Jalview-JS/JAL-3253-applet update for core_jalview

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/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