| OpenMS 2.5.0

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 | inline protected
asDateTime_(String date_string) | XMLHandler | inline protected
asDouble_(const String &in) | XMLHandler | inline protected
asFloat_(const String &in) | XMLHandler | inline protected
asInt_(const String &in) | XMLHandler | inline protected
asInt_(const XMLCh *in) | XMLHandler | inline protected
asUInt_(const String &in) | XMLHandler | inline protected
attributeAsDouble_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsDouble_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsDoubleList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsDoubleList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsInt_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsInt_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsIntList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsIntList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsString_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsString_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsStringList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsStringList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
characters(const XMLCh *const chars, const XMLSize_t length) override | XMLHandler | protected
charge_ | PepXMLFile | private
checked_base_name_ | PepXMLFile | private
checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) | XMLHandler | protected
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 | inline protected
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 | inline protected
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 | mutable protected
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 | protected virtual
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 | private static
mz_ | PepXMLFile | private
native_spectrum_name_ | PepXMLFile | private
open_tags_ | XMLHandler | protected
optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
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 | protected virtual
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, double rt_tolerance=0.01) | 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 | protected virtual
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const | XMLHandler | protected
writeXMLEscape(const String &to_escape) | XMLHandler | inline protected static
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 | private static
~PepXMLFile() override | PepXMLFile |
~XMLFile() | XMLFile | virtual
~XMLHandler() override | XMLHandler | protected