/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
 * 
 * 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/>.
 */
package jalview.analysis;

import java.util.*;

import jalview.datamodel.*;

/**
 * Routines for approximate Sequence Id resolution by name using string
 * containment (on word boundaries) rather than equivalence. It also attempts to
 * resolve ties where no exact match is available by picking the the id closest
 * to the query.
 */
public class SequenceIdMatcher
{
  private Hashtable names;

  public SequenceIdMatcher(SequenceI[] seqs)
  {
    names = new Hashtable();
    for (int i = 0; i < seqs.length; i++)
    {
      // TODO: deal with ID collisions - SequenceI should be appended to list associated with this key.
      names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
      // add in any interesting identifiers
      if (seqs[i].getDBRef() != null)
      {
        DBRefEntry dbr[] = seqs[i].getDBRef();
        SeqIdName sid = null;
        for (int r = 0; r < dbr.length; r++)
        {
          sid = new SeqIdName(dbr[r].getAccessionId());
          if (!names.contains(sid))
          {
            names.put(sid, seqs[i]);
          }
        }
      }
    }
  }

  /**
   * returns the closest SequenceI in matches to SeqIdName and returns all the
   * matches to the names hash.
   * 
   * @param candName
   *          SeqIdName
   * @param matches
   *          Vector of SequenceI objects
   * @return SequenceI closest SequenceI to SeqIdName
   */
  private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
  {
    SequenceI[] st= pickbestMatches(candName, matches);
    return st==null || st.length==0 ? null : st[0];
  }
  /**
   * returns the closest SequenceI in matches to SeqIdName and returns all the
   * matches to the names hash.
   * 
   * @param candName
   *          SeqIdName
   * @param matches
   *          Vector of SequenceI objects
   * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[] ties }
   */
  private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
  {
    ArrayList best=new ArrayList();
    SequenceI match = null;
    if (candName == null || matches == null || matches.size() == 0)
    {
      return null;
    }
    match = (SequenceI) matches.elementAt(0);
    matches.removeElementAt(0);
    best.add(match);
    names.put(new SeqIdName(match.getName()), match);
    int matchlen = match.getName().length();
    int namlen = candName.id.length();
    while (matches.size() > 0)
    {
      // look through for a better one.
      SequenceI cand = (SequenceI) matches.elementAt(0);
      matches.remove(0);
      names.put(new SeqIdName(cand.getName()), cand);
      int q,w,candlen = cand.getName().length();
      // keep the one with an id 'closer' to the given seqnam string
      if ((q=Math.abs(matchlen - namlen)) > (w=Math.abs(candlen - namlen))
              && candlen > matchlen)
      {
        best.clear();
        match = cand;
        matchlen = candlen;
        best.add(match);
      }
      if (q==w && candlen==matchlen)
      {
        // record any ties
        best.add(cand);
      }
    }
    if (best.size()==0) { return null; };
    return (SequenceI[]) best.toArray(new SequenceI[0]);
  }

  /**
   * get SequenceI with closest SequenceI.getName() to seq.getName()
   * 
   * @param seq
   *          SequenceI
   * @return SequenceI
   */
  public SequenceI findIdMatch(SequenceI seq)
  {
    SeqIdName nam = new SeqIdName(seq.getName());
    return findIdMatch(nam);
  }

  public SequenceI findIdMatch(String seqnam)
  {
    SeqIdName nam = new SeqIdName(seqnam);
    return findIdMatch(nam);
  }

  /**
   *  Find all matches for a given sequence name.
   *  @param seqnam string to query Matcher with.
   */
  public SequenceI[] findAllIdMatches(String seqnam)
  {

    SeqIdName nam = new SeqIdName(seqnam);
    return findAllIdMatches(nam);
  }

  /**
   * findIdMatch
   * 
   * Return pointers to sequences (or sequence object containers) which have
   * same Id as a given set of different sequence objects
   * 
   * @param seqs
   *          SequenceI[]
   * @return SequenceI[]
   */
  public SequenceI[] findIdMatch(SequenceI[] seqs)
  {
    SequenceI[] namedseqs = null;
    int i = 0;
    SeqIdName nam;

    if (seqs.length > 0)
    {
      namedseqs = new SequenceI[seqs.length];
      do
      {
        nam = new SeqIdName(seqs[i].getName());

        if (names.containsKey(nam))
        {
          namedseqs[i] = findIdMatch(nam);
        }
        else
        {
          namedseqs[i] = null;
        }
      } while (++i < seqs.length);
    }

    return namedseqs;
  }

  /**
   * core findIdMatch search method
   * 
   * @param nam
   *          SeqIdName
   * @return SequenceI
   */
  private SequenceI findIdMatch(
          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
  {
    Vector matches = new Vector();
    while (names.containsKey(nam))
    {
      matches.addElement(names.remove(nam));
    }
    return pickbestMatch(nam, matches);
  }
  /**
   * core findIdMatch search method for finding all equivalent matches
   * 
   * @param nam
   *          SeqIdName
   * @return SequenceI[]
   */
  private SequenceI[] findAllIdMatches(
          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
  {
    Vector matches = new Vector();
    while (names.containsKey(nam))
    {
      matches.addElement(names.remove(nam));
    }
    SequenceI[] r=pickbestMatches(nam, matches);
    return r;
  }


  private class SeqIdName
  {
    String id;

    SeqIdName(String s)
    {
      if (s != null)
      {
        id = new String(s);
      }
      else
      {
        id = "";
      }
    }

    public int hashCode()
    {
      return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
              .hashCode());
    }

    public boolean equals(Object s)
    {
      if (s instanceof SeqIdName)
      {
        return this.equals((SeqIdName) s);
      }
      else
      {
        if (s instanceof String)
        {
          return this.equals((String) s);
        }
      }

      return false;
    }

    /**
     * Characters that define the end of a unique sequence ID at the beginning
     * of an arbitrary ID string JBPNote: This is a heuristic that will fail for
     * arbritrarily extended sequence id's (like portions of an aligned set of
     * repeats from one sequence)
     */
    private String WORD_SEP = "~. |#\\/<>!\""+((char)0x00A4)+"$%^*)}[@',?_";

    /**
     * matches if one ID properly contains another at a whitespace boundary.
     * TODO: (JBPNote) These are not efficient. should use char[] for speed
     * todo: (JBPNote) Set separator characters appropriately
     * 
     * @param s
     *          SeqIdName
     * @return boolean
     */
    public boolean equals(SeqIdName s)
    {
      // TODO: JAL-732 patch for cases when name includes a list of IDs, and the match contains one ID flanked
      if (id.length() > s.id.length())
      {
        return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id
                .length())) > -1) : false;
      }
      else
      {
        return s.id.startsWith(id) ? (s.id.equals(id) ? true : (WORD_SEP
                .indexOf(s.id.charAt(id.length())) > -1)) : false;
      }
    }

    public boolean equals(String s)
    {
      if (id.length() > s.length())
      {
        return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
                : false;
      }
      else
      {
        return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
                .indexOf(s.charAt(id.length())) > -1)) : false;
      }
    }
  }
}