46 class MetaInfoInterface;
83 virtual LOADDETAIL getLoadDetail()
const override;
86 virtual void setLoadDetail(
const LOADDETAIL d)
override;
89 void endElement(
const XMLCh*
const uri,
const XMLCh*
const local_name,
const XMLCh*
const qname)
override;
92 void startElement(
const XMLCh*
const uri,
const XMLCh*
const local_name,
const XMLCh*
const qname,
const xercesc::Attributes& attributes)
override;
95 void characters(
const XMLCh*
const chars,
const XMLSize_t length)
override;
98 void writeTo(std::ostream& os)
override;
115 consumer_ = consumer;
179 inline void writeUserParam_(std::ostream& os,
const MetaInfoInterface& meta,
int indent = 4,
String tag =
"nameValue");
187 void doPopulateSpectraWithData_(
SpectrumData & spectrum_data);
195 void populateSpectraWithData_();
void setOptions(const PeakFileOptions &options)
Sets the options.
Definition: MzXMLHandler.h:101
A more convenient string class.
Definition: String.h:58
String precision_
Definition: MzXMLHandler.h:147
PeakMap MapType
XML handler for MzDataFile.
Definition: MzDataHandler.h:59
IMSDataConsumer IMSDataConsumer
Definition: IMSDataConsumer.h:127
PeakFileOptions options_
Options for loading and storing.
Definition: MzXMLHandler.h:131
MSSpectrum SpectrumType
Definition: MzDataHandler.h:60
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
MSExperiment PeakMap
Two-dimensional map of raw data points or peaks.
Definition: StandardTypes.h:61
MapType::PeakType PeakType
Peak type.
Definition: MzXMLHandler.h:121
MSSpectrum SpectrumType
Spectrum type.
Definition: MzXMLHandler.h:123
Int nesting_level_
Definition: MzXMLHandler.h:135
Data necessary to generate a single spectrum.
Definition: MzXMLHandler.h:144
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
MapType * exp_
map pointer for reading
Definition: MzXMLHandler.h:126
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
UInt getScanCount()
Gets the scan count.
Definition: MzXMLHandler.h:107
std::vector< SpectrumData > spectrum_data_
Vector of spectrum data stored for later parallel processing.
Definition: MzXMLHandler.h:155
const MapType * cexp_
map pointer for writing
Definition: MzXMLHandler.h:128
const ProgressLogger & logger_
Progress logging class.
Definition: MzXMLHandler.h:171
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
UInt scan_count_
Consumer class to work on spectra.
Definition: MzXMLHandler.h:168
Definition: MzXMLHandler.h:66
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
SpectrumType spectrum
Definition: MzXMLHandler.h:150
String compressionType_
Definition: MzXMLHandler.h:148
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
bool skip_data
Definition: MzXMLHandler.h:151
~MzXMLHandler() override
Destructor.
Definition: MzXMLHandler.h:79
UInt peak_count_
Definition: MzXMLHandler.h:146
bool skip_spectrum_
Flag that indicates whether this spectrum should be skipped (due to options)
Definition: MzXMLHandler.h:159
UInt spec_write_counter_
spectrum counter (spectra without peaks are not written)
Definition: MzXMLHandler.h:162
Base class for XML handlers.
Definition: XMLHandler.h:151
std::vector< boost::shared_ptr< DataProcessing > > data_processing_
data processing auxiliary variable
Definition: MzXMLHandler.h:198
Interfaces::IMSDataConsumer * consumer_
Consumer class to work on spectra.
Definition: MzXMLHandler.h:165
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
void setMSDataConsumer(Interfaces::IMSDataConsumer *consumer)
Set the IMSDataConsumer consumer which will consume the read data.
Definition: MzXMLHandler.h:113
String char_rest_
Definition: MzXMLHandler.h:149