Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-4257

allow adjustment of gap opening and extension for built in nw alignment

    XMLWordPrintable

    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.11.3.0
    • Fix Version/s: 2.11.4.0
    • Component/s: analysis, gui, Scriptable API
    • Labels:
      None

      Description

      JAL-4159 highlighted the need to have adjustable gap opening and extension parameters when calculating N&W alignments. The defaults should always remain 'Conservative' (12 & 2), but the Java class api needs to allow alternative parameters to be provided.

      Suggest enhancements to GUI are based on the new analysis/calculation api introduced in Jalview 2.12.

        Attachments

          Issue Links

          blocks

          New Feature - A new feature of the product, which has yet to be developed. JAL-4159 PaSiMap inclusion

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-4466 allow pairwise alignment gap parameters to be adjusted

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

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
              Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: