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MzMLFile Class Reference
[File IO]

File adapter for MzML files. More...

#include <OpenMS/FORMAT/MzMLFile.h>

Inheritance diagram for MzMLFile:
XMLFile ProgressLogger

List of all members.

Public Member Functions

 MzMLFile ()
 Default constructor.
 ~MzMLFile ()
 Destructor.
PeakFileOptions & getOptions ()
 Mutable access to the options for loading/storing.
const PeakFileOptions & getOptions () const
 Non-mutable access to the options for loading/storing.
template<typename MapType >
void load (const String &filename, MapType &map)
 Loads a map from a MzML file.
template<typename MapType >
void store (const String &filename, const MapType &map) const
 Stores a map in a MzML file.
bool isValid (const String &filename, std::ostream &os=std::cerr)
 Checks if a file validates against the XML schema.
bool isSemanticallyValid (const String &filename, StringList &errors, StringList &warnings)
 Checks if a file is valid with respect to the mapping file and the controlled vocabulary.

Private Attributes

PeakFileOptions options_
 Options for loading / storing.
String indexed_schema_location_
 Location of indexed mzML schema.

Detailed Description

File adapter for MzML files.

This implementation does currently not support the whole functionality of MzML. Some minor features are still missing:

Todo:
Implement chromatograms (Andreas)

Constructor & Destructor Documentation

MzMLFile (  ) 

Default constructor.

~MzMLFile (  ) 

Destructor.

Member Function Documentation

PeakFileOptions& getOptions (  ) 

Mutable access to the options for loading/storing.

Referenced by FileHandler::loadExperiment(), and FileHandler::storeExperiment().

const PeakFileOptions& getOptions (  )  const

Non-mutable access to the options for loading/storing.

bool isSemanticallyValid ( const String &  filename,
StringList &  errors,
StringList &  warnings 
)

Checks if a file is valid with respect to the mapping file and the controlled vocabulary.

Parameters:
filename File name of the file to be checked.
errors Errors during the validation are returned in this output parameter.
warnings Warnings during the validation are returned in this output parameter.
Exceptions:
Exception::FileNotFound is thrown if the file could not be opened
bool isValid ( const String &  filename,
std::ostream &  os = std::cerr 
)

Checks if a file validates against the XML schema.

Exceptions:
Exception::FileNotFound is thrown if the file cannot be found.
void load ( const String &  filename,
MapType &  map 
) [inline]

Loads a map from a MzML file.

map has to be a MSExperiment or have the same interface.

Exceptions:
Exception::FileNotFound is thrown if the file could not be opened
Exception::ParseError is thrown if an error occurs during parsing

References BaseException::getFile(), BaseException::getFunction(), BaseException::getLine(), BaseException::getName(), and MzMLHandler< MapType >::setOptions().

Referenced by FileHandler::loadExperiment(), and TOPPRNPxlXICFilter::main_().

void store ( const String &  filename,
const MapType &  map 
) const [inline]

Stores a map in a MzML file.

map has to be a MSExperiment or have the same interface.

Exceptions:
Exception::UnableToCreateFile is thrown if the file could not be created

References MzMLHandler< MapType >::setOptions().

Referenced by TOPPRNPxlXICFilter::main_(), TOPPViewBase::runTOPPTool_(), FileHandler::storeExperiment(), and CachedmzML::writeMetadata().

Member Data Documentation

String indexed_schema_location_ [private]

Location of indexed mzML schema.

PeakFileOptions options_ [private]

Options for loading / storing.

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1