- /**
- * Make a new alignment from an array of SeqCigars
- * @param seqs SeqCigar[]
- */
- public Alignment(SeqCigar[] alseqs) {
-
- SequenceI[] seqs = new SequenceI[alseqs.length];
- for (int i=0; i<alseqs.length; i++) {
- seqs[i] = alseqs[i].getSeq(this.gapCharacter);
- }
- initAlignment(seqs);
- }
- /**
- * Make a new alignment from an CigarArray
- * JBPNote - can only do this when compactAlignment does not contain hidden regions.
- * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
- * @param compactAlignment CigarArray
- */
- public Alignment(CigarArray compactAlignment) {
- throw new Error("Alignment(CigarArray) not yet implemented");
- // this(compactAlignment.refCigars);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getSequences()