dme_tcm_workspace.hpp

/*
 * Copyright (C) 2008 Cold Spring Harbor Laboratory and Andrew D Smith
 * Author: Andrew D Smith
 *
 * 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 St, Fifth Floor, Boston, MA
 * 02110-1301 USA
 */

/********************************
 * HEADER FOR THE DME WORKSPACE *
 ********************************/

#ifndef DME_TCM_WORKSPACE_HPP
#define DME_TCM_WORKSPACE_HPP

#include <smithlab_utils.hpp>

#include "ScoringMatrix.hpp"
#include "Matrix.hpp"
#include "CTSet.hpp"

struct dme_tcm_lextree;

class dme_tcm_workspace {
  
public:
  dme_tcm_workspace(const std::vector<std::string> &foreground, 
		    const std::vector<std::string> &background, 
		    const int motif_width_param,
		    const float adjustment);
  ~dme_tcm_workspace();
  
  // Pass in the column type sets as precomputed scoring matrix column
  // types. They will be "complemented" internally to speed the
  // computation. Similar for the information content.
  DMEPath 
  run_dme_tcm(const std::vector<std::vector<float> > &column_types,
	      const std::vector<float> &bits,
	      const float min_information);
  
  // Pass in the column type sets as precomputed scoring matrix column
  // types. They will be "complemented" internally to speed the
  // computation. Similar for the information content.
  DMEPath 
  run_dme_tcm_local(const std::vector<std::vector<std::vector<float> > > &refined_column_types,
		 const std::vector<std::vector<float> > &refined_bits,
		 const float min_information,
		 const size_t n_changes);
  
  void deactivate(const ScoringMatrix &sm);
  
private:
  void refined_enumeration(const size_t depth, const size_t prev_frontier,
			   const float surplus_information,
			   const size_t remaining_changes);
  void enumeration(const size_t depth, 
		   const size_t prev_frontier,
		   const float surplus_information);
  
  // These are set initially and not changed
  std::vector<std::vector<float> > score;
  std::vector<std::vector<dme_tcm_lextree*> > nodes;
  dme_tcm_lextree *tree;
  size_t motif_width;          // width of motif
  std::vector<size_t> prefix;
  
  // standard search variables
  std::vector<std::vector<float> > scoremat;
  std::vector<float> coltype_bits;
  size_t n_types;
  
  // local search variables
  std::vector<std::vector<std::vector<float> > > refined_scoremat;
  std::vector<size_t> n_refined_types;
  std::vector<std::vector<float> > refined_coltype_bits;
  
  // for both standard and local search (reset right away at each
  // public function call)
  std::vector<size_t> best_path;
  float best_score;
};

#endif