Representation of a protein identification run. More...
#include <OpenMS/METADATA/ProteinIdentification.h>
Classes | |
struct | ProteinGroup |
Bundles multiple (e.g. indistinguishable) proteins in a group. More... | |
struct | SearchParameters |
Search parameters of the DB search. More... | |
Public Types | |
enum | PeakMassType { MONOISOTOPIC, AVERAGE, SIZE_OF_PEAKMASSTYPE } |
Peak mass type. More... | |
enum | DigestionEnzyme { TRYPSIN, PEPSIN_A, PROTEASE_K, CHYMOTRYPSIN, NO_ENZYME, UNKNOWN_ENZYME, SIZE_OF_DIGESTIONENZYME } |
typedef ProteinHit | HitType |
Hit type definition. More... | |
Public Member Functions | |
Constructors, destructors, assignment operator <br> | |
ProteinIdentification () | |
Default constructor. More... | |
virtual | ~ProteinIdentification () |
Destructor. More... | |
ProteinIdentification (const ProteinIdentification &source) | |
Copy constructor. More... | |
ProteinIdentification & | operator= (const ProteinIdentification &source) |
Assignment operator. More... | |
bool | operator== (const ProteinIdentification &rhs) const |
Equality operator. More... | |
bool | operator!= (const ProteinIdentification &rhs) const |
Inequality operator. More... | |
Protein hit information (public members) | |
const std::vector< ProteinHit > & | getHits () const |
Returns the protein hits. More... | |
std::vector< ProteinHit > & | getHits () |
Returns the protein hits (mutable) More... | |
void | insertHit (const ProteinHit &input) |
Appends a protein hit. More... | |
void | setHits (const std::vector< ProteinHit > &hits) |
Sets the protein hits. More... | |
std::vector< ProteinHit >::iterator | findHit (const String &accession) |
Finds a protein hit by accession (returns past-the-end iterator if not found) More... | |
const std::vector< ProteinGroup > & | getProteinGroups () const |
Returns the protein groups. More... | |
std::vector< ProteinGroup > & | getProteinGroups () |
Returns the protein groups (mutable) More... | |
void | insertProteinGroup (const ProteinGroup &group) |
Appends a new protein group. More... | |
const std::vector< ProteinGroup > & | getIndistinguishableProteins () const |
Returns the indistinguishable proteins. More... | |
std::vector< ProteinGroup > & | getIndistinguishableProteins () |
Returns the indistinguishable proteins (mutable) More... | |
void | insertIndistinguishableProteins (const ProteinGroup &group) |
Appends new indistinguishable proteins. More... | |
DoubleReal | getSignificanceThreshold () const |
Returns the protein significance threshold value. More... | |
void | setSignificanceThreshold (DoubleReal value) |
Sets the protein significance threshold value. More... | |
const String & | getScoreType () const |
Returns the protein score type. More... | |
void | setScoreType (const String &type) |
Sets the protein score type. More... | |
bool | isHigherScoreBetter () const |
Returns true if a higher score represents a better score. More... | |
void | setHigherScoreBetter (bool higher_is_better) |
Sets the orientation of the score (is higher better?) More... | |
void | sort () |
Sorts the protein hits according to their score. More... | |
void | assignRanks () |
Sorts the protein hits by score and assigns ranks (best score has rank 1) More... | |
Size | computeCoverage (const std::vector< PeptideIdentification > &pep_ids) |
Compute the coverage (in percent) of all ProteinHits given PeptideHits. More... | |
General information | |
const DateTime & | getDateTime () const |
Returns the date of the protein identification run. More... | |
void | setDateTime (const DateTime &date) |
Sets the date of the protein identification run. More... | |
void | setSearchEngine (const String &search_engine) |
Sets the search engine type. More... | |
const String & | getSearchEngine () const |
Returns the type of search engine used. More... | |
void | setSearchEngineVersion (const String &search_engine_version) |
Sets the search engine version. More... | |
const String & | getSearchEngineVersion () const |
Returns the search engine version. More... | |
void | setSearchParameters (const SearchParameters &search_parameters) |
Sets the search parameters. More... | |
const SearchParameters & | getSearchParameters () const |
Returns the search parameters. More... | |
const String & | getIdentifier () const |
Returns the identifier. More... | |
void | setIdentifier (const String &id) |
Sets the identifier. More... | |
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MetaInfoInterface () | |
constructor More... | |
MetaInfoInterface (const MetaInfoInterface &rhs) | |
copy constructor More... | |
~MetaInfoInterface () | |
destructor More... | |
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) |
assignment operator More... | |
bool | operator== (const MetaInfoInterface &rhs) const |
Equality operator. More... | |
bool | operator!= (const MetaInfoInterface &rhs) const |
Equality operator. More... | |
const DataValue & | getMetaValue (const String &name) const |
returns the value corresponding to a string More... | |
const DataValue & | getMetaValue (UInt index) const |
returns the value corresponding to an index More... | |
bool | metaValueExists (const String &name) const |
returns if this MetaInfo is set More... | |
bool | metaValueExists (UInt index) const |
returns if this MetaInfo is set More... | |
void | setMetaValue (const String &name, const DataValue &value) |
sets the DataValue corresponding to a name More... | |
void | setMetaValue (UInt index, const DataValue &value) |
sets the DataValue corresponding to an index More... | |
void | removeMetaValue (const String &name) |
Removes the DataValue corresponding to name if it exists. More... | |
void | removeMetaValue (UInt index) |
Removes the DataValue corresponding to index if it exists. More... | |
void | getKeys (std::vector< String > &keys) const |
fills the given vector with a list of all keys for which a value is set More... | |
void | getKeys (std::vector< UInt > &keys) const |
fills the given vector with a list of all keys for which a value is set More... | |
bool | isMetaEmpty () const |
returns if the MetaInfo is empty More... | |
void | clearMetaInfo () |
removes all meta values More... | |
Static Public Attributes | |
static const std::string | NamesOfPeakMassType [SIZE_OF_PEAKMASSTYPE] |
Names corresponding to peak mass types. More... | |
static const std::string | NamesOfDigestionEnzyme [SIZE_OF_DIGESTIONENZYME] |
Names corresponding to digestion enzymes. More... | |
Protected Attributes | |
General information (search engine, parameters and database) | |
String | id_ |
String | search_engine_ |
String | search_engine_version_ |
SearchParameters | search_parameters_ |
DateTime | date_ |
Protein hit information (protected members) | |
String | protein_score_type_ |
bool | higher_score_better_ |
std::vector< ProteinHit > | protein_hits_ |
std::vector< ProteinGroup > | protein_groups_ |
std::vector< ProteinGroup > | indistinguishable_proteins_ |
Indistinguishable proteins: accessions [0] is "group leader", probability is meaningless. More... | |
DoubleReal | protein_significance_threshold_ |
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MetaInfo * | meta_ |
pointer to the MetaInfo object. 0 by default More... | |
Additional Inherited Members | |
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static MetaInfoRegistry & | metaRegistry () |
retuns a reference to the MetaInfoRegistry More... | |
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void | createIfNotExists_ () |
creates the MetaInfo object if it does not exist More... | |
Representation of a protein identification run.
This class stores the general information and the protein hits of a protein identification run.
The actual peptide hits are stored in PeptideIdentification instances that are part of spectra or features.
In order to be able to connect the ProteinIdentification and the corresponding peptide identifications, both classes have a string identifier. We recommend using the search engine name and the date as identifier. Setting this identifier is especially important when there are several protein identification runs for a map, i.e. several ProteinIdentification instances.
typedef ProteinHit HitType |
Hit type definition.
enum DigestionEnzyme |
enum PeakMassType |
Default constructor.
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Destructor.
ProteinIdentification | ( | const ProteinIdentification & | source | ) |
Copy constructor.
void assignRanks | ( | ) |
Sorts the protein hits by score and assigns ranks (best score has rank 1)
Size computeCoverage | ( | const std::vector< PeptideIdentification > & | pep_ids | ) |
Compute the coverage (in percent) of all ProteinHits given PeptideHits.
Exception::MissingInformation | if ProteinsHits do not have sequence information |
pep_ids
that are not contained in this ProteinIdentification set (should be 0) std::vector<ProteinHit>::iterator findHit | ( | const String & | accession | ) |
Finds a protein hit by accession (returns past-the-end iterator if not found)
const DateTime& getDateTime | ( | ) | const |
Returns the date of the protein identification run.
const std::vector<ProteinHit>& getHits | ( | ) | const |
Returns the protein hits.
Referenced by IDFilter::filterIdentificationsByBestNHits(), IDFilter::filterIdentificationsByScores(), and IDFilter::filterIdentificationsByThresholds().
std::vector<ProteinHit>& getHits | ( | ) |
Returns the protein hits (mutable)
const String& getIdentifier | ( | ) | const |
Returns the identifier.
const std::vector<ProteinGroup>& getIndistinguishableProteins | ( | ) | const |
Returns the indistinguishable proteins.
std::vector<ProteinGroup>& getIndistinguishableProteins | ( | ) |
Returns the indistinguishable proteins (mutable)
const std::vector<ProteinGroup>& getProteinGroups | ( | ) | const |
Returns the protein groups.
std::vector<ProteinGroup>& getProteinGroups | ( | ) |
Returns the protein groups (mutable)
const String& getScoreType | ( | ) | const |
Returns the protein score type.
const String& getSearchEngine | ( | ) | const |
Returns the type of search engine used.
const String& getSearchEngineVersion | ( | ) | const |
Returns the search engine version.
const SearchParameters& getSearchParameters | ( | ) | const |
Returns the search parameters.
Referenced by DBAdapter::loadExperiment().
DoubleReal getSignificanceThreshold | ( | ) | const |
Returns the protein significance threshold value.
void insertHit | ( | const ProteinHit & | input | ) |
Appends a protein hit.
void insertIndistinguishableProteins | ( | const ProteinGroup & | group | ) |
Appends new indistinguishable proteins.
void insertProteinGroup | ( | const ProteinGroup & | group | ) |
Appends a new protein group.
bool isHigherScoreBetter | ( | ) | const |
Returns true if a higher score represents a better score.
bool operator!= | ( | const ProteinIdentification & | rhs | ) | const |
Inequality operator.
ProteinIdentification& operator= | ( | const ProteinIdentification & | source | ) |
Assignment operator.
bool operator== | ( | const ProteinIdentification & | rhs | ) | const |
Equality operator.
void setDateTime | ( | const DateTime & | date | ) |
Sets the date of the protein identification run.
Referenced by DBAdapter::loadExperiment().
void setHigherScoreBetter | ( | bool | higher_is_better | ) |
Sets the orientation of the score (is higher better?)
Referenced by DBAdapter::loadExperiment().
void setHits | ( | const std::vector< ProteinHit > & | hits | ) |
Sets the protein hits.
Referenced by DBAdapter::loadExperiment(), and MRMFeatureFinderScoring::pickExperiment().
void setIdentifier | ( | const String & | id | ) |
Sets the identifier.
Referenced by MRMFeatureFinderScoring::pickExperiment().
void setScoreType | ( | const String & | type | ) |
Sets the protein score type.
Referenced by DBAdapter::loadExperiment().
void setSearchEngine | ( | const String & | search_engine | ) |
Sets the search engine type.
Referenced by DBAdapter::loadExperiment().
void setSearchEngineVersion | ( | const String & | search_engine_version | ) |
Sets the search engine version.
Referenced by DBAdapter::loadExperiment().
void setSearchParameters | ( | const SearchParameters & | search_parameters | ) |
Sets the search parameters.
Referenced by DBAdapter::loadExperiment().
void setSignificanceThreshold | ( | DoubleReal | value | ) |
Sets the protein significance threshold value.
Referenced by DBAdapter::loadExperiment().
void sort | ( | ) |
Sorts the protein hits according to their score.
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Indistinguishable proteins: accessions
[0] is "group leader", probability
is meaningless.
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Names corresponding to digestion enzymes.
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Names corresponding to peak mass types.
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OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |