| OpenMS 2.5.0

Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
MSPGenericFile Class Reference

Load MSP text file and save it into an `MSExperiment`. More...

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

Inheritance diagram for MSPGenericFile:

## Public Member Functions

| MSPGenericFile ()
| Default constructor. More...
| MSPGenericFile (const String &filename, MSExperiment &library)
| Constructor with filename and output library. More...
| ~MSPGenericFile ()=default
| Destructor. More...
void | getDefaultParameters (Param &params)
| Get the class' default parameters. More...
void | load (const String &filename, MSExperiment &library)
| Load the file's data and metadata, and save it into an `MSExperiment`. 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...

## Private Member Functions

void | updateMembers_ ()
| Overrides `DefaultParamHandler`'s method. More...
void | addSpectrumToLibrary (MSSpectrum &spectrum, MSExperiment &library)

## Private Attributes

std::set< String > | loaded_spectra_names_
| To keep track of which spectra have already been loaded and avoid duplicates. More...
std::vector< String > | synonyms_
String | synonyms_separator_
| The separator to be used in "Synon" metaValue. More...

## Friends

class | MSPGenericFile_friend
| To test private and protected methods. More...

## Additional Inherited Members

Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. 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< 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

Load MSP text file and save it into an `MSExperiment`.

This class is specialized for metabolites data. The required fields are: Name, Num Peaks, and the peaks data

Points (meaning x and y info) may be separated by a space or a colon. Peaks may be separated by a space or a semicolon.

An example of the expected format: > Name: foo > Num Peaks: 11 > 35 310; 36 1230; 37 27; 38 303; 47 5240; > 66 203; 67 68; 68 77; 82 63; 83 240; > 136 350;

Another supported format: > Name: bar > Num Peaks: 11 > 35:310 36:1230 37:27 38:303 47:5240 > 66:203 67:68 68:77 82:63 83:240 > 136:350

## Constructor & Destructor Documentation

## ◆ MSPGenericFile() [1/2]

MSPGenericFile | ( |  | ) |

Default constructor.

## ◆ MSPGenericFile() [2/2]

MSPGenericFile | ( | const String & | filename,
|  | MSExperiment & | library
| ) |  |

Constructor with filename and output library.

## ◆ ~MSPGenericFile()

~MSPGenericFile | ( |  | ) |

default

Destructor.

## Member Function Documentation

## ◆ addSpectrumToLibrary()

void addSpectrumToLibrary | ( | MSSpectrum & | spectrum,
|  | MSExperiment & | library
| ) |  |

private

Validate and add a spectrum to a spectral library

The spectrum is added to the library if all following criteria are met:

- Name field is present and not empty
- The number of peaks parsed matches the value of Num Peaks
- A spectrum of the same name has not already been added

Exceptions

  MissingInformation | If the spectrum doesn't have a name or Num Peaks info is missing
  ParseError | If Num Peaks' value doesn't match with the number of raw peaks parsed

Parameters

  | [in/out] | spectrum The spectrum to be added
  [out] | library | The spectrum is added into this `MSExperiment` library

Referenced by MSPGenericFile_friend::addSpectrumToLibrary().

## ◆ getDefaultParameters()

void getDefaultParameters | ( | Param & | params | ) |

Get the class' default parameters.

## ◆ load()

void load | ( | const String & | filename,
|  | MSExperiment & | library
| ) |  |

Load the file's data and metadata, and save it into an `MSExperiment`.

Parameters

  [in] | filename | Path to the MSP input file
  [out] | library | The variable into which the extracted information will be saved

Exceptions

  FileNotFound | If the file could not be found

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

private virtual

Overrides `DefaultParamHandler`'s method.

Reimplemented from DefaultParamHandler.

## Friends And Related Function Documentation

## ◆ MSPGenericFile_friend

friend class MSPGenericFile_friend

friend

To test private and protected methods.

## Member Data Documentation

## ◆ loaded_spectra_names_

std::set<String> loaded_spectra_names_

private

To keep track of which spectra have already been loaded and avoid duplicates.

## ◆ synonyms_

std::vector<String> synonyms_

private

## ◆ synonyms_separator_

String synonyms_separator_

private

The separator to be used in "Synon" metaValue.