jalview

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JAL-1807 attempt to add additional j2s project within default jalview project

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    /jalview2js/.project
revision for JAL-1749 - ensure view 2D structure menu is removed when no structures are available

fix for JAL-1776 renamed popup menu entry

updated version info in seqfetch.html

JAL-1553 reviewed & updated docs

JAL-1667 JAL-1668 updated reviewed and updated docs

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    /help/html/features/structurechooser.html
JAL-1788 updated docs

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    /help/html/features/bioJsonFormat.html
JAL-1813 only pair up A-Z with a-z if annotation is RNA

JAL-1769 updated test data

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    /test/jalview/bin/CommandLineOperations.java
JAL-1788 added help documentation for biojson

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    /help/html/features/bioJsonFormat.html
JAL-1759 corrected jmol applet lib name

JAL-1807 expanded import java.awt.* to allow code analysis

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    /src/jalview/appletgui/Tooltip.java
JAL-1759 code fix to enable testng ant task compile and run

JAL-1807 explicit imports (uk.ac)

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    /src/uk/ac/ebi/picr/model/UPEntry.java
JAL-1807 explicit imports (org.jibble)

JAL-1807 explicit imports (MCview)

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    /src/MCview/AppletPDBCanvas.java
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    /src/MCview/AppletPDBViewer.java
JAL-1807 explicit imports (jalview.ws.*)

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    /src/jalview/ws/DBRefFetcher.java
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    /src/jalview/ws/SequenceFetcher.java
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    /src/jalview/ws/dbsources/EmblCdsSouce.java
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    /src/jalview/ws/dbsources/EmblSource.java
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    /src/jalview/ws/dbsources/Pfam.java
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    /src/jalview/ws/dbsources/PfamSeed.java
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    /src/jalview/ws/dbsources/UnprotName.java
  1. … 28 more files in changeset.
JAL-1807 explicit imports (jalview.workers)

JAL-1807 explicit imports (jalview.viewmodel)

JAL-1807 explicit imports (jalview.util)

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    /src/jalview/util/BrowserLauncher.java
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    /src/jalview/util/ImageMaker.java
JAL-1807 explicit imports (jalview.structure)

JAL-1807 explicit imports (jalview.schemes)

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    /src/jalview/schemes/ColourSchemeI.java
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    /src/jalview/schemes/PIDColourScheme.java
JAL-1807 explicit imports (jalview.renderer)

JAL-1807 explicit imports (jalview.jbgui)

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    /src/jalview/jbgui/GAlignFrame.java
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    /src/jalview/jbgui/GDasSourceBrowser.java
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    /src/jalview/jbgui/GSequenceLink.java
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    /src/jalview/jbgui/GWsPreferences.java
JAL-1807 explicit imports (jalview.javascript)

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    /src/jalview/javascript/JsCallBack.java
JAL-1807 explicit imports (jalview.io.*)

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    /src/jalview/io/AnnotationFile.java
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    /src/jalview/io/AppletFormatAdapter.java
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    /src/jalview/io/FormatAdapter.java
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    /src/jalview/io/JalviewFileChooser.java
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    /src/jalview/io/ModellerDescription.java
  1. … 15 more files in changeset.
JAL-1807 explicit imports (jalview.gui)

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/AnnotationExporter.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/AnnotationRowFilter.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/CutAndPasteHtmlTransfer.java
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    /src/jalview/gui/CutAndPasteTransfer.java
  1. … 34 more files in changeset.
JAL-1807 explicit imports (jalview.ext.*)

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/varna/VarnaCommands.java
JAL-1807 explicit imports (jalview.datamodel)

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/AlignmentView.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceGroup.java
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    /src/jalview/datamodel/xdb/embl/EmblFile.java
JAL-1807 explicit imports (jalview.controller)