org.openscience.cdk.ChemModel Maven / Gradle / Ivy
/* Copyright (C) 1997-2007 Christoph Steinbeck
*
* Contact: [email protected]
*
* This program 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; either version 2.1
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk;
import java.io.Serializable;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.interfaces.IRingSet;
/**
* An object containing multiple MoleculeSet and
* the other lower level concepts like rings, sequences,
* fragments, etc.
*
* @cdk.module data
* @cdk.githash
*/
public class ChemModel extends ChemObject implements Serializable, IChemModel, IChemObjectListener, Cloneable {
/**
* Determines if a de-serialized object is compatible with this class.
*
* This value must only be changed if and only if the new version
* of this class is incompatible with the old version. See Sun docs
* for details.
*/
private static final long serialVersionUID = -5213425310451366185L;
/**
* A MoleculeSet.
*/
protected IAtomContainerSet setOfMolecules = null;
/**
* A ReactionSet.
*/
protected IReactionSet setOfReactions = null;
/**
* A RingSet.
*/
protected IRingSet ringSet = null;
/**
* A Crystal.
*/
protected ICrystal crystal = null;
/**
* Constructs an new ChemModel with a null setOfMolecules.
*/
public ChemModel() {}
/**
* Returns the MoleculeSet of this ChemModel.
*
* @return The MoleculeSet of this ChemModel
*
* @see #setMoleculeSet
*/
@Override
public IAtomContainerSet getMoleculeSet() {
return this.setOfMolecules;
}
/**
* Sets the MoleculeSet of this ChemModel.
*
* @param setOfMolecules the content of this model
*
* @see #getMoleculeSet
*/
@Override
public void setMoleculeSet(IAtomContainerSet setOfMolecules) {
if (this.setOfMolecules != null) this.setOfMolecules.removeListener(this);
this.setOfMolecules = setOfMolecules;
if (this.setOfMolecules != null) this.setOfMolecules.addListener(this);
notifyChanged();
}
/**
* Returns the RingSet of this ChemModel.
*
* @return the ringset of this model
*
* @see #setRingSet
*/
@Override
public IRingSet getRingSet() {
return this.ringSet;
}
/**
* Sets the RingSet of this ChemModel.
*
* @param ringSet the content of this model
*
* @see #getRingSet
*/
@Override
public void setRingSet(IRingSet ringSet) {
if (this.ringSet != null) this.ringSet.removeListener(this);
this.ringSet = ringSet;
if (this.ringSet != null) this.ringSet.addListener(this);
notifyChanged();
}
/**
* Gets the Crystal contained in this ChemModel.
*
* @return The crystal in this model
*
* @see #setCrystal
*/
@Override
public ICrystal getCrystal() {
return this.crystal;
}
/**
* Sets the Crystal contained in this ChemModel.
*
* @param crystal the Crystal to store in this model
*
* @see #getCrystal
*/
@Override
public void setCrystal(ICrystal crystal) {
if (this.crystal != null) this.crystal.removeListener(this);
this.crystal = crystal;
if (this.crystal != null) this.crystal.addListener(this);
notifyChanged();
}
/**
* Gets the ReactionSet contained in this ChemModel.
*
* @return The ReactionSet in this model
*
* @see #setReactionSet
*/
@Override
public IReactionSet getReactionSet() {
return this.setOfReactions;
}
/**
* Sets the ReactionSet contained in this ChemModel.
*
* @param sor the ReactionSet to store in this model
*
* @see #getReactionSet
*/
@Override
public void setReactionSet(IReactionSet sor) {
if (this.setOfReactions != null) this.setOfReactions.removeListener(this);
this.setOfReactions = sor;
if (this.setOfReactions != null) this.setOfReactions.addListener(this);
notifyChanged();
}
/**
* Returns a String representation of the contents of this
* IChemObject.
*
* @return String representation of content
*/
@Override
public String toString() {
StringBuffer buffer = new StringBuffer(64);
buffer.append("ChemModel(");
buffer.append(hashCode());
if (getMoleculeSet() != null) {
buffer.append(", ");
buffer.append(getMoleculeSet().toString());
}
if (getCrystal() != null) {
buffer.append(", ");
buffer.append(getCrystal().toString());
}
if (getReactionSet() != null) {
buffer.append(", ");
buffer.append(getReactionSet().toString());
}
buffer.append(')');
return buffer.toString();
}
/**
* Clones this ChemModel and its content.
*
* @return The cloned object
*/
@Override
public Object clone() throws CloneNotSupportedException {
ChemModel clone = (ChemModel) super.clone();
// clone the content
if (setOfMolecules != null) {
clone.setOfMolecules = (IAtomContainerSet) setOfMolecules.clone();
} else {
clone.setOfMolecules = null;
}
if (setOfReactions != null) {
clone.setOfReactions = (IReactionSet) ((ReactionSet) setOfReactions).clone();
} else {
clone.setOfReactions = null;
}
if (crystal != null) {
clone.crystal = (Crystal) ((Crystal) crystal).clone();
} else {
clone.crystal = null;
}
if (ringSet != null) {
clone.ringSet = (RingSet) ((RingSet) ringSet).clone();
} else {
clone.ringSet = null;
}
return clone;
}
/**
* Called by objects to which this object has
* registered as a listener.
*
*@param event A change event pointing to the source of the change
*/
@Override
public void stateChanged(IChemObjectChangeEvent event) {
notifyChanged(event);
}
/**
*{@inheritDoc}
*/
@Override
public boolean isEmpty() {
if (setOfMolecules != null && !setOfMolecules.isEmpty()) return false;
if (setOfReactions != null && !setOfReactions.isEmpty()) return false;
if (ringSet != null && !ringSet.isEmpty()) return false;
if (crystal != null && !crystal.isEmpty()) return false;
return true;
}
}