PrecursorIonSelectionPreprocessing#

class pyopenms.PrecursorIonSelectionPreprocessing#

Bases: object

Cython implementation of _PrecursorIonSelectionPreprocessing

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PrecursorIonSelectionPreprocessing.html: – Inherits from [‘DefaultParamHandler’]

__init__()#

Cython signature: void PrecursorIonSelectionPreprocessing()
Cython signature: void PrecursorIonSelectionPreprocessing(PrecursorIonSelectionPreprocessing &)

Methods

`__init__`	Cython signature: void PrecursorIonSelectionPreprocessing()
`dbPreprocessing`	Cython signature: void dbPreprocessing(String db_path, bool save)
`getDefaults`	Cython signature: Param getDefaults() Returns the default parameters
`getGaussMu`	Cython signature: double getGaussMu() Returns the Gauss Mu value
`getGaussSigma`	Cython signature: double getGaussSigma() Returns the Gauss Sigma value
`getMasses`	Cython signature: libcpp_vector[double] getMasses(String acc)
`getName`	Cython signature: String getName() Returns the name
`getPT`	Cython signature: double getPT(String prot_id, size_t peptide_index) Returns the PT value
`getParameters`	Cython signature: Param getParameters() Returns the parameters
`getRT`	Cython signature: double getRT(String prot_id, size_t peptide_index) Returns the RT value
`getRTProbability`	Cython signature: double getRTProbability(String prot_id, size_t peptide_index, Feature & feature)
`getSubsections`	Cython signature: libcpp_vector[String] getSubsections()
`getWeight`	Cython signature: double getWeight(double mass) Returns the weighted frequency of a mass
`loadPreprocessing`	Cython signature: void loadPreprocessing() Loads tryptic peptide masses of a given database
`setFixedModifications`	Cython signature: void setFixedModifications(StringList & modifications)
`setGaussianParameters`	Cython signature: void setGaussianParameters(double mu, double sigma)
`setName`	Cython signature: void setName(const String &) Sets the name
`setParameters`	Cython signature: void setParameters(Param & param) Sets the parameters

dbPreprocessing()#

Cython signature: void dbPreprocessing(String db_path, bool save)

Parameters

db_path – Path to database file (fasta)
save – Flag if preprocessing should be stored

Raises

Exception: FileNotFound is thrown if the file could not be found

Raises

Exception: UnableToCreateFile if preprocessing file can’t be written

Cython signature: void dbPreprocessing(String db_path, String rt_model_path, String dt_model_path, bool save)

Parameters: db_path – Path to database file (fasta)

:param rt_model_path :param dt_model_path :param save: Flag if preprocessing should be stored —– :raises:

Exception: FileNotFound is thrown if the file could not be found

Raises: Exception: UnableToCreateFile if preprocessing file can’t be written

getDefaults()#: Cython signature: Param getDefaults() Returns the default parameters

getGaussMu()#: Cython signature: double getGaussMu() Returns the Gauss Mu value

getGaussSigma()#: Cython signature: double getGaussSigma() Returns the Gauss Sigma value

getMasses()#: Cython signature: libcpp_vector[double] getMasses(String acc)

getName()#: Cython signature: String getName() Returns the name

getPT()#: Cython signature: double getPT(String prot_id, size_t peptide_index) Returns the PT value

getParameters()#: Cython signature: Param getParameters() Returns the parameters

getRT()#: Cython signature: double getRT(String prot_id, size_t peptide_index) Returns the RT value

getRTProbability()#

Cython signature: double getRTProbability(String prot_id, size_t peptide_index, Feature & feature)
Cython signature: double getRTProbability(double pred_rt, Feature & feature)

getSubsections()#: Cython signature: libcpp_vector[String] getSubsections()

getWeight()#: Cython signature: double getWeight(double mass) Returns the weighted frequency of a mass

loadPreprocessing()#: Cython signature: void loadPreprocessing() Loads tryptic peptide masses of a given database

setFixedModifications()#: Cython signature: void setFixedModifications(StringList & modifications)

setGaussianParameters()#: Cython signature: void setGaussianParameters(double mu, double sigma)

setName()#: Cython signature: void setName(const String &) Sets the name

setParameters()#: Cython signature: void setParameters(Param & param) Sets the parameters