jalview

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Commits this week: 2
Total Committers: 73
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Commits this week: 2

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Tuesday 23 May 2017
8:39 pm

Jim Procter

JAL-2549 RNAAliFold result to annotation file roundtrip test fails test due to JAL-2550 - Upper/lower case alphabet recognised as WUSS RNA annotation

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    /test/jalview/ws/jabaws/RNAStructExportImport.java
8:35 pm

Jim Procter

JAL-2549 skip ‘Unrecognised Service’ which resolves to a null entry in the get supported services list

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    /test/jalview/ws/jabaws/MinJabawsClientTests.java
8:35 pm

Jim Procter

JAL-2549 replace JABAWS 2.1 with 2.2 client and remove JPredWS client and tests

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    /.classpath
    • binary
    /lib/jabaws-min-client-2.2.0.jar
    • binary
    /lib/min-jabaws-client-2.1.0.jar
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    /src/jalview/ws/jws2/JPred301Client.java
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    /src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
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    /test/jalview/ws/jabaws/JpredJabaStructExportImport.java
Monday 22 May 2017
3:37 pm

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

JAL-2504 update the right feature colour when creating a new feature

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    /src/jalview/appletgui/FeatureRenderer.java
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    /src/jalview/gui/FeatureRenderer.java
2:39 pm

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

JAL-2544 unit tests for sort by feature score

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    /test/jalview/analysis/AlignmentSorterTest.java
2:33 pm

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

JAL-2544 check feature overlaps selection region

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    /src/jalview/analysis/AlignmentSorter.java
11:57 am

Kira Mourão

Merge remote-tracking branch 'origin/bug/JAL-2256' into develop

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11:34 am

Jim Procter

JAL-2418 patch build - broken htsjdk import

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    • -3
    • +1
    /src/jalview/datamodel/CigarArray.java
Friday 19 May 2017
4:59 pm

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

JAL-2526 removed redundant call to Sequence.findPosition()

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    • +27
    /src/jalview/gui/SeqPanel.java
Thursday 18 May 2017
4:33 pm

Jim Procter

Merge branch 'bug/JAL-2388_typeCheckAlignView.getUpdatedView' into develop

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4:31 pm

Jim Procter

JAL-2388 return empty hidden columns for fully visible alignment view

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    • -1
    • +1
    /src/jalview/datamodel/AlignmentView.java
2:09 pm

Kira Mourão

JAL-2256 Corrected AllCols/Rows iterator behaviour for single element

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    • +2
    /src/jalview/datamodel/AllColsIterator.java
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    /src/jalview/datamodel/AllRowsIterator.java
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    /test/jalview/datamodel/AllColsIteratorTest.java
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    /test/jalview/datamodel/AllRowsIteratorTest.java
12:18 pm

Jim Procter

JAL-2418 remove explicit test suite stats

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    /help/html/releases.html
Wednesday 17 May 2017
4:26 pm

Jim Procter

Merge branch 'develop' into documentation/JAL-2418_release2102

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4:10 pm

Jim Procter

Merge branch 'bug/JAL-2510amendFeatures' into develop

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    /resources/lang/Messages.properties
3:50 pm

Jim Procter

JAL-2447 add links to issues.jalview.org for experimental features

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    /help/html/features/chimera.html
3:41 pm

Jim Procter

Merge branch 'documentation/JAL-2418_release2102' into develop

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3:39 pm

Jim Procter

JAL-2447 experimental section in ‘Whats New’

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    /help/html/whatsNew.html
3:39 pm

Jim Procter

JAL-2447 JAL-2295 JAL-2296 documenting as experimental features

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    /help/html/features/chimera.html
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    /help/html/menus/desktopMenu.html
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    /help/html/releases.html
2:46 pm

Jim Procter

Merge branch 'develop' into documentation/JAL-2418_release2102

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2:31 pm

Jim Procter

Merge branch 'features/JAL-2447experimentalFlag' into develop

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    • +2
    /resources/lang/Messages.properties
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    /src/jalview/gui/Desktop.java
2:28 pm

Jim Procter

JAL-2418 release notes

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    /help/html/releases.html
1:07 pm

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

JAL-2504 use (and update) defaults for new feature only if not supplied

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/FeatureRenderer.java
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    /src/jalview/appletgui/Finder.java
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    /src/jalview/appletgui/SeqPanel.java
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    /src/jalview/gui/FeatureRenderer.java
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    /src/jalview/gui/Finder.java
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    /src/jalview/gui/PopupMenu.java
    • -1
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    /src/jalview/gui/SeqPanel.java
8:59 am

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

Merge branch 'develop' into bug/JAL-2510amendFeatures

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
Tuesday 16 May 2017
5:36 pm

Jim Procter

Merge branch 'documentation/JAL-2418_release2102' into develop

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5:27 pm

Jim Procter

JAL-2418 release notes

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    /help/html/releases.html
4:51 pm

Jim Procter

JAL-384 documentation on custom colours groovy examples

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    /help/help.jhm
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    /help/helpTOC.xml
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    /help/html/features/groovy.html
4:35 pm

Jim Procter

JAL-384 - groovy scripts for conserved/unconserved colourscheme requests

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    • +88
    /examples/groovy/colourConserved.groovy
    • -0
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    /examples/groovy/colourUnconserved.groovy
4:30 pm

Jim Procter

JAL-2418 release notes

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    • +35
    /help/html/releases.html
2:54 pm

Jim Procter

JAL-2418 JAL-2316 added to new features

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    /help/helpTOC.xml
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    /help/html/features/preferences.html
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    /help/html/releases.html