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/*
* $Id$
* $URL$
* ----------------------------------------------------------------------------
* 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;
/**
* The {@link ReferenceGlyph} element describes the graphical connection between
* an arbitrary {@link GraphicalObject} (or derived element) and a
* {@link GeneralGlyph} (which would be an arrow or some curve in most cases).
* A {@link ReferenceGlyph} inherits from {@link GraphicalObject}. Additionally,
* it has a mandatory attribute 'glyph' and two optional attributes 'reference'
* and 'role'. Optionally, the ReferenceGlyph also has an element 'curve'.
* The {@link ReferenceGlyph} should either contain a bounding box or a curve
* specification. If both are given, the bounding box should be ignored.
*
* @author Nicolas Rodriguez
* @author Sebastian Frölich
* @author Andreas Dräger
* @since 1.0
* @version $Rev$
*/
public class ReferenceGlyph extends AbstractReferenceGlyph {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -8810905237933499989L;
/**
*
*/
private Curve curve;
/**
*
*/
private String role;
/**
*
*/
private String glyph;
/**
*
*/
public ReferenceGlyph() {
super();
initDefaults();
}
/**
*
* @param level
* @param version
*/
public ReferenceGlyph(int level, int version) {
super(level, version);
initDefaults();
}
/**
*
* @param speciesReferenceGlyph
*/
public ReferenceGlyph(ReferenceGlyph speciesReferenceGlyph) {
super(speciesReferenceGlyph);
if (speciesReferenceGlyph.isSetCurve()) {
setCurve(speciesReferenceGlyph.getCurve().clone());
}
if (speciesReferenceGlyph.isSetRole()) {
setRole(speciesReferenceGlyph.getRole());
}
if (speciesReferenceGlyph.isSetGlyph()) {
setGlyph(new String(speciesReferenceGlyph.getGlyph()));
}
}
/**
*
* @param id
*/
public ReferenceGlyph(String id) {
super(id);
initDefaults();
}
/**
*
* @param id
* @param level
* @param version
*/
public ReferenceGlyph(String id, int level, int version) {
super(id, level, version);
initDefaults();
}
/**
* Initializes the default values using the namespace.
*/
@Override
public void initDefaults() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#clone()
*/
@Override
public ReferenceGlyph clone() {
return new ReferenceGlyph(this);
}
/**
*
* @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) {
ReferenceGlyph s = (ReferenceGlyph) object;
equals &= s.isSetRole() && isSetRole();
if (equals && isSetRole()) {
equals &= s.getRole().equals(getRole());
}
equals &= s.isSetGlyph() == isSetGlyph();
if (equals && isSetGlyph()) {
equals &= s.getGlyph().equals(getGlyph());
}
}
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
*/
public String getGlyph() {
return glyph;
}
/**
* @return
*/
public String getRole() {
return role;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 953;
int hashCode = super.hashCode();
if (isSetRole()) {
hashCode += prime * getRole().hashCode();
}
if (isSetGlyph()) {
hashCode += prime * getGlyph().hashCode();
}
return hashCode;
}
/**
* @return
*/
public boolean isSetCurve() {
return curve != null;
}
/**
* @return
*/
public boolean isSetGlyph() {
return glyph != null;
}
/**
* @return
*/
public boolean isSetRole() {
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.reference))
{
setReference(value);
}
else if (attributeName.equals(LayoutConstants.glyph))
{
setGlyph(value);
}
else if (attributeName.equals(LayoutConstants.role))
{
setRole(value);
}
else
{
return false;
}
}
return isAttributeRead;
}
/**
* The curve is an optional element of type {@link Curve}. When present, the glyph’s {@link BoundingBox}
* (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 ReferenceGlyph}.
*
* If the glyph represents a modification it should start at the glyph and end at the center of
* the {@link GeneralGlyph}.
*
* Otherwise it should begin at the center section of the {@link GeneralGlyph} and end at the reference
* glyph.
*
* @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 used to specify how the reference should be displayed.
* While as a string, the value of the role attribute is unconstrained, current
* implementations use the same values as defined in SpeciesReferenceRole.
* @param role
*/
public void setRole(String role) {
String oldRole = this.role;
this.role = role;
firePropertyChange(LayoutConstants.role, oldRole, this.role);
}
/**
* It contains a reference to the id of a {@link GraphicalObject} (or derived)
* object that is to be connected to the {@link GeneralGlyph}. This attribute is
* mandatory so as to ensure unambiguously which glyph has to be connected with
* this {@link GeneralGlyph}.
*
* @param glyph
*/
public void setGlyph(String glyph) {
String oldValue = this.glyph;
this.glyph = glyph;
firePropertyChange(LayoutConstants.speciesGlyph, oldValue, this.glyph);
}
/**
* The reference is an optional attribute that is used to connect the
* {@link ReferenceGlyph} with an element of the containing {@link Model}.
*
* @param reference
*/
@Override
public boolean setReference(String reference) {
return setReference(reference, LayoutConstants.reference);
}
/**
*
* @return
*/
public boolean unsetCurve() {
if (isSetCurve()) {
Curve oldCurve = getCurve();
curve = null;
oldCurve.fireNodeRemovedEvent();
return true;
}
return false;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetGlyph()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.glyph, glyph);
}
if (isSetReference()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.reference, getReference());
}
if (isSetRole()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.role, role);
}
return attributes;
}
}
