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  1. Jalview
  2. JAL-4386

Calculate tree using secondary structure annotation

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    Details

    • Type: New Feature
    • Status: In Progress
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: 2.11.3.2, 2.11.3.3, 2.11.4.0
    • Fix Version/s: 2.11.4.0, 2.11.5.0
    • Component/s: analysis, gui
    • Labels:
      None

      Description

      This feature calculate the similarity of secondary structure for each pair of aligned protein sequences and generate tree based on the similarity calculations.

      Since there can be more than one secondary structure per sequence, secondary structure based trees should link their leaves to both the sequence in the alignment and the annotation row(s) providing the secondary structure, so a sequence may appear more than once in the tree.

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          blocks

          New Feature - A new feature of the product, which has yet to be developed. JAL-4424 Add subtitle in PCA and Tree panel

          • Major - Major loss of function.
          • In Progress
          depends on

          Improvement - An improvement or enhancement to an existing feature or task. JAL-4528 Allow calculation of annotation track based trees involving just one or two sequences

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

          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

          • Major - Major loss of function.
          • In Progress

          New Feature - A new feature of the product, which has yet to be developed. JAL-4392 Consensus secondary structure visualization for alignments

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

          Task - A task that needs to be done. JAL-4518 sort and colour annotation rows in alignment view according to tree ordering

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-4509 Assign perceptually distinct colours for secondary structure providers

          • Major - Major loss of function.
          • In Progress
          mentioned on

          GitLab Commit - JAL-4386 @rcorreya001 - request a test for SequenceGroup.addOrRemoveAnnotation and documentation

          GitLab Commit - JAL-4386 account for null entries in sequence array passed to the score model...

          GitLab Commit - JAL-4386 Added secondary structure providers check boxes in show

          GitLab Commit - JAL-4386 allow score models to generate additional labelled entities to...

          GitLab Commit - JAL-4386 annotate internal nodes either side of partition with the set of labels on branches

          GitLab Commit - JAL-4386 Demonstration of the ColorUtils HSB methods in the normal tree

          GitLab Commit - JAL-4386 Demonstration of the ColorUtils HSB methods in the normal tree

          GitLab Commit - JAL-4386 fix viewstyle autotests

          GitLab Commit - JAL-4386 Fixed some identified bugs in recent changes

          GitLab Commit - JAL-4386 Fixed to the colour scheme ranges and application to the normal calculated tree

          GitLab Commit - JAL-4386 Fixed to the colour scheme ranges and application to the normal calculated tree

          GitLab Commit - JAL-4386 i8n secondary structure score model

          GitLab Commit - JAL-4386 JAL-4411 factored out the test for a particular annotation row being...

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

          GitLab Commit - JAL-4386 Merge multiple leaves for ss source

          GitLab Commit - JAL-4386 move provider label into a new attribute on BinaryNodes so it can be recovered easily

          GitLab Commit - JAL-4386 remove magic string in registerScoreModel...

          GitLab Commit - JAL-4386 Small refactor of helper NAME to Color methods

          GitLab Commit - JAL-4386 Small refactor of helper NAME to Color methods

          GitLab Commit - JAL-4386 Some methods to create consistent colours from a string id, with applicable colour schemes

          GitLab Commit - JAL-4386 Some methods to create consistent colours from a string id, with applicable colour schemes

          GitLab Commit - JAL-4386 TODOs re standardising and more efficient linking of PDB ID and provider to annotation row

          GitLab Commit - Merge branch 'spike/JAL-4517_customNodenamesInNewick' into...

          GitLab Commit - Resolved merge conflicts from develop into JAL-4386

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              Assignee:
              reniacorreya Renia Correya
              Reporter:
              reniacorreya Renia Correya
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                Dates

                Created:
                Updated: