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XTandemInfile Class Reference
[File IO]

XTandem input file adapter. More...

#include <OpenMS/FORMAT/XTandemInfile.h>

Inheritance diagram for XTandemInfile:
XMLFile

List of all members.

Public Types

enum  ErrorUnit { DALTONS = 0, PPM }
 

error unit, either Da or ppm

More...
enum  MassType { MONOISOTOPIC = 0, AVERAGE }
 

Mass type of the precursor, either monoisotopic or average.

More...

Public Member Functions

 XTandemInfile ()
 constructor
virtual ~XTandemInfile ()
 constructor
void setFragmentMassTolerance (double tolerance)
 setter for the fragment mass tolerance
double getFragmentMassTolerance () const
 returns the fragment mass tolerance
void setPrecursorMassTolerancePlus (double tol)
 sets the precursor mass tolerance (plus only)
double getPrecursorMassTolerancePlus () const
 returns the precursor mass tolerance (plus only)
void setPrecursorMassToleranceMinus (double tol)
 set the precursor mass tolerance (minus only)
double getPrecursorMassToleranceMinus () const
 returns the precursor mass tolerance (minus only)
void setPrecursorErrorType (MassType mono_isotopic)
 sets the precursor mass type
MassType getPrecursorErrorType () const
 returns the precursor mass type
void setFragmentMassErrorUnit (ErrorUnit unit)
 sets the fragment mass error unit (Da, ppm)
ErrorUnit getFragmentMassErrorUnit () const
 returns the fragment mass error unit (Da, ppm)
void setPrecursorMassErrorUnit (ErrorUnit unit)
 sets the precursor mass error unit (Da, ppm)
ErrorUnit getPrecursorMassErrorUnit () const
 returns the precursor mass error unit (Da, ppm)
void setNumberOfThreads (UInt threads)
 sets the number of threads used during the identifications
UInt getNumberOfThreads () const
 returns the number of threads
void setModifications (const ModificationDefinitionsSet &mods)
 sets the modifications using a modification definitions set
const ModificationDefinitionsSet & getModifications () const
 returns the modifications set, using a modification definitions set
void setOutputFilename (const String &output)
 sets the output filename
const String & getOutputFilename () const
 returns the output filename
void setInputFilename (const String &input_file)
 sets the input filename
const String & getInputFilename () const
 returns the input filename
void setTaxonomyFilename (const String &filename)
 set the filename of the taxonomy file
const String & getTaxonomyFilename () const
 returns the filename of the taxonomy file
void setDefaultParametersFilename (const String &filename)
 sets the default paramters file
const String & getDefaultParametersFilename () const
 returns the default parameters file
void setTaxon (const String &taxon)
 sets the taxon used in the taxonomy file
const String & getTaxon () const
 returns the taxon used in the taxonomy file
void setMaxPrecursorCharge (Int max_charge)
 sets the max precursor charge
Int getMaxPrecursorCharge () const
 returns the max precursor charge
void setNumberOfMissedCleavages (UInt missed_cleavages)
 sets the number of missed cleavages allowed
UInt getNumberOfMissedCleavages () const
 returns the number of missed cleavages allowed
void setMaxValidEValue (double value)
 sets the max valid E-value allowed in the list
double getMaxValidEValue () const
 returns the max valid E-value allowed in the list
bool isRefining () const
 get state of refine setting
void setSemiCleavage (const bool semi_cleavage)
 set state of semi cleavage
void setRefine (const bool refine)
 set state of refine setting
void write (const String &filename)
void load (const String &filename)

Protected Member Functions

 XTandemInfile (const XTandemInfile &rhs)
XTandemInfile & operator= (const XTandemInfile &rhs)
void writeTo_ (std::ostream &os)
void writeNote_ (std::ostream &os, const String &type, const String &label, const String &value)
void writeNote_ (std::ostream &os, const String &type, const String &label, const char *value)
void writeNote_ (std::ostream &os, const String &type, const String &label, bool value)

Protected Attributes

double fragment_mass_tolerance_
double precursor_mass_tolerance_plus_
double precursor_mass_tolerance_minus_
MassType precursor_mass_type_
ErrorUnit precursor_mass_error_unit_
ErrorUnit fragment_mass_error_unit_
MassType fragment_mass_type_
UInt max_precursor_charge_
double precursor_lower_mz_
double fragment_lower_mz_
UInt number_of_threads_
UInt batch_size_
ModificationDefinitionsSet modifications_
String input_filename_
String output_filename_
String taxonomy_file_
String taxon_
String cleavage_site_
bool refine_
bool semi_cleavage_
double refine_max_valid_evalue_
UInt number_of_missed_cleavages_
String default_parameters_file_
double max_valid_evalue_
std::vector
< Internal::XTandemInfileNote > 		notes_

Detailed Description

XTandem input file adapter.

This class is able to create a X!Tandem configuration file for a search

Member Enumeration Documentation

enum ErrorUnit

error unit, either Da or ppm

Enumerator:
DALTONS 
PPM 
enum MassType

Mass type of the precursor, either monoisotopic or average.

Enumerator:
MONOISOTOPIC 
AVERAGE 

Constructor & Destructor Documentation

XTandemInfile (  ) 

constructor

virtual ~XTandemInfile (  )  [virtual]

constructor

XTandemInfile ( const XTandemInfile &  rhs  )  [protected]

Member Function Documentation

const String& getDefaultParametersFilename (  )  const

returns the default parameters file

ErrorUnit getFragmentMassErrorUnit (  )  const

returns the fragment mass error unit (Da, ppm)

double getFragmentMassTolerance (  )  const

returns the fragment mass tolerance

const String& getInputFilename (  )  const

returns the input filename

Int getMaxPrecursorCharge (  )  const

returns the max precursor charge

double getMaxValidEValue (  )  const

returns the max valid E-value allowed in the list

const ModificationDefinitionsSet& getModifications (  )  const

returns the modifications set, using a modification definitions set

UInt getNumberOfMissedCleavages (  )  const

returns the number of missed cleavages allowed

UInt getNumberOfThreads (  )  const

returns the number of threads

const String& getOutputFilename (  )  const

returns the output filename

MassType getPrecursorErrorType (  )  const

returns the precursor mass type

ErrorUnit getPrecursorMassErrorUnit (  )  const

returns the precursor mass error unit (Da, ppm)

double getPrecursorMassToleranceMinus (  )  const

returns the precursor mass tolerance (minus only)

double getPrecursorMassTolerancePlus (  )  const

returns the precursor mass tolerance (plus only)

const String& getTaxon (  )  const

returns the taxon used in the taxonomy file

const String& getTaxonomyFilename (  )  const

returns the filename of the taxonomy file

bool isRefining (  )  const

get state of refine setting

void load ( const String &  filename  ) 

read the information from the given filename

Parameters:
filename the file which should be read from
Exceptions:
FileNotFound is thrown if the given file could not be found
ParseError is thrown if the given file could not be parsed
XTandemInfile& operator= ( const XTandemInfile &  rhs  )  [protected]
void setDefaultParametersFilename ( const String &  filename  ) 

sets the default paramters file

void setFragmentMassErrorUnit ( ErrorUnit  unit  ) 

sets the fragment mass error unit (Da, ppm)

void setFragmentMassTolerance ( double  tolerance  ) 

setter for the fragment mass tolerance

void setInputFilename ( const String &  input_file  ) 

sets the input filename

void setMaxPrecursorCharge ( Int  max_charge  ) 

sets the max precursor charge

void setMaxValidEValue ( double  value  ) 

sets the max valid E-value allowed in the list

void setModifications ( const ModificationDefinitionsSet &  mods  ) 

sets the modifications using a modification definitions set

void setNumberOfMissedCleavages ( UInt  missed_cleavages  ) 

sets the number of missed cleavages allowed

void setNumberOfThreads ( UInt  threads  ) 

sets the number of threads used during the identifications

void setOutputFilename ( const String &  output  ) 

sets the output filename

void setPrecursorErrorType ( MassType  mono_isotopic  ) 

sets the precursor mass type

void setPrecursorMassErrorUnit ( ErrorUnit  unit  ) 

sets the precursor mass error unit (Da, ppm)

void setPrecursorMassToleranceMinus ( double  tol  ) 

set the precursor mass tolerance (minus only)

void setPrecursorMassTolerancePlus ( double  tol  ) 

sets the precursor mass tolerance (plus only)

void setRefine ( const bool  refine  ) 

set state of refine setting

void setSemiCleavage ( const bool  semi_cleavage  ) 

set state of semi cleavage

void setTaxon ( const String &  taxon  ) 

sets the taxon used in the taxonomy file

void setTaxonomyFilename ( const String &  filename  ) 

set the filename of the taxonomy file

void write ( const String &  filename  ) 

writes the XTandemInfile to the given file

Parameters:
filename the name of the file which is written
Exceptions:
UnableToCreateFile is thrown if the given file could not be created
void writeNote_ ( std::ostream &  os,
const String &  type,
const String &  label,
const String &  value 
) [protected]
void writeNote_ ( std::ostream &  os,
const String &  type,
const String &  label,
const char *  value 
) [protected]
void writeNote_ ( std::ostream &  os,
const String &  type,
const String &  label,
bool  value 
) [protected]
void writeTo_ ( std::ostream &  os  )  [protected]

Member Data Documentation

UInt batch_size_ [protected]
String cleavage_site_ [protected]
String default_parameters_file_ [protected]
double fragment_lower_mz_ [protected]
ErrorUnit fragment_mass_error_unit_ [protected]
double fragment_mass_tolerance_ [protected]
MassType fragment_mass_type_ [protected]
String input_filename_ [protected]
UInt max_precursor_charge_ [protected]
double max_valid_evalue_ [protected]
ModificationDefinitionsSet modifications_ [protected]
std::vector<Internal::XTandemInfileNote> notes_ [protected]
UInt number_of_missed_cleavages_ [protected]
UInt number_of_threads_ [protected]
String output_filename_ [protected]
double precursor_lower_mz_ [protected]
ErrorUnit precursor_mass_error_unit_ [protected]
double precursor_mass_tolerance_minus_ [protected]
double precursor_mass_tolerance_plus_ [protected]
MassType precursor_mass_type_ [protected]
bool refine_ [protected]
double refine_max_valid_evalue_ [protected]
bool semi_cleavage_ [protected]
String taxon_ [protected]
String taxonomy_file_ [protected]
OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1