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