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ConsensusIDAlgorithmPEPMatrix Class Reference

Calculates a consensus from multiple ID runs based on PEPs and sequence similarities. More...

#include <OpenMS/ANALYSIS/ID/ConsensusIDAlgorithmPEPMatrix.h>

Inheritance diagram for ConsensusIDAlgorithmPEPMatrix:
ConsensusIDAlgorithmSimilarity ConsensusIDAlgorithm DefaultParamHandler

Public Member Functions

 ConsensusIDAlgorithmPEPMatrix ()
 Default constructor. More...
 
- Public Member Functions inherited from ConsensusIDAlgorithm
void apply (std::vector< PeptideIdentification > &ids, Size number_of_runs=0)
 Calculates the consensus ID for a set of peptide identifications of one spectrum or (consensus) feature. More...
 
virtual ~ConsensusIDAlgorithm ()
 Virtual destructor. More...
 
- 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...
 

Private Types

typedef ::seqan::Score< int,::seqan::ScoreMatrix< ::seqan::AminoAcid,::seqan::Default > > SeqAnScore
 SeqAn similarity scoring. More...
 
typedef ::seqan::String< ::seqan::AminoAcid > SeqAnSequence
 SeqAn amino acid sequence. More...
 

Private Member Functions

 ConsensusIDAlgorithmPEPMatrix (const ConsensusIDAlgorithmPEPMatrix &)
 Not implemented. More...
 
ConsensusIDAlgorithmPEPMatrixoperator= (const ConsensusIDAlgorithmPEPMatrix &)
 Not implemented. More...
 
virtual void updateMembers_ ()
 Docu in base class. More...
 
virtual double getSimilarity_ (AASequence seq1, AASequence seq2)
 Sequence similarity based on substitution matrix (ignores PTMs) More...
 

Private Attributes

SeqAnScore scoring_method_
 Similarity scoring method. More...
 
::seqan::Align< SeqAnSequence,::seqan::ArrayGaps > alignment_
 Alignment data structure. More...
 

Additional Inherited Members

- Protected Types inherited from ConsensusIDAlgorithmSimilarity
typedef std::map< std::pair< AASequence, AASequence >, doubleSimilarityCache
 Mapping: pair of peptide sequences -> sequence similarity. More...
 
- Protected Types inherited from ConsensusIDAlgorithm
typedef std::map< AASequence, std::pair< Int, std::vector< double > > > SequenceGrouping
 Mapping: peptide sequence -> (charge, scores) More...
 
- Protected Member Functions inherited from ConsensusIDAlgorithmSimilarity
 ConsensusIDAlgorithmSimilarity ()
 Default constructor. More...
 
- Protected Member Functions inherited from ConsensusIDAlgorithm
 ConsensusIDAlgorithm ()
 Default constructor. More...
 
void compareChargeStates_ (Int &recorded_charge, Int new_charge, const AASequence &peptide)
 Compare (and possibly update) charge state information. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Protected Attributes inherited from ConsensusIDAlgorithmSimilarity
SimilarityCache similarities_
 Cache for already computed sequence similarities. More...
 
- Protected Attributes inherited from ConsensusIDAlgorithm
Size considered_hits_
 Number of peptide hits considered per ID run (input parameter) More...
 
Size number_of_runs_
 Number of ID runs. More...
 
double min_support_
 Fraction of required support by other ID runs (input parameter) More...
 
bool count_empty_
 Count empty runs in "min_support" calculation? (input parameter) 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

Calculates a consensus from multiple ID runs based on PEPs and sequence similarities.

Note
The similarity scoring is based on an amino acid substitution matrix. Therefore only the raw amino acid sequences, without post-translational modifications (PTMs), can be considered for similarity scoring - PTMs are ignored during this step. However, PTMs on peptides are retained and separate results are produced for differently-modified peptides.

Member Typedef Documentation

typedef ::seqan::Score<int, ::seqan::ScoreMatrix< ::seqan::AminoAcid, ::seqan::Default> > SeqAnScore
private

SeqAn similarity scoring.

typedef ::seqan::String< ::seqan::AminoAcid> SeqAnSequence
private

SeqAn amino acid sequence.

Constructor & Destructor Documentation

Default constructor.

Not implemented.

Member Function Documentation

virtual double getSimilarity_ ( AASequence  seq1,
AASequence  seq2 
)
privatevirtual

Sequence similarity based on substitution matrix (ignores PTMs)

Implements ConsensusIDAlgorithmSimilarity.

Not implemented.

virtual void updateMembers_ ( )
privatevirtual

Docu in base class.

Reimplemented from ConsensusIDAlgorithm.

Member Data Documentation

::seqan::Align<SeqAnSequence, ::seqan::ArrayGaps> alignment_
private

Alignment data structure.

SeqAnScore scoring_method_
private

Similarity scoring method.


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:27 using doxygen 1.8.11