// check in case we went off the edge of the alignment
int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
// check in case we went off the edge of the alignment
int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);