File adapter for MSP files (NIST spectra library) More...
#include <OpenMS/FORMAT/MSPFile.h>
 
  
 | Public Member Functions | |
| MSPFile & | operator= (const MSPFile &rhs) | 
| assignment operator  More... | |
| void | load (const String &filename, std::vector< PeptideIdentification > &ids, RichPeakMap &exp) | 
| Loads a map from a MSPFile file.  More... | |
| void | store (const String &filename, const RichPeakMap &exp) const | 
| Stores a map in a MSPFile file.  More... | |
| MSPFile () | |
| Default constructor.  More... | |
| MSPFile (const MSPFile &rhs) | |
| Copy constructor.  More... | |
| virtual | ~MSPFile () | 
| Destructor.  More... | |
|  Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages.  More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor.  More... | |
| virtual | ~DefaultParamHandler () | 
| Destructor.  More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
| Protected Member Functions | |
| void | parseHeader_ (const String &header, RichPeakSpectrum &spec) | 
| reads the header information and stores it as metainfo in the spectrum  More... | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| virtual void | updateMembers_ () | 
| This method is used to update extra member variables at the end of the setParameters() method.  More... | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
| Additional Inherited Members | |
|  Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ | 
| Container for current parameters.  More... | |
| Param | defaults_ | 
| Container for default parameters. This member should be filled in the constructor of derived classes!  More... | |
| std::vector< String > | subsections_ | 
| Container for registered subsections. This member should be filled in the constructor of derived classes!  More... | |
| String | error_name_ | 
| Name that is displayed in error messages during the parameter checking.  More... | |
| bool | check_defaults_ | 
| If this member is set to false no checking if parameters in done;.  More... | |
| bool | warn_empty_defaults_ | 
| If this member is set to false no warning is emitted when defaults are empty;.  More... | |
File adapter for MSP files (NIST spectra library)
Parameters of this class are:| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| parse_headers | string | false | true, false | Flag whether header information should be parsed an stored for each spectrum | 
| parse_peakinfo | string | true | true, false | Flag whether the peak annotation information should be parsed and stored for each peak | 
| instrument | string | , it, qtof, toftof | If instrument given, only spectra of these type of instrument (Inst= in header) are parsed | 
| MSPFile | ( | ) | 
Default constructor.
Constructors and destructors
| 
 | virtual | 
Destructor.
| void load | ( | const String & | filename, | 
| std::vector< PeptideIdentification > & | ids, | ||
| RichPeakMap & | exp | ||
| ) | 
Loads a map from a MSPFile file.
| exp | RichPeakMap which contains the spectra after reading | 
| filename | the filename of the experiment | 
| ids | output parameter which contains the peptide identifications from the spectra anntations | 
| FileNotFound | is thrown if the file could not be found | 
| ParseError | is thrown if the given file could not be parsed | 
| ElementNotFound | is thrown if a annotated modification cannot be found in ModificationsDB (PSI-MOD definitions) | 
| 
 | protected | 
reads the header information and stores it as metainfo in the spectrum
| void store | ( | const String & | filename, | 
| const RichPeakMap & | exp | ||
| ) | const | 
Stores a map in a MSPFile file.
| UnableToCreateFile | is thrown if the given file could not be created | 
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |