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/* 
 * Copyright (C) 2008  Miguel Rojas 
 *               2014  Mark B Vine (orcid:0000-0002-7794-0426)
 *
 *  Contact: [email protected]
 *
 *  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.
 *
 *  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.reaction;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.dict.Dictionary;
import org.openscience.cdk.dict.DictionaryDatabase;
import org.openscience.cdk.dict.EntryReact;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.reaction.type.parameters.IParameterReact;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

/**
 * The base class for all chemical reactions objects in this cdk.
 * It provides methods for adding parameters
 *
 * @author         Miguel Rojas
 *
 * @cdk.created    2008-02-01
 * @cdk.module     reaction
 * @cdk.set        reaction-types
 * @cdk.githash
 */
@TestClass("org.openscience.cdk.reaction.ReactionEngineTest")
public class ReactionEngine {

    private static ILoggingTool    logger = LoggingToolFactory.createLoggingTool(ReactionEngine.class);

    private Dictionary             dictionary;
    public HashMap paramsMap;

    public IReactionMechanism      mechanism;

    public List   paramsMap2;

    /**
     * Constructor of the ReactionEngine object.
     */
    public ReactionEngine() {

        try {
            IReactionProcess reaction = (IReactionProcess) this;
            EntryReact entry = initiateDictionary("reaction-processes", (IReactionProcess) reaction);
            initiateParameterMap2(entry);
            reaction.setParameterList(getParameterList());
            extractMechanism(entry);
        } catch (Exception e) {
            e.printStackTrace();
        }

    }

    /**
     * Extract the mechanism necessary for this reaction.
     *
     * @param entry  The EntryReact object
     */
    private void extractMechanism(EntryReact entry) {
        String mechanismName = "org.openscience.cdk.reaction.mechanism." + entry.getMechanism();
        try {
            mechanism = (IReactionMechanism) this.getClass().getClassLoader().loadClass(mechanismName).newInstance();
            logger.info("Loaded mechanism: ", mechanismName);
        } catch (ClassNotFoundException exception) {
            logger.error("Could not find this IReactionMechanism: ", mechanismName);
            logger.debug(exception);
        } catch (InstantiationException | IllegalAccessException exception) {
            logger.error("Could not load this IReactionMechanism: ", mechanismName);
            logger.debug(exception);
        }
    }

    /**
     * Open the Dictionary OWLReact.
     *
     * @param nameDict  Name of the Dictionary
     * @param reaction  The IReactionProcess
     * @return          The entry for this reaction
     */
    private EntryReact initiateDictionary(String nameDict, IReactionProcess reaction) {
        DictionaryDatabase db = new DictionaryDatabase();
        dictionary = db.getDictionary(nameDict);
        String entryString = reaction.getSpecification().getSpecificationReference();
        entryString = entryString.substring(entryString.indexOf('#') + 1, entryString.length());

        return (EntryReact) dictionary.getEntry(entryString.toLowerCase());
    }

    /**
     * Creates a map with the name and type of the parameters.
     */
    private void initiateParameterMap2(EntryReact entry) {
        List> paramDic = entry.getParameterClass();

        paramsMap2 = new ArrayList();
        for (Iterator> it = paramDic.iterator(); it.hasNext();) {
            List param = it.next();
            String paramName = "org.openscience.cdk.reaction.type.parameters." + param.get(0);
            try {
                IParameterReact ipc = (IParameterReact) this.getClass().getClassLoader().loadClass(paramName)
                        .newInstance();
                ipc.setParameter(Boolean.parseBoolean(param.get(1)));
                ipc.setValue(param.get(2));

                logger.info("Loaded parameter class: ", paramName);
                paramsMap2.add(ipc);
            } catch (ClassNotFoundException exception) {
                logger.error("Could not find this IParameterReact: ", paramName);
                logger.debug(exception);
            } catch (InstantiationException | IllegalAccessException exception) {
                logger.error("Could not load this IParameterReact: ", paramName);
                logger.debug(exception);
            }
        }
    }

    /**
     * Returns the current parameter Map for this reaction.
     *
     * Must be done before calling
     * calculate as the parameters influence the calculation outcome.
     *
     * @param params A List of Objects containing the parameters for this reaction.
     * 				 The key must be included into the Dictionary reacton-processes
     * @throws CDKException if invalid number of type of parameters are passed to it
     *
     * @see #getParameterList
     */
    @TestMethod(value = "testSetParameterList_List")
    public void setParameterList(List params) throws CDKException {
        paramsMap2 = params;
    }

    /**
     * Returns the current parameter values.
     *
     * @return A List of Object containing the name and the type of the parameter
     * @see #setParameterList
     * */
    @TestMethod(value = "testGetParameterList")
    public List getParameterList() {
        return paramsMap2;
    }

    /**
     * Return the IParameterReact if it exists given the class.
     *
     * @param paramClass The class
     * @return           The IParameterReact
     */
    @TestMethod(value = "testGetParameterClass_Class")
    public IParameterReact getParameterClass(Class paramClass) {
        for (Iterator it = paramsMap2.iterator(); it.hasNext();) {
            IParameterReact ipr = it.next();
            if (ipr.getClass().equals(paramClass)) return ipr;
        }

        return null;
    }

}