InclusionExclusionList Class Reference

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...
virtual 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.

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