+ public HiddenSequences getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ public CigarArray getCompactAlignment()
+ {
+ SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+ }
+ CigarArray cal = new CigarArray(alseqs);
+ cal.addOperation(CigarArray.M, getWidth());
+ return cal;
+ }
+
+ public void setProperty(Object key, Object value)
+ {
+ if (alignmentProperties == null)
+ alignmentProperties = new Hashtable();
+
+ alignmentProperties.put(key, value);
+ }
+
+ public Object getProperty(Object key)
+ {
+ if (alignmentProperties != null)
+ return alignmentProperties.get(key);
+ else
+ return null;
+ }
+
+ public Hashtable getProperties()
+ {
+ return alignmentProperties;
+ }
+
+ AlignedCodonFrame[] codonFrameList = null;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * )
+ */
+ public void addCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons == null)
+ return;
+ if (codonFrameList == null)