//Copyright (c) 2014 - 2021, The Trustees of Indiana 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_PRSM_SEARCH_FASTA_MATCH_HPP_
#define TOPPIC_PRSM_SEARCH_FASTA_MATCH_HPP_

#include "prsm/prsm.hpp"

namespace toppic {

class SearchFastaMatch {
 public:
  SearchFastaMatch(std::string db_file_name);

  std::vector<std::pair<FastaSeqPtr, int>> process(PrsmPtr prsm_ptr_);

 private:
  std::string db_file_name_;
  FastaSeqPtrVec fasta_seq_vec_;
  std::vector<std::string> seq_vec_;
};

typedef std::shared_ptr<SearchFastaMatch> SearchFastaMatchPtr;

} //namespace toppic

#endif
