jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-2758 flag and tests for omitting uniprot accession prefix from sequence names

    • -9
    • +21
    /src/jalview/ws/dbsources/Uniprot.java
    • -1
    • +4
    /test/jalview/ws/dbsources/UniprotTest.java
JAL-2674 Last moves to iterators

    • -189
    • +96
    /src/jalview/datamodel/HiddenColumns.java
JAL-2647 stashing

    • -86
    • +216
    /src/jalview/datamodel/HiddenColumns.java
JAL-2753 add new jar to lib folder!

    • binary
    /lib/htsjdk-2.12.0.jar
JAL-2753 update to htsjdk 2.12.0 (requires Java 8)

JAL-2754 update to Java 1.8

JAL-2754 update to Java 1.8

JAL-2754 update to Java 1.8

JAL-2738 unit test for mapping failure case

JAL-2757 reset textbox after a non HTTP 200 response

JAL-2674 Removed a stray Vector

    • -3
    • +2
    /src/jalview/datamodel/HiddenColumns.java
JAL-2738 update spikes/mungo

    • -23
    • +61
    /src/jalview/analysis/AlignmentUtils.java
    • -0
    • +118
    /test/jalview/util/MapListTest.java
    • -0
    • +26
    /test/jalview/util/MathUtilsTest.java
JAL-2674 Rationalising iterators and retesting

    • -241
    • +263
    /src/jalview/datamodel/HiddenColumns.java
JAL-2738 warn (in console) when non chromosomal coordinates on sequence

JAL-2738 helper method for convolving mappings

    • -0
    • +22
    /src/jalview/util/MathUtils.java
    • -0
    • +26
    /test/jalview/util/MathUtilsTest.java
JAL-2755 transfer chromosomal reference from transcript to CDS

    • -23
    • +61
    /src/jalview/analysis/AlignmentUtils.java
JAL-2738 method to compound / traverse / convolve two mappings

    • -0
    • +118
    /test/jalview/util/MapListTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer

Blank interfaces added

    • -0
    • +46
    /src/jalview/analysis/TreeCalculator.java
    • -11
    • +14
    /src/jalview/gui/CalculationChooser.java
    • -0
    • +44
    /src/jalview/gui/TreeParams.java
JAL-2744 add score to feature details report, description to menu item

JAL-2674 Adjustments to hideColumns

    • -51
    • +56
    /src/jalview/datamodel/HiddenColumns.java
Merge branch 'features/JAL-1793VCF' into spikes/mungo

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/gui/PopupMenu.java

src/jalview/io/vcf/VCFLoader.java

JAL-2738 fix bug of premature exit from adding attributes

JAL-2523 start of refactoring...

JAL-2674 more adjustments to locateVisibleBoundsOfSequence

    • -33
    • +29
    /src/jalview/datamodel/HiddenColumns.java
    • -1
    • +1
    /src/jalview/renderer/ScaleRenderer.java
JAL-2674 Simplify locateVisibleBoundsOfSequence

Take advantage of sequence cursor changes where possible

    • -33
    • +43
    /src/jalview/datamodel/HiddenColumns.java
    • -6
    • +12
    /src/jalview/renderer/ScaleRenderer.java
JAL-2738 match consequence "Allele" to VCF allele; add non-SNP variants on nucleotide

    • -4
    • +15
    /src/jalview/analysis/AlignmentUtils.java
    • -146
    • +129
    /src/jalview/io/vcf/VCFLoader.java
JAL-2744 handle null features list

    • -9
    • +4
    /src/jalview/datamodel/HiddenColumns.java
JAL-2647 unit test