JAL-845 code/refactoring/tests related to linking DNA and protein
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 3 Feb 2015 10:53:56 +0000 (10:53 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 3 Feb 2015 10:53:56 +0000 (10:53 +0000)
commit10ff37d2cb03f342ddbed679951d3e2fef0a404b
tree15b59723cd4212862aefb4b01b149dfab530cc67
parent95ceead3cb4ea5aa5260e1fd4ab53658b64866e1
JAL-845 code/refactoring/tests related to linking DNA and protein
50 files changed:
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/bin/JalviewLite.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/CigarArray.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/CutAndPasteHtmlTransfer.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/IdPanel.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/VamsasApplication.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/vamsas/Sequencemapping.java
src/jalview/io/vamsas/Tree.java
src/jalview/javascript/JsSelectionSender.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/util/Comparison.java
src/jalview/util/MappingUtils.java
src/jalview/util/ShiftList.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/AWSThread.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/TestAlignSeq.java
test/jalview/datamodel/ColumnSelectionTest.java [new file with mode: 0644]
test/jalview/datamodel/SequenceTest.java
test/jalview/util/ShiftListTest.java [new file with mode: 0644]