org.sbml.jsbml.ext.spatial.CompartmentMapping Maven / Gradle / Ivy
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/*
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit
* for the latest version of JSBML and more information about SBML.
*
* Copyright (C) 2009-2022 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
* 4. The University of California, San Diego, La Jolla, CA, USA
* 5. The Babraham Institute, Cambridge, UK
*
* This library 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. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as .
* ----------------------------------------------------------------------------
*/
package org.sbml.jsbml.ext.spatial;
import java.text.MessageFormat;
import java.util.Map;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
import org.sbml.jsbml.xml.parsers.AbstractReaderWriter;
/**
* @author Alex Thomas
* @author Andreas Dräger
* @author Piero Dalle Pezze
* @since 1.0
*/
public class CompartmentMapping extends AbstractSpatialNamedSBase {
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger = Logger.getLogger(CompartmentMapping.class);
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -4623759168043277022L;
/**
*
*/
private String domainType;
/**
*
*/
private Double unitSize;
/**
*
*/
public CompartmentMapping() {
super();
}
/**
* @param cm
*/
public CompartmentMapping(CompartmentMapping cm) {
super(cm);
if (cm.isSetDomainType()) {
domainType = new String(cm.getDomainType());
}
if (cm.isSetUnitSize()) {
unitSize = new Double(cm.getUnitSize());
}
}
/**
* @param level
* @param version
*/
public CompartmentMapping(int level, int version) {
super(level, version);
}
/**
*
* @param id
* @param level
* @param version
*/
public CompartmentMapping(String id, int level, int version) {
super(id, level, version);
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#clone()
*/
@Override
public CompartmentMapping clone() {
return new CompartmentMapping(this);
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
boolean equal = super.equals(object);
if (equal) {
CompartmentMapping cm = (CompartmentMapping) object;
equal &= cm.isSetDomainType() == isSetDomainType();
if (equal && isSetDomainType()) {
equal &= cm.getDomainType().equals(getDomainType());
}
equal &= cm.isSetUnitSize() == isSetUnitSize();
if (equal && isSetUnitSize()) {
equal &= cm.getUnitSize() == getUnitSize();
}
}
return equal;
}
/**
* Returns the value of domainType
*
* @return the value of domainType
*/
public String getDomainType() {
if (isSetDomainType()) {
return domainType;
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(SpatialConstants.domainType, this);
}
/**
* Returns whether domainType is set
*
* @return whether domainType is set
*/
public boolean isSetDomainType() {
return domainType != null;
}
/**
* Sets the value of domainType
* @param domainType
*/
public void setDomainType(String domainType) {
String oldDomainType = this.domainType;
this.domainType = domainType;
firePropertyChange(SpatialConstants.domainType, oldDomainType, this.domainType);
}
/**
* Unsets the variable domainType
*
* @return {@code true}, if domainType was set before,
* otherwise {@code false}
*/
public boolean unsetDomainType() {
if (isSetDomainType()) {
String oldDomainType = domainType;
domainType = null;
firePropertyChange(SpatialConstants.domainType, oldDomainType, domainType);
return true;
}
return false;
}
/**
* Returns the value of unitSize
*
* @return the value of unitSize
*/
public double getUnitSize() {
if (isSetUnitSize()) {
return unitSize;
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(SpatialConstants.unitSize, this);
}
/**
* Returns whether unitSize is set
*
* @return whether unitSize is set
*/
public boolean isSetUnitSize() {
return unitSize != null;
}
/**
* Sets the value of unitSize
* @param unitSize
*/
public void setUnitSize(double unitSize) {
Double oldUnitSize = this.unitSize;
this.unitSize = unitSize;
firePropertyChange(SpatialConstants.unitSize, oldUnitSize, this.unitSize);
}
/**
* Unsets the variable unitSize
*
* @return {@code true}, if unitSize was set before,
* otherwise {@code false}
*/
public boolean unsetUnitSize() {
if (isSetUnitSize()) {
Double oldUnitSize = unitSize;
unitSize = null;
firePropertyChange(SpatialConstants.unitSize, oldUnitSize, unitSize);
return true;
}
return false;
}
/**
*
* @return the domainType instance of the {@link DomainType} class
*/
public DomainType getDomainTypeInstance() {
Model m = getModel();
if (m!=null) {
SpatialModelPlugin sm = (SpatialModelPlugin) m.getExtension(packageName);
sm.getGeometry().getListOfDomainTypes().get(getDomainType());
}
return null;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 1319;//Changed, it was 983
int hashCode = super.hashCode();
if (isSetDomainType()) {
hashCode += prime * getDomainType().hashCode();
}
if (isSetUnitSize()) {
hashCode += prime * getUnitSize();
}
return hashCode;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetDomainType()) {
attributes.remove("domainType");
attributes.put(SpatialConstants.shortLabel + ":domainType",
getDomainType());
}
if (isSetUnitSize()) {
attributes.remove("unitSize");
attributes.put(SpatialConstants.shortLabel + ":unitSize",
String.valueOf(getUnitSize()));
}
return attributes;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#readAttribute(java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public boolean readAttribute(String attributeName, String prefix, String value) {
boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.domainType)) {
try {
setDomainType(value);
} catch (Exception e) {
logger.warn(MessageFormat.format(
SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domainType, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.unitSize)) {
try {
setUnitSize(StringTools.parseSBMLDoubleStrict(value));
} catch (Exception e) {
AbstractReaderWriter.processInvalidAttribute(attributeName, null, value, prefix, this);
logger.warn(MessageFormat.format(
SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.unitSize, getElementName()));
}
}
else {
isAttributeRead = false;
}
}
return isAttributeRead;
}
}