[med-svn] [aevol] branch upstream updated (5090e7e -> 1503de1)
Andreas Tille
tille at debian.org
Mon Sep 11 18:55:03 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository aevol.
from 5090e7e New upstream version 4.4
new 1503de1 New upstream version 5.0
The 1 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:
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_phenotype.cpp => Habitat.cpp} | 131 +-
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, 52217 insertions(+), 52773 deletions(-)
create mode 100755 config.guess
create mode 100755 config.sub
rename doc/{aevol_misc_ancstats.1 => aevol_misc_ancestor_stats.1} (51%)
delete mode 100644 doc/aevol_misc_fixed_mutations.1
rename doc/{aevol_misc_view_generation.1 => aevol_misc_view.1} (56%)
delete mode 100644 examples/README
delete mode 100644 examples/lateral-transfer-by-replacement/README
delete mode 100644 examples/lateral-transfer-by-replacement/param.in
delete mode 100644 examples/with_space/param.in
rename examples/workflow/{README.txt => README} (56%)
create mode 100644 m4/ax_boost_base.m4
create mode 100644 m4/ax_boost_filesystem.m4
create mode 100644 m4/ax_boost_system.m4
create mode 100644 m4/ax_cxx_compile_stdcxx_11.m4
create mode 100644 m4/ax_cxx_compile_stdcxx_14.m4
create mode 100644 src/libaevol/AbstractFuzzy.cpp
create mode 100644 src/libaevol/AbstractFuzzy.h
copy src/libaevol/{ae_phenotype.cpp => AeTime.cpp} (66%)
copy src/libaevol/{ae_dump.h => AeTime.h} (61%)
create mode 100644 src/libaevol/Alignment.cpp
copy src/libaevol/{ae_dump.h => Alignment.h} (59%)
rename src/libaevol/{ae_vis_a_vis.cpp => Codon.cpp} (59%)
copy src/libaevol/{ae_dump.h => Codon.h} (61%)
copy src/libaevol/{ae_phenotype.cpp => Deletion.cpp} (51%)
create mode 100644 src/libaevol/Deletion.h
create mode 100644 src/libaevol/Dna.cpp
create mode 100644 src/libaevol/Dna.h
create mode 100644 src/libaevol/DnaReplicationReport.cpp
create mode 100644 src/libaevol/DnaReplicationReport.h
create mode 100644 src/libaevol/Dump.cpp
copy src/libaevol/{ae_dump.h => Dump.h} (63%)
copy src/libaevol/{f_line.cpp => Duplication.cpp} (53%)
create mode 100644 src/libaevol/Duplication.h
create mode 100644 src/libaevol/ExpManager.cpp
create mode 100644 src/libaevol/ExpManager.h
create mode 100644 src/libaevol/ExpManager_X11.cpp
rename src/libaevol/{ae_exp_manager_X11.h => ExpManager_X11.h} (64%)
create mode 100644 src/libaevol/ExpSetup.cpp
create mode 100644 src/libaevol/ExpSetup.h
create mode 100644 src/libaevol/Fuzzy.cpp
create mode 100644 src/libaevol/Fuzzy.h
copy src/libaevol/{ae_codon.cpp => FuzzyFactory.cpp} (51%)
copy src/libaevol/{ae_dump.h => FuzzyFactory.h} (50%)
copy src/libaevol/{ae_dump.h => Gaussian.h} (55%)
create mode 100644 src/libaevol/GeneticUnit.cpp
create mode 100644 src/libaevol/GeneticUnit.h
create mode 100644 src/libaevol/GridCell.cpp
create mode 100644 src/libaevol/GridCell.h
create mode 100644 src/libaevol/GzHelpers.h
copy src/libaevol/{ae_phenotype.cpp => Habitat.cpp} (51%)
create mode 100644 src/libaevol/Habitat.h
create mode 100644 src/libaevol/HabitatFactory.cpp
create mode 100644 src/libaevol/HabitatFactory.h
create mode 100644 src/libaevol/HorizontalTransfer.h
create mode 100644 src/libaevol/HybridFuzzy.cpp
create mode 100644 src/libaevol/HybridFuzzy.h
create mode 100644 src/libaevol/Individual.cpp
create mode 100644 src/libaevol/Individual.h
create mode 100644 src/libaevol/IndividualFactory.cpp
create mode 100644 src/libaevol/IndividualFactory.h
create mode 100644 src/libaevol/Individual_X11.cpp
rename src/libaevol/{ae_fuzzy_set_X11.h => Individual_X11.h} (69%)
copy src/libaevol/{ae_grid_cell.cpp => InsertionHT.cpp} (52%)
create mode 100644 src/libaevol/InsertionHT.h
copy src/libaevol/{f_line.cpp => Inversion.cpp} (52%)
create mode 100644 src/libaevol/Inversion.h
create mode 100644 src/libaevol/JumpPoly.h
rename src/libaevol/{ae_jumping_mt.cpp => JumpingMT.cpp} (58%)
rename src/libaevol/{ae_jumping_mt.h => JumpingMT.h} (67%)
create mode 100644 src/libaevol/LocalMutation.h
create mode 100644 src/libaevol/Logging.cpp
rename src/libaevol/{ae_logs.h => Logging.h} (71%)
create mode 100644 src/libaevol/Metrics.h
create mode 100644 src/libaevol/Mutation.cpp
rename src/libaevol/{ae_dump.h => Mutation.h} (56%)
create mode 100644 src/libaevol/MutationParams.cpp
create mode 100644 src/libaevol/MutationParams.h
create mode 100644 src/libaevol/NonCodingMetrics.h
rename src/libaevol/{tests/run_tests.cpp => Observable.cpp} (56%)
create mode 100644 src/libaevol/Observable.h
copy src/libaevol/{ae_object.h => ObservableEvent.h} (70%)
create mode 100644 src/libaevol/Observer.h
create mode 100644 src/libaevol/OutputManager.cpp
create mode 100644 src/libaevol/OutputManager.h
create mode 100644 src/libaevol/ParamLoader.cpp
create mode 100644 src/libaevol/ParamLoader.h
copy src/libaevol/{f_line.cpp => ParameterLine.cpp} (91%)
rename src/libaevol/{f_line.h => ParameterLine.h} (93%)
rename src/libaevol/{ae_utils.h => Phenotype.h} (52%)
rename src/libaevol/{ae_point_1d.h => PhenotypicSegment.h} (68%)
create mode 100644 src/libaevol/PhenotypicTarget.cpp
create mode 100644 src/libaevol/PhenotypicTarget.h
create mode 100644 src/libaevol/PhenotypicTargetHandler.cpp
create mode 100644 src/libaevol/PhenotypicTargetHandler.h
copy src/libaevol/{ae_object.h => Point.cpp} (70%)
copy src/libaevol/{ae_object.h => Point.h} (71%)
copy src/libaevol/{f_line.cpp => PointMutation.cpp} (60%)
create mode 100644 src/libaevol/PointMutation.h
create mode 100644 src/libaevol/Protein.cpp
rename src/libaevol/{ae_protein.h => Protein.h} (51%)
create mode 100644 src/libaevol/Rearrangement.h
copy src/libaevol/{ae_phenotype.cpp => ReplacementHT.cpp} (52%)
create mode 100644 src/libaevol/ReplacementHT.h
create mode 100644 src/libaevol/ReplicationReport.cpp
create mode 100644 src/libaevol/ReplicationReport.h
copy src/libaevol/{ae_codon.cpp => Rna.cpp} (59%)
rename src/libaevol/{ae_codon.h => Rna.h} (54%)
create mode 100644 src/libaevol/Selection.cpp
rename src/libaevol/{ae_selection.h => Selection.h} (59%)
rename src/libaevol/{f_line.cpp => SmallDeletion.cpp} (57%)
create mode 100644 src/libaevol/SmallDeletion.h
create mode 100644 src/libaevol/SmallInsertion.cpp
create mode 100644 src/libaevol/SmallInsertion.h
create mode 100644 src/libaevol/StatRecord.cpp
rename src/libaevol/{ae_stat_record.h => StatRecord.h} (52%)
create mode 100644 src/libaevol/Stats.cpp
create mode 100644 src/libaevol/Stats.h
create mode 100644 src/libaevol/Translocation.cpp
create mode 100644 src/libaevol/Translocation.h
create mode 100644 src/libaevol/Tree.cpp
rename src/libaevol/{ae_align.h => Tree.h} (63%)
copy src/libaevol/{ae_phenotype.cpp => Utils.cpp} (51%)
create mode 100644 src/libaevol/Utils.h
rename src/libaevol/{ae_grid_cell.cpp => VisAVis.cpp} (67%)
create mode 100644 src/libaevol/VisAVis.h
create mode 100644 src/libaevol/World.cpp
create mode 100644 src/libaevol/World.h
create mode 100644 src/libaevol/X11Window.cpp
rename src/libaevol/{ae_X11_window.h => X11Window.h} (51%)
delete mode 100644 src/libaevol/ae_X11_window.cpp
delete mode 100644 src/libaevol/ae_align.cpp
delete mode 100644 src/libaevol/ae_dna.cpp
delete mode 100644 src/libaevol/ae_dna.h
delete mode 100644 src/libaevol/ae_dna_replic_report.cpp
delete mode 100644 src/libaevol/ae_dna_replic_report.h
delete mode 100644 src/libaevol/ae_dump.cpp
delete mode 100644 src/libaevol/ae_environment.cpp
delete mode 100644 src/libaevol/ae_environment.h
delete mode 100644 src/libaevol/ae_exp_manager.cpp
delete mode 100644 src/libaevol/ae_exp_manager.h
delete mode 100644 src/libaevol/ae_exp_manager_X11.cpp
delete mode 100644 src/libaevol/ae_exp_setup.cpp
delete mode 100644 src/libaevol/ae_exp_setup.h
delete mode 100644 src/libaevol/ae_fuzzy_set.cpp
delete mode 100644 src/libaevol/ae_fuzzy_set.h
delete mode 100644 src/libaevol/ae_fuzzy_set_X11.cpp
delete mode 100644 src/libaevol/ae_gaussian.h
delete mode 100644 src/libaevol/ae_gene_mutation.cpp
delete mode 100644 src/libaevol/ae_gene_mutation.h
delete mode 100644 src/libaevol/ae_gene_tree.cpp
delete mode 100644 src/libaevol/ae_gene_tree.h
delete mode 100644 src/libaevol/ae_gene_tree_node.cpp
delete mode 100644 src/libaevol/ae_gene_tree_node.h
delete mode 100644 src/libaevol/ae_genetic_unit.cpp
delete mode 100644 src/libaevol/ae_genetic_unit.h
delete mode 100644 src/libaevol/ae_grid_cell.h
delete mode 100644 src/libaevol/ae_individual.cpp
delete mode 100644 src/libaevol/ae_individual.h
delete mode 100644 src/libaevol/ae_individual_X11.cpp
delete mode 100644 src/libaevol/ae_individual_X11.h
delete mode 100644 src/libaevol/ae_jump_poly.h
delete mode 100644 src/libaevol/ae_list.h
create mode 100644 src/libaevol/ae_logger.h
delete mode 100644 src/libaevol/ae_logs.cpp
delete mode 100644 src/libaevol/ae_macros.h
delete mode 100644 src/libaevol/ae_mutation.cpp
delete mode 100644 src/libaevol/ae_mutation.h
delete mode 100644 src/libaevol/ae_output_manager.cpp
delete mode 100644 src/libaevol/ae_output_manager.h
delete mode 100644 src/libaevol/ae_params_mut.cpp
delete mode 100644 src/libaevol/ae_params_mut.h
delete mode 100644 src/libaevol/ae_population.cpp
delete mode 100644 src/libaevol/ae_population.h
delete mode 100644 src/libaevol/ae_population_X11.cpp
delete mode 100644 src/libaevol/ae_protein.cpp
delete mode 100644 src/libaevol/ae_replication_report.cpp
delete mode 100644 src/libaevol/ae_replication_report.h
delete mode 100644 src/libaevol/ae_rna.cpp
delete mode 100644 src/libaevol/ae_rna.h
delete mode 100644 src/libaevol/ae_selection.cpp
delete mode 100644 src/libaevol/ae_spatial_structure.cpp
delete mode 100644 src/libaevol/ae_spatial_structure.h
delete mode 100644 src/libaevol/ae_stat_record.cpp
delete mode 100644 src/libaevol/ae_stats.cpp
delete mode 100644 src/libaevol/ae_stats.h
delete mode 100644 src/libaevol/ae_tree.cpp
delete mode 100644 src/libaevol/ae_tree.h
delete mode 100644 src/libaevol/ae_vis_a_vis.h
create mode 100644 src/libaevol/aevol.h
create mode 100644 src/libaevol/macros.h
rename src/libaevol/{ae_object.h => make_unique.h} (70%)
delete mode 100644 src/libaevol/param_loader.cpp
delete mode 100644 src/libaevol/param_loader.h
rename src/libaevol/{ae_codon.cpp => raevol/Habitat_R.cpp} (50%)
create mode 100644 src/libaevol/raevol/Habitat_R.h
create mode 100644 src/libaevol/raevol/Individual_R.cpp
rename src/libaevol/{ae_point_2d.h => raevol/Individual_R.h} (51%)
create mode 100644 src/libaevol/raevol/Individual_R_X11.cpp
rename src/libaevol/{ae_population_X11.h => raevol/Individual_R_X11.h} (70%)
create mode 100644 src/libaevol/raevol/PhenotypicTargetHandler_R.cpp
create mode 100644 src/libaevol/raevol/PhenotypicTargetHandler_R.h
rename src/libaevol/{ae_phenotype.cpp => raevol/PhenotypicTarget_R.cpp} (58%)
create mode 100644 src/libaevol/raevol/PhenotypicTarget_R.h
create mode 100644 src/libaevol/raevol/Protein_R.cpp
rename src/libaevol/{ae_env_segment.h => raevol/Protein_R.h} (55%)
create mode 100644 src/libaevol/raevol/Rna_R.cpp
rename src/libaevol/{ae_phenotype.h => raevol/Rna_R.h} (74%)
delete mode 100644 src/libaevol/tests/Makefile.am
delete mode 100644 src/libaevol/tests/Makefile.in
delete mode 100644 src/libaevol/tests/Test_ae_individual.cpp
delete mode 100644 src/libaevol/tests/Test_ae_individual.h
delete mode 100644 src/libaevol/tests/Test_ae_jumping_mt.cpp
delete mode 100644 src/libaevol/tests/Test_ae_jumping_mt.h
delete mode 100644 src/libaevol/tests/Test_ae_list.cpp
delete mode 100644 src/libaevol/tests/Test_ae_list.h
create mode 100644 src/post_treatments/IndivAnalysis.cpp
create mode 100644 src/post_treatments/IndivAnalysis.h
create mode 100644 src/post_treatments/ancestor_robustness.cpp
create mode 100644 src/post_treatments/ancestor_stats.cpp
delete mode 100644 src/post_treatments/ancstats.cpp
delete mode 100644 src/post_treatments/compute_pop_stats.cpp
delete mode 100644 src/post_treatments/fixed_mutations.cpp
delete mode 100644 src/post_treatments/gene_families.cpp
create mode 100644 src/post_treatments/mutagenesis.cpp
delete mode 100644 src/post_treatments/population_statistics.cpp
delete mode 100644 src/post_treatments/population_statistics.h
delete mode 100644 src/post_treatments/template.cpp
create mode 100644 src/post_treatments/view.cpp
delete mode 100644 src/post_treatments/view_generation.cpp
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