OpenMS
2.6.0
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File adapter for MSP files (NIST spectra library) More...
#include <OpenMS/FORMAT/MSPFile.h>
Public Member Functions | |
MSPFile () | |
Default constructor. More... | |
MSPFile (const MSPFile &rhs) | |
Copy constructor. More... | |
~MSPFile () override | |
Destructor. More... | |
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... | |
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, 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 &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< 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 |
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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
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override |
Destructor.
void load | ( | const String & | filename, |
std::vector< PeptideIdentification > & | ids, | ||
PeakMap & | exp | ||
) |
Loads a map from a MSPFile file.
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 |
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) |
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protected |
reads the header information and stores it as metainfo in the spectrum