}
/**
- * DOCUMENT ME!
+ * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
*
- * @return DOCUMENT ME!
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
*/
public int[] gapMap()
{
- // Returns an int array giving the position of each residue in the sequence in the alignment
String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
int[] map = new int[seq.length()];
int j = 0;