/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
/**
* Class DataSet.
*
- * @version $Revision$ $Date$
+ * @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)
+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.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 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.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._sequenceList != null) {
- if (temp._sequenceList == null) return false;
- if (this._sequenceList != temp._sequenceList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._sequenceList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._sequenceList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList); };
- return false;
- }
- if (!thcycle) {
- if (!this._sequenceList.equals(temp._sequenceList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
- org.castor.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.util.CycleBreaker.startingToCycle(this._sequenceMappingList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._sequenceMappingList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceMappingList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceMappingList); };
- return false;
- }
- if (!thcycle) {
- if (!this._sequenceMappingList.equals(temp._sequenceMappingList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceMappingList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceMappingList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceMappingList);
- org.castor.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.util.CycleBreaker.startingToCycle(this._dataSetAnnotationsList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dataSetAnnotationsList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetAnnotationsList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetAnnotationsList); };
- return false;
- }
- if (!thcycle) {
- if (!this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetAnnotationsList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetAnnotationsList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetAnnotationsList);
- org.castor.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.util.CycleBreaker.startingToCycle(this._alignmentList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._alignmentList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentList); };
- return false;
- }
- if (!thcycle) {
- if (!this._alignmentList.equals(temp._alignmentList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentList);
- org.castor.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.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._provenance != null) {
- if (temp._provenance == null) return false;
- if (this._provenance != temp._provenance) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); };
- return false;
- }
- if (!thcycle) {
- if (!this._provenance.equals(temp._provenance)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- }
- } else if (temp._provenance != null)
- return false;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
}
+ } else if (temp._id != null)
return false;
- }
-
- /**
- * 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.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_sequenceList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_sequenceList)) {
- result = 37 * result + _sequenceList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceList);
- }
- if (_sequenceMappingList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
- result = 37 * result + _sequenceMappingList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
- }
- if (_dataSetAnnotationsList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_dataSetAnnotationsList)) {
- result = 37 * result + _dataSetAnnotationsList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
- }
- if (_alignmentList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_alignmentList)) {
- result = 37 * result + _alignmentList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentList);
- }
- if (_treeList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
- result = 37 * result + _treeList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
- }
- if (_provenance != null
- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
- result = 37 * result + _provenance.hashCode();
- org.castor.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) {
+ if (this._sequenceList != null) {
+ if (temp._sequenceList == null)
+ return false;
+ if (this._sequenceList != temp._sequenceList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._sequenceList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._sequenceList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceList);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._sequenceList.equals(temp._sequenceList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
+ }
}
- 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]);
+ } 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.util.CycleBreaker
+ .startingToCycle(this._sequenceMappingList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._sequenceMappingList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceMappingList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceMappingList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._sequenceMappingList.equals(temp._sequenceMappingList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceMappingList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceMappingList);
+ return false;
+ }
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceMappingList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceMappingList);
+ }
}
- }
-
- /**
- * 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) + "]");
+ } 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.util.CycleBreaker
+ .startingToCycle(this._dataSetAnnotationsList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._dataSetAnnotationsList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetAnnotationsList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetAnnotationsList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._dataSetAnnotationsList
+ .equals(temp._dataSetAnnotationsList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetAnnotationsList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetAnnotationsList);
+ return false;
+ }
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetAnnotationsList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetAnnotationsList);
+ }
}
-
- 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]);
+ } 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.util.CycleBreaker
+ .startingToCycle(this._alignmentList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._alignmentList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._alignmentList.equals(temp._alignmentList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentList);
+ return false;
+ }
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentList);
+ }
}
- }
-
- /**
- * 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) + "]");
+ } 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.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._provenance != null) {
+ if (temp._provenance == null)
+ return false;
+ if (this._provenance != temp._provenance) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._provenance);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._provenance);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._provenance.equals(temp._provenance)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
}
- }
-
- /**
- * 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);
- }
+ } 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.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_sequenceList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_sequenceList)) {
+ result = 37 * result + _sequenceList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceList);
+ }
+ if (_sequenceMappingList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
+ result = 37 * result + _sequenceMappingList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
+ }
+ if (_dataSetAnnotationsList != null
+ && !org.castor.util.CycleBreaker
+ .startingToCycle(_dataSetAnnotationsList)) {
+ result = 37 * result + _dataSetAnnotationsList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
+ }
+ if (_alignmentList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_alignmentList)) {
+ result = 37 * result + _alignmentList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentList);
+ }
+ if (_treeList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
+ result = 37 * result + _treeList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
+ }
+ if (_provenance != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+ org.castor.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);
+ }
}
git://source.jalview.org / vamsas.git / blobdiff