Mascot input file adapter. More...
#include <OpenMS/FORMAT/MascotInfile.h>
Public Member Functions | |
| MascotInfile () | |
| constructor More... | |
| virtual | ~MascotInfile () |
| constructor More... | |
| void | store (const String &filename, const PeakSpectrum &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 More... | |
| void | store (const String &filename, const MSExperiment<> &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 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) 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... | |
| Real | getPrecursorMassTolerance () |
| returns the precursor mass tolerance More... | |
| void | setPrecursorMassTolerance (Real precursor_mass_tolerance) |
| sets the precursor mass tolerance in Da (default: 2.0) More... | |
| Real | getPeakMassTolerance () |
| returns the peak mass tolerance in Da More... | |
| void | setPeakMassTolerance (Real 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... | |
| 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... | |
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 MSExperiment<> &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 | |
| DoubleReal | 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 instument More... | |
| UInt | missed_cleavages_ |
| number of missed cleavages More... | |
| Real | precursor_mass_tolerance_ |
| precursor mass toerance in Da More... | |
| Real | 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... | |
| DoubleReal | retention_time_ |
| the retention time More... | |
Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| SignedSize | begin_ |
| SignedSize | end_ |
| SignedSize | value_ |
| QProgressDialog * | dlg_ |
| StopWatch | stop_watch_ |
| time_t | last_invoke_ |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. More... | |
Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
Mascot input file adapter.
Creates a file that can be used for Mascot search from a peak list or a whole experiment.
| MascotInfile | ( | ) |
constructor
|
virtual |
constructor
| const String& getBoundary | ( | ) |
returns the boundary used for the MIME format
| const String& getCharges | ( | ) |
returns the charges
| const String& getCleavage | ( | ) |
returns the enzyme used for cleavage
| const String& getDB | ( | ) |
returns the DB to use
| const String& getFormVersion | ( | ) |
returns the Mascot form version
| const String& getHits | ( | ) |
returns the number of hits to report back
| const String& getInstrument | ( | ) |
returns the instrument type
| const String& getMassType | ( | ) |
returns the used mass type ("Monoisotopic" or "Average")
| UInt getMissedCleavages | ( | ) |
returns the number of allowed missed cleavages
| const std::vector<String>& getModifications | ( | ) |
returns a vector containing the fixed modifications (default: none)
|
protected |
| Real getPeakMassTolerance | ( | ) |
returns the peak mass tolerance in Da
| Real getPrecursorMassTolerance | ( | ) |
returns the precursor mass tolerance
| const String& getSearchType | ( | ) |
returns the search type
| const String& getTaxonomy | ( | ) |
returns the taxonomy
| const std::vector<String>& getVariableModifications | ( | ) |
returns a vector containing the variable modifications (default: none)
|
inline |
loads a Mascot Generic File into a PeakMap
| filename | file name which the map should be read from |
| exp | the map which is filled with the data from the given file |
| FileNotFound | is thrown if the given file could not be found |
References File::exists(), and Peak2D::setPosition().
| void setBoundary | ( | const String & | boundary | ) |
sets the boundary used for the MIME format.
By default a 22 character random string is used
| void setCharges | ( | std::vector< Int > & | charges | ) |
sets the charges (default: 1+, 2+ and 3+)
| void setCleavage | ( | const String & | cleavage | ) |
sets the enzyme used for cleavage (default: Trypsin).
See <mascot path>/config/enzymes for possible settings.
| void setDB | ( | const String & | db | ) |
sets the DB to use (default: MSDB). See <mascot path>/config/mascot.dat in "Databases" section for possible settings
| void setFormVersion | ( | const String & | form_version | ) |
sets the Mascot form version (default: 1.01)
| void setHits | ( | const String & | hits | ) |
sets the number of hits to report back (default: 20)
| 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
| void setMassType | ( | const String & | mass_type | ) |
sets the used mass type "Monoisotopic" or "Average" (default: Monoisotopic)
| void setMissedCleavages | ( | UInt | missed_cleavages | ) |
sets the number of allowed missed cleavages (default: 1)
| void setModifications | ( | const std::vector< String > & | mods | ) |
sets the fixed modifications (default: none).
See <mascot path>/config/mod_file for possible settings.
| void setPeakMassTolerance | ( | Real | ion_mass_tolerance | ) |
sets the peak mass tolerance in Da (default: 1.0)
| void setPrecursorMassTolerance | ( | Real | precursor_mass_tolerance | ) |
sets the precursor mass tolerance in Da (default: 2.0)
| 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)
| void setTaxonomy | ( | const String & | taxonomy | ) |
sets the taxonomy (default: All entries).
See <mascot path>/config/taxonomy for possible settings.
| void setVariableModifications | ( | const std::vector< String > & | mods | ) |
sets the fixed modifications (default: none).
See <mascot path>/config/mod_file for possible settings.
| void store | ( | const String & | filename, |
| const PeakSpectrum & | 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<> & | experiment, | ||
| String | search_title | ||
| ) |
stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution
|
protected |
writes the full header
|
protected |
writes the MSExperiment
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protected |
writes a parameter header
|
protected |
writes the spectrum
|
protected |
the boundary used for the MIME format
|
protected |
charge states to use
|
protected |
Enzyme used for cleavage.
|
protected |
the DB to search in
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protected |
form version
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protected |
number of hits to report
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protected |
the used instument
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protected |
m/z tolerance of ions in Da
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protected |
Monoisotopic/average mass.
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protected |
number of missed cleavages
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protected |
fixed Modifications
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protected |
parent mass
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protected |
precursor mass toerance in Da
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protected |
the retention time
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protected |
the search title of the mascot search
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protected |
search type: MIS, SQ or PMF
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protected |
taxonomy
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protected |
variable Modifications
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |