int absAlignmentIndex = alignment.findIndex(sequence);
int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
- if (hiddenSequences[alignmentIndex] != null)
+ if (alignmentIndex < 0 || hiddenSequences[alignmentIndex] != null)
{
System.out.println("ERROR!!!!!!!!!!!");
+ return;
}
hiddenSequences[alignmentIndex] = sequence;
return startRow - visibleDistance;
}
- int index = startRow;
+ int index = Math.min(startRow, hiddenSequences.length - 1);
int count = 0;
while ((index > -1) && (count < visibleDistance))
{