[med-svn] [aevol] branch master updated (fef99a7 -> 8dc29b0)
Andreas Tille
tille at debian.org
Mon Sep 11 18:54:59 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository aevol.
from fef99a7 Updated version 4.4 from 'upstream/4.4'
new 208b731 Moved packaging from SVN to Git
new dc6e6e6 Fixed watch file
new 1503de1 New upstream version 5.0
new bd6f46c Updated version 5.0 from 'upstream/5.0'
new 6efc9fb New upstream version
new 5ac4e44 debhelper 10
new 66fa436 Standards-Version: 4.1.0 (no changes needed)
new 3655635 Add missing libboost Build-Depends
new 8c7ed1b hardening=+all
new 8dc29b0 Unique license name
The 10 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 +-
debian/changelog | 14 +
debian/compat | 2 +-
debian/control | 15 +-
debian/copyright | 18 +-
debian/rules | 4 +-
debian/watch | 4 +-
depcomp | 531 ++-
doc/Makefile.am | 6 +-
doc/Makefile.in | 170 +-
doc/aevol_create.1 | 22 +-
...xed_mutations.1 => aevol_misc_ancestor_stats.1} | 28 +-
doc/aevol_misc_ancstats.1 | 34 -
doc/aevol_misc_compute_pop_stats.1 | 2 +-
doc/aevol_misc_create_eps.1 | 28 +-
doc/aevol_misc_extract.1 | 41 +-
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 -
280 files changed, 52247 insertions(+), 52800 deletions(-)
create mode 100755 config.guess
create mode 100755 config.sub
rename doc/{aevol_misc_fixed_mutations.1 => aevol_misc_ancestor_stats.1} (51%)
delete mode 100644 doc/aevol_misc_ancstats.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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