JAL-2089 Merge branch releases/Release_2_10_Branch to master
authorJim Procter <jprocter@issues.jalview.org>
Thu, 6 Oct 2016 00:13:56 +0000 (01:13 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Thu, 6 Oct 2016 00:15:35 +0000 (01:15 +0100)
404 files changed:
1  2 
build.xml
doc/AddingGroovySupport.html
doc/building.html
examples/appletParameters.html
examples/applets.html
examples/embedded.html
examples/formComplete.html
examples/groovy/printtitle.groovy
examples/includes/nav_jv.html
examples/javascriptLaunch.html
examples/linkedapplets_ng.html
help/help.jhm
help/helpTOC.xml
help/html/calculations/consensus.html
help/html/calculations/conservation.html
help/html/calculations/pca.html
help/html/calculations/quality.html
help/html/calculations/redundancy.html
help/html/calculations/referenceseq.html
help/html/calculations/scorematrices.html
help/html/calculations/sorting.html
help/html/calculations/structureconsensus.html
help/html/calculations/tree.html
help/html/calculations/treeviewer.html
help/html/colourSchemes/annotationColouring.html
help/html/colourSchemes/conservation.html
help/html/colourSchemes/index.html
help/html/colourSchemes/rnahelicesColouring.html
help/html/editing/index.html
help/html/features/annotation.html
help/html/features/annotationsFormat.html
help/html/features/bioJsonFormat.html
help/html/features/chimera.html
help/html/features/clarguments.html
help/html/features/columnFilterByAnnotation.html
help/html/features/commandline.html
help/html/features/creatinFeatures.html
help/html/features/dasfeatures.html
help/html/features/dassettings.html
help/html/features/editingFeatures.html
help/html/features/featuresFormat.html
help/html/features/featuresettings.html
help/html/features/groovy.html
help/html/features/hiddenRegions.html
help/html/features/jmol.html
help/html/features/multipleViews.html
help/html/features/pdbsequencefetcher.html
help/html/features/pdbviewer.html
help/html/features/preferences.html
help/html/features/seqfeatures.html
help/html/features/seqfetch.html
help/html/features/seqmappings.html
help/html/features/splitView.html
help/html/features/structurechooser.html
help/html/features/varna.html
help/html/features/viewingpdbs.html
help/html/features/xsspannotation.html
help/html/index.html
help/html/io/export.html
help/html/io/exportseqreport.html
help/html/io/fileformats.html
help/html/io/index.html
help/html/io/modellerpir.html
help/html/io/tcoffeescores.html
help/html/keys.html
help/html/memory.html
help/html/menus/alignmentMenu.html
help/html/menus/alwannotation.html
help/html/menus/alwannotationpanel.html
help/html/menus/alwcalculate.html
help/html/menus/alwedit.html
help/html/menus/alwfile.html
help/html/menus/alwformat.html
help/html/menus/alwselect.html
help/html/menus/desktopMenu.html
help/html/menus/index.html
help/html/menus/popupMenu.html
help/html/menus/wsmenu.html
help/html/na/index.html
help/html/privacy.html
help/html/releases.html
help/html/vamsas/index.html
help/html/webServices/AACon.html
help/html/webServices/JABAWS.html
help/html/webServices/RNAalifold.html
help/html/webServices/dbreffetcher.html
help/html/webServices/index.html
help/html/webServices/jnet.html
help/html/webServices/msaclient.html
help/html/webServices/newsreader.html
help/html/webServices/proteinDisorder.html
help/html/webServices/shmr.html
help/html/webServices/urllinks.html
help/html/webServices/webServicesParams.html
help/html/webServices/webServicesPrefs.html
help/html/whatsNew.html
resources/embl_mapping.xml
schemas/jalview.xsd
src/MCview/AppletPDBCanvas.java
src/MCview/Atom.java
src/MCview/PDBCanvas.java
src/MCview/PDBChain.java
src/MCview/PDBViewer.java
src/MCview/PDBfile.java
src/MCview/Residue.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/Grouping.java
src/jalview/analysis/NJTree.java
src/jalview/analysis/Rna.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/SequenceIdMatcher.java
src/jalview/analysis/StructureFrequency.java
src/jalview/analysis/scoremodels/FeatureScoreModel.java
src/jalview/api/AlignCalcManagerI.java
src/jalview/api/AlignCalcWorkerI.java
src/jalview/api/AlignViewControllerI.java
src/jalview/api/AlignViewportI.java
src/jalview/api/FeatureRenderer.java
src/jalview/api/FeatureSettingsModelI.java
src/jalview/api/FeaturesDisplayedI.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/AnnotationColumnChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/AnnotationRowFilter.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/IdCanvas.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SequenceRenderer.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/JalviewLiteURLRetrieve.java
src/jalview/commands/TrimRegionCommand.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/AlignedCodon.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/CigarBase.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/DBRefSource.java
src/jalview/datamodel/FeatureProperties.java
src/jalview/datamodel/HiddenSequences.java
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/PDBEntry.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/SeqCigar.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceDummy.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/datamodel/xdb/embl/EmblFeature.java
src/jalview/datamodel/xdb/embl/EmblFile.java
src/jalview/datamodel/xdb/embl/EmblSequence.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/fts/api/FTSData.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationColumnChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AnnotationRowFilter.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/BlogReader.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/CutAndPasteHtmlTransfer.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureColourChooser.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/FontChooser.java
src/jalview/gui/Help.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.java
src/jalview/gui/JDatabaseTree.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/JalviewDialog.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/RedundancyPanel.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SequenceRenderer.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/TextColourChooser.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/VamsasApplication.java
src/jalview/io/AlignFile.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/ClustalFile.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/FormatAdapter.java
src/jalview/io/HtmlFile.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JSONFile.java
src/jalview/io/MSFfile.java
src/jalview/io/ModellerDescription.java
src/jalview/io/PIRFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/RnamlFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/WSWUBlastClient.java
src/jalview/io/packed/JalviewDataset.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/io/vamsas/DatastoreRegistry.java
src/jalview/io/vamsas/Sequencefeature.java
src/jalview/io/vamsas/Sequencemapping.java
src/jalview/io/vamsas/Tree.java
src/jalview/javascript/JSFunctionExec.java
src/jalview/javascript/JsSelectionSender.java
src/jalview/javascript/MouseOverStructureListener.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
src/jalview/jbgui/GCutAndPasteTransfer.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/schemes/RNAHelicesColour.java
src/jalview/schemes/RNAHelicesColourChooser.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/TCoffeeColourScheme.java
src/jalview/schemes/UserColourScheme.java
src/jalview/structure/StructureMapping.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/util/ColorUtils.java
src/jalview/util/Comparison.java
src/jalview/util/DBRefUtils.java
src/jalview/util/ImageMaker.java
src/jalview/util/MapList.java
src/jalview/util/MappingUtils.java
src/jalview/util/Platform.java
src/jalview/util/QuickSort.java
src/jalview/util/StringUtils.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
src/jalview/workers/AlignCalcManager.java
src/jalview/workers/AlignCalcWorker.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/ConservationThread.java
src/jalview/workers/StrucConsensusThread.java
src/jalview/ws/AWSThread.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/DasSequenceFeatureFetcher.java
src/jalview/ws/SequenceFetcher.java
src/jalview/ws/dbsources/EmblCdsSource.java
src/jalview/ws/dbsources/EmblSource.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/dbsources/GeneDbSource.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/dbsources/Pfam.java
src/jalview/ws/dbsources/PfamFull.java
src/jalview/ws/dbsources/PfamSeed.java
src/jalview/ws/dbsources/Rfam.java
src/jalview/ws/dbsources/RfamFull.java
src/jalview/ws/dbsources/RfamSeed.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/dbsources/UniprotName.java
src/jalview/ws/dbsources/Xfam.java
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
src/jalview/ws/ebi/EBIFetchClient.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/MsaWSClient.java
src/jalview/ws/jws1/MsaWSThread.java
src/jalview/ws/jws1/SeqSearchWSClient.java
src/jalview/ws/jws1/SeqSearchWSThread.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
src/jalview/ws/jws2/JPred301Client.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/jws2/MsaWSThread.java
src/jalview/ws/jws2/RNAalifoldClient.java
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
src/jalview/ws/seqfetcher/ASequenceFetcher.java
src/jalview/ws/seqfetcher/DbSourceProxy.java
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
test/MCview/AtomTest.java
test/MCview/PDBChainTest.java
test/MCview/PDBfileTest.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/CrossRefTest.java
test/jalview/analysis/DnaTest.java
test/jalview/analysis/GroupingTest.java
test/jalview/analysis/RnaTest.java
test/jalview/analysis/TestAlignSeq.java
test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
test/jalview/commands/EditCommandTest.java
test/jalview/datamodel/AlignedCodonFrameTest.java
test/jalview/datamodel/AlignmentAnnotationTests.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/datamodel/ColumnSelectionTest.java
test/jalview/datamodel/DBRefEntryTest.java
test/jalview/datamodel/MappingTest.java
test/jalview/datamodel/SearchResultsTest.java
test/jalview/datamodel/SeqCigarTest.java
test/jalview/datamodel/SequenceDummyTest.java
test/jalview/datamodel/SequenceTest.java
test/jalview/datamodel/xdb/embl/EmblFileTest.java
test/jalview/ext/jmol/JmolViewerTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
test/jalview/fts/service/pdb/PDBFTSPanelTest.java
test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/gui/AnnotationChooserTest.java
test/jalview/gui/JAL1353bugdemo.java
test/jalview/gui/PaintRefresherTest.java
test/jalview/gui/StructureChooserTest.java
test/jalview/io/AnnotatedPDBFileInputTest.java
test/jalview/io/AnnotationFileIOTest.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/FileIOTester.java
test/jalview/io/HtmlFileTest.java
test/jalview/io/IdentifyFileTest.java
test/jalview/io/JSONFileTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/JalviewExportPropertiesTests.java
test/jalview/io/NewickFileTests.java
test/jalview/io/RNAMLfileTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/schemes/DnaCodonTests.java
test/jalview/schemes/ResiduePropertiesTest.java
test/jalview/structure/Mapping.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/util/ColorUtilsTest.java
test/jalview/util/ComparisonTest.java
test/jalview/util/DBRefUtilsTest.java
test/jalview/util/MapListTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/util/QuickSortTest.java
test/jalview/util/StringUtilsTest.java
test/jalview/ws/PDBSequenceFetcherTest.java
test/jalview/ws/dbsources/UniprotTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/jws2/ParameterUtilsTest.java
test/jalview/ws/seqfetcher/DbRefFetcherTest.java
utils/InstallAnywhere/Jalview.iap_xml
utils/JettyExamplesDir.java
utils/getJavaVersion.java
utils/help2Website.java

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diff --cc help/help.jhm
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@@@ -47,11 -50,13 +50,14 @@@ import org.testng.annotations.AfterClas
  import org.testng.annotations.BeforeClass;
  import org.testng.annotations.Test;
  
+ import compbio.metadata.Argument;
  import compbio.metadata.WrongParameterException;
  
 +
  public class RNAStructExportImport
  {
+   private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
    public static String testseqs = "examples/RF00031_folded.stk";
  
    public static Jws2Discoverer disc;
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