File adapter for MRMFeatureQC files. More...

#include <OpenMS/FORMAT/MRMFeatureQCFile.h>

Inheritance diagram for MRMFeatureQCFile:

Collaboration diagram for MRMFeatureQCFile:

Public Member Functions
	MRMFeatureQCFile ()=default
	Default constructor. More...

	~MRMFeatureQCFile () override=default
	Destructor. More...

void	load (const String &filename, MRMFeatureQC &mrmfqc, const bool is_component_group) const
	Loads an MRMFeatureQC file. More...

void	store (const String &filename, const MRMFeatureQC &mrmfqc, const bool is_component_group)

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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 Member Functions
void	pushValuesFromLine_ (const StringList &line, const std::map< String, Size > &headers, std::vector< MRMFeatureQC::ComponentQCs > &c_qcs) const
	Save values from a line to a `ComponentQCs`. More...

void	pushValuesFromLine_ (const StringList &line, const std::map< String, Size > &headers, std::vector< MRMFeatureQC::ComponentGroupQCs > &cg_qcs) const
	Save values from a line to a `ComponentGroupQCs`. More...

void	setPairValue_ (const String &key, const String &value, const String &boundary, std::map< String, std::pair< double, double >> &meta_values_qc) const
	Set one of the values in a pair. More...

Int	getCastValue_ (const std::map< String, Size > &headers, const StringList &line, const String &header, const Int default_value) const
	Extracts a column's value from a line. More...

double	getCastValue_ (const std::map< String, Size > &headers, const StringList &line, const String &header, const double default_value) const
	Extracts a column's value from a line. More...

String	getCastValue_ (const std::map< String, Size > &headers, const StringList &line, const String &header, const String &default_value) const
	Extracts a column's value from a line. More...

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

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Private 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) const
	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...

Detailed Description

File adapter for MRMFeatureQC files.

Loads and stores .csv or .tsv files describing an MRMFeatureQC.

Constructor & Destructor Documentation

◆ MRMFeatureQCFile()

MRMFeatureQCFile ( )

default

Default constructor.

◆ ~MRMFeatureQCFile()

~MRMFeatureQCFile ( )

overridedefault

Destructor.

Member Function Documentation

◆ getCastValue_() [1/3]

double getCastValue_	(	const std::map< String, Size > &	headers,
		const StringList &	line,
		const String &	header,
		const double	default_value
	)		const

protected

Extracts a column's value from a line.

The method looks for the value found within line[headers[header]]. If the information is present and its value is valid, it will be converted to double and returned. Otherwise, default_value (provided by the user) is returned.

Parameters

[in]	headers	The mapping from columns' name to positions' indices
[in]	line	A list of strings containing a single row's values
[in]	header	The desired value's column name
[in]	default_value	A default value to return in case the information is not found or invalid

Returns: The found information (if found and valid) converted to double. Otherwise default_value.

◆ getCastValue_() [2/3]

Int getCastValue_	(	const std::map< String, Size > &	headers,
		const StringList &	line,
		const String &	header,
		const Int	default_value
	)		const

protected

Extracts a column's value from a line.

The method looks for the value found within line[headers[header]]. If the information is present and its value is valid, it will be converted to Int and returned. Otherwise, default_value (provided by the user) is returned.

Parameters

[in]	headers	The mapping from columns' name to positions' indices
[in]	line	A list of strings containing a single row's values
[in]	header	The desired value's column name
[in]	default_value	A default value to return in case the information is not found or invalid

Returns: The found information (if found and valid) converted to Int. Otherwise default_value.

◆ getCastValue_() [3/3]

String getCastValue_	(	const std::map< String, Size > &	headers,
		const StringList &	line,
		const String &	header,
		const String &	default_value
	)		const

protected

Extracts a column's value from a line.

The method looks for the value found within line[headers[header]]. If the information is present and its value is valid, it will be converted to String and returned. Otherwise, default_value (provided by the user) is returned.

Parameters

[in]	headers	The mapping from columns' name to positions' indices
[in]	line	A list of strings containing a single row's values
[in]	header	The desired value's column name
[in]	default_value	A default value to return in case the information is not found or invalid

Returns: The found information (if found and valid) converted to String. Otherwise default_value.

◆ load()

void load	(	const String &	filename,
		MRMFeatureQC &	mrmfqc,
		const bool	is_component_group
	)		const

Loads an MRMFeatureQC file.

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

Parameters

[in]	filename	The path to the input file
[in,out]	mrmfqc	The output class which will contain the criteria
[in]	is_component_group	true if the user intends to load ComponentGroupQCs data, false otherwise

◆ pushValuesFromLine_() [1/2]

void pushValuesFromLine_	(	const StringList &	line,
		const std::map< String, Size > &	headers,
		std::vector< MRMFeatureQC::ComponentGroupQCs > &	cg_qcs
	)		const

protected

Save values from a line to a ComponentGroupQCs.

Note: Lines missing the component_group_name value will be skipped.

Parameters

[in]	line	A line containing the values from a row in the input file
[in]	headers	A mapping from headers names to position indices
[out]	cg_qcs	The output will be saved in a new element of this vector

◆ pushValuesFromLine_() [2/2]

void pushValuesFromLine_	(	const StringList &	line,
		const std::map< String, Size > &	headers,
		std::vector< MRMFeatureQC::ComponentQCs > &	c_qcs
	)		const

protected

Save values from a line to a ComponentQCs.

Note: Lines missing the component_name value will be skipped.

Parameters

[in]	line	A line containing the values from a row in the input file
[in]	headers	A mapping from headers names to position indices
[out]	c_qcs	The output will be saved in a new element of this vector

◆ setPairValue_()

void setPairValue_	(	const String &	key,
		const String &	value,
		const String &	boundary,
		std::map< String, std::pair< double, double >> &	meta_values_qc
	)		const

protected

Set one of the values in a pair.

The method is given in input a map from Strings to pairs. Assuming the key is present within the map, its mapped value will be updated with the given value, in the correct boundary position. If the key is not found, a new pair will be created and both its values set (in this case, a default value of 0.0 is given to the other pair's element).

Parameters

[in]	key	The metavalue name
[in]	value	The mapped pair
[in]	boundary	"l" for lower bound or "u" for upper bound
[out]	meta_values_qc	The map containing the metavalues and pairs

◆ store()

void store	(	const String &	filename,
		const MRMFeatureQC &	mrmfqc,
		const bool	is_component_group
	)

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MRMFeatureQCFile()

◆ ~MRMFeatureQCFile()

Member Function Documentation

◆ getCastValue_() [1/3]

◆ getCastValue_() [2/3]

◆ getCastValue_() [3/3]

◆ load()

◆ pushValuesFromLine_() [1/2]

◆ pushValuesFromLine_() [2/2]

◆ setPairValue_()

◆ store()