/**
 * @file    unsetNotes.java
 * @brief   Unsets notes for each element
 * @author  Akira Funahashi (translated from libSBML C++ examples (using other Java examples provided by Nicolas Rodriguez))
 * @author  Akiya Jouraku
 *
 * <!--------------------------------------------------------------------------
 * This sample program is distributed under a different license than the rest
 * of libSBML.  This program uses the open-source MIT license, as follows:
 *
 * Copyright (c) 2013-2017 by the California Institute of Technology
 * (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
 * and the University of Heidelberg (Germany), with support from the National
 * Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
 *
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the "Software"),
 * to deal in the Software without restriction, including without limitation
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,
 * and/or sell copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
 * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 * DEALINGS IN THE SOFTWARE.
 *
 * Neither the name of the California Institute of Technology (Caltech), nor
 * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
 * of Heidelberg, nor the names of any contributors, may be used to endorse
 * or promote products derived from this software without specific prior
 * written permission.
 * ------------------------------------------------------------------------ -->
 */


import org.sbml.libsbml.Compartment;
import org.sbml.libsbml.Constraint;
import org.sbml.libsbml.Event;
import org.sbml.libsbml.InitialAssignment;
import org.sbml.libsbml.ModifierSpeciesReference;
import org.sbml.libsbml.Parameter;
import org.sbml.libsbml.SBMLWriter;
import org.sbml.libsbml.Species;
import org.sbml.libsbml.SpeciesReference;
import org.sbml.libsbml.SpeciesType;
import org.sbml.libsbml.EventAssignment;
import org.sbml.libsbml.FunctionDefinition;
import org.sbml.libsbml.KineticLaw;
import org.sbml.libsbml.Model;
import org.sbml.libsbml.Reaction;
import org.sbml.libsbml.Rule;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLReader;
import org.sbml.libsbml.UnitDefinition;
 

public class unsetNotes
{
  public static void main (String[] args)
  {        
    if (args.length != 2)
    {
      println("Usage: java unsetNotes <input-filename> <output-filename>");
      System.exit(1);
    }

    String filename       = args[0];
    SBMLDocument document;
    SBMLReader reader     = new SBMLReader();
    SBMLWriter writer     = new SBMLWriter();

    document = reader.readSBML(filename);

    long errors = document.getNumErrors();

    if (errors > 0)
    {
      document.printErrors();
      System.exit((int)errors);
    }

    Model m = document.getModel();
    m.unsetNotes();

    for(int i=0; i < m.getNumReactions(); i++)
    {
      Reaction re = m.getReaction(i);
      re.unsetNotes();

      for(int j=0; j < re.getNumReactants(); j++)
      { 
        SpeciesReference rt = re.getReactant(j);
        rt.unsetNotes();
      }

      for(int j=0; j < re.getNumProducts(); j++)
      { 
        SpeciesReference rt = re.getProduct(j);
        rt.unsetNotes();
      }

      for(int j=0; j < re.getNumModifiers(); j++)
      { 
        ModifierSpeciesReference md = re.getModifier(j);
        md.unsetNotes();
      }

      if(re.isSetKineticLaw())
      { 
        KineticLaw kl = re.getKineticLaw();
        kl.unsetNotes();

        /* Parameter */
        for(int j=0; j < kl.getNumParameters(); j++)
        { 
          Parameter pa = kl.getParameter(j);
          pa.unsetNotes();
        }
      }
    }
    
    for(int i=0; i < m.getNumSpecies(); i++)
    {
      Species sp = m.getSpecies(i);
      sp.unsetNotes();
    }   
    
    for(int i=0; i < m.getNumCompartments(); i++)
    { 
      Compartment sp = m.getCompartment(i);
      sp.unsetNotes();
    }   
    
    for(int i=0; i < m.getNumFunctionDefinitions(); i++)
    {
      FunctionDefinition sp = m.getFunctionDefinition(i);
      sp.unsetNotes();
    }

    for(int i=0; i < m.getNumUnitDefinitions(); i++)
    {
      UnitDefinition sp = m.getUnitDefinition(i);
      sp.unsetNotes();
    }

    for(int i=0; i < m.getNumParameters(); i++)
    {
      Parameter sp = m.getParameter(i);
      sp.unsetNotes();
    }

    for(int i=0; i < m.getNumRules(); i++)
    {
      Rule sp = m.getRule(i);
      sp.unsetNotes();
    }
    
    for(int i=0; i < m.getNumInitialAssignments(); i++)
    {
      InitialAssignment sp = m.getInitialAssignment(i);
      sp.unsetNotes();
    }

    for(int i=0; i < m.getNumEvents(); i++)
    { 
      Event sp = m.getEvent(i);
      sp.unsetNotes();

      for(int j=0; j < sp.getNumEventAssignments(); j++)
      {
        EventAssignment ea = sp.getEventAssignment(j);
        ea.unsetNotes();
      }
    }
    
    for(int i=0; i < m.getNumSpeciesTypes(); i++)
    {
      SpeciesType sp = m.getSpeciesType(i);
      sp.unsetNotes();
    }

    for(int i=0; i < m.getNumConstraints(); i++)
    {
      Constraint sp = m.getConstraint(i);
      sp.unsetNotes();
    }

    writer.writeSBML(document, args[1]);
    System.exit((int)errors);
  }

  static void println (String msg)
  {
    System.out.println(msg);
  }


  /**
   * Loads the SWIG-generated libSBML Java module when this class is
   * loaded, or reports a sensible diagnostic message about why it failed.
   */
  static
  {
    try
    {
      System.loadLibrary("sbmlj");
      // For extra safety, check that the jar file is in the classpath.
      Class.forName("org.sbml.libsbml.libsbml");
    }
    catch (UnsatisfiedLinkError e)
    {
      System.err.println("Error encountered while attempting to load libSBML:");
      System.err.println("Please check the value of your "
                         + (System.getProperty("os.name").startsWith("Mac OS")
                            ? "DYLD_LIBRARY_PATH" : "LD_LIBRARY_PATH") +
                         " environment variable and/or your" +
                         " 'java.library.path' system property (depending on" +
                         " which one you are using) to make sure it list the" +
                         " directories needed to find the " +
                         System.mapLibraryName("sbmlj") + " library file and" +
                         " libraries it depends upon (e.g., the XML parser).");
      System.exit(1);
    }
    catch (ClassNotFoundException e)
    {
      System.err.println("Error: unable to load the file 'libsbmlj.jar'." +
                         " It is likely that your -classpath command line " +
                         " setting or your CLASSPATH environment variable " +
                         " do not include the file 'libsbmlj.jar'.");
      e.printStackTrace();

      System.exit(1);
    }
    catch (SecurityException e)
    {
      System.err.println("Error encountered while attempting to load libSBML:");
      e.printStackTrace();
      System.err.println("Could not load the libSBML library files due to a"+
                         " security exception.\n");
      System.exit(1);
    }
  }
}

