jalview

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

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

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
    /test/jalview/gui/SplitFrameTest.java
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
    /examples/testdata/MN908947.jvp
JAL-3748 don’t trash start/end on SequenceI reconstructed from a SeqCigar via SeqsetUtils.SeqCharacterUnhash

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

    • -0
    • +23
    /test/jalview/datamodel/SeqCigarTest.java
JAL-3748 additional asserts to verify start/end after reconstructing sequence from seqCigar

    • -3
    • +11
    /test/jalview/datamodel/SeqCigarTest.java
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
    /src/jalview/ws/jws2/MsaWSThread.java
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
    /src/jalview/analysis/AlignmentUtils.java
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

Merge branch 'failingTest/JAL-3748_reconstructCDSafterProteinMSA' into cherry-pick/JAL-3700mapSequenceSelection

JAL-3748 store an AlignmentView for the complement within an viewport’s AlignView so it can be recovered after a web service operation

    • -0
    • +31
    /src/jalview/datamodel/AlignmentView.java
    • -0
    • +185
    /test/jalview/gui/SplitFrameTest.java
JAL-3675 logged JAL-3748 as known defect

JAL-3765 JAL-3718 release notes

changeset discussion

  1. Jim Procter: not related to JAL-3765 ! Actually related to JAL-3675!
Merge branch 'patch/JAL-3718_fixed_getdown_patched_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

JAL-3718 Fixed getdown auto-update. This commit Getdown jars and version files.

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3675 typo in release notes :(

JAL-3675 update release date and release notes for JAL-3732

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

JAL-3675 update release date and release notes for JAL-3280

Merge branch 'improvement/JAL-3280_Migrate_the_VersionChecker_service_to_build_properties' into releases/Release_2_11_1_Branch

JAL-3675 whats new, logging and release notes tidying for 2.11.1.1.

JAL-3676 rework logging docs.