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  1. Jalview
  2. JAL-4071

show counts for features observed at each column of the alignment

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    Details

    • Type: New Feature
    • Status: In Progress
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
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      Description

      It's often extremely useful to get an idea of where particular types of feature appear w.r.t. to each other in an alignment (see JAL-4070 for details). One option is via the groovy script 'visibleFeaturesCounter' which builds a custom annotation row calculator for the currently displayed features for an alignment.

      This was originally a PoC for the pluggable annotation calculator system, but the script's functionality should be incorporated into the core codebase.

      There are a few things that could be improved:
      1. Dynamic hide/show tracks for all features, or just a specific subset of features.
      2. Colour the tracks the same way as the features.
      3. Make the tracks more compact, so several feature count tracks can be seen at once.
      4. Tooltip for each histogram could report the set of sequence features observed at that column all at once (and of course this might be very useful to export, too).
      5. Mouseover/selection highlighting could reveal full extent of the sequence features at the moused-over position.

      ...

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Created:
                Updated: