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  1. Jalview
  2. JAL-4702

Support Jalview secondary structure trees in Archaeopteryx

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    Details

    • Type: New Feature
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: trees
    • Labels:
      None

      Description

      Jalview 2.11.5 can calculate trees from secondary structure similarity, where each leaf stands for an annotation row rather than a sequence, so a sequence with several structures can appear more than once. Those trees were left on the native tree panel because the Archaeopteryx integration could bind leaves to sequences only. Archaeopteryx already draws per-leaf strips through forester's DomainArchitecture, colours branches and reads node properties, so we just need the binding & data on the Jalview side to feed that rendering.

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          Task - A task that needs to be done. JAL-4517 store and restore trees linked to annotation rows in Jalview projects

          • Major - Major loss of function.
          • Closed
          mentioned on

          GitLab Commit - JAL-2798 JAL-4702 Restore project trees the merge left unreachable

          GitLab Commit - JAL-2798 JAL-4702 Restore project trees the merge left unreachable

          GitLab Commit - JAL-2838 JAL-4702 Lock the tree view map while iterating it

          GitLab Commit - JAL-2838 JAL-4702 Lock the tree view map while iterating it

          GitLab Commit - JAL-4702 Add annotation row sort to Aptx tree viewer

          GitLab Commit - JAL-4702 Add AnnotationLeafMap keying SS tree leaves for newick export

          GitLab Commit - JAL-4702 Associate annotation leaves by key or node property

          GitLab Commit - JAL-4702 Bind annotation leaves to Aptx selection and refilter in place

          GitLab Commit - JAL-4702 Colour Aptx leaf labels by secondary structure provider

          GitLab Commit - JAL-4702 Colour Aptx leaf labels by secondary structure provider

          GitLab Commit - JAL-4702 Count only the chosen provider's secondary structure rows

          GitLab Commit - JAL-4702 Cover SS tree binding release on frame close

          GitLab Commit - JAL-4702 Keep both leaves when two annotations share an id

          GitLab Commit - JAL-4702 Keep both leaves when two annotations share an id

          GitLab Commit - JAL-4702 Open calculated annotation trees with their bindings

          GitLab Commit - JAL-4702 Render secondary structure context in Archaeopteryx

          GitLab Commit - JAL-4702 Route annotation-based tree calculations to the native panel

          GitLab Commit - JAL-4702 Route SS similarity trees to Archaeopteryx

          GitLab Commit - JAL-4702 Skip Aptx restore for annotation-based project trees

          GitLab Commit - JAL-4702 Stabilise annotation tree identity and binding

          GitLab Commit - JAL-4702 Update help for Archaeopteryx secondary structure trees

          GitLab Commit - JAL-4702 Wait for the SS tree before asking for its provider panel

          GitLab Commit - JAL-4702 Wait for the SS tree before asking for its provider panel

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              Assignee:
              kjvdheide Koen van der Heide
              Reporter:
              kjvdheide Koen van der Heide
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                Dates

                Created:
                Updated: