jalview

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 possible release date 1st Feb 2022

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

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

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

    • -0
    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

    • -0
    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

close filehandles straight after parse, without setting an error

Conflicts:

src/jalview/project/Jalview2XML.java

(locale aware PDBID string compare)

close filehandles straight after parse, without setting an error

JAL-3937 update releases.html

JAL-3937 enable AIA download of intermediate certificates when needed

JAL-3937 enable AIA download of intermediate certificates when needed

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

    • -7
    • +9
    /test/jalview/io/EmblFlatFileTest.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

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

JAL-3934 update whats new

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

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

JAL-3934 trigger patch release for log4j version bump

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

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

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

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

JAL-3934 updated log4j from 2.16.0 to 2.17.0

    • binary
    /j11lib/log4j-1.2-api-2.17.0.jar
    • binary
    /j11lib/log4j-api-2.17.0.jar
    • binary
    /j11lib/log4j-core-2.17.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.17.0.jar
    • binary
    /j8lib/log4j-1.2-api-2.17.0.jar
    • binary
    /j8lib/log4j-api-2.17.0.jar
    • binary
    /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
JAL-3934 updated log4j from 2.16.0 to 2.17.0

    • binary
    /j11lib/log4j-1.2-api-2.17.0.jar
    • binary
    /j11lib/log4j-api-2.17.0.jar
    • binary
    /j11lib/log4j-core-2.17.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.17.0.jar
    • binary
    /j8lib/log4j-1.2-api-2.17.0.jar
    • binary
    /j8lib/log4j-api-2.17.0.jar
    • binary
    /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
Merge branch 'releases/Release_2_11_1_Branch'

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

JAL-3753 avoid appending unreplaced html content in help pages