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CMLWriter.java

/* $Revision$ $Author$ $Date$
 *
 * Copyright (C) 2001-2007  Egon Willighagen <egonw@users.sf.net>
 *                          Stefan Kuhn <shk3@users.sf.net>
 *                          Miguel Rojas-Cherto <miguelrojasch@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;

import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.List;

import nu.xom.Attribute;
import nu.xom.Document;
import nu.xom.Element;
import nu.xom.Serializer;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IPDBPolymer;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionScheme;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.io.cml.CustomSerializer;
import org.openscience.cdk.io.formats.CMLFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.io.setting.StringIOSetting;
import org.openscience.cdk.libio.cml.Convertor;
import org.openscience.cdk.libio.cml.ICMLCustomizer;
import org.openscience.cdk.tools.LoggingTool;

/**
 * Serializes a {@link IMoleculeSet} or a {@link IMolecule} object to CML 2 code.
 * Chemical Markup Language is an XML-based file format {@cdk.cite PMR99}.
 * Output can be redirected to other Writer objects like {@link StringWriter}
 * and {@link FileWriter}. An example:
 *
 * <pre>
 *   StringWriter output = new StringWriter();
 *   boolean makeFragment = true;
 *   CMLWriter cmlwriter = new CMLWriter(output, makeFragment);
 *   cmlwriter.write(molecule);
 *   cmlwriter.close();
 *   String cmlcode = output.toString();
 * </pre>
 *
 * <p>Output to a file called "molecule.cml" can done with:
 *
 * <pre>
 *   FileWriter output = new FileWriter("molecule.cml");
 *   CMLWriter cmlwriter = new CMLWriter(output);
 *   cmlwriter.write(molecule);
 *   cmlwriter.close();
 * </pre>
 *
 * <p>For atoms it outputs: coordinates, element type and formal charge.
 * For bonds it outputs: order, atoms (2, or more) and wedges.
 *
 * @cdk.module       libiocml
 * @cdk.githash
 * @cdk.builddepends xom-1.0.jar
 * @cdk.depends      jumbo50.jar
 * @cdk.require      java1.5+
 * @cdk.bug          1565563
 *
 * @see java.io.FileWriter
 * @see java.io.StringWriter
 *
 * @author Egon Willighagen
 *
 * @cdk.keyword file format, CML
 */
@TestClass("org.openscience.cdk.io.CMLWriterTest")
00112 public class CMLWriter extends DefaultChemObjectWriter {

    private OutputStream output;
    private Writer writer;

    private BooleanIOSetting cmlIds;
    private BooleanIOSetting namespacedOutput;
    private StringIOSetting namespacePrefix;
    private BooleanIOSetting schemaInstanceOutput;
    private StringIOSetting instanceLocation;
    private BooleanIOSetting indent;
    private BooleanIOSetting xmlDeclaration;
    
    private LoggingTool logger;
    
    private List<ICMLCustomizer> customizers = null;

    /**
     * Constructs a new CMLWriter class. Output will be stored in the Writer
     * class given as parameter. The CML code will be valid CML code with a
     * XML header. Only one object can be stored.
     *
     * @param out Writer to redirect the output to.
     */
00136     public CMLWriter(Writer out) {
        this.writer = out;
        output = new OutputStream() {
                  public void write(int anInt) throws IOException {
                        writer.write(anInt);
                  }
        };
        logger = new LoggingTool(this);
        initIOSettings();
    }

    public CMLWriter(OutputStream output) {
        this.output = output;
        writer = null;
        logger = new LoggingTool(this);
        initIOSettings();
    }
    
    public CMLWriter() {
        this(new StringWriter());
    }

    public void registerCustomizer(ICMLCustomizer customizer) {
      if (customizers == null) customizers = new ArrayList<ICMLCustomizer>();
      
      customizers.add(customizer);
      logger.info("Loaded Customizer: ", customizer.getClass().getName());
    }
    
    @TestMethod("testGetFormat")
00166     public IResourceFormat getFormat() {
        return CMLFormat.getInstance();
    }
    
00170     public void setWriter(Writer writer) throws CDKException {
        this.writer = writer;
    }

00174     public void setWriter(OutputStream output) throws CDKException {
      //TODO dont know what the intention here is, but without this line it is not working...
      this.output = output;
      setWriter(new OutputStreamWriter(output));
    }
    
    /**
     * Flushes the output and closes this object
     */
    @TestMethod("testClose")
00184     public void close() throws IOException {
        output.close();
    }

      @TestMethod("testAccepts")
    public boolean accepts(Class classObject) {
            Class[] interfaces = classObject.getInterfaces();
            for (int i=0; i<interfaces.length; i++) {
                  if (IAtom.class.equals(interfaces[i])) return true;
                  if (IBond.class.equals(interfaces[i])) return true;
                  if (ICrystal.class.equals(interfaces[i])) return true;
                  if (IChemModel.class.equals(interfaces[i])) return true;
                  if (IChemFile.class.equals(interfaces[i])) return true;
                  if (IChemSequence.class.equals(interfaces[i])) return true;
                  if (IMoleculeSet.class.equals(interfaces[i])) return true;
                  if (IReactionSet.class.equals(interfaces[i])) return true;
                  if (IReaction.class.equals(interfaces[i])) return true;
            }
            return false;
      }

    /**
     * Serializes the IChemObject to CML and redirects it to the output Writer.
     *
     * @param object A Molecule of MoleculeSet object
     */
00210     public void write(IChemObject object) throws CDKException {
       
        if (!(object instanceof IMolecule) &&
            !(object instanceof IAtomContainer) &&
            !(object instanceof IReaction) &&
            !(object instanceof IReactionSet) &&
            !(object instanceof IMoleculeSet) &&
            !(object instanceof IChemSequence) &&
            !(object instanceof IChemModel) &&
            !(object instanceof IChemFile) &&
            !(object instanceof ICrystal) &&
            !(object instanceof IAtom) &&
            !(object instanceof IBond)) {
             throw new CDKException("Cannot write this unsupported IChemObject: " + object.getClass().getName());
        }

        logger.debug("Writing object in CML of type: ", object.getClass().getName());
        
        customizeJob();
        
        Convertor convertor = new Convertor(
            cmlIds.isSet(), 
            (namespacePrefix.getSetting().length() >0) ? namespacePrefix.getSetting() : null
        );
        // adding the customizer
        if (customizers != null) {
            for (ICMLCustomizer customizer : customizers) {
                  convertor.registerCustomizer(customizer);
            }
        }
        
        // now convert the object
        Element root = null;
        if (object instanceof IPDBPolymer) {
            root = convertor.cdkPDBPolymerToCMLMolecule((IPDBPolymer)object);
      } else if (object instanceof IMolecule) {
            root = convertor.cdkMoleculeToCMLMolecule((IMolecule)object);
        } else if (object instanceof ICrystal) {
            root = convertor.cdkCrystalToCMLMolecule((ICrystal)object);
        } else if (object instanceof IAtom) {
            root = convertor.cdkAtomToCMLAtom(null, (IAtom)object);
        } else if (object instanceof IBond) {
            root = convertor.cdkBondToCMLBond((IBond)object);
        } else if (object instanceof IReaction) {
            root = convertor.cdkReactionToCMLReaction((IReaction)object);
        } else if (object instanceof IReactionScheme){
            root = convertor.cdkReactionSchemeToCMLReactionSchemeAndMoleculeList((IReactionScheme)object);
        } else if (object instanceof IReactionSet) {
            root = convertor.cdkReactionSetToCMLReactionList((IReactionSet)object);
        } else if (object instanceof IMoleculeSet) {
            root = convertor.cdkMoleculeSetToCMLList((IMoleculeSet)object);
        } else if (object instanceof IChemSequence) {
            root = convertor.cdkChemSequenceToCMLList((IChemSequence)object);
        } else if (object instanceof IChemModel) {
            root = convertor.cdkChemModelToCMLList((IChemModel)object);
        } else if (object instanceof IAtomContainer) {
            root = convertor.cdkAtomContainerToCMLMolecule((IAtomContainer)object);
        } else if (object instanceof IChemFile) {
            root = convertor.cdkChemFileToCMLList((IChemFile)object);
        }

        Document doc = new Document(root);
        try {
            Serializer serializer = null;
            if (xmlDeclaration.isSet()) {
                serializer = new Serializer(output, "ISO-8859-1");
            } else {
                serializer = new CustomSerializer(output, "ISO-8859-1");
            }
            if (indent.isSet()) {
                logger.info("Indenting XML output");
                serializer.setIndent(2);
            }
            
            if (schemaInstanceOutput.isSet()) {
                  root.addNamespaceDeclaration("xsi", "http://www.w3.org/2001/XMLSchema-instance");
                  root.addAttribute(new Attribute(
                        "xsi:schemaLocation=",
                        "http://www.w3.org/2001/XMLSchema-instance",
                        "http://www.xml-cml.org/schema/cml2/core " + instanceLocation.getSetting()
                  ));
            }
            
            serializer.write(doc);
        } catch (Exception exception) {
            throw new CDKException("Could not write XML output: " + exception.getMessage(), exception);
        }
    }

    private void initIOSettings() {
        cmlIds = new BooleanIOSetting("CMLIDs", IOSetting.LOW,
          "Should the output use CML identifiers?", 
          "true");

        namespacedOutput = new BooleanIOSetting("NamespacedOutput", IOSetting.LOW,
          "Should the output use namespaced output?", 
          "true");

        namespacePrefix = new StringIOSetting("NamespacePrefix", IOSetting.LOW,
          "What should the namespace prefix be? [empty is no prefix]",
          "");
          
        schemaInstanceOutput = new BooleanIOSetting("SchemaInstance", IOSetting.LOW,
          "Should the output use the Schema-Instance attribute?", 
          "false");
        
        instanceLocation = new StringIOSetting("InstanceLocation", IOSetting.LOW,
          "Where is the schema found?",
          "");

        indent = new BooleanIOSetting("Indenting", IOSetting.LOW,
          "Should the output be indented?", 
          "true");

        xmlDeclaration = new BooleanIOSetting("XMLDeclaration", IOSetting.LOW,
                "Should the output contain an XML declaration?",
                "true");
    }
    
    private void customizeJob() {
        fireIOSettingQuestion(cmlIds);
        fireIOSettingQuestion(namespacedOutput);
        if (namespacedOutput.isSet()) {
            fireIOSettingQuestion(namespacePrefix);
        }
        fireIOSettingQuestion(schemaInstanceOutput);
        if (schemaInstanceOutput.isSet()) {
            fireIOSettingQuestion(instanceLocation);
        }
        fireIOSettingQuestion(indent);
        fireIOSettingQuestion(xmlDeclaration);
    }

00343     public IOSetting[] getIOSettings() {
        IOSetting[] settings = new IOSetting[7];
        settings[0] = cmlIds;
        settings[1] = namespacedOutput;
        settings[2] = namespacePrefix;
        settings[3] = schemaInstanceOutput;
        settings[4] = instanceLocation;
        settings[5] = indent;
        settings[6] = xmlDeclaration;
        return settings;
    }

}

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