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

git://source.jalview.org / jalview.git / commit

author	Jim Procter <jprocter@dundee.ac.uk>
	Mon, 22 Dec 2014 16:16:17 +0000 (16:16 +0000)
committer	Jim Procter <jprocter@dundee.ac.uk>
	Mon, 22 Dec 2014 16:16:17 +0000 (16:16 +0000)
commit	2273eba5668e5340354da60fed329c6c716cc439
tree	8c33dcad3e491bec71663902b4583f5e830c9ca0	tree \| snapshot
parent	497958b4e5217efaa3ddeece38f38c3a6e98cb96	commit \| diff

Merge: 497958b 68dcaa7
(fake synthesised by jbp)

Merge branch 'develop' into JAL-1483_29dev
Conflicts:
       src/jalview/api/AlignmentViewPanel.java
       src/jalview/appletgui/SeqPanel.java
       src/jalview/gui/AlignFrame.java
       src/jalview/gui/AlignViewport.java
       src/jalview/gui/AnnotationExporter.java
       src/jalview/gui/FeatureRenderer.java
       src/jalview/gui/FeatureSettings.java
       src/jalview/gui/Jalview2XML.java
       src/jalview/gui/Jalview2XML_V1.java
       src/jalview/gui/PopupMenu.java
       src/jalview/gui/SeqPanel.java

172 files changed:

.classpath		diff \| blob \| history
.externalToolBuilders/Jalview Release indices [Builder].launch		diff \| blob \| history
.settings/org.eclipse.jdt.core.prefs		diff \| blob \| history
AUTHORS		diff \| blob \| history
THIRDPARTYLIBS		diff \| blob \| history
build.xml		diff \| blob \| history
examples/example_biojs.html		diff \| blob \| history
examples/uniref50.score_ascii	[new file with mode: 0644]	blob
help/help.jhm		diff \| blob \| history
help/helpTOC.xml		diff \| blob \| history
help/html/calculations/consensus.html		diff \| blob \| history
help/html/calculations/pca.html		diff \| blob \| history
help/html/colourSchemes/annotationColouring.html		diff \| blob \| history
help/html/colourSchemes/pid.html		diff \| blob \| history
help/html/features/annotation.html		diff \| blob \| history
help/html/features/chimera.html	[new file with mode: 0644]	blob
help/html/features/clarguments.html		diff \| blob \| history
help/html/features/dassettings.html		diff \| blob \| history
help/html/features/featuresFormat.html		diff \| blob \| history
help/html/features/featuresettings.html		diff \| blob \| history
help/html/features/hiddenRegions.html		diff \| blob \| history
help/html/features/jmol.html		diff \| blob \| history
help/html/features/multipleViews.html		diff \| blob \| history
help/html/features/preferences.html		diff \| blob \| history
help/html/features/seqfetch.html		diff \| blob \| history
help/html/features/varna.html		diff \| blob \| history
help/html/features/viewingpdbs.html		diff \| blob \| history
help/html/features/xsspannotation.html	[new file with mode: 0644]	blob
help/html/index.html		diff \| blob \| history
help/html/io/export.html		diff \| blob \| history
help/html/io/fileformats.html		diff \| blob \| history
help/html/jalviewjnlp.html	[deleted file]	blob \| history
help/html/memory.html		diff \| blob \| history
help/html/menus/alignmentMenu.html		diff \| blob \| history
help/html/menus/alwedit.html		diff \| blob \| history
help/html/menus/alwfile.html		diff \| blob \| history
help/html/menus/popupMenu.html		diff \| blob \| history
help/html/na/index.html		diff \| blob \| history
help/html/privacy.html		diff \| blob \| history
help/html/releases.html		diff \| blob \| history
help/html/vamsas/index.html		diff \| blob \| history
help/html/webServices/JABAWS.html		diff \| blob \| history
help/html/webServices/RNAalifold.html		diff \| blob \| history
help/html/webServices/dbreffetcher.html		diff \| blob \| history
help/html/webServices/jnet.html		diff \| blob \| history
help/html/whatsNew.html		diff \| blob \| history
resources/authors.props		diff \| blob \| history
resources/lang/Messages.properties		diff \| blob \| history
resources/lang/Messages_es.properties		diff \| blob \| history
resources/templates/BioJSTemplate.txt		diff \| blob \| history
src/MCview/PDBChain.java		diff \| blob \| history
src/MCview/PDBViewer.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/AnnotationSorter.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/api/AlignmentViewPanel.java		diff \| blob \| history
src/jalview/appletgui/APopupMenu.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/commands/EditCommand.java		diff \| blob \| history
src/jalview/commands/RemoveGapColCommand.java		diff \| blob \| history
src/jalview/commands/RemoveGapsCommand.java		diff \| blob \| history
src/jalview/commands/SlideSequencesCommand.java		diff \| blob \| history
src/jalview/commands/TrimRegionCommand.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AnnotatedCollectionI.java		diff \| blob \| history
src/jalview/datamodel/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/HiddenSequences.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/exceptions/JalviewException.java	[new file with mode: 0644]	blob
src/jalview/exceptions/NoFileSelectedException.java	[new file with mode: 0644]	blob
src/jalview/ext/jmol/PDBFileWithJmol.java		diff \| blob \| history
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationExporter.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/BlogReader.java		diff \| blob \| history
src/jalview/gui/ChimeraViewFrame.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureRenderer.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/Finder.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/HTMLOptions.java	[new file with mode: 0644]	blob
src/jalview/gui/Help.java		diff \| blob \| history
src/jalview/gui/IdCanvas.java		diff \| blob \| history
src/jalview/gui/IdPanel.java		diff \| blob \| history
src/jalview/gui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/Jalview2XML_V1.java		diff \| blob \| history
src/jalview/gui/JalviewChimeraBindingModel.java		diff \| blob \| history
src/jalview/gui/JvSwingUtils.java		diff \| blob \| history
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/RedundancyPanel.java		diff \| blob \| history
src/jalview/gui/SVGOptions.java	[new file with mode: 0644]	blob
src/jalview/gui/ScalePanel.java		diff \| blob \| history
src/jalview/gui/SeqCanvas.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SliderPanel.java		diff \| blob \| history
src/jalview/gui/WebserviceInfo.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/WsParamSetManager.java		diff \| blob \| history
src/jalview/gui/WsPreferences.java		diff \| blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/BioJsHTMLOutput.java		diff \| blob \| history
src/jalview/io/FormatAdapter.java		diff \| blob \| history
src/jalview/io/HtmlFile.java		diff \| blob \| history
src/jalview/io/HtmlSvgOutput.java	[new file with mode: 0644]	blob
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/RnamlFile.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GStructureViewer.java		diff \| blob \| history
src/jalview/json/binding/v1/BioJsAlignmentPojo.java		diff \| blob \| history
src/jalview/math/AlignmentDimension.java	[new file with mode: 0644]	blob
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/schemes/AnnotationColourGradient.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeProperty.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/util/ImageMaker.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/ws/DasSequenceFeatureFetcher.java		diff \| blob \| history
src/jalview/ws/HttpClientUtils.java		diff \| blob \| history
src/jalview/ws/jws1/JPredClient.java		diff \| blob \| history
src/jalview/ws/jws1/JPredThread.java		diff \| blob \| history
src/jalview/ws/jws1/WS1Client.java		diff \| blob \| history
src/jalview/ws/jws2/AADisorderClient.java		diff \| blob \| history
src/jalview/ws/jws2/JabaWsServerQuery.java		diff \| blob \| history
src/jalview/ws/jws2/JabawsCalcWorker.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Client.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Discoverer.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java		diff \| blob \| history
src/jalview/ws/rest/RestClient.java		diff \| blob \| history
test/jalview/commands/EditCommandTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/SequenceTest.java		diff \| blob \| history
test/jalview/ext/jmol/PDBFileWithJmolTest.java		diff \| blob \| history
test/jalview/ext/paradise/TestAnnotate3D.java		diff \| blob \| history
test/jalview/gui/HelpTest.java	[new file with mode: 0644]	blob
test/jalview/gui/PopupMenuTest.java		diff \| blob \| history
test/jalview/io/BioJsHTMLOutputTest.java	[new file with mode: 0644]	blob
test/jalview/io/HtmlFileTest.java	[new file with mode: 0644]	blob
test/jalview/io/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/io/RNAMLfileTest.java		diff \| blob \| history
test/jalview/io/StockholmFileTest.java		diff \| blob \| history
test/jalview/io/testProps.jvprops	[new file with mode: 0644]	blob
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java		diff \| blob \| history
utils/InstallAnywhere/Jalview.iap_xml		diff \| blob \| history

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