jalview

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JAL-2992 simpler heuristic for available height

JAL-2997 additional tests

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    /test/jalview/io/ClustalFileTest.java
JAL-2993 AlignFrame listen for keystrokes in OverviewPanel

JAL-2997 unit test

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    /test/jalview/io/ClustalFileTest.java
JAL-2997 handle tab-delimited trailing column number when parsing

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    /src/jalview/io/ClustalFile.java
JAL-2999 release notes and version bump for jalview 2.10.4b1

JAL-2895 replace $$Jalview-Version$$ in help.jhm with build version when indexing built in help pages

JAL-2920 release notes

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

JAL-2920 basic test for Description from features with/out description, variation and original attributes

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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-2920 simplified logic and added corner cases for missing attributes (probably not needed but..)

JAL-2906 update release date and release notes

JAL-2931 patch IA paths for new build box

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    /utils/InstallAnywhere/Jalview.iap_xml
JAL-2984 add pdb as sequence(s) if associate structure is declined

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    /src/jalview/gui/AlignFrame.java
Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch

JAL-2976 fixed bad equivalence check and implemented belt-and-braces check for quaqua in class name string of look and feel to decide when to fallback to violetlib-Aqua.

JAL-2321 release notes

Merge branch 'patch/JAL-2321_addsecstrForDroppedPDBFile' into releases/Release_2_10_4_Branch

JAL-2321 patch test to ensure structures are actually annotated when loaded directly to desktop

JAL-2321 ensure default is ‘parseImmediately=true’

JAL-2321 use configured values for structure derived annotation

JAL-2321 add secondary structure & temp factor if not already present on mapped sequences

JAL-2321 use StructureImportSettings singleton settings when JmolParser.parse() called from constructor

JAL-2321 isParseImmediately() allows the parse() method to determine if it was called by the constructor or after construction

JAL-2321 allow JmolParser to be configured before parsing data

JAL-2906 apply GPLv3 license source

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    /src/jalview/datamodel/RangeIterator.java
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    /src/jalview/jbgui/GStructureChooser.java
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    /test/jalview/gui/SeqCanvasTest.java
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    /test/jalview/ws/dbsources/PfamFullTest.java
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    /test/jalview/ws/dbsources/PfamSeedTest.java
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    /test/jalview/ws/dbsources/RfamFullTest.java
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    /test/jalview/ws/dbsources/RfamSeedTest.java
JAL-2960 don’t override a swing method and create infinite recursion ;) toFront now raiseViewer !

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    /src/jalview/gui/StructureViewerBase.java
Merge branch 'releases/Release_2_10_4_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_10_4_Branch

JAL-2906 small tweaks to release notes

JAL-2906 2.10.4 release for 8th May 2018