dme/dme_zoops_workspace.hpp at master · smithlabcode/dme · GitHub

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/* Copyright (C) 2025 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
 */

#ifndef DME_ZOOPS_WORKSPACE_HPP
#define DME_ZOOPS_WORKSPACE_HPP

#include <smithlab_utils.hpp>

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

struct dme_zoops_lextree;

class dme_zoops_workspace {

public:
  dme_zoops_workspace(const std::vector<std::string> &foreground,
                      const std::vector<std::string> &background,
                      const size_t motif_width_param, const float adjustment);
  ~dme_zoops_workspace();

  DMEPath
  run_dme_zoops(const std::vector<std::vector<float>> &column_types,
                const std::vector<float> &bits, const float min_information);

  DMEPath
  run_dme_zoops_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 float surplus_information,
                      const size_t remaining_changes);
  void
  enumeration(const size_t depth, const float surplus_information);

  float
  get_background_score() const;
  float
  get_background_refined_score() const;

  // These are set initially and not changed
  std::vector<std::vector<std::vector<float>>> fgscore;
  std::vector<std::vector<std::vector<dme_zoops_lextree *>>> fgnodes;
  std::vector<dme_zoops_lextree *> bgtrees;

  size_t fgsize;
  size_t bgsize;

  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;
  float max_score;

  // 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;
  float refined_max_score;

  // for both standard and local search (reset right away at each
  // public function call)
  std::vector<size_t> best_path;
  float best_score;
  float lambda;
};

#endif