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/*
* This file is part of the Vamsas Client version 0.2.
* Copyright 2010 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 -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
/**
* Class DataSet.
*
* @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
* $
*/
public class DataSet 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 _sequenceList.
*/
private java.util.Vector _sequenceList;
/**
* Field _sequenceMappingList.
*/
private java.util.Vector _sequenceMappingList;
/**
* Field _dataSetAnnotationsList.
*/
private java.util.Vector _dataSetAnnotationsList;
/**
* Field _alignmentList.
*/
private java.util.Vector _alignmentList;
/**
* Field _treeList.
*/
private java.util.Vector _treeList;
/**
* Field _provenance.
*/
private uk.ac.vamsas.objects.core.Provenance _provenance;
// ----------------/
// - Constructors -/
// ----------------/
public DataSet() {
super();
this._sequenceList = new java.util.Vector();
this._sequenceMappingList = new java.util.Vector();
this._dataSetAnnotationsList = new java.util.Vector();
this._alignmentList = new java.util.Vector();
this._treeList = new java.util.Vector();
}
// -----------/
// - Methods -/
// -----------/
/**
*
*
* @param vAlignment
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addAlignment(final uk.ac.vamsas.objects.core.Alignment vAlignment)
throws java.lang.IndexOutOfBoundsException {
this._alignmentList.addElement(vAlignment);
}
/**
*
*
* @param index
* @param vAlignment
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addAlignment(final int index,
final uk.ac.vamsas.objects.core.Alignment vAlignment)
throws java.lang.IndexOutOfBoundsException {
this._alignmentList.add(index, vAlignment);
}
/**
*
*
* @param vDataSetAnnotations
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addDataSetAnnotations(
final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
throws java.lang.IndexOutOfBoundsException {
this._dataSetAnnotationsList.addElement(vDataSetAnnotations);
}
/**
*
*
* @param index
* @param vDataSetAnnotations
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addDataSetAnnotations(final int index,
final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
throws java.lang.IndexOutOfBoundsException {
this._dataSetAnnotationsList.add(index, vDataSetAnnotations);
}
/**
*
*
* @param vSequence
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addSequence(final uk.ac.vamsas.objects.core.Sequence vSequence)
throws java.lang.IndexOutOfBoundsException {
this._sequenceList.addElement(vSequence);
}
/**
*
*
* @param index
* @param vSequence
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addSequence(final int index,
final uk.ac.vamsas.objects.core.Sequence vSequence)
throws java.lang.IndexOutOfBoundsException {
this._sequenceList.add(index, vSequence);
}
/**
*
*
* @param vSequenceMapping
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addSequenceMapping(
final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping)
throws java.lang.IndexOutOfBoundsException {
this._sequenceMappingList.addElement(vSequenceMapping);
}
/**
*
*
* @param index
* @param vSequenceMapping
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addSequenceMapping(final int index,
final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping)
throws java.lang.IndexOutOfBoundsException {
this._sequenceMappingList.add(index, vSequenceMapping);
}
/**
*
*
* @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 enumerateAlignment.
*
* @return an Enumeration over all uk.ac.vamsas.objects.core.Alignment
* elements
*/
public java.util.Enumeration enumerateAlignment() {
return this._alignmentList.elements();
}
/**
* Method enumerateDataSetAnnotations.
*
* @return an Enumeration over all
* uk.ac.vamsas.objects.core.DataSetAnnotations elements
*/
public java.util.Enumeration enumerateDataSetAnnotations() {
return this._dataSetAnnotationsList.elements();
}
/**
* Method enumerateSequence.
*
* @return an Enumeration over all uk.ac.vamsas.objects.core.Sequence elements
*/
public java.util.Enumeration enumerateSequence() {
return this._sequenceList.elements();
}
/**
* Method enumerateSequenceMapping.
*
* @return an Enumeration over all uk.ac.vamsas.objects.core.SequenceMapping
* elements
*/
public java.util.Enumeration enumerateSequenceMapping() {
return this._sequenceMappingList.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 DataSet) {
DataSet temp = (DataSet) obj;
boolean thcycle;
boolean tmcycle;
if (this._id != null) {
if (temp._id == null)
return false;
if (this._id != temp._id) {
thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
}
;
return false;
}
if (!thcycle) {
if (!this._id.equals(temp._id)) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
return false;
}
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
}
}
} else if (temp._id != null)
return false;
if (this._sequenceList != null) {
if (temp._sequenceList == null)
return false;
if (this._sequenceList != temp._sequenceList) {
thcycle = org.castor.core.util.CycleBreaker
.startingToCycle(this._sequenceList);
tmcycle = org.castor.core.util.CycleBreaker
.startingToCycle(temp._sequenceList);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._sequenceList);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._sequenceList);
}
;
return false;
}
if (!thcycle) {
if (!this._sequenceList.equals(temp._sequenceList)) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._sequenceList);
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._sequenceList);
return false;
}
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
}
}
} else if (temp._sequenceList != null)
return false;
if (this._sequenceMappingList != null) {
if (temp._sequenceMappingList == null)
return false;
if (this._sequenceMappingList != temp._sequenceMappingList) {
thcycle = org.castor.core.util.CycleBreaker
.startingToCycle(this._sequenceMappingList);
tmcycle = org.castor.core.util.CycleBreaker
.startingToCycle(temp._sequenceMappingList);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._sequenceMappingList);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._sequenceMappingList);
}
;
return false;
}
if (!thcycle) {
if (!this._sequenceMappingList.equals(temp._sequenceMappingList)) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._sequenceMappingList);
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._sequenceMappingList);
return false;
}
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._sequenceMappingList);
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._sequenceMappingList);
}
}
} else if (temp._sequenceMappingList != null)
return false;
if (this._dataSetAnnotationsList != null) {
if (temp._dataSetAnnotationsList == null)
return false;
if (this._dataSetAnnotationsList != temp._dataSetAnnotationsList) {
thcycle = org.castor.core.util.CycleBreaker
.startingToCycle(this._dataSetAnnotationsList);
tmcycle = org.castor.core.util.CycleBreaker
.startingToCycle(temp._dataSetAnnotationsList);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._dataSetAnnotationsList);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._dataSetAnnotationsList);
}
;
return false;
}
if (!thcycle) {
if (!this._dataSetAnnotationsList
.equals(temp._dataSetAnnotationsList)) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._dataSetAnnotationsList);
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._dataSetAnnotationsList);
return false;
}
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._dataSetAnnotationsList);
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._dataSetAnnotationsList);
}
}
} else if (temp._dataSetAnnotationsList != null)
return false;
if (this._alignmentList != null) {
if (temp._alignmentList == null)
return false;
if (this._alignmentList != temp._alignmentList) {
thcycle = org.castor.core.util.CycleBreaker
.startingToCycle(this._alignmentList);
tmcycle = org.castor.core.util.CycleBreaker
.startingToCycle(temp._alignmentList);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._alignmentList);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._alignmentList);
}
;
return false;
}
if (!thcycle) {
if (!this._alignmentList.equals(temp._alignmentList)) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._alignmentList);
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._alignmentList);
return false;
}
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._alignmentList);
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._alignmentList);
}
}
} else if (temp._alignmentList != null)
return false;
if (this._treeList != null) {
if (temp._treeList == null)
return false;
if (this._treeList != temp._treeList) {
thcycle = org.castor.core.util.CycleBreaker
.startingToCycle(this._treeList);
tmcycle = org.castor.core.util.CycleBreaker
.startingToCycle(temp._treeList);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
}
;
return false;
}
if (!thcycle) {
if (!this._treeList.equals(temp._treeList)) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
return false;
}
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
}
}
} else if (temp._treeList != null)
return false;
if (this._provenance != null) {
if (temp._provenance == null)
return false;
if (this._provenance != temp._provenance) {
thcycle = org.castor.core.util.CycleBreaker
.startingToCycle(this._provenance);
tmcycle = org.castor.core.util.CycleBreaker
.startingToCycle(temp._provenance);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
}
;
return false;
}
if (!thcycle) {
if (!this._provenance.equals(temp._provenance)) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
return false;
}
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
}
}
} else if (temp._provenance != null)
return false;
return true;
}
return false;
}
/**
* Method getAlignment.
*
* @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.Alignment at the given
* index
*/
public uk.ac.vamsas.objects.core.Alignment getAlignment(final int index)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._alignmentList.size()) {
throw new IndexOutOfBoundsException("getAlignment: Index value '" + index
+ "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
}
return (uk.ac.vamsas.objects.core.Alignment) _alignmentList.get(index);
}
/**
* Method getAlignment.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.Alignment[] getAlignment() {
uk.ac.vamsas.objects.core.Alignment[] array = new uk.ac.vamsas.objects.core.Alignment[0];
return (uk.ac.vamsas.objects.core.Alignment[]) this._alignmentList
.toArray(array);
}
/**
* Method getAlignmentAsReference.Returns a reference to '_alignmentList'. No
* type checking is performed on any modifications to the Vector.
*
* @return a reference to the Vector backing this class
*/
public java.util.Vector getAlignmentAsReference() {
return this._alignmentList;
}
/**
* Method getAlignmentCount.
*
* @return the size of this collection
*/
public int getAlignmentCount() {
return this._alignmentList.size();
}
/**
* Method getDataSetAnnotations.
*
* @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.DataSetAnnotations at
* the given index
*/
public uk.ac.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(
final int index) throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._dataSetAnnotationsList.size()) {
throw new IndexOutOfBoundsException(
"getDataSetAnnotations: Index value '" + index
+ "' not in range [0.."
+ (this._dataSetAnnotationsList.size() - 1) + "]");
}
return (uk.ac.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList
.get(index);
}
/**
* Method getDataSetAnnotations.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.DataSetAnnotations[] getDataSetAnnotations() {
uk.ac.vamsas.objects.core.DataSetAnnotations[] array = new uk.ac.vamsas.objects.core.DataSetAnnotations[0];
return (uk.ac.vamsas.objects.core.DataSetAnnotations[]) this._dataSetAnnotationsList
.toArray(array);
}
/**
* Method getDataSetAnnotationsAsReference.Returns a reference to
* '_dataSetAnnotationsList'. No type checking is performed on any
* modifications to the Vector.
*
* @return a reference to the Vector backing this class
*/
public java.util.Vector getDataSetAnnotationsAsReference() {
return this._dataSetAnnotationsList;
}
/**
* Method getDataSetAnnotationsCount.
*
* @return the size of this collection
*/
public int getDataSetAnnotationsCount() {
return this._dataSetAnnotationsList.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 'provenance'.
*
* @return the value of field 'Provenance'.
*/
public uk.ac.vamsas.objects.core.Provenance getProvenance() {
return this._provenance;
}
/**
* Method getSequence.
*
* @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.Sequence at the given
* index
*/
public uk.ac.vamsas.objects.core.Sequence getSequence(final int index)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._sequenceList.size()) {
throw new IndexOutOfBoundsException("getSequence: Index value '" + index
+ "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
}
return (uk.ac.vamsas.objects.core.Sequence) _sequenceList.get(index);
}
/**
* Method getSequence.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.Sequence[] getSequence() {
uk.ac.vamsas.objects.core.Sequence[] array = new uk.ac.vamsas.objects.core.Sequence[0];
return (uk.ac.vamsas.objects.core.Sequence[]) this._sequenceList
.toArray(array);
}
/**
* Method getSequenceAsReference.Returns a reference to '_sequenceList'. No
* type checking is performed on any modifications to the Vector.
*
* @return a reference to the Vector backing this class
*/
public java.util.Vector getSequenceAsReference() {
return this._sequenceList;
}
/**
* Method getSequenceCount.
*
* @return the size of this collection
*/
public int getSequenceCount() {
return this._sequenceList.size();
}
/**
* Method getSequenceMapping.
*
* @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.SequenceMapping at the
* given index
*/
public uk.ac.vamsas.objects.core.SequenceMapping getSequenceMapping(
final int index) throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._sequenceMappingList.size()) {
throw new IndexOutOfBoundsException("getSequenceMapping: Index value '"
+ index + "' not in range [0.."
+ (this._sequenceMappingList.size() - 1) + "]");
}
return (uk.ac.vamsas.objects.core.SequenceMapping) _sequenceMappingList
.get(index);
}
/**
* Method getSequenceMapping.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.SequenceMapping[] getSequenceMapping() {
uk.ac.vamsas.objects.core.SequenceMapping[] array = new uk.ac.vamsas.objects.core.SequenceMapping[0];
return (uk.ac.vamsas.objects.core.SequenceMapping[]) this._sequenceMappingList
.toArray(array);
}
/**
* Method getSequenceMappingAsReference.Returns a reference to
* '_sequenceMappingList'. No type checking is performed on any modifications
* to the Vector.
*
* @return a reference to the Vector backing this class
*/
public java.util.Vector getSequenceMappingAsReference() {
return this._sequenceMappingList;
}
/**
* Method getSequenceMappingCount.
*
* @return the size of this collection
*/
public int getSequenceMappingCount() {
return this._sequenceMappingList.size();
}
/**
* 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.core.util.CycleBreaker.startingToCycle(_id)) {
result = 37 * result + _id.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
}
if (_sequenceList != null
&& !org.castor.core.util.CycleBreaker.startingToCycle(_sequenceList)) {
result = 37 * result + _sequenceList.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequenceList);
}
if (_sequenceMappingList != null
&& !org.castor.core.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
result = 37 * result + _sequenceMappingList.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
}
if (_dataSetAnnotationsList != null
&& !org.castor.core.util.CycleBreaker
.startingToCycle(_dataSetAnnotationsList)) {
result = 37 * result + _dataSetAnnotationsList.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
}
if (_alignmentList != null
&& !org.castor.core.util.CycleBreaker.startingToCycle(_alignmentList)) {
result = 37 * result + _alignmentList.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentList);
}
if (_treeList != null
&& !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) {
result = 37 * result + _treeList.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList);
}
if (_provenance != null
&& !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
result = 37 * result + _provenance.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
}
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);
}
/**
* Method removeAlignment.
*
* @param vAlignment
* @return true if the object was removed from the collection.
*/
public boolean removeAlignment(
final uk.ac.vamsas.objects.core.Alignment vAlignment) {
boolean removed = _alignmentList.remove(vAlignment);
return removed;
}
/**
* Method removeAlignmentAt.
*
* @param index
* @return the element removed from the collection
*/
public uk.ac.vamsas.objects.core.Alignment removeAlignmentAt(final int index) {
java.lang.Object obj = this._alignmentList.remove(index);
return (uk.ac.vamsas.objects.core.Alignment) obj;
}
/**
*/
public void removeAllAlignment() {
this._alignmentList.clear();
}
/**
*/
public void removeAllDataSetAnnotations() {
this._dataSetAnnotationsList.clear();
}
/**
*/
public void removeAllSequence() {
this._sequenceList.clear();
}
/**
*/
public void removeAllSequenceMapping() {
this._sequenceMappingList.clear();
}
/**
*/
public void removeAllTree() {
this._treeList.clear();
}
/**
* Method removeDataSetAnnotations.
*
* @param vDataSetAnnotations
* @return true if the object was removed from the collection.
*/
public boolean removeDataSetAnnotations(
final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) {
boolean removed = _dataSetAnnotationsList.remove(vDataSetAnnotations);
return removed;
}
/**
* Method removeDataSetAnnotationsAt.
*
* @param index
* @return the element removed from the collection
*/
public uk.ac.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotationsAt(
final int index) {
java.lang.Object obj = this._dataSetAnnotationsList.remove(index);
return (uk.ac.vamsas.objects.core.DataSetAnnotations) obj;
}
/**
* Method removeSequence.
*
* @param vSequence
* @return true if the object was removed from the collection.
*/
public boolean removeSequence(
final uk.ac.vamsas.objects.core.Sequence vSequence) {
boolean removed = _sequenceList.remove(vSequence);
return removed;
}
/**
* Method removeSequenceAt.
*
* @param index
* @return the element removed from the collection
*/
public uk.ac.vamsas.objects.core.Sequence removeSequenceAt(final int index) {
java.lang.Object obj = this._sequenceList.remove(index);
return (uk.ac.vamsas.objects.core.Sequence) obj;
}
/**
* Method removeSequenceMapping.
*
* @param vSequenceMapping
* @return true if the object was removed from the collection.
*/
public boolean removeSequenceMapping(
final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping) {
boolean removed = _sequenceMappingList.remove(vSequenceMapping);
return removed;
}
/**
* Method removeSequenceMappingAt.
*
* @param index
* @return the element removed from the collection
*/
public uk.ac.vamsas.objects.core.SequenceMapping removeSequenceMappingAt(
final int index) {
java.lang.Object obj = this._sequenceMappingList.remove(index);
return (uk.ac.vamsas.objects.core.SequenceMapping) 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 vAlignment
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void setAlignment(final int index,
final uk.ac.vamsas.objects.core.Alignment vAlignment)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._alignmentList.size()) {
throw new IndexOutOfBoundsException("setAlignment: Index value '" + index
+ "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
}
this._alignmentList.set(index, vAlignment);
}
/**
*
*
* @param vAlignmentArray
*/
public void setAlignment(
final uk.ac.vamsas.objects.core.Alignment[] vAlignmentArray) {
// -- copy array
_alignmentList.clear();
for (int i = 0; i < vAlignmentArray.length; i++) {
this._alignmentList.add(vAlignmentArray[i]);
}
}
/**
* Sets the value of '_alignmentList' by copying the given Vector. All
* elements will be checked for type safety.
*
* @param vAlignmentList
* the Vector to copy.
*/
public void setAlignment(final java.util.Vector vAlignmentList) {
// copy vector
this._alignmentList.clear();
this._alignmentList.addAll(vAlignmentList);
}
/**
* Sets the value of '_alignmentList' by setting it to the given Vector. No
* type checking is performed.
*
* @deprecated
*
* @param alignmentVector
* the Vector to set.
*/
public void setAlignmentAsReference(final java.util.Vector alignmentVector) {
this._alignmentList = alignmentVector;
}
/**
*
*
* @param index
* @param vDataSetAnnotations
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void setDataSetAnnotations(final int index,
final uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._dataSetAnnotationsList.size()) {
throw new IndexOutOfBoundsException(
"setDataSetAnnotations: Index value '" + index
+ "' not in range [0.."
+ (this._dataSetAnnotationsList.size() - 1) + "]");
}
this._dataSetAnnotationsList.set(index, vDataSetAnnotations);
}
/**
*
*
* @param vDataSetAnnotationsArray
*/
public void setDataSetAnnotations(
final uk.ac.vamsas.objects.core.DataSetAnnotations[] vDataSetAnnotationsArray) {
// -- copy array
_dataSetAnnotationsList.clear();
for (int i = 0; i < vDataSetAnnotationsArray.length; i++) {
this._dataSetAnnotationsList.add(vDataSetAnnotationsArray[i]);
}
}
/**
* Sets the value of '_dataSetAnnotationsList' by copying the given Vector.
* All elements will be checked for type safety.
*
* @param vDataSetAnnotationsList
* the Vector to copy.
*/
public void setDataSetAnnotations(
final java.util.Vector vDataSetAnnotationsList) {
// copy vector
this._dataSetAnnotationsList.clear();
this._dataSetAnnotationsList.addAll(vDataSetAnnotationsList);
}
/**
* Sets the value of '_dataSetAnnotationsList' by setting it to the given
* Vector. No type checking is performed.
*
* @deprecated
*
* @param dataSetAnnotationsVector
* the Vector to set.
*/
public void setDataSetAnnotationsAsReference(
final java.util.Vector dataSetAnnotationsVector) {
this._dataSetAnnotationsList = dataSetAnnotationsVector;
}
/**
* 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 'provenance'.
*
* @param provenance
* the value of field 'provenance'.
*/
public void setProvenance(
final uk.ac.vamsas.objects.core.Provenance provenance) {
this._provenance = provenance;
}
/**
*
*
* @param index
* @param vSequence
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void setSequence(final int index,
final uk.ac.vamsas.objects.core.Sequence vSequence)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._sequenceList.size()) {
throw new IndexOutOfBoundsException("setSequence: Index value '" + index
+ "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
}
this._sequenceList.set(index, vSequence);
}
/**
*
*
* @param vSequenceArray
*/
public void setSequence(
final uk.ac.vamsas.objects.core.Sequence[] vSequenceArray) {
// -- copy array
_sequenceList.clear();
for (int i = 0; i < vSequenceArray.length; i++) {
this._sequenceList.add(vSequenceArray[i]);
}
}
/**
* Sets the value of '_sequenceList' by copying the given Vector. All elements
* will be checked for type safety.
*
* @param vSequenceList
* the Vector to copy.
*/
public void setSequence(final java.util.Vector vSequenceList) {
// copy vector
this._sequenceList.clear();
this._sequenceList.addAll(vSequenceList);
}
/**
* Sets the value of '_sequenceList' by setting it to the given Vector. No
* type checking is performed.
*
* @deprecated
*
* @param sequenceVector
* the Vector to set.
*/
public void setSequenceAsReference(final java.util.Vector sequenceVector) {
this._sequenceList = sequenceVector;
}
/**
*
*
* @param index
* @param vSequenceMapping
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void setSequenceMapping(final int index,
final uk.ac.vamsas.objects.core.SequenceMapping vSequenceMapping)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._sequenceMappingList.size()) {
throw new IndexOutOfBoundsException("setSequenceMapping: Index value '"
+ index + "' not in range [0.."
+ (this._sequenceMappingList.size() - 1) + "]");
}
this._sequenceMappingList.set(index, vSequenceMapping);
}
/**
*
*
* @param vSequenceMappingArray
*/
public void setSequenceMapping(
final uk.ac.vamsas.objects.core.SequenceMapping[] vSequenceMappingArray) {
// -- copy array
_sequenceMappingList.clear();
for (int i = 0; i < vSequenceMappingArray.length; i++) {
this._sequenceMappingList.add(vSequenceMappingArray[i]);
}
}
/**
* Sets the value of '_sequenceMappingList' by copying the given Vector. All
* elements will be checked for type safety.
*
* @param vSequenceMappingList
* the Vector to copy.
*/
public void setSequenceMapping(final java.util.Vector vSequenceMappingList) {
// copy vector
this._sequenceMappingList.clear();
this._sequenceMappingList.addAll(vSequenceMappingList);
}
/**
* Sets the value of '_sequenceMappingList' by setting it to the given Vector.
* No type checking is performed.
*
* @deprecated
*
* @param sequenceMappingVector
* the Vector to set.
*/
public void setSequenceMappingAsReference(
final java.util.Vector sequenceMappingVector) {
this._sequenceMappingList = sequenceMappingVector;
}
/**
*
*
* @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.DataSet
*/
public static uk.ac.vamsas.objects.core.DataSet unmarshal(
final java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException {
return (uk.ac.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(
uk.ac.vamsas.objects.core.DataSet.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);
}
}
|