jalview

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JAL-3393 Don't need PDF file using Illustrator. Replaced with SVG using Inkscape

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    /utils/install4j/jalview_dmg_background_layers.pdf
JAL-3407 2.11.1.0 release date bump - maybe tomorrow - maybe the next day !

JAL-3407 JAL-3130 back out java 9+ syntax that breaks java 8 builds

JAL-3210 merged from develop: build.gradle and gradle.properties

JAL-3210 debug logging commented out

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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-3210 test updated for changed signature of SequenceI.getDBRefs()

Merge branch 'develop' into Jalview-JS/develop

Conflicts:

.gitignore

build.gradle

gradle.properties

src/jalview/gui/AlignFrame.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureSettings.java

src/jalview/gui/JvSwingUtils.java

src/jalview/util/MessageManager.java

test/jalview/gui/AlignmentPanelTest.java

test/jalview/gui/JvSwingUtilsTest.java

test/jalview/gui/PopupMenuTest.java

utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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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/ext/ensembl/EnsemblSeqProxy.java
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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/AnnotationLabels.java
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    /src/jalview/gui/FeatureSettings.java
  1. … 19 more files in changeset.
JAL-3225 updated essential files for eclipse project if buildship fails

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    /utils/eclipse/eclipse_startup_files.zip
JAL-3225 updated essential files for eclipse project if buildship fails

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    /utils/eclipse/eclipse_startup_files.zip
JAL-3562 paranoid print out of tested values during wait suspect a platform issue making result different

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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3225 Also look for local.properties in file named ../${projectDir}_local.properties. This allows multiple instances of the same project in Eclipse by changing the eclipse_project_name propert (and other local properties)

JAL-3225 This one file needed for project if git clean -dfx run

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    /.settings/org.eclipse.buildship.core.prefs
JAL-3225 This one file needed for project if git clean -dfx run

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    /.settings/org.eclipse.buildship.core.prefs
JAL-3225 fix comparing Eclispe IDE j2s plugin and this branch j2s plugin

JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    /.settings/org.eclipse.buildship.core.prefs
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    /.settings/org.eclipse.jdt.core.jalview.prefs
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    /.settings/org.eclipse.jdt.groovy.core.prefs
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    /.settings/org.eclipse.jdt.ui.prefs
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    /utils/eclipse/org.eclipse.jdt.core.jalview.prefs
JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    /.settings/org.eclipse.buildship.core.prefs
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    /.settings/org.eclipse.jdt.core.jalview.prefs
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    /.settings/org.eclipse.jdt.groovy.core.prefs
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    /.settings/org.eclipse.jdt.ui.prefs
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    /utils/eclipse/org.eclipse.jdt.core.jalview.prefs
JAL-3562 even longer wait to see if idwidth test passes (still passes on OSX)

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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3562 belt and braces - wait before check, and also check validity of swing component

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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3562 wait until no more events on the queue as well

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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3562 - use isCalcInProgress rather than waiting for a non-null response from getConsensusSeq to indicate when alignFrame is ready to be poked and prodded by test code

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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3248 Added instructions for downloading and configuring as gradle project in Eclipse only, i.e. no command line tools needed

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    /doc/images/eclipse_add_gradle_nature.png
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    /doc/images/eclipse_egit_branch.png
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    /doc/images/eclipse_egit_connection.png
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    /doc/images/eclipse_egit_import.png
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    /doc/images/eclipse_installer.png
JAL-3210 fix an undefined copyPlugin var and improved warning in Eclipse console when copying plugin

JAL-3210 Fixed Eclipse IDE usage

Bamboo test #13

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    /src/jalview/gui/AlignmentPanel.java
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    /test/jalview/gui/SeqCanvasTest.java
unneeded debug message

JAL-3210 New site-resources dir too

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    /utils/jalviewjs/site-resources/applets-nocore.html
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    /utils/jalviewjs/site-resources/applets.html
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    /utils/jalviewjs/site-resources/css/ie6.css
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    /utils/jalviewjs/site-resources/css/ie7.css
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    /utils/jalviewjs/site-resources/css/reset.css
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    /utils/jalviewjs/site-resources/css/style.css
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    /utils/jalviewjs/site-resources/examples/2GIS.pdb
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    /utils/jalviewjs/site-resources/examples/3W5V.pdb
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    /utils/jalviewjs/site-resources/examples/backupfilestest.fa
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    /utils/jalviewjs/site-resources/examples/biojsonschema.json
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    /utils/jalviewjs/site-resources/examples/dna_interleaved.phy
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    /utils/jalviewjs/site-resources/examples/dna_sequential.phy
  1. … 29 more files in changeset.
JAL-3210 New version of swingjs and supporting .zip libraries. Swing-JS version 3.2.9.v1e

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    /swingjs/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.1.1/SwingJS-site.zip
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    /swingjs/ver/3.1.1/net.sf.j2s.core.3.1.1.jar
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    /swingjs/ver/3.2.1/SwingJS-site.zip
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    /swingjs/ver/3.2.1/net.sf.j2s.core_3.2.1.jar
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    /swingjs/ver/3.2.2/SwingJS-site.zip
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    /swingjs/ver/3.2.2/net.sf.j2s.core.jar
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    /swingjs/ver/3.2.3/SwingJS-site.zip
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    /swingjs/ver/3.2.3/net.sf.j2s.core.jar
  1. … 25 more files in changeset.
JAL-3210 adjustment to build.gradle, gradle.properties to look for net.sf.j2s.core-j11.jar

Bamboo test #13 AlignViewport resize and jscrollbar set

removing synchronize I just added.

Bamboo stalled?