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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) 2009-2019 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 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.distrib;
import java.util.Map;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
/**
* The {@link UncertSpan} class defines a span of values that define an uncertainty statistic such as confidence interval or
* range.
*
* It inherits from {@link UncertParameter}, and adds four optional attributes, varLower and varUpper, of type String,
* and valueLower and valueUpper, of type double. Exactly one of the attributes varLower and valueLower may be
* defined, and exactly one of the attributes varUpper and valueUpper may be defined. If no attributes are defined,
* the parameters of the span are undefined. If only one attribute is defined (one of the upper or lower attributes), that
* aspect of the span is defined, and the other end is undefined. The span is fully defined if two attributes (one lower
* and one upper) are defined.
*
* The value of the lower attribute (whichever is defined) must be lesser or equal to the value of the upper attribute
* (whichever is defined), at the initial conditions of the model. The Uncertainty element cannot affect the core
* mathematics of an SBML model, but if it is used in a mathematical context during simulation of the model, this
* restriction on the attribute values must be maintained, or the UncertSpan object as a whole will be undefined.
* Like the units attribute on an UncertParameter , the units attribute is provided if valueUpper and/or valueLower
* is defined. The units on both the upper and lower ends of the span must match each other, if defined. The units for
* span ends defined by reference may be obtained from the referenced SBML element.
*
* @author rodrigue
* @since 1.5
*/
public class UncertSpan extends UncertParameter {
/**
*
*/
private Double valueLower;
/**
*
*/
private Double valueUpper;
/**
*
*/
private String varLower;
/**
*
*/
private String varUpper;
/**
* Creates an UncertSpan instance
*/
public UncertSpan() {
super();
initDefaults();
}
/**
* Creates a UncertSpan instance with an id.
*
* @param id the identifier for the new element.
*/
public UncertSpan(String id) {
super(id);
initDefaults();
}
/**
* Creates a UncertSpan instance with a level and version.
*
* @param level SBML Level
* @param version SBML Version
*/
public UncertSpan(int level, int version) {
this(null, null, level, version);
}
/**
* Creates a UncertSpan instance with an id, level, and version.
*
* @param id the identifier for this element.
* @param level the SBML Level
* @param version the SBML Version
*/
public UncertSpan(String id, int level, int version) {
this(id, null, level, version);
}
/**
* Creates a UncertSpan instance with an id, name, level, and version.
*
* @param id the identifier for this element.
* @param name a human-readable name for this element that can be used for display purposes.
* @param level the SBML Level
* @param version the SBML Version
*/
public UncertSpan(String id, String name, int level, int version) {
super(id, name, level, version);
initDefaults();
}
/**
* Clone constructor
*/
public UncertSpan(UncertSpan obj) {
super(obj);
if (obj.isSetValueLower()) {
setValueLower(obj.getValueLower());
}
if (obj.isSetValueUpper()) {
setValueUpper(obj.getValueUpper());
}
if (obj.isSetVarLower()) {
setVarLower(obj.getVarLower());
}
if (obj.isSetValueUpper()) {
setVarUpper(obj.getVarUpper());
}
}
/**
* clones this class
*/
public UncertSpan clone() {
return new UncertSpan(this);
}
/**
* Initializes the default values using the namespace.
*/
public void initDefaults() {
setNamespace(DistribConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = DistribConstants.shortLabel;
setPackageVersion(-1);
}
/**
* Returns the value of {@link #valueLower}.
*
* @return the value of {@link #valueLower}.
*/
public double getValueLower() {
if (isSetValueLower()) {
return valueLower;
}
throw new PropertyUndefinedError(DistribConstants.valueLower, this);
}
/**
* Returns whether {@link #valueLower} is set.
*
* @return whether {@link #valueLower} is set.
*/
public boolean isSetValueLower() {
return valueLower != null;
}
/**
* Sets the value of valueLower
*
* @param valueLower the value of valueLower to be set.
*/
public void setValueLower(double valueLower) {
Double oldValueLower = this.valueLower;
this.valueLower = valueLower;
firePropertyChange(DistribConstants.valueLower, oldValueLower, this.valueLower);
}
/**
* Unsets the variable valueLower.
*
* @return {@code true} if valueLower was set before, otherwise {@code false}.
*/
public boolean unsetValueLower() {
if (isSetValueLower()) {
Double oldValueLower = this.valueLower;
this.valueLower = null;
firePropertyChange(DistribConstants.valueLower, oldValueLower, this.valueLower);
return true;
}
return false;
}
/**
* Returns the value of {@link #valueUpper}.
*
* @return the value of {@link #valueUpper}.
*/
public double getValueUpper() {
if (isSetValueUpper()) {
return valueUpper;
}
throw new PropertyUndefinedError(DistribConstants.valueUpper, this);
}
/**
* Returns whether {@link #valueUpper} is set.
*
* @return whether {@link #valueUpper} is set.
*/
public boolean isSetValueUpper() {
return valueUpper != null;
}
/**
* Sets the value of valueUpper
*
* @param valueUpper the value of valueUpper to be set.
*/
public void setValueUpper(double valueUpper) {
Double oldValueUpper = this.valueUpper;
this.valueUpper = valueUpper;
firePropertyChange(DistribConstants.valueUpper, oldValueUpper, this.valueUpper);
}
/**
* Unsets the variable valueUpper.
*
* @return {@code true} if valueUpper was set before, otherwise {@code false}.
*/
public boolean unsetValueUpper() {
if (isSetValueUpper()) {
Double oldValueUpper = this.valueUpper;
this.valueUpper = null;
firePropertyChange(DistribConstants.valueUpper, oldValueUpper, this.valueUpper);
return true;
}
return false;
}
/**
* Returns the value of {@link #varLower}.
*
* @return the value of {@link #varLower}.
*/
public String getVarLower() {
if (isSetVarLower()) {
return varLower;
}
return null;
}
/**
* Returns whether {@link #varLower} is set.
*
* @return whether {@link #varLower} is set.
*/
public boolean isSetVarLower() {
return varLower != null;
}
/**
* Sets the value of varLower
*
* @param varLower the value of varLower to be set.
*/
public void setVarLower(String varLower) {
String oldVarLower = this.varLower;
this.varLower = varLower;
firePropertyChange(DistribConstants.varLower, oldVarLower, this.varLower);
}
/**
* Unsets the variable varLower.
*
* @return {@code true} if varLower was set before, otherwise {@code false}.
*/
public boolean unsetVarLower() {
if (isSetVarLower()) {
String oldVarLower = this.varLower;
this.varLower = null;
firePropertyChange(DistribConstants.varLower, oldVarLower, this.varLower);
return true;
}
return false;
}
/**
* Returns the value of {@link #varUpper}.
*
* @return the value of {@link #varUpper}.
*/
public String getVarUpper() {
if (isSetVarUpper()) {
return varUpper;
}
return null;
}
/**
* Returns whether {@link #varUpper} is set.
*
* @return whether {@link #varUpper} is set.
*/
public boolean isSetVarUpper() {
return varUpper != null;
}
/**
* Sets the value of varUpper
*
* @param varUpper the value of varUpper to be set.
*/
public void setVarUpper(String varUpper) {
String oldVarUpper = this.varUpper;
this.varUpper = varUpper;
firePropertyChange(DistribConstants.varUpper, oldVarUpper, this.varUpper);
}
/**
* Unsets the variable varUpper.
*
* @return {@code true} if varUpper was set before, otherwise {@code false}.
*/
public boolean unsetVarUpper() {
if (isSetVarUpper()) {
String oldVarUpper = this.varUpper;
this.varUpper = null;
firePropertyChange(DistribConstants.varUpper, oldVarUpper, this.varUpper);
return true;
}
return false;
}
/* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 839;
int result = super.hashCode();
result = prime * result
+ ((valueLower == null) ? 0 : valueLower.hashCode());
result = prime * result
+ ((valueUpper == null) ? 0 : valueUpper.hashCode());
result = prime * result + ((varLower == null) ? 0 : varLower.hashCode());
result = prime * result + ((varUpper == null) ? 0 : varUpper.hashCode());
return result;
}
/* (non-Javadoc)
* @see java.lang.Object#equals(java.lang.Object)
*/
@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
if (!super.equals(obj)) {
return false;
}
if (getClass() != obj.getClass()) {
return false;
}
UncertSpan other = (UncertSpan) obj;
if (valueLower == null) {
if (other.valueLower != null) {
return false;
}
} else if (!valueLower.equals(other.valueLower)) {
return false;
}
if (valueUpper == null) {
if (other.valueUpper != null) {
return false;
}
} else if (!valueUpper.equals(other.valueUpper)) {
return false;
}
if (varLower == null) {
if (other.varLower != null) {
return false;
}
} else if (!varLower.equals(other.varLower)) {
return false;
}
if (varUpper == null) {
if (other.varUpper != null) {
return false;
}
} else if (!varUpper.equals(other.varUpper)) {
return false;
}
return true;
}
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetValueLower()) {
attributes.put(DistribConstants.shortLabel + ":" + DistribConstants.valueLower, valueLower.toString());
}
if (isSetValueUpper()) {
attributes.put(DistribConstants.shortLabel + ":" + DistribConstants.valueUpper, valueUpper.toString());
}
if (isSetVarLower()) {
attributes.put(DistribConstants.shortLabel + ":" + DistribConstants.varLower, varLower);
}
if (isSetVarUpper()) {
attributes.put(DistribConstants.shortLabel + ":" + DistribConstants.varUpper, varUpper);
}
return attributes;
}
@Override
public boolean readAttribute(String attributeName, String prefix,
String value) {
boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(DistribConstants.valueLower)) {
setValueLower(StringTools.parseSBMLDouble(value));
}
else if (attributeName.equals(DistribConstants.valueUpper)) {
setValueUpper(StringTools.parseSBMLDouble(value));
}
else if (attributeName.equals(DistribConstants.varUpper)) {
setVarUpper(value);
}
else if (attributeName.equals(DistribConstants.varLower)) {
setVarLower(value);
}
else {
isAttributeRead = false;
}
}
return isAttributeRead;
}
}