| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
MascotInfile Class Reference
Format » File IO

Mascot input file adapter. More...

`#include <OpenMS/FORMAT/MascotInfile.h>`

Inheritance diagram for MascotInfile:

## Public Member Functions

| MascotInfile ()
| constructor More...
virtual | ~MascotInfile ()
| constructor More...
void | store (const String &filename, const PeakSpectrum &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 More...
void | store (const String &filename, const PeakMap &experiment, String search_title)
| stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution More...
template<typename MapType >
void | load (const String &filename, MapType &exp)
const String & | getBoundary ()
| returns the boundary used for the MIME format More...
void | setBoundary (const String &boundary)
| sets the boundary used for the MIME format. By default a 22 character random string is used More...
const String & | getDB ()
| returns the DB to use More...
void | setDB (const String &db)
| sets the DB to use (default: MSDB). See <mascot path>/config/mascot.dat in "Databases" section for possible settings More...
const String & | getSearchType ()
| returns the search type More...
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) More...
const String & | getHits ()
| returns the number of hits to report back More...
void | setHits (const String &hits)
| sets the number of hits to report back (default: 20) More...
const String & | getCleavage ()
| returns the enzyme used for cleavage More...
void | setCleavage (const String &cleavage)
| sets the enzyme used for cleavage (default: Trypsin). See <mascot path>/config/enzymes for possible settings. More...
const String & | getMassType ()
| returns the used mass type ("Monoisotopic" or "Average") More...
void | setMassType (const String &mass_type)
| sets the used mass type "Monoisotopic" or "Average" (default: Monoisotopic) More...
const std::vector< String > & | getModifications ()
| returns a vector containing the fixed modifications (default: none) More...
void | setModifications (const std::vector< String > &mods)
| sets the fixed modifications (default: none). See <mascot path>/config/mod_file for possible settings. More...
const std::vector< String > & | getVariableModifications ()
| returns a vector containing the variable modifications (default: none) More...
void | setVariableModifications (const std::vector< String > &mods)
| sets the fixed modifications (default: none). See <mascot path>/config/mod_file for possible settings. More...
const String & | getInstrument ()
| returns the instrument type More...
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 More...
UInt | getMissedCleavages ()
| returns the number of allowed missed cleavages More...
void | setMissedCleavages (UInt missed_cleavages)
| sets the number of allowed missed cleavages (default: 1) More...
float | getPrecursorMassTolerance ()
| returns the precursor mass tolerance More...
void | setPrecursorMassTolerance (float precursor_mass_tolerance)
| sets the precursor mass tolerance in Da (default: 2.0) More...
float | getPeakMassTolerance ()
| returns the peak mass tolerance in Da More...
void | setPeakMassTolerance (float ion_mass_tolerance)
| sets the peak mass tolerance in Da (default: 1.0) More...
const String & | getTaxonomy ()
| returns the taxonomy More...
void | setTaxonomy (const String &taxonomy)
| sets the taxonomy (default: All entries). See <mascot path>/config/taxonomy for possible settings. More...
const String & | getFormVersion ()
| returns the Mascot form version More...
void | setFormVersion (const String &form_version)
| sets the Mascot form version (default: 1.01) More...
const String & | getCharges ()
| returns the charges More...
void | setCharges (std::vector< Int > &charges)
| sets the charges (default: 1+, 2+ and 3+) More...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Protected Member Functions

void | writeParameterHeader_ (const String &name, FILE *fp, bool line_break=true)
| writes a parameter header More...
void | writeHeader_ (FILE *fp)
| writes the full header More...
void | writeSpectrum_ (FILE *fp, const String &filename, const PeakSpectrum &peaks)
| writes the spectrum More...
void | writeMSExperiment_ (FILE *fp, const String &filename, const PeakMap &experiment)
| writes the MSExperiment More...
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

double | mz_
| parent mass More...
String | charges_
| charge states to use More...
String | search_title_
| the search title of the mascot search More...
String | db_
| the DB to search in More...
String | search_type_
| search type: MIS, SQ or PMF More...
String | hits_
| number of hits to report More...
String | cleavage_
| Enzyme used for cleavage. More...
String | mass_type_
| Monoisotopic/average mass. More...
std::vector< String > | mods_
| fixed Modifications More...
std::vector< String > | variable_mods_
| variable Modifications More...
String | instrument_
| the used instrument More...
UInt | missed_cleavages_
| number of missed cleavages More...
float | precursor_mass_tolerance_
| precursor mass tolerance in Da More...
float | ion_mass_tolerance_
| m/z tolerance of ions in Da More...
String | taxonomy_
| taxonomy More...
String | form_version_
| form version More...
String | boundary_
| the boundary used for the MIME format More...
double | retention_time_
| the retention time More...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. More...
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

Mascot input file adapter.

Deprecated:
  Use MascotGenericFile.h instead, which uses DefaultParamHandler, is more up to date and avoids weird behaviors of this class (especially in terms of MIME boundaries when writing MGF. This class is currently only used by MascotAdapter.cpp.

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

## Constructor & Destructor Documentation

## ◆ MascotInfile()

MascotInfile | ( |  | ) |

constructor

## ◆ ~MascotInfile()

virtual ~MascotInfile | ( |  | ) |

virtual

constructor

## Member Function Documentation

## ◆ getBoundary()

const String& getBoundary | ( |  | ) |

returns the boundary used for the MIME format

## ◆ getCharges()

const String& getCharges | ( |  | ) |

returns the charges

## ◆ getCleavage()

const String& getCleavage | ( |  | ) |

returns the enzyme used for cleavage

## ◆ getDB()

const String& getDB | ( |  | ) |

returns the DB to use

## ◆ getFormVersion()

const String& getFormVersion | ( |  | ) |

returns the Mascot form version

## ◆ getHits()

const String& getHits | ( |  | ) |

returns the number of hits to report back

## ◆ getInstrument()

const String& getInstrument | ( |  | ) |

returns the instrument type

## ◆ getMassType()

const String& getMassType | ( |  | ) |

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

## ◆ getMissedCleavages()

UInt getMissedCleavages | ( |  | ) |

returns the number of allowed missed cleavages

## ◆ getModifications()

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

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

## ◆ getNextSpectrum_()

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

## ◆ getPeakMassTolerance()

float getPeakMassTolerance | ( |  | ) |

returns the peak mass tolerance in Da

## ◆ getPrecursorMassTolerance()

float getPrecursorMassTolerance | ( |  | ) |

returns the precursor mass tolerance

## ◆ getSearchType()

const String& getSearchType | ( |  | ) |

returns the search type

## ◆ getTaxonomy()

const String& getTaxonomy | ( |  | ) |

returns the taxonomy

## ◆ getVariableModifications()

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

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

## ◆ load()

void load | ( | const String & | filename,
|  | MapType & | exp
| ) |  |

inline

loads a Mascot Generic File into a PeakMap

Parameters

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

Exceptions

  FileNotFound | is thrown if the given file could not be found

References MSExperiment::addSpectrum(), File::exists(), SpectrumSettings::getPrecursors(), MSExperiment::reset(), Peak1D::setIntensity(), MetaInfoInterface::setMetaValue(), MSSpectrum::setMSLevel(), Peak1D::setPosition(), and MSSpectrum::setRT().

## ◆ setBoundary()

void setBoundary | ( | const String & | boundary | ) |

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

## ◆ setCharges()

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

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

## ◆ setCleavage()

void setCleavage | ( | const String & | cleavage | ) |

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

## ◆ setDB()

void setDB | ( | const String & | db | ) |

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

## ◆ setFormVersion()

void setFormVersion | ( | const String & | form_version | ) |

sets the Mascot form version (default: 1.01)

## ◆ setHits()

void setHits | ( | const String & | hits | ) |

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

## ◆ setInstrument()

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

## ◆ setMassType()

void setMassType | ( | const String & | mass_type | ) |

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

## ◆ setMissedCleavages()

void setMissedCleavages | ( | UInt | missed_cleavages | ) |

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

## ◆ setModifications()

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

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

## ◆ setPeakMassTolerance()

void setPeakMassTolerance | ( | float | ion_mass_tolerance | ) |

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

## ◆ setPrecursorMassTolerance()

void setPrecursorMassTolerance | ( | float | precursor_mass_tolerance | ) |

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

## ◆ setSearchType()

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()

void setTaxonomy | ( | const String & | taxonomy | ) |

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

## ◆ setVariableModifications()

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

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

## ◆ store() [1/2]

void store | ( | const String & | filename,
|  | const PeakSpectrum & | 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

## ◆ store() [2/2]

void store | ( | const String & | filename,
|  | const PeakMap & | experiment,
|  | String | search_title
| ) |  |

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

## ◆ writeHeader_()

void writeHeader_ | ( | FILE * | fp | ) |

protected

writes the full header

## ◆ writeMSExperiment_()

void writeMSExperiment_ | ( | FILE * | fp,
|  | const String & | filename,
|  | const PeakMap & | experiment
| ) |  |

protected

writes the MSExperiment

## ◆ writeParameterHeader_()

void writeParameterHeader_ | ( | const String & | name,
|  | FILE * | fp,
|  | bool | line_break = `true`
| ) |  |

protected

writes a parameter header

## ◆ writeSpectrum_()

void writeSpectrum_ | ( | FILE * | fp,
|  | const String & | filename,
|  | const PeakSpectrum & | peaks
| ) |  |

protected

writes the spectrum

## Member Data Documentation

## ◆ boundary_

String boundary_

protected

the boundary used for the MIME format

## ◆ charges_

String charges_

protected

charge states to use

## ◆ cleavage_

String cleavage_

protected

Enzyme used for cleavage.

## ◆ db_

String db_

protected

the DB to search in

## ◆ form_version_

String form_version_

protected

form version

## ◆ hits_

String hits_

protected

number of hits to report

## ◆ instrument_

String instrument_

protected

the used instrument

## ◆ ion_mass_tolerance_

float ion_mass_tolerance_

protected

m/z tolerance of ions in Da

## ◆ mass_type_

String mass_type_

protected

Monoisotopic/average mass.

## ◆ missed_cleavages_

UInt missed_cleavages_

protected

number of missed cleavages

## ◆ mods_

std::vector<String> mods_

protected

fixed Modifications

## ◆ mz_

double mz_

protected

parent mass

## ◆ precursor_mass_tolerance_

float precursor_mass_tolerance_

protected

precursor mass tolerance in Da

## ◆ retention_time_

double retention_time_

protected

the retention time

## ◆ search_title_

String search_title_

protected

the search title of the mascot search

## ◆ search_type_

String search_type_

protected

search type: MIS, SQ or PMF

## ◆ taxonomy_

String taxonomy_

protected

taxonomy

## ◆ variable_mods_

std::vector<String> variable_mods_

protected

variable Modifications