jalview

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

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Monday 18 Apr
10:31 am

Ben Soares

JAL-3288 Replace all javax.swing.JInternalFrame with extended jalview.jbgui.ClassicJInternalFrame

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    • -3
    • +3
    /src/jalview/fts/core/GFTSPanel.java
    • -7
    • +7
    /src/jalview/gui/AlignFrame.java
    • -2
    • +2
    /src/jalview/gui/AlignViewport.java
    • -3
    • +3
    /src/jalview/gui/AnnotationChooser.java
    • -2
    • +2
    /src/jalview/gui/AnnotationColourChooser.java
    • -2
    • +2
    /src/jalview/gui/AnnotationColumnChooser.java
    • -3
    • +3
    /src/jalview/gui/AnnotationExporter.java
    • -2
    • +2
    /src/jalview/gui/AnnotationRowFilter.java
    • -2
    • +2
    /src/jalview/gui/AppVarna.java
    • -13
    • +15
    /src/jalview/gui/AquaInternalFrameManager.java
    • -3
    • +3
    /src/jalview/gui/CalculationChooser.java
    • -2
    • +2
    /src/jalview/gui/ChimeraViewFrame.java
    • -22
    • +35
    /src/jalview/gui/Desktop.java
    • -3
    • +3
    /src/jalview/gui/FeatureSettings.java
    • -5
    • +5
    /src/jalview/gui/Finder.java
  16. … 26 more files in changeset.
Thursday 07 Apr
12:35 am

Ben Soares

JAL-3991 Made info displayed only when needed (Java 11+)

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    • -2
    • +6
    /src/jalview/gui/Desktop.java
12:28 am

Ben Soares

JAL-3991 Added information output about the slightly alarming 'WARNING: An illegal reflective access operation has occurred' error that occurs for linux users. It can't be avoided so informing the user should help with alarm levels.

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    • -2
    • +3
    /src/jalview/gui/Desktop.java
12:08 am

Ben Soares

JAL-3991 JAVA_COMPILE_VERSION put into build_properties. Check for possible JVM mismatch in jalview.bin.LaunchUtils. STDERR warning from jalview.bin.Launcher. Console and optional popup warning in jalview.bin.Jalview.

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    • -0
    • +1
    /build.gradle
    • -0
    • +3
    /resources/lang/Messages.properties
    • -0
    • +4
    /resources/lang/Messages_es.properties
    • -0
    • +5
    /src/jalview/bin/Cache.java
    • -0
    • +41
    /src/jalview/bin/Jalview.java
    • -2
    • +9
    /src/jalview/bin/Launcher.java
    • -0
    • +113
    /src/jalview/util/LaunchUtils.java
Tuesday 05 Apr
6:37 pm

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

JAL-3981 patch tests and remove errant imports

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    • -4
    • +1
    /src/jalview/io/SequenceAnnotationReport.java
    • -13
    • +22
    /test/jalview/io/SequenceAnnotationReportTest.java
6:14 pm

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

JAL-3990 gradle spotlessApply

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    • -1
    • +2
    /src/jalview/gui/structurechooser/TDBResultAnalyser.java
    • -3
    • +3
    /src/jalview/io/SequenceAnnotationReport.java
    • -6
    • +4
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
    • -4
    • +2
    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
6:12 pm

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

JAL-3990 release notes for 2.11.2.1 patch release

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    • -5
    • +10
    /help/help/html/releases.html
5:57 pm

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

Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop

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Thursday 31 Mar
8:44 pm

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

JAL-3983 release note for JAL-3985

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    • -0
    • +4
    /help/help/html/releases.html
8:42 pm

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

Merge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop

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3:17 pm

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

JAL-3085 update tests and mock responses, new P0dtd1 testcase

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    • -343
    • +362
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
    • -5
    • +13
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
    • -1
    • +1
    /test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt
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    /test/jalview/fts/threedbeacons/p01308_tdb_fts_query_resp.txt
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    /test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
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    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1.txt
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    • +2506
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1_resp.txt
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    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2.txt
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    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2_resp.txt
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    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3.txt
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    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3_resp.txt
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    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4.txt
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    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4_resp.txt
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    /test/jalview/fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt
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    /test/jalview/fts/threedbeacons/p38398_tdb_fts_query_resp.txt
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    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
2:06 pm

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

JAL-3985 formatting

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    • -0
    • +3
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
2:06 pm

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

JAL-3985 split PDB id queries into multiple queries so server doesn’t 414

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    • -26
    • +62
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
Wednesday 30 Mar
6:35 pm

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

Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop

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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
4:56 pm

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

JAL-3983 known issue note for JAL-3984

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    • -0
    • +4
    /help/help/html/releases.html
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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    • -2
    • +2
    /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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    • +14
    /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
    • -4
    • +57
    /help/help/html/releases.html
Friday 25 Mar
2:31 pm

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

JAL-3980 JAL-3979 TODOs

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    • +2
    /src/jalview/datamodel/Sequence.java
2:30 pm

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

JAL-3980 defensive copy - inefficient but fixes bug

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    • -3
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    /src/jalview/io/SequenceAnnotationReport.java
2:16 pm

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

JAL-3981 Additional line breaks - sort of helps

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    • +3
    /src/jalview/io/SequenceAnnotationReport.java
Thursday 24 Mar
5:02 pm

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

JAL-3981 strategic newlines to help speed up Java's html parser

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    • -1
    • +1
    /src/jalview/gui/PopupMenu.java
    • -1
    • +3
    /src/jalview/io/SequenceAnnotationReport.java