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  1. Jalview
  2. JAL-4392

Consensus secondary structure visualization for alignments

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: 2.11.3.2, 2.11.3.3
    • Fix Version/s: 2.11.4.0, 2.11.5.0
    • Component/s: None
    • Labels:
      None

      Description

      Develop a feature that calculates and displays a consensus of secondary structures for sequence alignments.

        Attachments

          Issue Links

          blocks

          New Feature - A new feature of the product, which has yet to be developed. JAL-4436 Colour by secondary structure conservation

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. JAL-4426 Show number of sequences contributing to the consensus secondary structure in the status bar/tool tip

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

          New Feature - A new feature of the product, which has yet to be developed. JAL-4386 Calculate tree using secondary structure annotation

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-4425 optionally hide consensus/annotations when no data is available

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

          GitLab Commit - JAL-4392 Adding secondary structure provider Adding secondary structure

          GitLab Commit - JAL-4392 autohide the secondary structure consensus annotation by setting...

          GitLab Commit - JAL-4392 Bug fixing and code refactoring.

          GitLab Commit - JAL-4392 check if we are rendering a ss-consensus logo *just once* per row

          GitLab Commit - JAL-4392 Code Refactoring

          GitLab Commit - JAL-4392 Code refactoring

          GitLab Commit - JAL-4392 don't show SS consensus for DNA alignments

          GitLab Commit - JAL-4392 Feature implementation of group consensus secondary structures

          GitLab Commit - JAL-4392 Fix compilation error in test

          GitLab Commit - JAL-4392 Fixed failed test cases

          GitLab Commit - JAL-4392 Implemented show/hide group consensus secondary structure

          GitLab Commit - JAL-4392 JAL-3987 store and restore consensus secondary structure row...

          GitLab Commit - JAL-4392 JAL-4425 commented out code to allow consensus to be hidden...

          GitLab Commit - JAL-4392 JAL-4518 tree groups inherit colour so any group associated...

          GitLab Commit - JAL-4392 Print annotations

          GitLab Commit - JAL-4392 Secondary Structure Consensus save and load project

          GitLab Commit - JAL-4392 Updated the colouring of consensus logo

          GitLab Commit - JAL-4392 Updated the label "Show auto calculated annotations" to "Show

          GitLab Commit - JAL-4418 documentation for ss annotation row preference and auto show (JAL-4425 JAL-4392)

          GitLab Commit - JAL-4418 JAL-4392 show/hide group associated secondary structure consensus and...

          GitLab Commit - JAL-4531 JAL-4392 patch out Java 11+ methods not available in Java 8

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

            Activity

              People

              Assignee:
              reniacorreya Renia Correya
              Reporter:
              reniacorreya Renia Correya
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                Dates

                Created:
                Updated:
                Resolved: