LocalLinearMap Class Reference

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

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

List of all members.

Classes
struct	LLMParam
	Define parameters needed by the Local Linear Map (LLM) model. More...
Public Member Functions
	LocalLinearMap ()
	default constructor
virtual	~LocalLinearMap ()
	destructor
const LLMParam &	getLLMParam () const
	return parameters of the LocalLinearMap model
const Matrix< DoubleReal > &	getCodebooks () const
	return position of the codebook vectors (18-dim)
const Matrix< DoubleReal > &	getMatrixA () const
	return linear mappings of the codebooks
const std::vector< DoubleReal > &	getVectorWout () const
	return linear bias
const Matrix< UInt > &	getCord () const
	return coordinates of codebook vectors on the 2-d grid
void	normalizeVector (std::vector< DoubleReal > &aaIndexVariables)
	calculate and return normalized amino acid index variables from string representation of peptide
std::vector< DoubleReal >	neigh (const Matrix< UInt > &cord, Size win, DoubleReal radius)
	calculate neighborhood function based on distance of prototypes to winner prototype on two-dimensional grid structure and neighborhood width.
Private Member Functions
Matrix< UInt >	genCord_ (Size xdim, Size ydim)
	needed to store prototype coordinates
DoubleReal	dist_ (const Matrix< UInt > &u, const Matrix< UInt > &v, Size a, Size b)
	calculate distance between two prototypes
	LocalLinearMap (LocalLinearMap &rhs)
	Copy constructor not implemented => private.
LocalLinearMap &	operator= (const LocalLinearMap &llm)
	Assignment operator not implemented => private.
Private Attributes
LLMParam	param_
	parameters of the model
Matrix< DoubleReal >	code_
	codebook vectors
Matrix< DoubleReal >	A_
	linear mappings
std::vector< DoubleReal >	wout_
	linear bias
Matrix< UInt >	cord_
	coordinates of codebooks on grid

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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.

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Constructor & Destructor Documentation

LocalLinearMap

(

)

default constructor

virtual ~LocalLinearMap

(

)

[virtual]

destructor

LocalLinearMap

(

LocalLinearMap &

rhs

)

[private]

Copy constructor not implemented => private.

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Member Function Documentation

DoubleReal 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<DoubleReal>& 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<DoubleReal>& getMatrixA

(

)

const

return linear mappings of the codebooks

const std::vector<DoubleReal>& getVectorWout

(

)

const

return linear bias

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

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

void normalizeVector

(

std::vector< DoubleReal > &

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<DoubleReal> A_ [private]

linear mappings

Matrix<DoubleReal> code_ [private]

codebook vectors

Matrix<UInt> cord_ [private]

coordinates of codebooks on grid

LLMParam param_ [private]

parameters of the model

std::vector<DoubleReal> wout_ [private]

linear bias