jalview

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JAL-3210 updating. no test

    • binary
    /swingjs/SwingJS-site.zip-newer
    • binary
    /swingjs/net.sf.j2s.core.jar-3.2.4
JAL-3235 isolated the 'unsafe' override of entrySet to the saveProperties method, since we only need ordered output on save

JAL-2987 release notes

JAL-3407 update RELEASE and cut new release notes in releaseHistory.html

JAL-3407 JAL-3406 update credits in Jalview 2.11.1

JAL-3404 fix up test compilation errors

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-3404 explicit getModelForPdbFile lookup

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/util/StructureCommands.java
JAL-3990 fix typo in showStructures command for Chimera

JAL-3390 refactoring tidy of colourBySequence call stack

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3187 removal of variant feature (non-virtual) transfer to protein

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    /src/jalview/analysis/AlignmentUtils.java
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    /test/jalview/analysis/AlignmentUtilsTests.java
JAL-3390 move StructureCommands to utils package

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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/util/StructureCommands.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3390 improved Jmol colour by sequence command + tests + deprecations

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    /src/jalview/ext/jmol/JmolCommands.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3210 ben testing

JAL-3210 ben testing

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    /.settings/org.eclipse.jdt.core.prefs
JAL-3210 ben testing

JAL-3210 ben testing

JAL-3403 Fit To Window menu item for Jmol

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3390 StructureCommands atomspec helper, corrected Jmol atomspec/test

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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/rbvi/chimera/ChimeraCommands.java
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    /src/jalview/ext/rbvi/chimera/StructureCommands.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3210 ben testing

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    /.settings/org.eclipse.jdt.core.prefs
JAL-3210 ben testing

JAL-3210 ben testing

    • binary
    /swingjs/SwingJS-site.zip-dist
    • binary
    /swingjs/net.sf.j2s.core-3.2.4.jar
    • binary
    /swingjs/net.sf.j2s.core.jar-dist
JAL-3210 ben testing

JAL-3210 ben testing

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    /.settings/org.eclipse.jdt.core.prefs
    • binary
    /j11lib/Jmol-14.29.17-no_netscape.jar
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    /utils/publishHelp.xml
JAL-3402 suppress unmapped chains in View Chain menu

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    /src/jalview/gui/StructureViewerBase.java
JAL-3400 include sequence name in View | Show Chain menu

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3401 JAL-3253-applet

fixes too-early multiple calls to AlignPanel.repaint() and, via repaint

manager to the desktop, also SeqCanvas.paintComponent. See

Jalview2XML.java

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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/project/Jalview2XML.java
Platform.timeCheck - just resetting duration for reset/set-mark..set-mark/get sequence.

JAL-3383 JAL-3253-applet shortcut binary search when position is out of range.

JAL-3390 showSelectedChains pulled up to base class for Jmol/Chimera

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    • +0
    /src/jalview/gui/ChimeraViewFrame.java
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    • +17
    /src/jalview/gui/StructureViewerBase.java
Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

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    /resources/lang/Messages_es.properties
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • binary
    /utils/testnglibs/testng-sources.jar