JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...
authorjprocter <jprocter@compbio.dundee.ac.uk>
Wed, 30 May 2012 18:21:25 +0000 (19:21 +0100)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Wed, 30 May 2012 18:21:25 +0000 (19:21 +0100)
commitb81d4d7d46ea8b1c89df086fb847baab6b69d427
tree3afc026ba15c8b397e9d0c2c2dc37fe6f12ac29e
parent4908abbb92332aba961012da6841a3e70383c291
JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and use SequenceCollectionI and AnnotationCollectionI where possible to simplify code.
46 files changed:
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/Grouping.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/IdCanvas.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/AnnotatedCollectionI.java
src/jalview/datamodel/HiddenSequences.java
src/jalview/datamodel/SequenceCollectionI.java [new file with mode: 0644]
src/jalview/datamodel/SequenceGroup.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/TextColourChooser.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/VamsasApplication.java
src/jalview/io/AnnotationFile.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/ColourSchemeI.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/RNAHelicesColourChooser.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/schemes/TCoffeeColourScheme.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/rest/RestJobThread.java