+ }
+
+ /** Make an alignment from an array of Sequences.
+ *
+ * @param sequences
+ */
+ public Alignment(SequenceI[] seqs)
+ {
+ initAlignment(seqs);
+ }
+
+ /**
+ * Make a new alignment from an array of SeqCigars
+ * @param seqs SeqCigar[]
+ */
+ public Alignment(SeqCigar[] alseqs)
+ {
+ SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter,
+ new ColumnSelection(), null);
+ 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 static AlignmentI createAlignment(CigarArray compactAlignment)
+ {
+ throw new Error("Alignment(CigarArray) not yet implemented");
+ // this(compactAlignment.refCigars);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getSequences()
+ {
+ return sequences;
+ }
+
+ public SequenceI[] getSequencesArray()
+ {
+ SequenceI[] reply = new SequenceI[sequences.size()];
+ for (int i = 0; i < sequences.size(); i++)