jalview

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JAL-3594 very subtle grey tesselation of logo in the whitespace on getdown splashscreen added for release channel

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-3875 test case and patch to verify the query 3d beacons button is shown for proteins with uniprot ids but no canonical accessions

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    /src/jalview/gui/StructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-3907 changed two commented out lines to reflect location of future upgraded JRE zipfiles.

JAL-3907 added creation of symbolic links to workaround an install4j9 problem with parsing packed jre filenames with hyphens.

JAL-3907 adjusted download_jdks.sh and download_jres.sh scripts to use adoptium and added Java 17 download. Added JAVA_VERSION=17 as a gradle build property option.

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-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 '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
Merge branch 'bug/JAL-3885_sequence_fetched_not_displaying_PFAM_Seed' into develop

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-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-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
    • binary
    /j8lib/groovy-all-2.4.21-indy.jar