jalview

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Commits this week: 39
Total Committers: 68
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Commits this week: 39

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Friday 21 Feb
5:18 pm

Jim Procter

Merge branch 'bug/JAL-3536getCrossrefTwice' into develop

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3:12 pm

Jim Procter

JAL-3186 ensure transparency slider position is updated on revert

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    • -2
    • +16
    /src/jalview/gui/FeatureSettings.java
3:10 pm

Jim Procter

JAL-3186 avoid repainting twice in splitframe

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    • -1
    • +4
    /src/jalview/gui/AlignFrame.java
2:36 pm

Jim Procter

Merge branch 'features/JAL-3187_uitweaks' into develop

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2:34 pm

Jim Procter

Merge branch 'develop' into features/JAL-3187_uitweaks

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    • -5
    • +9
    /help/help/html/releases.html
    • -0
    • +5
    /src/jalview/gui/AlignFrame.java
    • -1
    • +1
    /src/jalview/gui/AlignViewport.java
Thursday 20 Feb
5:25 pm

Jim Procter

JAL-3187 nice to have enabling/disabling of apply/cancel when feature settings have not yet been modified for a view

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    • -1
    • +1
    /src/jalview/gui/FeatureSettings.java
5:24 pm

Jim Procter

JAL-3187 i18n

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    • -0
    • +2
    /resources/lang/Messages.properties
5:24 pm

Jim Procter

JAL-3187 use the recommended way of catching tab selection change events

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    • -29
    • +31
    /src/jalview/gui/SplitFrame.java
4:20 pm

Mungo Carstairs

JAL-3187 repaint complement after loading on features

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    • -0
    • +5
    /src/jalview/gui/AlignFrame.java
2:11 pm

Jim Procter

JAL-3187 individual feature settings panel has revert/apply when embedded in a tab, and split frame feature settings has an OK and Cancel.

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    • -0
    • +6
    /src/jalview/controller/FeatureSettingsControllerGuiI.java
    • -25
    • +66
    /src/jalview/gui/FeatureSettings.java
    • -1
    • +52
    /src/jalview/gui/SplitFrame.java
2:06 pm

Mungo Carstairs

JAL-2422 pull-up refactoring of structure commands (continued)

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    • -1
    • +1
    /resources/lang/Messages.properties
    • -1
    • +1
    /resources/lang/Messages_es.properties
    • -8
    • +0
    /src/jalview/api/structures/JalviewStructureDisplayI.java
    • -11
    • +11
    /src/jalview/appletgui/AppletJmol.java
    • -1
    • +1
    /src/jalview/appletgui/UserDefinedColours.java
    • -201
    • +37
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -23
    • +101
    /src/jalview/ext/jmol/JmolCommands.java
    • -41
    • +111
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -0
    • +627
    /src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
    • -210
    • +12
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -23
    • +3
    /src/jalview/gui/AppJmol.java
    • -23
    • +1
    /src/jalview/gui/ChimeraViewFrame.java
    • -0
    • +28
    /src/jalview/gui/ChimeraXViewFrame.java
    • -3
    • +4
    /src/jalview/gui/JalviewChimeraBindingModel.java
    • -0
    • +18
    /src/jalview/gui/JalviewChimeraXBindingModel.java
  16. … 11 more files in changeset.
Wednesday 19 Feb
6:46 pm

Jim Procter

JAL-3187 i18n for titles in windows/tabs

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    • -0
    • +1
    /resources/lang/Messages.properties
    • -9
    • +13
    /src/jalview/gui/SplitFrame.java
6:43 pm

Jim Procter

JAL-3535 todo re titles for CDS and Protein views in the feature settings dialog pane

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    • -0
    • +4
    /src/jalview/gui/SplitFrame.java
6:43 pm

Jim Procter

JAL-3187 - tabbed pane is nulled when feature settings is closed but not featureSettingsUI - check both are non-null or reconstruct

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    • -1
    • +1
    /src/jalview/gui/SplitFrame.java
4:40 pm

Ben Soares

Merge branch 'develop' into improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2

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    • -35
    • +52
    /build.gradle
4:37 pm

Ben Soares

JAL-3289 Improved the name of the channel_launch.jvl file to channel_launch-CHANNELNAMEWITHPLANKEY.jvl

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    • -4
    • +8
    /build.gradle
    • -1
    • +1
    /gradle.properties
    • -1
    • +1
    /utils/install4j/install4j8_template.install4j
3:22 pm

Jim Procter

(Notes for self) - Ben verified on linux, OSX, Windows. Need to check there are docs and logging to indicate that the hard limit is reached, so if people want to adjust the limit they can !

(Notes for self) - Ben verified on linux, OSX, Windows.
Need to check there are docs and logging to indicate that the hard limit is reached, so if people want to adjust the limit they can !

3:20 pm

Jim Procter

JAL-3477 New sensible default decisions on memory, and new jvmmemmax setting for setting absolute...
JAL-3477 New sensible default decisions on memory, and new jvmmemmax setting for setting absolute...
3:19 pm

Jim Procter

3:03 pm

Jim Procter

JAL-3187 JAL-2764 close feature settings when parent align frame is closed (need to check feature settings is open before closing it :) )

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    • -1
    • +5
    /src/jalview/gui/AlignFrame.java
    • -4
    • +9
    /src/jalview/gui/Desktop.java
2:22 pm

Ben Soares

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

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2:22 pm

Ben Soares

JAL-3337 Adding .settings/org.eclipse.jdt.core.jalview.prefs file needed for gradle eclipse

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    • -35
    • +52
    /build.gradle
12:05 pm

Jim Procter

Merge branch 'patch/JAL-3538_fontantialiasingbydefault' into develop

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12:05 pm

Jim Procter

JAL-3538 JAL-3407 release notes

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    • -4
    • +8
    /help/help/html/releases.html
12:03 pm

Jim Procter

JAL-3407 release next week :D

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    • -1
    • +1
    /help/help/html/releases.html
12:03 pm

Jim Procter

JAL-3538 anti-aliasing enabled by default

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    • -1
    • +1
    /src/jalview/gui/AlignViewport.java
    • -2
    • +2
    /src/jalview/gui/Preferences.java
9:06 am

Ben Soares

JAL-3449 helper task to perform getdown digest on any dir

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    • -0
    • +16
    /build.gradle
9:05 am

Ben Soares

JAL-3449 ensuring latest getdown jar files after merge

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    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
Tuesday 18 Feb
7:49 pm

Ben Soares

JAL-3449 merge from develop

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    • -5
    • +5
    /build.gradle
6:38 pm

Jim Procter

JAL-3529 attempt to guess database for a sequence’s AC record based on the sequence type if the alignment had no PFAM or RFAM accession

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    • -12
    • +17
    /src/jalview/io/StockholmFile.java