OpenMS
2.5.0
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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, 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_ |
Mascot input file adapter.
Creates a file that can be used for Mascot search from a peak list or a whole experiment.
MascotInfile | ( | ) |
constructor
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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)
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protected |
float getPeakMassTolerance | ( | ) |
returns the peak mass tolerance in Da
float 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)
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 MSExperiment::addSpectrum(), File::exists(), SpectrumSettings::getPrecursors(), MSExperiment::reset(), Peak1D::setIntensity(), MetaInfoInterface::setMetaValue(), MSSpectrum::setMSLevel(), Peak1D::setPosition(), and MSSpectrum::setRT().
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 | ( | float | ion_mass_tolerance | ) |
sets the peak mass tolerance in Da (default: 1.0)
void setPrecursorMassTolerance | ( | float | precursor_mass_tolerance | ) |
sets the precursor mass tolerance in Da (default: 2.0)
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)
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.
stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution
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
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protected |
writes the full header
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protected |
writes the MSExperiment
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protected |
writes a parameter header
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protected |
writes the spectrum
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protected |
the boundary used for the MIME format
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protected |
charge states to use
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protected |
Enzyme used for cleavage.
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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 instrument
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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 tolerance 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