{\r
if(hiddenSequences==null)\r
{\r
- System.out.println("H is null");\r
return 0;\r
}\r
int count = 0;\r
int index = 0;\r
int hiddenSeqs = 0;\r
if(hiddenSequences.length<=alignmentIndex)\r
- System.out.println(alignmentIndex+" "+hiddenSequences.length);\r
+ alignmentIndex = hiddenSequences.length-1;\r
\r
while(index <= alignmentIndex)\r
{\r