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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) 2009-2016 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.layout;
import java.text.MessageFormat;
import java.util.Map;
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.NamedSBase;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SimpleSpeciesReference;
/**
* The {@link SpeciesReferenceGlyph} class describes the graphical connection
* between a {@link SpeciesGlyph} and a {@link ReactionGlyph} (which would be
* an arrow or some curve in most cases).
*
* @author Nicolas Rodriguez
* @author Sebastian Frölich
* @author Andreas Dräger
* @since 1.0
*/
public class SpeciesReferenceGlyph extends AbstractReferenceGlyph {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -8810905237933499989L;
/**
*
*/
private Curve curve;
/**
*
*/
private SpeciesReferenceRole role;
/**
*
*/
private String speciesGlyph;
/**
*
*/
public SpeciesReferenceGlyph() {
super();
initDefaults();
}
/**
*
* @param level
* @param version
*/
public SpeciesReferenceGlyph(int level, int version) {
super(level, version);
initDefaults();
}
/**
*
* @param speciesReferenceGlyph
*/
public SpeciesReferenceGlyph(SpeciesReferenceGlyph speciesReferenceGlyph) {
super(speciesReferenceGlyph);
if (speciesReferenceGlyph.isSetCurve()) {
setCurve(speciesReferenceGlyph.getCurve().clone());
}
if (speciesReferenceGlyph.isSetSpeciesReferenceRole()) {
setRole(SpeciesReferenceRole.valueOf(speciesReferenceGlyph.getSpeciesReferenceRole().toString()));
}
if (speciesReferenceGlyph.isSetSpeciesGlyph()) {
setSpeciesGlyph(new String(speciesReferenceGlyph.getSpeciesGlyph()));
}
initDefaults();
}
/**
*
* @return
*/
public ReactionGlyph getReactionGlyph() {
TreeNode parent = getParent();
do {
if ((parent != null) && (parent instanceof ReactionGlyph)) {
return (ReactionGlyph) parent;
}
parent = parent.getParent();
} while (parent != null);
return null;
}
/**
*
* @param id
*/
public SpeciesReferenceGlyph(String id) {
super(id);
initDefaults();
}
/**
*
* @param id
* @param level
* @param version
*/
public SpeciesReferenceGlyph(String id, int level, int version) {
super(id, level, version);
initDefaults();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#clone()
*/
@Override
public SpeciesReferenceGlyph clone() {
return new SpeciesReferenceGlyph(this);
}
/**
* Initializes the default values using the namespace.
*/
@Override
public void initDefaults() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
/**
*
* @return
*/
public Curve createCurve() {
if (isSetCurve()) {
unsetCurve();
}
setCurve(new Curve(getLevel(), getVersion()));
return getCurve();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
boolean equals = super.equals(object);
if (equals) {
SpeciesReferenceGlyph s = (SpeciesReferenceGlyph) object;
equals &= s.isSetSpeciesReferenceRole() && isSetSpeciesReferenceRole();
if (equals && isSetSpeciesReferenceRole()) {
equals &= s.getSpeciesReferenceRole().equals(getSpeciesReferenceRole());
}
equals &= s.isSetSpeciesGlyph() == isSetSpeciesGlyph();
if (equals && isSetSpeciesGlyph()) {
equals &= s.getSpeciesGlyph().equals(getSpeciesGlyph());
}
}
return equals;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#getChildAt(int)
*/
@Override
public TreeNode getChildAt(int index) {
if (index < 0) {
throw new IndexOutOfBoundsException(Integer.toString(index));
}
int count = super.getChildCount(), pos = 0;
if (index < count) {
return super.getChildAt(index);
} else {
index -= count;
}
if (isSetCurve()) {
if (pos == index) {
return getCurve();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#getChildCount()
*/
@Override
public int getChildCount() {
int count = super.getChildCount();
if (isSetCurve()) {
count++;
}
return count;
}
/**
*
* @return
*/
public Curve getCurve() {
return curve;
}
/**
*
* @return String id of the speciesGlyph
*/
public String getSpeciesGlyph() {
return speciesGlyph;
}
/**
*
* @return
*/
public SpeciesGlyph getSpeciesGlyphInstance() {
if (!isSetSpeciesGlyph()) {
return null;
}
Model model = getModel();
return (model != null) ? (SpeciesGlyph) model.findNamedSBase(getSpeciesGlyph()) : null;
}
/**
*
* @return
*/
public String getSpeciesReference() {
return getReference();
}
/**
* Note that the return type of this method is {@link NamedSBase} because it
* could be possible to link some element from other packages to this glyph.
*
* @return
*/
public NamedSBase getSpeciesReferenceInstance() {
return getNamedSBaseInstance();
}
/**
* @return
*/
public SpeciesReferenceRole getSpeciesReferenceRole() {
return getRole();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 953;
int hashCode = super.hashCode();
if (isSetSpeciesReferenceRole()) {
hashCode += prime * getSpeciesReferenceRole().hashCode();
}
if (isSetSpeciesGlyph()) {
hashCode += prime * getSpeciesGlyph().hashCode();
}
return hashCode;
}
/**
* @return
*/
public boolean isSetCurve() {
return curve != null;
}
/**
* @return
*/
public boolean isSetSpeciesGlyph() {
return speciesGlyph != null;
}
/**
* @return
*/
public boolean isSetSpeciesReference() {
return isSetReference();
}
/**
* @return
*/
public boolean isSetSpeciesReferenceRole() {
return role != null;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#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(LayoutConstants.speciesReference))
{
setSpeciesReference(value);
}
else if (attributeName.equals(LayoutConstants.speciesGlyph))
{
setSpeciesGlyph(value);
}
else if (attributeName.equals(LayoutConstants.role))
{
try {
setRole(SpeciesReferenceRole.valueOf(value.toUpperCase()));
} catch (Exception e) {
throw new SBMLException("Could not recognized the value '" + value
+ "' for the attribute " + LayoutConstants.role
+ " on the 'SpeciesReferenceGlyph' element.");
}
}
else
{
return false;
}
}
return isAttributeRead;
}
/**
* The curve is an optional element of type {@link Curve}. When present, the glyphs
* bounding box (as inherited from the {@link GraphicalObject}) is to be disregarded.
*
* So as to make the drawing of these curves as easy as possible, the line segments
* should be ordered depending on the role of the {@link SpeciesReferenceGlyph}. If
* no role attribute is defined, the role to be assumed is taken from the role that
* the {@link SpeciesReference} referenced via the attribute speciesReference has,
* otherwise it is undefined.
*
* @param curve
*/
public void setCurve(Curve curve) {
Curve oldCurve = this.curve;
this.curve = curve;
firePropertyChange(LayoutConstants.curve, oldCurve, role);
registerChild(this.curve);
}
/**
* The role attribute is of type {@link SpeciesReferenceRole} and is used to specify
* how the species reference should be displayed. This attribute is optional and should
* only be necessary if the optional speciesReference attribute is not given or if the
* respective information from the model needs to be overridden.
*
* To define more specific interactions, the recommended practice is to use the sboTerm
* attribute on the {@link SpeciesReference}. If both role and sboTerm are specified and
* they conflict, it is the role that takes precedence.
*
* @param role
*/
public void setRole(SpeciesReferenceRole role) {
SpeciesReferenceRole oldRole = this.role;
this.role = role;
firePropertyChange(LayoutConstants.role, oldRole, role);
}
/**
*
* @param role
* @see #setRole(SpeciesReferenceRole)
*/
public void setSpeciesReferenceRole(SpeciesReferenceRole role) {
setRole(role);
}
/**
* @return
* @see #getSpeciesReferenceRole()
*/
public SpeciesReferenceRole getRole() {
return role;
}
/**
* The speciesGlyph attribute contains a reference to the id of a {@link SpeciesGlyph}
* object that is to be connected to the {@link ReactionGlyph}. This attribute is
* mandatory so as to ensure unambiguity about which {@link SpeciesGlyph} has to be
* connected with this {@link ReactionGlyph}.
*
* @param speciesGlyph
*/
public void setSpeciesGlyph(String speciesGlyph) {
String oldValue = this.speciesGlyph;
this.speciesGlyph = speciesGlyph;
firePropertyChange(LayoutConstants.speciesGlyph, oldValue, this.speciesGlyph);
}
/**
* See setSpeciesReference(String).
*
* @param speciesReference
*/
public void setSpeciesReference(SimpleSpeciesReference speciesReference) {
setSpeciesReference(speciesReference.getId());
}
/**
* The speciesReference is an optional attribute that allows modelers to
* connect the {@link SpeciesReferenceGlyph} with a particular {@link SpeciesReference}
* of the containing {@link Model}.
*
* @param speciesReference
*/
public void setSpeciesReference(String speciesReference) {
setReference(speciesReference, LayoutConstants.speciesReference);
}
/**
*
* @return
*/
public boolean unsetCurve() {
if (isSetCurve()) {
Curve oldCurve = getCurve();
curve = null;
oldCurve.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
*
*/
public void unsetSpeciesReference() {
unsetReference();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetSpeciesGlyph()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.speciesGlyph, speciesGlyph);
}
if (isSetSpeciesReference()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.speciesReference, getSpeciesReference());
}
if (isSetSpeciesReferenceRole()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.role, role.toString().toLowerCase());
}
return attributes;
}
}
