35 #ifndef OPENMS_FORMAT_MZXMLFILE_H 36 #define OPENMS_FORMAT_MZXMLFILE_H 80 template <
typename MapType>
91 parse_(filename, &handler);
101 template <
typename MapType>
105 save_(filename, &handler);
126 template <
typename MapType>
130 transformFirstPass_(filename_in, consumer, skip_full_count);
138 parse_(filename_in, &handler);
156 template <
typename MapType>
160 transformFirstPass_(filename_in, consumer, skip_full_count);
170 parse_(filename_in, &handler);
177 template <
typename MapType>
182 Size scount = 0, ccount = 0;
191 parse_(filename_in, &handler);
205 #endif // OPENMS_FOMAT_MZXMLFILE_H
PeakFileOptions options_
Definition: MzXMLFile.h:201
void store(const String &filename, const MapType &map) const
Stores a map in a MzXML file.
Definition: MzXMLFile.h:102
A more convenient string class.
Definition: String.h:57
File adapter for MzXML 2.1 files.
Definition: MzXMLFile.h:53
void reset()
Resets all internal values.
Definition: MSExperiment.h:660
void setMSDataConsumer(Interfaces::IMSDataConsumer< MapType > *consumer)
Set the IMSDataConsumer consumer which will consume the read data.
Definition: MzXMLHandler.h:129
void load(const String &filename, MapType &map)
Loads a map from a MzXML file.
Definition: MzXMLFile.h:81
XML handlers for MzXMLFile.
Definition: MzXMLHandler.h:62
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
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 transform(const String &filename_in, Interfaces::IMSDataConsumer< MapType > *consumer, bool skip_full_count=false)
Transforms a map while loading using the supplied MSDataConsumer.
Definition: MzXMLFile.h:127
void setMetadataOnly(bool only)
sets whether or not to load only meta data
UInt getScanCount()
Gets the scan count.
Definition: MzXMLHandler.h:123
void setOptions(const PeakFileOptions &options)
Sets the options.
Definition: MzXMLHandler.h:117
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: MzXMLFile.h:157
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.
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
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 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: MzXMLFile.h:178
void setSizeOnly(bool only)