JAL-2617: stop codons shown in CDS/Protein view from Ensembl locus...

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CR-JAL-113 1

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    Participant Role Time Spent Comments Latest Comment
    Author 1m    
    Reviewer - Complete 9m 1 possible threat if caller passes n+1 sequence. probably u...
    Total   10m 1  
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    Objectives

    1. Import P30419 via Ensembl
    2. Show CDS/Protein via Calculate->Show cross-references
    3. Scroll to column 90 in protein alignment - note that there are an extra 3 columns in the CDS compared to the protein - corresponding to the stop codon in CDS|ENST00000585561

    When stop codons are visible in the CDS window, mouseovers and selections behave in unexpected ways (i.e. scrolling of CDS view to show codons at edge of protein MSA). Columns containing stop codons are also not selected from protein MSA column selections since they have no mapping.

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    /src/jalview/analysis/AlignmentUtils.java Changed 1
    /src/jalview/util/MappingUtils.java Changed
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    /test/.../analysis/AlignmentUtilsTests.java Changed
    /test/jalview/util/MappingUtilsTest.java Changed
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