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OpenMS
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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;
178 inline void writeUserParam_(std::ostream& os,
const MetaInfoInterface& meta,
int indent = 4,
String tag =
"nameValue");
186 void doPopulateSpectraWithData_(
SpectrumData & spectrum_data);
194 void populateSpectraWithData_();
208 void initStaticMembers_();
MSSpectrum SpectrumType
Spectrum type.
Definition: MzXMLHandler.h:123
std::vector< boost::shared_ptr< DataProcessing > > data_processing_
data processing auxiliary variable
Definition: MzXMLHandler.h:197
static const XMLCh * s_filterline_
Definition: MzXMLHandler.h:230
static const XMLCh * s_completiontime_
Definition: MzXMLHandler.h:218
static const XMLCh * s_precursorintensity_
Definition: MzXMLHandler.h:223
const ProgressLogger & logger_
Progress logging class.
Definition: MzXMLHandler.h:171
Base class for XML handlers.
Definition: XMLHandler.h:148
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:67
static const XMLCh * s_version_
Definition: MzXMLHandler.h:214
static const XMLCh * s_centroided_
Definition: MzXMLHandler.h:241
static const XMLCh * s_count_
Definition: MzXMLHandler.h:211
UInt getScanCount()
Gets the scan count.
Definition: MzXMLHandler.h:107
PeakMap MapType
XML handler for MzDataFile.
Definition: MzDataHandler.h:59
A more convenient string class.
Definition: String.h:57
static const XMLCh * s_chargedeconvoluted_
Definition: MzXMLHandler.h:243
static const XMLCh * s_first_
Definition: MzXMLHandler.h:234
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
PeakFileOptions options_
Options for loading and storing.
Definition: MzXMLHandler.h:131
static const XMLCh * s_precision_
Definition: MzXMLHandler.h:219
static const XMLCh * s_contentType_
Definition: MzXMLHandler.h:221
UInt spec_write_counter_
spectrum counter (spectra without peaks are not written)
Definition: MzXMLHandler.h:162
static const XMLCh * s_precursorcharge_
Definition: MzXMLHandler.h:224
static const XMLCh * s_deisotoped_
Definition: MzXMLHandler.h:242
bool skip_data
Definition: MzXMLHandler.h:151
static const XMLCh * s_mslevel_
Definition: MzXMLHandler.h:226
static const XMLCh * s_value_
Definition: MzXMLHandler.h:210
UInt peak_count_
Definition: MzXMLHandler.h:146
int Int
Signed integer type.
Definition: Types.h:102
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
static const XMLCh * s_filesha1_
Definition: MzXMLHandler.h:217
static const XMLCh * s_retentiontime_
Definition: MzXMLHandler.h:231
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
static const XMLCh * s_startmz_
Definition: MzXMLHandler.h:232
Interfaces::IMSDataConsumer * consumer_
Consumer class to work on spectra.
Definition: MzXMLHandler.h:165
static const XMLCh * s_scantype_
Definition: MzXMLHandler.h:229
static const XMLCh * s_filename_
Definition: MzXMLHandler.h:215
static const XMLCh * s_byteorder_
Definition: MzXMLHandler.h:220
MSSpectrum SpectrumType
Definition: MzDataHandler.h:60
~MzXMLHandler() override
Destructor.
Definition: MzXMLHandler.h:79
UInt scan_count_
Consumer class to work on spectra.
Definition: MzXMLHandler.h:168
String precision_
Definition: MzXMLHandler.h:147
MSExperiment PeakMap
Two-dimensional map of raw data points or peaks.
Definition: StandardTypes.h:61
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
IMSDataConsumer IMSDataConsumer
Definition: IMSDataConsumer.h:125
const MapType * cexp_
map pointer for writing
Definition: MzXMLHandler.h:128
SpectrumType spectrum
Definition: MzXMLHandler.h:150
static const XMLCh * s_uri_
Definition: MzXMLHandler.h:238
static const XMLCh * s_polarity_
Definition: MzXMLHandler.h:228
static const XMLCh * s_last_
Definition: MzXMLHandler.h:235
String compressionType_
Definition: MzXMLHandler.h:148
static const XMLCh * s_filetype_
Definition: MzXMLHandler.h:216
MapType::PeakType PeakType
Peak type.
Definition: MzXMLHandler.h:121
Int nesting_level_
Definition: MzXMLHandler.h:135
void setOptions(const PeakFileOptions &options)
Sets the options.
Definition: MzXMLHandler.h:101
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
static const XMLCh * s_type_
Definition: MzXMLHandler.h:212
String char_rest_
Definition: MzXMLHandler.h:149
static const XMLCh * s_windowwideness_
Definition: MzXMLHandler.h:225
static const XMLCh * s_intensitycutoff_
Definition: MzXMLHandler.h:240
std::vector< SpectrumData > spectrum_data_
Vector of spectrum data stored for later parallel processing.
Definition: MzXMLHandler.h:155
static const XMLCh * s_email_
Definition: MzXMLHandler.h:237
static const XMLCh * s_num_
Definition: MzXMLHandler.h:239
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
static const XMLCh * s_phone_
Definition: MzXMLHandler.h:236
Definition: MzXMLHandler.h:66
static const XMLCh * s_name_
Definition: MzXMLHandler.h:213
void setMSDataConsumer(Interfaces::IMSDataConsumer *consumer)
Set the IMSDataConsumer consumer which will consume the read data.
Definition: MzXMLHandler.h:113
static const XMLCh * s_peakscount_
Definition: MzXMLHandler.h:227
static const XMLCh * s_compressionType_
Definition: MzXMLHandler.h:222
Data necessary to generate a single spectrum.
Definition: MzXMLHandler.h:144
MapType * exp_
map pointer for reading
Definition: MzXMLHandler.h:126
bool skip_spectrum_
Flag that indicates whether this spectrum should be skipped (due to options)
Definition: MzXMLHandler.h:159
static const XMLCh * s_endmz_
Definition: MzXMLHandler.h:233