| OpenMS 2.5.0

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

XTandem input file. More...

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

Inheritance diagram for XTandemInfile:

## 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 More...
| ~XTandemInfile () override
| constructor More...
void | setFragmentMassTolerance (double tolerance)
| setter for the fragment mass tolerance More...
double | getFragmentMassTolerance () const
| returns the fragment mass tolerance More...
void | setPrecursorMassTolerancePlus (double tol)
| sets the precursor mass tolerance (plus only) More...
double | getPrecursorMassTolerancePlus () const
| returns the precursor mass tolerance (plus only) More...
void | setPrecursorMassToleranceMinus (double tol)
| set the precursor mass tolerance (minus only) More...
double | getPrecursorMassToleranceMinus () const
| returns the precursor mass tolerance (minus only) More...
void | setPrecursorErrorType (MassType mono_isotopic)
| sets the precursor mass type More...
MassType | getPrecursorErrorType () const
| returns the precursor mass type More...
void | setFragmentMassErrorUnit (ErrorUnit unit)
| sets the fragment mass error unit (Da, ppm) More...
ErrorUnit | getFragmentMassErrorUnit () const
| returns the fragment mass error unit (Da, ppm) More...
void | setPrecursorMassErrorUnit (ErrorUnit unit)
| sets the precursor mass error unit (Da, ppm) More...
ErrorUnit | getPrecursorMassErrorUnit () const
| returns the precursor mass error unit (Da, ppm) More...
void | setNumberOfThreads (UInt threads)
| sets the number of threads used during the identifications More...
UInt | getNumberOfThreads () const
| returns the number of threads More...
void | setModifications (const ModificationDefinitionsSet &mods)
| sets the modifications using a modification definitions set More...
const ModificationDefinitionsSet & | getModifications () const
| returns the modifications set, using a modification definitions set More...
void | setOutputFilename (const String &output)
| sets the output filename More...
const String & | getOutputFilename () const
| returns the output filename More...
void | setInputFilename (const String &input_file)
| sets the input filename More...
const String & | getInputFilename () const
| returns the input filename More...
void | setTaxonomyFilename (const String &filename)
| set the filename of the taxonomy file More...
const String & | getTaxonomyFilename () const
| returns the filename of the taxonomy file More...
void | setDefaultParametersFilename (const String &filename)
| sets the default parameters file More...
const String & | getDefaultParametersFilename () const
| returns the default parameters file More...
void | setTaxon (const String &taxon)
| sets the taxon used in the taxonomy file More...
const String & | getTaxon () const
| returns the taxon used in the taxonomy file More...
void | setMaxPrecursorCharge (Int max_charge)
| sets the max precursor charge More...
Int | getMaxPrecursorCharge () const
| returns the max precursor charge More...
void | setNumberOfMissedCleavages (UInt missed_cleavages)
| sets the number of missed cleavages allowed More...
UInt | getNumberOfMissedCleavages () const
| returns the number of missed cleavages allowed More...
void | setOutputResults (String result)
| sets the output result type ("all", "valid" or "stochastic") More...
String | getOutputResults () const
| returns the output result type ("all", "valid" or "stochastic") More...
void | setMaxValidEValue (double value)
| sets the max valid E-value allowed in the list More...
double | getMaxValidEValue () const
| returns the max valid E-value allowed in the list More...
void | setSemiCleavage (const bool semi_cleavage)
| set state of semi cleavage More...
void | setAllowIsotopeError (const bool allow_isotope_error)
| set if misassignment of precursor to first and second 13C isotopic peak should also be considered More...
bool | getNoiseSuppression () const
| get state of noise suppression More...
void | setNoiseSuppression (const bool noise_suppression)
| set state of noise suppression More...
void | setCleavageSite (const String &cleavage_site)
| set the cleavage site with a X! Tandem conform regex More...
const String & | getCleavageSite () const
| returns the cleavage site regex More...
void | write (const String &filename, bool ignore_member_parameters=false, bool force_default_mods=false)
| Writes the X! Tandem input file to the given filename. More...
Public Member Functions inherited from XMLFile
| XMLFile ()
| Default constructor. More...
| XMLFile (const String &schema_location, const String &version)
| Constructor that sets the schema location. More...
virtual | ~XMLFile ()
| Destructor. More...
bool | isValid (const String &filename, std::ostream &os)
| Checks if a file validates against the XML schema. More...
const String & | getVersion () const
| return the version of the schema More...

## Protected Member Functions

| XTandemInfile (const XTandemInfile &rhs)
XTandemInfile & | operator= (const XTandemInfile &rhs)
void | writeTo_ (std::ostream &os, bool ignore_member_parameters)
void | writeNote_ (std::ostream &os, const String &label, const String &value)
void | writeNote_ (std::ostream &os, const String &label, const char *value)
void | writeNote_ (std::ostream &os, const String &label, bool value)
String | convertModificationSet_ (const std::set< ModificationDefinition > &mods, std::map< String, double > &affected_origins) const
| Converts the given set of Modifications into a format compatible to X!Tandem. More...
Protected Member Functions inherited from XMLFile
void | parse_ (const String &filename, XMLHandler *handler)
| Parses the XML file given by `filename` using the handler given by `handler`. More...
void | parseBuffer_ (const std::string &buffer, XMLHandler *handler)
| Parses the in-memory buffer given by `buffer` using the handler given by `handler`. More...
void | save_ (const String &filename, XMLHandler *handler) const
| Stores the contents of the XML handler given by `handler` in the file given by `filename`. More...
void | enforceEncoding_ (const String &encoding)

## Protected Attributes

double | fragment_mass_tolerance_
double | precursor_mass_tolerance_plus_
double | precursor_mass_tolerance_minus_
ErrorUnit | fragment_mass_error_unit_
ErrorUnit | precursor_mass_error_unit_
MassType | fragment_mass_type_
MassType | precursor_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 | semi_cleavage_
| semi cleavage More...
bool | allow_isotope_error_
UInt | number_of_missed_cleavages_
String | default_parameters_file_
String | output_results_
double | max_valid_evalue_
bool | force_default_mods_
Protected Attributes inherited from XMLFile
String | schema_location_
| XML schema file location. More...
String | schema_version_
| Version string. More...
String | enforced_encoding_
| Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...

## Detailed Description

XTandem input file.

This class is able to load/write a X!Tandem configuration file.

These files store parameters within 'note' tags, e.g.,

      <note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
    	<note type="input" label="output, proteins">yes</note>

## Member Enumeration Documentation

## ◆ ErrorUnit

enum ErrorUnit

error unit, either Da or ppm

Enumerator
DALTONS |
PPM |

## ◆ MassType

enum MassType

Mass type of the precursor, either monoisotopic or average.

Enumerator
MONOISOTOPIC |
AVERAGE |

## Constructor & Destructor Documentation

## ◆ XTandemInfile() [1/2]

XTandemInfile | ( |  | ) |

constructor

## ◆ ~XTandemInfile()

~XTandemInfile | ( |  | ) |

override

constructor

## ◆ XTandemInfile() [2/2]

XTandemInfile | ( | const XTandemInfile & | rhs | ) |

protected

## Member Function Documentation

## ◆ convertModificationSet_()

String convertModificationSet_ | ( | const std::set< ModificationDefinition > & | mods,
|  | std::map< String, double > & | affected_origins
| ) |  | const

protected

Converts the given set of Modifications into a format compatible to X!Tandem.

The set affected_origins can be used to avoid duplicate modifications, which are not supported in X! Tandem. Currently, a warning message is printed. Also, if a fixed mod is already given, a corresponding variable mods needs to have its delta mass reduced by the fixed modifications mass. This is also done automatically here.

Parameters

  mods | The modifications to convert
  affected_origins | Set of origins, which were used previously. Will be augmented with the current mods.

Returns
  An X! Tandem compatible string representation.

## ◆ getCleavageSite()

const String& getCleavageSite | ( |  | ) | const

returns the cleavage site regex

## ◆ getDefaultParametersFilename()

const String& getDefaultParametersFilename | ( |  | ) | const

returns the default parameters file

## ◆ getFragmentMassErrorUnit()

ErrorUnit getFragmentMassErrorUnit | ( |  | ) | const

returns the fragment mass error unit (Da, ppm)

## ◆ getFragmentMassTolerance()

double getFragmentMassTolerance | ( |  | ) | const

returns the fragment mass tolerance

## ◆ getInputFilename()

const String& getInputFilename | ( |  | ) | const

returns the input filename

## ◆ getMaxPrecursorCharge()

Int getMaxPrecursorCharge | ( |  | ) | const

returns the max precursor charge

## ◆ getMaxValidEValue()

double getMaxValidEValue | ( |  | ) | const

returns the max valid E-value allowed in the list

## ◆ getModifications()

const ModificationDefinitionsSet& getModifications | ( |  | ) | const

returns the modifications set, using a modification definitions set

## ◆ getNoiseSuppression()

bool getNoiseSuppression | ( |  | ) | const

get state of noise suppression

## ◆ getNumberOfMissedCleavages()

UInt getNumberOfMissedCleavages | ( |  | ) | const

returns the number of missed cleavages allowed

## ◆ getNumberOfThreads()

UInt getNumberOfThreads | ( |  | ) | const

returns the number of threads

## ◆ getOutputFilename()

const String& getOutputFilename | ( |  | ) | const

returns the output filename

## ◆ getOutputResults()

String getOutputResults | ( |  | ) | const

returns the output result type ("all", "valid" or "stochastic")

## ◆ getPrecursorErrorType()

MassType getPrecursorErrorType | ( |  | ) | const

returns the precursor mass type

## ◆ getPrecursorMassErrorUnit()

ErrorUnit getPrecursorMassErrorUnit | ( |  | ) | const

returns the precursor mass error unit (Da, ppm)

## ◆ getPrecursorMassToleranceMinus()

double getPrecursorMassToleranceMinus | ( |  | ) | const

returns the precursor mass tolerance (minus only)

## ◆ getPrecursorMassTolerancePlus()

double getPrecursorMassTolerancePlus | ( |  | ) | const

returns the precursor mass tolerance (plus only)

## ◆ getTaxon()

const String& getTaxon | ( |  | ) | const

returns the taxon used in the taxonomy file

## ◆ getTaxonomyFilename()

const String& getTaxonomyFilename | ( |  | ) | const

returns the filename of the taxonomy file

## ◆ operator=()

XTandemInfile& operator= | ( | const XTandemInfile & | rhs | ) |

protected

## ◆ setAllowIsotopeError()

void setAllowIsotopeError | ( | const bool | allow_isotope_error | ) |

set if misassignment of precursor to first and second 13C isotopic peak should also be considered

## ◆ setCleavageSite()

void setCleavageSite | ( | const String & | cleavage_site | ) |

set the cleavage site with a X! Tandem conform regex

## ◆ setDefaultParametersFilename()

void setDefaultParametersFilename | ( | const String & | filename | ) |

sets the default parameters file

## ◆ setFragmentMassErrorUnit()

void setFragmentMassErrorUnit | ( | ErrorUnit | unit | ) |

sets the fragment mass error unit (Da, ppm)

## ◆ setFragmentMassTolerance()

void setFragmentMassTolerance | ( | double | tolerance | ) |

setter for the fragment mass tolerance

## ◆ setInputFilename()

void setInputFilename | ( | const String & | input_file | ) |

sets the input filename

## ◆ setMaxPrecursorCharge()

void setMaxPrecursorCharge | ( | Int | max_charge | ) |

sets the max precursor charge

## ◆ setMaxValidEValue()

void setMaxValidEValue | ( | double | value | ) |

sets the max valid E-value allowed in the list

## ◆ setModifications()

void setModifications | ( | const ModificationDefinitionsSet & | mods | ) |

sets the modifications using a modification definitions set

## ◆ setNoiseSuppression()

void setNoiseSuppression | ( | const bool | noise_suppression | ) |

set state of noise suppression

## ◆ setNumberOfMissedCleavages()

void setNumberOfMissedCleavages | ( | UInt | missed_cleavages | ) |

sets the number of missed cleavages allowed

## ◆ setNumberOfThreads()

void setNumberOfThreads | ( | UInt | threads | ) |

sets the number of threads used during the identifications

## ◆ setOutputFilename()

void setOutputFilename | ( | const String & | output | ) |

sets the output filename

## ◆ setOutputResults()

void setOutputResults | ( | String | result | ) |

sets the output result type ("all", "valid" or "stochastic")

## ◆ setPrecursorErrorType()

void setPrecursorErrorType | ( | MassType | mono_isotopic | ) |

sets the precursor mass type

## ◆ setPrecursorMassErrorUnit()

void setPrecursorMassErrorUnit | ( | ErrorUnit | unit | ) |

sets the precursor mass error unit (Da, ppm)

## ◆ setPrecursorMassToleranceMinus()

void setPrecursorMassToleranceMinus | ( | double | tol | ) |

set the precursor mass tolerance (minus only)

## ◆ setPrecursorMassTolerancePlus()

void setPrecursorMassTolerancePlus | ( | double | tol | ) |

sets the precursor mass tolerance (plus only)

## ◆ setSemiCleavage()

void setSemiCleavage | ( | const bool | semi_cleavage | ) |

set state of semi cleavage

## ◆ setTaxon()

void setTaxon | ( | const String & | taxon | ) |

sets the taxon used in the taxonomy file

## ◆ setTaxonomyFilename()

void setTaxonomyFilename | ( | const String & | filename | ) |

set the filename of the taxonomy file

## ◆ write()

void write | ( | const String & | filename,
|  | bool | ignore_member_parameters = `false`,
|  | bool | force_default_mods = `false`
| ) |  |

Writes the X! Tandem input file to the given filename.

If `ignore_member_parameters` is true, only a very limited number of tags fed by member variables (i.e. in, out, database/taxonomy) is written.

Parameters

  filename | the name of the file which is written
  ignore_member_parameters | Do not write tags for class members
  force_default_mods | Force writing of mods covered by special parameters

Exceptions

  UnableToCreateFile | is thrown if the given file could not be created

## ◆ writeNote_() [1/3]

void writeNote_ | ( | std::ostream & | os,
|  | const String & | label,
|  | const String & | value
| ) |  |

protected

## ◆ writeNote_() [2/3]

void writeNote_ | ( | std::ostream & | os,
|  | const String & | label,
|  | const char * | value
| ) |  |

protected

## ◆ writeNote_() [3/3]

void writeNote_ | ( | std::ostream & | os,
|  | const String & | label,
|  | bool | value
| ) |  |

protected

## ◆ writeTo_()

void writeTo_ | ( | std::ostream & | os,
|  | bool | ignore_member_parameters
| ) |  |

protected

## Member Data Documentation

## ◆ allow_isotope_error_

bool allow_isotope_error_

protected

## ◆ batch_size_

UInt batch_size_

protected

## ◆ cleavage_site_

String cleavage_site_

protected

## ◆ default_parameters_file_

String default_parameters_file_

protected

## ◆ force_default_mods_

bool force_default_mods_

protected

## ◆ fragment_lower_mz_

double fragment_lower_mz_

protected

## ◆ fragment_mass_error_unit_

ErrorUnit fragment_mass_error_unit_

protected

## ◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

## ◆ fragment_mass_type_

MassType fragment_mass_type_

protected

## ◆ input_filename_

String input_filename_

protected

## ◆ max_precursor_charge_

UInt max_precursor_charge_

protected

## ◆ max_valid_evalue_

double max_valid_evalue_

protected

## ◆ modifications_

ModificationDefinitionsSet modifications_

protected

## ◆ number_of_missed_cleavages_

UInt number_of_missed_cleavages_

protected

## ◆ number_of_threads_

UInt number_of_threads_

protected

## ◆ output_filename_

String output_filename_

protected

## ◆ output_results_

String output_results_

protected

## ◆ precursor_lower_mz_

double precursor_lower_mz_

protected

## ◆ precursor_mass_error_unit_

ErrorUnit precursor_mass_error_unit_

protected

## ◆ precursor_mass_tolerance_minus_

double precursor_mass_tolerance_minus_

protected

## ◆ precursor_mass_tolerance_plus_

double precursor_mass_tolerance_plus_

protected

## ◆ precursor_mass_type_

MassType precursor_mass_type_

protected

## ◆ semi_cleavage_

bool semi_cleavage_

protected

semi cleavage

## ◆ taxon_

String taxon_

protected

## ◆ taxonomy_file_

String taxonomy_file_

protected