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Jalview-JS/JAL-3253-applet update for core_jalview
author
hansonr
<hansonr@STO24954W.ad.stolaf.edu>
Sun, 19 May 2019 03:35:12 +0000
(22:35 -0500)
committer
hansonr
<hansonr@STO24954W.ad.stolaf.edu>
Sun, 19 May 2019 03:35:12 +0000
(22:35 -0500)
_j2sclasslist.txt
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diff --git
a/_j2sclasslist.txt
b/_j2sclasslist.txt
index
9a790a0
..
5afab4a
100644
(file)
--- 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/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/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
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/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/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
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/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/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
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/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/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
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/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
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/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
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/JSAppletThread.js
swingjs/JSAppletViewer.js
swingjs/JSCharSet.js
+swingjs/JSDummyApplet.js
swingjs/JSFocusPeer.js
swingjs/JSFontMetrics.js
swingjs/JSFrameViewer.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/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
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/CellRendererPane.js
javax/swing/DefaultListSelectionModel.js
javax/swing/DefaultRowSorter.js