File adapter for MzML files. More...
#include <OpenMS/FORMAT/MzMLFile.h>
Public Member Functions | |
MzMLFile () | |
Default constructor. More... | |
~MzMLFile () | |
Destructor. More... | |
PeakFileOptions & | getOptions () |
Mutable access to the options for loading/storing. More... | |
const PeakFileOptions & | getOptions () 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 MzML file. More... | |
template<typename MapType > | |
void | store (const String &filename, const MapType &map) const |
Stores a map in a MzML file. More... | |
bool | isValid (const String &filename, std::ostream &os=std::cerr) |
Checks if a file validates against the XML schema. More... | |
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. More... | |
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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 String & | getVersion () const |
return the version of the schema More... | |
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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_ |
Options for loading / storing. More... | |
String | indexed_schema_location_ |
Location of indexed mzML schema. More... | |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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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) |
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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... | |
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LogType | type_ |
SignedSize | begin_ |
SignedSize | end_ |
SignedSize | value_ |
QProgressDialog * | dlg_ |
StopWatch | stop_watch_ |
time_t | last_invoke_ |
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static int | recursion_depth_ |
File adapter for MzML files.
This implementation does currently not support the whole functionality of MzML. Some minor features are still missing:
MzMLFile | ( | ) |
Default constructor.
~MzMLFile | ( | ) |
Destructor.
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.
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. |
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.
Exception::FileNotFound | is thrown if the file cannot be found. |
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inline |
Loads a map from a MzML file.
map
has to be a MSExperiment or have the same interface.
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 TOPPRNPxl::main_().
void setOptions | ( | const PeakFileOptions & | ) |
set options for loading/storing
|
inline |
Stores a map in a MzML file.
map
has to be a MSExperiment or have the same interface.
Exception::UnableToCreateFile | is thrown if the file could not be created |
References MzMLHandler< MapType >::setOptions().
Referenced by TOPPRNPxl::main_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), TOPPViewBase::runTOPPTool_(), FileHandler::storeExperiment(), and CachedmzML::writeMetadata().
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private |
Location of indexed mzML schema.
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private |
Options for loading / storing.
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |