//Copyright (c) 2014 - 2020, 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_TOPFD_COMMON_TOPFD_PROCESS_HPP_
#define TOPPIC_TOPFD_COMMON_TOPFD_PROCESS_HPP_

#include <string>
#include <vector>

#include "topfd/common/topfd_para.hpp"

#include "pwiz/data/msdata/DefaultReaderList.hpp"
#include "pwiz/data/msdata/MSDataFile.hpp"

#include "pwiz/data/msdata/SpectrumList_mzML.hpp"
#include "pwiz/data/msdata/SpectrumInfo.hpp"
#include "pwiz/utility/misc/Std.hpp"

namespace toppic {

namespace topfd_process {

int processOneFile(TopfdParaPtr para_ptr, 
                   const std::string &spec_file_name, 
                   int frac_id);

int process(TopfdParaPtr para_ptr,  
            std::vector<std::string> spec_file_lst); 

void getMsScanCount(std::string spectrum_file_name, std::vector<int> &scan_cnt_vec);

}
}

#endif
