package jalview.datamodel;

public abstract class CigarBase
{
  /**
   * Base class for compact idiosyncratic representation of gaps and aligned residues
   * Regards to Tom Oldfield for his DynamicArray class.
   * 17th July 2006
   * Not thread safe.
   */
  public CigarBase()
  {
    // nothing to be done (probably)
  }

  protected int length = 0;
  protected int _inc_length = 10; // extension range for addition of new operations
  protected char[] operation = null;
  protected int[] range = null;
  /**
   * Range of Hidden residues in seq (translated as deleted in seq)
   */
  public static final char D = 'D'; /**
  * Range of insertions to seq
  */
 public static final char I = 'I'; /**
  * Range of aligned residues
  */
 public static final char M = 'M';
  static protected final char _case_shift = 'a' - 'A';
  /**
   * Ugly function to get edited sequence string, start and end symbol positions and the deletion regions as an array of int pairs
   * May return null for an empty cigar string.
   * May return null for deletion ranges if there are none.
   * @param reference - the symbol sequence to apply the cigar operations to (or null if no sequence)
   * @param GapChar - the symbol to use for Insert operations
   * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3] {start, end, col} or null} the gapped sequence, first and last residue index, and the deletion ranges on the reference sequence
   */
  public Object[] getSequenceAndDeletions(String reference, char GapChar)
  {
    int rlength=0;
    int[][] deletions = new int[length][];
    int[][] trunc_deletions = null;
    StringBuffer sq = new StringBuffer();
    int cursor = 0, alcursor=0,start = 0, startpos=0, end = 0, endpos=0, delcount = -1;
    boolean consecutive_del = false;
    if (length == 0)
    {
      return null;
    }
    if (reference!=null)
      rlength=reference.length();
    boolean modstart = true;
    for (int i = 0; i < length; i++)
    {
      switch (operation[i])
      {
        case D:
          if (!consecutive_del)
          {
            deletions[++delcount] = new int[]
                {
                cursor, 0, alcursor};
          }
          cursor += range[i];
          deletions[delcount][1] = cursor - 1;
          consecutive_del = true;
          break;
        case I:
          consecutive_del = false;
          for (int r = 0; r < range[i]; r++)
          {
            sq.append(GapChar);
            alcursor++;
          }
          break;
        case M:
          consecutive_del = false;
          if (modstart)
          {
            start = cursor;
            startpos=alcursor;
            modstart = false;
          }
          if (reference!=null) {
            int sbend = cursor+range[i];
            if (sbend>=rlength) {
              sq.append(reference.substring(cursor, rlength));
              while (sbend-- >= rlength)
              {
                sq.append(GapChar);
              }
            } else {
              sq.append(reference.substring(cursor, sbend));
            }
          }
          alcursor+=range[i];
          cursor += range[i];
          end = cursor - 1;
          endpos = alcursor;
          break;
        default:
          throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
      }
    }
    if (++delcount > 0)
    {
      trunc_deletions = new int[delcount][];
      System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
    }
    deletions = null;
    return new Object[]
        {
        ((reference!=null) ? sq.toString() : null),
        new int[] {
        start, startpos, end, endpos}, trunc_deletions};
  }

  /**
   * turn a cigar string into a series of operation range pairs
   * @param cigarString String
   * @return object[] {char[] operation, int[] range}
   * @throws java.lang.Exception for improperly formated cigar strings or ones with unknown operations
   */
  public static Object[] parseCigarString(String cigarString)
      throws Exception
  {
    int ops = 0;
    for (int i = 0, l = cigarString.length(); i < l; i++)
    {
      char c = cigarString.charAt(i);
      if (c == M || c == (M - _case_shift) || c == I || c == (I - _case_shift) ||
          c == D || c == (D - _case_shift))
      {
        ops++;
      }
    }
    char[] operation = new char[ops];
    int[] range = new int[ops];
    int op = 0;
    int i = 0, l = cigarString.length();
    while (i < l)
    {
      char c;
      int j = i;
      do
      {
        c = cigarString.charAt(j++);
      }
      while (c >= '0' && c <= '9' && j < l);
      if (j >= l && c >= '0' && c <= '9')
      {
        throw new Exception("Unterminated cigar string.");
      }
      try
      {
        String rangeint = cigarString.substring(i, j - 1);
        range[op] = Integer.parseInt(rangeint);
        i = j;
      }
      catch (Exception e)
      {
        throw new Error("Implementation bug in parseCigarString");
      }
      if (c >= 'a' && c <= 'z')
      {
        c -= _case_shift;
      }
      if ( (c == M || c == I || c == D))
      {
        operation[op++] = c;
      }
      else
      {
        throw new Exception("Unexpected operation '" + c +
                            "' in cigar string (position " + i + " in '" +
                            cigarString + "'");
      }
    }
    return new Object[]
        {
        operation, range};
  }

  /**
   * inefficient add one operation to cigar string
   * @param op char
   * @param range int
   */
  public void addOperation(char op, int range)
  {
    if (op >= 'a' && op <= 'z')
    {
      op -= _case_shift;
    }
    if (op != M && op != D && op != I)
    {
      throw new Error("Implementation error. Invalid operation string.");
    }
    if (range<=0)
      throw new Error("Invalid range string (must be non-zero positive number)");
    int lngth = 0;
    if (operation == null)
    {
      this.operation = new char[_inc_length];
      this.range = new int[_inc_length];
    }
    if (length + 1 == operation.length)
    {
      char[] ops = this.operation;
      this.operation = new char[length + 1 + _inc_length];
      System.arraycopy(ops, 0, this.operation, 0, length);
      ops = null;
      int[] rng = this.range;
      this.range = new int[length + 1 + _inc_length];
      System.arraycopy(rng, 0, this.range, 0, length);
      rng = null;
    }
    if ((length>0) && (operation[length-1]==op))
      length--; // modify existing operation.
    else
      this.range[length]=0; // reset range
    this.operation[length] = op;
    this.range[length++] += range;
  }

  /**
   * semi-efficient insert an operation on the current cigar string set at column pos (from 1)
   * NOTE: Insertion operations simply extend width of cigar result - affecting registration of alignment
   * Deletion ops will shorten length of result - and affect registration of alignment
   * Match ops will also affect length of result - affecting registration of alignment
   * (ie "10M".insert(4,I,3)->"4M3I3M")
   * (ie "10M".insert(4,D,3)->"4M3D3M")
   * (ie "5I5M".insert(4,I,3)->"8I5M")
   * (ie "5I5M".insert(4,D,3)->"4I3M")
   * if pos is beyond width - I operations are added before the operation
   * (ie "10M".insert(4,M,3)->"13M")
   * (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts sequence left by 1 residue and extends it by 3
   * @param pos int
   * @param op char
   * @param range int
   */
  public void addOperationAt(int pos, char op, int range)
  {

  }

  /**
   * sum of ranges in cigar string
   * @return int number of residues hidden, matched, or gaps inserted into sequence
   */
  public int getFullWidth()
  {
    int w = 0;
    if (range != null)
    {
      for (int i = 0; i < length; i++)
      {
        w += range[i];
      }
    }
    return w;
  }

  /**
   * Visible length of aligned sequence
   * @return int length of including gaps and less hidden regions
   */
  public int getWidth()
  {
    int w = 0;
    if (range != null)
    {
      for (int i = 0; i < length; i++)
      {
        if (operation[i] == M || operation[i] == I)
        {
          w += range[i];
        }
      }
    }
    return w;
  }
  /**
   * mark a range of inserted residues
   * @param range int
   */
  public void addInsertion(int range)
  {
    this.addOperation(I, range);
  }

  /**
   * mark the next range residues as hidden (not aligned) or deleted
   * @param range int
   */
  public void addDeleted(int range)
  {
    this.addOperation(D, range);
  }

  /**
   * Modifies operation list to delete columns from start to end (inclusive)
   * editing will remove insertion operations, and convert matches to deletions
   * @param start alignment column
   * @param end alignment column
   * @return boolean true if residues were marked as deleted.
   */
  public boolean deleteRange(int start, int end)
  {
    boolean deleted = false;
    int op = 0, prevop = -1, firstm = -1,
        lastm = -1, postop = -1;
    int width = 0; // zero'th column
    if (length > 0)
    {
      // find operation bracketing start of the range
      do
      {
        if (operation[op] != D)
        {
          width += range[prevop = op];
        }
        op++;
      }
      while (op < length && width < start);
    }
    if (width < start)
    {
      // run off end - add more operations up to deletion.
      addInsertion(start - width);
    }
    else
    {
      // edit existing operations.
      op = prevop;
      width -= range[prevop];
      int[] oldrange = range;
      char[] oldops = operation;
      range = new int[oldrange.length];
      operation = new char[oldops.length];
      if (op < length)
      {
        do
        {
          if (operation[op] != D)
          {
            width += range[postop = op];
          }
          op++;
        }
        while (op < length && width <= end);
      }
    }
    if (deleted == true)
    {
      addDeleted(end - start + 1);
    }
    return deleted;
  }

  /**
   * Return an ENSEMBL style cigar string where D may indicates excluded parts of seq
   * @return String of form ([0-9]+[IMD])+
   */
  public String getCigarstring()
  {
    StringBuffer cigarString = new StringBuffer();
    for (int i = 0; i < length; i++)
    {
      cigarString.append("" + range[i]);
      cigarString.append(operation[i]);
    }
    return cigarString.toString();
  }
}