* @param c
* @return the colour for the given character
*/
- public Color findColour(char c);
+ Color findColour(char c);
/**
*
* @return context dependent colour for the given symbol at the position in
* the given sequence
*/
- public Color findColour(char c, int j, SequenceI seq);
+ Color findColour(char c, int j, SequenceI seq);
/**
* assign the given consensus profile for the colourscheme
*/
- public void setConsensus(ProfilesI hconsensus);
+ void setConsensus(ProfilesI hconsensus);
/**
* assign the given conservation to the colourscheme
*
* @param c
*/
- public void setConservation(jalview.analysis.Conservation c);
+ void setConservation(jalview.analysis.Conservation c);
/**
* enable or disable conservation shading for this colourscheme
*
* @param conservationApplied
*/
- public void setConservationApplied(boolean conservationApplied);
+ void setConservationApplied(boolean conservationApplied);
/**
*
* @return true if conservation shading is enabled for this colourscheme
*/
- public boolean conservationApplied();
+ boolean conservationApplied();
/**
* set scale factor for bleaching of colour in unconserved regions
*
* @param i
*/
- public void setConservationInc(int i);
+ void setConservationInc(int i);
/**
*
* @return scale factor for bleaching colour in unconserved regions
*/
- public int getConservationInc();
+ int getConservationInc();
/**
*
* @return percentage identity threshold for applying colourscheme
*/
- public int getThreshold();
+ int getThreshold();
/**
* set percentage identity threshold and type of %age identity calculation for
* @param ignoreGaps
* when true, calculate PID without including gapped positions
*/
- public void setThreshold(int ct, boolean ignoreGaps);
+ void setThreshold(int ct, boolean ignoreGaps);
/**
* recalculate dependent data using the given sequence collection, taking
* @param alignment
* @param hiddenReps
*/
- public void alignmentChanged(AnnotatedCollectionI alignment,
+ void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps);
/**
* @param hiddenRepSequences
* @return copy of current scheme with any inherited settings transfered
*/
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
-
}