JAL-98 use Profile to store consensus, ResidueCount for fast compact
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 3 Oct 2016 11:45:47 +0000 (12:45 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 3 Oct 2016 11:45:47 +0000 (12:45 +0100)
commit1c757dc1e6ee864277825c1ebd9c6a9fbe0da7b2
treeef5ff50f5fef17735d0a806cd6e54af698f4c9da
parent1e5b6995c96364c79329e618f7933caf177b353e
JAL-98 use Profile to store consensus, ResidueCount for fast compact
counting
23 files changed:
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/Profile.java
src/jalview/analysis/ResidueCount.java [new file with mode: 0644]
src/jalview/api/AlignViewportI.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/ext/android/ContainerHelpers.java
src/jalview/ext/android/SparseIntArray.java
src/jalview/ext/android/SparseShortArray.java [new file with mode: 0644]
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/Blosum62ColourScheme.java
src/jalview/schemes/ColourSchemeI.java
src/jalview/schemes/FollowerColourScheme.java
src/jalview/schemes/PIDColourScheme.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/util/SparseCount.java [new file with mode: 0644]
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/ComplementConsensusThread.java
src/jalview/workers/ConsensusThread.java
test/jalview/analysis/AAFrequencyTest.java
test/jalview/analysis/ResidueCountTest.java [new file with mode: 0644]
test/jalview/ext/android/SparseIntArrayTest.java [new file with mode: 0644]
test/jalview/ext/android/SparseShortArrayTest.java [new file with mode: 0644]
test/jalview/util/SparseCountTest.java [new file with mode: 0644]