jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
Merge branch 'feature/JAL-2745ebiHttps' into develop

Revert "JAL-2745 update SIFTS FTP URL to HTTPS" EBI ftp confirmed to remain accesible via HTTP This reverts commit c7f663521cb82b94d832015010fa488d3dc7ff58.

    • -1
    • +1
    /src/jalview/ws/sifts/SiftsClient.java
Revert "JAL-2745 update SIFTS FTP URL to HTTPS" EBI ftp confirmed to remain accesible via HTTP This reverts commit c7f663521cb82b94d832015010fa488d3dc7ff58.

    • -1
    • +1
    /src/jalview/ws/sifts/SiftsClient.java
JAL=2674 Removed getHiddenColumnsCopy

    • -1
    • +1
    /src/jalview/appletgui/ScalePanel.java
    • -1
    • +1
    /src/jalview/datamodel/CigarArray.java
    • -30
    • +140
    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 reverted attempt at visible regions iterator

    • -8
    • +14
    /src/jalview/appletgui/SeqCanvas.java
    • -126
    • +0
    /src/jalview/datamodel/HiddenColumns.java
Merge branch 'feature/JAL-2745ebiHttps' into develop

JAL-2745 update default EBI-eye search URL to HTTPS

JAL-2745 update default EBI-eye search URL to HTTPS

JAL-2745 update SIFTS FTP URL to HTTPS

    • -1
    • +1
    /src/jalview/ws/sifts/SiftsClient.java
JAL-2745 update SIFTS FTP URL to HTTPS

    • -1
    • +1
    /src/jalview/ws/sifts/SiftsClient.java
Merge branch 'feature/JAL-2745ebiHttps' into develop

JAL-2745 stderr rather than stdout for unexpected HTTP response

    • -1
    • +1
    /src/jalview/ws/ebi/EBIFetchClient.java
JAL-2745 stderr rather than stdout for unexpected HTTP response

    • -1
    • +1
    /src/jalview/ws/ebi/EBIFetchClient.java
JAL-2745 update obsolete DAS URL to https

JAL-2745 update www.ebi.ac.uk to https

    • -3
    • +11
    /src/jalview/ws/ebi/EBIFetchClient.java
JAL-2745 update www.ebi.ac.uk to https

    • -3
    • +11
    /src/jalview/ws/ebi/EBIFetchClient.java
JAL-2738 separate thread to load VCF; update FeatureSettings when done

    • -10
    • +41
    /src/jalview/io/vcf/VCFLoader.java
Merge branch 'develop' into features/JAL-1793VCF

JAL-2647 more iterators

    • -70
    • +61
    /src/jalview/appletgui/SeqCanvas.java
    • -24
    • +136
    /src/jalview/datamodel/HiddenColumns.java
    • -4
    • +5
    /src/jalview/gui/VamsasApplication.java
    • -7
    • +27
    /test/jalview/analysis/DnaTest.java
JAL-2036 set menus after fully loading AlignFrame

JAL-1796 GeneLociI as distinguished DBRefEntry

    • -1
    • +24
    /src/jalview/datamodel/DBRefEntry.java
    • -46
    • +0
    /src/jalview/datamodel/GeneLoci.java
    • -0
    • +38
    /src/jalview/datamodel/GeneLociI.java
    • -39
    • +44
    /src/jalview/datamodel/Sequence.java
    • -15
    • +48
    /src/jalview/ext/ensembl/EnsemblGene.java
    • -12
    • +24
    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-2744 simple Feature Details report from Popup menu

JAL-2744 refactor PopupMenu constructor to enable adding feature details

    • -13
    • +43
    /test/jalview/gui/PopupMenuTest.java
proof of concept for passing tree data to archaeopteryx

    • -0
    • +20
    /.settings/org.eclipse.jdt.core.prefs
JAL-2674 Removing most calls to getHiddenColumnsCopy

    • -10
    • +27
    /src/jalview/datamodel/HiddenColumns.java
    • -18
    • +17
    /test/jalview/gui/AlignFrameTest.java
    • -14
    • +15
    /test/jalview/util/MappingUtilsTest.java
JAL-2674 tidied up CigarArray

    • -11
    • +0
    /src/jalview/datamodel/CigarArray.java
Merge remote-tracking branch 'origin/bug/JAL-2742' into feature/JAL-2674take2

JAL-2742 uncomment test

JAL-2674 uncomment test

Merge remote-tracking branch 'origin/bug/JAL-2742' into feature/JAL-2674take2

Conflicts:

src/jalview/datamodel/CigarArray.java

    • -18
    • +12
    /src/jalview/datamodel/CigarArray.java