JAL-2386: Change Colour (All Groups) applies PID threshold but not Conservation

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CR-JAL-28 0

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    Objectives

    Behaviour of Change Colour with Apply to All Groups selected is inconsistent:

    • PID threshold is applied to all groups along with the selected colour scheme
    • Consensus slider value is not


    For example,

    • load uniref50.fa and colour by helix propensity
    • create a subgroup and colour by turn propensity
    • apply a PID threshold to the alignment colour scheme
    • select Colour | Apply Colour to All Groups and change to Hydrophobicity
      -> both colour and PID threshold are also applied to the sub-group
      Compare the same procedure but with By Conservation instead of PID:
      -> the Conservation threshold is not applied to the sub-group

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

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    /src/jalview/appletgui/AlignFrame.java Changed
    /src/jalview/gui/AlignFrame.java Changed
    /src/jalview/gui/PopupMenu.java Changed
    /src/jalview/gui/SliderPanel.java Changed
    /src/jalview/jbgui/GAlignFrame.java Changed
    /src/.../viewmodel/AlignmentViewport.java Changed
    /test/jalview/gui/AlignFrameTest.java Changed

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