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MzXMLFile Class Reference

File adapter for MzXML 2.1 files. More...

#include <OpenMS/FORMAT/MzXMLFile.h>

Inheritance diagram for MzXMLFile:
XMLFile ProgressLogger

Public Member Functions

 MzXMLFile ()
 Default constructor. More...
 
 ~MzXMLFile ()
 Destructor. More...
 
PeakFileOptionsgetOptions ()
 Mutable access to the options for loading/storing. More...
 
const PeakFileOptionsgetOptions () const
 Non-mutable access to the options for loading/storing. More...
 
void setOptions (const PeakFileOptions &)
 set options for loading/storing More...
 
template<typename MapType >
void load (const String &filename, MapType &map)
 Loads a map from a MzXML file. More...
 
template<typename MapType >
void store (const String &filename, const MapType &map) const
 Stores a map in a MzXML file. More...
 
- Public Member Functions inherited from XMLFile
 XMLFile ()
 Default constructor. More...
 
 XMLFile (const String &schema_location, const String &version)
 Constructor that sets the schema location. More...
 
virtual ~XMLFile ()
 Destructor. More...
 
bool isValid (const String &filename, std::ostream &os=std::cerr)
 Checks if a file validates against the XML schema. More...
 
const StringgetVersion () const
 return the version of the schema More...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress () const
 Ends the progress display. More...
 

Private Attributes

PeakFileOptions options_
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Protected Member Functions inherited from XMLFile
void parse_ (const String &filename, XMLHandler *handler)
 Parses the XML file given by filename using the handler given by handler. More...
 
void save_ (const String &filename, XMLHandler *handler) const
 Stores the contents of the XML handler given by handler in the file given by filename. More...
 
void enforceEncoding_ (const String &encoding)
 
- Protected Attributes inherited from XMLFile
String schema_location_
 XML schema file location. More...
 
String schema_version_
 Version string. More...
 
String enforced_encoding_
 Encoding string that replaces the encoding (system dependend or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
SignedSize begin_
 
SignedSize end_
 
SignedSize value_
 
QProgressDialog * dlg_
 
StopWatch stop_watch_
 
time_t last_invoke_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

File adapter for MzXML 2.1 files.

Constructor & Destructor Documentation

MzXMLFile ( )

Default constructor.

~MzXMLFile ( )

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.

void load ( const String filename,
MapType &  map 
)
inline

Loads a map from a MzXML file.

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

Exceptions
Exception::FileNotFoundis thrown if the file could not be opened
Exception::ParseErroris thrown if an error occurs during parsing

References MzXMLHandler< MapType >::setOptions().

Referenced by FileHandler::loadExperiment().

void setOptions ( const PeakFileOptions )

set options for loading/storing

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

Stores a map in a MzXML file.

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

Exceptions
Exception::UnableToCreateFileis thrown if the file could not be created

Referenced by FileHandler::storeExperiment().

Member Data Documentation

PeakFileOptions options_
private

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5