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
struct	PeptideEntry
struct	ProteinEntry
struct	ResolverResult
Public Member Functions
	ProteinResolver ()
	ProteinResolver (const ProteinResolver &rhs)
ProteinResolver &	operator= (const ProteinResolver &rhs)
virtual	~ProteinResolver ()
void	resolveConsensus (ConsensusMap &consensus)
	Computing protein groups from peptide identifications OR consensus map.
void	resolveID (std::vector< PeptideIdentification > &peptide_identifications)
	Computing protein groups from peptide identifications OR consensus map.
void	writePeptideTable (std::vector< PeptideEntry > &peptides, std::vector< Size > &reindexed_peptides, std::vector< PeptideIdentification > &identifications, String &output_file)
	NOT IMPLEMENTED YET.
void	writePeptideTable (std::vector< PeptideEntry > &peptides, std::vector< Size > &reindexed_peptides, ConsensusMap &consensus, String &output_file)
	Writing peptide table into text file.
void	writeProteinTable (std::vector< ProteinEntry > &proteins, std::vector< Size > &reindexed_proteins, String &output_file)
	Writing protein table into text file.
void	writeProteinGroups (std::vector< ISDGroup > &isd_groups, std::vector< MSDGroup > &msd_groups, String &output_file)
	Writing protein groups into text file.
void	countTargetDecoy (std::vector< MSDGroup > &msd_groups, ConsensusMap &consensus)
	brief
void	countTargetDecoy (std::vector< MSDGroup > &msd_groups, std::vector< PeptideIdentification > &peptide_nodes)
	brief
void	clearResult ()
void	setProteinData (std::vector< FASTAFile::FASTAEntry > &protein_data)
const std::vector < ResolverResult > &	getResults ()
const PeptideIdentification &	getPeptideIdentification (const ConsensusMap &consensus, const PeptideEntry *peptide)
const PeptideHit &	getPeptideHit (const ConsensusMap &consensus, const PeptideEntry *peptide)
const PeptideIdentification &	getPeptideIdentification (const std::vector< PeptideIdentification > &peptide_nodes, const PeptideEntry *peptide)
const PeptideHit &	getPeptideHit (const std::vector< PeptideIdentification > &peptide_nodes, const PeptideEntry *peptide)
Private Member Functions
void	computeIntensityOfMSD_ (std::vector< MSDGroup > &msd_groups)
void	traversProtein_ (ProteinEntry *prot_node, ISDGroup &group)
void	traversProtein_ (ProteinEntry *prot_node, MSDGroup &group)
void	traversPeptide_ (PeptideEntry *pep_node, ISDGroup &group)
void	traversPeptide_ (PeptideEntry *pep_node, MSDGroup &group)
Size	findPeptideEntry_ (String seq, std::vector< PeptideEntry > &nodes)
Size	binarySearchNodes_ (String &seq, std::vector< PeptideEntry > &nodes, Size start, Size end)
Size	includeMSMSPeptides_ (std::vector< PeptideIdentification > &peptide_identifications, std::vector< PeptideEntry > &peptide_nodes)
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)
void	primaryProteins_ (std::vector< PeptideEntry > &peptide_nodes, std::vector< Size > &reindexed_peptides)
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_

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.

Constructor & Destructor Documentation

ProteinResolver ( )

ProteinResolver ( const ProteinResolver & rhs )

virtual ~ProteinResolver ( ) [virtual]

Member Function Documentation

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

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

void buildingMSDGroups_	(	std::vector< MSDGroup > &	msd_groups,
		std::vector< ISDGroup > &	isd_groups
	)			`[private]`

void clearResult ( )

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

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

brief

Parameters:

	msd_groups
	consensus

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

brief

Parameters:

	msd_groups
	peptide_nodes

Size findPeptideEntry_	(	String	seq,
		std::vector< PeptideEntry > &	nodes
	)			`[private]`

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

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

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

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

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

Size includeMSMSPeptides_	(	ConsensusMap &	consensus,
		std::vector< PeptideEntry > &	peptide_nodes
	)			`[private]`

Size includeMSMSPeptides_	(	std::vector< PeptideIdentification > &	peptide_identifications,
		std::vector< PeptideEntry > &	peptide_nodes
	)			`[private]`

ProteinResolver& operator= ( const ProteinResolver & rhs )

void primaryProteins_	(	std::vector< PeptideEntry > &	peptide_nodes,
		std::vector< Size > &	reindexed_peptides
	)			`[private]`

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

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

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

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

void traversPeptide_	(	PeptideEntry *	pep_node,
		ISDGroup &	group
	)			`[private]`

void traversPeptide_	(	PeptideEntry *	pep_node,
		MSDGroup &	group
	)			`[private]`

void traversProtein_	(	ProteinEntry *	prot_node,
		ISDGroup &	group
	)			`[private]`

void traversProtein_	(	ProteinEntry *	prot_node,
		MSDGroup &	group
	)			`[private]`

void writePeptideTable	(	std::vector< PeptideEntry > &	peptides,
		std::vector< Size > &	reindexed_peptides,
		ConsensusMap &	consensus,
		String &	output_file
	)

Writing peptide table into text file.

Parameters:

	peptides
	reindexed_peptides
	consensus
	output

void writePeptideTable	(	std::vector< PeptideEntry > &	peptides,
		std::vector< Size > &	reindexed_peptides,
		std::vector< PeptideIdentification > &	identifications,
		String &	output_file
	)

NOT IMPLEMENTED YET.

Parameters:

	protein_nodes
	peptide_nodes
	reindexed_proteins
	reindexed_peptides
	peptide_identifications
	output	Writing peptide table into text file
	peptides
	reindexed_peptides
	identifications
	output_file

void writeProteinGroups	(	std::vector< ISDGroup > &	isd_groups,
		std::vector< MSDGroup > &	msd_groups,
		String &	output_file
	)

Writing protein groups into text file.

Parameters:

	isd_groups	ISD groups
	msd_groups	MSD groups
	output_file	Path of output file

void writeProteinTable	(	std::vector< ProteinEntry > &	proteins,
		std::vector< Size > &	reindexed_proteins,
		String &	output_file
	)

Writing protein table into text file.

Parameters:

	proteins
	reindexed_proteins
	output_file

Member Data Documentation

std::vector<FASTAFile::FASTAEntry> protein_data_ [private]

std::vector<ResolverResult> resolver_result_ [private]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1

ProteinResolver Class Reference

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation