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 know - * 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.
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 know 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.
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 know - * 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 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.
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 know - * 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. - *
- * The following steps came from Effective Java Programming - * Language Guide 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) { - result = 37 * result + _id.hashCode(); - } - if (_sequenceList != null) { - result = 37 * result + _sequenceList.hashCode(); - } - if (_dataSetAnnotationsList != null) { - result = 37 * result + _dataSetAnnotationsList.hashCode(); - } - if (_alignmentList != null) { - result = 37 * result + _alignmentList.hashCode(); - } - if (_treeList != null) { - result = 37 * result + _treeList.hashCode(); - } - if (_provenance != null) { - result = 37 * result + _provenance.hashCode(); - } - - 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) { + if (this._sequenceMappingList != null) { + if (temp._sequenceMappingList == null) + return false; + if (this._sequenceMappingList != temp._sequenceMappingList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._sequenceMappingList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._sequenceMappingList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._sequenceMappingList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._sequenceMappingList); + } + ; return false; + } + if (!thcycle) { + if (!this._sequenceMappingList.equals(temp._sequenceMappingList)) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._sequenceMappingList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._sequenceMappingList); + return false; + } + org.castor.util.CycleBreaker + .releaseCycleHandle(this._sequenceMappingList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._sequenceMappingList); + } } - 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 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 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) + "]"); + } else if (temp._sequenceMappingList != null) + return false; + if (this._dataSetAnnotationsList != null) { + if (temp._dataSetAnnotationsList == null) + return false; + if (this._dataSetAnnotationsList != temp._dataSetAnnotationsList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._dataSetAnnotationsList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._dataSetAnnotationsList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._dataSetAnnotationsList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._dataSetAnnotationsList); + } + ; + return false; + } + if (!thcycle) { + if (!this._dataSetAnnotationsList + .equals(temp._dataSetAnnotationsList)) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._dataSetAnnotationsList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._dataSetAnnotationsList); + return false; + } + org.castor.util.CycleBreaker + .releaseCycleHandle(this._dataSetAnnotationsList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._dataSetAnnotationsList); + } } - - 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]); + } else if (temp._dataSetAnnotationsList != null) + return false; + if (this._alignmentList != null) { + if (temp._alignmentList == null) + return false; + if (this._alignmentList != temp._alignmentList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._alignmentList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._alignmentList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._alignmentList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._alignmentList); + } + ; + return false; + } + if (!thcycle) { + if (!this._alignmentList.equals(temp._alignmentList)) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._alignmentList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._alignmentList); + return false; + } + org.castor.util.CycleBreaker + .releaseCycleHandle(this._alignmentList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._alignmentList); + } } - } - - /** - * 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 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) + "]"); + } else if (temp._alignmentList != null) + return false; + if (this._treeList != null) { + if (temp._treeList == null) + return false; + if (this._treeList != temp._treeList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._treeList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._treeList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + } + ; + return false; + } + if (!thcycle) { + if (!this._treeList.equals(temp._treeList)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + } } - - 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]); + } else if (temp._treeList != null) + return false; + if (this._provenance != null) { + if (temp._provenance == null) + return false; + if (this._provenance != temp._provenance) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._provenance); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._provenance); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } + ; + return false; + } + if (!thcycle) { + if (!this._provenance.equals(temp._provenance)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + } } - } - - /** - * 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); - } + } 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. + *
+ * 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 + * know 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. + *
+ * 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 + * know 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. + *
+ * 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 + * know 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. + *
+ * 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 + * know 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. + *
+ * 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 + * know 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. + *
+ * The following steps came from Effective Java Programming Language + * Guide 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); + } }