/Converter_types.h b/src/conversion/Converter_types.h
index 1f2da49..e2dcb87 100644
--- a/src/conversion/Converter_types.h
+++ b/src/conversion/Converter_types.h
@@ -1,14 +1,27 @@
-// $Id: Converter_types.h,v 1.6 2012/06/30 01:32:41 bobgian Exp $
+// $Id: Converter_types.h,v 1.7 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#ifndef CONVERTER_TYPES_H
#define CONVERTER_TYPES_H
diff --git a/src/conversion/DataSourceException.cpp b/src/conversion/DataSourceException.cpp
index 9974c6f..86a37d2 100644
--- a/src/conversion/DataSourceException.cpp
+++ b/src/conversion/DataSourceException.cpp
@@ -1,13 +1,25 @@
-// $Id: DataSourceException.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: DataSourceException.cpp,v 1.4 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "Converter_DataSourceException.h"
#include "stringx.h"
diff --git a/src/conversion/DataSourceIf.cpp b/src/conversion/DataSourceIf.cpp
index becf501..ea89684 100644
--- a/src/conversion/DataSourceIf.cpp
+++ b/src/conversion/DataSourceIf.cpp
@@ -1,14 +1,27 @@
-// $Id: DataSourceIf.cpp,v 1.6 2012/06/30 01:32:41 bobgian Exp $
+// $Id: DataSourceIf.cpp,v 1.7 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <string>
#include "Converter_DataSourceIf.h"
diff --git a/src/conversion/HapConverter.cpp b/src/conversion/HapConverter.cpp
index 6f02007..9e34ba2 100644
--- a/src/conversion/HapConverter.cpp
+++ b/src/conversion/HapConverter.cpp
@@ -1,14 +1,27 @@
-// $Id: HapConverter.cpp,v 1.24 2011/03/07 06:08:48 bobgian Exp $
+// $Id: HapConverter.cpp,v 1.25 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <cassert>
#include "Converter_HapConverter.h"
diff --git a/src/conversion/IndividualDS.cpp b/src/conversion/IndividualDS.cpp
index 4059962..2fcc7e3 100644
--- a/src/conversion/IndividualDS.cpp
+++ b/src/conversion/IndividualDS.cpp
@@ -1,14 +1,27 @@
-// $Id: IndividualDS.cpp,v 1.17 2011/03/07 06:08:48 bobgian Exp $
+// $Id: IndividualDS.cpp,v 1.18 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <cassert>
#include "Converter_IndividualDS.h"
#include "Converter_DataSourceException.h"
diff --git a/src/conversion/LamarcDS.cpp b/src/conversion/LamarcDS.cpp
index 75d672b..40e18dd 100644
--- a/src/conversion/LamarcDS.cpp
+++ b/src/conversion/LamarcDS.cpp
@@ -1,14 +1,27 @@
-// $Id: LamarcDS.cpp,v 1.40 2012/06/30 01:32:41 bobgian Exp $
+// $Id: LamarcDS.cpp,v 1.41 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <stdio.h>
#include <vector>
diff --git a/src/conversion/MigrateConverter.cpp b/src/conversion/MigrateConverter.cpp
index 325a40f..7ed0551 100644
--- a/src/conversion/MigrateConverter.cpp
+++ b/src/conversion/MigrateConverter.cpp
@@ -1,14 +1,27 @@
-// $Id: MigrateConverter.cpp,v 1.37 2011/03/07 06:08:48 bobgian Exp $
+// $Id: MigrateConverter.cpp,v 1.38 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
// refactored by Mary April 30 2002
#include <cassert>
diff --git a/src/conversion/ModelDS.cpp b/src/conversion/ModelDS.cpp
index 140c250..503b80d 100644
--- a/src/conversion/ModelDS.cpp
+++ b/src/conversion/ModelDS.cpp
@@ -1,14 +1,27 @@
-// $Id: ModelDS.cpp,v 1.4 2010/03/17 17:25:58 bobgian Exp $
+// $Id: ModelDS.cpp,v 1.5 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include "Converter_ModelDS.h"
#include "Converter_DataSourceException.h"
#include "stringx.h"
diff --git a/src/conversion/ParserUtil.cpp b/src/conversion/ParserUtil.cpp
index c306e87..6a620f6 100644
--- a/src/conversion/ParserUtil.cpp
+++ b/src/conversion/ParserUtil.cpp
@@ -1,14 +1,27 @@
-// $Id: ParserUtil.cpp,v 1.16 2012/06/30 01:32:41 bobgian Exp $
+// $Id: ParserUtil.cpp,v 1.17 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <string>
#include <cstring>
#include <cctype>
diff --git a/src/conversion/PhylipConverter.cpp b/src/conversion/PhylipConverter.cpp
index 3956f93..38b0578 100644
--- a/src/conversion/PhylipConverter.cpp
+++ b/src/conversion/PhylipConverter.cpp
@@ -1,14 +1,27 @@
-// $Id: PhylipConverter.cpp,v 1.31 2012/06/30 01:32:41 bobgian Exp $
+// $Id: PhylipConverter.cpp,v 1.32 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <iostream>
#include <fstream>
#include <sstream>
diff --git a/src/conversion/PopulationDS.cpp b/src/conversion/PopulationDS.cpp
index bee21fc..ce913e0 100644
--- a/src/conversion/PopulationDS.cpp
+++ b/src/conversion/PopulationDS.cpp
@@ -1,14 +1,27 @@
-// $Id: PopulationDS.cpp,v 1.22 2012/06/30 01:32:41 bobgian Exp $
+// $Id: PopulationDS.cpp,v 1.23 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <stdio.h>
#include "Converter_PopulationDS.h"
diff --git a/src/conversion/RegionDS.cpp b/src/conversion/RegionDS.cpp
index 777a971..25e5b0f 100644
--- a/src/conversion/RegionDS.cpp
+++ b/src/conversion/RegionDS.cpp
@@ -1,14 +1,27 @@
-// $Id: RegionDS.cpp,v 1.26 2011/04/23 02:02:48 bobgian Exp $
+// $Id: RegionDS.cpp,v 1.27 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <cmath>
#include <stdio.h>
diff --git a/src/conversion/Sequence.cpp b/src/conversion/Sequence.cpp
index 6bf3eee..e8887fe 100644
--- a/src/conversion/Sequence.cpp
+++ b/src/conversion/Sequence.cpp
@@ -1,14 +1,27 @@
-// $Id: Sequence.cpp,v 1.13 2010/03/17 17:25:58 bobgian Exp $
+// $Id: Sequence.cpp,v 1.14 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include "Converter_Sequence.h"
#include "Converter_DataSourceException.h"
#include "random.h"
diff --git a/src/conversion/SpaceConverter.cpp b/src/conversion/SpaceConverter.cpp
index 48465a9..8b66037 100644
--- a/src/conversion/SpaceConverter.cpp
+++ b/src/conversion/SpaceConverter.cpp
@@ -1,14 +1,27 @@
-// $Id: SpaceConverter.cpp,v 1.13 2012/06/30 01:32:41 bobgian Exp $
+// $Id: SpaceConverter.cpp,v 1.14 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <vector>
#include <iostream>
#include <sstream>
diff --git a/src/conversion/SpacingDS.cpp b/src/conversion/SpacingDS.cpp
index b3611fd..9e05ce1 100644
--- a/src/conversion/SpacingDS.cpp
+++ b/src/conversion/SpacingDS.cpp
@@ -1,14 +1,27 @@
-// $Id: SpacingDS.cpp,v 1.16 2012/06/30 01:32:41 bobgian Exp $
+// $Id: SpacingDS.cpp,v 1.17 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <algorithm>
#include "Converter_SpacingDS.h"
diff --git a/src/conversion/UserFileUtil.cpp b/src/conversion/UserFileUtil.cpp
index 812867e..1f91c05 100644
--- a/src/conversion/UserFileUtil.cpp
+++ b/src/conversion/UserFileUtil.cpp
@@ -1,14 +1,27 @@
-// $Id: UserFileUtil.cpp,v 1.4 2010/03/17 17:25:58 bobgian Exp $
+// $Id: UserFileUtil.cpp,v 1.5 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include "Converter_UserFileUtil.h"
//----------------------------------------------------------------------
diff --git a/src/conversion/XmlParserUtil.cpp b/src/conversion/XmlParserUtil.cpp
index 4633cbe..d259221 100644
--- a/src/conversion/XmlParserUtil.cpp
+++ b/src/conversion/XmlParserUtil.cpp
@@ -1,14 +1,27 @@
-// $Id: XmlParserUtil.cpp,v 1.7 2012/06/30 01:32:41 bobgian Exp $
+// $Id: XmlParserUtil.cpp,v 1.8 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Patrick Colacurcio, Peter Beerli, Mary Kuhner,
- Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+/* Authors: Patrick Colacurcio, Peter Beerli, Mary Kuhner, Jon Yamato
+and Joseph Felsenstein */
+
+
#include <sstream>
#include "Converter_XmlParserUtil.h"
diff --git a/src/conversion/nomenuglobals.cpp b/src/conversion/nomenuglobals.cpp
index 9b9dadc..beb7d8f 100644
--- a/src/conversion/nomenuglobals.cpp
+++ b/src/conversion/nomenuglobals.cpp
@@ -1,13 +1,25 @@
-// $Id: nomenuglobals.cpp,v 1.7 2011/03/08 19:22:00 bobgian Exp $
+// $Id: nomenuglobals.cpp,v 1.8 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "nomenuglobals.h"
#ifdef JSIM
#include "constants.h" // for datatype const string (DNA, etc)
diff --git a/src/conversion/nomenuglobals.h b/src/conversion/nomenuglobals.h
index faa2175..e3583af 100644
--- a/src/conversion/nomenuglobals.h
+++ b/src/conversion/nomenuglobals.h
@@ -1,13 +1,25 @@
-// $Id: nomenuglobals.h,v 1.9 2011/03/08 19:22:00 bobgian Exp $
+// $Id: nomenuglobals.h,v 1.10 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
// This file defines the behaviour of the converter when compiled with the JSIM flag
#ifndef CONV_JSIMGLOBALS_H
diff --git a/src/datalike/calculators.cpp b/src/datalike/calculators.cpp
index cde8eb2..647f8b2 100644
--- a/src/datalike/calculators.cpp
+++ b/src/datalike/calculators.cpp
@@ -1,13 +1,25 @@
-// $Id: calculators.cpp,v 1.27 2012/06/30 01:32:41 bobgian Exp $
+// $Id: calculators.cpp,v 1.29 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <functional>
#include <numeric>
@@ -96,7 +108,7 @@ DoubleVec1d FrequenciesFromData(const Locus& locus, model_type modelType)
// this function to get an initial estimate, we may want to default
// to a reasonable value, but if reporting the value we do not.
-void MigFSTLocus(const DataPack& dpack, const Locus& loc, long int numMigs,
+void MigFSTLocus(const DataPack&, const Locus& loc, long int numMigs,
DoubleVec1d& estimate, std::deque<bool>& isCalculated)
{
estimate.clear();
@@ -215,7 +227,7 @@ void MigFSTMultiregion(const DataPack & dpack, const DoubleVec2d & regionalmurat
// this function to get an initial estimate, we may want to default
// to a reasonable value, but if reporting the value we do not.
-void ThetaFSTLocus(const DataPack& dpack, const Locus& loc, const long int numThetas,
+void ThetaFSTLocus(const DataPack&, const Locus& loc, const long int numThetas,
vector<map<force_type,string> > tipids, DoubleVec1d& estimates,
std::deque<bool>& isCalculated)
{
@@ -334,7 +346,7 @@ void ThetaFSTMultiregion(const DataPack& dpack, const DoubleVec1d & regionalthet
// to correct them when appropriate. for example, if using this function to get an initial estimate,
// we may want to default to a reasonable value, but if reporting the value we do not.
-void ThetaWattersonLocus(const DataPack& dpack, const Locus& locus, const long int numThetas,
+void ThetaWattersonLocus(const DataPack&, const Locus& locus, const long int numThetas,
const vector<map<force_type,string> > tipids, DoubleVec1d& estimates,
std::deque<bool>& isCalculated)
{
diff --git a/src/datalike/calculators.h b/src/datalike/calculators.h
index 865562e..1a063c0 100644
--- a/src/datalike/calculators.h
+++ b/src/datalike/calculators.h
@@ -1,13 +1,25 @@
-// $Id: calculators.h,v 1.13 2011/03/07 06:08:48 bobgian Exp $
+// $Id: calculators.h,v 1.14 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef CALCULATORS_H
#define CALCULATORS_H
diff --git a/src/datalike/cellmanager.cpp b/src/datalike/cellmanager.cpp
index f928c45..3c897fd 100644
--- a/src/datalike/cellmanager.cpp
+++ b/src/datalike/cellmanager.cpp
@@ -1,13 +1,25 @@
-// $Id: cellmanager.cpp,v 1.5 2011/03/07 06:08:48 bobgian Exp $
+// $Id: cellmanager.cpp,v 1.6 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// This file contains the implementation code for the manager of data-likelihood
// storage, CellManager
diff --git a/src/datalike/cellmanager.h b/src/datalike/cellmanager.h
index 44e792b..55eea7f 100644
--- a/src/datalike/cellmanager.h
+++ b/src/datalike/cellmanager.h
@@ -1,13 +1,25 @@
-// $Id: cellmanager.h,v 1.3 2011/02/20 04:14:09 bobgian Exp $
+// $Id: cellmanager.h,v 1.4 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/******************************************************************
The CellManager maintains a private internal store of the arrays
diff --git a/src/datalike/datapack.cpp b/src/datalike/datapack.cpp
index 5a968c4..d63a05e 100644
--- a/src/datalike/datapack.cpp
+++ b/src/datalike/datapack.cpp
@@ -1,13 +1,25 @@
-// $Id: datapack.cpp,v 1.70 2013/10/25 17:00:52 mkkuhner Exp $
+// $Id: datapack.cpp,v 1.71 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <functional> // for plus<> used in CountOverallBaseFreqs
#include <iostream>
diff --git a/src/datalike/datapack.h b/src/datalike/datapack.h
index af3466b..df2d040 100644
--- a/src/datalike/datapack.h
+++ b/src/datalike/datapack.h
@@ -1,13 +1,25 @@
-// $Id: datapack.h,v 1.58 2012/06/30 01:32:41 bobgian Exp $
+// $Id: datapack.h,v 1.59 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// In general, a DataPack owns a container of pointer to Regions, which
// own a container of Locus objects, which own a container of TipData objects.
//
diff --git a/src/datalike/datatype.cpp b/src/datalike/datatype.cpp
index e412465..8a01aae 100644
--- a/src/datalike/datatype.cpp
+++ b/src/datalike/datatype.cpp
@@ -1,13 +1,25 @@
-// $Id: datatype.cpp,v 1.38 2013/10/25 17:00:52 mkkuhner Exp $
+// $Id: datatype.cpp,v 1.40 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cstring>
@@ -569,7 +581,7 @@ KAlleleType::KAlleleType()
//------------------------------------------------------------------------------------
bool KAlleleType::Proofread(const string& raw, StringVec1d& clean,
- string& baddata) const
+ string&) const //string 'baddata' not used.
{
unsigned long index;
char c;
diff --git a/src/datalike/datatype.h b/src/datalike/datatype.h
index f71daf8..11eddeb 100644
--- a/src/datalike/datatype.h
+++ b/src/datalike/datatype.h
@@ -1,13 +1,25 @@
-// $Id: datatype.h,v 1.29 2011/03/07 06:08:48 bobgian Exp $
+// $Id: datatype.h,v 1.30 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*********************************************************************
This class is the key control class for polymorphism based on
the type of the input data (SNP, DNA, microsatellite, etc.) It is
diff --git a/src/datalike/dlcalc.cpp b/src/datalike/dlcalc.cpp
index 8bafff7..9caf393 100644
--- a/src/datalike/dlcalc.cpp
+++ b/src/datalike/dlcalc.cpp
@@ -1,13 +1,25 @@
-// $Id: dlcalc.cpp,v 1.113 2012/06/30 01:32:41 bobgian Exp $
+// $Id: dlcalc.cpp,v 1.115 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
#include <fstream>
@@ -298,7 +310,7 @@ void DLCalculator::Randomize(Locus& destloc, rangeset rset, Tree& tree)
//------------------------------------------------------------------------------------
-void DLCalculator::MarkPanelBranches(Tree& tree, const Locus& locus)
+void DLCalculator::MarkPanelBranches(Tree& tree, const Locus&) //locus unused.
{
// Walk down the tree and mark each branch.
// The tips are marked at create time as 0 = panel, 1 = sample.
@@ -1148,7 +1160,7 @@ double SNPCalculator::SumPanel(Cell_ptr varcell, pair<long,long> sitespan, Cell_
//------------------------------------------------------------------------------------
-void SNPCalculator::SimulateData(Tree& tree, Locus& locus)
+void SNPCalculator::SimulateData(Tree&, Locus&)
{
assert(false);
//The default data simulator probably doesn't work with SNPs.
diff --git a/src/datalike/dlcalc.h b/src/datalike/dlcalc.h
index 1e66bb3..14e89d7 100644
--- a/src/datalike/dlcalc.h
+++ b/src/datalike/dlcalc.h
@@ -1,13 +1,25 @@
-// $Id: dlcalc.h,v 1.44 2011/10/11 16:42:16 mkkuhner Exp $
+// $Id: dlcalc.h,v 1.45 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DLCALCULATOR_H
#define DLCALCULATOR_H
diff --git a/src/datalike/dlcell.cpp b/src/datalike/dlcell.cpp
index 158f68e..8433098 100644
--- a/src/datalike/dlcell.cpp
+++ b/src/datalike/dlcell.cpp
@@ -1,13 +1,25 @@
-// $Id: dlcell.cpp,v 1.44 2012/06/30 01:32:41 bobgian Exp $
+// $Id: dlcell.cpp,v 1.46 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// This file contains the implementation code for the data-likelihood
// storage object.
@@ -510,7 +522,7 @@ void NullCell::Initialize (const StringVec1d&, const DataModel_ptr)
} // Initialize
-DoubleVec1d NullCell::GetStateFor(long posn, long cat) const
+DoubleVec1d NullCell::GetStateFor(long, long) const
{
throw implementation_error("No state for this data likelihood.");
}
diff --git a/src/datalike/dlcell.h b/src/datalike/dlcell.h
index 2c7b659..fef432a 100644
--- a/src/datalike/dlcell.h
+++ b/src/datalike/dlcell.h
@@ -1,13 +1,25 @@
-// $Id: dlcell.h,v 1.36 2011/03/08 08:16:33 bobgian Exp $
+// $Id: dlcell.h,v 1.38 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/******************************************************************
This file defines the branch data-likelihood storage object. It maintains the data
likelihoods internally as a bare array for speed reasons (ability to use memcpy).
@@ -242,16 +254,16 @@ class NullCell : public Cell
virtual long DiffersFrom(Cell_ptr) const { assert(false); return 0; };
// Simulation functions.
- virtual void SetAllCategoriesTo(DoubleVec1d& state, long posn) {};
+ virtual void SetAllCategoriesTo(DoubleVec1d&, long) {};
virtual DoubleVec1d GetStateFor(long posn, long cat) const;
- virtual void SetStateTo(long posn, long cat, DoubleVec1d state) {};
- virtual void AddTo(const Cell_ptr othercell) {};
- virtual void SubtractFrom(const Cell_ptr othercell) {};
- virtual void MultiplyBy(double mult) {};
- virtual void MultiplyBy(const Cell_ptr othercell) {};
+ virtual void SetStateTo(long, long, DoubleVec1d) {};
+ virtual void AddTo(const Cell_ptr) {};
+ virtual void SubtractFrom(const Cell_ptr) {};
+ virtual void MultiplyBy(double) {};
+ virtual void MultiplyBy(const Cell_ptr) {};
// For output.
- virtual LongVec1d GetOnes(long marker) const { return LongVec1d();};
+ virtual LongVec1d GetOnes(long) const { return LongVec1d();};
// Debugging functions.
virtual string DLsToString(long, long) const { return string(""); };
diff --git a/src/datalike/dlmodel.cpp b/src/datalike/dlmodel.cpp
index 23fecf6..22bea99 100644
--- a/src/datalike/dlmodel.cpp
+++ b/src/datalike/dlmodel.cpp
@@ -1,13 +1,25 @@
-// $Id: dlmodel.cpp,v 1.138 2012/06/30 01:32:41 bobgian Exp $
+// $Id: dlmodel.cpp,v 1.140 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <algorithm>
#include <cstring>
@@ -580,7 +592,7 @@ StringVec1d NucModel::ToXML(size_t nspaces) const
//------------------------------------------------------------------------------------
-DoubleVec1d NucModel::ChooseAncestralState(long marker)
+DoubleVec1d NucModel::ChooseAncestralState(long) //long 'marker' never used.
{
DoubleVec1d result(BASES, 0.0);
double r = registry.GetRandom().Float();
@@ -1304,7 +1316,7 @@ StringVec1d F84Model::ToXML(size_t nspaces) const
// The second argument is unused since nucleotides don't have differing
// number of states by marker position
-DoubleVec1d F84Model::SimulateMarker(double branchlength, long whichmarker, const DoubleVec1d& state) const
+DoubleVec1d F84Model::SimulateMarker(double branchlength, long, const DoubleVec1d& state) const //long 'whichmarker' not used.
{
double freqa(m_basefreqs[baseA]), freqc(m_basefreqs[baseC]), freqg(m_basefreqs[baseG]), freqt(m_basefreqs[baseT]);
double pur = freqa + freqg;
@@ -1962,8 +1974,8 @@ StringVec1d GTRModel::ToXML(size_t nspaces) const
//------------------------------------------------------------------------------------
-DoubleVec1d GTRModel::SimulateMarker(double branchlength, long whichmarker,
- const DoubleVec1d& state) const
+DoubleVec1d GTRModel::SimulateMarker(double, long,
+ const DoubleVec1d&) const //branchlength, whichmarker, and state not used.
{
throw implementation_error("Cannot simulate data with the GTR model yet.");
} // SimulateMarker
@@ -2444,7 +2456,7 @@ void StepwiseModel::CalculateSteps(long marker)
//------------------------------------------------------------------------------------
-DoubleVec1d StepwiseModel::SimulateMarker(double branchlength, long whichmarker, const DoubleVec1d& state) const
+DoubleVec1d StepwiseModel::SimulateMarker(double, long, const DoubleVec1d&) const //branchlength, whichmarker, and state unused.
{
throw implementation_error("Cannot simulate data with the stepwise model yet.");
} // SimulateMarker
@@ -2688,7 +2700,7 @@ StringVec1d BrownianModel::CreateDataModelReport() const
//------------------------------------------------------------------------------------
-DoubleVec1d BrownianModel::SimulateMarker(double branchlength, long whichmarker, const DoubleVec1d& state) const
+DoubleVec1d BrownianModel::SimulateMarker(double, long, const DoubleVec1d&) const //branchlength, whichmarker, and state not used.
{
throw implementation_error("Cannot simulate data with the Brownian model yet.");
} // SimulateMarker
@@ -3612,7 +3624,7 @@ void MixedKSModel::WriteAlpha(ofstream& sumout, long loc, long rep, long chain)
//------------------------------------------------------------------------------------
-DoubleVec1d MixedKSModel::SimulateMarker(double branchlength, long whichmarker, const DoubleVec1d& state) const
+DoubleVec1d MixedKSModel::SimulateMarker(double, long, const DoubleVec1d&) const //branchlength, whichmarker, and state not used.
{
throw implementation_error("Cannot simulate data with the MixedKS model yet.");
} // SimulateMarker
diff --git a/src/datalike/dlmodel.h b/src/datalike/dlmodel.h
index d4ddf83..5a37ae5 100644
--- a/src/datalike/dlmodel.h
+++ b/src/datalike/dlmodel.h
@@ -1,13 +1,25 @@
-// $Id: dlmodel.h,v 1.70 2012/06/30 01:32:41 bobgian Exp $
+// $Id: dlmodel.h,v 1.72 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*********************************************************************
DLModel is the key control class for polymorphism based on the
type of data likelihood model in use. It is subclassed based on
@@ -141,10 +153,10 @@ class DataModel
void ResetCatCells(); // this needs to be called before each tree evaluation
virtual double ComputeCatDL(long startmarker, long endmarker) = 0;
//opt datamodel, default do nothing
- virtual bool OptimizeDataModel(Tree* tree, const Locus& locus) {return false;};
+ virtual bool OptimizeDataModel(Tree*, const Locus&) {return false;};
virtual void WriteAlpha(std::ofstream&, long, long, long) {};
virtual void ResetAlpha() {};
- virtual void SetAlpha(double alphaVal, long rep, long chain) {};
+ virtual void SetAlpha(double, long, long) {};
// Factories
diff --git a/src/datalike/funcMax.cpp b/src/datalike/funcMax.cpp
index b607da5..9e49e5d 100644
--- a/src/datalike/funcMax.cpp
+++ b/src/datalike/funcMax.cpp
@@ -1,13 +1,25 @@
-// $Id: funcMax.cpp,v 1.10 2012/06/30 01:32:41 bobgian Exp $
+// $Id: funcMax.cpp,v 1.11 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <iostream>
#include <fstream>
diff --git a/src/datalike/funcMax.h b/src/datalike/funcMax.h
index 922cb5d..309a2cc 100644
--- a/src/datalike/funcMax.h
+++ b/src/datalike/funcMax.h
@@ -1,13 +1,25 @@
-// $Id: funcMax.h,v 1.8 2011/03/08 19:22:00 bobgian Exp $
+// $Id: funcMax.h,v 1.9 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef FUNCMAX_H
#define FUNCMAX_H
diff --git a/src/datalike/haplotypes.cpp b/src/datalike/haplotypes.cpp
index bdcf940..20c0080 100644
--- a/src/datalike/haplotypes.cpp
+++ b/src/datalike/haplotypes.cpp
@@ -1,13 +1,25 @@
-// $Id: haplotypes.cpp,v 1.13 2012/06/30 01:32:41 bobgian Exp $
+// $Id: haplotypes.cpp,v 1.14 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2006 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream> // debug only
diff --git a/src/datalike/haplotypes.h b/src/datalike/haplotypes.h
index 32efe15..00c75e9 100644
--- a/src/datalike/haplotypes.h
+++ b/src/datalike/haplotypes.h
@@ -1,13 +1,25 @@
-// $Id: haplotypes.h,v 1.10 2012/06/30 01:32:41 bobgian Exp $
+// $Id: haplotypes.h,v 1.11 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2006 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// This files defines the class that stores "haplotype" specific
// information.
diff --git a/src/datalike/locus.cpp b/src/datalike/locus.cpp
index b7ce4a5..da51eed 100644
--- a/src/datalike/locus.cpp
+++ b/src/datalike/locus.cpp
@@ -1,13 +1,25 @@
-// $Id: locus.cpp,v 1.82 2012/06/30 01:32:41 bobgian Exp $
+// $Id: locus.cpp,v 1.84 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <functional> // for Locus::CountNNucleotides()
#include <fstream>
@@ -509,7 +521,7 @@ void Locus::SetNewMapPositionIfMoving()
//------------------------------------------------------------------------------------
-void Locus::SimulateData(Tree& tree, long int nsites)
+void Locus::SimulateData(Tree& tree, long int) //nsites not used.
{
assert(m_simulate);
ClearVariability();
diff --git a/src/datalike/locus.h b/src/datalike/locus.h
index f1cd07c..2d246c3 100644
--- a/src/datalike/locus.h
+++ b/src/datalike/locus.h
@@ -1,13 +1,25 @@
-// $Id: locus.h,v 1.52 2012/06/30 01:32:41 bobgian Exp $
+// $Id: locus.h,v 1.53 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/***************************************************************
The Locus class contains data information for one locus.
diff --git a/src/datalike/locuscell.cpp b/src/datalike/locuscell.cpp
index 2f12302..e1f180c 100644
--- a/src/datalike/locuscell.cpp
+++ b/src/datalike/locuscell.cpp
@@ -1,13 +1,25 @@
-// $Id: locuscell.cpp,v 1.13 2012/06/30 01:32:41 bobgian Exp $
+// $Id: locuscell.cpp,v 1.14 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "locuscell.h"
diff --git a/src/datalike/locuscell.h b/src/datalike/locuscell.h
index 59ed3ad..b45e832 100644
--- a/src/datalike/locuscell.h
+++ b/src/datalike/locuscell.h
@@ -1,13 +1,25 @@
-// $Id: locuscell.h,v 1.9 2011/03/07 06:08:49 bobgian Exp $
+// $Id: locuscell.h,v 1.10 2018/01/03 21:32:57 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*************************************************************************
This class is a managed container of Cells belonging to a single
locus. It needs to be managed because Cells generally have to be
diff --git a/src/datalike/phenotypes.cpp b/src/datalike/phenotypes.cpp
index bddb596..dc465bd 100644
--- a/src/datalike/phenotypes.cpp
+++ b/src/datalike/phenotypes.cpp
@@ -1,13 +1,25 @@
-// $Id: phenotypes.cpp,v 1.5 2011/03/07 06:08:49 bobgian Exp $
+// $Id: phenotypes.cpp,v 1.6 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2006 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "errhandling.h"
diff --git a/src/datalike/phenotypes.h b/src/datalike/phenotypes.h
index 53980a1..df84240 100644
--- a/src/datalike/phenotypes.h
+++ b/src/datalike/phenotypes.h
@@ -1,13 +1,25 @@
-// $Id: phenotypes.h,v 1.5 2012/06/30 01:32:41 bobgian Exp $
+// $Id: phenotypes.h,v 1.6 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2006 Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Lucian Smith, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PHENOTYPES_H
#define PHENOTYPES_H
diff --git a/src/datalike/region.cpp b/src/datalike/region.cpp
index 06171da..eb3fb24 100644
--- a/src/datalike/region.cpp
+++ b/src/datalike/region.cpp
@@ -1,13 +1,25 @@
-// $Id: region.cpp,v 1.93 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: region.cpp,v 1.94 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <fstream> // for Region::WriteFlucFile
#include <functional> // for Region::CountNBases()
diff --git a/src/datalike/region.h b/src/datalike/region.h
index 851f890..735b1a6 100644
--- a/src/datalike/region.h
+++ b/src/datalike/region.h
@@ -1,13 +1,25 @@
-// $Id: region.h,v 1.54 2012/06/30 01:32:41 bobgian Exp $
+// $Id: region.h,v 1.55 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Region--a storage class, containing data information that applies
// to the genetic info of that region (regional quick theta estimate,
// number of tips, region name).
diff --git a/src/datalike/tipdata.cpp b/src/datalike/tipdata.cpp
index a107455..94ba07d 100644
--- a/src/datalike/tipdata.cpp
+++ b/src/datalike/tipdata.cpp
@@ -1,13 +1,25 @@
-// $Id: tipdata.cpp,v 1.14 2012/06/30 01:32:41 bobgian Exp $
+// $Id: tipdata.cpp,v 1.15 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <functional> // for Locus::CountNNucleotides()
diff --git a/src/datalike/tipdata.h b/src/datalike/tipdata.h
index 9bfc9dc..d1290f8 100644
--- a/src/datalike/tipdata.h
+++ b/src/datalike/tipdata.h
@@ -1,13 +1,25 @@
-// $Id: tipdata.h,v 1.9 2011/03/07 06:08:49 bobgian Exp $
+// $Id: tipdata.h,v 1.10 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/***************************************************************
The TipData class holds the linked genetic data for a tip in a tree of
haplotypes. It also stores, for the tip, its partition membership,
diff --git a/src/force/epoch.cpp b/src/force/epoch.cpp
index c66c947..714aacb 100644
--- a/src/force/epoch.cpp
+++ b/src/force/epoch.cpp
@@ -1,13 +1,25 @@
-// $Id: epoch.cpp,v 1.4 2011/04/23 02:02:48 bobgian Exp $
+// $Id: epoch.cpp,v 1.5 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
//------------------------------------------------------------------------------------
#include "epoch.h"
diff --git a/src/force/epoch.h b/src/force/epoch.h
index 1ebffab..0889551 100644
--- a/src/force/epoch.h
+++ b/src/force/epoch.h
@@ -1,13 +1,25 @@
-// $Id: epoch.h,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: epoch.h,v 1.4 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
//------------------------------------------------------------------------------------
#ifndef EPOCH_H
diff --git a/src/force/event.cpp b/src/force/event.cpp
index c0e5806..fe904f0 100644
--- a/src/force/event.cpp
+++ b/src/force/event.cpp
@@ -1,13 +1,25 @@
-// $Id: event.cpp,v 1.65 2013/10/25 17:00:52 mkkuhner Exp $
+// $Id: event.cpp,v 1.66 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <algorithm>
#include <cassert>
#include <functional> // for divides<> and less<> used in ThrowIfSubPopSizeTiny
diff --git a/src/force/event.h b/src/force/event.h
index d216855..2b1d866 100644
--- a/src/force/event.h
+++ b/src/force/event.h
@@ -1,13 +1,25 @@
-// $Id: event.h,v 1.37 2012/06/30 01:32:41 bobgian Exp $
+// $Id: event.h,v 1.38 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef EVENT_H
#define EVENT_H
diff --git a/src/force/force.cpp b/src/force/force.cpp
index d79133c..ceb780f 100644
--- a/src/force/force.cpp
+++ b/src/force/force.cpp
@@ -1,13 +1,25 @@
-// $Id: force.cpp,v 1.79 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: force.cpp,v 1.81 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <algorithm> // for stl::remove
#include <cassert>
#include <cmath>
@@ -638,7 +650,7 @@ RegionGammaForce::RegionGammaForce(vector<Parameter> parameters,
//------------------------------------------------------------------------------------
-vector<Event*> RegionGammaForce::MakeEvents(const ForceSummary& fs) const
+vector<Event*> RegionGammaForce::MakeEvents(const ForceSummary&) const
{
vector<Event*> tempvec; // Yes this returns an empty vector.
return tempvec;
@@ -654,7 +666,7 @@ long RegionGammaForce::ReportDimensionality() const
//------------------------------------------------------------------------------------
-Summary* RegionGammaForce::CreateSummary(IntervalData& interval, bool shortness) const
+Summary* RegionGammaForce::CreateSummary(IntervalData&, bool) const
{
return NULL; // Yes, we have no summary of our own.
@@ -910,14 +922,14 @@ PartitionForce::PartitionForce(
//------------------------------------------------------------------------------------
-long PartitionForce::ChoosePartition(long origpart, long chosenpart, bool islow, long midpoint) const
+long PartitionForce::ChoosePartition(long origpart, long, bool, long) const
{
return origpart;
} // PartitionForce::ChoosePartition
//------------------------------------------------------------------------------------
-void PartitionForce::ModifyEvents(const ForceSummary& fs, vector<Event*>& events) const
+void PartitionForce::ModifyEvents(const ForceSummary&, vector<Event*>& events) const
{
vector<Event*>::iterator it;
for (it = events.begin(); it != events.end(); ++it)
@@ -1207,7 +1219,7 @@ GrowthForce::GrowthForce(vector<Parameter> parameters,
//------------------------------------------------------------------------------------
-vector<Event*> GrowthForce::MakeEvents(const ForceSummary& fs) const
+vector<Event*> GrowthForce::MakeEvents(const ForceSummary&) const
{
vector<Event*> tempvec; // Yes this returns an empty vector.
return tempvec;
@@ -1216,7 +1228,7 @@ vector<Event*> GrowthForce::MakeEvents(const ForceSummary& fs) const
//------------------------------------------------------------------------------------
-Summary* GrowthForce::CreateSummary(IntervalData& interval, bool shortness) const
+Summary* GrowthForce::CreateSummary(IntervalData&, bool) const
{
return NULL; // Yes, we have no summary of our own.
@@ -1224,7 +1236,7 @@ Summary* GrowthForce::CreateSummary(IntervalData& interval, bool shortness) cons
//------------------------------------------------------------------------------------
-void GrowthForce::ModifyEvents(const ForceSummary& fs, vector<Event*>& events) const
+void GrowthForce::ModifyEvents(const ForceSummary&, vector<Event*>&) const
{
// this is now a no-op
} // GrowthForce::ModifyEvents()
@@ -1327,7 +1339,7 @@ LogisticSelectionForce::LogisticSelectionForce(vector<Parameter> parameters,
//------------------------------------------------------------------------------------
-vector<Event*> LogisticSelectionForce::MakeEvents(const ForceSummary& fs) const
+vector<Event*> LogisticSelectionForce::MakeEvents(const ForceSummary&) const
{
vector<Event*> tempvec; // Yes this returns an empty vector.
return tempvec;
@@ -1336,7 +1348,7 @@ vector<Event*> LogisticSelectionForce::MakeEvents(const ForceSummary& fs) const
//------------------------------------------------------------------------------------
-Summary* LogisticSelectionForce::CreateSummary(IntervalData& interval, bool shortness) const
+Summary* LogisticSelectionForce::CreateSummary(IntervalData&, bool) const
{
return NULL; // Yes, we have no summary of our own.
@@ -1344,7 +1356,7 @@ Summary* LogisticSelectionForce::CreateSummary(IntervalData& interval, bool shor
//------------------------------------------------------------------------------------
-void LogisticSelectionForce::ModifyEvents(const ForceSummary& fs, vector<Event*>& events) const
+void LogisticSelectionForce::ModifyEvents(const ForceSummary&, vector<Event*>&) const
{
// this is now a no-op
} // LogisticSelectionForce::ModifyEvents()
@@ -1554,7 +1566,7 @@ string StickExpGrowForce::GetXMLName() const
//------------------------------------------------------------------------------------
-vector<Event*> StickExpGrowForce::MakeEvents(const ForceSummary& fs) const
+vector<Event*> StickExpGrowForce::MakeEvents(const ForceSummary&) const
{
vector<Event*> tempvec; // Yes this returns an empty vector.
return tempvec;
@@ -1562,14 +1574,14 @@ vector<Event*> StickExpGrowForce::MakeEvents(const ForceSummary& fs) const
//------------------------------------------------------------------------------------
-void StickExpGrowForce::ModifyEvents(const ForceSummary& fs, vector<Event*>& events) const
+void StickExpGrowForce::ModifyEvents(const ForceSummary&, vector<Event*>&) const
{
// this is now a no-op
} // StickExpGrowForce::ModifyEvents()
//------------------------------------------------------------------------------------
-Summary* StickExpGrowForce::CreateSummary(IntervalData& interval, bool shortness) const
+Summary* StickExpGrowForce::CreateSummary(IntervalData&, bool) const
{
return NULL; // Yes, we have no summary of our own.
}
@@ -1674,7 +1686,7 @@ string StickSelectForce::GetXMLName() const
//------------------------------------------------------------------------------------
-vector<Event*> StickSelectForce::MakeEvents(const ForceSummary& fs) const
+vector<Event*> StickSelectForce::MakeEvents(const ForceSummary&) const
{
vector<Event*> tempvec; // Yes this returns an empty vector.
return tempvec;
@@ -1689,7 +1701,7 @@ string StickSelectForce::MakeOpeningTag(unsigned long nspaces) const
//------------------------------------------------------------------------------------
-Summary* StickSelectForce::CreateSummary(IntervalData& interval, bool shortness) const
+Summary* StickSelectForce::CreateSummary(IntervalData&, bool) const
{
return NULL; // Yes, we have no summary of our own.
}
@@ -1721,7 +1733,7 @@ long StickSelectForce::ReportDimensionality() const
//------------------------------------------------------------------------------------
//------------------------------------------------------------------------------------
-DivForce::DivForce(vector<Parameter> parameters, long int maxEvents,
+DivForce::DivForce(vector<Parameter> parameters, long int, //maxEvents unused.
vector<ParamGroup> identgroups,
vector<ParamGroup> multgroups,
const DoubleVec1d& paramgroupmults,
diff --git a/src/force/force.h b/src/force/force.h
index a0892e6..35b8eea 100644
--- a/src/force/force.h
+++ b/src/force/force.h
@@ -1,13 +1,25 @@
// $Id: force.h,v 1.9 2002/07/30 01:44:41 mkkuhner Exp
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef FORCE_H
#define FORCE_H
@@ -256,7 +268,7 @@ class Force
// The following functions manage the Events associated with a particular
// force. Events are owned by the recipient (an Arranger).
virtual std::vector<Event*> MakeEvents(const ForceSummary& fs) const = 0;
- virtual void ModifyEvents(const ForceSummary& fs,
+ virtual void ModifyEvents(const ForceSummary&,
std::vector<Event*>&) const {};
// The following function is used in creating the partition holder in each branch.
@@ -545,7 +557,7 @@ class MigForce : public PartitionForce
virtual string GetXMLName() const { return xmlstr::XML_TAG_MIGRATION; };
virtual std::vector<Event*> MakeEvents(const ForceSummary& fs) const;
virtual Summary* CreateSummary(IntervalData& interval, bool shortness) const;
- virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); };
+ virtual std::string MakeStatusXML(const std::string&) const { return string(""); };
virtual long int ReportDimensionality() const { return 3L; };
}; // MigForce
@@ -578,7 +590,7 @@ class DivMigForce : public PartitionForce
virtual string GetXMLName() const { return xmlstr::XML_TAG_DIVMIG; };
virtual std::vector<Event*> MakeEvents(const ForceSummary& fs) const;
virtual Summary* CreateSummary(IntervalData& interval, bool shortness) const;
- virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); };
+ virtual std::string MakeStatusXML(const std::string&) const { return string(""); };
virtual long int ReportDimensionality() const { return 3L; };
}; // DivMigForce
diff --git a/src/force/forceparam.cpp b/src/force/forceparam.cpp
index e1ee703..d782144 100644
--- a/src/force/forceparam.cpp
+++ b/src/force/forceparam.cpp
@@ -1,13 +1,25 @@
-// $Id: forceparam.cpp,v 1.42 2013/11/07 22:46:06 mkkuhner Exp $
+// $Id: forceparam.cpp,v 1.43 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
diff --git a/src/force/forceparam.h b/src/force/forceparam.h
index beb47bb..e544e4e 100644
--- a/src/force/forceparam.h
+++ b/src/force/forceparam.h
@@ -1,13 +1,25 @@
-// $Id: forceparam.h,v 1.28 2011/03/07 06:08:49 bobgian Exp $
+// $Id: forceparam.h,v 1.29 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/********************************************************************
ForceParameters is a collection class used for internal communication
throughout Lamarc.
diff --git a/src/force/forcesummary.cpp b/src/force/forcesummary.cpp
index 777e975..8247e4f 100644
--- a/src/force/forcesummary.cpp
+++ b/src/force/forcesummary.cpp
@@ -1,13 +1,25 @@
-// $Id: forcesummary.cpp,v 1.63 2013/11/07 22:46:06 mkkuhner Exp $
+// $Id: forcesummary.cpp,v 1.64 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cmath>
diff --git a/src/force/forcesummary.h b/src/force/forcesummary.h
index e85dcd8..6297105 100644
--- a/src/force/forcesummary.h
+++ b/src/force/forcesummary.h
@@ -1,13 +1,25 @@
-// $Id: forcesummary.h,v 1.34 2012/06/30 01:32:41 bobgian Exp $
+// $Id: forcesummary.h,v 1.35 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/********************************************************************
ForceSummary is the governing object for polymorphism along force lines.
It creates the basic tree and manages other force-specific objects.
diff --git a/src/force/paramstat.cpp b/src/force/paramstat.cpp
index b91ed10..cf7b6e1 100644
--- a/src/force/paramstat.cpp
+++ b/src/force/paramstat.cpp
@@ -1,13 +1,25 @@
-// $Id: paramstat.cpp,v 1.12 2012/06/30 01:32:41 bobgian Exp $
+// $Id: paramstat.cpp,v 1.14 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "paramstat.h"
@@ -83,7 +95,7 @@ string IdenticalHeadStatus::ConstraintDescription(long) const
//-------------------------------------------------------------------------------------
-void IdenticalHeadStatus::SetWithConstraints(long pindex, double newval,
+void IdenticalHeadStatus::SetWithConstraints(long, double newval,
DoubleVec1d& pvecnums,
const ULongVec1d& groupmembers,
double) const
diff --git a/src/force/paramstat.h b/src/force/paramstat.h
index 2cf817b..0c5cd8a 100644
--- a/src/force/paramstat.h
+++ b/src/force/paramstat.h
@@ -1,13 +1,25 @@
-// $Id: paramstat.h,v 1.9 2011/04/23 02:02:49 bobgian Exp $
+// $Id: paramstat.h,v 1.11 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef PARAMSTAT_H
#define PARAMSTAT_H
@@ -96,8 +108,8 @@ class InvalidStatus: public ParamStatusImpl
virtual void SetWithConstraints(long, double, std::vector<double>&, const std::vector<unsigned long>&, double) const
{ assert(false); };
- virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
- virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_identical); };
+ virtual std::string ToggleIndividualStatus(force_type) const { return ToString(pstat_unconstrained); };
+ virtual std::string ToggleGroupStatus(force_type) const { return ToString(pstat_identical); };
};
//-------------------------------------------------------------------------------------
@@ -118,8 +130,8 @@ class UnconstrainedStatus: public ParamStatusImpl
const std::vector<unsigned long>&, double) const
{ pvecnums[pindex] = newval; };
- virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_constant); };
- virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
+ virtual std::string ToggleIndividualStatus(force_type) const { return ToString(pstat_constant); };
+ virtual std::string ToggleGroupStatus(force_type) const { return ToString(pstat_constant); };
};
//-------------------------------------------------------------------------------------
@@ -160,8 +172,8 @@ class IdenticalStatus: public ParamStatusImpl
const std::vector<unsigned long>&, double) const
{ assert(false); };
- virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
- virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
+ virtual std::string ToggleIndividualStatus(force_type) const { return ToString(pstat_unconstrained); };
+ virtual std::string ToggleGroupStatus(force_type) const { return ToString(pstat_constant); };
};
//-------------------------------------------------------------------------------------
@@ -178,8 +190,8 @@ class IdenticalHeadStatus: public ParamStatusImpl
virtual bool Grouped() const { return true; };
virtual void SetWithConstraints(long pindex, double newval, std::vector<double>& pvecnums,
const std::vector<unsigned long>& groupmembers, double) const;
- virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
- virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
+ virtual std::string ToggleIndividualStatus(force_type) const { return ToString(pstat_unconstrained); };
+ virtual std::string ToggleGroupStatus(force_type) const { return ToString(pstat_constant); };
};
//-------------------------------------------------------------------------------------
@@ -198,8 +210,8 @@ class MultiplicativeStatus: public ParamStatusImpl
virtual void SetWithConstraints(long, double, std::vector<double>&, const std::vector<unsigned long>&, double) const
{ assert(false); };
- virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
- virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
+ virtual std::string ToggleIndividualStatus(force_type) const { return ToString(pstat_unconstrained); };
+ virtual std::string ToggleGroupStatus(force_type) const { return ToString(pstat_constant); };
};
//-------------------------------------------------------------------------------------
@@ -216,8 +228,8 @@ class MultiplicativeHeadStatus: public ParamStatusImpl
virtual bool Grouped() const { return true; };
virtual void SetWithConstraints(long pindex, double newval, std::vector<double>& pvecnums,
const std::vector<unsigned long>& groupmembers, double multiplier) const;
- virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
- virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
+ virtual std::string ToggleIndividualStatus(force_type) const { return ToString(pstat_unconstrained); };
+ virtual std::string ToggleGroupStatus(force_type) const { return ToString(pstat_constant); };
};
//-------------------------------------------------------------------------------------
diff --git a/src/force/priorreport.cpp b/src/force/priorreport.cpp
index bdfea12..a9b6b4a 100644
--- a/src/force/priorreport.cpp
+++ b/src/force/priorreport.cpp
@@ -1,13 +1,25 @@
-// $Id: priorreport.cpp,v 1.7 2012/06/30 01:32:41 bobgian Exp $
+// $Id: priorreport.cpp,v 1.8 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
#include <algorithm> // for std::find
diff --git a/src/force/priorreport.h b/src/force/priorreport.h
index dc96011..281e3a0 100644
--- a/src/force/priorreport.h
+++ b/src/force/priorreport.h
@@ -1,13 +1,25 @@
-// $Id: priorreport.h,v 1.3 2011/03/07 06:08:49 bobgian Exp $
+// $Id: priorreport.h,v 1.4 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/********************************************************************
PriorReport is a collection class that creates an output report on
the priors used during a Lamarc run.
diff --git a/src/force/stair.cpp b/src/force/stair.cpp
index f654218..13162b6 100644
--- a/src/force/stair.cpp
+++ b/src/force/stair.cpp
@@ -1,13 +1,25 @@
-// $Id: stair.cpp,v 1.3 2011/03/08 19:22:00 bobgian Exp $
+// $Id: stair.cpp,v 1.4 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include "stair.h"
//------------------------------------------------------------------------------------
diff --git a/src/force/stair.h b/src/force/stair.h
index 8252ca9..33e2841 100644
--- a/src/force/stair.h
+++ b/src/force/stair.h
@@ -1,13 +1,25 @@
-// $Id: stair.h,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: stair.h,v 1.5 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef STAIR_H
#define STAIR_H
diff --git a/src/force/timemanager.cpp b/src/force/timemanager.cpp
index 6246476..a8ff8d5 100644
--- a/src/force/timemanager.cpp
+++ b/src/force/timemanager.cpp
@@ -1,12 +1,24 @@
-// $Id: timemanager.cpp,v 1.15 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: timemanager.cpp,v 1.17 2018/01/03 21:32:58 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <iostream> // for debug PrintStick function
@@ -43,7 +55,7 @@ TimeManager::TimeManager(const TimeManager& src)
//------------------------------------------------------------------------------------
-TimeManager& TimeManager::operator=(const TimeManager& src)
+TimeManager& TimeManager::operator=(const TimeManager&)
{
// it is not necessary to copy randomSource, as it should
// already be correct
@@ -159,14 +171,14 @@ void TimeManager::PrintStickFreqsToFileForJoint300(std::ofstream&) const
//------------------------------------------------------------------------------------
// ConstantTimeManager
-DoubleVec1d ConstantTimeManager::XpartThetasAtT(double t, const ForceParameters& fp)
+DoubleVec1d ConstantTimeManager::XpartThetasAtT(double, const ForceParameters& fp)
{
return fp.GetRegionalThetas();
} // XpartThetasAtT
//------------------------------------------------------------------------------------
-DoubleVec1d ConstantTimeManager::PartitionThetasAtT(double t, force_type force, const ForceParameters& fp)
+DoubleVec1d ConstantTimeManager::PartitionThetasAtT(double, force_type force, const ForceParameters& fp)
{
DoubleVec1d thetas(fp.GetRegionalThetas());
return dynamic_cast<PartitionForce*>(*registry.GetForceSummary().GetForceByTag(force))->SumXPartsToParts(thetas);
@@ -537,9 +549,9 @@ double ExpGrowTimeManager::TimeOfInactiveCoal(double tstart,
//------------------------------------------------------------------------------------
-double ExpGrowTimeManager::TimeOfTraitMutation(double tstart,
- const LongVec1d& lineages, const ForceParameters& fp, long& tiptrait,
- long& roottrait, double)
+double ExpGrowTimeManager::TimeOfTraitMutation(double,
+ const LongVec1d&, const ForceParameters&, long&,
+ long&, double)
{
// Computes a displacement, a.k.a. "delta t" -- the length of the time
// interval, not the timestamp for the end of the interval.
@@ -585,7 +597,7 @@ DoubleVec1d LogSelectTimeManager::XpartThetasAtT(double t, const ForceParameters
//------------------------------------------------------------------------------------
-DoubleVec1d LogSelectTimeManager::PartitionThetasAtT(double t, force_type force, const ForceParameters& fp)
+DoubleVec1d LogSelectTimeManager::PartitionThetasAtT(double, force_type, const ForceParameters&)
{
// MDEBUG not done!
assert(false); // MDEBUG we are not ready for this yet
@@ -1986,7 +1998,7 @@ DoubleVec1d ExpGrowStickTimeManager::NextThetas(double nexttime, const ForcePara
//------------------------------------------------------------------------------------
//------------------------------------------------------------------------------------
-double SelectStickTimeManager::NextRootTime(double timenow, const ForceParameters& fp) const
+double SelectStickTimeManager::NextRootTime(double timenow, const ForceParameters&) const //fp unused.
{
// JDEBUG--constant length joints for now?
// double newlength = 0.002; // for lpl'ish data
@@ -2049,7 +2061,7 @@ DoubleVec1d SelectStickTimeManager::NextThetas(double nexttime, const ForceParam
//------------------------------------------------------------------------------------
-DoubleVec1d SelectStickTimeManager::NextThetas(double nexttime, const ForceParameters& fp,
+DoubleVec1d SelectStickTimeManager::NextThetas(double, const ForceParameters& fp, //'nexttime' unused.
const DoubleVec1d& discounts) const
{
DoubleVec1d newthetas;
diff --git a/src/force/timemanager.h b/src/force/timemanager.h
index 44fe6f8..86dd999 100644
--- a/src/force/timemanager.h
+++ b/src/force/timemanager.h
@@ -1,13 +1,25 @@
-// $Id: timemanager.h,v 1.8 2012/06/30 01:32:41 bobgian Exp $
+// $Id: timemanager.h,v 1.9 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TIMEMANAGER_H
#define TIMEMANAGER_H
diff --git a/src/force/timesize.cpp b/src/force/timesize.cpp
index 941f58e..74cf085 100644
--- a/src/force/timesize.cpp
+++ b/src/force/timesize.cpp
@@ -1,13 +1,25 @@
-// $Id: timesize.cpp,v 1.10 2012/06/30 01:32:41 bobgian Exp $
+// $Id: timesize.cpp,v 1.11 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "force.h"
diff --git a/src/force/timesize.h b/src/force/timesize.h
index 6820c7c..e4ce951 100644
--- a/src/force/timesize.h
+++ b/src/force/timesize.h
@@ -1,13 +1,25 @@
-// $Id: timesize.h,v 1.6 2011/03/07 06:08:50 bobgian Exp $
+// $Id: timesize.h,v 1.7 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TIMESIZE_H
#define TIMESIZE_H
diff --git a/src/guiconv/batchconverter.cpp b/src/guiconv/batchconverter.cpp
index 270a905..d8d5438 100644
--- a/src/guiconv/batchconverter.cpp
+++ b/src/guiconv/batchconverter.cpp
@@ -1,13 +1,25 @@
-// $Id: batchconverter.cpp,v 1.22 2011/03/08 19:22:00 bobgian Exp $
+// $Id: batchconverter.cpp,v 1.23 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "batchconverter.h"
#include "gc_cmdline.h"
#include "gc_data.h"
diff --git a/src/guiconv/batchconverter.h b/src/guiconv/batchconverter.h
index dc1092a..d46b49e 100644
--- a/src/guiconv/batchconverter.h
+++ b/src/guiconv/batchconverter.h
@@ -1,13 +1,25 @@
-// $Id: batchconverter.h,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: batchconverter.h,v 1.6 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef BATCHCONVERTER_H
#define BATCHCONVERTER_H
diff --git a/src/guiconv/gc_assigntab.cpp b/src/guiconv/gc_assigntab.cpp
index b5d4038..e8046dd 100644
--- a/src/guiconv/gc_assigntab.cpp
+++ b/src/guiconv/gc_assigntab.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_assigntab.cpp,v 1.28 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_assigntab.cpp,v 1.29 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include <stdio.h>
diff --git a/src/guiconv/gc_assigntab.h b/src/guiconv/gc_assigntab.h
index d6e5fd8..b08b8c3 100644
--- a/src/guiconv/gc_assigntab.h
+++ b/src/guiconv/gc_assigntab.h
@@ -1,13 +1,25 @@
-// $Id: gc_assigntab.h,v 1.16 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_assigntab.h,v 1.17 2018/01/03 21:32:58 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_ASSIGNTAB_H
#define GC_ASSIGNTAB_H
diff --git a/src/guiconv/gc_block_dialogs.cpp b/src/guiconv/gc_block_dialogs.cpp
index afd8302..bcb73d4 100644
--- a/src/guiconv/gc_block_dialogs.cpp
+++ b/src/guiconv/gc_block_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_block_dialogs.cpp,v 1.8 2011/06/22 18:22:22 jmcgill Exp $
+// $Id: gc_block_dialogs.cpp,v 1.9 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_block_dialogs.h"
diff --git a/src/guiconv/gc_block_dialogs.h b/src/guiconv/gc_block_dialogs.h
index 5373442..feab05a 100644
--- a/src/guiconv/gc_block_dialogs.h
+++ b/src/guiconv/gc_block_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_block_dialogs.h,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_block_dialogs.h,v 1.7 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_BLOCK_DIALOGS_H
#define GC_BLOCK_DIALOGS_H
diff --git a/src/guiconv/gc_cmdline.cpp b/src/guiconv/gc_cmdline.cpp
index fab9209..5fdd519 100644
--- a/src/guiconv/gc_cmdline.cpp
+++ b/src/guiconv/gc_cmdline.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_cmdline.cpp,v 1.23 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_cmdline.cpp,v 1.24 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "wx/cmdline.h"
#include "wx/log.h"
#include "conf.h"
diff --git a/src/guiconv/gc_cmdline.h b/src/guiconv/gc_cmdline.h
index 1acd2e5..59fce7b 100644
--- a/src/guiconv/gc_cmdline.h
+++ b/src/guiconv/gc_cmdline.h
@@ -1,13 +1,25 @@
-// $Id: gc_cmdline.h,v 1.13 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_cmdline.h,v 1.14 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_CMDLINE_H
#define GC_CMDLINE_H
diff --git a/src/guiconv/gc_color.cpp b/src/guiconv/gc_color.cpp
index 8a6d5bd..efb8fab 100644
--- a/src/guiconv/gc_color.cpp
+++ b/src/guiconv/gc_color.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_color.cpp,v 1.4 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_color.cpp,v 1.5 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_color.h"
#include "wx/colour.h"
diff --git a/src/guiconv/gc_color.h b/src/guiconv/gc_color.h
index ef8f35f..ad13797 100644
--- a/src/guiconv/gc_color.h
+++ b/src/guiconv/gc_color.h
@@ -1,13 +1,25 @@
-// $Id: gc_color.h,v 1.5 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_color.h,v 1.6 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_COLOR_H
#define GC_COLOR_H
diff --git a/src/guiconv/gc_data.cpp b/src/guiconv/gc_data.cpp
index 90a035c..6a0a073 100644
--- a/src/guiconv/gc_data.cpp
+++ b/src/guiconv/gc_data.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_data.cpp,v 1.38 2011/12/30 22:50:10 jmcgill Exp $
+// $Id: gc_data.cpp,v 1.39 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "cnv_strings.h"
diff --git a/src/guiconv/gc_data.h b/src/guiconv/gc_data.h
index bd30dab..75bda49 100644
--- a/src/guiconv/gc_data.h
+++ b/src/guiconv/gc_data.h
@@ -1,13 +1,25 @@
-// $Id: gc_data.h,v 1.32 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_data.h,v 1.33 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_DATA_H
#define GC_DATA_H
diff --git a/src/guiconv/gc_data_display.cpp b/src/guiconv/gc_data_display.cpp
index 1889cc6..de5399c 100644
--- a/src/guiconv/gc_data_display.cpp
+++ b/src/guiconv/gc_data_display.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_data_display.cpp,v 1.10 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_data_display.cpp,v 1.11 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
//#include <iostream>
#include <string>
diff --git a/src/guiconv/gc_data_display.h b/src/guiconv/gc_data_display.h
index dc82112..91d1727 100644
--- a/src/guiconv/gc_data_display.h
+++ b/src/guiconv/gc_data_display.h
@@ -1,13 +1,25 @@
-// $Id: gc_data_display.h,v 1.9 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_data_display.h,v 1.10 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_DATA_DISPLAY_H
#define GC_DATA_DISPLAY_H
diff --git a/src/guiconv/gc_dialog.cpp b/src/guiconv/gc_dialog.cpp
index 05c0762..326be14 100644
--- a/src/guiconv/gc_dialog.cpp
+++ b/src/guiconv/gc_dialog.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_dialog.cpp,v 1.30 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_dialog.cpp,v 1.31 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_data.h"
diff --git a/src/guiconv/gc_dialog.h b/src/guiconv/gc_dialog.h
index 99e426d..0d596ff 100644
--- a/src/guiconv/gc_dialog.h
+++ b/src/guiconv/gc_dialog.h
@@ -1,13 +1,25 @@
-// $Id: gc_dialog.h,v 1.20 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_dialog.h,v 1.21 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_DIALOG_H
#define GC_DIALOG_H
diff --git a/src/guiconv/gc_event_ids.h b/src/guiconv/gc_event_ids.h
index 4e5f822..ed78bb3 100644
--- a/src/guiconv/gc_event_ids.h
+++ b/src/guiconv/gc_event_ids.h
@@ -1,13 +1,25 @@
-// $Id: gc_event_ids.h,v 1.61 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_event_ids.h,v 1.62 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_EVENT_IDS_H
#define GC_EVENT_IDS_H
diff --git a/src/guiconv/gc_event_publisher.cpp b/src/guiconv/gc_event_publisher.cpp
index 414339a..ef126ed 100644
--- a/src/guiconv/gc_event_publisher.cpp
+++ b/src/guiconv/gc_event_publisher.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_event_publisher.cpp,v 1.20 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_event_publisher.cpp,v 1.21 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <set>
#include "gc_event_ids.h"
diff --git a/src/guiconv/gc_event_publisher.h b/src/guiconv/gc_event_publisher.h
index 42396c0..85a1e77 100644
--- a/src/guiconv/gc_event_publisher.h
+++ b/src/guiconv/gc_event_publisher.h
@@ -1,13 +1,25 @@
-// $Id: gc_event_publisher.h,v 1.17 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_event_publisher.h,v 1.18 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_EVENT_PUBLISHER_H
#define GC_EVENT_PUBLISHER_H
diff --git a/src/guiconv/gc_export_dialogs.cpp b/src/guiconv/gc_export_dialogs.cpp
index 3e58c67..4e2bc9c 100644
--- a/src/guiconv/gc_export_dialogs.cpp
+++ b/src/guiconv/gc_export_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_export_dialogs.cpp,v 1.7 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_export_dialogs.cpp,v 1.8 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_event_ids.h"
#include "gc_export_dialogs.h"
#include "gc_layout.h"
diff --git a/src/guiconv/gc_export_dialogs.h b/src/guiconv/gc_export_dialogs.h
index 52c7bda..11bf2d8 100644
--- a/src/guiconv/gc_export_dialogs.h
+++ b/src/guiconv/gc_export_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_export_dialogs.h,v 1.6 2011/03/08 19:22:00 bobgian Exp $
+// $Id: gc_export_dialogs.h,v 1.7 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_EXPORT_DIALOGS_H
#define GC_EXPORT_DIALOGS_H
diff --git a/src/guiconv/gc_file_dialogs.cpp b/src/guiconv/gc_file_dialogs.cpp
index b938759..98a1973 100644
--- a/src/guiconv/gc_file_dialogs.cpp
+++ b/src/guiconv/gc_file_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_file_dialogs.cpp,v 1.49 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_file_dialogs.cpp,v 1.50 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "errhandling.h"
diff --git a/src/guiconv/gc_file_dialogs.h b/src/guiconv/gc_file_dialogs.h
index bd18b27..ae6a6f4 100644
--- a/src/guiconv/gc_file_dialogs.h
+++ b/src/guiconv/gc_file_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_file_dialogs.h,v 1.25 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_file_dialogs.h,v 1.26 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_FILE_DIALOGS_H
#define GC_FILE_DIALOGS_H
diff --git a/src/guiconv/gc_file_list.cpp b/src/guiconv/gc_file_list.cpp
index 7bd797e..29112fa 100644
--- a/src/guiconv/gc_file_list.cpp
+++ b/src/guiconv/gc_file_list.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_file_list.cpp,v 1.23 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_file_list.cpp,v 1.24 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_event_publisher.h"
diff --git a/src/guiconv/gc_file_list.h b/src/guiconv/gc_file_list.h
index a95e0ef..678a584 100644
--- a/src/guiconv/gc_file_list.h
+++ b/src/guiconv/gc_file_list.h
@@ -1,13 +1,25 @@
-// $Id: gc_file_list.h,v 1.13 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_file_list.h,v 1.14 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_FILELIST_H
#define GC_FILELIST_H
diff --git a/src/guiconv/gc_frame.cpp b/src/guiconv/gc_frame.cpp
index 0621032..0caa579 100644
--- a/src/guiconv/gc_frame.cpp
+++ b/src/guiconv/gc_frame.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_frame.cpp,v 1.109 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_frame.cpp,v 1.110 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
//#include <iostream>
#include <stdio.h>
diff --git a/src/guiconv/gc_frame.h b/src/guiconv/gc_frame.h
index 12b2c2a..6711378 100644
--- a/src/guiconv/gc_frame.h
+++ b/src/guiconv/gc_frame.h
@@ -1,13 +1,25 @@
-// $Id: gc_frame.h,v 1.56 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_frame.h,v 1.57 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_FRAME_H
#define GC_FRAME_H
diff --git a/src/guiconv/gc_layout.cpp b/src/guiconv/gc_layout.cpp
index 62033f1..40f9437 100644
--- a/src/guiconv/gc_layout.cpp
+++ b/src/guiconv/gc_layout.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_layout.cpp,v 1.29 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_layout.cpp,v 1.30 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_layout.h"
const long gclayout::appHeight = 800;
diff --git a/src/guiconv/gc_layout.h b/src/guiconv/gc_layout.h
index 9923b65..9215e41 100644
--- a/src/guiconv/gc_layout.h
+++ b/src/guiconv/gc_layout.h
@@ -1,13 +1,25 @@
-// $Id: gc_layout.h,v 1.23 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_layout.h,v 1.24 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_LAYOUT_H
#define GC_LAYOUT_H
diff --git a/src/guiconv/gc_locitab.cpp b/src/guiconv/gc_locitab.cpp
index 60edd1d..7917225 100644
--- a/src/guiconv/gc_locitab.cpp
+++ b/src/guiconv/gc_locitab.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_locitab.cpp,v 1.10 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_locitab.cpp,v 1.11 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_event_publisher.h"
diff --git a/src/guiconv/gc_locitab.h b/src/guiconv/gc_locitab.h
index 1cece38..56fa177 100644
--- a/src/guiconv/gc_locitab.h
+++ b/src/guiconv/gc_locitab.h
@@ -1,13 +1,25 @@
-// $Id: gc_locitab.h,v 1.8 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_locitab.h,v 1.9 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_LOCITAB_H
#define GC_LOCITAB_H
diff --git a/src/guiconv/gc_locus_dialogs.cpp b/src/guiconv/gc_locus_dialogs.cpp
index ee00cac..aab17b5 100644
--- a/src/guiconv/gc_locus_dialogs.cpp
+++ b/src/guiconv/gc_locus_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_locus_dialogs.cpp,v 1.29 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_locus_dialogs.cpp,v 1.30 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_creation_info.h"
diff --git a/src/guiconv/gc_locus_dialogs.h b/src/guiconv/gc_locus_dialogs.h
index 015f54f..ac20242 100644
--- a/src/guiconv/gc_locus_dialogs.h
+++ b/src/guiconv/gc_locus_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_locus_dialogs.h,v 1.18 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_locus_dialogs.h,v 1.19 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_LOCUS_DIALOGS_H
#define GC_LOCUS_DIALOGS_H
diff --git a/src/guiconv/gc_logic.cpp b/src/guiconv/gc_logic.cpp
index 7198b3e..6779ae8 100644
--- a/src/guiconv/gc_logic.cpp
+++ b/src/guiconv/gc_logic.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_logic.cpp,v 1.58 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_logic.cpp,v 1.59 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <vector>
#include "gc_dialog.h"
diff --git a/src/guiconv/gc_logic.h b/src/guiconv/gc_logic.h
index 8d354b7..2fc694b 100644
--- a/src/guiconv/gc_logic.h
+++ b/src/guiconv/gc_logic.h
@@ -1,13 +1,25 @@
-// $Id: gc_logic.h,v 1.43 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_logic.h,v 1.44 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_LOGIC_H
#define GC_LOGIC_H
diff --git a/src/guiconv/gc_matrix_display.cpp b/src/guiconv/gc_matrix_display.cpp
index 26d09e0..a151689 100644
--- a/src/guiconv/gc_matrix_display.cpp
+++ b/src/guiconv/gc_matrix_display.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_matrix_display.cpp,v 1.1 2011/12/01 22:32:42 jmcgill Exp $
+// $Id: gc_matrix_display.cpp,v 1.2 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_matrix_display.h"
#include "gc_layout.h"
#include "wx/log.h"
diff --git a/src/guiconv/gc_matrix_display.h b/src/guiconv/gc_matrix_display.h
index c852292..7cb688b 100644
--- a/src/guiconv/gc_matrix_display.h
+++ b/src/guiconv/gc_matrix_display.h
@@ -1,13 +1,25 @@
-// $Id: gc_matrix_display.h,v 1.2 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_matrix_display.h,v 1.3 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_MATRIX_DISPLAY_H
#define GC_MATRIX_DISPLAY_H
diff --git a/src/guiconv/gc_menu_actors.cpp b/src/guiconv/gc_menu_actors.cpp
index 23d42d3..8334b17 100644
--- a/src/guiconv/gc_menu_actors.cpp
+++ b/src/guiconv/gc_menu_actors.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_menu_actors.cpp,v 1.7 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_menu_actors.cpp,v 1.8 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_datastore.h"
diff --git a/src/guiconv/gc_menu_actors.h b/src/guiconv/gc_menu_actors.h
index 914fe6f..757327d 100644
--- a/src/guiconv/gc_menu_actors.h
+++ b/src/guiconv/gc_menu_actors.h
@@ -1,13 +1,25 @@
-// $Id: gc_menu_actors.h,v 1.7 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_menu_actors.h,v 1.8 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_MENU_ACTORS_H
#define GC_MENU_ACTORS_H
diff --git a/src/guiconv/gc_migration_dialogs.cpp b/src/guiconv/gc_migration_dialogs.cpp
index 9b75d71..ad57390 100644
--- a/src/guiconv/gc_migration_dialogs.cpp
+++ b/src/guiconv/gc_migration_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_migration_dialogs.cpp,v 1.3 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_migration_dialogs.cpp,v 1.5 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_datastore.h"
@@ -298,13 +310,13 @@ gcMigrationConstraintChoice::GetRelevantId()
gcMigrationEditDialog::gcMigrationEditDialog( wxWindow * parent,
GCDataStore & dataStore,
size_t migrationId,
- wxString fromName,
wxString toName,
+ wxString fromName,
bool forJustCreatedObj)
:
gcUpdatingDialog( parent,
dataStore,
- wxString::Format(gcstr::editMigration, fromName.c_str(), toName.c_str()),
+ wxString::Format(gcstr::editMigration, toName.c_str(), fromName.c_str()),
forJustCreatedObj),
m_migrationId(migrationId)
{
@@ -347,7 +359,7 @@ bool DoDialogEditMigration( wxWindow * parent,
dataStore.GetStructures().GetMigration(migrationId).GetToId()).GetName();
}
- gcMigrationEditDialog dialog(parent,dataStore,migrationId, fromName, toName,forJustCreatedObj);
+ gcMigrationEditDialog dialog(parent,dataStore,migrationId, toName, fromName, forJustCreatedObj);
// migration rate
diff --git a/src/guiconv/gc_migration_dialogs.h b/src/guiconv/gc_migration_dialogs.h
index 0a523e7..1cd4a2a 100644
--- a/src/guiconv/gc_migration_dialogs.h
+++ b/src/guiconv/gc_migration_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_migration_dialogs.h,v 1.2 2011/12/30 22:50:10 jmcgill Exp $
+// $Id: gc_migration_dialogs.h,v 1.4 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_MIGRATION_DIALOGS_H
#define GC_MIGRATION_DIALOGS_H
@@ -121,8 +133,8 @@ class gcMigrationEditDialog : public gcUpdatingDialog
gcMigrationEditDialog( wxWindow * parentWindow,
GCDataStore & dataStore,
size_t migrationId,
- wxString fromName,
wxString toName,
+ wxString fromName,
bool forJustCreatedObj);
virtual ~gcMigrationEditDialog();
};
diff --git a/src/guiconv/gc_migtab.cpp b/src/guiconv/gc_migtab.cpp
index 52f84f0..663ca61 100644
--- a/src/guiconv/gc_migtab.cpp
+++ b/src/guiconv/gc_migtab.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_migtab.cpp,v 1.7 2014/08/29 18:14:55 mkkuhner Exp $
+// $Id: gc_migtab.cpp,v 1.8 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
/* NOTE: 8/29/2014 Mary edited gc_migtab.cpp to reverse the sense
of "from" and "to" in the migration matrix, since it was producing
XML files that were backwards to what LAMARC assumes. She did NOT
diff --git a/src/guiconv/gc_migtab.h b/src/guiconv/gc_migtab.h
index ca4c8c6..c2c90e5 100644
--- a/src/guiconv/gc_migtab.h
+++ b/src/guiconv/gc_migtab.h
@@ -1,13 +1,25 @@
-// $Id: gc_migtab.h,v 1.3 2014/08/29 18:14:55 mkkuhner Exp $
+// $Id: gc_migtab.h,v 1.4 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
/* NOTE: 8/29/2014 Mary edited gc_migtab.cpp to reverse the sense
of "from" and "to" in the migration matrix, since it was producing
XML files that were backwards to what LAMARC assumes. She did NOT
diff --git a/src/guiconv/gc_panel_dialogs.cpp b/src/guiconv/gc_panel_dialogs.cpp
index 706322d..0a5599a 100644
--- a/src/guiconv/gc_panel_dialogs.cpp
+++ b/src/guiconv/gc_panel_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_panel_dialogs.cpp,v 1.2 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_panel_dialogs.cpp,v 1.3 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_datastore.h"
diff --git a/src/guiconv/gc_panel_dialogs.h b/src/guiconv/gc_panel_dialogs.h
index cdf7fec..776577b 100644
--- a/src/guiconv/gc_panel_dialogs.h
+++ b/src/guiconv/gc_panel_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_panel_dialogs.h,v 1.2 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_panel_dialogs.h,v 1.3 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PANEL_DIALOGS_H
#define GC_PANEL_DIALOGS_H
diff --git a/src/guiconv/gc_parent_dialogs.cpp b/src/guiconv/gc_parent_dialogs.cpp
index 823aef9..f8dbcbe 100644
--- a/src/guiconv/gc_parent_dialogs.cpp
+++ b/src/guiconv/gc_parent_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_parent_dialogs.cpp,v 1.3 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_parent_dialogs.cpp,v 1.4 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_datastore.h"
diff --git a/src/guiconv/gc_parent_dialogs.h b/src/guiconv/gc_parent_dialogs.h
index e73c820..0548df9 100644
--- a/src/guiconv/gc_parent_dialogs.h
+++ b/src/guiconv/gc_parent_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_parent_dialogs.h,v 1.2 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_parent_dialogs.h,v 1.3 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_PARENT_DIALOGS_H
#define GC_PARENT_DIALOGS_H
diff --git a/src/guiconv/gc_poptab.cpp b/src/guiconv/gc_poptab.cpp
index ea140f4..c64ade4 100644
--- a/src/guiconv/gc_poptab.cpp
+++ b/src/guiconv/gc_poptab.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_poptab.cpp,v 1.9 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_poptab.cpp,v 1.10 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_event_publisher.h"
diff --git a/src/guiconv/gc_poptab.h b/src/guiconv/gc_poptab.h
index e148a9d..3f09841 100644
--- a/src/guiconv/gc_poptab.h
+++ b/src/guiconv/gc_poptab.h
@@ -1,13 +1,25 @@
-// $Id: gc_poptab.h,v 1.7 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_poptab.h,v 1.8 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_POPTAB_H
#define GC_POPTAB_H
diff --git a/src/guiconv/gc_population_dialogs.cpp b/src/guiconv/gc_population_dialogs.cpp
index db99e32..dfc5c69 100644
--- a/src/guiconv/gc_population_dialogs.cpp
+++ b/src/guiconv/gc_population_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_population_dialogs.cpp,v 1.22 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_population_dialogs.cpp,v 1.23 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_datastore.h"
diff --git a/src/guiconv/gc_population_dialogs.h b/src/guiconv/gc_population_dialogs.h
index 873df3f..e4b870a 100644
--- a/src/guiconv/gc_population_dialogs.h
+++ b/src/guiconv/gc_population_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_population_dialogs.h,v 1.16 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_population_dialogs.h,v 1.17 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_POPULATION_DIALOGS_H
#define GC_POPULATION_DIALOGS_H
diff --git a/src/guiconv/gc_quantum.cpp b/src/guiconv/gc_quantum.cpp
index f0e79d8..e0c8d65 100644
--- a/src/guiconv/gc_quantum.cpp
+++ b/src/guiconv/gc_quantum.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_quantum.cpp,v 1.15 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_quantum.cpp,v 1.16 2018/01/03 21:32:59 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_default.h"
#include "gc_quantum.h"
#include "wx/log.h"
diff --git a/src/guiconv/gc_quantum.h b/src/guiconv/gc_quantum.h
index 3174b27..055e086 100644
--- a/src/guiconv/gc_quantum.h
+++ b/src/guiconv/gc_quantum.h
@@ -1,13 +1,25 @@
-// $Id: gc_quantum.h,v 1.15 2012/06/30 01:32:41 bobgian Exp $
+// $Id: gc_quantum.h,v 1.16 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_QUANTUM_H
#define GC_QUANTUM_H
diff --git a/src/guiconv/gc_region_dialogs.cpp b/src/guiconv/gc_region_dialogs.cpp
index 13ab694..9e1ab86 100644
--- a/src/guiconv/gc_region_dialogs.cpp
+++ b/src/guiconv/gc_region_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_region_dialogs.cpp,v 1.24 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_region_dialogs.cpp,v 1.25 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_datastore.h"
diff --git a/src/guiconv/gc_region_dialogs.h b/src/guiconv/gc_region_dialogs.h
index 3b10c40..0de5a38 100644
--- a/src/guiconv/gc_region_dialogs.h
+++ b/src/guiconv/gc_region_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_region_dialogs.h,v 1.14 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_region_dialogs.h,v 1.15 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_REGION_DIALOGS_H
#define GC_REGION_DIALOGS_H
diff --git a/src/guiconv/gc_regiontab.cpp b/src/guiconv/gc_regiontab.cpp
index c8435fc..2016a63 100644
--- a/src/guiconv/gc_regiontab.cpp
+++ b/src/guiconv/gc_regiontab.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_regiontab.cpp,v 1.43 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_regiontab.cpp,v 1.44 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_event_publisher.h"
diff --git a/src/guiconv/gc_regiontab.h b/src/guiconv/gc_regiontab.h
index eb98a3a..3f7fadb 100644
--- a/src/guiconv/gc_regiontab.h
+++ b/src/guiconv/gc_regiontab.h
@@ -1,13 +1,25 @@
-// $Id: gc_regiontab.h,v 1.29 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_regiontab.h,v 1.30 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_REGIONTAB_H
#define GC_REGIONTAB_H
diff --git a/src/guiconv/gc_trait_dialogs.cpp b/src/guiconv/gc_trait_dialogs.cpp
index 94a22d5..74dbed9 100644
--- a/src/guiconv/gc_trait_dialogs.cpp
+++ b/src/guiconv/gc_trait_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_trait_dialogs.cpp,v 1.10 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_trait_dialogs.cpp,v 1.11 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_datastore.h"
#include "gc_strings.h"
#include "gc_structures_err.h"
diff --git a/src/guiconv/gc_trait_dialogs.h b/src/guiconv/gc_trait_dialogs.h
index 1dcb667..ad0ceea 100644
--- a/src/guiconv/gc_trait_dialogs.h
+++ b/src/guiconv/gc_trait_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_trait_dialogs.h,v 1.5 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_trait_dialogs.h,v 1.6 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_TRAIT_DIALOGS_H
#define GC_TRAIT_DIALOGS_H
diff --git a/src/guiconv/gc_unit_dialogs.cpp b/src/guiconv/gc_unit_dialogs.cpp
index faa71b5..eab38a9 100644
--- a/src/guiconv/gc_unit_dialogs.cpp
+++ b/src/guiconv/gc_unit_dialogs.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_unit_dialogs.cpp,v 1.8 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_unit_dialogs.cpp,v 1.9 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_strings.h"
#include "gc_unit_dialogs.h"
#include "wx/filedlg.h"
diff --git a/src/guiconv/gc_unit_dialogs.h b/src/guiconv/gc_unit_dialogs.h
index 5cde26f..d10b4e4 100644
--- a/src/guiconv/gc_unit_dialogs.h
+++ b/src/guiconv/gc_unit_dialogs.h
@@ -1,13 +1,25 @@
-// $Id: gc_unit_dialogs.h,v 1.5 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_unit_dialogs.h,v 1.6 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_UNIT_DIALOGS_H
#define GC_UNIT_DIALOGS_H
diff --git a/src/guiconv/guiconverter.cpp b/src/guiconv/guiconverter.cpp
index 5116914..8d414e7 100644
--- a/src/guiconv/guiconverter.cpp
+++ b/src/guiconv/guiconverter.cpp
@@ -1,13 +1,25 @@
-// $Id: guiconverter.cpp,v 1.35 2014/08/29 18:14:55 mkkuhner Exp $
+// $Id: guiconverter.cpp,v 1.36 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
/* NOTE: 8/29/2014 Mary edited gc_migtab.cpp to reverse the sense
of "from" and "to" in the migration matrix, since it was producing
XML files that were backwards to what LAMARC assumes. She did NOT
diff --git a/src/guiconv/guiconverter.h b/src/guiconv/guiconverter.h
index 99803bd..f3ff3bc 100644
--- a/src/guiconv/guiconverter.h
+++ b/src/guiconv/guiconverter.h
@@ -1,13 +1,25 @@
-// $Id: guiconverter.h,v 1.14 2014/08/29 18:14:55 mkkuhner Exp $
+// $Id: guiconverter.h,v 1.15 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GUICONVERTER_H
#define GUICONVERTER_H
diff --git a/src/guiutil/gc_clickpanel.cpp b/src/guiutil/gc_clickpanel.cpp
index 00d8f6d..0cca882 100644
--- a/src/guiutil/gc_clickpanel.cpp
+++ b/src/guiutil/gc_clickpanel.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_clickpanel.cpp,v 1.12 2012/06/30 01:32:42 bobgian Exp $
+// $Id: gc_clickpanel.cpp,v 1.13 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include "gc_color.h"
diff --git a/src/guiutil/gc_clickpanel.h b/src/guiutil/gc_clickpanel.h
index c3fc52d..86bb5fa 100644
--- a/src/guiutil/gc_clickpanel.h
+++ b/src/guiutil/gc_clickpanel.h
@@ -1,13 +1,25 @@
-// $Id: gc_clickpanel.h,v 1.8 2012/06/30 01:32:42 bobgian Exp $
+// $Id: gc_clickpanel.h,v 1.9 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_CLICKPANEL_H
#define GC_CLICKPANEL_H
diff --git a/src/guiutil/gc_gridpanel.cpp b/src/guiutil/gc_gridpanel.cpp
index 6b62200..2f9f751 100644
--- a/src/guiutil/gc_gridpanel.cpp
+++ b/src/guiutil/gc_gridpanel.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_gridpanel.cpp,v 1.30 2012/03/09 22:55:20 jmcgill Exp $
+// $Id: gc_gridpanel.cpp,v 1.31 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include <stdio.h>
diff --git a/src/guiutil/gc_gridpanel.h b/src/guiutil/gc_gridpanel.h
index 256e5d2..25ab76d 100644
--- a/src/guiutil/gc_gridpanel.h
+++ b/src/guiutil/gc_gridpanel.h
@@ -1,13 +1,25 @@
-// $Id: gc_gridpanel.h,v 1.23 2012/06/30 01:32:42 bobgian Exp $
+// $Id: gc_gridpanel.h,v 1.24 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_GRIDPANEL_H
#define GC_GRIDPANEL_H
diff --git a/src/guiutil/gc_text_ctrl.cpp b/src/guiutil/gc_text_ctrl.cpp
index 444e043..271a083 100644
--- a/src/guiutil/gc_text_ctrl.cpp
+++ b/src/guiutil/gc_text_ctrl.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_text_ctrl.cpp,v 1.8 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_text_ctrl.cpp,v 1.9 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_text_ctrl.h"
#include "gc_validators.h"
#include "wx/log.h"
diff --git a/src/guiutil/gc_text_ctrl.h b/src/guiutil/gc_text_ctrl.h
index 782a5cb..e7af05d 100644
--- a/src/guiutil/gc_text_ctrl.h
+++ b/src/guiutil/gc_text_ctrl.h
@@ -1,13 +1,25 @@
-// $Id: gc_text_ctrl.h,v 1.6 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_text_ctrl.h,v 1.7 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_TEXT_CTRL_H
#define GC_TEXT_CTRL_H
diff --git a/src/guiutil/gc_validators.cpp b/src/guiutil/gc_validators.cpp
index f84e193..f889b03 100644
--- a/src/guiutil/gc_validators.cpp
+++ b/src/guiutil/gc_validators.cpp
@@ -1,13 +1,25 @@
-// $Id: gc_validators.cpp,v 1.6 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_validators.cpp,v 1.7 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "gc_data.h"
#include "gc_validators.h"
diff --git a/src/guiutil/gc_validators.h b/src/guiutil/gc_validators.h
index aa8f0d6..eb38455 100644
--- a/src/guiutil/gc_validators.h
+++ b/src/guiutil/gc_validators.h
@@ -1,13 +1,25 @@
-// $Id: gc_validators.h,v 1.6 2011/03/08 19:22:01 bobgian Exp $
+// $Id: gc_validators.h,v 1.7 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef GC_VALIDATORS_H
#define GC_VALIDATORS_H
diff --git a/src/lamarcmenus/coalmenus.cpp b/src/lamarcmenus/coalmenus.cpp
index 57915e2..97ba6c5 100644
--- a/src/lamarcmenus/coalmenus.cpp
+++ b/src/lamarcmenus/coalmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: coalmenus.cpp,v 1.15 2010/03/17 17:25:58 bobgian Exp $
+// $Id: coalmenus.cpp,v 1.16 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/coalmenus.h b/src/lamarcmenus/coalmenus.h
index 57f60ec..1fd5821 100644
--- a/src/lamarcmenus/coalmenus.h
+++ b/src/lamarcmenus/coalmenus.h
@@ -1,13 +1,25 @@
-// $Id: coalmenus.h,v 1.15 2011/03/07 06:08:50 bobgian Exp $
+// $Id: coalmenus.h,v 1.16 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef COALMENUS_H
#define COALMENUS_H
diff --git a/src/lamarcmenus/constraintmenus.cpp b/src/lamarcmenus/constraintmenus.cpp
index b4b9878..23f2f11 100644
--- a/src/lamarcmenus/constraintmenus.cpp
+++ b/src/lamarcmenus/constraintmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: constraintmenus.cpp,v 1.11 2011/03/08 19:22:01 bobgian Exp $
+// $Id: constraintmenus.cpp,v 1.13 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <string>
@@ -333,12 +345,12 @@ string ToggleMenuItem2dGroup::GetVariableText(UIId id)
return ui.doGetPrintString(menuKey,id);
}
-string ToggleMenuItem2dGroup::GetGroupDescription(long gid)
+string ToggleMenuItem2dGroup::GetGroupDescription(long)
{
return "\n";
}
-string ToggleMenuItem2dGroup::GetEmptyDescription(long gid)
+string ToggleMenuItem2dGroup::GetEmptyDescription(long)
{
return "\n";
}
@@ -410,7 +422,7 @@ string ToggleMenuItemGroupedConstraints::GetGroupDescription(long gid)
return ("Group " + ToString(gid+1));
}
-string ToggleMenuItemGroupedConstraints::GetEmptyDescription(long gid)
+string ToggleMenuItemGroupedConstraints::GetEmptyDescription(long)
{
return (" **No parameters in this group**");
}
diff --git a/src/lamarcmenus/constraintmenus.h b/src/lamarcmenus/constraintmenus.h
index a47c7ef..31eb7a1 100644
--- a/src/lamarcmenus/constraintmenus.h
+++ b/src/lamarcmenus/constraintmenus.h
@@ -1,13 +1,25 @@
-// $Id: constraintmenus.h,v 1.8 2012/02/29 00:29:58 ewalkup Exp $
+// $Id: constraintmenus.h,v 1.10 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef CONSTRAINTMENUS_H
#define CONSTRAINTMENUS_H
@@ -140,8 +152,8 @@ class ToggleMenuItem2dGroup : public MenuDisplayQuantaWithHandler
// stuff for multi-line items
virtual bool HasMultiLineItems() {return false;};
- virtual std::vector<std::string> GetExtraText(UIId id) {return std::vector<std::string>();};
- virtual std::vector<std::string> GetExtraVariableText(UIId id) {return std::vector<std::string>();};
+ virtual std::vector<std::string> GetExtraText(UIId) {return std::vector<std::string>();};
+ virtual std::vector<std::string> GetExtraVariableText(UIId) {return std::vector<std::string>();};
};
diff --git a/src/lamarcmenus/datafilenamedialog.cpp b/src/lamarcmenus/datafilenamedialog.cpp
index 3348ba0..fa3d1ec 100644
--- a/src/lamarcmenus/datafilenamedialog.cpp
+++ b/src/lamarcmenus/datafilenamedialog.cpp
@@ -1,13 +1,25 @@
-// $Id: datafilenamedialog.cpp,v 1.14 2012/06/30 01:32:42 bobgian Exp $
+// $Id: datafilenamedialog.cpp,v 1.15 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include <iostream>
diff --git a/src/lamarcmenus/datafilenamedialog.h b/src/lamarcmenus/datafilenamedialog.h
index 7cecdd3..41893dd 100644
--- a/src/lamarcmenus/datafilenamedialog.h
+++ b/src/lamarcmenus/datafilenamedialog.h
@@ -1,13 +1,25 @@
-// $Id: datafilenamedialog.h,v 1.8 2012/06/30 01:32:42 bobgian Exp $
+// $Id: datafilenamedialog.h,v 1.9 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DATAFILENAMEDIALOG_H
#define DATAFILENAMEDIALOG_H
diff --git a/src/lamarcmenus/datamodelmenu.cpp b/src/lamarcmenus/datamodelmenu.cpp
index da6b783..5f70f9f 100644
--- a/src/lamarcmenus/datamodelmenu.cpp
+++ b/src/lamarcmenus/datamodelmenu.cpp
@@ -1,13 +1,25 @@
-// $Id: datamodelmenu.cpp,v 1.42 2011/03/07 06:08:50 bobgian Exp $
+// $Id: datamodelmenu.cpp,v 1.44 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <string>
@@ -182,7 +194,7 @@ string GTRRatesSubMenuItem::GetVariableText()
return ui.doGetPrintString(uistr::gtrRates,id);
}
-MenuInteraction_ptr GTRRatesSubMenuItem::GetHandler(std::string inputKey)
+MenuInteraction_ptr GTRRatesSubMenuItem::GetHandler(std::string)
{
NewMenu * gtrRateMenu = new GTRRatesMenu(ui,id);
return MenuInteraction_ptr(gtrRateMenu);
@@ -297,7 +309,7 @@ string BaseFrequenciesSubMenuItem::GetVariableText()
return ui.doGetPrintString(uistr::baseFrequencies,id);
}
-MenuInteraction_ptr BaseFrequenciesSubMenuItem::GetHandler(std::string inputKey)
+MenuInteraction_ptr BaseFrequenciesSubMenuItem::GetHandler(std::string)
{
NewMenu * baseFreqMenu = new BaseFrequenciesMenu(ui,id);
return MenuInteraction_ptr(baseFreqMenu);
@@ -362,7 +374,7 @@ CategoriesMenuGroup::GetKey(UIId id)
}
string
-CategoriesMenuGroup::GetText(UIId id)
+CategoriesMenuGroup::GetText(UIId)
{
return string("Mutation Rate pair: (rate, probability)");
}
@@ -435,7 +447,7 @@ string CategoriesSubMenuItem::GetVariableText()
return ui.doGetPrintString(uistr::categoryCount,id);
}
-MenuInteraction_ptr CategoriesSubMenuItem::GetHandler(std::string inputKey)
+MenuInteraction_ptr CategoriesSubMenuItem::GetHandler(std::string)
{
NewMenu * catsFreqMenu = new CategoriesMenu(ui,id);
return MenuInteraction_ptr(catsFreqMenu);
diff --git a/src/lamarcmenus/datamodelmenu.h b/src/lamarcmenus/datamodelmenu.h
index 435c50e..a362c91 100644
--- a/src/lamarcmenus/datamodelmenu.h
+++ b/src/lamarcmenus/datamodelmenu.h
@@ -1,13 +1,25 @@
-// $Id: datamodelmenu.h,v 1.28 2011/03/07 06:08:50 bobgian Exp $
+// $Id: datamodelmenu.h,v 1.29 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DATAMODELMENU_H
#define DATAMODELMENU_H
diff --git a/src/lamarcmenus/diseasemenus.cpp b/src/lamarcmenus/diseasemenus.cpp
index 1815151..d37ebd1 100644
--- a/src/lamarcmenus/diseasemenus.cpp
+++ b/src/lamarcmenus/diseasemenus.cpp
@@ -1,13 +1,25 @@
-// $Id: diseasemenus.cpp,v 1.17 2011/03/07 06:08:50 bobgian Exp $
+// $Id: diseasemenus.cpp,v 1.18 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/diseasemenus.h b/src/lamarcmenus/diseasemenus.h
index 6eb6420..aaa151b 100644
--- a/src/lamarcmenus/diseasemenus.h
+++ b/src/lamarcmenus/diseasemenus.h
@@ -1,13 +1,25 @@
-// $Id: diseasemenus.h,v 1.14 2011/03/07 06:08:50 bobgian Exp $
+// $Id: diseasemenus.h,v 1.15 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DISEASEMENUS_H
#define DISEASEMENUS_H
diff --git a/src/lamarcmenus/divmenus.cpp b/src/lamarcmenus/divmenus.cpp
index 7b681b8..f1508dd 100644
--- a/src/lamarcmenus/divmenus.cpp
+++ b/src/lamarcmenus/divmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: divmenus.cpp,v 1.6 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: divmenus.cpp,v 1.7 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/divmenus.h b/src/lamarcmenus/divmenus.h
index 8438171..43c908c 100644
--- a/src/lamarcmenus/divmenus.h
+++ b/src/lamarcmenus/divmenus.h
@@ -1,13 +1,25 @@
-// $Id: divmenus.h,v 1.2 2012/02/29 00:29:58 ewalkup Exp $
+// $Id: divmenus.h,v 1.3 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DIVMENUS_H
#define DIVMENUS_H
diff --git a/src/lamarcmenus/divmigmenus.cpp b/src/lamarcmenus/divmigmenus.cpp
index 7a9bbc0..b4eb366 100644
--- a/src/lamarcmenus/divmigmenus.cpp
+++ b/src/lamarcmenus/divmigmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: divmigmenus.cpp,v 1.2 2012/06/30 01:32:42 bobgian Exp $
+// $Id: divmigmenus.cpp,v 1.3 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/divmigmenus.h b/src/lamarcmenus/divmigmenus.h
index 6584760..8c89442 100644
--- a/src/lamarcmenus/divmigmenus.h
+++ b/src/lamarcmenus/divmigmenus.h
@@ -1,13 +1,25 @@
-// $Id: divmigmenus.h,v 1.1 2012/02/15 18:13:42 jmcgill Exp $
+// $Id: divmigmenus.h,v 1.2 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DIVMIGMENUS_H
#define DIVMIGMENUS_H
diff --git a/src/lamarcmenus/forcesmenus.cpp b/src/lamarcmenus/forcesmenus.cpp
index c305ebe..0860e59 100644
--- a/src/lamarcmenus/forcesmenus.cpp
+++ b/src/lamarcmenus/forcesmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: forcesmenus.cpp,v 1.30 2012/06/30 01:32:42 bobgian Exp $
+// $Id: forcesmenus.cpp,v 1.31 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <string>
diff --git a/src/lamarcmenus/forcesmenus.h b/src/lamarcmenus/forcesmenus.h
index d1323e9..9db7824 100644
--- a/src/lamarcmenus/forcesmenus.h
+++ b/src/lamarcmenus/forcesmenus.h
@@ -1,13 +1,25 @@
-// $Id: forcesmenus.h,v 1.11 2011/03/07 06:08:50 bobgian Exp $
+// $Id: forcesmenus.h,v 1.12 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef FORCESMENUS_H
#define FORCESMENUS_H
diff --git a/src/lamarcmenus/growthmenus.cpp b/src/lamarcmenus/growthmenus.cpp
index fb2534e..9e0858c 100644
--- a/src/lamarcmenus/growthmenus.cpp
+++ b/src/lamarcmenus/growthmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: growthmenus.cpp,v 1.16 2010/03/17 17:25:58 bobgian Exp $
+// $Id: growthmenus.cpp,v 1.17 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/growthmenus.h b/src/lamarcmenus/growthmenus.h
index 9986071..300833a 100644
--- a/src/lamarcmenus/growthmenus.h
+++ b/src/lamarcmenus/growthmenus.h
@@ -1,13 +1,25 @@
-// $Id: growthmenus.h,v 1.16 2011/03/07 06:08:50 bobgian Exp $
+// $Id: growthmenus.h,v 1.17 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef GROWTHMENUS_H
#define GROWTHMENUS_H
diff --git a/src/lamarcmenus/lamarc_strings.cpp b/src/lamarcmenus/lamarc_strings.cpp
index 38a5a0b..034e2f1 100644
--- a/src/lamarcmenus/lamarc_strings.cpp
+++ b/src/lamarcmenus/lamarc_strings.cpp
@@ -1,13 +1,24 @@
-// $Id: lamarc_strings.cpp,v 1.47 2012/02/15 18:13:42 jmcgill Exp $
+// $Id: lamarc_strings.cpp,v 1.48 2018/01/03 21:33:00 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <string>
#include "lamarc_strings.h"
diff --git a/src/lamarcmenus/lamarc_strings.h b/src/lamarcmenus/lamarc_strings.h
index c61693e..4af5ad4 100644
--- a/src/lamarcmenus/lamarc_strings.h
+++ b/src/lamarcmenus/lamarc_strings.h
@@ -1,13 +1,24 @@
-// $Id: lamarc_strings.h,v 1.32 2012/02/15 18:13:42 jmcgill Exp $
+// $Id: lamarc_strings.h,v 1.33 2018/01/03 21:33:00 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef LAMARC_STRINGS_H
#define LAMARC_STRINGS_H
diff --git a/src/lamarcmenus/lamarcheaderdialog.cpp b/src/lamarcmenus/lamarcheaderdialog.cpp
index ae31518..a187f1a 100644
--- a/src/lamarcmenus/lamarcheaderdialog.cpp
+++ b/src/lamarcmenus/lamarcheaderdialog.cpp
@@ -1,13 +1,25 @@
-// $Id: lamarcheaderdialog.cpp,v 1.17 2012/06/30 01:32:42 bobgian Exp $
+// $Id: lamarcheaderdialog.cpp,v 1.18 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
// Defines various symbols used to control debugging of experimental code blocks.
diff --git a/src/lamarcmenus/lamarcheaderdialog.h b/src/lamarcmenus/lamarcheaderdialog.h
index eac128a..7c1b03f 100644
--- a/src/lamarcmenus/lamarcheaderdialog.h
+++ b/src/lamarcmenus/lamarcheaderdialog.h
@@ -1,13 +1,25 @@
-// $Id: lamarcheaderdialog.h,v 1.7 2011/03/07 06:08:50 bobgian Exp $
+// $Id: lamarcheaderdialog.h,v 1.8 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef LAMARCHEADERDIALOG_H
#define LAMARCHEADERDIALOG_H
diff --git a/src/lamarcmenus/lamarcmenu.cpp b/src/lamarcmenus/lamarcmenu.cpp
index eaba680..c8433c9 100644
--- a/src/lamarcmenus/lamarcmenu.cpp
+++ b/src/lamarcmenus/lamarcmenu.cpp
@@ -1,13 +1,25 @@
-// $Id: lamarcmenu.cpp,v 1.22 2010/03/17 17:25:58 bobgian Exp $
+// $Id: lamarcmenu.cpp,v 1.23 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// the base menu is the NON-Interactive "menu"
// derived menus handele the different windowing systems
// (- Curses)
diff --git a/src/lamarcmenus/lamarcmenu.h b/src/lamarcmenus/lamarcmenu.h
index 604b012..c9636ae 100644
--- a/src/lamarcmenus/lamarcmenu.h
+++ b/src/lamarcmenus/lamarcmenu.h
@@ -1,13 +1,25 @@
-// $Id: lamarcmenu.h,v 1.7 2011/03/07 06:08:50 bobgian Exp $
+// $Id: lamarcmenu.h,v 1.8 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef LAMARCMENU_H_
#define LAMARCMENU_H_
diff --git a/src/lamarcmenus/lamarcmenuitems.cpp b/src/lamarcmenus/lamarcmenuitems.cpp
index 7390f69..363453f 100644
--- a/src/lamarcmenus/lamarcmenuitems.cpp
+++ b/src/lamarcmenus/lamarcmenuitems.cpp
@@ -1,13 +1,25 @@
-// $Id: lamarcmenuitems.cpp,v 1.35 2012/06/30 01:32:42 bobgian Exp $
+// $Id: lamarcmenuitems.cpp,v 1.36 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// the base menu is the NON-Interactive "menu"
// derived menus handele the different windowing systems
// (- Curses)
diff --git a/src/lamarcmenus/lamarcmenuitems.h b/src/lamarcmenus/lamarcmenuitems.h
index 5300f9d..0505926 100644
--- a/src/lamarcmenus/lamarcmenuitems.h
+++ b/src/lamarcmenus/lamarcmenuitems.h
@@ -1,13 +1,25 @@
-// $Id: lamarcmenuitems.h,v 1.24 2012/05/15 06:21:48 ewalkup Exp $
+// $Id: lamarcmenuitems.h,v 1.25 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef LAMARCMENUITEMS_H_
#define LAMARCMENUITEMS_H_
diff --git a/src/lamarcmenus/logselectmenus.cpp b/src/lamarcmenus/logselectmenus.cpp
index fae88bb..a16fb60 100644
--- a/src/lamarcmenus/logselectmenus.cpp
+++ b/src/lamarcmenus/logselectmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: logselectmenus.cpp,v 1.4 2011/03/08 19:22:01 bobgian Exp $
+// $Id: logselectmenus.cpp,v 1.5 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/logselectmenus.h b/src/lamarcmenus/logselectmenus.h
index 819de2b..bc8e731 100644
--- a/src/lamarcmenus/logselectmenus.h
+++ b/src/lamarcmenus/logselectmenus.h
@@ -1,13 +1,25 @@
-// $Id: logselectmenus.h,v 1.4 2011/03/08 19:22:01 bobgian Exp $
+// $Id: logselectmenus.h,v 1.5 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef LOGSELECTMENUS_H
#define LOGSELECTMENUS_H
diff --git a/src/lamarcmenus/migmenus.cpp b/src/lamarcmenus/migmenus.cpp
index e31bc03..f3c699a 100644
--- a/src/lamarcmenus/migmenus.cpp
+++ b/src/lamarcmenus/migmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: migmenus.cpp,v 1.13 2010/03/17 17:25:58 bobgian Exp $
+// $Id: migmenus.cpp,v 1.14 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/migmenus.h b/src/lamarcmenus/migmenus.h
index 6f9355a..a90427d 100644
--- a/src/lamarcmenus/migmenus.h
+++ b/src/lamarcmenus/migmenus.h
@@ -1,13 +1,25 @@
-// $Id: migmenus.h,v 1.13 2011/03/07 06:08:50 bobgian Exp $
+// $Id: migmenus.h,v 1.14 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef MIGMENUS_H
#define MIGMENUS_H
diff --git a/src/lamarcmenus/nomenufilereaddialog.cpp b/src/lamarcmenus/nomenufilereaddialog.cpp
index 3d470b5..21fc738 100644
--- a/src/lamarcmenus/nomenufilereaddialog.cpp
+++ b/src/lamarcmenus/nomenufilereaddialog.cpp
@@ -1,13 +1,25 @@
-// $Id: nomenufilereaddialog.cpp,v 1.4 2010/03/17 17:25:58 bobgian Exp $
+// $Id: nomenufilereaddialog.cpp,v 1.5 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "defaults.h"
diff --git a/src/lamarcmenus/nomenufilereaddialog.h b/src/lamarcmenus/nomenufilereaddialog.h
index c83089d..c4e7e42 100644
--- a/src/lamarcmenus/nomenufilereaddialog.h
+++ b/src/lamarcmenus/nomenufilereaddialog.h
@@ -1,13 +1,25 @@
-// $Id: nomenufilereaddialog.h,v 1.5 2012/06/30 01:32:42 bobgian Exp $
+// $Id: nomenufilereaddialog.h,v 1.6 2018/01/03 21:33:00 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef NOMENUDIALOG_H
#define NOMENUDIALOG_H
diff --git a/src/lamarcmenus/outfilemenus.cpp b/src/lamarcmenus/outfilemenus.cpp
index 33a42b0..a98423b 100644
--- a/src/lamarcmenus/outfilemenus.cpp
+++ b/src/lamarcmenus/outfilemenus.cpp
@@ -1,13 +1,25 @@
-// $Id: outfilemenus.cpp,v 1.21 2010/03/17 17:25:59 bobgian Exp $
+// $Id: outfilemenus.cpp,v 1.22 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "lamarc_strings.h"
#include "newmenuitems.h"
diff --git a/src/lamarcmenus/outfilemenus.h b/src/lamarcmenus/outfilemenus.h
index 76ea242..af96675 100644
--- a/src/lamarcmenus/outfilemenus.h
+++ b/src/lamarcmenus/outfilemenus.h
@@ -1,13 +1,25 @@
-// $Id: outfilemenus.h,v 1.15 2011/03/07 06:08:50 bobgian Exp $
+// $Id: outfilemenus.h,v 1.16 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef OUTFILEMENUS_H
#define OUTFILEMENUS_H
diff --git a/src/lamarcmenus/overviewmenus.cpp b/src/lamarcmenus/overviewmenus.cpp
index e3331b4..b5fe240 100644
--- a/src/lamarcmenus/overviewmenus.cpp
+++ b/src/lamarcmenus/overviewmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: overviewmenus.cpp,v 1.33 2011/08/19 23:30:31 ewalkup Exp $
+// $Id: overviewmenus.cpp,v 1.35 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <string>
#include <iostream>
@@ -29,22 +41,22 @@ using std::string;
//------------------------------------------------------------------------------------
-string ChainTable::Title(UIInterface & ui)
+string ChainTable::Title(UIInterface &)
{
return "Chain parameters:";
}
-long ChainTable::ColCount(UIInterface & ui)
+long ChainTable::ColCount(UIInterface &)
{
return 3;
}
-long ChainTable::RowCount(UIInterface & ui)
+long ChainTable::RowCount(UIInterface &)
{
return 4;
}
-string ChainTable::ColLabel(UIInterface & ui, long index)
+string ChainTable::ColLabel(UIInterface &, long index)
{
if (index == 0) return menustr::emptyString;
if (index == 1) return menustr::initial;
@@ -53,7 +65,7 @@ string ChainTable::ColLabel(UIInterface & ui, long index)
return menustr::emptyString;
}
-string ChainTable::RowLabel(UIInterface & ui, long index)
+string ChainTable::RowLabel(UIInterface &, long index)
{
if(index == 0) return menustr::chains;
if(index == 1) return menustr::discard;
@@ -63,7 +75,7 @@ string ChainTable::RowLabel(UIInterface & ui, long index)
return menustr::emptyString;
}
-string ChainTable::Cell(UIInterface & ui, long rowIndex, long colIndex)
+string ChainTable::Cell(UIInterface &, long rowIndex, long colIndex)
{
if (colIndex == 0) return menustr::emptyString;
if (colIndex == 1)
@@ -127,22 +139,22 @@ const string ForceEventTable::forceMaxEvents(long i)
return forceMaxEventCount[i];
}
-string ForceEventTable::Title(UIInterface & ui)
+string ForceEventTable::Title(UIInterface &)
{
return "Enabled Forces:";
}
-long ForceEventTable::ColCount(UIInterface & ui)
+long ForceEventTable::ColCount(UIInterface &)
{
return 1;
}
-long ForceEventTable::RowCount(UIInterface & ui)
+long ForceEventTable::RowCount(UIInterface &)
{
return (ui.GetCurrentVars().forces.GetActiveForces().size());
}
-string ForceEventTable::ColLabel(UIInterface & ui, long index)
+string ForceEventTable::ColLabel(UIInterface &, long index)
{
if(index == 0) return uistr::maxEvents;
assert(false); //Uncaught index.
@@ -189,17 +201,17 @@ ForceEventTable::~ForceEventTable()
//------------------------------------------------------------------------------------
// assuming only one disease present
-string StartParamTable::Title(UIInterface & ui)
+string StartParamTable::Title(UIInterface &)
{
return "Start parameters";
}
-string StartParamTable::RowHeader(UIInterface & ui)
+string StartParamTable::RowHeader(UIInterface &)
{
return "Population";
}
-long StartParamTable::ColCount(UIInterface & ui)
+long StartParamTable::ColCount(UIInterface &)
{
return 6;
}
@@ -302,22 +314,22 @@ StartParamTable::~StartParamTable()
//------------------------------------------------------------------------------------
-long TemperatureTable::ColCount(UIInterface & ui)
+long TemperatureTable::ColCount(UIInterface &)
{
return 1;
}
-long TemperatureTable::RowCount(UIInterface & ui)
+long TemperatureTable::RowCount(UIInterface &)
{
return 4;
}
-string TemperatureTable::Title(UIInterface & ui)
+string TemperatureTable::Title(UIInterface &)
{
return "Parallel Markov Chain info:";
}
-string TemperatureTable::ColLabel(UIInterface & ui, long index)
+string TemperatureTable::ColLabel(UIInterface &, long)
{
return menustr::emptyString;
}
@@ -529,7 +541,7 @@ DataOverviewMenuItemGroup::GetText(UIId id)
}
string
-DataOverviewMenuItemGroup::GetVariableText(UIId id)
+DataOverviewMenuItemGroup::GetVariableText(UIId)
{
//return ToString(ui.doGetModelType(uistr::dataModel,id));
return menustr::emptyString;
@@ -722,7 +734,7 @@ BayesianPriorsOverviewMenuItemGroup::GetVariableText(UIId id)
return ui.GetCurrentVars().forces.GetPriorTypeSummaryDescription(id.GetForceType(),id.GetIndex1(), false);
}
-MenuInteraction_ptr BayesianPriorsOverviewMenuItemGroup::MakeOneHandler(UIId id)
+MenuInteraction_ptr BayesianPriorsOverviewMenuItemGroup::MakeOneHandler(UIId)
{
return MenuInteraction_ptr(new DoNothingHandler());
}
@@ -774,7 +786,7 @@ TraitMappingOverviewMenuItemGroup::GetVariableText(UIId id)
return ToString(ui.GetCurrentVars().traitmodels.GetAnalysisType(regId));
}
-MenuInteraction_ptr TraitMappingOverviewMenuItemGroup::MakeOneHandler(UIId id)
+MenuInteraction_ptr TraitMappingOverviewMenuItemGroup::MakeOneHandler(UIId)
{
return MenuInteraction_ptr(new DoNothingHandler());
}
diff --git a/src/lamarcmenus/overviewmenus.h b/src/lamarcmenus/overviewmenus.h
index 75d3e2f..d341a53 100644
--- a/src/lamarcmenus/overviewmenus.h
+++ b/src/lamarcmenus/overviewmenus.h
@@ -1,13 +1,25 @@
-// $Id: overviewmenus.h,v 1.16 2011/03/07 06:08:50 bobgian Exp $
+// $Id: overviewmenus.h,v 1.17 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef OVERVIEWMENUS_H
#define OVERVIEWMENUS_H
diff --git a/src/lamarcmenus/popsizemenu.cpp b/src/lamarcmenus/popsizemenu.cpp
index 1d87671..7d73df1 100644
--- a/src/lamarcmenus/popsizemenu.cpp
+++ b/src/lamarcmenus/popsizemenu.cpp
@@ -1,13 +1,25 @@
-// $Id: popsizemenu.cpp,v 1.5 2010/03/17 17:25:59 bobgian Exp $
+// $Id: popsizemenu.cpp,v 1.6 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "lamarc_strings.h"
#include "popsizemenu.h"
diff --git a/src/lamarcmenus/popsizemenu.h b/src/lamarcmenus/popsizemenu.h
index 198aec1..80c3195 100644
--- a/src/lamarcmenus/popsizemenu.h
+++ b/src/lamarcmenus/popsizemenu.h
@@ -1,13 +1,25 @@
-// $Id: popsizemenu.h,v 1.4 2011/03/07 06:08:50 bobgian Exp $
+// $Id: popsizemenu.h,v 1.5 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef POPSIZEMENU_H
#define POPSIZEMENU_H
diff --git a/src/lamarcmenus/priormenus.cpp b/src/lamarcmenus/priormenus.cpp
index febaa5b..4bd1d26 100644
--- a/src/lamarcmenus/priormenus.cpp
+++ b/src/lamarcmenus/priormenus.cpp
@@ -1,13 +1,25 @@
-// $Id: priormenus.cpp,v 1.13 2013/06/03 17:23:13 jyamato Exp $
+// $Id: priormenus.cpp,v 1.14 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <string>
diff --git a/src/lamarcmenus/priormenus.h b/src/lamarcmenus/priormenus.h
index 967470c..ba3ffc2 100644
--- a/src/lamarcmenus/priormenus.h
+++ b/src/lamarcmenus/priormenus.h
@@ -1,13 +1,25 @@
-// $Id: priormenus.h,v 1.3 2011/03/07 06:08:50 bobgian Exp $
+// $Id: priormenus.h,v 1.4 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PRIORMENUS_H
#define PRIORMENUS_H
diff --git a/src/lamarcmenus/profilemenus.cpp b/src/lamarcmenus/profilemenus.cpp
index 9c461ed..5fe68c3 100644
--- a/src/lamarcmenus/profilemenus.cpp
+++ b/src/lamarcmenus/profilemenus.cpp
@@ -1,13 +1,25 @@
-// $Id: profilemenus.cpp,v 1.15 2013/10/25 17:00:53 mkkuhner Exp $
+// $Id: profilemenus.cpp,v 1.16 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <string>
diff --git a/src/lamarcmenus/profilemenus.h b/src/lamarcmenus/profilemenus.h
index d083e67..556500a 100644
--- a/src/lamarcmenus/profilemenus.h
+++ b/src/lamarcmenus/profilemenus.h
@@ -1,13 +1,25 @@
-// $Id: profilemenus.h,v 1.4 2011/03/07 06:08:50 bobgian Exp $
+// $Id: profilemenus.h,v 1.5 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PROFILEMENUS_H
#define PROFILEMENUS_H
diff --git a/src/lamarcmenus/recmenus.cpp b/src/lamarcmenus/recmenus.cpp
index 610db5d..437dafa 100644
--- a/src/lamarcmenus/recmenus.cpp
+++ b/src/lamarcmenus/recmenus.cpp
@@ -1,13 +1,25 @@
-// $Id: recmenus.cpp,v 1.11 2010/03/17 17:25:59 bobgian Exp $
+// $Id: recmenus.cpp,v 1.12 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/recmenus.h b/src/lamarcmenus/recmenus.h
index 1a9ff6d..fa95bfe 100644
--- a/src/lamarcmenus/recmenus.h
+++ b/src/lamarcmenus/recmenus.h
@@ -1,13 +1,25 @@
-// $Id: recmenus.h,v 1.12 2011/03/07 06:08:50 bobgian Exp $
+// $Id: recmenus.h,v 1.13 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef RECMENUS_H
#define RECMENUS_H
diff --git a/src/lamarcmenus/regiongammamenus.cpp b/src/lamarcmenus/regiongammamenus.cpp
index cff467d..0580212 100644
--- a/src/lamarcmenus/regiongammamenus.cpp
+++ b/src/lamarcmenus/regiongammamenus.cpp
@@ -1,13 +1,25 @@
-// $Id: regiongammamenus.cpp,v 1.3 2010/03/17 17:25:59 bobgian Exp $
+// $Id: regiongammamenus.cpp,v 1.4 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "constraintmenus.h"
diff --git a/src/lamarcmenus/regiongammamenus.h b/src/lamarcmenus/regiongammamenus.h
index bf2e4eb..2ea4c38 100644
--- a/src/lamarcmenus/regiongammamenus.h
+++ b/src/lamarcmenus/regiongammamenus.h
@@ -1,13 +1,25 @@
-// $Id: regiongammamenus.h,v 1.4 2011/03/08 19:22:01 bobgian Exp $
+// $Id: regiongammamenus.h,v 1.5 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef REGIONGAMMAMENUS_H
#define REGIONGAMMAMENUS_H
diff --git a/src/lamarcmenus/traitmodelmenu.cpp b/src/lamarcmenus/traitmodelmenu.cpp
index ed2b182..36b1473 100644
--- a/src/lamarcmenus/traitmodelmenu.cpp
+++ b/src/lamarcmenus/traitmodelmenu.cpp
@@ -1,13 +1,25 @@
-// $Id: traitmodelmenu.cpp,v 1.11 2012/06/30 01:32:42 bobgian Exp $
+// $Id: traitmodelmenu.cpp,v 1.12 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "lamarc_strings.h"
diff --git a/src/lamarcmenus/traitmodelmenu.h b/src/lamarcmenus/traitmodelmenu.h
index 9592b45..2dfe9c6 100644
--- a/src/lamarcmenus/traitmodelmenu.h
+++ b/src/lamarcmenus/traitmodelmenu.h
@@ -1,13 +1,25 @@
-// $Id: traitmodelmenu.h,v 1.5 2011/03/07 06:08:50 bobgian Exp $
+// $Id: traitmodelmenu.h,v 1.6 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TRAITMODELMENU_H
#define TRAITMODELMENU_H
diff --git a/src/lamarcmenus/treesummenus.cpp b/src/lamarcmenus/treesummenus.cpp
index fe6ef5c..4c83a70 100644
--- a/src/lamarcmenus/treesummenus.cpp
+++ b/src/lamarcmenus/treesummenus.cpp
@@ -1,13 +1,25 @@
-// $Id: treesummenus.cpp,v 1.13 2010/03/17 17:25:59 bobgian Exp $
+// $Id: treesummenus.cpp,v 1.14 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <fstream>
#include <string>
#include "menu_strings.h"
diff --git a/src/lamarcmenus/treesummenus.h b/src/lamarcmenus/treesummenus.h
index fe24628..a8c5939 100644
--- a/src/lamarcmenus/treesummenus.h
+++ b/src/lamarcmenus/treesummenus.h
@@ -1,13 +1,25 @@
-// $Id: treesummenus.h,v 1.13 2011/03/07 06:08:50 bobgian Exp $
+// $Id: treesummenus.h,v 1.14 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TREESUMMENUS_H
#define TREESUMMENUS_H
diff --git a/src/menu/dialog.cpp b/src/menu/dialog.cpp
index d45b28f..aa8352e 100644
--- a/src/menu/dialog.cpp
+++ b/src/menu/dialog.cpp
@@ -1,13 +1,25 @@
-// $Id: dialog.cpp,v 1.23 2010/03/17 17:25:59 bobgian Exp $
+// $Id: dialog.cpp,v 1.24 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include "menuinteraction.h"
#include "dialog.h"
diff --git a/src/menu/dialog.h b/src/menu/dialog.h
index b6716c0..e908059 100644
--- a/src/menu/dialog.h
+++ b/src/menu/dialog.h
@@ -1,13 +1,25 @@
-// $Id: dialog.h,v 1.17 2011/03/07 06:08:50 bobgian Exp $
+// $Id: dialog.h,v 1.18 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DIALOG_H
#define DIALOG_H
diff --git a/src/menu/dialognoinput.cpp b/src/menu/dialognoinput.cpp
index 80f3567..bdc56c6 100644
--- a/src/menu/dialognoinput.cpp
+++ b/src/menu/dialognoinput.cpp
@@ -1,13 +1,25 @@
-// $Id: dialognoinput.cpp,v 1.14 2012/06/30 01:32:42 bobgian Exp $
+// $Id: dialognoinput.cpp,v 1.15 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "dialog.h"
diff --git a/src/menu/dialognoinput.h b/src/menu/dialognoinput.h
index 91a4ba7..93124b0 100644
--- a/src/menu/dialognoinput.h
+++ b/src/menu/dialognoinput.h
@@ -1,13 +1,25 @@
-// $Id: dialognoinput.h,v 1.13 2012/06/30 01:32:42 bobgian Exp $
+// $Id: dialognoinput.h,v 1.14 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DIALOGNOINPUT_H
#define DIALOGNOINPUT_H
diff --git a/src/menu/dialogrepeat.cpp b/src/menu/dialogrepeat.cpp
index 2501921..4081bc3 100644
--- a/src/menu/dialogrepeat.cpp
+++ b/src/menu/dialogrepeat.cpp
@@ -1,13 +1,25 @@
-// $Id: dialogrepeat.cpp,v 1.12 2012/06/30 01:32:42 bobgian Exp $
+// $Id: dialogrepeat.cpp,v 1.13 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "dialog.h"
diff --git a/src/menu/dialogrepeat.h b/src/menu/dialogrepeat.h
index e7b6bdb..936ebae 100644
--- a/src/menu/dialogrepeat.h
+++ b/src/menu/dialogrepeat.h
@@ -1,13 +1,25 @@
-// $Id: dialogrepeat.h,v 1.11 2012/06/30 01:32:42 bobgian Exp $
+// $Id: dialogrepeat.h,v 1.12 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DIALOGREPEAT_H
#define DIALOGREPEAT_H
diff --git a/src/menu/display.cpp b/src/menu/display.cpp
index e26a279..41bd351 100644
--- a/src/menu/display.cpp
+++ b/src/menu/display.cpp
@@ -1,13 +1,25 @@
-// $Id: display.cpp,v 1.40 2012/06/30 01:32:42 bobgian Exp $
+// $Id: display.cpp,v 1.42 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// base class for all displays
// + derived classes (these may need to split away from this file
//
@@ -418,29 +430,29 @@ void ScrollingDisplay::DisplayDialogOutput(string output)
NoDisplay::NoDisplay() {};
NoDisplay::~NoDisplay() {};
-menu_return_type NoDisplay::DisplayNewMenu(NewMenu & menu)
+menu_return_type NoDisplay::DisplayNewMenu(NewMenu &)
{
return menu_REDISPLAY;
}
-menu_return_type NoDisplay::DisplayRaw(StringVec1d strings)
+menu_return_type NoDisplay::DisplayRaw(StringVec1d)
{
return menu_REDISPLAY;
}
-void NoDisplay::ShowMenuDisplayGroup(MenuDisplayGroup & m)
+void NoDisplay::ShowMenuDisplayGroup(MenuDisplayGroup &)
{
}
-void NoDisplay::ShowMenuDisplay2dGroup(ToggleMenuItem2dGroup & m)
+void NoDisplay::ShowMenuDisplay2dGroup(ToggleMenuItem2dGroup &)
{
}
-void NoDisplay::ShowMenuDisplayLine(MenuDisplayLine & m)
+void NoDisplay::ShowMenuDisplayLine(MenuDisplayLine &)
{
}
-void NoDisplay::ShowMenuDisplayTable(MenuDisplayTable & t)
+void NoDisplay::ShowMenuDisplayTable(MenuDisplayTable &)
{
}
@@ -449,7 +461,7 @@ string NoDisplay::GetUserInput()
throw impossible_error("Should never get input without display");
}
-void NoDisplay::DisplayDialogOutput(string output)
+void NoDisplay::DisplayDialogOutput(string)
{
}
diff --git a/src/menu/display.h b/src/menu/display.h
index d6c0337..8960209 100644
--- a/src/menu/display.h
+++ b/src/menu/display.h
@@ -1,13 +1,25 @@
-// $Id: display.h,v 1.23 2012/02/29 00:29:58 ewalkup Exp $
+// $Id: display.h,v 1.24 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef DISPLAY_H
#define DISPLAY_H
diff --git a/src/menu/matrixitem.cpp b/src/menu/matrixitem.cpp
index 170f9a1..d2c7f89 100644
--- a/src/menu/matrixitem.cpp
+++ b/src/menu/matrixitem.cpp
@@ -1,13 +1,25 @@
-// $Id: matrixitem.cpp,v 1.13 2012/06/30 01:32:42 bobgian Exp $
+// $Id: matrixitem.cpp,v 1.14 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "matrixitem.h"
#include "menuinteraction.h"
diff --git a/src/menu/matrixitem.h b/src/menu/matrixitem.h
index 83d60d4..a0da487 100644
--- a/src/menu/matrixitem.h
+++ b/src/menu/matrixitem.h
@@ -1,13 +1,25 @@
-// $Id: matrixitem.h,v 1.11 2011/03/07 06:08:50 bobgian Exp $
+// $Id: matrixitem.h,v 1.12 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef MATRIXITEM_H
#define MATRIXITEM_H
diff --git a/src/menu/menu_strings.cpp b/src/menu/menu_strings.cpp
index b4ebc85..da9c223 100644
--- a/src/menu/menu_strings.cpp
+++ b/src/menu/menu_strings.cpp
@@ -1,13 +1,24 @@
-// $Id: menu_strings.cpp,v 1.14 2010/03/02 23:12:29 bobgian Exp $
+// $Id: menu_strings.cpp,v 1.15 2018/01/03 21:33:01 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <string>
#include "menu_strings.h"
diff --git a/src/menu/menu_strings.h b/src/menu/menu_strings.h
index 91089a8..c4907d0 100644
--- a/src/menu/menu_strings.h
+++ b/src/menu/menu_strings.h
@@ -1,13 +1,24 @@
-// $Id: menu_strings.h,v 1.16 2011/03/07 06:08:51 bobgian Exp $
+// $Id: menu_strings.h,v 1.17 2018/01/03 21:33:01 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef MENU_STRINGS_H
#define MENU_STRINGS_H
diff --git a/src/menu/menudefs.h b/src/menu/menudefs.h
index b2b5b2d..e26d2b8 100644
--- a/src/menu/menudefs.h
+++ b/src/menu/menudefs.h
@@ -1,13 +1,25 @@
-// $Id: menudefs.h,v 1.12 2010/03/17 17:25:59 bobgian Exp $
+// $Id: menudefs.h,v 1.13 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef MENUDEFS_H
#define MENUDEFS_H
diff --git a/src/menu/menuerror.h b/src/menu/menuerror.h
index dc3147c..27ab44a 100644
--- a/src/menu/menuerror.h
+++ b/src/menu/menuerror.h
@@ -1,13 +1,25 @@
-// $Id: menuerror.h,v 1.7 2011/03/07 06:08:51 bobgian Exp $
+// $Id: menuerror.h,v 1.8 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef MENUERROR_H
#define MENUERROR_H
diff --git a/src/menu/menuinteraction.cpp b/src/menu/menuinteraction.cpp
index 0c1d374..a313589 100644
--- a/src/menu/menuinteraction.cpp
+++ b/src/menu/menuinteraction.cpp
@@ -1,13 +1,25 @@
-// $Id: menuinteraction.cpp,v 1.8 2010/03/17 17:25:59 bobgian Exp $
+// $Id: menuinteraction.cpp,v 1.9 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include "menuinteraction.h"
#include "ui_constants.h"
diff --git a/src/menu/menuinteraction.h b/src/menu/menuinteraction.h
index d8c0688..1e36807 100644
--- a/src/menu/menuinteraction.h
+++ b/src/menu/menuinteraction.h
@@ -1,13 +1,25 @@
-// $Id: menuinteraction.h,v 1.9 2011/03/07 06:08:51 bobgian Exp $
+// $Id: menuinteraction.h,v 1.10 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef MENUINTERACTION_H
#define MENUINTERACTION_H
diff --git a/src/menu/menuitem.cpp b/src/menu/menuitem.cpp
index 7cd4e88..6da7fb3 100644
--- a/src/menu/menuitem.cpp
+++ b/src/menu/menuitem.cpp
@@ -1,13 +1,25 @@
-// $Id: menuitem.cpp,v 1.25 2012/06/30 01:32:42 bobgian Exp $
+// $Id: menuitem.cpp,v 1.27 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// menuitem.cpp
// functions to control the menuitem (a single line in a menu)
//
@@ -34,7 +46,7 @@ MenuDisplayQuantaVec::NukeContents()
}
MenuInteraction_ptr
-MenuDisplayQuantaWithHandler::GetHandler(string key)
+MenuDisplayQuantaWithHandler::GetHandler(string)
{
return MenuInteraction_ptr(NULL);
}
@@ -99,7 +111,7 @@ DisplayOnlyGroupWrapper::GetInconsistentIds()
}
string
-DisplayOnlyGroupWrapper::GetKey(UIId id)
+DisplayOnlyGroupWrapper::GetKey(UIId)
{
return menustr::emptyString;
}
diff --git a/src/menu/menuitem.h b/src/menu/menuitem.h
index 991584e..457c617 100644
--- a/src/menu/menuitem.h
+++ b/src/menu/menuitem.h
@@ -1,13 +1,25 @@
-// $Id: menuitem.h,v 1.27 2012/02/29 00:29:58 ewalkup Exp $
+// $Id: menuitem.h,v 1.29 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Menuitem.h
// is line in the menu and consists of a (key, text, handlerobject)
//
@@ -112,8 +124,8 @@ class MenuDisplayGroup : public MenuDisplayQuantaWithHandler
// stuff for multi-line items
virtual bool HasMultiLineItems() {return false;};
- virtual std::vector<std::string> GetExtraText(UIId id) {return std::vector<std::string>();};
- virtual std::vector<std::string> GetExtraVariableText(UIId id) {return std::vector<std::string>();};
+ virtual std::vector<std::string> GetExtraText(UIId) {return std::vector<std::string>();};
+ virtual std::vector<std::string> GetExtraVariableText(UIId) {return std::vector<std::string>();};
};
// a several-line unit for display in a menu, not having any associated
@@ -144,7 +156,7 @@ class DisplayOnlyGroupWrapper : public MenuDisplayGroup
virtual std::string GetText(UIId id);
virtual std::string GetVariableText(UIId id);
// void DisplayItemOn(Display & display);
- virtual bool Handles(std::string inputKey) { return false;};
+ virtual bool Handles(std::string) { return false;};
};
class KeyedMenuItem : public MenuDisplayLine
diff --git a/src/menu/menutypedefs.h b/src/menu/menutypedefs.h
index 0e99249..57377bd 100644
--- a/src/menu/menutypedefs.h
+++ b/src/menu/menutypedefs.h
@@ -1,13 +1,25 @@
-// $Id: menutypedefs.h,v 1.4 2011/03/08 19:22:01 bobgian Exp $
+// $Id: menutypedefs.h,v 1.5 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef MENUTYPEDEFS_H
#define MENUTYPEDEFS_H
diff --git a/src/menu/newmenu.cpp b/src/menu/newmenu.cpp
index 2825f4d..956d61b 100644
--- a/src/menu/newmenu.cpp
+++ b/src/menu/newmenu.cpp
@@ -1,13 +1,25 @@
-// $Id: newmenu.cpp,v 1.30 2011/03/07 06:08:51 bobgian Exp $
+// $Id: newmenu.cpp,v 1.31 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <string>
#include <vector>
diff --git a/src/menu/newmenu.h b/src/menu/newmenu.h
index 2ae9528..1f63b55 100644
--- a/src/menu/newmenu.h
+++ b/src/menu/newmenu.h
@@ -1,13 +1,25 @@
-// $Id: newmenu.h,v 1.23 2012/06/30 01:32:42 bobgian Exp $
+// $Id: newmenu.h,v 1.24 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef NEWMENU_H
#define NEWMENU_H
diff --git a/src/menu/newmenuitems.cpp b/src/menu/newmenuitems.cpp
index c1dc023..7ac1085 100644
--- a/src/menu/newmenuitems.cpp
+++ b/src/menu/newmenuitems.cpp
@@ -1,13 +1,25 @@
-// $Id: newmenuitems.cpp,v 1.36 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: newmenuitems.cpp,v 1.38 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// menuitem.cpp
// functions to control the menuitem (a single line in a menu)
//
@@ -40,7 +52,7 @@ std::string SameLevelMenuItem::GetVariableText()
return menustr::emptyString;
}
-menu_return_type DoNothingHandler::InvokeMe(Display& display)
+menu_return_type DoNothingHandler::InvokeMe(Display&)
{
return menu_REDISPLAY;
}
@@ -54,7 +66,7 @@ FileDumpMenuItem::~FileDumpMenuItem()
{
}
-MenuInteraction_ptr FileDumpMenuItem::GetHandler(string inputKey)
+MenuInteraction_ptr FileDumpMenuItem::GetHandler(string)
{
return MenuInteraction_ptr(new FileDumpHandler(ui));
}
@@ -159,12 +171,12 @@ bool UndoMenuItem::IsVisible()
return undoable;
}
-MenuInteraction_ptr UndoMenuItem::GetHandler(string inputKey)
+MenuInteraction_ptr UndoMenuItem::GetHandler(string)
{
return MenuInteraction_ptr(new UndoHandler(ui));
}
-menu_return_type UndoHandler::InvokeMe(Display& display)
+menu_return_type UndoHandler::InvokeMe(Display&)
{
ui.Undo();
return menu_REDISPLAY;
@@ -190,12 +202,12 @@ bool RedoMenuItem::IsVisible()
return redoable;
}
-MenuInteraction_ptr RedoMenuItem::GetHandler(string inputKey)
+MenuInteraction_ptr RedoMenuItem::GetHandler(string)
{
return MenuInteraction_ptr(new RedoHandler(ui));
}
-menu_return_type RedoHandler::InvokeMe(Display& display)
+menu_return_type RedoHandler::InvokeMe(Display&)
{
ui.Redo();
return menu_REDISPLAY;
@@ -281,7 +293,7 @@ string SubMenuItem::GetVariableText()
return menustr::emptyString;
}
-MenuInteraction_ptr SubMenuItem::GetHandler(std::string inputKey)
+MenuInteraction_ptr SubMenuItem::GetHandler(std::string)
{
// EWFIX.P5 REFACTOR there was a memory leak here, which was fixed
// by having Create() return a shared pointer, but surely
diff --git a/src/menu/newmenuitems.h b/src/menu/newmenuitems.h
index 7cef045..808725b 100644
--- a/src/menu/newmenuitems.h
+++ b/src/menu/newmenuitems.h
@@ -1,13 +1,25 @@
-// $Id: newmenuitems.h,v 1.32 2012/06/30 01:32:42 bobgian Exp $
+// $Id: newmenuitems.h,v 1.34 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef NEWMENUITEM_H
#define NEWMENUITEM_H
@@ -196,7 +208,7 @@ class QuitHandler : public MenuInteraction
public:
QuitHandler() {};
virtual ~QuitHandler() {};
- virtual menu_return_type InvokeMe(Display & display)
+ virtual menu_return_type InvokeMe(Display &)
{ return menu_QUIT;};
};
@@ -205,7 +217,7 @@ class GoUpHandler : public MenuInteraction
public:
GoUpHandler() {};
virtual ~GoUpHandler() {};
- virtual menu_return_type InvokeMe(Display & display)
+ virtual menu_return_type InvokeMe(Display &)
{ return menu_GO_UP;};
};
diff --git a/src/menu/setmenuitem.cpp b/src/menu/setmenuitem.cpp
index 8db06e7..90d9498 100644
--- a/src/menu/setmenuitem.cpp
+++ b/src/menu/setmenuitem.cpp
@@ -1,13 +1,25 @@
-// $Id: setmenuitem.cpp,v 1.27 2011/03/07 06:08:51 bobgian Exp $
+// $Id: setmenuitem.cpp,v 1.28 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <string>
diff --git a/src/menu/setmenuitem.h b/src/menu/setmenuitem.h
index 31ea702..aec57b6 100644
--- a/src/menu/setmenuitem.h
+++ b/src/menu/setmenuitem.h
@@ -1,13 +1,25 @@
-// $Id: setmenuitem.h,v 1.30 2011/03/07 06:08:51 bobgian Exp $
+// $Id: setmenuitem.h,v 1.32 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Menuitem.h
// is line in the menu and consists of a (key, text, handlerobject)
//
@@ -146,7 +158,7 @@ class NewToggleHandler : public MenuInteraction
NewToggleHandler(UIInterface & myui, std::string myMenuKey, UIId myId)
: ui(myui),menuKey(myMenuKey),id(myId) {};
~NewToggleHandler() {};
- virtual menu_return_type InvokeMe(Display & display)
+ virtual menu_return_type InvokeMe(Display &)
{ ui.doToggle(menuKey,id); return menu_REDISPLAY;};
};
@@ -158,7 +170,7 @@ class ToggleMenuItemNoId : public SetMenuItemNoId
ToggleMenuItemNoId(std::string myKey, UIInterface & myui, std::string myMenuKey )
: SetMenuItemNoId(myKey,myui,myMenuKey) {};
~ToggleMenuItemNoId() {};
- virtual MenuInteraction_ptr GetHandler(std::string input)
+ virtual MenuInteraction_ptr GetHandler(std::string)
{ return MenuInteraction_ptr(new NewToggleHandler(ui,menuKey,GetId()));};
};
@@ -168,7 +180,7 @@ class ToggleMenuItemId : public SetMenuItemId
ToggleMenuItemId(std::string myKey, UIInterface & myui, std::string myMenuKey, UIId myId)
: SetMenuItemId(myKey,myui,myMenuKey,myId) {};
~ToggleMenuItemId() {};
- virtual MenuInteraction_ptr GetHandler(std::string input)
+ virtual MenuInteraction_ptr GetHandler(std::string)
{ return MenuInteraction_ptr(new NewToggleHandler(ui,menuKey,GetId()));};
};
diff --git a/src/menu/togglemenuitem.cpp b/src/menu/togglemenuitem.cpp
index 3465796..10e3ca6 100644
--- a/src/menu/togglemenuitem.cpp
+++ b/src/menu/togglemenuitem.cpp
@@ -1,13 +1,25 @@
-// $Id: togglemenuitem.cpp,v 1.13 2010/03/17 17:25:59 bobgian Exp $
+// $Id: togglemenuitem.cpp,v 1.14 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include "constants.h"
#include "togglemenuitem.h"
diff --git a/src/menu/togglemenuitem.h b/src/menu/togglemenuitem.h
index 6318374..5f75d42 100644
--- a/src/menu/togglemenuitem.h
+++ b/src/menu/togglemenuitem.h
@@ -1,13 +1,25 @@
-// $Id: togglemenuitem.h,v 1.16 2010/03/02 23:12:29 bobgian Exp $
+// $Id: togglemenuitem.h,v 1.17 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TOGGLEMENUITEM_H
#define TOGGLEMENUITEM_H
diff --git a/src/menu/twodtable.cpp b/src/menu/twodtable.cpp
index 68d5de1..d53777b 100644
--- a/src/menu/twodtable.cpp
+++ b/src/menu/twodtable.cpp
@@ -1,13 +1,25 @@
-// $Id: twodtable.cpp,v 1.7 2011/03/07 06:08:51 bobgian Exp $
+// $Id: twodtable.cpp,v 1.9 2018/01/03 21:33:01 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <string>
#include <vector>
#include "display.h"
@@ -35,7 +47,7 @@ bool TwoDTable::IsVisible()
return true;
}
-string TwoDTable::RowHeader(UIInterface & ui)
+string TwoDTable::RowHeader(UIInterface &)
{
return menustr::emptyString;
}
diff --git a/src/menu/twodtable.h b/src/menu/twodtable.h
index 269613c..c4f2290 100644
--- a/src/menu/twodtable.h
+++ b/src/menu/twodtable.h
@@ -1,13 +1,25 @@
-// $Id: twodtable.h,v 1.6 2011/03/07 06:08:51 bobgian Exp $
+// $Id: twodtable.h,v 1.7 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TWODTABLE_H
#define TWODTABLE_H
diff --git a/src/postlike/analyzer.cpp b/src/postlike/analyzer.cpp
index e75dc09..5304042 100644
--- a/src/postlike/analyzer.cpp
+++ b/src/postlike/analyzer.cpp
@@ -1,13 +1,25 @@
-// $Id: analyzer.cpp,v 1.33 2012/06/30 01:32:42 bobgian Exp $
+// $Id: analyzer.cpp,v 1.34 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// analyzer.cpp
//
// the analyzer generates
diff --git a/src/postlike/analyzer.h b/src/postlike/analyzer.h
index d6c6bc5..b22a78e 100644
--- a/src/postlike/analyzer.h
+++ b/src/postlike/analyzer.h
@@ -1,13 +1,25 @@
-// $Id: analyzer.h,v 1.33 2012/06/30 01:32:42 bobgian Exp $
+// $Id: analyzer.h,v 1.34 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// analyzer.h
//
// the analyzer generates
diff --git a/src/postlike/derivatives.cpp b/src/postlike/derivatives.cpp
index ba1bb7f..1405995 100644
--- a/src/postlike/derivatives.cpp
+++ b/src/postlike/derivatives.cpp
@@ -1,13 +1,25 @@
-// $Id: derivatives.cpp,v 1.55 2012/06/30 01:32:42 bobgian Exp $
+// $Id: derivatives.cpp,v 1.56 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// derivatives of parameter likelihood
// call sequence is in maximizer.cpp
diff --git a/src/postlike/likelihood.cpp b/src/postlike/likelihood.cpp
index b5f7082..3458169 100644
--- a/src/postlike/likelihood.cpp
+++ b/src/postlike/likelihood.cpp
@@ -1,13 +1,25 @@
-// $Id: likelihood.cpp,v 1.110 2013/10/25 17:00:53 mkkuhner Exp $
+// $Id: likelihood.cpp,v 1.111 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// parameter likelihood calculation
//
// <Single | Replicate | Region | GammaRegion>PostLike::Calculate()
diff --git a/src/postlike/likelihood.h b/src/postlike/likelihood.h
index 816464d..7d471c1 100644
--- a/src/postlike/likelihood.h
+++ b/src/postlike/likelihood.h
@@ -1,13 +1,25 @@
-// $Id: likelihood.h,v 1.59 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: likelihood.h,v 1.60 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// likelihood class --------------------------------------------------
//
// PostLike
diff --git a/src/postlike/maximizer.cpp b/src/postlike/maximizer.cpp
index 5c4555e..11d3b5d 100644
--- a/src/postlike/maximizer.cpp
+++ b/src/postlike/maximizer.cpp
@@ -1,13 +1,25 @@
-// $Id: maximizer.cpp,v 1.119 2012/06/30 01:32:42 bobgian Exp $
+// $Id: maximizer.cpp,v 1.121 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Broyden-Fletcher-Goldfarb-Shanno maximizer implementation
//
// started 2000 Peter Beerli
@@ -497,7 +509,7 @@ void Maximizer::CalcDirection ()
//------------------------------------------------------------------------------------
-void Maximizer::ExplainParamChange(long index, double oldVal, double newVal, string kind)
+void Maximizer::ExplainParamChange(long index, double oldVal, double newVal, string) //kind unused.
{
#ifdef TEST
cerr << "Parameter \"out of bounds\"--setting param " << index
diff --git a/src/postlike/maximizer.h b/src/postlike/maximizer.h
index 73a1c42..8304876 100644
--- a/src/postlike/maximizer.h
+++ b/src/postlike/maximizer.h
@@ -1,13 +1,25 @@
-// $Id: maximizer.h,v 1.36 2012/04/17 19:03:20 ewalkup Exp $
+// $Id: maximizer.h,v 1.37 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Maximizer Class ----------------------------------------------
//
// Maximizer for likelihood function (see PostLike::Calculate())
diff --git a/src/postlike/maximizer_strings.cpp b/src/postlike/maximizer_strings.cpp
index e96a545..808ce1b 100644
--- a/src/postlike/maximizer_strings.cpp
+++ b/src/postlike/maximizer_strings.cpp
@@ -1,13 +1,25 @@
-// $Id: maximizer_strings.cpp,v 1.7 2012/06/30 01:32:42 bobgian Exp $
+// $Id: maximizer_strings.cpp,v 1.8 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <string>
#include "maximizer_strings.h"
diff --git a/src/postlike/maximizer_strings.h b/src/postlike/maximizer_strings.h
index 55a957b..86fdde3 100644
--- a/src/postlike/maximizer_strings.h
+++ b/src/postlike/maximizer_strings.h
@@ -1,13 +1,25 @@
-// $Id: maximizer_strings.h,v 1.4 2011/03/07 06:08:51 bobgian Exp $
+// $Id: maximizer_strings.h,v 1.5 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2006 Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef MAXSTR_H
#define MAXSTR_H
diff --git a/src/postlike/plforces.cpp b/src/postlike/plforces.cpp
index 83e6225..68eaf39 100644
--- a/src/postlike/plforces.cpp
+++ b/src/postlike/plforces.cpp
@@ -1,13 +1,25 @@
-// $Id: plforces.cpp,v 1.76 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: plforces.cpp,v 1.77 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Posterior Likelihood forces classes
// - CoalescePL
// - coalesce with no-growth [using compressed summaries]
diff --git a/src/postlike/plforces.h b/src/postlike/plforces.h
index 2a5d9eb..bc4b069 100644
--- a/src/postlike/plforces.h
+++ b/src/postlike/plforces.h
@@ -1,13 +1,25 @@
-// $Id: plforces.h,v 1.39 2011/04/23 02:02:49 bobgian Exp $
+// $Id: plforces.h,v 1.41 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// PLforces class --------------------------------------------------
//
// know how to calculate waiting times and point probabilities
@@ -398,13 +410,13 @@ class DivMigPL:public PLForces
// evaluation, so the following two functions are not used.
// If they are ever needed, implementation is very similar to the
// MigPL versions.
- double DlnWait (const vector < double >¶m,
- const TreeSummary * treedata,
- const long &whichparam) { assert(false); return 0;};
+ double DlnWait (const vector < double >&,
+ const TreeSummary *,
+ const long &) { assert(false); return 0;};
- double DlnPoint (const vector < double >¶m,
- const TreeSummary * treedata,
- const long &whichparam) { assert(false); return 0;};
+ double DlnPoint (const vector < double >&,
+ const TreeSummary *,
+ const long &) { assert(false); return 0;};
};
//------------------------------------------------------------------------------------
@@ -465,20 +477,20 @@ class DivPL: public PLForces
virtual PLForces* Clone() const
{ return new DivPL(*this); };
- double lnWait (const vector < double >¶m,
- const TreeSummary * treedata) { return 1.0; };
+ double lnWait (const vector < double >&,
+ const TreeSummary * ) { return 1.0; };
- double lnPoint (const vector < double >¶m,
- const vector < double >&lparam,
- const TreeSummary * treedata) { return 1.0; };
+ double lnPoint (const vector < double >&,
+ const vector < double >&,
+ const TreeSummary *) { return 1.0; };
- double DlnWait (const vector < double >¶m,
- const TreeSummary * treedata,
- const long &whichparam) { return 1.0; };
+ double DlnWait (const vector < double >&,
+ const TreeSummary *,
+ const long &) { return 1.0; };
- double DlnPoint (const vector < double >¶m,
- const TreeSummary * treedata,
- const long &whichparam) { return 1.0; };
+ double DlnPoint (const vector < double >&,
+ const TreeSummary *,
+ const long &) { return 1.0; };
};
//------------------------------------------------------------------------------------
diff --git a/src/postlike/plotstat.cpp b/src/postlike/plotstat.cpp
index eb6fbd3..93c1fa7 100644
--- a/src/postlike/plotstat.cpp
+++ b/src/postlike/plotstat.cpp
@@ -1,13 +1,25 @@
-// $Id: plotstat.cpp,v 1.10 2010/03/17 17:25:59 bobgian Exp $
+// $Id: plotstat.cpp,v 1.11 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <vector>
#include "plotstat.h"
diff --git a/src/postlike/plotstat.h b/src/postlike/plotstat.h
index 602e601..5b57a9c 100644
--- a/src/postlike/plotstat.h
+++ b/src/postlike/plotstat.h
@@ -1,13 +1,25 @@
-// $Id: plotstat.h,v 1.12 2011/04/23 02:02:49 bobgian Exp $
+// $Id: plotstat.h,v 1.13 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PLOTSTAT_H
#define PLOTSTAT_H
diff --git a/src/postlike/profile.cpp b/src/postlike/profile.cpp
index f984745..5a355d1 100644
--- a/src/postlike/profile.cpp
+++ b/src/postlike/profile.cpp
@@ -1,13 +1,25 @@
-// $Id: profile.cpp,v 1.73 2012/06/30 01:32:42 bobgian Exp $
+// $Id: profile.cpp,v 1.74 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// profile.cpp [part of the analyzer module]
//
// - profiles (fixed and percentile)
diff --git a/src/report/curvefiles.cpp b/src/report/curvefiles.cpp
index 2899058..27bdbe2 100644
--- a/src/report/curvefiles.cpp
+++ b/src/report/curvefiles.cpp
@@ -1,13 +1,25 @@
-// $Id: curvefiles.cpp,v 1.5 2011/03/08 19:22:01 bobgian Exp $
+// $Id: curvefiles.cpp,v 1.6 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include <fstream>
#include <iostream>
diff --git a/src/report/curvefiles.h b/src/report/curvefiles.h
index 43586c9..7e5136b 100644
--- a/src/report/curvefiles.h
+++ b/src/report/curvefiles.h
@@ -1,13 +1,25 @@
-// $Id: curvefiles.h,v 1.2 2010/03/02 23:12:29 bobgian Exp $
+// $Id: curvefiles.h,v 1.3 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2008 Peeter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peeter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef CURVEFILES_H
#define CURVEFILES_H
diff --git a/src/report/outputfile.cpp b/src/report/outputfile.cpp
index 79f9def..54dedb1 100644
--- a/src/report/outputfile.cpp
+++ b/src/report/outputfile.cpp
@@ -1,13 +1,25 @@
-// $Id: outputfile.cpp,v 1.21 2012/06/30 01:32:42 bobgian Exp $
+// $Id: outputfile.cpp,v 1.22 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <exception>
#include <iostream>
diff --git a/src/report/outputfile.h b/src/report/outputfile.h
index 8bd453a..862355d 100644
--- a/src/report/outputfile.h
+++ b/src/report/outputfile.h
@@ -1,13 +1,25 @@
-// $Id: outputfile.h,v 1.10 2011/03/07 06:08:51 bobgian Exp $
+// $Id: outputfile.h,v 1.11 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef OUTPUTFILE_H
#define OUTPUTFILE_H
diff --git a/src/report/reportpage.cpp b/src/report/reportpage.cpp
index 2b3576a..dd70dc8 100644
--- a/src/report/reportpage.cpp
+++ b/src/report/reportpage.cpp
@@ -1,13 +1,25 @@
-// $Id: reportpage.cpp,v 1.129 2013/10/25 17:00:53 mkkuhner Exp $
+// $Id: reportpage.cpp,v 1.130 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// All versions of SetupColhdr() used for PrintTable() must
// put "\n" at EOL for each line. PrintTable() will not do it!
//
diff --git a/src/report/reportpage.h b/src/report/reportpage.h
index c888a44..f3387dc 100644
--- a/src/report/reportpage.h
+++ b/src/report/reportpage.h
@@ -1,13 +1,25 @@
-// $Id: reportpage.h,v 1.38 2012/06/30 01:32:42 bobgian Exp $
+// $Id: reportpage.h,v 1.40 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/******************************************************************
The base class ReportPage represents a single page of the output
report; subclasses produce specific pages.
@@ -27,7 +39,7 @@
using std::map;
using std::ofstream;
using std::string;
-class PlotStruct;
+struct PlotStruct;
class Parameter;
class RegionGammaInfo;
@@ -210,7 +222,7 @@ class ProfPage : public ReportPage
const DoubleVec1d modifiers,
vector<bool>& badLnLs);
StringVec3d WrapTable(StringVec2d& forcetable);
- void PrintTable(StringVec3d& wrappedtable);
+ virtual void PrintTable(StringVec3d& wrappedtable);
void PrintProfileLine(StringVec1d& line);
public:
diff --git a/src/report/runreport.cpp b/src/report/runreport.cpp
index 1923f0b..6c6194a 100644
--- a/src/report/runreport.cpp
+++ b/src/report/runreport.cpp
@@ -1,13 +1,25 @@
-// $Id: runreport.cpp,v 1.60 2012/06/30 01:32:42 bobgian Exp $
+// $Id: runreport.cpp,v 1.61 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
diff --git a/src/report/runreport.h b/src/report/runreport.h
index eb6dbc5..24ef544 100644
--- a/src/report/runreport.h
+++ b/src/report/runreport.h
@@ -1,13 +1,25 @@
-// $Id: runreport.h,v 1.20 2011/04/23 02:02:49 bobgian Exp $
+// $Id: runreport.h,v 1.21 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef RUNREPORT_H
#define RUNREPORT_H
diff --git a/src/report/spreadsheet.cpp b/src/report/spreadsheet.cpp
index 22cca89..42b2715 100644
--- a/src/report/spreadsheet.cpp
+++ b/src/report/spreadsheet.cpp
@@ -1,13 +1,25 @@
-// $Id: spreadsheet.cpp,v 1.4 2011/03/08 19:22:01 bobgian Exp $
+// $Id: spreadsheet.cpp,v 1.5 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include <fstream>
#include <iostream>
diff --git a/src/report/spreadsheet.h b/src/report/spreadsheet.h
index 88c7476..92d6280 100644
--- a/src/report/spreadsheet.h
+++ b/src/report/spreadsheet.h
@@ -1,13 +1,25 @@
-// $Id: spreadsheet.h,v 1.2 2010/03/02 23:12:29 bobgian Exp $
+// $Id: spreadsheet.h,v 1.3 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2008 Peeter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peeter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef SPREADSHEET_H
#define SPREADSHEET_H
diff --git a/src/report/xml_report.cpp b/src/report/xml_report.cpp
index e06d954..682eacd 100644
--- a/src/report/xml_report.cpp
+++ b/src/report/xml_report.cpp
@@ -1,13 +1,25 @@
-// $Id: xml_report.cpp,v 1.16 2012/06/30 01:32:42 bobgian Exp $
+// $Id: xml_report.cpp,v 1.17 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2008 Peeter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peeter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "chainmanager.h"
diff --git a/src/report/xml_report.h b/src/report/xml_report.h
index 8fa0c35..46f601a 100644
--- a/src/report/xml_report.h
+++ b/src/report/xml_report.h
@@ -1,13 +1,25 @@
-// $Id: xml_report.h,v 1.7 2011/03/07 06:08:51 bobgian Exp $
+// $Id: xml_report.h,v 1.8 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2008 Peeter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peeter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef XML_REPORT_H
#define XML_REPORT_H
diff --git a/src/tools/mathx.cpp b/src/tools/mathx.cpp
index 40430de..9537cc0 100644
--- a/src/tools/mathx.cpp
+++ b/src/tools/mathx.cpp
@@ -1,13 +1,25 @@
-// $Id: mathx.cpp,v 1.54 2012/06/30 01:32:42 bobgian Exp $
+// $Id: mathx.cpp,v 1.55 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cmath>
#include <iostream>
@@ -778,7 +790,8 @@ pair<DoubleVec1d, DoubleVec2d> EigenCalculator::Eigen(DoubleVec2d a)
{
eigvals[i] = a[i][i];
}
- return make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs);
+ // changed 2018.1.3 on recommendation of Debian distro team
+ return make_pair(eigvals, eigvecs);
} // Eigen
//------------------------------------------------------------------------------------
diff --git a/src/tools/mathx.h b/src/tools/mathx.h
index 28b3039..f8c2ea9 100644
--- a/src/tools/mathx.h
+++ b/src/tools/mathx.h
@@ -1,13 +1,25 @@
-// $Id: mathx.h,v 1.33 2012/06/30 01:32:42 bobgian Exp $
+// $Id: mathx.h,v 1.34 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef MATHX_H
#define MATHX_H
diff --git a/src/tools/random.cpp b/src/tools/random.cpp
index d6d0bea..c392502 100644
--- a/src/tools/random.cpp
+++ b/src/tools/random.cpp
@@ -1,13 +1,25 @@
-// $Id: random.cpp,v 1.20 2011/04/23 02:02:49 bobgian Exp $
+// $Id: random.cpp,v 1.21 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Mary 9/1/2010 Changed to use Boost random number generator (Mersenne Twister)
// due to suspicions that the homebrew was showing too much pattern.
diff --git a/src/tools/random.h b/src/tools/random.h
index 3739b8b..aa85ca6 100644
--- a/src/tools/random.h
+++ b/src/tools/random.h
@@ -1,13 +1,25 @@
-// $Id: random.h,v 1.17 2011/03/07 06:08:51 bobgian Exp $
+// $Id: random.h,v 1.18 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef RANDOM_H
#define RANDOM_H
diff --git a/src/tools/rangex.cpp b/src/tools/rangex.cpp
index 999eba5..ba8a41a 100644
--- a/src/tools/rangex.cpp
+++ b/src/tools/rangex.cpp
@@ -1,13 +1,25 @@
-// $Id: rangex.cpp,v 1.31 2013/11/07 22:56:31 jyamato Exp $
+// $Id: rangex.cpp,v 1.32 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
diff --git a/src/tools/rangex.h b/src/tools/rangex.h
index a130c5a..d815597 100644
--- a/src/tools/rangex.h
+++ b/src/tools/rangex.h
@@ -1,13 +1,25 @@
-// $Id: rangex.h,v 1.23 2013/08/22 18:03:12 jmcgill Exp $
+// $Id: rangex.h,v 1.24 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef RANGEX_H
#define RANGEX_H
diff --git a/src/tools/stringx.cpp b/src/tools/stringx.cpp
index e7ae68e..3881ef6 100644
--- a/src/tools/stringx.cpp
+++ b/src/tools/stringx.cpp
@@ -1,13 +1,25 @@
-// $Id: stringx.cpp,v 1.130 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: stringx.cpp,v 1.131 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cctype>
#include <functional>
@@ -15,6 +27,7 @@
#include <string>
#include <cstring>
#include <cstdio>
+#include <climits>
// NOTE: older versions required including <direct.h> here and
// using _getcwd() below for MSWINDOWS compiles
diff --git a/src/tools/stringx.h b/src/tools/stringx.h
index 35ece72..3b95f20 100644
--- a/src/tools/stringx.h
+++ b/src/tools/stringx.h
@@ -1,13 +1,25 @@
-// $Id: stringx.h,v 1.78 2014/08/29 19:29:20 mkkuhner Exp $
+// $Id: stringx.h,v 1.79 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef STRINGX_H
#define STRINGX_H
diff --git a/src/tools/timex.cpp b/src/tools/timex.cpp
index 0871133..fdb141c 100644
--- a/src/tools/timex.cpp
+++ b/src/tools/timex.cpp
@@ -1,13 +1,25 @@
-// $Id: timex.cpp,v 1.6 2011/03/07 06:08:51 bobgian Exp $
+// $Id: timex.cpp,v 1.7 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include "timex.h"
#ifdef DMALLOC_FUNC_CHECK
diff --git a/src/tools/timex.h b/src/tools/timex.h
index 8ed1606..95b53ad 100644
--- a/src/tools/timex.h
+++ b/src/tools/timex.h
@@ -1,13 +1,25 @@
-// $Id: timex.h,v 1.7 2011/04/23 02:02:49 bobgian Exp $
+// $Id: timex.h,v 1.8 2018/01/03 21:33:02 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TIMEX_H
#define TIMEX_H
diff --git a/src/tools/tools.h b/src/tools/tools.h
index d473a7e..38e4935 100644
--- a/src/tools/tools.h
+++ b/src/tools/tools.h
@@ -1,13 +1,25 @@
-// $Id: tools.h,v 1.4 2011/03/08 19:22:01 bobgian Exp $
+// $Id: tools.h,v 1.5 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
// This is just a catch-all include file for all of the program
// specific extensions to the standard library
diff --git a/src/tools/vector_constants.cpp b/src/tools/vector_constants.cpp
index 2720771..1afce3a 100644
--- a/src/tools/vector_constants.cpp
+++ b/src/tools/vector_constants.cpp
@@ -1,13 +1,25 @@
-// $Id: vector_constants.cpp,v 1.17 2010/03/17 17:25:59 bobgian Exp $
+// $Id: vector_constants.cpp,v 1.18 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// vector constants, used for profile tables
// Peter Beerli December 2002 modelled after Elizabeth Walkup's ui_string.[h][cpp] class
diff --git a/src/tools/vector_constants.h b/src/tools/vector_constants.h
index 1cec9dc..efd6e92 100644
--- a/src/tools/vector_constants.h
+++ b/src/tools/vector_constants.h
@@ -1,13 +1,24 @@
-// $Id: vector_constants.h,v 1.11 2011/03/07 06:08:51 bobgian Exp $
+// $Id: vector_constants.h,v 1.12 2018/01/03 21:33:03 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
// modelled after ui_interface/ui_strings.h
diff --git a/src/tools/vectorx.cpp b/src/tools/vectorx.cpp
index a7c94fd..fed4f5a 100644
--- a/src/tools/vectorx.cpp
+++ b/src/tools/vectorx.cpp
@@ -1,13 +1,25 @@
-// $Id: vectorx.cpp,v 1.14 2011/04/23 02:02:49 bobgian Exp $
+// $Id: vectorx.cpp,v 1.15 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cmath>
diff --git a/src/tools/vectorx.h b/src/tools/vectorx.h
index 39c2480..77dc0c7 100644
--- a/src/tools/vectorx.h
+++ b/src/tools/vectorx.h
@@ -1,13 +1,25 @@
-// $Id: vectorx.h,v 1.22 2011/03/07 06:08:51 bobgian Exp $
+// $Id: vectorx.h,v 1.23 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Vector utilities
//
// VECTOR SETTERS
diff --git a/src/tree/argtree.cpp b/src/tree/argtree.cpp
index 63315bc..fba7a08 100644
--- a/src/tree/argtree.cpp
+++ b/src/tree/argtree.cpp
@@ -1,13 +1,25 @@
-// $Id: argtree.cpp,v 1.6 2012/07/07 02:29:42 bobgian Exp $
+// $Id: argtree.cpp,v 1.8 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2012 Jim McGill, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Jim McGill, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream> // for debug cerr
#include <map>
@@ -371,7 +383,7 @@ void ARGTree::ToLamarcTree(Tree& stump, vector<ARGEdge> argedges)
if (forcefound)
{
// add to target map array
- Branch_ptr nullptr;
+ Branch_ptr null_ptr;
if (recfound)
{
// recombination case - returns a pair of branches
@@ -388,7 +400,7 @@ void ARGTree::ToLamarcTree(Tree& stump, vector<ARGEdge> argedges)
else
{
// everything else
- targetpair p = make_pair(recbranches.first, nullptr);
+ targetpair p = make_pair(recbranches.first, null_ptr);
targetmap.insert(make_pair(argedges[edge].GetSource(), p));
}
@@ -404,7 +416,7 @@ void ARGTree::ToLamarcTree(Tree& stump, vector<ARGEdge> argedges)
else
{
// everything else
- targetpair q = make_pair(recbranches.second, nullptr);
+ targetpair q = make_pair(recbranches.second, null_ptr);
targetmap.insert(make_pair(argedges[edge+1].GetSource(), q));
}
}
@@ -421,7 +433,7 @@ void ARGTree::ToLamarcTree(Tree& stump, vector<ARGEdge> argedges)
else
{
// everything else
- targetpair p = make_pair(newbranch, nullptr);
+ targetpair p = make_pair(newbranch, null_ptr);
targetmap.insert(make_pair(argedges[edge].GetSource(), p));
}
}
diff --git a/src/tree/argtree.h b/src/tree/argtree.h
index 2934e26..dd266c7 100644
--- a/src/tree/argtree.h
+++ b/src/tree/argtree.h
@@ -1,13 +1,25 @@
-// $Id: argtree.h,v 1.3 2012/06/30 01:32:42 bobgian Exp $
+// $Id: argtree.h,v 1.4 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2012 Jim McGill, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Jim McGill, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef ARGTREE_H
#define ARGTREE_H
diff --git a/src/tree/arranger.cpp b/src/tree/arranger.cpp
index 033e0f0..ff4dec4 100644
--- a/src/tree/arranger.cpp
+++ b/src/tree/arranger.cpp
@@ -1,13 +1,25 @@
-// $Id: arranger.cpp,v 1.122 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: arranger.cpp,v 1.123 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "local_build.h"
diff --git a/src/tree/arranger.h b/src/tree/arranger.h
index 4515341..6fee380 100644
--- a/src/tree/arranger.h
+++ b/src/tree/arranger.h
@@ -1,13 +1,25 @@
-// $Id: arranger.h,v 1.62 2013/06/03 17:23:13 jyamato Exp $
+// $Id: arranger.h,v 1.64 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef ARRANGER_H
#define ARRANGER_H
@@ -380,9 +392,9 @@ class ZilchArranger: public Arranger
public:
ZilchArranger(double timing) : Arranger(timing) {};
virtual ~ZilchArranger() {};
- virtual void SetParameters(ChainState & chainstate) {};
- virtual void Rearrange(ChainState & chstate) {};
- virtual void ScoreRearrangement(ChainState & chstate) {};
+ virtual void SetParameters(ChainState &) {};
+ virtual void Rearrange(ChainState &) {};
+ virtual void ScoreRearrangement(ChainState &) {};
virtual bool AcceptAndSynchronize(ChainState &, double temperature, bool badtree);
virtual Arranger* Clone() const;
virtual std::string GetName() const { return arrangerstrings::ZILCH; };
diff --git a/src/tree/arranger_types.cpp b/src/tree/arranger_types.cpp
index 192a584..2a5f58e 100644
--- a/src/tree/arranger_types.cpp
+++ b/src/tree/arranger_types.cpp
@@ -1,13 +1,25 @@
-// $Id: arranger_types.cpp,v 1.13 2013/06/03 17:23:13 jyamato Exp $
+// $Id: arranger_types.cpp,v 1.14 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <string>
#include "arranger_types.h"
diff --git a/src/tree/arranger_types.h b/src/tree/arranger_types.h
index 67d3b01..2fd804a 100644
--- a/src/tree/arranger_types.h
+++ b/src/tree/arranger_types.h
@@ -1,13 +1,25 @@
-// $Id: arranger_types.h,v 1.15 2013/06/03 17:23:13 jyamato Exp $
+// $Id: arranger_types.h,v 1.16 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef ARRANGER_TYPES_H
#define ARRANGER_TYPES_H
diff --git a/src/tree/arrangervec.cpp b/src/tree/arrangervec.cpp
index 2113ae1..c3d3c0a 100644
--- a/src/tree/arrangervec.cpp
+++ b/src/tree/arrangervec.cpp
@@ -1,13 +1,25 @@
-// $Id: arrangervec.cpp,v 1.34 2013/06/03 17:23:13 jyamato Exp $
+// $Id: arrangervec.cpp,v 1.35 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
#include <map>
@@ -122,7 +134,7 @@ void ArrangerVec::CopyAllMembers(const ArrangerVec & cp)
for(it = cp.arrangers.begin(); it != cp.arrangers.end(); it++)
{
Arranger* arr = it->second->Clone();
- arrangers.insert(std::make_pair<string, Arranger*>(arr->GetName(), arr));
+ arrangers.insert(std::make_pair(arr->GetName(), arr));
}
}
}
diff --git a/src/tree/arrangervec.h b/src/tree/arrangervec.h
index 604004b..c4662cd 100644
--- a/src/tree/arrangervec.h
+++ b/src/tree/arrangervec.h
@@ -1,13 +1,25 @@
-// $Id: arrangervec.h,v 1.28 2013/06/03 17:23:13 jyamato Exp $
+// $Id: arrangervec.h,v 1.29 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef ARRANGERVEC_H
#define ARRANGERVEC_H
diff --git a/src/tree/branch.cpp b/src/tree/branch.cpp
index ca94619..51a7e45 100644
--- a/src/tree/branch.cpp
+++ b/src/tree/branch.cpp
@@ -1,13 +1,25 @@
-// $Id: branch.cpp,v 1.109 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: branch.cpp,v 1.110 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <algorithm>
#include <cassert>
#include <iostream> // for debug cerr
diff --git a/src/tree/branch.h b/src/tree/branch.h
index 259af40..f2c109c 100644
--- a/src/tree/branch.h
+++ b/src/tree/branch.h
@@ -1,13 +1,25 @@
-// $Id: branch.h,v 1.69 2012/06/30 01:32:42 bobgian Exp $
+// $Id: branch.h,v 1.71 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*******************************************************************
Class Branch represents a branch in the tree, and is polymorphic on the type of event at its top
@@ -166,8 +178,8 @@ class Branch : public boost::enable_shared_from_this<Branch>
virtual long int Cuttable() const { return 0; };
virtual bool CanRemove(Branch_ptr) { return true; };
virtual long int CountDown() const { return 0; };
- virtual void UpdateBranchRange(const rangeset & fcsites, bool dofc) {};
- virtual void UpdateRootBranchRange(const rangeset & fcsites, bool dofc) {};
+ virtual void UpdateBranchRange(const rangeset &, bool ) {};
+ virtual void UpdateRootBranchRange(const rangeset &, bool) {};
virtual bool IsEquivalentTo(const Branch_ptr) const; // Virtual, but there is only 1 definition.
virtual bool HasSamePartitionsAs(const Branch_ptr) const;
virtual bool PartitionsConsistentWith(const Branch_ptr) const;
@@ -427,7 +439,7 @@ class PartitionBranch : public Branch
virtual long int Cuttable() const { return 0; };
virtual branch_group BranchGroup() const { return bgroupBody; };
virtual void UpdateBranchRange(const rangeset & fcsites, bool dofc);
- virtual void UpdateRootBranchRange(const rangeset & fcsites, bool dofc) { assert(false); };
+ virtual void UpdateRootBranchRange(const rangeset &, bool) { assert(false); };
// Debugging function.
virtual bool CheckInvariant() const;
@@ -626,7 +638,7 @@ class RBranch : public Branch
virtual long int Cuttable() const { return 1; };
virtual long int CountDown() const { return 1; };
virtual void UpdateBranchRange(const rangeset & fcsites, bool dofc);
- virtual void UpdateRootBranchRange(const rangeset & fcsites, bool dofc) { assert(false); };
+ virtual void UpdateRootBranchRange(const rangeset &, bool) { assert(false); };
virtual void ReplaceChild(Branch_ptr oldchild, Branch_ptr newchild);
virtual bool IsRemovableRecombinationLeg(const rangeset &) const;
virtual Branch_ptr GetRecPartner() const;
diff --git a/src/tree/branchbuffer.cpp b/src/tree/branchbuffer.cpp
index 1f799c3..57ddffa 100644
--- a/src/tree/branchbuffer.cpp
+++ b/src/tree/branchbuffer.cpp
@@ -1,13 +1,25 @@
-// $Id: branchbuffer.cpp,v 1.27 2012/06/30 01:32:43 bobgian Exp $
+// $Id: branchbuffer.cpp,v 1.28 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream> // debugging
diff --git a/src/tree/branchbuffer.h b/src/tree/branchbuffer.h
index daa56be..76efdaf 100644
--- a/src/tree/branchbuffer.h
+++ b/src/tree/branchbuffer.h
@@ -1,13 +1,25 @@
-// $Id: branchbuffer.h,v 1.17 2012/06/30 01:32:43 bobgian Exp $
+// $Id: branchbuffer.h,v 1.18 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// This file defines a time ordered container of Branch_ptr, BranchBuffer. The BranchBuffer
// is a storage buffer used during rearrangement to store active and inactive branches.
diff --git a/src/tree/branchtag.cpp b/src/tree/branchtag.cpp
index 45ba60a..c6808df 100644
--- a/src/tree/branchtag.cpp
+++ b/src/tree/branchtag.cpp
@@ -1,13 +1,25 @@
-// $Id: branchtag.cpp,v 1.6 2012/06/30 01:32:43 bobgian Exp $
+// $Id: branchtag.cpp,v 1.7 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#ifdef DMALLOC_FUNC_CHECK
diff --git a/src/tree/branchtag.h b/src/tree/branchtag.h
index df87e92..0ebe634 100644
--- a/src/tree/branchtag.h
+++ b/src/tree/branchtag.h
@@ -1,13 +1,25 @@
-// $Id: branchtag.h,v 1.4 2011/03/07 06:08:52 bobgian Exp $
+// $Id: branchtag.h,v 1.5 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*******************************************************************
Class BranchTag tracks and manages the semi-unique ID number of each
"branch". Semi-unique, in that if two (or more) branches represent the
diff --git a/src/tree/chain.cpp b/src/tree/chain.cpp
index e4f6bc7..cd29d83 100644
--- a/src/tree/chain.cpp
+++ b/src/tree/chain.cpp
@@ -1,13 +1,25 @@
-// $Id: chain.cpp,v 1.99 2013/11/07 22:52:33 jyamato Exp $
+// $Id: chain.cpp,v 1.100 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <algorithm>
#include <cassert>
#include <fstream>
diff --git a/src/tree/chain.h b/src/tree/chain.h
index 40913a5..34fdd0f 100644
--- a/src/tree/chain.h
+++ b/src/tree/chain.h
@@ -1,13 +1,25 @@
-// $Id: chain.h,v 1.34 2012/06/30 01:32:43 bobgian Exp $
+// $Id: chain.h,v 1.35 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*******************************************************************
Chain is a helper class of the ChainManager whose main
responsiblities are to choose the right arranger to use, call that
diff --git a/src/tree/chainstate.cpp b/src/tree/chainstate.cpp
index 0c36ff7..9205599 100644
--- a/src/tree/chainstate.cpp
+++ b/src/tree/chainstate.cpp
@@ -1,13 +1,25 @@
-// $Id: chainstate.cpp,v 1.20 2012/06/30 01:32:43 bobgian Exp $
+// $Id: chainstate.cpp,v 1.21 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "chainstate.h"
diff --git a/src/tree/chainstate.h b/src/tree/chainstate.h
index ee0e2ec..48ab7a1 100644
--- a/src/tree/chainstate.h
+++ b/src/tree/chainstate.h
@@ -1,13 +1,25 @@
-// $Id: chainstate.h,v 1.13 2011/03/07 06:08:52 bobgian Exp $
+// $Id: chainstate.h,v 1.14 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// ChainState encapsulates the parts of Chain's internal state that
// need to be used by Arranger, Event, CollectionManager and Collector.
// It is owned and managed by Chain.
diff --git a/src/tree/collector.cpp b/src/tree/collector.cpp
index c132ce2..44967a3 100644
--- a/src/tree/collector.cpp
+++ b/src/tree/collector.cpp
@@ -1,13 +1,25 @@
-// $Id: collector.cpp,v 1.32 2012/06/30 01:32:43 bobgian Exp $
+// $Id: collector.cpp,v 1.33 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
#include <fstream>
@@ -205,7 +217,7 @@ void ParamCollector::Score(ChainState& chstate)
void ParamCollector::AddParamSummary(ForceParameters fp, long ncopy)
{
- m_paramsum.push_back(make_pair<ForceParameters, long>(fp, ncopy));
+ m_paramsum.push_back(make_pair(fp, ncopy));
}
//------------------------------------------------------------------------------------
diff --git a/src/tree/collector.h b/src/tree/collector.h
index 5fb80fa..33be706 100644
--- a/src/tree/collector.h
+++ b/src/tree/collector.h
@@ -1,13 +1,25 @@
-// $Id: collector.h,v 1.20 2012/06/30 01:32:43 bobgian Exp $
+// $Id: collector.h,v 1.22 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// Collector classes store information from the ongoing chain for
// later analysis. They are related via a base class for convenience
// in initialization, but mostly used via pointer-to-derived because
@@ -43,8 +55,8 @@ class Collector
Collector();
virtual ~Collector() {};
virtual void Score(ChainState& chstate) = 0;
- virtual void CorrectForFatalAttraction(long region) { };
- virtual void UpdateArrangers(ArrangerVec& arrangers, ChainState& chstate) const { };
+ virtual void CorrectForFatalAttraction(long) { };
+ virtual void UpdateArrangers(ArrangerVec&, ChainState&) const { };
virtual void WriteCollectionWhenScore(std::ofstream* out);
virtual void WriteLastSummary() = 0;
virtual void WriteAllSummaries(std::ofstream& out) = 0;
diff --git a/src/tree/collmanager.cpp b/src/tree/collmanager.cpp
index 4154224..9742d6e 100644
--- a/src/tree/collmanager.cpp
+++ b/src/tree/collmanager.cpp
@@ -1,13 +1,25 @@
-// $Id: collmanager.cpp,v 1.35 2012/07/05 04:31:23 bobgian Exp $
+// $Id: collmanager.cpp,v 1.36 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
diff --git a/src/tree/collmanager.h b/src/tree/collmanager.h
index 8dd290d..f3c502d 100644
--- a/src/tree/collmanager.h
+++ b/src/tree/collmanager.h
@@ -1,13 +1,25 @@
-// $Id: collmanager.h,v 1.18 2012/07/05 04:31:23 bobgian Exp $
+// $Id: collmanager.h,v 1.19 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2003 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// The CollectionManager class contains all the Collectors and hands out
// information about them.
diff --git a/src/tree/fc_status.cpp b/src/tree/fc_status.cpp
index 88875a8..e573370 100644
--- a/src/tree/fc_status.cpp
+++ b/src/tree/fc_status.cpp
@@ -1,12 +1,24 @@
-// $Id: fc_status.cpp,v 1.15 2012/06/30 01:32:43 bobgian Exp $
+// $Id: fc_status.cpp,v 1.16 2018/01/03 21:33:03 mkkuhner Exp $
/*
- * Copyright 2010 Mary Kuhner, Jon Yamato, Joseph Felsenstein, and Bob Giansiracusa
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Mary Kuhner, Jon Yamato, Joseph Felsenstein, and Bob Giansiracusa */
+
//------------------------------------------------------------------------------------
diff --git a/src/tree/fc_status.h b/src/tree/fc_status.h
index 2d4a7ac..d5fc60c 100644
--- a/src/tree/fc_status.h
+++ b/src/tree/fc_status.h
@@ -1,12 +1,24 @@
-// $Id: fc_status.h,v 1.14 2012/06/30 01:32:43 bobgian Exp $
+// $Id: fc_status.h,v 1.15 2018/01/03 21:33:03 mkkuhner Exp $
/*
- * Copyright 2010 Mary Kuhner, Jon Yamato, Joseph Felsenstein, and Bob Giansiracusa
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Mary Kuhner, Jon Yamato, Joseph Felsenstein, and Bob Giansiracusa */
+
//------------------------------------------------------------------------------------
diff --git a/src/tree/individual.cpp b/src/tree/individual.cpp
index a3db677..2b39a93 100644
--- a/src/tree/individual.cpp
+++ b/src/tree/individual.cpp
@@ -1,13 +1,25 @@
-// $Id: individual.cpp,v 1.30 2012/10/02 02:27:06 bobgian Exp $
+// $Id: individual.cpp,v 1.31 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "branch.h"
diff --git a/src/tree/individual.h b/src/tree/individual.h
index d9a110e..abb9f91 100644
--- a/src/tree/individual.h
+++ b/src/tree/individual.h
@@ -1,13 +1,25 @@
-// $Id: individual.h,v 1.21 2012/06/30 01:32:43 bobgian Exp $
+// $Id: individual.h,v 1.22 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// This file defines the class that stores "individual" specific information.
#ifndef INDIVIDUAL_H
diff --git a/src/tree/intervaldata.cpp b/src/tree/intervaldata.cpp
index 7bcd5f9..4bd4c71 100644
--- a/src/tree/intervaldata.cpp
+++ b/src/tree/intervaldata.cpp
@@ -1,13 +1,25 @@
-// $Id: intervaldata.cpp,v 1.25 2012/06/30 01:32:43 bobgian Exp $
+// $Id: intervaldata.cpp,v 1.26 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <fstream>
#include <iostream>
diff --git a/src/tree/intervaldata.h b/src/tree/intervaldata.h
index 2a6f420..e9d61cc 100644
--- a/src/tree/intervaldata.h
+++ b/src/tree/intervaldata.h
@@ -1,13 +1,25 @@
-// $Id: intervaldata.h,v 1.25 2012/06/30 01:32:43 bobgian Exp $
+// $Id: intervaldata.h,v 1.26 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*
This file contains two closely related classes used in storing
TreeSummaries. The first class, Interval, represents all data
diff --git a/src/tree/newick.h b/src/tree/newick.h
index f09fbd4..4a13a1c 100644
--- a/src/tree/newick.h
+++ b/src/tree/newick.h
@@ -1,13 +1,25 @@
-// $Id: newick.h,v 1.10 2013/11/07 22:52:33 jyamato Exp $
+// $Id: newick.h,v 1.12 2018/01/03 21:33:03 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef NEWICK_H
#define NEWICK_H
@@ -43,7 +55,7 @@ class NullUserTree : public UserTree
virtual ~NullUserTree() {};
- virtual void ToLamarcTree(Tree& stump) { assert(false); }; // instantiating NULL tree
+ virtual void ToLamarcTree(Tree&) { assert(false); }; // instantiating NULL tree
};
//------------------------------------------------------------------------------------
diff --git a/src/tree/parameter.cpp b/src/tree/parameter.cpp
index 2be1d19..f6b168e 100644
--- a/src/tree/parameter.cpp
+++ b/src/tree/parameter.cpp
@@ -1,13 +1,25 @@
-// $Id: parameter.cpp,v 1.50 2012/06/30 01:32:43 bobgian Exp $
+// $Id: parameter.cpp,v 1.51 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "local_build.h" // for definition of LAMARC_NEW_FEATURE_RELATIVE_SAMPLING
diff --git a/src/tree/parameter.h b/src/tree/parameter.h
index 883423f..1787899 100644
--- a/src/tree/parameter.h
+++ b/src/tree/parameter.h
@@ -1,13 +1,25 @@
-// $Id: parameter.h,v 1.46 2012/06/30 01:32:43 bobgian Exp $
+// $Id: parameter.h,v 1.47 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*************************************************************************
The Parameter class and its helper ResultStruct are used to store
information about individual parameters of the force model. For
diff --git a/src/tree/partition.cpp b/src/tree/partition.cpp
index fe8cb78..23eeec2 100644
--- a/src/tree/partition.cpp
+++ b/src/tree/partition.cpp
@@ -1,13 +1,25 @@
-// $Id: partition.cpp,v 1.5 2011/03/08 19:22:01 bobgian Exp $
+// $Id: partition.cpp,v 1.6 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "force.h"
#include "partition.h"
diff --git a/src/tree/partition.h b/src/tree/partition.h
index f7768ec..e3fe10e 100644
--- a/src/tree/partition.h
+++ b/src/tree/partition.h
@@ -1,13 +1,25 @@
-// $Id: partition.h,v 1.10 2011/03/12 20:03:02 bobgian Exp $
+// $Id: partition.h,v 1.11 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PARTITION_H
#define PARTITION_H
diff --git a/src/tree/prior.cpp b/src/tree/prior.cpp
index 752cc92..bf9c7b2 100644
--- a/src/tree/prior.cpp
+++ b/src/tree/prior.cpp
@@ -1,13 +1,25 @@
-// $Id: prior.cpp,v 1.13 2013/06/03 17:23:13 jyamato Exp $
+// $Id: prior.cpp,v 1.14 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "local_build.h" // for definition of LAMARC_NEW_FEATURE_RELATIVE_SAMPLING
@@ -79,18 +91,18 @@ bool Prior::operator==(const Prior src) const
std::pair<double, double> Prior::RandomDraw() const
{
Random& rnd = registry.GetRandom();
- double newparam, newlnparam;
+ double newparam = 0, newlnparam = 0;
switch (m_priortype)
{
case LINEAR:
newparam = rnd.Float() * (m_upperbound - m_lowerbound) + m_lowerbound;
newlnparam = log(newparam);
- return std::make_pair<double, double>(newparam, newlnparam);
+ return std::make_pair(newparam, newlnparam);
break;
case LOGARITHMIC:
newlnparam = rnd.Float() * (m_lnupper - m_lnlower) + m_lnlower;
newparam = exp(newlnparam);
- return std::make_pair<double, double>(newparam, newlnparam);
+ return std::make_pair(newparam, newlnparam);
break;
}
string e = "Unknown prior type " + ToString(m_priortype) +
@@ -103,7 +115,7 @@ std::pair<double, double> Prior::RandomDraw() const
std::pair<double,double> Prior::RandomDrawWithReflection(double current, double windowfraction) const
{
Random& rnd = registry.GetRandom();
- double newparam, newlnparam;
+ double newparam = 0, newlnparam = 0;
double delta = windowfraction * (m_upperbound - m_lowerbound);
switch (m_priortype)
{
@@ -117,7 +129,7 @@ std::pair<double,double> Prior::RandomDrawWithReflection(double current, double
{
newparam = 2.0 * m_upperbound - newparam;
}
- return std::make_pair<double,double>(newparam, log(newparam));
+ return std::make_pair(newparam, log(newparam));
break;
case LOGARITHMIC:
string e = "Cannot use prior type " + ToString(m_priortype) +
@@ -135,7 +147,7 @@ std::pair<double,double> Prior::RandomDrawWithReflection(double current, double
std::pair<double, double> Prior::RandomDrawWithinBounds(double lower, double upper) const
{
Random& rnd = registry.GetRandom();
- double newparam, newlnparam;
+ double newparam = 0, newlnparam = 0;
double lowbound = std::max(m_lowerbound, lower);
double upbound = std::min(m_upperbound, upper);
switch (m_priortype)
@@ -143,15 +155,18 @@ std::pair<double, double> Prior::RandomDrawWithinBounds(double lower, double upp
case LINEAR:
newparam = rnd.Float() * (upbound - lowbound) + lowbound;
newlnparam = log(newparam);
- return std::make_pair<double, double>(newparam, newlnparam);
+ return std::make_pair(newparam, newlnparam);
break;
case LOGARITHMIC:
lowbound = log(lowbound);
upbound = log(upbound);
newlnparam = rnd.Float() * (upbound - lowbound) + lowbound;
newparam = exp(newlnparam);
- return std::make_pair<double, double>(newparam, newlnparam);
+ return std::make_pair(newparam, newlnparam);
break;
}
+ string e = "Unknown prior type " + ToString(m_priortype) +
+ " in Parameter::RandomDrawWithinBounds";
+ throw implementation_error(e);
} // RandomDrawWithinBounds
diff --git a/src/tree/prior.h b/src/tree/prior.h
index affcdc5..551c8ad 100644
--- a/src/tree/prior.h
+++ b/src/tree/prior.h
@@ -1,13 +1,25 @@
-// $Id: prior.h,v 1.9 2013/06/03 17:23:13 jyamato Exp $
+// $Id: prior.h,v 1.10 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
//A prior is a shape. Currently, we have two possible shapes: a rectangle
// in linear space, and a rectangle in log space. Those are simple enough
// that we don't really need a class for them, but if we want more complex
diff --git a/src/tree/range.cpp b/src/tree/range.cpp
index da81e30..39a084b 100644
--- a/src/tree/range.cpp
+++ b/src/tree/range.cpp
@@ -1,13 +1,25 @@
-// $Id: range.cpp,v 1.50 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: range.cpp,v 1.51 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream> // For debugging.
#include <iomanip> // For setw().
diff --git a/src/tree/range.h b/src/tree/range.h
index 1dbd7f4..75ad693 100644
--- a/src/tree/range.h
+++ b/src/tree/range.h
@@ -1,13 +1,25 @@
-// $Id: range.h,v 1.48 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: range.h,v 1.50 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
//------------------------------------------------------------------------------------
// General comments about the meanings of terms as they apply to the Biglink versus Littlelink implementations.
//------------------------------------------------------------------------------------
@@ -261,9 +273,9 @@ class Range
// Tests.
virtual bool operator==(const Range & other) const;
- virtual bool SameLiveSites(const rangeset & src) const { return true; };
+ virtual bool SameLiveSites(const rangeset &) const { return true; };
virtual bool LiveSitesOnly() const { return true; };
- virtual bool IsSiteLive(long int site) const { return true; };
+ virtual bool IsSiteLive(long int) const { return true; };
// Getters.
// Functions which ASSERT here are defined to return a RANGESET (or LINKRANGESET) simply to satisfy the compiler
@@ -292,7 +304,7 @@ class Range
virtual void UpdateMRange(const Range * const childrangeptr);
virtual void UpdateRRange(const Range * const childrangeptr, const rangeset & fcsites, bool dofc);
- virtual bool AreLowSitesOnInactiveBranch(long int recpoint) const
+ virtual bool AreLowSitesOnInactiveBranch(long int) const
{ assert(false); return false; };
virtual bool AreDiseaseSitesTransmitted() const { return true; };
@@ -313,8 +325,8 @@ class Range
virtual void PrintInfo() const;
virtual void PrintNewTargetLinks() const;
virtual bool NoLiveAndNoTransmittedDiseaseSites() const { return false; };
- virtual bool DifferentCurTargetLinks(const linkrangeset & src) const { return false; };
- virtual bool DifferentNewTargetLinks(const linkrangeset & src) const { return false; };
+ virtual bool DifferentCurTargetLinks(const linkrangeset &) const { return false; };
+ virtual bool DifferentNewTargetLinks(const linkrangeset &) const { return false; };
};
diff --git a/src/tree/rectree.cpp b/src/tree/rectree.cpp
index 72ec9d5..aae670d 100644
--- a/src/tree/rectree.cpp
+++ b/src/tree/rectree.cpp
@@ -1,13 +1,25 @@
-// $Id: rectree.cpp,v 1.81 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: rectree.cpp,v 1.82 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream> // debugging
diff --git a/src/tree/sticksum.h b/src/tree/sticksum.h
index f4790c3..e6c8389 100644
--- a/src/tree/sticksum.h
+++ b/src/tree/sticksum.h
@@ -1,14 +1,24 @@
-// $Id: sticksum.h,v 1.5 2011/04/23 02:02:50 bobgian Exp $
+// $Id: sticksum.h,v 1.6 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2006 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph
- * Felsenstein
- *
- * This software is distributed free of charge for non-commercial
- * use and is copyrighted. Of course, we do not guarantee that the
- * software works, and are not responsible for any damage you may
- * cause or have.
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
/********************************************************************
Class StickSummary.
diff --git a/src/tree/summary.cpp b/src/tree/summary.cpp
index e882bbb..a65d433 100644
--- a/src/tree/summary.cpp
+++ b/src/tree/summary.cpp
@@ -1,13 +1,25 @@
-// $Id: summary.cpp,v 1.54 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: summary.cpp,v 1.55 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <cmath>
#include <iostream>
diff --git a/src/tree/summary.h b/src/tree/summary.h
index be18871..7633cdd 100644
--- a/src/tree/summary.h
+++ b/src/tree/summary.h
@@ -1,13 +1,25 @@
-// $Id: summary.h,v 1.41 2012/06/30 01:32:43 bobgian Exp $
+// $Id: summary.h,v 1.43 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*
This is a Force-polymorphic class which works with the IntervalData
class (non-polymorphic) to provide needed summary information about
@@ -31,7 +43,7 @@
#include "registry.h" // For use of GetDataPack() and GetForceSummary() to set npop & m_nparams.
#include "vectorx.h"
-class Interval;
+struct Interval;
class Summary
{
@@ -199,7 +211,7 @@ class EpochSummary : public Summary
virtual ~EpochSummary() {};
virtual Summary * Clone(IntervalData& interval) const;
- virtual void AdjustSummary(const DoubleVec1d & totals, long region) {};
+ virtual void AdjustSummary(const DoubleVec1d &, long) {};
virtual string GetType() const { return lamarcstrings::DIVERGENCE; };
};
diff --git a/src/tree/tempident.cpp b/src/tree/tempident.cpp
index 54d9813..332d2d9 100644
--- a/src/tree/tempident.cpp
+++ b/src/tree/tempident.cpp
@@ -1,13 +1,25 @@
-// $Id: tempident.cpp,v 1.23 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: tempident.cpp,v 1.24 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <map>
diff --git a/src/tree/tempident.h b/src/tree/tempident.h
index 380477f..7721ded 100644
--- a/src/tree/tempident.h
+++ b/src/tree/tempident.h
@@ -1,13 +1,25 @@
-// $Id: tempident.h,v 1.17 2012/06/30 01:32:43 bobgian Exp $
+// $Id: tempident.h,v 1.18 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*******************************************************************
TemperatureIdentity contains the temperature-dependent parts of
a Chain; having this as a separate object facilitates swapping two
diff --git a/src/tree/timelist.cpp b/src/tree/timelist.cpp
index b469060..3e7880b 100644
--- a/src/tree/timelist.cpp
+++ b/src/tree/timelist.cpp
@@ -1,13 +1,25 @@
-// $Id: timelist.cpp,v 1.60 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: timelist.cpp,v 1.61 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <functional> // for mem_fun
#include <iostream> // debugging
diff --git a/src/tree/timelist.h b/src/tree/timelist.h
index 8ddb2b3..a16ed60 100644
--- a/src/tree/timelist.h
+++ b/src/tree/timelist.h
@@ -1,13 +1,25 @@
-// $Id: timelist.h,v 1.30 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: timelist.h,v 1.31 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// This files defines a time ordered container of Branch_ptr,
// TimeList. The TimeList is a wrapped std::list of all Branch
// derived things associated with a particular tree.
diff --git a/src/tree/tree.cpp b/src/tree/tree.cpp
index 49a6fb0..e0422a9 100644
--- a/src/tree/tree.cpp
+++ b/src/tree/tree.cpp
@@ -1,13 +1,25 @@
-// $Id: tree.cpp,v 1.115 2013/06/03 17:23:13 jyamato Exp $
+// $Id: tree.cpp,v 1.117 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <algorithm> // for std::max and min
#include <cassert>
#include <iostream> // debugging
@@ -532,7 +544,7 @@ vector<Branch_ptr> Tree::FindBranchesBetween(double startint, double endint)
//------------------------------------------------------------------------------------
-void Tree::NextInterval(Branch_ptr branch)
+void Tree::NextInterval(Branch_ptr)
{
// Deliberately blank; needed only in rectree.
}
diff --git a/src/tree/tree.h b/src/tree/tree.h
index 6b4c13a..af5c059 100644
--- a/src/tree/tree.h
+++ b/src/tree/tree.h
@@ -1,13 +1,25 @@
-// $Id: tree.h,v 1.83 2013/06/03 17:23:13 jyamato Exp $
+// $Id: tree.h,v 1.85 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
/*******************************************************************
Class Tree represents a genealogy (not necessarily a "tree" in the recombinant cases). It has two subtypes,
a PlainTree (no recombination) and a RecTree (with recombination) because the recombination machinery is too
@@ -196,8 +208,8 @@ class Tree
DoubleVec1d PartitionThetasAtT(double time, force_type force, const ForceParameters & fp) const;
// TreeSizeArranger.
- virtual void SetCurTargetLinkweightFrom(const BranchBuffer & brbuffer) { }; // no-op
- virtual void ClearCurTargetLinkweight() { }; // no-op
+ virtual void SetCurTargetLinkweightFrom(const BranchBuffer &) { }; // no-op
+ virtual void ClearCurTargetLinkweight() { }; // no-op
// Simulation.
virtual bool SimulateDataIfNeeded();
diff --git a/src/tree/treesum.cpp b/src/tree/treesum.cpp
index 52f89d8..54dc98a 100644
--- a/src/tree/treesum.cpp
+++ b/src/tree/treesum.cpp
@@ -1,13 +1,25 @@
-// $Id: treesum.cpp,v 1.116 2013/11/08 21:46:21 mkkuhner Exp $
+// $Id: treesum.cpp,v 1.117 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <fstream>
#include <iostream>
diff --git a/src/tree/treesum.h b/src/tree/treesum.h
index 3796b26..18a4555 100644
--- a/src/tree/treesum.h
+++ b/src/tree/treesum.h
@@ -1,13 +1,25 @@
// $id: treesum.h,v 1.15 2002/10/29 22:01:19 ewalkup Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef TREESUM_H
#define TREESUM_H
diff --git a/src/ui_interface/chainparam_interface.cpp b/src/ui_interface/chainparam_interface.cpp
index 6dda761..2cb2c1f 100644
--- a/src/ui_interface/chainparam_interface.cpp
+++ b/src/ui_interface/chainparam_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: chainparam_interface.cpp,v 1.36 2011/01/12 17:27:20 mkkuhner Exp $
+// $Id: chainparam_interface.cpp,v 1.37 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <iostream>
#include "arranger.h"
diff --git a/src/ui_interface/chainparam_interface.h b/src/ui_interface/chainparam_interface.h
index cde96d1..2364bd4 100644
--- a/src/ui_interface/chainparam_interface.h
+++ b/src/ui_interface/chainparam_interface.h
@@ -1,13 +1,24 @@
-// $Id: chainparam_interface.h,v 1.35 2011/03/07 06:08:53 bobgian Exp $
+// $Id: chainparam_interface.h,v 1.36 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef CHAINPARAM_INTERFACE_H
#define CHAINPARAM_INTERFACE_H
diff --git a/src/ui_interface/constraint_interface.cpp b/src/ui_interface/constraint_interface.cpp
index efb39cc..ebd01f3 100644
--- a/src/ui_interface/constraint_interface.cpp
+++ b/src/ui_interface/constraint_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: constraint_interface.cpp,v 1.9 2011/03/08 19:22:01 bobgian Exp $
+// $Id: constraint_interface.cpp,v 1.10 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <algorithm> // for std::min()
#include "constraint_interface.h"
diff --git a/src/ui_interface/constraint_interface.h b/src/ui_interface/constraint_interface.h
index 69d302a..6353617 100644
--- a/src/ui_interface/constraint_interface.h
+++ b/src/ui_interface/constraint_interface.h
@@ -1,13 +1,24 @@
-// $Id: constraint_interface.h,v 1.5 2011/03/08 19:22:01 bobgian Exp $
+// $Id: constraint_interface.h,v 1.6 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef CONSTRAINT_INTERFACE_H
#define CONSTRAINT_INTERFACE_H
diff --git a/src/ui_interface/data_interface.cpp b/src/ui_interface/data_interface.cpp
index cd01fb1..74d12b8 100644
--- a/src/ui_interface/data_interface.cpp
+++ b/src/ui_interface/data_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: data_interface.cpp,v 1.33 2012/06/30 01:32:43 bobgian Exp $
+// $Id: data_interface.cpp,v 1.34 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <iostream>
diff --git a/src/ui_interface/data_interface.h b/src/ui_interface/data_interface.h
index 8c87bbf..d28d514 100644
--- a/src/ui_interface/data_interface.h
+++ b/src/ui_interface/data_interface.h
@@ -1,13 +1,24 @@
-// $Id: data_interface.h,v 1.23 2012/02/15 18:13:42 jmcgill Exp $
+// $Id: data_interface.h,v 1.24 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef DATA_INTERFACE_H
#define DATA_INTERFACE_H
diff --git a/src/ui_interface/datamodel_interface.cpp b/src/ui_interface/datamodel_interface.cpp
index ef93895..88b49bf 100644
--- a/src/ui_interface/datamodel_interface.cpp
+++ b/src/ui_interface/datamodel_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: datamodel_interface.cpp,v 1.39 2011/03/07 06:08:53 bobgian Exp $
+// $Id: datamodel_interface.cpp,v 1.40 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <string>
diff --git a/src/ui_interface/datamodel_interface.h b/src/ui_interface/datamodel_interface.h
index eced294..7d3169f 100644
--- a/src/ui_interface/datamodel_interface.h
+++ b/src/ui_interface/datamodel_interface.h
@@ -1,13 +1,24 @@
-// $Id: datamodel_interface.h,v 1.29 2011/03/07 06:08:53 bobgian Exp $
+// $Id: datamodel_interface.h,v 1.30 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef DATAMODEL_INTERFACE_H
#define DATAMODEL_INTERFACE_H
diff --git a/src/ui_interface/force_interface.cpp b/src/ui_interface/force_interface.cpp
index a660431..b727e83 100644
--- a/src/ui_interface/force_interface.cpp
+++ b/src/ui_interface/force_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: force_interface.cpp,v 1.63 2012/06/30 01:32:43 bobgian Exp $
+// $Id: force_interface.cpp,v 1.64 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <algorithm> // for std::min()
diff --git a/src/ui_interface/force_interface.h b/src/ui_interface/force_interface.h
index bab832f..bfbb935 100644
--- a/src/ui_interface/force_interface.h
+++ b/src/ui_interface/force_interface.h
@@ -1,13 +1,24 @@
-// $Id: force_interface.h,v 1.39 2012/06/30 01:32:43 bobgian Exp $
+// $Id: force_interface.h,v 1.40 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef FORCE_INTERFACE_H
#define FORCE_INTERFACE_H
diff --git a/src/ui_interface/front_end_warnings.cpp b/src/ui_interface/front_end_warnings.cpp
index 81c559b..05342b5 100644
--- a/src/ui_interface/front_end_warnings.cpp
+++ b/src/ui_interface/front_end_warnings.cpp
@@ -1,13 +1,25 @@
-// $Id: front_end_warnings.cpp,v 1.3 2011/03/08 19:22:01 bobgian Exp $
+// $Id: front_end_warnings.cpp,v 1.4 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "front_end_warnings.h"
#include "vectorx.h"
diff --git a/src/ui_interface/front_end_warnings.h b/src/ui_interface/front_end_warnings.h
index 97fe3a6..a8180d9 100644
--- a/src/ui_interface/front_end_warnings.h
+++ b/src/ui_interface/front_end_warnings.h
@@ -1,13 +1,24 @@
-// $Id: front_end_warnings.h,v 1.3 2011/03/07 06:08:53 bobgian Exp $
+// $Id: front_end_warnings.h,v 1.4 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef FRONT_END_WARNINGS_H
#define FRONT_END_WARNINGS_H
diff --git a/src/ui_interface/prior_interface.cpp b/src/ui_interface/prior_interface.cpp
index 7761a0e..17aade6 100644
--- a/src/ui_interface/prior_interface.cpp
+++ b/src/ui_interface/prior_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: prior_interface.cpp,v 1.13 2012/06/30 01:32:43 bobgian Exp $
+// $Id: prior_interface.cpp,v 1.14 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_interface/prior_interface.h b/src/ui_interface/prior_interface.h
index 07cdedb..ae76c11 100644
--- a/src/ui_interface/prior_interface.h
+++ b/src/ui_interface/prior_interface.h
@@ -1,13 +1,24 @@
-// $Id: prior_interface.h,v 1.8 2012/06/30 01:32:43 bobgian Exp $
+// $Id: prior_interface.h,v 1.9 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef PRIOR_INTERFACE_H
#define PRIOR_INTERFACE_H
diff --git a/src/ui_interface/profile_interface.cpp b/src/ui_interface/profile_interface.cpp
index a3c82ac..490f40f 100644
--- a/src/ui_interface/profile_interface.cpp
+++ b/src/ui_interface/profile_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: profile_interface.cpp,v 1.27 2011/03/07 06:08:53 bobgian Exp $
+// $Id: profile_interface.cpp,v 1.28 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <iostream>
diff --git a/src/ui_interface/profile_interface.h b/src/ui_interface/profile_interface.h
index 2f99c8f..52038e1 100644
--- a/src/ui_interface/profile_interface.h
+++ b/src/ui_interface/profile_interface.h
@@ -1,13 +1,24 @@
-// $Id: profile_interface.h,v 1.21 2011/03/07 06:08:53 bobgian Exp $
+// $Id: profile_interface.h,v 1.22 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef PROFILE_INTERFACE_H
#define PROFILE_INTERFACE_H
diff --git a/src/ui_interface/setget.h b/src/ui_interface/setget.h
index 1e9c328..fadc28b 100644
--- a/src/ui_interface/setget.h
+++ b/src/ui_interface/setget.h
@@ -1,13 +1,24 @@
-// $Id: setget.h,v 1.45 2011/03/07 06:08:53 bobgian Exp $
+// $Id: setget.h,v 1.47 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef SETGET_H
#define SETGET_H
@@ -48,23 +59,23 @@ class SetGet
virtual const string & UIKey()
{ return uikey;};
// Get a string describing what will be set/gotten
- virtual string Description(UIVars& vars, UIId id)
+ virtual string Description(UIVars&, UIId)
{ return UIKey();};
//Get a string describing the min/max values possible.
- virtual string Min(UIVars& vars, UIId id) { return ToString(FLAGDOUBLE);};
- virtual string Max(UIVars& vars, UIId id) { return ToString(FLAGDOUBLE);};
+ virtual string Min(UIVars&, UIId) { return ToString(FLAGDOUBLE);};
+ virtual string Max(UIVars&, UIId) { return ToString(FLAGDOUBLE);};
// Get a string that represents the value stored in the backend
virtual std::string GetPrintString(UIVars& vars, UIId id) = 0;
- virtual std::string NextToggleValue(UIVars& vars, UIId id)
+ virtual std::string NextToggleValue(UIVars&, UIId)
{ throw implementation_error("no toggle possible");};
// returns true if the values associated with id for this
// menu item are internally consistent -- used to verify
// that two or more values are mutually OK.
- virtual bool IsConsistent(UIVars& vars, UIId id)
+ virtual bool IsConsistent(UIVars&, UIId)
{
return true;
};
- virtual void SetFromString(UIVars& vars, UIId id, string stringVal)
+ virtual void SetFromString(UIVars&, UIId, string)
{ throw implementation_error("no SetFromString possible");};
};
@@ -84,7 +95,7 @@ class GetTemplate : public SetGet
virtual std::string GetPrintString(UIVars& vars, UIId id)
{ return MakePrintString(vars,Get(vars,id));};
// how these values should be printed out
- virtual std::string MakePrintString(UIVars& vars,ValType v)
+ virtual std::string MakePrintString(UIVars&,ValType v)
{ return ToString(v);};
};
@@ -255,7 +266,7 @@ class SetGetBool : public SetGetTemplate<bool>
public:
SetGetBool(const std::string & key): SetGetTemplate<bool>(key) {};
virtual ~SetGetBool() {};
- virtual bool GetValFromString(UIVars& vars,string input)
+ virtual bool GetValFromString(UIVars&,string input)
{ return ProduceBoolOrBarf(input);};
virtual std::string NextToggleValue(UIVars& vars,UIId id)
{ bool v = Get(vars,id); return ToString(!v);};
@@ -270,7 +281,7 @@ class SetGetDouble : public SetGetTemplate<double>
public:
SetGetDouble(const std::string & key): SetGetTemplate<double>(key) {};
virtual ~SetGetDouble() {};
- virtual double GetValFromString(UIVars& vars,string input)
+ virtual double GetValFromString(UIVars&,string input)
{ return ProduceDoubleOrBarf(input);};
};
@@ -283,7 +294,7 @@ class SetGetGrowthScheme : public SetGetTemplate<growth_scheme>
public:
SetGetGrowthScheme(const std::string & key): SetGetTemplate<growth_scheme>(key) {};
virtual ~SetGetGrowthScheme() {};
- virtual growth_scheme GetValFromString(UIVars& vars,string input)
+ virtual growth_scheme GetValFromString(UIVars&,string input)
{ return ProduceGrowthSchemeOrBarf(input);};
};
@@ -296,7 +307,7 @@ class SetGetGrowthType : public SetGetTemplate<growth_type>
public:
SetGetGrowthType(const std::string & key): SetGetTemplate<growth_type>(key) {};
virtual ~SetGetGrowthType() {};
- virtual growth_type GetValFromString(UIVars& vars,string input)
+ virtual growth_type GetValFromString(UIVars&,string input)
{ return ProduceGrowthTypeOrBarf(input);};
};
@@ -309,7 +320,7 @@ class SetGetSelectionType : public SetGetTemplate<selection_type>
public:
SetGetSelectionType(const std::string & key): SetGetTemplate<selection_type>(key) {};
virtual ~SetGetSelectionType() {};
- virtual selection_type GetValFromString(UIVars& vars,string input)
+ virtual selection_type GetValFromString(UIVars&,string input)
{ return ProduceSelectionTypeOrBarf(input);};
};
@@ -322,7 +333,7 @@ class SetGetLong : public SetGetTemplate<long int>
public:
SetGetLong(const std::string & key): SetGetTemplate<long int>(key) {};
virtual ~SetGetLong() {};
- virtual long int GetValFromString(UIVars& vars,string input)
+ virtual long int GetValFromString(UIVars&,string input)
{ return ProduceLongOrBarf(input);};
};
@@ -335,7 +346,7 @@ class SetGetMethodType : public SetGetTemplate<method_type>
public:
SetGetMethodType(const std::string & key): SetGetTemplate<method_type>(key) {};
virtual ~SetGetMethodType() {};
- virtual method_type GetValFromString(UIVars& vars,string input)
+ virtual method_type GetValFromString(UIVars&,string input)
{ return ProduceMethodTypeOrBarf(input);};
};
@@ -348,7 +359,7 @@ class SetGetString : public SetGetTemplate<std::string>
public:
SetGetString(const std::string & key): SetGetTemplate<std::string>(key) {};
virtual ~SetGetString() {};
- virtual string GetValFromString(UIVars& vars,string input)
+ virtual string GetValFromString(UIVars&,string input)
{ return input;};
};
@@ -361,7 +372,7 @@ class SetGetModelType : public SetGetTemplate<model_type>
public:
SetGetModelType(const std::string & key): SetGetTemplate<model_type>(key) {};
virtual ~SetGetModelType() {};
- virtual model_type GetValFromString(UIVars& vars,string input)
+ virtual model_type GetValFromString(UIVars&,string input)
{ return ProduceModelTypeOrBarf(input);};
};
@@ -374,7 +385,7 @@ class SetGetProftype : public SetGetTemplate<proftype>
public:
SetGetProftype(const std::string & key): SetGetTemplate<proftype>(key) {};
virtual ~SetGetProftype() {};
- virtual proftype GetValFromString(UIVars& vars,string input)
+ virtual proftype GetValFromString(UIVars&,string input)
{ return ProduceProftypeOrBarf(input);};
virtual std::string NextToggleValue(UIVars& vars,UIId id)
{
@@ -400,7 +411,7 @@ class SetGetIndividualParamstatus : public SetGetTemplate<ParamStatus>
public:
SetGetIndividualParamstatus(const std::string & key): SetGetTemplate<ParamStatus>(key) {};
virtual ~SetGetIndividualParamstatus() {};
- virtual ParamStatus GetValFromString(UIVars& vars,string input)
+ virtual ParamStatus GetValFromString(UIVars&,string input)
{ return ProduceParamstatusOrBarf(input);};
virtual std::string NextToggleValue(UIVars& vars,UIId id)
{
@@ -413,7 +424,7 @@ class SetGetGroupParamstatus : public SetGetTemplate<ParamStatus>
public:
SetGetGroupParamstatus(const std::string & key): SetGetTemplate<ParamStatus>(key) {};
virtual ~SetGetGroupParamstatus() {};
- virtual ParamStatus GetValFromString(UIVars& vars,string input)
+ virtual ParamStatus GetValFromString(UIVars&,string input)
{ return ProduceParamstatusOrBarf(input);};
virtual std::string NextToggleValue(UIVars& vars,UIId id)
{
@@ -431,7 +442,7 @@ class SetGetVerbosityType : public SetGetTemplate<verbosity_type>
SetGetVerbosityType(const std::string & key)
: SetGetTemplate<verbosity_type>(key) {};
virtual ~SetGetVerbosityType() {};
- virtual verbosity_type GetValFromString(UIVars& vars,string input)
+ virtual verbosity_type GetValFromString(UIVars&,string input)
{ return ProduceVerbosityTypeOrBarf(input);};
virtual std::string NextToggleValue(UIVars& vars, UIId id)
{
@@ -465,7 +476,7 @@ class SetGetVerbosityTypeNoNone : public SetGetTemplate<verbosity_type>
SetGetVerbosityTypeNoNone(const std::string & key)
: SetGetTemplate<verbosity_type>(key) {};
virtual ~SetGetVerbosityTypeNoNone() {};
- virtual verbosity_type GetValFromString(UIVars& vars, string input)
+ virtual verbosity_type GetValFromString(UIVars&, string input)
{ return ProduceVerbosityTypeOrBarf(input);};
virtual std::string NextToggleValue(UIVars& vars, UIId id)
{
@@ -497,7 +508,7 @@ class SetGetPriorType : public SetGetTemplate<priortype>
SetGetPriorType(const std::string & key)
: SetGetTemplate<priortype>(key) {};
virtual ~SetGetPriorType() {};
- virtual priortype GetValFromString(UIVars& vars, string input)
+ virtual priortype GetValFromString(UIVars&, string input)
{ return ProducePriorTypeOrBarf(input);};
virtual std::string NextToggleValue(UIVars& vars, UIId id)
{
@@ -528,7 +539,7 @@ class SetGetLongVec1d : public SetGetTemplate<LongVec1d>
SetGetLongVec1d(const std::string & key)
: SetGetTemplate<LongVec1d>(key) {};
virtual ~SetGetLongVec1d() {};
- virtual LongVec1d GetValFromString(UIVars& vars, string input)
+ virtual LongVec1d GetValFromString(UIVars&, string input)
{ return ProduceLongVec1dOrBarf(input); };
};
@@ -542,7 +553,7 @@ class SetGetProftypeVec1d : public SetGetTemplate<ProftypeVec1d>
SetGetProftypeVec1d(const std::string & key)
: SetGetTemplate<ProftypeVec1d>(key) {};
virtual ~SetGetProftypeVec1d() {};
- virtual ProftypeVec1d GetValFromString(UIVars& vars, string input)
+ virtual ProftypeVec1d GetValFromString(UIVars&, string input)
{ return ProduceProftypeVec1dOrBarf(input); };
};
@@ -554,7 +565,7 @@ class SetGetBoolEnabled : public SetGetBool
public:
SetGetBoolEnabled(const std::string & key) : SetGetBool(key) {};
virtual ~SetGetBoolEnabled() {};
- virtual std::string MakePrintString(UIVars& vars, bool val)
+ virtual std::string MakePrintString(UIVars&, bool val)
{
if(val) return "Enabled";
return "Disabled";
@@ -569,7 +580,7 @@ class SetGetBoolOnOff : public SetGetBool
public:
SetGetBoolOnOff(const std::string & key) : SetGetBool(key) {};
virtual ~SetGetBoolOnOff() {};
- virtual std::string MakePrintString(UIVars& vars, bool val)
+ virtual std::string MakePrintString(UIVars&, bool val)
{
if(val) return "On";
return "Off";
@@ -584,7 +595,7 @@ class SetGetBoolReadWrite : public SetGetBool
public:
SetGetBoolReadWrite(const std::string & key) : SetGetBool(key) {};
virtual ~SetGetBoolReadWrite() {};
- virtual std::string MakePrintString(UIVars& vars, bool val)
+ virtual std::string MakePrintString(UIVars&, bool val)
{
if(val) return "Write";
return "Read";
@@ -597,10 +608,10 @@ class SetGetNoval : public SetGetTemplate<noval>
SetGetNoval(const std::string & key)
: SetGetTemplate<noval>(key) {};
virtual ~SetGetNoval() {};
- virtual noval Get(UIVars& vars, UIId id) { return noval_none;};
- virtual noval GetValFromString(UIVars& vars, string input)
+ virtual noval Get(UIVars&, UIId) { return noval_none;};
+ virtual noval GetValFromString(UIVars&, string)
{ return noval_none;};
- virtual std::string NextToggleValue(UIVars& vars, UIId id)
+ virtual std::string NextToggleValue(UIVars&, UIId)
{ return ToString(noval_none);};
};
diff --git a/src/ui_interface/setgetmachine.cpp b/src/ui_interface/setgetmachine.cpp
index e244a17..d51634c 100644
--- a/src/ui_interface/setgetmachine.cpp
+++ b/src/ui_interface/setgetmachine.cpp
@@ -1,13 +1,24 @@
-// $Id: setgetmachine.cpp,v 1.95 2012/06/30 01:32:43 bobgian Exp $
+// $Id: setgetmachine.cpp,v 1.96 2018/01/03 21:33:04 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <string>
diff --git a/src/ui_interface/setgetmachine.h b/src/ui_interface/setgetmachine.h
index d6c151f..54162df 100644
--- a/src/ui_interface/setgetmachine.h
+++ b/src/ui_interface/setgetmachine.h
@@ -1,13 +1,25 @@
-// $Id: setgetmachine.h,v 1.30 2012/06/30 01:32:43 bobgian Exp $
+// $Id: setgetmachine.h,v 1.31 2018/01/03 21:33:04 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef SETGETMACHINE_H
#define SETGETMACHINE_H
diff --git a/src/ui_interface/traitmodel_interface.cpp b/src/ui_interface/traitmodel_interface.cpp
index 16d45b7..dd11c0b 100644
--- a/src/ui_interface/traitmodel_interface.cpp
+++ b/src/ui_interface/traitmodel_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: traitmodel_interface.cpp,v 1.7 2011/03/07 06:08:53 bobgian Exp $
+// $Id: traitmodel_interface.cpp,v 1.8 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_interface/traitmodel_interface.h b/src/ui_interface/traitmodel_interface.h
index 16f1c95..1ebfee5 100644
--- a/src/ui_interface/traitmodel_interface.h
+++ b/src/ui_interface/traitmodel_interface.h
@@ -1,13 +1,24 @@
-// $Id: traitmodel_interface.h,v 1.5 2011/03/07 06:08:53 bobgian Exp $
+// $Id: traitmodel_interface.h,v 1.6 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef TRAITMODEL_INTERFACE_H
#define TRAITMODEL_INTERFACE_H
diff --git a/src/ui_interface/ui_constants.cpp b/src/ui_interface/ui_constants.cpp
index b2439b4..39c76f7 100644
--- a/src/ui_interface/ui_constants.cpp
+++ b/src/ui_interface/ui_constants.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_constants.cpp,v 1.9 2010/03/02 23:12:31 bobgian Exp $
+// $Id: ui_constants.cpp,v 1.10 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include "ui_constants.h"
diff --git a/src/ui_interface/ui_constants.h b/src/ui_interface/ui_constants.h
index c8eb456..906c9dc 100644
--- a/src/ui_interface/ui_constants.h
+++ b/src/ui_interface/ui_constants.h
@@ -1,13 +1,24 @@
-// $Id: ui_constants.h,v 1.12 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_constants.h,v 1.13 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_CONSTANTS_H
#define UI_CONSTANTS_H
diff --git a/src/ui_interface/ui_id.cpp b/src/ui_interface/ui_id.cpp
index 720a815..7a5ce82 100644
--- a/src/ui_interface/ui_id.cpp
+++ b/src/ui_interface/ui_id.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_id.cpp,v 1.11 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_id.cpp,v 1.12 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_interface/ui_id.h b/src/ui_interface/ui_id.h
index 15c6c97..025d9ab 100644
--- a/src/ui_interface/ui_id.h
+++ b/src/ui_interface/ui_id.h
@@ -1,13 +1,24 @@
-// $Id: ui_id.h,v 1.9 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_id.h,v 1.10 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UIID_H
#define UIID_H
diff --git a/src/ui_interface/ui_interface.cpp b/src/ui_interface/ui_interface.cpp
index dcc6927..3d94bbd 100644
--- a/src/ui_interface/ui_interface.cpp
+++ b/src/ui_interface/ui_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_interface.cpp,v 1.51 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_interface.cpp,v 1.52 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <string>
#include <fstream>
diff --git a/src/ui_interface/ui_interface.h b/src/ui_interface/ui_interface.h
index 88db694..b8e23ff 100644
--- a/src/ui_interface/ui_interface.h
+++ b/src/ui_interface/ui_interface.h
@@ -1,13 +1,24 @@
-// $Id: ui_interface.h,v 1.43 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_interface.h,v 1.44 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_INTERFACE_H
#define UI_INTERFACE_H
diff --git a/src/ui_interface/ui_regid.cpp b/src/ui_interface/ui_regid.cpp
index deda3ae..0ce4318 100644
--- a/src/ui_interface/ui_regid.cpp
+++ b/src/ui_interface/ui_regid.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_regid.cpp,v 1.7 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_regid.cpp,v 1.8 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_interface/ui_regid.h b/src/ui_interface/ui_regid.h
index 35481f3..7a21edb 100644
--- a/src/ui_interface/ui_regid.h
+++ b/src/ui_interface/ui_regid.h
@@ -1,13 +1,24 @@
-// $Id: ui_regid.h,v 1.5 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_regid.h,v 1.6 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
//This is not much more than a struct right now, but has some complexity in
// the constructors. If you give it a region, locus, and the UIVars, it uses
diff --git a/src/ui_interface/ui_strings.cpp b/src/ui_interface/ui_strings.cpp
index 38968c0..edefc65 100644
--- a/src/ui_interface/ui_strings.cpp
+++ b/src/ui_interface/ui_strings.cpp
@@ -1,13 +1,25 @@
-// $Id: ui_strings.cpp,v 1.103 2012/06/30 01:32:43 bobgian Exp $
+// $Id: ui_strings.cpp,v 1.104 2018/01/03 21:33:05 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <string>
#include "local_build.h"
diff --git a/src/ui_interface/ui_strings.h b/src/ui_interface/ui_strings.h
index d418336..07837d7 100644
--- a/src/ui_interface/ui_strings.h
+++ b/src/ui_interface/ui_strings.h
@@ -1,13 +1,24 @@
-// $Id: ui_strings.h,v 1.89 2012/03/23 20:33:37 ewalkup Exp $
+// $Id: ui_strings.h,v 1.90 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_STRINGS_H
#define UI_STRINGS_H
diff --git a/src/ui_interface/ui_warnings.cpp b/src/ui_interface/ui_warnings.cpp
index 2ebd15f..c824756 100644
--- a/src/ui_interface/ui_warnings.cpp
+++ b/src/ui_interface/ui_warnings.cpp
@@ -1,13 +1,25 @@
-// $Id: ui_warnings.cpp,v 1.4 2012/06/30 01:32:43 bobgian Exp $
+// $Id: ui_warnings.cpp,v 1.5 2018/01/03 21:33:05 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <string>
#include "ui_warnings.h"
diff --git a/src/ui_interface/ui_warnings.h b/src/ui_interface/ui_warnings.h
index 648689c..c2bbb45 100644
--- a/src/ui_interface/ui_warnings.h
+++ b/src/ui_interface/ui_warnings.h
@@ -1,13 +1,24 @@
-// $Id: ui_warnings.h,v 1.3 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_warnings.h,v 1.4 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_WARNINGS_H
#define UI_WARNINGS_H
diff --git a/src/ui_interface/userparam_interface.cpp b/src/ui_interface/userparam_interface.cpp
index d2ab24e..dae7396 100644
--- a/src/ui_interface/userparam_interface.cpp
+++ b/src/ui_interface/userparam_interface.cpp
@@ -1,13 +1,24 @@
-// $Id: userparam_interface.cpp,v 1.35 2012/06/30 01:32:43 bobgian Exp $
+// $Id: userparam_interface.cpp,v 1.36 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <iostream>
diff --git a/src/ui_interface/userparam_interface.h b/src/ui_interface/userparam_interface.h
index 36e6a20..09a4999 100644
--- a/src/ui_interface/userparam_interface.h
+++ b/src/ui_interface/userparam_interface.h
@@ -1,13 +1,24 @@
-// $Id: userparam_interface.h,v 1.38 2012/06/30 01:32:43 bobgian Exp $
+// $Id: userparam_interface.h,v 1.39 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef USERPARAM_INTERFACE_H
#define USERPARAM_INTERFACE_H
diff --git a/src/ui_util/undoredochain.cpp b/src/ui_util/undoredochain.cpp
index b5f6331..ffb7006 100644
--- a/src/ui_util/undoredochain.cpp
+++ b/src/ui_util/undoredochain.cpp
@@ -1,13 +1,24 @@
-// $Id: undoredochain.cpp,v 1.25 2012/06/30 01:32:43 bobgian Exp $
+// $Id: undoredochain.cpp,v 1.26 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <stack>
#include <iostream>
diff --git a/src/ui_util/undoredochain.h b/src/ui_util/undoredochain.h
index 49ca4a8..3413cb4 100644
--- a/src/ui_util/undoredochain.h
+++ b/src/ui_util/undoredochain.h
@@ -1,13 +1,24 @@
-// $Id: undoredochain.h,v 1.19 2011/03/07 06:08:53 bobgian Exp $
+// $Id: undoredochain.h,v 1.20 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UNDOREDOCHAIN_H
#define UNDOREDOCHAIN_H
diff --git a/src/ui_vars/report_strings.cpp b/src/ui_vars/report_strings.cpp
index 5337b4d..5442bef 100644
--- a/src/ui_vars/report_strings.cpp
+++ b/src/ui_vars/report_strings.cpp
@@ -1,13 +1,25 @@
-// $Id: report_strings.cpp,v 1.7 2011/03/08 19:22:01 bobgian Exp $
+// $Id: report_strings.cpp,v 1.8 2018/01/03 21:33:05 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "report_strings.h"
using std::string;
diff --git a/src/ui_vars/report_strings.h b/src/ui_vars/report_strings.h
index 4056e75..ce6f636 100644
--- a/src/ui_vars/report_strings.h
+++ b/src/ui_vars/report_strings.h
@@ -1,13 +1,25 @@
-// $Id: report_strings.h,v 1.7 2011/03/08 19:22:01 bobgian Exp $
+// $Id: report_strings.h,v 1.8 2018/01/03 21:33:05 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef REPORT_STRINGS_H
#define REPORT_STRINGS_H
diff --git a/src/ui_vars/ui_vars.cpp b/src/ui_vars/ui_vars.cpp
index f9c7604..7f3d3df 100644
--- a/src/ui_vars/ui_vars.cpp
+++ b/src/ui_vars/ui_vars.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_vars.cpp,v 1.26 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_vars.cpp,v 1.27 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_vars/ui_vars.h b/src/ui_vars/ui_vars.h
index 3d0874e..61ddc01 100644
--- a/src/ui_vars/ui_vars.h
+++ b/src/ui_vars/ui_vars.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars.h,v 1.15 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_vars.h,v 1.16 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_VARS_H
#define UI_VARS_H
diff --git a/src/ui_vars/ui_vars_chainparams.cpp b/src/ui_vars/ui_vars_chainparams.cpp
index 6add31c..6872eef 100644
--- a/src/ui_vars/ui_vars_chainparams.cpp
+++ b/src/ui_vars/ui_vars_chainparams.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_vars_chainparams.cpp,v 1.39 2012/05/15 06:21:48 ewalkup Exp $
+// $Id: ui_vars_chainparams.cpp,v 1.40 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_vars/ui_vars_chainparams.h b/src/ui_vars/ui_vars_chainparams.h
index ea9d7e2..689c748 100644
--- a/src/ui_vars/ui_vars_chainparams.h
+++ b/src/ui_vars/ui_vars_chainparams.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars_chainparams.h,v 1.17 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_vars_chainparams.h,v 1.18 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_VARS_CHAINPARAMS_H
#define UI_VARS_CHAINPARAMS_H
diff --git a/src/ui_vars/ui_vars_component.cpp b/src/ui_vars/ui_vars_component.cpp
index 000c5d7..3fcde7a 100644
--- a/src/ui_vars/ui_vars_component.cpp
+++ b/src/ui_vars/ui_vars_component.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_vars_component.cpp,v 1.5 2010/03/02 23:12:32 bobgian Exp $
+// $Id: ui_vars_component.cpp,v 1.6 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <cstddef> // for NULL
diff --git a/src/ui_vars/ui_vars_component.h b/src/ui_vars/ui_vars_component.h
index cfd15f8..2c5cb39 100644
--- a/src/ui_vars/ui_vars_component.h
+++ b/src/ui_vars/ui_vars_component.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars_component.h,v 1.8 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_vars_component.h,v 1.9 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_VARS_COMPONENT_H
#define UI_VARS_COMPONENT_H
diff --git a/src/ui_vars/ui_vars_datamodel.cpp b/src/ui_vars/ui_vars_datamodel.cpp
index 68c3bd6..624209e 100644
--- a/src/ui_vars/ui_vars_datamodel.cpp
+++ b/src/ui_vars/ui_vars_datamodel.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_vars_datamodel.cpp,v 1.41 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_vars_datamodel.cpp,v 1.42 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_vars/ui_vars_datamodel.h b/src/ui_vars/ui_vars_datamodel.h
index 8a74085..764f12d 100644
--- a/src/ui_vars/ui_vars_datamodel.h
+++ b/src/ui_vars/ui_vars_datamodel.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars_datamodel.h,v 1.24 2011/03/07 06:08:53 bobgian Exp $
+// $Id: ui_vars_datamodel.h,v 1.25 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_VARS_DATAMODEL_H
#define UI_VARS_DATAMODEL_H
diff --git a/src/ui_vars/ui_vars_datapackplus.cpp b/src/ui_vars/ui_vars_datapackplus.cpp
index 578177e..ce93bac 100644
--- a/src/ui_vars/ui_vars_datapackplus.cpp
+++ b/src/ui_vars/ui_vars_datapackplus.cpp
@@ -1,13 +1,25 @@
-// $Id: ui_vars_datapackplus.cpp,v 1.36 2013/11/08 21:46:22 mkkuhner Exp $
+// $Id: ui_vars_datapackplus.cpp,v 1.37 2018/01/03 21:33:05 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <set>
diff --git a/src/ui_vars/ui_vars_datapackplus.h b/src/ui_vars/ui_vars_datapackplus.h
index f16782b..ba18016 100644
--- a/src/ui_vars/ui_vars_datapackplus.h
+++ b/src/ui_vars/ui_vars_datapackplus.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars_datapackplus.h,v 1.23 2012/06/30 01:32:43 bobgian Exp $
+// $Id: ui_vars_datapackplus.h,v 1.24 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_VARS_DATAPACK_PLUS_H
#define UI_VARS_DATAPACK_PLUS_H
diff --git a/src/ui_vars/ui_vars_forces.cpp b/src/ui_vars/ui_vars_forces.cpp
index 23923ee..52fb91a 100644
--- a/src/ui_vars/ui_vars_forces.cpp
+++ b/src/ui_vars/ui_vars_forces.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_vars_forces.cpp,v 1.94 2013/11/08 21:46:22 mkkuhner Exp $
+// $Id: ui_vars_forces.cpp,v 1.95 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <algorithm>
diff --git a/src/ui_vars/ui_vars_forces.h b/src/ui_vars/ui_vars_forces.h
index 6e509a8..ed39c66 100644
--- a/src/ui_vars/ui_vars_forces.h
+++ b/src/ui_vars/ui_vars_forces.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars_forces.h,v 1.56 2013/10/25 17:00:53 mkkuhner Exp $
+// $Id: ui_vars_forces.h,v 1.57 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
// This file contains two classes (one with subclasses) which are derived from UIVarsComponent.
// UIVarsSingleForce represents one force; it has a subtype UIVars2DForce for forces whose
diff --git a/src/ui_vars/ui_vars_prior.cpp b/src/ui_vars/ui_vars_prior.cpp
index 8882208..c74ce89 100644
--- a/src/ui_vars/ui_vars_prior.cpp
+++ b/src/ui_vars/ui_vars_prior.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_vars_prior.cpp,v 1.16 2012/06/30 01:32:43 bobgian Exp $
+// $Id: ui_vars_prior.cpp,v 1.17 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_vars/ui_vars_prior.h b/src/ui_vars/ui_vars_prior.h
index bce5362..850c610 100644
--- a/src/ui_vars/ui_vars_prior.h
+++ b/src/ui_vars/ui_vars_prior.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars_prior.h,v 1.9 2012/06/30 01:32:43 bobgian Exp $
+// $Id: ui_vars_prior.h,v 1.10 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_VARS_PRIOR_H
#define UI_VARS_PRIOR_H
diff --git a/src/ui_vars/ui_vars_traitmodels.cpp b/src/ui_vars/ui_vars_traitmodels.cpp
index 4f6ed5e..8eee672 100644
--- a/src/ui_vars/ui_vars_traitmodels.cpp
+++ b/src/ui_vars/ui_vars_traitmodels.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_vars_traitmodels.cpp,v 1.18 2012/06/30 01:32:43 bobgian Exp $
+// $Id: ui_vars_traitmodels.cpp,v 1.19 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
diff --git a/src/ui_vars/ui_vars_traitmodels.h b/src/ui_vars/ui_vars_traitmodels.h
index 39ffa0c..6850c0b 100644
--- a/src/ui_vars/ui_vars_traitmodels.h
+++ b/src/ui_vars/ui_vars_traitmodels.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars_traitmodels.h,v 1.11 2012/06/30 01:32:43 bobgian Exp $
+// $Id: ui_vars_traitmodels.h,v 1.12 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_VARS_TRAITMODELS_H
#define UI_VARS_TRAITMODELS_H
diff --git a/src/ui_vars/ui_vars_userparams.cpp b/src/ui_vars/ui_vars_userparams.cpp
index d3c95ed..a61f659 100644
--- a/src/ui_vars/ui_vars_userparams.cpp
+++ b/src/ui_vars/ui_vars_userparams.cpp
@@ -1,13 +1,24 @@
-// $Id: ui_vars_userparams.cpp,v 1.36 2013/10/25 17:00:53 mkkuhner Exp $
+// $Id: ui_vars_userparams.cpp,v 1.37 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#include <cassert>
#include <fstream> //For summary file testing.
diff --git a/src/ui_vars/ui_vars_userparams.h b/src/ui_vars/ui_vars_userparams.h
index 4e4fd98..75c7c3b 100644
--- a/src/ui_vars/ui_vars_userparams.h
+++ b/src/ui_vars/ui_vars_userparams.h
@@ -1,13 +1,24 @@
-// $Id: ui_vars_userparams.h,v 1.24 2012/06/30 01:32:43 bobgian Exp $
+// $Id: ui_vars_userparams.h,v 1.25 2018/01/03 21:33:05 mkkuhner Exp $
/*
- * Copyright 2004 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
- *
- * This software is distributed free of charge for non-commercial use
- * and is copyrighted. Of course, we do not guarantee that the software
- * works, and are not responsible for any damage you may cause or have.
- *
- */
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
#ifndef UI_VARS_USERPARAMS_H
#define UI_VARS_USERPARAMS_H
diff --git a/src/xml/lamarc_input_schema.h b/src/xml/lamarc_input_schema.h
index 7f1ea59..5172938 100644
--- a/src/xml/lamarc_input_schema.h
+++ b/src/xml/lamarc_input_schema.h
@@ -1,13 +1,25 @@
-// $Id: lamarc_input_schema.h,v 1.19 2010/03/17 17:26:00 bobgian Exp $
+// $Id: lamarc_input_schema.h,v 1.20 2018/01/03 21:33:05 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// NOTE -- this file is no longer used by lamarc. It is kept in the
// cvs archive since it is a useful reference. -- ewalkup
diff --git a/src/xml/lamarcschema.cpp b/src/xml/lamarcschema.cpp
index 7124eaf..19df503 100644
--- a/src/xml/lamarcschema.cpp
+++ b/src/xml/lamarcschema.cpp
@@ -1,13 +1,25 @@
-// $Id: lamarcschema.cpp,v 1.37 2012/06/30 01:32:43 bobgian Exp $
+// $Id: lamarcschema.cpp,v 1.38 2018/01/03 21:33:05 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "local_build.h"
#include "parsetreeschema.h"
#include "xml_strings.h"
diff --git a/src/xml/parsetreeschema.cpp b/src/xml/parsetreeschema.cpp
index 06dcf59..67027b1 100644
--- a/src/xml/parsetreeschema.cpp
+++ b/src/xml/parsetreeschema.cpp
@@ -1,13 +1,25 @@
-// $Id: parsetreeschema.cpp,v 1.6 2011/03/08 19:22:01 bobgian Exp $
+// $Id: parsetreeschema.cpp,v 1.7 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <cassert>
#include <iostream>
diff --git a/src/xml/parsetreeschema.h b/src/xml/parsetreeschema.h
index 3a4e319..0c4fedc 100644
--- a/src/xml/parsetreeschema.h
+++ b/src/xml/parsetreeschema.h
@@ -1,13 +1,25 @@
-// $Id: parsetreeschema.h,v 1.5 2011/03/07 06:08:54 bobgian Exp $
+// $Id: parsetreeschema.h,v 1.6 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PARSETREESCHEMA_H
#define PARSETREESCHEMA_H
diff --git a/src/xml/parsetreetodata.cpp b/src/xml/parsetreetodata.cpp
index f03e4dc..1a01303 100644
--- a/src/xml/parsetreetodata.cpp
+++ b/src/xml/parsetreetodata.cpp
@@ -1,13 +1,25 @@
-// $Id: parsetreetodata.cpp,v 1.57 2013/11/08 21:46:22 mkkuhner Exp $
+// $Id: parsetreetodata.cpp,v 1.58 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include <boost/algorithm/string.hpp>
diff --git a/src/xml/parsetreetodata.h b/src/xml/parsetreetodata.h
index aed444e..cc0b9fa 100644
--- a/src/xml/parsetreetodata.h
+++ b/src/xml/parsetreetodata.h
@@ -1,13 +1,25 @@
-// $Id: parsetreetodata.h,v 1.19 2012/06/30 01:32:43 bobgian Exp $
+// $Id: parsetreetodata.h,v 1.20 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PARSETREETODATA_H
#define PARSETREETODATA_H
diff --git a/src/xml/parsetreetosettings.cpp b/src/xml/parsetreetosettings.cpp
index 996b10d..4cf3d89 100644
--- a/src/xml/parsetreetosettings.cpp
+++ b/src/xml/parsetreetosettings.cpp
@@ -1,13 +1,25 @@
-// $Id: parsetreetosettings.cpp,v 1.85 2013/06/03 17:23:13 jyamato Exp $
+// $Id: parsetreetosettings.cpp,v 1.86 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "local_build.h"
diff --git a/src/xml/parsetreetosettings.h b/src/xml/parsetreetosettings.h
index fb213f2..2cc999b 100644
--- a/src/xml/parsetreetosettings.h
+++ b/src/xml/parsetreetosettings.h
@@ -1,13 +1,25 @@
-// $Id: parsetreetosettings.h,v 1.17 2011/03/07 06:08:54 bobgian Exp $
+// $Id: parsetreetosettings.h,v 1.18 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PARSETREETOSETTINGS_H
#define PARSETREETOSETTINGS_H
diff --git a/src/xml/parsetreewalker.cpp b/src/xml/parsetreewalker.cpp
index 63909ea..bc87abf 100644
--- a/src/xml/parsetreewalker.cpp
+++ b/src/xml/parsetreewalker.cpp
@@ -1,13 +1,25 @@
-// $Id: parsetreewalker.cpp,v 1.11 2013/08/22 18:03:12 jmcgill Exp $
+// $Id: parsetreewalker.cpp,v 1.12 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include "menu_strings.h" // for menustr::emptyString
#include "parsetreewalker.h"
#include "stringx.h" // for StripLeadingSpaces and similar
diff --git a/src/xml/parsetreewalker.h b/src/xml/parsetreewalker.h
index eddeadc..cbc1d44 100644
--- a/src/xml/parsetreewalker.h
+++ b/src/xml/parsetreewalker.h
@@ -1,13 +1,25 @@
-// $Id: parsetreewalker.h,v 1.10 2013/08/22 18:03:12 jmcgill Exp $
+// $Id: parsetreewalker.h,v 1.11 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef PARSETREEWALKER_H
#define PARSETREEWALKER_H
diff --git a/src/xml/tixml_base.cpp b/src/xml/tixml_base.cpp
index 593111e..4170417 100644
--- a/src/xml/tixml_base.cpp
+++ b/src/xml/tixml_base.cpp
@@ -1,17 +1,30 @@
-// $Id: tixml_base.cpp,v 1.7 2011/03/08 19:22:01 bobgian Exp $
+// $Id: tixml_base.cpp,v 1.8 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include "errhandling.h"
#include "stringx.h"
#include "tinyxml.h"
#include "tixml_base.h"
+#include <climits>
const std::string tibasestr::EXTRA_TAG_0 = "incorrect xml: extra tag \"";
const std::string tibasestr::EXTRA_TAG_1 = "\".";
diff --git a/src/xml/tixml_base.h b/src/xml/tixml_base.h
index 428b9de..9e3aa6d 100644
--- a/src/xml/tixml_base.h
+++ b/src/xml/tixml_base.h
@@ -1,13 +1,25 @@
-// $Id: tixml_base.h,v 1.5 2012/06/30 01:32:43 bobgian Exp $
+// $Id: tixml_base.h,v 1.6 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#ifndef TIXML_BASE_H
#define TIXML_BASE_H
diff --git a/src/xml/toxml.cpp b/src/xml/toxml.cpp
index 7482314..7867d23 100644
--- a/src/xml/toxml.cpp
+++ b/src/xml/toxml.cpp
@@ -1,13 +1,25 @@
-// $Id: toxml.cpp,v 1.25 2012/06/30 01:32:43 bobgian Exp $
+// $Id: toxml.cpp,v 1.26 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "toxml.h"
diff --git a/src/xml/toxml.h b/src/xml/toxml.h
index 18f1c71..45ccb53 100644
--- a/src/xml/toxml.h
+++ b/src/xml/toxml.h
@@ -1,13 +1,25 @@
-// $Id: toxml.h,v 1.14 2012/06/30 01:32:43 bobgian Exp $
+// $Id: toxml.h,v 1.15 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
// PopulationXML is a helper class used by Region::MakePopXML() to create an
// XML infile for lamarc identical (in execution) to the one used to begin
// the program run. PopulationXML's chief job is to manage a container of
diff --git a/src/xml/xml.cpp b/src/xml/xml.cpp
index 7b01a35..446c67e 100644
--- a/src/xml/xml.cpp
+++ b/src/xml/xml.cpp
@@ -1,13 +1,25 @@
-// $Id: xml.cpp,v 1.124 2010/09/27 03:19:46 bobgian Exp $
+// $Id: xml.cpp,v 1.125 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#include <cassert>
#include "errhandling.h"
diff --git a/src/xml/xml.h b/src/xml/xml.h
index 25089c7..48e9594 100644
--- a/src/xml/xml.h
+++ b/src/xml/xml.h
@@ -1,13 +1,25 @@
-// $Id: xml.h,v 1.50 2011/03/07 06:08:54 bobgian Exp $
+// $Id: xml.h,v 1.51 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef XML_H
#define XML_H
diff --git a/src/xml/xml_strings.cpp b/src/xml/xml_strings.cpp
index 4b74257..2c13f66 100644
--- a/src/xml/xml_strings.cpp
+++ b/src/xml/xml_strings.cpp
@@ -1,13 +1,25 @@
-// $Id: xml_strings.cpp,v 1.74 2012/06/30 01:32:43 bobgian Exp $
+// $Id: xml_strings.cpp,v 1.75 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Mary Kuhner, Jon Yamato, and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Mary Kuhner, Jon Yamato, and Joseph Felsenstein */
+
+
#include <string>
#include "local_build.h" // for definition of LAMARC_NEW_FEATURE_RELATIVE_SAMPLING
diff --git a/src/xml/xml_strings.h b/src/xml/xml_strings.h
index a500165..7a27ddb 100644
--- a/src/xml/xml_strings.h
+++ b/src/xml/xml_strings.h
@@ -1,13 +1,25 @@
-// $Id: xml_strings.h,v 1.80 2012/06/30 01:32:43 bobgian Exp $
+// $Id: xml_strings.h,v 1.81 2018/01/03 21:33:06 mkkuhner Exp $
/*
- Copyright 2002 Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein
+Copyright 2002-2005 Mary K. Kuhner, Peter Beerli, and Joseph Felsenstein
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
- This software is distributed free of charge for non-commercial use
- and is copyrighted. Of course, we do not guarantee that the software
- works, and are not responsible for any damage you may cause or have.
*/
+/* Authors: Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein */
+
+
#ifndef XMLSTRINGS_H
#define XMLSTRINGS_H
diff --git a/tools/README b/tools/README
new file mode 100644
index 0000000..7dcafbb
--- /dev/null
+++ b/tools/README
@@ -0,0 +1,2 @@
+this is the place to put tools we might use to build lamarc, but might not
+want to distribute to our users.
diff --git a/tools/apache-forrest-0.7.tar.gz b/tools/apache-forrest-0.7.tar.gz
new file mode 100644
index 0000000..c990dff
Binary files /dev/null and b/tools/apache-forrest-0.7.tar.gz differ
diff --git a/website/apacheInput/skinconf.xml b/website/apacheInput/skinconf.xml
new file mode 100644
index 0000000..83090b7
--- /dev/null
+++ b/website/apacheInput/skinconf.xml
@@ -0,0 +1,446 @@
+<?xml version="1.0"?>
+<!--
+ Copyright 2002-2005 The Apache Software Foundation or its licensors,
+ as applicable.
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+
+<!--
+Skin configuration file. This file contains details of your project,
+which will be used to configure the chosen Forrest skin.
+-->
+
+<!DOCTYPE skinconfig PUBLIC "-//APACHE//DTD Skin Configuration V0.7-1//EN" "http://forrest.apache.org/dtd/skinconfig-v07-1.dtd">
+<skinconfig>
+ <!-- To enable lucene search add provider="lucene" (default is google).
+ Add box-location="alt" to move the search box to an alternate location
+ (if the skin supports it) and box-location="all" to show it in all
+ available locations on the page. Remove the <search> element to show
+ no search box. @domain will enable sitesearch for the specific domain with google.
+ In other words google will search the @domain for the query string.
+ -->
+ <search name="lamarc" domain="evolution.genetics.washington.edu/lamarc/" provider="google"/>
+
+ <!-- Disable the print link? If enabled, invalid HTML 4.0.1 -->
+ <disable-print-link>true</disable-print-link>
+ <!-- Disable the PDF link? -->
+ <disable-pdf-link>false</disable-pdf-link>
+ <!-- Disable the POD link? -->
+ <disable-pod-link>true</disable-pod-link>
+ <!-- Disable the Text link? FIXME: NOT YET IMPLEMENETED. -->
+ <disable-txt-link>true</disable-txt-link>
+ <!-- Disable the xml source link? -->
+ <!-- The xml source link makes it possible to access the xml rendition
+ of the source frim the html page, and to have it generated statically.
+ This can be used to enable other sites and services to reuse the
+ xml format for their uses. Keep this disabled if you don't want other
+ sites to easily reuse your pages.-->
+ <disable-xml-link>true</disable-xml-link>
+
+ <!-- Disable navigation icons on all external links? -->
+ <disable-external-link-image>true</disable-external-link-image>
+
+ <!-- Disable w3c compliance links?
+ Use e.g. align="center" to move the compliance links logos to
+ an alternate location default is left.
+ (if the skin supports it) -->
+ <disable-compliance-links>false</disable-compliance-links>
+
+ <!-- Render mailto: links unrecognisable by spam harvesters? -->
+ <obfuscate-mail-links>true</obfuscate-mail-links>
+ <obfuscate-mail-value>.at.</obfuscate-mail-value>
+
+ <!-- Disable the javascript facility to change the font size -->
+ <disable-font-script>true</disable-font-script>
+
+ <!-- mandatory project logo
+ default skin: renders it at the top -->
+ <project-name>Lamarc</project-name>
+ <project-description>Likelihood Analysis with Metropolis Algorithm using Random Coalescence</project-description>
+ <project-url>http://evolution.gs.washington.edu/lamarc/</project-url>
+ <project-logo>images/lamarc.gif</project-logo>
+ <!-- Alternative static image:
+ <project-logo>images/project-logo.gif</project-logo> -->
+
+ <!-- optional group logo
+ default skin: renders it at the top-left corner -->
+ <!--
+ <group-name>Felsenstein Lab</group-name>
+ <group-description>Felsenstein Lab Web Pages</group-description>
+ <group-url>http://evolution.gs.washington.edu/</group-url>
+ -->
+ <!--
+ <group-logo>images/group.png</group-logo>
+ -->
+ <!-- Alternative static image:
+ <group-logo>images/group-logo.gif</group-logo> -->
+
+ <!-- optional host logo (e.g. sourceforge logo)
+ default skin: renders it at the bottom-left corner -->
+ <host-url></host-url>
+ <host-logo></host-logo>
+
+ <!-- relative url of a favicon file, normally favicon.ico -->
+ <favicon-url></favicon-url>
+
+ <!-- The following are used to construct a copyright statement -->
+ <year>2006</year>
+ <vendor>Mary K. Kuhner, Peter Beerli, Joe Felsenstein, Eric Rynes, Lucian Smith, Elizabeth A. Walkup, and Jon Yamato.</vendor>
+ <!-- The optional copyright-link URL will be used as a link in the
+ copyright statement
+ <copyright-link>http://www.apache.org/licenses/</copyright-link>
+ -->
+
+ <!-- Some skins use this to form a 'breadcrumb trail' of links.
+ Use location="alt" to move the trail to an alternate location
+ (if the skin supports it).
+ Omit the location attribute to display the trail in the default location.
+ Use location="none" to not display the trail (if the skin supports it).
+ For some skins just set the attributes to blank.
+
+ NOTE: If a breadcrumb entry points at a local file the href must
+ be complete, that is it must point to the file itself, not to a
+ directory.
+ -->
+ <trail>
+ <link1 name="Genome Sciences @ UW" href="http://www.gs.washington.edu/"/>
+ <link2 name="Felsenstein Lab" href="http://evolution.gs.washington.edu/"/>
+ <link3 name="Lamarc Project" href="http://evolution.gs.washington.edu/lamarc/"/>
+ </trail>
+
+ <!-- Configure the TOC, i.e. the Table of Contents.
+ @max-depth
+ how many "section" levels need to be included in the
+ generated Table of Contents (TOC).
+ @min-sections
+ Minimum required to create a TOC.
+ @location ("page","menu","page,menu", "none")
+ Where to show the TOC.
+ -->
+ <toc max-depth="2" min-sections="1" location="page"/>
+
+ <!-- Heading types can be clean|underlined|boxed -->
+ <headings type="underlined"/>
+
+ <!-- The optional feedback element will be used to construct a
+ feedback link in the footer with the page pathname appended:
+ <a href="@href">{@to}</a>
+ -->
+ <feedback to="lamarc at gs.washington.edu"
+ href="mailto:lamarc at gs.washington.edu?subject=Feedback " >
+ Send feedback about the website to:
+ </feedback>
+
+ <!-- Optional message of the day (MOTD).
+ Note: This is only implemented in the pelt skin.
+ If the optional <motd> element is used, then messages will be appended
+ depending on the URI string pattern.
+ motd-option : Specifies a pattern to match and provides small text content.
+ motd-title : This text will be added in brackets after the <html><title>
+ motd-page : This text will be added in a panel on the face of the page,
+ with the "motd-page-url" being the hyperlink "More".
+ Values for the "location" attribute are:
+ page : on the face of the page, e.g. in the spare space of the toc
+ alt : at the bottom of the left-hand navigation panel
+ both : both
+ -->
+<!--
+ <motd>
+ <motd-option pattern="docs_0_80">
+ <motd-title>v0.8-dev</motd-title>
+ <motd-page location="both">
+ This is documentation for development version v0.8
+ </motd-page>
+ <motd-page-url>/versions/index.html</motd-page-url>
+ </motd-option>
+ <motd-option pattern="docs_0_70">
+ <motd-title>v0.7</motd-title>
+ <motd-page location="both">
+ This is documentation for current version v0.7
+ </motd-page>
+ <motd-page-url>/versions/index.html</motd-page-url>
+ </motd-option>
+ </motd>
+-->
+
+ <!--
+ extra-css - here you can define custom css-elements that are
+ A) overriding the fallback elements or
+ B) adding the css definition from new elements that you may have
+ used in your documentation.
+ -->
+ <extra-css>
+ <!--Example of reason B:
+ To define the css definition of a new element that you may have used
+ in the class attribute of a <p> node.
+ e.g. <p class="quote"/>
+ -->
+ p.quote {
+ margin-left: 2em;
+ padding: .5em;
+ background-color: #f0f0f0;
+ font-family: monospace;
+ }
+ <!--Example:
+ To override the colours of links only in the footer.
+ -->
+ #footer a { color: #0F3660; }
+ #footer a:visited { color: #009999; }
+ </extra-css>
+
+ <colors>
+ <!-- These values are used for the generated CSS files.
+ They essentially "override" the default colors defined in the chosen skin.
+ There are four duplicate "groups" of colors below, denoted by comments:
+ Color group: Forrest, Krysalis, Collabnet, and Lenya using Pelt.
+ They are provided for example only. To customize the colors of any skin,
+ uncomment one of these groups of color elements and change the values
+ of the particular color elements that you wish to change.
+ Note that by default, all color groups are commented-out which means that
+ the default colors provided by the skin are being used.
+ -->
+
+ <!-- Color group: Forrest: example colors similar to forrest.apache.org
+ Some of the element names are obscure, so comments are added to show how
+ the "pelt" skin uses them, other skins might use these elements in a different way.
+ Tip: temporarily change the value of an element to red (#ff0000) and see the effect.
+ pelt: breadtrail: the strip at the top of the page and the second strip under the tabs
+ pelt: header: top strip containing project and group logos
+ pelt: heading|subheading: section headings within the content
+ pelt: navstrip: the strip under the tabs which contains the published date
+ pelt: menu: the left-hand navigation panel
+ pelt: toolbox: the selected menu item
+ pelt: searchbox: the background of the searchbox
+ pelt: border: line border around selected menu item
+ pelt: body: any remaining parts, e.g. the bottom of the page
+ pelt: footer: the second from bottom strip containing credit logos and published date
+ pelt: feedback: the optional bottom strip containing feedback link
+ -->
+ <color name="navstrip" value="#4a6d8c" font="#ffffff" link="#0F3660" vlink="#0F3660" hlink="#000066"/>
+ <color name="toolbox" value="#4a6d8c"/>
+ <color name="border" value="#4a6d8c"/>
+<!--
+ <color name="breadtrail" value="#cedfef" font="#0F3660" link="#0F3660" vlink="#0F3660" hlink="#000066"/>
+ <color name="header" value="#294563"/>
+ <color name="tab-selected" value="#4a6d8c" link="#0F3660" vlink="#0F3660" hlink="#000066"/>
+ <color name="tab-unselected" value="#b5c7e7" link="#0F3660" vlink="#0F3660" hlink="#000066"/>
+ <color name="subtab-selected" value="#4a6d8c" link="#0F3660" vlink="#0F3660" hlink="#000066"/>
+ <color name="subtab-unselected" value="#4a6d8c" link="#0F3660" vlink="#0F3660" hlink="#000066"/>
+ <color name="heading" value="#294563"/>
+ <color name="subheading" value="#4a6d8c"/>
+ <color name="published" value="#4C6C8F" font="#FFFFFF"/>
+ <color name="feedback" value="#4C6C8F" font="#FFFFFF" align="center"/>
+ <color name="navstrip" value="#4a6d8c" font="#ffffff" link="#0F3660" vlink="#0F3660" hlink="#000066"/>
+ <color name="menu" value="#4a6d8c" font="#cedfef" link="#ffffff" vlink="#ffffff" hlink="#ffcf00"/>
+ <color name="toolbox" value="#4a6d8c"/>
+ <color name="border" value="#294563"/>
+ <color name="dialog" value="#4a6d8c"/>
+ <color name="searchbox" value="#4a6d8c" font="#000000"/>
+ <color name="body" value="#ffffff" link="#0F3660" vlink="#009999" hlink="#000066"/>
+ <color name="table" value="#7099C5"/>
+ <color name="table-cell" value="#f0f0ff"/>
+ <color name="highlight" value="#ffff00"/>
+ <color name="fixme" value="#cc6600"/>
+ <color name="note" value="#006699"/>
+ <color name="warning" value="#990000"/>
+ <color name="code" value="#CFDCED"/>
+ <color name="footer" value="#cedfef"/>
+-->
+
+ <!-- Color group: Krysalis -->
+<!--
+ <color name="header" value="#FFFFFF"/>
+
+ <color name="tab-selected" value="#a5b6c6" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="tab-unselected" value="#F7F7F7" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="subtab-selected" value="#a5b6c6" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="subtab-unselected" value="#a5b6c6" link="#000000" vlink="#000000" hlink="#000000"/>
+
+ <color name="heading" value="#a5b6c6"/>
+ <color name="subheading" value="#CFDCED"/>
+
+ <color name="navstrip" value="#CFDCED" font="#000000" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="toolbox" value="#a5b6c6"/>
+ <color name="border" value="#a5b6c6"/>
+
+ <color name="menu" value="#F7F7F7" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="dialog" value="#F7F7F7"/>
+
+ <color name="body" value="#ffffff" link="#0F3660" vlink="#009999" hlink="#000066"/>
+
+ <color name="table" value="#a5b6c6"/>
+ <color name="table-cell" value="#ffffff"/>
+ <color name="highlight" value="#ffff00"/>
+ <color name="fixme" value="#cc6600"/>
+ <color name="note" value="#006699"/>
+ <color name="warning" value="#990000"/>
+ <color name="code" value="#a5b6c6"/>
+
+ <color name="footer" value="#a5b6c6"/>
+-->
+
+ <!-- Color group: Collabnet -->
+<!--
+ <color name="header" value="#003366"/>
+
+ <color name="tab-selected" value="#dddddd" link="#555555" vlink="#555555" hlink="#555555"/>
+ <color name="tab-unselected" value="#999999" link="#ffffff" vlink="#ffffff" hlink="#ffffff"/>
+ <color name="subtab-selected" value="#cccccc" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="subtab-unselected" value="#cccccc" link="#555555" vlink="#555555" hlink="#555555"/>
+
+ <color name="heading" value="#003366"/>
+ <color name="subheading" value="#888888"/>
+
+ <color name="navstrip" value="#dddddd" font="#555555"/>
+ <color name="toolbox" value="#dddddd" font="#555555"/>
+ <color name="border" value="#999999"/>
+
+ <color name="menu" value="#ffffff"/>
+ <color name="dialog" value="#eeeeee"/>
+
+ <color name="body" value="#ffffff"/>
+
+ <color name="table" value="#ccc"/>
+ <color name="table-cell" value="#ffffff"/>
+ <color name="highlight" value="#ffff00"/>
+ <color name="fixme" value="#cc6600"/>
+ <color name="note" value="#006699"/>
+ <color name="warning" value="#990000"/>
+ <color name="code" value="#003366"/>
+
+ <color name="footer" value="#ffffff"/>
+-->
+ <!-- Color group: Lenya using pelt-->
+<!--
+
+ <color name="header" value="#ffffff"/>
+
+ <color name="tab-selected" value="#E5E4D9" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="tab-unselected" value="#F5F4E9" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="subtab-selected" value="#000000" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="subtab-unselected" value="#E5E4D9" link="#000000" vlink="#000000" hlink="#000000"/>
+
+ <color name="heading" value="#E5E4D9"/>
+ <color name="subheading" value="#000000"/>
+ <color name="published" value="#000000"/>
+ <color name="navstrip" value="#E5E4D9" font="#000000"/>
+ <color name="toolbox" value="#CFDCED" font="#000000"/>
+ <color name="border" value="#999999"/>
+
+ <color name="menu" value="#E5E4D9" font="#000000" link="#000000" vlink="#000000" hlink="#000000"/>
+ <color name="dialog" value="#CFDCED"/>
+ <color name="body" value="#ffffff" />
+
+ <color name="table" value="#ccc"/>
+ <color name="table-cell" value="#ffffff"/>
+ <color name="highlight" value="#ffff00"/>
+ <color name="fixme" value="#cc6600"/>
+ <color name="note" value="#006699"/>
+ <color name="warning" value="#990000"/>
+ <color name="code" value="#003366"/>
+
+ <color name="footer" value="#E5E4D9"/>
+-->
+ </colors>
+
+ <!-- Settings specific to PDF output. -->
+ <pdf>
+ <!--
+ Supported page sizes are a0, a1, a2, a3, a4, a5, executive,
+ folio, legal, ledger, letter, quarto, tabloid (default letter).
+ Supported page orientations are portrait, landscape (default
+ portrait).
+ Supported text alignments are left, right, justify (default left).
+ -->
+ <page size="letter" orientation="portrait" text-align="left"/>
+
+ <!--
+ Pattern of the page numbering in the footer - Default is "Page x".
+ first occurrence of '1' digit represents the current page number,
+ second occurrence of '1' digit represents the total page number,
+ anything else is considered as the static part of the numbering pattern.
+ Examples : x is the current page number, y the total page number.
+ <page-numbering-format>none</page-numbering-format> Do not displays the page numbering
+ <page-numbering-format>1</page-numbering-format> Displays "x"
+ <page-numbering-format>p1.</page-numbering-format> Displays "px."
+ <page-numbering-format>Page 1/1</page-numbering-format> Displays "Page x/y"
+ <page-numbering-format>(1-1)</page-numbering-format> Displays "(x-y)"
+ -->
+ <page-numbering-format>Page 1</page-numbering-format>
+
+ <!--
+ Margins can be specified for top, bottom, inner, and outer
+ edges. If double-sided="false", the inner edge is always left
+ and the outer is always right. If double-sided="true", the
+ inner edge will be left on odd pages, right on even pages,
+ the outer edge vice versa.
+ Specified below are the default settings.
+ -->
+ <margins double-sided="false">
+ <top>1in</top>
+ <bottom>1in</bottom>
+ <inner>1.25in</inner>
+ <outer>1in</outer>
+ </margins>
+
+ <!--
+ Print the URL text next to all links going outside the file
+ -->
+ <show-external-urls>true</show-external-urls>
+
+ <!--
+ Disable the copyright footer on each page of the PDF.
+ A footer is composed for each page. By default, a "credit" with role=pdf
+ will be used, as explained below. Otherwise a copyright statement
+ will be generated. This latter can be disabled.
+ -->
+ <disable-copyright-footer>false</disable-copyright-footer>
+ </pdf>
+
+ <!--
+ Credits are typically rendered as a set of small clickable
+ images in the page footer.
+
+ Use box-location="alt" to move the credits to an alternate location
+ (if the skin supports it).
+
+ For example, pelt skin:
+ - box-location="alt" will place the logo at the end of the
+ left-hand coloured menu panel.
+ - box-location="alt2" will place them underneath that panel
+ in the left-hand whitespace.
+ - Otherwise they are placed next to the compatibility icons
+ at the bottom of the screen.
+
+ Comment out the whole <credit>-element if you want no credits in the
+ web pages
+ -->
+ <credits>
+ <credit>
+ <name>Built with Apache Forrest</name>
+ <url>http://forrest.apache.org/</url>
+ <image>images/built-with-forrest-button.png</image>
+ <width>88</width>
+ <height>31</height>
+ </credit>
+ <!-- A credit with @role="pdf" will be used to compose a footer
+ for each page in the PDF, using either "name" or "url" or both.
+ -->
+ <credit role="pdf">
+ <name>Built with Apache Forrest</name>
+ <url>http://forrest.apache.org/</url>
+ </credit>
+ </credits>
+
+</skinconfig>
diff --git a/website/apacheInput/xdocs/documentation/index.xml b/website/apacheInput/xdocs/documentation/index.xml
new file mode 100644
index 0000000..72b0988
--- /dev/null
+++ b/website/apacheInput/xdocs/documentation/index.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE document PUBLIC "-//APACHE//DTD Documentation V2.0//EN" "http://forrest.apache.org/dtd/document-v20.dtd">
+<document>
+ <header>
+ <title>Documentation</title>
+ </header>
+ <body>
+ <section id="sectionid">
+ <title>A Section</title>
+ <p>
+ EWFIX
+ </p>
+ </section>
+ </body>
+</document>
diff --git a/website/apacheInput/xdocs/download/index.xml b/website/apacheInput/xdocs/download/index.xml
new file mode 100644
index 0000000..763a669
--- /dev/null
+++ b/website/apacheInput/xdocs/download/index.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE document PUBLIC "-//APACHE//DTD Documentation V2.0//EN" "http://forrest.apache.org/dtd/document-v20.dtd">
+<document>
+ <header>
+ <title>Download</title>
+ </header>
+ <body>
+ <section id="sectionid2">
+ <title>A Section</title>
+ <p>
+ EWFIX
+ </p>
+ </section>
+ </body>
+</document>
diff --git a/website/apacheInput/xdocs/images/icon.png b/website/apacheInput/xdocs/images/icon.png
new file mode 100644
index 0000000..3be8bbb
Binary files /dev/null and b/website/apacheInput/xdocs/images/icon.png differ
diff --git a/website/apacheInput/xdocs/images/lamarc.gif b/website/apacheInput/xdocs/images/lamarc.gif
new file mode 100644
index 0000000..8e6f0e9
Binary files /dev/null and b/website/apacheInput/xdocs/images/lamarc.gif differ
diff --git a/website/apacheInput/xdocs/index.xml b/website/apacheInput/xdocs/index.xml
new file mode 100644
index 0000000..4110333
--- /dev/null
+++ b/website/apacheInput/xdocs/index.xml
@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Copyright 2002-2004 The Apache Software Foundation or its licensors,
+ as applicable.
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+<!DOCTYPE document PUBLIC "-//APACHE//DTD Documentation V2.0//EN" "http://forrest.apache.org/dtd/document-v20.dtd">
+<document>
+ <header>
+ <title>Welcome to Lamarc</title>
+ </header>
+ <body>
+ <section id="about">
+ <title>About Lamarc</title>
+ <p>
+ </p>
+ </section>
+
+ <section id="news">
+ <title>Lamarc News</title>
+ <p>
+ </p>
+ </section>
+
+ <section id="contact">
+ <title>Contacting Lamarc Personnel</title>
+ <p>
+ </p>
+ </section>
+
+ <section id="team">
+ <title>The Lamarc Team</title>
+ <p>
+ </p>
+ </section>
+
+ <section id="credits">
+ <title>Our Thanks To...</title>
+ <p>
+ </p>
+ </section>
+
+ </body>
+</document>
diff --git a/website/apacheInput/xdocs/more/index.xml b/website/apacheInput/xdocs/more/index.xml
new file mode 100644
index 0000000..4cf9cc1
--- /dev/null
+++ b/website/apacheInput/xdocs/more/index.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE document PUBLIC "-//APACHE//DTD Documentation V2.0//EN" "http://forrest.apache.org/dtd/document-v20.dtd">
+<document>
+ <header>
+ <title>Additional Resources</title>
+ </header>
+ <body>
+ <section id="other-webs">
+ <title>Useful Websites</title>
+ <p>
+ <a href="http://www.csit.fsu.edu/~beerli/">Peter Beerli</a>
+ maintains a
+ <a href="http://www.csit.fsu.edu/~beerli/popgensoftware/">
+ list of programs</a>
+ which infer population parameters using the coalescent.
+ </p>
+ </section>
+ <section id="contact">
+ <title>Contact the Lamarc Team</title>
+ <p>You can contact the lamarc team at
+ <a href="mailto:lamarc at gs.washington.edu">
+ lamarc at gs.washington.edu</a>
+ </p>
+ </section>
+ </body>
+</document>
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diff --git a/website/apacheInput/xdocs/publications/evolution2000-pb-mkk.pdf b/website/apacheInput/xdocs/publications/evolution2000-pb-mkk.pdf
new file mode 100644
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diff --git a/website/apacheInput/xdocs/publications/fluctuate1.1.pdf b/website/apacheInput/xdocs/publications/fluctuate1.1.pdf
new file mode 100644
index 0000000..3677d7b
Binary files /dev/null and b/website/apacheInput/xdocs/publications/fluctuate1.1.pdf differ
diff --git a/website/apacheInput/xdocs/publications/g_explain.pdf b/website/apacheInput/xdocs/publications/g_explain.pdf
new file mode 100644
index 0000000..6c428d9
Binary files /dev/null and b/website/apacheInput/xdocs/publications/g_explain.pdf differ
diff --git a/website/apacheInput/xdocs/publications/genetics763.pdf b/website/apacheInput/xdocs/publications/genetics763.pdf
new file mode 100644
index 0000000..336fa55
Binary files /dev/null and b/website/apacheInput/xdocs/publications/genetics763.pdf differ
diff --git a/website/apacheInput/xdocs/publications/index.xml b/website/apacheInput/xdocs/publications/index.xml
new file mode 100644
index 0000000..dea105f
--- /dev/null
+++ b/website/apacheInput/xdocs/publications/index.xml
@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE document PUBLIC "-//APACHE//DTD Documentation V2.0//EN" "http://forrest.apache.org/dtd/document-v20.dtd">
+<document>
+ <header>
+ <title>Publications</title>
+ </header>
+ <body>
+ <section id="articles">
+ <title>Scholarly Articles</title>
+ <ul>
+ <li>
+ <p><a href="./metro-hastings.pdf">Estimating effective
+ population size and mutation rate from sequence data
+ using Metropolis-Hastings sampling</a> appeared
+ in EWFIX genetics 1995
+ </p>
+ <p>
+ EWFIX -- description
+ </p>
+ </li>
+ <li><a href="./fluctuate1.1.pdf">EWFIX -- fluctuate </a></li>
+ <li>
+ <p><a href="./fluctuate1.1.pdf">Maximum likelihood
+ estimation of population growth rates based on
+ the coalescent</a> appeared
+ in EWFIX genetics 1998
+ </p>
+ <p>
+ EWFIX -- description
+ </p>
+ </li>
+ <li>
+ <p><a href="./genetics763.pdf">Maximum-Likelihood
+ Estimation of Migration Rates and Effective Population
+ Numbers in Two Populations Using a Coalescent Approach</a>
+ appeared in EWFIX
+ </p>
+ <p>
+ EWFIX -- description
+ </p>
+ </li>
+ <li>
+ <p><a href="./beerli-felsenstein-2001.pdf">Maximum likelihood
+ estimation of a migration matrix and effective population
+ sizes in n subpopulations by using a coalescent approach</a>
+ appeared in EWFIX
+ </p>
+ <p>
+ EWFIX -- description
+ </p>
+ </li>
+ </ul>
+ </section>
+ <section id="posters">
+ <title>Posters</title>
+ <ul>
+ <li>
+ <p>Poster entitled <a href="./evolution2000-pb-mkk.pdf">Hard and Easy Data Sets
+ for Coalescent Likelihood Methods</a>, presented at the Evolution
+ 2000 meeting in Bloomington, Indiana.
+ </p>
+ <p>
+ EWFIX -- description
+ </p>
+ </li>
+ </ul>
+ </section>
+ <section id="whitepapers">
+ <title>White Papers</title>
+ <ul>
+ <li><a href="./g_explain.pdf">EWFIX -- growth -- broken</a></li>
+ </ul>
+ </section>
+ </body>
+</document>
diff --git a/website/apacheInput/xdocs/publications/metro-hastings.pdf b/website/apacheInput/xdocs/publications/metro-hastings.pdf
new file mode 100644
index 0000000..1e483d9
Binary files /dev/null and b/website/apacheInput/xdocs/publications/metro-hastings.pdf differ
diff --git a/website/apacheInput/xdocs/site.xml b/website/apacheInput/xdocs/site.xml
new file mode 100644
index 0000000..3d76325
--- /dev/null
+++ b/website/apacheInput/xdocs/site.xml
@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Copyright 2002-2004 The Apache Software Foundation or its licensors,
+ as applicable.
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+
+<!--
+Forrest site.xml
+
+This file contains an outline of the site's information content. It is used to:
+- Generate the website menus (though these can be overridden - see docs)
+- Provide semantic, location-independent aliases for internal 'site:' URIs, eg
+<link href="site:changes"> links to changes.html (or ../changes.html if in
+ subdir).
+- Provide aliases for external URLs in the external-refs section. Eg, <link
+ href="ext:cocoon"> links to http://cocoon.apache.org/
+
+See http://forrest.apache.org/docs/linking.html for more info
+-->
+
+<site label="Lamarc" href="" xmlns="http://apache.org/forrest/linkmap/1.0" tab="welcome">
+ <!-- Note: No matter what you configure here, Forrest will always try to load
+ index.html when you request http://yourHost/.
+ 'How can I use a start-up-page other than index.html?' in the FAQs has more
+ information tells you how to change that.
+ -->
+ <about label="About">
+ <index label="Index" href="index.html" description="Welcome to Lamarc"/>
+ </about>
+
+ <download label="Download" href="download/" tab="download">
+ <index label="Index" href="index.html" description="get Lamarc and related programs"/>
+ </download>
+
+ <documentation label="Documentation" href="documentation/" tab="documentation">
+ <index label="Index" href="index.html" description="scholarly papers on Lamarc and related programs"/>
+ </documentation>
+
+ <publications label="Publications" href="publications/" tab="publications">
+ <index label="Index" href="index.html" description="scholarly papers on Lamarc and related programs"/>
+ </publications>
+
+ <more label="Additional Resources" href="more/" tab="more">
+ <index label="Index" href="index.html" description="web sites and more"/>
+ </more>
+
+</site>
diff --git a/website/apacheInput/xdocs/tabs.xml b/website/apacheInput/xdocs/tabs.xml
new file mode 100644
index 0000000..480eb4d
--- /dev/null
+++ b/website/apacheInput/xdocs/tabs.xml
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Copyright 2002-2004 The Apache Software Foundation or its licensors,
+ as applicable.
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+<!DOCTYPE tabs PUBLIC "-//APACHE//DTD Cocoon Documentation Tab V1.1//EN" "http://forrest.apache.org/dtd/tab-cocoon-v11.dtd">
+
+<tabs software="Lamarc"
+ title="Lamarc"
+ copyright=""
+ xmlns:xlink="http://www.w3.org/1999/xlink">
+
+ <!-- The rules for tabs are:
+ @dir will always have '/@indexfile' added.
+ @indexfile gets appended to @dir if the tab is selected. Defaults to 'index.html'
+ @href is not modified unless it is root-relative and obviously specifies a
+ directory (ends in '/'), in which case /index.html will be added
+ If @id's are present, site.xml entries with a matching @tab will be in that tab.
+
+ Tabs can be embedded to a depth of two. The second level of tabs will only
+ be displayed when their parent tab is selected.
+ -->
+
+ <tab id="welcome" label="Welcome" dir="" />
+ <tab id="download" label="Download" dir="download"/>
+ <tab id="documentation" label="Documentation" dir="documentation"/>
+ <tab id="publications" label="Publications" dir="publications"/>
+ <tab id="more" label="Additional Resources" dir="more"/>
+
+</tabs>
--
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