| OpenMS 2.5.0

Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
ConsensusIDAlgorithmPEPMatrix Class Reference
Analysis » Identification

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

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

Inheritance diagram for ConsensusIDAlgorithmPEPMatrix:

## 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...
| ~ConsensusIDAlgorithm () override
| 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 DefaultParamHandler & | operator= (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 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...

## 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...
ConsensusIDAlgorithmPEPMatrix & | operator= (const ConsensusIDAlgorithmPEPMatrix &)
| Not implemented. More...
void | updateMembers_ () override
| Docu in base class. More...
double | getSimilarity_ (AASequence seq1, AASequence seq2) override
| 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 >, double > | SimilarityCache
| 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< 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...

## 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.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
matrix | string | identity | identity, PAM30MS | Substitution matrix to use for alignment-based similarity scoring
penalty | int | 5 | min: 1 | Alignment gap penalty (the same value is used for gap opening and extension)
filter:considered_hits | int | 0 | min: 0 | The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits).
filter:min_support | float | 0.0 | min: 0.0 max: 1.0 | For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed).
filter:count_empty | string | false | true, false | Count empty ID runs (i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Member Typedef Documentation

## ◆ SeqAnScore

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

private

SeqAn similarity scoring.

## ◆ SeqAnSequence

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

private

SeqAn amino acid sequence.

## Constructor & Destructor Documentation

## ◆ ConsensusIDAlgorithmPEPMatrix() [1/2]

ConsensusIDAlgorithmPEPMatrix | ( |  | ) |

Default constructor.

## ◆ ConsensusIDAlgorithmPEPMatrix() [2/2]

ConsensusIDAlgorithmPEPMatrix | ( | const ConsensusIDAlgorithmPEPMatrix & |  | ) |

private

Not implemented.

## Member Function Documentation

## ◆ getSimilarity_()

double getSimilarity_ | ( | AASequence | seq1,
|  | AASequence | seq2
| ) |  |

override private virtual

Sequence similarity based on substitution matrix (ignores PTMs)

Implements ConsensusIDAlgorithmSimilarity.

## ◆ operator=()

ConsensusIDAlgorithmPEPMatrix& operator= | ( | const ConsensusIDAlgorithmPEPMatrix & |  | ) |

private

Not implemented.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override private virtual

Docu in base class.

Reimplemented from ConsensusIDAlgorithm.

## Member Data Documentation

## ◆ alignment_

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

private

Alignment data structure.

## ◆ scoring_method_

SeqAnScore scoring_method_

private

Similarity scoring method.