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  1. Jalview
  2. JAL-753

allow sequences with partial ID string matches to be annotated from GFF/jalview features files

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    Details

    • Type: Improvement
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.7
    • Component/s: JVL-Ajax, jvlite
    • Labels:
      None

      Description

      Occasionally, sequence IDs within an alignment are formed as compound ID strings like 'uniprot|q12456|pdb|1xyz|long name'. The jalview.analysis.SequenceIdMatcher includes routines for matching a single ID against such compound strings, and it would be useful to optionally employ this matcher when importing sequence annotation.

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          blocks

          Task - A task that needs to be done. JAL-856 document new javascript functions for jalview 2.7

          • Major - Major loss of function.
          • Resolved

          Improvement - An improvement or enhancement to an existing feature or task. JAL-942 user preference to allow relaxed ID matching when loading gff and jalview sequence feature files

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

          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

          Bug - A problem which impairs or prevents the functions of the product. JAL-3195 Relaxed id resolution failing for features files

          • Major - Major loss of function.
          • In Progress

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1965 case insensitive and word based ID matching for tree, annotation and feature file import

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

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Created:
                Updated:
                Resolved: