+ } else if (temp._provenance != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Method getAlignment.
+ *
+ * @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.Alignment at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Alignment getAlignment(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size()) {
+ throw new IndexOutOfBoundsException("getAlignment: Index value '" + index
+ + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Alignment) _alignmentList.get(index);
+ }
+
+ /**
+ * Method getAlignment.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.Alignment[] getAlignment() {
+ uk.ac.vamsas.objects.core.Alignment[] array = new uk.ac.vamsas.objects.core.Alignment[0];
+ return (uk.ac.vamsas.objects.core.Alignment[]) this._alignmentList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAlignmentAsReference.Returns a reference to '_alignmentList'. No
+ * type checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getAlignmentAsReference() {
+ return this._alignmentList;
+ }
+
+ /**
+ * Method getAlignmentCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlignmentCount() {
+ return this._alignmentList.size();
+ }
+
+ /**
+ * Method getDataSetAnnotations.
+ *
+ * @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.DataSetAnnotations at
+ * the given index
+ */
+ public uk.ac.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(
+ final int index) throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._dataSetAnnotationsList.size()) {
+ throw new IndexOutOfBoundsException(
+ "getDataSetAnnotations: Index value '" + index
+ + "' not in range [0.."
+ + (this._dataSetAnnotationsList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList
+ .get(index);
+ }
+
+ /**
+ * Method getDataSetAnnotations.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.DataSetAnnotations[] getDataSetAnnotations() {
+ uk.ac.vamsas.objects.core.DataSetAnnotations[] array = new uk.ac.vamsas.objects.core.DataSetAnnotations[0];
+ return (uk.ac.vamsas.objects.core.DataSetAnnotations[]) this._dataSetAnnotationsList
+ .toArray(array);
+ }
+
+ /**
+ * Method getDataSetAnnotationsAsReference.Returns a reference to
+ * '_dataSetAnnotationsList'. No type checking is performed on any
+ * modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getDataSetAnnotationsAsReference() {
+ return this._dataSetAnnotationsList;
+ }
+
+ /**
+ * Method getDataSetAnnotationsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getDataSetAnnotationsCount() {
+ return this._dataSetAnnotationsList.size();
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return the value of field 'Provenance'.
+ */
+ public uk.ac.vamsas.objects.core.Provenance getProvenance() {
+ return this._provenance;
+ }
+
+ /**
+ * Method getSequence.
+ *
+ * @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.Sequence at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Sequence getSequence(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size()) {
+ throw new IndexOutOfBoundsException("getSequence: Index value '" + index
+ + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Sequence) _sequenceList.get(index);
+ }
+
+ /**
+ * Method getSequence.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.Sequence[] getSequence() {
+ uk.ac.vamsas.objects.core.Sequence[] array = new uk.ac.vamsas.objects.core.Sequence[0];
+ return (uk.ac.vamsas.objects.core.Sequence[]) this._sequenceList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequenceAsReference.Returns a reference to '_sequenceList'. No
+ * type checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getSequenceAsReference() {
+ return this._sequenceList;
+ }
+
+ /**
+ * Method getSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceCount() {
+ return this._sequenceList.size();
+ }
+
+ /**
+ * Method getSequenceMapping.
+ *
+ * @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.SequenceMapping at the
+ * given index
+ */
+ public uk.ac.vamsas.objects.core.SequenceMapping getSequenceMapping(
+ final int index) throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceMappingList.size()) {
+ throw new IndexOutOfBoundsException("getSequenceMapping: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceMappingList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.SequenceMapping) _sequenceMappingList
+ .get(index);
+ }
+
+ /**
+ * Method getSequenceMapping.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.SequenceMapping[] getSequenceMapping() {
+ uk.ac.vamsas.objects.core.SequenceMapping[] array = new uk.ac.vamsas.objects.core.SequenceMapping[0];
+ return (uk.ac.vamsas.objects.core.SequenceMapping[]) this._sequenceMappingList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequenceMappingAsReference.Returns a reference to
+ * '_sequenceMappingList'. No type checking is performed on any modifications
+ * to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getSequenceMappingAsReference() {
+ return this._sequenceMappingList;
+ }
+
+ /**
+ * Method getSequenceMappingCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceMappingCount() {
+ return this._sequenceMappingList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @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.Tree at the given index
+ */
+ public uk.ac.vamsas.objects.core.Tree getTree(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.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.Tree[] getTree() {
+ uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0];
+ return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeAsReference.Returns a reference to '_treeList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getTreeAsReference() {
+ return this._treeList;
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount() {
+ return this._treeList.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 (_sequenceList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_sequenceList)) {
+ result = 37 * result + _sequenceList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceList);
+ }
+ if (_sequenceMappingList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
+ result = 37 * result + _sequenceMappingList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
+ }
+ if (_dataSetAnnotationsList != null
+ && !org.castor.util.CycleBreaker
+ .startingToCycle(_dataSetAnnotationsList)) {
+ result = 37 * result + _dataSetAnnotationsList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
+ }
+ if (_alignmentList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_alignmentList)) {
+ result = 37 * result + _alignmentList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentList);
+ }
+ if (_treeList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
+ result = 37 * result + _treeList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
+ }
+ if (_provenance != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+
+ 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);
+ }
+
+ /**
+ * Method removeAlignment.
+ *
+ * @param vAlignment
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignment(
+ final uk.ac.vamsas.objects.core.Alignment vAlignment) {
+ boolean removed = _alignmentList.remove(vAlignment);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Alignment removeAlignmentAt(final int index) {
+ java.lang.Object obj = this._alignmentList.remove(index);
+ return (uk.ac.vamsas.objects.core.Alignment) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlignment() {
+ this._alignmentList.clear();
+ }
+
+ /**
+ */
+ public void removeAllDataSetAnnotations() {
+ this._dataSetAnnotationsList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequence() {
+ this._sequenceList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequenceMapping() {
+ this._sequenceMappingList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree() {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeDataSetAnnotations.
+ *
+ * @param vDataSetAnnotations
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeDataSetAnnotations(
+ final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) {
+ boolean removed = _dataSetAnnotationsList.remove(vDataSetAnnotations);
+ return removed;
+ }
+
+ /**
+ * Method removeDataSetAnnotationsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotationsAt(
+ final int index) {
+ java.lang.Object obj = this._dataSetAnnotationsList.remove(index);
+ return (uk.ac.vamsas.objects.core.DataSetAnnotations) obj;
+ }
+
+ /**
+ * Method removeSequence.
+ *
+ * @param vSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequence(
+ final uk.ac.vamsas.objects.core.Sequence vSequence) {
+ boolean removed = _sequenceList.remove(vSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Sequence removeSequenceAt(final int index) {
+ java.lang.Object obj = this._sequenceList.remove(index);
+ return (uk.ac.vamsas.objects.core.Sequence) obj;
+ }
+
+ /**
+ * Method removeSequenceMapping.
+ *
+ * @param vSequenceMapping
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceMapping(
+ final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping) {
+ boolean removed = _sequenceMappingList.remove(vSequenceMapping);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceMappingAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.SequenceMapping removeSequenceMappingAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceMappingList.remove(index);
+ return (uk.ac.vamsas.objects.core.SequenceMapping) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(final uk.ac.vamsas.objects.core.Tree vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Tree removeTreeAt(final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (uk.ac.vamsas.objects.core.Tree) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlignment(final int index,
+ final uk.ac.vamsas.objects.core.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size()) {
+ throw new IndexOutOfBoundsException("setAlignment: Index value '" + index
+ + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
+ }
+
+ this._alignmentList.set(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentArray
+ */
+ public void setAlignment(
+ final uk.ac.vamsas.objects.core.Alignment[] vAlignmentArray) {
+ // -- copy array
+ _alignmentList.clear();
+
+ for (int i = 0; i < vAlignmentArray.length; i++) {
+ this._alignmentList.add(vAlignmentArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_alignmentList' by copying the given Vector. All
+ * elements will be checked for type safety.
+ *
+ * @param vAlignmentList
+ * the Vector to copy.
+ */
+ public void setAlignment(final java.util.Vector vAlignmentList) {
+ // copy vector
+ this._alignmentList.clear();
+
+ this._alignmentList.addAll(vAlignmentList);
+ }
+
+ /**
+ * Sets the value of '_alignmentList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param alignmentVector
+ * the Vector to set.
+ */
+ public void setAlignmentAsReference(final java.util.Vector alignmentVector) {
+ this._alignmentList = alignmentVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDataSetAnnotations
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setDataSetAnnotations(final int index,
+ final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._dataSetAnnotationsList.size()) {
+ throw new IndexOutOfBoundsException(
+ "setDataSetAnnotations: Index value '" + index
+ + "' not in range [0.."
+ + (this._dataSetAnnotationsList.size() - 1) + "]");
+ }
+
+ this._dataSetAnnotationsList.set(index, vDataSetAnnotations);
+ }
+
+ /**
+ *
+ *
+ * @param vDataSetAnnotationsArray
+ */
+ public void setDataSetAnnotations(
+ final uk.ac.vamsas.objects.core.DataSetAnnotations[] vDataSetAnnotationsArray) {
+ // -- copy array
+ _dataSetAnnotationsList.clear();
+
+ for (int i = 0; i < vDataSetAnnotationsArray.length; i++) {
+ this._dataSetAnnotationsList.add(vDataSetAnnotationsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_dataSetAnnotationsList' by copying the given Vector.
+ * All elements will be checked for type safety.
+ *
+ * @param vDataSetAnnotationsList
+ * the Vector to copy.
+ */
+ public void setDataSetAnnotations(
+ final java.util.Vector vDataSetAnnotationsList) {
+ // copy vector
+ this._dataSetAnnotationsList.clear();
+
+ this._dataSetAnnotationsList.addAll(vDataSetAnnotationsList);
+ }
+
+ /**
+ * Sets the value of '_dataSetAnnotationsList' by setting it to the given
+ * Vector. No type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param dataSetAnnotationsVector
+ * the Vector to set.
+ */
+ public void setDataSetAnnotationsAsReference(
+ final java.util.Vector dataSetAnnotationsVector) {
+ this._dataSetAnnotationsList = dataSetAnnotationsVector;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance
+ * the value of field 'provenance'.
+ */
+ public void setProvenance(
+ final uk.ac.vamsas.objects.core.Provenance provenance) {
+ this._provenance = provenance;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequence(final int index,
+ final uk.ac.vamsas.objects.core.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size()) {
+ throw new IndexOutOfBoundsException("setSequence: Index value '" + index
+ + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
+ }
+
+ this._sequenceList.set(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceArray
+ */
+ public void setSequence(
+ final uk.ac.vamsas.objects.core.Sequence[] vSequenceArray) {
+ // -- copy array
+ _sequenceList.clear();
+
+ for (int i = 0; i < vSequenceArray.length; i++) {
+ this._sequenceList.add(vSequenceArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_sequenceList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vSequenceList
+ * the Vector to copy.
+ */
+ public void setSequence(final java.util.Vector vSequenceList) {
+ // copy vector
+ this._sequenceList.clear();
+
+ this._sequenceList.addAll(vSequenceList);
+ }
+
+ /**
+ * Sets the value of '_sequenceList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param sequenceVector
+ * the Vector to set.
+ */
+ public void setSequenceAsReference(final java.util.Vector sequenceVector) {
+ this._sequenceList = sequenceVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceMapping
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequenceMapping(final int index,
+ final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceMappingList.size()) {
+ throw new IndexOutOfBoundsException("setSequenceMapping: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequenceMappingList.size() - 1) + "]");
+ }
+
+ this._sequenceMappingList.set(index, vSequenceMapping);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceMappingArray
+ */
+ public void setSequenceMapping(
+ final uk.ac.vamsas.objects.core.SequenceMapping[] vSequenceMappingArray) {
+ // -- copy array
+ _sequenceMappingList.clear();
+
+ for (int i = 0; i < vSequenceMappingArray.length; i++) {
+ this._sequenceMappingList.add(vSequenceMappingArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_sequenceMappingList' by copying the given Vector. All
+ * elements will be checked for type safety.
+ *
+ * @param vSequenceMappingList
+ * the Vector to copy.
+ */
+ public void setSequenceMapping(final java.util.Vector vSequenceMappingList) {
+ // copy vector
+ this._sequenceMappingList.clear();
+
+ this._sequenceMappingList.addAll(vSequenceMappingList);
+ }
+
+ /**
+ * Sets the value of '_sequenceMappingList' by setting it to the given Vector.
+ * No type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param sequenceMappingVector
+ * the Vector to set.
+ */
+ public void setSequenceMappingAsReference(
+ final java.util.Vector sequenceMappingVector) {
+ this._sequenceMappingList = sequenceMappingVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTree(final int index,
+ final uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(final uk.ac.vamsas.objects.core.Tree[] vTreeArray) {
+ // -- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_treeList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vTreeList
+ * the Vector to copy.
+ */
+ public void setTree(final java.util.Vector vTreeList) {
+ // copy vector
+ this._treeList.clear();
+
+ this._treeList.addAll(vTreeList);
+ }
+
+ /**
+ * Sets the value of '_treeList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param treeVector
+ * the Vector to set.
+ */
+ public void setTreeAsReference(final java.util.Vector treeVector) {
+ this._treeList = treeVector;
+ }
+
+ /**
+ * 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.DataSet
+ */
+ public static uk.ac.vamsas.objects.core.DataSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.DataSet.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);
+ }