+ 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)
+ {
+ codonFrameList = new AlignedCodonFrame[]
+ { codons };
+ return;
+ }
+ AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
+ System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
+ t[codonFrameList.length] = codons;
+ codonFrameList = t;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+ */
+ public AlignedCodonFrame getCodonFrame(int index)
+ {
+ return codonFrameList[index];
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ */
+ public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+ {
+ if (seq == null || codonFrameList == null)
+ return null;
+ Vector cframes = new Vector();
+ for (int f = 0; f < codonFrameList.length; f++)
+ {
+ if (codonFrameList[f].involvesSequence(seq))
+ cframes.addElement(codonFrameList[f]);
+ }
+ if (cframes.size() == 0)
+ return null;
+ AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
+ cframes.copyInto(cfr);
+ return cfr;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ */
+ public AlignedCodonFrame[] getCodonFrames()
+ {
+ return codonFrameList;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ */
+ public boolean removeCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons == null || codonFrameList == null)
+ return false;
+ boolean removed = false;
+ int i = 0, iSize = codonFrameList.length;
+ while (i < iSize)
+ {
+ if (codonFrameList[i] == codons)
+ {
+ removed = true;
+ if (i + 1 < iSize)
+ {
+ System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
+ - i - 1);
+ }
+ iSize--;
+ }
+ else
+ {
+ i++;
+ }
+ }
+ return removed;
+ }
+