[med-svn] [aevol] 04/10: Updated version 5.0 from 'upstream/5.0'
Andreas Tille
tille at debian.org
Mon Sep 11 18:55:01 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository aevol.
commit bd6f46cc5a576670977cbd3fef478f957ce5f4a7
Merge: dc6e6e6 1503de1
Author: Andreas Tille <tille at debian.org>
Date: Mon Sep 11 20:23:02 2017 +0200
Updated version 5.0 from 'upstream/5.0'
with Debian dir 40dde30488a44dcb20c0006ff2ca7bbaabf26b90
AUTHORS | 5 +-
INSTALL | 19 +-
Makefile.am | 9 +-
Makefile.in | 364 +-
NEWS | 11 +
README | 8 +-
aclocal.m4 | 830 ++--
compile | 232 +-
config.guess | 1420 ++++++
config.sub | 1799 ++++++++
configure | 4583 ++++++++++++++------
configure.ac | 228 +-
depcomp | 531 ++-
doc/Makefile.am | 6 +-
doc/Makefile.in | 170 +-
doc/aevol_create.1 | 22 +-
...misc_ancstats.1 => aevol_misc_ancestor_stats.1} | 28 +-
doc/aevol_misc_compute_pop_stats.1 | 2 +-
doc/aevol_misc_create_eps.1 | 28 +-
doc/aevol_misc_extract.1 | 41 +-
doc/aevol_misc_fixed_mutations.1 | 34 -
doc/aevol_misc_gene_families.1 | 2 +-
doc/aevol_misc_lineage.1 | 37 +-
doc/aevol_misc_robustness.1 | 41 +-
...ol_misc_view_generation.1 => aevol_misc_view.1} | 22 +-
doc/aevol_modify.1 | 16 +-
doc/aevol_propagate.1 | 66 +-
doc/aevol_run.1 | 28 +-
examples/README | 57 -
examples/basic/param.in | 22 +-
examples/lateral-transfer-by-replacement/README | 32 -
examples/lateral-transfer-by-replacement/param.in | 93 -
examples/with_space/param.in | 74 -
examples/workflow/{README.txt => README} | 184 +-
examples/workflow/wild_type/param.in | 22 +-
install-sh | 35 +-
m4/ax_boost_base.m4 | 285 ++
m4/ax_boost_filesystem.m4 | 118 +
m4/ax_boost_system.m4 | 121 +
m4/ax_cxx_compile_stdcxx_11.m4 | 142 +
m4/ax_cxx_compile_stdcxx_14.m4 | 142 +
missing | 4 +-
src/Makefile.am | 7 +-
src/Makefile.in | 397 +-
src/aevol_create.cpp | 395 +-
src/aevol_modify.cpp | 1700 ++++----
src/aevol_propagate.cpp | 520 +--
src/aevol_run.cpp | 465 +-
src/libaevol/AbstractFuzzy.cpp | 5 +
src/libaevol/AbstractFuzzy.h | 83 +
src/libaevol/{ae_phenotype.cpp => AeTime.cpp} | 74 +-
src/libaevol/{ae_dump.h => AeTime.h} | 135 +-
src/libaevol/Alignment.cpp | 316 ++
src/libaevol/{ae_dump.h => Alignment.h} | 135 +-
src/libaevol/{ae_vis_a_vis.cpp => Codon.cpp} | 99 +-
src/libaevol/{ae_dump.h => Codon.h} | 110 +-
src/libaevol/{ae_phenotype.cpp => Deletion.cpp} | 127 +-
src/libaevol/Deletion.h | 102 +
src/libaevol/Dna.cpp | 3293 ++++++++++++++
src/libaevol/Dna.h | 201 +
src/libaevol/DnaReplicationReport.cpp | 327 ++
src/libaevol/DnaReplicationReport.h | 99 +
src/libaevol/Dump.cpp | 242 ++
src/libaevol/{ae_dump.h => Dump.h} | 122 +-
src/libaevol/{f_line.cpp => Duplication.cpp} | 104 +-
src/libaevol/Duplication.h | 104 +
src/libaevol/ExpManager.cpp | 676 +++
src/libaevol/ExpManager.h | 239 +
src/libaevol/ExpManager_X11.cpp | 1257 ++++++
.../{ae_exp_manager_X11.h => ExpManager_X11.h} | 161 +-
src/libaevol/ExpSetup.cpp | 356 ++
src/libaevol/ExpSetup.h | 359 ++
src/libaevol/Fuzzy.cpp | 440 ++
src/libaevol/Fuzzy.h | 158 +
src/libaevol/{ae_codon.cpp => FuzzyFactory.cpp} | 162 +-
src/libaevol/{ae_dump.h => FuzzyFactory.h} | 173 +-
src/libaevol/{ae_dump.h => Gaussian.h} | 139 +-
src/libaevol/GeneticUnit.cpp | 3489 +++++++++++++++
src/libaevol/GeneticUnit.h | 563 +++
src/libaevol/GridCell.cpp | 162 +
src/libaevol/GridCell.h | 209 +
src/libaevol/GzHelpers.h | 79 +
src/libaevol/{ae_codon.cpp => Habitat.cpp} | 142 +-
src/libaevol/Habitat.h | 150 +
src/libaevol/HabitatFactory.cpp | 51 +
src/libaevol/HabitatFactory.h | 28 +
src/libaevol/HorizontalTransfer.h | 84 +
src/libaevol/HybridFuzzy.cpp | 229 +
src/libaevol/HybridFuzzy.h | 91 +
src/libaevol/Individual.cpp | 1743 ++++++++
src/libaevol/Individual.h | 630 +++
src/libaevol/IndividualFactory.cpp | 229 +
src/libaevol/IndividualFactory.h | 148 +
src/libaevol/Individual_X11.cpp | 840 ++++
.../{ae_fuzzy_set_X11.h => Individual_X11.h} | 97 +-
src/libaevol/{ae_grid_cell.cpp => InsertionHT.cpp} | 122 +-
src/libaevol/InsertionHT.h | 136 +
src/libaevol/{f_line.cpp => Inversion.cpp} | 99 +-
src/libaevol/Inversion.h | 118 +
src/libaevol/JumpPoly.h | 62 +
src/libaevol/{ae_jumping_mt.cpp => JumpingMT.cpp} | 282 +-
src/libaevol/{ae_jumping_mt.h => JumpingMT.h} | 110 +-
src/libaevol/LocalMutation.h | 83 +
src/libaevol/Logging.cpp | 446 ++
src/libaevol/{ae_logs.h => Logging.h} | 111 +-
src/libaevol/Makefile.am | 188 +-
src/libaevol/Makefile.in | 1396 +++---
src/libaevol/Metrics.h | 208 +
src/libaevol/Mutation.cpp | 264 ++
src/libaevol/{ae_dump.h => Mutation.h} | 154 +-
src/libaevol/MutationParams.cpp | 268 ++
src/libaevol/MutationParams.h | 571 +++
src/libaevol/NonCodingMetrics.h | 174 +
.../{tests/run_tests.cpp => Observable.cpp} | 101 +-
src/libaevol/Observable.h | 101 +
src/libaevol/{ae_object.h => ObservableEvent.h} | 44 +-
src/libaevol/Observer.h | 89 +
src/libaevol/OutputManager.cpp | 252 ++
src/libaevol/OutputManager.h | 244 ++
src/libaevol/ParamLoader.cpp | 2104 +++++++++
src/libaevol/ParamLoader.h | 321 ++
src/libaevol/{f_line.cpp => ParameterLine.cpp} | 21 +-
src/libaevol/{f_line.h => ParameterLine.h} | 40 +-
src/libaevol/{ae_utils.h => Phenotype.h} | 81 +-
.../{ae_point_1d.h => PhenotypicSegment.h} | 147 +-
src/libaevol/PhenotypicTarget.cpp | 148 +
src/libaevol/PhenotypicTarget.h | 152 +
src/libaevol/PhenotypicTargetHandler.cpp | 395 ++
src/libaevol/PhenotypicTargetHandler.h | 228 +
src/libaevol/{ae_object.h => Point.cpp} | 45 +-
src/libaevol/{ae_object.h => Point.h} | 47 +-
src/libaevol/{f_line.cpp => PointMutation.cpp} | 85 +-
src/libaevol/PointMutation.h | 103 +
src/libaevol/Protein.cpp | 703 +++
src/libaevol/{ae_protein.h => Protein.h} | 190 +-
src/libaevol/Rearrangement.h | 83 +
.../{ae_phenotype.cpp => ReplacementHT.cpp} | 131 +-
src/libaevol/ReplacementHT.h | 141 +
src/libaevol/ReplicationReport.cpp | 270 ++
src/libaevol/ReplicationReport.h | 275 ++
src/libaevol/{ae_codon.cpp => Rna.cpp} | 119 +-
src/libaevol/{ae_codon.h => Rna.h} | 160 +-
src/libaevol/SFMT-src-1.4/Makefile.in | 304 +-
src/libaevol/Selection.cpp | 759 ++++
src/libaevol/{ae_selection.h => Selection.h} | 157 +-
src/libaevol/{f_line.cpp => SmallDeletion.cpp} | 93 +-
src/libaevol/SmallDeletion.h | 109 +
src/libaevol/SmallInsertion.cpp | 107 +
src/libaevol/SmallInsertion.h | 114 +
src/libaevol/StatRecord.cpp | 939 ++++
src/libaevol/{ae_stat_record.h => StatRecord.h} | 231 +-
src/libaevol/Stats.cpp | 860 ++++
src/libaevol/Stats.h | 179 +
src/libaevol/Translocation.cpp | 91 +
src/libaevol/Translocation.h | 139 +
src/libaevol/Tree.cpp | 216 +
src/libaevol/{ae_align.h => Tree.h} | 133 +-
src/libaevol/{ae_phenotype.cpp => Utils.cpp} | 142 +-
src/libaevol/Utils.h | 106 +
src/libaevol/{ae_grid_cell.cpp => VisAVis.cpp} | 77 +-
src/libaevol/VisAVis.h | 348 ++
src/libaevol/World.cpp | 502 +++
src/libaevol/World.h | 312 ++
src/libaevol/X11Window.cpp | 555 +++
src/libaevol/{ae_X11_window.h => X11Window.h} | 200 +-
src/libaevol/ae_X11_window.cpp | 558 ---
src/libaevol/ae_align.cpp | 316 --
src/libaevol/ae_dna.cpp | 3388 ---------------
src/libaevol/ae_dna.h | 246 --
src/libaevol/ae_dna_replic_report.cpp | 200 -
src/libaevol/ae_dna_replic_report.h | 257 --
src/libaevol/ae_dump.cpp | 254 --
src/libaevol/ae_enums.h | 81 +-
src/libaevol/ae_environment.cpp | 835 ----
src/libaevol/ae_environment.h | 439 --
src/libaevol/ae_exp_manager.cpp | 827 ----
src/libaevol/ae_exp_manager.h | 605 ---
src/libaevol/ae_exp_manager_X11.cpp | 809 ----
src/libaevol/ae_exp_setup.cpp | 219 -
src/libaevol/ae_exp_setup.h | 382 --
src/libaevol/ae_fuzzy_set.cpp | 1026 -----
src/libaevol/ae_fuzzy_set.h | 210 -
src/libaevol/ae_fuzzy_set_X11.cpp | 124 -
src/libaevol/ae_gaussian.h | 201 -
src/libaevol/ae_gene_mutation.cpp | 292 --
src/libaevol/ae_gene_mutation.h | 193 -
src/libaevol/ae_gene_tree.cpp | 234 -
src/libaevol/ae_gene_tree.h | 215 -
src/libaevol/ae_gene_tree_node.cpp | 1216 ------
src/libaevol/ae_gene_tree_node.h | 189 -
src/libaevol/ae_genetic_unit.cpp | 4168 ------------------
src/libaevol/ae_genetic_unit.h | 857 ----
src/libaevol/ae_grid_cell.h | 202 -
src/libaevol/ae_individual.cpp | 1567 -------
src/libaevol/ae_individual.h | 1581 -------
src/libaevol/ae_individual_X11.cpp | 890 ----
src/libaevol/ae_individual_X11.h | 141 -
src/libaevol/ae_jump_poly.h | 58 -
src/libaevol/ae_list.h | 981 -----
src/libaevol/ae_logger.h | 91 +
src/libaevol/ae_logs.cpp | 427 --
src/libaevol/ae_macros.h | 113 -
src/libaevol/ae_mutation.cpp | 959 ----
src/libaevol/ae_mutation.h | 195 -
src/libaevol/ae_output_manager.cpp | 360 --
src/libaevol/ae_output_manager.h | 277 --
src/libaevol/ae_params_mut.cpp | 267 --
src/libaevol/ae_params_mut.h | 567 ---
src/libaevol/ae_population.cpp | 405 --
src/libaevol/ae_population.h | 504 ---
src/libaevol/ae_population_X11.cpp | 230 -
src/libaevol/ae_protein.cpp | 521 ---
src/libaevol/ae_replication_report.cpp | 390 --
src/libaevol/ae_replication_report.h | 331 --
src/libaevol/ae_rna.cpp | 156 -
src/libaevol/ae_rna.h | 224 -
src/libaevol/ae_selection.cpp | 870 ----
src/libaevol/ae_spatial_structure.cpp | 227 -
src/libaevol/ae_spatial_structure.h | 301 --
src/libaevol/ae_stat_record.cpp | 1052 -----
src/libaevol/ae_stats.cpp | 729 ----
src/libaevol/ae_stats.h | 184 -
src/libaevol/ae_string.cpp | 246 +-
src/libaevol/ae_string.h | 195 +-
src/libaevol/ae_tree.cpp | 417 --
src/libaevol/ae_tree.h | 214 -
src/libaevol/ae_vis_a_vis.h | 358 --
src/libaevol/aevol.h | 89 +
src/libaevol/macros.h | 112 +
src/libaevol/{ae_object.h => make_unique.h} | 45 +-
src/libaevol/param_loader.cpp | 1971 ---------
src/libaevol/param_loader.h | 308 --
.../{ae_codon.cpp => raevol/Habitat_R.cpp} | 145 +-
src/libaevol/raevol/Habitat_R.h | 149 +
src/libaevol/raevol/Individual_R.cpp | 492 +++
.../{ae_point_2d.h => raevol/Individual_R.h} | 216 +-
src/libaevol/raevol/Individual_R_X11.cpp | 601 +++
.../Individual_R_X11.h} | 109 +-
src/libaevol/raevol/PhenotypicTargetHandler_R.cpp | 442 ++
src/libaevol/raevol/PhenotypicTargetHandler_R.h | 198 +
.../PhenotypicTarget_R.cpp} | 122 +-
src/libaevol/raevol/PhenotypicTarget_R.h | 132 +
src/libaevol/raevol/Protein_R.cpp | 218 +
.../{ae_env_segment.h => raevol/Protein_R.h} | 227 +-
src/libaevol/raevol/Rna_R.cpp | 280 ++
src/libaevol/{ae_phenotype.h => raevol/Rna_R.h} | 119 +-
src/libaevol/tests/Makefile.am | 47 -
src/libaevol/tests/Makefile.in | 659 ---
src/libaevol/tests/Test_ae_individual.cpp | 327 --
src/libaevol/tests/Test_ae_individual.h | 162 -
src/libaevol/tests/Test_ae_jumping_mt.cpp | 122 -
src/libaevol/tests/Test_ae_jumping_mt.h | 157 -
src/libaevol/tests/Test_ae_list.cpp | 290 --
src/libaevol/tests/Test_ae_list.h | 164 -
src/post_treatments/IndivAnalysis.cpp | 197 +
src/post_treatments/IndivAnalysis.h | 68 +
src/post_treatments/Makefile.am | 50 +-
src/post_treatments/Makefile.in | 459 +-
src/post_treatments/ancestor_robustness.cpp | 303 ++
src/post_treatments/ancestor_stats.cpp | 741 ++++
src/post_treatments/ancstats.cpp | 889 ----
src/post_treatments/compute_pop_stats.cpp | 259 --
src/post_treatments/create_eps.cpp | 1282 +++---
src/post_treatments/extract.cpp | 799 ++--
src/post_treatments/fixed_mutations.cpp | 629 ---
src/post_treatments/gene_families.cpp | 872 ----
src/post_treatments/lineage.cpp | 784 ++--
src/post_treatments/mutagenesis.cpp | 1185 +++++
src/post_treatments/population_statistics.cpp | 542 ---
src/post_treatments/population_statistics.h | 133 -
src/post_treatments/robustness.cpp | 373 +-
src/post_treatments/template.cpp | 193 -
src/post_treatments/view.cpp | 158 +
src/post_treatments/view_generation.cpp | 167 -
274 files changed, 52213 insertions(+), 52788 deletions(-)
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