package uk.ac.ebi.intenz.domain.enzyme;
   
   import java.util.Map;
   import java.util.StringTokenizer;
   import java.util.TreeMap;
   
   import uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant;
   import uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant;
   import uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant;
  
  /**
   * An enzyme link is used to store cross-reference information.
   * <p/>
   * Most of the links use a static URL which differs only in the EC number used to identify the enzyme.
   * These links can be obtained by accessing the class constants.<br/>
   * Other cross-references contain a static URL but need a different identifier. For example,
   * a SwissProt cross-reference needs a protein accession number. These links are provided
   * via the according factory methods. In case of SwissProt and MIM links it is also possible
   * to provide a name for the protein or disease respectively.<br/>
   * <p/>
   * The terms <i>link</i> and <i>cross-reference</i> are used synonymously.
   * <p/>
   * Instances of this class are immutable.
   *
   * @author Michael Darsow
   * @version $Revision: 1.2 $ $Date: 2008/01/28 12:33:00 $
   */
  public class EnzymeLink implements Comparable<EnzymeLink>, Commented, Viewable {
    /**
     * Static link to the BRENDA database.
     */
    public static final EnzymeLink BRENDA =
  	  new EnzymeLink(XrefDatabaseConstant.BRENDA, XrefDatabaseConstant.BRENDA.getUrl(),
  			  "", "BRENDA", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
    
    /**
     * Link to MetaCyc.
     */
    public static final EnzymeLink METACYC =
  	  new EnzymeLink(XrefDatabaseConstant.METACYC, XrefDatabaseConstant.METACYC.getUrl(),
  			  "", "MetaCyc", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
  
    /**
     * Static link to the KEGG database.
     */
    public static final EnzymeLink KEGG =
  	  new EnzymeLink(XrefDatabaseConstant.KEGG, XrefDatabaseConstant.KEGG.getUrl(),
  			  "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
  
    /**
     * Static link to the ENZYME database at expasy.org.
     */
    public static final EnzymeLink EXPASY =
  	  new EnzymeLink(XrefDatabaseConstant.ENZYME, XrefDatabaseConstant.ENZYME.getUrl(),
  			  "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
  
    /**
     * Static link to the GM pages (NC-IUBMB).
     */
    public static final EnzymeLink NC_IUBMB =
  	  new EnzymeLink(XrefDatabaseConstant.NC_IUBMB, XrefDatabaseConstant.NC_IUBMB.getUrl(),
  			  "", "", EnzymeSourceConstant.IUBMB, EnzymeViewConstant.INTENZ);
  
    /**
     * Static link to the ERGO database.
     * @deprecated the ERGO website is not working any more.
     */
     @Deprecated
    public static final EnzymeLink ERGO =
  	  new EnzymeLink(XrefDatabaseConstant.ERGO, XrefDatabaseConstant.ERGO.getUrl(),
  			  "", "ERGO", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
  
    /**
     * Static link to the ERGO (formerly WIT) database.
     */
    public static final EnzymeLink WIT =
  	  new EnzymeLink(XrefDatabaseConstant.WIT, XrefDatabaseConstant.WIT.getUrl(),
  			  "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
  
    /**
     * Static link to the Gene Ontology database.
     */
    public static final EnzymeLink GO =
  	  new EnzymeLink(XrefDatabaseConstant.GO, XrefDatabaseConstant.GO.getUrl(),
  			  "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
  
    /**
     * Static link to the NIST 74 database.
     */
    public static final EnzymeLink NIST74 =
  	  new EnzymeLink(XrefDatabaseConstant.NIST74, XrefDatabaseConstant.NIST74.getUrl(),
  			  "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
  
    /**
     * Static link to the UM-BBD database.
     */
    public static final EnzymeLink UMBBD =
  	  new EnzymeLink(XrefDatabaseConstant.UMBBD, XrefDatabaseConstant.UMBBD.getUrl(),
  			  "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
 
   /**
    * Static link to the PDB database.
    */
   public static final EnzymeLink PDB =
 	  new EnzymeLink(XrefDatabaseConstant.PDB, XrefDatabaseConstant.PDB.getUrl(),
 			  "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
 
   /**
    * Static link to the CSA database.
    */
   public static final EnzymeLink CSA =
 	  new EnzymeLink(XrefDatabaseConstant.CSA, XrefDatabaseConstant.CSA.getUrl(),
 			  "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
 
   public static final EnzymeLink EXPLORENZ = new EnzymeLink(
     XrefDatabaseConstant.EXPLORENZ,
     XrefDatabaseConstant.EXPLORENZ.getUrl(),
     "", "", EnzymeSourceConstant.IUBMB, EnzymeViewConstant.INTENZ);
 
   public static final EnzymeLink UNIPATHWAY = new EnzymeLink(
     XrefDatabaseConstant.UNIPATHWAY,
     XrefDatabaseConstant.UNIPATHWAY.getUrl(),
     "", "", EnzymeSourceConstant.INTENZ, EnzymeViewConstant.INTENZ);
 
   private static Map<XrefDatabaseConstant, EnzymeLink> STATIC_LINKS;
 
   static {
     STATIC_LINKS = new TreeMap<XrefDatabaseConstant, EnzymeLink>();
     STATIC_LINKS.put(BRENDA.getXrefDatabaseConstant(), BRENDA);
     STATIC_LINKS.put(METACYC.getXrefDatabaseConstant(), METACYC);
     STATIC_LINKS.put(KEGG.getXrefDatabaseConstant(), KEGG);
     STATIC_LINKS.put(EXPASY.getXrefDatabaseConstant(), EXPASY);
     STATIC_LINKS.put(EXPLORENZ.getXrefDatabaseConstant(), EXPLORENZ);
     STATIC_LINKS.put(NIST74.getXrefDatabaseConstant(), NIST74);
     STATIC_LINKS.put(UMBBD.getXrefDatabaseConstant(), UMBBD);
     STATIC_LINKS.put(UNIPATHWAY.getXrefDatabaseConstant(), UNIPATHWAY);
     STATIC_LINKS.put(CSA.getXrefDatabaseConstant(), CSA);
     STATIC_LINKS.put(PDB.getXrefDatabaseConstant(), PDB);
   }
 
   /**
    * All sources are controlled vocabulary.
    */
   private XrefDatabaseConstant xrefDatabaseConstant;
 
   /**
    * Some links have specific URLs.
    */
   private String specificUrl;
 
   /**
    * Some links need an accession number (e.g. EC number).
    */
   private String accession;
 
   /**
    * Some links have name associated (e.g. MIM links).
    */
   private String name;
 
   private EnzymeSourceConstant source;
 
   /**
    * Defines in which view this link will be displayed.
    */
   private EnzymeViewConstant view;
 
     private String dataComment;
 
     /**
    * Object cannot be created outside this class.
    *
    * @param xrefDatabaseConstant The data xrefDatabaseConstant name.
    * @param specificUrl          The URL of the given xrefDatabaseConstant.
    * @param accession            The accession (if needed).
    * @param name                 The name (if available).
    */
   private EnzymeLink(XrefDatabaseConstant xrefDatabaseConstant, String specificUrl, String accession, String name,
                      EnzymeSourceConstant source, EnzymeViewConstant view) {
     this.xrefDatabaseConstant = xrefDatabaseConstant;
     this.specificUrl = specificUrl;
     this.accession = accession;
     this.name = name;
     this.source = source;
     this.view = view;
   }
 
   /**
    * Returns an <code>EnzymeLink</code> instance.
    *
    * @param xrefDatabaseConstant The link's xrefDatabaseConstant.
    * @param specificUrl          The link's URL.
    * @param accession            The accession of this link.
    * @param name                 The name of this link.
    * @return the <code>EnzymeLink</code> instance.
    * @throws NullPointerException     if <code>xrefDatabaseConstant</code> is <code>null</code>.
    * @throws IllegalArgumentException if the arguments are not sufficient to create a link.
    */
   public static EnzymeLink valueOf(XrefDatabaseConstant xrefDatabaseConstant,
 		  String specificUrl, String accession, String name,
           EnzymeSourceConstant source, EnzymeViewConstant view) {
     if (xrefDatabaseConstant == null) throw new NullPointerException("Parameter 'xrefDatabaseConstant' must not be null.");
     if (source == null) throw new NullPointerException("Parameter 'source' must not be null.");
     if (view == null) throw new NullPointerException("Parameter 'view' must not be null.");
 
     // Static links.
 //      if (view.toString().equals("") && STATIC_LINKS.containsKey(xrefDatabaseConstant))
     // Links based on EC number, except when they are passed as accession (BRENDA):
     if (STATIC_LINKS.containsKey(xrefDatabaseConstant)){
     	if (accession == null){
             return STATIC_LINKS.get(xrefDatabaseConstant);
     	} else {
     		// A static link to an EC number, but we have an accession? Preliminary ECs
     		return new EnzymeLink(xrefDatabaseConstant,
     				xrefDatabaseConstant.getUrl(),
     				accession, accession, source, view);
     	}
     }
 
     if ((specificUrl == null || specificUrl.equals("")) && (accession == null || accession.equals("")) &&
         (name == null || name.equals("")))
       throw new IllegalArgumentException("Either parameter specificUrl, accession or name must contain a value.");
 
     return new EnzymeLink(xrefDatabaseConstant, specificUrl, accession, name, source, view);
   }
 
   /**
    * Returns a commented <code>EnzymeLink</code> instance.
    * @param xrefDatabaseConstant
    * @param specificUrl
    * @param accession
    * @param name
    * @param source
    * @param view
    * @param dataComment
    * @return
    */
   public static EnzymeLink valueOf(XrefDatabaseConstant xrefDatabaseConstant, String specificUrl, String accession, String name,
                                    EnzymeSourceConstant source, EnzymeViewConstant view, String dataComment){
       EnzymeLink el = EnzymeLink.valueOf(xrefDatabaseConstant, specificUrl, accession, name, source, view);
       el.setDataComment(dataComment);
       return el;
   }
 
   /**
    * Checks if the given link is a static link.
    *
    * @param databaseConstant The database constant to be checked.
    * @return <code>true</code> if the link is a static link.
    * @throws NullPointerException if <code>link</code> is <code>null</code>.
    */
   public static boolean isStaticLink(XrefDatabaseConstant databaseConstant) {
     if (databaseConstant == null) throw new NullPointerException("Parameter 'databaseConstant' must not be null.");
     return STATIC_LINKS.containsKey(databaseConstant);
   }
 
   public static EnzymeLink getStaticLink(XrefDatabaseConstant databaseConstant) {
     if (databaseConstant == null) throw new NullPointerException("Parameter 'databaseConstant' must not be null.");
     return STATIC_LINKS.get(databaseConstant);
   }
 
   /**
    * Used for ordering links in a collection.
    * <p/>
    * Static and other links are ordered by their xrefDatabaseConstant name,
    * SwissProt and MIM cross-references by their name
    * and PROSITE links by their accession. Other links are ordered by their specific URL
    * if the xrefDatabaseConstant name is the same.
    * Noted: Changed so that only SwissProt compares on the basis of name and OMIM compares on the
    * basis of accession like PROSITE.
    *
    * @param link The object to be compared to this.
    * @return neg, 0 or pos. value to indicate the order of these two objects.
    * @throws NullPointerException if <code>o</code> is <code>null</code>.
    */
   public int compareTo(EnzymeLink link) {
     if (xrefDatabaseConstant == link.getXrefDatabaseConstant()) {
       if (name.equals(link.getName())) {
         if (accession.equals(link.getAccession())) {
           return specificUrl.compareTo(link.getSpecificUrl());
         }
         return accession.compareTo(link.getAccession());
       }
       return name.compareTo(link.getName());
     }
     // NC-IUBMB always listed first:
     return xrefDatabaseConstant.equals(XrefDatabaseConstant.NC_IUBMB)?
         -1 : link.getXrefDatabaseConstant().equals(XrefDatabaseConstant.NC_IUBMB)?
         1 : xrefDatabaseConstant.compareTo(link.getXrefDatabaseConstant());
   }
 
   /**
    * Checks for equality.
    *
    * @param o The object to be compared to this.
    * @return <code>true</code> if <code>o</code> is equal this object.
    */
   public boolean equals(Object o) {
     if (this == o) return true;
     if (!(o instanceof EnzymeLink)) return false;
 
     final EnzymeLink enzymeLink = (EnzymeLink) o;
 
     if (accession != null ? !accession.equals(enzymeLink.accession) : enzymeLink.accession != null) return false;
     if (name != null ? !name.equals(enzymeLink.name) : enzymeLink.name != null) return false;
     if (source != null ? !source.equals(enzymeLink.source) : enzymeLink.source != null) return false;
     if (specificUrl != null ? !specificUrl.equals(enzymeLink.specificUrl) : enzymeLink.specificUrl != null) return false;
     if (view != null ? !view.equals(enzymeLink.view) : enzymeLink.view != null) return false;
     if (xrefDatabaseConstant != null ? !xrefDatabaseConstant.equals(enzymeLink.xrefDatabaseConstant) : enzymeLink.xrefDatabaseConstant !=
                                                                                                        null)
       return false;
 
     return true;
   }
 
   /**
    * Generates a hash code for this object.
    *
    * @return the hash code.
    */
   public int hashCode() {
     int result;
     result = (xrefDatabaseConstant != null ? xrefDatabaseConstant.hashCode() : 0);
     result = 29 * result + (specificUrl != null ? specificUrl.hashCode() : 0);
     result = 29 * result + (accession != null ? accession.hashCode() : 0);
     result = 29 * result + (name != null ? name.hashCode() : 0);
     result = 29 * result + (source != null ? source.hashCode() : 0);
     result = 29 * result + (view != null ? view.hashCode() : 0);
     return result;
   }
 
   /**
    * Provides a string representation of an <code>EnzymeLink</code>.
    *
    * @return the string representation.
    */
   public String toString() {
     StringBuffer output = new StringBuffer();
     output.append(this.xrefDatabaseConstant);
     output.append(", ");
     output.append(this.specificUrl);
     output.append(", ");
     output.append(this.accession);
     output.append(", ");
     output.append(this.name);
     output.append(", ");
     output.append(this.view.toString());
     output.append(", ");
     output.append(this.source.toString());
 
     return output.toString();
   }
 
 
   // ----------------  GETTER ------------------
 
   /**
    * Creates a unique name for this link.
    * <p/>
    * This method will be used to populate lists (esp. combo box content).
    *
    * @return the unique name.
    */
   public String getListOrderCriterion() {
     if (xrefDatabaseConstant == XrefDatabaseConstant.SWISSPROT ||
         xrefDatabaseConstant == XrefDatabaseConstant.PROSITE ||
         xrefDatabaseConstant == XrefDatabaseConstant.CAS) {
       return accession;
     }
 
     if (xrefDatabaseConstant == XrefDatabaseConstant.MEROPS || xrefDatabaseConstant == XrefDatabaseConstant.UMBBD) return specificUrl;
 
     if (xrefDatabaseConstant == XrefDatabaseConstant.DIAGRAM) return name;
 
     return xrefDatabaseConstant.getDatabaseCode();
   }
 
   /**
    * Links with the EC number as identifier need to call this method to get the correct URL.
    *
    * @param ec The EC number.
    * @return the full URL.
    * @throws NullPointerException if <code>ec</code> is <code>null</code>.
    */
   public String getFullUrl(String ec) {
     if (ec == null) throw new NullPointerException();
     if (STATIC_LINKS.keySet().contains(xrefDatabaseConstant)){
     	boolean withAccession = EnzymeCommissionNumber.isPreliminary(ec)
     		&& accession != null && accession.length() > 0;
         return specificUrl + (withAccession? accession : ec);
     }
     if (xrefDatabaseConstant == XrefDatabaseConstant.PROSITE ||
         xrefDatabaseConstant == XrefDatabaseConstant.SWISSPROT ||
         xrefDatabaseConstant == XrefDatabaseConstant.MIM ||
         xrefDatabaseConstant == XrefDatabaseConstant.PDB ||
         xrefDatabaseConstant == XrefDatabaseConstant.GO ||
         xrefDatabaseConstant == XrefDatabaseConstant.BRENDA ||
         xrefDatabaseConstant == XrefDatabaseConstant.METACYC){
         StringBuffer sb = new StringBuffer(xrefDatabaseConstant.getUrl());
         sb.append(accession);
         return sb.toString();
     }
     if (xrefDatabaseConstant == XrefDatabaseConstant.NC_IUBMB){
     	StringTokenizer st = new StringTokenizer(ec, ".");
         StringBuffer sb = new StringBuffer(xrefDatabaseConstant.getUrl());
     	sb.append(st.nextToken()).append('/')        // ec1
     		.append(st.nextToken()).append('/')      // ec2
     		.append(st.nextToken()).append('/')      // ec3
     		.append(st.nextToken()).append(".html"); // ec4
     	return sb.toString();
     }
     return specificUrl;
   }
 
   public XrefDatabaseConstant getXrefDatabaseConstant() {
     return xrefDatabaseConstant;
   }
 
   public String getSpecificUrl() {
     return specificUrl;
   }
 
   public String getAccession() {
     return accession;
   }
 
   public String getName() {
     return name;
   }
 
   public EnzymeViewConstant getView() {
     return view;
   }
 
   public EnzymeSourceConstant getSource() {
     return source;
   }
 
     public String getDataComment() {
         return dataComment;
     }
 
     public void setDataComment(String comment) {
         dataComment = comment;
     }
 }