jalview

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Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3253-applet JAL-3414 Display Settings dialog slow to open

SwingJS-site.zip

corrects code in JSDialog that called parent.addNotify() every time, not

just before it has been connected.

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3253-applet JAL-3397 delete fix

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    /src/intervalstore/nonc/IntervalStore.java
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    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3253-applet JAL-3397 JAL-3383 fast IntervalStore for JavaScript

fully commented and cleaned code

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    /src/jalview/datamodel/features/FeatureStoreJS.java
JAL-3253-applet JAL-3397 JAL-3383 fast IntervalStore for JavaScript

needs testing in JavaScript

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    /src/intervalstore/api/IntervalI.java
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    /src/intervalstore/api/IntervalStoreI.java
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    /src/intervalstore/nonc/IntervalStore.java
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    /src/jalview/analysis/CrossRef.java
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    /src/jalview/datamodel/features/FeatureStoreJS.java
JAL-3210 updating. no test

JAL-3210 testing

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    /.settings/org.eclipse.buildship.core.prefs
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    /.settings/org.eclipse.jdt.groovy.core.prefs
    • binary
    /swingjs/net.sf.j2s.core.jar-newer
JAL-3362 keep Java 1.8 build happy by specifying generic type arguments

Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into merge-212

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/project/Jalview2XML.java
JAL-3210 test commit

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    /.settings/org.eclipse.buildship.core.prefs
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    /.settings/org.eclipse.jdt.core.prefs
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    /.settings/org.eclipse.jdt.groovy.core.prefs
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    /.settings/org.eclipse.jdt.ui.prefs
JAL-3210 updating. no test

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-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