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... | |
virtual | ~XTandemInfile () |
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... | |
bool | isRefining () const |
get state of refine setting 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... | |
void | setRefine (const bool refine) |
set state of refine setting More... | |
void | setCleavageSite (const String &cleavage_site) |
set the cleavage site with a xtandem conform regex More... | |
const String & | getCleavageSite () const |
returns the cleavage site regex More... | |
void | write (const String &filename) |
Writes the XTandemInfile to the given file. More... | |
void | load (const String &filename) |
Reads the information from the given filename. More... | |
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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) |
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) |
String | convertModificationSet_ (const std::set< ModificationDefinition > &mods) const |
Converts the given set of Modifications into a format compatible to X!Tandem. More... | |
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void | parse_ (const String &filename, XMLHandler *handler) |
Parses the XML file given by filename 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 create a X!Tandem configuration files to be used with Xtandem.
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.
mods | The modifications to convert. |
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
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
bool isRefining | ( | ) | const |
get state of refine setting
void load | ( | const String & | filename | ) |
Reads the information from the given filename.
filename | the file which should be read from |
FileNotFound | is thrown if the given file could not be found |
ParseError | is thrown if the given file could not be parsed |
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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 xtandem 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 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 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.
filename | the name of the file which is written |
UnableToCreateFile | is thrown if the given file could not be created |
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Holds additional nodes that were not translated to member variables, but are conserved for storing. <note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
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Enable/disable xtandem refinement.
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semi cleavage
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OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:47 using doxygen 1.8.5 |