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

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

author	gmungoc <g.m.carstairs@dundee.ac.uk>
	Fri, 30 Mar 2018 14:56:41 +0000 (15:56 +0100)
committer	gmungoc <g.m.carstairs@dundee.ac.uk>
	Fri, 30 Mar 2018 14:56:41 +0000 (15:56 +0100)
commit	04a4d60a50394d846d0479c442facebe360b5b9c
tree	9f6bb376a6ce55288c06f241f1051093d73dafe3	tree \| snapshot
parent	653e250e0a2a5dd455ae4c52794c4ce0de340418	commit \| diff

Updated with latest from mchmmer branch

221 files changed:

.classpath		diff \| blob \| history
RELEASE		diff \| blob \| history
benchmarking/README		diff \| blob \| history
benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java		diff \| blob \| history
build.xml		diff \| blob \| history
examples/testdata/4IM2_missing.pdb	[new file with mode: 0644]	blob
examples/testdata/4IM2_missing_noid.pdb	[new file with mode: 0644]	blob
examples/testdata/4IM2_nterm.pdb	[new file with mode: 0644]	blob
examples/uniref50.hmm	[new file with mode: 0644]	blob
help/help.jhm		diff \| blob \| history
help/helpTOC.xml		diff \| blob \| history
help/html/features/preferences.html		diff \| blob \| history
help/html/features/splitView.html		diff \| blob \| history
help/html/menus/alwhmmer.html	[new file with mode: 0644]	blob
help/html/releases.html		diff \| blob \| history
help/html/whatsNew.html		diff \| blob \| history
resources/lang/Messages.properties		diff \| blob \| history
src/MCview/PDBChain.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/Dna.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/api/structures/JalviewStructureDisplayI.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/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/IdCanvas.java		diff \| blob \| history
src/jalview/appletgui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/appletgui/OverviewCanvas.java		diff \| blob \| history
src/jalview/appletgui/OverviewPanel.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqCanvas.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/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/CigarArray.java		diff \| blob \| history
src/jalview/datamodel/DBRefSource.java		diff \| blob \| history
src/jalview/datamodel/HMMNode.java	[new file with mode: 0644]	blob
src/jalview/datamodel/HiddenColumns.java		diff \| blob \| history
src/jalview/datamodel/HiddenColumnsCursor.java	[new file with mode: 0644]	blob
src/jalview/datamodel/HiddenCursorPosition.java	[new file with mode: 0644]	blob
src/jalview/datamodel/HiddenMarkovModel.java	[new file with mode: 0644]	blob
src/jalview/datamodel/RangeElementsIterator.java	[new file with mode: 0644]	blob
src/jalview/datamodel/RangeIterator.java	[new file with mode: 0644]	blob
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/StartRegionIterator.java	[new file with mode: 0644]	blob
src/jalview/datamodel/VisibleColsCollection.java		diff \| blob \| history
src/jalview/datamodel/VisibleColsIterator.java	[deleted file]	blob \| history
src/jalview/datamodel/VisibleContigsIterator.java	[new file with mode: 0644]	blob
src/jalview/ext/ensembl/EnsemblGenomes.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/EnsemblRestClient.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java		diff \| blob \| history
src/jalview/ext/jmol/JmolCommands.java		diff \| blob \| history
src/jalview/fts/service/uniprot/UniProtFTSRestClient.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/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.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/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/OptsAndParamsPage.java		diff \| blob \| history
src/jalview/gui/OverviewCanvas.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/RotatableCanvas.java		diff \| blob \| history
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/SplitFrame.java		diff \| blob \| history
src/jalview/gui/StructureChooser.java		diff \| blob \| history
src/jalview/gui/StructureViewer.java		diff \| blob \| history
src/jalview/gui/StructureViewerBase.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/hmmer/HMMAlign.java	[new file with mode: 0644]	blob
src/jalview/hmmer/HMMBuild.java	[new file with mode: 0644]	blob
src/jalview/hmmer/HMMERParamStore.java	[new file with mode: 0644]	blob
src/jalview/hmmer/HMMERPreset.java	[new file with mode: 0644]	blob
src/jalview/hmmer/HMMSearch.java	[new file with mode: 0644]	blob
src/jalview/hmmer/HmmerCommand.java	[new file with mode: 0644]	blob
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/AnnotationFile.java		diff \| blob \| history
src/jalview/io/FileFormat.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/FormatAdapter.java		diff \| blob \| history
src/jalview/io/HMMFile.java	[new file with mode: 0644]	blob
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/ResidueShaderI.java		diff \| blob \| history
src/jalview/renderer/ScaleRenderer.java		diff \| blob \| history
src/jalview/schemes/HmmerColourScheme.java	[new file with mode: 0644]	blob
src/jalview/schemes/HmmerGlobalBackground.java	[new file with mode: 0644]	blob
src/jalview/schemes/HmmerLocalBackground.java	[new file with mode: 0644]	blob
src/jalview/schemes/JalviewColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/structure/StructureMapping.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/util/HMMProbabilityDistributionAnalyser.java	[new file with mode: 0644]	blob
src/jalview/util/MapList.java		diff \| blob \| history
src/jalview/util/MappingUtils.java		diff \| blob \| history
src/jalview/util/ProbabilityAnalyserKickstarter.java	[new file with mode: 0644]	blob
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensions.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensionsHideHidden.java		diff \| blob \| history
src/jalview/viewmodel/OverviewDimensionsShowHidden.java		diff \| blob \| history
src/jalview/viewmodel/ViewportRanges.java		diff \| blob \| history
src/jalview/workers/AlignCalcManager.java		diff \| blob \| history
src/jalview/workers/ConsensusThread.java		diff \| blob \| history
src/jalview/workers/InformationThread.java	[new file with mode: 0644]	blob
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/dbsources/Pfam.java		diff \| blob \| history
src/jalview/ws/dbsources/PfamFull.java		diff \| blob \| history
src/jalview/ws/dbsources/PfamSeed.java		diff \| blob \| history
src/jalview/ws/dbsources/Rfam.java		diff \| blob \| history
src/jalview/ws/dbsources/RfamFull.java		diff \| blob \| history
src/jalview/ws/dbsources/RfamSeed.java		diff \| blob \| history
src/jalview/ws/dbsources/Uniprot.java		diff \| blob \| history
src/jalview/ws/dbsources/Xfam.java		diff \| blob \| history
src/jalview/ws/jws1/JPredThread.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/params/ValueConstrainI.java		diff \| blob \| history
src/jalview/ws/params/simple/DoubleParameter.java	[new file with mode: 0644]	blob
src/jalview/ws/params/simple/LogarithmicParameter.java	[new file with mode: 0644]	blob
src/jalview/ws/params/simple/StringParameter.java	[new file with mode: 0644]	blob
src/jalview/ws/sifts/SiftsClient.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/DnaTest.java		diff \| blob \| history
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java		diff \| blob \| history
test/jalview/datamodel/AlignmentAnnotationTests.java		diff \| blob \| history
test/jalview/datamodel/AlignmentTest.java		diff \| blob \| history
test/jalview/datamodel/AlignmentViewTest.java		diff \| blob \| history
test/jalview/datamodel/ColumnSelectionTest.java		diff \| blob \| history
test/jalview/datamodel/HMMNodeTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/HiddenColumnsCursorTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/HiddenColumnsTest.java		diff \| blob \| history
test/jalview/datamodel/HiddenMarkovModelTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/HiddenSequencesTest.java		diff \| blob \| history
test/jalview/datamodel/RangeElementsIteratorTest.java	[moved from test/jalview/datamodel/VisibleColsIteratorTest.java with 84% similarity]	diff \| blob \| history
test/jalview/datamodel/ResidueCountTest.java		diff \| blob \| history
test/jalview/datamodel/SequenceGroupTest.java		diff \| blob \| history
test/jalview/datamodel/SequenceTest.java		diff \| blob \| history
test/jalview/datamodel/StartRegionIteratorTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/VisibleContigsIteratorTest.java	[new file with mode: 0644]	blob
test/jalview/ext/ensembl/EnsemblGeneTest.java		diff \| blob \| history
test/jalview/ext/jmol/JmolCommandsTest.java		diff \| blob \| history
test/jalview/gui/AlignFrameTest.java		diff \| blob \| history
test/jalview/gui/AlignViewportTest.java		diff \| blob \| history
test/jalview/gui/AnnotationColumnChooserTest.java		diff \| blob \| history
test/jalview/gui/PairwiseAlignmentPanelTest.java		diff \| blob \| history
test/jalview/gui/PopupMenuTest.java		diff \| blob \| history
test/jalview/gui/SequenceRendererTest.java		diff \| blob \| history
test/jalview/hmmer/HMMERTest.java	[new file with mode: 0644]	blob
test/jalview/hmmer/testProps.jvprops	[new file with mode: 0644]	blob
test/jalview/io/AnnotatedPDBFileInputTest.java		diff \| blob \| history
test/jalview/io/CrossRef2xmlTests.java		diff \| blob \| history
test/jalview/io/FileFormatsTest.java		diff \| blob \| history
test/jalview/io/FormatAdapterTest.java		diff \| blob \| history
test/jalview/io/HMMFileTest.java	[new file with mode: 0644]	blob
test/jalview/io/JSONFileTest.java		diff \| blob \| history
test/jalview/io/Jalview2xmlBase.java		diff \| blob \| history
test/jalview/io/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/io/StockholmFileTest.java		diff \| blob \| history
test/jalview/io/test_MADE1_hmm.txt	[new file with mode: 0644]	blob
test/jalview/io/test_PKinase_hmm.txt	[new file with mode: 0644]	blob
test/jalview/io/test_fn3_hmm.txt	[new file with mode: 0644]	blob
test/jalview/io/vcf/VCFLoaderTest.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/HmmerGlobalBackgroundTest.java	[new file with mode: 0644]	blob
test/jalview/schemes/HmmerLocalBackgroundTest.java	[new file with mode: 0644]	blob
test/jalview/schemes/PIDColourSchemeTest.java		diff \| blob \| history
test/jalview/structure/StructureSelectionManagerTest.java		diff \| blob \| history
test/jalview/util/Binned.csv	[new file with mode: 0644]	blob
test/jalview/util/HMMProbabilityDistributionAnalyserTest.java	[new file with mode: 0644]	blob
test/jalview/util/MapListTest.java		diff \| blob \| history
test/jalview/util/MappingUtilsTest.java		diff \| blob \| history
test/jalview/util/Raw.csv	[new file with mode: 0644]	blob
test/jalview/util/test_Fams_for_probability_analysis	[new file with mode: 0644]	blob
test/jalview/util/test_hmms_for_probability_analysis	[new file with mode: 0644]	blob
test/jalview/ws/PDBSequenceFetcherTest.java		diff \| blob \| history
test/jalview/ws/dbsources/PfamFullTest.java	[new file with mode: 0644]	blob
test/jalview/ws/dbsources/PfamSeedTest.java	[new file with mode: 0644]	blob
test/jalview/ws/dbsources/RfamFullTest.java	[new file with mode: 0644]	blob
test/jalview/ws/dbsources/RfamSeedTest.java	[new file with mode: 0644]	blob
test/jalview/ws/dbsources/XfamFetcherTest.java		diff \| blob \| history
test/jalview/ws/sifts/SiftsClientTest.java		diff \| blob \| history

RSS Atom