/* $Revision$ $Author$ $Date$
*
* 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
*/
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
*/
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
*/
public IteratingPCCompoundXMLReader(InputStream in, IChemObjectBuilder builder) throws Exception {
this(new InputStreamReader(in), builder);
}
@TestMethod("testGetFormat")
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")
public void close() throws IOException {
primarySource.close();
}
public void remove() {
throw new UnsupportedOperationException();
}
@TestMethod("testSetReader_Reader")
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")
public void setReader(InputStream reader) throws CDKException {
setReader(new InputStreamReader(reader));
}
}