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OpenMS
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This is the complete list of members for ImzMLHandler, including all inherited members.
| ActionMode enum name | XMLHandler | |
| applyRefGroup_(const std::string &id) | ImzMLHandler | private |
| asBool_(const std::string &in) const | XMLHandler | inlineprotected |
| asDateTime_(std::string date_string) const | XMLHandler | inlineprotected |
| asDouble_(const std::string &in) const | XMLHandler | inlineprotected |
| asFloat_(const std::string &in) const | XMLHandler | inlineprotected |
| asInt_(const std::string &in) const | XMLHandler | inlineprotected |
| asInt_(const XMLCh *in) const | XMLHandler | inlineprotected |
| asUInt_(const std::string &in) const | XMLHandler | inlineprotected |
| attributeAsDouble_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsDouble_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsDoubleList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsDoubleList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsInt_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsInt_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsIntList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsIntList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsString_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsString_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsStringList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsStringList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| bin_data_ | MzMLHandler | protected |
| BinaryData typedef | MzMLHandler | protected |
| cached_terms_ | MzMLHandler | mutableprotected |
| cexp_ | MzMLHandler | protected |
| characters(const XMLCh *const chars, const XMLSize_t length) override | MzMLHandler | |
| checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) const | XMLHandler | |
| chrom_count_total_ | MzMLHandler | protected |
| chromatogram_ | MzMLHandler | protected |
| chromatogram_count_ | MzMLHandler | protected |
| chromatogram_data_ | MzMLHandler | protected |
| ChromatogramPeakType typedef | MzMLHandler | protected |
| chromatograms_offsets_ | MzMLHandler | protected |
| ChromatogramType typedef | MzMLHandler | protected |
| connectDecodeConsumer(Interfaces::IMSDataConsumer *downstream, bool append_spectra_to_map, bool decode_ibd=true) | ImzMLHandler | |
| consumer_ | MzMLHandler | protected |
| cur_array_ | ImzMLHandler | private |
| cur_int_meta_ | ImzMLHandler | private |
| cur_mz_meta_ | ImzMLHandler | private |
| cur_ref_id_ | ImzMLHandler | private |
| cur_x_ | ImzMLHandler | private |
| cur_x_seen_ | ImzMLHandler | private |
| cur_y_ | ImzMLHandler | private |
| cur_y_seen_ | ImzMLHandler | private |
| cur_z_ | ImzMLHandler | private |
| current_id_ | MzMLHandler | protected |
| cv_ | MzMLHandler | protected |
| cv_terms_ | XMLHandler | protected |
| CvPair typedef | ImzMLHandler | private |
| cvParamToValue(const ControlledVocabulary &cv, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::string &unit_accession) const | XMLHandler | |
| cvParamToValue(const ControlledVocabulary &cv, const CVTerm &raw_term) const | XMLHandler | |
| cvStringToEnum_(const Size section, const std::string &term, const char *message, const SignedSize result_on_error=0) | XMLHandler | protected |
| decode_bridge_ | ImzMLHandler | private |
| decode_ibd_ | ImzMLHandler | private |
| default_array_length_ | MzMLHandler | protected |
| default_processing_ | MzMLHandler | protected |
| endElement(const XMLCh *uri, const XMLCh *localname, const XMLCh *qname) override | ImzMLHandler | |
| equal_(const XMLCh *a, const XMLCh *b) const | XMLHandler | inlineprotected |
| error(const xercesc::SAXParseException &exception) override | XMLHandler | |
| error(ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const | XMLHandler | |
| exp_ | MzMLHandler | protected |
| expectList_(const std::string &str) const | XMLHandler | inlineprivate |
| fatalError(const xercesc::SAXParseException &exception) override | XMLHandler | |
| fatalError(ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const | XMLHandler | |
| file_ | XMLHandler | protected |
| fillChromatogramData_() | MzMLHandler | protected |
| fromXSDString(const std::string &type, const std::string &value) | XMLHandler | inlinestatic |
| getChildWithName_(const std::string &parent_accession, const std::string &name) const | MzMLHandler | protected |
| getCounts(Size &spectra_counts, Size &chromatogram_counts) | MzMLHandler | |
| getImzMLMeta() const noexcept | ImzMLHandler | inline |
| getImzMLMeta() noexcept | ImzMLHandler | inline |
| getIndex() const noexcept | ImzMLHandler | inline |
| getLoadDetail() const override | MzMLHandler | virtual |
| getOptions() | MzMLHandler | |
| handleCVParam_(const std::string &parent_parent_tag, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::string &unit_accession="") | MzMLHandler | protected |
| handleIMSCvParam_(const std::string &acc, const std::string &val) | ImzMLHandler | private |
| handleUserParam_(const std::string &parent_parent_tag, const std::string &parent_tag, const std::string &name, const std::string &type, const std::string &value, const std::string &unit_accession="") | MzMLHandler | protected |
| ibd_ | ImzMLHandler | private |
| ImzMLHandler(PeakMap &exp, const std::string &filename, const ProgressLogger &logger) | ImzMLHandler | |
| ImzMLHandler(const ImzMLHandler &)=delete | ImzMLHandler | |
| ImzMLInterceptConsumer | ImzMLHandler | friend |
| in_bda_ | ImzMLHandler | private |
| in_ref_group_ | ImzMLHandler | private |
| in_scan_ | ImzMLHandler | private |
| in_spectrum_ | ImzMLHandler | private |
| in_spectrum_list_ | MzMLHandler | protected |
| index_ | ImzMLHandler | private |
| instruments_ | MzMLHandler | protected |
| LD_ALLDATA enum value | XMLHandler | |
| LD_COUNTS_WITHOPTIONS enum value | XMLHandler | |
| LD_RAWCOUNTS enum value | XMLHandler | |
| LOAD enum value | XMLHandler | |
| load_detail_ | XMLHandler | protected |
| LOADDETAIL enum name | XMLHandler | |
| logger_ | MzMLHandler | protected |
| mapping_ | MzMLHandler | protected |
| meta_ | ImzMLHandler | private |
| MzMLHandler(MapType &exp, const std::string &filename, const std::string &version, const ProgressLogger &logger) | MzMLHandler | |
| MzMLHandler(const MapType &exp, const std::string &filename, const std::string &version, const ProgressLogger &logger) | MzMLHandler | |
| MzMLHandler(const std::string &filename, const std::string &version, const ProgressLogger &logger) | MzMLHandler | protected |
| open_tags_ | XMLHandler | protected |
| openIBD(const std::string &ibd_path) | ImzMLHandler | |
| operator=(const ImzMLHandler &)=delete | ImzMLHandler | |
| optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsString_(std::string &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsString_(std::string &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| options_ | MzMLHandler | protected |
| PeakType typedef | MzMLHandler | protected |
| populateChromatogramsWithData_() | MzMLHandler | protected |
| populateChromatogramsWithData_(std::vector< MzMLHandlerHelper::BinaryData > &input_data, Size &length, const PeakFileOptions &peak_file_options, ChromatogramType &chromatogram) | MzMLHandler | protected |
| populateSpectraWithData_() | MzMLHandler | protected |
| populateSpectraWithData_(std::vector< MzMLHandlerHelper::BinaryData > &input_data, Size &length, const PeakFileOptions &peak_file_options, SpectrumType &spectrum) | MzMLHandler | protected |
| processing_ | MzMLHandler | protected |
| ref_groups_ | ImzMLHandler | private |
| ref_param_ | MzMLHandler | protected |
| reset() | XMLHandler | |
| rt_set_ | MzMLHandler | protected |
| samples_ | MzMLHandler | protected |
| scan_count_ | MzMLHandler | protected |
| scan_count_total_ | MzMLHandler | protected |
| selected_ion_count_ | MzMLHandler | protected |
| setLoadDetail(const LOADDETAIL d) override | MzMLHandler | virtual |
| setMSDataConsumer(Interfaces::IMSDataConsumer *consumer) | MzMLHandler | |
| setOptions(const PeakFileOptions &opt) | MzMLHandler | |
| skip_chromatogram_ | MzMLHandler | protected |
| skip_spectrum_ | MzMLHandler | protected |
| sm_ | XMLHandler | protected |
| software_ | MzMLHandler | protected |
| source_files_ | MzMLHandler | protected |
| spec_ | MzMLHandler | protected |
| spec_ims_ | ImzMLHandler | private |
| spectra_offsets_ | MzMLHandler | protected |
| spectrum_data_ | MzMLHandler | protected |
| SpectrumType typedef | MzMLHandler | protected |
| startElement(const XMLCh *uri, const XMLCh *localname, const XMLCh *qname, const xercesc::Attributes &attrs) override | ImzMLHandler | |
| STORE enum value | XMLHandler | |
| validateCV_(const ControlledVocabulary::CVTerm &c, const std::string &path, const Internal::MzMLValidator &validator) const | MzMLHandler | protected |
| version_ | XMLHandler | protected |
| warning(const xercesc::SAXParseException &exception) override | XMLHandler | |
| warning(ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const | XMLHandler | |
| writeBinaryDataArray_(std::ostream &os, const PeakFileOptions &options, std::vector< DataType > &data, bool is32bit, std::string array_type) | MzMLHandler | protected |
| writeBinaryFloatDataArray_(std::ostream &os, const PeakFileOptions &options, const OpenMS::DataArrays::FloatDataArray &array, const Size spec_chrom_idx, const Size array_idx, bool is_spectrum, const Internal::MzMLValidator &validator) | MzMLHandler | protected |
| writeChromatogram_(std::ostream &os, const ChromatogramType &chromatogram, Size chrom_idx, const Internal::MzMLValidator &validator) | MzMLHandler | protected |
| writeContainerData_(std::ostream &os, const PeakFileOptions &pf_options_, const ContainerT &container, const std::string &array_type) | MzMLHandler | protected |
| writeCV_(const ControlledVocabulary::CVTerm &c, const DataValue &metaValue) const | MzMLHandler | protected |
| writeDataProcessing_(std::ostream &os, const std::string &id, const std::vector< ConstDataProcessingPtr > &dps, const Internal::MzMLValidator &validator) | MzMLHandler | protected |
| writeHeader_(std::ostream &os, const MapType &exp, std::vector< std::vector< ConstDataProcessingPtr > > &dps, const Internal::MzMLValidator &validator) | MzMLHandler | protected |
| writePrecursor_(std::ostream &os, const Precursor &precursor, const Internal::MzMLValidator &validator) | MzMLHandler | protected |
| writeProduct_(std::ostream &os, const Product &product, const Internal::MzMLValidator &validator) | MzMLHandler | protected |
| writeSoftware_(std::ostream &os, const std::string &id, const Software &software, const Internal::MzMLValidator &validator) | MzMLHandler | protected |
| writeSourceFile_(std::ostream &os, const std::string &id, const SourceFile &software, const Internal::MzMLValidator &validator) | MzMLHandler | protected |
| writeSpectrum_(std::ostream &os, const SpectrumType &spec, Size spec_idx, const Internal::MzMLValidator &validator, bool renew_native_ids, std::vector< std::vector< ConstDataProcessingPtr > > &dps) | MzMLHandler | protected |
| writeTo(std::ostream &os) override | MzMLHandler | virtual |
| writeUserParam_(std::ostream &os, const MetaInfoInterface &meta, UInt indent, const std::string &path, const Internal::MzMLValidator &validator, const std::set< std::string > &exclude={}) const | MzMLHandler | protected |
| OpenMS::Internal::XMLHandler::writeUserParam_(const std::string &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const | XMLHandler | protected |
| writeXMLEscape(const std::string &to_escape) | XMLHandler | inlinestatic |
| XMLHandler(const std::string &filename, const std::string &version) | XMLHandler | |
| XMLHandler() | XMLHandler | private |
| ~ImzMLHandler() override | ImzMLHandler | |
| ~MzMLHandler() override | MzMLHandler | |
| ~XMLHandler() override | XMLHandler |
1.9.8 