#include <OpenMS/FORMAT/MascotInfile.h>
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 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+) | |
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< String > | mods_ |
fixed Modifications | |
std::vector< String > | variable_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 |
MascotInfile | ( | ) |
constructor
virtual ~MascotInfile | ( | ) | [virtual] |
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
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] |
DoubleReal mz_ [protected] |
parent mass
String search_title_ [protected] |
the search title of the mascot search
String search_type_ [protected] |
search type: MIS, SQ or PMF
String mass_type_ [protected] |
Monoisotopic/average mass.
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 form_version_ [protected] |
form version
DoubleReal retention_time_ [protected] |
the retention time
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |