jalview

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Merge branch 'feature/JAL-666_exportoverview' into features/JAL-666_exportoverview

JAL-666 patch JAL-1947 in applet where overview is under sampled when lost of sequences are hidden in the viewport (hangover from applet not supporting hidden rows)

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    /src/jalview/appletgui/OverviewPanel.java
JAL-666 patch possible buglet in applet where overview is under sampled when lost of sequences are hidden in the viewport (hangover from applet not supporting hidden rows)

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    /src/jalview/appletgui/OverviewPanel.java
JAL-666 JAL-1667 regularise use of API calls between applet and application overviews

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    /src/jalview/appletgui/OverviewPanel.java
JAL-1667 make transferSettings an API method

JAL-1667 JAL-666 rename the GUI FeatureRenderer classes that hold the editing logic for sequence features.

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    /src/jalview/appletgui/AppletJmol.java
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    /src/jalview/appletgui/FeatureRendererAndEditor.java
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    /src/jalview/appletgui/OverviewPanel.java
  1. … 9 more files in changeset.
JAL-1943 don't try to unmarshal non-xml files in V1 project

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    /src/jalview/gui/Jalview2XML_V1.java
JAL-1932 TrimRegionCommand bug fix, tests and purge of unused code

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/commands/TrimRegionCommand.java
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    /test/jalview/commands/TrimRegionCommandTest.java
JAL-1925 version change

JAL-1925 update what's new and release notes

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

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

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

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

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

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