package uk.ac.ebi.intenz.biopax.level2;
   
   import java.io.IOException;
   import java.io.OutputStream;
   import java.lang.reflect.InvocationTargetException;
   import java.util.Collection;
   import org.apache.log4j.Logger;
   import org.biopax.paxtools.model.Model;
   import uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry;
  
  /**
   * Utility class to dump IntEnz entries as BioPAX model.
   * @author rafalcan
   */
  public class Biopax extends uk.ac.ebi.rhea.biopax.level2.Biopax {
  
      private static final Logger LOGGER = Logger.getLogger(Biopax.class);
  
      public static final String INTENZ_PREFIX = "intenz";
      public static final String INTENZ_NS = "http://www.ebi.ac.uk/intenz/#";
  
  	/**
  	 * Creates an empty ontology model with the needed namespaces.
  	 * @return an OWL model.
       *
  	 */
      public static Model createModel(){
  		Model biopaxModel = uk.ac.ebi.rhea.biopax.level2.Biopax.createModel();
  		biopaxModel.setXmlBase(INTENZ_NS);
  		biopaxModel.getNameSpacePrefixMap().put("", INTENZ_NS);
  		biopaxModel.getNameSpacePrefixMap().put(INTENZ_PREFIX, INTENZ_NS);
  		return biopaxModel;
  	}
  
      /**
       * Writes a collection of enzyme entries to an output stream.
       * @param enzymes
       * @param os
       * @throws java.io.IOException
       * @throws java.lang.IllegalAccessException
       * @throws java.lang.reflect.InvocationTargetException
       */
      public static void write(Collection<EnzymeEntry> enzymes, OutputStream os)
      throws IOException, IllegalAccessException, InvocationTargetException {
          Model model = Biopax.createModel();
      	for (EnzymeEntry entry : enzymes) {
              try {
                  new BiopaxCatalysis(entry, model);
                  LOGGER.info("Added to BioPAX model - EC " + entry.getEc());
              } catch(Exception e){
                  LOGGER.error("Unable to convert to BioPAX - EC " + entry.getEc(), e);
              }
          }
          write(model, os);
      }
  }