/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 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.datamodel;

import java.util.*;

public class HiddenSequences
{
  Hashtable hiddenSequences;
  AlignmentI alignment;

  public HiddenSequences(AlignmentI al)
  {
    alignment = al;
  }

  public int getSize()
  {
    return hiddenSequences == null ? 0 : hiddenSequences.size();
  }

  public int getWidth()
  {
    Enumeration en = hiddenSequences.elements();
    int width = 0;
    while(en.hasMoreElements())
    {
      SequenceI seq = (SequenceI)en.nextElement();
      if(seq.getLength()>width)
        width = seq.getLength();
    }
    return width;
  }

  public void hideSequence(SequenceI sequence)
  {
    if(hiddenSequences==null)
      hiddenSequences = new Hashtable();

    int alignmentIndex = alignment.findIndex(sequence);
    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);

    hiddenSequences.put(new Integer(alignmentIndex), sequence);

    alignment.deleteSequence(sequence);
  }

  public void showAll()
  {
   for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)
     showSequence(i);
  }

  public void showSequence(int alignmentIndex)
  {
    SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
    if(repSequence!=null
       && repSequence.getHiddenSequences()==null
       && alignmentIndex>0)
      repSequence = alignment.getSequenceAt(alignmentIndex-1);

    if(repSequence!=null
       && repSequence.getHiddenSequences()==null)
      repSequence = null;

    int start = adjustForHiddenSeqs(alignmentIndex-1);
    int end = adjustForHiddenSeqs(alignmentIndex);

    for(int index = end; index > start; index--)
    {
      SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(
          index));

      if(seq!=null)
      {
        alignment.getSequences().insertElementAt(seq, alignmentIndex);
        if(repSequence!=null)
        {
          repSequence.showHiddenSequence(seq);
        }
      }
    }
  }

  public Hashtable getHiddenSequences()
  {
    return hiddenSequences;
  }

  public SequenceI getHiddenSequence(int alignmentIndex)
  {
    return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));
  }

  public int findIndexWithoutHiddenSeqs(int alignmentIndex)
  {
    int index = 0;
    int hiddenSeqs = 0;
    while(index <= alignmentIndex)
    {
     if(hiddenSequences.containsKey(new Integer(index)))
     {
       hiddenSeqs ++;
     }
      index ++;
    };

    return (alignmentIndex - hiddenSeqs) ;
  }

  public int adjustForHiddenSeqs(int alignmentIndex)
  {
    int index = 0;
    while(index <= alignmentIndex)
    {
     if(hiddenSequences.containsKey(new Integer(index)))
     {
       alignmentIndex ++;
     }
      index ++;
    };

    return alignmentIndex ;
  }

  public AlignmentI getFullAlignment()
  {
    int isize = alignment.getHeight()+hiddenSequences.size();
    SequenceI [] seq = new Sequence[isize];

    Enumeration en = hiddenSequences.keys();
    while(en.hasMoreElements())
    {
      Integer key = (Integer)en.nextElement();
      seq[key.intValue()] = (SequenceI)hiddenSequences.get(key);
    }

    int index = 0;
    for(int i=0; i<isize; i++)
    {
      if(seq[i]!=null)
      {
        continue;
      }

      seq[i] = alignment.getSequenceAt(index);
      index++;
    }

    return new Alignment(seq);
  }

  public boolean isHidden(SequenceI seq)
  {
    return hiddenSequences.contains(seq);
  }
}