/*
- * 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 Tree.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class Tree extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- */
- private java.lang.String _id;
-
- /**
- * Field _modifiable.
- */
- private java.lang.String _modifiable;
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _newickList.
- */
- private java.util.Vector _newickList;
-
- /**
- * node identity and mapping data between tree
- * representations and vamsas document objects
- */
- private java.util.Vector _treenodeList;
-
- /**
- * Field _propertyList.
- */
- private java.util.Vector _propertyList;
-
- /**
- * Field _provenance.
- */
- private uk.ac.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Tree() {
- super();
- this._newickList = new java.util.Vector();
- this._treenodeList = new java.util.Vector();
- this._propertyList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vNewick
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addNewick(
- final uk.ac.vamsas.objects.core.Newick vNewick)
- throws java.lang.IndexOutOfBoundsException {
- this._newickList.addElement(vNewick);
- }
-
- /**
- *
- *
- * @param index
- * @param vNewick
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addNewick(
- final int index,
- final uk.ac.vamsas.objects.core.Newick vNewick)
- throws java.lang.IndexOutOfBoundsException {
- this._newickList.add(index, vNewick);
- }
-
- /**
- *
- *
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.addElement(vProperty);
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final int index,
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.add(index, vProperty);
- }
-
- /**
- *
- *
- * @param vTreenode
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTreenode(
- final uk.ac.vamsas.objects.core.Treenode vTreenode)
- throws java.lang.IndexOutOfBoundsException {
- this._treenodeList.addElement(vTreenode);
- }
-
- /**
- *
- *
- * @param index
- * @param vTreenode
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTreenode(
- final int index,
- final uk.ac.vamsas.objects.core.Treenode vTreenode)
- throws java.lang.IndexOutOfBoundsException {
- this._treenodeList.add(index, vTreenode);
- }
-
- /**
- * Method enumerateNewick.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Newick elements
- */
- public java.util.Enumeration enumerateNewick(
- ) {
- return this._newickList.elements();
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Property elements
- */
- public java.util.Enumeration enumerateProperty(
- ) {
- return this._propertyList.elements();
- }
-
- /**
- * Method enumerateTreenode.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Treenode elements
- */
- public java.util.Enumeration enumerateTreenode(
- ) {
- return this._treenodeList.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 Tree extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Primary Key for vamsas object referencing
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _modifiable.
+ */
+ private java.lang.String _modifiable;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _newickList.
+ */
+ private java.util.Vector _newickList;
+
+ /**
+ * node identity and mapping data between tree representations and vamsas
+ * document objects
+ */
+ private java.util.Vector _treenodeList;
+
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
+ /**
+ * Field _provenance.
+ */
+ private uk.ac.vamsas.objects.core.Provenance _provenance;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Tree() {
+ super();
+ this._newickList = new java.util.Vector();
+ this._treenodeList = new java.util.Vector();
+ this._propertyList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vNewick
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addNewick(final uk.ac.vamsas.objects.core.Newick vNewick)
+ throws java.lang.IndexOutOfBoundsException {
+ this._newickList.addElement(vNewick);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vNewick
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addNewick(final int index,
+ final uk.ac.vamsas.objects.core.Newick vNewick)
+ throws java.lang.IndexOutOfBoundsException {
+ this._newickList.add(index, vNewick);
+ }
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final int index,
+ final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vTreenode
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTreenode(final uk.ac.vamsas.objects.core.Treenode vTreenode)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treenodeList.addElement(vTreenode);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTreenode
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTreenode(final int index,
+ final uk.ac.vamsas.objects.core.Treenode vTreenode)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treenodeList.add(index, vTreenode);
+ }
+
+ /**
+ * Method enumerateNewick.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Newick elements
+ */
+ public java.util.Enumeration enumerateNewick() {
+ return this._newickList.elements();
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements
+ */
+ public java.util.Enumeration enumerateProperty() {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Method enumerateTreenode.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Treenode elements
+ */
+ public java.util.Enumeration enumerateTreenode() {
+ return this._treenodeList.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 Tree) {
+
+ Tree temp = (Tree) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._id != null) {
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
return false;
-
- if (obj instanceof Tree) {
-
- Tree temp = (Tree)obj;
- boolean thcycle;
- boolean tmcycle;
- if (this._id != null) {
- if (temp._id == null) return false;
- if (this._id != temp._id) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
- return false;
- if (this._modifiable != null) {
- if (temp._modifiable == null) return false;
- if (this._modifiable != temp._modifiable) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._modifiable);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._modifiable);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); };
- return false;
- }
- if (!thcycle) {
- if (!this._modifiable.equals(temp._modifiable)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- }
- } else if (temp._modifiable != null)
- return false;
- if (this._title != null) {
- if (temp._title == null) return false;
- if (this._title != temp._title) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._title);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._title);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._title); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); };
- return false;
- }
- if (!thcycle) {
- if (!this._title.equals(temp._title)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
- }
- }
- } else if (temp._title != null)
- return false;
- if (this._newickList != null) {
- if (temp._newickList == null) return false;
- if (this._newickList != temp._newickList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._newickList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._newickList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); };
- return false;
- }
- if (!thcycle) {
- if (!this._newickList.equals(temp._newickList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
- }
- }
- } else if (temp._newickList != null)
- return false;
- if (this._treenodeList != null) {
- if (temp._treenodeList == null) return false;
- if (this._treenodeList != temp._treenodeList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._treenodeList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._treenodeList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList); };
- return false;
- }
- if (!thcycle) {
- if (!this._treenodeList.equals(temp._treenodeList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList);
- }
- }
- } else if (temp._treenodeList != null)
- return false;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- if (this._propertyList != temp._propertyList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._propertyList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._propertyList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); };
- return false;
- }
- if (!thcycle) {
- if (!this._propertyList.equals(temp._propertyList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- }
- }
- } else if (temp._propertyList != 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;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
}
+ } else if (temp._id != null)
return false;
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return the value of field 'Modifiable'.
- */
- public java.lang.String getModifiable(
- ) {
- return this._modifiable;
- }
-
- /**
- * Method getNewick.
- *
- * @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.Newick at
- * the given index
- */
- public uk.ac.vamsas.objects.core.Newick getNewick(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._newickList.size()) {
- throw new IndexOutOfBoundsException("getNewick: Index value '" + index + "' not in range [0.." + (this._newickList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Newick) _newickList.get(index);
- }
-
- /**
- * Method getNewick.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.Newick[] getNewick(
- ) {
- uk.ac.vamsas.objects.core.Newick[] array = new uk.ac.vamsas.objects.core.Newick[0];
- return (uk.ac.vamsas.objects.core.Newick[]) this._newickList.toArray(array);
- }
-
- /**
- * Method getNewickAsReference.Returns a reference to
- * '_newickList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getNewickAsReference(
- ) {
- return this._newickList;
- }
-
- /**
- * Method getNewickCount.
- *
- * @return the size of this collection
- */
- public int getNewickCount(
- ) {
- return this._newickList.size();
- }
-
- /**
- * Method getProperty.
- *
- * @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.Property
- * at the given index
- */
- public uk.ac.vamsas.objects.core.Property getProperty(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
- }
-
- /**
- * Method getProperty.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.Property[] getProperty(
- ) {
- uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
- return (uk.ac.vamsas.objects.core.Property[]) this._propertyList.toArray(array);
- }
-
- /**
- * Method getPropertyAsReference.Returns a reference to
- * '_propertyList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getPropertyAsReference(
- ) {
- return this._propertyList;
- }
-
- /**
- * Method getPropertyCount.
- *
- * @return the size of this collection
- */
- public int getPropertyCount(
- ) {
- return this._propertyList.size();
- }
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return the value of field 'Provenance'.
- */
- public uk.ac.vamsas.objects.core.Provenance getProvenance(
- ) {
- return this._provenance;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Method getTreenode.
- *
- * @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.Treenode
- * at the given index
- */
- public uk.ac.vamsas.objects.core.Treenode getTreenode(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treenodeList.size()) {
- throw new IndexOutOfBoundsException("getTreenode: Index value '" + index + "' not in range [0.." + (this._treenodeList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Treenode) _treenodeList.get(index);
- }
-
- /**
- * Method getTreenode.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.Treenode[] getTreenode(
- ) {
- uk.ac.vamsas.objects.core.Treenode[] array = new uk.ac.vamsas.objects.core.Treenode[0];
- return (uk.ac.vamsas.objects.core.Treenode[]) this._treenodeList.toArray(array);
- }
-
- /**
- * Method getTreenodeAsReference.Returns a reference to
- * '_treenodeList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getTreenodeAsReference(
- ) {
- return this._treenodeList;
- }
-
- /**
- * Method getTreenodeCount.
- *
- * @return the size of this collection
- */
- public int getTreenodeCount(
- ) {
- return this._treenodeList.size();
- }
-
- /**
- * Overrides the java.lang.Object.hashCode method.
- * <p>
- * The following steps came from <b>Effective Java Programming
- * Language Guide</b> by Joshua Bloch, Chapter 3
- *
- * @return a hash code value for the object.
- */
- public int hashCode(
- ) {
- int result = super.hashCode();
-
- long tmp;
- if (_id != null
- && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_modifiable != null
- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
- result = 37 * result + _modifiable.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
- }
- if (_title != null
- && !org.castor.util.CycleBreaker.startingToCycle(_title)) {
- result = 37 * result + _title.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_title);
+ if (this._modifiable != null) {
+ if (temp._modifiable == null)
+ return false;
+ if (this._modifiable != temp._modifiable) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._modifiable);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._modifiable);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._modifiable.equals(temp._modifiable)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
}
- if (_newickList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) {
- result = 37 * result + _newickList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_newickList);
+ } else if (temp._modifiable != null)
+ return false;
+ if (this._title != null) {
+ if (temp._title == null)
+ return false;
+ if (this._title != temp._title) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._title.equals(temp._title)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
+ }
}
- if (_treenodeList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) {
- result = 37 * result + _treenodeList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList);
+ } else if (temp._title != null)
+ return false;
+ if (this._newickList != null) {
+ if (temp._newickList == null)
+ return false;
+ if (this._newickList != temp._newickList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._newickList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._newickList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._newickList.equals(temp._newickList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
+ }
}
- if (_propertyList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ } else if (temp._newickList != null)
+ return false;
+ if (this._treenodeList != null) {
+ if (temp._treenodeList == null)
+ return false;
+ if (this._treenodeList != temp._treenodeList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._treenodeList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._treenodeList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._treenodeList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._treenodeList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._treenodeList.equals(temp._treenodeList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._treenodeList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._treenodeList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList);
+ }
}
- if (_provenance != null
- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
- result = 37 * result + _provenance.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
+ } else if (temp._treenodeList != null)
+ return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
}
-
- 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._propertyList != 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);
+ }
}
- 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 removeAllNewick(
- ) {
- this._newickList.clear();
- }
-
- /**
- */
- public void removeAllProperty(
- ) {
- this._propertyList.clear();
- }
-
- /**
- */
- public void removeAllTreenode(
- ) {
- this._treenodeList.clear();
- }
-
- /**
- * Method removeNewick.
- *
- * @param vNewick
- * @return true if the object was removed from the collection.
- */
- public boolean removeNewick(
- final uk.ac.vamsas.objects.core.Newick vNewick) {
- boolean removed = _newickList.remove(vNewick);
- return removed;
- }
-
- /**
- * Method removeNewickAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Newick removeNewickAt(
- final int index) {
- java.lang.Object obj = this._newickList.remove(index);
- return (uk.ac.vamsas.objects.core.Newick) obj;
- }
-
- /**
- * Method removeProperty.
- *
- * @param vProperty
- * @return true if the object was removed from the collection.
- */
- public boolean removeProperty(
- final uk.ac.vamsas.objects.core.Property vProperty) {
- boolean removed = _propertyList.remove(vProperty);
- return removed;
- }
-
- /**
- * Method removePropertyAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Property removePropertyAt(
- final int index) {
- java.lang.Object obj = this._propertyList.remove(index);
- return (uk.ac.vamsas.objects.core.Property) obj;
- }
-
- /**
- * Method removeTreenode.
- *
- * @param vTreenode
- * @return true if the object was removed from the collection.
- */
- public boolean removeTreenode(
- final uk.ac.vamsas.objects.core.Treenode vTreenode) {
- boolean removed = _treenodeList.remove(vTreenode);
- return removed;
+ } else if (temp._provenance != null)
+ return false;
+ return true;
}
-
- /**
- * Method removeTreenodeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Treenode removeTreenodeAt(
- final int index) {
- java.lang.Object obj = this._treenodeList.remove(index);
- return (uk.ac.vamsas.objects.core.Treenode) obj;
+ return false;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Primary Key for vamsas object referencing
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId() {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'modifiable'.
+ *
+ * @return the value of field 'Modifiable'.
+ */
+ public java.lang.String getModifiable() {
+ return this._modifiable;
+ }
+
+ /**
+ * Method getNewick.
+ *
+ * @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.Newick at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Newick getNewick(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._newickList.size()) {
+ throw new IndexOutOfBoundsException("getNewick: Index value '" + index
+ + "' not in range [0.." + (this._newickList.size() - 1) + "]");
}
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
+ return (uk.ac.vamsas.objects.core.Newick) _newickList.get(index);
+ }
+
+ /**
+ * Method getNewick.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.Newick[] getNewick() {
+ uk.ac.vamsas.objects.core.Newick[] array = new uk.ac.vamsas.objects.core.Newick[0];
+ return (uk.ac.vamsas.objects.core.Newick[]) this._newickList.toArray(array);
+ }
+
+ /**
+ * Method getNewickAsReference.Returns a reference to '_newickList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getNewickAsReference() {
+ return this._newickList;
+ }
+
+ /**
+ * Method getNewickCount.
+ *
+ * @return the size of this collection
+ */
+ public int getNewickCount() {
+ return this._newickList.size();
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @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.Property at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Property getProperty(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
}
- /**
- * Sets the value of field 'modifiable'.
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(
- final java.lang.String modifiable) {
- this._modifiable = modifiable;
+ return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.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.Property[] getProperty() {
+ uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
+ return (uk.ac.vamsas.objects.core.Property[]) this._propertyList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPropertyAsReference.Returns a reference to '_propertyList'. No
+ * type checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getPropertyAsReference() {
+ return this._propertyList;
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount() {
+ return this._propertyList.size();
+ }
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return the value of field 'Provenance'.
+ */
+ public uk.ac.vamsas.objects.core.Provenance getProvenance() {
+ return this._provenance;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle() {
+ return this._title;
+ }
+
+ /**
+ * Method getTreenode.
+ *
+ * @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.Treenode at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Treenode getTreenode(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treenodeList.size()) {
+ throw new IndexOutOfBoundsException("getTreenode: Index value '" + index
+ + "' not in range [0.." + (this._treenodeList.size() - 1) + "]");
}
- /**
- *
- *
- * @param index
- * @param vNewick
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setNewick(
- final int index,
- final uk.ac.vamsas.objects.core.Newick vNewick)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._newickList.size()) {
- throw new IndexOutOfBoundsException("setNewick: Index value '" + index + "' not in range [0.." + (this._newickList.size() - 1) + "]");
- }
-
- this._newickList.set(index, vNewick);
+ return (uk.ac.vamsas.objects.core.Treenode) _treenodeList.get(index);
+ }
+
+ /**
+ * Method getTreenode.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.Treenode[] getTreenode() {
+ uk.ac.vamsas.objects.core.Treenode[] array = new uk.ac.vamsas.objects.core.Treenode[0];
+ return (uk.ac.vamsas.objects.core.Treenode[]) this._treenodeList
+ .toArray(array);
+ }
+
+ /**
+ * Method getTreenodeAsReference.Returns a reference to '_treenodeList'. No
+ * type checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getTreenodeAsReference() {
+ return this._treenodeList;
+ }
+
+ /**
+ * Method getTreenodeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreenodeCount() {
+ return this._treenodeList.size();
+ }
+
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ * <p>
+ * The following steps came from <b>Effective Java Programming Language
+ * Guide</b> by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
}
-
- /**
- *
- *
- * @param vNewickArray
- */
- public void setNewick(
- final uk.ac.vamsas.objects.core.Newick[] vNewickArray) {
- //-- copy array
- _newickList.clear();
-
- for (int i = 0; i < vNewickArray.length; i++) {
- this._newickList.add(vNewickArray[i]);
- }
+ if (_modifiable != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
+ result = 37 * result + _modifiable.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
}
-
- /**
- * Sets the value of '_newickList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vNewickList the Vector to copy.
- */
- public void setNewick(
- final java.util.Vector vNewickList) {
- // copy vector
- this._newickList.clear();
-
- this._newickList.addAll(vNewickList);
+ if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) {
+ result = 37 * result + _title.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_title);
}
-
- /**
- * Sets the value of '_newickList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param newickVector the Vector to set.
- */
- public void setNewickAsReference(
- final java.util.Vector newickVector) {
- this._newickList = newickVector;
+ if (_newickList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) {
+ result = 37 * result + _newickList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_newickList);
}
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setProperty(
- final int index,
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- this._propertyList.set(index, vProperty);
+ if (_treenodeList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) {
+ result = 37 * result + _treenodeList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList);
}
-
- /**
- *
- *
- * @param vPropertyArray
- */
- public void setProperty(
- final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
- //-- copy array
- _propertyList.clear();
-
- for (int i = 0; i < vPropertyArray.length; i++) {
- this._propertyList.add(vPropertyArray[i]);
- }
+ if (_propertyList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
}
-
- /**
- * Sets the value of '_propertyList' by copying the given
- * Vector. All elements will be checked for type safety.
- *
- * @param vPropertyList the Vector to copy.
- */
- public void setProperty(
- final java.util.Vector vPropertyList) {
- // copy vector
- this._propertyList.clear();
-
- this._propertyList.addAll(vPropertyList);
+ if (_provenance != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
}
- /**
- * Sets the value of '_propertyList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param propertyVector the Vector to set.
- */
- public void setPropertyAsReference(
- final java.util.Vector propertyVector) {
- this._propertyList = propertyVector;
+ 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 field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(
- final uk.ac.vamsas.objects.core.Provenance provenance) {
- this._provenance = provenance;
+ 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 removeAllNewick() {
+ this._newickList.clear();
+ }
+
+ /**
+ */
+ public void removeAllProperty() {
+ this._propertyList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTreenode() {
+ this._treenodeList.clear();
+ }
+
+ /**
+ * Method removeNewick.
+ *
+ * @param vNewick
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeNewick(final uk.ac.vamsas.objects.core.Newick vNewick) {
+ boolean removed = _newickList.remove(vNewick);
+ return removed;
+ }
+
+ /**
+ * Method removeNewickAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Newick removeNewickAt(final int index) {
+ java.lang.Object obj = this._newickList.remove(index);
+ return (uk.ac.vamsas.objects.core.Newick) obj;
+ }
+
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final uk.ac.vamsas.objects.core.Property vProperty) {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ }
+
+ /**
+ * Method removeTreenode.
+ *
+ * @param vTreenode
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTreenode(
+ final uk.ac.vamsas.objects.core.Treenode vTreenode) {
+ boolean removed = _treenodeList.remove(vTreenode);
+ return removed;
+ }
+
+ /**
+ * Method removeTreenodeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Treenode removeTreenodeAt(final int index) {
+ java.lang.Object obj = this._treenodeList.remove(index);
+ return (uk.ac.vamsas.objects.core.Treenode) obj;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * Primary Key for vamsas object referencing
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'modifiable'.
+ *
+ * @param modifiable
+ * the value of field 'modifiable'.
+ */
+ public void setModifiable(final java.lang.String modifiable) {
+ this._modifiable = modifiable;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vNewick
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setNewick(final int index,
+ final uk.ac.vamsas.objects.core.Newick vNewick)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._newickList.size()) {
+ throw new IndexOutOfBoundsException("setNewick: Index value '" + index
+ + "' not in range [0.." + (this._newickList.size() - 1) + "]");
}
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
+ this._newickList.set(index, vNewick);
+ }
- /**
- *
- *
- * @param index
- * @param vTreenode
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setTreenode(
- final int index,
- final uk.ac.vamsas.objects.core.Treenode vTreenode)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treenodeList.size()) {
- throw new IndexOutOfBoundsException("setTreenode: Index value '" + index + "' not in range [0.." + (this._treenodeList.size() - 1) + "]");
- }
-
- this._treenodeList.set(index, vTreenode);
- }
+ /**
+ *
+ *
+ * @param vNewickArray
+ */
+ public void setNewick(final uk.ac.vamsas.objects.core.Newick[] vNewickArray) {
+ // -- copy array
+ _newickList.clear();
- /**
- *
- *
- * @param vTreenodeArray
- */
- public void setTreenode(
- final uk.ac.vamsas.objects.core.Treenode[] vTreenodeArray) {
- //-- copy array
- _treenodeList.clear();
-
- for (int i = 0; i < vTreenodeArray.length; i++) {
- this._treenodeList.add(vTreenodeArray[i]);
- }
+ for (int i = 0; i < vNewickArray.length; i++) {
+ this._newickList.add(vNewickArray[i]);
}
-
- /**
- * Sets the value of '_treenodeList' by copying the given
- * Vector. All elements will be checked for type safety.
- *
- * @param vTreenodeList the Vector to copy.
- */
- public void setTreenode(
- final java.util.Vector vTreenodeList) {
- // copy vector
- this._treenodeList.clear();
-
- this._treenodeList.addAll(vTreenodeList);
+ }
+
+ /**
+ * Sets the value of '_newickList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vNewickList
+ * the Vector to copy.
+ */
+ public void setNewick(final java.util.Vector vNewickList) {
+ // copy vector
+ this._newickList.clear();
+
+ this._newickList.addAll(vNewickList);
+ }
+
+ /**
+ * Sets the value of '_newickList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param newickVector
+ * the Vector to set.
+ */
+ public void setNewickAsReference(final java.util.Vector newickVector) {
+ this._newickList = newickVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setProperty(final int index,
+ final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
}
- /**
- * Sets the value of '_treenodeList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param treenodeVector the Vector to set.
- */
- public void setTreenodeAsReference(
- final java.util.Vector treenodeVector) {
- this._treenodeList = treenodeVector;
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
+ // -- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++) {
+ this._propertyList.add(vPropertyArray[i]);
}
-
- /**
- * 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.Tree
- */
- public static uk.ac.vamsas.objects.core.Tree unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.Tree) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Tree.class, reader);
+ }
+
+ /**
+ * Sets the value of '_propertyList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vPropertyList
+ * the Vector to copy.
+ */
+ public void setProperty(final java.util.Vector vPropertyList) {
+ // copy vector
+ this._propertyList.clear();
+
+ this._propertyList.addAll(vPropertyList);
+ }
+
+ /**
+ * Sets the value of '_propertyList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param propertyVector
+ * the Vector to set.
+ */
+ public void setPropertyAsReference(final java.util.Vector propertyVector) {
+ this._propertyList = propertyVector;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTreenode
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTreenode(final int index,
+ final uk.ac.vamsas.objects.core.Treenode vTreenode)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treenodeList.size()) {
+ throw new IndexOutOfBoundsException("setTreenode: Index value '" + index
+ + "' not in range [0.." + (this._treenodeList.size() - 1) + "]");
}
- /**
- *
- *
- * @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);
+ this._treenodeList.set(index, vTreenode);
+ }
+
+ /**
+ *
+ *
+ * @param vTreenodeArray
+ */
+ public void setTreenode(
+ final uk.ac.vamsas.objects.core.Treenode[] vTreenodeArray) {
+ // -- copy array
+ _treenodeList.clear();
+
+ for (int i = 0; i < vTreenodeArray.length; i++) {
+ this._treenodeList.add(vTreenodeArray[i]);
}
+ }
+
+ /**
+ * Sets the value of '_treenodeList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vTreenodeList
+ * the Vector to copy.
+ */
+ public void setTreenode(final java.util.Vector vTreenodeList) {
+ // copy vector
+ this._treenodeList.clear();
+
+ this._treenodeList.addAll(vTreenodeList);
+ }
+
+ /**
+ * Sets the value of '_treenodeList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param treenodeVector
+ * the Vector to set.
+ */
+ public void setTreenodeAsReference(final java.util.Vector treenodeVector) {
+ this._treenodeList = treenodeVector;
+ }
+
+ /**
+ * 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.Tree
+ */
+ public static uk.ac.vamsas.objects.core.Tree unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.Tree) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.Tree.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