ActionMode enum name | XMLHandler | |
actual_peptide_ | MzIdentMLHandler | private |
actual_protein_ | MzIdentMLHandler | 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) | MzIdentMLHandler | virtual |
cid_ | MzIdentMLHandler | protected |
cpep_id_ | MzIdentMLHandler | protected |
cpro_id_ | MzIdentMLHandler | protected |
current_id_hit_ | MzIdentMLHandler | protected |
current_mod_location_ | MzIdentMLHandler | private |
current_spectrum_id_ | MzIdentMLHandler | protected |
cv_ | MzIdentMLHandler | protected |
cv_terms_ | XMLHandler | protected |
cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0) | XMLHandler | inlineprotected |
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) | MzIdentMLHandler | virtual |
equal_(const XMLCh *a, const XMLCh *b) const | XMLHandler | inlineprotected |
error(const xercesc::SAXParseException &exception) | XMLHandler | |
error(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | |
error_message_ | XMLHandler | mutableprotected |
errorString() | XMLHandler | |
fatalError(const xercesc::SAXParseException &exception) | XMLHandler | |
fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | |
file_ | XMLHandler | protected |
getChildWithName_(const String &parent_accession, const String &name) const | MzIdentMLHandler | protected |
handleCVParam_(const String &parent_parent_tag, const String &parent_tag, const String &accession, const xercesc::Attributes &attributes, const String &cv_ref) | MzIdentMLHandler | protected |
handleUserParam_(const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value) | MzIdentMLHandler | protected |
id_ | MzIdentMLHandler | protected |
LOAD enum value | XMLHandler | |
logger_ | MzIdentMLHandler | protected |
MzIdentMLHandler(const Identification &id, const String &filename, const String &version, const ProgressLogger &logger) | MzIdentMLHandler | |
MzIdentMLHandler(const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger) | MzIdentMLHandler | |
MzIdentMLHandler(Identification &id, const String &filename, const String &version, const ProgressLogger &logger) | MzIdentMLHandler | |
MzIdentMLHandler(std::vector< ProteinIdentification > &pro_id, std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger) | MzIdentMLHandler | |
MzIdentMLHandler() | MzIdentMLHandler | private |
MzIdentMLHandler(const MzIdentMLHandler &rhs) | MzIdentMLHandler | private |
open_tags_ | XMLHandler | protected |
operator=(const MzIdentMLHandler &rhs) | MzIdentMLHandler | private |
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 |
pep_id_ | MzIdentMLHandler | protected |
pep_sequences_ | MzIdentMLHandler | private |
ph_2_sdat_ | MzIdentMLHandler | private |
pp_identifier_2_sil_ | MzIdentMLHandler | private |
pro_id_ | MzIdentMLHandler | protected |
reset() | XMLHandler | |
sil_2_sdat_ | MzIdentMLHandler | private |
sil_2_sdb_ | MzIdentMLHandler | private |
sil_2_sip_ | MzIdentMLHandler | private |
sm_ | XMLHandler | protected |
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) | MzIdentMLHandler | virtual |
STORE enum value | XMLHandler | |
tag_ | MzIdentMLHandler | protected |
trimOpenMSfileURI(const String file) const | MzIdentMLHandler | protected |
unimod_ | MzIdentMLHandler | protected |
version_ | XMLHandler | protected |
warning(const xercesc::SAXParseException &exception) | XMLHandler | |
warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | |
writeEnzyme_(String &s, Enzyme enzy, UInt miss, UInt indent) const | MzIdentMLHandler | protected |
writeFragmentAnnotations_(String &s, const std::vector< PeptideHit::PeakAnnotation > &annotations, UInt indent, bool is_ppxl) const | MzIdentMLHandler | protected |
writeMetaInfos_(String &s, const MetaInfoInterface &meta, UInt indent) const | MzIdentMLHandler | protected |
writeModParam_(String &s, const std::vector< String > &mod_names, bool fixed, UInt indent) const | MzIdentMLHandler | protected |
writeTo(std::ostream &os) | MzIdentMLHandler | virtual |
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const | XMLHandler | protected |
writeXMLEscape(const String &to_escape) | XMLHandler | inlinestatic |
XMLHandler(const String &filename, const String &version) | XMLHandler | |
~MzIdentMLHandler() | MzIdentMLHandler | virtual |
~XMLHandler() | XMLHandler | virtual |