package uk.ac.ebi.intenz.domain.enzyme;
   
   import java.util.ArrayList;
   import java.util.Iterator;
   import java.util.List;
   import java.util.Set;
   import java.util.SortedSet;
   import java.util.TreeSet;
   
  import uk.ac.ebi.biobabel.util.collections.OperatorSet;
  import uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant;
  import uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant;
  import uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant;
  import uk.ac.ebi.intenz.domain.constants.Status;
  import uk.ac.ebi.intenz.domain.constants.View;
  import uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant;
  import uk.ac.ebi.intenz.domain.exceptions.EnzymeNameException;
  import uk.ac.ebi.intenz.domain.exceptions.EnzymeReactionException;
  import uk.ac.ebi.intenz.domain.exceptions.EnzymeReferenceException;
  import uk.ac.ebi.intenz.domain.history.HistoryGraph;
  import uk.ac.ebi.intenz.domain.history.HistoryNode;
  import uk.ac.ebi.intenz.domain.reference.Reference;
  import uk.ac.ebi.rhea.domain.Reaction;
  
  /**
   * This class stores the information of an IntEnz enzyme.
   * <p/>
   * Such an enzyme includes information from three different sources:
   * <p/>
   * <ul>
   * <li>NC-IUBMB (the official data)</li>
   * <li>enzyme.dat (Amos' enzyme file)</li>
   * <li>BRENDA (enzyme database from the University of Cologne)</li>
   * </ul>
   *
   * @author Michael Darsow
   * @version $Revision: 1.4 $ $Date: 2009/04/20 13:44:24 $
   */
  public class EnzymeEntry {
  
    /**
     * The enzyme's unique ID.
     */
    private Long id;
  
    /**
     * If an enzyme gets approved it must have a valid EC number.
     */
    private EnzymeCommissionNumber ec;
  
    /**
     * An enzyme belongs to a class of enzymes.
     */
    private String className;
  
    /**
     * An enzyme belongs to a subclass of a class of enzymes.
     */
    private String subclassName;
  
    /**
     * The sub-subclass is the lowest hierarchical level to which an enzyme belongs.
     */
    private String subSubclassName;
  
    /**
     * The common name of an enzyme.
     */
    private List<EnzymeName> commonNames;
  
    /**
     * The systematic name of this enzyme.
     */
    private EnzymeName systematicName;
  
    /**
     * Synonyms will be ordered by their order number internally.
     */
    private List<EnzymeName> synonyms;
  
    /**
     * An enzyme may catalyse more than one reaction.
     * @deprecated use enzymaticReactions istead
     */
    private List<Reaction> reactions;
  
    /**
     * Map to reactions catalyzed by this enzyme.
     */
    private EnzymaticReactions enzymaticReactions;
  
    /**
     * List of all cofactors.
     */
    private Set<Object> cofactors;
  
    /**
     * Stores links of this enzyme.
     */
   private SortedSet<EnzymeLink> links;
 
   /**
    * Some enzymes contain comments.
    */
   private List<EnzymeComment> comments;
 
   /**
    * At least one reference must be present to describe the enzyme.
    */
   private List<Reference> references;
 
   /**
    * The note can be added by a curator but it will not be publicly visible.
    */
   private String note;
 
   /**
    * Stores the enzyme's history as a graph for all history events stored in the database (since 2002).
    */
   private HistoryGraph historyGraph;
 
   /**
    * The status of this enzyme (can be suggested, proposed or approved).
    */
   private Status status;
 
   /**
    * The source of the enzyme (can be IUBMB, SIB, BRENDA or INTENZ).
    */
   private EnzymeSourceConstant source;
 
   /**
    * A flag to indicate whether this enzyme is isActive (not transferred or deleted) or not.
    */
   private boolean isActive;
 
   /**
    * Has this enzyme been lazy-loaded or does it contain the whole set of information?
    */
   private boolean isGhost;
 
   /**
    * The default source is <code>INTENZ</code>.
    * Every new instance is active by default.
    */
   @SuppressWarnings("unchecked")
   public EnzymeEntry() {
     id = new Long(-1);
     ec = EnzymeCommissionNumber.UNDEF;
     className = "";
     subclassName = "";
     subSubclassName = "";
     commonNames = new ArrayList<EnzymeName>();
     systematicName = EnzymeName.UNDEF;
     reactions = new ArrayList<Reaction>();
     cofactors = new OperatorSet();
     synonyms = new ArrayList<EnzymeName>();
     links = new TreeSet<EnzymeLink>();
     comments = new ArrayList<EnzymeComment>();
     references = new ArrayList<Reference>();
     note = "";
     HistoryNode currentNode = new HistoryNode();
     currentNode.setEnzymeEntry(this);
     historyGraph = new HistoryGraph(currentNode);
     status = Status.SUGGESTED;
     source = EnzymeSourceConstant.INTENZ;
     isActive = true;
     isGhost = false;
   }
 
   /**
    * Adds a reaction to the list of reactions.
    * <p/>
    * Duplicates are not stored.
    *
    * @param reaction The reaction to be added.
    * @throws NullPointerException if <code>reaction</code> is <code>null</code>.
    * @deprecated use addEnzymaticReaction instead
    */
   public void addReaction(Reaction reaction) {
     if (reaction == null) throw new NullPointerException("Parameter 'reaction' must not be null.");
     for (Iterator<Reaction> it = reactions.iterator(); it.hasNext();) {
       Reaction storedReaction = it.next();
       if (storedReaction.equals(reaction)) return;
     }
 
     reactions.add(reaction);
   }
 
     /**
      * Adds a reaction to the list of alternative reactions.
      * @param reaction
      * @param view
      * @param iubmb the IUBMB flag.
      */
     public void addEnzymaticReaction(Reaction reaction, String view,
     		boolean iubmb){
         if (enzymaticReactions == null)
             enzymaticReactions = new EnzymaticReactions();
         enzymaticReactions.add(reaction, view, iubmb);
     }
 
   /**
    * Adds a cofactor to the list of cofactors.
    * <p/>
    * Duplicates are not stored.
    *
    * @param cofactor The cofactor to be added.
    * @throws NullPointerException if <code>cofactor</code> is <code>null</code>.
    * @deprecated use {@link #addCofactor(Object)} instead
    */
   public void addCofactor(Cofactor cofactor) {
     if (cofactor == null)
         throw new NullPointerException("Parameter 'cofactor' must not be null.");
     if (!cofactors.contains(cofactor))
         cofactors.add(cofactor);
   }
 
   /**
    * Adds a cofactor to the list of cofactors.
    * @param cofactor A <code>Cofactor</code> or <code>OperatorSet</code> object.
    */
   public void addCofactor(Object cofactor){
 	  if (cofactor == null)
 		  throw new NullPointerException("Parameter 'cofactor' must not be null.");
 	  if (!(cofactor instanceof Cofactor) && !(cofactor instanceof OperatorSet))
 		  throw new IllegalArgumentException("The cofactor class is " + cofactor.getClass());
 	  cofactors.add(cofactor);
   }
 
   /**
    * Removes a reaction from the list of reactions.
    *
    * @param equation The reaction to be removed.
    * @throws NullPointerException if <code>equation</code> is <code>null</code>.
    * @deprecated use removeEnzymaticReaction instead
    */
   public void removeReaction(String equation) {
     if (equation == null) throw new NullPointerException("Parameter 'equation' must not be null.");
     for (Iterator<Reaction> it = reactions.iterator(); it.hasNext();) {
       Reaction reaction = it.next();
       if (reaction.getTextualRepresentation().equals(equation)) {
         reactions.remove(reaction);
         return;
       }
     }
   }
 
     public void removeEnzymaticReaction(Reaction reaction){
         enzymaticReactions.removeReaction(reaction);
     }
 
   /**
    * Removes a cofactor from the list of cofactors.
    *
    * @param cofactorString The cofactor string to be removed.
    * @throws NullPointerException if <code>cofactorString</code> is <code>null</code>.
    * @deprecated use removeCofactor(Object) instead
    */
   public void removeCofactor(String cofactorString) {
       if (cofactorString == null) throw new NullPointerException("Parameter 'cofactorString' must not be null.");
       for (Iterator<Object> it = cofactors.iterator(); it.hasNext();) {
           Cofactor cofactor = (Cofactor) it.next(); // FIXME: what if it is a OperatorSet?
           if (cofactor.getCompound().getName().equals(cofactorString)) {
               cofactors.remove(cofactor);
               return;
           }
       }
   }
 
   /**
    * Removes a cofactor from the list of cofactors.
    * @param cofactor
    * @deprecated use {@link #removeCofactor(Object)} instead
    */
   public void removeCofactor(Cofactor cofactor){
       if (cofactor == null)
           throw new NullPointerException("Cannot remove a null cofactor");
       cofactors.remove(cofactor);
   }
 
 
   /**
    * Removes a cofactor from the list of cofactors.
    * @param cofactor
    */
   public void removeCofactor(Object cofactor){
       if (cofactor == null)
           throw new NullPointerException("Cannot remove a null cofactor");
       cofactors.remove(cofactor);
   }
 
   /**
    * Adds a synonsm to the list of synonyms.
    *
    * @param synonym The synonym to be added.
    * @throws NullPointerException if <code>synonym</code> is <code>null</code>.
    */
   public void addSynonym(EnzymeName synonym) {
     if (synonym == null) throw new NullPointerException("Parameter 'synonym' must not be null.");
     synonyms.add(synonym);
   }
 
   /**
    * Removes a synonsm from the list of synonyms.
    *
    * @param synonym The synonym to be removed.
    * @throws NullPointerException if <code>synonym</code> is <code>null</code>.
    */
   public void removeSynonym(String synonym) {
     if (synonym == null) throw new NullPointerException("Parameter 'synonym' must not be null.");
     synonyms.remove(synonym);
   }
 
   /**
    * Adds a link to the list of additional links.
    * <p/>
    * Duplicates are not stored.
    *
    * @param link The link to be added.
    * @throws NullPointerException if <code>link</code> is <code>null</code>.
    */
   public void addLink(EnzymeLink link) {
     if (link == null) throw new NullPointerException("Parameter 'link' must not be null.");
     // Don't save duplicates.
     if (!links.contains(link)) links.add(link);
   }
 
   /**
    * Removes a link from the list of additional links.
    *
    * @param link The link to be removed.
    * @throws NullPointerException if <code>link</code> is <code>null</code>.
    */
   public void removeLink(EnzymeLink link) {
     if (link == null) throw new NullPointerException("Parameter 'link' must not be null.");
     links.remove(link);
   }
 
   /**
    * Adds a reference to the list of references.
    *
    * @param reference The reference to be added.
    * @throws NullPointerException if <code>reference</code> is <code>null</code>.
    */
   public void addReference(Reference reference) {
     if (reference == null) throw new NullPointerException("Parameter 'reference' must not be null.");
     for (Iterator<Reference> it = references.iterator(); it.hasNext();) {
       Reference storedReference = it.next();
       if (storedReference.equals(reference)) return;
     }
 
     references.add(reference);
   }
 
   /**
    * Removes a reference from the list of references.
    *
    * @param reference The reference to be removed.
    * @throws NullPointerException if <code>reference</code> is <code>null</code>.
    */
   public void removeReference(Reference reference) {
     if (reference == null) throw new NullPointerException("Parameter 'reference' must not be null.");
     for (Iterator<Reference> it = references.iterator(); it.hasNext();) {
       Reference storedReference = it.next();
       if (reference.equals(storedReference)) {
         references.remove(storedReference);
         return;
       }
     }
   }
 
   /**
    * Standard equals method.
    *
    * @param o Object to be compared to this one.
    * @return <code>true</code> if the objects are equal.
    */
     @Override
   public boolean equals(Object o) {
     if (this == o) return true;
     if (!(o instanceof EnzymeEntry)) return false;
 
     final EnzymeEntry enzymeEntry = (EnzymeEntry) o;
 
     if (isActive != enzymeEntry.isActive) return false;
     if (isGhost != enzymeEntry.isGhost) return false;
     if (className != null ? !className.equals(enzymeEntry.className) : enzymeEntry.className != null) return false;
     if (cofactors != null ? !cofactors.equals(enzymeEntry.cofactors) : enzymeEntry.cofactors != null) return false;
     if (comments != null ? !comments.equals(enzymeEntry.comments) : enzymeEntry.comments != null) return false;
     if (commonNames != null ? !commonNames.equals(enzymeEntry.commonNames) : enzymeEntry.commonNames != null) return false;
     if (ec != null ? !ec.equals(enzymeEntry.ec) : enzymeEntry.ec != null) return false;
     if (historyGraph != null ? !historyGraph.equals(enzymeEntry.historyGraph) : enzymeEntry.historyGraph != null) return false;
     if (id != null ? !id.equals(enzymeEntry.id) : enzymeEntry.id != null) return false;
     if (links != null ? !links.equals(enzymeEntry.links) : enzymeEntry.links != null) return false;
     if (note != null ? !note.equals(enzymeEntry.note) : enzymeEntry.note != null) return false;
 //    if (reactions != null ? !reactions.equals(enzymeEntry.reactions) : enzymeEntry.reactions != null) return false;
     if (enzymaticReactions != null ?
         !enzymaticReactions.equals(enzymeEntry.enzymaticReactions) :
 		enzymeEntry.enzymaticReactions != null) return false;
     if (references != null ? !references.equals(enzymeEntry.references) : enzymeEntry.references != null) return false;
     if (source != null ? !source.equals(enzymeEntry.source) : enzymeEntry.source != null) return false;
     if (status != null ? !status.equals(enzymeEntry.status) : enzymeEntry.status != null) return false;
     if (subSubclassName != null ? !subSubclassName.equals(enzymeEntry.subSubclassName) : enzymeEntry.subSubclassName !=
                                                                                          null)
       return false;
     if (subclassName != null ? !subclassName.equals(enzymeEntry.subclassName) : enzymeEntry.subclassName != null) return false;
     if (synonyms != null ? !synonyms.equals(enzymeEntry.synonyms) : enzymeEntry.synonyms != null) return false;
     if (systematicName != null ? !systematicName.equals(enzymeEntry.systematicName) : enzymeEntry.systematicName !=
                                                                                       null)
       return false;
 
     return true;
   }
 
   /**
    * Returns the hash code of this object.
    *
    * @return the hash code of this object.
    */
     @Override
   public int hashCode() {
     int result;
     result = (id != null ? id.hashCode() : 0);
     result = 29 * result + (ec != null ? ec.hashCode() : 0);
     result = 29 * result + (className != null ? className.hashCode() : 0);
     result = 29 * result + (subclassName != null ? subclassName.hashCode() : 0);
     result = 29 * result + (subSubclassName != null ? subSubclassName.hashCode() : 0);
     result = 29 * result + (commonNames != null ? commonNames.hashCode() : 0);
     result = 29 * result + (systematicName != null ? systematicName.hashCode() : 0);
     result = 29 * result + (synonyms != null ? synonyms.hashCode() : 0);
     result = 29 * result + (reactions != null ? reactions.hashCode() : 0);
     result = 29 * result + (cofactors != null ? cofactors.hashCode() : 0);
     result = 29 * result + (links != null ? links.hashCode() : 0);
     result = 29 * result + (comments != null ? comments.hashCode() : 0);
     result = 29 * result + (references != null ? references.hashCode() : 0);
     result = 29 * result + (note != null ? note.hashCode() : 0);
     result = 29 * result + (historyGraph != null ? historyGraph.hashCode() : 0);
     result = 29 * result + (status != null ? status.hashCode() : 0);
     result = 29 * result + (source != null ? source.hashCode() : 0);
     result = 29 * result + (isActive ? 1 : 0);
     result = 29 * result + (isGhost ? 1 : 0);
     return result;
   }
 
   // ----------------  GETTER & SETTER ------------------
 
   public Long getId() {
     return id;
   }
 
   public void setId(Long id) {
     this.id = id;
   }
 
   public EnzymeCommissionNumber getEc() {
     return ec;
   }
 
   /**
    * Sets the EC number.
    *
    * @param ec The new EC number.
    * @throws NullPointerException if <code>ec</code> is <code>null</code>.
    */
   public void setEc(EnzymeCommissionNumber ec) {
     if (ec == null) throw new NullPointerException("Parameter 'ec' must not be null.");
     this.ec = ec;
   }
 
   public String getClassName() {
     return className;
   }
 
   /**
    * Sets the class name.
    *
    * @param className The class name.
    * @throws NullPointerException     if <code>className</code> is <code>null</code>
    * @throws IllegalArgumentException if <code>className</code> is empty.
    */
   public void setClassName(String className) {
     if (className == null) throw new NullPointerException("Parameter 'className' must not be null.");
     if (className.equals("")) throw new IllegalArgumentException("Parameter 'className' must not be empty.");
     this.className = className;
   }
 
   public String getSubclassName() {
     return subclassName;
   }
 
   /**
    * Sets the subclass name.
    *
    * @param subclassName The subclass name.
    * @throws NullPointerException     if <code>subclassName</code> is <code>null</code>
    * @throws IllegalArgumentException if <code>subclassName</code> is empty.
    */
   public void setSubclassName(String subclassName) {
     if (subclassName == null) throw new NullPointerException("Parameter 'subclassName' must not be null.");
     if (subclassName.equals("")) throw new IllegalArgumentException("Parameter 'subclassName' must not be empty.");
     this.subclassName = subclassName;
   }
 
   public String getSubSubclassName() {
     return subSubclassName;
   }
 
   /**
    * Sets the sub-subclass name.
    *
    * @param subSubclassName The sub-subclass name.
    * @throws NullPointerException if <code>subSubclassName</code> is <code>null</code>.
    */
   public void setSubSubclassName(String subSubclassName) {
     if (subSubclassName == null) throw new NullPointerException("Parameter 'subSubclassName' must not be null.");
     this.subSubclassName = subSubclassName;
   }
 
   public List<EnzymeName> getCommonNames() {
     return commonNames;
   }
   
   /**
    * @return the IntEnz common name.
    */
   public EnzymeName getCommonName(){
 	  return getCommonName(null);
   }
 
   /**
    * Returns the first common name which <code>view</code> value matches the
    * parameter's view value.
    * @param view web view (defaults to INTENZ)
    * @return the common name.
    * @throws IllegalArgumentException if <code>view</code> is not either
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.INTENZ},
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.IUBMB} or
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.SIB} .
    */
   public EnzymeName getCommonName(EnzymeViewConstant view) {
     if (view == null) view = EnzymeViewConstant.INTENZ;
     if (view != EnzymeViewConstant.INTENZ && view != EnzymeViewConstant.IUBMB && view != EnzymeViewConstant.SIB)
       throw new IllegalArgumentException("Parameter 'view' must be either 'EnzymeViewConstant.INTENZ', 'EnzymeViewConstant.IUBMB' or 'EnzymeViewConstant.SIB'");
     if (commonNames == null || commonNames.size() == 0) return EnzymeName.UNDEF;
     for (int iii = 0; iii < commonNames.size(); iii++) {
       EnzymeName enzymeName = commonNames.get(iii);
       if (view.toString().equals(EnzymeViewConstant.INTENZ.toString()) &&
           EnzymeViewConstant.isInIntEnzView(enzymeName.getView().toString()))
         return enzymeName;
       if (view.toString().equals(EnzymeViewConstant.IUBMB.toString()) &&
           EnzymeViewConstant.isInIUBMBView(enzymeName.getView().toString()))
         return enzymeName;
       if (view.toString().equals(EnzymeViewConstant.SIB.toString()) &&
           EnzymeViewConstant.isInSIBView(enzymeName.getView().toString()))
         return enzymeName;
     }
     return commonNames.get(0);
   }
 
   /**
    * Sets the list of common names.
    * <p/>
    * An enzyme must have at least one or at most two common names.
    * Empty strings will be omitted.
    *
    * @param commonNames List of common names.
    * @throws NullPointerException if <code>commonNames</code> is <code>null</code>.
    * @throws EnzymeNameException  if the list of common names does contain less than 1 or more than 2 common names or
    *                              if the type of a name in the list is not defined as {@link EnzymeNameTypeConstant.COMMON_NAME}.
    */
   public void setCommonNames(List<EnzymeName> commonNames) throws EnzymeNameException {
     if (commonNames == null) throw new NullPointerException("Parameter 'commonNames' must not be null.");
     if (commonNames.size() > 2)
       throw new EnzymeNameException("At most two common names can be part of this list.");
     for (int iii = 0; iii < commonNames.size(); iii++) {
       EnzymeName enzymeName = commonNames.get(iii);
       if (enzymeName.getType() != EnzymeNameTypeConstant.COMMON_NAME)
         throw new EnzymeNameException("The name's type " +
                                       "must be of type 'uk.ac.ebi.intenz.domain.constants.EnzymeNameTypeConstant.COMMON_NAME'.");
       if (enzymeName.getName().equals("")) commonNames.remove(iii--);
     }
     if (commonNames.size() < 1)
       throw new EnzymeNameException("At least one common name must be part of this list.");
 
     this.commonNames = commonNames;
   }
 
   /**
    * Adds a common name to the list of common names.
    * <p/>
    * If the list already contains two elements an {@link uk.ac.ebi.intenz.webapp.exceptions.EnzymeNameException} is thrown.
    * Empty strings will be omitted.
    *
    * @param commonName The common name to be added.
    * @throws EnzymeNameException if the list of common names already contains two elements.
    */
   public void addCommonName(EnzymeName commonName) throws EnzymeNameException {
     if (commonName == null) throw new NullPointerException("Parameter 'commonName' must not be null.");
     if (commonNames.size() == 2) throw new EnzymeNameException("The list of common names already contains two common names.");
     if (commonName.getName().equals("")) return;
     commonNames.add(commonName);
   }
 
   public EnzymeName getSystematicName() {
     return systematicName;
   }
 
   /**
    * Sets the systematic name of the enzyme.
    *
    * @param systematicName The systematic name.
    * @throws NullPointerException if <code>systematicName</code> is <code>null</code>.
    */
   public void setSystematicName(EnzymeName systematicName) {
     if (systematicName == null) throw new NullPointerException("Parameter 'systematicName' must not be null.");
     this.systematicName = systematicName;
   }
 
   /** @deprecated use getEnzymaticReactions instead */
   public List<Reaction> getReactions() {
     return reactions;
   }
 
   /**
    * Returns a list of reactions which <code>view</code> values match the parameter's view value.
    *
    * @return the {@link java.util.ArrayList} of reactions.
    * @throws NullPointerException     if <code>view</code> is <code>null</code>.
    * @throws IllegalArgumentException if <code>view</code> is not either
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.INTENZ},
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.IUBMB} or
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.SIB} .
    * @deprecated use {@link #getReactions(View)} or {@link #getReactions(String)} instead.
    */
   public List<Reaction> getReactions(EnzymeViewConstant view) {
 	  return getReactions(view.toString());
   }
   
   public List<Reaction> getReactions(String view){
     View theView = View.valueOf(view);
     return getReactions(theView);
   }
 
   public List<Reaction> getReactions(View view){
 	return enzymaticReactions.getReactions(view);
   }
   
   /**
    * Gets a collection of enzymatic reactions for the given view.
    * @param view a web view.
    * @return an {@link EnzymaticReactions} object containing only reactions in
    * 		the given view.
    * @since 4.3.0
    */
   public EnzymaticReactions getEnzymaticReactions(View view){
 	  return enzymaticReactions.forView(view);
   }
 
   /**
    * Sets the list of reactions.
    * <p/>
    * Empty reaction strings will be omitted.
    *
    * @param reactions The list of reactions.
    * @throws EnzymeReactionException if the list of reactions is empty.
    */
   public void setReactions(List<Reaction> reactions) throws EnzymeReactionException {
     if (reactions == null) throw new NullPointerException("Parameter 'reactions' must not be null.");
     if (reactions.isEmpty())
         throw new EnzymeReactionException("At least one reaction must be part of this list.");
     for (int iii = 0; iii < reactions.size(); iii++) {
       Reaction reaction = reactions.get(iii);
       if (reaction.getTextualRepresentation().equals("")) reactions.remove(iii--);
     }
     this.reactions = reactions;
   }
 
   public EnzymaticReactions getEnzymaticReactions(){
 	  return enzymaticReactions;
   }
 
   public void setEnzymaticReactions(EnzymaticReactions enzymaticReactions) {
 	this.enzymaticReactions = enzymaticReactions;
   }
 
   public Set<Object> getCofactors() {
     return cofactors;
   }
 
   public void setCofactors(Set<Object> cofactors) {
     this.cofactors = cofactors;
   }
 
   public List<EnzymeName> getSynonyms() {
     return synonyms;
   }
   
   public List<EnzymeName> getSynonyms(String view){
 	  View theView = View.valueOf(view);
 	  return getSynonyms(theView);
   }
   
   public List<EnzymeName> getSynonyms(View theView){
 	  if (synonyms == null) return new ArrayList<EnzymeName>();
 	  if (synonyms.size() == 0) return synonyms;
 	  boolean isInView = false;
 	  List<EnzymeName> names = new ArrayList<EnzymeName>();
 	  for (EnzymeName name : synonyms){
 		  switch (theView) {
 		  case INTENZ:
 			  isInView = name.getView().isInIntEnzView();
 			  break;
 		  case IUBMB:
 			  isInView = name.getView().isInIUBMBView();
 			  break;
 		  case SIB:
 			  isInView = name.getView().isInSIBView();
 			  break;
 		  }
 		  if (isInView) names.add(name);
 	  }
 	  return names;
   }
 
   /**
    * Returns a list of synonyms which <code>view</code> values match the parameter's view value.
    *
    * @return the {@link java.util.ArrayList} of synonyms.
    * @throws NullPointerException     if <code>view</code> is <code>null</code>.
    * @throws IllegalArgumentException if <code>view</code> is not either
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.INTENZ},
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.IUBMB} or
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.SIB} .
    * @deprecated use {@link #getSynonyms(String)} or {@link #getSynonyms(View)} instead.
    */
   public List<EnzymeName> getSynonyms(EnzymeViewConstant view) {
     return getSynonyms(view.toString());
   }
 
   /**
    * Sets the list of synonyms.
    *
    * @param synonyms The list of synonyms.
    * @throws NullPointerException if <code>synonyms</code> is <code>null</code>.
    */
   public void setSynonyms(List<EnzymeName> synonyms) {
     if (synonyms == null) throw new NullPointerException("Parameter 'synonyms' must not be null.");
     this.synonyms = synonyms;
   }
 
   public List<EnzymeComment> getComments() {
     return comments;
   }
   
   public List<EnzymeComment> getComments(String view){
 	  View theView = View.valueOf(view);
 	  return getComments(theView);
   }
 
   public List<EnzymeComment> getComments(View theView){
 	  if (comments == null) return new ArrayList<EnzymeComment>();
 	  if (comments.size() == 0) return comments;
 	  boolean isInView = false;
 	  List<EnzymeComment> commentsInView = new ArrayList<EnzymeComment>();
 	  for (EnzymeComment comment : comments){
 		  switch (theView) {
 		  case INTENZ:
 			  isInView = comment.getView().isInIntEnzView();
 			  break;
 		  case IUBMB:
 			  isInView = comment.getView().isInIUBMBView();
 			  break;
 		  case SIB:
 			  isInView = comment.getView().isInSIBView();
 			  break;
 		  }
 		  if (isInView) commentsInView.add(comment);
 	  }
 	  return commentsInView;
   }
 
   /**
    * Returns a list of comments which <code>view</code> values match the parameter's view value.
    *
    * @return the {@link java.util.ArrayList} of comments.
    * @throws NullPointerException     if <code>view</code> is <code>null</code>.
    * @throws IllegalArgumentException if <code>view</code> is not either
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.INTENZ},
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.IUBMB} or
    *                                  {@link uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant.SIB} .
    * @deprecated use {@link #getComments(String)} instead
    * */
   public List<EnzymeComment> getComments(EnzymeViewConstant view) {
     if (view == null) throw new NullPointerException("Parameter 'view' must not be null.");
     if (view != EnzymeViewConstant.INTENZ && view != EnzymeViewConstant.IUBMB && view != EnzymeViewConstant.SIB)
       throw new IllegalArgumentException("Parameter 'view' must be either 'EnzymeViewConstant.INTENZ', 'EnzymeViewConstant.IUBMB' or 'EnzymeViewConstant.SIB'");
     if (comments == null) return new ArrayList<EnzymeComment>();
     if (comments.size() == 0) return comments;
     List<EnzymeComment> groupedComments = new ArrayList<EnzymeComment>();
     for (int iii = 0; iii < comments.size(); iii++) {
       EnzymeComment comment = comments.get(iii);
       if (view.toString().equals(EnzymeViewConstant.INTENZ.toString()) &&
           EnzymeViewConstant.isInIntEnzView(comment.getView().toString())) {
         groupedComments.add(comment);
         continue;
       }
       if (view.toString().equals(EnzymeViewConstant.IUBMB.toString()) &&
           EnzymeViewConstant.isInIUBMBView(comment.getView().toString())) {
         groupedComments.add(comment);
         continue;
       }
       if (view.toString().equals(EnzymeViewConstant.SIB.toString()) &&
           EnzymeViewConstant.isInSIBView(comment.getView().toString())) {
         groupedComments.add(comment);
         continue;
       }
     }
     return groupedComments;
   }
 
   /**
    * Sets the list of comments.
    *
    * @param comments The list of comments.
    * @throws NullPointerException if <code>comments</code> is <code>null</code>.
    */
   public void setComments(List<EnzymeComment> comments) {
     if (comments == null) throw new NullPointerException("Parameter 'comments' must not be null.");
     this.comments = comments;
   }
 
   public SortedSet<EnzymeLink> getLinks() {
     return links;
   }
   
   public SortedSet<EnzymeLink> getLinks(String view){
 	  View theView = View.valueOf(view);
 	  return getLinks(theView);
   }
   
   /**
    * CAS numbers for IntEnz and IUBMB views.
    * @return
    */
   public SortedSet<EnzymeLink> getCasNumbers(){
 	  SortedSet<EnzymeLink> cas = new TreeSet<EnzymeLink>();
 	  for (EnzymeLink link : links){
 		  if (link.getXrefDatabaseConstant().equals(XrefDatabaseConstant.CAS)){
 			  cas.add(link);
 		  }
 	  }
 	  return cas;
   }
 
   public SortedSet<EnzymeLink> getUniProtLinks(){
       SortedSet<EnzymeLink> uniProtLinks = new TreeSet<EnzymeLink>();
  	  for (EnzymeLink link : links){
 		  if (link.getXrefDatabaseConstant().equals(XrefDatabaseConstant.SWISSPROT))
             uniProtLinks.add(link);
       }
       return uniProtLinks;
   }
   
   /**
    * Return the links to entries in external databases.
    * These exclude:
    * <ul>
    * <li>CAS numbers (they are just identifiers, without
    * any URL to go to). Use getCasNumbers.</li>
    * <li>UniProt links. Use getUniProtLinks.</li>
    * </ul>
    * @param theView
    * @return
    */
   public SortedSet<EnzymeLink> getLinks(View theView){
 	  boolean isInView = false;
 	  SortedSet<EnzymeLink> linksInView = new TreeSet<EnzymeLink>();
 	  for (EnzymeLink link : links){
 		  if (link.getXrefDatabaseConstant().equals(XrefDatabaseConstant.CAS) ||
               link.getXrefDatabaseConstant().equals(XrefDatabaseConstant.SWISSPROT))
 			  continue;
 		  switch (theView) {
 		  case INTENZ:
 			  isInView = link.getView().isInIntEnzView();
 			  break;
 		  case IUBMB:
 			  isInView = link.getView().isInIUBMBView();
 			  break;
 		  case SIB:
 			  isInView = link.getView().isInSIBView();
 			  break;
 		  }
 		  if (isInView) linksInView.add(link);
 	  }
 	  // Automatic links (not in the database):
       if (status.equals(Status.PRELIMINARY)){
           if (theView == View.INTENZ)
               linksInView.add(EnzymeLink.EXPASY);
       } else {
           switch (theView) {
           case INTENZ:
               linksInView.add(EnzymeLink.CSA);
               linksInView.add(EnzymeLink.NC_IUBMB);
               linksInView.add(EnzymeLink.UNIPATHWAY);
               linksInView.add(EnzymeLink.EXPLORENZ);
               linksInView.add(EnzymeLink.METACYC);
           case IUBMB:
               linksInView.add(EnzymeLink.PDB);
               linksInView.add(EnzymeLink.BRENDA);
               linksInView.add(EnzymeLink.EXPASY);
               linksInView.add(EnzymeLink.KEGG);
               break;
           }
       }
 	  return linksInView;
   }
 
   /**
    * 
    * @param view
    * @return
    * @deprecated use {@link #getLinks(String)} instead
    */
   public SortedSet<EnzymeLink> getLinks(EnzymeViewConstant view) {
     if (view == null) throw new NullPointerException("Parameter 'view' must not be null.");
     if (view != EnzymeViewConstant.INTENZ && view != EnzymeViewConstant.IUBMB && view != EnzymeViewConstant.SIB)
       throw new IllegalArgumentException("Parameter 'view' must be either 'EnzymeViewConstant.INTENZ', 'EnzymeViewConstant.IUBMB' or 'EnzymeViewConstant.SIB'");
     if (links == null) return new TreeSet<EnzymeLink>();
     if (links.size() == 0) return links;
     SortedSet<EnzymeLink> groupedLinks = new TreeSet<EnzymeLink>();
     for (Iterator<EnzymeLink> it = links.iterator(); it.hasNext();) {
       EnzymeLink link = it.next();
       if (view.toString().equals(EnzymeViewConstant.INTENZ.toString()) &&
           EnzymeViewConstant.isInIntEnzView(link.getView().toString())) {
         groupedLinks.add(link);
         continue;
       }
       if (view.toString().equals(EnzymeViewConstant.IUBMB.toString()) &&
           EnzymeViewConstant.isInIUBMBView(link.getView().toString())) {
         groupedLinks.add(link);
         continue;
       }
       if (view.toString().equals(EnzymeViewConstant.SIB.toString()) &&
           EnzymeViewConstant.isInSIBView(link.getView().toString())) {
         groupedLinks.add(link);
         continue;
       }
     }
     return groupedLinks;
   }
 
   /**
    * Sets the list of links.
    *
    * @param links The list of links.
    * @throws NullPointerException if <code>links</code> is <code>null</code>.
    */
   public void setLinks(SortedSet<EnzymeLink> links) {
     if (links == null) throw new NullPointerException("Parameter 'links' must not be null.");
     this.links = links;
   }
 
   public List<Reference> getReferences() {
     return references;
   }
 
   /**
    * Sets the list of refernces.
    *
    * @param references The list of references.
    * @throws EnzymeReferenceException if <code>references</code> is <code>null</code>.
    */
   public void setReferences(List<Reference> references) throws EnzymeReferenceException {
     if (references == null) throw new NullPointerException("Parameter 'references' must not be null.");
     if (references.size() < 1)
       throw new EnzymeReferenceException("At least one reference must be part of this list.");
     this.references = references;
   }
 
   public String getNote() {
     return note;
   }
 
   /**
    * Sets the note.
    *
    * @param note the note.
    * @throws NullPointerException if <code>note</code> is <code>null</code>.
    */
   public void setNote(String note) {
     if (note == null) throw new NullPointerException("Parameter 'note' must not be null.");
     this.note = note;
   }
 
   public HistoryGraph getHistory() {
     return historyGraph;
   }
 
   /**
    * Sets the history graph.
    *
    * @param historyGraph the history graph.
    * @throws NullPointerException if <code>historyGraph</code> is <code>null</code>.
    */
   public void setHistory(HistoryGraph historyGraph) {
     if (historyGraph == null) throw new NullPointerException("Parameter 'historyGraph' must not be null.");
     this.historyGraph = historyGraph;
   }
 
   public Status getStatus() {
     return status;
   }
 
   /**
    * Sets the enzyme's status.
    *
    * @param status The enzyme's status.
    * @throws NullPointerException if <code>status</code> is <code>null</code>.
    */
   public void setStatus(Status status) {
     if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");
     this.status = status;
   }
 
   public EnzymeSourceConstant getSource() {
     return source;
   }
 
   /**
    * Sets the enzyme's source.
    *
    * @param source The enzyme's source.
    * @throws NullPointerException if <code>source</code> is <code>null</code>.
    */
   public void setSource(EnzymeSourceConstant source) {
     if (source == null) throw new NullPointerException("Parameter 'source' must not be null.");
     this.source = source;
   }
 
   public boolean isActive() {
     return isActive;
   }
 
   public void setActive(boolean active) {
     this.isActive = active;
   }
 
   public boolean isGhost() {
     return isGhost;
   }
 
   public void setGhost(boolean ghost) {
     isGhost = ghost;
   }
 
   public boolean hasNames() {
     if (commonNames != null && commonNames.size() > 0) return true;
     if (synonyms != null && synonyms.size() > 0) return true;
     if (systematicName != null && !systematicName.getName().equals("")) return true;
     return false;
   }
 
   // ------------------- PRIVATE METHODS ------------------------
 
 }