JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 20 Feb 2017 16:07:45 +0000 (16:07 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 20 Feb 2017 16:07:45 +0000 (16:07 +0000)
commitfcb39fa3bc47777bf4e0eb209f765dd254dc3cb9
tree3d4ebcc79d197b370f629c00498af2d81c6d406d
parent69b6e688c0a87bffc1fc7ae970fa0f8cd2976007
JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of
PairwiseDistanceModel
23 files changed:
resources/scoreModel/dna.scm
src/jalview/analysis/NJTree.java
src/jalview/analysis/PCA.java
src/jalview/analysis/scoremodels/FeatureDistanceModel.java [moved from src/jalview/analysis/scoremodels/FeatureScoreModel.java with 97% similarity]
src/jalview/analysis/scoremodels/PIDDistanceModel.java [moved from src/jalview/analysis/scoremodels/PIDScoreModel.java with 92% similarity]
src/jalview/analysis/scoremodels/PairwiseDistanceModel.java [moved from src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java with 59% similarity]
src/jalview/analysis/scoremodels/PairwiseScoreModelI.java [new file with mode: 0644]
src/jalview/analysis/scoremodels/SWDistanceModel.java [moved from src/jalview/analysis/scoremodels/SWScoreModel.java with 91% similarity]
src/jalview/analysis/scoremodels/ScoreMatrix.java
src/jalview/analysis/scoremodels/ScoreModels.java
src/jalview/api/analysis/DistanceModelI.java [moved from src/jalview/api/analysis/ScoreModelI.java with 89% similarity]
src/jalview/appletgui/TreePanel.java
src/jalview/datamodel/BinarySequence.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/TreeChooser.java
src/jalview/gui/TreePanel.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/ws/sifts/SiftsClient.java
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java [moved from test/jalview/analysis/scoremodels/FeatureScoreModelTest.java with 97% similarity]
test/jalview/analysis/scoremodels/ScoreMatrixTest.java
test/jalview/analysis/scoremodels/ScoreModelsTest.java
test/jalview/schemes/ScoreMatrixPrinter.java