MascotInfile

class pyopenms.MascotInfile

Bases: object

Cython implementation of _MascotInfile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MascotInfile.html: – Inherits from [‘ProgressLogger’]

__init__()

Cython signature: void MascotInfile()
Cython signature: void MascotInfile(MascotInfile &)

Methods

`__init__`	Cython signature: void MascotInfile()
`endProgress`	Cython signature: void endProgress() Ends the progress display
`getBoundary`	Cython signature: String getBoundary() Returns the boundary used for the MIME format
`getCharges`	Cython signature: String getCharges() Returns the charges
`getCleavage`	Cython signature: String getCleavage() Returns the enzyme used for cleavage
`getDB`	Cython signature: String getDB() Returns the DB to use
`getFormVersion`	Cython signature: String getFormVersion() Returns the Mascot form version
`getHits`	Cython signature: String getHits() Returns the number of hits to report back
`getInstrument`	Cython signature: String getInstrument() Returns the instrument type
`getLogType`	Cython signature: LogType getLogType() Returns the type of progress log being used
`getMassType`	Cython signature: String getMassType() Returns the used mass type ("Monoisotopic" or "Average")
`getMissedCleavages`	Cython signature: unsigned int getMissedCleavages() Returns the number of allowed missed cleavages
`getModifications`	Cython signature: libcpp_vector[String] getModifications() Returns a vector containing the fixed modifications (default none)
`getPeakMassTolerance`	Cython signature: float getPeakMassTolerance() Returns the peak mass tolerance in Da
`getPrecursorMassTolerance`	Cython signature: float getPrecursorMassTolerance() Returns the precursor mass tolerance
`getSearchType`	Cython signature: String getSearchType() Returns the search type
`getTaxonomy`	Cython signature: String getTaxonomy() Returns the taxonomy
`getVariableModifications`	Cython signature: libcpp_vector[String] getVariableModifications() Returns a vector containing the variable modifications (default none)
`load`	Cython signature: void load(const String & filename, MSExperiment & exp)
`nextProgress`	Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)
`setBoundary`	Cython signature: void setBoundary(const String & boundary) Sets the boundary used for the MIME format.By default a 22 character random string is used
`setCharges`	Cython signature: void setCharges(libcpp_vector[int] & charges) Sets the charges (default 1+, 2+ and 3+)
`setCleavage`	Cython signature: void setCleavage(const String & cleavage) Sets the enzyme used for cleavage (default Trypsin).
`setDB`	Cython signature: void setDB(const String & db) Sets the DB (default MSDB).
`setFormVersion`	Cython signature: void setFormVersion(const String & form_version) Sets the Mascot form version (default 1.01)
`setHits`	Cython signature: void setHits(const String & hits) Sets the number of hits to report back (default 20)
`setInstrument`	Cython signature: void setInstrument(const String & instrument) Sets the instrument type (Default Default).
`setLogType`	Cython signature: void setLogType(LogType) Sets the progress log that should be used.
`setMassType`	Cython signature: void setMassType(const String & mass_type) Sets the used mass type "Monoisotopic" or "Average" (default Monoisotopic)
`setMissedCleavages`	Cython signature: void setMissedCleavages(unsigned int missed_cleavages) Sets the number of allowed missed cleavages (default 1)
`setModifications`	Cython signature: void setModifications(libcpp_vector[String] & mods) Sets the fixed modifications (default none).
`setPeakMassTolerance`	Cython signature: void setPeakMassTolerance(float ion_mass_tolerance) Sets the peak mass tolerance in Da (default 1.0)
`setPrecursorMassTolerance`	Cython signature: void setPrecursorMassTolerance(float precursor_mass_tolerance) Sets the precursor mass tolerance in Da (default 2.0)
`setProgress`	Cython signature: void setProgress(ptrdiff_t value) Sets the current progress
`setSearchType`	Cython signature: void setSearchType(const String & search_type) Sets the search type (default MIS).
`setTaxonomy`	Cython signature: void setTaxonomy(const String & taxonomy) Sets the taxonomy (default All entries).
`setVariableModifications`	Cython signature: void setVariableModifications(libcpp_vector[String] & mods) Sets the fixed modifications (default none).
`startProgress`	Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)
`store`	Cython signature: void store(const String & filename, MSSpectrum & spec, double mz, double retention_time, String search_title)

endProgress(): Cython signature: void endProgress() Ends the progress display

getBoundary(): Cython signature: String getBoundary() Returns the boundary used for the MIME format

getCharges(): Cython signature: String getCharges() Returns the charges

getCleavage(): Cython signature: String getCleavage() Returns the enzyme used for cleavage

getDB(): Cython signature: String getDB() Returns the DB to use

getFormVersion(): Cython signature: String getFormVersion() Returns the Mascot form version

getHits(): Cython signature: String getHits() Returns the number of hits to report back

getInstrument(): Cython signature: String getInstrument() Returns the instrument type

getLogType(): Cython signature: LogType getLogType() Returns the type of progress log being used

getMassType(): Cython signature: String getMassType() Returns the used mass type (“Monoisotopic” or “Average”)

getMissedCleavages(): Cython signature: unsigned int getMissedCleavages() Returns the number of allowed missed cleavages

getModifications(): Cython signature: libcpp_vector[String] getModifications() Returns a vector containing the fixed modifications (default none)

getPeakMassTolerance(): Cython signature: float getPeakMassTolerance() Returns the peak mass tolerance in Da

getPrecursorMassTolerance(): Cython signature: float getPrecursorMassTolerance() Returns the precursor mass tolerance

getSearchType(): Cython signature: String getSearchType() Returns the search type

getTaxonomy(): Cython signature: String getTaxonomy() Returns the taxonomy

getVariableModifications(): Cython signature: libcpp_vector[String] getVariableModifications() Returns a vector containing the variable modifications (default none)

load()

Cython signature: void load(const String & filename, MSExperiment & exp)

Parameters

filename – File name which the map should be read from
exp – The map which is filled with the data from the given file

Raises

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

nextProgress(): Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)

setBoundary(): Cython signature: void setBoundary(const String & boundary) Sets the boundary used for the MIME format.By default a 22 character random string is used

setCharges(): Cython signature: void setCharges(libcpp_vector[int] & charges) Sets the charges (default 1+, 2+ and 3+)

setCleavage(): Cython signature: void setCleavage(const String & cleavage) Sets the enzyme used for cleavage (default Trypsin). See mascot path /config/enzymes for possible settings

setDB(): Cython signature: void setDB(const String & db) Sets the DB (default MSDB). See mascot path /config/mascot.dat in “Databases” section for possible settings

setFormVersion(): Cython signature: void setFormVersion(const String & form_version) Sets the Mascot form version (default 1.01)

setHits(): Cython signature: void setHits(const String & hits) Sets the number of hits to report back (default 20)

setInstrument(): Cython signature: void setInstrument(const String & instrument) Sets the instrument type (Default Default). Possible instruments are ESI-QUAD-TOF, MALDI-TOF-PSD, ESI-TRAP, ESI-QUAD, ESI-FTICR, MALDI-TOF-TOF, ESI-4SECTOR, FTMS-ECD, MALDI-QUAD-TOF, MALDI-QIT-TOF

setLogType(): Cython signature: void setLogType(LogType) Sets the progress log that should be used. The default type is NONE!

setMassType(): Cython signature: void setMassType(const String & mass_type) Sets the used mass type “Monoisotopic” or “Average” (default Monoisotopic)

setMissedCleavages(): Cython signature: void setMissedCleavages(unsigned int missed_cleavages) Sets the number of allowed missed cleavages (default 1)

setModifications(): Cython signature: void setModifications(libcpp_vector[String] & mods) Sets the fixed modifications (default none). See mascot path /config/mod_file for possible settings

setPeakMassTolerance(): Cython signature: void setPeakMassTolerance(float ion_mass_tolerance) Sets the peak mass tolerance in Da (default 1.0)

setPrecursorMassTolerance(): Cython signature: void setPrecursorMassTolerance(float precursor_mass_tolerance) Sets the precursor mass tolerance in Da (default 2.0)

setProgress(): Cython signature: void setProgress(ptrdiff_t value) Sets the current progress

setSearchType(): Cython signature: void setSearchType(const String & search_type) Sets the search type (default MIS). So far only MIS is supported!Valid types are “MIS” (MS/MS Ion Search), “PMF” (Peptide Mass Fingerprint) , “SQ” (Sequence Query)

setTaxonomy(): Cython signature: void setTaxonomy(const String & taxonomy) Sets the taxonomy (default All entries). See mascot path /config/taxonomy for possible settings

setVariableModifications(): Cython signature: void setVariableModifications(libcpp_vector[String] & mods) Sets the fixed modifications (default none). See mascot path /config/mod_file for possible settings

startProgress(): Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)

store()

Cython signature: void store(const String & filename, MSSpectrum & spec, double mz, double retention_time, String search_title) Stores the peak list in a MascotInfile that can be used as input for MASCOT shell execution
Cython signature: void store(const String & filename, MSExperiment & experiment, String search_title) Stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution