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MascotInfile Class Reference
[File IO]

#include <OpenMS/FORMAT/MascotInfile.h>

Inheritance diagram for MascotInfile:

ProgressLogger

List of all members.


Detailed Description

Mascot input file adapter.

Creates a file that can be used for Mascot search from a peak list or a whole experiment.

Public Member Functions

 MascotInfile ()
 constructor
virtual ~MascotInfile ()
 constructor
void store (const String &filename, const DPeakArray< Peak1D > &spec, DoubleReal mz, DoubleReal retention_time, String search_title)
 stores the peak list in a MascotInfile that can be used as input for MASCOT shell execution
void store (const String &filename, const MSExperiment< Peak1D > &experiment, String search_title)
 stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution
template<typename MapType>
void load (const String &filename, MapType &map) throw (Exception::FileNotFound, Exception::ParseError)
 loads a Mascot Generic File into a PeakMap
const StringgetBoundary ()
 returns the boundary used for the MIME format
void setBoundary (const String &boundary)
 sets the boundary used for the MIME format.
By default a 22 character random string is used
const StringgetDB ()
 returns the DB to use
void setDB (const String &db)
 sets the DB to use (default: MSDB). See <mascot path>/config/mascot.dat in "Databases" section for possible settings
const StringgetSearchType ()
 returns the search type
void setSearchType (const String &search_type)
 sets the seach type (default: MIS). So far only MIS is supported!
Valid types are "MIS" (MS/MS Ion Search), "PMF" (Peptide Mass Fingerprint) , "SQ" (Sequence Query)
const StringgetHits ()
 returns the number of hits to report back
void setHits (const String &hits)
 sets the number of hits to report back (default: 20)
const StringgetCleavage ()
 returns the enzyme used for cleavage
void setCleavage (const String &cleavage)
 sets the enzyme used for cleavage (default: Trypsin).
See <mascot path>/config/enzymes for possible settings.
const StringgetMassType ()
 returns the used mass type ("Monoisotopic" or "Average")
void setMassType (const String &mass_type)
 sets the used mass type "Monoisotopic" or "Average" (default: Monoisotopic)
const std::vector< String > & getModifications ()
 returns a vector containing the fixed modifications (default: none)
void setModifications (const std::vector< String > &mods)
 sets the fixed modifications (default: none).
See <mascot path>/config/mod_file for possible settings.
const std::vector< String > & getVariableModifications ()
 returns a vector containing the variable modifications (default: none)
void setVariableModifications (const std::vector< String > &mods)
 sets the fixed modifications (default: none).
See <mascot path>/config/mod_file for possible settings.
const StringgetInstrument ()
 returns the instrument type
void setInstrument (const String &instrument)
 sets the instrument type (Default: Default).
Possible instruments: 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
UInt getMissedCleavages ()
 returns the number of allowed missed cleavages
void setMissedCleavages (UInt missed_cleavages)
 sets the number of allowed missed cleavages (default: 1)
Real getPrecursorMassTolerance ()
 returns the precursor mass tolerance
void setPrecursorMassTolerance (Real precursor_mass_tolerance)
 sets the precursor mass tolerance in Da (default: 2.0)
Real getPeakMassTolerance ()
 returns the peak mass tolerance in Da
void setPeakMassTolerance (Real ion_mass_tolerance)
 sets the peak mass tolerance in Da (default: 1.0)
const StringgetTaxonomy ()
 returns the taxonomy
void setTaxonomy (const String &taxonomy)
 sets the taxonomy (default: All entries).
See <mascot path>/config/taxonomy for possible settings.
const StringgetFormVersion ()
 returns the Mascot form version
void setFormVersion (const String &form_version)
 sets the Mascot form version (default: 1.01)
const StringgetCharges ()
 returns the charges
void setCharges (std::vector< Int > &charges)
 sets the charges (default: 1+, 2+ and 3+)

Protected Member Functions

void writeParameterHeader_ (const String &name, FILE *fp, bool line_break=true)
 writes a parameter header
void writeHeader_ (FILE *fp)
 writes the full header
void writeSpectrum_ (FILE *fp, const String &filename, const DPeakArray< Peak1D > &peaks)
 writes the spectrum
void writeMSExperiment_ (FILE *fp, const String &filename, const MSExperiment< Peak1D > &experiment)
 writes the MSExperiment
bool getNextSpectrum_ (std::istream &is, std::vector< std::pair< double, double > > &spectrum, UInt &charge, double &precursor_mz, double &precursor_int, double &rt, String &title)

Protected Attributes

DoubleReal mz_
 parent mass
String charges_
 charge states to use
String search_title_
 the search title of the mascot search
String db_
 the DB to search in
String search_type_
 search type: MIS, SQ or PMF
String hits_
 number of hits to report
String cleavage_
 Enzyme used for cleavage.
String mass_type_
 Monoisotopic/average mass.
std::vector< Stringmods_
 fixed Modifications
std::vector< Stringvariable_mods_
 variable Modifications
String instrument_
 the used instument
UInt missed_cleavages_
 number of missed cleavages
Real precursor_mass_tolerance_
 precursor mass toerance in Da
Real ion_mass_tolerance_
 m/z tolerance of ions in Da
String taxonomy_
 taxonomy
String form_version_
 form version
String boundary_
 the boundary used for the MIME format
DoubleReal retention_time_
 the retention time


Constructor & Destructor Documentation

MascotInfile (  ) 

constructor

virtual ~MascotInfile (  )  [virtual]

constructor


Member Function Documentation

void store ( const String filename,
const DPeakArray< Peak1D > &  spec,
DoubleReal  mz,
DoubleReal  retention_time,
String  search_title 
)

stores the peak list in a MascotInfile that can be used as input for MASCOT shell execution

void store ( const String filename,
const MSExperiment< Peak1D > &  experiment,
String  search_title 
)

stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution

void load ( const String filename,
MapType &  map 
) throw (Exception::FileNotFound, Exception::ParseError) [inline]

loads a Mascot Generic File into a PeakMap

const String& getBoundary (  ) 

returns the boundary used for the MIME format

void setBoundary ( const String boundary  ) 

sets the boundary used for the MIME format.
By default a 22 character random string is used

const String& getDB (  ) 

returns the DB to use

void setDB ( const String db  ) 

sets the DB to use (default: MSDB). See <mascot path>/config/mascot.dat in "Databases" section for possible settings

const String& getSearchType (  ) 

returns the search type

void setSearchType ( const String search_type  ) 

sets the seach type (default: MIS). So far only MIS is supported!
Valid types are "MIS" (MS/MS Ion Search), "PMF" (Peptide Mass Fingerprint) , "SQ" (Sequence Query)

const String& getHits (  ) 

returns the number of hits to report back

void setHits ( const String hits  ) 

sets the number of hits to report back (default: 20)

const String& getCleavage (  ) 

returns the enzyme used for cleavage

void setCleavage ( const String cleavage  ) 

sets the enzyme used for cleavage (default: Trypsin).
See <mascot path>/config/enzymes for possible settings.

const String& getMassType (  ) 

returns the used mass type ("Monoisotopic" or "Average")

void setMassType ( const String mass_type  ) 

sets the used mass type "Monoisotopic" or "Average" (default: Monoisotopic)

const std::vector<String>& getModifications (  ) 

returns a vector containing the fixed modifications (default: none)

void setModifications ( const std::vector< String > &  mods  ) 

sets the fixed modifications (default: none).
See <mascot path>/config/mod_file for possible settings.

const std::vector<String>& getVariableModifications (  ) 

returns a vector containing the variable modifications (default: none)

void setVariableModifications ( const std::vector< String > &  mods  ) 

sets the fixed modifications (default: none).
See <mascot path>/config/mod_file for possible settings.

const String& getInstrument (  ) 

returns the instrument type

void setInstrument ( const String instrument  ) 

sets the instrument type (Default: Default).
Possible instruments: 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

UInt getMissedCleavages (  ) 

returns the number of allowed missed cleavages

void setMissedCleavages ( UInt  missed_cleavages  ) 

sets the number of allowed missed cleavages (default: 1)

Real getPrecursorMassTolerance (  ) 

returns the precursor mass tolerance

void setPrecursorMassTolerance ( Real  precursor_mass_tolerance  ) 

sets the precursor mass tolerance in Da (default: 2.0)

Real getPeakMassTolerance (  ) 

returns the peak mass tolerance in Da

void setPeakMassTolerance ( Real  ion_mass_tolerance  ) 

sets the peak mass tolerance in Da (default: 1.0)

const String& getTaxonomy (  ) 

returns the taxonomy

void setTaxonomy ( const String taxonomy  ) 

sets the taxonomy (default: All entries).
See <mascot path>/config/taxonomy for possible settings.

const String& getFormVersion (  ) 

returns the Mascot form version

void setFormVersion ( const String form_version  ) 

sets the Mascot form version (default: 1.01)

const String& getCharges (  ) 

returns the charges

void setCharges ( std::vector< Int > &  charges  ) 

sets the charges (default: 1+, 2+ and 3+)

void writeParameterHeader_ ( const String name,
FILE *  fp,
bool  line_break = true 
) [protected]

writes a parameter header

void writeHeader_ ( FILE *  fp  )  [protected]

writes the full header

void writeSpectrum_ ( FILE *  fp,
const String filename,
const DPeakArray< Peak1D > &  peaks 
) [protected]

writes the spectrum

void writeMSExperiment_ ( FILE *  fp,
const String filename,
const MSExperiment< Peak1D > &  experiment 
) [protected]

writes the MSExperiment

bool getNextSpectrum_ ( std::istream &  is,
std::vector< std::pair< double, double > > &  spectrum,
UInt charge,
double &  precursor_mz,
double &  precursor_int,
double &  rt,
String title 
) [protected]


Member Data Documentation

DoubleReal mz_ [protected]

parent mass

String charges_ [protected]

charge states to use

String search_title_ [protected]

the search title of the mascot search

String db_ [protected]

the DB to search in

String search_type_ [protected]

search type: MIS, SQ or PMF

String hits_ [protected]

number of hits to report

String cleavage_ [protected]

Enzyme used for cleavage.

String mass_type_ [protected]

Monoisotopic/average mass.

std::vector<String> mods_ [protected]

fixed Modifications

std::vector<String> variable_mods_ [protected]

variable Modifications

String instrument_ [protected]

the used instument

UInt missed_cleavages_ [protected]

number of missed cleavages

Real precursor_mass_tolerance_ [protected]

precursor mass toerance in Da

Real ion_mass_tolerance_ [protected]

m/z tolerance of ions in Da

String taxonomy_ [protected]

taxonomy

String form_version_ [protected]

form version

String boundary_ [protected]

the boundary used for the MIME format

DoubleReal retention_time_ [protected]

the retention time


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1