/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3 of the License, or (at your option) any later version.
 * 
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 */
package jalview.datamodel;

import java.util.*;

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 };
  }

  protected void compact_operations()
  {
    int i = 1;
    if (operation == null)
    {
      return;
    }
    char last = operation[0];
    while (i < length)
    {
      if (last == operation[i])
      {
        range[i - 1] += range[i];
        int r = length - i;
        if (r > 0)
        {
          System.arraycopy(range, i + 1, range, i, r);
          System.arraycopy(operation, i + 1, operation, i, r);
        }
        length--;
      }
      else
      {
        last = operation[i++];
      }
    }
  }

  /**
   * 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 };
  }

  /**
   * add an 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)
    {
      return; // No Operation to add.
    }
    if (range < 0)
    {
      throw new Error(
              "Invalid range string (must be zero or 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") - (replace?) (ie
   * "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment) (ie
   * "5I5M".insert(4,I,3)->"8I5M") - real insertion (ie
   * "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms
   * changed to Ds (ie "10M".insert(4,M,3)->"13M") - lengthens - Is changed to
   * M, Ds changed to M. (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts
   * sequence left by 1 residue and extends it by 3 (
   * "10D5M".insert(-1,M,3)->"3M7D5M") ( "10D5M".insert(0,M,3)->"7D8M") (
   * "10D5M".insert(1,M,3)->"10D8M") ( "1M10D5M".insert(0,M,3)->"1M10D8M") (
   * "1M10D5M".insert(1,M,3)->"
   * 
   * if pos is beyond width - I operations are added before the operation
   * 
   * @param pos
   *          int -1, 0-length of visible region, or greater to append new ops
   *          (with insertions in between)
   * @param op
   *          char
   * @param range
   *          int public void addOperationAt(int pos, char op, int range) { int
   *          cursor = -1; // mark the position for the current operation being
   *          edited. int o = 0; boolean last_d = false; // previous op was a
   *          deletion. if (pos < -1) throw new
   *          Error("pos<-1 is not supported."); while (o<length) { if
   *          (operation[o] != D) { if ( (cursor + this.range[o]) < pos) {
   *          cursor += this.range[o]; o++; last_d=false; } else { break; } }
   *          else { last_d=true; o++; } } if (o==length) { // must insert more
   *          operations before pos if (pos-cursor>0) addInsertion(pos-cursor);
   *          // then just add the new operation. Regardless of what it is.
   *          addOperation(op, range); } else { int diff = pos - cursor;
   * 
   *          int e_length = length-o; // new edit operation array length. //
   *          diff<0 - can only happen before first insertion or match. -
   *          affects op and all following // dif==0 - only when at first
   *          position of existing op - // diff>0 - must preserve some existing
   *          operations int[] e_range = new int[e_length];
   *          System.arraycopy(this.range, o, e_range, 0, e_length); char[] e_op
   *          = new char[e_length]; System.arraycopy(this.operation, o, e_op, 0,
   *          e_length); length = o; // can now use add_operation to extend
   *          list. int e_o=0; // current operation being edited. switch (op) {
   *          case M: switch (e_op[e_o]) { case M: if (last_d && diff <= 0) { //
   *          reduce D's, if possible if (range<=this.range[o-1]) { this.range[o
   *          - 1] -= range; } else { this.range[o-1]=0; } if
   *          (this.range[o-1]==0) o--; // lose this op. } e_range[e_o] +=
   *          range; // just add more matched residues break; case I: // change
   *          from insertion to match if (last_d && diff<=0) { // reduce D's, if
   *          possible if (range<=this.range[o-1]) { this.range[o - 1] -= range;
   *          } else { this.range[o-1]=0; } if (this.range[o-1]==0) o--; // lose
   *          this op. } e_range[e_o] break; default: throw new Inp }
   * 
   *          break; case I: break; case D: } break; default: throw new
   *          Error("Implementation Error: Unknown operation in addOperation!");
   *          } // finally, add remaining ops. while (e_o<e_length) {
   *          addOperation(e_op[e_o], e_range[e_o]); e_o++; } } }
   */
  /**
   * Mark residues from start to end (inclusive) as deleted from the alignment,
   * and removes any insertions.
   * 
   * @param start
   *          int
   * @param end
   *          int
   * @return deleted int - number of symbols marked as deleted
   */
  public int deleteRange(int start, int end)
  {
    int deleted = 0;
    if (length == 0)
    {
      // nothing to do here
      return deleted;
    }
    if (start < 0 || start > end)
    {
      throw new Error(
              "Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
    }
    // find beginning
    int cursor = 0; // mark the position for the current operation being edited.
    int rlength = 1 + end - start; // number of positions to delete
    int oldlen = length;
    int o = 0;
    boolean editing = false;
    char[] oldops = operation;
    int[] oldrange = range;
    length = 0;
    operation = null;
    range = null;
    compact_operations();
    while (o < oldlen && cursor <= end && rlength > 0)
    {
      if (oldops[o] == D)
      {
        // absorbed into new deleted region.
        addDeleted(oldrange[o++]);
        continue;
      }

      int remain = oldrange[o]; // number of op characters left to edit
      if (!editing)
      {
        if ((cursor + remain) <= start)
        {
          addOperation(oldops[o], oldrange[o]);
          cursor += oldrange[o++];
          continue; // next operation
        }
        editing = true;
        // add operations before hidden region
        if (start - cursor > 0)
        {
          addOperation(oldops[o], start - cursor);
          remain -= start - cursor;
        }
      }
      // start inserting new ops
      if (o < oldlen && editing && rlength > 0 && remain > 0)
      {
        switch (oldops[o])
        {
        case M:
          if (rlength > remain)
          {
            addDeleted(remain);
            deleted += remain;
          }
          else
          {
            deleted += rlength;
            addDeleted(rlength);
            if (remain - rlength > 0)
            {
              this.addOperation(M, remain - rlength); // add remaining back.
            }
            rlength = 0;
            remain = 0;
          }
          break;
        case I:
          if (remain - rlength > 0)
          {
            // only remove some gaps
            addInsertion(remain - rlength);
            rlength = 0;
          }
          break;
        case D:
          throw new Error("Implementation error."); // do nothing;
        default:
          throw new Error("Implementation Error! Unknown operation '"
                  + oldops[o] + "'");
        }
        rlength -= remain;
        remain = oldrange[++o]; // number of op characters left to edit
      }
    }
    // add remaining
    while (o < oldlen)
    {
      addOperation(oldops[o], oldrange[o++]);
    }
    // if (cursor<(start+1)) {
    // ran out of ops - nothing to do here ?
    // addInsertion(start-cursor);
    // }
    return deleted;
  }

  /**
   * Deleted regions mean that there will be discontinuous sequence numbering in
   * the sequence returned by getSeq(char).
   * 
   * @return true if there deletions
   */
  public boolean hasDeletedRegions()
  {
    for (int i = 0; i < length; i++)
    {
      if (operation[i] == D)
      {
        return true;
      }
    }
    return false;
  }

  /**
   * enumerate the ranges on seq that are marked as deleted in this cigar
   * 
   * @return int[] { vis_start, sym_start, length }
   */
  public int[] getDeletedRegions()
  {
    if (length == 0)
    {
      return null;
    }
    Vector dr = new Vector();
    int cursor = 0, vcursor = 0;
    for (int i = 0; i < length; i++)
    {
      switch (operation[i])
      {
      case M:
        cursor += range[i];
      case I:
        vcursor += range[i];
        break;
      case D:
        dr.addElement(new int[]
        { vcursor, cursor, range[i] });
        cursor += range[i];
      }
    }
    if (dr.size() == 0)
    {
      return null;
    }
    int[] delregions = new int[dr.size() * 3];
    for (int i = 0, l = dr.size(); i < l; i++)
    {
      int[] reg = (int[]) dr.elementAt(i);
      delregions[i * 3] = reg[0];
      delregions[i * 3 + 1] = reg[1];
      delregions[i * 3 + 2] = reg[2];
    }
    return delregions;
  }

  /**
   * 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();
  }
}
