String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
strucAnn = new Hashtable();
}
- Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> newStruc = new Vector<>();
parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
{
DBRefEntry dbrf = null;
- List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> dbrs = new ArrayList<>();
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
}
}
+
// output annotations
while (i < s.length && s[i] != null)
{
String key = type2id(alAnot[j].label);
boolean isrna = alAnot[j].isValidStruc();
-
if (isrna)
{
// hardwire to secondary structure if there is RNA secondary
for (int k = 0; k < ann.length; k++)
{
seq += outputCharacter(key, k, isrna, ann, s[i]);
- }
+
+ }
out.append(seq);
out.append(newline);
}
out.append(newline);
}
}
+
+
out.append("//");
out.append(newline);
out.append("# STOCKHOLM 1.0");
out.append(newline);
print(getSeqsAsArray(), false);
-
+
out.append("//");
out.append(newline);
return out.toString();