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
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.
2:40 pm

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

JAL-3982 todo notes

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    /src/jalview/rest/HighlightGenomicRangeEndpoint.java
2:14 pm

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

JAL-3860 prototype for highlight species/assembly/chromosome/position

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    /src/jalview/datamodel/GenomicAssemblies.java
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    /src/jalview/rest/API.java
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    /src/jalview/rest/HighlightGenomicRangeEndpoint.java
Tuesday 29 Mar
11:20 pm

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

JAL-3982 JAL-3860 encapsulate genomic coordinates mapping/liftover logic

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    /src/jalview/datamodel/GenomicAssemblies.java
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    /src/jalview/io/vcf/VCFLoader.java
8:06 pm

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

JAL-3860 JAL-3892 extract genomic assembly mapping logic to static store

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    • +158
    /src/jalview/datamodel/GenomicAssemblies.java
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    /src/jalview/io/vcf/VCFLoader.java
Friday 25 Mar
4:16 pm

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

JAL-3982 highlight any 3D structure mappings for positions mapped via CDS/transcript relationships

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    • +64
    /src/jalview/structure/StructureSelectionManager.java
Wednesday 23 Mar
9:38 pm

Ben Soares

JAL-3851 Fix getRequestBody()

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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/InputAlignmentEndpoint.java
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    /src/jalview/rest/RestHandler.java
Tuesday 22 Mar
7:00 pm

Ben Soares

Merge branch 'feature/JAL-3851_rest_api_for_genome_browser' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

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6:42 pm

Ben Soares

JAL-3851 merged to develop 2022-03-22

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    /doc/api_specification.md
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/SequenceFetcher.java
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    /src/jalview/httpserver/AbstractRequestHandler.java
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    /src/jalview/httpserver/HttpServer.java
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    /src/jalview/rest/API.java
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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/AbstractEndpointAsync.java
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    /src/jalview/rest/FetchSequencesEndpoint.java
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    /src/jalview/rest/GetCrossReferencesEndpoint.java
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    /src/jalview/rest/HighlightSequenceEndpoint.java
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    /src/jalview/rest/InputAlignmentEndpoint.java
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    /src/jalview/rest/RestHandler.java
  16. … 3 more files in changeset.
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

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    • 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
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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/PushRule.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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    • +5
    /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
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
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    /resources/edu/stanford/ejalbert/launching/misc/linuxUnixConfig.properties
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    /resources/lang/Messages.properties
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    /src/jalview/bin/Jalview.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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    /THIRDPARTYLIBS
12:34 am

Ben Soares

JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2

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    /build.gradle
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    /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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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/io/HTMLOutput.java
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    /src/jalview/jbgui/GPreferences.java
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    /src/jalview/util/BrowserLauncher.java