LibSBML printMath.java

/**
 * @file    printMath.java
 * @brief   Prints Rule, Reaction, and Event formulas in a given SBML Document
 * @author  Nicolas Rodriguez (translated from libSBML C++ examples)
 * @author  Sarah Keating
 * @author  Ben Bornstein
 * @author  Michael Hucka
 *
 * 
 */


import org.sbml.libsbml.ASTNode;
import org.sbml.libsbml.Event;
import org.sbml.libsbml.Delay;
import org.sbml.libsbml.Trigger;
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.libsbml;
 

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

    String filename       = args[0];
    SBMLReader reader     = new SBMLReader();
    SBMLDocument document;
    Model        model;
    int          level, version;

    document = reader.readSBML(filename);

    if (document.getNumErrors() > 0)
    {
      document.printErrors();
      println("Printing skipped.  Please correct the above problems first.");
      System.exit(1);
    }

    model = document.getModel();

    if (model == null)
    {
      println("There does not appear to be a model in this file");
      System.exit(0);
    }

    level   = (int) document.getLevel();
    version = (int) document.getVersion();

    println("File: " + filename +
            " (Level " + level + ", version " + version + ")");

    printMath(model);
  }

 
  static void printFunctionDefinition (int n, FunctionDefinition fd)
  {
    if (fd.isSetMath())
    {
      print("FunctionDefinition " + n + ", " + fd.getId() + "(");

      ASTNode math = fd.getMath();

      /* Print function arguments. */
      if (math.getNumChildren() > 1)
      {
        print(" " + math.getLeftChild().getName());
                
        for (int i = 1; i < math.getNumChildren() - 1; ++i)
        {
          print(",  " + math.getChild(i).getName());
        }
      }

      print(") := ");

      /* Print function body. */
      if (math.getNumChildren() == 0)
      {
        println("(no body defined)");
      }
      else
      {
        math = math.getChild(math.getNumChildren() - 1);
        println(libsbml.formulaToString(math));
      }
    }
  }


  static void printRuleMath (int n, Rule r)
  {
    if (r.isSetMath())
    {
      String formula = libsbml.formulaToString(r.getMath());
      String var     = r.getVariable();

      if (r.getVariable().length() > 0)
      println("Rule " + n + ", formula: " + var + " = " + formula);
      else
      println("Rule " + n + ", formula: " + formula + " = 0");
    }
  }
    
    
  static void printReactionMath (int n, Reaction r)
  {
    if (r.isSetKineticLaw())
    {
      KineticLaw kl = r.getKineticLaw();
            
      if ( kl.isSetMath() )
      {
        String formula = libsbml.formulaToString( kl.getMath() );
        println("Reaction " + n + ", formula: " + formula);
      }
    }
  }

    
  static void printEventAssignmentMath (int n, EventAssignment ea)
  {
    if (ea.isSetMath())
    {
      String variable = ea.getVariable();
      String formula  = libsbml.formulaToString( ea.getMath() );
            
      println("  EventAssignment " + n + ", trigger: " + variable + " = " +
              formula);
    }
  }


  static void printEventMath (int n, Event e)
  {
    String formula;


    if (e.isSetDelay())
    {
      formula = libsbml.formulaToString(e.getDelay().getMath());
      println("Event " + n + " delay: " + formula);
    }

    if (e.isSetTrigger())
    {
      formula = libsbml.formulaToString(e.getTrigger().getMath());
      println("Event " + n + " trigger: " + formula);
    }

    for (int i = 0; i < e.getNumEventAssignments(); ++i)
    {
      printEventAssignmentMath(i + 1, e.getEventAssignment(i));
    }

    println("\n");
  }
    
    
  static void printMath (Model model)
  {
    for (int n = 0; n < model.getNumFunctionDefinitions(); ++n)
    {
      printFunctionDefinition(n + 1, model.getFunctionDefinition(n));
      println("");
    }

    for (int n = 0; n < model.getNumRules(); ++n)
    {
      printRuleMath(n + 1, model.getRule(n));
      println("");
    }

    for (int n = 0; n < model.getNumReactions(); ++n)
    {
      printReactionMath(n + 1, model.getReaction(n));
      println("");
    }

    for (int n = 0; n < model.getNumEvents(); ++n)
    {
      printEventMath(n + 1, model.getEvent(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
  {
    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);
    }
  }
}

LibSBML, an application programming interface (API) library for SBML.

SBML Team http://www.sbml.org/ sbml-team@googlegroups.com