/usr/include/OpenMS/FORMAT/LibSVMEncoder.h is in libopenms-dev 1.11.1-3.
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// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Sandro Andreotti $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_LIBSVMENCODER_H
#define OPENMS_FORMAT_LIBSVMENCODER_H
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <svm.h>
#include <vector>
#include <utility>
namespace OpenMS
{
/**
@brief Serves for encoding sequences into feature vectors
The class can be used to construct composition vectors for
sequences. Additionally the vectors can be encoded into
the libsvm format.
*/
class OPENMS_DLLAPI LibSVMEncoder
{
public:
/// Constructor
LibSVMEncoder();
/// Destructor
~LibSVMEncoder();
/**
@brief stores a composition vector of 'sequence' in 'encoded_vector'
The allowed characters given by 'allowed_characters' are counted in the sequence 'sequence'
and the relative frequency of the letters are sored in the composition vector.
The first entry of the vector (<UInt, DoubleReal>) corresponds to the first letter of
'allowed_characters' that has a non zero frequency in 'sequence' and its corresponding
relative frequency...
*/
void encodeCompositionVector(const String & sequence, std::vector<std::pair<Int, DoubleReal> > & encoded_vector, const String & allowed_characters = "ACDEFGHIKLMNPQRSTVWY");
/**
@brief stores composition vectors of the sequences given by 'sequence' in 'composition_vectors'
The allowed characters given by 'allowed_characters' are counted in the sequences 'sequences'
and the relative frequency of the letters are sored in the composition vectors.
The first entry of the first vector (<UInt, DoubleReal>) corresponds to the first letter of
'allowed_characters' that has a non zero frequency in the first 'sequence' and its corresponding
relative frequency...
*/
void encodeCompositionVectors(const std::vector<String> & sequences, const String & allowed_characters, std::vector<std::vector<std::pair<Int, DoubleReal> > > & composition_vectors);
/// encodes the feature vector in LibSVM compliant format
svm_node * encodeLibSVMVector(const std::vector<std::pair<Int, DoubleReal> > & feature_vector);
/// encodes the feature vectors in LibSVM compliant format
void encodeLibSVMVectors(const std::vector<std::vector<std::pair<Int, DoubleReal> > > & feature_vectors, std::vector<svm_node *> & libsvm_vectors);
/// encodes the LibSVM compliant vectors into a LibSVM compliant structure
svm_problem * encodeLibSVMProblem(const std::vector<svm_node *> & vectors,
std::vector<DoubleReal> & labels);
/// creates composition vectors for 'sequences' and stores them in LibSVM compliant format
svm_problem * encodeLibSVMProblemWithCompositionVectors(const std::vector<String> & sequences,
std::vector<DoubleReal> & labels,
const String & allowed_characters);
/// creates composition vectors with additional length information for 'sequences' and stores them in LibSVM compliant format
svm_problem * encodeLibSVMProblemWithCompositionAndLengthVectors(const std::vector<String> & sequences,
std::vector<DoubleReal> & labels,
const String & allowed_characters,
UInt maximum_sequence_length);
/// creates composition vectors with additional length and average weight information for 'sequences' and stores them in LibSVM compliant format
svm_problem * encodeLibSVMProblemWithCompositionLengthAndWeightVectors(const std::vector<String> & sequences,
std::vector<DoubleReal> & labels,
const String & allowed_characters);
/// stores the LibSVM-encoded data in a text file that can be used by the LibSVM applications (svm-scale, svm-train,...)
bool storeLibSVMProblem(const String & filename, const svm_problem * problem) const;
/// loads the LibSVM-encoded data stored in 'filename'
svm_problem * loadLibSVMProblem(const String & filename);
/// encodes the borders of the sequence as k_mer oligos and stores them in 'libsvm_vector'
void encodeOligoBorders(String sequence,
UInt k_mer_length,
const String & allowed_characters,
UInt border_length,
std::vector<std::pair<Int, DoubleReal> > & libsvm_vector,
bool strict = false,
bool unpaired = false,
bool length_encoding = false);
/// creates oligo border vectors vectors for 'sequences' and stores them in LibSVM compliant format
svm_problem * encodeLibSVMProblemWithOligoBorderVectors(const std::vector<String> & sequences,
std::vector<DoubleReal> & labels,
UInt k_mer_length,
const String & allowed_characters,
UInt border_length,
bool strict = false,
bool unpaired = false,
bool length_encoding = false);
/// creates oligo border vectors vectors for 'sequences' and stores them in 'vectors'
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, DoubleReal> > > & vectors);
/**
@brief stores a string representation of the encoded sequence 'vector' in 'output'
This function can be used if one wants to print one feature vector that is used in
the libsvm.
*/
void libSVMVectorToString(svm_node * vector, String & output);
/**
@brief stores a string representation of the encoded sequences in 'vectors' in 'output'
This function can be used if one wants to print the feature vectors that are used in
the libsvm.
*/
void libSVMVectorsToString(svm_problem * vector, String & output);
/**
@brief encodes an AASequence instance in oligo encoding
This function is used to get the oligo encoding for AASequence
'sequence'. If a residue is modified, it gets an extra oligo function.
*/
void encodeOligo(const AASequence & sequence,
UInt k_mer_length,
const String & allowed_characters,
std::vector<std::pair<Int, DoubleReal> > & values,
bool is_right_border = false);
/**
@brief frees all the memory of the svm_problem instance
This function is used to free all the memory used by 'problem'
*/
static void destroyProblem(svm_problem * problem);
private:
/// comparator for oligos encoded by encodeOligo
static bool cmpOligos_(std::pair<Int, DoubleReal> a,
std::pair<Int, DoubleReal> b);
};
} // namespace OpenMS
#endif // OPENMS_FORMAT_LIBSVMENCODER_H
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