[med-svn] [Git][med-team/libarb][master] 6 commits: Link SL/CB header files that are needed by ARBDB
Andreas Tille
gitlab at salsa.debian.org
Fri Jun 7 05:55:03 BST 2019
Andreas Tille pushed to branch master at Debian Med / libarb
Commits:
0b2f7f17 by Andreas Tille at 2019-06-07T04:45:10Z
Link SL/CB header files that are needed by ARBDB
- - - - -
2471c41e by Andreas Tille at 2019-06-07T04:52:31Z
ARBDB needs another header file (aw_awar_defs.hxx)
- - - - -
1557d956 by Andreas Tille at 2019-06-07T04:53:18Z
New upstream version 6.0.6
- - - - -
596ca4c8 by Andreas Tille at 2019-06-07T04:53:20Z
Update upstream source from tag 'upstream/6.0.6'
Update to upstream version '6.0.6'
with Debian dir 14d16f23df7e55b1d2b2a3df1e711375e8ad2ca5
- - - - -
a5c3b6f5 by Andreas Tille at 2019-06-07T04:54:32Z
Link header file
- - - - -
2812ff18 by Andreas Tille at 2019-06-07T04:54:42Z
ARBDB builds as well
- - - - -
7 changed files:
- Makefile
- PROBE_COM/Makefile
- SOURCE_TOOLS/build_info.pl
- SOURCE_TOOLS/generate_all_links.sh
- + WINDOW/aw_awar_defs.hxx
- debian/copyright
- debian/rules
Changes:
=====================================
Makefile
=====================================
@@ -705,7 +705,7 @@ ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
@echo '$(ARBHOME)/$@:1: has been generated.'
@echo 'Please edit $@ to configure your system!'
@echo --------------------------------------------------------------------------------
- @false
+ # @false
else
@echo '$(ARBHOME)/$<:1: is more recent than'
@echo '$(ARBHOME)/$@:1:'
@@ -805,7 +805,7 @@ check_TOOLS:
"$(LINK_SHARED_LIB)" \
-check_ENVIRONMENT : check_PATH check_TOOLS
+check_ENVIRONMENT :
@echo "-------------------- Environment [start]"
@echo "ARBHOME='$(ARBHOME)'"
@echo "PATH='$(PATH)'"
@@ -824,7 +824,7 @@ force_tab_check:
# ---------------------
-check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
+check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER
@echo Your setup seems to be ok.
checks: check_setup check_tabs
@@ -843,64 +843,16 @@ checks: check_setup check_tabs
# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in . at DD_links_non_perl
ARCHS = \
- $(ARCHS_PT_SERVER) \
- AISC/AISC.a \
- AISC_MKPTPS/AISC_MKPTPS.a \
ARBDB/libARBDB.a \
CORE/libCORE.a \
- ARB_GDE/ARB_GDE.a \
- AWT/libAWT.a \
- AWTC/AWTC.a \
- AWTI/AWTI.a \
- CONSENSUS_TREE/CONSENSUS_TREE.a \
- CONVERTALN/CONVERTALN.a \
- DBSERVER/DBSERVER.a \
- DIST/DIST.a \
- EDIT4/EDIT4.a \
- EISPACK/EISPACK.a \
- GDE/GDE.a \
- GENOM/GENOM.a \
- GENOM_IMPORT/GENOM_IMPORT.a \
- GL/GL.a \
- ISLAND_HOPPING/ISLAND_HOPPING.a \
- MERGE/MERGE.a \
- MULTI_PROBE/MULTI_PROBE.a \
- NALIGNER/NALIGNER.a \
- NAMES/NAMES.a \
- NAMES_COM/server.a \
- NTREE/NTREE.a \
- PARSIMONY/PARSIMONY.a \
- PERLTOOLS/PERLTOOLS.a \
- PHYLO/PHYLO.a \
- PRIMER_DESIGN/PRIMER_DESIGN.a \
PROBE_COM/server.a \
- PROBE_DESIGN/PROBE_DESIGN.a \
- PROBE_SET/PROBE_SET.a \
- READSEQ/READSEQ.a \
- RNA3D/RNA3D.a \
- RNACMA/RNACMA.a \
- SECEDIT/SECEDIT.a \
- SEQ_QUALITY/SEQ_QUALITY.a \
- SERVERCNTRL/SERVERCNTRL.a \
- SL/SL.a \
- STAT/STAT.a \
- TOOLS/TOOLS.a \
- TREEGEN/TREEGEN.a \
- UNIT_TESTER/UNIT_TESTER.a \
- WETC/WETC.a \
- WINDOW/libWINDOW.a \
- XML/XML.a \
# -----------------------
# library packets
ARCHS_CLIENT_PROBE = PROBE_COM/client.a PROBE_COM/common.a
-ARCHS_CLIENT_NAMES = NAMES_COM/client.a NAMES_COM/common.a
ARCHS_SERVER_PROBE = PROBE_COM/server.a $(ARCHS_CLIENT_PROBE)
-ARCHS_SERVER_NAMES = NAMES_COM/server.a $(ARCHS_CLIENT_NAMES)
-
-ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
# communication libs need aisc and aisc_mkpts:
@@ -1291,9 +1243,8 @@ WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
# Additional dependencies for subtargets:
PROBE_COM/PROBE_COM.dummy : comtools
-NAMES_COM/NAMES_COM.dummy : comtools
-com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
+com: PROBE_COM/PROBE_COM.dummy
PROBE_COM/server.dummy:
@echo Unwanted request to make target $<
@@ -1553,18 +1504,15 @@ genheaders: TEMPLATES/TEMPLATES.dummy
clrdotdepends:
-rm PROBE_COM/.depends
-rm NAMES_COM/.depends
- -rm PERL2ARB/.depends
comdepends: comtools clrdotdepends
@echo "$(SEP) Partially build com interface"
- $(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
- $(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
+ $(MAKE) PROBE_COM/PROBE_COM.depends # NAMES_COM/NAMES_COM.depends
+ $(MAKE) PROBE_COM/server.depends # NAMES_COM/server.depends
depends: genheaders comdepends
@echo "$(SEP) Updating other dependencies"
$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
- HELP_SOURCE/HELP_SOURCE.depends \
- SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
$(MAKE) libdepends
@@ -1652,8 +1600,8 @@ tags: $(TAG_SOURCE_LISTS)
LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
-links: checks $(LINKSTAMP) arbmainwrapper
-links_no_checks: $(LINKSTAMP) arbmainwrapper
+links: checks # $(LINKSTAMP) arbmainwrapper
+links_no_checks: # $(LINKSTAMP) arbmainwrapper
forcelinks:
-rm $(LINKSTAMP)
@@ -1676,7 +1624,7 @@ redo_links: clean_links
#********************************************************************************
header_libs:
- $(MAKE) -C HEADERLIBS all
+ echo "No headerlibs - just create libarb core" # $(MAKE) -C HEADERLIBS all
#********************************************************************************
@@ -1708,7 +1656,7 @@ endif
binlink:
- $(MAKE) -C bin $(BIN_TARGET)
+ echo "No binaries, build library only" # $(MAKE) -C bin $(BIN_TARGET)
preplib:
(cd lib;$(MAKE) all)
@@ -1728,7 +1676,7 @@ preplib:
ifeq ($(WITHPERL),1)
links_non_perl: PERLTOOLS/PERLTOOLS.dummy
perltools: links_non_perl
-perl: realperl
+perl:
else
links_non_perl: links
perl:
@@ -1744,27 +1692,14 @@ TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
endif
realperl: perltools
- (( \
- echo "$(SEP) Make PERL2ARB" ; \
- $(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
- "AUTODEPENDS=1" \
- "dflags=$(dflags)" \
- "cross_cflags=$(cross_cflags) $(cxxflags) $(dflags)" \
- "cross_lflags=$(cross_lflags)" \
- "COMPILER_VERSION=$(COMPILER_VERSION)" \
- all && \
- $(TEST_PERL_SCRIPTS) && \
- echo "$(SEP) Make PERL2ARB [done]" ; \
- ) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) || (cat PERL2ARB.log;rm PERL2ARB.log;false)
+ echo "PERL2ARB is not needed for libarb"
perl_clean:
- @$(MAKE) -C PERL2ARB -r -f Makefile.main \
- "AUTODEPENDS=0" \
- clean
+ echo "PERL2ARB is not needed for libarb thus nothing to clean"
PERL2ARB/PERL2ARB.clean:
- $(MAKE) perl_clean
- $(MAKE) -C PERL_SCRIPTS/test clean
+ # $(MAKE) perl_clean
+ # $(MAKE) -C PERL_SCRIPTS/test clean
# ---------------------------------------- bindings to script languages
@@ -1810,7 +1745,7 @@ rmbak:
-exec rm -v {} \;
bin_reinit:
- $(MAKE) bin/bin.clean
+ #$(MAKE) bin/bin.clean
$(MAKE) -C "bin" all
clean_directories:
@@ -1826,19 +1761,14 @@ objclean:
# bin.clean and HELP_SOURCE.clean interfere
clean3:
- $(MAKE) bin/bin.clean
- $(MAKE) HELP_SOURCE/HELP_SOURCE.clean
+ # $(MAKE) bin/bin.clean
+ # $(MAKE) HELP_SOURCE/HELP_SOURCE.clean
clean2: $(ARCHS:.a=.clean) \
clean3 \
rmbak \
libclean \
objclean \
- lib/lib.clean \
- GDEHELP/GDEHELP.clean \
- HEADERLIBS/HEADERLIBS.clean \
- SOURCE_TOOLS/SOURCE_TOOLS.clean \
- SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
UNIT_TESTER/UNIT_TESTER.clean \
TEMPLATES/TEMPLATES.clean \
perl_clean \
@@ -1847,7 +1777,7 @@ clean2: $(ARCHS:.a=.clean) \
rm -f *.last_gcc *.last_compiler config.makefile.bak
# links are needed for cleanup
-clean: redo_links motif_xpm_hack_clean
+clean: redo_links
$(MAKE) clean2
$(MAKE) clean_cov_all clean_links
@@ -1860,8 +1790,6 @@ reloc_clean: links
$(MAKE) \
perl_clean \
GDEHELP/GDEHELP.clean \
- HELP_SOURCE/genhelp/genhelp.clean \
- bin/bin.clean \
libclean \
objclean
@@ -1896,7 +1824,7 @@ perl4ever: clean
rebuild: clean
$(MAKE) all
-relink: bin/bin.clean libclean
+relink: libclean
$(MAKE) build
tarfile: rebuild
@@ -1979,10 +1907,10 @@ arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
arb_external: convert tools gde readseq tg pst xmlin
-arb_no_perl: arbapplications help arb_external
+arb_no_perl: arbapplications arb_external
-arb: motif_xpm_hack
- $(MAKE) "WITHPERL=1" perl arb_no_perl
+arb:
+ $(MAKE) "WITHPERL=1" perl # arb_no_perl
motif_xpm_hack:
$(MAKE) -r -C "lib/motifHack" all
@@ -2121,7 +2049,6 @@ UNITS_TESTED = \
SL/FAST_ALIGNER/FAST_ALIGNER.test \
SL/PRONUC/PRONUC.test \
WINDOW/libWINDOW.test \
- HELP_SOURCE/arb_help2xml.test \
CONVERTALN/CONVERTALN.test \
SL/SEQIO/SEQIO.test \
SL/PTCLEAN/PTCLEAN.test \
@@ -2312,7 +2239,7 @@ post_commit_check:
# --------------------------------------------------------------------------------
build: arb
- $(MAKE) binlink preplib compile_compatibility
+ $(MAKE) db core
all:
@echo "Build time" > $(TIMELOG)
=====================================
PROBE_COM/Makefile
=====================================
@@ -20,7 +20,11 @@ AISC_COMPILER=../AISC/aisc
AISC_PROTOTYPER=../AISC_MKPTPS/aisc_mkpt
AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER) $(AISC_PROTOTYPER)
+ifeq (,$(wildcard AISC/export2sub))
+include ../AISC_COM/AISC/export2sub
+else
include AISC/export2sub
+endif
$(MAIN): server.a
@@ -33,7 +37,7 @@ depends:
clean:
@rm -f .depends
- @$(MAKE) -r -f AISC/Makefile clean
+ #@$(MAKE) -r -f AISC/Makefile clean
# DO NOT DELETE
=====================================
SOURCE_TOOLS/build_info.pl
=====================================
@@ -275,36 +275,6 @@ my $in_SVN = (-d $ARBHOME.'/.svn');
# update revision info?
my ($revision,$is_tag,$branch) = (undef,undef,undef);
-if ($in_SVN) {
- # in SVN checkout -> update revision info
- $revision = getRevision();
- ($is_tag,$branch) = getBranchOrTag();
-
- # $branch = $RC_BRANCH; # @@@ fake
- # $branch = $STABLE_BRANCH; # @@@ fake
- # $branch = 'gtk_only'; # @@@ fake
- # ($is_tag,$branch) = (1, 'arb-5.20.1'); # @@@ fake
- # ($is_tag,$branch) = (1, 'arb-5.19'); # @@@ fake
- # ($is_tag,$branch) = (1, 'evalSomething'); # @@@ fake
- # ($is_tag,$branch) = (1, 'arb-5.20'); # @@@ fake
- # ($is_tag,$branch) = (1, 'arb-5.20-rc1'); # @@@ fake
- # ($is_tag,$branch) = (1, 'arb-5.20-rc2'); # @@@ fake
-
- my @svn_revision = (
- '#define ARB_SVN_REVISION "'.$revision.'"',
- '#define ARB_SVN_BRANCH "'.$branch.'"',
- '#define ARB_SVN_BRANCH_IS_TAG '.$is_tag,
- );
-
- update($svn_revision_h, at svn_revision);
-}
-else {
- if (not -f $svn_revision_h) {
- die "Missing file '$svn_revision_h'";
- }
- # use revision info as in source tarball
- ($revision,$is_tag,$branch) = getBranchOrTagFromHeader($svn_revision_h);
-}
my $date = `date '+%d.%b.%Y'`;
chomp($date);
@@ -395,46 +365,6 @@ my $short_version = undef;
my $always_show_revision = 1;
my $orgbranch = $branch; # real branch or branch estimated from tag
-if ($is_tag==1) {
- if ($branch =~ /^arb-[0-9]+\.[0-9]+/o) {
- if ($branch =~ /-rc[0-9]+$/o) { $orgbranch = $RC_BRANCH; }
- else { $orgbranch = $STABLE_BRANCH; }
- }
- else {
- $orgbranch = 'unknown';
- }
-}
-
-if ($orgbranch eq $STABLE_BRANCH or $orgbranch eq $RC_BRANCH) {
- $always_show_revision = 0;
- $svn_tag = 'arb-'.$version_info{MAJOR}.'.'.$version_info{MINOR};
- if ($orgbranch eq $RC_BRANCH) {
- $svn_tag .= '-rc'.$version_info{CANDIDATE};
- }
- else {
- if ($version_info{PATCHLEVEL} > 0) { $svn_tag .= '.'.$version_info{PATCHLEVEL}; }
- }
- $short_version = $svn_tag;
-
- if ($is_tag==1) {
- # check real SVN-tag vs generated SVN-tag
- if ($branch ne $svn_tag) {
- die "Version info and SVN-branch-tag mismatch:\n".
- "(version suggests svn-tag = '$svn_tag'\n".
- " real svn-tag = '$branch')";
- }
- }
- print "SVN_URL='$ENV{SVN_URL}'\n";
- print "SVN_REVISION='$ENV{SVN_REVISION}'\n";
-}
-elsif ($is_tag==1) {
- $short_version = 'arb-special-'.$branch; # use custom tag
-}
-else {
- $short_version = 'arb-devel';
- if ($branch ne 'trunk') { $short_version .= '-'.$branch; }
- $short_version .= '-'.$version_info{MAJOR}.'.'.$version_info{MINOR};
-}
defined $short_version || die "expected known short_version!";
defined $revision || die "expected known revision!";
=====================================
SOURCE_TOOLS/generate_all_links.sh
=====================================
@@ -1,7 +1,7 @@
#!/bin/bash
SELF=$ARBHOME/SOURCE_TOOLS/generate_all_links.sh
-READLINK=${ARBHOME}/SH/arb_readlink
+READLINK=readlink
finderr() {
@@ -126,7 +126,9 @@ makedir lib/help &&
(test -z $MOTIF_LIBPATH || symlink_file $MOTIF_LIBPATH lib/libXm.so.3) &&
# Links in bin directory
-( cd bin ; make all; cd .. ) &&
+if [ -d bin ] ; then
+ ( cd bin ; make all; cd .. ) &&
+fi
# ...COMS
@@ -146,64 +148,11 @@ symlink_maybe_no_target GENH/aisc.h PROBE_COM/PT_server.h &&
# TEMPLATES directory
-symlink_file ../TEMPLATES/arb_algo.h INCLUDE/arb_algo.h &&
-symlink_file ../TEMPLATES/arb_backtrace.h INCLUDE/arb_backtrace.h &&
-symlink_file ../TEMPLATES/arb_debug.h INCLUDE/arb_debug.h &&
-symlink_file ../TEMPLATES/arb_defs.h INCLUDE/arb_defs.h &&
-symlink_file ../TEMPLATES/arb_early_check.h INCLUDE/arb_early_check.h &&
-symlink_file ../TEMPLATES/arb_error.h INCLUDE/arb_error.h &&
-symlink_file ../TEMPLATES/arb_forward_list.h INCLUDE/arb_forward_list.h &&
-symlink_file ../TEMPLATES/arb_global_defs.h INCLUDE/arb_global_defs.h &&
-symlink_file ../TEMPLATES/arb_simple_assert.h INCLUDE/arb_simple_assert.h &&
-symlink_file ../TEMPLATES/arb_sleep.h INCLUDE/arb_sleep.h &&
-symlink_file ../TEMPLATES/arb_stdstr.h INCLUDE/arb_stdstr.h &&
-symlink_file ../TEMPLATES/arb_str.h INCLUDE/arb_str.h &&
-symlink_file ../TEMPLATES/arb_unit_test.h INCLUDE/arb_unit_test.h &&
-symlink_file ../TEMPLATES/arb_unordered_map.h INCLUDE/arb_unordered_map.h &&
-symlink_file ../TEMPLATES/arb_version.h INCLUDE/arb_version.h &&
-symlink_file ../TEMPLATES/arbtools.h INCLUDE/arbtools.h &&
-symlink_file ../TEMPLATES/attributes.h INCLUDE/attributes.h &&
-symlink_file ../TEMPLATES/bytestring.h INCLUDE/bytestring.h &&
-symlink_file ../TEMPLATES/cache.h INCLUDE/cache.h &&
-symlink_file ../TEMPLATES/ChecksumCollector.h INCLUDE/ChecksumCollector.h &&
-symlink_file ../TEMPLATES/command_output.h INCLUDE/command_output.h &&
-symlink_file ../TEMPLATES/config_parser.h INCLUDE/config_parser.h &&
-symlink_file ../TEMPLATES/cxxforward.h INCLUDE/cxxforward.h &&
-symlink_file ../TEMPLATES/downcast.h INCLUDE/downcast.h &&
-symlink_file ../TEMPLATES/dupstr.h INCLUDE/dupstr.h &&
-symlink_file ../TEMPLATES/gccver.h INCLUDE/gccver.h &&
-symlink_file ../TEMPLATES/malloc.h INCLUDE/malloc.h &&
-symlink_file ../TEMPLATES/mode_text.h INCLUDE/mode_text.h &&
-symlink_file ../TEMPLATES/output.h INCLUDE/output.h &&
-symlink_file ../TEMPLATES/perf_timer.h INCLUDE/perf_timer.h &&
-symlink_file ../TEMPLATES/SigHandler.h INCLUDE/SigHandler.h &&
-symlink_file ../TEMPLATES/smartptr.h INCLUDE/smartptr.h &&
-symlink_file ../TEMPLATES/static_assert.h INCLUDE/static_assert.h &&
-symlink_file ../TEMPLATES/SuppressOutput.h INCLUDE/SuppressOutput.h &&
-symlink_file ../TEMPLATES/ttypes.h INCLUDE/ttypes.h &&
-symlink_file ../TEMPLATES/ut_valgrinded.h INCLUDE/ut_valgrinded.h &&
-symlink_file ../TEMPLATES/valgrind.h INCLUDE/valgrind.h &&
-
-symlink_maybe_no_target ../TEMPLATES/arb_build.h INCLUDE/arb_build.h &&
-symlink_maybe_no_target ../TEMPLATES/svn_revision.h INCLUDE/svn_revision.h &&
-
# INCLUDE directory
-
-symlink_maybe_no_target ../NAMES_COM/names_client.h INCLUDE/names_client.h &&
-symlink_maybe_no_target ../NAMES_COM/names_prototypes.h INCLUDE/names_prototypes.h &&
-symlink_maybe_no_target ../NAMES_COM/names_server.h INCLUDE/names_server.h &&
-
symlink_maybe_no_target ../PROBE_COM/PT_com.h INCLUDE/PT_com.h &&
symlink_maybe_no_target ../PROBE_COM/PT_server.h INCLUDE/PT_server.h &&
symlink_maybe_no_target ../PROBE_COM/PT_server_prototypes.h INCLUDE/PT_server_prototypes.h &&
-symlink_file ../AISC_COM/C/aisc_func_types.h INCLUDE/aisc_func_types.h &&
-symlink_file ../AISC_COM/C/aisc_global.h INCLUDE/aisc_global.h &&
-symlink_file ../AISC_COM/C/client.h INCLUDE/client.h &&
-symlink_file ../AISC_COM/C/client_types.h INCLUDE/client_types.h &&
-symlink_file ../AISC_COM/C/client_privat.h INCLUDE/client_privat.h &&
-symlink_file ../AISC_COM/C/server.h INCLUDE/server.h &&
-symlink_file ../AISC_COM/C/struct_man.h INCLUDE/struct_man.h &&
symlink_file ../ARBDB/ad_cb.h INCLUDE/ad_cb.h &&
symlink_file ../ARBDB/ad_cb_prot.h INCLUDE/ad_cb_prot.h &&
symlink_file ../ARBDB/ad_config.h INCLUDE/ad_config.h &&
=====================================
WINDOW/aw_awar_defs.hxx
=====================================
@@ -0,0 +1,65 @@
+#ifndef AW_AWAR_DEFS_HXX
+#define AW_AWAR_DEFS_HXX
+
+#define AWAR_DB "tmp/nt/arbdb/"
+#define AWAR_DB_PATH AWAR_DB "file_name"
+#define AWAR_DB_TYPE AWAR_DB "type"
+#define AWAR_DB_FILTER AWAR_DB "filter"
+#define AWAR_DB_NAME AWAR_DB_PATH "_without_path" // awar is automatically updated when AWAR_DB_PATH changes
+
+#define AWAR_DEFAULT_ALIGNMENT "presets/use" // has to match ../ARBDB/arbdb.h at GB_DEFAULT_ALIGNMENT
+
+#define AWAR_TREE "focus/tree_name"
+#define AWAR_TREE_REFRESH "tmp/focus/tree_refresh" // touch this awar to refresh the tree display
+#define AWAR_CONFIGURATION "focus/configuration"
+
+#define AWAR_SECURITY_LEVEL "tmp/etc/security_level"
+
+#define AWAR_GDE_EXPORT_FILTER "tmp/gde/export_filter"
+#define AWAR_GDE_FILTER "tmp/gde/filter"
+
+#define AWAR_DB_COMMENT "description"
+
+#define AWAR_PT_SERVER "nt/pt_server"
+#define AWAR_TARGET_STRING "nt/target_string"
+#define AWAR_PRIMER_TARGET_STRING "nt/primer_target_string"
+#define AWAR_GENE_CONTENT "nt/gene_content"
+#define AWAR_MAX_MISMATCHES "nt/max_mismatches"
+#define AWAR_ITARGET_STRING "nt/itarget_string"
+#define AWAR_EXPERT "nt/expert"
+
+#define AWAR_SAI_COLOR_STR "tmp/sai_color_str" // to visualize SAIs in probe Match window
+
+// local awars for edit and edit4:
+
+#define AWAR_SPECIES_NAME_LOCAL "tmp/edit/species_name" // string: name of selected species
+#define AWAR_CURSOR_POSITION_LOCAL "tmp/edit/cursor_position" // int: position in sequence [0..N-1]
+#define AWAR_EDITOR_ALIGNMENT "tmp/edit/alignment" // string: alignment used by editor
+
+// global awars
+
+#define AWAR_CURSOR_POSITION "tmp/focus/cursor_position" // int: position in sequence range=[1;len]
+#define AWAR_SET_CURSOR_POSITION "tmp/focus/set_cursor_position" // int: set position in sequence (remote control for ARB_EDIT4) range=[0;len-1]
+
+#define AWAR_SPECIES_NAME "tmp/focus/species_name" // string: name of selected species
+#define AWAR_INFO_BUTTON_TEXT "tmp/focus/info_button_text" // string: to display selected species
+#define AWAR_ORGANISM_NAME "tmp/focus/organism_name" // string: name of selected organism (differs from AWAR_SPECIES_NAME only for pseudo-gene-species)
+/* - normally AWAR_ORGANISM_NAME contains the same value as AWAR_SPECIES_NAME
+ - if AWAR_SPECIES_NAME contains the name of a pseudo gene-species then AWAR_ORGANISM_NAME
+ contains the name of the species the pseudo gene-species originated from */
+// #define AWAR_EXPERIMENT_NAME "tmp/focus/experiment_name" // string : name of selected experiment
+#define AWAR_SAI_NAME "tmp/focus/sai_name" // string : name of selected SAI (e.g. in EDIT4 and 'Manage SAI')
+#define AWAR_SAI_GLOBAL "tmp/focus/sai_global" // string : name of selected SAI in EDIT4/Visualize SAI Tool - used in RNA3D Tool
+
+#define AWAR_HELIX_NAME "tmp/focus/helix_name" // string: name of selected helix, for helix numbers append _NR, get default by GBT_get_default_helix
+
+#define AWAR_ERROR_MESSAGES "tmp/message/displayed" // error-messages: display awar
+
+#define AWAR_FOOTER "tmp/LeftFooter" // mode line (showing help for selected mode)
+#define AWAR_FOOTER_MAX_LEN 100 // max allowed textlen for mode line
+
+#define AWAR_AWM_MASK "tmp/awm_mask"
+
+#else
+#error aw_awar_defs.hxx included twice
+#endif
=====================================
debian/copyright
=====================================
@@ -103,7 +103,30 @@ Files-Excluded: arbsrc*/AISC_COM/C
arbsrc*/UNIT_TESTER/reporter.pl
arbsrc*/UNIT_TESTER/sym2testcode.pl
arbsrc*/UNIT_TESTER/test_helpers.h
- arbsrc*/W*
+ arbsrc*/WETC
+ arbsrc*/WINDOW/AW_*
+ arbsrc*/WINDOW/Makefile
+ arbsrc*/WINDOW/aw_Xm.hxx
+ arbsrc*/WINDOW/aw_advice.hxx
+ arbsrc*/WINDOW/aw_at.hxx
+ arbsrc*/WINDOW/aw_awar.hxx
+ arbsrc*/WINDOW/aw_awars.hxx
+ arbsrc*/WINDOW/aw_b*
+ arbsrc*/WINDOW/aw_c*
+ arbsrc*/WINDOW/aw_d*
+ arbsrc*/WINDOW/aw_e*
+ arbsrc*/WINDOW/aw_f*
+ arbsrc*/WINDOW/aw_g*
+ arbsrc*/WINDOW/aw_k*
+ arbsrc*/WINDOW/aw_m*
+ arbsrc*/WINDOW/aw_n*
+ arbsrc*/WINDOW/aw_p*
+ arbsrc*/WINDOW/aw_q*
+ arbsrc*/WINDOW/aw_r*
+ arbsrc*/WINDOW/aw_s*
+ arbsrc*/WINDOW/aw_w*
+ arbsrc*/WINDOW/aw_x*
+ arbsrc*/WINDOW/needs_libs.libWINDOW_so
arbsrc*/X*
arbsrc*/bin
arbsrc*/doc
=====================================
debian/rules
=====================================
@@ -37,7 +37,7 @@ config.makefile: config.makefile.template
override_dh_auto_build:
ln -s TEMPLATES INCLUDE
- for header in CORE/*.h UNIT_TESTER/*.h ; do ln -s ../$${header} INCLUDE/`basename $${header}` ; done
+ for header in CORE/*.h UNIT_TESTER/*.h SL/CB/*.h WINDOW/*.hxx ; do ln -s ../$${header} INCLUDE/`basename $${header}` ; done
ln -s /usr/include/valgrind/valgrind.h INCLUDE/valgrind.h
ln -s ../AISC_COM/AISC PROBE_COM/AISC
mkdir bin
View it on GitLab: https://salsa.debian.org/med-team/libarb/compare/fc9ff293669e9be6caa269bd0700b3c1c765a86b...2812ff18aad03b6ca814cfdbdbdf4e79175668e0
--
View it on GitLab: https://salsa.debian.org/med-team/libarb/compare/fc9ff293669e9be6caa269bd0700b3c1c765a86b...2812ff18aad03b6ca814cfdbdbdf4e79175668e0
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