+ } else if (temp._vxrefList != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Method getDbRef.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.DbRef at the given index
+ */
+ public uk.ac.vamsas.objects.core.DbRef getDbRef(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._dbRefList.size()) {
+ throw new IndexOutOfBoundsException("getDbRef: Index value '" + index
+ + "' not in range [0.." + (this._dbRefList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.DbRef) _dbRefList.get(index);
+ }
+
+ /**
+ * Method getDbRef.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 uk.ac.vamsas.objects.core.DbRef[] getDbRef() {
+ uk.ac.vamsas.objects.core.DbRef[] array = new uk.ac.vamsas.objects.core.DbRef[0];
+ return (uk.ac.vamsas.objects.core.DbRef[]) this._dbRefList.toArray(array);
+ }
+
+ /**
+ * Method getDbRefAsReference.Returns a reference to '_dbRefList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getDbRefAsReference() {
+ return this._dbRefList;
+ }
+
+ /**
+ * Method getDbRefCount.
+ *
+ * @return the size of this collection
+ */
+ public int getDbRefCount() {
+ return this._dbRefList.size();
+ }
+
+ /**
+ * Returns the value of field 'dictionary'. The field 'dictionary' has the
+ * following description: symbol class for sequence
+ *
+ *
+ * @return the value of field 'Dictionary'.
+ */
+ public java.lang.String getDictionary() {
+ return this._dictionary;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Primary Key for vamsas object referencing
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId() {
+ return this._id;
+ }
+
+ /**
+ * Method getVxref.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.Vxref at the given index
+ */
+ public uk.ac.vamsas.objects.core.Vxref getVxref(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._vxrefList.size()) {
+ throw new IndexOutOfBoundsException("getVxref: Index value '" + index
+ + "' not in range [0.." + (this._vxrefList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Vxref) _vxrefList.get(index);
+ }
+
+ /**
+ * Method getVxref.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 uk.ac.vamsas.objects.core.Vxref[] getVxref() {
+ uk.ac.vamsas.objects.core.Vxref[] array = new uk.ac.vamsas.objects.core.Vxref[0];
+ return (uk.ac.vamsas.objects.core.Vxref[]) this._vxrefList.toArray(array);
+ }
+
+ /**
+ * Method getVxrefAsReference.Returns a reference to '_vxrefList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getVxrefAsReference() {
+ return this._vxrefList;
+ }
+
+ /**
+ * Method getVxrefCount.
+ *
+ * @return the size of this collection
+ */
+ public int getVxrefCount() {
+ return this._vxrefList.size();
+ }
+
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ * <p>
+ * The following steps came from <b>Effective Java Programming Language
+ * Guide</b> by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_dictionary != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_dictionary)) {
+ result = 37 * result + _dictionary.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_dictionary);
+ }
+ if (_dbRefList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_dbRefList)) {
+ result = 37 * result + _dbRefList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_dbRefList);
+ }
+ if (_vxrefList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_vxrefList)) {
+ result = 37 * result + _vxrefList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_vxrefList);
+ }
+
+ return result;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ */
+ public void removeAllDbRef() {
+ this._dbRefList.clear();
+ }
+
+ /**
+ */
+ public void removeAllVxref() {
+ this._vxrefList.clear();
+ }
+
+ /**
+ * Method removeDbRef.
+ *
+ * @param vDbRef
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeDbRef(final uk.ac.vamsas.objects.core.DbRef vDbRef) {
+ boolean removed = _dbRefList.remove(vDbRef);
+ return removed;
+ }
+
+ /**
+ * Method removeDbRefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.DbRef removeDbRefAt(final int index) {
+ java.lang.Object obj = this._dbRefList.remove(index);
+ return (uk.ac.vamsas.objects.core.DbRef) obj;
+ }
+
+ /**
+ * Method removeVxref.
+ *
+ * @param vVxref
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeVxref(final uk.ac.vamsas.objects.core.Vxref vVxref) {
+ boolean removed = _vxrefList.remove(vVxref);
+ return removed;
+ }
+
+ /**
+ * Method removeVxrefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Vxref removeVxrefAt(final int index) {
+ java.lang.Object obj = this._vxrefList.remove(index);
+ return (uk.ac.vamsas.objects.core.Vxref) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDbRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setDbRef(final int index,
+ final uk.ac.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._dbRefList.size()) {
+ throw new IndexOutOfBoundsException("setDbRef: Index value '" + index
+ + "' not in range [0.." + (this._dbRefList.size() - 1) + "]");
+ }
+
+ this._dbRefList.set(index, vDbRef);
+ }
+
+ /**
+ *
+ *
+ * @param vDbRefArray
+ */
+ public void setDbRef(final uk.ac.vamsas.objects.core.DbRef[] vDbRefArray) {
+ // -- copy array
+ _dbRefList.clear();
+
+ for (int i = 0; i < vDbRefArray.length; i++) {
+ this._dbRefList.add(vDbRefArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_dbRefList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vDbRefList
+ * the Vector to copy.
+ */
+ public void setDbRef(final java.util.Vector vDbRefList) {
+ // copy vector
+ this._dbRefList.clear();
+
+ this._dbRefList.addAll(vDbRefList);
+ }
+
+ /**
+ * Sets the value of '_dbRefList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param dbRefVector
+ * the Vector to set.
+ */
+ public void setDbRefAsReference(final java.util.Vector dbRefVector) {
+ this._dbRefList = dbRefVector;
+ }
+
+ /**
+ * Sets the value of field 'dictionary'. The field 'dictionary' has the
+ * following description: symbol class for sequence
+ *
+ *
+ * @param dictionary
+ * the value of field 'dictionary'.
+ */
+ public void setDictionary(final java.lang.String dictionary) {
+ this._dictionary = dictionary;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * Primary Key for vamsas object referencing
+ *
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vVxref
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setVxref(final int index,
+ final uk.ac.vamsas.objects.core.Vxref vVxref)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._vxrefList.size()) {
+ throw new IndexOutOfBoundsException("setVxref: Index value '" + index
+ + "' not in range [0.." + (this._vxrefList.size() - 1) + "]");
+ }
+
+ this._vxrefList.set(index, vVxref);
+ }
+
+ /**
+ *
+ *
+ * @param vVxrefArray
+ */
+ public void setVxref(final uk.ac.vamsas.objects.core.Vxref[] vVxrefArray) {
+ // -- copy array
+ _vxrefList.clear();
+
+ for (int i = 0; i < vVxrefArray.length; i++) {
+ this._vxrefList.add(vVxrefArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_vxrefList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vVxrefList
+ * the Vector to copy.
+ */
+ public void setVxref(final java.util.Vector vVxrefList) {
+ // copy vector
+ this._vxrefList.clear();
+
+ this._vxrefList.addAll(vVxrefList);
+ }
+
+ /**
+ * Sets the value of '_vxrefList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param vxrefVector
+ * the Vector to set.
+ */
+ public void setVxrefAsReference(final java.util.Vector vxrefVector) {
+ this._vxrefList = vxrefVector;
+ }
+
+ /**
+ * 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 uk.ac.vamsas.objects.core.SequenceTyp
+ */
+ public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.Sequence.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);
+ }