OpenMS
IdXMLFile Member List

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

ActionMode enum nameXMLHandlerprotected
addProteinGroups_(MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::unordered_map< std::string, UInt > &accession_to_id, XMLHandler::ActionMode mode)IdXMLFileprotected
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
checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) constXMLHandlerprotected
CMD enum valueProgressLogger
createFlankingAAXMLString_(const std::vector< PeptideEvidence > &pes, std::ostream &os)IdXMLFileprotectedstatic
createPositionXMLString_(const std::vector< PeptideEvidence > &pes, std::ostream &os)IdXMLFileprotectedstatic
current_analysis_result_IdXMLFileprotected
current_logger_ProgressLoggermutableprotected
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
document_id_IdXMLFileprotected
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) overrideIdXMLFileprotected
endProgress(UInt64 bytes_processed=0) constProgressLogger
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
getLogType() constProgressLogger
getProteinGroups_(std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name)IdXMLFileprotected
getVersion() constXMLFile
GUI enum valueProgressLogger
id_IdXMLFileprotected
IdXMLFile()IdXMLFile
Internal::ConsensusXMLHandler classIdXMLFilefriend
Internal::FeatureXMLHandler classIdXMLFilefriend
isValid(const String &filename, std::ostream &os)XMLFile
last_invoke_ProgressLoggermutableprotected
last_meta_IdXMLFileprotected
LD_ALLDATA enum valueXMLHandlerprotected
LD_COUNTS_WITHOPTIONS enum valueXMLHandlerprotected
LD_RAWCOUNTS enum valueXMLHandlerprotected
load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)IdXMLFile
load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, String &document_id)IdXMLFile
LOAD enum valueXMLHandlerprotected
load_detail_XMLHandlerprotected
LOADDETAIL enum nameXMLHandlerprotected
LogType enum nameProgressLogger
nextProgress() constProgressLogger
NONE enum valueProgressLogger
open_tags_XMLHandlerprotected
operator=(const ProgressLogger &other)ProgressLogger
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
param_IdXMLFileprotected
parameters_IdXMLFileprotected
parse_(const String &filename, XMLHandler *handler)XMLFileprotected
parseBuffer_(const std::string &buffer, XMLHandler *handler)XMLFileprotected
parseFragmentAnnotation_(const String &s, std::vector< PeptideHit::PeakAnnotation > &annotations)IdXMLFileprotectedstatic
pep_hit_IdXMLFileprotected
pep_id_IdXMLFileprotected
pep_ids_IdXMLFileprotected
peptide_evidences_IdXMLFileprotected
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
prot_hit_IdXMLFileprotected
prot_id_IdXMLFileprotected
prot_id_in_run_IdXMLFileprotected
prot_ids_IdXMLFileprotected
proteinid_to_accession_IdXMLFileprotected
recursion_depth_ProgressLoggerprotectedstatic
reset()XMLHandlerprotected
save_(const String &filename, XMLHandler *handler) constXMLFileprotected
schema_location_XMLFileprotected
schema_version_XMLFileprotected
setLoadDetail(const LOADDETAIL d)XMLHandlerprotectedvirtual
setLogger(ProgressLoggerImpl *logger)ProgressLogger
setLogType(LogType type) constProgressLogger
setProgress(SignedSize value) constProgressLogger
sm_XMLHandlerprotected
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) overrideIdXMLFileprotected
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
STORE enum valueXMLHandlerprotected
store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")IdXMLFile
type_ProgressLoggermutableprotected
version_XMLHandlerprotected
warning(const xercesc::SAXParseException &exception) overrideXMLHandlerprotected
warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandlerprotected
writeFragmentAnnotations_(const String &tag_name, std::ostream &os, const std::vector< PeptideHit::PeakAnnotation > &annotations, UInt indent)IdXMLFileprotectedstatic
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
~ProgressLogger()ProgressLoggervirtual
~XMLFile()XMLFilevirtual
~XMLHandler() overrideXMLHandlerprotected