/* Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
 *                    2014  Mark B Vine (orcid:0000-0002-7794-0426)
 *
 * 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 org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MDLRXNFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.Iterator;
import java.util.StringTokenizer;

/**
 * Reads a molecule from an MDL RXN file {@cdk.cite DAL92}.
 *
 * @cdk.module io
 * @cdk.githash
 * @cdk.iooptions
 *
 * @author     Egon Willighagen
 * @cdk.created    2003-07-24
 *
 * @cdk.keyword    file format, MDL RXN
 * @deprecated Use V2000 or V3000
 */
@Deprecated
public class MDLRXNReader extends DefaultChemObjectReader {

    BufferedReader              input  = null;
    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLRXNReader.class);

    /**
     * Constructs a new MDLReader that can read Molecule from a given Reader.
     *
     * @param  in  The Reader to read from
     */
    public MDLRXNReader(Reader in) {
        this(in, Mode.RELAXED);
    }

    public MDLRXNReader(Reader in, Mode mode) {
        if (in instanceof BufferedReader) {
            input = (BufferedReader) in;
        } else {
            input = new BufferedReader(in);
        }
        super.mode = mode;
    }

    public MDLRXNReader(InputStream input) {
        this(input, Mode.RELAXED);
    }

    public MDLRXNReader(InputStream input, Mode mode) {
        this(new InputStreamReader(input), mode);
    }

    public MDLRXNReader() {
        this(new StringReader(""));
    }

    @Override
    public IResourceFormat getFormat() {
        return MDLRXNFormat.getInstance();
    }

    @Override
    public void setReader(Reader input) throws CDKException {
        if (input instanceof BufferedReader) {
            this.input = (BufferedReader) input;
        } else {
            this.input = new BufferedReader(input);
        }
    }

    @Override
    public void setReader(InputStream input) throws CDKException {
        setReader(new InputStreamReader(input));
    }

    @Override
    public boolean accepts(Class<? extends IChemObject> classObject) {
        if (IChemFile.class.equals(classObject)) return true;
        if (IChemModel.class.equals(classObject)) return true;
        if (IReaction.class.equals(classObject)) return true;
        if (IReactionSet.class.equals(classObject)) return true;
        Class<?>[] interfaces = classObject.getInterfaces();
        for (int i = 0; i < interfaces.length; i++) {
            if (IChemModel.class.equals(interfaces[i])) return true;
            if (IChemFile.class.equals(interfaces[i])) return true;
            if (IReaction.class.equals(interfaces[i])) return true;
            if (IReactionSet.class.equals(interfaces[i])) return true;
        }
        Class superClass = classObject.getSuperclass();
        if (superClass != null) return this.accepts(superClass);
        return false;
    }

    /**
      * Takes an object which subclasses IChemObject, e.g.Molecule, and will read
      * this (from file, database, internet etc). If the specific implementation
      * does not support a specific IChemObject it will throw an Exception.
      *
      * @param  object                              The object that subclasses
      *      IChemObject
      * @return                                     The IChemObject read
      * @exception  CDKException
      */
    @Override
    public <T extends IChemObject> T read(T object) throws CDKException {
        if (object instanceof IChemFile) {
            return (T) readChemFile((IChemFile) object);
        } else if (object instanceof IChemModel) {
            return (T) readChemModel((IChemModel) object);
        } else if (object instanceof IReactionSet) {
            return (T) readReactionSet((IReactionSet) object);
        } else if (object instanceof IReaction) {
            return (T) readReaction(object.getBuilder());
        } else {
            throw new CDKException("Only supported are Reaction, ReactionSet, ChemModel and ChemFile, and not "
                    + object.getClass().getName() + ".");
        }
    }

    public boolean accepts(IChemObject object) {
        if (object instanceof IReaction) {
            return true;
        } else if (object instanceof IChemModel) {
            return true;
        } else if (object instanceof IChemFile) {
            return true;
        } else if (object instanceof IReactionSet) {
            return true;
        }
        return false;
    }

    /**
    * Read a ChemFile from a file in MDL RDF format.
    *
    * @param  chemFile The IChemFile
    * @return          The IChemFile that was read from the RDF file.
    */
    private IChemFile readChemFile(IChemFile chemFile) throws CDKException {
        IChemSequence chemSequence = chemFile.getBuilder().newInstance(IChemSequence.class);

        IChemModel chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
        chemSequence.addChemModel(readChemModel(chemModel));
        chemFile.addChemSequence(chemSequence);
        return chemFile;
    }

    /**
    * Read a IChemModel from a file in MDL RDF format.
    *
    * @param  chemModel The IChemModel
    * @return           The IChemModel that was read from the RDF file
    */
    private IChemModel readChemModel(IChemModel chemModel) throws CDKException {
        IReactionSet setOfReactions = chemModel.getReactionSet();
        if (setOfReactions == null) {
            setOfReactions = chemModel.getBuilder().newInstance(IReactionSet.class);
        }
        chemModel.setReactionSet(readReactionSet(setOfReactions));
        return chemModel;
    }

    /**
    * Read a IReactionSet from a file in MDL RDF format.
    *
    * @param  setOfReactions The IReactionSet
    * @return                The IReactionSet that was read from the RDF file
    */
    private IReactionSet readReactionSet(IReactionSet setOfReactions) throws CDKException {

        IReaction r = readReaction(setOfReactions.getBuilder());
        if (r != null) {
            setOfReactions.addReaction(r);
        }

        try {
            String line;
            while ((line = input.readLine()) != null) {
                logger.debug("line: ", line);
                // apparently, this is a SDF file, continue with
                // reading mol files
                if (line.equals("$$$$")) {
                    r = readReaction(setOfReactions.getBuilder());

                    if (r != null) {
                        setOfReactions.addReaction(r);
                    }
                } else {
                    // here the stuff between 'M  END' and '$$$$'
                    if (r != null) {
                        // ok, the first lines should start with '>'
                        String fieldName = null;
                        if (line.startsWith("> ")) {
                            // ok, should extract the field name
                            int index = line.indexOf('<');
                            if (index != -1) {
                                int index2 = line.substring(index).indexOf('>');
                                if (index2 != -1) {
                                    fieldName = line.substring(index + 1, index + index2);
                                }
                            }
                            // end skip all other lines
                            while ((line = input.readLine()) != null && line.startsWith(">")) {
                                logger.debug("data header line: ", line);
                            }
                        }
                        if (line == null) {
                            throw new CDKException("Expecting data line here, but found null!");
                        }
                        String data = line;
                        while ((line = input.readLine()) != null && line.trim().length() > 0) {
                            if (line.equals("$$$$")) {
                                logger.error("Expecting data line here, but found end of molecule: ", line);
                                break;
                            }
                            logger.debug("data line: ", line);
                            data += line;
                            // preserve newlines, unless the line is exactly 80 chars; in that case it
                            // is assumed to continue on the next line. See MDL documentation.
                            if (line.length() < 80) data += "\n";
                        }
                        if (fieldName != null) {
                            logger.info("fieldName, data: ", fieldName, ", ", data);
                            r.setProperty(fieldName, data);
                        }
                    }
                }
            }
        } catch (CDKException cdkexc) {
            throw cdkexc;
        } catch (IOException exception) {
            String error = "Error while parsing SDF";
            logger.error(error);
            logger.debug(exception);
            throw new CDKException(error, exception);
        }

        return setOfReactions;
    }

    /**
     * Read a Reaction from a file in MDL RXN format
     *
     * @return  The Reaction that was read from the MDL file.
     */
    private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
        logger.debug("Reading new reaction");
        int linecount = 0;
        IReaction reaction = builder.newInstance(IReaction.class);
        try {
            input.readLine(); // first line should be $RXN
            input.readLine(); // second line
            input.readLine(); // third line
            input.readLine(); // fourth line
        } catch (IOException exception) {
            logger.debug(exception);
            throw new CDKException("Error while reading header of RXN file", exception);
        }

        int reactantCount = 0;
        int productCount = 0;
        try {
            String countsLine = input.readLine();
            linecount++;
            if (countsLine == null) {
                return null;
            }
            logger.debug("Line " + linecount + ": " + countsLine);
            if (countsLine.startsWith("$$$$")) {
                logger.debug("File is empty, returning empty reaction");
                return reaction;
            }
            /*
             * this line contains the number of reactants and products
             */
            StringTokenizer tokenizer = new StringTokenizer(countsLine);
            reactantCount = Integer.valueOf(tokenizer.nextToken()).intValue();
            logger.info("Expecting " + reactantCount + " reactants in file");
            productCount = Integer.valueOf(tokenizer.nextToken()).intValue();
            logger.info("Expecting " + productCount + " products in file");
        } catch (IOException | NumberFormatException exception) {
            logger.debug(exception);
            throw new CDKException("Error while counts line of RXN file", exception);
        }

        // now read the reactants
        try {
            for (int i = 1; i <= reactantCount; i++) {
                StringBuffer molFile = new StringBuffer();
                input.readLine(); // announceMDLFileLine
                String molFileLine = "";
                do {
                    molFileLine = input.readLine();
                    molFile.append(molFileLine);
                    molFile.append('\n');
                } while (!molFileLine.equals("M  END"));

                // read MDL molfile content
                MDLReader reader = new MDLReader(new StringReader(molFile.toString()));
                IAtomContainer reactant = (IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
                reader.close();

                // add reactant
                reaction.addReactant(reactant);
            }
        } catch (CDKException exception) {
            // rethrow exception from MDLReader
            throw exception;
        } catch (IOException | IllegalArgumentException exception) {
            logger.debug(exception);
            throw new CDKException("Error while reading reactant", exception);
        }

        // now read the products
        try {
            for (int i = 1; i <= productCount; i++) {
                StringBuffer molFile = new StringBuffer();
                input.readLine(); // String announceMDLFileLine =
                String molFileLine = "";
                do {
                    molFileLine = input.readLine();
                    molFile.append(molFileLine);
                    molFile.append('\n');
                } while (!molFileLine.equals("M  END"));

                // read MDL molfile content
                MDLReader reader = new MDLReader(new StringReader(molFile.toString()), super.mode);
                IAtomContainer product = (IAtomContainer) reader.read(builder.newInstance(IAtomContainer.class));
                reader.close();

                // add reactant
                reaction.addProduct(product);
            }
        } catch (CDKException exception) {
            // rethrow exception from MDLReader
            throw exception;
        } catch (IOException | IllegalArgumentException exception) {
            logger.debug(exception);
            throw new CDKException("Error while reading products", exception);
        }

        // now try to map things, if wanted
        logger.info("Reading atom-atom mapping from file");
        // distribute all atoms over two AtomContainer's
        IAtomContainer reactingSide = builder.newInstance(IAtomContainer.class);
        Iterator<IAtomContainer> molecules = reaction.getReactants().atomContainers().iterator();
        while (molecules.hasNext()) {
            reactingSide.add(molecules.next());
        }
        IAtomContainer producedSide = builder.newInstance(IAtomContainer.class);
        molecules = reaction.getProducts().atomContainers().iterator();
        while (molecules.hasNext()) {
            producedSide.add(molecules.next());
        }

        // map the atoms
        int mappingCount = 0;
        //        IAtom[] reactantAtoms = reactingSide.getAtoms();
        //        IAtom[] producedAtoms = producedSide.getAtoms();
        for (int i = 0; i < reactingSide.getAtomCount(); i++) {
            for (int j = 0; j < producedSide.getAtomCount(); j++) {
                IAtom eductAtom = reactingSide.getAtom(i);
                IAtom productAtom = producedSide.getAtom(j);
                if (eductAtom.getProperty(CDKConstants.ATOM_ATOM_MAPPING) != null
                        && eductAtom.getProperty(CDKConstants.ATOM_ATOM_MAPPING).equals(
                                productAtom.getProperty(CDKConstants.ATOM_ATOM_MAPPING))) {
                    reaction.addMapping(builder.newInstance(IMapping.class, eductAtom, productAtom));
                    mappingCount++;
                    break;
                }
            }
        }
        logger.info("Mapped atom pairs: " + mappingCount);

        return reaction;
    }

    @Override
    public void close() throws IOException {
        input.close();
    }
}
