/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
/**
* Class VamsasDocument.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class VamsasDocument extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Vamsas Document Version Number
- */
- private java.lang.String _version;
-
- /**
- * Field _lockFile.
- */
- private uk.ac.vamsas.objects.core.LockFile _lockFile;
-
- /**
- * Field _provenance.
- */
- private uk.ac.vamsas.objects.core.Provenance _provenance;
-
- /**
- * contains unassociated trees and a number of analysis sets
- *
- */
- private java.util.Vector _VAMSASList;
-
- /**
- * Field _applicationDataList.
- */
- private java.util.Vector _applicationDataList;
-
- /**
- * Field _attachmentList.
- */
- private java.util.Vector _attachmentList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VamsasDocument() {
- super();
- this._VAMSASList = new java.util.Vector();
- this._applicationDataList = new java.util.Vector();
- this._attachmentList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vApplicationData
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addApplicationData(
- final uk.ac.vamsas.objects.core.ApplicationData vApplicationData)
- throws java.lang.IndexOutOfBoundsException {
- this._applicationDataList.addElement(vApplicationData);
- }
-
- /**
- *
- *
- * @param index
- * @param vApplicationData
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addApplicationData(
- final int index,
- final uk.ac.vamsas.objects.core.ApplicationData vApplicationData)
- throws java.lang.IndexOutOfBoundsException {
- this._applicationDataList.add(index, vApplicationData);
- }
-
- /**
- *
- *
- * @param vAttachment
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAttachment(
- final uk.ac.vamsas.objects.core.Attachment vAttachment)
- throws java.lang.IndexOutOfBoundsException {
- this._attachmentList.addElement(vAttachment);
- }
-
- /**
- *
- *
- * @param index
- * @param vAttachment
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAttachment(
- final int index,
- final uk.ac.vamsas.objects.core.Attachment vAttachment)
- throws java.lang.IndexOutOfBoundsException {
- this._attachmentList.add(index, vAttachment);
- }
-
- /**
- *
- *
- * @param vVAMSAS
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addVAMSAS(
- final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS)
- throws java.lang.IndexOutOfBoundsException {
- this._VAMSASList.addElement(vVAMSAS);
- }
-
- /**
- *
- *
- * @param index
- * @param vVAMSAS
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addVAMSAS(
- final int index,
- final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS)
- throws java.lang.IndexOutOfBoundsException {
- this._VAMSASList.add(index, vVAMSAS);
- }
-
- /**
- * Method enumerateApplicationData.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.ApplicationData elements
- */
- public java.util.Enumeration enumerateApplicationData(
- ) {
- return this._applicationDataList.elements();
- }
-
- /**
- * Method enumerateAttachment.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Attachment elements
- */
- public java.util.Enumeration enumerateAttachment(
- ) {
- return this._attachmentList.elements();
- }
-
- /**
- * Method enumerateVAMSAS.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.VAMSAS elements
- */
- public java.util.Enumeration enumerateVAMSAS(
- ) {
- return this._VAMSASList.elements();
- }
-
- /**
- * Overrides the java.lang.Object.equals method.
- *
- * @param obj
- * @return true if the objects are equal.
- */
- public boolean equals(
- final java.lang.Object obj) {
- if ( this == obj )
- return true;
-
- if (super.equals(obj)==false)
+public class VamsasDocument extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Vamsas Document Version Number
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _lockFile.
+ */
+ private uk.ac.vamsas.objects.core.LockFile _lockFile;
+
+ /**
+ * Field _provenance.
+ */
+ private uk.ac.vamsas.objects.core.Provenance _provenance;
+
+ /**
+ * contains unassociated trees and a number of analysis sets
+ *
+ */
+ private java.util.Vector _VAMSASList;
+
+ /**
+ * Field _applicationDataList.
+ */
+ private java.util.Vector _applicationDataList;
+
+ /**
+ * Field _attachmentList.
+ */
+ private java.util.Vector _attachmentList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public VamsasDocument() {
+ super();
+ this._VAMSASList = new java.util.Vector();
+ this._applicationDataList = new java.util.Vector();
+ this._attachmentList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vApplicationData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addApplicationData(
+ final uk.ac.vamsas.objects.core.ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException {
+ this._applicationDataList.addElement(vApplicationData);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vApplicationData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addApplicationData(final int index,
+ final uk.ac.vamsas.objects.core.ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException {
+ this._applicationDataList.add(index, vApplicationData);
+ }
+
+ /**
+ *
+ *
+ * @param vAttachment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAttachment(
+ final uk.ac.vamsas.objects.core.Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._attachmentList.addElement(vAttachment);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAttachment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAttachment(final int index,
+ final uk.ac.vamsas.objects.core.Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._attachmentList.add(index, vAttachment);
+ }
+
+ /**
+ *
+ *
+ * @param vVAMSAS
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addVAMSAS(final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException {
+ this._VAMSASList.addElement(vVAMSAS);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vVAMSAS
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addVAMSAS(final int index,
+ final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException {
+ this._VAMSASList.add(index, vVAMSAS);
+ }
+
+ /**
+ * Method enumerateApplicationData.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.ApplicationData
+ * elements
+ */
+ public java.util.Enumeration enumerateApplicationData() {
+ return this._applicationDataList.elements();
+ }
+
+ /**
+ * Method enumerateAttachment.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Attachment
+ * elements
+ */
+ public java.util.Enumeration enumerateAttachment() {
+ return this._attachmentList.elements();
+ }
+
+ /**
+ * Method enumerateVAMSAS.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.VAMSAS elements
+ */
+ public java.util.Enumeration enumerateVAMSAS() {
+ return this._VAMSASList.elements();
+ }
+
+ /**
+ * Overrides the java.lang.Object.equals method.
+ *
+ * @param obj
+ * @return true if the objects are equal.
+ */
+ public boolean equals(final java.lang.Object obj) {
+ if (this == obj)
+ return true;
+
+ if (super.equals(obj) == false)
+ return false;
+
+ if (obj instanceof VamsasDocument) {
+
+ VamsasDocument temp = (VamsasDocument) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._version != null) {
+ if (temp._version == null)
+ return false;
+ if (this._version != temp._version) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ ;
return false;
-
- if (obj instanceof VamsasDocument) {
-
- VamsasDocument temp = (VamsasDocument)obj;
- boolean thcycle;
- boolean tmcycle;
- if (this._version != null) {
- if (temp._version == null) return false;
- if (this._version != temp._version) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._version);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._version);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._version); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); };
- return false;
- }
- if (!thcycle) {
- if (!this._version.equals(temp._version)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
- }
- }
- } else if (temp._version != null)
- return false;
- 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);
- }
- }
- } 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);
- }
- }
- } 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);
- }
- }
- } 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);
- }
- }
- } 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);
- }
- }
- } else if (temp._attachmentList != null)
- return false;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._version.equals(temp._version)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
}
+ } else if (temp._version != null)
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) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.ApplicationData) _applicationDataList.get(index);
- }
-
- /**
- * Method getApplicationData.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.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. <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.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. <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.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.
- * <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 (_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.
+ * <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.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.
+ * <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.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.
+ * <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.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.
+ * <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 (_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);
+ }
}
git://source.jalview.org / vamsas.git / blobdiff