jalview

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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 improvement/JAL-3594_BG_and_UoD_logos_added

Merge branch 'improvement/JAL-3594_logos_for_jalview_test' into develop

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 improvement/JAL-3594_logos_for_jalview_test

JAL-3594 New Jalview Test logos and .icns/.ico creation helper script

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    /doc/README-DMG_background_image_creation.md
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    /doc/README-DMG_creation.md
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    /doc/README_convert_PNG_to_ICNS_and_ICO
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    /utils/channels/release/images/jalview_logo.svg
  1. … 15 more files in changeset.
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

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    /src/jalview/gui/StructureChooser.java
JAL-3594 Changed logo for Jalview Test

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    /utils/channels/test-release/images/jalview_test-release_logo.svg
  1. … 21 more files in changeset.
JAL-1260 Added .gbk to GenBank extensions. Added GenBank extensions to the installer.

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    /utils/install4j/file_associations_auto-Info_plist.xml
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    /utils/install4j/file_associations_auto-install4j8.xml
JAL-3878 Skip getting results of failed jobs.

JAL-3878 Add job log messages reporting.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Fix null pointer exception when preparing empty sequences for job.

JAL-3878 Fetch sequences for alignment on menu action, not creation.

JAL-3878 Split web services menu entries by programs and hosts.

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    /src/jalview/ws2/operations/Operation.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-3885 Made the database JComboBox have StringPair entries to allow a display value, set to the single item dbname if there's a single item

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    /src/jalview/gui/SequenceFetcher.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-3878 Add isInteractive() method to Operation interface.

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    /src/jalview/ws2/operations/Operation.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-3878 Add getName() to Operation interface.

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    /src/jalview/ws2/operations/Operation.java
JAL-3783 Updated groovy-all-2.4. Currently newer stable releases cause a problem with shadowJar.

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    /j11lib/groovy-all-2.4.21-indy.jar
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    /j8lib/groovy-all-2.4.21-indy.jar
JAL-3878 Wire web services logic to UI elements.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java