LibSVMEncoder.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <svm.h>

#include <vector>
#include <utility>

namespace OpenMS
{
  class OPENMS_DLLAPI LibSVMEncoder
  {
public:
    LibSVMEncoder();
    ~LibSVMEncoder();

    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);

private:
    static bool cmpOligos_(std::pair<Int, double> a,
                           std::pair<Int, double> b);

  };

} // namespace OpenMS