/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*/
package jalview.schemes;
-import java.awt.*;
+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);
+ public Color findColour(char c, int j, SequenceI seq);
public void setConsensus(java.util.Hashtable[] h);
public void setThreshold(int ct, boolean ignoreGaps);
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps);
+
}