/**
 * @file    printUnits.java
 * @brief   Prints some unit information about the model
 * @author  Akira Funahashi (translated from libSBML C++ examples (using other Java examples provided by Nicolas Rodriguez))
 * @author  Sarah Keating
 * @author  Michael Hucka
 *
 * $Id: printUnits.java 8704 2009-01-04 02:26:05Z mhucka $
 * $HeadURL: http://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/examples/java/printUnits.java $
 *
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 */


import org.sbml.libsbml.libsbml;
import org.sbml.libsbml.Model;
import org.sbml.libsbml.ModelCreator;
import org.sbml.libsbml.ModelHistory;
import org.sbml.libsbml.SBMLWriter;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLReader;
import org.sbml.libsbml.Species; 
import org.sbml.libsbml.Compartment; 
import org.sbml.libsbml.Parameter; 
import org.sbml.libsbml.InitialAssignment; 
import org.sbml.libsbml.Rule; 
import org.sbml.libsbml.Reaction; 
import org.sbml.libsbml.KineticLaw; 
import org.sbml.libsbml.SpeciesReference; 
import org.sbml.libsbml.Event;
import org.sbml.libsbml.EventAssignment; 
import org.sbml.libsbml.UnitDefinition;

public class printUnits
{
  public static void main (String[] args)
  {        
    if (args.length != 1)
    {
      println("\nUsage: java printUnits filename\n");
      System.exit(1);
    }

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

    SBMLDocument d = reader.readSBML(filename);

    if (d.getNumErrors() > 0)
    {
      println("Encountered the following SBML errors:");
      d.printErrors();
      System.exit(1);
    }

    Model model = d.getModel();

    if (model == null)
    {
      println("No model present.");
      System.exit(1);
    }


    for (int n = 0; n < model.getNumCompartments(); n++)
    {
      Compartment c = model.getCompartment(n);

      println("Compartment #" + (n+1) + " --");
      println("  id in model: " + c.getId());

      printUD(c.getDerivedUnitDefinition());
    }
    
    for (int n = 0; n < model.getNumSpecies(); n++)
    {
      Species s = model.getSpecies(n);

      println("Species #" + (n+1) + " --");
      println("  id in model: " + s.getId());

      printUD(s.getDerivedUnitDefinition());
    }

    for (int n = 0; n < model.getNumParameters(); n++)
    {
      Parameter p = model.getParameter(n);

      println("Parameter #" + (n+1) + " --");
      println("  id in model: " + p.getId());

      printUD(p.getDerivedUnitDefinition());
    }

    for (int n = 0; n < model.getNumInitialAssignments(); n++)
    {
      InitialAssignment ia = model.getInitialAssignment(n);

      println("InitialAssignment #" + (n+1) + " --");
      println("  id in model: " + ia.getId());

      printUD(ia.getDerivedUnitDefinition());

      if (ia.containsUndeclaredUnits())
      {
        println(" undeclared parameters?: yes");
      }
      else
      {
        println(" undeclared parameters?: no");
      }

      print("\n");
    }
    
    for (int n = 0; n < model.getNumRules(); n++)
    {
      Rule r = model.getRule(n);

      println("Rule #" + (n+1) + " --");
      println("  id in model: " + r.getId());

      printUD(r.getDerivedUnitDefinition());

      if (r.containsUndeclaredUnits())
      {
        println(" undeclared parameters?: yes");
      }
      else
      {
        println(" undeclared parameters?: no");
      }

      print("\n");
    }

    for (int n = 0; n < model.getNumEvents(); n++)
    {
      Event e = model.getEvent(n);

      println("Event #" + (n+1) + " --");
      println("  id in model: " + e.getId());
      
      if (e.isSetDelay())
      {
        println("Delay:");

        printUD(e.getDelay().getDerivedUnitDefinition());

        if (e.getDelay().containsUndeclaredUnits())
        {
          println(" undeclared parameters?: yes");
        }
        else
        {
          println(" undeclared parameters?: no");
        }

        print("\n");

        for (int nn = 0; nn < e.getNumEventAssignments(); nn++)
        {
          EventAssignment ea = e.getEventAssignment(nn);

          println("EventAssignment #" + (n+1) + " --");
          println("  id in model: " + ea.getId());

          printUD(ea.getDerivedUnitDefinition());

          if (ea.containsUndeclaredUnits())
          {
            println(" undeclared parameters?: yes");
          }
          else
          {
            println(" undeclared parameters?: no");
          }

          print("\n");

        }
      }
    }

    for (int n = 0; n < model.getNumReactions(); n++)
    {
      Reaction rn = model.getReaction(n);

      println("Reaction #" + (n+1) + " --");
      println("  id in model: " + rn.getId());

      if (rn.isSetKineticLaw())
      {
        printUD(rn.getKineticLaw().getDerivedUnitDefinition());

        if (rn.getKineticLaw().containsUndeclaredUnits())
        {
          println(" undeclared parameters?: yes");
        }
        else
        {
          println(" undeclared parameters?: no");
        }
      }
      print("\n");
      for (int nn = 0; nn < rn.getNumReactants(); nn++)
      {
        SpeciesReference sr = rn.getReactant(nn);

        if (sr.isSetStoichiometryMath())
        {
          println("Reactant #" + (n+1) + " --");
          println("  id in model: " + sr.getSpecies());

          printUD(sr.getStoichiometryMath().getDerivedUnitDefinition());

          if (sr.getStoichiometryMath().containsUndeclaredUnits())
          {
            println(" undeclared parameters?: yes");
          }
          else
          {
            println(" undeclared parameters?: no");
          }
       
          print("\n");
        }
      }
      for (int nn = 0; nn < rn.getNumProducts(); nn++)
      {
        SpeciesReference sr = rn.getProduct(nn);

        if (sr.isSetStoichiometryMath())
        {
          println("Product #" + (n+1) + " --");
          println("  id in model: " + sr.getSpecies());

          printUD(sr.getStoichiometryMath().getDerivedUnitDefinition());

          if (sr.getStoichiometryMath().containsUndeclaredUnits())
          {
            println(" undeclared parameters?: yes");
          }
          else
          {
            println(" undeclared parameters?: no");
          }
       
          print("\n");
        }
      }
    }

  }

  static void printUD (UnitDefinition ud)
  {
    for (int p = 0; p < ud.getNumUnits(); p++)
    {
      int kind = ud.getUnit(p).getKind();
      int exp = ud.getUnit(p).getExponent();
      print(libsbml.UnitKind_toString(kind) + "(exponent = " +  exp + ")");

      if ( p + 1 < ud.getNumUnits())
      {
        print(", ");
      }
    }
    print("\n\n");
  }

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

  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
  {
    String varname;

    if (System.getProperty("mrj.version") != null)
      varname = "DYLD_LIBRARY_PATH";	// We're on a Mac.
    else
      varname = "LD_LIBRARY_PATH";	// We're not on a Mac.

    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: could not link with the libSBML library."+
			 "  It is likely\nyour " + varname +
			 " environment variable does not include\nthe"+
			 " directory containing the libsbml library file.");
      System.exit(1);
    }
    catch (ClassNotFoundException e)
    {
      System.err.println("Error: unable to load the file libsbmlj.jar."+
			 "  It is likely\nyour " + varname + " environment"+
			 " variable or CLASSPATH variable\ndoes not include"+
			 " the directory containing the libsbmlj.jar file.");
      System.exit(1);
    }
    catch (SecurityException e)
    {
      System.err.println("Could not load the libSBML library files due to a"+
			 " security exception.");
    }
  }
}
