fasta_out.flush();
}
/**
- *validate a SequenceType object as an info:iubmb.org/aminoacid SequenceType
+ *validate a SequenceType Vobject as an info:iubmb.org/aminoacid SequenceType
*This version resolves references to Sequence objects from AlignmentSequence
*TODO: Define info: urn for dictionary string (could also be regex of valid characters!)
* @param s
* @param dict TODO
- * @return true if a valid amino acid sequence object
+ * @return true if a valid amino acid sequence Vobject
*/
private static boolean valid_aadictionary_string(String s, String dict) {
if (s==null)
}
public static Sequence newSequence(String Name, String Sequence, String Dictionary, int start, int end) {
- //TODO: make hierarchy reflecting the SeqType object.
+ //TODO: make hierarchy reflecting the SeqType Vobject.
Sequence seq= new Sequence();
seq.setDictionary(Dictionary);
seq.setName(Name);
if ((end-start)!=Sequence.length())
seq.setEnd(start+Sequence.length());
} else {
- // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence object
+ // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence Vobject
if ((start-end)!=Sequence.length())
seq.setEnd(end+Sequence.length());
}