org.sbml.jsbml.ext.layout.Layout Maven / Gradle / Ivy
/*
* $Id$
* $URL$
* ----------------------------------------------------------------------------
* 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.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.NamedSBase;
import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.Species;
import org.sbml.jsbml.UniqueNamedSBase;
import org.sbml.jsbml.util.ListOfWithName;
import org.sbml.jsbml.util.filters.NameFilter;
/**
* The {@link Layout} class stores layout information for some or all elements of the
* {@link org.sbml.jsbml.Model} as well as additional objects that need not be connected to the {@link org.sbml.jsbml.Model}.
* The {@link Layout} has two attributes: id and name. Additionally, a {@link Dimensions}
* element specifies the size of the {@link Layout}. The actual layout elements are contained
* in several lists, namely: a ListOf{@link CompartmentGlyph}s, a ListOf{@link SpeciesGlyph}s,
* a ListOf{@link ReactionGlyph}s, a ListOf{@link TextGlyph}s, and a
* ListOfAdditional{@link GraphicalObject}s. Each of these lists can only occur once, and, if present,
* are not allowed to be empty.
*
* @author Nicolas Rodriguez
* @author Sebastian Frölich
* @author Andreas Dräger
* @author Clemens Wrzodek
* @since 1.0
* @version $Rev$
*/
public class Layout extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 8866612784809904674L;
/**
*
*/
private Dimensions dimensions;
/**
*
*/
private ListOf listOfAdditionalGraphicalObjects;
/**
*
*/
private ListOf listOfCompartmentGlyphs;
/**
*
*/
private ListOf listOfReactionGlyphs;
/**
*
*/
private ListOf listOfSpeciesGlyphs;
/**
*
*/
private ListOf listOfTextGlyphs;
/**
*
*/
public Layout() {
super();
initDefault();
}
/**
*
* @param level
* @param version
*/
public Layout(int level, int version) {
super(level, version);
initDefault();
}
/**
* @param layout
*
*/
public Layout(Layout layout) {
super(layout);
if (layout.listOfAdditionalGraphicalObjects != null) {
setListOfAdditionalGraphicalObjects(layout.getListOfAdditionalGraphicalObjects().clone());
}
if (layout.dimensions != null) {
setDimensions(layout.getDimensions().clone());
}
if (layout.listOfCompartmentGlyphs != null) {
setListOfCompartmentGlyphs(layout.getListOfCompartmentGlyphs().clone());
}
if (layout.listOfReactionGlyphs != null) {
setListOfReactionGlyphs(layout.getListOfReactionGlyphs().clone());
}
if (layout.listOfSpeciesGlyphs != null) {
setListOfSpeciesGlyphs(layout.getListOfSpeciesGlyphs().clone());
}
if (layout.listOfTextGlyphs != null) {
setListOfTextGlyphs(layout.getListOfTextGlyphs().clone());
}
}
/**
*
* @param id
* @param level
* @param version
*/
public Layout(String id, int level, int version) {
super(id, level, version);
initDefault();
}
/**
* Adds an arbitrary additional {@link GraphicalObject}.
* @param object
* @libsbml.deprecated same as {@link #addGraphicalObject(GraphicalObject)}
*/
public void addAdditionalGraphicalObject(GraphicalObject object) {
addGraphicalObject(object);
}
/**
* Adds a new {@link CompartmentGlyph} to the {@link #listOfCompartmentGlyphs}.
* The {@link #listOfCompartmentGlyphs} is initialized if necessary.
*
* @param compartmentGlyph the element to add to the list
* @return {@code true} (as specified by {@link java.util.Collection#add})
*/
public boolean addCompartmentGlyph(CompartmentGlyph compartmentGlyph) {
return getListOfCompartmentGlyphs().add(compartmentGlyph);
}
/**
* Adds a {@link GeneralGlyph} object.
*
* @param object
*/
public void addGeneralGlyph(GeneralGlyph object) {
if (object != null) {
getListOfAdditionalGraphicalObjects().add(object);
}
}
/**
* Adds an arbitrary additional {@link GraphicalObject}.
* @param object
*/
public void addGraphicalObject(GraphicalObject object) {
if (object != null) {
getListOfAdditionalGraphicalObjects().add(object);
}
}
/**
* Adds a {@link ReactionGlyph} to this layout
*
* @param reactionGlyph
*/
public void addReactionGlyph(ReactionGlyph reactionGlyph) {
if (reactionGlyph != null) {
getListOfReactionGlyphs().add(reactionGlyph);
}
}
/**
*
* @param speciesGlyph
*/
public void addSpeciesGlyph(SpeciesGlyph speciesGlyph) {
if (speciesGlyph != null) {
getListOfSpeciesGlyphs().add(speciesGlyph);
}
}
/**
*
* @param TextGlyph
*/
public void addTextGlyph(TextGlyph TextGlyph) {
if (TextGlyph != null) {
getListOfTextGlyphs().add(TextGlyph);
}
}
/*
* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#clone()
*/
@Override
public Layout clone() {
return new Layout(this);
}
/**
*
* @param compartment
* @return
*/
public boolean containsGlyph(Compartment compartment) {
return containsGlyph(listOfCompartmentGlyphs, compartment);
}
/**
*
* @param listOfGlyphs
* @param nsb
* @return
*/
private boolean containsGlyph(ListOf listOfGlyphs,
NamedSBase nsb) {
if ((nsb != null) && (listOfGlyphs != null) && !listOfGlyphs.isEmpty()) {
NamedSBaseReferenceFilter filter = new NamedSBaseReferenceFilter(nsb.getId());
filter.setFilterForReference(true);
return listOfGlyphs.firstHit(filter) != null;
}
return false;
}
/**
*
* @param reaction
* @return
*/
public boolean containsGlyph(Reaction reaction) {
return containsGlyph(listOfReactionGlyphs, reaction);
}
/**
*
* @param species
* @return
*/
public boolean containsGlyph(Species species) {
return containsGlyph(listOfSpeciesGlyphs, species);
}
// TODO - add methods to create GraphicalObject
// TODO - check the libsbml Layout java API to see if we could add some methods
/**
* Creates and adds a new {@link CompartmentGlyph}.
*
* @param id
* the identifier of the {@link CompartmentGlyph} to be created.
* @return a new {@link CompartmentGlyph}.
* @see #createCompartmentGlyph(String, String)
*/
public CompartmentGlyph createCompartmentGlyph(String id) {
return createCompartmentGlyph(id, null);
}
/**
* Creates and adds a new {@link CompartmentGlyph}.
*
* @param id
* the identifier of the {@link CompartmentGlyph} to be created.
* @param compartment
* {@link Compartment} ID.
* @return a new {@link CompartmentGlyph}.
*/
public CompartmentGlyph createCompartmentGlyph(String id, String compartment) {
CompartmentGlyph glyph = new CompartmentGlyph(id, getLevel(), getVersion());
glyph.setCompartment(compartment);
addCompartmentGlyph(glyph);
return glyph;
}
/**
* Creates, sets and returns {@link Dimensions} based on the
* given values.
*
* @param width
* @param height
* @param depth
* @return a new {@link Dimensions} object.
* @see #createDimensions(String, double, double, double)
*/
public Dimensions createDimensions(double width, double height, double depth) {
return createDimensions(null, width, height, depth);
}
/**
* Creates, sets and returns {@link Dimensions} based on the
* given values.
*
* @param id
* the identifier of the {@link Dimensions} to be created.
* @param width
* @param height
* @param depth
* @return a new {@link Dimensions} object.
*/
public Dimensions createDimensions(String id, double width,
double height, double depth) {
Dimensions d = new Dimensions(id, getLevel(), getVersion());
d.setWidth(width);
d.setHeight(height);
d.setDepth(depth);
setDimensions(d);
return d;
}
/**
* Creates and adds a new {@link GeneralGlyph}.
*
* @param id
* the identifier of the {@link GeneralGlyph} to be created.
* @return a new {@link GeneralGlyph}.
* @see #createGeneralGlyph(String, String)
*/
public GeneralGlyph createGeneralGlyph(String id) {
return createGeneralGlyph(id, null);
}
/**
* Creates and adds a new {@link GeneralGlyph}.
*
* @param id
* the identifier of the {@link GeneralGlyph} to be created.
* @param reference
* the identifier of an element in the model that this GeneralGlyph will represent.
* @return a new {@link GeneralGlyph}.
*/
public GeneralGlyph createGeneralGlyph(String id, String reference) {
GeneralGlyph glyph = new GeneralGlyph(id, getLevel(), getVersion());
glyph.setReference(reference);
addGeneralGlyph(glyph);
return glyph;
}
/**
* Creates and adds a new {@link ReactionGlyph}.
*
* @param id
* the identifier of the {@link ReactionGlyph} to be created.
* @return a new {@link ReactionGlyph}.
* @see #createReactionGlyph(String, String)
*/
public ReactionGlyph createReactionGlyph(String id) {
return createReactionGlyph(id, null);
}
/**
* Creates and adds a new {@link ReactionGlyph}.
*
* @param id
* the identifier of the {@link ReactionGlyph} to be created.
* @param reaction
* {@link Reaction} ID.
* @return a new {@link ReactionGlyph}.
*/
public ReactionGlyph createReactionGlyph(String id, String reaction) {
ReactionGlyph glyph = new ReactionGlyph(id, getLevel(), getVersion());
glyph.setReaction(reaction);
addReactionGlyph(glyph);
return glyph;
}
/**
* Creates and adds a new {@link SpeciesGlyph} with the given identifier.
*
* @param id
* the identifier for the {@link SpeciesGlyph} to be created.
* @return a new {@link SpeciesGlyph}.
* @see #createSpeciesGlyph(String, String)
*/
public SpeciesGlyph createSpeciesGlyph(String id) {
return createSpeciesGlyph(id, null);
}
/**
* Creates and adds a new {@link SpeciesGlyph}.
*
* @param id
* the identifier for the {@link SpeciesGlyph} to be created.
* @param species
* {@link Species} ID.
* @return a new {@link SpeciesGlyph}.
*/
public SpeciesGlyph createSpeciesGlyph(String id, String species) {
SpeciesGlyph glyph = new SpeciesGlyph(id, getLevel(), getVersion());
glyph.setSpecies(species);
addSpeciesGlyph(glyph);
return glyph;
}
/**
* Creates and adds a new {@link TextGlyph}.
*
* @param id
* the identifier for the {@link TextGlyph} to be created.
* @return a new {@link TextGlyph}.
* @see #createTextGlyph(String, String)
*/
public TextGlyph createTextGlyph(String id) {
return createTextGlyph(id, null);
}
/**
* Creates and adds a new {@link TextGlyph}.
*
* @param id
* the identifier for the {@link TextGlyph} to be created.
* @param text
* the text for the new glyph
* @return a new {@link TextGlyph}.
*/
public TextGlyph createTextGlyph(String id, String text) {
TextGlyph glyph = new TextGlyph(id, getLevel(), getVersion());
glyph.setText(text);
addTextGlyph(glyph);
return glyph;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
boolean equals = super.equals(object);
if (equals) {
Layout layout = (Layout) object;
equals &= layout.isSetDimensions() == isSetDimensions();
if (equals && isSetDimensions()) {
equals &= layout.getDimensions().equals(getDimensions());
}
equals &= layout.isSetListOfAdditionalGraphicalObjects() == isSetListOfAdditionalGraphicalObjects();
if (equals && isSetListOfAdditionalGraphicalObjects()) {
equals &= layout.getListOfAdditionalGraphicalObjects().equals(getListOfAdditionalGraphicalObjects());
}
if (equals && isSetListOfCompartmentGlyphs()) {
equals &= layout.getListOfCompartmentGlyphs().equals(getListOfCompartmentGlyphs());
}
if (equals && isSetListOfReactionGlyphs()) {
equals &= layout.getListOfReactionGlyphs().equals(getListOfReactionGlyphs());
}
if (equals && isSetListOfSpeciesGlyphs()) {
equals &= layout.getListOfSpeciesGlyphs().equals(getListOfSpeciesGlyphs());
}
if (equals && isSetListOfTextGlyphs()) {
equals &= layout.getListOfTextGlyphs().equals(getListOfTextGlyphs());
}
}
return equals;
}
/**
* Searches all instances of {@link CompartmentGlyph} within this {@link Layout} that
* refer to the {@link Compartment} with the given id.
*
* @param compartmentID
* @return a {@link List} containing all identified elements. It can be
* empty but not {@code null}.
*/
public List findCompartmentGlyphs(String compartmentID) {
return findGlyphs(listOfCompartmentGlyphs, compartmentID);
}
/**
*
* @param listOfGlyphs
* @param id
* @return
*/
@SuppressWarnings("unchecked")
private List findGlyphs(ListOf listOfGlyphs, String id) {
// TODO - use the Model findUniqueNamedSBase method if model is not null ?
if (isSetListOfReactionGlyphs() && (listOfGlyphs != null) && (!listOfGlyphs.isEmpty())) {
NamedSBaseReferenceFilter filter = new NamedSBaseReferenceFilter(id);
filter.setFilterForReference(true);
return (List) listOfReactionGlyphs.filter(filter);
}
return new ArrayList(0);
}
/**
* Searches all instances of {@link ReactionGlyph} within this {@link Layout} that
* refer to the {@link Reaction} with the given id.
*
* @param reactionID
* @return a {@link List} containing all identified elements. It can be
* empty but not {@code null}.
*/
public List findReactionGlyphs(String reactionID) {
return findGlyphs(listOfReactionGlyphs, reactionID);
}
/**
* Searches all instances of {@link SpeciesGlyph} within this {@link Layout} that
* refer to the {@link Species} with the given id.
*
* @param speciesID
* @return a {@link List} containing all identified elements. It can be
* empty but not {@code null}.
*/
public List findSpeciesGlyphs(String speciesID) {
return findGlyphs(listOfSpeciesGlyphs, speciesID);
}
/**
* Searches within the {@link #listOfTextGlyphs} for {@link TextGlyph}s whose
* {@link TextGlyph#getOriginOfText()} points to the given id.
*
* @param id
* the identifier of the element for which {@link TextGlyph}s are to be
* found.
* @return all {@link TextGlyph}s associated to an element with the given id.
*/
public List findTextGlyphs(String id) {
return findGlyphs(listOfTextGlyphs, id);
}
/**
*
* @param i
* @return
*/
public GraphicalObject getAdditionalGraphicalObject(int i) {
if (isSetListOfAdditionalGraphicalObjects()) {
// Do not check the range of indices here! Better throw IndexOutOfBoundsException!
return listOfAdditionalGraphicalObjects.get(i);
}
return null;
}
/**
*
* @return
*/
public int getAdditionalGraphicalObjectCount() {
return isSetListOfAdditionalGraphicalObjects() ? listOfAdditionalGraphicalObjects.size() : 0;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#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 (isSetDimensions()) {
if (index == pos) {
return getDimensions();
}
pos++;
}
if (isSetAddGraphicalObjects()) {
if (index == pos) {
return getListOfAdditionalGraphicalObjects();
}
pos++;
}
if (isSetListOfCompartmentGlyphs()) {
if (index == pos) {
return getListOfCompartmentGlyphs();
}
pos++;
}
if (isSetListOfSpeciesGlyphs()) {
if (index == pos) {
return getListOfSpeciesGlyphs();
}
pos++;
}
if (isSetListOfReactionGlyphs()) {
if (index == pos) {
return getListOfReactionGlyphs();
}
pos++;
}
if (isSetListOfTextGlyphs()) {
if (index == pos) {
return getListOfTextGlyphs();
}
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#getChildCount()
*/
@Override
public int getChildCount() {
int count = super.getChildCount();
if (isSetDimensions()) {
count++;
}
if (isSetListOfCompartmentGlyphs()) {
count++;
}
if (isSetListOfSpeciesGlyphs()) {
count++;
}
if (isSetListOfReactionGlyphs()) {
count++;
}
if (isSetListOfTextGlyphs()) {
count++;
}
if (isSetAddGraphicalObjects()) {
count++;
}
return count;
}
/**
* Gets an element from the listOfCompartmentGlyphs at the given index.
*
* @param i the index of the {@link CompartmentGlyph} element to get.
* @return an element from the listOfCompartmentGlyphs at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size).
*/
public CompartmentGlyph getCompartmentGlyph(int i) {
if (!isSetListOfCompartmentGlyphs()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
return getListOfCompartmentGlyphs().get(i);
}
/**
* Gets an element from the listOfCompartmentGlyphs, with the given id.
*
* @param id the id of the {@link CompartmentGlyph} element to get.
* @return an element from the listOfCompartmentGlyphs with the given id or null.
*/
public CompartmentGlyph getCompartmentGlyph(String id) {
if (isSetListOfCompartmentGlyphs()) {
return getListOfCompartmentGlyphs().firstHit(new NameFilter(id));
}
return null;
}
/**
* Returns the number of {@link CompartmentGlyph}s of this {@link Layout}.
*
* @return the number of {@link CompartmentGlyph}s of this {@link Layout}.
*/
public int getCompartmentGlyphCount() {
return isSetListOfCompartmentGlyphs() ? listOfCompartmentGlyphs.size() : 0;
}
/**
*
* @return
*/
public Dimensions getDimensions() {
return dimensions;
}
/**
*
* @return
*/
public ListOf getListOfAdditionalGraphicalObjects() {
if (!isSetListOfAdditionalGraphicalObjects()) {
listOfAdditionalGraphicalObjects = new ListOfWithName(LayoutConstants.listOfAdditionalGraphicalObjects);
listOfAdditionalGraphicalObjects.setSBaseListType(ListOf.Type.other);
listOfAdditionalGraphicalObjects.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfAdditionalGraphicalObjects.setPackageName(null);
listOfAdditionalGraphicalObjects.setPackageName(LayoutConstants.shortLabel);
registerChild(listOfAdditionalGraphicalObjects);
}
return listOfAdditionalGraphicalObjects;
}
/**
*
* @return
*/
public ListOf getListOfCompartmentGlyphs() {
if (!isSetListOfCompartmentGlyphs()) {
listOfCompartmentGlyphs = ListOf.newInstance(this, CompartmentGlyph.class);
listOfCompartmentGlyphs.setSBaseListType(ListOf.Type.other);
listOfCompartmentGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfCompartmentGlyphs.setPackageName(null);
listOfCompartmentGlyphs.setPackageName(LayoutConstants.shortLabel);
registerChild(listOfCompartmentGlyphs);
}
return listOfCompartmentGlyphs;
}
/**
*
* @return
*/
public ListOf getListOfReactionGlyphs() {
if (!isSetListOfReactionGlyphs()) {
listOfReactionGlyphs = ListOf.newInstance(this, ReactionGlyph.class);
listOfReactionGlyphs.setSBaseListType(ListOf.Type.other);
listOfReactionGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfReactionGlyphs.setPackageName(null);
listOfReactionGlyphs.setPackageName(LayoutConstants.shortLabel);
registerChild(listOfReactionGlyphs);
}
return listOfReactionGlyphs;
}
/**
*
* @return
*/
public ListOf getListOfSpeciesGlyphs() {
if (!isSetListOfSpeciesGlyphs()) {
listOfSpeciesGlyphs = ListOf.newInstance(this, SpeciesGlyph.class);
listOfSpeciesGlyphs.setSBaseListType(ListOf.Type.other);
listOfSpeciesGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSpeciesGlyphs.setPackageName(null);
listOfSpeciesGlyphs.setPackageName(LayoutConstants.shortLabel);
registerChild(listOfSpeciesGlyphs);
}
return listOfSpeciesGlyphs;
}
/**
*
* @return
*/
public ListOf getListOfTextGlyphs() {
if (!isSetListOfTextGlyphs()) {
listOfTextGlyphs = ListOf.newInstance(this, TextGlyph.class);
listOfTextGlyphs.setSBaseListType(ListOf.Type.other);
listOfTextGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfTextGlyphs.setPackageName(null);
listOfTextGlyphs.setPackageName(LayoutConstants.shortLabel);
registerChild(listOfTextGlyphs);
}
return listOfTextGlyphs;
}
/**
* Returns the number of {@link CompartmentGlyph}s of this {@link Layout}.
*
* @return the number of {@link CompartmentGlyph}s of this {@link Layout}.
* @libsbml.deprecated same as {@link #getCompartmentGlyphCount()}
*/
public int getNumCompartmentGlyphs() {
return getCompartmentGlyphCount();
}
/**
* Returns the number of {@link ReactionGlyph}s of this {@link Layout}.
*
* @return the number of {@link ReactionGlyph}s of this {@link Layout}.
* @libsbml.deprecated same as {@link #getReactionGlyphCount()}
*/
public int getNumReactionGlyphs() {
return getReactionGlyphCount();
}
/**
* Returns the number of {@link SpeciesGlyph}s of this {@link Layout}.
*
* @return the number of {@link SpeciesGlyph}s of this {@link Layout}.
* @libsbml.deprecated same as {@link #getSpeciesGlyphCount()}
*/
public int getNumSpeciesGlyphs() {
return getSpeciesGlyphCount();
}
/**
* Returns the number of {@link TextGlyph}s of this {@link Layout}.
*
* @return the number of {@link TextGlyph}s of this {@link Layout}.
* @libsbml.deprecated same as {@link #getTextGlyphCount()}
*/
public int getNumTextGlyphs() {
return getTextGlyphCount();
}
/**
*
* @param i
* @return
*/
public ReactionGlyph getReactionGlyph(int i) {
return getListOfReactionGlyphs().get(i);
}
/**
*
* @param id
* @return
*/
public ReactionGlyph getReactionGlyph(String id) {
if (isSetListOfReactionGlyphs()) {
return listOfReactionGlyphs.firstHit(new NameFilter(id));
}
return null;
}
/**
* Returns the number of {@link ReactionGlyph}s of this {@link Layout}.
*
* @return the number of {@link ReactionGlyph}s of this {@link Layout}.
*/
public int getReactionGlyphCount() {
return isSetListOfReactionGlyphs() ? listOfReactionGlyphs.size() : 0;
}
/**
*
* @param i
* @return
*/
public SpeciesGlyph getSpeciesGlyph(int i) {
return getListOfSpeciesGlyphs().get(i);
}
/**
*
* @param id
* @return
*/
public SpeciesGlyph getSpeciesGlyph(String id) {
if (isSetListOfSpeciesGlyphs()) {
return listOfSpeciesGlyphs.firstHit(new NameFilter(id));
}
return null;
}
/**
* Returns the number of {@link SpeciesGlyph}s of this {@link Layout}.
*
* @return the number of {@link SpeciesGlyph}s of this {@link Layout}.
*/
public int getSpeciesGlyphCount() {
return isSetListOfSpeciesGlyphs() ? listOfSpeciesGlyphs.size() : 0;
}
/**
*
* @param i
* @return
*/
public TextGlyph getTextGlyph(int i) {
return getListOfTextGlyphs().get(i);
}
/**
*
* @param id
* @return
*/
public TextGlyph getTextGlyph(String id) {
if (isSetListOfTextGlyphs()) {
return listOfTextGlyphs.firstHit(new NameFilter(id));
}
return null;
}
/**
* Returns the number of {@link TextGlyph}s of this {@link Layout}.
*
* @return the number of {@link TextGlyph}s of this {@link Layout}.
*/
public int getTextGlyphCount() {
return isSetListOfTextGlyphs() ? listOfTextGlyphs.size() : 0;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 947;
int hashCode = super.hashCode();
if (isSetDimensions()) {
hashCode += prime * getDimensions().hashCode();
}
if (isSetListOfAdditionalGraphicalObjects()) {
hashCode += prime * getListOfAdditionalGraphicalObjects().hashCode();
}
if (isSetListOfCompartmentGlyphs()) {
hashCode += prime * getListOfCompartmentGlyphs().hashCode();
}
if (isSetListOfReactionGlyphs()) {
hashCode += prime * getListOfReactionGlyphs().hashCode();
}
if (isSetListOfSpeciesGlyphs()) {
hashCode += prime * getListOfSpeciesGlyphs().hashCode();
}
if (isSetListOfTextGlyphs()) {
hashCode += prime * getListOfTextGlyphs().hashCode();
}
return hashCode;
}
/**
*
*/
private void initDefault() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.NamedSBase#isIdMandatory()
*/
@Override
public boolean isIdMandatory() {
// See "Including Layout Information in SBML Files" Version 2.2, p. 6
return true;
}
/**
* @return
*/
public boolean isSetAddGraphicalObjects() {
return (listOfAdditionalGraphicalObjects != null) && (listOfAdditionalGraphicalObjects.size() > 0);
}
/**
* @return
*/
public boolean isSetDimensions() {
return dimensions != null;
}
/**
* @return
*/
public boolean isSetListOfAdditionalGraphicalObjects() {
return (listOfAdditionalGraphicalObjects != null) && (listOfAdditionalGraphicalObjects.size() > 0);
}
/**
* @return
*/
public boolean isSetListOfCompartmentGlyphs() {
return (listOfCompartmentGlyphs != null) && (listOfCompartmentGlyphs.size() > 0);
}
/**
* @return
*/
public boolean isSetListOfReactionGlyphs() {
return (listOfReactionGlyphs != null) && (listOfReactionGlyphs.size() > 0);
}
/**
*
* @return
*/
public boolean isSetListOfSpeciesGlyphs() {
return (listOfSpeciesGlyphs != null) && (listOfSpeciesGlyphs.size() > 0);
}
/**
* @return
*/
public boolean isSetListOfTextGlyphs() {
return (listOfTextGlyphs != null) && (listOfTextGlyphs.size() > 0);
}
/**
* @param attributeName
* @param prefix
* @param value
* @return
*/
@Override
public boolean readAttribute(String attributeName, String prefix,
String value) {
boolean isAttributeRead = super.readAttribute(attributeName, prefix,
value);
return isAttributeRead;
}
/**
* Removes an element from the listOfCompartmentGlyphs.
*
* @param compartmentGlyph the element to be removed from the list.
* @return true if the list contained the specified element and it was removed.
* @see List#remove(Object)
*/
public boolean removeCompartmentGlyph(CompartmentGlyph compartmentGlyph) {
if (isSetListOfCompartmentGlyphs()) {
return getListOfCompartmentGlyphs().remove(compartmentGlyph);
}
return false;
}
/**
* Removes an element from the listOfCompartmentGlyphs at the given index.
*
* @param i the index where to remove the {@link CompartmentGlyph}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size).
*/
public CompartmentGlyph removeCompartmentGlyph(int i) {
if (!isSetListOfCompartmentGlyphs()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
return getListOfCompartmentGlyphs().remove(i);
}
/**
* Removes an element from the listOfCompartmentGlyphs.
*
* @param compartmentGlyphId the id of the element to be removed from the list.
* @return the removed element, if it was successfully found and removed or {@code null}.
*/
public CompartmentGlyph removeCompartmentGlyph(String compartmentGlyphId) {
if (isSetListOfCompartmentGlyphs()) {
return getListOfCompartmentGlyphs().remove(compartmentGlyphId);
}
return null;
}
/**
* @param toBeRemoved
* @return the given element in case of a successful operation, {@code null}
* otherwise.
*/
public GeneralGlyph removeGeneralGlyph(GeneralGlyph toBeRemoved) {
if (isSetListOfAdditionalGraphicalObjects()
&& getListOfAdditionalGraphicalObjects().contains(toBeRemoved)
&& toBeRemoved.removeFromParent()) {
return toBeRemoved;
}
return null;
}
/**
* Removes an element from the {@link #listOfAdditionalGraphicalObjects} at
* the given index.
*
* @param i the index where to remove the {@link GeneralGlyph}.
* @return the removed object
* @throws IndexOutOfBoundsException if the listOf is not set or if the index
* is out of bound (index < 0 || index > list.size).
* @throws ClassCastException if the additional graphical object at the given
* index is not an instance of {@link GeneralGlyph}. Note that the element is
* still removed, but an exception will be thrown. The element will not be
* re-inserted.
*/
public GeneralGlyph removeGeneralGlyph(int i) {
if (!isSetListOfAdditionalGraphicalObjects()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
return (GeneralGlyph) getListOfAdditionalGraphicalObjects().remove(i);
}
/**
*
* @param id
* @return
* @throws ClassCastException if the additional graphical object with the
* given id is not an instance of {@link GeneralGlyph}. Note that the element
* is still removed, but an exception will be thrown. The element will not be
* re-inserted.
*/
public GeneralGlyph removeGeneralGlyph(String id) {
if (isSetListOfAdditionalGraphicalObjects()) {
return (GeneralGlyph) getListOfAdditionalGraphicalObjects().remove(id);
}
return null;
}
/**
* Removes an element from the {@link #listOfReactionGlyphs} at the given index.
*
* @param i the index where to remove the {@link ReactionGlyph}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size).
*/
public ReactionGlyph removeReactionGlyph(int i) {
if (!isSetListOfReactionGlyphs()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
return getListOfReactionGlyphs().remove(i);
}
/**
* Removes an element from the listOfReactionGlyphs.
*
* @param reactionGlyph the element to be removed from the list.
* @return true if the list contained the specified element and it was removed.
* @see List#remove(Object)
*/
public boolean removeReactionGlyph(ReactionGlyph reactionGlyph) {
if (isSetListOfReactionGlyphs()) {
return getListOfReactionGlyphs().remove(reactionGlyph);
}
return false;
}
/**
* Removes an element from the listOfReactionGlyphs.
*
* @param reactionGlyphId the id of the element to be removed from the list.
* @return the removed element, if it was successfully found and removed or {@code null}.
*/
public ReactionGlyph removeReactionGlyph(String reactionGlyphId) {
if (isSetListOfReactionGlyphs()) {
return getListOfReactionGlyphs().remove(reactionGlyphId);
}
return null;
}
/**
* Removes all singleton {@link SpeciesGlyph}s (no {@link SpeciesReferenceGlyph}
* in {@link ReactionGlyph}) and also removes their associated {@link TextGlyph}s
* @return
*/
public boolean removeSingletons() {
// Collect species glyphs that are used first
Set speciesGlyphsToKeep = new HashSet();
if (isSetListOfReactionGlyphs()) {
for (ReactionGlyph rxnGlyph : getListOfReactionGlyphs()) {
for (SpeciesReferenceGlyph srg : rxnGlyph.getListOfSpeciesReferenceGlyphs()) {
speciesGlyphsToKeep.add(srg.getSpeciesGlyph());
}
}
Iterator it = getListOfSpeciesGlyphs().iterator();
while(it.hasNext()) {
if (!speciesGlyphsToKeep.contains(it.next().getId())) {
it.remove();
}
}
Iterator it2 = getListOfTextGlyphs().iterator();
while(it2.hasNext()) {
GraphicalObject go = it2.next().getGraphicalObjectInstance();
if ((go instanceof SpeciesGlyph) &&
(!speciesGlyphsToKeep.contains(go.getId()))) {
it2.remove();
}
}
return true;
}
return false;
}
/**
* Removes an element from the listOfSpeciesGlyphs at the given index.
*
* @param i the index where to remove the {@link SpeciesGlyph}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesGlyph removeSpeciesGlyph(int i) {
if (!isSetListOfSpeciesGlyphs()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
return getListOfSpeciesGlyphs().remove(i);
}
/**
* Removes an element from the listOfSpeciesGlyphs.
*
* @param speciesGlyph the element to be removed from the list.
* @return true if the list contained the specified element and it was removed.
* @see List#remove(Object)
*/
public boolean removeSpeciesGlyph(SpeciesGlyph speciesGlyph) {
if (isSetListOfSpeciesGlyphs()) {
return getListOfSpeciesGlyphs().remove(speciesGlyph);
}
return false;
}
/**
* Removes an element from the listOfSpeciesGlyphs.
*
* @param speciesGlyphId the id of the element to be removed from the list.
* @return the removed element, if it was successfully found and removed or {@code null}.
*/
public SpeciesGlyph removeSpeciesGlyph(String speciesGlyphId) {
if (isSetListOfSpeciesGlyphs()) {
return getListOfSpeciesGlyphs().remove(speciesGlyphId);
}
return null;
}
/**
* Removes an element from the listOfTextGlyphs at the given index.
*
* @param i the index where to remove the {@link TextGlyph}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size).
*/
public TextGlyph removeTextGlyph(int i) {
if (!isSetListOfTextGlyphs()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
return getListOfTextGlyphs().remove(i);
}
/**
* Removes an element from the listOfTextGlyphs.
*
* @param textGlyphId the id of the element to be removed from the list.
* @return the removed element, if it was successfully found and removed or {@code null}.
*/
public TextGlyph removeTextGlyph(String textGlyphId) {
if (isSetListOfTextGlyphs()) {
return getListOfTextGlyphs().remove(textGlyphId);
}
return null;
}
/**
* Removes an element from the listOfTextGlyphs.
*
* @param textGlyph the element to be removed from the list.
* @return true if the list contained the specified element and it was removed.
* @see List#remove(Object)
*/
public boolean removeTextGlyph(TextGlyph textGlyph) {
if (isSetListOfTextGlyphs()) {
return getListOfTextGlyphs().remove(textGlyph);
}
return false;
}
/**
* This element is optional. If set, this list cannot be empty.
*
* @param addGraphicalObjects
*/
public void setAddGraphicalObjects(ListOf addGraphicalObjects) {
setListOfAdditionalGraphicalObjects(addGraphicalObjects);
}
/**
* The dimensions element of type {@link Dimensions} specifies the dimensions of this
* layout. This element is required. It holds the dimensions of all layout elements
* (care should be taken when using {@link CubicBezier}s, that the described curve also
* lies within the given dimensions).
*
* @param dimensions
*/
public void setDimensions(Dimensions dimensions) {
if (this.dimensions != null) {
this.dimensions.fireNodeRemovedEvent();
}
this.dimensions = dimensions;
registerChild(this.dimensions);
}
/**
* This element is optional. If set, this list cannot be empty. Most objects for
* which layout information is to be included in an SBML file have a corresponding
* object in {@link org.sbml.jsbml.Model}. As there might be cases where the user wants to
* include object types in the layout that do fall in any of the other categories
* described below, we include a listOfAdditionalGraphicalObjects in each {@link Layout}
* object. This list holds an arbitrary number of {@link GraphicalObject} elements.
* The {@link GraphicalObject} only defines a bounding box in a specific place in the
* {@link Layout} without giving additional information about its contents.
*
* The listOfAdditionalGraphicalObjects, when present, must contain one or more of the
* following elements: {@link GraphicalObject} or {@link GeneralGlyph}. When using a
* {@link GraphicalObject} it is recommended that some form of meta-information is provided.
* For additional relationships such as SBML events or rules, the {@link GeneralGlyph} can
* be used.
*
* @param additionalGraphicalObjects
*/
public void setListOfAdditionalGraphicalObjects(ListOf additionalGraphicalObjects)
{
unsetListOfAdditionalGraphicalObjects();
if (additionalGraphicalObjects != null) {
boolean registerDone = false;
// in case, the ListOf was created by hand by a user without the proper class, we need to make a copy of the list
if ((! (additionalGraphicalObjects instanceof ListOfWithName))
|| (! additionalGraphicalObjects.getElementName().equals(LayoutConstants.listOfAdditionalGraphicalObjects)))
{
listOfAdditionalGraphicalObjects = getListOfAdditionalGraphicalObjects(); // initializing a new ListOfWithName with the proper settings
registerDone = true;
// Need to reset the parent of all the given list to prevent warning when we add them to the real new list
for (GraphicalObject go : additionalGraphicalObjects) {
go.setParent(null);
}
// now adding all the cloned GraphicalObject to the real new list
listOfAdditionalGraphicalObjects.addAll(additionalGraphicalObjects);
}
if (!registerDone) {
listOfAdditionalGraphicalObjects = additionalGraphicalObjects;
listOfAdditionalGraphicalObjects.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfAdditionalGraphicalObjects.setPackageName(null);
listOfAdditionalGraphicalObjects.setPackageName(LayoutConstants.shortLabel);
listOfAdditionalGraphicalObjects.setSBaseListType(ListOf.Type.other);
registerChild(listOfAdditionalGraphicalObjects);
}
}
}
/**
* This element is optional. If set, this list cannot be empty. Also, not all
* {@link Compartment}s of a {@link org.sbml.jsbml.Model} will need a corresponding {@link CompartmentGlyph}.
*
* @param compartmentGlyphs
*/
public void setListOfCompartmentGlyphs(ListOf compartmentGlyphs) {
unsetListOfCompartmentGlyphs();
listOfCompartmentGlyphs = compartmentGlyphs;
if (listOfCompartmentGlyphs != null) {
listOfCompartmentGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfCompartmentGlyphs.setPackageName(null);
listOfCompartmentGlyphs.setPackageName(LayoutConstants.shortLabel);
listOfCompartmentGlyphs.setSBaseListType(ListOf.Type.other);
registerChild(listOfCompartmentGlyphs);
}
}
/**
* This element is optional. If set, this list cannot be empty. Also, not all {@link Reaction}s
* of a {@link org.sbml.jsbml.Model} need a corresponding {@link ReactionGlyph}.
*
* @param reactionGlyphs
*/
public void setListOfReactionGlyphs(ListOf reactionGlyphs) {
unsetListOfReactionGlyphs();
listOfReactionGlyphs = reactionGlyphs;
if (listOfReactionGlyphs != null) {
listOfReactionGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfReactionGlyphs.setPackageName(null);
listOfReactionGlyphs.setPackageName(LayoutConstants.shortLabel);
listOfReactionGlyphs.setSBaseListType(ListOf.Type.other);
registerChild(listOfReactionGlyphs);
}
}
/**
* This element is optional. If set, this list cannot be empty. Also, not all {@link Species}
* of a {@link org.sbml.jsbml.Model} need a corresponding {@link SpeciesGlyph}.
*
* @param speciesGlyphs
*/
public void setListOfSpeciesGlyphs(ListOf speciesGlyphs) {
unsetListOfSpeciesGlyphs();
listOfSpeciesGlyphs = speciesGlyphs;
if (listOfSpeciesGlyphs != null) {
listOfSpeciesGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSpeciesGlyphs.setPackageName(null);
listOfSpeciesGlyphs.setPackageName(LayoutConstants.shortLabel);
listOfSpeciesGlyphs.setSBaseListType(ListOf.Type.other);
registerChild(listOfSpeciesGlyphs);
}
}
/**
* This element is optional. If set, this list cannot be empty.
*
* @param textGlyphs
*/
public void setListOfTextGlyphs(ListOf textGlyphs) {
unsetListOfTextGlyphs();
listOfTextGlyphs = textGlyphs;
if (listOfTextGlyphs != null) {
listOfTextGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfTextGlyphs.setPackageName(null);
listOfTextGlyphs.setPackageName(LayoutConstants.shortLabel);
listOfTextGlyphs.setSBaseListType(ListOf.Type.other);
registerChild(listOfTextGlyphs);
}
}
/**
* Removes the {@link #listOfAdditionalGraphicalObjects} from this {@link org.sbml.jsbml.Model} and notifies
* all registered instances of {@link org.sbml.jsbml.util.TreeNodeChangeListener}.
*
* @return {@code true} if calling this method lead to a change in this
* data structure.
*/
public boolean unsetListOfAdditionalGraphicalObjects() {
if (listOfAdditionalGraphicalObjects != null) {
ListOf oldListOfAdditionalGraphicalObjects = listOfAdditionalGraphicalObjects;
listOfAdditionalGraphicalObjects = null;
oldListOfAdditionalGraphicalObjects.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Removes the {@link #listOfCompartmentGlyphs} from this {@link org.sbml.jsbml.Model} and notifies
* all registered instances of {@link org.sbml.jsbml.util.TreeNodeChangeListener}.
*
* @return {@code true} if calling this method lead to a change in this
* data structure.
*/
public boolean unsetListOfCompartmentGlyphs() {
if (listOfCompartmentGlyphs != null) {
ListOf oldListOfCompartmentGlyphs = listOfCompartmentGlyphs;
listOfCompartmentGlyphs = null;
oldListOfCompartmentGlyphs.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Removes the {@link #listOfReactionGlyphs} from this {@link org.sbml.jsbml.Model} and notifies
* all registered instances of {@link org.sbml.jsbml.util.TreeNodeChangeListener}.
*
* @return {@code true} if calling this method lead to a change in this
* data structure.
*/
public boolean unsetListOfReactionGlyphs() {
if (listOfReactionGlyphs != null) {
ListOf oldListOfReactionGlyphs = listOfReactionGlyphs;
listOfReactionGlyphs = null;
oldListOfReactionGlyphs.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Removes the {@link #listOfSpeciesGlyphs} from this {@link org.sbml.jsbml.Model} and notifies
* all registered instances of {@link org.sbml.jsbml.util.TreeNodeChangeListener}.
*
* @return {@code true} if calling this method lead to a change in this
* data structure.
*/
public boolean unsetListOfSpeciesGlyphs() {
if (listOfSpeciesGlyphs != null) {
ListOf oldListOfSpeciesGlyphs = listOfSpeciesGlyphs;
listOfSpeciesGlyphs = null;
oldListOfSpeciesGlyphs.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Removes the {@link #listOfTextGlyphs} from this {@link org.sbml.jsbml.Model} and notifies
* all registered instances of {@link org.sbml.jsbml.util.TreeNodeChangeListener}.
*
* @return {@code true} if calling this method lead to a change in this
* data structure.
*/
public boolean unsetListOfTextGlyphs() {
if (listOfTextGlyphs != null) {
ListOf oldListOfTextGlyphs = listOfTextGlyphs;
listOfTextGlyphs = null;
oldListOfTextGlyphs.fireNodeRemovedEvent();
return true;
}
return false;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetId()) {
attributes.remove("id");
attributes.put(LayoutConstants.shortLabel + ":id", getId());
}
if (isSetName()) {
attributes.remove("name");
attributes.put(LayoutConstants.shortLabel + ":name", getName());
}
return attributes;
}
}