X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=classlists%2Fjvexamplefile.txt;h=ae01fe13056b70013838c09c17f680bba6c80e93;hb=2ea1fb1e8751ac7272c421820000449525664f02;hp=444b0bf6184f7e07a158d3fd6452032b456aea0a;hpb=2359e3ec0c8ebbd3c62b029453bd77122cdede4f;p=jalview.git diff --git a/classlists/jvexamplefile.txt b/classlists/jvexamplefile.txt index 444b0bf..ae01fe1 100644 --- a/classlists/jvexamplefile.txt +++ b/classlists/jvexamplefile.txt @@ -1,3 +1,4 @@ + com/stevesoft/pat/Any.js com/stevesoft/pat/Bracket.js com/stevesoft/pat/Branch.js @@ -22,10 +23,12 @@ com/stevesoft/pat/Pattern.js com/stevesoft/pat/PatternSub.js com/stevesoft/pat/Pthings.js com/stevesoft/pat/Range.js +com/stevesoft/pat/RegHolder.js com/stevesoft/pat/RegOpt.js com/stevesoft/pat/RegRes.js com/stevesoft/pat/Regex.js com/stevesoft/pat/ReplaceRule.js +com/stevesoft/pat/Replacer.js com/stevesoft/pat/Rthings.js com/stevesoft/pat/Skip.js com/stevesoft/pat/StrPos.js @@ -56,19 +59,26 @@ intervalstore/impl/NCList.js intervalstore/impl/NCNode.js jalview/analysis/AAFrequency.js jalview/analysis/AlignSeq.js +jalview/analysis/AlignmentAnnotationUtils.js jalview/analysis/AlignmentUtils.js jalview/analysis/AnnotationSorter.js +jalview/analysis/AverageDistanceTree.js jalview/analysis/Conservation.js jalview/analysis/CrossRef.js jalview/analysis/GeneticCodeI.js jalview/analysis/GeneticCodes.js +jalview/analysis/Grouping.js +jalview/analysis/NJTree.js +jalview/analysis/SeqsetUtils.js jalview/analysis/SequenceIdMatcher.js +jalview/analysis/TreeBuilder.js jalview/analysis/TreeModel.js jalview/analysis/scoremodels/DistanceScoreModel.js jalview/analysis/scoremodels/FeatureDistanceModel.js jalview/analysis/scoremodels/PIDModel.js jalview/analysis/scoremodels/ScoreMatrix.js jalview/analysis/scoremodels/ScoreModels.js +jalview/analysis/scoremodels/SimilarityParams.js jalview/analysis/scoremodels/SimilarityScoreModel.js jalview/api/AlignCalcManagerI.js jalview/api/AlignCalcWorkerI.js @@ -93,6 +103,7 @@ jalview/api/StructureSelectionManagerProvider.js jalview/api/ViewStyleI.js jalview/api/analysis/PairwiseScoreModelI.js jalview/api/analysis/ScoreModelI.js +jalview/api/analysis/SimilarityParamsI.js jalview/api/structures/JalviewStructureDisplayI.js jalview/bin/ArgsParser.js jalview/bin/BuildDetails.js @@ -104,13 +115,18 @@ jalview/datamodel/ASequenceI.js jalview/datamodel/Alignment.js jalview/datamodel/AlignmentAnnotation.js jalview/datamodel/AlignmentI.js +jalview/datamodel/AlignmentView.js jalview/datamodel/AnnotatedCollectionI.js jalview/datamodel/Annotation.js jalview/datamodel/BinaryNode.js +jalview/datamodel/CigarArray.js +jalview/datamodel/CigarBase.js +jalview/datamodel/CigarSimple.js jalview/datamodel/ColumnSelection.js jalview/datamodel/ContiguousI.js jalview/datamodel/DBRefEntry.js jalview/datamodel/DBRefSource.js +jalview/datamodel/GraphLine.js jalview/datamodel/HiddenColumns.js jalview/datamodel/HiddenColumnsCursor.js jalview/datamodel/HiddenCursorPosition.js @@ -128,6 +144,7 @@ jalview/datamodel/ResidueCount.js jalview/datamodel/SearchResultMatchI.js jalview/datamodel/SearchResults.js jalview/datamodel/SearchResultsI.js +jalview/datamodel/SeqCigar.js jalview/datamodel/Sequence.js jalview/datamodel/SequenceCollectionI.js jalview/datamodel/SequenceCursor.js @@ -135,6 +152,7 @@ jalview/datamodel/SequenceFeature.js jalview/datamodel/SequenceGroup.js jalview/datamodel/SequenceI.js jalview/datamodel/SequenceNode.js +jalview/datamodel/StartRegionIterator.js jalview/datamodel/StructureViewerModel.js jalview/datamodel/VisibleColsCollection.js jalview/datamodel/VisibleContigsIterator.js @@ -144,6 +162,7 @@ jalview/datamodel/features/FeatureAttributes.js jalview/datamodel/features/FeatureLocationI.js jalview/datamodel/features/FeatureMatcherSet.js jalview/datamodel/features/FeatureMatcherSetI.js +jalview/datamodel/features/FeatureSources.js jalview/datamodel/features/FeatureStore.js jalview/datamodel/features/SequenceFeatures.js jalview/datamodel/features/SequenceFeaturesI.js @@ -173,16 +192,20 @@ jalview/fts/service/uniprot/UniprotFTSPanel.js jalview/gui/AlignFrame.js jalview/gui/AlignViewport.js jalview/gui/AlignmentPanel.js +jalview/gui/AnnotationColumnChooser.js jalview/gui/AnnotationLabels.js jalview/gui/AnnotationPanel.js +jalview/gui/AnnotationRowFilter.js jalview/gui/AppJmol.js jalview/gui/AppJmolBinding.js +jalview/gui/CalculationChooser.js jalview/gui/ColourMenuHelper.js jalview/gui/ComboBoxTooltipRenderer.js jalview/gui/Desktop.js jalview/gui/FeatureRenderer.js jalview/gui/FeatureSettings.js jalview/gui/FeatureTypeSettings.js +jalview/gui/FontChooser.js jalview/gui/IProgressIndicator.js jalview/gui/IdCanvas.js jalview/gui/IdPanel.js @@ -195,6 +218,7 @@ jalview/gui/JvSwingUtils.js jalview/gui/OverviewCanvas.js jalview/gui/OverviewPanel.js jalview/gui/PaintRefresher.js +jalview/gui/PopupMenu.js jalview/gui/Preferences.js jalview/gui/ProgressBar.js jalview/gui/ProgressPanel.js @@ -204,6 +228,7 @@ jalview/gui/SeqPanel.js jalview/gui/SequenceFetcher.js jalview/gui/SequenceRenderer.js jalview/gui/SliderPanel.js +jalview/gui/StructureChooser.js jalview/gui/StructureViewer.js jalview/gui/StructureViewerBase.js jalview/gui/TreeCanvas.js @@ -212,8 +237,10 @@ jalview/gui/ViewSelectionMenu.js jalview/io/AlignFile.js jalview/io/AlignmentFileReaderI.js jalview/io/AlignmentFileWriterI.js +jalview/io/AnnotationFile.js jalview/io/AppletFormatAdapter.js jalview/io/DataSourceType.js +jalview/io/FastaFile.js jalview/io/FileFormat.js jalview/io/FileFormatI.js jalview/io/FileFormats.js @@ -221,15 +248,18 @@ jalview/io/FileLoader.js jalview/io/FileParse.js jalview/io/FormatAdapter.js jalview/io/IdentifyFile.js +jalview/io/JPredFile.js jalview/io/JalviewFileChooser.js jalview/io/JalviewFileFilter.js jalview/io/JalviewFileView.js +jalview/io/JnetAnnotationMaker.js jalview/io/NewickFile.js jalview/io/PDBFeatureSettings.js jalview/io/PIRFile.js jalview/io/ScoreMatrixFile.js jalview/io/SequenceAnnotationReport.js jalview/io/StructureFile.js +jalview/io/TCoffeeScoreFile.js jalview/io/cache/JvCacheableInputBox.js jalview/javascript/json/JSON.js jalview/javascript/log4j/ConsoleAppender.js @@ -246,11 +276,15 @@ jalview/jbgui/BackupFilesPresetEntry.js jalview/jbgui/GAlignFrame.js jalview/jbgui/GAlignmentPanel.js jalview/jbgui/GDesktop.js +jalview/jbgui/GFontChooser.js jalview/jbgui/GPreferences.js jalview/jbgui/GSliderPanel.js +jalview/jbgui/GStructureChooser.js jalview/jbgui/GStructureViewer.js jalview/jbgui/GTreePanel.js jalview/jbgui/IntKeyStringValueEntry.js +jalview/math/Matrix.js +jalview/math/MatrixI.js jalview/project/Jalview2XML.js jalview/renderer/AnnotationRenderer.js jalview/renderer/AwtRenderPanelI.js @@ -320,6 +354,7 @@ jalview/util/MapList.js jalview/util/MessageManager.js jalview/util/Platform.js jalview/util/QuickSort.js +jalview/util/SetUtils.js jalview/util/StringUtils.js jalview/util/UrlLink.js jalview/util/dialogrunner/DialogRunnerI.js @@ -330,6 +365,7 @@ jalview/viewmodel/OverviewDimensionsHideHidden.js jalview/viewmodel/ViewportListenerI.js jalview/viewmodel/ViewportProperties.js jalview/viewmodel/ViewportRanges.js +jalview/viewmodel/annotationfilter/AnnotationFilterParameter.js jalview/viewmodel/seqfeatures/FeatureRendererModel.js jalview/viewmodel/seqfeatures/FeatureRendererSettings.js jalview/viewmodel/seqfeatures/FeaturesDisplayed.js @@ -362,12 +398,41 @@ jalview/xml/binding/jalview/Annotation.js jalview/xml/binding/jalview/AnnotationElement.js jalview/xml/binding/jalview/Feature.js jalview/xml/binding/jalview/JalviewModel.js +jalview/xml/binding/jalview/ObjectFactory.js jalview/xml/binding/jalview/Pdbentry.js jalview/xml/binding/jalview/Sequence.js jalview/xml/binding/jalview/SequenceSet.js jalview/xml/binding/jalview/SequenceType.js jalview/xml/binding/jalview/VAMSAS.js jalview/xml/binding/jalview/WebServiceParameterSet.js +jalview/xml/binding/uniprot/CitationType.js +jalview/xml/binding/uniprot/CommentType.js +jalview/xml/binding/uniprot/ConsortiumType.js +jalview/xml/binding/uniprot/DbReferenceType.js +jalview/xml/binding/uniprot/Entry.js +jalview/xml/binding/uniprot/EventType.js +jalview/xml/binding/uniprot/EvidenceType.js +jalview/xml/binding/uniprot/EvidencedStringType.js +jalview/xml/binding/uniprot/FeatureType.js +jalview/xml/binding/uniprot/GeneNameType.js +jalview/xml/binding/uniprot/GeneType.js +jalview/xml/binding/uniprot/IsoformType.js +jalview/xml/binding/uniprot/KeywordType.js +jalview/xml/binding/uniprot/LocationType.js +jalview/xml/binding/uniprot/NameListType.js +jalview/xml/binding/uniprot/OrganismNameType.js +jalview/xml/binding/uniprot/OrganismType.js +jalview/xml/binding/uniprot/PersonType.js +jalview/xml/binding/uniprot/PositionType.js +jalview/xml/binding/uniprot/PropertyType.js +jalview/xml/binding/uniprot/ProteinExistenceType.js +jalview/xml/binding/uniprot/ProteinType.js +jalview/xml/binding/uniprot/ReferenceType.js +jalview/xml/binding/uniprot/SequenceType.js +jalview/xml/binding/uniprot/SourceDataType.js +jalview/xml/binding/uniprot/SourceType.js +jalview/xml/binding/uniprot/SubcellularLocationType.js +jalview/xml/binding/uniprot/Uniprot.js java/awt/AWTKeyStroke.js java/awt/AlphaComposite.js java/awt/CardLayout.js @@ -514,6 +579,7 @@ java/util/Comparator.js java/util/Deque.js java/util/DualPivotQuicksort.js java/util/Enumeration.js +java/util/Formatter.js java/util/GregorianCalendar.js java/util/Iterator.js java/util/LinkedHashMap.js @@ -539,6 +605,7 @@ java/util/TimSort.js java/util/TimeZone.js java/util/TreeMap.js java/util/TreeSet.js +java/util/WeakHashMap.js java/util/concurrent/AbstractExecutorService.js java/util/concurrent/BlockingQueue.js java/util/concurrent/ConcurrentHashMap.js @@ -764,6 +831,7 @@ javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js javax/xml/bind/annotation/adapters/XmlAdapter.js javax/xml/bind/helpers/AbstractUnmarshallerImpl.js javax/xml/bind/helpers/DefaultValidationEventHandler.js +javax/xml/datatype/DatatypeFactory.js javax/xml/datatype/XMLGregorianCalendar.js javax/xml/namespace/QName.js javax/xml/stream/XMLInputFactory.js @@ -772,6 +840,25 @@ mc_view/Atom.js mc_view/Bond.js mc_view/PDBChain.js mc_view/Residue.js +net/miginfocom/layout/AC.js +net/miginfocom/layout/AnimSpec.js +net/miginfocom/layout/BoundSize.js +net/miginfocom/layout/CC.js +net/miginfocom/layout/ComponentWrapper.js +net/miginfocom/layout/ConstraintParser.js +net/miginfocom/layout/ContainerWrapper.js +net/miginfocom/layout/DimConstraint.js +net/miginfocom/layout/Grid.js +net/miginfocom/layout/LC.js +net/miginfocom/layout/LayoutUtil.js +net/miginfocom/layout/LinkHandler.js +net/miginfocom/layout/PlatformDefaults.js +net/miginfocom/layout/ResizeConstraint.js +net/miginfocom/layout/UnitValue.js +net/miginfocom/swing/MigLayout.js +net/miginfocom/swing/SwingComponentWrapper.js +net/miginfocom/swing/SwingContainerWrapper.js +org/apache/xerces/jaxp/datatype/DatatypeFactoryImpl.js org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js org/jmol/adapter/readers/cif/CifReader.js org/jmol/adapter/readers/cif/MMCifReader.js @@ -1085,10 +1172,12 @@ swingjs/plaf/TextListener.js swingjs/xml/JSJAXBClass.js swingjs/xml/JSJAXBContext.js swingjs/xml/JSJAXBContextFactory.js +swingjs/xml/JSJAXBDatatypeFactory.js swingjs/xml/JSJAXBField.js swingjs/xml/JSJAXBUnmarshaller.js swingjs/xml/JSSAXAttributes.js swingjs/xml/JSSAXParser.js swingjs/xml/JSXMLGregorianCalendarImpl.js swingjs/xml/JSXMLInputFactory.js +swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Any.js swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Boundary.js