OpenMS  2.8.0
Public Member Functions | Protected Member Functions | List of all members
MSPFile Class Reference

File adapter for MSP files (NIST spectra library) More...

#include <OpenMS/FORMAT/MSPFile.h>

Inheritance diagram for MSPFile:
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Collaboration diagram for MSPFile:
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Public Member Functions

 MSPFile ()
 Default constructor. More...
 
 MSPFile (const MSPFile &rhs)
 Copy constructor. More...
 
 ~MSPFile () override
 Destructor. More...
 
MSPFileoperator= (const MSPFile &rhs)
 assignment operator More...
 
void load (const String &filename, std::vector< PeptideIdentification > &ids, PeakMap &exp)
 Loads a map from a MSPFile file. More...
 
void store (const String &filename, const PeakMap &exp) const
 Stores a map in a MSPFile file. 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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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, PeakSpectrum &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

- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 
- 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< Stringsubsections_
 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...
 

Detailed Description

File adapter for MSP files (NIST spectra library)

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
parse_headers stringfalse true, falseFlag whether header information should be parsed an stored for each spectrum
parse_peakinfo stringtrue true, falseFlag whether the peak annotation information should be parsed and stored for each peak
parse_firstpeakinfo_only stringtrue true, falseFlag whether only the first (default for 1:1 correspondence in SpecLibSearcher) or all peak annotation information should be parsed and stored for each peak.
instrument string , it, qtof, toftofIf instrument given, only spectra of these type of instrument (Inst= in header) are parsed

Note:

Constructor & Destructor Documentation

◆ MSPFile() [1/2]

MSPFile ( )

Default constructor.

Constructors and destructors

◆ MSPFile() [2/2]

MSPFile ( const MSPFile rhs)

Copy constructor.

◆ ~MSPFile()

~MSPFile ( )
override

Destructor.

Member Function Documentation

◆ load()

void load ( const String filename,
std::vector< PeptideIdentification > &  ids,
PeakMap exp 
)

Loads a map from a MSPFile file.

Parameters
expPeakMap which contains the spectra after reading
filenamethe filename of the experiment
idsoutput parameter which contains the peptide identifications from the spectra annotations
Exceptions
FileNotFoundis thrown if the file could not be found
ParseErroris thrown if the given file could not be parsed
ElementNotFoundis thrown if a annotated modification cannot be found in ModificationsDB (PSI-MOD definitions)

◆ operator=()

MSPFile& operator= ( const MSPFile rhs)

assignment operator

◆ parseHeader_()

void parseHeader_ ( const String header,
PeakSpectrum spec 
)
protected

reads the header information and stores it as metainfo in the spectrum

◆ store()

void store ( const String filename,
const PeakMap exp 
) const

Stores a map in a MSPFile file.

Exceptions
UnableToCreateFileis thrown if the given file could not be created