| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | List of all members
MSPFile Class Reference
Format » File IO

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

`#include <OpenMS/FORMAT/MSPFile.h>`

Inheritance diagram for MSPFile:

## Public Member Functions

MSPFile & | operator= (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...
| MSPFile ()
| Default constructor. More...
| MSPFile (const MSPFile &rhs)
| Copy constructor. More...
| ~MSPFile () override
| 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 &param)
| 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, 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

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...

## Detailed Description

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

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## 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

  exp | PeakMap which contains the spectra after reading
  filename | the filename of the experiment
  ids | output parameter which contains the peptide identifications from the spectra annotations

Exceptions

  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)

## ◆ 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

  UnableToCreateFile | is thrown if the given file could not be created