jalview

Clone Tools

Stats

Commits this week: 0
Total Committers: 73
Last Commit:
Commits this week: 0

Lines of code count not available

Commit Activity

Commits By Day In Week
52 week commits volume
Commits By Day In Week
Commits by day
Commits By Day In Week
Commits by hour
Commits By Hour In Day
Commit calendar
 

Most active committers (90 days)

loading
loading
  • last updated a few seconds ago
All Commits Reviews
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
Wednesday 27 Feb 2019
1:53 pm

Ben Soares

JAL-3196 tidying for demo

Options
    • binary
    /getdown/getdown-core-1.8.3-SNAPSHOT.jar
    • binary
    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • -5
    • +13
    /gradle/jalview/build.gradle
    • -7
    • +6
    /gradle/jalview/gradle.properties
    • -1
    • +1
    /gradle/jalview/jalview.install4j
    • -11
    • +38
    /gradle/jalview/jalview_getdown.install4j
    • binary
    /resources/images/jalview_logo_background_getdown-640x480.png
12:31 pm

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

JAL-3202 discard zero percentages in extracted profile

Conflicts:

src/jalview/renderer/AnnotationRenderer.java

Options
    • -13
    • +41
    /src/jalview/analysis/AAFrequency.java
    • -3
    • +11
    /src/jalview/renderer/AnnotationRenderer.java
    • -0
    • +183
    /test/jalview/analysis/AAFrequencyTest.java
12:31 pm

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

JAL-3202 discard zero percentages in extracted profile

Options
    • -13
    • +41
    /src/jalview/analysis/AAFrequency.java
    • -3
    • +11
    /src/jalview/renderer/AnnotationRenderer.java
    • -0
    • +183
    /test/jalview/analysis/AAFrequencyTest.java
9:15 am

Ben Soares

JAL-3196 deleting old file

Options
    • -173
    • +0
    /gradle/jalview/OLD_build.gradle
3:11 am

Ben Soares

JAL-3196 fixed getdown progress bar position

Options
    • -1
    • +1
    /gradle/jalview/gradle.properties
2:54 am

Ben Soares

JAL-3196 Substantial addition of getdown automation in getdown, and new getdown-based launchers packaged by install4j

Options
    • -0
    • +3
    /.gitignore
    • -90
    • +73
    /getdown/files/getdown.txt
    • binary
    /getdown/files/resource/jalview_logo_background_getdown-640x480.png
    • binary
    /getdown/files/resource/jalview_logo_background_getdown-progress.png
    • -117
    • +140
    /gradle/jalview/build.gradle
    • -4
    • +34
    /gradle/jalview/gradle.properties
    • -4
    • +4
    /gradle/jalview/jalview.install4j
    • -0
    • +1411
    /gradle/jalview/jalview_getdown.install4j
    • binary
    /resources/images/jalview_logo_background_getdown-640x480.png
    • binary
    /resources/images/jalview_logo_background_getdown-progress.png
    • binary
    /resources/images/jetset_jalview_splash.bmp
    • binary
    /resources/images/jetset_jalview_splash.png
Tuesday 26 Feb 2019
11:39 am

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

JAL-3201 JAL-2386 don't pre-select 'apply to all groups'

Options
    • -1
    • +10
    /src/jalview/gui/SliderPanel.java
10:41 am

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

JAL-3201 group colour schemes distinct instances

Options
    • -2
    • +5
    /src/jalview/gui/SeqPanel.java
    • -1
    • +1
    /src/jalview/viewmodel/AlignmentViewport.java
    • -4
    • +29
    /test/jalview/gui/AlignViewportTest.java
Monday 25 Feb 2019
7:32 pm

Ben Soares

JAL-3196 new background image

Options
    • binary
    /resources/images/jalview_logo_background_fade-640x480.png
3:54 pm

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

JAL-3032 Jalview (as JS) parse query params to main arguments

Options
    • -2
    • +11
    /src/jalview/bin/Jalview.java
3:24 pm

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

JAL-3032 JalviewJS2 converts url query parameters to 'applet' args

Options
    • -9
    • +12
    /src/jalview/bin/JalviewJS2.java
1:46 pm

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

JAL-3200 fast lookup of DSSP3 notation

Options
    • -22
    • +26
    /src/jalview/schemes/ResidueProperties.java
    • -0
    • +10
    /test/jalview/schemes/ResiduePropertiesTest.java
Sunday 24 Feb 2019
7:58 pm

Ben Soares

JAL-3196 some changes

Options
    • -2
    • +3
    /getdown/files/getdown.txt
    • -3
    • +4
    /gradle/jalview/build.gradle
    • -1
    • +1
    /gradle/jalview/gradle.properties
8:58 am

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

JAL-3198 don't recalculate group conservation for Id Panel selection

Options
    • -2
    • +2
    /src/jalview/gui/IdPanel.java
8:10 am

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

JAL-3198 SequenceGroup 'bulk constructor' without duplicates check

Options
    • -1
    • +13
    /src/jalview/datamodel/SequenceGroup.java
    • -6
    • +2
    /src/jalview/gui/AlignFrame.java
    • -10
    • +1
    /src/jalview/gui/ScalePanel.java
    • -2
    • +36
    /test/jalview/datamodel/SequenceGroupTest.java
Saturday 23 Feb 2019
12:36 pm

Ben Soares

JAL-3196 Initial addition of getdown

Options
    • binary
    /getdown/files/getdown-launcher.jar
    • -0
    • +94
    /getdown/files/getdown.txt
    • binary
    /getdown/getdown-core-1.8.3-SNAPSHOT.jar
12:20 pm

Ben Soares

JAL-3196 changed test Launcher to default to maxMem

Options
    • -22
    • +26
    /src/jalview/bin/Launcher.java
12:18 pm

Ben Soares

JAL-3196 extra output file used for gradle incremental builds

Options
    • -0
    • +1
    /.gitignore
12:14 pm

Ben Soares

JAL-3196 updates to install4j config

Options
    • -13
    • +37
    /gradle/jalview/build.gradle
    • -0
    • +2
    /gradle/jalview/gradle.properties
    • -8
    • +44
    /gradle/jalview/jalview.install4j
    • binary
    /resources/images/jalview_logo_background_fade-small.png
Friday 22 Feb 2019
11:27 am

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

JAL-2915 don't recalculate Overview on scroll to position, ever!

Options
    • -1
    • +1
    /src/jalview/gui/AlignFrame.java
    • -11
    • +7
    /src/jalview/gui/AlignmentPanel.java
    • -1
    • +1
    /src/jalview/gui/SeqPanel.java
10:04 am

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

JAL-2738 don't set AF as feature score

Options
    • -30
    • +1
    /src/jalview/io/vcf/VCFLoader.java
    • -26
    • +64
    /test/jalview/io/vcf/VCFLoaderTest.java
9:19 am

Ben Soares

JAL-3141 improved message for asking whether to delete files (file modification time and size added to info to help user decide

Options
    • -1
    • +2
    /resources/lang/Messages.properties
    • -1
    • +2
    /resources/lang/Messages_es.properties
    • -2
    • +6
    /src/jalview/io/BackupFiles.java
Thursday 21 Feb 2019
5:59 pm

Ben Soares

JAL-3141 Sensible refactoring for confirming deleting 'newer' old backup files

Options
    • -2
    • +8
    /resources/lang/Messages.properties
    • -2
    • +8
    /resources/lang/Messages_es.properties
    • -188
    • +227
    /src/jalview/io/BackupFiles.java
2:49 pm

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

JAL-3187 handle no mapping / complement features without NPE

Options
    • -0
    • +4
    /src/jalview/datamodel/MappedFeatures.java
    • -5
    • +11
    /src/jalview/gui/SeqPanel.java
    • -7
    • +13
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
    • -4
    • +9
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
Wednesday 20 Feb 2019
4:40 pm

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

Merge branch 'feature/JAL-3143ensemblJSON' into feature/JAL-3187linkedFeatures

Options
    • -5
    • +8
    /src/jalview/analysis/AlignmentUtils.java
    • -6
    • +10
    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
12:15 pm

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

JAL-3187 read peptide variant from CSQ:HGVSp if present (VCF/VEP data)

Options
    • -3
    • +24
    /src/jalview/datamodel/MappedFeatures.java
Tuesday 19 Feb 2019
12:01 pm

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

Merge branch 'feature/JAL-3187linkedFeatures' into merge/JAL-3187_JAL-3010

Conflicts:

src/jalview/gui/FeatureSettings.java

src/jalview/renderer/seqfeatures/FeatureRenderer.java

Options
    • -0
    • +6
    /src/jalview/gui/FeatureSettings.java
11:15 am

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

JAL-3187 hacks to get peptide variant in to Jmol hover tooltip

Options
    • -1
    • +2
    /src/jalview/analysis/AlignmentUtils.java
    • -2
    • +2
    /src/jalview/appletgui/SeqPanel.java
    • -0
    • +154
    /src/jalview/datamodel/MappedFeatures.java
    • -9
    • +26
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -4
    • +75
    /src/jalview/gui/SeqPanel.java
    • -4
    • +5
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
    • -1
    • +9
    /src/jalview/structure/SequenceListener.java
    • -6
    • +13
    /src/jalview/structure/StructureSelectionManager.java
    • -4
    • +26
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
Monday 18 Feb 2019
9:19 am

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

JAL-3187 reset ViewStyle on Cancel in FeatureSettings

Options
    • -0
    • +6
    /src/jalview/gui/FeatureSettings.java
    • -0
    • +3
    /src/jalview/viewmodel/styles/ViewStyle.java
Sunday 17 Feb 2019
6:19 pm

Ben Soares

JAL-3141 User warning when deleting old backup files that are newer than the previous backup file

Options
    • -1
    • +1
    /resources/lang/Messages.properties
    • -1
    • +1
    /resources/lang/Messages_es.properties
    • -1
    • +1
    /src/jalview/io/BackupFiles.java