PeptDeepInput.h

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// Copyright (c) 2002-present, OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Satyam Yadav, Justin Sing $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <cstddef>
#include <cstdint>
#include <string>
#include <vector>
 
namespace OpenMS
{
  namespace ML
  {
    struct OPENMS_DLLAPI PeptDeepInputConfig
    {
      bool add_terminal_tokens = true;
 
      size_t fixed_sequence_length = 0;
    };
 
    struct OPENMS_DLLAPI PeptDeepInputBatch
    {
      size_t batch_size = 0;
      size_t sequence_length = 0;
 
      std::vector<int64_t> aa_indices;
      std::vector<float> mod_x;
 
      std::vector<float> charges;
      std::vector<float> nces;
      std::vector<int64_t> instrument_indices;
    };
 
    class OPENMS_DLLAPI PeptDeepInputBuilder
    {
    public:
      static PeptDeepInputBatch buildPeptideBatch(
        const std::vector<OpenMS::AASequence>& parsed_peptides,
        const PeptDeepInputConfig& config = PeptDeepInputConfig());
 
      static PeptDeepInputBatch buildPrecursorBatch(
        const std::vector<OpenMS::AASequence>& parsed_peptides,
        const std::vector<float>& charges,
        const PeptDeepInputConfig& config = PeptDeepInputConfig());
 
      static PeptDeepInputBatch buildProductMetaBatch(
        const std::vector<OpenMS::AASequence>& parsed_peptides,
        const std::vector<float>& charges,
        const std::vector<float>& nces,
        const std::vector<int64_t>& instrument_indices,
        const PeptDeepInputConfig& config = PeptDeepInputConfig());
    };
  } // namespace ML
} // namespace OpenMS