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jim procter <j.procter@dundee.ac.uk> in jalview

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'bug/r2_11_2/JAL-3904_structureviewermenu' into develop

JAL-3905 Fix: wait for response when sending mouseovers. Combined remove old label and add new label and also added warning in javadoc about out-of-order execution

JAL-3904 override buildActionMenu to add in additional menu actions after rebuild

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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
JAL-3904 failing test

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    /src/jalview/gui/StructureViewerBase.java
JAL-2909 JAL-3894 hack in support to import regions of an unindexed SAM file.

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    /src/jalview/datamodel/CigarParser.java
Merge branch 'develop' into features/JAL-2909_bamImport_2_11_2

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3616 show name of structure viewer in ‘new view’ button

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    /src/jalview/jbgui/GStructureChooser.java
JAL-3616 explicit configure external viewer config

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3829 3d beacons logo - misi varadi gave permission to re-use but most likely it is CC-0

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    /resources/images/3d-beacons-logo-transparent.png
Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

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    /src/jalview/gui/StructureChooser.java
Merge branch 'bug/JAL-3885_sequence_fetched_not_displaying_PFAM_Seed' into develop

JAL-2909 increase commandlinetests timeout

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    /test/jalview/bin/CommandLineOperations.java
JAL-2909 fix up tests and ensure we don’t test bam as a writable format

JAL-2909 pass a dummy sequence object to receive features. Ideally we should test that features look like they are expected too here !

JAL-2909 mininal merge of bam import demo to Jalview 2.11.2 develop Merge remote-tracking branch 'origin/features/JAL-2909_bamImport2_11' into features/JAL-2909_bamImport_2_11_2

Conflicts:

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/AppletFormatAdapter.java

src/jalview/io/FileFormat.java

src/jalview/io/FileLoader.java

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    /src/jalview/io/AlignmentFileReaderI.java
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    /src/jalview/io/AppletFormatAdapter.java
JAL-3884 squish alarming but harmless errors when uniprot doesn’t have a record

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    /src/jalview/ws/dbsources/Uniprot.java
JAL-3881 split on any nonalphanumeric symbol (plus _) to generate putative sequence identifiers with which to query databases

JAL-3829 report when 3d-beacons doesn’t provide any models

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    /src/jalview/gui/StructureChooser.java
JAL-3746 update the example corefile for jalviewjs

JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop up menu item

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3821 data file for failing test

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    /test/jalview/io/J03321_rna.embl.txt