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ChromatogramExtractor Class Reference

The ChromatogramExtractor extracts chromatograms from a mzML file. More...

#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>

Inheritance diagram for ChromatogramExtractor:
ProgressLogger

Public Member Functions

 ChromatogramExtractor ()
 Constructor. More...
 
 ~ChromatogramExtractor ()
 Destructor. More...
 
template<typename ExperimentT >
void extractChromatograms (const ExperimentT &input, ExperimentT &output, OpenMS::TargetedExperiment &transition_exp, double extract_window, bool ppm, TransformationDescription trafo, double rt_extraction_window, String filter)
 Extract chromatograms defined by the TargetedExperiment from the input map and write them to the output map. More...
 
template<typename SpectrumT >
void extract_value_tophat (const SpectrumT &input, const double &mz, Size &peak_idx, double &integrated_intensity, const double &extract_window, const bool ppm)
 
template<typename SpectrumT >
void extract_value_bartlett (const SpectrumT &input, const double &mz, Size &peak_idx, double &integrated_intensity, const double &extract_window, const bool ppm)
 
void extract_value_tophat (const std::vector< double >::const_iterator &mz_start, std::vector< double >::const_iterator &mz_it, const std::vector< double >::const_iterator &mz_end, std::vector< double >::const_iterator &int_it, const double &mz, double &integrated_intensity, double &extract_window, bool ppm)
 
- 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...
 

Private Member Functions

template<class SpectrumSettingsT , class ChromatogramT >
void prepareSpectra_ (SpectrumSettingsT &settings, std::vector< ChromatogramT > &chromatograms, OpenMS::TargetedExperiment &transition_exp)
 This populates the chromatograms vector with empty chromatograms (but sets their meta-information) More...
 
bool outsideExtractionWindow_ (const ReactionMonitoringTransition &transition, double current_rt, const TransformationDescription &trafo, double rt_extraction_window)
 

Private Attributes

std::map< OpenMS::String, doublePeptideRTMap_
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- 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

The ChromatogramExtractor extracts chromatograms from a mzML file.

It will take as input a set of (TraML) transitions and will extract the signal of the provided map at the product ion m/z values specified by the transitions. The map is thus assumed to be an MS2 map from a SWATH / DIA experiment.

Constructor & Destructor Documentation

Constructor.

~ChromatogramExtractor ( )
inline

Destructor.

Member Function Documentation

void extract_value_bartlett ( const SpectrumT &  input,
const double mz,
Size peak_idx,
double integrated_intensity,
const double extract_window,
const bool  ppm 
)
inline
void extract_value_tophat ( const SpectrumT &  input,
const double mz,
Size peak_idx,
double integrated_intensity,
const double extract_window,
const bool  ppm 
)
inline
void extract_value_tophat ( const std::vector< double >::const_iterator &  mz_start,
std::vector< double >::const_iterator &  mz_it,
const std::vector< double >::const_iterator &  mz_end,
std::vector< double >::const_iterator &  int_it,
const double mz,
double integrated_intensity,
double extract_window,
bool  ppm 
)
inline
void extractChromatograms ( const ExperimentT &  input,
ExperimentT &  output,
OpenMS::TargetedExperiment transition_exp,
double  extract_window,
bool  ppm,
TransformationDescription  trafo,
double  rt_extraction_window,
String  filter 
)
inline
bool outsideExtractionWindow_ ( const ReactionMonitoringTransition transition,
double  current_rt,
const TransformationDescription trafo,
double  rt_extraction_window 
)
inlineprivate
void prepareSpectra_ ( SpectrumSettingsT &  settings,
std::vector< ChromatogramT > &  chromatograms,
OpenMS::TargetedExperiment transition_exp 
)
inlineprivate

Member Data Documentation

std::map<OpenMS::String, double> PeptideRTMap_
private

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5