OpenMS
2.5.0
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XTandem input file. More...
#include <OpenMS/FORMAT/XTandemInfile.h>
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) |
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>
enum ErrorUnit |
enum MassType |
XTandemInfile | ( | ) |
constructor
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constructor
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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.
mods | The modifications to convert |
affected_origins | Set of origins, which were used previously. Will be augmented with the current mods. |
const String& getCleavageSite | ( | ) | const |
returns the cleavage site regex
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
bool getNoiseSuppression | ( | ) | const |
get state of noise suppression
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
String getOutputResults | ( | ) | const |
returns the output result type ("all", "valid" or "stochastic")
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
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void setAllowIsotopeError | ( | const bool | allow_isotope_error | ) |
set if misassignment of precursor to first and second 13C isotopic peak should also be considered
void setCleavageSite | ( | const String & | cleavage_site | ) |
set the cleavage site with a X! Tandem conform regex
void setDefaultParametersFilename | ( | const String & | filename | ) |
sets the default parameters 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 setNoiseSuppression | ( | const bool | noise_suppression | ) |
set state of noise suppression
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 setOutputResults | ( | String | result | ) |
sets the output result type ("all", "valid" or "stochastic")
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 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, |
bool | ignore_member_parameters = false , |
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bool | force_default_mods = false |
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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.
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 |
UnableToCreateFile | is thrown if the given file could not be created |
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semi cleavage
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