/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.util;

import java.util.*;

import jalview.datamodel.*;

public class DBRefUtils
{
  /**
   * Utilities for handling DBRef objects and their collections.
   */
  /**
   *
   * @param dbrefs Vector of DBRef objects to search
   * @param sources String[] array of source DBRef IDs to retrieve
   * @return Vector
   */
  public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources)
  {
    if (dbrefs == null)
    {
      return null;
    }
    if (sources == null)
    {
      return dbrefs;
    }
    Hashtable srcs = new Hashtable();
    Vector res = new Vector();

    for (int i = 0; i < sources.length; i++)
    {
      srcs.put(new String(sources[i]), new Integer(i));
    }
    for (int i = 0, j = dbrefs.length; i < j; i++)
    {
      if (srcs.containsKey(dbrefs[i].getSource()))
      {
        res.addElement(dbrefs[i]);
      }
    }

    if (res.size() > 0)
    {
      DBRefEntry[] reply = new DBRefEntry[res.size()];
      for (int i = 0; i < res.size(); i++)
      {
        reply[i] = (DBRefEntry) res.elementAt(i);
      }
      return reply;
    }
    res = null;
    // there are probable  memory leaks in the hashtable!
    return null;
  }

  /**
   * isDasCoordinateSystem
   *
   * @param string String
   * @param dBRefEntry DBRefEntry
   * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name
   */
  public static Hashtable DasCoordinateSystemsLookup = null;
  public static boolean isDasCoordinateSystem(String string,
                                              DBRefEntry dBRefEntry)
  {
    if (DasCoordinateSystemsLookup == null)
    { // Initialise
      DasCoordinateSystemsLookup = new Hashtable();
      DasCoordinateSystemsLookup.put("pdbresnum",
                                     jalview.datamodel.DBRefSource.PDB);
      DasCoordinateSystemsLookup.put("uniprot",
                                     jalview.datamodel.DBRefSource.UNIPROT);
      DasCoordinateSystemsLookup.put("EMBL",
              jalview.datamodel.DBRefSource.EMBL);
      //DasCoordinateSystemsLookup.put("EMBL",
      //        jalview.datamodel.DBRefSource.EMBLCDS);
    }

    String coordsys = (String) DasCoordinateSystemsLookup.get(string.
        toLowerCase());
    if (coordsys != null)
    {
      return coordsys.equals(dBRefEntry.getSource());
    }
    return false;
  }
  public static Hashtable CanonicalSourceNameLookup=null;
  /**
   * look up source in an internal list of database reference sources
   * and return the canonical jalview name for the source, or the original
   * string if it has no canonical form.
   * @param source
   * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or original source
   */
  public static String getCanonicalName(String source)
  {
    if (CanonicalSourceNameLookup==null) {
      CanonicalSourceNameLookup = new Hashtable();
      CanonicalSourceNameLookup.put("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
      CanonicalSourceNameLookup.put("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
      CanonicalSourceNameLookup.put("pdb", jalview.datamodel.DBRefSource.PDB);
    }
    String canonical = (String) CanonicalSourceNameLookup.get(source.
        toLowerCase());
    if (canonical==null)
    {
      return source;
    }
    return canonical;
  }
  /**
   * find RefEntry corresponding to a particular pattern
   * the equals method of each entry is used, from String attributes right down to Mapping attributes.
   * @param ref Set of references to search
   * @param entry pattern to collect - null any entry for wildcard match
   * @return
   */
  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
  {
    return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList);
  }
  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry, DbRefComp comparator)
  {
    if (ref==null || entry==null)
      return null;
    Vector rfs = new Vector();
    for (int i=0; i<ref.length;i++)
    {
      if (comparator.matches(entry, ref[i]))
      {
              rfs.addElement(ref[i]);
      }
    }
    // TODO Auto-generated method stub
    if (rfs.size()>0)
    {
      DBRefEntry[] rf = new DBRefEntry[rfs.size()];
      rfs.copyInto(rf);
      return rf;
    }
    return null;
  }
  public interface DbRefComp {
    public boolean matches(DBRefEntry refa, DBRefEntry refb);
  }
  /**
   * match on all non-null fields in refa
   */
  public static DbRefComp matchNonNullonA = new DbRefComp()
    {
          public boolean matches(DBRefEntry refa, DBRefEntry refb)
          {
            if (refa.getSource()==null || refb.getSource().equals(refa.getSource()))
            {
              if (refa.getVersion()==null || refb.getVersion().equals(refa.getVersion()))
              {
                if (refa.getAccessionId()==null || refb.getAccessionId().equals(refa.getAccessionId()))
                {
                  if (refa.getMap()==null || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
                  {
                    return true; 
                  }
                }
              }
            }
            return false;
          }
    };
    /**
     * either field is null or field matches for all of source, version, accession id and map.
     */
    public static DbRefComp matchEitherNonNull = new DbRefComp()
    {
          public boolean matches(DBRefEntry refa, DBRefEntry refb)
          {
            if ((refa.getSource()==null || refb.getSource()==null) 
                    || refb.getSource().equals(refa.getSource()))
            {
              if ((refa.getVersion()==null || refb.getVersion()==null) 
                      || refb.getVersion().equals(refa.getVersion()))
              {
                if ((refa.getAccessionId()==null || refb.getAccessionId()==null) 
                        || refb.getAccessionId().equals(refa.getAccessionId()))
                {
                  if ((refa.getMap()==null || refb.getMap()==null) 
                          || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
                  {
                    return true; 
                  }
                }
              }
            }
            return false;
          }
    };
    /**
     * accession ID and DB must be identical. Version is ignored. Map is either not defined or is a match (or is compatible?)
     */
    public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
    {
          public boolean matches(DBRefEntry refa, DBRefEntry refb)
          {
            if (refa.getSource()!=null && refb.getSource()!=null 
                    && refb.getSource().equals(refa.getSource()))
            {
              // We dont care about version
              //if ((refa.getVersion()==null || refb.getVersion()==null) 
              //        || refb.getVersion().equals(refa.getVersion()))
              //{
              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
                      || refb.getAccessionId().equals(refa.getAccessionId()))
                {
                  if ((refa.getMap()==null || refb.getMap()==null) 
                          || (refa.getMap()!=null && refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
                  {
                    return true; 
                  }
                }
              }
            return false;
          }
    };
    /**
     * accession ID and DB must be identical. Version is ignored. 
     * No map on either or map but no maplist on either or maplist of map on a is the complement of maplist of map on b.
     */
    public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
    {
          public boolean matches(DBRefEntry refa, DBRefEntry refb)
          {
            if (refa.getSource()!=null && refb.getSource()!=null 
                    && refb.getSource().equals(refa.getSource()))
            {
              // We dont care about version
              //if ((refa.getVersion()==null || refb.getVersion()==null) 
              //        || refb.getVersion().equals(refa.getVersion()))
              //{
              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
                      || refb.getAccessionId().equals(refa.getAccessionId()))
                {
                  if ((refa.getMap()==null && refb.getMap()==null) 
                          || (refa.getMap()!=null && refb.getMap()!=null))
                    if ((refb.getMap().getMap()==null && refa.getMap().getMap()==null)
                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
                            && refb.getMap().getMap().getInverse().equals(refa.getMap().getMap())))
                  {
                    return true; 
                  }
                }
              }
            return false;
          }
    };
    /**
     * accession ID and DB must be identical. Version is ignored. 
     * No map on both or or map but no maplist on either or maplist of map on a is equivalent to the maplist of map on b.
     */
    public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
    {
          public boolean matches(DBRefEntry refa, DBRefEntry refb)
          {
            if (refa.getSource()!=null && refb.getSource()!=null 
                    && refb.getSource().equals(refa.getSource()))
            {
              // We dont care about version
              //if ((refa.getVersion()==null || refb.getVersion()==null) 
              //        || refb.getVersion().equals(refa.getVersion()))
              //{
              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
                      || refb.getAccessionId().equals(refa.getAccessionId()))
                {
                  if (refa.getMap()==null && refb.getMap()==null)
                  {
                    return true;
                  }
                  if (refa.getMap()!=null && refb.getMap()!=null
                          && ((refb.getMap().getMap()==null && refa.getMap().getMap()==null)
                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
                            && refb.getMap().getMap().equals(refa.getMap().getMap()))))
                  {
                    return true; 
                  }
                }
              }
            return false;
          }
    };
    /**
     * accession ID and DB must be identical. Version is ignored. 
     * No map on either or map but no maplist on either or maplist of map on a is equivalent to the maplist of map on b.
     */
    public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
    {
          public boolean matches(DBRefEntry refa, DBRefEntry refb)
          {
            if (refa.getSource()!=null && refb.getSource()!=null 
                    && refb.getSource().equals(refa.getSource()))
            {
              // We dont care about version
              //if ((refa.getVersion()==null || refb.getVersion()==null) 
              //        || refb.getVersion().equals(refa.getVersion()))
              //{
              if (refa.getAccessionId()!=null && refb.getAccessionId()!=null 
                      && refb.getAccessionId().equals(refa.getAccessionId()))
                {
                  if (refa.getMap()==null || refb.getMap()==null)
                  {
                    return true;
                  }
                  if ((refa.getMap()!=null && refb.getMap()!=null)
                          && (refb.getMap().getMap()==null && refa.getMap().getMap()==null)
                            || (refb.getMap().getMap()!=null && refa.getMap().getMap()!=null
                            && refb.getMap().getMap().equals(refa.getMap().getMap())))
                  {
                    return true; 
                  }
                }
              }
            return false;
          }
    };
    /**
     * used by file parsers to generate DBRefs from annotation within file (eg stockholm)
     * @param dbname
     * @param version
     * @param acn
     * @param seq where to anotate with reference
     * @return parsed version of entry that was added to seq (if any)
     */
    public static DBRefEntry parseToDbRef(SequenceI seq, String dbname, String version,
            String acn)
    {
      DBRefEntry ref = null;
      if (dbname!=null)
      {
        String locsrc = jalview.util.DBRefUtils
        .getCanonicalName(dbname);
        if (locsrc.equals(jalview.datamodel.DBRefSource.PDB))
        {
          // check for chaincode and mapping
          // PFAM style stockhom PDB citation
          com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex("([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
          if (r.search(acn.trim()))
          {
            String pdbid = r.stringMatched(1);
            String chaincode = r.stringMatched(2);
            String mapstart = r.stringMatched(3);
            String mapend = r.stringMatched(4);
            if (chaincode.equals(" "))
            {
              chaincode = "_";
            }
            // construct pdb ref.
            ref = new DBRefEntry(locsrc, version, pdbid+chaincode);
            PDBEntry pdbr = new PDBEntry();
            pdbr.setId(pdbid);
            seq.addPDBId(pdbr);
          }
        } else {
          // default:
          ref = new DBRefEntry(locsrc, version, acn);
        }
      }
      if (ref!=null)
      {
        seq.addDBRef(ref);
      }
      return ref;
    }
        
          
}