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Clarification on SequenceAnnotation.getIntervals() order



  • Official comment
    Tom Edwards

    Hi Pam,

    The order in which you add the intervals within the annotation is the order in which they will be 'processed' by our translation system. In your example you have intervals like this:

    new SequenceAnnotationInterval(11, 20, Direction.rightToLeft),
    new SequenceAnnotationInterval(31, 40, Direction.rightToLeft)

    The way this will be translated is that the interval #1 will be looked at first and because it's direction is right-to-left, the translation will start at point 20 and move backwards to point 11. Then the translation will continue into interval #2, and again, because it's direction is right-to-left, it will start from point 40 and translate to point 31.

    Something to be aware of is that right-to-left intervals are considered to be on the reverse strand (so they will use the reverse-complement nucleotides).

    Hope that answers your question,

  • Pamela Russell

    It does answer my question, thank you!


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