jalview

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JAL-3474 removed all .cvsignore files stored in the repo

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    /help/help/html/colourSchemes/.cvsignore
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    /help/help/html/webServices/.cvsignore
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JAL-3468 unit tests updated for changes

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    /test/jalview/gui/JvSwingUtilsTest.java
Merge branch 'bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException' into improvement/JAL-3416_GTK_look_and_feel

JAL-3210 Automatic buildship/eclipse update to site when making changes to code

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    /.settings/org.eclipse.jdt.core.jalview.prefs
JAL-3210 Added jdt prefs from applet branch. Made IDE tasks more visible

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    /.settings/org.eclipse.jdt.core.jalview.prefs
JAL-3468 truncate feature description to 40 chars in tooltip/menu item

JAL-3473 Checked value of def and min. Set def to min if lower than min.

JAL-3473 Checked value of def and min. Set def to min if lower than min.

JAL-3473 Checked value of def and min. Set def to min if lower than min.

Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build

JAL-3210 unimportant error message

JAL-3210 new transpiler fixes problem that it could have a null-pointer exception for comparison to history, where, apparently, IProject.getProject().getLocation() is null.

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    /swingjs/_j2sclasslist.txt
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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/_j2sclasslist.txt
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3210 new transpiler fixes problem that it could have a null-pointer exception for comparison to history, where, apparently, IProject.getProject().getLocation() is null.

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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3210 catch exception for eclipse

JAL-3210 _j2sclasslist.txt moved into swingjs

JAL-3210 Fixed jalviewjs dependencies. Changed linkCheck to tee output to .out file. Tidying jalviewjs paths.

JAL-3210 Fixed local.properties setting. Some tidying.

JAL-3210 firming up relative paths with jalviewDir. Some comments on possibility of using eclipse plugins differently

JAL-3210 Some tidying and now using swingjs/*

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    /utils/jalviewjs/Java2ScriptCompilationParticipant.java
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    /utils/jalviewjs/Java2ScriptCompiler.java
JAL-3210 Now add/override gradle.properties with local.properties

Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build

JAL-3210 tidying j2s and swingjs

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    /utils/jalviewjs/SwingJS-site.zip_4.12
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    /utils/jalviewjs/SwingJS-site.zip_4.13
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    /utils/jalviewjs/eclipse/cleanEclipseOptions
JAL-3210 .j2s fix to exclude /utils directory

JAL-3210 transpiler resource recursion fix for package foo in path .../foo/.../foo

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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

JAL-3210 transpiler fix for package foo with path .../foo/.../foo

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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
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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3210 Added eclipse instance info in j2s-transpile.out log.

JAL-3469 add "Number=." fields (all values) to all alleles in VCF record

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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3210 Tidied more build.gradle. Different j2s versions for different eclipse versions -- temporary. Only 2019-06 working.

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    /utils/jalviewjs/SwingJS-site.zip_4.12
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    /utils/jalviewjs/SwingJS-site.zip_4.13
JAL-3210 Using j2s plugins that work for 4.12. net.sf.j2s.core-3.2.4.08.jar not working yet