JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Thu, 23 Feb 2017 15:48:57 +0000 (15:48 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Thu, 23 Feb 2017 15:48:57 +0000 (15:48 +0000)
commit7f5ab7d1f58d870622968e0e6a430f33403b8e4f
tree04cd59868da02927faddc614f638f5eaa96079f6
parentd6a30c6516e8e2f923c8c2f6dce7592cb3b7d974
JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to
allow distance and similarity models to be used for Tree and PCA
28 files changed:
src/jalview/analysis/NJTree.java
src/jalview/analysis/PCA.java
src/jalview/analysis/scoremodels/FeatureDistanceModel.java
src/jalview/analysis/scoremodels/PIDDistanceModel.java
src/jalview/analysis/scoremodels/PairwiseDistanceModel.java [deleted file]
src/jalview/analysis/scoremodels/SWDistanceModel.java
src/jalview/analysis/scoremodels/ScoreMatrix.java
src/jalview/analysis/scoremodels/ScoreModels.java
src/jalview/api/analysis/DistanceModelI.java [deleted file]
src/jalview/api/analysis/DistanceScoreModelI.java [new file with mode: 0644]
src/jalview/api/analysis/PairwiseScoreModelI.java [moved from src/jalview/analysis/scoremodels/PairwiseScoreModelI.java with 95% similarity]
src/jalview/api/analysis/ScoreModelI.java [new file with mode: 0644]
src/jalview/api/analysis/SimilarityScoreModelI.java [new file with mode: 0644]
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/TreePanel.java
src/jalview/datamodel/SequenceNode.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreeChooser.java
src/jalview/gui/TreePanel.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/viewmodel/PCAModel.java
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
test/jalview/analysis/scoremodels/ScoreMatrixTest.java
test/jalview/analysis/scoremodels/ScoreModelsTest.java
test/jalview/util/ComparisonTest.java