X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=_j2sclasslist.txt;h=f51640c512f8a3f2c97f4c28b6d1c1968ed3ead7;hb=refs%2Fheads%2FJAL-3253-applet-test;hp=8fd841565803b3a88037f17b05fbeb0d3f8743d0;hpb=38f731cfd7d8bfcbf50dc48f36980c0cfe0cfba1;p=jalview.git diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt index 8fd8415..f51640c 100644 --- a/_j2sclasslist.txt +++ b/_j2sclasslist.txt @@ -2,11 +2,13 @@ jalview/analysis/AAFrequency.js jalview/analysis/AlignSeq.js jalview/analysis/AlignmentAnnotationUtils.js jalview/analysis/AlignmentUtils.js +jalview/analysis/AlignmentSorter.js jalview/analysis/AnnotationSorter.js jalview/analysis/Conservation.js jalview/analysis/CrossRef.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 @@ -20,12 +22,14 @@ jalview/api/AlignCalcManagerI.js jalview/api/AlignCalcWorkerI.js jalview/api/AlignViewControllerGuiI.js jalview/api/AlignViewControllerI.js +jalview/api/AlignFrameI.js jalview/api/AlignViewportI.js jalview/api/AlignmentViewPanel.js jalview/api/BuildDetailsI.js jalview/api/FeatureColourI.js jalview/api/FeatureRenderer.js jalview/api/FeaturesDisplayedI.js +jalview/api/JalviewApp.js jalview/api/OOMHandlerI.js jalview/api/SequenceRenderer.js jalview/api/StructureSelectionManagerProvider.js @@ -33,11 +37,15 @@ jalview/api/ViewStyleI.js jalview/api/analysis/PairwiseScoreModelI.js jalview/api/analysis/ScoreModelI.js jalview/api/analysis/SimilarityParamsI.js +jalview/bin/AppletParams.js +jalview/bin/ApplicationSingletonProvider.js jalview/bin/ArgsParser.js jalview/bin/BuildDetails.js jalview/bin/Cache.js jalview/bin/Jalview.js -jalview/bin/JalviewJS2.js +jalview/bin/JalviewAppLoader.js +jalview/commands/CommandI.js +jalview/commands/OrderCommand.js jalview/controller/AlignViewController.js jalview/datamodel/ASequence.js jalview/datamodel/ASequenceI.js @@ -82,7 +90,9 @@ jalview/datamodel/features/FeatureMatcherI.js jalview/datamodel/features/FeatureMatcherSet.js jalview/datamodel/features/FeatureMatcherSetI.js jalview/datamodel/features/FeatureStore.js -jalview/datamodel/features/RangeComparator.js +jalview/datamodel/features/FeatureStoreI.js +jalview/datamodel/features/FeatureStoreJS.js + jalview/datamodel/features/SequenceFeatures.js jalview/datamodel/features/SequenceFeaturesI.js jalview/gui/AlignFrame.js @@ -123,9 +133,11 @@ jalview/io/FileFormats.js jalview/io/FileLoader.js jalview/io/FileParse.js jalview/io/IdentifyFile.js +jalview/io/NewickFile.js jalview/io/PIRFile.js jalview/io/ScoreMatrixFile.js jalview/io/SequenceAnnotationReport.js +jalview/javascript/JalviewLiteJSApi.js jalview/javascript/log4j/ConsoleAppender.js jalview/javascript/log4j/Layout.js jalview/javascript/log4j/Level.js @@ -154,6 +166,8 @@ jalview/schemes/ClustalxColourScheme.js jalview/schemes/ColourSchemeI.js jalview/schemes/ColourSchemeProperty.js jalview/schemes/ColourSchemes.js +jalview/schemes/ColourSchemeLoader.js +jalview/schemes/UserColourScheme.js jalview/schemes/Consensus.js jalview/schemes/FeatureColour.js jalview/schemes/HelixColourScheme.js @@ -170,6 +184,7 @@ 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/CommandListener.js jalview/structure/SelectionListener.js @@ -549,6 +564,13 @@ javax/swing/DefaultDesktopManager.js javax/swing/DefaultListCellRenderer.js javax/swing/DefaultSingleSelectionModel.js javax/swing/DesktopManager.js +javax/swing/FocusManager.js +javax/swing/InternalFrameFocusTraversalPolicy.js +javax/swing/LayoutComparator.js +javax/swing/LayoutFocusTraversalPolicy.js +javax/swing/SortingFocusTraversalPolicy.js +javax/swing/SwingContainerOrderFocusTraversalPolicy.js +javax/swing/SwingDefaultFocusTraversalPolicy.js javax/swing/InputMap.js javax/swing/JApplet.js javax/swing/JButton.js @@ -608,6 +630,7 @@ javax/swing/WindowConstants.js javax/swing/border/AbstractBorder.js javax/swing/border/BevelBorder.js javax/swing/border/Border.js +javax/swing/border/CompoundBorder.js javax/swing/border/EmptyBorder.js javax/swing/border/EtchedBorder.js javax/swing/border/LineBorder.js @@ -711,6 +734,7 @@ swingjs/JSApplet.js swingjs/JSAppletThread.js swingjs/JSAppletViewer.js swingjs/JSCharSet.js +swingjs/JSDummyApplet.js swingjs/JSFocusPeer.js swingjs/JSFontMetrics.js swingjs/JSFrameViewer.js @@ -791,8 +815,7 @@ swingjs/xml/JSXMLInputFactory.js swingjs/xml/JSXMLStreamReader.js intervalstore/api/IntervalI.js intervalstore/api/IntervalStoreI.js -intervalstore/impl/BinarySearcher.js -intervalstore/impl/IntervalStore.js +intervalstore/nonc/IntervalStore.js jalview/analysis/GeneticCodeI.js jalview/analysis/GeneticCodes.js jalview/api/FeaturesSourceI.js @@ -804,3 +827,156 @@ jalview/util/LinkedIdentityHashSet.js jalview/util/ParseHtmlBodyAndLinks.js java/util/function/Function.js swingjs/a2s/A2SContainer.js + +jalview/fts/api/FTSData.js +jalview/fts/api/FTSDataColumnI.js +jalview/fts/api/FTSRestClientI.js +jalview/fts/core/DecimalFormatTableCellRenderer.js +jalview/fts/core/FTSDataColumnPreferences.js +jalview/fts/core/FTSRestClient.js +jalview/fts/core/FTSRestRequest.js +jalview/fts/core/FTSRestResponse.js +jalview/fts/service/pdb/PDBFTSRestClient.js +jalview/gui/StructureChooser.js +jalview/javascript/json/JSON.js +jalview/javascript/web/Client.js +jalview/javascript/web/ClientResponse.js +jalview/javascript/web/WebResource.js +jalview/jbgui/BackupFilesPresetEntry.js +jalview/jbgui/GStructureChooser.js +jalview/jbgui/IntKeyStringValueEntry.js +java/awt/CardLayout.js +java/awt/TextComponent.js +java/awt/image/ImageConsumer.js +java/io/ObjectStreamField.js +java/net/URI.js +java/util/ComparableTimSort.js +java/util/LinkedHashSet.js +java/util/WeakHashMap.js +javajs/util/Base64.js +javax/net/ssl/HttpsURLConnection.js +javax/swing/CellRendererPane.js +javax/swing/DefaultListSelectionModel.js +javax/swing/DefaultRowSorter.js +javax/swing/DropMode.js +javax/swing/Icon.js +javax/swing/ImageIcon.js +javax/swing/JTable.js +javax/swing/JTextField.js +javax/swing/ListSelectionModel.js +javax/swing/RowSorter.js +javax/swing/SortOrder.js +javax/swing/event/CaretEvent.js +javax/swing/event/CaretListener.js +javax/swing/event/CellEditorListener.js +javax/swing/event/DocumentListener.js +javax/swing/event/ListSelectionEvent.js +javax/swing/event/ListSelectionListener.js +javax/swing/event/MouseInputListener.js +javax/swing/event/RowSorterEvent.js +javax/swing/event/RowSorterListener.js +javax/swing/event/SwingPropertyChangeSupport.js +javax/swing/event/TableColumnModelEvent.js +javax/swing/event/TableColumnModelListener.js +javax/swing/event/TableModelEvent.js +javax/swing/plaf/InputMapUIResource.js +javax/swing/table/DefaultTableCellRenderer.js +javax/swing/table/DefaultTableColumnModel.js +javax/swing/table/DefaultTableModel.js +javax/swing/table/JTableHeader.js +javax/swing/table/TableCellRenderer.js +javax/swing/table/TableColumn.js +javax/swing/table/TableColumnModel.js +javax/swing/table/TableRowSorter.js +javax/swing/text/Caret.js +javax/swing/text/DefaultCaret.js +javax/swing/text/DefaultEditorKit.js +javax/swing/text/Document.js +javax/swing/text/EditorKit.js +javax/swing/text/Element.js +javax/swing/text/JTextComponent.js +javax/swing/text/Position.js +javax/swing/text/TextAction.js +javax/swing/text/View.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 +sun/swing/StringUIClientPropertyKey.js +sun/swing/SwingUtilities2.js +sun/swing/UIClientPropertyKey.js +sun/swing/table/DefaultTableCellHeaderRenderer.js +swingjs/JSAbstractDocument.js +swingjs/JSImage.js +swingjs/JSImagekit.js +swingjs/JSPlainDocument.js +swingjs/api/JSMinimalAbstractDocument.js +swingjs/json/JSON.js +swingjs/plaf/BasicHTML.js +swingjs/plaf/CellHolder.js +swingjs/plaf/JSTableHeaderUI.js +swingjs/plaf/JSTableUI.js +swingjs/plaf/JSTextFieldUI.js +swingjs/plaf/JSTextUI.js +swingjs/plaf/TextListener.js + +com/stevesoft/pat/Bracket.js +com/stevesoft/pat/CaseMgr.js +com/stevesoft/pat/FastMulti.js +com/stevesoft/pat/NUnicodeAlpha.js +com/stevesoft/pat/NUnicodeCurrency.js +com/stevesoft/pat/NUnicodeDigit.js +com/stevesoft/pat/NUnicodeMath.js +com/stevesoft/pat/NUnicodePunct.js +com/stevesoft/pat/NUnicodeW.js +com/stevesoft/pat/NUnicodeWhite.js +com/stevesoft/pat/NoPattern.js +com/stevesoft/pat/Or.js +com/stevesoft/pat/OrMark.js +com/stevesoft/pat/Pattern.js +com/stevesoft/pat/PatternSub.js +com/stevesoft/pat/Pthings.js +com/stevesoft/pat/Range.js +com/stevesoft/pat/RegOpt.js +com/stevesoft/pat/RegRes.js +com/stevesoft/pat/Regex.js +com/stevesoft/pat/Rthings.js +com/stevesoft/pat/StrPos.js +com/stevesoft/pat/StringLike.js +com/stevesoft/pat/SubMark.js +com/stevesoft/pat/UniValidator.js +com/stevesoft/pat/UnicodeAlpha.js +com/stevesoft/pat/UnicodeCurrency.js +com/stevesoft/pat/UnicodeDigit.js +com/stevesoft/pat/UnicodeLower.js +com/stevesoft/pat/UnicodeMath.js +com/stevesoft/pat/UnicodePunct.js +com/stevesoft/pat/UnicodeUpper.js +com/stevesoft/pat/UnicodeW.js +com/stevesoft/pat/UnicodeWhite.js +com/stevesoft/pat/Validator.js +com/stevesoft/pat/oneChar.js +com/stevesoft/pat/parsePerl.js +com/stevesoft/pat/patInt.js +com/stevesoft/pat/wrap/StringWrap.js + +jalview/api/DBRefEntryI.js +jalview/api/SequenceStructureBinding.js +jalview/api/structures/JalviewStructureDisplayI.js +jalview/datamodel/DBRefEntry.js +jalview/datamodel/Mapping.js +jalview/datamodel/features/FeatureAttributes.js