From 4ba1c57b4ce0b3708b245633a109442dc88f586c Mon Sep 17 00:00:00 2001 From: hansonr Date: Sat, 18 May 2019 22:35:12 -0500 Subject: [PATCH] Jalview-JS/JAL-3253-applet update for core_jalview --- _j2sclasslist.txt | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt index 9a790a0..5afab4a 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 @@ -123,9 +131,11 @@ 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 +164,8 @@ 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 +182,7 @@ 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 @@ -711,6 +724,7 @@ swingjs/JSApplet.js swingjs/JSAppletThread.js swingjs/JSAppletViewer.js swingjs/JSCharSet.js +swingjs/JSDummyApplet.js swingjs/JSFocusPeer.js swingjs/JSFontMetrics.js swingjs/JSFrameViewer.js @@ -826,12 +840,12 @@ java/awt/CardLayout.js java/awt/TextComponent.js java/awt/image/ImageConsumer.js java/io/ObjectStreamField.js -java/net/HttpsURLConnection.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 -- 1.7.10.2