OpenMS
PepXMLFile Member List

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

ActionMode enum nameXMLHandlerprotected
analysis_summary_PepXMLFileprivate
asBool_(const String &in) constXMLHandlerinlineprotected
asDateTime_(String date_string) constXMLHandlerinlineprotected
asDouble_(const String &in) constXMLHandlerinlineprotected
asFloat_(const String &in) constXMLHandlerinlineprotected
asInt_(const String &in) constXMLHandlerinlineprotected
asInt_(const XMLCh *in) constXMLHandlerinlineprotected
asUInt_(const String &in) constXMLHandlerinlineprotected
attributeAsDouble_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsDouble_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsDoubleList_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsDoubleList_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsInt_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsInt_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsIntList_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsIntList_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsString_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsString_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsStringList_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsStringList_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
characters(const XMLCh *const chars, const XMLSize_t length) overrideXMLHandlerprotected
charge_PepXMLFileprivate
checked_base_name_PepXMLFileprivate
checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) constXMLHandlerprotected
current_analysis_result_PepXMLFileprivate
current_base_name_PepXMLFileprivate
current_modifications_PepXMLFileprivate
current_peptide_PepXMLFileprivate
current_proteins_PepXMLFileprivate
current_sequence_PepXMLFileprivate
cv_terms_XMLHandlerprotected
cvParamToValue(const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession) constXMLHandlerprotected
cvParamToValue(const ControlledVocabulary &cv, const CVTerm &raw_term) constXMLHandlerprotected
cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0)XMLHandlerprotected
date_PepXMLFileprivate
decoy_prefix_PepXMLFileprivate
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) overridePepXMLFileprotected
enforced_encoding_XMLFileprotected
enforceEncoding_(const String &encoding)XMLFileprotected
enzyme_PepXMLFileprivate
enzyme_cuttingsite_PepXMLFileprivate
equal_(const XMLCh *a, const XMLCh *b) constXMLHandlerinlineprotected
error(const xercesc::SAXParseException &exception) overrideXMLHandlerprotected
error(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandlerprotected
exp_name_PepXMLFileprivate
expectList_(const String &str) constXMLHandlerinlineprivate
experiment_label_PepXMLFileprivate
fatalError(const xercesc::SAXParseException &exception) overrideXMLHandlerprotected
fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandlerprotected
file_XMLHandlerprotected
fixed_modifications_PepXMLFileprivate
fromXSDString(const String &type, const String &value)XMLHandlerinlineprotectedstatic
getLoadDetail() constXMLHandlerprotectedvirtual
getVersion() constXMLFile
has_decoys_PepXMLFileprivate
hydrogen_PepXMLFileprivate
hydrogen_mass_PepXMLFileprivate
isValid(const String &filename, std::ostream &os)XMLFile
keep_native_name_PepXMLFileprivate
keepNativeSpectrumName(bool keep)PepXMLFileinline
LD_ALLDATA enum valueXMLHandlerprotected
LD_COUNTS_WITHOPTIONS enum valueXMLHandlerprotected
LD_RAWCOUNTS enum valueXMLHandlerprotected
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 valueXMLHandlerprotected
load_detail_XMLHandlerprotected
LOADDETAIL enum nameXMLHandlerprotected
lookup_PepXMLFileprivate
lookupAddFromHeader_(double modification_mass, Size modification_position, std::vector< AminoAcidModification > const &header_mods)PepXMLFileprivate
makeScanMap_()PepXMLFileprivate
mod_tol_PepXMLFileprivatestatic
mz_PepXMLFileprivate
native_spectrum_name_PepXMLFileprivate
open_tags_XMLHandlerprotected
optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
params_PepXMLFileprivate
parse_(const String &filename, XMLHandler *handler)XMLFileprotected
parse_unknown_scores_PepXMLFileprivate
parseBuffer_(const std::string &buffer, XMLHandler *handler)XMLFileprotected
peptide_hit_PepXMLFileprivate
peptides_PepXMLFileprivate
PepXMLFile()PepXMLFile
preferred_fixed_modifications_PepXMLFileprivate
preferred_variable_modifications_PepXMLFileprivate
prot_id_PepXMLFileprivate
proteins_PepXMLFileprivate
readRTMZCharge_(const xercesc::Attributes &attributes)PepXMLFileprivate
reset()XMLHandlerprotected
rt_PepXMLFileprivate
save_(const String &filename, XMLHandler *handler) constXMLFileprotected
scan_map_PepXMLFileprivate
scannr_PepXMLFileprivate
schema_location_XMLFileprotected
schema_version_XMLFileprotected
search_engine_PepXMLFileprivate
search_id_PepXMLFileprivate
search_score_summary_PepXMLFileprivate
search_summary_PepXMLFileprivate
seen_experiment_PepXMLFileprivate
setLoadDetail(const LOADDETAIL d)XMLHandlerprotectedvirtual
setParseUnknownScores(bool parse_unknown_scores)PepXMLFile
setPreferredFixedModifications(const std::vector< const ResidueModification * > &mods)PepXMLFile
setPreferredVariableModifications(const std::vector< const ResidueModification * > &mods)PepXMLFile
sm_XMLHandlerprotected
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) overridePepXMLFileprotected
status_PepXMLFileprivate
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, double rt_tolerance=0.01)PepXMLFile
STORE enum valueXMLHandlerprotected
swath_assay_PepXMLFileprivate
use_precursor_data_PepXMLFileprivate
variable_modifications_PepXMLFileprivate
version_XMLHandlerprotected
warning(const xercesc::SAXParseException &exception) overrideXMLHandlerprotected
warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandlerprotected
writeTo(std::ostream &)XMLHandlerprotectedvirtual
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) constXMLHandlerprotected
writeXMLEscape(const String &to_escape)XMLHandlerinlineprotectedstatic
wrong_experiment_PepXMLFileprivate
XMLFile()XMLFile
XMLFile(const String &schema_location, const String &version)XMLFile
XMLHandler(const String &filename, const String &version)XMLHandlerprotected
XMLHandler()XMLHandlerprivate
xtandem_artificial_mod_tol_PepXMLFileprivatestatic
~PepXMLFile() overridePepXMLFile
~XMLFile()XMLFilevirtual
~XMLHandler() overrideXMLHandlerprotected