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  1. Jalview
  2. JAL-1965

case insensitive and word based ID matching for tree, annotation and feature file import

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.10.0, 2.11.0
    • Fix Version/s: None
    • Component/s: analysis, file format issue
    • Labels:
      None

      Description

      For 2.9 and before, the jalview.analysis.SequenceIdMatcher routine required the following:

      * one ID starts with the other ID string
      * if one ID is longer, the next character is non-alphanumeric (e.g. a pipe symbol)

      This doesn't quite work for IDs like PDB|1QIP|A and 1QIP|A. Furthermore, if the ID is lower case, then the matcher will also fail. Instead, when matching IDs Jalview should allow case insensitive matching and whole word, ie _match_ matches 'match', '_match' and 'match_', but not '_match2_'.

      Prompted by thread on Jalview-discuss:
      http://www.jalview.org/pipermail/jalview-discuss/2015-November/001251.html




        Attachments

          Issue Links

          depends on

          Bug - A problem which impairs or prevents the functions of the product. JAL-1537 relaxed id matches do not associate with all occurences

          • Blocker - Blocks development and/or testing work, production could not run.
          • In Progress
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2038 Drag-and-drop to associate pdb files with sequences of same name is broken

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-753 allow sequences with partial ID string matches to be annotated from GFF/jalview features files

          • Major - Major loss of function.
          • Resolved

          Bug - A problem which impairs or prevents the functions of the product. JAL-872 structure associated with alignment fails for alignments of repeats

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1427 Relaxed reference sequence ID matching when loading annotation files

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

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: