/**
 * @file    appendAnnotation.java
 * @brief   Adds annotation to a model and a species
 * @author  Akira Funahashi (translated from libSBML C++ examples (using other Java examples provided by Nicolas Rodriguez))
 * @author  Akiya Jouraku
 *
 * $Id: appendAnnotation.java 13075 2011-03-01 03:58:36Z mhucka $
 * $HeadURL: http://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/examples/java/appendAnnotation.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.libsbmlConstants;
import org.sbml.libsbml.CVTerm;
import org.sbml.libsbml.Date;
import org.sbml.libsbml.ModelCreator;
import org.sbml.libsbml.ModelHistory;
import org.sbml.libsbml.SBMLWriter;
import org.sbml.libsbml.Species;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLReader;
 

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

    SBMLDocument d;
    SBMLReader reader     = new SBMLReader();
    SBMLWriter writer     = new SBMLWriter();

    d = reader.readSBML(args[0]);

    long errors = d.getNumErrors();

    if (errors > 0)
    {
      println("Read Error(s):");
      d.printErrors();
      println("Correct the above and re-run.");
    }
	else
	{
	    String model_history_annotation = 
	       "<annotation>\n" +
	       "  <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
	       "    <rdf:Description rdf:about=\"#\">\n" +
	       "      <dc:creator rdf:parseType=\"Resource\">\n" +
	       "        <rdf:Bag>\n" +
	       "          <rdf:li rdf:parseType=\"Resource\">\n" +
	       "            <vCard:N rdf:parseType=\"Resource\">\n" +
	       "              <vCard:Family>Keating</vCard:Family>\n" +
	       "              <vCard:Given>Sarah</vCard:Given>\n" +
	       "            </vCard:N>\n" +
	       "            <vCard:EMAIL>sbml-team@caltech.edu</vCard:EMAIL>\n" +
	       "            <vCard:ORG>\n" +
	       "              <vCard:Orgname>University of Hertfordshire</vCard:Orgname>\n" + 
	       "            </vCard:ORG>\n" +
	       "          </rdf:li>\n" +
	       "        </rdf:Bag>\n" +
	       "      </dc:creator>\n" +
	       "      <dcterms:created rdf:parseType=\"Resource\">\n" +
	       "        <dcterms:W3CDTF>1999-11-13T06:54:32Z</dcterms:W3CDTF>\n" +
	       "      </dcterms:created>\n" +
	       "      <dcterms:modified rdf:parseType=\"Resource\">\n" +
	       "        <dcterms:W3CDTF>2007-11-31T06:54:00-02:00</dcterms:W3CDTF>\n" +
	       "      </dcterms:modified>\n" +
	       "    </rdf:Description>\n" +
	       "  </rdf:RDF>\n" +
	       "</annotation>\n";

	    d.getModel().appendAnnotation(model_history_annotation);
	    /*
	     * The above code can be replaced by the following code.
	     *
         ModelHistory h = new ModelHistory();

         ModelCreator c = new ModelCreator();
         c.setFamilyName("Keating");
         c.setGivenName("Sarah");
         c.setEmail("sbml-team@caltech.edu");
         c.setOrganisation("University of Hertfordshire");

         h.addCreator(c);

         Date date = new Date("1999-11-13T06:54:32");
         Date date2 = new Date("2007-11-31T06:54:00-02:00");

         h.setCreatedDate(date);
         h.setModifiedDate(date2);

         d.getModel().setModelHistory(h);
         *
         */
	    
	    long n = d.getModel().getNumSpecies();

	    if (n > 0)
	    { 
	      Species s = d.getModel().getSpecies(0);

	      String cvterms_annotation =
	        "<annotation>\n" +
	        "  <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
	        "    <rdf:Description rdf:about=\"#\">\n" +
	        "      <bqbiol:isVersionOf>\n" +
	        "        <rdf:Bag>\n" +
	        "          <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n" +
	        "          <rdf:li rdf:resource=\"http://www.ebi.ac.uk/interpro/#IPR002394\"/>\n" +
	        "        </rdf:Bag>\n" +
	        "      </bqbiol:isVersionOf>\n" +
	        "      <bqbiol:is>\n" +
	        "        <rdf:Bag>\n" +
	        "          <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005895\"/>\n" +
	        "        </rdf:Bag>\n" +
	        "      </bqbiol:is>\n" +
	        "    </rdf:Description>\n" +
	        "  </rdf:RDF>\n" +
	        "</annotation>\n";

	      s.appendAnnotation(cvterms_annotation);
	      
	      /*
	       * The above code can be replaced by the following code.
	       *
          CVTerm cv = new CVTerm();
          cv.setQualifierType(libsbmlConstants.BIOLOGICAL_QUALIFIER);
          cv.setBiologicalQualifierType(libsbmlConstants.BQB_IS_VERSION_OF);
          cv.addResource("http://www.geneontology.org/#GO:0005892");

          CVTerm cv2 = new CVTerm();
          cv2.setQualifierType(libsbmlConstants.BIOLOGICAL_QUALIFIER);
          cv2.setBiologicalQualifierType(libsbmlConstants.BQB_IS);
          cv2.addResource("http://www.geneontology.org/#GO:0005895");

          CVTerm cv1 = new CVTerm();
          cv1.setQualifierType(libsbmlConstants.BIOLOGICAL_QUALIFIER);
          cv1.setBiologicalQualifierType(libsbmlConstants.BQB_IS_VERSION_OF);
          cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394");

          s.addCVTerm(cv);
          s.addCVTerm(cv2);
          s.addCVTerm(cv1);
	       * 
	       */
	    }
	}
	writer.writeSBML(d, args[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
  {
    String varname;
    String shlibname;

    if (System.getProperty("os.name").startsWith("Mac OS"))
    {
      varname = "DYLD_LIBRARY_PATH";    // We're on a Mac.
      shlibname = "'libsbmlj.jnilib'";
    }
    else
    {
      varname = "LD_LIBRARY_PATH";      // We're not on a Mac.
      shlibname = "'libsbmlj.so' and/or 'libsbml.so'";
    }

    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:");
      e.printStackTrace();
      System.err.println("Please check the value of your " + varname +
                         " 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 " + shlibname + " library file and the" +
                         " 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'.");
      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);
    }
  }
}
