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  1. Jalview
  2. JAL-2371

Separate colour threshold/fading from colour schemes

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    Details

    • Type: Task
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: 2.10.1
    • Fix Version/s: 2.10.2
    • Component/s: Scriptable API
    • Labels:
      None

      Description

      Currently, each colour scheme has code to modify the residue colour if 'above PID' threshold or 'By Conservation' shading is in force.
      Logically these are distinct operations.
      Separation of threshold/fading from colour scheme would simplify colour scheme coding.
      In particular, a user-contributed colour scheme (e.g via Groovy) should be able to participate in threshold/fading without having to code for this.

        Attachments

          Issue Links

          blocks

          Bug - A problem which impairs or prevents the functions of the product. JAL-2405 Protein specific colours enabled in selected group colour menu for nucleotide alignment

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2400 Text white/black threshold improvements in refactored colours menu

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2360 Make available colour schemes dependent on sequence collection

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-2512 Overview doesn't show non-gap positions in light grey for 'None' colourscheme

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-2570 existing SequenceGroup loses colourscheme when resized in splitframe

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-2650 Conservation colouring not applied in new view with a user defined colourscheme

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2660 New View with Above PID colouring incorrect if ignoreGaps is false

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2724 Cannot apply annotation shading across all groups in a view

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-3201 Per-group clustal colourscheme changes when different groups in the alignment are selected

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2704 Gap colour should not be affected by PID or Conservation shading

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2394 Simplify colourschemeI interface to avoid requiring boilerplate is/newInstance/update mathods

          • Major - Major loss of function.
          • Open

            Activity

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated:
                Resolved: