jalview

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Wednesday 26 Jan
7:36 pm

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

Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/util/MapList.java

test/jalview/util/MapListTest.java

test/jalview/util/MappingUtilsTest.java

Options
    • -55
    • +41
    /src/jalview/analysis/AlignmentUtils.java
    • -2
    • +4
    /src/jalview/datamodel/SearchResults.java
    • -1
    • +6
    /src/jalview/gui/PopupMenu.java
    • -53
    • +53
    /src/jalview/util/MappingUtils.java
    • -7
    • +7
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
    • -3
    • +4
    /test/jalview/util/MapListTest.java
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    • +114
    /test/jalview/util/MappingUtilsTest.java
6:34 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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6:32 pm

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

Merge branch 'releases/Release_2_11_1_Branch'

Options
Wednesday 19 Jan
1:45 pm

Mateusz Warowny

JAL-3878 Move listeners list from the WebServiceDiscoverer interface.

Listeners list defined in the interface was globally shared

among all discoverer instances. Listeners should be kept by

the discoverer instance instead.

Options
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    • +62
    /src/jalview/ws2/OperationsChangeListenerList.java
    • -29
    • +2
    /src/jalview/ws2/WebServiceDiscovererI.java
    • -0
    • +22
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
Tuesday 18 Jan
12:24 pm

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

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)

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    • -7
    • +9
    /help/help/html/releases.html
11:44 am

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

JAL-3940 errant heading in release notes..

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    • +11
    /help/help/html/releases.html
8:14 am

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

Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files' into releases/Release_2_11_1_Branch

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Monday 17 Jan
12:50 pm

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

JAL-3703 patch Windows save file test for 2.11.1 codebase

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    • +4
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
12:39 pm

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

Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files' into releases/Release_2_11_1_Branch

Options
12:38 pm

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

JAL-3940 fix issues in release notes

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    • -1
    • +1
    /help/help/html/releases.html
12:36 pm

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

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release

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    • +18
    /help/help/html/releases.html
12:24 pm

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

JAL-3940 bump version and update release notes - release set for Tuesday 18th January 2022

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    /RELEASE
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    /help/help/html/releases.html
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    • +5
    /help/help/html/whatsNew.html
12:20 pm

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

JAL-3940 update release notes for JAL-3702,JAL-3935 in 2.11.1.7 release

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    • +10
    /help/help/html/releases.html
11:57 am

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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11:54 am

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

JAL-3746 possible release date 1st Feb 2022

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    • +10
    /help/help/html/releases.html
11:54 am

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

JAL-3746 Release notes for patch JAL-3702 JAL-3915

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    • +6
    /help/help/html/releases.html
11:45 am

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

Merge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_fails' into develop

Options
Wednesday 12 Jan
12:32 pm

Ben Soares

JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

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    • -1
    • +2
    /test/jalview/io/BackupFilesTest.java
    • -0
    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
12:32 pm

Ben Soares

JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

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    • -1
    • +7
    /test/jalview/io/BackupFilesTest.java
    • -0
    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
Tuesday 11 Jan
8:13 pm

Ben Soares

JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

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    • -2
    • +19
    /src/jalview/io/AlignFile.java
    • -3
    • +8
    /src/jalview/io/FastaFile.java
    • -1
    • +3
    /src/jalview/io/FeaturesFile.java
8:13 pm

Ben Soares

JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

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    • -2
    • +19
    /src/jalview/io/AlignFile.java
    • -3
    • +8
    /src/jalview/io/FastaFile.java
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    • +3
    /src/jalview/io/FeaturesFile.java
    • -2
    • +2
    /src/jalview/io/FileParse.java
4:04 pm

Ben Soares

close filehandles straight after parse, without setting an error

Conflicts:

src/jalview/project/Jalview2XML.java

(locale aware PDBID string compare)

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    • -7
    • +8
    /src/jalview/io/AlignFile.java
    • -3
    • +5
    /src/jalview/project/Jalview2XML.java
4:04 pm

Ben Soares

close filehandles straight after parse, without setting an error

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    • -7
    • +8
    /src/jalview/io/AlignFile.java
    • -4
    • +4
    /src/jalview/project/Jalview2XML.java
2:45 pm

Ben Soares

JAL-3937 update releases.html

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    • +16
    /help/help/html/releases.html
Monday 10 Jan
8:58 pm

Ben Soares

JAL-3937 enable AIA download of intermediate certificates when needed

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    • -0
    • +3
    /src/jalview/bin/Jalview.java
8:31 pm

Ben Soares

JAL-3937 enable AIA download of intermediate certificates when needed

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    • +3
    /src/jalview/bin/Jalview.java
Thursday 06 Jan
12:29 pm

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

JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSource to EMBLFlatFile parser

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    /src/jalview/io/EMBLLikeFlatFile.java
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    /test/jalview/io/EmblFlatFileTest.java
10:58 am

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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9:58 am

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

JAL-3746 update release history for 2.11.1.5 and 2.11.1.6 patch releases

Options
    • -0
    • +46
    /help/help/html/releases.html
9:56 am

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

JAL-3934 update whats new

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    /help/help/html/whatsNew.html