Helper class for peptide and protein quantification based on feature data annotated with IDs. More...
#include <OpenMS/ANALYSIS/QUANTITATION/ProteinResolver.h>
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. 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 () |
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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 ¶m) |
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) |
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 | 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_ |
Additional Inherited Members | |
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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... | |
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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... | |
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.
ProteinResolver | ( | ) |
ProteinResolver | ( | const ProteinResolver & | rhs | ) |
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void clearResult | ( | ) |
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void countTargetDecoy | ( | std::vector< MSDGroup > & | msd_groups, |
ConsensusMap & | consensus | ||
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NOT IMPLEMENTED YET.
protein_nodes | |
peptide_nodes | |
reindexed_proteins | |
reindexed_peptides | |
peptide_identifications | |
output | Writing peptide table into text file |
peptides | |
reindexed_peptides | |
identifications | |
output_file | Writing peptide table into text file |
peptides | |
reindexed_peptides | |
consensus | |
output | Writing protein table into text file |
proteins | |
reindexed_proteins | |
output_file | Writing protein groups into text file |
isd_groups | ISD groups |
msd_groups | MSD groups |
output_file | Path of output file brief |
msd_groups | |
consensus |
void countTargetDecoy | ( | std::vector< MSDGroup > & | msd_groups, |
std::vector< PeptideIdentification > & | peptide_nodes | ||
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brief
msd_groups | |
peptide_nodes |
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const std::vector<ResolverResult>& getResults | ( | ) |
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ProteinResolver& operator= | ( | const ProteinResolver & | rhs | ) |
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void resolveConsensus | ( | ConsensusMap & | consensus | ) |
Computing protein groups from peptide identifications OR consensus map.
Computes ISD and MSD groups.
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.
peptide_identifications | Vector of PeptideIdentification in case idXML is given as input |
void setProteinData | ( | std::vector< FASTAFile::FASTAEntry > & | protein_data | ) |
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OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |