/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.schemes;
import java.awt.Color;
import java.util.Map;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
public interface ColourSchemeI
{
public Color findColour(char c);
public Color findColour(char c, int j, SequenceI seq);
public void setConsensus(java.util.Hashtable[] h);
public void setConservation(jalview.analysis.Conservation c);
public boolean conservationApplied();
public void setConservationInc(int i);
public int getConservationInc();
public int getThreshold();
public void setThreshold(int ct, boolean ignoreGaps);
public void alignmentChanged(AnnotatedCollectionI alignment,
Map hiddenReps);
}