LibSBML readSBML.java

/**
 * @file    readSBML.java
 * @brief   Similar to validateSBML, but without the validation
 * @author  Nicolas Rodriguez (translated from libSBML C++ examples)
 * @author  Ben Bornstein
 * @author  Michael Hucka
 *
 * 
 */


import java.io.File;

import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLReader;
 

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

    String filename = args[0];
    SBMLReader reader     = new SBMLReader();
    SBMLDocument document;
    long start, stop, size;

    start    = System.currentTimeMillis();
    document = reader.readSBML(filename);
    stop     = System.currentTimeMillis();

    size     = new File(args[0]).length();

    println("        filename: " + filename);
    println("       file size: " + size);
    println("  read time (ms): " + (stop - start));
    println("        error(s): " + document.getNumErrors());

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


  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