/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2002-2007 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.config.atomtypes;
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.List;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
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;
/**
* XML Reader for the CDKBasedAtomTypeConfigurator.
*
* @see org.openscience.cdk.config.CDKBasedAtomTypeConfigurator
*
* @cdk.module core
* @cdk.githash
*/
@TestClass("org.openscience.cdk.config.atomtypes.AtomTypeReaderTest")
public class AtomTypeReader {
private XMLReader parser;
private Reader input;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(AtomTypeReader.class);
/**
* Instantiates the XML based AtomTypeReader.
*
* @param input The Reader to read the IAtomType's from.
*/
public AtomTypeReader(Reader input) {
this.init();
this.input = input;
}
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 exception) {
logger.warn("Could not instantiate JAXP/SAX XML reader!");
logger.debug(exception);
}
}
// 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 exception) {
logger.warn("Could not instantiate Aelfred2 XML reader!");
logger.debug(exception);
}
}
// 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 exception) {
logger.warn("Could not instantiate Xerces XML reader!");
logger.debug(exception);
}
}
if (!success) {
logger.error("Could not instantiate any XML parser!");
}
}
/**
* Reads the atom types from the data file.
*
* @param builder The IChemObjectBuilder used to create new IAtomType's.
* @return a List with atom types. Is empty if some reading error occured.
*/
@TestMethod("testReadAtomTypes2,testReadAtomTypes_CDK,testReadAtomTypes_FF,testReadAtomTypes_IChemObjectBuilder")
public List<IAtomType> readAtomTypes(IChemObjectBuilder builder) {
List<IAtomType> isotopes = new ArrayList<IAtomType>();
try {
parser.setFeature("http://xml.org/sax/features/validation", false);
logger.info("Deactivated validation");
} catch (SAXException exception) {
logger.warn("Cannot deactivate validation: ", exception.getMessage());
logger.debug(exception);
}
AtomTypeHandler handler = new AtomTypeHandler(builder);
parser.setContentHandler(handler);
try {
parser.parse(new InputSource(input));
isotopes = handler.getAtomTypes();
} catch (IOException exception) {
logger.error("IOException: ",exception.getMessage());
logger.debug(exception);
} catch (SAXException saxe) {
logger.error("SAXException: ", saxe.getMessage());
logger.debug(saxe);
}
return isotopes;
}
}