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As default the multiplication with codon frequencies has been moved up one level
Removed dependencies computation from Forest and created a standalone class Added accessors to Forest Removed unneeded methods Write results do nothing if file not defined Adjusted member visibility to various variables Removed custom code for memalign Added more tasking git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4784 95c5a404-1f88-0410-a6b0-c3f062b6f34a
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- AlignedAllocator.cpp 8 additions, 1 deletionAlignedAllocator.cpp
- BayesTest.cpp 4 additions, 4 deletionsBayesTest.cpp
- BayesTest.h 3 additions, 3 deletionsBayesTest.h
- BranchSiteModel.cpp 10 additions, 8 deletionsBranchSiteModel.cpp
- BranchSiteModel.h 66 additions, 34 deletionsBranchSiteModel.h
- CmdLine.cpp 4 additions, 1 deletionCmdLine.cpp
- CodeMLoptimizer.h 1 addition, 1 deletionCodeMLoptimizer.h
- Forest.cpp 66 additions, 18 deletionsForest.cpp
- Forest.h 42 additions, 19 deletionsForest.h
- ForestExport.h 2 additions, 2 deletionsForestExport.h
- Genes.h 2 additions, 2 deletionsGenes.h
- HighLevelCoordinator.cpp 9 additions, 7 deletionsHighLevelCoordinator.cpp
- Newick.cpp 25 additions, 18 deletionsNewick.cpp
- Phylip.cpp 2 additions, 1 deletionPhylip.cpp
- PhyloTree.h 2 additions, 1 deletionPhyloTree.h
- ProbabilityMatrixSet.cpp 17 additions, 3 deletionsProbabilityMatrixSet.cpp
- ProbabilityMatrixSet.h 10 additions, 15 deletionsProbabilityMatrixSet.h
- TreeAndSetsDependencies.cpp 234 additions, 8 deletionsTreeAndSetsDependencies.cpp
- TreeAndSetsDependencies.h 60 additions, 6 deletionsTreeAndSetsDependencies.h
- WriteResults.cpp 25 additions, 34 deletionsWriteResults.cpp
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