Serves for encoding sequences into feature vectors. More...

#include <OpenMS/FORMAT/LibSVMEncoder.h>

Public Member Functions
	LibSVMEncoder ()=default
	Constructor. More...

	~LibSVMEncoder ()=default
	Destructor. More...

void	encodeCompositionVector (const String &sequence, std::vector< std::pair< Int, double > > &encoded_vector, const String &allowed_characters="ACDEFGHIKLMNPQRSTVWY")
	stores a composition vector of 'sequence' in 'encoded_vector' More...

void	encodeCompositionVectors (const std::vector< String > &sequences, const String &allowed_characters, std::vector< std::vector< std::pair< Int, double > > > &composition_vectors)
	stores composition vectors of the sequences given by 'sequence' in 'composition_vectors' More...

svm_node *	encodeLibSVMVector (const std::vector< std::pair< Int, double > > &feature_vector)
	encodes the feature vector in LibSVM compliant format More...

void	encodeLibSVMVectors (const std::vector< std::vector< std::pair< Int, double > > > &feature_vectors, std::vector< svm_node * > &libsvm_vectors)
	encodes the feature vectors in LibSVM compliant format More...

svm_problem *	encodeLibSVMProblem (const std::vector< svm_node * > &vectors, std::vector< double > &labels)
	encodes the LibSVM compliant vectors into a LibSVM compliant structure More...

svm_problem *	encodeLibSVMProblemWithCompositionVectors (const std::vector< String > &sequences, std::vector< double > &labels, const String &allowed_characters)
	creates composition vectors for 'sequences' and stores them in LibSVM compliant format More...

svm_problem *	encodeLibSVMProblemWithCompositionAndLengthVectors (const std::vector< String > &sequences, std::vector< double > &labels, const String &allowed_characters, UInt maximum_sequence_length)
	creates composition vectors with additional length information for 'sequences' and stores them in LibSVM compliant format More...

svm_problem *	encodeLibSVMProblemWithCompositionLengthAndWeightVectors (const std::vector< String > &sequences, std::vector< double > &labels, const String &allowed_characters)
	creates composition vectors with additional length and average weight information for 'sequences' and stores them in LibSVM compliant format More...

bool	storeLibSVMProblem (const String &filename, const svm_problem *problem) const
	stores the LibSVM-encoded data in a text file that can be used by the LibSVM applications (svm-scale, svm-train,...) More...

svm_problem *	loadLibSVMProblem (const String &filename)
	loads the LibSVM-encoded data stored in 'filename' More...

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)
	encodes the borders of the sequence as k_mer oligos and stores them in 'libsvm_vector' More...

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)
	creates oligo border vectors vectors for 'sequences' and stores them in LibSVM compliant format More...

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)
	creates oligo border vectors vectors for 'sequences' and stores them in 'vectors' More...

void	libSVMVectorToString (svm_node *vector, String &output)
	stores a string representation of the encoded sequence 'vector' in 'output' More...

void	libSVMVectorsToString (svm_problem *vector, String &output)
	stores a string representation of the encoded sequences in 'vectors' in 'output' More...

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)
	encodes an AASequence instance in oligo encoding More...

Static Public Member Functions
static void	destroyProblem (svm_problem *problem)
	frees all the memory of the svm_problem instance More...

static std::vector< double >	predictPeptideRT (const std::vector< String > &sequences, SVMWrapper &svm, const String &allowed_characters="ACDEFGHIKLMNPQRSTVWY", UInt maximum_sequence_length=50)

Static Private Member Functions
static bool	cmpOligos_ (std::pair< Int, double > a, std::pair< Int, double > b)
	comparator for oligos encoded by encodeOligo More...

Detailed Description

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.

Constructor & Destructor Documentation

◆ LibSVMEncoder()

LibSVMEncoder ( )

default

Constructor.

◆ ~LibSVMEncoder()

~LibSVMEncoder ( )

default

Destructor.

Member Function Documentation

◆ cmpOligos_()

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

staticprivate

comparator for oligos encoded by encodeOligo

◆ destroyProblem()

static void destroyProblem ( svm_problem * problem )

static

frees all the memory of the svm_problem instance

This function is used to free all the memory used by 'problem'

Referenced by LibSVMEncoder::predictPeptideRT().

◆ encodeCompositionVector()

void encodeCompositionVector	(	const String &	sequence,
		std::vector< std::pair< Int, double > > &	encoded_vector,
		const String &	allowed_characters = `"ACDEFGHIKLMNPQRSTVWY"`
	)

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 stored in the composition vector. The first entry of the vector (<UInt, double>) corresponds to the first letter of 'allowed_characters' that has a non zero frequency in 'sequence' and its corresponding relative frequency...

◆ encodeCompositionVectors()

void encodeCompositionVectors	(	const std::vector< String > &	sequences,
		const String &	allowed_characters,
		std::vector< std::vector< std::pair< Int, double > > > &	composition_vectors
	)

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 stored in the composition vectors. The first entry of the first vector (<UInt, double>) corresponds to the first letter of 'allowed_characters' that has a non zero frequency in the first 'sequence' and its corresponding relative frequency...

◆ encodeLibSVMProblem()

svm_problem* encodeLibSVMProblem	(	const std::vector< svm_node * > &	vectors,
		std::vector< double > &	labels
	)

encodes the LibSVM compliant vectors into a LibSVM compliant structure

◆ encodeLibSVMProblemWithCompositionAndLengthVectors()

svm_problem* encodeLibSVMProblemWithCompositionAndLengthVectors	(	const std::vector< String > &	sequences,
		std::vector< double > &	labels,
		const String &	allowed_characters,
		UInt	maximum_sequence_length
	)

creates composition vectors with additional length information for 'sequences' and stores them in LibSVM compliant format

Note: The resulting svm_problem needs to be destroyed by calling LibSVMEncoder::destroyProblem

Referenced by LibSVMEncoder::predictPeptideRT().

◆ encodeLibSVMProblemWithCompositionLengthAndWeightVectors()

svm_problem* encodeLibSVMProblemWithCompositionLengthAndWeightVectors	(	const std::vector< String > &	sequences,
		std::vector< double > &	labels,
		const String &	allowed_characters
	)

creates composition vectors with additional length and average weight information for 'sequences' and stores them in LibSVM compliant format

Note: The resulting svm_problem needs to be destroyed by calling LibSVMEncoder::destroyProblem

◆ encodeLibSVMProblemWithCompositionVectors()

svm_problem* encodeLibSVMProblemWithCompositionVectors	(	const std::vector< String > &	sequences,
		std::vector< double > &	labels,
		const String &	allowed_characters
	)

creates composition vectors for 'sequences' and stores them in LibSVM compliant format

◆ encodeLibSVMProblemWithOligoBorderVectors()

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`
	)

creates oligo border vectors vectors for 'sequences' and stores them in LibSVM compliant format

◆ encodeLibSVMVector()

svm_node* encodeLibSVMVector ( const std::vector< std::pair< Int, double > > & feature_vector )

encodes the feature vector in LibSVM compliant format

◆ encodeLibSVMVectors()

void encodeLibSVMVectors	(	const std::vector< std::vector< std::pair< Int, double > > > &	feature_vectors,
		std::vector< svm_node * > &	libsvm_vectors
	)

encodes the feature vectors in LibSVM compliant format

◆ encodeOligo()

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`
	)

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.

◆ encodeOligoBorders()

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`
	)

encodes the borders of the sequence as k_mer oligos and stores them in 'libsvm_vector'

◆ encodeProblemWithOligoBorderVectors()

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
	)

creates oligo border vectors vectors for 'sequences' and stores them in 'vectors'

◆ libSVMVectorsToString()

void libSVMVectorsToString	(	svm_problem *	vector,
		String &	output
	)

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.

◆ libSVMVectorToString()

void libSVMVectorToString	(	svm_node *	vector,
		String &	output
	)

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.

◆ loadLibSVMProblem()

svm_problem* loadLibSVMProblem ( const String & filename )

loads the LibSVM-encoded data stored in 'filename'

◆ predictPeptideRT()

static std::vector<double> predictPeptideRT	(	const std::vector< String > &	sequences,
		SVMWrapper &	svm,
		const String &	allowed_characters = `"ACDEFGHIKLMNPQRSTVWY"`,
		UInt	maximum_sequence_length = `50`
	)

inlinestatic

References LibSVMEncoder::destroyProblem(), LibSVMEncoder::encodeLibSVMProblemWithCompositionAndLengthVectors(), and SVMWrapper::predict().

◆ storeLibSVMProblem()

bool storeLibSVMProblem	(	const String &	filename,
		const svm_problem *	problem
	)		const

stores the LibSVM-encoded data in a text file that can be used by the LibSVM applications (svm-scale, svm-train,...)

Public Member Functions

Static Public Member Functions

Static Private Member Functions