jalview

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JAL-1791 remove blanket sign of examples/*.jar

JAL-1791 id rather than name attrib

JAL-1791 sign the applet with/out timestamps

JAL-1791 add explicit proxy for benefit of jalview's build server when timestamping signed jars

JAL-1791 fix ant target dependencies

JAL-1791 make timestamping optional using -Dtimestamp

JAL-1791 add jalview.tsaurl for specifying timestamp server when signing jars

Merge branch 'bug/JAL-1923_290b2_group_annots' into Release_2_9_0b1_Branch

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    /src/jalview/gui/TreeCanvas.java
JAL-1923 formatting

JAL-1923 add groups to codon-complement and notify annotation update for all linked views

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    /src/jalview/gui/TreeCanvas.java
JAL-1923 fix: don’t add group twice

Merge branch 'develop' into Release_2_9_0b1_Branch

JAL-1684 updated fragment alignment for example and added aligned protein and cDNA

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    /examples/estrogenReceptorCdna_aln.fa
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    /examples/estrogenReceptorCdna_frag.fa
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    /examples/estrogenReceptorProtein_aln.fa
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    /examples/estrogenReceptorProtein_frag.fa
Merge branch 'Release_2_9_0b1_Branch' of https://source.jalview.org/git/jalview.git into Release_2_9_0b1_Branch

JAL-1684 example uncommented on 2.9.0b1 branch

JAL-1894 update year/version in copyright

  1. … 886 more files in changeset.
Merge branch 'develop' into Release_2_9_0b1_Branch

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

Merge branch 'develop' into Release_2_9_0b1_Branch

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/io/JSONFile.java
  1. … 8 more files in changeset.
JAL-1894 add licensing

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    /test/jalview/bin/JalviewLiteTest.java
JAL-1912 JAL-1896 release notes updated

JAL-1894 update what's new

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

JAL-1912 JAL-1896 release notes updated

JAL-1544 typo fix

JAL-1894 formatting

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    /test/jalview/bin/JalviewLiteTest.java
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    /test/jalview/io/FeaturesFileTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-1894 organise imports

merge

JAL-1894 source formatting

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-1894 organise imports