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.ApplicationData[] getApplicationData( - ) { - uk.ac.vamsas.objects.core.ApplicationData[] array = new uk.ac.vamsas.objects.core.ApplicationData[0]; - return (uk.ac.vamsas.objects.core.ApplicationData[]) this._applicationDataList.toArray(array); - } - - /** - * Method getApplicationDataAsReference.Returns a reference to - * '_applicationDataList'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getApplicationDataAsReference( - ) { - return this._applicationDataList; - } - - /** - * Method getApplicationDataCount. - * - * @return the size of this collection - */ - public int getApplicationDataCount( - ) { - return this._applicationDataList.size(); - } - - /** - * Method getAttachment. - * - * @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.Attachment at the given index - */ - public uk.ac.vamsas.objects.core.Attachment getAttachment( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._attachmentList.size()) { - throw new IndexOutOfBoundsException("getAttachment: Index value '" + index + "' not in range [0.." + (this._attachmentList.size() - 1) + "]"); - } - - return (uk.ac.vamsas.objects.core.Attachment) _attachmentList.get(index); - } - - /** - * Method getAttachment.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.Attachment[] getAttachment( - ) { - uk.ac.vamsas.objects.core.Attachment[] array = new uk.ac.vamsas.objects.core.Attachment[0]; - return (uk.ac.vamsas.objects.core.Attachment[]) this._attachmentList.toArray(array); - } - - /** - * Method getAttachmentAsReference.Returns a reference to - * '_attachmentList'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getAttachmentAsReference( - ) { - return this._attachmentList; - } - - /** - * Method getAttachmentCount. - * - * @return the size of this collection - */ - public int getAttachmentCount( - ) { - return this._attachmentList.size(); - } - - /** - * Returns the value of field 'lockFile'. - * - * @return the value of field 'LockFile'. - */ - public uk.ac.vamsas.objects.core.LockFile getLockFile( - ) { - return this._lockFile; - } - - /** - * Returns the value of field 'provenance'. - * - * @return the value of field 'Provenance'. - */ - public uk.ac.vamsas.objects.core.Provenance getProvenance( - ) { - return this._provenance; - } - - /** - * Method getVAMSAS. - * - * @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.VAMSAS at - * the given index - */ - public uk.ac.vamsas.objects.core.VAMSAS getVAMSAS( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._VAMSASList.size()) { - throw new IndexOutOfBoundsException("getVAMSAS: Index value '" + index + "' not in range [0.." + (this._VAMSASList.size() - 1) + "]"); - } - - return (uk.ac.vamsas.objects.core.VAMSAS) _VAMSASList.get(index); - } - - /** - * Method getVAMSAS.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.VAMSAS[] getVAMSAS( - ) { - uk.ac.vamsas.objects.core.VAMSAS[] array = new uk.ac.vamsas.objects.core.VAMSAS[0]; - return (uk.ac.vamsas.objects.core.VAMSAS[]) this._VAMSASList.toArray(array); - } - - /** - * Method getVAMSASAsReference.Returns a reference to - * '_VAMSASList'. No type checking is performed on any - * modifications to the Vector. - * - * @return a reference to the Vector backing this class - */ - public java.util.Vector getVAMSASAsReference( - ) { - return this._VAMSASList; - } - - /** - * Method getVAMSASCount. - * - * @return the size of this collection - */ - public int getVAMSASCount( - ) { - return this._VAMSASList.size(); - } - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Vamsas Document Version - * Number - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion( - ) { - return this._version; - } - - /** - * 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 (_version != null - && !org.castor.util.CycleBreaker.startingToCycle(_version)) { - result = 37 * result + _version.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_version); - } - if (_lockFile != null - && !org.castor.util.CycleBreaker.startingToCycle(_lockFile)) { - result = 37 * result + _lockFile.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_lockFile); - } - if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { - result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + if (this._lockFile != null) { + if (temp._lockFile == null) + return false; + if (this._lockFile != temp._lockFile) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._lockFile); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._lockFile); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile); + } + ; + return false; + } + if (!thcycle) { + if (!this._lockFile.equals(temp._lockFile)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile); + } } - if (_VAMSASList != null - && !org.castor.util.CycleBreaker.startingToCycle(_VAMSASList)) { - result = 37 * result + _VAMSASList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_VAMSASList); + } else if (temp._lockFile != 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); + } } - if (_applicationDataList != null - && !org.castor.util.CycleBreaker.startingToCycle(_applicationDataList)) { - result = 37 * result + _applicationDataList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_applicationDataList); + } else if (temp._provenance != null) + return false; + if (this._VAMSASList != null) { + if (temp._VAMSASList == null) + return false; + if (this._VAMSASList != temp._VAMSASList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._VAMSASList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._VAMSASList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); + } + ; + return false; + } + if (!thcycle) { + if (!this._VAMSASList.equals(temp._VAMSASList)) { + org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); + return false; + } + org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); + } } - if (_attachmentList != null - && !org.castor.util.CycleBreaker.startingToCycle(_attachmentList)) { - result = 37 * result + _attachmentList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_attachmentList); + } else if (temp._VAMSASList != null) + return false; + if (this._applicationDataList != null) { + if (temp._applicationDataList == null) + return false; + if (this._applicationDataList != temp._applicationDataList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._applicationDataList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._applicationDataList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._applicationDataList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._applicationDataList); + } + ; + return false; + } + if (!thcycle) { + if (!this._applicationDataList.equals(temp._applicationDataList)) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._applicationDataList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._applicationDataList); + return false; + } + org.castor.util.CycleBreaker + .releaseCycleHandle(this._applicationDataList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._applicationDataList); + } } - - 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) { + } else if (temp._applicationDataList != null) + return false; + if (this._attachmentList != null) { + if (temp._attachmentList == null) + return false; + if (this._attachmentList != temp._attachmentList) { + thcycle = org.castor.util.CycleBreaker + .startingToCycle(this._attachmentList); + tmcycle = org.castor.util.CycleBreaker + .startingToCycle(temp._attachmentList); + if (thcycle != tmcycle) { + if (!thcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._attachmentList); + } + ; + if (!tmcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._attachmentList); + } + ; return false; + } + if (!thcycle) { + if (!this._attachmentList.equals(temp._attachmentList)) { + org.castor.util.CycleBreaker + .releaseCycleHandle(this._attachmentList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._attachmentList); + return false; + } + org.castor.util.CycleBreaker + .releaseCycleHandle(this._attachmentList); + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._attachmentList); + } } - 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 removeAllApplicationData( - ) { - this._applicationDataList.clear(); - } - - /** - */ - public void removeAllAttachment( - ) { - this._attachmentList.clear(); - } - - /** - */ - public void removeAllVAMSAS( - ) { - this._VAMSASList.clear(); - } - - /** - * Method removeApplicationData. - * - * @param vApplicationData - * @return true if the object was removed from the collection. - */ - public boolean removeApplicationData( - final uk.ac.vamsas.objects.core.ApplicationData vApplicationData) { - boolean removed = _applicationDataList.remove(vApplicationData); - return removed; - } - - /** - * Method removeApplicationDataAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.ApplicationData removeApplicationDataAt( - final int index) { - java.lang.Object obj = this._applicationDataList.remove(index); - return (uk.ac.vamsas.objects.core.ApplicationData) obj; - } - - /** - * Method removeAttachment. - * - * @param vAttachment - * @return true if the object was removed from the collection. - */ - public boolean removeAttachment( - final uk.ac.vamsas.objects.core.Attachment vAttachment) { - boolean removed = _attachmentList.remove(vAttachment); - return removed; + } else if (temp._attachmentList != null) + return false; + return true; } - - /** - * Method removeAttachmentAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.Attachment removeAttachmentAt( - final int index) { - java.lang.Object obj = this._attachmentList.remove(index); - return (uk.ac.vamsas.objects.core.Attachment) obj; + return false; + } + + /** + * Method getApplicationData. + * + * @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.ApplicationData at the + * given index + */ + public uk.ac.vamsas.objects.core.ApplicationData getApplicationData( + final int index) throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._applicationDataList.size()) { + throw new IndexOutOfBoundsException("getApplicationData: Index value '" + + index + "' not in range [0.." + + (this._applicationDataList.size() - 1) + "]"); } - /** - * Method removeVAMSAS. - * - * @param vVAMSAS - * @return true if the object was removed from the collection. - */ - public boolean removeVAMSAS( - final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS) { - boolean removed = _VAMSASList.remove(vVAMSAS); - return removed; + return (uk.ac.vamsas.objects.core.ApplicationData) _applicationDataList + .get(index); + } + + /** + * Method getApplicationData.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.ApplicationData[] getApplicationData() { + uk.ac.vamsas.objects.core.ApplicationData[] array = new uk.ac.vamsas.objects.core.ApplicationData[0]; + return (uk.ac.vamsas.objects.core.ApplicationData[]) this._applicationDataList + .toArray(array); + } + + /** + * Method getApplicationDataAsReference.Returns a reference to + * '_applicationDataList'. No type checking is performed on any modifications + * to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getApplicationDataAsReference() { + return this._applicationDataList; + } + + /** + * Method getApplicationDataCount. + * + * @return the size of this collection + */ + public int getApplicationDataCount() { + return this._applicationDataList.size(); + } + + /** + * Method getAttachment. + * + * @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.Attachment at the given + * index + */ + public uk.ac.vamsas.objects.core.Attachment getAttachment(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._attachmentList.size()) { + throw new IndexOutOfBoundsException("getAttachment: Index value '" + + index + "' not in range [0.." + (this._attachmentList.size() - 1) + + "]"); } - /** - * Method removeVAMSASAt. - * - * @param index - * @return the element removed from the collection - */ - public uk.ac.vamsas.objects.core.VAMSAS removeVAMSASAt( - final int index) { - java.lang.Object obj = this._VAMSASList.remove(index); - return (uk.ac.vamsas.objects.core.VAMSAS) obj; + return (uk.ac.vamsas.objects.core.Attachment) _attachmentList.get(index); + } + + /** + * Method getAttachment.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.Attachment[] getAttachment() { + uk.ac.vamsas.objects.core.Attachment[] array = new uk.ac.vamsas.objects.core.Attachment[0]; + return (uk.ac.vamsas.objects.core.Attachment[]) this._attachmentList + .toArray(array); + } + + /** + * Method getAttachmentAsReference.Returns a reference to '_attachmentList'. + * No type checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getAttachmentAsReference() { + return this._attachmentList; + } + + /** + * Method getAttachmentCount. + * + * @return the size of this collection + */ + public int getAttachmentCount() { + return this._attachmentList.size(); + } + + /** + * Returns the value of field 'lockFile'. + * + * @return the value of field 'LockFile'. + */ + public uk.ac.vamsas.objects.core.LockFile getLockFile() { + return this._lockFile; + } + + /** + * Returns the value of field 'provenance'. + * + * @return the value of field 'Provenance'. + */ + public uk.ac.vamsas.objects.core.Provenance getProvenance() { + return this._provenance; + } + + /** + * Method getVAMSAS. + * + * @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.VAMSAS at the given + * index + */ + public uk.ac.vamsas.objects.core.VAMSAS getVAMSAS(final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._VAMSASList.size()) { + throw new IndexOutOfBoundsException("getVAMSAS: Index value '" + index + + "' not in range [0.." + (this._VAMSASList.size() - 1) + "]"); } - /** - * - * - * @param index - * @param vApplicationData - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setApplicationData( - final int index, - final uk.ac.vamsas.objects.core.ApplicationData vApplicationData) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._applicationDataList.size()) { - throw new IndexOutOfBoundsException("setApplicationData: Index value '" + index + "' not in range [0.." + (this._applicationDataList.size() - 1) + "]"); - } - - this._applicationDataList.set(index, vApplicationData); + return (uk.ac.vamsas.objects.core.VAMSAS) _VAMSASList.get(index); + } + + /** + * Method getVAMSAS.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.VAMSAS[] getVAMSAS() { + uk.ac.vamsas.objects.core.VAMSAS[] array = new uk.ac.vamsas.objects.core.VAMSAS[0]; + return (uk.ac.vamsas.objects.core.VAMSAS[]) this._VAMSASList.toArray(array); + } + + /** + * Method getVAMSASAsReference.Returns a reference to '_VAMSASList'. No type + * checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getVAMSASAsReference() { + return this._VAMSASList; + } + + /** + * Method getVAMSASCount. + * + * @return the size of this collection + */ + public int getVAMSASCount() { + return this._VAMSASList.size(); + } + + /** + * Returns the value of field 'version'. The field 'version' has the following + * description: Vamsas Document Version Number + * + * @return the value of field 'Version'. + */ + public java.lang.String getVersion() { + return this._version; + } + + /** + * 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 (_version != null + && !org.castor.util.CycleBreaker.startingToCycle(_version)) { + result = 37 * result + _version.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_version); } - - /** - * - * - * @param vApplicationDataArray - */ - public void setApplicationData( - final uk.ac.vamsas.objects.core.ApplicationData[] vApplicationDataArray) { - //-- copy array - _applicationDataList.clear(); - - for (int i = 0; i < vApplicationDataArray.length; i++) { - this._applicationDataList.add(vApplicationDataArray[i]); - } + if (_lockFile != null + && !org.castor.util.CycleBreaker.startingToCycle(_lockFile)) { + result = 37 * result + _lockFile.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_lockFile); } - - /** - * Sets the value of '_applicationDataList' by copying the - * given Vector. All elements will be checked for type safety. - * - * @param vApplicationDataList the Vector to copy. - */ - public void setApplicationData( - final java.util.Vector vApplicationDataList) { - // copy vector - this._applicationDataList.clear(); - - this._applicationDataList.addAll(vApplicationDataList); + if (_provenance != null + && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + result = 37 * result + _provenance.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); } - - /** - * Sets the value of '_applicationDataList' by setting it to - * the given Vector. No type checking is performed. - * @deprecated - * - * @param applicationDataVector the Vector to set. - */ - public void setApplicationDataAsReference( - final java.util.Vector applicationDataVector) { - this._applicationDataList = applicationDataVector; + if (_VAMSASList != null + && !org.castor.util.CycleBreaker.startingToCycle(_VAMSASList)) { + result = 37 * result + _VAMSASList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_VAMSASList); } - - /** - * - * - * @param index - * @param vAttachment - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAttachment( - final int index, - final uk.ac.vamsas.objects.core.Attachment vAttachment) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._attachmentList.size()) { - throw new IndexOutOfBoundsException("setAttachment: Index value '" + index + "' not in range [0.." + (this._attachmentList.size() - 1) + "]"); - } - - this._attachmentList.set(index, vAttachment); + if (_applicationDataList != null + && !org.castor.util.CycleBreaker.startingToCycle(_applicationDataList)) { + result = 37 * result + _applicationDataList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_applicationDataList); } - - /** - * - * - * @param vAttachmentArray - */ - public void setAttachment( - final uk.ac.vamsas.objects.core.Attachment[] vAttachmentArray) { - //-- copy array - _attachmentList.clear(); - - for (int i = 0; i < vAttachmentArray.length; i++) { - this._attachmentList.add(vAttachmentArray[i]); - } + if (_attachmentList != null + && !org.castor.util.CycleBreaker.startingToCycle(_attachmentList)) { + result = 37 * result + _attachmentList.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_attachmentList); } - /** - * Sets the value of '_attachmentList' by copying the given - * Vector. All elements will be checked for type safety. - * - * @param vAttachmentList the Vector to copy. - */ - public void setAttachment( - final java.util.Vector vAttachmentList) { - // copy vector - this._attachmentList.clear(); - - this._attachmentList.addAll(vAttachmentList); + 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; } - - /** - * Sets the value of '_attachmentList' by setting it to the - * given Vector. No type checking is performed. - * @deprecated - * - * @param attachmentVector the Vector to set. + 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 setAttachmentAsReference( - final java.util.Vector attachmentVector) { - this._attachmentList = attachmentVector; - } + public void removeAllApplicationData() { + this._applicationDataList.clear(); + } - /** - * Sets the value of field 'lockFile'. - * - * @param lockFile the value of field 'lockFile'. + /** */ - public void setLockFile( - final uk.ac.vamsas.objects.core.LockFile lockFile) { - this._lockFile = lockFile; - } + public void removeAllAttachment() { + this._attachmentList.clear(); + } - /** - * 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; + public void removeAllVAMSAS() { + this._VAMSASList.clear(); + } + + /** + * Method removeApplicationData. + * + * @param vApplicationData + * @return true if the object was removed from the collection. + */ + public boolean removeApplicationData( + final uk.ac.vamsas.objects.core.ApplicationData vApplicationData) { + boolean removed = _applicationDataList.remove(vApplicationData); + return removed; + } + + /** + * Method removeApplicationDataAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.ApplicationData removeApplicationDataAt( + final int index) { + java.lang.Object obj = this._applicationDataList.remove(index); + return (uk.ac.vamsas.objects.core.ApplicationData) obj; + } + + /** + * Method removeAttachment. + * + * @param vAttachment + * @return true if the object was removed from the collection. + */ + public boolean removeAttachment( + final uk.ac.vamsas.objects.core.Attachment vAttachment) { + boolean removed = _attachmentList.remove(vAttachment); + return removed; + } + + /** + * Method removeAttachmentAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.Attachment removeAttachmentAt(final int index) { + java.lang.Object obj = this._attachmentList.remove(index); + return (uk.ac.vamsas.objects.core.Attachment) obj; + } + + /** + * Method removeVAMSAS. + * + * @param vVAMSAS + * @return true if the object was removed from the collection. + */ + public boolean removeVAMSAS(final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS) { + boolean removed = _VAMSASList.remove(vVAMSAS); + return removed; + } + + /** + * Method removeVAMSASAt. + * + * @param index + * @return the element removed from the collection + */ + public uk.ac.vamsas.objects.core.VAMSAS removeVAMSASAt(final int index) { + java.lang.Object obj = this._VAMSASList.remove(index); + return (uk.ac.vamsas.objects.core.VAMSAS) obj; + } + + /** + * + * + * @param index + * @param vApplicationData + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setApplicationData(final int index, + final uk.ac.vamsas.objects.core.ApplicationData vApplicationData) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._applicationDataList.size()) { + throw new IndexOutOfBoundsException("setApplicationData: Index value '" + + index + "' not in range [0.." + + (this._applicationDataList.size() - 1) + "]"); } - /** - * - * - * @param index - * @param vVAMSAS - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setVAMSAS( - final int index, - final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._VAMSASList.size()) { - throw new IndexOutOfBoundsException("setVAMSAS: Index value '" + index + "' not in range [0.." + (this._VAMSASList.size() - 1) + "]"); - } - - this._VAMSASList.set(index, vVAMSAS); + this._applicationDataList.set(index, vApplicationData); + } + + /** + * + * + * @param vApplicationDataArray + */ + public void setApplicationData( + final uk.ac.vamsas.objects.core.ApplicationData[] vApplicationDataArray) { + // -- copy array + _applicationDataList.clear(); + + for (int i = 0; i < vApplicationDataArray.length; i++) { + this._applicationDataList.add(vApplicationDataArray[i]); } - - /** - * - * - * @param vVAMSASArray - */ - public void setVAMSAS( - final uk.ac.vamsas.objects.core.VAMSAS[] vVAMSASArray) { - //-- copy array - _VAMSASList.clear(); - - for (int i = 0; i < vVAMSASArray.length; i++) { - this._VAMSASList.add(vVAMSASArray[i]); - } + } + + /** + * Sets the value of '_applicationDataList' by copying the given Vector. All + * elements will be checked for type safety. + * + * @param vApplicationDataList + * the Vector to copy. + */ + public void setApplicationData(final java.util.Vector vApplicationDataList) { + // copy vector + this._applicationDataList.clear(); + + this._applicationDataList.addAll(vApplicationDataList); + } + + /** + * Sets the value of '_applicationDataList' by setting it to the given Vector. + * No type checking is performed. + * + * @deprecated + * + * @param applicationDataVector + * the Vector to set. + */ + public void setApplicationDataAsReference( + final java.util.Vector applicationDataVector) { + this._applicationDataList = applicationDataVector; + } + + /** + * + * + * @param index + * @param vAttachment + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setAttachment(final int index, + final uk.ac.vamsas.objects.core.Attachment vAttachment) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._attachmentList.size()) { + throw new IndexOutOfBoundsException("setAttachment: Index value '" + + index + "' not in range [0.." + (this._attachmentList.size() - 1) + + "]"); } - /** - * Sets the value of '_VAMSASList' by copying the given Vector. - * All elements will be checked for type safety. - * - * @param vVAMSASList the Vector to copy. - */ - public void setVAMSAS( - final java.util.Vector vVAMSASList) { - // copy vector - this._VAMSASList.clear(); - - this._VAMSASList.addAll(vVAMSASList); + this._attachmentList.set(index, vAttachment); + } + + /** + * + * + * @param vAttachmentArray + */ + public void setAttachment( + final uk.ac.vamsas.objects.core.Attachment[] vAttachmentArray) { + // -- copy array + _attachmentList.clear(); + + for (int i = 0; i < vAttachmentArray.length; i++) { + this._attachmentList.add(vAttachmentArray[i]); } - - /** - * Sets the value of '_VAMSASList' by setting it to the given - * Vector. No type checking is performed. - * @deprecated - * - * @param VAMSASVector the Vector to set. - */ - public void setVAMSASAsReference( - final java.util.Vector VAMSASVector) { - this._VAMSASList = VAMSASVector; + } + + /** + * Sets the value of '_attachmentList' by copying the given Vector. All + * elements will be checked for type safety. + * + * @param vAttachmentList + * the Vector to copy. + */ + public void setAttachment(final java.util.Vector vAttachmentList) { + // copy vector + this._attachmentList.clear(); + + this._attachmentList.addAll(vAttachmentList); + } + + /** + * Sets the value of '_attachmentList' by setting it to the given Vector. No + * type checking is performed. + * + * @deprecated + * + * @param attachmentVector + * the Vector to set. + */ + public void setAttachmentAsReference(final java.util.Vector attachmentVector) { + this._attachmentList = attachmentVector; + } + + /** + * Sets the value of field 'lockFile'. + * + * @param lockFile + * the value of field 'lockFile'. + */ + public void setLockFile(final uk.ac.vamsas.objects.core.LockFile lockFile) { + this._lockFile = lockFile; + } + + /** + * 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 vVAMSAS + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setVAMSAS(final int index, + final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._VAMSASList.size()) { + throw new IndexOutOfBoundsException("setVAMSAS: Index value '" + index + + "' not in range [0.." + (this._VAMSASList.size() - 1) + "]"); } - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Vamsas Document Version Number - * - * @param version the value of field 'version'. - */ - public void setVersion( - final java.lang.String version) { - this._version = version; - } + this._VAMSASList.set(index, vVAMSAS); + } - /** - * 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.VamsasDocument - */ - public static uk.ac.vamsas.objects.core.VamsasDocument unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.VamsasDocument.class, reader); - } + /** + * + * + * @param vVAMSASArray + */ + public void setVAMSAS(final uk.ac.vamsas.objects.core.VAMSAS[] vVAMSASArray) { + // -- copy array + _VAMSASList.clear(); - /** - * - * - * @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); + for (int i = 0; i < vVAMSASArray.length; i++) { + this._VAMSASList.add(vVAMSASArray[i]); } + } + + /** + * Sets the value of '_VAMSASList' by copying the given Vector. All elements + * will be checked for type safety. + * + * @param vVAMSASList + * the Vector to copy. + */ + public void setVAMSAS(final java.util.Vector vVAMSASList) { + // copy vector + this._VAMSASList.clear(); + + this._VAMSASList.addAll(vVAMSASList); + } + + /** + * Sets the value of '_VAMSASList' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param VAMSASVector + * the Vector to set. + */ + public void setVAMSASAsReference(final java.util.Vector VAMSASVector) { + this._VAMSASList = VAMSASVector; + } + + /** + * Sets the value of field 'version'. The field 'version' has the following + * description: Vamsas Document Version Number + * + * @param version + * the value of field 'version'. + */ + public void setVersion(final java.lang.String version) { + this._version = version; + } + + /** + * 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.VamsasDocument + */ + public static uk.ac.vamsas.objects.core.VamsasDocument unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.VamsasDocument.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); + } }