Version 4.0.0

Coder.h

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/* seqpp/Coder.h
 *
 * Copyright (C) 2003 Laboratoire Statistique & Génome
 *
 * 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., 675 Mass Ave, Cambridge, MA 02139, USA.
 */
#ifndef CODER_H
#define CODER_H

#include <vector>
#include <iostream>

using namespace std;

class Coder
{
 private:

  short _order;
  short _size;

  long * _pow;
  long * _jump;
  long ** _pow_r;
  
  vector<long> _vect;
  
  short compute_length() const;
  
 public:
  long _code;
  short _sizeword;
  
  Coder( short order, short size );

  Coder( short order, short size,
         long first_code, short sizeword );
  
  Coder( )
  {
    _order = -1; _size = 0; 
    _pow = NULL; _jump = NULL; 
    _pow_r = NULL;
  }  
  
  Coder( const Coder& c );
  
  ~Coder( );  
  
    
  void init( long code, short sizeword ){
    _code = code;
    _sizeword = sizeword;
  }

  void init( long code ){
    _code = code;
    _sizeword = this->compute_length();
  }
  
  void init( const vector<short>& X );

  void init( const short * X );

  void restrict_init( const short * X,  short pseudo_order );

  void clear(){
    _code = -1;
    _sizeword = 0;
  }

  
  void push_back( short i ){
    _code = (_code+1)*_size + i;
    _sizeword++;
  }
  long virtual_push_back( short i ) const{
    return (_code+1)*_size + i;
  }


  void push_front( short i ){
    _code += _pow[_sizeword] + _pow_r[i][_order-_sizeword];
    _sizeword++;
  }
  long virtual_push_front( short i ) const{
    return (_code + _pow[_sizeword] + _pow_r[i][_order-_sizeword]);
  }

  void erase_back(){
    _code = _code/_size - 1;
    _sizeword--;
  }
  short pop_back();
   
          
  void erase_front(){
    _sizeword--;
    _code = _code - _pow_r[  (_code-_jump[_sizeword])/_pow[_sizeword]  ][ _order-_sizeword ] - _pow[_sizeword];
  }
  short pop_front();

  bool empty() const{
    return (_code==-1);
  }

  short length() const{
    return _sizeword;
  }

  long tell_nbvalue() const{
    return _jump[_order+1];
  }

  long tell_jump( short i ) const{
    return _jump[i];
  }
  long tell_jump( ) const{
    return _jump[_order];
  }
  
  long * get_jump() const{
    return _jump;
  }

  vector<long> & list_suffixed( short sizeprefix );
  vector<long> & list_suffixed( ){
    return list_suffixed( _order+1 - _sizeword );
  }

  vector<long> & bound_prefixed( short sizesuffix );
  vector<long> & bound_prefixed( ){
    return bound_prefixed( _order+1 - _sizeword );
  }
};
#endif

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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin

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