Clone Tools
  • last updated a few seconds ago
Constraints: committers
Constraints: files
Constraints: dates
JAL-3700 mapped sequence group includes short (or all gapped) sequences

    • -13
    • +17
    • -25
    • +24
JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

    • -7
    • +8
JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for - needs cherry-pick to 2.11.2)

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

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

    • -2
    • +2
JAL-3763 Javadoc, check for null, additional tests

JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

    • -2
    • +4
    • -26
    • +129
JAL-3700 JAL-3763 create datasets for test sequences

    • -4
    • +8
JAL-3763 failsafe check for null

JAL-3763 refactored getCoveringMapping for virtual feature discovery

JAL-3763 always make a new dataset sequence for CDS sequence

    • -55
    • +41
JAL-3751 only merge strictly contiguous ranges of mappings

    • -112
    • +88
    • -0
    • +7
JAL-3748 not testing for sequence’s containment in mapped range breaks CDS reconstruction but allows testAlignProteinAsDna_incompleteStartCodon to pass

JAL-3748 fix compilation error

JAL-3748 maximal test for JAL-3748 using covid19 CDS/Protein

    • -0
    • +34
JAL-3748 more tests verifying reconstruction of AlignemntView for linked CDS/Protein alignment and selected region

JAL-3748 reusable assert to trace specific issues with recovering the correct Sequence/Mapping (highlights points of failure for AlignmentUtilsTests with patch

JAL-3748 allow AlignedCodonFrame.covers to optionally only require coverage for either originating or mapped sequence.

JAL-3748 test data for SplitFrameTest

    • binary
JAL-3748 don’t trash start/end on SequenceI reconstructed from a SeqCigar via SeqsetUtils.SeqCharacterUnhash

    • -3
    • +17
JAL-3748 simple test for SeqCigar preservation of start/end and name for different ways of constructing SeqCigar and reconstructing alignment sequences

    • -0
    • +23
JAL-3748 additional asserts to verify start/end after reconstructing sequence from seqCigar

    • -3
    • +11
JAL-3700 additions and corrections to unit tests (trivial) Conflicts: test/jalview/util/MappingUtilsTest.java

    • -172
    • +306
JAL-3748 preserve sequence IDs from original alignment view when alignment returned by web service or analysis method.

JAL-3748 recover complement alignment from complement alignmentView rather than let ‘alignAs’ to do the work

    • -14
    • +18
JAL-3748 make findAlignedSequence require mapped from/to to properly contain the given CDS or protein sequence

JAL-3748 pass a list to findAlignedSequence to return mapping that relates CDS and the returned Peptide sequence to avoid searching twice

    • -2
    • +3
JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq,true) to select the protein that matches a CDS sequence

JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true) to verify mapping matches seq’s dataset sequence start/end rather than seq