ProteinIdentification
- class pyopenms.ProteinIdentification
Bases:
objectCython implementation of _ProteinIdentification
- Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1ProteinIdentification.html
– Inherits from [‘MetaInfoInterface’]
- __init__()
Cython signature: void ProteinIdentification()
Cython signature: void ProteinIdentification(ProteinIdentification &)
Methods
Cython signature: void ProteinIdentification()
Cython signature: void addPrimaryMSRunPath(StringList & s)
Cython signature: void assignRanks() Sorts the protein hits by score and assigns ranks (best score has rank 1)
Cython signature: void clearMetaInfo() Removes all meta values
Cython signature: void computeCoverage(libcpp_vector[PeptideIdentification] pep_ids) Compute the coverage (in percent) of all ProteinHits given PeptideHits
Cython signature: DateTime getDateTime() Returns the date of the protein identification run
Cython signature: libcpp_vector[ProteinHit] getHits() Returns the protein hits
Cython signature: String getIdentifier() Returns the identifier
Cython signature: libcpp_vector[ProteinGroup] getIndistinguishableProteins() Returns the indistinguishable proteins
Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
Cython signature: void getPrimaryMSRunPath(StringList & output)
Cython signature: libcpp_vector[ProteinGroup] getProteinGroups() Returns the protein groups
Cython signature: String getScoreType() Returns the protein score type
Cython signature: String getSearchEngine() Returns the type of search engine used
Cython signature: String getSearchEngineVersion() Returns the search engine version
Cython signature: SearchParameters getSearchParameters() Returns the search parameters
Cython signature: double getSignificanceThreshold() Returns the protein significance threshold value
Cython signature: void insertHit(ProteinHit input) Appends a protein hit
Cython signature: void insertIndistinguishableProteins(ProteinGroup group) Appends new indistinguishable proteins
Cython signature: void insertProteinGroup(ProteinGroup group) Appends a new protein group
Cython signature: bool isHigherScoreBetter() Returns true if a higher score represents a better score
Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
Cython signature: void setDateTime(DateTime date) Sets the date of the protein identification run
Cython signature: void setHigherScoreBetter(bool higher_is_better) Sets the orientation of the score (is higher better?)
Cython signature: void setHits(libcpp_vector[ProteinHit] hits) Sets the protein hits
Cython signature: void setIdentifier(String id_) Sets the identifier
Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
Cython signature: void setPrimaryMSRunPath(StringList & s)
Cython signature: void setScoreType(String type) Sets the protein score type
Cython signature: void setSearchEngine(String search_engine) Sets the search engine type
Cython signature: void setSearchEngineVersion(String search_engine_version) Sets the search engine version
Cython signature: void setSearchParameters(SearchParameters search_parameters) Sets the search parameters
Cython signature: void setSignificanceThreshold(double value) Sets the protein significance threshold value
Cython signature: void sort() Sorts the protein hits according to their score
- PeakMassType
alias of
pyopenms.pyopenms_4.__PeakMassType
- addPrimaryMSRunPath()
Cython signature: void addPrimaryMSRunPath(StringList & s)
Cython signature: void addPrimaryMSRunPath(StringList & s, bool raw)
- assignRanks()
Cython signature: void assignRanks() Sorts the protein hits by score and assigns ranks (best score has rank 1)
- clearMetaInfo()
Cython signature: void clearMetaInfo() Removes all meta values
- computeCoverage()
Cython signature: void computeCoverage(libcpp_vector[PeptideIdentification] pep_ids) Compute the coverage (in percent) of all ProteinHits given PeptideHits
- getDateTime()
Cython signature: DateTime getDateTime() Returns the date of the protein identification run
- getHits()
Cython signature: libcpp_vector[ProteinHit] getHits() Returns the protein hits
- getIdentifier()
Cython signature: String getIdentifier() Returns the identifier
- getIndistinguishableProteins()
Cython signature: libcpp_vector[ProteinGroup] getIndistinguishableProteins() Returns the indistinguishable proteins
- getKeys()
Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
- getMetaValue()
Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
- getPrimaryMSRunPath()
Cython signature: void getPrimaryMSRunPath(StringList & output)
Cython signature: void getPrimaryMSRunPath(StringList & output, bool raw)
- getProteinGroups()
Cython signature: libcpp_vector[ProteinGroup] getProteinGroups() Returns the protein groups
- getScoreType()
Cython signature: String getScoreType() Returns the protein score type
- getSearchEngine()
Cython signature: String getSearchEngine() Returns the type of search engine used
- getSearchEngineVersion()
Cython signature: String getSearchEngineVersion() Returns the search engine version
- getSearchParameters()
Cython signature: SearchParameters getSearchParameters() Returns the search parameters
- getSignificanceThreshold()
Cython signature: double getSignificanceThreshold() Returns the protein significance threshold value
- insertHit()
Cython signature: void insertHit(ProteinHit input) Appends a protein hit
- insertIndistinguishableProteins()
Cython signature: void insertIndistinguishableProteins(ProteinGroup group) Appends new indistinguishable proteins
- insertProteinGroup()
Cython signature: void insertProteinGroup(ProteinGroup group) Appends a new protein group
- isHigherScoreBetter()
Cython signature: bool isHigherScoreBetter() Returns true if a higher score represents a better score
- isMetaEmpty()
Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
- metaRegistry()
Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
- metaValueExists()
Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
- removeMetaValue()
Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
- setDateTime()
Cython signature: void setDateTime(DateTime date) Sets the date of the protein identification run
- setHigherScoreBetter()
Cython signature: void setHigherScoreBetter(bool higher_is_better) Sets the orientation of the score (is higher better?)
- setHits()
Cython signature: void setHits(libcpp_vector[ProteinHit] hits) Sets the protein hits
- setMetaValue()
Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
- setPrimaryMSRunPath()
Cython signature: void setPrimaryMSRunPath(StringList & s)
- Parameters
raw – Store paths to the raw files (or equivalent) rather than mzMLs - Cython signature: void setPrimaryMSRunPath(StringList & s, bool raw)
- setScoreType()
Cython signature: void setScoreType(String type) Sets the protein score type
- setSearchEngine()
Cython signature: void setSearchEngine(String search_engine) Sets the search engine type
- setSearchEngineVersion()
Cython signature: void setSearchEngineVersion(String search_engine_version) Sets the search engine version
- setSearchParameters()
Cython signature: void setSearchParameters(SearchParameters search_parameters) Sets the search parameters
- setSignificanceThreshold()
Cython signature: void setSignificanceThreshold(double value) Sets the protein significance threshold value
- sort()
Cython signature: void sort() Sorts the protein hits according to their score