/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
/**
* Class Sequence.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class Sequence extends uk.ac.vamsas.objects.core.SequenceType
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- *
- */
- private java.lang.String _id;
-
- /**
- * symbol class for sequence
- *
- */
- private java.lang.String _dictionary;
-
- /**
- * Store a list of database references
- * for this sequence record - with optional mapping
- * from database sequence to the given sequence record
- */
- private java.util.Vector _dbRefList;
-
- /**
- * explicitly named cross reference to
- * other objects in the document.
- */
- private java.util.Vector _vxrefList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Sequence() {
- super();
- this._dbRefList = new java.util.Vector();
- this._vxrefList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vDbRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addDbRef(
- final uk.ac.vamsas.objects.core.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException {
- this._dbRefList.addElement(vDbRef);
- }
-
- /**
- *
- *
- * @param index
- * @param vDbRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addDbRef(
- final int index,
- final uk.ac.vamsas.objects.core.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException {
- this._dbRefList.add(index, vDbRef);
- }
-
- /**
- *
- *
- * @param vVxref
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addVxref(
- final uk.ac.vamsas.objects.core.Vxref vVxref)
- throws java.lang.IndexOutOfBoundsException {
- this._vxrefList.addElement(vVxref);
- }
-
- /**
- *
- *
- * @param index
- * @param vVxref
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addVxref(
- final int index,
- final uk.ac.vamsas.objects.core.Vxref vVxref)
- throws java.lang.IndexOutOfBoundsException {
- this._vxrefList.add(index, vVxref);
- }
-
- /**
- * Method enumerateDbRef.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.DbRef elements
- */
- public java.util.Enumeration enumerateDbRef(
- ) {
- return this._dbRefList.elements();
- }
-
- /**
- * Method enumerateVxref.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Vxref elements
- */
- public java.util.Enumeration enumerateVxref(
- ) {
- return this._vxrefList.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 Sequence extends uk.ac.vamsas.objects.core.SequenceType implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Primary Key for vamsas object referencing
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * symbol class for sequence
+ *
+ */
+ private java.lang.String _dictionary;
+
+ /**
+ * Store a list of database references for this sequence record - with
+ * optional mapping from database sequence to the given sequence record
+ */
+ private java.util.Vector _dbRefList;
+
+ /**
+ * explicitly named cross reference to other objects in the document.
+ */
+ private java.util.Vector _vxrefList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Sequence() {
+ super();
+ this._dbRefList = new java.util.Vector();
+ this._vxrefList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vDbRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDbRef(final uk.ac.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException {
+ this._dbRefList.addElement(vDbRef);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDbRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDbRef(final int index,
+ final uk.ac.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException {
+ this._dbRefList.add(index, vDbRef);
+ }
+
+ /**
+ *
+ *
+ * @param vVxref
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addVxref(final uk.ac.vamsas.objects.core.Vxref vVxref)
+ throws java.lang.IndexOutOfBoundsException {
+ this._vxrefList.addElement(vVxref);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vVxref
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addVxref(final int index,
+ final uk.ac.vamsas.objects.core.Vxref vVxref)
+ throws java.lang.IndexOutOfBoundsException {
+ this._vxrefList.add(index, vVxref);
+ }
+
+ /**
+ * Method enumerateDbRef.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.DbRef elements
+ */
+ public java.util.Enumeration enumerateDbRef() {
+ return this._dbRefList.elements();
+ }
+
+ /**
+ * Method enumerateVxref.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Vxref elements
+ */
+ public java.util.Enumeration enumerateVxref() {
+ return this._vxrefList.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 Sequence) {
+
+ Sequence temp = (Sequence) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._id != null) {
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
return false;
-
- if (obj instanceof Sequence) {
-
- Sequence temp = (Sequence)obj;
- boolean thcycle;
- boolean tmcycle;
- if (this._id != null) {
- if (temp._id == null) return false;
- if (this._id != temp._id) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
- return false;
- if (this._dictionary != null) {
- if (temp._dictionary == null) return false;
- if (this._dictionary != temp._dictionary) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._dictionary);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dictionary);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary); };
- return false;
- }
- if (!thcycle) {
- if (!this._dictionary.equals(temp._dictionary)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
- }
- }
- } else if (temp._dictionary != null)
- return false;
- if (this._dbRefList != null) {
- if (temp._dbRefList == null) return false;
- if (this._dbRefList != temp._dbRefList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._dbRefList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dbRefList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); };
- return false;
- }
- if (!thcycle) {
- if (!this._dbRefList.equals(temp._dbRefList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
- }
- }
- } else if (temp._dbRefList != null)
- return false;
- if (this._vxrefList != null) {
- if (temp._vxrefList == null) return false;
- if (this._vxrefList != temp._vxrefList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._vxrefList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._vxrefList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); };
- return false;
- }
- if (!thcycle) {
- if (!this._vxrefList.equals(temp._vxrefList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
- }
- }
- } else if (temp._vxrefList != null)
- return false;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
}
+ } else if (temp._id != null)
return false;
- }
-
- /**
- * Method getDbRef.
- *
- * @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.DbRef at
- * the given index
- */
- public uk.ac.vamsas.objects.core.DbRef getDbRef(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._dbRefList.size()) {
- throw new IndexOutOfBoundsException("getDbRef: Index value '" + index + "' not in range [0.." + (this._dbRefList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.DbRef) _dbRefList.get(index);
- }
-
- /**
- * Method getDbRef.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.DbRef[] getDbRef(
- ) {
- uk.ac.vamsas.objects.core.DbRef[] array = new uk.ac.vamsas.objects.core.DbRef[0];
- return (uk.ac.vamsas.objects.core.DbRef[]) this._dbRefList.toArray(array);
- }
-
- /**
- * Method getDbRefAsReference.Returns a reference to
- * '_dbRefList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getDbRefAsReference(
- ) {
- return this._dbRefList;
- }
-
- /**
- * Method getDbRefCount.
- *
- * @return the size of this collection
- */
- public int getDbRefCount(
- ) {
- return this._dbRefList.size();
- }
-
- /**
- * Returns the value of field 'dictionary'. The field
- * 'dictionary' has the following description: symbol class for
- * sequence
- *
- *
- * @return the value of field 'Dictionary'.
- */
- public java.lang.String getDictionary(
- ) {
- return this._dictionary;
- }
-
- /**
- * 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 getVxref.
- *
- * @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.Vxref at
- * the given index
- */
- public uk.ac.vamsas.objects.core.Vxref getVxref(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._vxrefList.size()) {
- throw new IndexOutOfBoundsException("getVxref: Index value '" + index + "' not in range [0.." + (this._vxrefList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Vxref) _vxrefList.get(index);
- }
-
- /**
- * Method getVxref.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.Vxref[] getVxref(
- ) {
- uk.ac.vamsas.objects.core.Vxref[] array = new uk.ac.vamsas.objects.core.Vxref[0];
- return (uk.ac.vamsas.objects.core.Vxref[]) this._vxrefList.toArray(array);
- }
-
- /**
- * Method getVxrefAsReference.Returns a reference to
- * '_vxrefList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getVxrefAsReference(
- ) {
- return this._vxrefList;
- }
-
- /**
- * Method getVxrefCount.
- *
- * @return the size of this collection
- */
- public int getVxrefCount(
- ) {
- return this._vxrefList.size();
- }
-
- /**
- * Overrides the java.lang.Object.hashCode method.
- * <p>
- * The following steps came from <b>Effective Java Programming
- * Language Guide</b> by Joshua Bloch, Chapter 3
- *
- * @return a hash code value for the object.
- */
- public int hashCode(
- ) {
- int result = super.hashCode();
-
- long tmp;
- if (_id != null
- && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_dictionary != null
- && !org.castor.util.CycleBreaker.startingToCycle(_dictionary)) {
- result = 37 * result + _dictionary.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_dictionary);
- }
- if (_dbRefList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_dbRefList)) {
- result = 37 * result + _dbRefList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_dbRefList);
- }
- if (_vxrefList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_vxrefList)) {
- result = 37 * result + _vxrefList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_vxrefList);
- }
-
- return result;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
+ if (this._dictionary != null) {
+ if (temp._dictionary == null)
+ return false;
+ if (this._dictionary != temp._dictionary) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._dictionary);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._dictionary);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._dictionary.equals(temp._dictionary)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
+ }
}
- 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 removeAllDbRef(
- ) {
- this._dbRefList.clear();
- }
-
- /**
- */
- public void removeAllVxref(
- ) {
- this._vxrefList.clear();
- }
-
- /**
- * Method removeDbRef.
- *
- * @param vDbRef
- * @return true if the object was removed from the collection.
- */
- public boolean removeDbRef(
- final uk.ac.vamsas.objects.core.DbRef vDbRef) {
- boolean removed = _dbRefList.remove(vDbRef);
- return removed;
- }
-
- /**
- * Method removeDbRefAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.DbRef removeDbRefAt(
- final int index) {
- java.lang.Object obj = this._dbRefList.remove(index);
- return (uk.ac.vamsas.objects.core.DbRef) obj;
- }
-
- /**
- * Method removeVxref.
- *
- * @param vVxref
- * @return true if the object was removed from the collection.
- */
- public boolean removeVxref(
- final uk.ac.vamsas.objects.core.Vxref vVxref) {
- boolean removed = _vxrefList.remove(vVxref);
- return removed;
- }
-
- /**
- * Method removeVxrefAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Vxref removeVxrefAt(
- final int index) {
- java.lang.Object obj = this._vxrefList.remove(index);
- return (uk.ac.vamsas.objects.core.Vxref) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vDbRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setDbRef(
- final int index,
- final uk.ac.vamsas.objects.core.DbRef vDbRef)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._dbRefList.size()) {
- throw new IndexOutOfBoundsException("setDbRef: Index value '" + index + "' not in range [0.." + (this._dbRefList.size() - 1) + "]");
- }
-
- this._dbRefList.set(index, vDbRef);
- }
-
- /**
- *
- *
- * @param vDbRefArray
- */
- public void setDbRef(
- final uk.ac.vamsas.objects.core.DbRef[] vDbRefArray) {
- //-- copy array
- _dbRefList.clear();
-
- for (int i = 0; i < vDbRefArray.length; i++) {
- this._dbRefList.add(vDbRefArray[i]);
- }
- }
-
- /**
- * Sets the value of '_dbRefList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vDbRefList the Vector to copy.
- */
- public void setDbRef(
- final java.util.Vector vDbRefList) {
- // copy vector
- this._dbRefList.clear();
-
- this._dbRefList.addAll(vDbRefList);
- }
-
- /**
- * Sets the value of '_dbRefList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param dbRefVector the Vector to set.
- */
- public void setDbRefAsReference(
- final java.util.Vector dbRefVector) {
- this._dbRefList = dbRefVector;
- }
-
- /**
- * Sets the value of field 'dictionary'. The field 'dictionary'
- * has the following description: symbol class for sequence
- *
- *
- * @param dictionary the value of field 'dictionary'.
- */
- public void setDictionary(
- final java.lang.String dictionary) {
- this._dictionary = dictionary;
- }
-
- /**
- * 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 vVxref
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setVxref(
- final int index,
- final uk.ac.vamsas.objects.core.Vxref vVxref)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._vxrefList.size()) {
- throw new IndexOutOfBoundsException("setVxref: Index value '" + index + "' not in range [0.." + (this._vxrefList.size() - 1) + "]");
+ } else if (temp._dictionary != null)
+ return false;
+ if (this._dbRefList != null) {
+ if (temp._dbRefList == null)
+ return false;
+ if (this._dbRefList != temp._dbRefList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._dbRefList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._dbRefList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._dbRefList.equals(temp._dbRefList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
+ }
}
-
- this._vxrefList.set(index, vVxref);
- }
-
- /**
- *
- *
- * @param vVxrefArray
- */
- public void setVxref(
- final uk.ac.vamsas.objects.core.Vxref[] vVxrefArray) {
- //-- copy array
- _vxrefList.clear();
-
- for (int i = 0; i < vVxrefArray.length; i++) {
- this._vxrefList.add(vVxrefArray[i]);
+ } else if (temp._dbRefList != null)
+ return false;
+ if (this._vxrefList != null) {
+ if (temp._vxrefList == null)
+ return false;
+ if (this._vxrefList != temp._vxrefList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._vxrefList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._vxrefList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._vxrefList.equals(temp._vxrefList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
+ }
}
- }
-
- /**
- * Sets the value of '_vxrefList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vVxrefList the Vector to copy.
- */
- public void setVxref(
- final java.util.Vector vVxrefList) {
- // copy vector
- this._vxrefList.clear();
-
- this._vxrefList.addAll(vVxrefList);
- }
-
- /**
- * Sets the value of '_vxrefList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param vxrefVector the Vector to set.
- */
- public void setVxrefAsReference(
- final java.util.Vector vxrefVector) {
- this._vxrefList = vxrefVector;
- }
-
- /**
- * 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.SequenceTyp
- */
- public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Sequence.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ } else if (temp._vxrefList != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Method getDbRef.
+ *
+ * @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.DbRef at the given index
+ */
+ public uk.ac.vamsas.objects.core.DbRef getDbRef(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._dbRefList.size()) {
+ throw new IndexOutOfBoundsException("getDbRef: Index value '" + index
+ + "' not in range [0.." + (this._dbRefList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.DbRef) _dbRefList.get(index);
+ }
+
+ /**
+ * Method getDbRef.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.DbRef[] getDbRef() {
+ uk.ac.vamsas.objects.core.DbRef[] array = new uk.ac.vamsas.objects.core.DbRef[0];
+ return (uk.ac.vamsas.objects.core.DbRef[]) this._dbRefList.toArray(array);
+ }
+
+ /**
+ * Method getDbRefAsReference.Returns a reference to '_dbRefList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getDbRefAsReference() {
+ return this._dbRefList;
+ }
+
+ /**
+ * Method getDbRefCount.
+ *
+ * @return the size of this collection
+ */
+ public int getDbRefCount() {
+ return this._dbRefList.size();
+ }
+
+ /**
+ * Returns the value of field 'dictionary'. The field 'dictionary' has the
+ * following description: symbol class for sequence
+ *
+ *
+ * @return the value of field 'Dictionary'.
+ */
+ public java.lang.String getDictionary() {
+ return this._dictionary;
+ }
+
+ /**
+ * 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 getVxref.
+ *
+ * @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.Vxref at the given index
+ */
+ public uk.ac.vamsas.objects.core.Vxref getVxref(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._vxrefList.size()) {
+ throw new IndexOutOfBoundsException("getVxref: Index value '" + index
+ + "' not in range [0.." + (this._vxrefList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Vxref) _vxrefList.get(index);
+ }
+
+ /**
+ * Method getVxref.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.Vxref[] getVxref() {
+ uk.ac.vamsas.objects.core.Vxref[] array = new uk.ac.vamsas.objects.core.Vxref[0];
+ return (uk.ac.vamsas.objects.core.Vxref[]) this._vxrefList.toArray(array);
+ }
+
+ /**
+ * Method getVxrefAsReference.Returns a reference to '_vxrefList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getVxrefAsReference() {
+ return this._vxrefList;
+ }
+
+ /**
+ * Method getVxrefCount.
+ *
+ * @return the size of this collection
+ */
+ public int getVxrefCount() {
+ return this._vxrefList.size();
+ }
+
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ * <p>
+ * The following steps came from <b>Effective Java Programming Language
+ * Guide</b> by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_dictionary != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_dictionary)) {
+ result = 37 * result + _dictionary.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_dictionary);
+ }
+ if (_dbRefList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_dbRefList)) {
+ result = 37 * result + _dbRefList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_dbRefList);
+ }
+ if (_vxrefList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_vxrefList)) {
+ result = 37 * result + _vxrefList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_vxrefList);
+ }
+
+ 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 removeAllDbRef() {
+ this._dbRefList.clear();
+ }
+
+ /**
+ */
+ public void removeAllVxref() {
+ this._vxrefList.clear();
+ }
+
+ /**
+ * Method removeDbRef.
+ *
+ * @param vDbRef
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeDbRef(final uk.ac.vamsas.objects.core.DbRef vDbRef) {
+ boolean removed = _dbRefList.remove(vDbRef);
+ return removed;
+ }
+
+ /**
+ * Method removeDbRefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.DbRef removeDbRefAt(final int index) {
+ java.lang.Object obj = this._dbRefList.remove(index);
+ return (uk.ac.vamsas.objects.core.DbRef) obj;
+ }
+
+ /**
+ * Method removeVxref.
+ *
+ * @param vVxref
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeVxref(final uk.ac.vamsas.objects.core.Vxref vVxref) {
+ boolean removed = _vxrefList.remove(vVxref);
+ return removed;
+ }
+
+ /**
+ * Method removeVxrefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Vxref removeVxrefAt(final int index) {
+ java.lang.Object obj = this._vxrefList.remove(index);
+ return (uk.ac.vamsas.objects.core.Vxref) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDbRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setDbRef(final int index,
+ final uk.ac.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._dbRefList.size()) {
+ throw new IndexOutOfBoundsException("setDbRef: Index value '" + index
+ + "' not in range [0.." + (this._dbRefList.size() - 1) + "]");
+ }
+
+ this._dbRefList.set(index, vDbRef);
+ }
+
+ /**
+ *
+ *
+ * @param vDbRefArray
+ */
+ public void setDbRef(final uk.ac.vamsas.objects.core.DbRef[] vDbRefArray) {
+ // -- copy array
+ _dbRefList.clear();
+
+ for (int i = 0; i < vDbRefArray.length; i++) {
+ this._dbRefList.add(vDbRefArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_dbRefList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vDbRefList
+ * the Vector to copy.
+ */
+ public void setDbRef(final java.util.Vector vDbRefList) {
+ // copy vector
+ this._dbRefList.clear();
+
+ this._dbRefList.addAll(vDbRefList);
+ }
+
+ /**
+ * Sets the value of '_dbRefList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param dbRefVector
+ * the Vector to set.
+ */
+ public void setDbRefAsReference(final java.util.Vector dbRefVector) {
+ this._dbRefList = dbRefVector;
+ }
+
+ /**
+ * Sets the value of field 'dictionary'. The field 'dictionary' has the
+ * following description: symbol class for sequence
+ *
+ *
+ * @param dictionary
+ * the value of field 'dictionary'.
+ */
+ public void setDictionary(final java.lang.String dictionary) {
+ this._dictionary = dictionary;
+ }
+
+ /**
+ * 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 vVxref
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setVxref(final int index,
+ final uk.ac.vamsas.objects.core.Vxref vVxref)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._vxrefList.size()) {
+ throw new IndexOutOfBoundsException("setVxref: Index value '" + index
+ + "' not in range [0.." + (this._vxrefList.size() - 1) + "]");
+ }
+
+ this._vxrefList.set(index, vVxref);
+ }
+
+ /**
+ *
+ *
+ * @param vVxrefArray
+ */
+ public void setVxref(final uk.ac.vamsas.objects.core.Vxref[] vVxrefArray) {
+ // -- copy array
+ _vxrefList.clear();
+
+ for (int i = 0; i < vVxrefArray.length; i++) {
+ this._vxrefList.add(vVxrefArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_vxrefList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vVxrefList
+ * the Vector to copy.
+ */
+ public void setVxref(final java.util.Vector vVxrefList) {
+ // copy vector
+ this._vxrefList.clear();
+
+ this._vxrefList.addAll(vVxrefList);
+ }
+
+ /**
+ * Sets the value of '_vxrefList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param vxrefVector
+ * the Vector to set.
+ */
+ public void setVxrefAsReference(final java.util.Vector vxrefVector) {
+ this._vxrefList = vxrefVector;
+ }
+
+ /**
+ * 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.SequenceTyp
+ */
+ public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.Sequence.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