Provides functionality for writing inclusion or exclusion lists. More...

#include <OpenMS/ANALYSIS/TARGETED/InclusionExclusionList.h>

Inheritance diagram for InclusionExclusionList:

Collaboration diagram for InclusionExclusionList:

Classes
struct	IEWindow

class	WindowDistance_
	Determine distance between two spectra. More...

Public Member Functions
Constructors and destructors
	InclusionExclusionList ()
	default constructor More...

void	writeTargets (const std::vector< FASTAFile::FASTAEntry > &fasta_entries, const String &out_path, const IntList &charges, const String &rt_model_path)
	Writes inclusion or exclusion list of tryptic peptides of the given proteins (tab-delimited). More...

void	writeTargets (const FeatureMap &map, const String &out_path)
	Writes inclusion or exclusion list of given feature map. More...

void	writeTargets (const std::vector< PeptideIdentification > &pep_ids, const String &out_path, const IntList &charges)
	Writes inclusion or exclusion list of given peptide ids (tab-delimited). More...

Public Member Functions inherited from DefaultParamHandler
	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...

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	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...

Protected Types
typedef std::vector< IEWindow >	WindowList

Protected Member Functions
void	mergeOverlappingWindows_ (WindowList &list) const
	Merges overlapping windows using m/z tolerance. More...

void	writeToFile_ (const String &out_path, const WindowList &windows) const
	Writes the windows to the given file. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Attributes inherited from DefaultParamHandler
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...

Detailed Description

Provides functionality for writing inclusion or exclusion lists.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
missed_cleavages	int	0		Number of missed cleavages used for protein digestion.
RT:unit	string	minutes	minutes, seconds	Create lists with units as seconds instead of minutes
RT:use_relative	string	true	true, false	Use relative RT window, which depends on RT of precursor.
RT:window_relative	float	0.05	min: 0.0 max: 10.0	[for RT:use_relative == true] The relative factor X for the RT exclusion window, e.g. the window is calculated as [rt - rtX, rt + rtX].
RT:window_absolute	float	90.0	min: 0.0	[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec], e.g. the window is calculated as [rt - X, rt + X].
merge:mz_tol	float	10.0	min: 0.0	Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance. Unit of this is defined in 'mz_tol_unit'.
merge:mz_tol_unit	string	ppm	ppm, Da	Unit of 'mz_tol'
merge:rt_tol	float	1.1	min: 0.0	Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows). Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds].

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Todo:: allow modifications (fixed?)

Member Typedef Documentation

◆ WindowList

typedef std::vector<IEWindow> WindowList

protected

Constructor & Destructor Documentation

◆ InclusionExclusionList()

InclusionExclusionList ( )

default constructor

Member Function Documentation

◆ mergeOverlappingWindows_()

void mergeOverlappingWindows_ ( WindowList & list ) const

protected

Merges overlapping windows using m/z tolerance.

We employ single linkage clustering to merge windows that:

are close in m/z
overlap in RT All clusters found by this are merged such that:
RT windows are extended
m/z value is averaged over all windows

◆ writeTargets() [1/3]

void writeTargets	(	const FeatureMap &	map,
		const String &	out_path
	)

Writes inclusion or exclusion list of given feature map.

Exceptions

Exception::UnableToCreateFile is thrown if the output file cannot be created

◆ writeTargets() [2/3]

void writeTargets	(	const std::vector< FASTAFile::FASTAEntry > &	fasta_entries,
		const String &	out_path,
		const IntList &	charges,
		const String &	rt_model_path
	)

Writes inclusion or exclusion list of tryptic peptides of the given proteins (tab-delimited).

Exceptions

Exception::UnableToCreateFile is thrown if the output file cannot be created

◆ writeTargets() [3/3]

void writeTargets	(	const std::vector< PeptideIdentification > &	pep_ids,
		const String &	out_path,
		const IntList &	charges
	)

Writes inclusion or exclusion list of given peptide ids (tab-delimited).

Exceptions

Exception::UnableToCreateFile	is thrown if the output file cannot be created
Exception::InvalidSize	is thrown if a peptide id contains more than one hit
Exception::MissingInformation	is thrown if a peptide id contains no RT information

◆ writeToFile_()

void writeToFile_	(	const String &	out_path,
		const WindowList &	windows
	)		const

protected

Writes the windows to the given file.

Format for each window is: <mz>\t<rt_start>\t<rt_stop>\n

Exceptions

Exception::UnableToCreateFile when file cannot be created

Classes

Public Member Functions

Protected Types

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ WindowList

Constructor & Destructor Documentation

◆ InclusionExclusionList()

Member Function Documentation

◆ mergeOverlappingWindows_()

◆ writeTargets() [1/3]

◆ writeTargets() [2/3]

◆ writeTargets() [3/3]

◆ writeToFile_()