MQExporterHelper Class Reference

Helper class for common functions and NON trivial values needed for exporting MaxQuant outputs. More...

#include <OpenMS/QC/MQExporterHelper.h>

Classes
struct	MQCommonOutputs

Static Public Member Functions
static OpenMS::String	extractGeneName (const OpenMS::String &prot_description)
	Extract a gene name from a protein description by looking for the substring 'GN='. More...
static OpenMS::Size	proteinGroupID_ (std::map< OpenMS::String, OpenMS::Size > &database, const OpenMS::String &protein_accession)
	Returns a unique ID (number) for each distinct protein accession, or creates a new ID by augmenting the given database. More...
static std::map< OpenMS::Size, OpenMS::Size >	makeFeatureUIDtoConsensusMapIndex_ (const OpenMS::ConsensusMap &cmap)
	Creates map that has the information which FeatureUID is mapped to which ConsensusFeature in ConsensusMap. More...
static bool	hasValidPepID_ (const OpenMS::Feature &f, const OpenMS::Size c_feature_number, const std::multimap< OpenMS::String, std::pair< OpenMS::Size, OpenMS::Size >> &UIDs, const OpenMS::ProteinIdentification::Mapping &mp_f)
	Checks if Feature has valid PeptideIdentifications. More...
static bool	hasPeptideIdentifications_ (const OpenMS::ConsensusFeature &cf)
	Checks if ConsensusFeature has valid PeptideIdentifications. More...
static bool	isValid (const std::string &filename_)
	Checks if file is writable (i.e. the path in the ctor was not empty and could be created) More...

Detailed Description

Helper class for common functions and NON trivial values needed for exporting MaxQuant outputs.

Member Function Documentation

extractGeneName()

static OpenMS::String extractGeneName ( const OpenMS::String &  prot_description )

static

Extract a gene name from a protein description by looking for the substring 'GN='.

If no such substring exists, an empty string is returned.

hasPeptideIdentifications_()

static bool hasPeptideIdentifications_ ( const OpenMS::ConsensusFeature &  cf )

static

Checks if ConsensusFeature has valid PeptideIdentifications.

If there are no PeptideIdentifications, the functions returns false to show that something went wrong.

Parameters

cf	is used to extract PeptideIdentifications

Returns

Returns true if the ConsensusFeature has any PepIDs; otherwise false

hasValidPepID_()

static bool hasValidPepID_ ( const OpenMS::Feature &  f, const OpenMS::Size  c_feature_number, const std::multimap< OpenMS::String, std::pair< OpenMS::Size, OpenMS::Size >> &  UIDs, const OpenMS::ProteinIdentification::Mapping &  mp_f  )

static

Checks if Feature has valid PeptideIdentifications.

If there are no PeptideIdentifications or the best hit of the Feature cannot be found in corresponding ConsensusFeature, the functions returns false to show that something went wrong.

Parameters

f	Feature to extract PeptideIdentifications
c_feature_number	Index of corresponding ConsensusFeature in ConsensusMap
UIDs	UIDs of all PeptideIdentifications of the ConsensusMap
mp_f	Mapping between the FeatureMap and ProteinIdentifications for the UID

Returns

Returns true if the PeptideIdentifications exist and are valid

isValid()

static bool isValid ( const std::string &  filename_ )

static

Checks if file is writable (i.e. the path in the ctor was not empty and could be created)

Returns

Returns true if file is writable

makeFeatureUIDtoConsensusMapIndex_()

static std::map<OpenMS::Size, OpenMS::Size> makeFeatureUIDtoConsensusMapIndex_ ( const OpenMS::ConsensusMap &  cmap )

static

Creates map that has the information which FeatureUID is mapped to which ConsensusFeature in ConsensusMap.

Exceptions

Exception::Precondition

if FeatureHandle exists twice in ConsensusMap

Parameters

cmap	ConsensusMap that includes ConsensusFeatures

Returns

Returns map, the index is a FeatureID, the value is the index of the ConsensusFeature in the vector of ConsensusMap

proteinGroupID_()

static OpenMS::Size proteinGroupID_ ( std::map< OpenMS::String, OpenMS::Size > &  database, const OpenMS::String &  protein_accession  )

static

Returns a unique ID (number) for each distinct protein accession, or creates a new ID by augmenting the given database.

Obtains a unique, consecutive number for each distinct protein, which can be used as a protein ID in the MaxQuant output files (in lack of a proper proteingroup ID which maps to proteinGroups.txt)

Parameters

database	A map from accession to ID (which can be augmented by this function)
protein_accession	The protein accession which needs translation to an ID

Returns

The ID for the protein_accession