*/\r
package jalview.schemes;\r
\r
-import java.util.*;\r
-\r
import java.awt.*;\r
\r
import jalview.datamodel.*;\r
\r
public Color findColour(String s, int j)\r
{\r
+ char res = s.charAt(0);\r
+ if ('a' <= res && res <= 'z')\r
+ {\r
+ s = String.valueOf(res -= ('a' - 'A'));\r
+ }\r
+\r
+\r
if ( (threshold != 0) && !aboveThreshold(s, j))\r
{\r
return Color.white;\r
}\r
\r
- Color c = Color.white;\r
- Hashtable hash = (Hashtable) consensus.elementAt(j);\r
+ currentColour = Color.white;\r
\r
double sc = 0;\r
\r
- if ( (Integer.parseInt(hash.get("maxCount").toString()) != -1) &&\r
- hash.contains(s))\r
+ if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&\r
+ consensus[j].contains(s))\r
{\r
- sc = ( ( (Integer) hash.get(s)).intValue() * 100.0) /\r
- ( (Integer) hash.get(\r
- "size")).intValue();\r
+ sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
\r
- // MC Should be isGap\r
- if (!jalview.util.Comparison.isGap( (s.charAt(0))))\r
+ if (!jalview.util.Comparison.isGap( res ))\r
{\r
for (int i = 0; i < thresholds.length; i++)\r
{\r
if (sc > thresholds[i])\r
{\r
- c = pidColours[i];\r
+ currentColour = pidColours[i];\r
\r
break;\r
}\r
}\r
}\r
\r
- return c;\r
+ if(conservationColouring)\r
+ applyConservation(j);\r
+\r
+ return currentColour;\r
}\r
}\r