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OMSSAXMLFile Member List

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

ActionMode enum nameXMLHandlerprotected
actual_mod_site_OMSSAXMLFileprivate
actual_mod_type_OMSSAXMLFileprivate
actual_peptide_evidence_OMSSAXMLFileprivate
actual_peptide_evidences_OMSSAXMLFileprivate
actual_peptide_hit_OMSSAXMLFileprivate
actual_peptide_id_OMSSAXMLFileprivate
actual_protein_hit_OMSSAXMLFileprivate
actual_protein_id_OMSSAXMLFileprivate
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) overrideOMSSAXMLFileprotected
checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) constXMLHandlerprotected
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
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) overrideOMSSAXMLFileprotected
enforced_encoding_XMLFileprotected
enforceEncoding_(const String &encoding)XMLFileprotected
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
expectList_(const String &str) constXMLHandlerinlineprivate
fatalError(const xercesc::SAXParseException &exception) overrideXMLHandlerprotected
fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandlerprotected
file_XMLHandlerprotected
fromXSDString(const String &type, const String &value)XMLHandlerinlineprotectedstatic
getLoadDetail() constXMLHandlerprotectedvirtual
getVersion() constXMLFile
isValid(const String &filename, std::ostream &os)XMLFile
LD_ALLDATA enum valueXMLHandlerprotected
LD_COUNTS_WITHOPTIONS enum valueXMLHandlerprotected
LD_RAWCOUNTS enum valueXMLHandlerprotected
LOAD enum valueXMLHandlerprotected
load(const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)OMSSAXMLFile
load_detail_XMLHandlerprotected
load_empty_hits_OMSSAXMLFileprivate
load_proteins_OMSSAXMLFileprivate
LOADDETAIL enum nameXMLHandlerprotected
mod_def_set_OMSSAXMLFileprivate
modifications_OMSSAXMLFileprivate
mods_map_OMSSAXMLFileprivate
mods_to_num_OMSSAXMLFileprivate
OMSSAXMLFile()OMSSAXMLFile
OMSSAXMLFile(const OMSSAXMLFile &rhs)OMSSAXMLFileprivate
open_tags_XMLHandlerprotected
operator=(const OMSSAXMLFile &rhs)OMSSAXMLFileprivate
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
parse_(const String &filename, XMLHandler *handler)XMLFileprotected
parseBuffer_(const std::string &buffer, XMLHandler *handler)XMLFileprotected
peptide_identifications_OMSSAXMLFileprivate
readMappingFile_()OMSSAXMLFileprivate
reset()XMLHandlerprotected
save_(const String &filename, XMLHandler *handler) constXMLFileprotected
schema_location_XMLFileprotected
schema_version_XMLFileprotected
setLoadDetail(const LOADDETAIL d)XMLHandlerprotectedvirtual
setModificationDefinitionsSet(const ModificationDefinitionsSet &rhs)OMSSAXMLFile
sm_XMLHandlerprotected
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) overrideOMSSAXMLFileprotected
STORE enum valueXMLHandlerprotected
tag_OMSSAXMLFileprivate
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
XMLFile()XMLFile
XMLFile(const String &schema_location, const String &version)XMLFile
XMLHandler(const String &filename, const String &version)XMLHandlerprotected
XMLHandler()XMLHandlerprivate
~OMSSAXMLFile() overrideOMSSAXMLFile
~XMLFile()XMLFilevirtual
~XMLHandler() overrideXMLHandlerprotected