/*
 * 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.commands;

import java.util.*;

import jalview.datamodel.*;

/**
 *
 * <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;
  public static final int REPLACE = 4;

  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, null);
  }

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

    performEdit(0, null);
  }

  final public String getDescription()
  {
    return description;
  }

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

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

  /**
   * append a new editCommand
   * Note. this shouldn't be called if the edit is an operation affects more alignment objects than the one referenced
   * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter.
   * @param command
   * @param seqs
   * @param position
   * @param number
   * @param al
   * @param performEdit
   */
  final public void appendEdit(int command,
          SequenceI[] seqs,
          int position,
          int number,
          AlignmentI al,
          boolean performEdit)
  {
    appendEdit(command, seqs, position, number, al, performEdit, null);
  }
  /**
   * append a new edit command with a set of alignment views that may be operated on
   * @param command
   * @param seqs
   * @param position
   * @param number
   * @param al
   * @param performEdit
   * @param views
   */
  final public void appendEdit(int command,
                               SequenceI[] seqs,
                               int position,
                               int number,
                               AlignmentI al,
                               boolean performEdit, AlignmentI[] views)
  {
    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, views);
    }
  }

  final void performEdit(int commandIndex, AlignmentI[] views)
  {
    int eSize = edits.length;
    for (int e = commandIndex; e < eSize; e++)
    {
      switch(edits[e].command)
      {
        case INSERT_GAP:
        insertGap(edits[e]);
          break;
        case DELETE_GAP:
        deleteGap(edits[e]);
          break;
        case CUT:
        cut(edits[e], views);
          break;
        case PASTE:
        paste(edits[e], views);
          break;
        case REPLACE:
          replace(edits[e]);
          break;
      }
    }
  }

  final public void doCommand(AlignmentI[] views)
  {
    performEdit(0,views);
  }

  final public void undoCommand(AlignmentI[] views)
  {
    int e = 0, eSize = edits.length;
    for (e = eSize - 1; e > -1; e--)
    {
      switch (edits[e].command)
      {
        case INSERT_GAP:
        deleteGap(edits[e]);
          break;
        case DELETE_GAP:
        insertGap(edits[e]);
          break;
        case CUT:
        paste(edits[e], views);
          break;
        case PASTE:
        cut(edits[e], views);
          break;
        case REPLACE:
          replace(edits[e]);
          break;
      }
    }
  }

  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, false, null);
  }

  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, false, null);
  }

  void cut(Edit command, AlignmentI[] views)
  {
    boolean seqDeleted=false;
    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]);
        seqDeleted=true;
      }
    }

    adjustAnnotations(command, false, seqDeleted, views);
  }

  void paste(Edit command, AlignmentI[] views)
  {
    StringBuffer tmp;
    boolean newDSNeeded;
    boolean seqWasDeleted=false;
    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]);
        }
        seqWasDeleted=true;
      }
      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)
        { // use new ds mechanism here
          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, seqWasDeleted, views);

    command.string = null;
  }

  void replace(Edit command)
  {
    StringBuffer tmp;
    String oldstring;
    int start = command.position;
    int end = command.number;

    command.number = start + command.string[0].length;
    for (int i = 0; i < command.seqs.length; i++)
    {
      oldstring = command.seqs[i].getSequenceAsString();
      tmp = new StringBuffer(oldstring.substring(0, start));
      tmp.append(command.string[i]);
      tmp.append(oldstring.substring(end));
      command.seqs[i].setSequence(tmp.toString());
      command.string[i] = oldstring.substring(start, end).toCharArray();
      tmp = null;
      oldstring = null;
    }
  }

  final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility, AlignmentI[] views)
  {
    AlignmentAnnotation[] annotations = null;

    if (modifyVisibility && !insert)
    {
      // only occurs if a sequence was added or deleted.
      command.deletedAnnotationRows = new Hashtable();
    }
    if (command.fullAlignmentHeight)
    {
      annotations = command.al.getAlignmentAnnotation();
    }
    else
    {
      int aSize = 0;
      AlignmentAnnotation[] tmp;
      for (int s = 0; s < command.seqs.length; s++)
      {
        if (modifyVisibility)
        {
          // Rows are only removed or added to sequence object.
          if (!insert) {
            // remove rows
            tmp = command.seqs[s].getAnnotation();
            if (tmp!=null) {
              int alen=tmp.length;
              for (int aa =0; aa<tmp.length; aa++)
              {
                if (!command.al.deleteAnnotation(tmp[aa]))
                {
                  // strip out annotation not in the current al (will be put back on insert in all views)
                  tmp[aa] = null;
                  alen--;
                }
              }
              command.seqs[s].setAlignmentAnnotation(null);
              if (alen!=tmp.length)
              {
                // save the non-null annotation references only
                AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
                for (int aa=0,aapos=0;aa<tmp.length;aa++)
                {
                  if (tmp[aa]!=null)
                  {
                    saved[aapos++] = tmp[aa];
                    tmp[aa] = null;
                  }
                }
                tmp = saved;
                command.deletedAnnotationRows.put(command.seqs[s], saved);
                // and then remove any annotation in the other views
                for (int alview=0; views!=null && alview<views.length; alview++)
                {
                  if (views[alview]!=command.al)
                  {
                    AlignmentAnnotation[] toremove = views[alview].getAlignmentAnnotation();
                    if (toremove==null || toremove.length==0)
                    {
                      continue;
                    }
                    // remove any alignment annotation on this sequence that's on that alignment view.
                    for (int aa = 0; aa<toremove.length; aa++)
                    {
                      if (toremove[aa].sequenceRef==command.seqs[s])
                      {
                        views[alview].deleteAnnotation(toremove[aa]);
                      }
                    }
                  }
                }
              } else {
                // save all the annotation
                command.deletedAnnotationRows.put(command.seqs[s], tmp);
              }
            }
          } else {
            // recover rows
            if (command.deletedAnnotationRows!=null && command.deletedAnnotationRows.containsKey(command.seqs[s]))
            {
              AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows.get(command.seqs[s]);
              command.seqs[s].setAlignmentAnnotation(revealed);
              if (revealed!=null) {
                for (int aa =0; aa<revealed.length; aa++)
                {
                  // iterate through al adding original annotation
                  command.al.addAnnotation(revealed[aa]);
                }
                for (int aa =0; aa<revealed.length; aa++)
                {
                  command.al.setAnnotationIndex(revealed[aa], aa);
                }
                // and then duplicate added annotation on every other alignment view
                for (int vnum=0; views!=null && vnum<views.length; vnum++)
                {
                  if (views[vnum]!=command.al)
                  {
                    int avwidth = views[vnum].getWidth()+1;
                    // duplicate in this view
                    for (int a=0; a<revealed.length; a++)
                    {
                      AlignmentAnnotation newann = new AlignmentAnnotation(revealed[a]);
                      command.seqs[s].addAlignmentAnnotation(newann);
                      newann.padAnnotation(avwidth);
                      views[vnum].addAnnotation(newann);
                      views[vnum].setAnnotationIndex(newann, a);
                    }
                  }
                }
              }
            }
          }
          continue;
        }

        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 || annotations[a].annotations == null)
      {
        continue;
      }

      int tSize = 0;

      aSize = annotations[a].annotations.length;
      if (insert)
      {
        temp = new Annotation[aSize + command.number];
        if(annotations[a].padGaps)
          for (int aa = 0; aa < temp.length; aa++)
          {
            temp[aa] = new Annotation(
                command.gapChar+"",
                null, ' ', 0);
          }
      }
      else
      {
        if (command.position < aSize)
        {
          if (command.position + command.number >= aSize)
          {
            tSize = aSize;
          }
          else
          {
            tSize = aSize - command.number;
          }
        }
        else
        {
          tSize = aSize;
        }

        if (tSize < 0)
        {
          tSize = aSize;
        }
        temp = new Annotation[tSize];
      }


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

            temp = new Annotation[annotations[a].annotations.length +
                restore.length];
            System.arraycopy(annotations[a].annotations,
                             0, temp, 0,
                             annotations[a].annotations.length);
            System.arraycopy(restore, 0, temp,
                             annotations[a].annotations.length, restore.length);
          }
          else
          {
            temp = annotations[a].annotations;
          }
        }
      }
      else
      {
        if (tSize != aSize || command.position < 2)
        {
          int copylen = Math.min(command.position, annotations[a].annotations.length);
          if (copylen>0)
            System.arraycopy(annotations[a].annotations,
                           0, temp, 0, copylen); //command.position);

          Annotation[] deleted = new Annotation[command.number];
          if (copylen>=command.position) {
            copylen = Math.min(command.number, annotations[a].annotations.length-command.position);
            if (copylen>0)
            {
              System.arraycopy(annotations[a].annotations,
                      command.position, deleted, 0, copylen); // command.number);
            }
          }

          command.deletedAnnotations.put(annotations[a].annotationId,
                                         deleted);
          if (annotations[a].annotations.length>command.position+command.number) {
            System.arraycopy(annotations[a].annotations,
                           command.position + command.number,
                           temp, command.position,
                           annotations[a].annotations.length - command.position - command.number); // aSize
          }
        }
        else
        {
          int dSize = aSize - command.position;

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

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

            tSize = Math.min(annotations[a].annotations.length,
                             command.position);
            temp = new Annotation[tSize];
            System.arraycopy(annotations[a].annotations,
                             0, temp, 0, tSize);
          }
          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 deletedAnnotationRows;
    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);
    }

    Edit(int command,
         SequenceI[] seqs,
         int position,
         int number,
         AlignmentI al,
         String replace)
    {
      this.command = command;
      this.seqs = seqs;
      this.position = position;
      this.number = number;
      this.al = al;
      this.gapChar = al.getGapCharacter();
      string = new char[seqs.length][];
      for (int i = 0; i < seqs.length; i++)
      {
        string[i] = replace.toCharArray();
      }

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