PepXMLFile Member List

This is the complete list of members for PepXMLFile, including all inherited members.

ActionMode enum name	XMLHandler	protected
analysis_summary_	PepXMLFile	private
asBool_(const String &in)	XMLHandler	inlineprotected
asDateTime_(String date_string)	XMLHandler	inlineprotected
asDouble_(const String &in)	XMLHandler	inlineprotected
asFloat_(const String &in)	XMLHandler	inlineprotected
asInt_(const String &in)	XMLHandler	inlineprotected
asInt_(const XMLCh *in)	XMLHandler	inlineprotected
asUInt_(const String &in)	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
characters(const XMLCh *const chars, const XMLSize_t length) override	XMLHandler	protected
charge_	PepXMLFile	private
checked_base_name_	PepXMLFile	private
current_analysis_result_	PepXMLFile	private
current_base_name_	PepXMLFile	private
current_modifications_	PepXMLFile	private
current_peptide_	PepXMLFile	private
current_proteins_	PepXMLFile	private
current_sequence_	PepXMLFile	private
cv_terms_	XMLHandler	protected
cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0)	XMLHandler	inlineprotected
date_	PepXMLFile	private
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override	PepXMLFile	protected
enforced_encoding_	XMLFile	protected
enforceEncoding_(const String &encoding)	XMLFile	protected
enzyme_	PepXMLFile	private
equal_(const XMLCh *a, const XMLCh *b) const	XMLHandler	inlineprotected
error(const xercesc::SAXParseException &exception) override	XMLHandler	protected
error(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const	XMLHandler	protected
error_message_	XMLHandler	mutableprotected
errorString()	XMLHandler	protected
exp_name_	PepXMLFile	private
experiment_label_	PepXMLFile	private
fatalError(const xercesc::SAXParseException &exception) override	XMLHandler	protected
fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const	XMLHandler	protected
file_	XMLHandler	protected
fixed_modifications_	PepXMLFile	private
getLoadDetail() const	XMLHandler	protectedvirtual
getVersion() const	XMLFile
hydrogen_	PepXMLFile	private
hydrogen_mass_	PepXMLFile	private
isValid(const String &filename, std::ostream &os)	XMLFile
keep_native_name_	PepXMLFile	private
keepNativeSpectrumName(bool keep)	PepXMLFile	inline
LD_ALLDATA enum value	XMLHandler	protected
LD_COUNTS_WITHOPTIONS enum value	XMLHandler	protected
LD_RAWCOUNTS enum value	XMLHandler	protected
load(const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name, const SpectrumMetaDataLookup &lookup)	PepXMLFile
load(const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name="")	PepXMLFile
LOAD enum value	XMLHandler	protected
load_detail_	XMLHandler	protected
LOADDETAIL enum name	XMLHandler	protected
lookup_	PepXMLFile	private
makeScanMap_()	PepXMLFile	private
matchModification_(const double mass, const String &origin, String &modification_description)	PepXMLFile	private
mod_tol_	PepXMLFile	privatestatic
mz_	PepXMLFile	private
native_spectrum_name_	PepXMLFile	private
open_tags_	XMLHandler	protected
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_(String &value, const xercesc::Attributes &a, const char *name) const	XMLHandler	inlineprotected
optionalAttributeAsString_(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
params_	PepXMLFile	private
parse_(const String &filename, XMLHandler *handler)	XMLFile	protected
parseBuffer_(const std::string &buffer, XMLHandler *handler)	XMLFile	protected
peptide_hit_	PepXMLFile	private
peptides_	PepXMLFile	private
PepXMLFile()	PepXMLFile
prot_id_	PepXMLFile	private
proteins_	PepXMLFile	private
readRTMZCharge_(const xercesc::Attributes &attributes)	PepXMLFile	private
reset()	XMLHandler	protected
rt_	PepXMLFile	private
save_(const String &filename, XMLHandler *handler) const	XMLFile	protected
scan_map_	PepXMLFile	private
schema_location_	XMLFile	protected
schema_version_	XMLFile	protected
search_engine_	PepXMLFile	private
search_id_	PepXMLFile	private
search_score_summary_	PepXMLFile	private
search_summary_	PepXMLFile	private
seen_experiment_	PepXMLFile	private
setLoadDetail(const LOADDETAIL d)	XMLHandler	protectedvirtual
sm_	XMLHandler	protected
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override	PepXMLFile	protected
status_	PepXMLFile	private
STORE enum value	XMLHandler	protected
store(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, const String &mz_file="", const String &mz_name="", bool peptideprophet_analyzed=false)	PepXMLFile
swath_assay_	PepXMLFile	private
use_precursor_data_	PepXMLFile	private
variable_modifications_	PepXMLFile	private
version_	XMLHandler	protected
warning(const xercesc::SAXParseException &exception) override	XMLHandler	protected
warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const	XMLHandler	protected
writeTo(std::ostream &)	XMLHandler	protectedvirtual
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const	XMLHandler	protected
writeXMLEscape(const String &to_escape)	XMLHandler	inlineprotectedstatic
wrong_experiment_	PepXMLFile	private
XMLFile()	XMLFile
XMLFile(const String &schema_location, const String &version)	XMLFile
XMLHandler(const String &filename, const String &version)	XMLHandler	protected
xtandem_artificial_mod_tol_	PepXMLFile	privatestatic
~PepXMLFile() override	PepXMLFile
~XMLFile()	XMLFile	virtual
~XMLHandler() override	XMLHandler	protected