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  1. Jalview
  2. JAL-4435

Label sequence groups and shade tree internal nodes with diversity information

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.11.4.0
    • Fix Version/s: 2.11.5.0
    • Component/s: annotation, trees
    • Labels:
      None
    • Sprint:
      2.11.5.0 alpha

      Description

      Work on JAL-4386 demonstrated creating multiple nodes for a sequence, one for each secondary structure annotation track, is useful when exploring the differences between different sources of truth for secondary structure (ie experiment, AlphaFold, SWISS-MODEL, etc) across a family of proteins.

      Jalview's tree viewer and the sequence groups it creates could be enhanced to report summaries of those sources of truth - e.g. one branch only contains alphafold predictions, another only contains PDB and SWISS-MODEL predictions.

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          Issue Links

          depends on

          New Feature - A new feature of the product, which has yet to be developed. JAL-3987 Consensus secondary structure annotation rows for sequences with multiple sources of structural data

          • Blocker - Blocks development and/or testing work, production could not run.
          • Closed
          related with

          Improvement - An improvement or enhancement to an existing feature or task. JAL-628 Colour By Chain assigns distinct colours across multiple structures and chains

          • Blocker - Blocks development and/or testing work, production could not run.
          • Open
          mentioned on

          GitLab Commit - JAL-4386 JAL-4435 TODO and refactored TreeViewer constructor with added alignmentannotation[]

          GitLab Commit - JAL-4435 Added coloured dashed lines for secondary structure providers.

          GitLab Commit - JAL-4435 Added Show Secondary Structure Providers menu in tree panel

          GitLab Commit - JAL-4435 Added SS provider list in tree panel

          GitLab Commit - JAL-4435 Added ss provider toggle buttons

          GitLab Commit - JAL-4435 Append numbers to group names if there is a naming conflict

          GitLab Commit - JAL-4435 Cache a branch label, re-set ancestor cached labels when name changes

          GitLab Commit - JAL-4435 Changes to ColorUtils and StringUtils (MD5 is a bit rubbish)

          GitLab Commit - JAL-4435 Colour correction for provider toggle button

          GitLab Commit - JAL-4435 Correction in map annotation rows to tree nodes

          GitLab Commit - JAL-4435 Corrections on coloured line visualisation

          GitLab Commit - JAL-4435 Corrections on coloured line visualisation

          GitLab Commit - JAL-4435 Documentation for label tree internal nodes with diversity

          GitLab Commit - JAL-4435 Map annotation row to tree node

          GitLab Commit - JAL-4435 Menu option and colouring for sec struct providers

          GitLab Commit - JAL-4435 Reformatting tree node labels and tree sub group names

          GitLab Commit - JAL-4435 Removing secondary structure providers list

          GitLab Commit - JAL-4435 Some fixes for the tree visualisation

          GitLab Commit - JAL-4435 Use the colours

          GitLab Commit - JAL-4435 WIP - to squash

          GitLab Commit - JAL-4531 JAL-4435 fix broken doc links

          GitLab Commit - JAL-4531 release notes for...

          GitLab Commit - JAL-4531 updated docs and release notes - new image for JAL-4435

          GitLab Commit - Merge branch 'feature/JAL-4435_JAL-4509_JAL-4542_JAL-4518_documentation' into...

          GitLab Merge request - JAL-4435 Documentation for label tree internal nodes with diversity

            Activity

              People

              Assignee:
              reniacorreya Renia Correya
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: