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  1. Jalview
  2. JAL-2474

Impact analysis: migration to SequenceFeatures store

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    Details

    • Type: Task
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.10.3
    • Component/s: Datamodel
    • Labels:
      None

      Description

      This issue is to capture the impact of changing Sequence.sequenceFeatures from an unordered array to a structured data store of
        SequenceFeatures // all features for one sequence
            FeatureStore // all features for one sequence and type
                // with internal structure including NCList for any nested features

      Approach:
      - inspect all calls to Sequence.getSequenceFeatures() and setSequenceFeatures() in Jalview
      - look for optimisation opportunities (get features by type and/or range)
      - identify any further impact on / methods wanted on SequenceFeatures
      - identify regression testing required if migration proceeds

        Attachments

          Issue Links

          blocks

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2480 Encapsulate performant access to sequence features

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

          Epic - Created by Jira Software - do not edit or delete. Issue type for a big user story that needs to be broken down. JAL-2446 Add NCList data structure to Jalview

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. JAL-2444 Define requirements for efficient sequence feature datastore

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. JAL-2505 Make 'key' members of SequenceFeature final

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2490 Performant lookup of features at position

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2492 Performant lookup of non-positional features

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2525 Performant lookup of features by Ontology term

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated:
                Resolved: