jalview

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Commits this week: 7
Total Committers: 73
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Commits this week: 7

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Wednesday 30 Mar
7:22 pm

Ben Soares

JAL-3847 Add some dependencies that gradle 7 mildly complains about

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    • +5
    /build.gradle
4:54 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984

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    /help/help/html/releases.html
4:52 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop

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4:51 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but we live in hope..

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    • -7
    • +7
    /src/jalview/gui/TextColourChooser.java
4:23 pm

Jim Procter

4:22 pm

Jim Procter

make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
4:20 pm

Jim Procter

JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
4:15 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3983 update release notes for JAL-3973

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    /help/help/html/releases.html
4:12 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3973 exclude the original RELEASE file so gradle doesn't complain of duplicate entries in the tarball

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    • -0
    • +2
    /build.gradle
3:49 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'bug/JAL-3973_source_tarball_not_building' into develop

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3:45 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3983 release 2.11.2.1 date and release notes

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    /RELEASE
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    • +57
    /help/help/html/releases.html
Tuesday 15 Mar
5:13 pm

Ben Soares

JAL-360 JAL-3975 make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after JvOptionPane action.

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    • +15
    /src/jalview/gui/FeatureEditor.java
    • -3
    • +4
    /src/jalview/gui/JvOptionPane.java
Sunday 13 Mar
9:00 pm

Ben Soares

Append git.hash and git.branch to RELEASE file stored in tarball. When compiling, if not in git repo use git.branch and git.hash from RELEASE file.

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    • -4
    • +29
    /build.gradle
Friday 11 Mar
9:31 am

Ben Soares

JAL-3973 This fixes the gradle build when not in a git repo. (Part 1 of the issue)

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    • -4
    • +14
    /build.gradle
Thursday 10 Mar
1:29 am

Jalview Development Admin <jalview-dev-owner@jalview.org>

JAL-3746 bump release date to 10th March - after UoD network maintenance

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    /help/help/html/releases.html
1:28 am

Jalview Development Admin <jalview-dev-owner@jalview.org>

JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(

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    /utils/install4j/install4j9_template.install4j
Wednesday 09 Mar
4:51 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert

Options
    • binary
    /j11lib/Jmol-NO_LOG4J-14.31.53.jar
    • binary
    /j8lib/Jmol-NO_LOG4J-14.31.53.jar
10:11 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 JAL-3841 fix README typo

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    /README
8:09 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 more docs tweaking and release notes

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    /help/help/html/features/preferences.html
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    /help/help/html/releases.html
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    /help/help/html/whatsNew.html
7:59 am

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'spike/try_spotless_JAL-3438' into develop

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Tuesday 08 Mar
9:58 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 apply copyright to tests

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    /test/jalview/analysis/AlignmentSorterTest.java
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    /test/jalview/analysis/GeneticCodesTest.java
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    /test/jalview/analysis/scoremodels/PIDModelTest.java
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    /test/jalview/analysis/scoremodels/ScoreMatrixTest.java
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    /test/jalview/analysis/scoremodels/ScoreModelsTest.java
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    /test/jalview/bin/HiDPISettingTest1.java
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    /test/jalview/datamodel/ConcurrentModificationTest.java
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    /test/jalview/datamodel/MappedFeaturesTest.java
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    /test/jalview/datamodel/SequenceGroupTest.java
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    /test/jalview/datamodel/features/FeatureAttributesTest.java
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    /test/jalview/datamodel/features/FeatureMatcherSetTest.java
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    /test/jalview/datamodel/features/FeatureMatcherTest.java
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    /test/jalview/datamodel/features/FeatureStoreTest.java
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    /test/jalview/datamodel/features/SequenceFeaturesTest.java
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    /test/jalview/ext/android/SparseDoubleArrayTest.java
  16. … 59 more files in changeset.
9:56 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 apply copyright to source

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    /src/jalview/bin/Console.java
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    /src/jalview/bin/HiDPISetting.java
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    /src/jalview/bin/JalviewJS2.java
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    /src/jalview/bin/ScreenInfo.java
    • -0
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    /src/jalview/datamodel/AlignExportSettingsAdapter.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
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    /src/jalview/fts/api/StructureFTSRestClientI.java
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    /src/jalview/fts/service/alphafold/AlphafoldRestClient.java
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    /src/jalview/fts/service/threedbeacons/.gitignore
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    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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    /src/jalview/gui/ChimeraXViewFrame.java
  16. … 31 more files in changeset.
9:30 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3438 spotless for 2.11.2.0

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    /src/com/stevesoft/pat/ChangeRule.java
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    /src/com/stevesoft/pat/Ctrl.java
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    /src/com/stevesoft/pat/Custom.java
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    /src/com/stevesoft/pat/FastBracket.java
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    /src/com/stevesoft/pat/FastMulti.java
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    /src/com/stevesoft/pat/FileRegex.java
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    /src/com/stevesoft/pat/Pattern.java
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    /src/com/stevesoft/pat/PopRule.java
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    /src/com/stevesoft/pat/Prop.java
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    /src/com/stevesoft/pat/PushRule.java
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    /src/com/stevesoft/pat/RegOpt.java
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    /src/com/stevesoft/pat/RegRes.java
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    /src/com/stevesoft/pat/Regex.java
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    /src/com/stevesoft/pat/RegexTokenizer.java
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    /src/com/stevesoft/pat/RegexWriter.java
  16. … 647 more files in changeset.
8:39 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes

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    /README
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    /help/help/html/releases.html
6:53 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3108 updated Ensembl client and model species names

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    /help/help/html/releases.html
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    /src/jalview/ext/ensembl/EnsemblRestClient.java
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    /src/jalview/ext/ensembl/Species.java
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    /test/jalview/ext/ensembl/EnsemblGeneTest.java
6:18 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 new release date for 2.11.2

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    /help/help/html/releases.html
6:13 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes

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    /help/help/html/releases.html
5:41 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'bug/JAL-3103_browser_launcher_problems_macos_and_linux' into develop

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    /resources/lang/Messages.properties
12:26 pm

Ben Soares

JAL-3103 updated help doc to remove default browser choice

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    /help/help/html/features/preferences.html
12:14 pm

Ben Soares

JAL-3103 Removed code and unused widgets for defaultBrowser

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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java