/*
* 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 -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
/**
* Class SequenceMapping.
*
* @version $Revision$ $Date$
*/
public class SequenceMapping extends uk.ac.vamsas.objects.core.MapType
implements java.io.Serializable {
// --------------------------/
// - Class/Member Variables -/
// --------------------------/
/**
* Object on which the local range is defined.
*/
private java.lang.Object _loc;
/**
* Object on which the mapped range is defined.
*/
private java.lang.Object _map;
/**
* Field _id.
*/
private java.lang.String _id;
/**
* Field _provenance.
*/
private uk.ac.vamsas.objects.core.Provenance _provenance;
// ----------------/
// - Constructors -/
// ----------------/
public SequenceMapping() {
super();
}
// -----------/
// - Methods -/
// -----------/
/**
* 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 SequenceMapping) {
SequenceMapping temp = (SequenceMapping) obj;
boolean thcycle;
boolean tmcycle;
if (this._loc != null) {
if (temp._loc == null)
return false;
if (this._loc != temp._loc) {
thcycle = org.castor.util.CycleBreaker.startingToCycle(this._loc);
tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._loc);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.util.CycleBreaker.releaseCycleHandle(this._loc);
}
;
if (!tmcycle) {
org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc);
}
;
return false;
}
if (!thcycle) {
if (!this._loc.equals(temp._loc)) {
org.castor.util.CycleBreaker.releaseCycleHandle(this._loc);
org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc);
return false;
}
org.castor.util.CycleBreaker.releaseCycleHandle(this._loc);
org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc);
}
}
} else if (temp._loc != null)
return false;
if (this._map != null) {
if (temp._map == null)
return false;
if (this._map != temp._map) {
thcycle = org.castor.util.CycleBreaker.startingToCycle(this._map);
tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._map);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.util.CycleBreaker.releaseCycleHandle(this._map);
}
;
if (!tmcycle) {
org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);
}
;
return false;
}
if (!thcycle) {
if (!this._map.equals(temp._map)) {
org.castor.util.CycleBreaker.releaseCycleHandle(this._map);
org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);
return false;
}
org.castor.util.CycleBreaker.releaseCycleHandle(this._map);
org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);
}
}
} else if (temp._map != 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._provenance != null) {
if (temp._provenance == null)
return false;
if (this._provenance != temp._provenance) {
thcycle = org.castor.util.CycleBreaker
.startingToCycle(this._provenance);
tmcycle = org.castor.util.CycleBreaker
.startingToCycle(temp._provenance);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
}
;
if (!tmcycle) {
org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
}
;
return false;
}
if (!thcycle) {
if (!this._provenance.equals(temp._provenance)) {
org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
return false;
}
org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
}
}
} else if (temp._provenance != null)
return false;
return true;
}
return false;
}
/**
* Returns the value of field 'id'.
*
* @return the value of field 'Id'.
*/
public java.lang.String getId() {
return this._id;
}
/**
* Returns the value of field 'loc'. The field 'loc' has the following
* description: Object on which the local range is defined.
*
* @return the value of field 'Loc'.
*/
public java.lang.Object getLoc() {
return this._loc;
}
/**
* Returns the value of field 'map'. The field 'map' has the following
* description: Object on which the mapped range is defined.
*
* @return the value of field 'Map'.
*/
public java.lang.Object getMap() {
return this._map;
}
/**
* Returns the value of field 'provenance'.
*
* @return the value of field 'Provenance'.
*/
public uk.ac.vamsas.objects.core.Provenance getProvenance() {
return this._provenance;
}
/**
* 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 (_loc != null && !org.castor.util.CycleBreaker.startingToCycle(_loc)) {
result = 37 * result + _loc.hashCode();
org.castor.util.CycleBreaker.releaseCycleHandle(_loc);
}
if (_map != null && !org.castor.util.CycleBreaker.startingToCycle(_map)) {
result = 37 * result + _map.hashCode();
org.castor.util.CycleBreaker.releaseCycleHandle(_map);
}
if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
result = 37 * result + _id.hashCode();
org.castor.util.CycleBreaker.releaseCycleHandle(_id);
}
if (_provenance != null
&& !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
result = 37 * result + _provenance.hashCode();
org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
}
return result;
}
/**
* Method isValid.
*
* @return true if this object is valid according to the schema
*/
public boolean isValid() {
try {
validate();
} catch (org.exolab.castor.xml.ValidationException vex) {
return false;
}
return true;
}
/**
*
*
* @param out
* @throws org.exolab.castor.xml.MarshalException
* if object is null or if any SAXException is thrown during
* marshaling
* @throws org.exolab.castor.xml.ValidationException
* if this object is an invalid instance according to the schema
*/
public void marshal(final java.io.Writer out)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException {
Marshaller.marshal(this, out);
}
/**
*
*
* @param handler
* @throws java.io.IOException
* if an IOException occurs during marshaling
* @throws org.exolab.castor.xml.ValidationException
* if this object is an invalid instance according to the schema
* @throws org.exolab.castor.xml.MarshalException
* if object is null or if any SAXException is thrown during
* marshaling
*/
public void marshal(final org.xml.sax.ContentHandler handler)
throws java.io.IOException, org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException {
Marshaller.marshal(this, handler);
}
/**
* Sets the value of field 'id'.
*
* @param id
* the value of field 'id'.
*/
public void setId(final java.lang.String id) {
this._id = id;
}
/**
* Sets the value of field 'loc'. The field 'loc' has the following
* description: Object on which the local range is defined.
*
* @param loc
* the value of field 'loc'.
*/
public void setLoc(final java.lang.Object loc) {
this._loc = loc;
}
/**
* Sets the value of field 'map'. The field 'map' has the following
* description: Object on which the mapped range is defined.
*
* @param map
* the value of field 'map'.
*/
public void setMap(final java.lang.Object map) {
this._map = map;
}
/**
* Sets the value of field 'provenance'.
*
* @param provenance
* the value of field 'provenance'.
*/
public void setProvenance(
final uk.ac.vamsas.objects.core.Provenance provenance) {
this._provenance = provenance;
}
/**
* 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.MapType
*/
public static uk.ac.vamsas.objects.core.MapType unmarshal(
final java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException {
return (uk.ac.vamsas.objects.core.MapType) Unmarshaller.unmarshal(
uk.ac.vamsas.objects.core.SequenceMapping.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);
}
}