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 paramters 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 | 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 | setRefine (const bool refine) | 
| set state of refine setting  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... | |
|  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=std::cerr) | 
| 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... | |
|  Protected Member Functions inherited from XMLFile | |
| void | parse_ (const String &filename, XMLHandler *handler) | 
| Parses the XML file given by filenameusing the handler given byhandler.  More... | |
| void | save_ (const String &filename, XMLHandler *handler) const | 
| Stores the contents of the XML handler given by handlerin the file given byfilename.  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& 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 | ) | 
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 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.
| 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 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |