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 () |
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 ¶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 | |
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... | |
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 |