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  1. OMG Issue

BSA — SeqRegionInvalid not just for wrong StrandTypes

  • Key: BSA-50
  • Legacy Issue Number: 3961
  • Status: closed  
  • Source: ( Philip Lijnzaad)
  • Summary:

    Many methods have an Interval as an input parameter (directly, or indirectly
    as part of a SeqAnnotation)

    Since Interval can-be-a [Composite]SeqRegion, it would seem logical that all
    these methods can raise SeqRegionInvalid as well.

    Currently, SeqRegionInvalid can only be raised if the StrandType isn't
    appropriate; we think that it's natural to also raise it for wrong
    CompositeSeqRegion (e.g., when the CompositeSeqRegion has internal overlaps
    in cases wher this does not make sense).

    So the issue is 1) allow raising SeqRegionInvalid for reasons other than
    wrong strandtype and 2) add this exception to the relevant methods, which


    • add_annotation
    • seq_interval
    • reverse_complement_interval


    • get_seq_region


    • get_row_column_interval
    • get_row_interval


    • create_seq_annotation
      (this one also needs SeqRegionOutOfBounds)
  • Reported: BSA 1.0b1 — Tue, 17 Oct 2000 04:00 GMT
  • Disposition: Resolved — BSA 1.0
  • Disposition Summary:

    Accepted. The text changes were pervasive, but minor.

  • Updated: Fri, 6 Mar 2015 20:57 GMT