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ProteinResolver Class Reference

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:
DefaultParamHandler

Classes

struct  ISDGroup
 
struct  MSDGroup
 
struct  PeptideEntry
 
struct  ProteinEntry
 
struct  ResolverResult
 

Public Member Functions

 ProteinResolver ()
 
 ProteinResolver (const ProteinResolver &rhs)
 
ProteinResolveroperator= (const ProteinResolver &rhs)
 
virtual ~ProteinResolver ()
 
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 DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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)
 
static const PeptideHitgetPeptideHit (const ConsensusMap &consensus, const PeptideEntry *peptide)
 
static const
PeptideIdentification
getPeptideIdentification (const std::vector< PeptideIdentification > &peptide_nodes, const PeptideEntry *peptide)
 
static const PeptideHitgetPeptideHit (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< ResolverResultresolver_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< Stringsubsections_
 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.

Constructor & Destructor Documentation

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 
)

NOT IMPLEMENTED YET.

Parameters
protein_nodes
peptide_nodes
reindexed_proteins
reindexed_peptides
peptide_identifications
outputWriting peptide table into text file
peptides
reindexed_peptides
identifications
output_fileWriting peptide table into text file
peptides
reindexed_peptides
consensus
outputWriting protein table into text file
proteins
reindexed_proteins
output_fileWriting protein groups into text file
isd_groupsISD groups
msd_groupsMSD groups
output_filePath of output file brief
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
static const PeptideHit& getPeptideHit ( const ConsensusMap consensus,
const PeptideEntry peptide 
)
static
static const PeptideHit& getPeptideHit ( const std::vector< PeptideIdentification > &  peptide_nodes,
const PeptideEntry peptide 
)
static
static const PeptideIdentification& getPeptideIdentification ( const ConsensusMap consensus,
const PeptideEntry peptide 
)
static
static const PeptideIdentification& getPeptideIdentification ( const std::vector< PeptideIdentification > &  peptide_nodes,
const PeptideEntry peptide 
)
static
const std::vector<ResolverResult>& getResults ( )
Size includeMSMSPeptides_ ( std::vector< PeptideIdentification > &  peptide_identifications,
std::vector< PeptideEntry > &  peptide_nodes 
)
private
Size includeMSMSPeptides_ ( ConsensusMap consensus,
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
consensusConsensusMap 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_identificationsVector 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

Member Data Documentation

std::vector<FASTAFile::FASTAEntry> protein_data_
private
std::vector<ResolverResult> resolver_result_
private

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5