+ /**
+ * Method getAlcodMapCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodMapCount(
+ ) {
+ return this._alcodMapList.size();
+ }
+
+ /**
+ * Method getAlcodon.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.Alcodon at the given index
+ */
+ public jalview.schemabinding.version2.Alcodon getAlcodon(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonList.size()) {
+ throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
+ }
+
+ /**
+ * Method getAlcodon.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Alcodon[] getAlcodon(
+ ) {
+ jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
+ return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array);
+ }
+
+ /**
+ * Method getAlcodonCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodonCount(
+ ) {
+ return this._alcodonList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method removeAlcodMap.
+ *
+ * @param vAlcodMap
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodMap(
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap) {
+ boolean removed = _alcodMapList.remove(vAlcodMap);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodMapAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
+ final int index) {
+ java.lang.Object obj = this._alcodMapList.remove(index);
+ return (jalview.schemabinding.version2.AlcodMap) obj;
+ }
+
+ /**
+ * Method removeAlcodon.
+ *
+ * @param vAlcodon
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodon(
+ final jalview.schemabinding.version2.Alcodon vAlcodon) {
+ boolean removed = _alcodonList.remove(vAlcodon);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodonAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
+ final int index) {
+ java.lang.Object obj = this._alcodonList.remove(index);
+ return (jalview.schemabinding.version2.Alcodon) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlcodMap(
+ ) {
+ this._alcodMapList.clear();
+ }
+
+ /**
+ */
+ public void removeAllAlcodon(
+ ) {
+ this._alcodonList.clear();
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodMap
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAlcodMap(
+ final int index,
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodMapList.size()) {
+ throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
+ }
+
+ this._alcodMapList.set(index, vAlcodMap);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodMapArray
+ */
+ public void setAlcodMap(
+ final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) {
+ //-- copy array
+ _alcodMapList.clear();
+
+ for (int i = 0; i < vAlcodMapArray.length; i++) {
+ this._alcodMapList.add(vAlcodMapArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodon
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAlcodon(
+ final int index,
+ final jalview.schemabinding.version2.Alcodon vAlcodon)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonList.size()) {
+ throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
+ }
+
+ this._alcodonList.set(index, vAlcodon);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodonArray
+ */
+ public void setAlcodon(
+ final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) {
+ //-- copy array
+ _alcodonList.clear();
+
+ for (int i = 0; i < vAlcodonArray.length; i++) {
+ this._alcodonList.add(vAlcodonArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.AlcodonFrame
+ */
+ public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);