Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-2403

refactor ScoreMatrix.computePairwiseScores(String[])

    XMLWordPrintable

    Details

      Description

      The PCA calculation uses ScoreMatrix.computePairwiseScores(String[]), but the tree uses the ScoreModelI for computing matrices, which works on an alignment view rather than the stringified visible region.

      As a further refinement to JAL-2379, PCA should use the same interface (which allows input data recovery) and the ScoreModelI interface updated to provide a MatrixI instance.

        Attachments

          Issue Links

          blocks

          New Feature - A new feature of the product, which has yet to be developed. JAL-1483 feature based tree/pca calculation

          • Critical - Crashes, loss of data, severe memory leak.
          • Closed
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2424 AlignmentView.getVisibleContigs() out by 1

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-838 extend jalview's PID routine to allow different types of PIDs to be calculated

          • Major - Major loss of function.
          • In Progress

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3205 Use symmetry to speed up similarity calculations

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

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
              Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: