Jim Procter

JAL-3690 for a laugh, lets enable web services!

JAL-3690 update to next patched 3.2.9 j2s c336e447

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3690 update j2s from hanson1 branch 0b8b02bb

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

    • -2
    • +8
    /test/jalview/io/vcf/VCFLoaderTest.java
Merge branch 'releases/Release_2_11_1_Branch'

JAL-3766 what’s new and release notes for 2.11.1.3

JAL-3759 fix compilation error for test

    • -1
    • +1
    /test/jalview/analysis/GroupingTest.java
JAL-3766 release notes for JAL-3759

JAL-3759 exclude hidden columns when processing column selection

    • -3
    • +18
    /src/jalview/analysis/Grouping.java
Merge branch 'documentation/JAL-3766_relnotes' into releases/Release_2_11_1_Branch

Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_11_1_Branch

JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

    • -7
    • +8
    /test/jalview/io/EmblFlatFileTest.java
JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1.3 - needs cherry-pick to 2.11.2)

Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides' into releases/Release_2_11_1_Branch

Merge branch 'portforward/JAL-3765_patch_to_2112' into develop

update test for JAL-3763 redact shared DS sequences for contiguous CDS

JAL-3768 noticed failure of test when run as part of suite via gradle - whilst patching JAL-3700 JAL-3748 JAL-3763 for 2.11.1.3

JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via alignAs if guide peptide doesn’t include C terminus.

    • -2
    • +2
    /src/jalview/analysis/AlignmentUtils.java
JAL-3766 release notes for JAL-3611 JAL-3765

Merge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_11_1_Branch

Merge branch 'bug/JAL-3765_Find_bugs_in_21112' into releases/Release_2_11_1_Branch

JAL-3766 cut new patch release

Merge branch 'releases/Release_2_11_1_Branch'

JAL-3765 fix test

    • -0
    • +13
    /test/jalview/analysis/FinderTest.java
JAL-3765 fix test

    • -10
    • +13
    /test/jalview/analysis/FinderTest.java
fix for JAL-3765

fix for JAL-3765

JAL-3765 simple test that findAll finds all matches for a pattern when it is present multiple times in a sequence

    • -0
    • +10
    /test/jalview/analysis/FinderTest.java
not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!