Extracts chromatographic peaks from a mass trace. More...
#include <OpenMS/FILTERING/DATAREDUCTION/ElutionPeakDetection.h>
Public Member Functions | |
ElutionPeakDetection () | |
Default Constructor. More... | |
virtual | ~ElutionPeakDetection () |
Destructor. More... | |
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DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
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ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. 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... | |
Main computation methods | |
double | chrom_fwhm_ |
double | chrom_peak_snr_ |
double | noise_threshold_int_ |
double | min_fwhm_ |
double | max_fwhm_ |
String | pw_filtering_ |
bool | mt_snr_filtering_ |
void | detectPeaks (MassTrace &mt, std::vector< MassTrace > &single_mtraces) |
Extracts chromatographic peaks from a single MassTrace and stores the splits into a vector of new mass traces. More... | |
void | detectPeaks (std::vector< MassTrace > &mt_vec, std::vector< MassTrace > &single_mtraces) |
void | filterByPeakWidth (std::vector< MassTrace > &, std::vector< MassTrace > &) |
double | computeMassTraceNoise (const MassTrace &) |
double | computeMassTraceSNR (const MassTrace &) |
double | computeApexSNR (const MassTrace &) |
void | findLocalExtrema (const MassTrace &, const Size &, std::vector< Size > &, std::vector< Size > &) |
void | smoothData (MassTrace &mt, int win_size) const |
adds smoothed_intensities to internal data of mt More... | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | detectElutionPeaks_ (MassTrace &, std::vector< MassTrace > &) |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
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static int | recursion_depth_ |
Extracts chromatographic peaks from a mass trace.
Mass traces may consist of several consecutively (partly overlapping) eluting peaks, e.g., stemming from isomeric compounds with exactly the same mass but different retentional behaviour. This method first applies smoothing on the mass trace's intensities, then detects local minima/maxima in order to separate the chromatographic peaks from each other. This results in a vector that gathers the splitted mass traces (see ElutionPeakDetection parameters).
Default Constructor.
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virtual |
Destructor.
Extracts chromatographic peaks from a single MassTrace and stores the splits into a vector of new mass traces.
Applies the aforementioned detection method on a series of mass traces as input Smoothed intensities are added to mt_vec
void findLocalExtrema | ( | const MassTrace & | , |
const Size & | , | ||
std::vector< Size > & | , | ||
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void smoothData | ( | MassTrace & | mt, |
int | win_size | ||
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adds smoothed_intensities to internal data of mt
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protectedvirtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
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OpenMS / TOPP release 2.0.0 | Documentation generated on Sat May 16 2015 16:13:49 using doxygen 1.8.9.1 |