jalview

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Commits this week: 5
Total Committers: 72
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Commits this week: 5

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Thursday 21 Jan
11:42 pm

Ben Soares

JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_Branch

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    • -7
    • +1
    /build.gradle
    • -74
    • +0
    /utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist
    • binary
    /utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet
    • -1
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    /utils/install4j/Uninstall Old Jalview.app/Contents/PkgInfo
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    /utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt
    • binary
    /utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.icns
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    /utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc
    • -5
    • +0
    /utils/install4j/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf
    • -177
    • +0
    /utils/install4j/Uninstall Old Jalview.app/Contents/_CodeSignature/CodeResources
    • binary
    /utils/install4j/Uninstall Old Jalview.scpt
    • -15
    • +1
    /utils/install4j/install4j8_template.install4j
5:18 pm

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

JAL-3038 corrected code that reads editable JComboBox text input

Options
    • -3
    • +3
    /src/jalview/gui/Desktop.java
3:44 pm

Mateusz Warowny

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

Options
    • -10
    • +26
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Tuesday 19 Jan
5:29 pm

Mateusz Warowny

JAL-3690 AlignCalcManager - add full support for oneshot workers

Options
    • -87
    • +124
    /src/jalview/workers/AlignCalcManager2.java
5:29 pm

Mateusz Warowny

JAL-3690 AlignCalcManager - add full support for oneshot workers

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    • -87
    • +124
    /src/jalview/workers/AlignCalcManager2.java
4:10 pm

Mateusz Warowny

JAL-3690 AACon ws menu entry fix.

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    • -1
    • +3
    /src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
4:10 pm

Mateusz Warowny

JAL-3690 AACon ws menu entry fix.

Options
    • -1
    • +3
    /src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
Monday 18 Jan
4:50 pm

Mateusz Warowny

JAL-3690 Allow unregistered workers to be run with CalcManager.

Options
    • -5
    • +10
    /src/jalview/workers/AlignCalcManager2.java
4:50 pm

Mateusz Warowny

JAL-3690 Allow unregistered workers to be run with CalcManager.

Options
    • -5
    • +10
    /src/jalview/workers/AlignCalcManager2.java
4:50 pm

Mateusz Warowny

JAL-3690 Fix typo in enum name in slivka client.

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    • binary
    /j11lib/slivka-client.jar
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
4:50 pm

Mateusz Warowny

JAL-3690 Fix typo in enum name in slivka client.

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    • binary
    /j11lib/slivka-client.jar
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
    • binary
    /utils/jalviewjs/libjs/slivka-client-site.zip
12:51 pm

Mateusz Warowny

Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services' into feature/JAL-3690_callback-based-web-services

Options
Friday 15 Jan
6:21 pm

Mateusz Warowny

JAL-3690 Fixed slivka wsmenu categories.

Options
    • -5
    • +5
    /src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
    • -2
    • +3
    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
    • -33
    • +51
    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
6:21 pm

Mateusz Warowny

JAL-3690 Fixed slivka wsmenu categories.

Options
    • -5
    • +5
    /src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
    • -2
    • +3
    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
    • -34
    • +47
    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Thursday 14 Jan
5:39 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

JAL-3796 update signature for uninstaller on OSX

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    • binary
    /utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet
3:34 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

JAL-3796 update to Install4j 8.0.10 and add config for code notarization

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    • -1
    • +13
    /build.gradle
    • -0
    • +2
    /gradle.properties
    • -2
    • +23
    /utils/install4j/install4j8_template.install4j
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

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    • -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

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    • -8
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    /swingjs/README.txt
    • binary
    /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/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/SwingJS-site.zip
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
    • -0
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    /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

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    • -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

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    • -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

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    • -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

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    • -8
    • +35
    /src/jalview/util/Comparison.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
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

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    • 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()

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    • -6
    • +6
    /src/jalview/schemes/ClustalxColourScheme.java
4:38 pm

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

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

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    • -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

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    • -22
    • +22
    /src/jalview/util/MapList.java