/*
- * 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;
/**
* contains unassociated trees and a number of analysis sets
- *
*
- * @version $Revision$ $Date$
+ *
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class VAMSAS 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 _treeList.
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _dataSetList.
- */
- private java.util.Vector _dataSetList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VAMSAS() {
- super();
- this._treeList = new java.util.Vector();
- this._dataSetList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vDataSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addDataSet(
- final uk.ac.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException {
- this._dataSetList.addElement(vDataSet);
- }
-
- /**
- *
- *
- * @param index
- * @param vDataSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addDataSet(
- final int index,
- final uk.ac.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException {
- this._dataSetList.add(index, vDataSet);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final int index,
- final uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.add(index, vTree);
- }
-
- /**
- * Method enumerateDataSet.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.DataSet elements
- */
- public java.util.Enumeration enumerateDataSet(
- ) {
- return this._dataSetList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Tree elements
- */
- public java.util.Enumeration enumerateTree(
- ) {
- return this._treeList.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 VAMSAS 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 _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _dataSetList.
+ */
+ private java.util.Vector _dataSetList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public VAMSAS() {
+ super();
+ this._treeList = new java.util.Vector();
+ this._dataSetList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vDataSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDataSet(final uk.ac.vamsas.objects.core.DataSet vDataSet)
+ throws java.lang.IndexOutOfBoundsException {
+ this._dataSetList.addElement(vDataSet);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDataSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDataSet(final int index,
+ final uk.ac.vamsas.objects.core.DataSet vDataSet)
+ throws java.lang.IndexOutOfBoundsException {
+ this._dataSetList.add(index, vDataSet);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final int index,
+ final uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ * Method enumerateDataSet.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.DataSet elements
+ */
+ public java.util.Enumeration enumerateDataSet() {
+ return this._dataSetList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Tree elements
+ */
+ public java.util.Enumeration enumerateTree() {
+ return this._treeList.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 VAMSAS) {
+
+ VAMSAS temp = (VAMSAS) 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 VAMSAS) {
-
- VAMSAS temp = (VAMSAS)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._treeList != null) {
- if (temp._treeList == null) return false;
- if (this._treeList != temp._treeList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._treeList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._treeList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); };
- return false;
- }
- if (!thcycle) {
- if (!this._treeList.equals(temp._treeList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- }
- }
- } else if (temp._treeList != null)
- return false;
- if (this._dataSetList != null) {
- if (temp._dataSetList == null) return false;
- if (this._dataSetList != temp._dataSetList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._dataSetList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dataSetList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList); };
- return false;
- }
- if (!thcycle) {
- if (!this._dataSetList.equals(temp._dataSetList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
- }
- }
- } else if (temp._dataSetList != 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;
- }
-
- /**
- * Method getDataSet.
- *
- * @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.DataSet
- * at the given index
- */
- public uk.ac.vamsas.objects.core.DataSet getDataSet(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._dataSetList.size()) {
- throw new IndexOutOfBoundsException("getDataSet: Index value '" + index + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.DataSet) _dataSetList.get(index);
- }
-
- /**
- * Method getDataSet.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.DataSet[] getDataSet(
- ) {
- uk.ac.vamsas.objects.core.DataSet[] array = new uk.ac.vamsas.objects.core.DataSet[0];
- return (uk.ac.vamsas.objects.core.DataSet[]) this._dataSetList.toArray(array);
- }
-
- /**
- * Method getDataSetAsReference.Returns a reference to
- * '_dataSetList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getDataSetAsReference(
- ) {
- return this._dataSetList;
- }
-
- /**
- * Method getDataSetCount.
- *
- * @return the size of this collection
- */
- public int getDataSetCount(
- ) {
- return this._dataSetList.size();
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return the value of field 'Modifiable'.
- */
- public java.lang.String getModifiable(
- ) {
- return this._modifiable;
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the uk.ac.vamsas.objects.core.Tree at
- * the given index
- */
- public uk.ac.vamsas.objects.core.Tree getTree(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Tree) _treeList.get(index);
- }
-
- /**
- * Method getTree.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public uk.ac.vamsas.objects.core.Tree[] getTree(
- ) {
- uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0];
- return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeAsReference.Returns a reference to
- * '_treeList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getTreeAsReference(
- ) {
- return this._treeList;
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount(
- ) {
- return this._treeList.size();
- }
-
- /**
- * Overrides the java.lang.Object.hashCode method.
- * <p>
- * The following steps came from <b>Effective Java Programming
- * Language Guide</b> by Joshua Bloch, Chapter 3
- *
- * @return a hash code value for the object.
- */
- public int hashCode(
- ) {
- int result = super.hashCode();
-
- long tmp;
- if (_id != null
- && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_modifiable != null
- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
- result = 37 * result + _modifiable.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
- }
- if (_treeList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
- result = 37 * result + _treeList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
- }
- if (_dataSetList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_dataSetList)) {
- result = 37 * result + _dataSetList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetList);
- }
-
- return result;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
+ if (this._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);
+ }
}
- 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 removeAllDataSet(
- ) {
- this._dataSetList.clear();
- }
-
- /**
- */
- public void removeAllTree(
- ) {
- this._treeList.clear();
- }
-
- /**
- * Method removeDataSet.
- *
- * @param vDataSet
- * @return true if the object was removed from the collection.
- */
- public boolean removeDataSet(
- final uk.ac.vamsas.objects.core.DataSet vDataSet) {
- boolean removed = _dataSetList.remove(vDataSet);
- return removed;
- }
-
- /**
- * Method removeDataSetAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.DataSet removeDataSetAt(
- final int index) {
- java.lang.Object obj = this._dataSetList.remove(index);
- return (uk.ac.vamsas.objects.core.DataSet) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(
- final uk.ac.vamsas.objects.core.Tree vTree) {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Tree removeTreeAt(
- final int index) {
- java.lang.Object obj = this._treeList.remove(index);
- return (uk.ac.vamsas.objects.core.Tree) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vDataSet
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setDataSet(
- final int index,
- final uk.ac.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._dataSetList.size()) {
- throw new IndexOutOfBoundsException("setDataSet: Index value '" + index + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
- }
-
- this._dataSetList.set(index, vDataSet);
- }
-
- /**
- *
- *
- * @param vDataSetArray
- */
- public void setDataSet(
- final uk.ac.vamsas.objects.core.DataSet[] vDataSetArray) {
- //-- copy array
- _dataSetList.clear();
-
- for (int i = 0; i < vDataSetArray.length; i++) {
- this._dataSetList.add(vDataSetArray[i]);
- }
- }
-
- /**
- * Sets the value of '_dataSetList' by copying the given
- * Vector. All elements will be checked for type safety.
- *
- * @param vDataSetList the Vector to copy.
- */
- public void setDataSet(
- final java.util.Vector vDataSetList) {
- // copy vector
- this._dataSetList.clear();
-
- this._dataSetList.addAll(vDataSetList);
- }
-
- /**
- * Sets the value of '_dataSetList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param dataSetVector the Vector to set.
- */
- public void setDataSetAsReference(
- final java.util.Vector dataSetVector) {
- this._dataSetList = dataSetVector;
- }
-
- /**
- * 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 vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setTree(
- final int index,
- final uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ } else if (temp._modifiable != null)
+ return false;
+ if (this._treeList != null) {
+ if (temp._treeList == null)
+ return false;
+ if (this._treeList != temp._treeList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._treeList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._treeList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._treeList.equals(temp._treeList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
}
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(
- final uk.ac.vamsas.objects.core.Tree[] vTreeArray) {
- //-- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++) {
- this._treeList.add(vTreeArray[i]);
+ } else if (temp._treeList != null)
+ return false;
+ if (this._dataSetList != null) {
+ if (temp._dataSetList == null)
+ return false;
+ if (this._dataSetList != temp._dataSetList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._dataSetList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._dataSetList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._dataSetList.equals(temp._dataSetList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
+ }
}
- }
-
- /**
- * Sets the value of '_treeList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vTreeList the Vector to copy.
- */
- public void setTree(
- final java.util.Vector vTreeList) {
- // copy vector
- this._treeList.clear();
-
- this._treeList.addAll(vTreeList);
- }
-
- /**
- * Sets the value of '_treeList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param treeVector the Vector to set.
- */
- public void setTreeAsReference(
- final java.util.Vector treeVector) {
- this._treeList = treeVector;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled uk.ac.vamsas.objects.core.VAMSAS
- */
- public static uk.ac.vamsas.objects.core.VAMSAS unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.VAMSAS.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ } else if (temp._dataSetList != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Method getDataSet.
+ *
+ * @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.DataSet at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.DataSet getDataSet(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._dataSetList.size()) {
+ throw new IndexOutOfBoundsException("getDataSet: Index value '" + index
+ + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.DataSet) _dataSetList.get(index);
+ }
+
+ /**
+ * Method getDataSet.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.DataSet[] getDataSet() {
+ uk.ac.vamsas.objects.core.DataSet[] array = new uk.ac.vamsas.objects.core.DataSet[0];
+ return (uk.ac.vamsas.objects.core.DataSet[]) this._dataSetList
+ .toArray(array);
+ }
+
+ /**
+ * Method getDataSetAsReference.Returns a reference to '_dataSetList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getDataSetAsReference() {
+ return this._dataSetList;
+ }
+
+ /**
+ * Method getDataSetCount.
+ *
+ * @return the size of this collection
+ */
+ public int getDataSetCount() {
+ return this._dataSetList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Primary Key for vamsas object referencing
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId() {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'modifiable'.
+ *
+ * @return the value of field 'Modifiable'.
+ */
+ public java.lang.String getModifiable() {
+ return this._modifiable;
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.Tree at the given index
+ */
+ public uk.ac.vamsas.objects.core.Tree getTree(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.Tree[] getTree() {
+ uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0];
+ return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeAsReference.Returns a reference to '_treeList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getTreeAsReference() {
+ return this._treeList;
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount() {
+ return this._treeList.size();
+ }
+
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ * <p>
+ * The following steps came from <b>Effective Java Programming Language
+ * Guide</b> by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_modifiable != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
+ result = 37 * result + _modifiable.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
+ }
+ if (_treeList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
+ result = 37 * result + _treeList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
+ }
+ if (_dataSetList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_dataSetList)) {
+ result = 37 * result + _dataSetList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetList);
+ }
+
+ return result;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid() {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllDataSet() {
+ this._dataSetList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree() {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeDataSet.
+ *
+ * @param vDataSet
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeDataSet(final uk.ac.vamsas.objects.core.DataSet vDataSet) {
+ boolean removed = _dataSetList.remove(vDataSet);
+ return removed;
+ }
+
+ /**
+ * Method removeDataSetAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.DataSet removeDataSetAt(final int index) {
+ java.lang.Object obj = this._dataSetList.remove(index);
+ return (uk.ac.vamsas.objects.core.DataSet) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(final uk.ac.vamsas.objects.core.Tree vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Tree removeTreeAt(final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (uk.ac.vamsas.objects.core.Tree) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDataSet
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setDataSet(final int index,
+ final uk.ac.vamsas.objects.core.DataSet vDataSet)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._dataSetList.size()) {
+ throw new IndexOutOfBoundsException("setDataSet: Index value '" + index
+ + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
+ }
+
+ this._dataSetList.set(index, vDataSet);
+ }
+
+ /**
+ *
+ *
+ * @param vDataSetArray
+ */
+ public void setDataSet(final uk.ac.vamsas.objects.core.DataSet[] vDataSetArray) {
+ // -- copy array
+ _dataSetList.clear();
+
+ for (int i = 0; i < vDataSetArray.length; i++) {
+ this._dataSetList.add(vDataSetArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_dataSetList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vDataSetList
+ * the Vector to copy.
+ */
+ public void setDataSet(final java.util.Vector vDataSetList) {
+ // copy vector
+ this._dataSetList.clear();
+
+ this._dataSetList.addAll(vDataSetList);
+ }
+
+ /**
+ * Sets the value of '_dataSetList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param dataSetVector
+ * the Vector to set.
+ */
+ public void setDataSetAsReference(final java.util.Vector dataSetVector) {
+ this._dataSetList = dataSetVector;
+ }
+
+ /**
+ * 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 vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTree(final int index,
+ final uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(final uk.ac.vamsas.objects.core.Tree[] vTreeArray) {
+ // -- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_treeList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vTreeList
+ * the Vector to copy.
+ */
+ public void setTree(final java.util.Vector vTreeList) {
+ // copy vector
+ this._treeList.clear();
+
+ this._treeList.addAll(vTreeList);
+ }
+
+ /**
+ * Sets the value of '_treeList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param treeVector
+ * the Vector to set.
+ */
+ public void setTreeAsReference(final java.util.Vector treeVector) {
+ this._treeList = treeVector;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled uk.ac.vamsas.objects.core.VAMSAS
+ */
+ public static uk.ac.vamsas.objects.core.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.VAMSAS.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