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