* allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
*/
int truePos = sequencePos - (start - 1);
- while (alignedBases < truePos
- && alignedColumn < alignedSeq.length)
+ while (alignedBases < truePos && alignedColumn < alignedSeq.length)
{
if (alignedSeq[alignedColumn++] != gap)
{
*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
map = null;
return new AlignedCodonIterator(seq, gapChar);
}
+ /**
+ * Readable representation for debugging only, not guaranteed not to change
+ */
+ @Override
+ public String toString()
+ {
+ return String.format("%s %s", this.map.toString(), this.to == null ? ""
+ : this.to.getName());
+ }
+
}