jalview

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Commits this week: 3

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Monday 08 Aug
6:31 pm

Jim Procter

Friday 22 Jul
4:40 pm

Ben Soares

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace. This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses...

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace.
This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses. I notice that the new API server is sending back a 400 for bad input (including for non-existent query fields and wrong types for non-string query fields), which is invoking the warning triangle which puts the HTTP error message into the tooltip so this block is now getting more use!

The reason for wanting a full stacktrace in debug mode is that both the API and the changed client are new, so any errors in the next few months will be more quickly diagnosed if we can allow the user to easily obtain a stacktrace of the exception.

12:34 pm

Jim Procter

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a con...

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a convenient [search] button is shown so one doesn't have to click into the query field and press enter to trigger the search again.

12:32 pm

Jim Procter

should be Console.warn

should be Console.warn

12:31 pm

Jim Procter

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalvi...

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalview still work (up until legacy.uniprot.org goes away).

11:38 am

Jim Procter

shouldn't this be a warn ?

shouldn't this be a warn ?

11:36 am

Jim Procter

this comment block should really be after the imports ?

this comment block should really be after the imports ?

11:35 am

Jim Procter

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

11:33 am

Jim Procter

JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
Wednesday 30 Mar
4:23 pm

Jim Procter

4:22 pm

Jim Procter

make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
4:20 pm

Jim Procter

JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
2:40 pm

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

JAL-3982 todo notes

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    /src/jalview/rest/HighlightGenomicRangeEndpoint.java
2:14 pm

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

JAL-3860 prototype for highlight species/assembly/chromosome/position

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    /src/jalview/datamodel/GenomicAssemblies.java
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    /src/jalview/rest/API.java
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    /src/jalview/rest/HighlightGenomicRangeEndpoint.java
Tuesday 29 Mar
11:20 pm

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

JAL-3982 JAL-3860 encapsulate genomic coordinates mapping/liftover logic

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    /src/jalview/datamodel/GenomicAssemblies.java
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    /src/jalview/io/vcf/VCFLoader.java
8:06 pm

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

JAL-3860 JAL-3892 extract genomic assembly mapping logic to static store

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    /src/jalview/datamodel/GenomicAssemblies.java
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    /src/jalview/io/vcf/VCFLoader.java
Friday 25 Mar
4:16 pm

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

JAL-3982 highlight any 3D structure mappings for positions mapped via CDS/transcript relationships

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    /src/jalview/structure/StructureSelectionManager.java
Wednesday 23 Mar
9:38 pm

Ben Soares

JAL-3851 Fix getRequestBody()

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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/InputAlignmentEndpoint.java
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    /src/jalview/rest/RestHandler.java
Tuesday 22 Mar
7:00 pm

Ben Soares

Merge branch 'feature/JAL-3851_rest_api_for_genome_browser' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

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6:42 pm

Ben Soares

JAL-3851 merged to develop 2022-03-22

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    /doc/api_specification.md
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/httpserver/AbstractRequestHandler.java
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    /src/jalview/rest/API.java
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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/AbstractEndpointAsync.java
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    /src/jalview/rest/FetchSequencesEndpoint.java
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    /src/jalview/rest/GetCrossReferencesEndpoint.java
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    /src/jalview/rest/HighlightSequenceEndpoint.java
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    /src/jalview/rest/InputAlignmentEndpoint.java
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    /src/jalview/rest/RestHandler.java
  16. … 3 more files in changeset.
Thursday 10 Mar
1:29 am

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

JAL-3746 bump release date to 10th March - after UoD network maintenance

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    /help/help/html/releases.html
1:28 am

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

JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(

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    /utils/install4j/install4j9_template.install4j
Wednesday 09 Mar
4:51 pm

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

JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert

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    /j11lib/Jmol-NO_LOG4J-14.31.53.jar
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    /j8lib/Jmol-NO_LOG4J-14.31.53.jar
10:11 am

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

JAL-3746 JAL-3841 fix README typo

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    /README
8:09 am

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

JAL-3746 more docs tweaking and release notes

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    /help/help/html/features/preferences.html
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    /help/help/html/releases.html
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    /help/help/html/whatsNew.html
7:59 am

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

Merge branch 'spike/try_spotless_JAL-3438' into develop

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Tuesday 08 Mar
9:58 pm

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

JAL-3746 apply copyright to tests

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    /test/jalview/analysis/AlignmentSorterTest.java
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    /test/jalview/analysis/GeneticCodesTest.java
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    /test/jalview/analysis/scoremodels/PIDModelTest.java
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    /test/jalview/analysis/scoremodels/ScoreMatrixTest.java
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    /test/jalview/analysis/scoremodels/ScoreModelsTest.java
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    /test/jalview/bin/HiDPISettingTest1.java
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    /test/jalview/datamodel/ConcurrentModificationTest.java
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    /test/jalview/datamodel/MappedFeaturesTest.java
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    /test/jalview/datamodel/SequenceGroupTest.java
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    /test/jalview/datamodel/features/FeatureAttributesTest.java
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    /test/jalview/datamodel/features/FeatureMatcherSetTest.java
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    /test/jalview/datamodel/features/FeatureMatcherTest.java
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    /test/jalview/datamodel/features/FeatureStoreTest.java
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    /test/jalview/datamodel/features/SequenceFeaturesTest.java
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    /test/jalview/ext/android/SparseDoubleArrayTest.java
  16. … 59 more files in changeset.
9:56 pm

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

JAL-3746 apply copyright to source

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    /src/jalview/bin/Console.java
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    /src/jalview/bin/JalviewJS2.java
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    /src/jalview/bin/ScreenInfo.java
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    /src/jalview/datamodel/AlignExportSettingsAdapter.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
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    /src/jalview/fts/api/StructureFTSRestClientI.java
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    /src/jalview/fts/service/alphafold/AlphafoldRestClient.java
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    /src/jalview/fts/service/threedbeacons/.gitignore
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    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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    /src/jalview/gui/ChimeraXViewFrame.java
  16. … 31 more files in changeset.
9:30 pm

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

JAL-3438 spotless for 2.11.2.0

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  16. … 647 more files in changeset.
8:39 pm

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

JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes

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