//Copyright (c) 2014 - 2025, The Trustees of Indiana University, Tulane University.
//
//Licensed under the Apache License, Version 2.0 (the "License");
//you may not use this file except in compliance with the License.
//You may obtain a copy of the License at
//
//    http://www.apache.org/licenses/LICENSE-2.0
//
//Unless required by applicable law or agreed to in writing, software
//distributed under the License is distributed on an "AS IS" BASIS,
//WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
//See the License for the specific language governing permissions and
//limitations under the License.

#ifndef TOPPIC_FILTER_MNG_DIAG_FILTER_MNG_HPP_
#define TOPPIC_FILTER_MNG_DIAG_FILTER_MNG_HPP_

#include <boost/thread.hpp>

#include "para/prsm_para.hpp"

namespace toppic {

class DiagFilterMng {
 public:
  DiagFilterMng(PrsmParaPtr prsm_para_ptr,
                const std::string & index_file_para,
                int filtering_result_num,
                int thread_num,
                const std::string & output_file_ext,
                const std::string & residue_mod_file_name = "",
                int var_num = 0);

  std::string getIndexFilePara() {return index_file_para_;}

  PrsmParaPtr prsm_para_ptr_;

  std::string index_file_para_;

  /** parameters for fast filteration */
  int max_proteoform_mass_ = 50000;

  // Candidate protein number for each spectrum
  size_t filter_result_num_ = 20;
  int db_block_size_ = 5000000;
  int filter_scale_ = 100;
  int thread_num_ = 1;

  std::string output_file_ext_;
  std::string residue_mod_file_name_;

  int var_num_;

  // for counting spectra
  int n_spec_block_ = 0;
  boost::mutex mutex_;
  std::vector<int> cnts_;

  // file name vector
  std::vector<std::string> multi_ptm_file_vec_{"multi_ptm_index"};

};

typedef std::shared_ptr<DiagFilterMng> DiagFilterMngPtr;

}  // namespace toppic

#endif /* DIAG_FILTER_MNG_HPP_ */
