MRMFeaturePickerFile Class Reference

_MRMFeaturePickerFile_ loads components and components groups parameters from a .csv file. More...

#include <OpenMS/FORMAT/MRMFeaturePickerFile.h>

Inheritance diagram for MRMFeaturePickerFile:

Collaboration diagram for MRMFeaturePickerFile:

Public Member Functions
	MRMFeaturePickerFile ()=default
	Constructor. More...
	~MRMFeaturePickerFile () override=default
	Destructor. More...
void	load (const String &filename, std::vector< MRMFeaturePicker::ComponentParams > &cp_list, std::vector< MRMFeaturePicker::ComponentGroupParams > &cgp_list)
	Loads the file's data and saves it into vectors of `ComponentParams` and `ComponentGroupParams`. More...
Public Member Functions inherited from CsvFile
	CsvFile ()
	Default constructor. More...
	~CsvFile () override
	destructor More...
	CsvFile (const String &filename, char is=',', bool ie=false, Int first_n=-1)
	Constructor with filename. More...
void	load (const String &filename, char is=',', bool ie=false, Int first_n=-1)
	Loads data from a text file. More...
void	store (const String &filename)
	Stores the buffer's content into a file. More...
void	addRow (const StringList &list)
	Add a row to the buffer. More...
void	clear ()
	Clears the buffer. More...
bool	getRow (Size row, StringList &list)
	writes all items from a row to list More...
std::vector< String >::size_type	rowCount () const
	Returns the number of rows that were loaded from the file. More...

Protected Member Functions
bool	extractParamsFromLine_ (const StringList &line, const std::map< String, Size > &headers, MRMFeaturePicker::ComponentParams &cp, MRMFeaturePicker::ComponentGroupParams &cgp) const
	Extracts the information from a `StringList` and saves it into the correct data structures. More...
void	setCastValue_ (const String &key, const String &value, Param &params) const
	Helper method which takes care of converting the given value to the desired type, based on the header (here `key`) information. More...

Detailed Description

_MRMFeaturePickerFile_ loads components and components groups parameters from a .csv file.

The structures defined in [MRMFeaturePicker](MRMFeaturePicker) are used.

It is required that columns `component_name` and `component_group_name` are present. Lines whose `component_name`'s or `component_group_name`'s value is an empty string, will be skipped. The class supports the absence of information within other columns.

A reduced example of the expected format (fewer columns are shown here): > component_name,component_group_name,TransitionGroupPicker:stop_after_feature,TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length > arg-L.arg-L_1.Heavy,arg-L,2,15 > arg-L.arg-L_1.Light,arg-L,2,17 > orn.orn_1.Heavy,orn,3,21 > orn.orn_1.Light,orn,3,13

Constructor & Destructor Documentation

MRMFeaturePickerFile()

MRMFeaturePickerFile ( )

default

Constructor.

~MRMFeaturePickerFile()

~MRMFeaturePickerFile ( )

overridedefault

Destructor.

Member Function Documentation

extractParamsFromLine_()

bool extractParamsFromLine_ ( const StringList &  line, const std::map< String, Size > &  headers, MRMFeaturePicker::ComponentParams &  cp, MRMFeaturePicker::ComponentGroupParams &  cgp  ) const

protected

Extracts the information from a `StringList` and saves it into the correct data structures.

Parameters

[in]	line	The line parsed from the input file
[in]	headers	A mapping from a given header to its value's position
[out]	cp	The extracted component parameters
[out]	cgp	The extracted component group parameters

Returns

Returns `false` if `component_name` or `component_group_name` are empty strings. Otherwise, it returns `true`.

load()

void load	(	const String &	filename,
		std::vector< MRMFeaturePicker::ComponentParams > &	cp_list,
		std::vector< MRMFeaturePicker::ComponentGroupParams > &	cgp_list
	)

Loads the file's data and saves it into vectors of `ComponentParams` and `ComponentGroupParams`.

The file is expected to contain at least two columns: `component_name` and `component_group_name`. Otherwise, an exception is thrown.

If a component group (identified by its name) is found multiple times, only the first one is saved.

Parameters

[in]	filename	Path to the .csv input file
[out]	cp_list	Component params are saved in this list
[out]	cgp_list	Component Group params are saved in this list

Exceptions

Exception::MissingInformation	If the required columns are not found.
Exception::FileNotFound	If input file is not found.

setCastValue_()

void setCastValue_ ( const String &  key, const String &  value, Param &  params  ) const

protected

Helper method which takes care of converting the given value to the desired type, based on the header (here `key`) information.

Parameters

[in]	key	The header name with which the correct conversion is chosen
[in]	value	The value to be converted
[in,out]	params	The object where the new value is saved