/*
- * 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;
import org.exolab.castor.xml.Unmarshaller;
/**
- * Store a list of database references
- * for this sequence record - with optional mapping
- * from database sequence to the given sequence record
+ * Store a list of database references for this sequence record - with optional
+ * mapping from database sequence to the given sequence record
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-29 13:23:12 +0100 (Fri, 29 Jun 2007)
+ * $
*/
-public class DbRef extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * TODO Database Naming
- * Convention: either start using LSID (so
- * change type to URI) or leave this as an
- * uncontrolled/unspecified string ID
- *
- */
- private java.lang.String _source;
-
- /**
- * Version must be specified -
- *
- */
- private java.lang.String _version;
-
- /**
- * TODO: make some specification
- * of the database field from which this
- * accessionId is taken from - should that be a
- * special property of the dbRef object ?
- *
- */
- private java.lang.String _accessionId;
-
- /**
- * Primary Key for vamsas object
- * referencing
- */
- private java.lang.String _id;
-
- /**
- * the local mapType maps from the parent
- * sequence coordinate frame to the reference
- * frame defined by the dbRef element.
- * The mapped mapType is the mapped range defined
- * on the dbRef element's reference frame.
- * Conventionally, the unit attribute defaults to 1, or
- * will be inferred from the local sequence's
- * dictionary type and any dictionary type associated
- * with the database being mapped to.
- * However, it may be used to avoid ambiguity.
- *
- */
- private java.util.Vector _mapList;
-
- /**
- * Field _linkList.
- */
- private java.util.Vector _linkList;
-
- /**
- * Field _propertyList.
- */
- private java.util.Vector _propertyList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public DbRef() {
- super();
- this._mapList = new java.util.Vector();
- this._linkList = new java.util.Vector();
- this._propertyList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vLink
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addLink(
- final uk.ac.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException {
- this._linkList.addElement(vLink);
- }
-
- /**
- *
- *
- * @param index
- * @param vLink
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addLink(
- final int index,
- final uk.ac.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException {
- this._linkList.add(index, vLink);
- }
-
- /**
- *
- *
- * @param vMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addMap(
- final uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException {
- this._mapList.addElement(vMap);
- }
-
- /**
- *
- *
- * @param index
- * @param vMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addMap(
- final int index,
- final uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException {
- this._mapList.add(index, vMap);
- }
-
- /**
- *
- *
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.addElement(vProperty);
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final int index,
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.add(index, vProperty);
- }
-
- /**
- * Method enumerateLink.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Link elements
- */
- public java.util.Enumeration enumerateLink(
- ) {
- return this._linkList.elements();
- }
-
- /**
- * Method enumerateMap.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Map elements
- */
- public java.util.Enumeration enumerateMap(
- ) {
- return this._mapList.elements();
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Property elements
- */
- public java.util.Enumeration enumerateProperty(
- ) {
- return this._propertyList.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 DbRef extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * TODO Database Naming Convention: either start using LSID (so change type to
+ * URI) or leave this as an uncontrolled/unspecified string ID
+ *
+ */
+ private java.lang.String _source;
+
+ /**
+ * Version must be specified -
+ *
+ */
+ private java.lang.String _version;
+
+ /**
+ * TODO: make some specification of the database field from which this
+ * accessionId is taken from - should that be a special property of the dbRef
+ * object ?
+ *
+ */
+ private java.lang.String _accessionId;
+
+ /**
+ * Primary Key for vamsas object referencing
+ */
+ private java.lang.String _id;
+
+ /**
+ * the local mapType maps from the parent sequence coordinate frame to the
+ * reference frame defined by the dbRef element. The mapped mapType is the
+ * mapped range defined on the dbRef element's reference frame.
+ * Conventionally, the unit attribute defaults to 1, or will be inferred from
+ * the local sequence's dictionary type and any dictionary type associated
+ * with the database being mapped to. However, it may be used to avoid
+ * ambiguity.
+ *
+ */
+ private java.util.Vector _mapList;
+
+ /**
+ * Field _linkList.
+ */
+ private java.util.Vector _linkList;
+
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DbRef() {
+ super();
+ this._mapList = new java.util.Vector();
+ this._linkList = new java.util.Vector();
+ this._propertyList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vLink
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addLink(final uk.ac.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException {
+ this._linkList.addElement(vLink);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vLink
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addLink(final int index,
+ final uk.ac.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException {
+ this._linkList.add(index, vLink);
+ }
+
+ /**
+ *
+ *
+ * @param vMap
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addMap(final uk.ac.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException {
+ this._mapList.addElement(vMap);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vMap
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addMap(final int index, final uk.ac.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException {
+ this._mapList.add(index, vMap);
+ }
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final int index,
+ final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ * Method enumerateLink.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Link elements
+ */
+ public java.util.Enumeration enumerateLink() {
+ return this._linkList.elements();
+ }
+
+ /**
+ * Method enumerateMap.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Map elements
+ */
+ public java.util.Enumeration enumerateMap() {
+ return this._mapList.elements();
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements
+ */
+ public java.util.Enumeration enumerateProperty() {
+ return this._propertyList.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 DbRef) {
+
+ DbRef temp = (DbRef) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._source != null) {
+ if (temp._source == null)
+ return false;
+ if (this._source != temp._source) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._source);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._source);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
+ }
+ ;
return false;
-
- if (obj instanceof DbRef) {
-
- DbRef temp = (DbRef)obj;
- boolean thcycle;
- boolean tmcycle;
- if (this._source != null) {
- if (temp._source == null) return false;
- if (this._source != temp._source) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._source);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._source);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._source); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._source); };
- return false;
- }
- if (!thcycle) {
- if (!this._source.equals(temp._source)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
- }
- }
- } else if (temp._source != null)
- return false;
- if (this._version != null) {
- if (temp._version == null) return false;
- if (this._version != temp._version) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._version);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._version);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._version); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); };
- return false;
- }
- if (!thcycle) {
- if (!this._version.equals(temp._version)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
- }
- }
- } else if (temp._version != null)
- return false;
- if (this._accessionId != null) {
- if (temp._accessionId == null) return false;
- if (this._accessionId != temp._accessionId) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._accessionId);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._accessionId);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId); };
- return false;
- }
- if (!thcycle) {
- if (!this._accessionId.equals(temp._accessionId)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
- }
- }
- } else if (temp._accessionId != null)
- return false;
- 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._mapList != null) {
- if (temp._mapList == null) return false;
- if (this._mapList != temp._mapList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._mapList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._mapList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList); };
- return false;
- }
- if (!thcycle) {
- if (!this._mapList.equals(temp._mapList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
- }
- }
- } else if (temp._mapList != null)
- return false;
- if (this._linkList != null) {
- if (temp._linkList == null) return false;
- if (this._linkList != temp._linkList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._linkList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._linkList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); };
- return false;
- }
- if (!thcycle) {
- if (!this._linkList.equals(temp._linkList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
- }
- }
- } else if (temp._linkList != null)
- return false;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- if (this._propertyList != temp._propertyList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._propertyList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._propertyList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); };
- return false;
- }
- if (!thcycle) {
- if (!this._propertyList.equals(temp._propertyList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- }
- }
- } else if (temp._propertyList != null)
- return false;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._source.equals(temp._source)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
+ }
}
+ } else if (temp._source != null)
return false;
- }
-
- /**
- * Returns the value of field 'accessionId'. The field
- * 'accessionId' has the following description: TODO: make some
- * specification
- * of the database field from which this
- * accessionId is taken from - should that be a
- * special property of the dbRef object ?
- *
- *
- * @return the value of field 'AccessionId'.
- */
- public java.lang.String getAccessionId(
- ) {
- return this._accessionId;
- }
-
- /**
- * 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;
- }
-
- /**
- * Method getLink.
- *
- * @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.Link at
- * the given index
- */
- public uk.ac.vamsas.objects.core.Link getLink(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._linkList.size()) {
- throw new IndexOutOfBoundsException("getLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Link) _linkList.get(index);
- }
-
- /**
- * Method getLink.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.Link[] getLink(
- ) {
- uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0];
- return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array);
- }
-
- /**
- * Method getLinkAsReference.Returns a reference to
- * '_linkList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getLinkAsReference(
- ) {
- return this._linkList;
- }
-
- /**
- * Method getLinkCount.
- *
- * @return the size of this collection
- */
- public int getLinkCount(
- ) {
- return this._linkList.size();
- }
-
- /**
- * Method getMap.
- *
- * @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.Map at
- * the given index
- */
- public uk.ac.vamsas.objects.core.Map getMap(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._mapList.size()) {
- throw new IndexOutOfBoundsException("getMap: Index value '" + index + "' not in range [0.." + (this._mapList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Map) _mapList.get(index);
- }
-
- /**
- * Method getMap.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.Map[] getMap(
- ) {
- uk.ac.vamsas.objects.core.Map[] array = new uk.ac.vamsas.objects.core.Map[0];
- return (uk.ac.vamsas.objects.core.Map[]) this._mapList.toArray(array);
- }
-
- /**
- * Method getMapAsReference.Returns a reference to '_mapList'.
- * No type checking is performed on any modifications to the
- * Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getMapAsReference(
- ) {
- return this._mapList;
- }
-
- /**
- * Method getMapCount.
- *
- * @return the size of this collection
- */
- public int getMapCount(
- ) {
- return this._mapList.size();
- }
-
- /**
- * Method getProperty.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the uk.ac.vamsas.objects.core.Property
- * at the given index
- */
- public uk.ac.vamsas.objects.core.Property getProperty(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
- }
-
- /**
- * Method getProperty.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public uk.ac.vamsas.objects.core.Property[] getProperty(
- ) {
- uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
- return (uk.ac.vamsas.objects.core.Property[]) this._propertyList.toArray(array);
- }
-
- /**
- * Method getPropertyAsReference.Returns a reference to
- * '_propertyList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getPropertyAsReference(
- ) {
- return this._propertyList;
- }
-
- /**
- * Method getPropertyCount.
- *
- * @return the size of this collection
- */
- public int getPropertyCount(
- ) {
- return this._propertyList.size();
- }
-
- /**
- * Returns the value of field 'source'. The field 'source' has
- * the following description: TODO Database Naming
- * Convention: either start using LSID (so
- * change type to URI) or leave this as an
- * uncontrolled/unspecified string ID
- *
- *
- * @return the value of field 'Source'.
- */
- public java.lang.String getSource(
- ) {
- return this._source;
- }
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: Version must be specified -
- *
- *
- * @return the value of field 'Version'.
- */
- public java.lang.String getVersion(
- ) {
- return this._version;
- }
-
- /**
- * 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 (_source != null
- && !org.castor.util.CycleBreaker.startingToCycle(_source)) {
- result = 37 * result + _source.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_source);
- }
- if (_version != null
- && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
- result = 37 * result + _version.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_version);
- }
- if (_accessionId != null
- && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) {
- result = 37 * result + _accessionId.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId);
+ if (this._version != null) {
+ if (temp._version == null)
+ return false;
+ if (this._version != temp._version) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._version.equals(temp._version)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
}
- if (_id != null
- && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ } else if (temp._version != null)
+ return false;
+ if (this._accessionId != null) {
+ if (temp._accessionId == null)
+ return false;
+ if (this._accessionId != temp._accessionId) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._accessionId);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._accessionId);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._accessionId);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._accessionId);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._accessionId.equals(temp._accessionId)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._accessionId);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._accessionId);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
+ }
}
- if (_mapList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) {
- result = 37 * result + _mapList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_mapList);
+ } else if (temp._accessionId != null)
+ return false;
+ 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);
+ }
}
- if (_linkList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {
- result = 37 * result + _linkList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);
+ } else if (temp._id != null)
+ return false;
+ if (this._mapList != null) {
+ if (temp._mapList == null)
+ return false;
+ if (this._mapList != temp._mapList) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._mapList);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._mapList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._mapList.equals(temp._mapList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
+ }
}
- if (_propertyList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ } else if (temp._mapList != null)
+ return false;
+ if (this._linkList != null) {
+ if (temp._linkList == null)
+ return false;
+ if (this._linkList != temp._linkList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._linkList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._linkList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._linkList.equals(temp._linkList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
+ }
}
-
- return result;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
+ } else if (temp._linkList != null)
+ return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllLink(
- ) {
- this._linkList.clear();
- }
-
- /**
- */
- public void removeAllMap(
- ) {
- this._mapList.clear();
- }
-
- /**
- */
- public void removeAllProperty(
- ) {
- this._propertyList.clear();
- }
-
- /**
- * Method removeLink.
- *
- * @param vLink
- * @return true if the object was removed from the collection.
- */
- public boolean removeLink(
- final uk.ac.vamsas.objects.core.Link vLink) {
- boolean removed = _linkList.remove(vLink);
- return removed;
- }
-
- /**
- * Method removeLinkAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Link removeLinkAt(
- final int index) {
- java.lang.Object obj = this._linkList.remove(index);
- return (uk.ac.vamsas.objects.core.Link) obj;
+ } else if (temp._propertyList != null)
+ return false;
+ return true;
}
-
- /**
- * Method removeMap.
- *
- * @param vMap
- * @return true if the object was removed from the collection.
- */
- public boolean removeMap(
- final uk.ac.vamsas.objects.core.Map vMap) {
- boolean removed = _mapList.remove(vMap);
- return removed;
+ return false;
+ }
+
+ /**
+ * Returns the value of field 'accessionId'. The field 'accessionId' has the
+ * following description: TODO: make some specification of the database field
+ * from which this accessionId is taken from - should that be a special
+ * property of the dbRef object ?
+ *
+ *
+ * @return the value of field 'AccessionId'.
+ */
+ public java.lang.String getAccessionId() {
+ return this._accessionId;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Method getLink.
+ *
+ * @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.Link at the given index
+ */
+ public uk.ac.vamsas.objects.core.Link getLink(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._linkList.size()) {
+ throw new IndexOutOfBoundsException("getLink: Index value '" + index
+ + "' not in range [0.." + (this._linkList.size() - 1) + "]");
}
- /**
- * Method removeMapAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Map removeMapAt(
- final int index) {
- java.lang.Object obj = this._mapList.remove(index);
- return (uk.ac.vamsas.objects.core.Map) obj;
+ return (uk.ac.vamsas.objects.core.Link) _linkList.get(index);
+ }
+
+ /**
+ * Method getLink.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.Link[] getLink() {
+ uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0];
+ return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array);
+ }
+
+ /**
+ * Method getLinkAsReference.Returns a reference to '_linkList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getLinkAsReference() {
+ return this._linkList;
+ }
+
+ /**
+ * Method getLinkCount.
+ *
+ * @return the size of this collection
+ */
+ public int getLinkCount() {
+ return this._linkList.size();
+ }
+
+ /**
+ * Method getMap.
+ *
+ * @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.Map at the given index
+ */
+ public uk.ac.vamsas.objects.core.Map getMap(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._mapList.size()) {
+ throw new IndexOutOfBoundsException("getMap: Index value '" + index
+ + "' not in range [0.." + (this._mapList.size() - 1) + "]");
}
- /**
- * Method removeProperty.
- *
- * @param vProperty
- * @return true if the object was removed from the collection.
- */
- public boolean removeProperty(
- final uk.ac.vamsas.objects.core.Property vProperty) {
- boolean removed = _propertyList.remove(vProperty);
- return removed;
+ return (uk.ac.vamsas.objects.core.Map) _mapList.get(index);
+ }
+
+ /**
+ * Method getMap.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.Map[] getMap() {
+ uk.ac.vamsas.objects.core.Map[] array = new uk.ac.vamsas.objects.core.Map[0];
+ return (uk.ac.vamsas.objects.core.Map[]) this._mapList.toArray(array);
+ }
+
+ /**
+ * Method getMapAsReference.Returns a reference to '_mapList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getMapAsReference() {
+ return this._mapList;
+ }
+
+ /**
+ * Method getMapCount.
+ *
+ * @return the size of this collection
+ */
+ public int getMapCount() {
+ return this._mapList.size();
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.Property at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Property getProperty(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
}
- /**
- * Method removePropertyAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Property removePropertyAt(
- final int index) {
- java.lang.Object obj = this._propertyList.remove(index);
- return (uk.ac.vamsas.objects.core.Property) obj;
+ return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.Property[] getProperty() {
+ uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
+ return (uk.ac.vamsas.objects.core.Property[]) this._propertyList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPropertyAsReference.Returns a reference to '_propertyList'. No
+ * type checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getPropertyAsReference() {
+ return this._propertyList;
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount() {
+ return this._propertyList.size();
+ }
+
+ /**
+ * Returns the value of field 'source'. The field 'source' has the following
+ * description: TODO Database Naming Convention: either start using LSID (so
+ * change type to URI) or leave this as an uncontrolled/unspecified string ID
+ *
+ *
+ * @return the value of field 'Source'.
+ */
+ public java.lang.String getSource() {
+ return this._source;
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version' has the following
+ * description: Version must be specified -
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion() {
+ return this._version;
+ }
+
+ /**
+ * 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 (_source != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_source)) {
+ result = 37 * result + _source.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_source);
}
-
- /**
- * Sets the value of field 'accessionId'. The field
- * 'accessionId' has the following description: TODO: make some
- * specification
- * of the database field from which this
- * accessionId is taken from - should that be a
- * special property of the dbRef object ?
- *
- *
- * @param accessionId the value of field 'accessionId'.
- */
- public void setAccessionId(
- final java.lang.String accessionId) {
- this._accessionId = accessionId;
+ if (_version != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
+ result = 37 * result + _version.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_version);
}
-
- /**
- * 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;
+ if (_accessionId != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) {
+ result = 37 * result + _accessionId.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId);
}
-
- /**
- *
- *
- * @param index
- * @param vLink
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setLink(
- final int index,
- final uk.ac.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._linkList.size()) {
- throw new IndexOutOfBoundsException("setLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]");
- }
-
- this._linkList.set(index, vLink);
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
}
-
- /**
- *
- *
- * @param vLinkArray
- */
- public void setLink(
- final uk.ac.vamsas.objects.core.Link[] vLinkArray) {
- //-- copy array
- _linkList.clear();
-
- for (int i = 0; i < vLinkArray.length; i++) {
- this._linkList.add(vLinkArray[i]);
- }
+ if (_mapList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) {
+ result = 37 * result + _mapList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_mapList);
}
-
- /**
- * Sets the value of '_linkList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vLinkList the Vector to copy.
- */
- public void setLink(
- final java.util.Vector vLinkList) {
- // copy vector
- this._linkList.clear();
-
- this._linkList.addAll(vLinkList);
+ if (_linkList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {
+ result = 37 * result + _linkList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);
}
-
- /**
- * Sets the value of '_linkList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param linkVector the Vector to set.
- */
- public void setLinkAsReference(
- final java.util.Vector linkVector) {
- this._linkList = linkVector;
+ if (_propertyList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
}
- /**
- *
- *
- * @param index
- * @param vMap
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setMap(
- final int index,
- final uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._mapList.size()) {
- throw new IndexOutOfBoundsException("setMap: Index value '" + index + "' not in range [0.." + (this._mapList.size() - 1) + "]");
- }
-
- this._mapList.set(index, vMap);
+ 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;
}
-
- /**
- *
- *
- * @param vMapArray
- */
- public void setMap(
- final uk.ac.vamsas.objects.core.Map[] vMapArray) {
- //-- copy array
- _mapList.clear();
-
- for (int i = 0; i < vMapArray.length; i++) {
- this._mapList.add(vMapArray[i]);
- }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllLink() {
+ this._linkList.clear();
+ }
+
+ /**
+ */
+ public void removeAllMap() {
+ this._mapList.clear();
+ }
+
+ /**
+ */
+ public void removeAllProperty() {
+ this._propertyList.clear();
+ }
+
+ /**
+ * Method removeLink.
+ *
+ * @param vLink
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeLink(final uk.ac.vamsas.objects.core.Link vLink) {
+ boolean removed = _linkList.remove(vLink);
+ return removed;
+ }
+
+ /**
+ * Method removeLinkAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Link removeLinkAt(final int index) {
+ java.lang.Object obj = this._linkList.remove(index);
+ return (uk.ac.vamsas.objects.core.Link) obj;
+ }
+
+ /**
+ * Method removeMap.
+ *
+ * @param vMap
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeMap(final uk.ac.vamsas.objects.core.Map vMap) {
+ boolean removed = _mapList.remove(vMap);
+ return removed;
+ }
+
+ /**
+ * Method removeMapAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Map removeMapAt(final int index) {
+ java.lang.Object obj = this._mapList.remove(index);
+ return (uk.ac.vamsas.objects.core.Map) obj;
+ }
+
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final uk.ac.vamsas.objects.core.Property vProperty) {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ }
+
+ /**
+ * Sets the value of field 'accessionId'. The field 'accessionId' has the
+ * following description: TODO: make some specification of the database field
+ * from which this accessionId is taken from - should that be a special
+ * property of the dbRef object ?
+ *
+ *
+ * @param accessionId
+ * the value of field 'accessionId'.
+ */
+ public void setAccessionId(final java.lang.String accessionId) {
+ this._accessionId = accessionId;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vLink
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setLink(final int index,
+ final uk.ac.vamsas.objects.core.Link vLink)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._linkList.size()) {
+ throw new IndexOutOfBoundsException("setLink: Index value '" + index
+ + "' not in range [0.." + (this._linkList.size() - 1) + "]");
}
- /**
- * Sets the value of '_mapList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vMapList the Vector to copy.
- */
- public void setMap(
- final java.util.Vector vMapList) {
- // copy vector
- this._mapList.clear();
-
- this._mapList.addAll(vMapList);
- }
+ this._linkList.set(index, vLink);
+ }
- /**
- * Sets the value of '_mapList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param mapVector the Vector to set.
- */
- public void setMapAsReference(
- final java.util.Vector mapVector) {
- this._mapList = mapVector;
- }
+ /**
+ *
+ *
+ * @param vLinkArray
+ */
+ public void setLink(final uk.ac.vamsas.objects.core.Link[] vLinkArray) {
+ // -- copy array
+ _linkList.clear();
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setProperty(
- final int index,
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- this._propertyList.set(index, vProperty);
+ for (int i = 0; i < vLinkArray.length; i++) {
+ this._linkList.add(vLinkArray[i]);
}
-
- /**
- *
- *
- * @param vPropertyArray
- */
- public void setProperty(
- final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
- //-- copy array
- _propertyList.clear();
-
- for (int i = 0; i < vPropertyArray.length; i++) {
- this._propertyList.add(vPropertyArray[i]);
- }
+ }
+
+ /**
+ * Sets the value of '_linkList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vLinkList
+ * the Vector to copy.
+ */
+ public void setLink(final java.util.Vector vLinkList) {
+ // copy vector
+ this._linkList.clear();
+
+ this._linkList.addAll(vLinkList);
+ }
+
+ /**
+ * Sets the value of '_linkList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param linkVector
+ * the Vector to set.
+ */
+ public void setLinkAsReference(final java.util.Vector linkVector) {
+ this._linkList = linkVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vMap
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setMap(final int index, final uk.ac.vamsas.objects.core.Map vMap)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._mapList.size()) {
+ throw new IndexOutOfBoundsException("setMap: Index value '" + index
+ + "' not in range [0.." + (this._mapList.size() - 1) + "]");
}
- /**
- * Sets the value of '_propertyList' by copying the given
- * Vector. All elements will be checked for type safety.
- *
- * @param vPropertyList the Vector to copy.
- */
- public void setProperty(
- final java.util.Vector vPropertyList) {
- // copy vector
- this._propertyList.clear();
-
- this._propertyList.addAll(vPropertyList);
- }
+ this._mapList.set(index, vMap);
+ }
- /**
- * Sets the value of '_propertyList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param propertyVector the Vector to set.
- */
- public void setPropertyAsReference(
- final java.util.Vector propertyVector) {
- this._propertyList = propertyVector;
- }
+ /**
+ *
+ *
+ * @param vMapArray
+ */
+ public void setMap(final uk.ac.vamsas.objects.core.Map[] vMapArray) {
+ // -- copy array
+ _mapList.clear();
- /**
- * Sets the value of field 'source'. The field 'source' has the
- * following description: TODO Database Naming
- * Convention: either start using LSID (so
- * change type to URI) or leave this as an
- * uncontrolled/unspecified string ID
- *
- *
- * @param source the value of field 'source'.
- */
- public void setSource(
- final java.lang.String source) {
- this._source = source;
+ for (int i = 0; i < vMapArray.length; i++) {
+ this._mapList.add(vMapArray[i]);
}
-
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: Version must be specified -
- *
- *
- * @param version the value of field 'version'.
- */
- public void setVersion(
- final java.lang.String version) {
- this._version = version;
+ }
+
+ /**
+ * Sets the value of '_mapList' by copying the given Vector. All elements will
+ * be checked for type safety.
+ *
+ * @param vMapList
+ * the Vector to copy.
+ */
+ public void setMap(final java.util.Vector vMapList) {
+ // copy vector
+ this._mapList.clear();
+
+ this._mapList.addAll(vMapList);
+ }
+
+ /**
+ * Sets the value of '_mapList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param mapVector
+ * the Vector to set.
+ */
+ public void setMapAsReference(final java.util.Vector mapVector) {
+ this._mapList = mapVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setProperty(final int index,
+ final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
}
- /**
- * 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.DbRef
- */
- public static uk.ac.vamsas.objects.core.DbRef unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DbRef.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);
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
+ // -- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++) {
+ this._propertyList.add(vPropertyArray[i]);
}
+ }
+
+ /**
+ * Sets the value of '_propertyList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vPropertyList
+ * the Vector to copy.
+ */
+ public void setProperty(final java.util.Vector vPropertyList) {
+ // copy vector
+ this._propertyList.clear();
+
+ this._propertyList.addAll(vPropertyList);
+ }
+
+ /**
+ * Sets the value of '_propertyList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param propertyVector
+ * the Vector to set.
+ */
+ public void setPropertyAsReference(final java.util.Vector propertyVector) {
+ this._propertyList = propertyVector;
+ }
+
+ /**
+ * Sets the value of field 'source'. The field 'source' has the following
+ * description: TODO Database Naming Convention: either start using LSID (so
+ * change type to URI) or leave this as an uncontrolled/unspecified string ID
+ *
+ *
+ * @param source
+ * the value of field 'source'.
+ */
+ public void setSource(final java.lang.String source) {
+ this._source = source;
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has the following
+ * description: Version must be specified -
+ *
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * 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.DbRef
+ */
+ public static uk.ac.vamsas.objects.core.DbRef unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.DbRef.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