jalview

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JAL-3252 some debugging

JAL-3240 known issue for release notes

JAL-3239 release note

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    /src/jalview/gui/SequenceRenderer.java
JAL-3244 release note

Merge remote-tracking branch 'origin/bug/JAL-3239monospacedEps' into develop

JAL-3244 delete obsolete method

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-3239 draw EPS or SVG one character at a time (even monospaced)

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    /src/jalview/gui/SequenceRenderer.java
Merge branch 'bug/JAL-3244jmolWindows' into develop

JAL-3244 renamed Platform method for clarity

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    /src/jalview/gui/ChimeraViewFrame.java
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    /test/jalview/util/PlatformTest.java
adding another getdown file (produced during a getdown build) to gitignore

Fixed -Djvl=true in install4j JVM invocation

Extra JVL file association in the installer. Shadowed gradle-launcher.jar and classpath adjusted in install4j template. 'jre' folder made a compiler variable in install4j template.

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    /getdown/src/getdown/launcher/pom.xml
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    /resources/images/JalviewVersionLocator.png
JAL-3244 ignore file path separator when comparing pdb file paths

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    /test/jalview/util/PlatformTest.java
Merge branch 'task/JAL-3243_PDB_free_text_error' into develop

Merging in JAL-3243 replacement .jar files for jersey and javax.ws.rs.

JAL-3243 Replaced javax.ws jar compatible with jersey-*-1.19.1.jar

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    /j11lib/jersey-client-1.19.1.jar
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    /j11lib/jersey-core-1.19.1.jar
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    /j11lib/jersey-json-1.19.1.jar
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    /j11lib/jsr311-api-1.1.1.jar
JAL-3196 Correcting the source for getdown (already corrected in util/install4j/install4j_template.install4j and getdown/lib/getdown-launcher.jar)

JAL-3241 simplified enum constructors for classloadability in Java 11

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    /src/jalview/util/ImageMaker.java
JAL-2738 JAL-2743 update unit test to match new VCF properties

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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3003 help page mention EPS doesn't support transparency

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    /help/help/html/features/featuresettings.html
JAL-3236 see also previous commit - tweak the install4j template so our installers get built !

Added a unixInstaller and unixArchive media-type to the install4j template. unixArchive is now specified in the gradle.properties (unixInstaller can be added).

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    /doc/building-OLD.html
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

Removing old commented out 'org.gradle.java.home=' line from gradle.properties

Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-2743 class Javadoc

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    /src/jalview/ext/ensembl/EnsemblMap.java
JAL-2738 JAL-2743 properties to map VCF header to species or assembly

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    /src/jalview/io/vcf/VCFLoader.java
Also removing eclipse .project and .settings from the branch. Run 'gradle cleanEclipse eclipse' to produce fresh new eclipse project files (and either 'Refresh' project in eclipse, or 'Import... -> Existing gradle project') or just run 'gradle eclipse' to keep some of your existing project settings.

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    /.settings/org.eclipse.jdt.core.prefs
Removing .classpath from this branch

JAL-3150 examples/exampleFile.jvp for updated manual/tutorial exercises

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    /examples/exampleFile.jvp