org.openscience.cdk.ReactionSet Maven / Gradle / Ivy
/* Copyright (C) 2003-2007 Egon Willighagen
*
* 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 java.util.Iterator;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
/**
* A set of reactions, for example those taking part in a reaction.
*
* To retrieve the reactions from the set, there are two options:
*
*
* Iterator reactions = reactionSet.reactions();
* while (reactions.hasNext()) {
* IReaction reaction = (IReaction)reactions.next();
* }
*
*
* and
*
* {@code
* for (int i=0; i < reactionSet.getReactionCount(); i++) {
* IReaction reaction = reactionSet.getReaction(i);
* }
* }
*
* @cdk.module data
* @cdk.githash
*
* @cdk.keyword reaction
*/
public class ReactionSet extends ChemObject implements Serializable, IReactionSet, 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 = 1555749911904585204L;
/**
* Array of Reactions.
*/
private IReaction[] reactions;
/**
* Number of Reactions contained by this container.
*/
private int reactionCount;
/**
* Amount by which the Reactions array grows when elements are added and
* the array is not large enough for that.
*/
private int growArraySize = 5;
/**
* Constructs an empty ReactionSet.
*/
public ReactionSet() {
reactionCount = 0;
reactions = new IReaction[growArraySize];
}
/**
* Adds an reaction to this container.
*
* @param reaction The reaction to be added to this container
*/
@Override
public void addReaction(IReaction reaction) {
if (reactionCount + 1 >= reactions.length) growReactionArray();
reactions[reactionCount] = reaction;
reactionCount++;
notifyChanged();
}
/**
* Remove a reaction from this set.
*
* @param pos The position of the reaction to be removed.
*/
@Override
public void removeReaction(int pos) {
reactions[pos].removeListener(this);
for (int i = pos; i < reactionCount - 1; i++) {
reactions[i] = reactions[i + 1];
}
reactions[reactionCount - 1] = null;
reactionCount--;
notifyChanged();
}
/**
*
* Returns the Reaction at position number in the
* container.
*
* @param number The position of the Reaction to be returned
* @return The Reaction at position number
*/
@Override
public IReaction getReaction(int number) {
return reactions[number];
}
/**
* Get an iterator for this reaction set.
*
* @return A new Iterator for this ReactionSet.
*/
@Override
public Iterable reactions() {
return new Iterable() {
@Override
public Iterator iterator() {
return new ReactionIterator();
}
};
}
/**
* The inner Iterator class.
*
*/
private class ReactionIterator implements Iterator {
private int pointer = 0;
@Override
public boolean hasNext() {
if (pointer < reactionCount) return true;
return false;
}
@Override
public IReaction next() {
return reactions[pointer++];
}
@Override
public void remove() {
removeReaction(--pointer);
}
}
/**
* Grows the reaction array by a given size.
*
* @see growArraySize
*/
private void growReactionArray() {
growArraySize = reactions.length;
IReaction[] newreactions = new IReaction[reactions.length + growArraySize];
System.arraycopy(reactions, 0, newreactions, 0, reactions.length);
reactions = newreactions;
}
/**
* Returns the number of Reactions in this Container.
*
* @return The number of Reactions in this Container
*/
@Override
public int getReactionCount() {
return this.reactionCount;
}
@Override
public String toString() {
StringBuffer buffer = new StringBuffer(32);
buffer.append("ReactionSet(");
buffer.append(this.hashCode());
buffer.append(", R=").append(getReactionCount()).append(", ");
for (IReaction reaction : reactions()) {
buffer.append(reaction.toString());
}
buffer.append(')');
return buffer.toString();
}
/**
* Clones this ReactionSet and the contained Reactions
* too.
*
* @return The cloned ReactionSet
*/
@Override
public Object clone() throws CloneNotSupportedException {
ReactionSet clone = (ReactionSet) super.clone();
// clone the reactions
clone.reactionCount = this.reactionCount;
clone.reactions = new IReaction[clone.reactionCount];
for (int f = 0; f < clone.reactionCount; f++) {
clone.reactions[f] = (IReaction) ((IReaction) reactions[f]).clone();
}
return clone;
}
/**
* Removes all Reactions from this container.
*/
@Override
public void removeAllReactions() {
for (int pos = this.reactionCount - 1; pos >= 0; pos--) {
this.reactions[pos] = null;
}
this.reactionCount = 0;
notifyChanged();
}
@Override
public void stateChanged(IChemObjectChangeEvent event) {
notifyChanged(event);
}
@Override
public void removeReaction(IReaction relevantReaction) {
for (int i = reactionCount - 1; i >= 0; i--) {
if (reactions[i] == relevantReaction) removeReaction(i);
}
}
/**
*{@inheritDoc}
*/
@Override
public boolean isEmpty() {
return reactionCount == 0;
}
}