/*
 * 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.analysis;

import java.util.*;

import jalview.datamodel.*;

/**
 * <p>Title: </p>
 *
 * <p>Description: </p>
 *
 * <p>Copyright: Copyright (c) 2004</p>
 *
 * <p>Company: Dundee University</p>
 *
 * @author not attributable
 * @version 1.0
 */
public class SeqsetUtils
{

  /**
   * Store essential properties of a sequence in a hashtable for later recovery
   *  Keys are Name, Start, End, SeqFeatures, PdbId
   * @param seq SequenceI
   * @return Hashtable
   */
  public static Hashtable SeqCharacterHash(SequenceI seq)
  {
    Hashtable sqinfo = new Hashtable();
    sqinfo.put("Name", seq.getName());
    sqinfo.put("Start", new Integer(seq.getStart()));
    sqinfo.put("End", new Integer(seq.getEnd()));
    if (seq.getDescription() != null)
    {
      sqinfo.put("Description", seq.getDescription());
    }
    Vector sfeat = new Vector();
    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
    if (sfarray != null && sfarray.length > 0)
    {
      for (int i = 0; i < sfarray.length; i++)
      {
        sfeat.addElement(sfarray[i]);
      }
    }
    sqinfo.put("SeqFeatures", sfeat);
    sqinfo.put("PdbId",
               (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
    sqinfo.put("datasetSequence",
               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() :
               new Sequence("THISISAPLACEHOLDER", ""));
    return sqinfo;
  }

  /**
   * Recover essential properties of a sequence from a hashtable
   * TODO: replace these methods with something more elegant.
   * @param sq SequenceI
   * @param sqinfo Hashtable
   * @return boolean true if name was not updated from sqinfo Name entry
   */
  public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
  {
    boolean namePresent = true;
    if (sqinfo == null)
    {
      return false;
    }
    String oldname = (String) sqinfo.get("Name");
    Integer start = (Integer) sqinfo.get("Start");
    Integer end = (Integer) sqinfo.get("End");
    Vector sfeatures = (Vector) sqinfo.get(
        "SeqFeatures");
    Vector pdbid = (Vector) sqinfo.get("PdbId");
    String description = (String) sqinfo.get("Description");
    Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
    if (oldname == null)
    {
      namePresent = false;
    }
    else
    {
      sq.setName(oldname);
    }
    if (pdbid != null && pdbid.size() > 0)
    {
      sq.setPDBId(pdbid);
    }

    if ( (start != null) && (end != null))
    {
      sq.setStart(start.intValue());
      sq.setEnd(end.intValue());
    }

    if ( (sfeatures != null) && (sfeatures.size() > 0))
    {
      SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()];
      for (int is=0,isize=sfeatures.size();is<isize;is++)
      { 
        sfarray[is] = (SequenceFeature) sfeatures.elementAt(is);
      }
      sq.setSequenceFeatures(sfarray);
    }
    if (description != null)
    {
      sq.setDescription(description);
    }
    if ( (seqds != null) &&
        ! (seqds.getName().equals("THISISAPLACEHOLDER") &&
           seqds.getLength() == 0))
    {
      sq.setDatasetSequence(seqds);
    }

    return namePresent;
  }

  /**
   * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
   * @param i int
   * @return String
   */
  public static String unique_name(int i)
  {
    return new String("Sequence" + i);
  }

  /**
   * Generates a hash of SeqCharacterHash properties for each sequence
   * in a sequence set, and optionally renames the sequences to an
   * unambiguous 'safe' name.
   * @param sequences SequenceI[]
   * @param write_names boolean set this to rename each of the sequences to its unique_name(index) name
   * @return Hashtable to be passed to @see deuniquify to recover original names (and properties) for renamed sequences
   */
  public static Hashtable uniquify(SequenceI[] sequences, boolean write_names)
  {
    // Generate a safely named sequence set and a hash to recover the sequence names
    Hashtable map = new Hashtable();
    //String[] un_names = new String[sequences.length];

    for (int i = 0; i < sequences.length; i++)
    {
      String safename = unique_name(i);
      map.put(safename, SeqCharacterHash(sequences[i]));

      if (write_names)
      {
        sequences[i].setName(safename);
      }
    }

    return map;
  }

  /**
   * recover unsafe sequence names and original properties for a sequence
   * set using a map generated by @see uniquify(sequences,true)
   * @param map Hashtable
   * @param sequences SequenceI[]
   * @return boolean
   */
  public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
  {
    return deuniquify(map, sequences, true);
  }
  /**
   * recover unsafe sequence names and original properties for a sequence
   * set using a map generated by @see uniquify(sequences,true)
   * @param map Hashtable
   * @param sequences SequenceI[]
   * @param quiet when false, don't complain about sequences without any data in the map. 
   * @return boolean
   */
    public static boolean deuniquify(Hashtable map, SequenceI[] sequences, boolean quiet)
    {
          jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
        sequences);
    SequenceI msq = null;
    Enumeration keys = map.keys();
    Vector unmatched = new Vector();
    for (int i = 0, j = sequences.length; i < j; i++)
    {
      unmatched.addElement(sequences[i]);
    }
    while (keys.hasMoreElements())
    {
      Object key = keys.nextElement();
      if (key instanceof String)
      {
        if ( (msq = matcher.findIdMatch( (String) key)) != null)
        {
          Hashtable sqinfo = (Hashtable) map.get(key);
          unmatched.removeElement(msq);
          SeqCharacterUnhash(msq, sqinfo);
        }
        else
        {
          if (!quiet)
            {
            System.err.println("Can't find '" + ( (String) key) +
                             "' in uniquified alignment");
            }
        }
      }
    }
    if (unmatched.size() > 0 && !quiet)
    {
      System.err.println("Did not find matches for :");
      for (Enumeration i = unmatched.elements(); i.hasMoreElements();
           System.out.println( ( (SequenceI) i.nextElement()).getName()))
      {
        ;
      }
      return false;
    }

    return true;
  }

  /**
   * returns a subset of the sequenceI seuqences,
   * including only those that contain at least one residue.
   * @param sequences SequenceI[]
   * @return SequenceI[]
   */
  public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
  {
    // Identify first row of alignment with residues for prediction
    boolean ungapped[] = new boolean[sequences.length];
    int msflen = 0;
    for (int i = 0, j = sequences.length; i < j; i++)
    {
      String tempseq = jalview.analysis.AlignSeq.extractGaps(
          jalview.util.Comparison.GapChars,
          sequences[i].getSequenceAsString());

      if (tempseq.length() == 0)
      {
        ungapped[i] = false;
      }
      else
      {
        ungapped[i] = true;
        msflen++;
      }
    }
    if (msflen == 0)
    {
      return null; // no minimal set
    }
    // compose minimal set
    SequenceI[] mset = new SequenceI[msflen];
    for (int i = 0, j = sequences.length, k = 0; i < j; i++)
    {
      if (ungapped[i])
      {
        mset[k++] = sequences[i];
      }
    }
    ungapped = null;
    return mset;
  }
}