org.openscience.cdk.ChemFile 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.IChemFile;
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 Object containing a number of ChemSequences. This is supposed to be the
* top level container, which can contain all the concepts stored in a chemical
* document
*
*@author steinbeck
* @cdk.githash
*@cdk.module data
*/
public class ChemFile extends ChemObject implements Serializable, Cloneable, IChemFile, IChemObjectListener {
/**
* 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 = 1926781734333430132L;
/**
* Array of ChemSquences.
*/
protected IChemSequence[] chemSequences;
/**
* Number of ChemSequences contained by this container.
*/
protected int chemSequenceCount;
/**
* Amount by which the chemsequence array grows when elements are added and
* the array is not large enough for that.
*/
protected int growArraySize = 4;
/**
* Constructs an empty ChemFile.
*/
public ChemFile() {
chemSequenceCount = 0;
chemSequences = new ChemSequence[growArraySize];
}
/**
* Adds a ChemSequence to this container.
*
*@param chemSequence The chemSequence to be added to this container
*@see #chemSequences
*/
@Override
public void addChemSequence(IChemSequence chemSequence) {
chemSequence.addListener(this);
if (chemSequenceCount + 1 >= chemSequences.length) {
growChemSequenceArray();
}
chemSequences[chemSequenceCount] = chemSequence;
chemSequenceCount++;
notifyChanged();
}
/**
* Removes a ChemSequence from this container.
*
* @param pos The position from which to remove
* @see #chemSequences
* @see #addChemSequence(org.openscience.cdk.interfaces.IChemSequence)
*/
@Override
public void removeChemSequence(int pos) {
chemSequences[pos].removeListener(this);
for (int i = pos; i < chemSequenceCount - 1; i++) {
chemSequences[i] = chemSequences[i + 1];
}
chemSequences[chemSequenceCount - 1] = null;
chemSequenceCount--;
notifyChanged();
}
/**
* Returns the Iterable to ChemSequences of this container.
*
*@return The Iterable to ChemSequences of this container
*@see #addChemSequence
*/
@Override
public Iterable chemSequences() {
return new Iterable() {
@Override
public Iterator iterator() {
return new ChemSequenceIterator();
}
};
}
/**
* The inner Iterator class.
*
*/
private class ChemSequenceIterator implements Iterator {
private int pointer = 0;
@Override
public boolean hasNext() {
return pointer < chemSequenceCount;
}
@Override
public IChemSequence next() {
return chemSequences[pointer++];
}
@Override
public void remove() {
removeChemSequence(--pointer);
}
}
/**
* Returns the ChemSequence at position number in the container.
*
*@param number The position of the ChemSequence to be returned.
*@return The ChemSequence at position number.
*@see #addChemSequence
*/
@Override
public IChemSequence getChemSequence(int number) {
return chemSequences[number];
}
/**
* Grows the ChemSequence array by a given size.
*
*@see #growArraySize
*/
protected void growChemSequenceArray() {
growArraySize = chemSequences.length;
IChemSequence[] newchemSequences = new ChemSequence[chemSequences.length + growArraySize];
System.arraycopy(chemSequences, 0, newchemSequences, 0, chemSequences.length);
chemSequences = newchemSequences;
}
/**
* Returns the number of ChemSequences in this Container.
*
*@return The number of ChemSequences in this Container
*/
@Override
public int getChemSequenceCount() {
return this.chemSequenceCount;
}
/**
* Returns a String representation of this class. It implements
* RFC #9.
*
*@return String representation of the Object
*/
@Override
public String toString() {
StringBuffer buffer = new StringBuffer();
buffer.append("ChemFile(#S=");
buffer.append(chemSequenceCount);
if (chemSequenceCount > 0) {
for (IChemSequence iChemSequence : chemSequences()) {
buffer.append(", ");
buffer.append(iChemSequence.toString());
}
}
buffer.append(')');
return buffer.toString();
}
/**
* Allows for getting an clone of this object.
*
*@return a clone of this object
*/
@Override
public Object clone() throws CloneNotSupportedException {
ChemFile clone = (ChemFile) super.clone();
// clone the chemModels
clone.chemSequenceCount = getChemSequenceCount();
clone.chemSequences = new ChemSequence[clone.chemSequenceCount];
for (int f = 0; f < clone.chemSequenceCount; f++) {
clone.chemSequences[f] = (ChemSequence) ((ChemSequence) chemSequences[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);
}
}