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LocalLinearMap Class Reference

Trained Local Linear Map (LLM) model for peak intensity prediction. More...

#include <OpenMS/ANALYSIS/PIP/LocalLinearMap.h>

Classes

struct  LLMParam
 Define parameters needed by the Local Linear Map (LLM) model. More...
 

Public Member Functions

 LocalLinearMap ()
 default constructor More...
 
virtual ~LocalLinearMap ()
 destructor More...
 
const LLMParamgetLLMParam () const
 return parameters of the LocalLinearMap model More...
 
const Matrix< double > & getCodebooks () const
 return position of the codebook vectors (18-dim) More...
 
const Matrix< double > & getMatrixA () const
 return linear mappings of the codebooks More...
 
const std::vector< double > & getVectorWout () const
 return linear bias More...
 
const Matrix< UInt > & getCord () const
 return coordinates of codebook vectors on the 2-d grid More...
 
void normalizeVector (std::vector< double > &aaIndexVariables)
 calculate and return normalized amino acid index variables from string representation of peptide More...
 
std::vector< doubleneigh (const Matrix< UInt > &cord, Size win, double radius)
 calculate neighborhood function based on distance of prototypes to winner prototype on two-dimensional grid structure and neighborhood width. More...
 

Private Member Functions

Matrix< UIntgenCord_ (Size xdim, Size ydim)
 needed to store prototype coordinates More...
 
double dist_ (const Matrix< UInt > &u, const Matrix< UInt > &v, Size a, Size b)
 calculate distance between two prototypes More...
 
 LocalLinearMap (LocalLinearMap &rhs)
 Copy constructor not implemented => private. More...
 
LocalLinearMapoperator= (const LocalLinearMap &llm)
 Assignment operator not implemented => private. More...
 

Private Attributes

LLMParam param_
 parameters of the model More...
 
Matrix< doublecode_
 codebook vectors More...
 
Matrix< doubleA_
 linear mappings More...
 
std::vector< doublewout_
 linear bias More...
 
Matrix< UIntcord_
 coordinates of codebooks on grid More...
 

Detailed Description

Trained Local Linear Map (LLM) model for peak intensity prediction.

This class offers a model for predictions of peptide peak heights (referred to as intensities) by a Local Linear Map (LLM) model and is the basis of PeakIntensityPredictor.

A general introduction to the Peak Intensity Predictor (PIP) can be found in the PIP Tutorial.

The model trained needs two files for storing the position of the codebook vectors and the linear mappings (codebooks.data, linearMapping.data) This is the default model used by PeakIntensityPredictor.

Constructor & Destructor Documentation

default constructor

virtual ~LocalLinearMap ( )
virtual

destructor

LocalLinearMap ( LocalLinearMap rhs)
private

Copy constructor not implemented => private.

Member Function Documentation

double dist_ ( const Matrix< UInt > &  u,
const Matrix< UInt > &  v,
Size  a,
Size  b 
)
private

calculate distance between two prototypes

Matrix<UInt> genCord_ ( Size  xdim,
Size  ydim 
)
private

needed to store prototype coordinates

const Matrix<double>& getCodebooks ( ) const

return position of the codebook vectors (18-dim)

const Matrix<UInt>& getCord ( ) const

return coordinates of codebook vectors on the 2-d grid

const LLMParam& getLLMParam ( ) const

return parameters of the LocalLinearMap model

const Matrix<double>& getMatrixA ( ) const

return linear mappings of the codebooks

const std::vector<double>& getVectorWout ( ) const

return linear bias

std::vector<double> neigh ( const Matrix< UInt > &  cord,
Size  win,
double  radius 
)

calculate neighborhood function based on distance of prototypes to winner prototype on two-dimensional grid structure and neighborhood width.

void normalizeVector ( std::vector< double > &  aaIndexVariables)

calculate and return normalized amino acid index variables from string representation of peptide

LocalLinearMap& operator= ( const LocalLinearMap llm)
private

Assignment operator not implemented => private.

Member Data Documentation

Matrix<double> A_
private

linear mappings

Matrix<double> code_
private

codebook vectors

Matrix<UInt> cord_
private

coordinates of codebooks on grid

LLMParam param_
private

parameters of the model

std::vector<double> wout_
private

linear bias


OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11