/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:VAMSAS.java 264 2006-12-14 17:42:54Z JimP $
+ * 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 java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
/**
* contains unassociated trees and a number of analysis sets
- *
*
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ *
+ * @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();
- _treeList = new Vector();
- _dataSetList = new Vector();
- } //-- uk.ac.vamsas.objects.core.VAMSAS()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addDataSet
- *
- *
- *
- * @param vDataSet
- */
- public void addDataSet(uk.ac.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException
- {
- _dataSetList.addElement(vDataSet);
- } //-- void addDataSet(uk.ac.vamsas.objects.core.DataSet)
-
- /**
- * Method addDataSet
- *
- *
- *
- * @param index
- * @param vDataSet
- */
- public void addDataSet(int index, uk.ac.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException
- {
- _dataSetList.insertElementAt(vDataSet, index);
- } //-- void addDataSet(int, uk.ac.vamsas.objects.core.DataSet)
-
- /**
- * Method addTree
- *
- *
- *
- * @param vTree
- */
- public void addTree(uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.addElement(vTree);
- } //-- void addTree(uk.ac.vamsas.objects.core.Tree)
-
- /**
- * Method addTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void addTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, uk.ac.vamsas.objects.core.Tree)
-
- /**
- * Method enumerateDataSet
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateDataSet()
- {
- return _dataSetList.elements();
- } //-- java.util.Enumeration enumerateDataSet()
-
- /**
- * Method enumerateTree
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateTree()
- {
- return _treeList.elements();
- } //-- java.util.Enumeration enumerateTree()
-
- /**
- * Note: hashCode() has not been overriden
- *
- * @param obj
- * @return boolean
- */
- public boolean equals(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;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(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;
}
- else if (temp._id != null)
- return false;
- if (this._modifiable != null) {
- if (temp._modifiable == null) return false;
- else if (!(this._modifiable.equals(temp._modifiable)))
- 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);
}
- else if (temp._modifiable != null)
- return false;
- if (this._treeList != null) {
- if (temp._treeList == null) return false;
- else if (!(this._treeList.equals(temp._treeList)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
}
- else if (temp._treeList != null)
- return false;
- if (this._dataSetList != null) {
- if (temp._dataSetList == null) return false;
- else if (!(this._dataSetList.equals(temp._dataSetList)))
- return false;
+ ;
+ 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;
}
- else if (temp._dataSetList != null)
- return false;
- return true;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
}
+ } else if (temp._modifiable != null)
return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getDataSet
- *
- *
- *
- * @param index
- * @return DataSet
- */
- public uk.ac.vamsas.objects.core.DataSet getDataSet(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dataSetList.size())) {
- throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.DataSet getDataSet(int)
-
- /**
- * Method getDataSet
- *
- *
- *
- * @return DataSet
- */
- public uk.ac.vamsas.objects.core.DataSet[] getDataSet()
- {
- int size = _dataSetList.size();
- uk.ac.vamsas.objects.core.DataSet[] mArray = new uk.ac.vamsas.objects.core.DataSet[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.DataSet[] getDataSet()
-
- /**
- * Method getDataSetCount
- *
- *
- *
- * @return int
- */
- public int getDataSetCount()
- {
- return _dataSetList.size();
- } //-- int getDataSetCount()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return String
- * @return the value of field 'modifiable'.
- */
- public java.lang.String getModifiable()
- {
- return this._modifiable;
- } //-- java.lang.String getModifiable()
-
- /**
- * Method getTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public uk.ac.vamsas.objects.core.Tree getTree(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _treeList.size())) {
- throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Tree getTree(int)
-
- /**
- * Method getTree
- *
- *
- *
- * @return Tree
- */
- public uk.ac.vamsas.objects.core.Tree[] getTree()
- {
- int size = _treeList.size();
- uk.ac.vamsas.objects.core.Tree[] mArray = new uk.ac.vamsas.objects.core.Tree[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Tree[] getTree()
-
- /**
- * Method getTreeCount
- *
- *
- *
- * @return int
- */
- public int getTreeCount()
- {
- return _treeList.size();
- } //-- int getTreeCount()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ 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);
+ }
}
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAllDataSet
- *
- */
- public void removeAllDataSet()
- {
- _dataSetList.removeAllElements();
- } //-- void removeAllDataSet()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeDataSet
- *
- *
- *
- * @param index
- * @return DataSet
- */
- public uk.ac.vamsas.objects.core.DataSet removeDataSet(int index)
- {
- java.lang.Object obj = _dataSetList.elementAt(index);
- _dataSetList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.DataSet) obj;
- } //-- uk.ac.vamsas.objects.core.DataSet removeDataSet(int)
-
- /**
- * Method removeTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public uk.ac.vamsas.objects.core.Tree removeTree(int index)
- {
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Tree) obj;
- } //-- uk.ac.vamsas.objects.core.Tree removeTree(int)
-
- /**
- * Method setDataSet
- *
- *
- *
- * @param index
- * @param vDataSet
- */
- public void setDataSet(int index, uk.ac.vamsas.objects.core.DataSet vDataSet)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dataSetList.size())) {
- throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
- }
- _dataSetList.setElementAt(vDataSet, index);
- } //-- void setDataSet(int, uk.ac.vamsas.objects.core.DataSet)
-
- /**
- * Method setDataSet
- *
- *
- *
- * @param dataSetArray
- */
- public void setDataSet(uk.ac.vamsas.objects.core.DataSet[] dataSetArray)
- {
- //-- copy array
- _dataSetList.removeAllElements();
- for (int i = 0; i < dataSetArray.length; i++) {
- _dataSetList.addElement(dataSetArray[i]);
- }
- } //-- void setDataSet(uk.ac.vamsas.objects.core.DataSet)
-
- /**
- * 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(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'modifiable'.
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(java.lang.String modifiable)
- {
- this._modifiable = modifiable;
- } //-- void setModifiable(java.lang.String)
-
- /**
- * Method setTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void setTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _treeList.size())) {
- throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
- }
- _treeList.setElementAt(vTree, index);
- } //-- void setTree(int, uk.ac.vamsas.objects.core.Tree)
-
- /**
- * Method setTree
- *
- *
- *
- * @param treeArray
- */
- public void setTree(uk.ac.vamsas.objects.core.Tree[] treeArray)
- {
- //-- copy array
- _treeList.removeAllElements();
- for (int i = 0; i < treeArray.length; i++) {
- _treeList.addElement(treeArray[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);
+ }
}
- } //-- void setTree(uk.ac.vamsas.objects.core.Tree)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return VAMSAS
- */
- public static uk.ac.vamsas.objects.core.VAMSAS unmarshal(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);
- } //-- uk.ac.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
+ } 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