package uk.ac.ebi.intenz.domain.constants;
   
   import java.util.*;
   
   import uk.ac.ebi.intenz.domain.exceptions.DomainException;
   
   /**
    * This class represents an enumeration of all supported link source types.
    * <p/>
   * Instances of this class are immutable.
   *
   * @author Michael Darsow
   * @version $Revision: 1.4 $ $Date: 2008/07/09 09:49:05 $
   */
  public class XrefDatabaseConstant implements Comparable<XrefDatabaseConstant> {
    private String databaseCode;
  
    private String displayName;
  
    private String url;
  
    private boolean isXref;
  
    public static final XrefDatabaseConstant UNDEF = new XrefDatabaseConstant("UNDEF", "UNDEFINED",
                                                                              "", false);
  
    /**
     * <a href="http://www.brenda.uni-koeln.de/">BRENDA</a> collects functional
     * data about enzymes. NOTE: this is now considered as xref, as the identifiers
     * we are linking to are their preliminary EC numbers.
     */
    public static final XrefDatabaseConstant BRENDA = new XrefDatabaseConstant(
  		  "BRENDA", "BRENDA",
  		  "http://www.brenda-enzymes.info/php/result_flat.php4?ecno=", true);
  
    public static final XrefDatabaseConstant METACYC = new XrefDatabaseConstant(
  		  "MCYC", "MetaCyc",
  		  "http://www.metacyc.org/META/NEW-IMAGE?type=EC-NUMBER&object=EC-", true);
    
    /**
     * <a href="http://www.cas.org/">CAS</a> is commercial and cannot be linked to.
     */
    public static final XrefDatabaseConstant CAS = new XrefDatabaseConstant("CAS", "CAS", "", false);
  
    /**
     * <a href="http://ca.expasy.org/enzyme/">ENZYME</a> is the EXPASY version of the NC-IUBMB Nomenclature containing some
     * additional information (cofactors, improved comments and additional links).
     */
    public static final XrefDatabaseConstant ENZYME =
  		  new XrefDatabaseConstant("EXPASY", "ENZYME@ExPASy",
  				  "http://enzyme.expasy.org/EC/", false);
  
    /**
     * Gerry Moss' web pages (Nomenclature Comitee of the IUBMB).
     */
    public static final XrefDatabaseConstant NC_IUBMB = new XrefDatabaseConstant("NCIUBMB", "NC-IUBMB",
            "http://www.chem.qmul.ac.uk/iubmb/enzyme/EC", false);
  
    /**
     * <a href="http://geneontology.org/">GO</a> is the Gene Ontology database.
     */
  //  public static final XrefDatabaseConstant GO = new XrefDatabaseConstant("GO", "GO",
  //                                                                         "http://www.ebi.ac.uk/ego/GSearch?query=", false);
    public static final XrefDatabaseConstant GO = new XrefDatabaseConstant("GO", "GO",
            "http://www.ebi.ac.uk/ego/DisplayGoTerm?id=", true);
  
    /**
     * <a href="http://www.ebi.ac.uk/thornton-srv/databases/CSA/">Catalytic Site Atlas</a>
     * provides catalytic residues details.
     */
    public static final XrefDatabaseConstant CSA = new XrefDatabaseConstant("CSA", "CSA",
        "http://www.ebi.ac.uk/thornton-srv/databases/CSA_NEW/SearchResults_EC.php?ECID=", false);
  
    /**
     * <a href="http://wwwbiotech.nist.gov:8030/enzyme/ename.html">NIST74</a> provides further information about the
     * catalytic activity.
     */
    public static final XrefDatabaseConstant NIST74 = new XrefDatabaseConstant("NIST74", "NIST 74",
                                                                               "http://xpdb.nist.gov/enzyme_thermodynamics/enzyme_compose_query.pl?EC=", false);
  
    /**
     * <a href="http://www.genome.ad.jp/kegg/kegg2.html">KEGG</a> comprises several databases storing information
     * especially related to enzymes (e.g. LIGAND, REACTION) and genes and genomes in general.
     */
    public static final XrefDatabaseConstant KEGG = new XrefDatabaseConstant("KEGG", "KEGG",
                                                                             "http://www.genome.ad.jp/dbget-bin/www_bget?ec:", false);
  
    /**
     * <a href="http://merops.sanger.ac.uk/">MEROPS</a> is a resource for peptidases.
     */
    public static final XrefDatabaseConstant MEROPS = new XrefDatabaseConstant("MEROPS", "MEROPS", "", false);
  
    /**
     * <a href="http://www.ncbi.nlm.nih.gov/omim/">OMIM</a> stores information about human genetic diseases.
     */
    public static final XrefDatabaseConstant MIM = new XrefDatabaseConstant("MIM", "OMIM", "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=", true);
  
    /**
     * <a href="http://ca.expasy.org/prosite/">PROSITE</a> is located at the SIB and contains information about protein
    * families and domains.
    */
   public static final XrefDatabaseConstant PROSITE = new XrefDatabaseConstant("PROSITE", "PROSITE",
                                                                               "http://www.expasy.org/prosite/", true);
 
   /**
    * <a href="http://ca.expasy.org/sprot/">Swiss-Prot</a> is THE protein sequence database.
    */
   public static final XrefDatabaseConstant SWISSPROT = new XrefDatabaseConstant("SWISSPROT", "Swiss-Prot",
                                                                                 "http://www.uniprot.org/uniprot/", true);
 
   /**
    * <a href="http://umbbd.ethz.ch">UM-BBD</a> is a comprehensive resource about enzymes also
    * containing enzymes which haven't got an EC number yet.
    * <p/>
    * UM-BBD links can be static (using EC number) or non-static (using UM-BBD identifier). Therefore a UM-BBD link
    * will not be part of the list of static links.
    */
   public static final XrefDatabaseConstant UMBBD = new XrefDatabaseConstant("UMBBD", "UM-BBD",
                                                                             "http://umbbd.ethz.ch/servlets/pageservlet?ptype=e&ECcode=", false);
 
   public static final XrefDatabaseConstant DIAGRAM = new XrefDatabaseConstant("DIAGR", "DIAGRAM",
                                                                               "", true);
 
   /**
    * <a href="http://ca.expasy.org/sprot/">ERGO</a> is a not very reliable enzyme source ... (I couldn't get any
    * information about it because the server was down).
    * @deprecated This website does not work any more (if it ever did).
    */
    @Deprecated
   public static final XrefDatabaseConstant ERGO = new XrefDatabaseConstant("ERGO", "ERGO",
                                                                            "http://www.ergo-light.com/ERGO/CGI/fr.cgi?org=&user=&fr=", false);
 
   /**
    * <a href="http://ca.expasy.org/sprot/">ERGO</a> formerly WIT.
    */
   public static final XrefDatabaseConstant WIT = new XrefDatabaseConstant("WIT", "WIT",
                                                                           "http://www.ergo-light.com/ERGO/CGI/fr.cgi?org=&user=&fr=", false);
 
   /**
    * Link to the <a href="http://www.rcsb.org/pdb/index.html">Protein Data Bank (PDB)</a>.
    */
   public static final XrefDatabaseConstant PDB = new XrefDatabaseConstant("PDB", "EC2PDB", "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/enzymes/GetPage.pl?ec_number=", false);
 
     /**
      * Link to ExplorEnz (Dublin's MySQL implementation of NC-IUBMB).
      */
   public static final XrefDatabaseConstant EXPLORENZ = new XrefDatabaseConstant(
     "EXP", "ExplorEnz", "http://www.enzyme-database.org/query.php?ec=", false);
 
   public static final XrefDatabaseConstant UNIPATHWAY =
         new XrefDatabaseConstant("UP", "UniPathway",
         "http://www.unipathway.org/enzyme/entry?ec=", false);
 
   private static XrefDatabaseConstant[] PRIVATE_LINK_SOURCES = {
     NC_IUBMB,
     BRENDA,
     DIAGRAM,
     ENZYME,
     ERGO,
     EXPLORENZ,
     GO,
     KEGG,
     MEROPS,
     METACYC,
     MIM,
     NIST74,
     PROSITE,
     SWISSPROT,
     UMBBD,
     UNIPATHWAY,
     WIT,
     CSA,
     PDB,
     CAS,
     UNDEF
   };
 
   private static XrefDatabaseConstant[] PRIVATE_UNIQUE_LINK_SOURCES = {
     NC_IUBMB,
     BRENDA,
     ENZYME,
     EXPLORENZ,
     GO,
     KEGG,
     METACYC,
     NIST74,
     UMBBD,
     UNIPATHWAY,
     WIT
   };
 
   /**
    * All link sources ordered alphabetically. This set is immutable.
    */
   public static final List<XrefDatabaseConstant> LINK_SOURCE_CONSTANTS =
 	  Collections.unmodifiableList(Arrays.asList(PRIVATE_LINK_SOURCES));
 
   /**
    * This set contains all link which can only occur once in an enzyme entry.
    */
   public static final Set<XrefDatabaseConstant> UNIQUE_LINK_SOURCES =
 	  Collections.unmodifiableSet(new HashSet<XrefDatabaseConstant>(Arrays.asList(PRIVATE_UNIQUE_LINK_SOURCES)));
 
   /**
    * Object cannot be created outside this class.
    *
    * @param sourceCode  The line type code.
    * @param displayName The full name of this source.
    * @param url         The URL of this link source (if available).
    */
   private XrefDatabaseConstant(String sourceCode, String displayName, String url, boolean isXref) {
     this.databaseCode = sourceCode;
     this.displayName = displayName;
     this.url = url;
     this.isXref = isXref;
   }
 
   public static XrefDatabaseConstant valueOf(String sourceCode) throws DomainException {
     if (sourceCode == null) throw new NullPointerException("Parameter 'databaseCode' must not be null.");
     if (sourceCode.equals("")) throw new IllegalArgumentException("Parameter 'databaseCode' must not be empty.");
     for (Iterator<XrefDatabaseConstant> it = LINK_SOURCE_CONSTANTS.iterator(); it.hasNext();) {
       XrefDatabaseConstant xrefDatabaseConstant = it.next();
       if (xrefDatabaseConstant.getDatabaseCode().equals(sourceCode)) return xrefDatabaseConstant;
     }
     throw new DomainException("org.apache.struts.action.GLOBAL_MESSAGE", "errors.application.xrefs.source_code");
   }
 
   public int compareTo(XrefDatabaseConstant linkSourceConstant) {
     return this.getDatabaseCode().compareTo(linkSourceConstant.getDatabaseCode());
   }
 
   /**
    * Checks if the given link source code exists in this enumeration.
    *
    * @param sourceCode The source code of the link.
    * @return <code>true</code> if the source code exists.
    * @throws NullPointerException if <code>databaseCode</code> is <code>null</code>.
    */
   public static boolean contains(String sourceCode) {
     if (sourceCode == null) throw new NullPointerException("Parameter 'databaseCode' must not be null.");
     for (Iterator<XrefDatabaseConstant> it = LINK_SOURCE_CONSTANTS.iterator(); it.hasNext();) {
       XrefDatabaseConstant sourceConstant = it.next();
       if (sourceCode.equals(sourceConstant.getDatabaseCode())) return true;
     }
     return false;
   }
 
   public static boolean isUniqueXrefDatabaseName(String databaseName) {
     if (databaseName == null) throw new NullPointerException("Parameter 'databaseName' must not be null.");
     String databaseCode = getDatabaseCodeOf(databaseName);
     return isUniqueXrefDatabaseCode(databaseCode);
   }
 
   public static boolean isUniqueXrefDatabaseCode(String databaseCode) {
     if (databaseCode == null) throw new NullPointerException("Parameter 'databaseCode' must not be null.");
     if (!XrefDatabaseConstant.contains(databaseCode)) throw new IllegalArgumentException("The databaseCode paramter is invalid.");
     for (Iterator<XrefDatabaseConstant> it = UNIQUE_LINK_SOURCES.iterator(); it.hasNext();) {
       XrefDatabaseConstant xrefDatabaseConstant = it.next();
       if (xrefDatabaseConstant.databaseCode.equals(databaseCode)) return true;
     }
     return false;
   }
 
   /**
    * Returns <code>true</code> if this link belongs to the XREFS table.
    * <p/>
    * If the source code is not a valid source code an exception is thrown (see below).
    *
    * @param sourceCode The source code of this link constant.
    * @return <code>true</code> if this link belongs to the XREFS table.
    * @throws NullPointerException     if <code>databaseCode</code> is <code>null</code>.
    * @throws IllegalArgumentException if <code>databaseCode</code> is invalid.
    */
   public static boolean isXref(String sourceCode) {
     if (sourceCode == null) throw new NullPointerException();
     if (!XrefDatabaseConstant.contains(sourceCode)) throw new IllegalArgumentException("The databaseCode paramter is invalid.");
     for (Iterator<XrefDatabaseConstant> it = LINK_SOURCE_CONSTANTS.iterator(); it.hasNext();) {
       XrefDatabaseConstant sourceConstant = it.next();
       if (sourceCode.equals(sourceConstant.getDatabaseCode())) return sourceConstant.isXref();
     }
     return false;
   }
 
   /**
    * Standard equals method.
    *
    * @param o Object to be compared to this one.
    * @return <code>true</code> if the objects are equal.
    */
   public boolean equals(Object o) {
     if (this == o) return true;
     if (!(o instanceof XrefDatabaseConstant)) return false;
 
     final XrefDatabaseConstant xrefDatabaseConstant = (XrefDatabaseConstant) o;
 
     if (databaseCode != null ? !databaseCode.equals(xrefDatabaseConstant.databaseCode) : xrefDatabaseConstant.databaseCode !=
                                                                                          null) return false;
     if (url != null ? !url.equals(xrefDatabaseConstant.url) : xrefDatabaseConstant.url != null) return false;
 
     return true;
   }
 
   /**
    * Returns the hash code of this object.
    *
    * @return the hash code of this object.
    */
   public int hashCode() {
     int result;
     result = (databaseCode != null ? databaseCode.hashCode() : 0);
     result = 29 * result + (url != null ? url.hashCode() : 0);
     return result;
   }
 
   /**
    * Returns the display name.
    *
    * @return the display name.
    */
   public String toString() {
     return displayName;
   }
 
 
   // ----------------  GETTER ------------------
 
   /**
    * Returns the URL of the given source code.
    * <p/>
    * If the source code is not a valid source code an exception is thrown (see below).
    *
    * @param sourceCode The source code of this link constant.
    * @return the URL.
    * @throws NullPointerException     if <code>databaseCode</code> is <code>null</code>.
    * @throws IllegalArgumentException if <code>databaseCode</code> is invalid.
    */
   public static String getUrlOf(String sourceCode) {
     if (sourceCode == null) throw new NullPointerException("Parameter 'databaseCode' must not be null.");
     if (!XrefDatabaseConstant.contains(sourceCode)) throw new IllegalArgumentException("The 'databaseCode' paramter is invalid.");
     for (Iterator<XrefDatabaseConstant> it = LINK_SOURCE_CONSTANTS.iterator(); it.hasNext();) {
       XrefDatabaseConstant sourceConstant = it.next();
       if (sourceCode.equals(sourceConstant.getDatabaseCode())) return sourceConstant.getUrl();
     }
     return "";
   }
 
   /**
    * Returns the display name of the source defined by <code>databaseCode</code>.
    *
    * @param sourceCode The source's code.
    * @return the display name.
    * @throws NullPointerException if <code>databaseCode</code> is <code>null</code>.
    */
   public static String getDisplayNameOf(String sourceCode) {
     if (sourceCode == null) throw new NullPointerException("Parameter 'databaseCode' must not be null.");
     if (!XrefDatabaseConstant.contains(sourceCode)) throw new IllegalArgumentException("The 'databaseCode' paramter is invalid.");
     for (Iterator<XrefDatabaseConstant> it = LINK_SOURCE_CONSTANTS.iterator(); it.hasNext();) {
       XrefDatabaseConstant sourceConstant = it.next();
       if (sourceCode.equals(sourceConstant.getDatabaseCode())) return sourceConstant.getDisplayName();
     }
     return "";
   }
 
   public static String getDatabaseCodeOf(String databaseName) {
     if (databaseName == null) throw new NullPointerException("Parameter 'databaseName' must not be null.");
     for (Iterator<XrefDatabaseConstant> it = LINK_SOURCE_CONSTANTS.iterator(); it.hasNext();) {
       XrefDatabaseConstant sourceConstant = it.next();
       if (databaseName.equals(sourceConstant.getDisplayName())) return sourceConstant.getDatabaseCode();
     }
     throw new IllegalArgumentException("The 'databaseName' parameter is invalid:" + databaseName);
   }
 
   public String getDatabaseCode() {
     return databaseCode;
   }
 
   public String getDisplayName() {
     return displayName;
   }
 
   public String getUrl() {
     return url;
   }
 
   public boolean isXref() {
     return isXref;
   }
 
 }