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  1. Jalview
  2. JAL-1463

efficient encoding of programmatically generated alignment and sequence annotation rows

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: 2.11.3
    • Fix Version/s: 3.0, 2.12.0
    • Component/s: Datamodel
    • Labels:

      Description

      The Jalview 2 Alignment Annotation row includes a free-text string shown as a tooltip. This is used by a number of the alignment and sequence analysis routines to report summary statistics such as amino acid profiles.

      Many of these strings could be dynamically generated at the point of need based on more compact representations. For arbitrary description text, compression should be employed to store them efficiently.

        Attachments

          Issue Links

          blocks

          New Feature - A new feature of the product, which has yet to be developed. JAL-1462 support for complex html/interactive tooltips

          • Major - Major loss of function.
          • In Progress

          Improvement - An improvement or enhancement to an existing feature or task. JAL-711 Consensus line should use IUB codes

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3455 AlignAnnotations.areLabelsSecondaryStructure woefully inefficient

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2646 Show tooltip for T-Coffee reliability scores

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-736 show conserved physicochemical properties in conservation row

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

          Story - Created by Jira Software - do not edit or delete. Issue type for a user story. JAL-2402 merging group and view specific shader settings with the colour by annotation dialog

          • Major - Major loss of function.
          • Open

          New Feature - A new feature of the product, which has yet to be developed. JAL-3623 Combined row-wise and positional per-sequence annotation shading

          • Major - Major loss of function.
          • In Progress

          New Feature - A new feature of the product, which has yet to be developed. JAL-1553 Select columns by annotation row dialog box

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-4381 Dynamic value colouring of annotations, e.g. linegraph, can be misleading

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

          New Feature - A new feature of the product, which has yet to be developed. JAL-1681 Codon consensus on protein view linked to cDNA alignment

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1680 more efficient group conservation calculation

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2651 Store calculation results for autoannotation rows in Jalview XML objects

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1373 sensible precision when calculating consensus percentages

          • Major - Major loss of function.
          • Resolved

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              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: