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LibSVMEncoder Class Reference

#include <OpenMS/FORMAT/LibSVMEncoder.h>

List of all members.


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.

Public Member Functions

 LibSVMEncoder ()
 Constructor.
 ~LibSVMEncoder ()
 Destructor.
void encodeCompositionVector (const String &sequence, std::vector< std::pair< Int, DoubleReal > > &encoded_vector, const String &allowed_characters="ACDEFGHIKLMNPQRSTVWY")
 stores a composition vector of 'sequence' in 'encoded_vector'
void encodeCompositionVectors (const std::vector< String > &sequences, const String &allowed_characters, std::vector< std::vector< std::pair< Int, DoubleReal > > > &composition_vectors)
 stores composition vectors of the sequences given by 'sequence' in 'composition_vectors'
svm_node * encodeLibSVMVector (const std::vector< std::pair< Int, DoubleReal > > &feature_vector)
 encodes the feature vector 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 feature vectors in LibSVM compliant format
svm_problem * encodeLibSVMProblem (const std::vector< svm_node * > &vectors, std::vector< DoubleReal > &labels)
 encodes the LibSVM compliant vectors into a LibSVM compliant structure
svm_problem * encodeLibSVMProblemWithCompositionVectors (const std::vector< String > &sequences, std::vector< DoubleReal > &labels, const String &allowed_characters)
 creates composition vectors 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 information for 'sequences' and stores them in LibSVM compliant format
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,...)
svm_problem * loadLibSVMProblem (const String &filename)
 loads the LibSVM-encoded data stored in 'filename'
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)
 encodes the borders of the sequence as k_mer oligos and stores them in 'libsvm_vector'
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 LibSVM compliant format
void libSVMVectorToString (svm_node *vector, String &output)
 stores a string representation of the encoded sequence 'vector' in 'output'
void libSVMVectorsToString (svm_problem *vector, String &output)
 stores a string representation of the encoded sequences in 'vectors' in 'output'


Constructor & Destructor Documentation

LibSVMEncoder (  ) 

Constructor.

~LibSVMEncoder (  ) 

Destructor.


Member Function Documentation

void encodeCompositionVector ( const String sequence,
std::vector< std::pair< Int, DoubleReal > > &  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 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 encodeCompositionVectors ( const std::vector< String > &  sequences,
const String allowed_characters,
std::vector< std::vector< std::pair< Int, DoubleReal > > > &  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 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...

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

encodes the feature vector 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 feature vectors in LibSVM compliant format

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

encodes the LibSVM compliant vectors into a LibSVM compliant structure

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

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

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,...)

svm_problem* loadLibSVMProblem ( const String filename  ) 

loads the LibSVM-encoded data stored in 'filename'

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 
)

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

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 LibSVM compliant format

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.

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.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1