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You are running Crucible 4.2.1 with FishEye 4.2.1 (20161109135523 2016-11-09)

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Tuesday 01 Dec
3:03 pm

Ben Soares

Merge branch 'develop' into merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch

Options
2:57 pm

Ben Soares

JAL-3609 JAL-3775 Updated getdown with re-factored HiDPISetting and ScreenInfo. No real functionality change.

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    • -1
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    /getdown/lib/FJVL_VERSION
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    /getdown/lib/JVL_VERSION
    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • -1
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    /getdown/src/getdown/ant/pom.xml
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    /getdown/src/getdown/core/pom.xml
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    • +39
    /getdown/src/getdown/core/src/main/java/jalview/bin/HiDPISetting.java
    • -0
    • +21
    /getdown/src/getdown/core/src/main/java/jalview/bin/ScreenInfo.java
    • -1
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    /getdown/src/getdown/launcher/pom.xml
    • -1
    • +1
    /getdown/src/getdown/mvn_cmd
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    /getdown/src/getdown/pom.xml
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
2:52 pm

Ben Soares

JAL-3609 JAL-3775 Tests for jalview.bin.HiDPISetting

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    /src/jalview/gui/Desktop.java
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    /test/jalview/bin/HiDPISettingTest1.java
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    /test/jalview/bin/HiDPISettingTest2.java
    • -0
    • +15
    /test/jalview/bin/hidpiTestProps.jvprops
2:34 pm

Ben Soares

JAL-3609 JAL-3775 Refactoring a bit of jalview.bin.HiDPISetting so screen display can be mocked in tests by Mockito

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    • -7
    • +39
    /src/jalview/bin/HiDPISetting.java
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    /src/jalview/bin/ScreenInfo.java
2:30 pm

Ben Soares

JAL-3775 Adding Mockito jars for tests. Needed for HiDPISettingTest1

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    • binary
    /utils/testnglibs/byte-buddy-1.10.15.jar
    • binary
    /utils/testnglibs/byte-buddy-agent-1.10.15.jar
    • binary
    /utils/testnglibs/mockito-core-3.6.0.jar
    • binary
    /utils/testnglibs/objenesis-3.1.jar
2:27 pm

Mungo Carstairs

JAL-3774 better translation

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    /resources/lang/Messages_es.properties
2:25 pm

Ben Soares

JAL-3530 Added a -nowebservicediscovery command line argument.

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    • -12
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    /src/jalview/bin/Jalview.java
2:16 pm

Mungo Carstairs

JAL-3774 missing i18n added, overlong translation shortened

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/Finder.java
Monday 30 Nov
4:14 pm

Jim Procter

JAL-3690 for a laugh, lets enable web services!

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    • -1
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    /src/jalview/bin/Jalview.java
3:59 pm

Jim Procter

JAL-3690 update to next patched 3.2.9 j2s c336e447

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    /swingjs/SwingJS-site.zip
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    /swingjs/timestamp
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /swingjs/ver/3.2.9/timestamp
3:56 pm

Jim Procter

JAL-3690 update j2s from hanson1 branch 0b8b02bb

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    /swingjs/SwingJS-site.zip
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    /swingjs/net.sf.j2s.core-j11.jar
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    /swingjs/net.sf.j2s.core.jar
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    /swingjs/timestamp
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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/timestamp
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
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    /swingjs/ver/3.2.9/timestamp
Sunday 29 Nov
5:55 pm

Mungo Carstairs

JAL-3774 fixed focus Finder from split frame

Options
    • -0
    • +1
    /resources/lang/Messages.properties
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    • +1
    /resources/lang/Messages_es.properties
    • -1
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Finder.java
    • -13
    • +17
    /src/jalview/gui/SplitFrame.java
Friday 27 Nov
5:24 pm

Ben Soares

JAL-3660 Fix for specified output format when using command line arg to convert a file

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    • -8
    • +28
    /src/jalview/bin/Jalview.java
5:24 pm

Ben Soares

JAL-3660 Fix for specified output format when using command line arg to convert a file

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    • -8
    • +29
    /src/jalview/bin/Jalview.java
Thursday 26 Nov
2:17 pm

Mungo Carstairs

JAL-3761 locateInFrom/To revised with tests; unused methods removed

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    /src/jalview/datamodel/Mapping.java
    • -318
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    /src/jalview/util/MapList.java
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    /test/jalview/util/MapListTest.java
Friday 20 Nov
1:04 pm

Mungo Carstairs

JAL-3779 apply properties to all groups with given name, not just first

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    • -105
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    /src/jalview/io/AnnotationFile.java
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    /test/jalview/io/AnnotationFileIOTest.java
11:59 am

Mungo Carstairs

JAL-3761 extra check that VCF feature is fully mappable to sequence

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    /src/jalview/io/vcf/VCFLoader.java
11:58 am

Mungo Carstairs

JAL-3761 debugged and working (but not tidied) locateInFrom2/To2

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    /src/jalview/util/MapList.java
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    /test/jalview/util/MapListTest.java
Thursday 19 Nov
5:58 pm

Ben Soares

JAL-3521 removed unnecessary parts of the ext project in build.gradle

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    /build.gradle
4:17 pm

Ben Soares

JAL-3521 Minimal plugins and tasks needed to run tests and build jalview.jar

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    /build.gradle
Friday 13 Nov
6:10 pm

Ben Soares

JAL-3775 Re-compiled Getdown jars

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    /getdown/lib/JVL_VERSION
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    /getdown/lib/getdown-launcher-local.jar
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    /getdown/lib/getdown-launcher.jar
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    /getdown/src/getdown/ant/pom.xml
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    /getdown/src/getdown/launcher/pom.xml
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    /getdown/src/getdown/mvn_cmd
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    /getdown/src/getdown/pom.xml
    • binary
    /j11lib/getdown-core.jar
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    /j8lib/getdown-core.jar
6:09 pm

Ben Soares

JAL-3775 Eclipse re-formatting commit

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    /src/jalview/gui/Preferences.java
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    /src/jalview/io/BackupFiles.java
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    /src/jalview/jbgui/GPreferences.java
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    /src/jalview/project/Jalview2XML.java
3:51 pm

Mateusz Warowny

JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

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    /src/jalview/api/PollableAlignCalcWorkerI.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/PCAPanel.java
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    /src/jalview/gui/ProgressBar.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/WebserviceInfo.java
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    /src/jalview/workers/AlignCalcManager.java
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    /src/jalview/workers/AlignCalcManager2.java
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    /src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
Thursday 12 Nov
3:13 pm

Mateusz Warowny

JAL-3690 - fixed state inconsistency when restarting the calcworker

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    /src/jalview/workers/AlignCalcManager2.java
2:36 pm

Jim Procter

Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
2:27 pm

Ben Soares

JAL-3628 Error when saving alert box has been moved in develop for JS, adding Platform.isHeadless test to new isSaveAlignmentSuccessful method.

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    /src/jalview/gui/AlignFrame.java
10:03 am

Mungo Carstairs

JAL-3761 locateInFrom2 work in progress commit

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    /src/jalview/util/MapList.java
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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MapListTest.java
Wednesday 11 Nov
6:42 pm

Mateusz Warowny

JAL-3690 partially reworked AlignCalcManager

todo:

- modify SeqAnnotationServiceCalcWorker to implement PollableAlignCalcWorkerI

- fix race condition where worker state gets overriden by the old job (QUEUED to IDLE)

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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/api/PollableAlignCalcWorkerI.java
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    /src/jalview/workers/AlignCalcManager2.java
Friday 06 Nov
5:05 pm

Ben Soares

JAL-3609 formatting save after cherry-picks

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    /getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
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    /src/jalview/bin/MemorySetting.java
Thursday 05 Nov
4:01 pm

Ben Soares

JAL-3608 cherry pick of 92cb745e7

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    /src/jalview/bin/Cache.java
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    /src/jalview/bin/Jalview.java