FeatureFinder Class Reference

The main feature finder class. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h>

Inheritance diagram for FeatureFinder:

Collaboration diagram for FeatureFinder:

Public Member Functions
	FeatureFinder ()
	Default constructor. More...
	~FeatureFinder () override
	Destructor. More...
void	run (const String &algorithm_name, PeakMap &input_map, FeatureMap &features, const Param &param, const FeatureMap &seeds)
	Executes the FeatureFinder using the given algorithm. More...
const Flag &	getPeakFlag (const IndexPair &index) const
	Returns a non-mutable reference to a peak flag. More...
Flag &	getPeakFlag (const IndexPair &index)
	Returns mutable reference to a peak flag. More...
Param	getParameters (const String &algorithm_name) const
	Returns the default parameters for the algorithm with name algorithm_name. More...
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
virtual	~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 (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Protected Attributes
std::vector< std::vector< Flag > >	flags_
	Container for flags attached to input data. More...
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Public Types inherited from FeatureFinderDefs
enum	Flag { UNUSED , USED }
	Flags that indicate if a peak is already used in a feature. More...
typedef IsotopeCluster::IndexPair	IndexPair
	Index to peak consisting of two UInts (scan index / peak index) More...
typedef IsotopeCluster::ChargedIndexSet	ChargedIndexSet
	Index to peak consisting of two UInts (scan index / peak index) with charge information. More...
typedef IsotopeCluster::IndexSet	IndexSet
	A set of peak indices. More...
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

The main feature finder class.

• Stores the flags for (indices of) data points ("used", "unused")
• The algorithm itself is a factory product (derived from FeatureFinderAlgorithm)
• The main method is run(), which is a template so that we can deal with different types of input and output
• The run() method takes five arguments: algorithm_name, input_map, output, parameters, seeds

Constructor & Destructor Documentation

FeatureFinder()

FeatureFinder

(

)

Default constructor.

~FeatureFinder()

~FeatureFinder ( )

override

Destructor.

Member Function Documentation

getParameters()

Param getParameters

(

const String &

algorithm_name

)

const

Returns the default parameters for the algorithm with name algorithm_name.

getPeakFlag() [1/2]

Flag& getPeakFlag ( const IndexPair &  index )

inline

Returns mutable reference to a peak flag.

getPeakFlag() [2/2]

const Flag& getPeakFlag ( const IndexPair &  index ) const

inline

Returns a non-mutable reference to a peak flag.

run()

void run	(	const String &	algorithm_name,
		PeakMap &	input_map,
		FeatureMap &	features,
		const Param &	param,
		const FeatureMap &	seeds
	)

Executes the FeatureFinder using the given algorithm.

There are several constraints for the input_map. They are tested before the algorithm starts. It must only contain MS 1 level scans and you have to call updateRanges() before passing it to this method. The input map is sorted by RT & m/z if that's not the case. Furthermore we throw an Exception if the data contains negative m/z values, as this will disturb most algorithms.

Parameters

algorithm_name	Name of the feature finding algorithm to use
input_map	Input peak map
features	Output feature map
param	Algorithm parameters
seeds	List of seeds to use

Implemented in FeatureFinder_impl.h

Member Data Documentation

flags_

std::vector<std::vector<Flag> > flags_

protected

Container for flags attached to input data.