source.jalview.org Git - jalview.git/commit

Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/api/AlignViewportI.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/WsJobParameters.java
src/jalview/io/AlignmentFileReaderI.java
src/jalview/io/FileLoader.java
src/jalview/io/StockholmFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GPreferences.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/jws2/Jws2Discoverer.java
test/jalview/analysis/AAFrequencyTest.java
test/jalview/gui/AlignFrameTest.java
test/jalview/gui/AlignViewportTest.java

author	Jim Procter <jprocter@issues.jalview.org>
	Mon, 18 May 2020 14:26:30 +0000 (15:26 +0100)
committer	Jim Procter <jprocter@issues.jalview.org>
	Mon, 18 May 2020 14:26:30 +0000 (15:26 +0100)
commit	c794c5033adeee182b03a5ea92c0a7495a29661f
tree	47cec5f821cda1882438b035a29de51f31bbb1e2	tree \| snapshot
parent	e1dbbc5edc07f65706eeb1dda9f4c9bcdee9d3a5	commit \| diff
parent	3609d4b908fa64cab35f2348401baab3347188fc	commit \| diff

resources/lang/Messages.properties	diff1 \|	diff2 \|	blob \| history
resources/lang/Messages_es.properties	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/AAFrequency.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/AlignmentSorter.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/AlignmentUtils.java	diff1 \|	diff2 \|	blob \| history
src/jalview/analysis/Dna.java	diff1 \|	diff2 \|	blob \| history
src/jalview/api/AlignViewportI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AlignFrame.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AlignViewport.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AlignmentPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/AnnotationPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/OverviewPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/appletgui/TitledPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/bin/Jalview.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/Alignment.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/Sequence.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/SequenceGroup.java	diff1 \|	diff2 \|	blob \| history
src/jalview/datamodel/SequenceI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ext/ensembl/EnsemblFeatures.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ext/ensembl/EnsemblInfo.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ext/ensembl/EnsemblXref.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AlignFrame.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AlignViewport.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/AnnotationLabels.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/CalculationChooser.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/Desktop.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/JvSwingUtils.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/OverviewPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/PopupMenu.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/Preferences.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/RestServiceEditorPane.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/SliderPanel.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/SplitFrame.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/WsJobParameters.java	diff1 \|	diff2 \|	blob \| history
src/jalview/gui/WsParamSetManager.java	diff1 \|	diff2 \|	blob \| history
src/jalview/hmmer/HmmerCommand.java	\|	diff2 \|	blob \| history
src/jalview/io/AlignFile.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/AlignmentFileWriterI.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/FileFormat.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/FileLoader.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/HMMFile.java	\|	diff2 \|	blob \| history
src/jalview/io/IdentifyFile.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/SequenceAnnotationReport.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/StockholmFile.java	diff1 \|	diff2 \|	blob \| history
src/jalview/io/packed/ParsePackedSet.java	diff1 \|	diff2 \|	blob \| history
src/jalview/jbgui/GAlignFrame.java	diff1 \|	diff2 \|	blob \| history
src/jalview/jbgui/GPreferences.java	diff1 \|	diff2 \|	blob \| history
src/jalview/jbgui/GUserDefinedColours.java	diff1 \|	diff2 \|	blob \| history
src/jalview/project/Jalview2XML.java	diff1 \|	diff2 \|	blob \| history
src/jalview/renderer/AnnotationRenderer.java	diff1 \|	diff2 \|	blob \| history
src/jalview/schemes/ResidueProperties.java	diff1 \|	diff2 \|	blob \| history
src/jalview/util/Platform.java	diff1 \|	diff2 \|	blob \| history
src/jalview/viewmodel/AlignmentViewport.java	diff1 \|	diff2 \|	blob \| history
src/jalview/workers/ConsensusThread.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ws/dbsources/EmblXmlSource.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ws/dbsources/Uniprot.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ws/jws2/JabaParamStore.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ws/jws2/Jws2Discoverer.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ws/jws2/MsaWSClient.java	diff1 \|	diff2 \|	blob \| history
src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java	\|	diff2 \|	blob \| history
src/org/json/JSONObject.java	diff1 \|	\|	blob \| history
test/jalview/analysis/AAFrequencyTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/analysis/AlignmentUtilsTests.java	diff1 \|	diff2 \|	blob \| history
test/jalview/analysis/CrossRefTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/datamodel/AlignmentTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/datamodel/SequenceTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/fts/service/pdb/PDBFTSPanelTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/gui/AlignFrameTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/gui/AlignViewportTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/gui/PopupMenuTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/gui/StructureChooserTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/io/FileFormatsTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/io/StockholmFileTest.java	diff1 \|	diff2 \|	blob \| history
test/jalview/project/Jalview2xmlTests.java	diff1 \|	diff2 \|	blob \| history
test/jalview/schemes/PIDColourSchemeTest.java	diff1 \|	diff2 \|	blob \| history