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

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

author	gmungoc <g.m.carstairs@dundee.ac.uk>
	Mon, 13 Aug 2018 10:10:16 +0000 (11:10 +0100)
committer	gmungoc <g.m.carstairs@dundee.ac.uk>
	Mon, 13 Aug 2018 10:10:16 +0000 (11:10 +0100)
commit	2b618ede76f5a9d2f1be7db9aad8bb3a2b10e23b
tree	8d597aa17ee84552ecb835db12bc384ea53e6e5c	tree \| snapshot
parent	ac4a041c0706baca6fd04570bf37e8264457ea86	commit \| diff

update spikes/mungo from JAL-3076 patch branch

163 files changed:

.classpath		diff \| blob \| history
.gitignore		diff \| blob \| history
RELEASE		diff \| blob \| history
THIRDPARTYLIBS		diff \| blob \| history
build.xml		diff \| blob \| history
help/help.jhm		diff \| blob \| history
help/helpTOC.xml		diff \| blob \| history
help/html/editing/index.html		diff \| blob \| history
help/html/features/clarguments.html		diff \| blob \| history
help/html/features/preferences.html		diff \| blob \| history
help/html/features/search.html		diff \| blob \| history
help/html/features/searchclearhist.png		diff \| blob \| history
help/html/features/seqfeatures.html		diff \| blob \| history
help/html/features/seqfetch.html		diff \| blob \| history
help/html/menus/alignmentMenu.html		diff \| blob \| history
help/html/menus/alwview.html		diff \| blob \| history
help/html/menus/wsmenu.html		diff \| blob \| history
help/html/releases.html		diff \| blob \| history
help/html/webServices/dbreffetcher.html		diff \| blob \| history
help/html/webServices/index.html		diff \| blob \| history
nbbuild.xml		diff \| blob \| history
resources/lang/Messages.properties		diff \| blob \| history
resources/lang/Messages_es.properties		diff \| blob \| history
schemas/jalview.xsd		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/api/AlignCalcWorkerI.java		diff \| blob \| history
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignViewport.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/OverviewPanel.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/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AlignmentOrder.java		diff \| blob \| history
src/jalview/datamodel/AnnotatedCollectionI.java		diff \| blob \| history
src/jalview/datamodel/ResidueCount.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceCollectionI.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureAttributes.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeatures.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeaturesI.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblCdna.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblCds.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblFeatures.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGene.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGenome.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblInfo.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblLookup.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblMap.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblProtein.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblRestClient.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSeqProxy.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblXref.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/CalculationChooser.java		diff \| blob \| history
src/jalview/gui/ColourMenuHelper.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/FeatureTypeSettings.java		diff \| blob \| history
src/jalview/gui/JDatabaseTree.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/Jalview2XML_V1.java		diff \| blob \| history
src/jalview/gui/JvSwingUtils.java		diff \| blob \| history
src/jalview/gui/OptsAndParamsPage.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/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SplitFrame.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/WsParamSetManager.java		diff \| blob \| history
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/FileFormat.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/cache/JvCacheableInputBox.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GRestInputParamEditDialog.java		diff \| blob \| history
src/jalview/jbgui/GRestServiceEditorPane.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/ResidueShaderI.java		diff \| blob \| history
src/jalview/schemabinding/version2/JSeq.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java		diff \| blob \| history
src/jalview/schemes/JalviewColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/util/MapList.java		diff \| blob \| history
src/jalview/util/MappingUtils.java		diff \| blob \| history
src/jalview/util/Platform.java		diff \| blob \| history
src/jalview/util/StringUtils.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/workers/AlignCalcManager.java		diff \| blob \| history
src/jalview/workers/ConsensusThread.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/SequenceFetcher.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Client.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/jws2/dm/JabaOption.java		diff \| blob \| history
src/jalview/ws/params/OptionI.java		diff \| blob \| history
src/jalview/ws/params/ValueConstrainI.java		diff \| blob \| history
src/jalview/ws/params/simple/BooleanOption.java		diff \| blob \| history
src/jalview/ws/params/simple/IntegerParameter.java		diff \| blob \| history
src/jalview/ws/params/simple/Option.java		diff \| blob \| history
src/jalview/ws/params/simple/StringChoiceParameter.java		diff \| blob \| history
src/jalview/ws/rest/InputType.java		diff \| blob \| history
test/jalview/analysis/AAFrequencyTest.java		diff \| blob \| history
test/jalview/analysis/AlignmentUtilsTests.java		diff \| blob \| history
test/jalview/analysis/CrossRefTest.java		diff \| blob \| history
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java		diff \| blob \| history
test/jalview/datamodel/AlignmentTest.java		diff \| blob \| history
test/jalview/datamodel/AlignmentViewTest.java		diff \| blob \| history
test/jalview/datamodel/HiddenSequencesTest.java		diff \| blob \| history
test/jalview/datamodel/ResidueCountTest.java		diff \| blob \| history
test/jalview/datamodel/SequenceGroupTest.java		diff \| blob \| history
test/jalview/datamodel/features/FeatureAttributesTest.java		diff \| blob \| history
test/jalview/datamodel/features/SequenceFeaturesTest.java		diff \| blob \| history
test/jalview/ext/ensembl/EnsemblCdnaTest.java		diff \| blob \| history
test/jalview/ext/ensembl/EnsemblCdsTest.java		diff \| blob \| history
test/jalview/ext/ensembl/EnsemblGeneTest.java		diff \| blob \| history
test/jalview/ext/ensembl/EnsemblGenomeTest.java		diff \| blob \| history
test/jalview/ext/ensembl/EnsemblRestClientTest.java		diff \| blob \| history
test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java		diff \| blob \| history
test/jalview/ext/ensembl/EnsemblSeqProxyTest.java		diff \| blob \| history
test/jalview/gui/AlignFrameTest.java		diff \| blob \| history
test/jalview/gui/AlignViewportTest.java		diff \| blob \| history
test/jalview/gui/PairwiseAlignmentPanelTest.java		diff \| blob \| history
test/jalview/gui/SequenceRendererTest.java		diff \| blob \| history
test/jalview/io/FileFormatsTest.java		diff \| blob \| history
test/jalview/io/FileLoaderTest.java		diff \| blob \| history
test/jalview/io/FormatAdapterTest.java		diff \| blob \| history
test/jalview/io/JSONFileTest.java		diff \| blob \| history
test/jalview/io/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/io/StockholmFileTest.java		diff \| blob \| history
test/jalview/renderer/OverviewResColourFinderTest.java		diff \| blob \| history
test/jalview/renderer/ResidueColourFinderTest.java		diff \| blob \| history
test/jalview/renderer/ScaleRendererTest.java		diff \| blob \| history
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java		diff \| blob \| history
test/jalview/schemes/ClustalxColourSchemeTest.java		diff \| blob \| history
test/jalview/schemes/PIDColourSchemeTest.java		diff \| blob \| history
test/jalview/util/MapListTest.java		diff \| blob \| history
test/jalview/util/MappingUtilsTest.java		diff \| blob \| history
test/jalview/util/StringUtilsTest.java		diff \| blob \| history
test/jalview/ws/PDBSequenceFetcherTest.java		diff \| blob \| history
test/jalview/ws/SequenceFetcherTest.java		diff \| blob \| history
test/jalview/ws/dbsources/RemoteFormatTest.java		diff \| blob \| history
test/jalview/ws/gui/Jws2ParamView.java		diff \| blob \| history
utils/i18nAnt.xml		diff \| blob \| history

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