org.openscience.cdk.formula.MolecularFormulaSet Maven / Gradle / Ivy
/* Copyright (C) 2007 Miguel Rojasch
*
* 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.formula;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IMolecularFormulaSet;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
/**
* Class defining an set object of MolecularFormulas. It maintains
* a list of list IMolecularFormula.
*
* @cdk.module data
* @author miguelrojasch
* @cdk.created 2007-11-20
* @cdk.keyword molecular formula
* @cdk.githash
*/
public class MolecularFormulaSet implements Iterable, IMolecularFormulaSet, 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 = -2043178712150212550L;
/** Internal List of IMolecularFormula. */
private List components;
/**
* Constructs an empty MolecularFormulaSet.
*
* @see #MolecularFormulaSet(IMolecularFormula)
*/
public MolecularFormulaSet() {
components = new ArrayList();
}
/**
* Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another
* MolecularFormulaSet (A shallow copy, i.e., with the same objects as in
* the original MolecularFormulaSet).
*
* @param formula An MolecularFormula to copy from
* @see #MolecularFormulaSet()
*/
public MolecularFormulaSet(IMolecularFormula formula) {
components = new ArrayList();
components.add(0, formula);
}
/**
* Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
*
* @param formulaSet The MolecularFormulaSet
*/
@Override
public void add(IMolecularFormulaSet formulaSet) {
for (IMolecularFormula mf : formulaSet.molecularFormulas()) {
addMolecularFormula(mf);
}
/*
* notifyChanged() is called by addAtomContainer()
*/
}
/**
* Adds an molecularFormula to this chemObject.
*
* @param formula The molecularFormula to be added to this chemObject
*/
@Override
public void addMolecularFormula(IMolecularFormula formula) {
components.add(formula);
}
/**
* Returns an Iterable for looping over all IMolecularFormula
* in this MolecularFormulaSet.
*
* @return An Iterable with the IMolecularFormula in this MolecularFormulaSet
*/
@Override
public Iterable molecularFormulas() {
return components;
}
/**
* Returns an Iterator for looping over all IMolecularFormula
* in this MolecularFormulaSet.
*
* @return An Iterator with the IMolecularFormula in this MolecularFormulaSet
*/
@Override
public Iterator iterator() {
return components.iterator();
}
/**
* Returns the number of MolecularFormulas in this MolecularFormulaSet.
*
* @return The number of MolecularFormulas in this MolecularFormulaSet
*/
@Override
public int size() {
return components.size();
}
/**
* True, if the MolecularFormulaSet contains the given IMolecularFormula object.
*
* @param formula The IMolecularFormula this MolecularFormulaSet is searched for
* @return True, if the MolecularFormulaSet contains the given IMolecularFormula object
*/
@Override
public boolean contains(IMolecularFormula formula) {
return components.contains(formula);
}
/**
*
* Returns the MolecularFormula at position number in the
* chemObject.
*
* @param position The position of the IMolecularFormula to be returned.
* @return The IMolecularFormula at position number .
*/
@Override
public IMolecularFormula getMolecularFormula(int position) {
return components.get(position);
}
/**
* Removes all IMolecularFormula from this chemObject.
*/
@Override
public void removeAllMolecularFormulas() {
components.clear();
}
/**
* Removes an IMolecularFormula from this chemObject.
*
* @param formula The IMolecularFormula to be removed from this chemObject
*/
@Override
public void removeMolecularFormula(IMolecularFormula formula) {
components.remove(formula);
}
/**
* Removes an MolecularFormula from this chemObject.
*
* @param position The position of the MolecularFormula to be removed from this chemObject
*/
@Override
public void removeMolecularFormula(int position) {
components.remove(position);
}
/**
* Clones this MolecularFormulaSet object and its content.
*
* @return The cloned object
*/
@Override
public Object clone() throws CloneNotSupportedException {
// /* it is not a super class of chemObject */
// MolecularFormulaSet clone = (MolecularFormulaSet) super.clone();
// // start from scratch
// clone.removeAllMolecularFormulas();
// // clone all molecularFormulas
// Iterator iterForm = this.molecularFormulas();
// while(iterForm.hasNext()){
// clone.addMolecularFormula((IMolecularFormula) iterForm.next().clone());
// }
MolecularFormulaSet clone = new MolecularFormulaSet();
for (IMolecularFormula mf : this.molecularFormulas()) {
clone.addMolecularFormula((IMolecularFormula) mf.clone());
}
return clone;
}
@Override
public IChemObjectBuilder getBuilder() {
return DefaultChemObjectBuilder.getInstance();
}
}