jalview

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Commits this week: 5
Total Committers: 73
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Commits this week: 5

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Monday 31 Aug 2020
10:33 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3730 retry ping before failing; sysout logging changed to Cache.log

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    • +10
    /src/jalview/ext/ensembl/EnsemblMap.java
    • -27
    • +43
    /src/jalview/ext/ensembl/EnsemblRestClient.java
    • -4
    • +4
    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
Monday 24 Aug 2020
11:00 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3018 updated reviewed REST version to 12.0

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    • -2
    • +2
    /src/jalview/ext/ensembl/EnsemblRestClient.java
Monday 17 Aug 2020
10:55 am

Jim Procter

Merge branch 'task/JAL-3597memoryLeakTest' into develop

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Thursday 13 Aug 2020
11:05 pm

Ben Soares

JAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts heap size

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    • -5
    • +10
    /test/jalview/gui/FreeUpMemoryTest.java
Wednesday 12 Aug 2020
11:15 am

Jim Procter

Merge branch 'task/JAL-3608_property_set_laf_and_tests' into develop

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    • -0
    • +5
    /build.gradle
    • -1
    • +10
    /src/jalview/bin/Cache.java
    • -37
    • +178
    /src/jalview/bin/Jalview.java
Tuesday 04 Aug 2020
7:30 pm

Ben Soares

JAL-3477 Improved command line arguments description in memory.html

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    • -4
    • +5
    /help/help/html/memory.html
6:13 pm

Ben Soares

JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html

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    • -3
    • +3
    /help/help/html/features/clarguments.html
    • -80
    • +79
    /src/jalview/bin/Jalview.java
Monday 03 Aug 2020
11:20 am

Ben Soares

JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

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    • -0
    • +19
    /help/help/html/features/clarguments.html
    • -1
    • +10
    /help/help/html/memory.html
10:40 am

Jim Procter

Merge branch 'bug/JAL-2983negativeSliderMin' into develop

Conflicts:

src/jalview/gui/FeatureSettings.java

src/jalview/gui/FeatureTypeSettings.java

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    • -20
    • +13
    /src/jalview/gui/AnnotationColourChooser.java
    • -15
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    /src/jalview/gui/AnnotationColumnChooser.java
    • -2
    • +2
    /src/jalview/gui/FeatureSettings.java
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    • +28
    /src/jalview/gui/FeatureTypeSettings.java
Wednesday 29 Jul 2020
6:47 pm

Jim Procter

JAL-3371 JAL-2983 don't modify 'extent' of slider - this is managed by look and feel

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    • -3
    • +1
    /src/jalview/gui/Slider.java
Tuesday 28 Jul 2020
1:36 pm

Jim Procter

Merge branch 'feature/JAL-3615gzipXfam' into develop

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12:17 pm

Jim Procter

JAL-3615 JAL-2656 missing import after cherrypick

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    • -0
    • +1
    /src/jalview/io/FileParse.java
11:32 am

Jim Procter

JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header

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    • -8
    • +24
    /src/jalview/io/FileParse.java
11:29 am

Jim Procter

JAL-2656 recognise Gzipped file input streams by their content, not their filename

Conflicts:

src/jalview/io/FileParse.java

cherypicked from 2.11.1.1 release patch

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    • -21
    • +58
    /src/jalview/io/FileParse.java
11:18 am

Jim Procter

JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

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    • -1
    • +1
    /test/jalview/ws/dbsources/PfamFullTest.java
    • -1
    • +1
    /test/jalview/ws/dbsources/PfamSeedTest.java
    • -1
    • +1
    /test/jalview/ws/dbsources/RfamFullTest.java
    • -1
    • +1
    /test/jalview/ws/dbsources/RfamSeedTest.java
Monday 27 Jul 2020
3:10 pm

Jim Procter

JAL-3697 show total number of features not shown

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    • -1
    • +1
    /src/jalview/gui/SeqPanel.java
3:05 pm

Jim Procter

JAL-3696 log the error message from the exception to the console

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    • -1
    • +1
    /src/jalview/io/vcf/VCFLoader.java
2:59 pm

Jim Procter

JAL-3695 htsjdk 2.12 -> 2.23 (library change only, no code change. needs gradle refresh in eclipse)

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    • binary
    /j11lib/htsjdk-2.12.0.jar
    • binary
    /j11lib/htsjdk-2.23.0.jar
    • binary
    /j8lib/htsjdk-2.12.0.jar
    • binary
    /j8lib/htsjdk-2.23.0.jar
Monday 20 Jul 2020
9:17 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB

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    • -46
    • +49
    /test/jalview/gui/FreeUpMemoryTest.java
Tuesday 14 Jul 2020
5:08 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1421 last change tidied up properly

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    • -1
    • +1
    /src/jalview/gui/TreeCanvas.java
9:44 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1421 types added to nameHash and nodeHash maps

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    • -35
    • +30
    /src/jalview/gui/TreeCanvas.java
9:43 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3597 additional references nulled, bug in test corrected

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    • -0
    • +6
    /src/jalview/gui/PCAPanel.java
    • -0
    • +12
    /src/jalview/gui/TreePanel.java
    • -0
    • +1
    /src/jalview/renderer/AnnotationRenderer.java
    • -0
    • +1
    /src/jalview/viewmodel/AlignmentViewport.java
    • -33
    • +74
    /test/jalview/gui/FreeUpMemoryTest.java
Wednesday 08 Jul 2020
12:47 am

Ben Soares

JAL-3608 Changes from code review CR-JAL-236

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    • -13
    • +9
    /src/jalview/bin/Jalview.java
Tuesday 07 Jul 2020
8:50 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1424 streamlined message checker, corrected applet lookup keys

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    • -5
    • +5
    /src/jalview/appletgui/APopupMenu.java
    • -7
    • +7
    /src/jalview/appletgui/AlignFrame.java
    • -4
    • +4
    /src/jalview/appletgui/AppletJmol.java
    • -4
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    /src/mc_view/AppletPDBViewer.java
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    /utils/MessageBundleChecker.java
Monday 06 Jul 2020
3:59 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1424 slight tidying of reporting

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    • -20
    • +35
    /utils/MessageBundleChecker.java
3:57 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3311 JAL-3141 JAL-3144 tidying obsolete message bundle entries

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    • +1
    /resources/lang/Messages.properties
    • -36
    • +1
    /resources/lang/Messages_es.properties
    • -2
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    /src/jalview/controller/AlignViewController.java
    • -7
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    /src/jalview/fts/core/FTSRestClient.java
    • -6
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    /src/jalview/gui/VamsasApplication.java
    • -4
    • +2
    /src/jalview/io/VamsasAppDatastore.java
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    /src/jalview/io/vamsas/Rangetype.java
12:57 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3518 Spanish text for 'write features'

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    /resources/lang/Messages_es.properties
12:37 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3570 JAL-3187 spanish translations for tabbed feature settings

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    /resources/lang/Messages_es.properties
10:05 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3570 updated external help links

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    /help/help/html/index.html
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    /help/help/html/webServices/AACon.html
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    /help/help/html/webServices/msaclient.html
Thursday 02 Jul 2020
5:24 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2656 JAL-3615 check response headers to test for gzipped url reply

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    /src/jalview/io/FileParse.java
    • -1
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    /src/jalview/ws/dbsources/Pfam.java
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    /src/jalview/ws/dbsources/Rfam.java
    • -34
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    /test/jalview/io/FileParseTest.java