Jim Procter

JAL-3816 release notes for JAL-3806

Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch

JAL-3816 JAL-3814 JAL-3813 JAL-3812 JAL-3811 JAL-3818 release notes and date for 2.11.1.4 release

Merge branch 'bug/JAL-3818_jmolDeadlock' into releases/Release_2_11_1_Branch

Merge branch 'releases/Release_2_11_1_4_debianpatches' into releases/Release_2_11_1_Branch

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
JAL-3821 patch for 2.11.2 to retrieve RNA ENA records as RNA

Merge branch 'feature/JAL-3692enaEndpoint' into patch/for2.11.2/JAL-3821_ena_rna_moltype

    • -1
    • +0
    /resources/lang/Messages_es.properties
JAL-3821 rough and ready patch translates t/T to u/U when mol_type includes rna

JAL-3816 bump version number and cut release notes

JAL-3815 default /etc/jalview_properties under utils/debian

    • -0
    • +60
    /utils/debian/etc/jalview_properties
Merge branch 'task/JAL-3521_Slimmed_down_build.gradle_for_debian' into releases/Release_2_11_1_4_debianpatches

Merge branch 'releases/Release_2_11_1_4_debianpatches' into task/JAL-3521_Slimmed_down_build.gradle_for_debian

JAL-3814 don’t automatically launch the news browser when the desktop is first opened

JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging www.jalview.org/services/identifiers to get a list of URL link templates for viewing database crossreferences

    • -5
    • +0
    /src/jalview/ws/utils/UrlDownloadClient.java
JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository

JAL-3811 document SHOW_JWS2_SERVICES user preference and provide new menu option for ‘one off’ JABAWS discovery if preference is disabled.

JAL-3814 NONEWS property

JAL-3808 handle 1:1 mappings in exonerate gff2 using the ‘similarity’ feature extent to determine direction of mapping generated from alignment

    • -22
    • +138
    /src/jalview/io/gff/ExonerateHelper.java
JAL-3808 example exonerate cdna2genome and coding2genome test data and test

    • -0
    • +74
    /examples/testdata/test_cdna2genome_showquerygff.gff2
    • -0
    • +81
    /examples/testdata/test_cdna2genome_showtargetgff.gff2
    • -0
    • +76
    /examples/testdata/test_coding2genome_showquerygff.gff2
    • -0
    • +82
    /examples/testdata/test_coding2genome_showtargetgff.gff2
    • -0
    • +42
    /test/jalview/io/FeaturesFileTest.java
JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

    • -0
    • +17
    /test/jalview/datamodel/SequenceTest.java
JAL-3690 recoded AWSThread to use javax.swing.Timer (see https://github.com/BobHanson/java2script/issues/195#issuecomment-747695834 )- web service submission works, but doesn’t seem to be happening as a background task.

JAL-3690 patch out use of java.streams/spliterator not supported in java2script (yet)

JAL-3690 tweak J2S direct DB access registration for jalview, compbio and other sites

JAL-3690 direct access to slivka, compbio, jalview.org and localhost/loopback.

JAL-3690 patch out need for java.time in j2s (see https://github.com/BobHanson/java2script/issues/194 )

JAL-3690 patch out spinning animation for web service jobs

JAL-3690 disable proxy server for JalviewJS