jalview

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JAL-3700 mapped sequence group includes short (or all gapped) sequences

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

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    /test/jalview/io/EmblFlatFileTest.java
JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1.3 - 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 2.11.1.3

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

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3763 Javadoc, check for null, additional tests

JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

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    /src/jalview/datamodel/SearchResults.java
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    /test/jalview/datamodel/AlignedCodonFrameTest.java
JAL-3700 JAL-3763 create datasets for test sequences

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    /test/jalview/util/MappingUtilsTest.java
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

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3751 only merge strictly contiguous ranges of mappings

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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
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

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    /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

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

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    /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

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

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    /test/jalview/datamodel/SeqCigarTest.java
JAL-3700 additions and corrections to unit tests (trivial) Conflicts: test/jalview/util/MappingUtilsTest.java

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    /test/jalview/util/MappingUtilsTest.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

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    /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

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    /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