jalview

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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

Merge branch 'bug/JAL-2899' into releases/Release_2_10_4_Branch

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-2906 removed mention of experimental features, updated what’s new for 2.10.4 release, and help TOC.

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    /help/html/features/chimera.html
JAL-2976 patch NPE when trying to open Uniprot FTS

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    /src/jalview/fts/core/FTSRestClient.java
JAL-2929 JAL-2922 release notes

JAL-2976 typo in installAnywhere build for VAqua dependency

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    /utils/InstallAnywhere/Jalview.iap_xml
JAL-2960 release notes

JAL-2948 transfer features/annotation is now available for all users

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    /src/jalview/gui/ChimeraViewFrame.java
JAL-2960 raise the structure view after adding structures to it

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    /src/jalview/gui/StructureViewerBase.java
JAL-2976 Vaqua fallback release notes JAL-2906

Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch

JAL-2976 fallback to Vaqua for Macs that don’t work for Quaqua

JAL-2976 Vaqua(4) as a dependency

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    /utils/InstallAnywhere/Jalview.iap_xml
JAL-2899 release notes

JAL-2973 JAL-2974 known defects for 2.10.4 (JAL-2906)

JAL-2925 release notes

JAL-2593 JAL-2945 JAL-2952 JAL-2954 release notes for 2.10.4 JAL-2906

JAL-2906 reformat release notes