X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FDbRef.java;h=1683cb832a9ba5cea72f79fb4862f9694026b685;hb=1eea4b639911330e7cd65e17c5421cc584f0d22e;hp=5b69fd5e74a984b41ca7fd8c72f2dbd090b0fa19;hpb=667c5f732b74c1a0e0ac50cd26d93634811663ee;p=vamsas.git
diff --git a/src/uk/ac/vamsas/objects/core/DbRef.java b/src/uk/ac/vamsas/objects/core/DbRef.java
index 5b69fd5..1683cb8 100644
--- a/src/uk/ac/vamsas/objects/core/DbRef.java
+++ b/src/uk/ac/vamsas/objects/core/DbRef.java
@@ -1,806 +1,1102 @@
/*
- * This class was automatically generated with
- * Castor 0.9.9M2, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.2.
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see .
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
/**
- * 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
-{
+public class DbRef extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
- //--------------------------/
- //- 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;
- /**
- * 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;
- /**
- * 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;
+ /**
+ * 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;
-
- /**
- * From: Offset to first
- * position in dataset sequence record that
- * this database entry maps to To: Offset
- * to last position in dataset sequence
- * record that this database entry maps to
- * Start: Offset to first last position in
- * database entry that first (or offset)
- * position in sequence maps to End: Offset
- * to last position in database entry that
- * last (offset) position in sequence maps
- * to
- */
- private java.util.Vector _mapList;
+ /**
+ * Primary Key for vamsas object referencing
+ */
+ private java.lang.String _id;
- /**
- * Field _linkList
- */
- private java.util.Vector _linkList;
+ /**
+ * 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 _propertyList
- */
- private java.util.Vector _propertyList;
+ /**
+ * Field _linkList.
+ */
+ private java.util.Vector _linkList;
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
- //----------------/
- //- Constructors -/
- //----------------/
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
- public DbRef()
- {
- super();
- _mapList = new Vector();
- _linkList = new Vector();
- _propertyList = new Vector();
- } //-- uk.ac.vamsas.objects.core.DbRef()
+ public DbRef() {
+ super();
+ this._mapList = new java.util.Vector();
+ this._linkList = new java.util.Vector();
+ this._propertyList = new java.util.Vector();
+ }
+ // -----------/
+ // - Methods -/
+ // -----------/
- //-----------/
- //- 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);
+ }
- /**
- * Method addLink
- *
- *
- *
- * @param vLink
- */
- public void addLink(uk.ac.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException
- {
- _linkList.addElement(vLink);
- } //-- void addLink(uk.ac.vamsas.objects.core.Link)
-
- /**
- * Method addLink
- *
- *
- *
- * @param index
- * @param vLink
- */
- public void addLink(int index, uk.ac.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException
- {
- _linkList.insertElementAt(vLink, index);
- } //-- void addLink(int, uk.ac.vamsas.objects.core.Link)
-
- /**
- * Method addMap
- *
- *
- *
- * @param vMap
- */
- public void addMap(uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException
- {
- _mapList.addElement(vMap);
- } //-- void addMap(uk.ac.vamsas.objects.core.Map)
-
- /**
- * Method addMap
- *
- *
- *
- * @param index
- * @param vMap
- */
- public void addMap(int index, uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException
- {
- _mapList.insertElementAt(vMap, index);
- } //-- void addMap(int, uk.ac.vamsas.objects.core.Map)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method enumerateLink
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateLink()
- {
- return _linkList.elements();
- } //-- java.util.Enumeration enumerateLink()
-
- /**
- * Method enumerateMap
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateMap()
- {
- return _mapList.elements();
- } //-- java.util.Enumeration enumerateMap()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * Note: hashCode() has not been overriden
- *
- * @param obj
- * @return boolean
- */
- public boolean equals(java.lang.Object obj)
- {
- if ( this == obj )
- return true;
-
- if (super.equals(obj)==false)
+ /**
+ *
+ *
+ * @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;
- if (this._source != null) {
- if (temp._source == null) return false;
- else if (!(this._source.equals(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;
}
- else if (temp._source != null)
- return false;
- if (this._version != null) {
- if (temp._version == null) return false;
- else if (!(this._version.equals(temp._version)))
- 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);
}
- else if (temp._version != null)
- return false;
- if (this._accessionId != null) {
- if (temp._accessionId == null) return false;
- else if (!(this._accessionId.equals(temp._accessionId)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
}
- else if (temp._accessionId != null)
- return false;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
+ ;
+ 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;
}
- else if (temp._id != null)
- return false;
- if (this._mapList != null) {
- if (temp._mapList == null) return false;
- else if (!(this._mapList.equals(temp._mapList)))
- 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);
}
- else if (temp._mapList != null)
- return false;
- if (this._linkList != null) {
- if (temp._linkList == null) return false;
- else if (!(this._linkList.equals(temp._linkList)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._accessionId);
}
- else if (temp._linkList != null)
- return false;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
+ ;
+ 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;
}
- else if (temp._propertyList != null)
- return false;
- return true;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
+ }
}
+ } else if (temp._accessionId != null)
return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * 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 String
- * @return the value of field 'accessionId'.
- */
- public java.lang.String getAccessionId()
- {
- return this._accessionId;
- } //-- java.lang.String getAccessionId()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Method getLink
- *
- *
- *
- * @param index
- * @return Link
- */
- public uk.ac.vamsas.objects.core.Link getLink(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _linkList.size())) {
- throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Link getLink(int)
-
- /**
- * Method getLink
- *
- *
- *
- * @return Link
- */
- public uk.ac.vamsas.objects.core.Link[] getLink()
- {
- int size = _linkList.size();
- uk.ac.vamsas.objects.core.Link[] mArray = new uk.ac.vamsas.objects.core.Link[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Link[] getLink()
-
- /**
- * Method getLinkCount
- *
- *
- *
- * @return int
- */
- public int getLinkCount()
- {
- return _linkList.size();
- } //-- int getLinkCount()
-
- /**
- * Method getMap
- *
- *
- *
- * @param index
- * @return Map
- */
- public uk.ac.vamsas.objects.core.Map getMap(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _mapList.size())) {
- throw new IndexOutOfBoundsException("getMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Map) _mapList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Map getMap(int)
-
- /**
- * Method getMap
- *
- *
- *
- * @return Map
- */
- public uk.ac.vamsas.objects.core.Map[] getMap()
- {
- int size = _mapList.size();
- uk.ac.vamsas.objects.core.Map[] mArray = new uk.ac.vamsas.objects.core.Map[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Map) _mapList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Map[] getMap()
-
- /**
- * Method getMapCount
- *
- *
- *
- * @return int
- */
- public int getMapCount()
- {
- return _mapList.size();
- } //-- int getMapCount()
-
- /**
- * Method getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * 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 String
- * @return the value of field 'source'.
- */
- public java.lang.String getSource()
- {
- return this._source;
- } //-- java.lang.String getSource()
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: Version must be specified -
- *
- *
- * @return String
- * @return the value of field 'version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- } //-- java.lang.String getVersion()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ 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);
+ }
}
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAllLink
- *
- */
- public void removeAllLink()
- {
- _linkList.removeAllElements();
- } //-- void removeAllLink()
-
- /**
- * Method removeAllMap
- *
- */
- public void removeAllMap()
- {
- _mapList.removeAllElements();
- } //-- void removeAllMap()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeLink
- *
- *
- *
- * @param index
- * @return Link
- */
- public uk.ac.vamsas.objects.core.Link removeLink(int index)
- {
- java.lang.Object obj = _linkList.elementAt(index);
- _linkList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Link) obj;
- } //-- uk.ac.vamsas.objects.core.Link removeLink(int)
-
- /**
- * Method removeMap
- *
- *
- *
- * @param index
- * @return Map
- */
- public uk.ac.vamsas.objects.core.Map removeMap(int index)
- {
- java.lang.Object obj = _mapList.elementAt(index);
- _mapList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Map) obj;
- } //-- uk.ac.vamsas.objects.core.Map removeMap(int)
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Property) obj;
- } //-- uk.ac.vamsas.objects.core.Property removeProperty(int)
-
- /**
- * 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(java.lang.String accessionId)
- {
- this._accessionId = accessionId;
- } //-- void setAccessionId(java.lang.String)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Method setLink
- *
- *
- *
- * @param index
- * @param vLink
- */
- public void setLink(int index, uk.ac.vamsas.objects.core.Link vLink)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _linkList.size())) {
- throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
- }
- _linkList.setElementAt(vLink, index);
- } //-- void setLink(int, uk.ac.vamsas.objects.core.Link)
-
- /**
- * Method setLink
- *
- *
- *
- * @param linkArray
- */
- public void setLink(uk.ac.vamsas.objects.core.Link[] linkArray)
- {
- //-- copy array
- _linkList.removeAllElements();
- for (int i = 0; i < linkArray.length; i++) {
- _linkList.addElement(linkArray[i]);
- }
- } //-- void setLink(uk.ac.vamsas.objects.core.Link)
-
- /**
- * Method setMap
- *
- *
- *
- * @param index
- * @param vMap
- */
- public void setMap(int index, uk.ac.vamsas.objects.core.Map vMap)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _mapList.size())) {
- throw new IndexOutOfBoundsException("setMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
- }
- _mapList.setElementAt(vMap, index);
- } //-- void setMap(int, uk.ac.vamsas.objects.core.Map)
-
- /**
- * Method setMap
- *
- *
- *
- * @param mapArray
- */
- public void setMap(uk.ac.vamsas.objects.core.Map[] mapArray)
- {
- //-- copy array
- _mapList.removeAllElements();
- for (int i = 0; i < mapArray.length; i++) {
- _mapList.addElement(mapArray[i]);
+ } 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);
+ }
}
- } //-- void setMap(uk.ac.vamsas.objects.core.Map)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ } 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);
+ }
}
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
- */
- public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[i]);
+ } 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);
+ }
}
- } //-- void setProperty(uk.ac.vamsas.objects.core.Property)
-
- /**
- * 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(java.lang.String source)
- {
- this._source = source;
- } //-- void setSource(java.lang.String)
-
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: Version must be specified -
- *
- *
- * @param version the value of field 'version'.
+ } else if (temp._propertyList != null)
+ return false;
+ return true;
+ }
+ 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.
+ *
+ * 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
+ * know 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.
+ *
+ * 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
+ * know 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.
+ *
+ * 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
+ * know 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.
+ *
+ * The following steps came from Effective Java Programming Language
+ * Guide 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 (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_mapList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) {
+ result = 37 * result + _mapList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_mapList);
+ }
+ if (_linkList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {
+ result = 37 * result + _linkList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);
+ }
+ if (_propertyList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+
+ return result;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid() {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public void setVersion(java.lang.String version)
- {
- this._version = version;
- } //-- void setVersion(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return DbRef
+ public void removeAllLink() {
+ this._linkList.clear();
+ }
+
+ /**
*/
- public static uk.ac.vamsas.objects.core.DbRef unmarshal(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);
- } //-- uk.ac.vamsas.objects.core.DbRef unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
+ public void removeAllMap() {
+ this._mapList.clear();
+ }
+
+ /**
*/
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
+ 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) + "]");
+ }
+
+ this._linkList.set(index, vLink);
+ }
+
+ /**
+ *
+ *
+ * @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]);
+ }
+ }
+
+ /**
+ * 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) + "]");
+ }
+
+ this._mapList.set(index, vMap);
+ }
+
+ /**
+ *
+ *
+ * @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]);
+ }
+ }
+
+ /**
+ * 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) + "]");
+ }
+
+ 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);
+ }
}