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
5:32 pm

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

JAL-3976 fix mock PDBFTS query & responses

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    • -1
    • +1
    /test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt
    • -1
    • +2377
    /test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt
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.
Wednesday 23 Mar
12:22 pm

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

JAL-3976 skip entries with null values when analyzing

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    • -10
    • +13
    /src/jalview/gui/structurechooser/TDBResultAnalyser.java
12:22 pm

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

JAL-3976 update tests

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    • -2
    • +4
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
    • -2377
    • +1
    /test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt
    • -1
    • +1
    /test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
Thursday 10 Mar
5:40 pm

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

Merge branch 'master' into releases/Release_2_11_2_Branch

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    • -47
    • +0
    /doc/old_ant_build_README
    • binary
    /examples/testdata/MN908947.jvp
    • binary
    /j11digestonly/htsjdk-2.12.0.jar
    • binary
    /j11digestonly/intervalstore-v1.0.jar
    • binary
    /j8digestonly/htsjdk-2.12.0.jar
    • binary
    /j8digestonly/intervalstore-v1.0.jar
    • -224
    • +0
    /test/jalview/gui/SplitFrameTest.java
1:34 am

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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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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    • -1
    • +1
    /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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    • -1
    • +1
    /utils/install4j/install4j9_template.install4j
Wednesday 09 Mar
5:31 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
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
10:12 am

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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10:11 am

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

JAL-3746 JAL-3841 fix README typo

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    • -1
    • +1
    /README
8:14 am

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
8:09 am

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

JAL-3746 more docs tweaking and release notes

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    • -6
    • +1
    /help/help/html/features/preferences.html
    • -45
    • +45
    /help/help/html/releases.html
    • -18
    • +20
    /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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    • -0
    • +20
    /test/jalview/analysis/AlignmentSorterTest.java
    • -0
    • +20
    /test/jalview/analysis/GeneticCodesTest.java
    • -0
    • +20
    /test/jalview/analysis/scoremodels/PIDModelTest.java
    • -0
    • +20
    /test/jalview/analysis/scoremodels/ScoreMatrixTest.java
    • -0
    • +20
    /test/jalview/analysis/scoremodels/ScoreModelsTest.java
    • -0
    • +20
    /test/jalview/bin/HiDPISettingTest1.java
    • -0
    • +20
    /test/jalview/datamodel/ConcurrentModificationTest.java
    • -0
    • +20
    /test/jalview/datamodel/MappedFeaturesTest.java
    • -0
    • +20
    /test/jalview/datamodel/SequenceGroupTest.java
    • -0
    • +20
    /test/jalview/datamodel/features/FeatureAttributesTest.java
    • -0
    • +20
    /test/jalview/datamodel/features/FeatureMatcherSetTest.java
    • -0
    • +20
    /test/jalview/datamodel/features/FeatureMatcherTest.java
    • -0
    • +20
    /test/jalview/datamodel/features/FeatureStoreTest.java
    • -0
    • +20
    /test/jalview/datamodel/features/SequenceFeaturesTest.java
    • -0
    • +20
    /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

Options
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    • +20
    /src/jalview/bin/Console.java
    • -0
    • +20
    /src/jalview/bin/HiDPISetting.java
    • -0
    • +20
    /src/jalview/bin/JalviewJS2.java
    • -0
    • +20
    /src/jalview/bin/ScreenInfo.java
    • -0
    • +20
    /src/jalview/datamodel/AlignExportSettingsAdapter.java
    • -0
    • +20
    /src/jalview/ext/pymol/PymolCommands.java
    • -0
    • +20
    /src/jalview/ext/pymol/PymolManager.java
    • -0
    • +20
    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
    • -0
    • +20
    /src/jalview/fts/api/StructureFTSRestClientI.java
    • -0
    • +20
    /src/jalview/fts/service/alphafold/AlphafoldRestClient.java
    • -0
    • +20
    /src/jalview/fts/service/threedbeacons/.gitignore
    • -0
    • +20
    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
    • -0
    • +20
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
    • -0
    • +20
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -0
    • +20
    /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
    • -31
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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.
8:40 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
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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    • +33
    /README
    • -34
    • +48
    /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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    • +5
    /help/help/html/releases.html
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    • +2
    /src/jalview/ext/ensembl/EnsemblRestClient.java
    • -3
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    /src/jalview/ext/ensembl/Species.java
    • -1
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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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    • -1
    • +1
    /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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    • +4
    /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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    • +1
    /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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    • +0
    /src/jalview/gui/Preferences.java
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    • +0
    /src/jalview/jbgui/GPreferences.java
12:03 pm

Ben Soares

JAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods

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    /THIRDPARTYLIBS
    • binary
    /j11lib/BrowserLauncher2-1_3.jar
    • binary
    /j8lib/BrowserLauncher2-1_3.jar
    • -35
    • +0
    /resources/edu/stanford/ejalbert/launching/misc/linuxUnixConfig.properties
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    /resources/edu/stanford/ejalbert/launching/misc/sunOSConfig.properties
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    /resources/edu/stanford/ejalbert/launching/windows/windowsConfig.properties
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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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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
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    /src/jalview/util/BrowserLauncher.java
12:39 am

Ben Soares

JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS

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    • +1
    /THIRDPARTYLIBS