parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
for (int k = 0; k < ann.length; k++)
{
seq += outputCharacter(key, k, isrna, ann, s[i]);
for (int k = 0; k < ann.length; k++)
{
seq += outputCharacter(key, k, isrna, ann, s[i]);
out.append("# STOCKHOLM 1.0");
out.append(newline);
print(getSeqsAsArray(), false);
out.append("# STOCKHOLM 1.0");
out.append(newline);
print(getSeqsAsArray(), false);