/*
 * 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.commands;

import jalview.datamodel.*;

import java.util.Hashtable;

/**
 *
 * <p>Title: EditCommmand</p>
 *
 * <p>Description: Essential information for performing
 * undo and redo for cut/paste insert/delete gap
 * which can be stored in the HistoryList </p>
 *
 * <p>Copyright: Copyright (c) 2006</p>
 *
 * <p>Company: Dundee University</p>
 *
 * @author not attributable
 * @version 1.0
 */
public class EditCommand implements CommandI
{
  public static final int INSERT_GAP = 0;
  public static final int DELETE_GAP = 1;
  public static final int CUT = 2;
  public static final int PASTE = 3;

  Edit[] edits;

  String description;

  public EditCommand()
  {}

  public EditCommand(String description)
  {
    this.description = description;
  }

  public EditCommand( String description,
                      int command,
                      SequenceI[] seqs,
                      int position,
                      int number,
                      AlignmentI al)
   {
     this.description = description;
     if ( command==CUT || command==PASTE)
     {
       edits = new Edit[]{new Edit(command, seqs, position, number, al)};
     }

     performEdit(0);
  }


  final public String getDescription()
  {
    return description;
  }

  public int getSize()
  {
    return edits==null?0:edits.length;
  }

  final public AlignmentI getAlignment()
  {
    return edits[0].al;
  }


  final public void appendEdit(int command,
                         SequenceI[] seqs,
                         int position,
                         int number,
                         AlignmentI al,
                         boolean performEdit)
  {
    Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());
    if(al.getHeight()==seqs.length)
    {
      edit.al = al;
      edit.fullAlignmentHeight = true;
    }

    if (edits != null)
    {
      Edit[] temp = new Edit[edits.length + 1];
      System.arraycopy(edits, 0, temp, 0, edits.length);
      edits = temp;
      edits[edits.length - 1] = edit;
    }
    else
      edits = new Edit[] {  edit  };

    if (performEdit)
      performEdit(edits.length - 1);
  }

  final void performEdit(int commandIndex)
  {
    int eSize = edits.length;
    for (int e = commandIndex; e < eSize; e++)
    {
      if (edits[e].command==INSERT_GAP)
      {
        insertGap(edits[e]);
      }
      else if (edits[e].command==DELETE_GAP)
      {
        deleteGap(edits[e]);
      }
      else if(edits[e].command==CUT)
      {
        cut(edits[e]);
      }
      else if(edits[e].command==PASTE)
      {
        paste(edits[e]);
      }
    }
  }

  final public void doCommand()
  {
    performEdit(0);
  }

  final public void undoCommand()
  {
    int e = 0, eSize = edits.length;
    for (e = eSize-1; e > -1; e--)
    {
      if (edits[e].command==INSERT_GAP)
      {
        deleteGap(edits[e]);
      }
      else if (edits[e].command==DELETE_GAP)
      {
        insertGap(edits[e]);
      }
      else if (edits[e].command==CUT)
      {
        paste(edits[e]);
      }
      else if (edits[e].command==PASTE)
      {
        cut(edits[e]);
      }
    }
  }

  final void insertGap(Edit command)
  {
    for(int s=0; s<command.seqs.length; s++)
    {
        command.seqs[s].insertCharAt(command.position,
                                     command.number,
                                     command.gapChar);
    }

    adjustAnnotations(command, true);
  }

  final void deleteGap(Edit command)
  {
    for (int s = 0; s < command.seqs.length; s++)
    {
      command.seqs[s].deleteChars(command.position, command.position+command.number);
    }

    adjustAnnotations(command, false);
  }

  void cut(Edit command)
  {
    command.string = new char [command.seqs.length][];

    for(int i=0; i<command.seqs.length; i++)
    {
      if(command.seqs[i].getLength()>command.position)
      {
        command.string[i] = command.seqs[i].getSequence(command.position,
            command.position + command.number);

        if(command.seqs[i].getDatasetSequence()!=null
        || command.seqs[i].getSequenceFeatures()!=null)
        {
          for (int s = command.position; s < command.position + command.number; s++)
          {
            if (jalview.schemes.ResidueProperties
                .aaIndex[command.seqs[i].getCharAt(s)] != 23)
            {
              adjustFeatures(command, i,
                             command.seqs[i].findPosition(command.position),
                             command.seqs[i].findPosition(command.position +
                                                          command.number),
                             false);
              break;
            }
          }
        }
        command.seqs[i].deleteChars(command.position,
                                    command.position + command.number);
      }

      if(command.seqs[i].getLength()<1)
      {
        command.al.deleteSequence(command.seqs[i]);
      }
    }

    adjustAnnotations(command, false);
  }

  void paste(Edit command)
  {
    StringBuffer tmp;
    boolean newDSNeeded;
    int start=0, end=0;

    for(int i=0; i<command.seqs.length; i++)
    {
      newDSNeeded = false;
      if(command.seqs[i].getLength()<1)
      {
        // ie this sequence was deleted, we need to
        // read it to the alignment
        if (command.alIndex[i] < command.al.getHeight())
          command.al.getSequences().insertElementAt(command.seqs[i],
              command.alIndex[i]);
        else
          command.al.addSequence(command.seqs[i]);
      }
      tmp = new StringBuffer();
      tmp.append(command.seqs[i].getSequence());

      if(command.string!=null && command.string[i]!=null)
      {
        if(command.position>=tmp.length())
        {
          //This occurs if padding is on, and residues
          //are removed from end of alignment
          int length = command.position-tmp.length();
          while (length > 0)
          {
            tmp.append(command.gapChar);
            length--;
          }
        }
        tmp.insert(command.position, command.string[i]);

        for (int s = 0; s < command.string[i].length; s++)
        {
          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
          {
            newDSNeeded = true;
            start = command.seqs[i].findPosition(command.position);
            end = command.seqs[i].findPosition(command.position+command.number);
            break;
          }
        }
        command.string[i] = null;
      }


      command.seqs[i].setSequence(tmp.toString());

      if(newDSNeeded)
      {
        if (command.seqs[i].getDatasetSequence() != null)
        {
          Sequence ds = new Sequence(command.seqs[i].getName(),
                                     jalview.analysis.AlignSeq.extractGaps(
                                         jalview.util.Comparison.GapChars,
                                         command.seqs[i].getSequenceAsString()
                                     ),
                                     command.seqs[i].getStart(),
                                     command.seqs[i].getEnd());
          ds.setDescription(command.seqs[i].getDescription());
          command.seqs[i].setDatasetSequence(ds);
        }

        adjustFeatures(command, i, start, end, true);
      }
    }


    adjustAnnotations(command, true);

    command.string = null;
  }


  final void adjustAnnotations(Edit command, boolean insert)
  {

    AlignmentAnnotation [] annotations = null;

    if (command.fullAlignmentHeight)
    {
      annotations = command.al.getAlignmentAnnotation();
    }
    else
    {
      int aSize = 0;
      AlignmentAnnotation [] tmp;
      for(int s=0; s<command.seqs.length; s++)
      {
        if(command.seqs[s].getAnnotation()==null)
          continue;

        if (aSize == 0)
            annotations = command.seqs[s].getAnnotation();
        else
        {
          tmp = new AlignmentAnnotation
              [aSize + command.seqs[s].getAnnotation().length];

          System.arraycopy(annotations,0,tmp,0,aSize);

          System.arraycopy(command.seqs[s].getAnnotation(),
              0,tmp,aSize,command.seqs[s].getAnnotation().length);

          annotations = tmp;
        }


        aSize = annotations.length;
      }
    }

    if(annotations==null)
      return;


      if(!insert)
        command.deletedAnnotations = new Hashtable();

      int aSize;
      Annotation [] temp;
      for (int a = 0; a < annotations.length; a++)
      {
        if(annotations[a].autoCalculated)
        {
          continue;
        }

        aSize = annotations[a].annotations.length;
        if(insert)
          temp = new Annotation[aSize + command.number];
        else
        {
          if(command.position<aSize)
          {
            if (aSize - command.number + command.position > 0)
              temp = new Annotation[aSize - command.number + command.position];
            else
              temp = new Annotation[aSize];
          }
          else
            temp = new Annotation[aSize];
        }

        if(insert)
        {
          if(command.position < annotations[a].annotations.length)
          {
            System.arraycopy(annotations[a].annotations,
                             0, temp, 0, command.position);

            if (command.deletedAnnotations != null
                &&
                command.deletedAnnotations.containsKey(annotations[a].annotationId))
            {
              Annotation[] restore = (Annotation[])
                  command.deletedAnnotations.get(annotations[a].annotationId);

              System.arraycopy(restore,
                               0,
                               temp,
                               command.position,
                               command.number);

            }

            System.arraycopy(annotations[a].annotations,
                             command.position, temp,
                             command.position + command.number,
                             aSize - command.position);
          }
          else
            temp = annotations[a].annotations;
        }
        else
        {
          if(command.position < aSize &&  aSize - command.number+command.position>0)
          {
            System.arraycopy(annotations[a].annotations,
                             0, temp, 0, command.position);

            Annotation[] deleted = new Annotation[command.number];
            System.arraycopy(annotations[a].annotations,
                             command.position, deleted, 0, command.number);

            command.deletedAnnotations.put(annotations[a].annotationId,
                                           deleted);

            System.arraycopy(annotations[a].annotations,
                             command.position + command.number,
                             temp, command.position,
                             aSize - command.position - command.number);
          }
          else
            temp = annotations[a].annotations;
        }

        annotations[a].annotations = temp;
     }
  }

  final void adjustFeatures(Edit command, int index, int i, int j, boolean insert)
  {
    SequenceI seq = command.seqs[index];
    SequenceI sequence = seq.getDatasetSequence();
    if(sequence==null)
      sequence = seq;

    if(insert)
    {
      if (command.editedFeatures != null
          && command.editedFeatures.containsKey(seq))
        sequence.setSequenceFeatures(
            (SequenceFeature[]) command.editedFeatures.get(seq)
            );

      return;
    }


    SequenceFeature [] sf = sequence.getSequenceFeatures();


    if(sf==null)
    {
      return;
    }

    SequenceFeature [] oldsf = new SequenceFeature[sf.length];

    int cSize = j - i;

    for (int s = 0; s < sf.length; s++)
    {
      SequenceFeature copy = new SequenceFeature(sf[s]);

      oldsf[s] = copy;

      if (sf[s].getEnd() < i)
        continue;

      if (sf[s].getBegin() > j)
      {
        sf[s].setBegin(copy.getBegin() - cSize);
        sf[s].setEnd(copy.getEnd() - cSize);
        continue;
      }

      if (sf[s].getBegin() >= i)
        sf[s].setBegin(i);

      if (sf[s].getEnd() < j)
        sf[s].setEnd(j - 1);

      sf[s].setEnd(sf[s].getEnd() - (cSize));

      if (sf[s].getBegin() > sf[s].getEnd())
        sequence.deleteFeature(sf[s]);
    }

    if (command.editedFeatures == null)
      command.editedFeatures = new Hashtable();

    command.editedFeatures.put(seq, oldsf);

  }


  class Edit
  {
    boolean fullAlignmentHeight = false;
    Hashtable deletedAnnotations;
    Hashtable editedFeatures;
    AlignmentI al;
    int command;
    char [][] string;
    SequenceI[] seqs;
    int [] alIndex;
    int position, number;
    char gapChar;

    Edit(int command,
         SequenceI[] seqs,
         int position,
         int number,
         char gapChar)
    {
      this.command = command;
      this.seqs = seqs;
      this.position = position;
      this.number = number;
      this.gapChar = gapChar;
    }


    Edit(int command,
         SequenceI[] seqs,
         int position,
         int number,
         AlignmentI al)
    {
      this.gapChar = al.getGapCharacter();
      this.command = command;
      this.seqs = seqs;
      this.position = position;
      this.number = number;
      this.al = al;

      alIndex = new int[seqs.length];
      for(int i=0; i<seqs.length; i++)
      {
        alIndex[i] = al.findIndex(seqs[i]);
      }

      fullAlignmentHeight = (al.getHeight()==seqs.length);
    }
  }

}