/*\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
* @return DOCUMENT ME!\r
*/\r
- public Color findColour(String n)\r
+ public Color findColour(char c)\r
{\r
// System.out.println("called"); log.debug\r
- return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+ return colors[ResidueProperties.nucleotideIndex[c]];\r
}\r
\r
/**\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public Color findColour(String n, int j)\r
+ public Color findColour(char c, int j)\r
{\r
- if ((threshold == 0) || aboveThreshold(n, j))\r
+ Color currentColour;\r
+ if ((threshold == 0) || aboveThreshold(c, j))\r
{\r
try\r
{\r
- return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+ currentColour = colors[ ResidueProperties.nucleotideIndex[c]];\r
}\r
catch (Exception ex)\r
{\r
{\r
return Color.white;\r
}\r
+\r
+ if(conservationColouring)\r
+ currentColour = applyConservation(currentColour, j);\r
+\r
+ return currentColour;\r
}\r
}\r