Helper class for peptide and protein quantification based on feature data annotated with IDs. More...

#include <OpenMS/ANALYSIS/QUANTITATION/ProteinResolver.h>

Inheritance diagram for ProteinResolver:

Classes
struct	ISDGroup

struct	MSDGroup
	representation of an msd group. Contains peptides, proteins and a pointer to its ISD group More...

struct	PeptideEntry
	represents a peptide. First in silico. If experimental is set to true it is MS/MS derived. More...

struct	ProteinEntry
	represents a protein from FASTA file More...

struct	ResolverResult

Public Member Functions
	ProteinResolver ()

	ProteinResolver (const ProteinResolver &rhs)

ProteinResolver &	operator= (const ProteinResolver &rhs)

	~ProteinResolver () override

void	resolveConsensus (ConsensusMap &consensus)
	Computing protein groups from peptide identifications OR consensus map. More...

void	resolveID (std::vector< PeptideIdentification > &peptide_identifications)
	Computing protein groups from peptide identifications OR consensus map. More...

void	countTargetDecoy (std::vector< MSDGroup > &msd_groups, ConsensusMap &consensus)
	NOT IMPLEMENTED YET. More...

void	countTargetDecoy (std::vector< MSDGroup > &msd_groups, std::vector< PeptideIdentification > &peptide_nodes)
	brief More...

void	clearResult ()

void	setProteinData (std::vector< FASTAFile::FASTAEntry > &protein_data)

const std::vector< ResolverResult > &	getResults ()

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...

Static Public Member Functions
static const PeptideIdentification &	getPeptideIdentification (const ConsensusMap &consensus, const PeptideEntry *peptide)
	overloaded functions – return a const reference to a PeptideIdentification object or a peptideHit either from a consensusMap or a vector<PeptideIdentification> More...

static const PeptideHit &	getPeptideHit (const ConsensusMap &consensus, const PeptideEntry *peptide)

static const PeptideIdentification &	getPeptideIdentification (const std::vector< PeptideIdentification > &peptide_nodes, const PeptideEntry *peptide)

static const PeptideHit &	getPeptideHit (const std::vector< PeptideIdentification > &peptide_nodes, const PeptideEntry *peptide)

Private Member Functions
void	computeIntensityOfMSD_ (std::vector< MSDGroup > &msd_groups)

void	traverseProtein_ (ProteinEntry *prot_node, MSDGroup &group)
	traverse protein and peptide nodes for building MSD groups More...

void	traversePeptide_ (PeptideEntry *pep_node, MSDGroup &group)

Size	findPeptideEntry_ (String seq, std::vector< PeptideEntry > &nodes)
	searches given sequence in all nodes and returns its index or nodes.size() if not found. More...

Size	binarySearchNodes_ (String &seq, std::vector< PeptideEntry > &nodes, Size start, Size end)
	helper function for findPeptideEntry. More...

Size	includeMSMSPeptides_ (std::vector< PeptideIdentification > &peptide_identifications, std::vector< PeptideEntry > &peptide_nodes)
	includes all MS/MS derived peptides into the graph –idXML More...

Size	includeMSMSPeptides_ (ConsensusMap &consensus, std::vector< PeptideEntry > &peptide_nodes)

void	reindexingNodes_ (std::vector< MSDGroup > &msd_groups, std::vector< Size > &reindexed_proteins, std::vector< Size > &reindexed_peptides)
	Proteins and Peptides get reindexed, based on whether they belong to msd groups or not. Indexes of Proteins which are in an ISD group but in none of the MSD groups will not be used anymore. More...

void	primaryProteins_ (std::vector< PeptideEntry > &peptide_nodes, std::vector< Size > &reindexed_peptides)
	marks Proteins which have a unique peptide as primary. Uses reindexed vector, thus reindexingNodes has to be called before. More...

void	buildingMSDGroups_ (std::vector< MSDGroup > &msd_groups, std::vector< ISDGroup > &isd_groups)

void	buildingISDGroups_ (std::vector< ProteinEntry > &protein_nodes, std::vector< PeptideEntry > &peptide_nodes, std::vector< ISDGroup > &isd_groups)

Private Attributes
std::vector< ResolverResult >	resolver_result_

std::vector< FASTAFile::FASTAEntry >	protein_data_

Additional Inherited Members
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...

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

Helper class for peptide and protein quantification based on feature data annotated with IDs.

This class is used by ProteinResolver. See there for further documentation.

Class Documentation

◆ OpenMS::ProteinResolver::ISDGroup

struct OpenMS::ProteinResolver::ISDGroup

Class Members
Size	index
list< Size >	msd_groups
list< PeptideEntry * >	peptides
list< ProteinEntry * >	proteins

◆ OpenMS::ProteinResolver::MSDGroup

struct OpenMS::ProteinResolver::MSDGroup

representation of an msd group. Contains peptides, proteins and a pointer to its ISD group

Class Members
Size	index
float	intensity	intensity of the MSD Group. Defined as the median of the peptide intensities.
ISDGroup *	isd_group
Size	number_of_decoy
Size	number_of_target
Size	number_of_target_plus_decoy
list< PeptideEntry * >	peptides
list< ProteinEntry * >	proteins

◆ OpenMS::ProteinResolver::PeptideEntry

struct OpenMS::ProteinResolver::PeptideEntry

represents a peptide. First in silico. If experimental is set to true it is MS/MS derived.

Class Members
bool	experimental
Size	index
float	intensity
Size	isd_group
Size	msd_group
String	origin
Size	peptide_hit
Size	peptide_identification
list< ProteinEntry * >	proteins
String	sequence
bool	traversed

Constructor & Destructor Documentation

◆ ProteinResolver() [1/2]

ProteinResolver ( )

◆ ProteinResolver() [2/2]

ProteinResolver ( const ProteinResolver & rhs )

◆ ~ProteinResolver()

~ProteinResolver ( )

override

Member Function Documentation

◆ binarySearchNodes_()

Size binarySearchNodes_	(	String &	seq,
		std::vector< PeptideEntry > &	nodes,
		Size	start,
		Size	end
	)

private

helper function for findPeptideEntry.

◆ buildingISDGroups_()

void buildingISDGroups_	(	std::vector< ProteinEntry > &	protein_nodes,
		std::vector< PeptideEntry > &	peptide_nodes,
		std::vector< ISDGroup > &	isd_groups
	)

private

◆ buildingMSDGroups_()

void buildingMSDGroups_	(	std::vector< MSDGroup > &	msd_groups,
		std::vector< ISDGroup > &	isd_groups
	)

private

◆ clearResult()

void clearResult ( )

◆ computeIntensityOfMSD_()

void computeIntensityOfMSD_ ( std::vector< MSDGroup > & msd_groups )

private

◆ countTargetDecoy() [1/2]

void countTargetDecoy	(	std::vector< MSDGroup > &	msd_groups,
		ConsensusMap &	consensus
	)

NOT IMPLEMENTED YET.

Parameters

protein_nodes
peptide_nodes
reindexed_proteins
reindexed_peptides
peptide_identifications
output

Writing peptide table into text file

Parameters

peptides
reindexed_peptides
identifications
output_file

Writing peptide table into text file

Parameters

peptides
reindexed_peptides
consensus
output

Writing protein table into text file

Parameters

proteins
reindexed_proteins
output_file

Writing protein groups into text file

Parameters

isd_groups	ISD groups
msd_groups	MSD groups
output_file	Path of output file

brief

Parameters

msd_groups
consensus

◆ countTargetDecoy() [2/2]

void countTargetDecoy	(	std::vector< MSDGroup > &	msd_groups,
		std::vector< PeptideIdentification > &	peptide_nodes
	)

brief

Parameters

msd_groups
peptide_nodes

◆ findPeptideEntry_()

Size findPeptideEntry_	(	String	seq,
		std::vector< PeptideEntry > &	nodes
	)

private

searches given sequence in all nodes and returns its index or nodes.size() if not found.

◆ getPeptideHit() [1/2]

static const PeptideHit& getPeptideHit	(	const ConsensusMap &	consensus,
		const PeptideEntry *	peptide
	)

static

◆ getPeptideHit() [2/2]

static const PeptideHit& getPeptideHit	(	const std::vector< PeptideIdentification > &	peptide_nodes,
		const PeptideEntry *	peptide
	)

static

◆ getPeptideIdentification() [1/2]

static const PeptideIdentification& getPeptideIdentification	(	const ConsensusMap &	consensus,
		const PeptideEntry *	peptide
	)

static

overloaded functions – return a const reference to a PeptideIdentification object or a peptideHit either from a consensusMap or a vector<PeptideIdentification>

◆ getPeptideIdentification() [2/2]

static const PeptideIdentification& getPeptideIdentification	(	const std::vector< PeptideIdentification > &	peptide_nodes,
		const PeptideEntry *	peptide
	)

static

◆ getResults()

const std::vector<ResolverResult>& getResults ( )

◆ includeMSMSPeptides_() [1/2]

Size includeMSMSPeptides_	(	ConsensusMap &	consensus,
		std::vector< PeptideEntry > &	peptide_nodes
	)

private

TODO include run information for each peptide includes all MS/MS derived peptides into the graph –consensusXML

◆ includeMSMSPeptides_() [2/2]

Size includeMSMSPeptides_	(	std::vector< PeptideIdentification > &	peptide_identifications,
		std::vector< PeptideEntry > &	peptide_nodes
	)

private

includes all MS/MS derived peptides into the graph –idXML

◆ operator=()

ProteinResolver& operator= ( const ProteinResolver & rhs )

◆ primaryProteins_()

void primaryProteins_	(	std::vector< PeptideEntry > &	peptide_nodes,
		std::vector< Size > &	reindexed_peptides
	)

private

marks Proteins which have a unique peptide as primary. Uses reindexed vector, thus reindexingNodes has to be called before.

◆ reindexingNodes_()

void reindexingNodes_	(	std::vector< MSDGroup > &	msd_groups,
		std::vector< Size > &	reindexed_proteins,
		std::vector< Size > &	reindexed_peptides
	)

private

Proteins and Peptides get reindexed, based on whether they belong to msd groups or not. Indexes of Proteins which are in an ISD group but in none of the MSD groups will not be used anymore.

◆ resolveConsensus()

void resolveConsensus ( ConsensusMap & consensus )

Computing protein groups from peptide identifications OR consensus map.

Computes ISD and MSD groups.

Parameters

consensus ConsensusMap in case consensusXML file is given as input

◆ resolveID()

void resolveID ( std::vector< PeptideIdentification > & peptide_identifications )

Computing protein groups from peptide identifications OR consensus map.

Computes ISD and MSD groups.

Parameters

peptide_identifications Vector of PeptideIdentification in case idXML is given as input

◆ setProteinData()

void setProteinData ( std::vector< FASTAFile::FASTAEntry > & protein_data )

◆ traversePeptide_()

void traversePeptide_	(	PeptideEntry *	pep_node,
		MSDGroup &	group
	)

private

◆ traverseProtein_()

void traverseProtein_	(	ProteinEntry *	prot_node,
		MSDGroup &	group
	)

private

traverse protein and peptide nodes for building MSD groups

Member Data Documentation

◆ protein_data_

std::vector<FASTAFile::FASTAEntry> protein_data_

private

◆ resolver_result_

std::vector<ResolverResult> resolver_result_

private

Classes

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::ProteinResolver::ISDGroup

◆ OpenMS::ProteinResolver::MSDGroup

◆ OpenMS::ProteinResolver::PeptideEntry

Constructor & Destructor Documentation

◆ ProteinResolver() [1/2]

◆ ProteinResolver() [2/2]

◆ ~ProteinResolver()

Member Function Documentation

◆ binarySearchNodes_()

◆ buildingISDGroups_()

◆ buildingMSDGroups_()

◆ clearResult()

◆ computeIntensityOfMSD_()

◆ countTargetDecoy() [1/2]

◆ countTargetDecoy() [2/2]

◆ findPeptideEntry_()

◆ getPeptideHit() [1/2]

◆ getPeptideHit() [2/2]

◆ getPeptideIdentification() [1/2]

◆ getPeptideIdentification() [2/2]

◆ getResults()

◆ includeMSMSPeptides_() [1/2]

◆ includeMSMSPeptides_() [2/2]

◆ operator=()

◆ primaryProteins_()

◆ reindexingNodes_()

◆ resolveConsensus()

◆ resolveID()

◆ setProteinData()

◆ traversePeptide_()

◆ traverseProtein_()

Member Data Documentation

◆ protein_data_

◆ resolver_result_