- /**
- * 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);