jalview

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Commits this week: 23
Total Committers: 68
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Commits this week: 23

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Tuesday 11 Aug
3:54 pm

Jim Procter

JAL-3675 update release notes for JAL-3673 and tested merge of additional patch for JAL-2983

Options
    • -0
    • +4
    /help/help/html/releases.html
3:01 pm

Jim Procter

Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch

Options
2:50 pm

Mungo Carstairs

JAL-3705 JAL-3251 unused attribute repurposed/renamed to mappedFromId

Options
    • -4
    • +1
    /schemas/vamsas.xsd
    • -2
    • +2
    /src/jalview/project/Jalview2XML.java
    • -10
    • +10
    /src/jalview/xml/binding/jalview/Mapping.java
2:31 pm

Mungo Carstairs

JAL-3705 unit test and "fix" borrowing unused schema attribute

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    • -50
    • +50
    /src/jalview/project/Jalview2XML.java
    • -14
    • +76
    /test/jalview/io/CrossRef2xmlTests.java
12:10 pm

Mungo Carstairs

JAL-3706 handle e.g. mapped exon feature extending beyond mapped range

Options
    • -2
    • +11
    /src/jalview/datamodel/MappedFeatures.java
    • -1
    • +8
    /test/jalview/datamodel/MappedFeaturesTest.java
10:35 am

Mungo Carstairs

JAL-3371 more fine-grained slider; set Param slider to initial default

Options
    • -3
    • +5
    /src/jalview/gui/OptsAndParamsPage.java
    • -1
    • +7
    /src/jalview/gui/Slider.java
Monday 10 Aug
4:04 pm

Mungo Carstairs

JAL-3706 handle virtual feature extending to unmapped stop codon

Options
    • -3
    • +22
    /src/jalview/datamodel/MappedFeatures.java
    • -4
    • +3
    /src/jalview/datamodel/SequenceFeature.java
    • -4
    • +3
    /src/jalview/gui/PopupMenu.java
    • -31
    • +12
    /src/jalview/io/SequenceAnnotationReport.java
    • -3
    • +44
    /test/jalview/datamodel/MappedFeaturesTest.java
    • -9
    • +6
    /test/jalview/io/SequenceAnnotationReportTest.java
3:10 pm

Jim Procter

JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations

Options
    • -1
    • +3
    /src/jalview/io/FeaturesFile.java
    • -3
    • +4
    /src/jalview/io/FileFormats.java
    • -1
    • +2
    /src/jalview/io/FormatAdapter.java
    • -2
    • +3
    /src/jalview/io/IdentifyFile.java
    • -1
    • +2
    /src/jalview/io/JPredFile.java
    • -1
    • +3
    /src/jalview/io/JnetAnnotationMaker.java
    • -1
    • +2
    /src/jalview/io/MSFfile.java
    • -2
    • +3
    /src/jalview/io/packed/ParsePackedSet.java
    • -2
    • +3
    /src/jalview/io/vcf/VCFLoader.java
3:02 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch' into patch/JAL-3691_No_score_models_available

Options
3:01 pm

Jim Procter

JAL-3628 JAL-3708 call Cache.initLogger() before using Cache.log in static methods with no class-level guarantee logs are initialised

Options
    • -0
    • +2
    /src/jalview/io/BackupFiles.java
Thursday 06 Aug
9:49 am

Mungo Carstairs

JAL-3490 match count independent of contiguous matches count

Options
    • -4
    • +1
    /src/jalview/analysis/Finder.java
    • -1
    • +1
    /src/jalview/appletgui/AlignmentPanel.java
    • -2
    • +2
    /src/jalview/appletgui/Finder.java
    • -2
    • +22
    /src/jalview/datamodel/SearchResults.java
    • -2
    • +15
    /src/jalview/datamodel/SearchResultsI.java
    • -2
    • +2
    /src/jalview/gui/Finder.java
    • -2
    • +3
    /src/jalview/gui/SeqPanel.java
    • -34
    • +40
    /test/jalview/analysis/FinderTest.java
    • -3
    • +3
    /test/jalview/datamodel/SearchResultsTest.java
9:49 am

Mungo Carstairs

JAL-3490 match count independent of contiguous matches count

Options
    • -4
    • +1
    /src/jalview/analysis/Finder.java
    • -1
    • +1
    /src/jalview/appletgui/AlignmentPanel.java
    • -2
    • +2
    /src/jalview/appletgui/Finder.java
    • -2
    • +22
    /src/jalview/datamodel/SearchResults.java
    • -2
    • +15
    /src/jalview/datamodel/SearchResultsI.java
    • -2
    • +2
    /src/jalview/gui/Finder.java
    • -2
    • +3
    /src/jalview/gui/SeqPanel.java
    • -34
    • +40
    /test/jalview/analysis/FinderTest.java
    • -3
    • +3
    /test/jalview/datamodel/SearchResultsTest.java
Wednesday 05 Aug
10:57 pm

Ben Soares

JAL-3691 Changed .toUppoerCase().startsWith(...) to .regionMatches(true,...) as upper-cased 'i' in Turkish is not 'I'.

Options
    • -4
    • +5
    /src/jalview/io/ScoreMatrixFile.java
5:41 pm

Jim Procter

JAL-3628 init log after loading testProps for each backupfile test

Options
    • -0
    • +1
    /test/jalview/io/BackupFilesTest.java
5:41 pm

Jim Procter

JAL-3628 init log after loading testProps for each backupfile test

Options
    • -0
    • +1
    /test/jalview/io/BackupFilesTest.java
5:29 pm

Jim Procter

Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch

Options
5:01 pm

Mungo Carstairs

JAL-3692 unit test updated for ?gzip download endpoint URL

Options
    • -2
    • +2
    /test/jalview/ws/ebi/EBIFetchClientTest.java
5:01 pm

Mungo Carstairs

JAL-3692 unit test updated for ?gzip download endpoint URL

Options
    • -2
    • +2
    /test/jalview/ws/ebi/EBIFetchClientTest.java
4:53 pm

Mungo Carstairs

JAL-3692 parse multiline feature qualifiers and escaped quotes

Options
    • -32
    • +90
    /src/jalview/io/EmblFlatFile.java
    • -2
    • +8
    /src/jalview/ws/dbsources/EmblFlatfileSource.java
    • -3
    • +2
    /src/jalview/ws/ebi/EBIFetchClient.java
    • -2
    • +15
    /test/jalview/io/EmblFlatFileTest.java
4:53 pm

Mungo Carstairs

JAL-3692 parse multiline feature qualifiers and escaped quotes

Options
    • -32
    • +90
    /src/jalview/io/EmblFlatFile.java
    • -2
    • +8
    /src/jalview/ws/dbsources/EmblFlatfileSource.java
    • -3
    • +2
    /src/jalview/ws/ebi/EBIFetchClient.java
    • -2
    • +15
    /test/jalview/io/EmblFlatFileTest.java
4:41 pm

Jim Procter

JAL-3675 release notes for JAL-3477, JAL-3667, JAL-3541, JAL-3685, JAL-3676, JAL-3677 and bumped release date for 2.11.1.1 to next Tuesday(ish)

Options
    • -5
    • +44
    /help/help/html/releases.html
4:10 pm

Jim Procter

4:09 pm

Jim Procter

4:09 pm

Jim Procter

doesn't matter for 2.11.1.1 but should be dropped for 2.11.2 unless it really is needed.

doesn't matter for 2.11.1.1 but should be dropped for 2.11.2 unless it really is needed.

4:08 pm

Jim Procter

Ben Soares - I don't think you need this. The logger provides a overload to pass exceptions which will give the full stack trace - e.g. catch (Exception ex) { Cache.log.debug("ignored raised except...

Ben Soares - I don't think you need this. The logger provides a overload to pass exceptions which will give the full stack trace - e.g. catch (Exception ex) { Cache.log.debug("ignored raised exception during blah",ex); }

3:58 pm

Jim Procter

3:57 pm

Jim Procter

JAL-3628 Cache.getStackTraceAsString
JAL-3628 Cache.getStackTraceAsString
3:47 pm

Jim Procter

Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

Options
    • -11
    • +16
    /resources/lang/Messages.properties
    • -0
    • +5
    /resources/lang/Messages_es.properties
    • -92
    • +109
    /src/jalview/bin/Jalview.java
3:36 pm

Jim Procter

2:27 pm

Mungo Carstairs

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