jalview

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Commits this week: 19
Total Committers: 68
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Commits this week: 19

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Today
1 hr ago

Ben Soares

JAL-3394 jalviews scheme added

Options
    • -18
    • +0
    /utils/install4j/auto_file_associations-i4j8.pl
    • -1
    • +11
    /utils/install4j/install4j8_template.install4j
4 hrs ago

Ben Soares

JAL-3394 file not needed

Options
    • -39
    • +0
    /utils/install4j/Info_plist_file_associations.xml
4 hrs ago

Ben Soares

JAL-3447 Satisfactory file associations. cif, mcif and pdb now not opened by Jalview by default -- but are associated. In Windows and linux installer, are deselected by default. 'jalview://' as a URL scheme now associated in Windows and macOS.

Options
    • -59
    • +46
    /utils/install4j/auto_file_associations-i4j8.pl
    • -54
    • +54
    /utils/install4j/file_associations_auto-Info_plist.xml
    • -153
    • +176
    /utils/install4j/file_associations_auto-install4j8.xml
    • -2
    • +2
    /utils/install4j/file_associations_template-Info_plist.xml
    • -3
    • +4
    /utils/install4j/file_associations_template-install4j8.xml
    • -58
    • +23
    /utils/install4j/install4j8_template.install4j
4 hrs ago

Ben Soares

JAL-3447 Change to install4j template version, JAL-3394 removed redundant compiler variable. Fixed help when run in Eclipse and removed redundant helpDir

Options
    • -19
    • +17
    /build.gradle
    • -0
    • +1
    /gradle.properties
5 hrs ago

Mungo Carstairs

JAL-3490 unit test for ignore hidden regions with selection group

Options
    • -5
    • +1
    /src/jalview/analysis/Finder.java
    • -4
    • +31
    /test/jalview/analysis/FinderTest.java
6 hrs ago

Jim Procter

JAL-2305 moved failing CrossRef tests to Functional_Failing group

Options
    • -3
    • +3
    /test/jalview/analysis/CrossRefTest.java
7 hrs ago

Jim Procter

JAL-3407 update release date for Jalview 2.11.1

Options
    • -1
    • +1
    /help/help/html/releases.html
Wednesday 11 Dec
2:38 pm

Mungo Carstairs

JAL-3490 tests for skip hidden regions (and a bug fix)

Options
    • -3
    • +8
    /src/jalview/analysis/Finder.java
    • -1
    • +91
    /test/jalview/analysis/FinderTest.java
1:09 pm

Mungo Carstairs

JAL-3490 extract constants for number of rows in layout

Options
    • -3
    • +9
    /src/jalview/jbgui/GFinder.java
12:55 pm

Mungo Carstairs

JAL-3490 revised layout and search algorithm (more tests to be added)

Options
    • -1
    • +3
    /resources/lang/Messages.properties
    • -1
    • +3
    /resources/lang/Messages_es.properties
    • -170
    • +317
    /src/jalview/analysis/Finder.java
    • -8
    • +21
    /src/jalview/api/FinderI.java
    • -2
    • +4
    /src/jalview/appletgui/Finder.java
    • -1
    • +1
    /src/jalview/fts/core/GFTSPanel.java
    • -3
    • +2
    /src/jalview/gui/AlignFrame.java
    • -2
    • +1
    /src/jalview/gui/AnnotationColumnChooser.java
    • -26
    • +27
    /src/jalview/gui/Finder.java
    • -1
    • +1
    /src/jalview/gui/SplitFrame.java
    • -18
    • +18
    /src/jalview/io/cache/JvCacheableInputBox.java
    • -93
    • +101
    /src/jalview/jbgui/GFinder.java
    • -56
    • +69
    /test/jalview/analysis/FinderTest.java
    • -1
    • +1
    /test/jalview/controller/AlignViewControllerTest.java
    • -2
    • +2
    /test/jalview/io/cache/JvCacheableInputBoxTest.java
Tuesday 10 Dec
4:29 pm

Ben Soares

JAL-3394 Simplified media output from install4j

Options
    • -58
    • +17
    /utils/install4j/install4j8_template.install4j
Monday 09 Dec
2:31 pm

Mungo Carstairs

JAL-3490 pull up getViewAsVisibleContigs to base class and interface

Options
    • -0
    • +13
    /src/jalview/api/AlignViewportI.java
    • -26
    • +0
    /src/jalview/gui/AlignViewport.java
    • -0
    • +18
    /src/jalview/viewmodel/AlignmentViewport.java
9:05 am

Ben Soares

JAL-3449 More whitespace in installer. Tidying

Options
    • -6
    • +5
    /build.gradle
    • -169
    • +0
    /utils/install4j/auto_file_associations.pl
    • -1862
    • +0
    /utils/install4j/bs_install4j_template.install4j
    • -1085
    • +0
    /utils/install4j/file_associations_auto-install4j.xml
    • -35
    • +0
    /utils/install4j/file_associations_template-install4j.xml
    • -0
    • +8
    /utils/install4j/install4j8_template.install4j
    • -2140
    • +0
    /utils/install4j/install4j_template.install4j
2:29 am

Ben Soares

JAL-3449 Fixed Info.plist file insertion. Simplified install4j conf filename

Options
    • -0
    • +1
    /.gitignore
    • -2
    • +1
    /build.gradle
    • -4
    • +4
    /utils/install4j/install4j8_template.install4j
12:35 am

Ben Soares

JAL-3449 Now parsing install4j XML file to edit values. Should be safer

Options
    • -89
    • +33
    /build.gradle
Sunday 08 Dec
9:09 pm

Ben Soares

JAL-3449 Work in progress improving XML replacements by gradle

Options
    • -37
    • +72
    /build.gradle
    • -0
    • +6
    /utils/install4j/install4j8_template.install4j
Friday 06 Dec
5:42 pm

Ben Soares

JAL-3394 disableSigning=true when DEV

Options
    • -35
    • +7
    /build.gradle
5:34 pm

Ben Soares

JAL-3394 Changed most of the token replacement for adding compiler variables

Options
    • -3
    • +41
    /build.gradle
    • -34
    • +51
    /utils/install4j/install4j8_template.install4j
5:34 pm

Ben Soares

JAL-3449 Added more versions to getdown splashscreen and fixed Jalview's Java Console installer version reporting

Options
    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • -3
    • +11
    /getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/StatusPanel.java
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
    • -4
    • +6
    /src/jalview/bin/Cache.java
Thursday 05 Dec
4:30 pm

Mateusz Warowny

JAL-3066 Comment on ambiguous parameter parsing.

Options
    • -0
    • +2
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
4:30 pm

Mateusz Warowny

JAL-3066 Change Slivka connection to https

Options
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
Monday 02 Dec
4:22 pm

Bob Hanson

JAL-3487 help/splash <html> wrap issue + associated tooltip breaking

Options
    • binary
    /swingjs/SwingJS-site.zip
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.5/SwingJS-site.zip
    • -1
    • +1
    /swingjs/ver/3.2.5/timestamp
4:17 pm

Bob Hanson

jmol-app.zip update for java2script 3.2.5.v1

Options
    • binary
    /libjs/jmol-app.zip
4:16 pm

Bob Hanson

JAL-3487 splash/help fix

Options
    • -135
    • +164
    /src/jalview/gui/SplashScreen.java
Friday 29 Nov
3:53 pm

Mungo Carstairs

JAL-3490 Finder match across entirely gapped hidden regions

Options
    • -19
    • +38
    /src/jalview/analysis/Finder.java
    • -7
    • +53
    /test/jalview/analysis/FinderTest.java
1:16 pm

Mungo Carstairs

JAL-3489 ensure all chains mapped when loading local multimeric PDB file

Options
    • -1
    • +1
    /src/jalview/gui/AlignFrame.java
    • -5
    • +8
    /src/jalview/gui/AssociatePdbFileWithSeq.java
    • -1
    • +1
    /src/jalview/gui/StructureChooser.java
Thursday 28 Nov
5:08 pm

Mateusz Warowny

JAL-3066 Fix incorrect URL resolving with /slivka prefix.

Options
    • binary
    /j11lib/slivka-client.jar
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
Wednesday 27 Nov
5:46 am

Bob Hanson

SwingJS transpiler to 3.2.5.v1 (fixed java.util.stream)

- required transpiler fixes and redesign of final variables for stream

objects

- required redesign of $init$ and $static$ to exactly reproduce the full

class loading sequence of (1) method definition with default static

values, (2) superclass-sequenced initialization of static fields (3)

superclass-sequenced initialization of static fields, (4)

superclass-sequenced constructor initialization, in that order, able to

handle any complex situation

-includes fixes for JLabelUI HTML label wrapping issues

Options
    • binary
    /swingjs/SwingJS-site.zip
    • -1
    • +14
    /swingjs/_j2sclasslist.txt
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.1.1/SwingJS-site.zip
    • binary
    /swingjs/ver/3.1.1/net.sf.j2s.core.3.1.1.jar
    • binary
    /swingjs/ver/3.2.1/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.1/net.sf.j2s.core_3.2.1.jar
    • binary
    /swingjs/ver/3.2.2/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.2/net.sf.j2s.core.jar
    • -1
    • +0
    /swingjs/ver/3.2.2/timestamp
    • binary
    /swingjs/ver/3.2.3/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.3/net.sf.j2s.core.jar
    • -1
    • +0
    /swingjs/ver/3.2.3/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
  16. … 6 more files in changeset.
5:43 am

Bob Hanson

SwingJS transpiler to 3.2.5.v1 (fixed java.util.stream)

- required transpiler fixes and redesign of final variables for stream

objects

- required redesign of $init$ and $static$ to exactly reproduce the full

class loading sequence of (1) method definition with default static

values, (2) superclass-sequenced initialization of static fields (3)

superclass-sequenced initialization of static fields, (4)

superclass-sequenced constructor initialization, in that order, able to

handle any complex situation

-includes fixes for JLabelUI HTML label wrapping issues

Options
    • binary
    /swingjs/SwingJS-site.zip
    • -1
    • +16
    /swingjs/_j2sclasslist.txt
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.1.1/SwingJS-site.zip
    • binary
    /swingjs/ver/3.1.1/net.sf.j2s.core.3.1.1.jar
    • binary
    /swingjs/ver/3.2.1/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.1/net.sf.j2s.core_3.2.1.jar
    • binary
    /swingjs/ver/3.2.2/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.2/net.sf.j2s.core.jar
    • -1
    • +0
    /swingjs/ver/3.2.2/timestamp
    • binary
    /swingjs/ver/3.2.3/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.3/net.sf.j2s.core.jar
    • -1
    • +0
    /swingjs/ver/3.2.3/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
  16. … 8 more files in changeset.
5:31 am

Bob Hanson

JAL-3487 HTML label not wrapping

Options
    • binary
    /swingjs/SwingJS-site.zip
    • -1
    • +14
    /swingjs/_j2sclasslist.txt
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.1.1/SwingJS-site.zip
    • binary
    /swingjs/ver/3.1.1/net.sf.j2s.core.3.1.1.jar
    • binary
    /swingjs/ver/3.2.1/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.1/net.sf.j2s.core_3.2.1.jar
    • binary
    /swingjs/ver/3.2.2/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.2/net.sf.j2s.core.jar
    • -1
    • +0
    /swingjs/ver/3.2.2/timestamp
    • binary
    /swingjs/ver/3.2.3/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.3/net.sf.j2s.core.jar
    • -1
    • +0
    /swingjs/ver/3.2.3/timestamp
    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
  16. … 6 more files in changeset.