/*\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
import java.awt.*;\r
\r
import jalview.datamodel.*;\r
+import jalview.analysis.AAFrequency;\r
\r
public class PIDColourScheme\r
extends ResidueColourScheme\r
return Color.white;\r
}\r
\r
-\r
-\r
- Color c = Color.white;\r
+ currentColour = Color.white;\r
\r
double sc = 0;\r
\r
- if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&\r
- consensus[j].contains(s))\r
- {\r
- sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
+ if(consensus.length<=j)\r
+ return Color.white;\r
\r
- if (!jalview.util.Comparison.isGap( res ))\r
+ if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&\r
+ consensus[j].contains(s))\r
{\r
- for (int i = 0; i < thresholds.length; i++)\r
+ sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
+\r
+ if (!jalview.util.Comparison.isGap(res))\r
{\r
- if (sc > thresholds[i])\r
+ for (int i = 0; i < thresholds.length; i++)\r
{\r
- c = pidColours[i];\r
+ if (sc > thresholds[i])\r
+ {\r
+ currentColour = pidColours[i];\r
\r
- break;\r
+ break;\r
+ }\r
}\r
}\r
}\r
- }\r
\r
- return c;\r
+ if(conservationColouring)\r
+ applyConservation(j);\r
+\r
+ return currentColour;\r
}\r
}\r