LibSVMEncoder.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/ANALYSIS/SVM/SVMWrapper.h>
 
#include <vector>
#include <utility>
 
struct svm_problem;
struct svm_parameter;
struct svm_model;
 
namespace OpenMS
{
  class OPENMS_DLLAPI LibSVMEncoder
  {
public:
    LibSVMEncoder() = default;
    ~LibSVMEncoder() = default;
 
    void encodeCompositionVector(const String & sequence, std::vector<std::pair<Int, double> > & encoded_vector, const String & allowed_characters = "ACDEFGHIKLMNPQRSTVWY");
 
    void encodeCompositionVectors(const std::vector<String> & sequences, const String & allowed_characters, std::vector<std::vector<std::pair<Int, double> > > & composition_vectors);
    svm_node * encodeLibSVMVector(const std::vector<std::pair<Int, double> > & feature_vector);
 
    void encodeLibSVMVectors(const std::vector<std::vector<std::pair<Int, double> > > & feature_vectors, std::vector<svm_node *> & libsvm_vectors);
 
    svm_problem * encodeLibSVMProblem(const std::vector<svm_node *> & vectors,
                                      std::vector<double> & labels);
 
    svm_problem * encodeLibSVMProblemWithCompositionVectors(const std::vector<String> & sequences,
                                                            std::vector<double> & labels,
                                                            const String & allowed_characters);
 
    svm_problem * encodeLibSVMProblemWithCompositionAndLengthVectors(const std::vector<String> & sequences,
                                                                     std::vector<double> & labels,
                                                                     const String & allowed_characters,
                                                                     UInt maximum_sequence_length);
 
    svm_problem * encodeLibSVMProblemWithCompositionLengthAndWeightVectors(const std::vector<String> & sequences,
                                                                           std::vector<double> & labels,
                                                                           const String & allowed_characters);
 
    bool storeLibSVMProblem(const String & filename, const svm_problem * problem) const;
 
    svm_problem * loadLibSVMProblem(const String & filename);
 
    void encodeOligoBorders(String                                                                                       sequence,
                            UInt                                                                             k_mer_length,
                            const String & allowed_characters,
                            UInt                                        border_length,
                            std::vector<std::pair<Int, double> > & libsvm_vector,
                            bool                                                                                             strict = false,
                            bool                                                                                             unpaired = false,
                            bool                                                                                             length_encoding = false);
 
    svm_problem * encodeLibSVMProblemWithOligoBorderVectors(const std::vector<String> & sequences,
                                                            std::vector<double> & labels,
                                                            UInt                           k_mer_length,
                                                            const String & allowed_characters,
                                                            UInt                           border_length,
                                                            bool                                                   strict = false,
                                                            bool                                                   unpaired = false,
                                                            bool                                                   length_encoding = false);
 
    void encodeProblemWithOligoBorderVectors(const std::vector<AASequence> & sequences,
                                             UInt                                                       k_mer_length,
                                             const String & allowed_characters,
                                             UInt                                                       border_length,
                                             std::vector<std::vector<std::pair<Int, double> > > & vectors);
 
    void libSVMVectorToString(svm_node * vector, String & output);
 
    void libSVMVectorsToString(svm_problem * vector, String & output);
 
    void encodeOligo(const AASequence & sequence,
                     UInt k_mer_length,
                     const String & allowed_characters,
                     std::vector<std::pair<Int, double> > & values,
                     bool is_right_border = false);
 
    static void destroyProblem(svm_problem* &problem, bool free_nodes = true);
 
    static std::vector<double> predictPeptideRT(const std::vector<String> & sequences,
                                                SVMWrapper& svm,
                                                const String & allowed_characters = "ACDEFGHIKLMNPQRSTVWY",
                                                UInt maximum_sequence_length = 50)
    {
      std::vector<double> predicted_retention_times;
 
      LibSVMEncoder encoder;
      std::vector<double> temp_rts;
      temp_rts.resize(sequences.size(), 0);
      svm_problem * prediction_data =
          encoder.encodeLibSVMProblemWithCompositionAndLengthVectors(sequences,
                                                                     temp_rts,
                                                                     allowed_characters,
                                                                     maximum_sequence_length);
      svm.predict(prediction_data, predicted_retention_times);
      LibSVMEncoder::destroyProblem(prediction_data);
      return predicted_retention_times;
    }
 
private:
    static bool cmpOligos_(std::pair<Int, double> a,
                           std::pair<Int, double> b);
 
  };
 
} // namespace OpenMS