JAL-3130 Lots of deprecation fixes. See utils/deprecation_auto_fixes.sh for commands...
authorBen Soares <bsoares@dundee.ac.uk>
Wed, 20 Mar 2019 16:13:14 +0000 (16:13 +0000)
committerBen Soares <bsoares@dundee.ac.uk>
Wed, 20 Mar 2019 16:17:37 +0000 (16:17 +0000)
commit3027bfb4b1b13af8686abcd419888e03141bd672
tree120af9eff5bcf6196f49dcccee43e028884b70a3
parent36ad4645318399ebd59df2c019a62e0fb9c79aaf
JAL-3130 Lots of deprecation fixes.  See utils/deprecation_auto_fixes.sh for commands used to fix the bulk of these (a couple of manual fixes at the end too).
66 files changed:
build-j11.xml
src/MCview/AppletPDBCanvas.java
src/MCview/Atom.java
src/MCview/PDBCanvas.java
src/com/stevesoft/pat/RegOpt.java
src/com/stevesoft/pat/RegexTokenizer.java
src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/ParseProperties.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/StructureFrequency.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/bin/JalviewLite.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/BinarySequence.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/ext/htsjdk/VCFReader.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/BlogReader.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/WsPreferences.java
src/jalview/io/AnnotationFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/JPredFile.java
src/jalview/io/JnetAnnotationMaker.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/vamsas/Rangetype.java
src/jalview/io/vamsas/Sequencefeature.java
src/jalview/io/vamsas/Tree.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
src/jalview/jbgui/GCutAndPasteTransfer.java
src/jalview/jbgui/GDesktop.java
src/jalview/project/Jalview2XML.java
src/jalview/schemes/FeatureColour.java
src/jalview/util/Platform.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/ws/jws2/RNAalifoldClient.java
src/uk/ac/ebi/www/InputParams.java
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
test/jalview/datamodel/ColumnSelectionTest.java
test/jalview/datamodel/SequenceFeatureTest.java
test/jalview/gui/SeqPanelTest.java
test/jalview/io/StockholmFileTest.java
utils/deprecation_auto_fixes.sh [new file with mode: 0644]