jalview

Clone Tools

Stats

Commits this week: 4
Total Committers: 73
Last Commit:
Commits this week: 4

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
Tuesday 22 Oct 2019
10:57 am

Ben Soares

JAL-3210 project name explicitly set. updated README_GRADLE_JALVIEWJS...md file. fixed eclipseRootDir detection for macos.

Options
    • -38
    • +0
    /README_GRADLE_JALVIEWJS-2019-10-15.md
    • -0
    • +70
    /README_GRADLE_JALVIEWJS-2019-10-22.md
    • -1
    • +7
    /build.gradle
    • -1
    • +1
    /gradle.properties
    • -0
    • +1
    /settings.gradle
12:36 am

Ben Soares

JAL-3210 added absolute path for transpile log

Options
    • -2
    • +2
    /build.gradle
12:23 am

Ben Soares

JAL-3210 Improved/fixed the tempdir creation/storage for eclipse workspace

Options
    • -10
    • +26
    /build.gradle
    • -1
    • +1
    /gradle.properties
Monday 21 Oct 2019
9:16 pm

Ben Soares

JAL-3210 Different j2s plugin for different versions of eclipse. Not great, but good for now

Options
    • -1
    • +22
    /build.gradle
    • -1
    • +1
    /gradle.properties
    • binary
    /utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects-1.4.0.jar
    • binary
    /utils/jalviewjs/eclipse/dropins/net.sf.j2s.core_3.2.4-FOR_4.13.jar
    • binary
    /utils/jalviewjs/eclipse/dropins_4.12/com.seeq.eclipse.importprojects-1.4.0.jar
    • binary
    /utils/jalviewjs/eclipse/dropins_4.12/net.sf.j2s.core-3.2.4-FOR_4.12.jar
    • binary
    /utils/jalviewjs/eclipse/dropins_4.13/com.seeq.eclipse.importprojects-1.4.0.jar
    • binary
    /utils/jalviewjs/eclipse/dropins_4.13/net.sf.j2s.core_3.2.4-FOR_4.13.jar
7:51 pm

Ben Soares

JAL-3210 Changed eclipse workspace dir to be a system temp dir [held in build/jalviewjs/eclipse_workspace_location] that persists until a gradle clean

Options
    • -11
    • +33
    /build.gradle
    • -2
    • +3
    /gradle.properties
    • binary
    /utils/jalviewjs/eclipse/dropins/net.sf.j2s.core_3.2.4-FOR_4.13.jar
    • binary
    /utils/jalviewjs/eclipse/dropins/net.sf.j2s.core_3.2.4.jar
1:41 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3463 Thread.sleep()

setting sleep() to throw InterruptedException()

Options
    • binary
    /swingjs/SwingJS-site.zip
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • -1
    • +1
    /swingjs/ver/3.2.4/timestamp
11:41 am

Ben Soares

JAL-3416 first attemp at using com.sun.java.swing.plaf.gtk.GTKLookAndFeel in Linux/solaris. Some issues

Options
    • -0
    • +14
    /src/jalview/bin/Jalview.java
3:53 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3463 alert for Thread.sleep; JAL-3378 java.util.logging.Logger implemented.

Options
    • binary
    /swingjs/SwingJS-site.zip
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/ver/3.2.4/timestamp
Thursday 17 Oct 2019
5:05 pm

Mateusz Warowny

JAL-3066 Slivka client update for changed api endpoints.

Options
    • binary
    /j11lib/slivka-client.jar
4:48 pm

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

JAL-3436 null large object reference, tidy method visibility

Options
    • -7
    • +9
    /src/jalview/project/Jalview2XML.java
4:10 pm

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

JAL-3436 save filePath from fileObject, tidy updateRecentlyOpened

Options
    • -64
    • +64
    /src/jalview/gui/AlignFrame.java
    • -48
    • +48
    /src/jalview/io/FileLoader.java
2:02 pm

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

JAL-3436 move/rename/private fields refactoring only

Options
    • -2
    • +2
    /src/jalview/gui/AlignFrame.java
    • -64
    • +61
    /src/jalview/project/Jalview2XML.java
1:55 pm

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

Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

Options
1:37 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3436 broken reader - SwingJS issue (wrong JAL number in last commit)

- java.util.logging.Logger not fully implemented.

- this fix just removes Logger calls from javax.xml classes.

- see JAL-3461 for full fix TODO

Options
    • -1
    • +1
    /swingjs/timestamp
1:33 pm

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

JAL-3261 broken reader - SwingJS issue

- java.util.logging.Logger not fully implemented.

- this fix just removes Logger calls from javax.xml classes.

- see JAL-3461 for full fix TODO

Options
    • binary
    /swingjs/SwingJS-site.zip
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • -1
    • +1
    /swingjs/ver/3.2.4/timestamp
11:36 am

Ben Soares

JAL-3210 changed classes for net.sf.j2s.core

Options
    • -0
    • +185
    /utils/jalviewjs/Java2ScriptCompilationParticipant.java
    • -0
    • +586
    /utils/jalviewjs/Java2ScriptCompiler.java
10:35 am

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

Merge branch 'Jalview-jJS/JAL-3253-applet-JAL-3436' into Jalview-JS/JAL-3253-applet

Options
10:27 am

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

JAL-3368 'web' colour parsing reinstated (for now)

Options
    • -31
    • +44
    /src/jalview/util/Platform.java
9:59 am

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

JAL-3368 removed parsing web colours (now on a separate branch)

Options
    • -15
    • +55
    /src/jalview/util/ColorUtils.java
    • -51
    • +0
    /src/jalview/util/Platform.java
    • -1
    • +27
    /src/jalview/util/StringUtils.java
    • -13
    • +11
    /test/jalview/util/ColorUtilsTest.java
    • -1
    • +19
    /test/jalview/util/StringUtilsTest.java
1:33 am

Ben Soares

JAL-3210 Added site transfer dir. New net.sf.j2s.core.jar ONLY WORKS WITH ECLIPSE 2019-09+

Options
    • -22
    • +20
    /build.gradle
    • -4
    • +5
    /gradle.properties
    • binary
    /utils/jalviewjs/eclipse/dropins/net.sf.j2s.core-3.2.4.jar
    • binary
    /utils/jalviewjs/eclipse/dropins/net.sf.j2s.core_3.2.4.jar
Wednesday 16 Oct 2019
11:36 am

Ben Soares

Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build

Merging in Jalview-JS/develop (should be no changes -- just checking)

Options
Tuesday 15 Oct 2019
5:02 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3442 (Aug 28 commit) option to use/not use cache

Options
    • -4
    • +9
    /src/jalview/renderer/OverviewResColourFinder.java
4:54 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

Commit 113cc13-2019.09.28 with added transparency fix

Options
    • -2
    • +15
    /src/jalview/renderer/seqfeatures/FeatureColourFinder.java
    • binary
    /swingjs/SwingJS-site.zip
    • -0
    • +2
    /swingjs/_j2sclasslist.txt
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • -0
    • +2
    /swingjs/ver/3.2.4/_j2sclasslist.txt
    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/ver/3.2.4/timestamp
4:11 pm

Jim Procter

JAL-3407 update release date for Jalview 2.11.1

Options
    • -1
    • +1
    /help/help/html/releases.html
2:18 pm

Ben Soares

JAL-3210 Added README_GRADLE_JALVIEWJS-2019-10-15.md

Options
    • -0
    • +38
    /README_GRADLE_JALVIEWJS-2019-10-15.md
11:14 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3368 JAL-2365 JAL-2642

Options
    • -39
    • +35
    /src/jalview/util/Platform.java
11:10 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3368 retaining branch for future SwingJS reference

Options
    • -25
    • +21
    /src/jalview/util/Platform.java
10:06 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3437 Desktop File...Load Project fails in JalviewJS

- just needed to use the File object rather than the file name in the

call to Jalview2XML.loadJalviewAlign

Options
    • -1
    • +1
    /src/jalview/gui/Desktop.java
Monday 14 Oct 2019
3:40 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3445 branch for BSML file reading development

Options
    • -0
    • +225
    /src/jalview/io/BSMLFile.java
    • -0
    • +15
    /src/jalview/io/FileFormat.java
    • -0
    • +9
    /src/jalview/io/IdentifyFile.java
    • -0
    • +3
    /test/jalview/io/JSONFileTest.java
3:33 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3453 test changes needed to allow tests to proceed unheeded by dialogs.

Options
    • -0
    • +1
    /test/jalview/schemes/ColourSchemesTest.java
    • -0
    • +3
    /test/jalview/schemes/PIDColourSchemeTest.java
    • -0
    • +5
    /test/jalview/ws/dbsources/RemoteFormatTest.java
    • -1
    • +3
    /test/jalview/ws/jabaws/RNAStructExportImport.java