/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2002-2007 The Chemistry Development Kit (CDK) project
*
* 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;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.io.formats.INChIFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.inchi.INChIHandler;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.XMLReader;
/**
* Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document. See
* {@cdk.cite HEL01}. Recently a new INChI format was introduced an files generated
* with the latest INChI generator cannot be parsed with this class. This class
* needs to be updated.
*
* <P>The elements that are read are given in the INChIHandler class.
*
* @cdk.module extra
* @cdk.githash
*
* @author Egon Willighagen <egonw@sci.kun.nl>
* @cdk.created 2004-05-17
*
* @cdk.keyword file format, INChI
* @cdk.keyword chemical identifier
* @cdk.require java1.4+
*
* @see org.openscience.cdk.io.inchi.INChIHandler
*/
@TestClass("org.openscience.cdk.io.INChIReaderTest")
public class INChIReader extends DefaultChemObjectReader {
private XMLReader parser;
private InputStream input;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(INChIReader.class);
/**
* Construct a INChI reader from a InputStream object.
*
* @param input the InputStream with the content
*/
public INChIReader(InputStream input) {
this.input = input;
init();
}
public INChIReader() {
this(new ByteArrayInputStream(new byte[0]));
}
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return INChIFormat.getInstance();
}
/**
* This method must not be used; XML reading requires the use of an InputStream.
* Use setReader(InputStream) instead.
*/
@TestMethod("testSetReader_Reader")
public void setReader(Reader reader) throws CDKException {
throw new CDKException("Invalid method call; use SetReader(InputStream) instead.");
}
@TestMethod("testSetReader_InputStream")
public void setReader(InputStream input) throws CDKException {
this.input = input;
}
/**
* Initializes this reader.
*/
private void init() {
boolean success = false;
// If JAXP is prefered (comes with Sun JVM 1.4.0 and higher)
if (!success) {
try {
javax.xml.parsers.SAXParserFactory spf = javax.xml.parsers.SAXParserFactory.newInstance();
spf.setNamespaceAware(true);
javax.xml.parsers.SAXParser saxParser = spf.newSAXParser();
parser = saxParser.getXMLReader();
logger.info("Using JAXP/SAX XML parser.");
success = true;
} catch (Exception e) {
logger.warn("Could not instantiate JAXP/SAX XML reader!");
logger.debug(e);
}
}
// Aelfred is first alternative.
if (!success) {
try {
parser = (XMLReader)this.getClass().getClassLoader().
loadClass("gnu.xml.aelfred2.XmlReader").
newInstance();
logger.info("Using Aelfred2 XML parser.");
success = true;
} catch (Exception e) {
logger.warn("Could not instantiate Aelfred2 XML reader!");
logger.debug(e);
}
}
// Xerces is second alternative
if (!success) {
try {
parser = (XMLReader)this.getClass().getClassLoader().
loadClass("org.apache.xerces.parsers.SAXParser").
newInstance();
logger.info("Using Xerces XML parser.");
success = true;
} catch (Exception e) {
logger.warn("Could not instantiate Xerces XML reader!");
logger.debug(e);
}
}
if (!success) {
logger.error("Could not instantiate any XML parser!");
}
}
@TestMethod("testAccepts")
public boolean accepts(Class classObject) {
Class[] interfaces = classObject.getInterfaces();
for (int i=0; i<interfaces.length; i++) {
if (IChemFile.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* Reads a IChemObject of type object from input.
* Supported types are: ChemFile.
*
* @param object type of requested IChemObject
* @return the content in a ChemFile object
*/
public IChemObject read(IChemObject object) throws CDKException {
if (object instanceof IChemFile) {
return (IChemObject)readChemFile();
} else {
throw new CDKException("Only supported is reading of ChemFile objects.");
}
}
// private functions
/**
* Reads a ChemFile object from input.
*
* @return ChemFile with the content read from the input
*/
private IChemFile readChemFile() {
IChemFile cf = null;
try {
parser.setFeature("http://xml.org/sax/features/validation", false);
logger.info("Deactivated validation");
} catch (SAXException e) {
logger.warn("Cannot deactivate validation.");
}
INChIHandler handler = new INChIHandler();
parser.setContentHandler(handler);
try {
parser.parse(new InputSource(input));
cf = handler.getChemFile();
} catch (IOException e) {
logger.error("IOException: ", e.getMessage());
logger.debug(e);
} catch (SAXException saxe) {
logger.error("SAXException: ", saxe.getClass().getName());
logger.debug(saxe);
}
return cf;
}
@TestMethod("testClose")
public void close() throws IOException {
input.close();
}
}