jalview

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JAL-2988 update InstallAnywhere install dependencies for VAqua5

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    /utils/InstallAnywhere/Jalview.iap_xml
JAL-2988 workaround for jalview save as dialogs - clear filename before displaying

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    /src/jalview/io/JalviewFileChooser.java
JAL-2988 JAL-2976 update to latest VAqua release: VAqua5

Merge branch 'task/JAL-3047_clover2104b1_cherrypick' into releases/Release_2_10_4_Branch

JAL-3047 don't set classes unconditionally (forgot to delete it in earlier patch)

JAL-3047 don’t let the makedist task complete if a clover build was performed

JAL-3047 ‘cloverclasses’ build directory for instrumented classes (allow incremental compile and avoid releasing instrumented classes in production builds)

JAL-3047 enable clover for testng

JAL-3047 ignore clover output dir

JAL-3009 release notes

Merge branch 'bugs/JAL-3009_blockingNetworkThreads' into releases/Release_2_10_4_Branch

JAL-2999 what's new and tweak release notes order

JAL-2920 format/comment tidy

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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-2920 wrap description in <html/> if it includes <br/>

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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
Merge branch 'releases/Release_2_10_4_Branch' of https://source.jalview.org/git/jalview.git into releases/Release_2_10_4_Branch

JAL-2920 unit tests for 3 or more original or variant bases

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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-2999 refine release notes

JAL-2999 release 2.10.4b1 on Thursday (promise!)

JAL-2920 release notes

Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch

JAL-2920 revised TODO for JAL-3025

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    /src/jalview/ws/dbsources/Uniprot.java
JAL-2920 don’t output variant/original sequence as three-letter codes for more than three bases (pragmatic deviation from HGVC nomenclature)

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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-2920 JAL-3017 uniprot XML schema included in mappings doc

JAL-1920 JAL-3017 use newline not <br/> in description and update test to cover multi-position variants and newline code

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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-2999 update release notes and patch date to 5th June 2018

JAL-3017 parse multiple variant elements for uniprot feature Conflicts: src/jalview/datamodel/xdb/uniprot/UniprotFeature.java Merged JAL-3017 into upstream JAL-2920 patches for HGVC nomenclature note - should properly deal with delins variants http://varnomen.hgvs.org/recommendations/protein/variant/delins/

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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-3017 parse multiple variant elements for uniprot feature

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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-2999 2.10.4b1 release 31st May

JAL-3009 news reader thread should be in background. TODO: patch newsreader so it uses GUI thread for displaying itself ?

JAL-3009 Identifiers.Org retrieval on background thread.