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 |