35 #ifndef OPENMS_FORMAT_MZMLFILE_H
36 #define OPENMS_FORMAT_MZMLFILE_H
82 template <
typename MapType>
93 safeParse_(filename, &handler);
99 void loadSize(
const String & filename,
Size& scount,
Size& ccount);
108 template <
typename MapType>
113 save_(filename, &handler);
134 template <
typename MapType>
138 transformFirstPass_(filename_in, consumer, skip_full_count);
146 safeParse_(filename_in, &handler);
164 template <
typename MapType>
168 transformFirstPass_(filename_in, consumer, skip_full_count);
178 safeParse_(filename_in, &handler);
187 bool isValid(
const String& filename, std::ostream& os = std::cerr);
204 template <
typename MapType>
209 Size scount = 0, ccount = 0;
218 safeParse_(filename_in, &handler);
240 #endif // OPENMS_FOMAT_MZMLFILE_H
A more convenient string class.
Definition: String.h:57
void reset()
Resets all internal values.
Definition: MSExperiment.h:660
PeakFileOptions options_
Options for loading / storing.
Definition: MzMLFile.h:232
Base class for XML handlers.
Definition: XMLHandler.h:99
void setLoadedFileType(const String &file_name)
set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably do...
void transformFirstPass_(const String &filename_in, Interfaces::IMSDataConsumer< MapType > *consumer, bool skip_full_count)
Perform first pass through the file and retrieve the meta-data to initialize the consumer.
Definition: MzMLFile.h:205
void transform(const String &filename_in, Interfaces::IMSDataConsumer< MapType > *consumer, MapType &map, bool skip_full_count=false)
Transforms a map while loading using the supplied MSDataConsumer.
Definition: MzMLFile.h:165
void setMetadataOnly(bool only)
sets whether or not to load only meta data
File adapter for MzML files.
Definition: MzMLFile.h:55
XML handler for MzMLFile.
Definition: MzMLHandler.h:108
void load(const String &filename, MapType &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
Definition: MzMLFile.h:83
void store(const String &filename, const MapType &map) const
Stores a map in a MzML file.
Definition: MzMLFile.h:109
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
void getCounts(Size &spectra_counts, Size &chromatogram_counts)
Get the spectra and chromatogram counts of a file.
Definition: MzMLHandler.h:236
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:68
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
void setLoadedFilePath(const String &file_name)
set the file_name_ according to absolute path of the file loaded from preferably done whilst loading ...
virtual void setExpectedSize(Size expectedSpectra, Size expectedChromatograms)=0
Set expected size of spectra and chromatograms to be consumed.
void setOptions(const PeakFileOptions &opt)
Set the peak file options.
Definition: MzMLHandler.h:222
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:53
Options for loading files containing peak data.
Definition: PeakFileOptions.h:48
void transform(const String &filename_in, Interfaces::IMSDataConsumer< MapType > *consumer, bool skip_full_count=false)
Transforms a map while loading using the supplied MSDataConsumer.
Definition: MzMLFile.h:135
virtual void setExperimentalSettings(const ExperimentalSettings &exp)=0
Set experimental settings (meta-data) of the data to be consumed.
void setAlwaysAppendData(bool only)
sets whether or not to always append the data to the given map (even if a consumer is given) ...
void setMSDataConsumer(Interfaces::IMSDataConsumer< MapType > *consumer)
Set the IMSDataConsumer consumer which will consume the read data.
Definition: MzMLHandler.h:243
String indexed_schema_location_
Location of indexed mzML schema.
Definition: MzMLFile.h:235
void setSizeOnly(bool only)