jalview

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Commits this week: 8
Total Committers: 73
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Commits this week: 8

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Monday 06 May 2019
7:42 pm

Ben Soares

JAL-3252 some debugging

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    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/FileUtil.java
9:49 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3240 known issue for release notes

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    /help/help/html/releases.html
9:23 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3239 release note

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    /help/help/html/releases.html
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    /src/jalview/gui/SequenceRenderer.java
9:21 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3244 release note

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    /help/help/html/releases.html
9:18 am

gmungoc <g.m.carstairs@dundee.ac.uk>

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

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9:07 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3244 delete obsolete method

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
Thursday 02 May 2019
2:37 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3239 draw EPS or SVG one character at a time (even monospaced)

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    /src/jalview/gui/SequenceRenderer.java
12:36 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'bug/JAL-3244jmolWindows' into develop

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12:34 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3244 renamed Platform method for clarity

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    /src/jalview/gui/AppJmol.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/project/Jalview2XML.java
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    /src/jalview/util/Platform.java
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    /test/jalview/util/PlatformTest.java
12:17 pm

Ben Soares

adding another getdown file (produced during a getdown build) to gitignore

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    /.gitignore
Wednesday 01 May 2019
5:36 pm

Ben Soares

Fixed -Djvl=true in install4j JVM invocation

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    /.gitignore
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    /utils/install4j/install4j_template.install4j
5:18 pm

Ben Soares

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/lib/getdown-launcher.jar
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    /getdown/src/getdown/launcher/pom.xml
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    /getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java
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    /resources/images/JalviewVersionLocator.png
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    /utils/install4j/install4j_template.install4j
5:04 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3244 ignore file path separator when comparing pdb file paths

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    /src/jalview/gui/AppJmol.java
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    /src/jalview/structure/StructureSelectionManager.java
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    /src/jalview/util/Platform.java
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    /test/jalview/util/PlatformTest.java
2:37 pm

Ben Soares

Merge branch 'task/JAL-3243_PDB_free_text_error' into develop

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

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Tuesday 30 Apr 2019
6:05 pm

Ben Soares

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

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    /j11lib/javax.ws.rs-api-2.1.1.jar
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    /j11lib/jersey-client-1.19.1.jar
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    /j11lib/jersey-client-1.19.jar
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    /j11lib/jersey-core-1.19.1.jar
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    /j11lib/jersey-core-1.19.jar
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    /j11lib/jersey-json-1.19.1.jar
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    /j11lib/jersey-json-1.19.jar
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    /j11lib/jsr311-api-1.1.1.jar
12:51 pm

Ben Soares

JAL-3196 Correcting the source for getdown (already corrected in util/install4j/install4j_template.install4j and getdown/lib/getdown-launcher.jar)

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    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java
11:57 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3241 simplified enum constructors for classloadability in Java 11

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    /src/jalview/util/ImageMaker.java
Monday 29 Apr 2019
3:17 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2738 JAL-2743 update unit test to match new VCF properties

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
2:47 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3003 help page mention EPS doesn't support transparency

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    /help/help/html/features/featuresettings.html
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    /help/help/html/io/export.html
Friday 26 Apr 2019
5:47 pm

Jim Procter

JAL-3236 see also previous commit - tweak the install4j template so our installers get built !

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    /utils/install4j/install4j_template.install4j
5:25 pm

Ben Soares

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
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    /doc/building.html
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    /gradle.properties
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    /utils/install4j/install4j_template.install4j
4:23 pm

Ben Soares

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

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4:22 pm

Ben Soares

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

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    /gradle.properties
3:11 pm

Jim Procter

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

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2:55 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

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

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2:53 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2743 class Javadoc

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    /src/jalview/ext/ensembl/EnsemblMap.java
2:52 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2738 JAL-2743 properties to map VCF header to species or assembly

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    /src/jalview/io/vcf/VCFLoader.java
2:13 pm

Ben Soares

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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    /.project
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    /.settings/org.eclipse.jdt.core.prefs
1:20 pm

Ben Soares

Removing .classpath from this branch

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    /.classpath
12:34 pm

Jim Procter

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

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    /examples/exampleFile.jvp