/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 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 jalview.util.ShiftList;

import java.util.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class HistoryItem
{
  /** DOCUMENT ME!! */
  public static final int EDIT = 0;

  /** DOCUMENT ME!! */
  public static final int SORT = 1;

  /** DOCUMENT ME!! */
  public static final int HIDE = 2;

  /** DOCUMENT ME!! */
  public static final int PASTE = 3;

  final int type;

  AlignmentI alignment;
  String description;

  Vector sequences;
  Vector seqAsString;
  Vector alignIndex;

  Vector hiddenSeqs;
  Vector hiddenSeqsAsString;
  /**
   * public field - set directly if history involves a frame shift
   * should contain the <em>inverse</em> frame shift operations.
   */
  public ShiftList alColumnChanges=null;

  /**
   * Creates a new HistoryItem object.
   *
   * @param description DOCUMENT ME!
   * @param al DOCUMENT ME!
   * @param type DOCUMENT ME!
   */
  public HistoryItem(String description, AlignmentI al, int type)
  {
    alignment = al;
    this.type = type;
    this.description = description;
    sequences = new Vector();
    alignIndex = new Vector();
    seqAsString = new Vector();

    for (int i = 0; i < al.getHeight(); i++)
    {
      SequenceI seq = al.getSequenceAt(i);
      sequences.addElement(seq);
      alignIndex.addElement(i + "");
      seqAsString.addElement(seq.getStart()
                             +" "+seq.getEnd()
                             +" "+seq.getSequence().toString());
    }

    if(alignment.getHiddenSequences()!=null
       && alignment.getHiddenSequences().getSize()>0)
    {
      hiddenSeqs = new Vector();
      hiddenSeqsAsString = new Vector();
      Enumeration en = alignment.getHiddenSequences().hiddenSequences.elements();
      while (en.hasMoreElements())
      {
        SequenceI key = (SequenceI) en.nextElement();
        hiddenSeqs.addElement(key);
        hiddenSeqsAsString.addElement(key.getSequence().toString());
      }
    }
  }
  /**
   * DOCUMENT ME!
   *
   * @return DOCUMENT ME!
   */
  public String getDescription()
  {
    return description;
  }

  /**
   * restore state - adjusting gui hiddenColumn view as necessary
   * @param columnSelection
   */
  public void restore(ColumnSelection columnSelection)
  {
    if (type == HistoryItem.SORT)
    {
      for (int i = 0; i < sequences.size(); i++)
      {
        alignment.getSequences().setElementAt(sequences.elementAt(i), i);
      }
    }
    else
    {
      StringTokenizer st;
      for (int i = 0; i < sequences.size(); i++)
      {
        SequenceI restore = (SequenceI) sequences.elementAt(i);


        if (restore.getLength() == 0)
        {
          //This is for edits which remove all residues in a sequence
          alignment.getSequences().insertElementAt(restore,
              Integer.parseInt(alignIndex.elementAt(i).toString()));
        }

        st = new StringTokenizer(seqAsString.elementAt(i).toString());
        restore.setStart(Integer.parseInt(st.nextToken()));
        restore.setEnd(Integer.parseInt(st.nextToken()));
        restore.setSequence(st.nextToken());
      }

      if(hiddenSeqs!=null)
      {
        for(int hs=0; hs<hiddenSeqs.size(); hs++)
        {
          SequenceI key = (SequenceI) hiddenSeqs.elementAt(hs);
          key.setSequence(hiddenSeqsAsString.elementAt(hs).toString());
        }
      }

      if (type == HistoryItem.PASTE)
      {
        for (int i = alignment.getHeight() - 1;
             i > (sequences.size() - 1); i--)
        {
          alignment.deleteSequence(i);
        }
      }
      if (alColumnChanges!=null) {
        columnSelection.compensateForEdits(alColumnChanges);
      }
    }

  }
  /**
   * note a frame shift that must be compensated for
   * @param pos start position for shift (in original reference frame)
   * @param shift length of shift
   */
  public void addShift(int pos, int shift) {
    if (alColumnChanges==null)
      alColumnChanges = new ShiftList();
    alColumnChanges.addShift(pos, -shift);
  }
}