-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\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
* You should have received a copy of the GNU General Public License\r
* along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
\r
-import java.util.*;\r
import java.awt.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
+import jalview.analysis.AAFrequency;\r
\r
-public class Blosum62ColourScheme extends ResidueColourScheme\r
+public class Blosum62ColourScheme\r
+ extends ResidueColourScheme\r
{\r
-\r
- // need to keep an eye on the changing visible consensus sequence\r
- AlignViewport av;\r
-\r
- public Blosum62ColourScheme(AlignViewport av)\r
+ public Blosum62ColourScheme()\r
{\r
super();\r
- this.av = av;\r
}\r
\r
- public Color findColour(String s, int j, Vector aa)\r
+ public Color findColour(String s, int j)\r
{\r
- Hashtable hash;\r
+ char res = s.charAt(0);\r
+ if ('a' <= res && res <= 'z' )\r
+ {\r
+ // TO UPPERCASE !!!\r
+ s = String.valueOf( res -= ('a' - 'A') );\r
+ }\r
\r
- if (aa != null)\r
- hash = (Hashtable)aa.elementAt(j);\r
- else\r
+ if (consensus == null ||\r
+ j >= consensus.length ||\r
+ consensus[j] == null ||\r
+ (threshold != 0 && !aboveThreshold(s, j)))\r
+ {\r
return Color.white;\r
+ }\r
\r
- if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
+ if (!jalview.util.Comparison.isGap( res ))\r
{\r
- String max = (String)hash.get("maxResidue");\r
+ String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);\r
\r
- if (max.indexOf(s)>-1)\r
- return new Color(154, 154, 255);\r
- else {\r
+ if (max.indexOf(s) > -1)\r
+ {\r
+ currentColour = new Color(154, 154, 255);\r
+ }\r
+ else\r
+ {\r
+ int c = 0;\r
+ int max_aa = 0;\r
+ int n = max.length();\r
\r
- int c = 0,\r
- max_aa=0,\r
- n=max.length();\r
- do {\r
- c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);\r
- } while (++max_aa<n);\r
+ do\r
+ {\r
+ c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
+ max_aa + 1), s);\r
+ }\r
+ while (++max_aa < n);\r
\r
- if (c>0)\r
- return new Color(204, 204, 255);\r
+ if (c > 0)\r
+ {\r
+ currentColour = new Color(204, 204, 255);\r
+ }\r
else\r
- return Color.white;\r
+ {\r
+ currentColour = Color.white;\r
+ }\r
}\r
+\r
+ if(conservationColouring)\r
+ applyConservation(j);\r
}\r
else\r
- return Color.white;\r
-\r
- }\r
+ {\r
+ return Color.white;\r
+ }\r
\r
- public boolean canThreshold()\r
- {\r
- return false;\r
+ return currentColour;\r
}\r
-\r
}\r