org.openscience.cdk.ChemSequence 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 org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.IChemSequence;
import java.io.Serializable;
import java.util.Iterator;
/**
* A sequence of ChemModels, which can, for example, be used to
* store the course of a reaction. Each state of the reaction would be
* stored in one ChemModel.
*
* @cdk.module data
* @cdk.githash
*
* @cdk.keyword animation
* @cdk.keyword reaction
*/
public class ChemSequence extends ChemObject implements Serializable, IChemSequence, 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 = 2199218627455492000L;
/**
* Array of ChemModels.
*/
protected IChemModel[] chemModels;
/**
* Number of ChemModels contained by this container.
*/
protected int chemModelCount;
/**
* Amount by which the chemModels array grows when elements are added and
* the array is not large enough for that.
*/
protected int growArraySize = 4;
/**
* Constructs an empty ChemSequence.
*/
public ChemSequence() {
chemModelCount = 0;
chemModels = new ChemModel[growArraySize];
}
/**
* Adds an chemModel to this container.
*
* @param chemModel The chemModel to be added to this container
*
* @see #getChemModel
*/
@Override
public void addChemModel(IChemModel chemModel) {
if (chemModelCount + 1 >= chemModels.length) {
growChemModelArray();
}
chemModels[chemModelCount] = chemModel;
chemModelCount++;
chemModel.addListener(this);
notifyChanged();
}
/**
* Remove a ChemModel from this ChemSequence.
*
* @param pos The position of the ChemModel to be removed.
*/
@Override
public void removeChemModel(int pos) {
chemModels[pos].removeListener(this);
for (int i = pos; i < chemModelCount - 1; i++) {
chemModels[i] = chemModels[i + 1];
}
chemModels[chemModelCount - 1] = null;
chemModelCount--;
notifyChanged();
}
/**
* Returns an Iterable to ChemModels in this container.
*
* @return The Iterable to ChemModels in this container
* @see #addChemModel
*/
@Override
public Iterable chemModels() {
return new Iterable() {
@Override
public Iterator iterator() {
return new ChemModelIterator();
}
};
}
/**
* The inner Iterator class.
*
*/
private class ChemModelIterator implements Iterator {
private int pointer = 0;
@Override
public boolean hasNext() {
return pointer < chemModelCount;
}
@Override
public IChemModel next() {
return chemModels[pointer++];
}
@Override
public void remove() {
removeChemModel(--pointer);
}
}
/**
*
* Returns the ChemModel at position number in the
* container.
*
* @param number The position of the ChemModel to be returned.
* @return The ChemModel at position number.
*
* @see #addChemModel
*/
@Override
public IChemModel getChemModel(int number) {
return chemModels[number];
}
/**
* Grows the chemModel array by a given size.
*
* @see growArraySize
*/
protected void growChemModelArray() {
ChemModel[] newchemModels = new ChemModel[chemModels.length + growArraySize];
System.arraycopy(chemModels, 0, newchemModels, 0, chemModels.length);
chemModels = newchemModels;
}
/**
* Returns the number of ChemModels in this Container.
*
* @return The number of ChemModels in this Container
*/
@Override
public int getChemModelCount() {
return this.chemModelCount;
}
@Override
public String toString() {
StringBuffer buffer = new StringBuffer(32);
buffer.append("ChemSequence(#M=");
buffer.append(chemModelCount);
if (chemModelCount > 0) {
buffer.append(", ");
for (int i = 0; i < chemModelCount; i++) {
buffer.append(chemModels[i].toString());
}
}
buffer.append(')');
return buffer.toString();
}
@Override
public Object clone() throws CloneNotSupportedException {
ChemSequence clone = (ChemSequence) super.clone();
// clone the chemModels
clone.chemModelCount = getChemModelCount();
clone.chemModels = new ChemModel[clone.chemModelCount];
for (int f = 0; f < clone.chemModelCount; f++) {
clone.chemModels[f] = (ChemModel) ((ChemModel) chemModels[f]).clone();
}
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);
}
}