/*
 * 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.datamodel;

public class CigarArray
    extends CigarBase
{
  /**
   * Do CIGAR operations on a set of sequences from many other cigars
   * BAD THINGS WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY
   * or a CIGARCIGAR is given a CIGARARRAY to insert gaps into.
   */
  /**
   * array of subject cigars
   */
  public CigarSimple refCigars[] = null;
  private boolean seqcigararray = false;
  private CigarArray()
  {
    super();
  }

  /**
   * isSeqCigarArray()
   * @return boolean true if all refCigars resolve to a SeqCigar or a CigarCigar
   */
  public boolean isSeqCigarArray()
  {
    return seqcigararray;
  }

  /**
   * Apply CIGAR operations to several cigars in parallel
   * will throw an error if any of cigar are actually CigarArrays.
   * @param cigar Cigar[]
   */
  public CigarArray(CigarSimple[] cigars)
  {
    super();
    seqcigararray = true;
    if (cigars != null && cigars.length > 0)
    {
      refCigars = new CigarSimple[cigars.length];
      for (int c = 0; c < cigars.length; c++)
      {
        refCigars[c] = cigars[c];
        if (! ( (cigars[c] instanceof SeqCigar)
               || cigars[c] instanceof CigarCigar))
        {
          seqcigararray = false;
        }
      }
    }
  }

  /**
   * @see Cigar.getSequenceAndDeletions
   * @param GapChar char
   * @return Object[][]
   */
  protected Object[][] getArrayofSequenceAndDeletions(char GapChar)
  {
    if (refCigars == null || refCigars.length == 0 || length == 0)
    {
      return null;
    }
    Object[][] sqanddels = new Object[refCigars.length][];
    for (int c = 0; c < refCigars.length; c++)
    {
      String refString = refCigars[c].getSequenceString(GapChar);
      if (refString != null)
      {
        sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
      }
      else
      {
        sqanddels[c] = null;
      }
    }
    return sqanddels;
  }

  /**
   * NOTE: this is an improper sequence string function
   * @return String formed by newline concatenated results of applying CIGAR operations to each reference object in turn.
   * @param GapChar char
   * @return '\n' separated strings (empty results included as \n\n)
   */
  public String getSequenceString(char GapChar)
  {
    if (length == 0 || refCigars == null)
    {
      return "";
    }
    StringBuffer seqStrings = new StringBuffer();
    Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
    for (int c = 0; c < refCigars.length; c++)
    {
      if (sqanddels[c] != null)
      {
        seqStrings.append( (String) sqanddels[c][0]);
        sqanddels[c][0] = null;
      }
      seqStrings.append('\n');
    }
    return seqStrings.toString();
  }

  /**
   * return string results of applying cigar string to all reference cigars
   * @param GapChar char
   * @return String[]
   */
  public String[] getSequenceStrings(char GapChar)
  {

    if (length == 0 || refCigars == null || refCigars.length == 0)
    {
      return null;
    }
    Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
    String[] seqs = new String[sqanddels.length];
    for (int c = 0; c < refCigars.length; c++)
    {
      seqs[c] = (String) sqanddels[c][0];
    }
    return seqs;
  }

  /**
   * Combines the CigarArray cigar operations with the operations in each
   * reference cigar - creating a new reference cigar
   * @return Cigar[]

     public CigarBase[] getEditedCigars() {

    return new CigarBase[] {};
     }
   */
  /**
   * applyDeletions
   * edits underlying refCigars to propagate deleted regions, and removes deletion
   * operations from CigarArray operation list.
   * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured
   */
  public int[] applyDeletions()
  {
    java.util.Vector delpos = null;
    if (length == 0)
    {
      return null;
    }
    int cursor = 0; // range counter for deletions
    int vcursor = 0; // visible column index
    int offset = 0; // shift in visible column index as deletions are made
    int i = 0;
    while (i < length)
    {
      if (operation[i] != D)
      {
        if (operation[i] == M)
        {
          cursor += range[i];
        }
        vcursor += range[i++];
      }
      else
      {
        if (delpos == null)
        {
          delpos = new java.util.Vector();
        }
        int delstart = cursor, delend = cursor + range[i] - 1; // inclusive
        delpos.addElement(new int[]
                          {vcursor + offset, range[i]}); // index of right hand column after hidden region boundary
        offset += range[i] - 1; // shift in visible column coordinates
        System.arraycopy(operation, i + 1, operation, i, length - i);
        System.arraycopy(range, i + 1, range, i, length - i);
        length--;
        /*        int dmax=0;
         for (int s=0; s<refCigars.length; s++) {
           int d = refCigars[s].deleteRange(delstart, delend);
           if (d>dmax)
             dmax=d;
         }
         offset+=dmax; // shift in visible column coordinates
         */
        for (int s = 0; s < refCigars.length; s++)
        {
          int d = refCigars[s].deleteRange(delstart, delend);
        }

      }
    }
    if (delpos != null)
    {
      int[] pos = new int[delpos.size() * 2];
      for (int k = 0, l = delpos.size(); k < l; k++)
      {
        int[] dr = ( (int[]) delpos.elementAt(k));
        pos[k * 2] = dr[0];
        pos[k * 2 + 1] = dr[1];
        delpos.setElementAt(null, k);
      }
      delpos = null;
      return pos;
    }
    return null;
  }

  /**
   *
   * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does not resolve to set of seqCigars)
   */
  public SeqCigar[] getSeqCigarArray()
  {
    if (!isSeqCigarArray())
    {
      return null;
    }
    SeqCigar[] sa = new SeqCigar[refCigars.length];
    for (int i = 0; i < refCigars.length; i++)
    {
      sa[i] = (SeqCigar) refCigars[i];
    }
    return sa;
  }
}