jalview

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JAL-3394 jalviews scheme added

JAL-3394 file not needed

JAL-3447 Satisfactory file associations. cif, mcif and pdb now not opened by Jalview by default -- but are associated. In Windows and linux installer, are deselected by default. 'jalview://' as a URL scheme now associated in Windows and macOS.

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    /utils/install4j/file_associations_auto-Info_plist.xml
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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-Info_plist.xml
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    /utils/install4j/file_associations_template-install4j8.xml
JAL-3447 Change to install4j template version, JAL-3394 removed redundant compiler variable. Fixed help when run in Eclipse and removed redundant helpDir

JAL-3490 unit test for ignore hidden regions with selection group

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    /test/jalview/analysis/FinderTest.java
JAL-2305 moved failing CrossRef tests to Functional_Failing group

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    /test/jalview/analysis/CrossRefTest.java
JAL-3407 update release date for Jalview 2.11.1

JAL-3490 tests for skip hidden regions (and a bug fix)

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    /test/jalview/analysis/FinderTest.java
JAL-3490 extract constants for number of rows in layout

JAL-3490 revised layout and search algorithm (more tests to be added)

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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/Finder.java
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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/jbgui/GFinder.java
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    /test/jalview/analysis/FinderTest.java
JAL-3394 Simplified media output from install4j

JAL-3490 pull up getViewAsVisibleContigs to base class and interface

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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/gui/AlignViewport.java
JAL-3449 More whitespace in installer. Tidying

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    /utils/install4j/bs_install4j_template.install4j
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    /utils/install4j/file_associations_auto-install4j.xml
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    /utils/install4j/file_associations_template-install4j.xml
JAL-3449 Fixed Info.plist file insertion. Simplified install4j conf filename

JAL-3449 Now parsing install4j XML file to edit values. Should be safer

JAL-3449 Work in progress improving XML replacements by gradle

JAL-3394 disableSigning=true when DEV

JAL-3394 Changed most of the token replacement for adding compiler variables

JAL-3449 Added more versions to getdown splashscreen and fixed Jalview's Java Console installer version reporting

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    /getdown/lib/getdown-launcher-local.jar
JAL-3066 Comment on ambiguous parameter parsing.

JAL-3066 Change Slivka connection to https

JAL-3487 help/splash <html> wrap issue + associated tooltip breaking

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    /swingjs/ver/3.2.5/SwingJS-site.zip
jmol-app.zip update for java2script 3.2.5.v1

JAL-3487 splash/help fix

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    /src/jalview/gui/SplashScreen.java
JAL-3490 Finder match across entirely gapped hidden regions

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    /src/jalview/analysis/Finder.java
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    /test/jalview/analysis/FinderTest.java
JAL-3489 ensure all chains mapped when loading local multimeric PDB file

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    /src/jalview/gui/AssociatePdbFileWithSeq.java
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    /src/jalview/gui/StructureChooser.java
JAL-3066 Fix incorrect URL resolving with /slivka prefix.

SwingJS transpiler to 3.2.5.v1 (fixed java.util.stream)

- required transpiler fixes and redesign of final variables for stream

objects

- required redesign of $init$ and $static$ to exactly reproduce the full

class loading sequence of (1) method definition with default static

values, (2) superclass-sequenced initialization of static fields (3)

superclass-sequenced initialization of static fields, (4)

superclass-sequenced constructor initialization, in that order, able to

handle any complex situation

-includes fixes for JLabelUI HTML label wrapping issues

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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
  1. … 6 more files in changeset.
SwingJS transpiler to 3.2.5.v1 (fixed java.util.stream)

- required transpiler fixes and redesign of final variables for stream

objects

- required redesign of $init$ and $static$ to exactly reproduce the full

class loading sequence of (1) method definition with default static

values, (2) superclass-sequenced initialization of static fields (3)

superclass-sequenced initialization of static fields, (4)

superclass-sequenced constructor initialization, in that order, able to

handle any complex situation

-includes fixes for JLabelUI HTML label wrapping issues

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    /swingjs/ver/3.1.1/SwingJS-site.zip
    • binary
    /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
  1. … 8 more files in changeset.
JAL-3487 HTML label not wrapping

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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
  1. … 6 more files in changeset.