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  1. Jalview
  2. JAL-3779

Annotation file: PROPERTIES apply only to the first SEQUENCE_GROUP defined



    • Type: Bug
    • Status: Being tested
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s:
    • Fix Version/s: 2.11.2
    • Component/s: annotation
    • Labels:
    • Environment:
      MAC OS Catalina
    • Urgency:


      The annotation file of JalView enables to define multiple sequence regions in multiple sequences as a SEQUENCE_GROUP with one name, e.g. a group:
      SEQUENCE_GROUP feature1 230 403 -1 sequence1
      SEQUENCE_GROUP feature1 235 450 -1 sequence2
      SEQUENCE_GROUP feature2 901 955 -1 sequence1

      This property of JalView annotation files is nice as it allows to annotate multiple sequence groups across multiple sequences with unique position in the alignment but same name (I use this feature to inspect the position of annotated genes in alignments of whole mitochondrial genomes).

      However, when one tries to set the properties of such sequence groups (which would help substantially with visual inspection of the annotated alignments) only the first sequence group definition line for each sequence group name is affected. In the example above, annotation file with additional following line:
      PROPERTIES feature1 outlineColour=red
      will set the box outline color for feature1 in sequence1 but not influence feature1 in sequence2.

      I believe this is a bug as JalView allows definition of same-name sequence groups across different sequences but does not allow to set the properties for these groups - only for the first defined feature belonging to each group.

      In case this is not considered by the JalView authors as a bug (perhaps because sequence groups with the same name were not intended to be defined on multiple lines of JalView annotation file - this is not clear to me from the documentation for alignment annotation files) I'd be happy to learn if there is other intended way how to define same-name features with unique locations across multiple sequences and how to assign these features with properties.

      Thanks for consideration and for building this really versatile visualization tool!




            soares Ben Soares
            alesbucek Ales Bucek
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