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  1. Jalview
  2. JAL-2526

SequenceCursor for more efficient Sequence.findPosition, findIndex

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.10.3
    • Component/s: Efficiency
    • Labels:

      Description

      Sequence.findPosition(i) locates the sequence position for a column position.
      It does this by counting non-gapped positions from char[0] to char[i-1].

      If the calling code is iterating over columns, this could be made much more efficient by 'remembering' the last column/position e.g. in an iterator.

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          depends on

          Task - A task that needs to be done. JAL-2562 Verify and fix tests, javadoc and use of SequenceI.findPosition

          • Major - Major loss of function.
          • Open
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-1034 sluggish zoom to highlight or select region with large alignments

          • Critical - Crashes, loss of data, severe memory leak.
          • Open

          Bug - A problem which impairs or prevents the functions of the product. JAL-2544 Sort by features buggy with gapped selection region

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2547 Sequence feature tooltips on gaps

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2986 Sequence.findIndex wrong when 'end' > sequence length

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2563 Status bar doesn't show positions with ambiguous amino acids

          • Trivial - Cosmetic problem like misspelt words or misaligned text.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-3296 Changing sequence start should invalidate cursor

          • Trivial - Cosmetic problem like misspelt words or misaligned text.
          • Closed

          Task - A task that needs to be done. JAL-2290 Avoid repeated calculation of unchanged sequence tooltip

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2598 Don't expose sequence character array

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated:
                Resolved: