| OpenMS 2.5.0

Classes | Public Member Functions | Private Member Functions | Private Attributes | List of all members
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 LLMParam & | getLLMParam () 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< 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. More...

## Private Member Functions

Matrix< UInt > | genCord_ (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...
LocalLinearMap & | operator= (const LocalLinearMap &llm)
| Assignment operator not implemented => private. More...

## Private Attributes

LLMParam | param_
| parameters of the model More...
Matrix< double > | code_
| codebook vectors More...
Matrix< double > | A_
| linear mappings More...
std::vector< double > | wout_
| linear bias More...
Matrix< UInt > | cord_
| 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.

## Class Documentation

## ◆ OpenMS::LocalLinearMap::LLMParam

struct OpenMS::LocalLinearMap::LLMParam

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

Parameters xdim and ydim define the size of the two dimensional grid structure. Parameter radius gives the width of the Gaussian neighborhood function.

Class Members
double | radius | width of Gaussian neighborhood function
UInt | xdim | size of first coordinate
UInt | ydim | size of second coordinate

## Constructor & Destructor Documentation

## ◆ LocalLinearMap() [1/2]

LocalLinearMap | ( |  | ) |

default constructor

## ◆ ~LocalLinearMap()

virtual ~LocalLinearMap | ( |  | ) |

virtual

destructor

## ◆ LocalLinearMap() [2/2]

LocalLinearMap | ( | LocalLinearMap & | rhs | ) |

private

Copy constructor not implemented => private.

## Member Function Documentation

## ◆ dist_()

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

private

calculate distance between two prototypes

## ◆ genCord_()

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

private

needed to store prototype coordinates

## ◆ getCodebooks()

const Matrix<double>& getCodebooks | ( |  | ) | const

return position of the codebook vectors (18-dim)

## ◆ getCord()

const Matrix<UInt>& getCord | ( |  | ) | const

return coordinates of codebook vectors on the 2-d grid

## ◆ getLLMParam()

const LLMParam& getLLMParam | ( |  | ) | const

return parameters of the LocalLinearMap model

## ◆ getMatrixA()

const Matrix<double>& getMatrixA | ( |  | ) | const

return linear mappings of the codebooks

## ◆ getVectorWout()

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

return linear bias

## ◆ neigh()

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.

## ◆ normalizeVector()

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

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

## ◆ operator=()

LocalLinearMap& operator= | ( | const LocalLinearMap & | llm | ) |

private

Assignment operator not implemented => private.

## Member Data Documentation

## ◆ A_

Matrix<double> A_

private

linear mappings

## ◆ code_

Matrix<double> code_

private

codebook vectors

## ◆ cord_

Matrix<UInt> cord_

private

coordinates of codebooks on grid

## ◆ param_

LLMParam param_

private

parameters of the model

## ◆ wout_

std::vector<double> wout_

private

linear bias