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SILACFiltering Class Reference

Filtering for SILAC data. More...

#include <OpenMS/FILTERING/DATAREDUCTION/SILACFiltering.h>

Inheritance diagram for SILACFiltering:
ProgressLogger

Classes

struct  BlacklistEntry
 structure for blacklist More...
 
class  SpectrumInterpolation
 Wrapper class for spectrum interpolation. More...
 

Public Types

typedef std::vector< SILACFilterFilters
 
- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 

Public Member Functions

 SILACFiltering (MSExperiment< Peak1D > &exp, const PeakWidthEstimator::Result &, const DoubleReal intensity_cutoff, const String debug_filebase_="")
 detailed constructor More...
 
void addFilter (SILACFilter &filter)
 adds a new filter to the filtering More...
 
void filterDataPoints ()
 starts the filtering based on the added filters More...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress () const
 Ends the progress display. More...
 

Public Attributes

Filters filters_
 holds all filters used in the filtering More...
 
const PeakWidthEstimator::Result peak_width
 peak-width equation More...
 
std::multimap< DoubleReal,
BlacklistEntry
blacklist
 holds the range that is blacklisted for other filters and the filter that generated the blacklist entry More...
 

Private Member Functions

void pickSeeds_ ()
 pick data seeds More...
 
void filterSeeds_ ()
 apply filtering to picked data seeds More...
 

Private Attributes

DoubleReal intensity_cutoff_
 minimal intensity of SILAC features More...
 
MSExperiment< Peak1D > & exp_
 raw data More...
 
MSExperiment< Peak1Dpicked_exp_
 picked data More...
 
MSExperiment< Peak1Dpicked_exp_seeds_
 picked data seeds More...
 
const String debug_filebase_
 

Additional Inherited Members

- Protected Attributes inherited from ProgressLogger
LogType type_
 
SignedSize begin_
 
SignedSize end_
 
SignedSize value_
 
QProgressDialog * dlg_
 
StopWatch stop_watch_
 
time_t last_invoke_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

Filtering for SILAC data.

This filtering can be used to extract SILAC features from an MS experiment. Several SILACFilters can be added to the filtering to search for specific SILAC patterns.

See Also
SILACFilter

Member Typedef Documentation

typedef std::vector<SILACFilter> Filters

Constructor & Destructor Documentation

SILACFiltering ( MSExperiment< Peak1D > &  exp,
const PeakWidthEstimator::Result ,
const DoubleReal  intensity_cutoff,
const String  debug_filebase_ = "" 
)

detailed constructor

Parameters
expraw data
intensity_cutoffminimal intensity of SILAC features

Member Function Documentation

void addFilter ( SILACFilter filter)

adds a new filter to the filtering

Parameters
filterfilter to add
void filterDataPoints ( )

starts the filtering based on the added filters

void filterSeeds_ ( )
private

apply filtering to picked data seeds

void pickSeeds_ ( )
private

pick data seeds

Member Data Documentation

std::multimap<DoubleReal, BlacklistEntry> blacklist

holds the range that is blacklisted for other filters and the filter that generated the blacklist entry

const String debug_filebase_
private

Filename base for debugging output

MSExperiment<Peak1D>& exp_
private

raw data

Filters filters_

holds all filters used in the filtering

DoubleReal intensity_cutoff_
private

minimal intensity of SILAC features

const PeakWidthEstimator::Result peak_width

peak-width equation

MSExperiment<Peak1D> picked_exp_
private

picked data

MSExperiment<Peak1D> picked_exp_seeds_
private

picked data seeds


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5