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Monday 17 Jan
11:54 am

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

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

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    • -9
    • +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

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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
    • -1
    • +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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    • -1
    • +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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    • -0
    • +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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    • -6
    • +3
    /src/jalview/io/EMBLLikeFlatFile.java
    • -7
    • +9
    /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

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    • -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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    • -6
    • +4
    /help/help/html/whatsNew.html
9:47 am

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

Merge branch 'critical/JAL-3933_log4j_update_for_develop_branch' into develop

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9:45 am

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

Merge branch 'task/JAL-3934_update_log4j_again' into releases/Release_2_11_1_Branch

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9:42 am

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

JAL-3934 trigger patch release for log4j version bump

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    • +1
    /RELEASE
    • -0
    • +14
    /help/help/html/releases.html
Thursday 23 Dec 2021
4:49 pm

Mateusz Warowny

Merge branch 'JAL-3927_ws_preferences_dialog_fix' into alpha/JAL-3066_Jalview_212_slivka-integration

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4:48 pm

Mateusz Warowny

Merge branch 'update/JAL-3066_updated_testng' into alpha/JAL-3066_Jalview_212_slivka-integration

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4:48 pm

Mateusz Warowny

JAL-3878 Use AlignViewport interface instead of concrete implementation in AlignmentWorker

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    • -2
    • +3
    /src/jalview/ws2/operations/AlignmentWorker.java
Wednesday 22 Dec 2021
11:17 am

Ben Soares

Merge branch 'develop' into critical/JAL-3933_log4j_update_for_develop_branch

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11:12 am

Ben Soares

JAL-3934 updated log4j from 2.16.0 to 2.17.0

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    • binary
    /j11lib/log4j-1.2-api-2.16.0.jar
    • binary
    /j11lib/log4j-1.2-api-2.17.0.jar
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    /j11lib/log4j-api-2.16.0.jar
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    /j11lib/log4j-api-2.17.0.jar
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    /j11lib/log4j-core-2.16.0.jar
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    /j11lib/log4j-core-2.17.0.jar
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    /j11lib/log4j-slf4j18-impl-2.16.0.jar
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    /j11lib/log4j-slf4j18-impl-2.17.0.jar
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    /j8lib/log4j-1.2-api-2.16.0.jar
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    /j8lib/log4j-1.2-api-2.17.0.jar
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    /j8lib/log4j-api-2.16.0.jar
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    /j8lib/log4j-api-2.17.0.jar
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    /j8lib/log4j-core-2.16.0.jar
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    /j8lib/log4j-core-2.17.0.jar
    • binary
    /j8lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/log4j-slf4j18-impl-2.17.0.jar
11:12 am

Ben Soares

JAL-3934 updated log4j from 2.16.0 to 2.17.0

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    • binary
    /j11lib/log4j-1.2-api-2.16.0.jar
    • binary
    /j11lib/log4j-1.2-api-2.17.0.jar
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    /j11lib/log4j-api-2.16.0.jar
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    /j11lib/log4j-api-2.17.0.jar
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    /j11lib/log4j-core-2.16.0.jar
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    /j11lib/log4j-core-2.17.0.jar
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    /j11lib/log4j-slf4j18-impl-2.16.0.jar
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    /j11lib/log4j-slf4j18-impl-2.17.0.jar
    • binary
    /j8lib/log4j-1.2-api-2.16.0.jar
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    /j8lib/log4j-1.2-api-2.17.0.jar
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    /j8lib/log4j-api-2.16.0.jar
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    /j8lib/log4j-api-2.17.0.jar
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    /j8lib/log4j-core-2.16.0.jar
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    /j8lib/log4j-core-2.17.0.jar
    • binary
    /j8lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/log4j-slf4j18-impl-2.17.0.jar
10:32 am

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

Merge branch 'releases/Release_2_11_1_Branch'

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Monday 20 Dec 2021
2:03 pm

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

JAL-3842 remove replacement tokens in html text - not properly resolved in this release branch

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    • -5
    • +0
    /help/help/html/whatsNew.html
12:15 pm

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

JAL-3753 avoid appending unreplaced html content in help pages

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    • -1
    • +1
    /build.gradle
9:50 am

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

JAL-3842 patch what’s new text

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    • -6
    • +7
    /help/help/html/whatsNew.html
8:04 am

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

JAL-3842 release 2.11.1.5 release notes

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    • +8
    /help/help/html/releases.html
    • -17
    • +8
    /help/help/html/whatsNew.html
7:45 am

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

Merge branch 'critical/JAL-3933_log4shell_mitigation' into releases/Release_2_11_1_Branch

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