/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.datamodel;

import jalview.api.DBRefEntryI;
import jalview.util.DBRefUtils;
import jalview.util.MapList;

import java.util.Arrays;
import java.util.List;

public class DBRefEntry implements DBRefEntryI
{
  /*
   * the mapping to chromosome (genome) is held as an instance with
   * source = speciesId
   * version = assemblyId
   * accessionId = "chromosome:" + chromosomeId
   * map = mapping from sequence to reference assembly
   */
  public static final String CHROMOSOME = "chromosome";

  String source = "";

  String version = "", ucversion;

  String accessionId = "";
  
  String sourceKey;

  String canonicalSourceName;


  /**
   * maps from associated sequence to the database sequence's coordinate system
   */
  Mapping map = null;

  public DBRefEntry()
  {

  }

  public DBRefEntry(String source, String version, String accessionId)
  {
    this(source, version, accessionId, null);
  }

  /**
   * 
   * @param source
   *          canonical source (uppercase only)
   * @param version
   *          (source dependent version string)
   * @param accessionId
   *          (source dependent accession number string)
   * @param map
   *          (mapping from local sequence numbering to source accession
   *          numbering)
   */
  public DBRefEntry(String source, String version, String accessionId,
          Mapping map)
  {
	  // BH 2019.01.25 made these always non-null. 
	  // Is there a difference between "" and null for version? 
	  // evidence is that source CANNOT be null. 
    setSource(source);
    setVersion(version);
    setAccessionId(accessionId);
    this.map = map;
  }

  public DBRefEntry(DBRefEntryI entry)
  {
	  this(entry.getSource(), entry.getVersion(), entry.getAccessionId(), entry.getMap() == null ? null : new Mapping(entry.getMap()));
//    this((entry.getSource() == null ? "" : new String(entry.getSource())),
//            (entry.getVersion() == null ? ""
//                    : new String(entry.getVersion())),
//            (entry.getAccessionId() == null ? ""
//                    : new String(entry.getAccessionId())),
//            (entry.getMap() == null ? null : new Mapping(entry.getMap())));
  }

  @Override
  public boolean equals(Object o)
  {
    // TODO should also override hashCode to ensure equal objects have equal
    // hashcodes
	  
	  
//    if (o == null || !(o instanceof DBRefEntry))
//    {
//      return false;
//    }
//    DBRefEntry entry = (DBRefEntry) o;
//    if (entry == this)
//    {
//      return true;
//    }
    Mapping em;
    return (o != null && o instanceof DBRefEntry 
    		&& (o == this 
    		|| equalRef((DBRefEntry) o) 
    		  && (map == null) == ((em = ((DBRefEntry) o).map) == null) 
    		  && (map == null || map.equals(em))));
//    	
//    {
//      return true;
//    }
//    return false;
  }

  /**
   * Answers true if this object is either equivalent to, or can be 'improved'
   * by, the given entry. Specifically, answers true if
   * <ul>
   * <li>source and accession are identical (ignoring case)</li>
   * <li>version is identical (ignoring case), or this version is of the format
   * "someSource:0", in which case the version for the other entry replaces
   * it</li>
   * <li>mappings are not compared but if this entry has no mapping, replace
   * with that for the other entry</li>
   * </ul>
   * 
   * @param other
   * @return
   */
  @Override
  public boolean updateFrom(DBRefEntryI other)
  {
    if (other == null)
    {
      return false;
    }
    if (other == this)
    {
      return true;
    }

    /*
     * source must either match or be both null
     */
    String otherSource = other.getSource();
    if ((source == null && otherSource != null)
            || (source != null && otherSource == null)
            || (source != null && !source.equalsIgnoreCase(otherSource)))
    {
      return false;
    }

    /*
     * accession id must either match or be both null
     */
    String otherAccession = other.getAccessionId();
    if ((accessionId == null && otherAccession != null)
            || (accessionId != null && otherAccession == null)
            || (accessionId != null
                    && !accessionId.equalsIgnoreCase(otherAccession)))
    {
      return false;
    }

    /*
     * if my version is null, "0" or "source:0" then replace with other version,
     * otherwise the versions have to match
     */
    String otherVersion = other.getVersion();

    if ((version == null || version.equals("0") || version.endsWith(":0"))
            && otherVersion != null)
    {
      setVersion(otherVersion);
    }
    else
    {
      if (version != null && (otherVersion == null
              || !version.equalsIgnoreCase(otherVersion)))
      {
        return false;
      }
    }

    /*
     * if I have no mapping, take that of the other dbref
     */
    if (map == null)
    {
      setMap(other.getMap());
    }
    return true;
  }

  /**
   * test for similar DBRef attributes, except for the map object.
   * 
   * @param entry
   * @return true if source, accession and version are equal with those of entry
   */
  @Override
  public boolean equalRef(DBRefEntryI entry)
  {
    // TODO is this method and equals() not needed?
    if (entry == null)
    {
      return false;
    }
    if (entry == this)
    {
      return true;
    }
    
    // BH 2019.01.25  source, accessionId, and version cannot be null. 
    // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
    
    if (entry != null
            && (source != null && entry.getSource() != null
                    && source.equalsIgnoreCase(entry.getSource()))
            && (accessionId != null && entry.getAccessionId() != null
                    && accessionId.equalsIgnoreCase(entry.getAccessionId()))
            && (version != null && entry.getVersion() != null
                    && version.equalsIgnoreCase(entry.getVersion())))
    {
      return true;
    }
    return false;
  }

  @Override
  public String getSource()
  {
    return source;
  }

  public String getSourceKey() 
  {
	return sourceKey;
  }

  @Override
  public String getVersion()
  {
    return version;
  }

  @Override
  public String getAccessionId()
  {
    return accessionId;
  }

  @Override
  public void setAccessionId(String accessionId)
  {
    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
  }

  @Override
  public void setSource(String source)
  {
    this.source = (source == null ? "" : source).toUpperCase();
    this.canonicalSourceName = 	DBRefUtils.getCanonicalName(this.source);
    this.sourceKey = ";" + canonicalSourceName + ";";
  }

  @Override
  public void setVersion(String version)
  {
    this.version = (version == null ? "" : version);
    this.ucversion = this.version.toUpperCase();
  }

  @Override
  public Mapping getMap()
  {
    return map;
  }

  /**
   * @param map
   *          the map to set
   */
  public void setMap(Mapping map)
  {
    this.map = map;
  }

  public boolean hasMap()
  {
    return map != null;
  }

  /**
   * 
   * @return source+":"+accessionId
   */
  public String getSrcAccString()
  {
    return ((source != null) ? source : "") + ":"
            + ((accessionId != null) ? accessionId : "");
  }

  @Override
  public String toString()
  {
    return getSrcAccString();
  }

  @Override
  public boolean isPrimaryCandidate()
  {
    /*
     * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.  
     */
    if (map != null)
    {
      SequenceI mto = map.getTo();
      if (mto != null)
      {
        return false;
      }
      MapList ml = map.getMap();
      if (ml.getFromRatio() != ml.getToRatio()
              || ml.getFromRatio() != 1)
      {
        return false;
      }
      // check map is between identical single contiguous ranges
      List<int[]> fromRanges, toRanges;
      if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1)
      {
        return false;
      }
      if (fromRanges.get(0)[0] != toRanges.get(0)[0]
              || fromRanges.get(0)[1] != toRanges.get(0)[1])
      {
        return false;
      }
    }
    if (version == null || version == "")
    {
      // no version string implies the reference has not been verified at all.
      return false;
    }
    // tricky - this test really needs to search the sequence's set of dbrefs to
    // see if there is a primary reference that derived this reference.
    String[] sources = DBRefSource.allSources();
    for (int i = sources.length; --i >= 0;)
    {
      if (ucversion.startsWith(sources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
      {
        // by convention, many secondary references inherit the primary
        // reference's
        // source string as a prefix for any version information from the
        // secondary reference.
        return false;
      }
    }
    return true;
  }

  /**
   * Mappings to chromosome are held with accessionId as "chromosome:id"
   * 
   * @return
   */
  public boolean isChromosome()
  {
    return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
  }

  public Object getCanonicalSourceName() {
	return canonicalSourceName;
  }


}