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Viewing changes to src/org/openscience/cdk/ChemFile.java

  • Committer: Bazaar Package Importer
  • Author(s): Paul Cager
  • Date: 2008-04-09 21:17:53 UTC
  • Revision ID: james.westby@ubuntu.com-20080409211753-46lmjw5z8mx5pd8d
Tags: upstream-1.0.2
Import upstream version 1.0.2

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src/org/openscience/cdk/ChemFile.java
 
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/*
 
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 *  $RCSfile$
 
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 *  $Author: egonw $
 
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 *  $Date: 2007-02-16 14:03:31 +0100 (Fri, 16 Feb 2007) $
 
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 *  $Revision: 7958 $
 
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 *
 
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 *  Copyright (C) 1997-2007  Christoph Steinbeck <steinbeck@users.sf.net>
 
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 *
 
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 *  Contact: cdk-devel@lists.sourceforge.net
 
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 *
 
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 *  This program is free software; you can redistribute it and/or
 
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 *  modify it under the terms of the GNU Lesser General Public License
 
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 *  as published by the Free Software Foundation; either version 2.1
 
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 *  of the License, or (at your option) any later version.
 
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 *
 
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 *  This program is distributed in the hope that it will be useful,
 
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 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 
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 *  GNU Lesser General Public License for more details.
 
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 *
 
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 *  You should have received a copy of the GNU Lesser General Public License
 
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 *  along with this program; if not, write to the Free Software
 
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 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 
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 */
 
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package org.openscience.cdk;
 
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import java.io.Serializable;
 
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import org.openscience.cdk.interfaces.IChemFile;
 
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import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 
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import org.openscience.cdk.interfaces.IChemObjectListener;
 
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import org.openscience.cdk.interfaces.IChemSequence;
 
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/**
 
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 *  A Object containing a number of ChemSequences. This is supposed to be the
 
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 *  top level container, which can contain all the concepts stored in a chemical
 
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 *  document
 
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 *
 
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 *@author        steinbeck
 
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 *@cdk.module    data
 
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 */
 
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public class ChemFile extends ChemObject implements Serializable, Cloneable,
 
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                IChemFile, IChemObjectListener
 
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{
 
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        /**
 
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     * Determines if a de-serialized object is compatible with this class.
 
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     *
 
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     * This value must only be changed if and only if the new version
 
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     * of this class is imcompatible with the old version. See Sun docs
 
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     * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
 
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     * /serialization/spec/version.doc.html>details</a>.
 
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         */
 
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        private static final long serialVersionUID = 1926781734333430132L;
 
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        /**
 
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         *  Array of ChemSquences.
 
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         */
 
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        protected IChemSequence[] chemSequences;
 
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        /**
 
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         *  Number of ChemSequences contained by this container.
 
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         */
 
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        protected int chemSequenceCount;
 
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        /**
 
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         *  Amount by which the chemsequence array grows when elements are added and
 
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         *  the array is not large enough for that.
 
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         */
 
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        protected int growArraySize = 4;
 
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        /**
 
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         *  Constructs an empty ChemFile.
 
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         */
 
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        public ChemFile()
 
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        {
 
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                chemSequenceCount = 0;
 
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                chemSequences = new ChemSequence[growArraySize];
 
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        }
 
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        /**
 
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         *  Adds a ChemSequence to this container.
 
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         *
 
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         *@param  chemSequence  The chemSequence to be added to this container
 
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         *@see                  #chemSequences
 
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         */
 
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        public void addChemSequence(IChemSequence chemSequence)
 
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        {
 
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                chemSequence.addListener(this);
 
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                if (chemSequenceCount + 1 >= chemSequences.length)
 
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                {
 
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                        growChemSequenceArray();
 
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                }
 
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                chemSequences[chemSequenceCount] = chemSequence;
 
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                chemSequenceCount++;
 
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                notifyChanged();
 
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        }
 
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        /**
 
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         *  Removes a ChemSequence from this container.
 
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         *
 
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         *@param  chemSequence  The chemSequence to be added to this container
 
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         *@see                  #chemSequences
 
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         */
 
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        public void removeChemSequence(int pos)
 
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        {
 
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                chemSequences[pos].removeListener(this);
 
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                for (int i = pos; i < chemSequenceCount - 1; i++) {
 
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                        chemSequences[i] = chemSequences[i + 1];
 
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                }
 
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                chemSequences[chemSequenceCount - 1] = null;
 
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                chemSequenceCount--;
 
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                notifyChanged();
 
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        }
 
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        /**
 
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         *  Returns the Iterator to ChemSequences of this container.
 
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         *
 
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         *@return    The Iterator to ChemSequences of this container
 
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         *@see       #addChemSequence
 
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         */
 
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        public java.util.Iterator chemSequences()
 
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        {
 
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                return new ChemSequenceIterator();
 
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        }
 
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        /**
 
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     * The inner Iterator class.
 
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     *
 
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     */
 
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    private class ChemSequenceIterator implements java.util.Iterator {
 
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        private int pointer = 0;
 
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        public boolean hasNext() {
 
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            if (pointer < chemSequenceCount) return true;
 
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            return false;
 
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        }
 
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        public Object next() {
 
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            return chemSequences[pointer++];
 
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        }
 
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        public void remove() {
 
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            removeChemSequence(--pointer);
 
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        }
 
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    }
 
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        /**
 
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         *  Returns the ChemSequence at position <code>number</code> in the container.
 
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         *
 
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         *@param  number  The position of the ChemSequence to be returned.
 
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         *@return         The ChemSequence at position <code>number</code>.
 
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         *@see            #addChemSequence
 
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         */
 
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        public IChemSequence getChemSequence(int number)
 
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        {
 
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                return (ChemSequence)chemSequences[number];
 
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        }
 
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        /**
 
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         *  Grows the ChemSequence array by a given size.
 
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         *
 
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         *@see    #growArraySize
 
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         */
 
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        protected void growChemSequenceArray()
 
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        {
 
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                growArraySize = chemSequences.length;
 
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                IChemSequence[] newchemSequences = new ChemSequence[chemSequences.length + growArraySize];
 
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                System.arraycopy(chemSequences, 0, newchemSequences, 0, chemSequences.length);
 
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                chemSequences = newchemSequences;
 
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        }
 
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        /**
 
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         *  Returns the number of ChemSequences in this Container.
 
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         *
 
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         *@return    The number of ChemSequences in this Container
 
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         */
 
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        public int getChemSequenceCount()
 
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        {
 
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                return this.chemSequenceCount;
 
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        }
 
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        /**
 
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         * Returns a String representation of this class. It implements
 
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         * RFC #9.
 
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         *
 
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         *@return    String representation of the Object
 
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         */
 
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        public String toString()
 
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        {
 
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                StringBuffer buffer = new StringBuffer();
 
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                buffer.append("ChemFile(#S=");
 
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                java.util.Iterator seqs = chemSequences();
 
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                buffer.append(chemSequenceCount);
 
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                buffer.append(", ");
 
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                while (seqs.hasNext())
 
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                {
 
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                        IChemSequence sequence = (IChemSequence)seqs.next();
 
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                        buffer.append(sequence.toString());
 
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                }
 
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                buffer.append(')');
 
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                return buffer.toString();
 
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        }
 
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        /**
 
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         *  Allows for getting an clone of this object.
 
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         *
 
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         *@return    a clone of this object
 
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         */
 
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        public Object clone() throws CloneNotSupportedException
 
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        {
 
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                ChemFile clone = (ChemFile) super.clone();
 
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                // clone the chemModels
 
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                clone.chemSequenceCount = getChemSequenceCount();
 
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                clone.chemSequences = new ChemSequence[clone.chemSequenceCount];
 
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                for (int f = 0; f < clone.chemSequenceCount; f++)
 
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                {
 
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                        clone.chemSequences[f] = (ChemSequence)((ChemSequence)chemSequences[f]).clone();
 
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                }
 
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                return clone;
 
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        }
 
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        /**
 
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         *  Called by objects to which this object has
 
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         *  registered as a listener.
 
235
         *
 
236
         *@param  event  A change event pointing to the source of the change
 
237
         */
 
238
        public void stateChanged(IChemObjectChangeEvent event)
 
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        {
 
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                notifyChanged(event);
 
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        }
 
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}
 
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