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IteratingPCCompoundXMLReader.java

/* $Revision$ $Author$ $Date$
 * 
 * Copyright (C) 2008  Egon Willighagen <egonw@users.sf.net>
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * 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.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 *
 * 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.io.iterator;

import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.util.NoSuchElementException;

import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat;
import org.openscience.cdk.io.pubchemxml.PubChemXMLHelper;
import org.xmlpull.v1.XmlPullParser;
import org.xmlpull.v1.XmlPullParserException;
import org.xmlpull.v1.XmlPullParserFactory;

/**
 * Iterating PubChem PCCompound ASN.1 XML reader.
 *
 * @cdk.module io
 * @cdk.githash
 *
 * @see org.openscience.cdk.io.PCCompoundASNReader
 * 
 * @author       Egon Willighagen <egonw@users.sf.net>
 * @cdk.created  2008-05-05
 *
 * @cdk.keyword  file format, ASN
 * @cdk.keyword  PubChem
 */
00059 public class IteratingPCCompoundXMLReader extends DefaultIteratingChemObjectReader {
      
      private Reader primarySource;
    private XmlPullParser parser;
    private PubChemXMLHelper parserHelper;
    private IChemObjectBuilder builder;
    
    private boolean nextAvailableIsKnown;
    private boolean hasNext;
    private IMolecule nextMolecule;
    
    /**
     * Constructs a new IteratingPCCompoundXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
     *
     * @param in      The input stream
     * @param builder The builder
     * @throws org.xmlpull.v1.XmlPullParserException if there is an error isn setting up the XML parser
     */
00077     public IteratingPCCompoundXMLReader(Reader in, IChemObjectBuilder builder) throws IOException, XmlPullParserException {
        this.builder = builder;
        parserHelper = new PubChemXMLHelper(builder);
        
        // initiate the pull parser
        XmlPullParserFactory factory = XmlPullParserFactory.newInstance(
                System.getProperty(XmlPullParserFactory.PROPERTY_NAME), null
        );
        factory.setNamespaceAware(true);
        parser = factory.newPullParser();
        primarySource = in;
        parser.setInput(primarySource);

        nextMolecule = null;
        nextAvailableIsKnown = false;
        hasNext = false;
    }

    /**
     * Constructs a new IteratingPCCompoundXLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
     *
     * @param in The input stream
     * @param builder The builder. In general, use {@link org.openscience.cdk.DefaultChemObjectBuilder}
     * @throws Exception if there is a problem creating an InputStreamReader
     */
00102     public IteratingPCCompoundXMLReader(InputStream in, IChemObjectBuilder builder) throws Exception {
        this(new InputStreamReader(in), builder);
    }


    @TestMethod("testGetFormat")
00108     public IResourceFormat getFormat() {
        return PubChemCompoundsXMLFormat.getInstance();
    }

    public boolean hasNext() {
        if (!nextAvailableIsKnown) {
            hasNext = false;
            
            try {
                if (parser.next() == XmlPullParser.END_DOCUMENT) return false;
                
                  while (parser.next() != XmlPullParser.END_DOCUMENT) {
                        if (parser.getEventType() == XmlPullParser.START_TAG) {
//                            System.out.println("start: '" + parser.getName() + "'");
                              if (parser.getName().equals("PC-Compound")) {
                                    hasNext = true;
                                    break;
                              }
                        }
                  }
                  if (hasNext) {
                        nextMolecule = parserHelper.parseMolecule(parser, builder);                   
                  }
                  
                  } catch (Exception e) {
                        e.printStackTrace();
                        hasNext = false;
                  }
            
            if (!hasNext) nextMolecule = null;
            nextAvailableIsKnown = true;
        }
        return hasNext;
    }
    
      public IChemObject next() {
        if (!nextAvailableIsKnown) {
            hasNext();
        }
        nextAvailableIsKnown = false;
        if (!hasNext) {
            throw new NoSuchElementException();
        }
        return nextMolecule;
    }
    
    @TestMethod("testClose")
00155     public void close() throws IOException {
      primarySource.close();
    }
    
00159     public void remove() {
        throw new UnsupportedOperationException();
    }

      @TestMethod("testSetReader_Reader")
00164     public void setReader(Reader reader) throws CDKException {
            primarySource = reader;
        try {
              parser.setInput(primarySource);
        } catch (XmlPullParserException e) {
              throw new CDKException("Error while opening the input:" + e.getMessage(), e);
        }
        nextMolecule = null;
        nextAvailableIsKnown = false;
        hasNext = false;
    }

      @TestMethod("testSetReader_InputStream")
00177     public void setReader(InputStream reader) throws CDKException {
          setReader(new InputStreamReader(reader));
    }
}


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