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## uk.ac.man.bioinf.apps.cinema.color
Interface ColorMapMetaData

All Known Implementing Classes:
  AminoAcidColorMapMetaData, ColormapColorMapMetaData, DefaultColorMapMetaData, GrayScaleVariance, InstancePerAlignmentColorMapMetaData, IntenseColorMapMetaData, Js_TestColorMapMetaData, NullColorMapMetaData, PedanticColorMapMetaData, PercentageIDVarianceColorMapMetaData, TaylorColorMapMetaData, ThreadedPercentageIDVarianceColorMapMetaData, VariableColorMapMetaData, VariationsColorMapMetaData, WhiteColorMapMetaData, ZenecaColorMapMetaData

public interface ColorMapMetaData

ColorMapMetaData.java Many of the colour maps available need to be treated in different ways. So for instance some colour maps can use a single shared instance, others needs a new one for each alignment. It does not really make sense to try and encapsulate this sort of knowledge within the ColorMap class, but it is needed within Cinema... Created: Tue Jul 18 14:57:08 2000

Version:
  $Id: ColorMapMetaData.java,v 1.3 2001/04/11 17:04:41 lord Exp $
Author:
  Phillip Lord

Method Summary
`String` | `getColorMapName()` This should return the string that ColorMap instances created via this class, return as their name, via the getName method
`ColorMap` | `getConsensusInstance(ConsensusSequence sequence, JAlignmentViewer viewer)` Returns an instance of this type for this consensus sequence
`ColorMap` | `getInstance(SequenceAlignment alignment, JAlignmentViewer viewer)` Returns a instance of this Color map for the given alignment instance.
`void` | `setModule(CinemaModule module)`

Method Detail

### setModule

    public void setModule(CinemaModule module)

### getColorMapName

    public String getColorMapName()

  This should return the string that ColorMap instances created via this class, return as their name, via the getName method

  Returns:
    the name

### getInstance

    public ColorMap getInstance(SequenceAlignment alignment,
                                JAlignmentViewer viewer)

  Returns a instance of this Color map for the given alignment instance.

  Returns:
    the ColorMap

### getConsensusInstance

    public ColorMap getConsensusInstance(ConsensusSequence sequence,
                                         JAlignmentViewer viewer)

  Returns an instance of this type for this consensus sequence

  Parameters:
    `sequence` - the consensus sequence
  Returns:
    the ColorMap instance

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