jalview

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Commits this week: 17
Total Committers: 73
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Commits this week: 17

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Monday 13 Dec 2021
6:17 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 isCanonical should by default be false - ensure JalviewJS offers 3d-beacons search for example project

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    • -1
    • +1
    /src/jalview/datamodel/DBRefEntry.java
5:49 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
5:49 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve been given it

Options
    • -1
    • +1
    /src/jalview/gui/StructureViewerBase.java
    • -0
    • +9
    /src/jalview/ws/dbsources/EBIAlfaFold.java
4:54 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 update Jalview 2.12 branch from build.gradle for 2.11.2

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    • -225
    • +383
    /build.gradle
    • -13
    • +28
    /gradle.properties
4:54 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 update Jalview 2.12 branch from build.gradle for 2.11.2

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    • -225
    • +383
    /build.gradle
    • -13
    • +28
    /gradle.properties
4:26 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
2:15 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 preserve lowercase pdbid in group name for transferred features

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    • -5
    • +6
    /src/jalview/structure/StructureSelectionManager.java
Wednesday 08 Dec 2021
6:58 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'to_merge/r2_11_2/JAL-3904_improved_alignpanelAPI_autoshowview' into develop

Options
6:53 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 pymol docs - work in progress

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    • -0
    • +1
    /help/help/help.jhm
    • -1
    • +2
    /help/help/helpTOC.xml
    • -2
    • +3
    /help/help/html/features/chimera.html
    • -0
    • +234
    /help/help/html/features/pymol.html
6:52 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 don’t use the url encoded pdbId in feature group when transferring features from associated structure to a sequence

Options
    • -5
    • +5
    /src/jalview/structure/StructureSelectionManager.java
    • -3
    • +8
    /src/mc_view/PDBChain.java
3:59 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3616 update messages/tooltips/menu items to use getViewerName() for chimera/x/pymol

Options
    • -3
    • +3
    /resources/lang/Messages.properties
    • -3
    • +3
    /src/jalview/gui/ChimeraViewFrame.java
    • -1
    • +1
    /src/jalview/gui/PymolViewer.java
3:48 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 JAL-3931 view pymol commands/responses in Log.trace

Options
    • -0
    • +8
    /src/jalview/ext/pymol/PymolManager.java
3:45 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the structure identifier that Jalview uses to refer to each file

Options
    • -0
    • +15
    /src/jalview/gui/PymolBindingModel.java
3:44 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 URLencode pdbid to remove problematic characters - propagate urlEncoded ID to the features transferred from the structure file

Options
    • -1
    • +3
    /src/jalview/gui/StructureViewerBase.java
    • -0
    • +17
    /src/jalview/ws/dbsources/EBIAlfaFold.java
    • -1
    • +2
    /src/mc_view/PDBChain.java
Tuesday 07 Dec 2021
1:22 pm

Ben Soares

JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

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    • -25
    • +25
    /utils/install4j/file_associations_auto-install4j8.xml
    • -1
    • +1
    /utils/install4j/file_associations_template-install4j8.xml
    • -5
    • +5
    /utils/install4j/install4j9_template.install4j
12:39 pm

Ben Soares

JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

Options
    • -25
    • +25
    /utils/install4j/file_associations_auto-install4j8.xml
    • -1
    • +1
    /utils/install4j/file_associations_template-install4j8.xml
    • -4
    • +4
    /utils/install4j/install4j8_template.install4j
Monday 06 Dec 2021
10:05 am

Ben Soares

Merge branch 'develop' into task/JAL-3911_getdown_improvements

Options
Thursday 02 Dec 2021
11:23 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3904 use new AlignPanel API method

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    • -2
    • +3
    /src/jalview/gui/ViewSelectionMenu.java
11:22 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3904 simple method to make an alignPanel the currently viewed one in the alignframe

Options
    • -3
    • +6
    /src/jalview/gui/AlignmentPanel.java
Wednesday 01 Dec 2021
2:10 pm

Mateusz Warowny

JAL-3878 Use annotations from the representative sequence in the new alignment.

Options
    • -2
    • +3
    /src/jalview/ws2/gui/JPredMenuBuilder.java
    • -2
    • +1
    /src/jalview/ws2/operations/JPredWorker.java
Monday 29 Nov 2021
8:00 pm

Ben Soares

JAL-3594 correct Jalview Develop logo SVG added in [not actually used in application]

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    • -57
    • +70
    /utils/channels/develop/images/jalview_develop_logo.svg
Thursday 25 Nov 2021
6:12 pm

Mateusz Warowny

JAL-3927 Make url checks asynchronous in preferences dialog

Options
    • -9
    • +22
    /src/jalview/gui/SlivkaPreferences.java
2:50 pm

Mateusz Warowny

JAL-3878 Add jpred operation and worker to the services.

Options
    • -0
    • +157
    /src/jalview/ws2/gui/JPredMenuBuilder.java
    • -1
    • +1
    /src/jalview/ws2/operations/AbstractWorker.java
    • -0
    • +35
    /src/jalview/ws2/operations/JPredOperation.java
    • -0
    • +334
    /src/jalview/ws2/operations/JPredWorker.java
    • -1
    • +21
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
    • -16
    • +22
    /src/jalview/ws2/slivka/SlivkaWebService.java
11:08 am

Ben Soares

JAL-3553 added filesize to json

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    • -3
    • +8
    /build.gradle
Wednesday 24 Nov 2021
4:31 pm

Mateusz Warowny

JAL-3878 Make openEditsParamsDialog an interface static method.

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    • -39
    • +3
    /src/jalview/ws2/gui/AlignmentMenuBuilder.java
    • -40
    • +4
    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
    • -0
    • +43
    /src/jalview/ws2/gui/MenuEntryProviderI.java
Tuesday 23 Nov 2021
3:54 pm

Mateusz Warowny

JAL-3066 Fix ambiguous assertEquals casting values to double.

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    • -17
    • +17
    /test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
3:35 pm

Mateusz Warowny

JAL-3878 Add annotation operation and worker to the services.

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    • -0
    • +181
    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
    • -0
    • +50
    /src/jalview/ws2/gui/ProgressBarUpdater.java
    • -0
    • +41
    /src/jalview/ws2/operations/AnnotationOperation.java
    • -0
    • +602
    /src/jalview/ws2/operations/AnnotationWorker.java
    • -15
    • +19
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
    • -42
    • +35
    /src/jalview/ws2/slivka/SlivkaWebService.java
3:31 pm

Mateusz Warowny

JAL-3878 Handle nulls when filtering annotation workers by name.

Options
    • -2
    • +2
    /src/jalview/workers/AlignCalcManager2.java
3:10 pm

Ben Soares

JAL-3066 Vastly updated testng libs

Options
    • binary
    /utils/testnglibs/testng-7.4.0-sources.jar
    • binary
    /utils/testnglibs/testng-7.4.0.jar
    • binary
    /utils/testnglibs/testng-sources.jar
    • binary
    /utils/testnglibs/testng.jar
3:10 pm

Ben Soares

JAL-3066 Vastly updated testng libs

Options
    • binary
    /utils/testnglibs/testng-7.4.0-sources.jar
    • binary
    /utils/testnglibs/testng-7.4.0.jar
    • binary
    /utils/testnglibs/testng-sources.jar
    • binary
    /utils/testnglibs/testng.jar