invade codenew

Brought to you by: rokofler

Commit [r20] Maximize Restore History

included reference regions into output

Authored by: rokofler 2022-01-17

Browse code at this revision

Parent: [r19]

Child: [r21]

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changed	/src/trunk/inv/Main.java
changed	/src/trunk/inv/classic/ClassicSimulationFramework.java
changed	/src/trunk/inv/corelib/Population.java
changed	/src/trunk/inv/corelib/genome/HaploidGenome.java
changed	/src/trunk/inv/corelib/io/output/HOHEWriter.java
changed	/src/trunk/inv/corelib/io/output/MHPWriter.java
changed	/src/trunk/inv/corelib/io/output/OutputManagerCluster.java
changed	/src/trunk/inv/corelib/io/output/SFSWriter.java
changed	/src/trunk/inv/corelib/io/output/SpectrumWriter.java
changed	/src/trunk/inv/corelib/io/parser/BasepopLoader.java
changed	/src/trunk/inv/corelib/io/parser/ClusterDefinitionParser.java
added	/src/trunk/inv/corelib/io/parser/RefDefinitionParser.java
changed	/src/trunk/inv/corelib/statistic/ChromosomeBasedInsertion.java
changed	/src/trunk/inv/corelib/statistic/PopulationStatisticCalculator.java
changed	/src/trunk/inv/corelib/statistic/SpecimenSummary.java
changed	/src/trunk/inv/corelib/statistic/SpecimenSummaryBuilder.java
changed	/src/trunk/inv/invasion/InvasionComandLineParser.java
changed	/src/trunk/inv/invasion/InvasionSimulationFramework.java
changed	/src/trunk/inv/unittest/UnitTesterMain.java
changed	/src/trunk/inv/unittest/testcases/genome/Test_HaploidGenome.java
changed	/src/trunk/inv/unittest/testcases/genome/Test_HaploidGenome_Recombine.java
changed	/src/trunk/inv/unittest/testcases/genome/Test_HaploidGenome_RecombineAndJump.java
changed	/src/trunk/inv/unittest/testcases/misc/Test_FitnessFunctionH.java
changed	/src/trunk/inv/unittest/testcases/misc/Test_FitnessFunctionSiteSpecific.java
added	/src/trunk/inv/unittest/testcases/parser/Test_RefParser.java

/src/trunk/inv/Main.java Diff Switch to side-by-side view

/src/trunk/inv/classic/ClassicSimulationFramework.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/Population.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/genome/HaploidGenome.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/io/output/HOHEWriter.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/io/output/MHPWriter.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/io/output/OutputManagerCluster.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/io/output/SFSWriter.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/io/output/SpectrumWriter.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/io/parser/BasepopLoader.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/io/parser/ClusterDefinitionParser.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/io/parser/RefDefinitionParser.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/statistic/ChromosomeBasedInsertion.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/statistic/PopulationStatisticCalculator.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/statistic/SpecimenSummary.java Diff Switch to side-by-side view

/src/trunk/inv/corelib/statistic/SpecimenSummaryBuilder.java Diff Switch to side-by-side view

/src/trunk/inv/invasion/InvasionComandLineParser.java Diff Switch to side-by-side view

/src/trunk/inv/invasion/InvasionSimulationFramework.java Diff Switch to side-by-side view

/src/trunk/inv/unittest/UnitTesterMain.java Diff Switch to side-by-side view

/src/trunk/inv/unittest/testcases/genome/Test_HaploidGenome.java Diff Switch to side-by-side view

/src/trunk/inv/unittest/testcases/genome/Test_HaploidGenome_Recombine.java Diff Switch to side-by-side view

/src/trunk/inv/unittest/testcases/genome/Test_HaploidGenome_RecombineAndJump.java Diff Switch to side-by-side view

/src/trunk/inv/unittest/testcases/misc/Test_FitnessFunctionH.java Diff Switch to side-by-side view

/src/trunk/inv/unittest/testcases/misc/Test_FitnessFunctionSiteSpecific.java Diff Switch to side-by-side view

/src/trunk/inv/unittest/testcases/parser/Test_RefParser.java Diff Switch to side-by-side view

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