jalview

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Commits this week: 18

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Wednesday 28 Jul
11:36 am

Mateusz Warowny

Merge branch 'improvement/JAL-3848_slivka_0.8' into alpha/JAL-3066_Jalview_212_slivka-integration

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    /j11lib/slivka-client.jar
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    /src/jalview/ws/jws2/JPredThread.java
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    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
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    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Tuesday 27 Jul
4:36 pm

Mateusz Warowny

Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

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    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
2:26 pm

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

JAL-3674 Jmol seems to sometimes return a null for some commands, handle it at source

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    /src/jalview/structures/models/AAStructureBindingModel.java
2:25 pm

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

JAL-3855 suppress NPE when trying to retrieve SIFTS mappings for Alphafold PDB IDs

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    /src/jalview/structure/StructureSelectionManager.java
1:52 pm

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

JAL-3855 ALPHAFOLD database source based on the PDB retriever

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    /src/jalview/ws/dbsources/EBIAlfaFold.java
1:35 pm

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

JAL-3855 check if an alpha fold ID and retrieve using that source

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    /src/jalview/gui/AppJmol.java
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    /src/jalview/gui/StructureViewerBase.java
1:34 pm

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

JAL-3855 check for existence of an alpha fold model when pinging the PDBe

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    /src/jalview/fts/service/alphafold/AlphafoldRestClient.java
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    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
1:33 pm

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

JAL-3855 convenience method to check a URL will return a 200

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    /src/jalview/util/HttpUtils.java
12:00 pm

Mateusz Warowny

Merge commit '0b438477b16470202bddfecb54e0587036b37202' into alpha/JAL-3066_Jalview_212_slivka-integration

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Sunday 25 Jul
5:48 pm

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

JAL-3854 patched SeqSeqUtils.deUniquify to not use instanceOf - seems to work

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    /src/jalview/analysis/SeqsetUtils.java
4:23 pm

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

JAL-2994 disable tests for FileUtils path search methods on bamboo

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    /test/jalview/util/FileUtilsTest.java
4:08 pm

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

JAL-3848 slivka preferences in javascript

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    /src/jalview/jbgui/GPreferences.java
4:07 pm

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

JAL-3848 reinstate Fetch DB References submenu

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    /src/jalview/gui/AlignFrame.java
3:51 pm

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

JAL-3848 add compbio and jalview to direct connection list for J2S

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    /src/jalview/bin/Jalview.java
3:45 pm

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

JAL-3848 update jalview core with slivka classes, example file import and structure view

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    /utils/jalviewjs/classlists/jalview.txt
3:04 pm

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

JAL-3853 - tweak test again - since failed a few commits after f6cb90d43782ca99cf2b1cbee2dc76bca3d1d466

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    /test/jalview/io/SequenceAnnotationReportTest.java
2:47 pm

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

JAL-3848 update swingJS runtime and transpiler to 3.3.1

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    /swingjs/differences.txt
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    /swingjs/ver/3.3.1-j11/DEV_NOTES.txt
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    /swingjs/ver/3.3.1-j11/_j2sclasslist.txt
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    /swingjs/ver/3.3.1-j11/differences.txt
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    /swingjs/ver/3.3.1/DEV_NOTES.txt
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2:16 pm

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

Merge branch 'improvement/JAL-3848_slivka_0.8' of https://source.jalview.org/git/jalview into improvement/JAL-3848_slivka_0.8

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Friday 23 Jul
1:12 pm

Mateusz Warowny

JAL-3848 Update slivka client javajs library.

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    /utils/jalviewjs/libjs/slivka-client-site.zip
Thursday 22 Jul
8:44 pm

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

JAL-3848 enable slivka services dialog in JalviewJS

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    /src/jalview/gui/Preferences.java
8:41 pm

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

JAL-3853 JAL-1870 toggle to enable/disable posterior probability transparency when rendering per sequence annotation row scores .. needs more work

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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/AnnotationRowFilter.java
8:40 pm

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

JAL-3853 JAL-1870 patch tests for annotation colour gradient without transparency/per sequence annotation score encoding

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    /src/jalview/schemes/AnnotationColourGradient.java
8:37 pm

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

JAL-1950 patch groovy bootstrap for importing hmmer3 json

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    /examples/groovy/hmmertestimport.groovy
8:36 pm

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

JAL-3853 patch sequence annotation report code and tweak the test. When merging from 2.11.2 develop there will be conflicts that need merging re HTMLXML tags

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    /src/jalview/io/SequenceAnnotationReport.java
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    /test/jalview/io/SequenceAnnotationReportTest.java
6:04 pm

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

JAL-3848 ensure annotation from a service gets a calcId so it can be updated and tracked across multiple views - nb - service.getId() probably isn’t the right value to use for this!

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    /src/jalview/io/AnnotationFile.java
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    /src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
6:02 pm

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

JAL-3848 don’t include sequence limits in sequence id as it confuses slivka-0.8’s jalview-feature-file creation script

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    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
6:00 pm

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

JAL-3848 - actually test the Slivka and JABAWS disorder services - nb still need asserts to verify the disorder annotation from Slivka looks like Jabaws

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    /test/jalview/ws/jabaws/DisorderAnnotExportImport.java
Wednesday 21 Jul
5:08 pm

Mateusz Warowny

JAL-3848 print exception for failed align jobs

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    /src/jalview/ws/gui/MsaWSThread.java
5:06 pm

Mateusz Warowny

JAL-3848 add latest slivka-client fixes.

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    /j11lib/slivka-client.jar
12:50 pm

Ben Soares

JAL-3850 fixed full class name

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    /build.gradle