jalview

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Commits this week: 5
Total Committers: 70
Last Commit:
Commits this week: 5

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Monday 11 Jan
9:30 pm

Ben Soares

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

Options
    • -4
    • +37
    /build.gradle
    • -1
    • +13
    /gradle.properties
9:30 pm

Ben Soares

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

Options
    • -4
    • +37
    /build.gradle
    • -1
    • +14
    /gradle.properties
9:28 pm

Ben Soares

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

Options
    • -8
    • +0
    /swingjs/README.txt
    • binary
    /swingjs/SwingJS-site.zip
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • -0
    • +10
    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
    • -0
    • +1541
    /swingjs/ver/3.2.10-j11/differences.txt
    • binary
    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
    • -0
    • +1
    /swingjs/ver/3.2.10-j11/timestamp
    • -0
    • +10
    /swingjs/ver/3.2.10/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.10/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.2.10/_j2sclasslist.txt
    • -0
    • +1541
    /swingjs/ver/3.2.10/differences.txt
  16. … 24 more files in changeset.
9:28 pm

Ben Soares

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

Options
    • -8
    • +0
    /swingjs/README.txt
    • binary
    /swingjs/SwingJS-site.zip
    • -0
    • +1541
    /swingjs/differences.txt
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • -0
    • +10
    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
    • -0
    • +1541
    /swingjs/ver/3.2.10-j11/differences.txt
    • binary
    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
    • -0
    • +1
    /swingjs/ver/3.2.10-j11/timestamp
    • -0
    • +10
    /swingjs/ver/3.2.10/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.10/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.2.10/_j2sclasslist.txt
  16. … 32 more files in changeset.
5:08 pm

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

JAL-3117 raise AlignFrame or SplitFrame when Overview clicked

Options
    • -15
    • +33
    /src/jalview/gui/AlignFrame.java
    • -50
    • +63
    /src/jalview/gui/AlignmentPanel.java
    • -5
    • +5
    /src/jalview/gui/ViewSelectionMenu.java
    • -14
    • +14
    /src/jalview/jbgui/GAlignFrame.java
    • -1
    • +1
    /test/jalview/gui/FreeUpMemoryTest.java
Friday 08 Jan
4:53 pm

Ben Soares

JAL-3419 improved look of tabs

Options
    • -1
    • +9
    /src/jalview/bin/Jalview.java
4:06 pm

Jim Procter

JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

Options
    • -8
    • +35
    /src/jalview/util/Comparison.java
4:05 pm

Jim Procter

JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

Options
    • -0
    • +17
    /test/jalview/datamodel/SequenceTest.java
12:02 pm

Ben Soares

JAL-3416 Added FlatLightLaf, use with -Dlaf=flat property

Options
    • binary
    /j11lib/flatlaf-0.46.jar
    • -3
    • +16
    /src/jalview/bin/Jalview.java
Tuesday 29 Dec 2020
4:38 pm

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

JAL-3788 synchronize concurrent findColour() and alignmentChanged()

Options
    • -6
    • +6
    /src/jalview/schemes/ClustalxColourScheme.java
Saturday 26 Dec 2020
8:51 am

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

JAL-3761 more consistent parameter naming

Options
    • -22
    • +22
    /src/jalview/util/MapList.java
Tuesday 22 Dec 2020
12:55 pm

Ben Soares

JAL-3790 New getdown version and jar files

Options
    • -1
    • +1
    /getdown/lib/FJVL_VERSION
    • -1
    • +1
    /getdown/lib/JVL_VERSION
    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • -1
    • +1
    /getdown/src/getdown/ant/pom.xml
    • -1
    • +1
    /getdown/src/getdown/core/pom.xml
    • -1
    • +1
    /getdown/src/getdown/launcher/pom.xml
    • -1
    • +1
    /getdown/src/getdown/mvn_cmd
    • -1
    • +1
    /getdown/src/getdown/pom.xml
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
12:54 pm

Ben Soares

JAL-3790 Enable copy to clipboard when mouse click on the getdown splashscreen StatusPanel

Options
    • -21
    • +43
    /getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/StatusPanel.java
11:52 am

Ben Soares

JAL-3789 tidied net.sf.j2s.core.Java2ScriptCompiler code for submission

Options
    • -281
    • +0
    /Java2ScriptCompilationParticipant.java
    • -886
    • +752
    /Java2ScriptCompiler.java
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
12:37 am

Ben Soares

JAL-3789 Removed debugging printlns

Options
    • -4
    • +4
    /Java2ScriptCompilationParticipant.java
    • -23
    • +0
    /Java2ScriptCompiler.java
Monday 21 Dec 2020
2:14 pm

Ben Soares

JAL-3789 First attempt for configurable property to look at

Options
    • -0
    • +281
    /Java2ScriptCompilationParticipant.java
    • -0
    • +946
    /Java2ScriptCompiler.java
    • -0
    • +2
    /build.gradle
    • -1
    • +2
    /gradle.properties
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
Saturday 19 Dec 2020
7:22 am

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

JAL-1713 restore project with no Overview, regardless of Preferences

Options
    • -5
    • +7
    /src/jalview/project/Jalview2XML.java
    • -24
    • +46
    /test/jalview/project/Jalview2xmlTests.java
Friday 18 Dec 2020
11:37 am

Jim Procter

JAL-3690 recoded AWSThread to use javax.swing.Timer (see https://github.com/BobHanson/java2script/issues/195#issuecomment-747695834 )- web service submission works, but doesn’t seem to be happening as a background task.

Options
    • -9
    • +15
    /src/jalview/ws/AWSThread.java
Thursday 17 Dec 2020
8:44 pm

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

JAL-1713 close and replace auto-opened Overview with restored Overview

Options
    • -0
    • +12
    /src/jalview/gui/AlignmentPanel.java
    • -0
    • +8
    /src/jalview/gui/OverviewPanel.java
    • -153
    • +166
    /src/jalview/project/Jalview2XML.java
    • -1
    • +3
    /test/jalview/project/Jalview2xmlTests.java
4:31 pm

Jim Procter

JAL-3690 patch out use of java.streams/spliterator not supported in java2script (yet)

Options
    • -8
    • +24
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Tuesday 15 Dec 2020
7:04 pm

Jim Procter

JAL-3690 tweak J2S direct DB access registration for jalview, compbio and other sites

Options
    • -4
    • +2
    /utils/jalviewjs/coretemplate.html
    • -2
    • +2
    /utils/jalviewjs/template.html
6:46 pm

Jim Procter

JAL-3690 direct access to slivka, compbio, jalview.org and localhost/loopback.

Options
    • -0
    • +4
    /utils/jalviewjs/coretemplate.html
    • -0
    • +3
    /utils/jalviewjs/template.html
6:45 pm

Jim Procter

JAL-3690 patch out need for java.time in j2s (see https://github.com/BobHanson/java2script/issues/194 )

Options
    • -6
    • +14
    /src/jalview/ws/api/JobId.java
6:42 pm

Jim Procter

JAL-3690 patch out spinning animation for web service jobs

Options
    • -3
    • +7
    /src/jalview/gui/WebserviceInfo.java
11:53 am

Jim Procter

JAL-3690 disable proxy server for JalviewJS

Options
    • -1
    • +1
    /utils/jalviewjs/template.html
Monday 14 Dec 2020
11:18 pm

Ben Soares

JAL-3280 Fixed the version checking URL formulation (getdown build_properties) for jalviewjs, can also use it for jalviewjs in future

Options
    • -13
    • +35
    /src/jalview/bin/Cache.java
7:58 pm

Jim Procter

Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

Options
    • -1
    • +2
    /src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
    • -240
    • +257
    /src/jalview/analysis/AlignmentSorter.java
    • -12
    • +8
    /src/jalview/appletgui/AlignFrame.java
    • -1
    • +1
    /src/jalview/appletgui/AlignViewport.java
    • -0
    • +12
    /src/jalview/appletgui/AnnotationPanel.java
    • -1
    • +2
    /src/jalview/appletgui/TitledPanel.java
    • -424
    • +668
    /src/jalview/bin/Jalview.java
    • -1
    • +2
    /src/jalview/datamodel/Alignment.java
    • -459
    • +825
    /src/jalview/gui/AlignFrame.java
    • -29
    • +47
    /src/jalview/gui/AlignViewport.java
    • -28
    • +20
    /src/jalview/gui/AnnotationLabels.java
    • -30
    • +136
    /src/jalview/gui/CalculationChooser.java
    • -348
    • +416
    /src/jalview/gui/Desktop.java
    • -27
    • +34
    /src/jalview/gui/JvSwingUtils.java
    • -30
    • +25
    /src/jalview/gui/OverviewPanel.java
  16. … 42 more files in changeset.
5:56 pm

Ben Soares

JAL-3783 Reverting to using groovy-all-2.4.12-indy.jar to fix serious problem with Groovy console using shadowJar

Options
    • binary
    /j11lib/groovy-2.5.7.jar
    • binary
    /j11lib/groovy-all-2.4.12-indy.jar
    • binary
    /j11lib/groovy-ant-2.5.7.jar
    • binary
    /j11lib/groovy-bsf-2.5.7.jar
    • binary
    /j11lib/groovy-cli-commons-2.5.7.jar
    • binary
    /j11lib/groovy-cli-picocli-2.5.7.jar
    • binary
    /j11lib/groovy-console-2.5.7.jar
    • binary
    /j11lib/groovy-datetime-2.5.7.jar
    • binary
    /j11lib/groovy-dateutil-2.5.7.jar
    • binary
    /j11lib/groovy-docgenerator-2.5.7.jar
    • binary
    /j11lib/groovy-groovydoc-2.5.7.jar
    • binary
    /j11lib/groovy-groovysh-2.5.7.jar
    • binary
    /j11lib/groovy-jaxb-2.5.7.jar
    • binary
    /j11lib/groovy-jmx-2.5.7.jar
    • binary
    /j11lib/groovy-json-2.5.7.jar
  16. … 12 more files in changeset.
5:24 pm

Ben Soares

JAL-3628 Test for doubly saved single backup file scheme

Options
    • -23
    • +71
    /test/jalview/io/BackupFilesTest.java
    • -0
    • +112
    /test/jalview/io/testProps_singlefilebackup.jvprops
4:27 pm

Jim Procter

Merge branch 'Jalview-JS/develop_j2s_v3_2_9_j11' into Jalview-JS/develop

Options