[med-svn] [lamarc] branch master updated (6607f83 -> e8734fd)
Andreas Tille
tille at debian.org
Thu Jan 4 20:52:58 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository lamarc.
from 6607f83 Remove duplicate from install targets
new fe57504 Fix install location of docs
new e045f73 Add upstream metadata
new ed688db hardening=+all
new 19f8279 Location of html doc
new 0f70698 New upstream version 2.1.10.1+dfsg
new dcf98f0 Update upstream source from tag 'upstream/2.1.10.1+dfsg'
new e8734fd New upstream version with clarified license
The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 +-
debian/changelog | 2 +-
debian/copyright | 16 +-
debian/patches/fix_install_target.patch | 48 +-
debian/patches/use_debian_packaged_boost.patch | 6 +-
debian/rules | 16 +-
debian/upstream/metadata | 22 +-
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 +-
src/conversion/Converter_SpacingDS.h | 25 +-
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 +-
src/conversion/IndividualDS.cpp | 25 +-
src/conversion/LamarcDS.cpp | 25 +-
src/conversion/MigrateConverter.cpp | 25 +-
src/conversion/ModelDS.cpp | 25 +-
src/conversion/ParserUtil.cpp | 25 +-
src/conversion/PhylipConverter.cpp | 25 +-
src/conversion/PopulationDS.cpp | 25 +-
src/conversion/RegionDS.cpp | 25 +-
src/conversion/Sequence.cpp | 25 +-
src/conversion/SpaceConverter.cpp | 25 +-
src/conversion/SpacingDS.cpp | 25 +-
src/conversion/UserFileUtil.cpp | 25 +-
src/conversion/XmlParserUtil.cpp | 25 +-
src/conversion/nomenuglobals.cpp | 22 +-
src/conversion/nomenuglobals.h | 22 +-
src/datalike/calculators.cpp | 28 +-
src/datalike/calculators.h | 22 +-
src/datalike/cellmanager.cpp | 22 +-
src/datalike/cellmanager.h | 22 +-
src/datalike/datapack.cpp | 22 +-
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src/datalike/datatype.cpp | 24 +-
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src/datalike/dlcalc.cpp | 26 +-
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src/datalike/dlcell.cpp | 24 +-
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src/datalike/dlmodel.cpp | 36 +-
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src/datalike/funcMax.cpp | 22 +-
src/datalike/funcMax.h | 22 +-
src/datalike/haplotypes.cpp | 22 +-
src/datalike/haplotypes.h | 22 +-
src/datalike/locus.cpp | 24 +-
src/datalike/locus.h | 22 +-
src/datalike/locuscell.cpp | 22 +-
src/datalike/locuscell.h | 22 +-
src/datalike/phenotypes.cpp | 22 +-
src/datalike/phenotypes.h | 22 +-
src/datalike/region.cpp | 22 +-
src/datalike/region.h | 22 +-
src/datalike/tipdata.cpp | 22 +-
src/datalike/tipdata.h | 22 +-
src/force/epoch.cpp | 22 +-
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src/force/event.cpp | 22 +-
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src/force/force.cpp | 54 +-
src/force/force.h | 26 +-
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src/force/forcesummary.cpp | 22 +-
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src/force/paramstat.cpp | 24 +-
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src/force/priorreport.cpp | 22 +-
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src/force/timemanager.cpp | 44 +-
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src/force/timesize.cpp | 22 +-
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src/guiconv/batchconverter.cpp | 22 +-
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src/guiconv/gc_assigntab.cpp | 22 +-
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src/guiconv/gc_data_display.cpp | 22 +-
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src/guiconv/gc_dialog.cpp | 22 +-
src/guiconv/gc_dialog.h | 22 +-
src/guiconv/gc_event_ids.h | 22 +-
src/guiconv/gc_event_publisher.cpp | 22 +-
src/guiconv/gc_event_publisher.h | 22 +-
src/guiconv/gc_export_dialogs.cpp | 22 +-
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src/guiconv/gc_file_dialogs.cpp | 22 +-
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src/guiconv/gc_file_list.cpp | 22 +-
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src/guiconv/gc_frame.cpp | 22 +-
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src/guiconv/gc_layout.cpp | 22 +-
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src/guiconv/gc_locitab.cpp | 22 +-
src/guiconv/gc_locitab.h | 22 +-
src/guiconv/gc_locus_dialogs.cpp | 22 +-
src/guiconv/gc_locus_dialogs.h | 22 +-
src/guiconv/gc_logic.cpp | 22 +-
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src/guiconv/gc_matrix_display.cpp | 22 +-
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src/guiconv/gc_menu_actors.cpp | 22 +-
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src/guiconv/gc_migration_dialogs.cpp | 28 +-
src/guiconv/gc_migration_dialogs.h | 24 +-
src/guiconv/gc_migtab.cpp | 22 +-
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src/guiconv/gc_panel_dialogs.cpp | 22 +-
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src/guiconv/gc_parent_dialogs.cpp | 22 +-
src/guiconv/gc_parent_dialogs.h | 22 +-
src/guiconv/gc_poptab.cpp | 22 +-
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src/guiconv/gc_population_dialogs.cpp | 22 +-
src/guiconv/gc_population_dialogs.h | 22 +-
src/guiconv/gc_quantum.cpp | 22 +-
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src/guiconv/gc_region_dialogs.cpp | 22 +-
src/guiconv/gc_region_dialogs.h | 22 +-
src/guiconv/gc_regiontab.cpp | 22 +-
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src/guiconv/gc_trait_dialogs.cpp | 22 +-
src/guiconv/gc_trait_dialogs.h | 22 +-
src/guiconv/gc_unit_dialogs.cpp | 22 +-
src/guiconv/gc_unit_dialogs.h | 22 +-
src/guiconv/guiconverter.cpp | 22 +-
src/guiconv/guiconverter.h | 22 +-
src/guiutil/gc_clickpanel.cpp | 22 +-
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src/guiutil/gc_gridpanel.cpp | 22 +-
src/guiutil/gc_gridpanel.h | 22 +-
src/guiutil/gc_text_ctrl.cpp | 22 +-
src/guiutil/gc_text_ctrl.h | 22 +-
src/guiutil/gc_validators.cpp | 22 +-
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src/lamarcmenus/coalmenus.cpp | 22 +-
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src/lamarcmenus/nomenufilereaddialog.cpp | 22 +-
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src/lamarcmenus/outfilemenus.cpp | 22 +-
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src/lamarcmenus/overviewmenus.cpp | 62 +-
src/lamarcmenus/overviewmenus.h | 22 +-
src/lamarcmenus/popsizemenu.cpp | 22 +-
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src/lamarcmenus/priormenus.cpp | 22 +-
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src/lamarcmenus/profilemenus.cpp | 22 +-
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src/lamarcmenus/recmenus.cpp | 22 +-
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src/lamarcmenus/regiongammamenus.cpp | 22 +-
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src/lamarcmenus/traitmodelmenu.cpp | 22 +-
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src/lamarcmenus/treesummenus.cpp | 22 +-
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src/menu/dialog.cpp | 22 +-
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src/menu/menu_strings.cpp | 27 +-
src/menu/menu_strings.h | 27 +-
src/menu/menudefs.h | 22 +-
src/menu/menuerror.h | 22 +-
src/menu/menuinteraction.cpp | 22 +-
src/menu/menuinteraction.h | 22 +-
src/menu/menuitem.cpp | 26 +-
src/menu/menuitem.h | 28 +-
src/menu/menutypedefs.h | 22 +-
src/menu/newmenu.cpp | 22 +-
src/menu/newmenu.h | 22 +-
src/menu/newmenuitems.cpp | 36 +-
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
.../apacheInput/xdocs}/images/lamarc.gif | Bin
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 +
668 files changed, 42032 insertions(+), 3918 deletions(-)
create mode 100644 CONTENTS
create mode 100644 COPYING
create mode 100644 HISTORY
create mode 100644 INSTALL
create mode 100644 MAINTAINER.README
create mode 100644 Makefile.in
create mode 100644 README
create mode 100644 aclocal.m4
copy config/{conf.h.in => conf.h} (67%)
create mode 100755 config/config.guess
create mode 100755 config/config.sub
create mode 100755 config/depcomp
create mode 100644 config/dynacounter.bash
create mode 100755 config/install-sh
create mode 100755 config/missing
create mode 100755 configure
create mode 100755 depcomp
create mode 100644 doc/pipeline.txt
create mode 100755 firstLinuxBuild.sh
create mode 100755 install-sh
create mode 100755 makedebug.sh
create mode 100755 makegcov.sh
create mode 100755 makeopt.sh
create mode 100755 missing
create mode 100644 projects/macos/MacOSPrefix.h
create mode 100644 projects/macos/MacOSPrefixDebug.h
create mode 100644 projects/macos/carb.r
create mode 100644 projects/macos/lam_conv make
create mode 100644 projects/macos/lamarc make
create mode 100755 projects/macos/make_mwerks.pl
create mode 100644 projects/macos/mwerks_xml_template
create mode 100644 projects/win32/README
create mode 100644 projects/win32/gui_lam_conv.vcproj
create mode 100644 projects/win32/lam_conv.vcproj
create mode 100644 projects/win32/lamarc.vcproj
create mode 100755 projects/win32/make_vcproj.pl
create mode 100644 projects/win32/vcproj_template
create mode 100755 scripts/buildDmg.sh
create mode 100644 scripts/pyParallel/README
create mode 100644 scripts/pyParallel/combine_regions.py
create mode 100644 scripts/pyParallel/combine_replicates.py
create mode 100644 scripts/pyParallel/divide_data.py
create mode 100644 scripts/pyParallel/parallelCommon.py
create mode 100644 scripts/xmingw32/binutils-2.15.91-20040904-1-src.tar.gz
create mode 100644 scripts/xmingw32/gcc-core-3.4.2-20040916-1-src.tar.gz
create mode 100644 scripts/xmingw32/gcc-g++-3.4.2-20040916-1-src.tar.gz
create mode 100644 scripts/xmingw32/gcc-g77-3.4.2-20040916-1-src.tar.gz
create mode 100644 scripts/xmingw32/mingw-runtime-3.7.tar.gz
create mode 100644 scripts/xmingw32/w32api-3.2.tar.gz
create mode 100644 scripts/xmingw32/xmingw32.bat.in
create mode 100644 scripts/xmingw32/xmingw32.mak
create mode 100644 scripts/xmingw32/xmingw32.sh.in
delete mode 100644 src/BUGS
create mode 100644 tools/README
create mode 100644 tools/apache-forrest-0.7.tar.gz
create mode 100644 website/apacheInput/skinconf.xml
create mode 100644 website/apacheInput/xdocs/documentation/index.xml
create mode 100644 website/apacheInput/xdocs/download/index.xml
create mode 100644 website/apacheInput/xdocs/images/icon.png
copy {doc/html => website/apacheInput/xdocs}/images/lamarc.gif (100%)
create mode 100644 website/apacheInput/xdocs/index.xml
create mode 100644 website/apacheInput/xdocs/more/index.xml
create mode 100644 website/apacheInput/xdocs/publications/beerli-felsenstein-2001.pdf
create mode 100644 website/apacheInput/xdocs/publications/evolution2000-pb-mkk.pdf
create mode 100644 website/apacheInput/xdocs/publications/fluctuate1.1.pdf
create mode 100644 website/apacheInput/xdocs/publications/g_explain.pdf
create mode 100644 website/apacheInput/xdocs/publications/genetics763.pdf
create mode 100644 website/apacheInput/xdocs/publications/index.xml
create mode 100644 website/apacheInput/xdocs/publications/metro-hastings.pdf
create mode 100644 website/apacheInput/xdocs/site.xml
create mode 100644 website/apacheInput/xdocs/tabs.xml
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