*/\r
public boolean aboveThreshold(String s, int j)\r
{\r
- if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&\r
+ char c = s.charAt(0);\r
+ if ('a' <= c && c <= 'z')\r
+ {\r
+ // TO UPPERCASE !!!\r
+ //Faster than toUpperCase\r
+ c -= ('a' - 'A');\r
+ s = String.valueOf(c);\r
+ }\r
+\r
+\r
+ if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&\r
consensus[j].contains(s))\r
{\r
if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)\r
*\r
* @param consensus DOCUMENT ME!\r
*/\r
- public void setConsensus(Vector vconsensus)\r
+ public void setConsensus(Hashtable [] consensus)\r
{\r
- if(vconsensus==null)\r
+ if(consensus==null)\r
return;\r
\r
- int i, iSize=vconsensus.size();\r
- consensus = new Hashtable[iSize];\r
- for(i=0; i<iSize; i++)\r
- consensus[i] = (Hashtable)vconsensus.elementAt(i);\r
+ this.consensus = consensus;\r
}\r
\r
\r
+\r
public void setConservation(Conservation cons)\r
{\r
if(cons==null)\r