/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
*/\r
package jalview.schemes;\r
\r
-import java.util.*;\r
-\r
import java.awt.*;\r
\r
public interface ColourSchemeI\r
{\r
- public Color findColour(String aa);\r
+ public Color findColour(char c);\r
+\r
+ public Color findColour(char c, int j);\r
+\r
+ public void setConsensus(java.util.Hashtable [] h);\r
+\r
+ public void setConservation(jalview.analysis.Conservation c);\r
+\r
+ public boolean conservationApplied();\r
+\r
+ public void setConservationInc(int i);\r
+\r
+ public int getConservationInc();\r
+\r
+ public int getThreshold();\r
+\r
+ public void setThreshold(int ct, boolean ignoreGaps);\r
\r
- public Color findColour(String s, int j);\r
\r
- public void setConsensus(Vector v);\r
}\r