From e46258ec9c1d56a23167aa2ba0ff4778a418d0b5 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 1 Jun 2022 11:40:57 +0100 Subject: [PATCH] JAL-3066 update classlist for jalviewjs --- utils/jalviewjs/classlists/jalview.txt | 244 ++++++++++++++++++++++++++------ 1 file changed, 200 insertions(+), 44 deletions(-) diff --git a/utils/jalviewjs/classlists/jalview.txt b/utils/jalviewjs/classlists/jalview.txt index 739f070..8b37728 100644 --- a/utils/jalviewjs/classlists/jalview.txt +++ b/utils/jalviewjs/classlists/jalview.txt @@ -10,41 +10,50 @@ jalview/analysis/AlignmentAnnotationUtils.js jalview/analysis/AlignmentSorter.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/NJTree.js +jalview/analysis/PCA.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/AlignCalcManagerI2.js jalview/api/AlignCalcWorkerI.js jalview/api/AlignViewControllerGuiI.js jalview/api/AlignViewControllerI.js jalview/api/AlignViewportI.js +jalview/api/AlignmentColsCollectionI.js +jalview/api/AlignmentRowsCollectionI.js jalview/api/AlignmentViewPanel.js jalview/api/BuildDetailsI.js jalview/api/DBRefEntryI.js jalview/api/FeatureColourI.js jalview/api/FeatureRenderer.js -jalview/api/FeatureSettingsModelI.js +jalview/api/FeatureSettingsControllerI.js jalview/api/FeaturesDisplayedI.js -jalview/api/FeaturesSourceI.js jalview/api/JalviewJSApi.js jalview/api/OOMHandlerI.js jalview/api/PollableAlignCalcWorkerI.js +jalview/api/RendererListenerI.js +jalview/api/RotatableCanvasI.js jalview/api/SequenceRenderer.js jalview/api/SequenceStructureBinding.js 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/AppletParams.js jalview/bin/ApplicationSingletonProvider.js @@ -52,16 +61,23 @@ jalview/bin/ArgsParser.js jalview/bin/BuildDetails.js jalview/bin/Cache.js jalview/bin/Jalview.js +jalview/bin/JalviewJS2.js jalview/bin/JalviewJSApp.js jalview/bin/JalviewTaskbar.js +jalview/commands/CommandI.js +jalview/commands/OrderCommand.js jalview/controller/AlignViewController.js +jalview/controller/FeatureSettingsControllerGuiI.js jalview/datamodel/ASequence.js jalview/datamodel/ASequenceI.js jalview/datamodel/Alignment.js jalview/datamodel/AlignmentAnnotation.js jalview/datamodel/AlignmentI.js -jalview/datamodel/AlignmentOrder.js jalview/datamodel/AlignmentView.js +jalview/datamodel/AllColsCollection.js +jalview/datamodel/AllColsIterator.js +jalview/datamodel/AllRowsCollection.js +jalview/datamodel/AllRowsIterator.js jalview/datamodel/AnnotatedCollectionI.js jalview/datamodel/Annotation.js jalview/datamodel/BinaryNode.js @@ -72,18 +88,19 @@ 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 jalview/datamodel/HiddenSequences.js jalview/datamodel/Mapping.js jalview/datamodel/PDBEntry.js +jalview/datamodel/Point.js jalview/datamodel/Profile.js jalview/datamodel/ProfileI.js jalview/datamodel/Profiles.js jalview/datamodel/ProfilesI.js jalview/datamodel/Range.js +jalview/datamodel/RangeElementsIterator.js jalview/datamodel/RangeIterator.js jalview/datamodel/ResidueCount.js jalview/datamodel/SearchResultMatchI.js @@ -97,9 +114,17 @@ jalview/datamodel/SequenceFeature.js jalview/datamodel/SequenceGroup.js jalview/datamodel/SequenceI.js jalview/datamodel/SequenceNode.js +jalview/datamodel/SequencePoint.js +jalview/datamodel/StartRegionIterator.js jalview/datamodel/StructureViewerModel.js +jalview/datamodel/VisibleColsCollection.js +jalview/datamodel/VisibleContigsIterator.js +jalview/datamodel/VisibleRowsCollection.js +jalview/datamodel/VisibleRowsIterator.js jalview/datamodel/features/FeatureAttributes.js jalview/datamodel/features/FeatureLocationI.js +jalview/datamodel/features/FeatureMatcherSet.js +jalview/datamodel/features/FeatureMatcherSetI.js jalview/datamodel/features/FeatureStore.js jalview/datamodel/features/SequenceFeatures.js jalview/datamodel/features/SequenceFeaturesI.js @@ -108,6 +133,9 @@ jalview/ext/ensembl/EnsemblGene.js jalview/ext/ensembl/EnsemblRestClient.js jalview/ext/ensembl/EnsemblSeqProxy.js jalview/ext/ensembl/EnsemblSequenceFetcher.js +jalview/ext/jmol/JalviewJmolBinding.js +jalview/ext/jmol/JmolCommands.js +jalview/ext/jmol/JmolParser.js jalview/fts/api/FTSData.js jalview/fts/api/FTSDataColumnI.js jalview/fts/api/FTSRestClientI.js @@ -121,73 +149,72 @@ jalview/gui/APQHandlers.js jalview/gui/AlignFrame.js jalview/gui/AlignViewport.js jalview/gui/AlignmentPanel.js -jalview/gui/AnnotationColumnChooser.js +jalview/gui/AnnotationExporter.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/CutAndPasteTransfer.js jalview/gui/Desktop.js jalview/gui/FeatureRenderer.js +jalview/gui/FeatureSettings.js jalview/gui/IProgressIndicator.js jalview/gui/IProgressIndicatorHandler.js jalview/gui/IdCanvas.js jalview/gui/IdPanel.js jalview/gui/IdwidthAdjuster.js -jalview/gui/JalviewBooleanRadioButtons.js jalview/gui/JalviewChangeSupport.js jalview/gui/JvOptionPane.js jalview/gui/JvSwingUtils.js -jalview/gui/OptsAndParamsPage.js -jalview/gui/OptsParametersContainerI.js +jalview/gui/OverviewCanvas.js +jalview/gui/OverviewPanel.js +jalview/gui/PCAPanel.js jalview/gui/PaintRefresher.js +jalview/gui/PairwiseAlignPanel.js jalview/gui/PopupMenu.js jalview/gui/Preferences.js jalview/gui/ProgressBar.js +jalview/gui/ProgressPanel.js +jalview/gui/RotatableCanvas.js jalview/gui/ScalePanel.js jalview/gui/SeqCanvas.js jalview/gui/SeqPanel.js jalview/gui/SequenceFetcher.js jalview/gui/SequenceRenderer.js jalview/gui/SliderPanel.js -jalview/gui/SlivkaPreferences.js jalview/gui/StructureChooser.js jalview/gui/StructureViewer.js +jalview/gui/StructureViewerBase.js +jalview/gui/TextColourChooser.js jalview/gui/TreeCanvas.js jalview/gui/TreePanel.js +jalview/gui/UserDefinedColours.js jalview/gui/ViewSelectionMenu.js jalview/gui/WebserviceInfo.js -jalview/gui/WsJobParameters.js -jalview/gui/WsParamSetManager.js jalview/hmmer/HmmerCommand.js jalview/io/AlignFile.js jalview/io/AlignmentFileReaderI.js jalview/io/AlignmentFileWriterI.js jalview/io/AnnotationFile.js jalview/io/AppletFormatAdapter.js -jalview/io/BackupFilenameParts.js -jalview/io/BackupFiles.js -jalview/io/BackupFilesPresetEntry.js jalview/io/DataSourceType.js jalview/io/FastaFile.js -jalview/io/FeaturesFile.js jalview/io/FileFormat.js +jalview/io/FileFormatException.js jalview/io/FileFormatI.js jalview/io/FileFormats.js jalview/io/FileLoader.js jalview/io/FileParse.js jalview/io/FormatAdapter.js jalview/io/IdentifyFile.js -jalview/io/IntKeyStringValueEntry.js -jalview/io/JalviewFileChooser.js -jalview/io/JalviewFileFilter.js -jalview/io/JalviewFileView.js jalview/io/NewickFile.js jalview/io/PIRFile.js jalview/io/ScoreMatrixFile.js jalview/io/SequenceAnnotationReport.js -jalview/io/StockholmFile.js -jalview/io/cache/JvCacheableInputBox.js +jalview/io/StructureFile.js jalview/javascript/json/JSON.js jalview/javascript/log4j/ConsoleAppender.js jalview/javascript/log4j/Layout.js @@ -201,20 +228,29 @@ jalview/javascript/web/ClientResponse.js jalview/javascript/web/WebResource.js jalview/jbgui/GAlignFrame.js jalview/jbgui/GAlignmentPanel.js +jalview/jbgui/GCutAndPasteTransfer.js jalview/jbgui/GDesktop.js +jalview/jbgui/GPCAPanel.js +jalview/jbgui/GPairwiseAlignPanel.js jalview/jbgui/GPreferences.js jalview/jbgui/GSliderPanel.js jalview/jbgui/GStructureChooser.js +jalview/jbgui/GStructureViewer.js jalview/jbgui/GTreePanel.js +jalview/jbgui/GUserDefinedColours.js jalview/jbgui/GWebserviceInfo.js +jalview/math/Matrix.js +jalview/math/MatrixI.js jalview/project/Jalview2XML.js jalview/renderer/AnnotationRenderer.js jalview/renderer/AwtRenderPanelI.js +jalview/renderer/OverviewRenderer.js jalview/renderer/OverviewResColourFinder.js jalview/renderer/ResidueColourFinder.js jalview/renderer/ResidueShader.js jalview/renderer/ResidueShaderI.js jalview/renderer/ScaleRenderer.js +jalview/renderer/seqfeatures/FeatureColourFinder.js jalview/renderer/seqfeatures/FeatureRenderer.js jalview/schemes/Blosum62ColourScheme.js jalview/schemes/BuriedColourScheme.js @@ -224,7 +260,6 @@ jalview/schemes/ColourSchemeProperty.js jalview/schemes/ColourSchemes.js jalview/schemes/Consensus.js jalview/schemes/FeatureColour.js -jalview/schemes/FeatureSettingsAdapter.js jalview/schemes/HMMMatchScoreColourScheme.js jalview/schemes/HelixColourScheme.js jalview/schemes/HmmerColourScheme.js @@ -244,6 +279,7 @@ jalview/schemes/StrandColourScheme.js jalview/schemes/TCoffeeColourScheme.js jalview/schemes/TaylorColourScheme.js jalview/schemes/TurnColourScheme.js +jalview/schemes/UserColourScheme.js jalview/schemes/ZappoColourScheme.js jalview/structure/AtomSpec.js jalview/structure/CommandListener.js @@ -251,8 +287,13 @@ jalview/structure/SelectionListener.js jalview/structure/SelectionSource.js jalview/structure/SequenceListener.js jalview/structure/StructureImportSettings.js +jalview/structure/StructureListener.js +jalview/structure/StructureMapping.js +jalview/structure/StructureMappingcommandSet.js jalview/structure/StructureSelectionManager.js jalview/structure/VamsasSource.js +jalview/structures/models/AAStructureBindingModel.js +jalview/structures/models/SequenceStructureBindingModel.js jalview/urls/CustomUrlProvider.js jalview/urls/IdOrgSettings.js jalview/urls/IdentifiersUrlProvider.js @@ -263,7 +304,7 @@ jalview/urls/UrlProviderImpl.js jalview/urls/api/UrlProviderFactoryI.js jalview/urls/api/UrlProviderI.js jalview/urls/desktop/DesktopUrlProviderFactory.js -jalview/util/BrowserLauncher.js +jalview/util/CaseInsensitiveString.js jalview/util/ColorUtils.js jalview/util/Comparison.js jalview/util/DBRefUtils.js @@ -272,18 +313,21 @@ jalview/util/Format.js jalview/util/LinkedIdentityHashSet.js jalview/util/MapList.js jalview/util/MessageManager.js -jalview/util/ParseHtmlBodyAndLinks.js jalview/util/Platform.js jalview/util/QuickSort.js +jalview/util/ShiftList.js jalview/util/StringUtils.js jalview/util/UrlLink.js jalview/util/dialogrunner/DialogRunnerI.js jalview/util/jarInputStreamProvider.js jalview/viewmodel/AlignmentViewport.js +jalview/viewmodel/OverviewDimensions.js +jalview/viewmodel/OverviewDimensionsHideHidden.js +jalview/viewmodel/OverviewDimensionsShowHidden.js +jalview/viewmodel/PCAModel.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 @@ -297,6 +341,7 @@ jalview/workers/InformationThread.js jalview/workers/StrucConsensusThread.js jalview/ws/AWSThread.js jalview/ws/AWsJob.js +jalview/ws/DBRefFetcher.js jalview/ws/JobStateSummary.js jalview/ws/SequenceFetcher.js jalview/ws/ServiceChangeListener.js @@ -305,6 +350,7 @@ jalview/ws/WSClientI.js jalview/ws/WSDiscovererI.js jalview/ws/WSMenuEntryProviderI.js jalview/ws/api/CancellableI.js +jalview/ws/api/JPredServiceI.js jalview/ws/api/JalviewServiceEndpointProviderI.js jalview/ws/api/JalviewWebServiceI.js jalview/ws/api/JobId.js @@ -327,10 +373,12 @@ jalview/ws/dbsources/Rfam.js jalview/ws/dbsources/RfamSeed.js jalview/ws/dbsources/Uniprot.js jalview/ws/dbsources/Xfam.js +jalview/ws/ebi/EBIFetchClient.js jalview/ws/gui/AnnotationWsJob.js jalview/ws/gui/MsaWSJob.js jalview/ws/gui/MsaWSThread.js jalview/ws/gui/WsJob.js +jalview/ws/jws2/JPredClient.js jalview/ws/jws2/Jws2Client.js jalview/ws/jws2/Jws2ClientFactory.js jalview/ws/jws2/Jws2Discoverer.js @@ -344,9 +392,7 @@ jalview/ws/params/ArgumentI.js jalview/ws/params/AutoCalcSetting.js jalview/ws/params/OptionI.js jalview/ws/params/ParamDatastoreI.js -jalview/ws/params/ParamManager.js jalview/ws/params/ParameterI.js -jalview/ws/params/ValueConstrainI.js jalview/ws/params/WsParamSetI.js jalview/ws/params/simple/BooleanOption.js jalview/ws/params/simple/DoubleParameter.js @@ -357,8 +403,10 @@ jalview/ws/seqfetcher/ASequenceFetcher.js jalview/ws/seqfetcher/DbSourceProxy.js jalview/ws/seqfetcher/DbSourceProxyImpl.js jalview/ws/sifts/SiftsSettings.js +jalview/ws/slivkaws/RNAalifoldServiceInstance.js jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.js jalview/ws/slivkaws/SlivkaDatastore.js +jalview/ws/slivkaws/SlivkaJPredServiceInstance.js jalview/ws/slivkaws/SlivkaMsaServiceInstance.js jalview/ws/slivkaws/SlivkaParamSet.js jalview/ws/slivkaws/SlivkaWSDiscoverer.js @@ -369,13 +417,39 @@ 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/CofactorType.js +jalview/xml/binding/uniprot/CommentType.js +jalview/xml/binding/uniprot/DbReferenceType.js +jalview/xml/binding/uniprot/Entry.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/InteractantType.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/applet/AppletContext.js java/applet/AppletStub.js java/applet/JSApplet.js @@ -565,6 +639,7 @@ java/lang/Iterable.js java/lang/Readable.js java/lang/Runtime.js java/lang/RuntimePermission.js +java/lang/Shutdown.js java/lang/StringBuffer.js java/lang/StringBuilder.js java/lang/Thread.js @@ -587,8 +662,20 @@ java/net/HttpURLConnection.js java/net/URI.js java/net/URL.js java/net/URLConnection.js +java/net/URLDecoder.js java/net/URLStreamHandler.js java/net/URLStreamHandlerFactory.js +java/nio/Bits.js +java/nio/Buffer.js +java/nio/ByteBuffer.js +java/nio/ByteOrder.js +java/nio/CharBuffer.js +java/nio/HeapByteBuffer.js +java/nio/HeapCharBuffer.js +java/nio/charset/Charset.js +java/nio/charset/CharsetDecoder.js +java/nio/charset/CoderResult.js +java/nio/charset/CodingErrorAction.js java/security/AccessController.js java/security/BasicPermission.js java/security/Guard.js @@ -654,6 +741,7 @@ java/util/Map.js java/util/NavigableMap.js java/util/NavigableSet.js java/util/Objects.js +java/util/Optional.js java/util/PriorityQueue.js java/util/Properties.js java/util/PropertyResourceBundle.js @@ -666,6 +754,7 @@ java/util/Set.js java/util/SortedMap.js java/util/SortedSet.js java/util/Spliterator.js +java/util/Stack.js java/util/StringTokenizer.js java/util/TimSort.js java/util/TimeZone.js @@ -712,7 +801,6 @@ java/util/concurrent/locks/ReadWriteLock.js java/util/concurrent/locks/ReentrantLock.js java/util/concurrent/locks/ReentrantReadWriteLock.js java/util/function/Consumer.js -java/util/function/Function.js java/util/function/Predicate.js java/util/function/Supplier.js java/util/jar/JarEntry.js @@ -743,11 +831,13 @@ java/util/zip/ZipConstants.js java/util/zip/ZipEntry.js java/util/zip/ZipInputStream.js javajs/api/BytePoster.js +javajs/api/EigenInterface.js +javajs/api/GenericCifDataParser.js javajs/api/GenericLineReader.js javajs/api/GenericOutputChannel.js +javajs/api/Interface.js javajs/api/JSONEncodable.js javajs/async/SwingJSUtils.js -javajs/http/ClientProtocolException.js javajs/http/HttpClient.js javajs/http/HttpClientFactory.js javajs/http/SimpleHttpClient.js @@ -759,7 +849,9 @@ javajs/util/AjaxURLStreamHandlerFactory.js javajs/util/BS.js javajs/util/Base64.js javajs/util/CU.js +javajs/util/CifDataParser.js javajs/util/DF.js +javajs/util/Eigen.js javajs/util/Encoding.js javajs/util/JSThread.js javajs/util/LimitedLineReader.js @@ -767,11 +859,13 @@ javajs/util/Lst.js javajs/util/M3.js javajs/util/M34.js javajs/util/M4.js +javajs/util/Measure.js javajs/util/OC.js javajs/util/P3.js javajs/util/P3i.js javajs/util/P4.js javajs/util/PT.js +javajs/util/Quat.js javajs/util/Rdr.js javajs/util/SB.js javajs/util/T3.js @@ -791,7 +885,6 @@ javax/swing/ArrayTable.js javax/swing/Autoscroller.js javax/swing/BorderFactory.js javax/swing/BoundedRangeModel.js -javax/swing/Box.js javax/swing/BoxLayout.js javax/swing/ButtonGroup.js javax/swing/ButtonModel.js @@ -803,6 +896,7 @@ javax/swing/ComboBoxModel.js javax/swing/ComponentInputMap.js javax/swing/DefaultBoundedRangeModel.js javax/swing/DefaultButtonModel.js +javax/swing/DefaultCellEditor.js javax/swing/DefaultComboBoxModel.js javax/swing/DefaultDesktopManager.js javax/swing/DefaultListCellRenderer.js @@ -820,11 +914,12 @@ javax/swing/JApplet.js javax/swing/JButton.js javax/swing/JCheckBox.js javax/swing/JCheckBoxMenuItem.js +javax/swing/JColorChooser.js javax/swing/JComboBox.js javax/swing/JComponent.js javax/swing/JDesktopPane.js javax/swing/JDialog.js -javax/swing/JFileChooser.js +javax/swing/JEditorPane.js javax/swing/JFormattedTextField.js javax/swing/JFrame.js javax/swing/JInternalFrame.js @@ -846,10 +941,12 @@ javax/swing/JScrollPane.js javax/swing/JSeparator.js javax/swing/JSlider.js javax/swing/JSpinner.js +javax/swing/JSplitPane.js javax/swing/JTabbedPane.js javax/swing/JTable.js javax/swing/JTextArea.js javax/swing/JTextField.js +javax/swing/JTextPane.js javax/swing/JToggleButton.js javax/swing/JToolTip.js javax/swing/JViewport.js @@ -869,7 +966,6 @@ javax/swing/Popup.js javax/swing/PopupFactory.js javax/swing/RepaintManager.js javax/swing/RootPaneContainer.js -javax/swing/RowFilter.js javax/swing/RowSorter.js javax/swing/ScrollPaneConstants.js javax/swing/ScrollPaneLayout.js @@ -880,8 +976,6 @@ javax/swing/SortOrder.js javax/swing/SortingFocusTraversalPolicy.js javax/swing/SpinnerModel.js javax/swing/SpinnerNumberModel.js -javax/swing/Spring.js -javax/swing/SpringLayout.js javax/swing/SwingConstants.js javax/swing/SwingContainerOrderFocusTraversalPolicy.js javax/swing/SwingDefaultFocusTraversalPolicy.js @@ -901,7 +995,20 @@ javax/swing/border/CompoundBorder.js javax/swing/border/EmptyBorder.js javax/swing/border/EtchedBorder.js javax/swing/border/LineBorder.js +javax/swing/border/MatteBorder.js javax/swing/border/TitledBorder.js +javax/swing/colorchooser/AbstractColorChooserPanel.js +javax/swing/colorchooser/CenterLayout.js +javax/swing/colorchooser/ColorChooserComponentFactory.js +javax/swing/colorchooser/ColorSelectionModel.js +javax/swing/colorchooser/DefaultColorSelectionModel.js +javax/swing/colorchooser/DefaultPreviewPanel.js +javax/swing/colorchooser/DefaultRGBChooserPanel.js +javax/swing/colorchooser/DefaultSwatchChooserPanel.js +javax/swing/colorchooser/MainSwatchPanel.js +javax/swing/colorchooser/RecentSwatchPanel.js +javax/swing/colorchooser/SmartGridLayout.js +javax/swing/colorchooser/SwatchPanel.js javax/swing/event/AncestorEvent.js javax/swing/event/AncestorListener.js javax/swing/event/CaretEvent.js @@ -933,8 +1040,6 @@ javax/swing/event/TableModelEvent.js javax/swing/event/TableModelListener.js javax/swing/event/UndoableEditEvent.js javax/swing/event/UndoableEditListener.js -javax/swing/filechooser/FileFilter.js -javax/swing/filechooser/FileView.js javax/swing/plaf/ActionMapUIResource.js javax/swing/plaf/BorderUIResource.js javax/swing/plaf/ColorUIResource.js @@ -967,6 +1072,7 @@ javax/swing/text/DefaultCaret.js javax/swing/text/DefaultEditorKit.js javax/swing/text/DefaultFormatter.js javax/swing/text/DefaultFormatterFactory.js +javax/swing/text/DefaultStyledDocument.js javax/swing/text/Document.js javax/swing/text/DocumentFilter.js javax/swing/text/EditorKit.js @@ -975,6 +1081,7 @@ javax/swing/text/GapContent.js javax/swing/text/GapVector.js javax/swing/text/InternationalFormatter.js javax/swing/text/JTextComponent.js +javax/swing/text/Keymap.js javax/swing/text/MutableAttributeSet.js javax/swing/text/NumberFormatter.js javax/swing/text/PlainDocument.js @@ -986,11 +1093,15 @@ javax/swing/text/SimpleAttributeSet.js javax/swing/text/Style.js javax/swing/text/StyleConstants.js javax/swing/text/StyleContext.js +javax/swing/text/StyledDocument.js +javax/swing/text/StyledEditorKit.js javax/swing/text/TabExpander.js javax/swing/text/TextAction.js javax/swing/text/Utilities.js javax/swing/text/View.js +javax/swing/text/ViewFactory.js javax/swing/text/WrappedPlainView.js +javax/swing/tree/TreeCellEditor.js javax/swing/tree/TreeNode.js javax/swing/undo/AbstractUndoableEdit.js javax/swing/undo/CompoundEdit.js @@ -1008,14 +1119,16 @@ 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/FactoryFinder.js -javax/xml/datatype/SecuritySupport.js javax/xml/datatype/XMLGregorianCalendar.js javax/xml/namespace/QName.js javax/xml/stream/XMLInputFactory.js javax/xml/stream/XMLStreamConstants.js javax/xml/stream/XMLStreamReader.js +mc_view/Atom.js +mc_view/Bond.js +mc_view/PDBChain.js +mc_view/PDBfile.js +mc_view/Residue.js net/miginfocom/layout/AC.js net/miginfocom/layout/AnimSpec.js net/miginfocom/layout/BoundSize.js @@ -1034,8 +1147,9 @@ 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 org/jmol/adapter/readers/pdb/PdbReader.js org/jmol/adapter/smarter/Atom.js org/jmol/adapter/smarter/AtomIterator.js @@ -1048,18 +1162,24 @@ org/jmol/adapter/smarter/Resolver.js org/jmol/adapter/smarter/SmarterJmolAdapter.js org/jmol/adapter/smarter/Structure.js org/jmol/adapter/smarter/StructureIterator.js +org/jmol/adapter/smarter/XtalSymmetry.js org/jmol/api/AtomIndexIterator.js org/jmol/api/EventManager.js org/jmol/api/FontManager.js org/jmol/api/GenericFileInterface.js +org/jmol/api/GenericMenuInterface.js org/jmol/api/GenericMouseInterface.js org/jmol/api/GenericPlatform.js org/jmol/api/Interface.js +org/jmol/api/JmolAbstractButton.js org/jmol/api/JmolAdapter.js org/jmol/api/JmolAdapterAtomIterator.js org/jmol/api/JmolAdapterBondIterator.js org/jmol/api/JmolAdapterStructureIterator.js +org/jmol/api/JmolAppConsoleInterface.js org/jmol/api/JmolCallbackListener.js +org/jmol/api/JmolDropEditor.js +org/jmol/api/JmolFilesReaderInterface.js org/jmol/api/JmolGraphicsInterface.js org/jmol/api/JmolMeasurementClient.js org/jmol/api/JmolPropertyManager.js @@ -1072,13 +1192,18 @@ org/jmol/api/JmolSelectionListener.js org/jmol/api/JmolStatusListener.js org/jmol/api/JmolViewer.js org/jmol/api/PlatformViewer.js +org/jmol/api/SC.js org/jmol/api/SymmetryInterface.js org/jmol/api/Translator.js org/jmol/atomdata/AtomDataServer.js org/jmol/atomdata/RadiusData.js org/jmol/awt/AwtFile.js org/jmol/awt/AwtFont.js +org/jmol/awt/AwtJmolPopup.js +org/jmol/awt/AwtPopupHelper.js +org/jmol/awt/AwtSwingComponent.js org/jmol/awt/Display.js +org/jmol/awt/FileDropper.js org/jmol/awt/Image.js org/jmol/awt/Mouse.js org/jmol/awt/Platform.js @@ -1094,6 +1219,9 @@ org/jmol/c/PAL.js org/jmol/c/STER.js org/jmol/c/STR.js org/jmol/c/VDW.js +org/jmol/console/GenericConsole.js +org/jmol/console/JmolButton.js +org/jmol/console/JmolConsole.js org/jmol/g3d/CylinderRenderer.js org/jmol/g3d/G3DRenderer.js org/jmol/g3d/Graphics3D.js @@ -1110,6 +1238,7 @@ org/jmol/i18n/GT.js org/jmol/i18n/Language.js org/jmol/i18n/Resource.js org/jmol/io/FileReader.js +org/jmol/io/FilesReader.js org/jmol/modelset/Atom.js org/jmol/modelset/AtomCollection.js org/jmol/modelset/AtomIteratorWithinModel.js @@ -1140,8 +1269,16 @@ org/jmol/modelsetbio/BioPolymer.js org/jmol/modelsetbio/BioResolver.js org/jmol/modelsetbio/Helix.js org/jmol/modelsetbio/Monomer.js +org/jmol/modelsetbio/NucleicMonomer.js +org/jmol/modelsetbio/PhosphorusMonomer.js org/jmol/modelsetbio/ProteinStructure.js org/jmol/modelsetbio/Sheet.js +org/jmol/popup/GenericPopup.js +org/jmol/popup/JmolGenericPopup.js +org/jmol/popup/JmolPopup.js +org/jmol/popup/MainPopupResourceBundle.js +org/jmol/popup/PopupHelper.js +org/jmol/popup/PopupResource.js org/jmol/render/BallsRenderer.js org/jmol/render/BbcageRenderer.js org/jmol/render/CageRenderer.js @@ -1155,6 +1292,7 @@ org/jmol/render/ShapeRenderer.js org/jmol/render/SticksRenderer.js org/jmol/render/TextRenderer.js org/jmol/render/UccageRenderer.js +org/jmol/renderbio/BackboneRenderer.js org/jmol/renderbio/BioShapeRenderer.js org/jmol/renderbio/CartoonRenderer.js org/jmol/renderbio/RocketsRenderer.js @@ -1171,6 +1309,7 @@ org/jmol/script/ScriptFunction.js org/jmol/script/ScriptManager.js org/jmol/script/ScriptMathProcessor.js org/jmol/script/ScriptParam.js +org/jmol/script/ScriptQueueThread.js org/jmol/script/ScriptTokenParser.js org/jmol/script/T.js org/jmol/scriptext/CmdExt.js @@ -1189,6 +1328,7 @@ org/jmol/shape/Shape.js org/jmol/shape/Sticks.js org/jmol/shape/TextShape.js org/jmol/shape/Uccage.js +org/jmol/shapebio/Backbone.js org/jmol/shapebio/BioShape.js org/jmol/shapebio/BioShapeCollection.js org/jmol/shapebio/Cartoon.js @@ -1198,6 +1338,7 @@ org/jmol/symmetry/SymmetryInfo.js org/jmol/symmetry/UnitCell.js org/jmol/thread/HoverWatcherThread.js org/jmol/thread/JmolThread.js +org/jmol/thread/SpinThread.js org/jmol/thread/TimeoutThread.js org/jmol/util/BSUtil.js org/jmol/util/BoxInfo.js @@ -1206,6 +1347,7 @@ org/jmol/util/ColorEncoder.js org/jmol/util/CommandHistory.js org/jmol/util/DefaultLogger.js org/jmol/util/Edge.js +org/jmol/util/EigenSort.js org/jmol/util/Elements.js org/jmol/util/Escape.js org/jmol/util/Font.js @@ -1226,6 +1368,8 @@ org/jmol/util/SimpleEdge.js org/jmol/util/SimpleNode.js org/jmol/util/SimpleUnitCell.js org/jmol/util/TempArray.js +org/jmol/util/Tensor.js +org/jmol/util/Txt.js org/jmol/viewer/ActionManager.js org/jmol/viewer/AnimationManager.js org/jmol/viewer/ColorManager.js @@ -1246,9 +1390,10 @@ org/jmol/viewer/Viewer.js org/jmol/viewer/binding/Binding.js org/jmol/viewer/binding/JmolBinding.js org/json/JSONArray.js -org/json/JSONException.js org/json/JSONObject.js org/json/JSONTokener.js +org/openscience/jmol/app/jmolpanel/console/AppConsole.js +org/openscience/jmol/app/jmolpanel/console/EnterListener.js org/xml/sax/AttributeList.js org/xml/sax/Attributes.js org/xml/sax/ContentHandler.js @@ -1279,6 +1424,12 @@ sun/font/FontDesignMetrics.js sun/java2d/StateTrackable.js sun/java2d/StateTrackableDelegate.js sun/misc/Unsafe.js +sun/nio/cs/ArrayDecoder.js +sun/nio/cs/HistoricallyNamedCharset.js +sun/nio/cs/StandardCharsets.js +sun/nio/cs/ThreadLocalCoders.js +sun/nio/cs/UTF_8.js +sun/nio/cs/Unicode.js sun/swing/DefaultLookup.js sun/swing/StringUIClientPropertyKey.js sun/swing/SwingLazyValue.js @@ -1320,6 +1471,7 @@ sun/util/spi/CalendarProvider.js swingjs/JSApp.js swingjs/JSAppletThread.js swingjs/JSAppletViewer.js +swingjs/JSCharSet.js swingjs/JSDummyApplet.js swingjs/JSFocusPeer.js swingjs/JSFontMetrics.js @@ -1364,18 +1516,21 @@ swingjs/plaf/BasicComboBoxRenderer.js swingjs/plaf/BasicHTML.js swingjs/plaf/ButtonListener.js swingjs/plaf/CellHolder.js +swingjs/plaf/CenterLayout.js swingjs/plaf/DefaultMenuLayout.js swingjs/plaf/HTML5LookAndFeel.js swingjs/plaf/JSAppletUI.js swingjs/plaf/JSButtonUI.js swingjs/plaf/JSCheckBoxMenuItemUI.js swingjs/plaf/JSCheckBoxUI.js +swingjs/plaf/JSColorChooserUI.js swingjs/plaf/JSComboBoxUI.js swingjs/plaf/JSComboPopupList.js swingjs/plaf/JSComponentUI.js swingjs/plaf/JSDesktopIconUI.js swingjs/plaf/JSDesktopPaneUI.js swingjs/plaf/JSDialogUI.js +swingjs/plaf/JSEditorPaneUI.js swingjs/plaf/JSEventHandler.js swingjs/plaf/JSFormattedTextFieldUI.js swingjs/plaf/JSFrameUI.js @@ -1402,11 +1557,13 @@ swingjs/plaf/JSScrollPaneUI.js swingjs/plaf/JSSeparatorUI.js swingjs/plaf/JSSliderUI.js swingjs/plaf/JSSpinnerUI.js +swingjs/plaf/JSSplitPaneUI.js swingjs/plaf/JSTabbedPaneUI.js swingjs/plaf/JSTableHeaderUI.js swingjs/plaf/JSTableUI.js swingjs/plaf/JSTextAreaUI.js swingjs/plaf/JSTextFieldUI.js +swingjs/plaf/JSTextPaneUI.js swingjs/plaf/JSTextUI.js swingjs/plaf/JSToolTipUI.js swingjs/plaf/JSViewportUI.js @@ -1417,7 +1574,6 @@ 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 -- 1.7.10.2