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OptimizePick Class Reference
[PeakPicking]

#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePick.h>

List of all members.


Detailed Description

This class provides the non-linear optimization of the peak paramters.

Given a vector of peak shapes, this class optimizes all peak shapes parameters using a non-linear optimization. For the non-linear optimization we use the Levenberg-Marquardt algorithm provided by the gsl.

Public Types

typedef std::vector
< DRawDataPoint< 1 > > 
RawDataVector
 Raw data vector type.
typedef RawDataVector::iterator RawDataPointIterator
 Raw data iterator type.

Public Member Functions

 OptimizePick ()
 Constructor.
 OptimizePick (const struct OptimizationFunctions::PenaltyFactors &penalties_, const int max_iteration_, const double eps_abs_, const double eps_rel_)
 Constructor to set the penalty factors, the number of optimization iterations as well as the threshold for the absolute and the relative error.
 ~OptimizePick ()
 Destructor.
struct
OptimizationFunctions::PenaltyFactors
getPenalties () const
 Non-mutable access to the penalty factors.
struct
OptimizationFunctions::PenaltyFactors
getPenalties ()
 Mutable access to the penalty factors.
void setPenalties (const struct OptimizationFunctions::PenaltyFactors &penalties)
 Mutable access to the penalty factors.
UInt getNumberIterations () const
 Non-mutable access to the number of iterations.
unsigned int & getNumberIterations ()
 Mutable access to the number of iterations.
void setNumberIterations (const int max_iteration)
 Mutable access to the number of iterations.
DoubleReal getMaxAbsError () const
 Non-mutable access to the maximum absolute error.
double & getMaxAbsError ()
 Mutable access to the maximum absolute error.
void setMaxAbsError (double eps_abs)
 Mutable access to the maximum absolute error.
DoubleReal getMaxRelError () const
 Non-mutable access to the maximum relative error.
double & getMaxRelError ()
 Mutable access to the maximum relative error.
void setMaxRelError (double eps_rel)
 Mutable access to the maximum relative error.
void optimize (std::vector< PeakShape > &peaks)
 Start the optimization of the peak shapes peaks. The original peak shapes will be subsituted by the optimized peak shapes.

Protected Member Functions

double correlate_ (const PeakShape &peak, double left_endpoint, double right_endpoint)
 Returns the squared pearson coefficient.

Protected Attributes

struct
OptimizationFunctions::PenaltyFactors 
penalties_
 Penalty factors.
unsigned int max_iteration_
 Maximum number of iterations during optimization.
double eps_abs_
 Maximum absolute and relative error used in the optimization.
double eps_rel_


Member Typedef Documentation

typedef std::vector<DRawDataPoint<1> > RawDataVector

Raw data vector type.

typedef RawDataVector::iterator RawDataPointIterator

Raw data iterator type.


Constructor & Destructor Documentation

OptimizePick (  )  [inline]

Constructor.

OptimizePick ( const struct OptimizationFunctions::PenaltyFactors penalties_,
const int  max_iteration_,
const double  eps_abs_,
const double  eps_rel_ 
)

Constructor to set the penalty factors, the number of optimization iterations as well as the threshold for the absolute and the relative error.

~OptimizePick (  ) 

Destructor.


Member Function Documentation

struct OptimizationFunctions::PenaltyFactors& getPenalties (  )  const [inline, read]

Non-mutable access to the penalty factors.

struct OptimizationFunctions::PenaltyFactors& getPenalties (  )  [inline, read]

Mutable access to the penalty factors.

void setPenalties ( const struct OptimizationFunctions::PenaltyFactors penalties  )  [inline]

Mutable access to the penalty factors.

UInt getNumberIterations (  )  const [inline]

Non-mutable access to the number of iterations.

unsigned int& getNumberIterations (  )  [inline]

Mutable access to the number of iterations.

void setNumberIterations ( const int  max_iteration  )  [inline]

Mutable access to the number of iterations.

DoubleReal getMaxAbsError (  )  const [inline]

Non-mutable access to the maximum absolute error.

double& getMaxAbsError (  )  [inline]

Mutable access to the maximum absolute error.

void setMaxAbsError ( double  eps_abs  )  [inline]

Mutable access to the maximum absolute error.

DoubleReal getMaxRelError (  )  const [inline]

Non-mutable access to the maximum relative error.

double& getMaxRelError (  )  [inline]

Mutable access to the maximum relative error.

void setMaxRelError ( double  eps_rel  )  [inline]

Mutable access to the maximum relative error.

void optimize ( std::vector< PeakShape > &  peaks  ) 

Start the optimization of the peak shapes peaks. The original peak shapes will be subsituted by the optimized peak shapes.

double correlate_ ( const PeakShape peak,
double  left_endpoint,
double  right_endpoint 
) [protected]

Returns the squared pearson coefficient.

Computes the correlation of the peak and the original data given by the peak enpoints. If the value is near 1, the fitted peakshape and the raw data are expected to be very similar.


Member Data Documentation

struct OptimizationFunctions::PenaltyFactors penalties_ [read, protected]

Penalty factors.

unsigned int max_iteration_ [protected]

Maximum number of iterations during optimization.

double eps_abs_ [protected]

Maximum absolute and relative error used in the optimization.

double eps_rel_ [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:48 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1