Ben Soares

JAL-3416 make flat default laf for linux

JAL-3416 updated FlatLaf to 1.6 and added some tabbed pane properties

    • binary
    /j11lib/flatlaf-1.6.jar
    • binary
    /j8lib/flatlaf-1.6.jar
Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

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

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 improvement/JAL-3594_logos_for_jalview_test

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

    • -0
    • +18
    /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.
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.

    • -0
    • +39
    /utils/install4j/file_associations_auto-Info_plist.xml
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    /utils/install4j/file_associations_auto-install4j8.xml
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

    • -42
    • +112
    /src/jalview/gui/SequenceFetcher.java
JAL-3783 Updated groovy-all-2.4. Currently newer stable releases cause a problem with shadowJar.

    • binary
    /j11lib/groovy-all-2.4.21-indy.jar
    • binary
    /j8lib/groovy-all-2.4.21-indy.jar
JAL-3594 added BG and UoD logo and banner to splashscreens, and adjusted status text box

JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

    • -4
    • +6
    /src/jalview/analysis/AlignmentUtils.java
    • -1
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    /src/jalview/analysis/Conservation.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/commands/EditCommand.java
  1. … 88 more files in changeset.
JAL-3521 'Debian-safe' version of minimal build.gradle and patch. Using existing doc/*.html and build_properties from source tarball.

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    /utils/debian/build_gradle.patch
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    /utils/debian/debian_build.gradle
JAL-3521 Created a patch file to transform build.gradle into debian_build.gradle

    • -0
    • +2739
    /utils/debian/build_gradle.patch
JAL-3521 working minimal build.gradle for debian and 2.11.2. Flexmark plugin might be a problem

JAL-3521 not quite working minimal build.gradle for debian and 2.11.2

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    /utils/debian/debian_build.gradle
Merge branch 'merge/develop_JAL-1260' into develop

JAL-1260 rudimentary parsing of LOCUS line to at least get accession id

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    /src/jalview/io/GenBankFile.java
JAL-1260 rudimentary parsing of LOCUS line to at least get accession id

    • -32
    • +14
    /src/jalview/io/GenBankFile.java
JAL-3874 attempt to add source jars to eclipse through buildship

    • binary
    /j11sources/Jmol-14.31.53-sources.jar
JAL-3779 Added to documentation

JAL-3774 combined changes from bug/JAL-3774_splitFrameFinder: i) fixed focus Finder from split frame. ii) missing i18n added, overlong translation shortened. iii) better translation.

    • -1
    • +3
    /resources/lang/Messages_es.properties
JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

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    • +1
    /resources/lang/Messages_es.properties
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    • +17
    /src/jalview/gui/OptsAndParamsPage.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/jws2/Jws2Client.java
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    /src/jalview/ws/jws2/MsaWSClient.java
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    /src/jalview/ws/jws2/dm/JabaOption.java
JAL-3761 listToArray became rangeListToArray

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    /test/jalview/util/MappingUtilsTest.java
JAL-3761 listToArray became rangeListToArray

    • -14
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    /src/jalview/io/EmblFlatFile.java
JAL-3818 formatting

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
Merge branch 'develop' into merge/develop_ben2

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