act_cons_element_ | ConsensusXMLHandler | [protected] |
asBool_(const String &in) | XMLHandler | [inline, protected] |
asDateTime_(const String &in) | 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] |
attributeAsInt_(const xercesc::Attributes &a, const char *name) const | XMLHandler | [inline, protected] |
attributeAsInt_(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] |
calignment_ | ConsensusXMLHandler | [protected] |
characters(const XMLCh *const chars, unsigned int length) | ConsensusXMLHandler | [inline, virtual] |
consensus_element_range_ | ConsensusXMLHandler | [protected] |
consensus_map_ | ConsensusXMLHandler | [protected] |
consensus_map_flag_ | ConsensusXMLHandler | [protected] |
ConsensusElementType typedef | ConsensusXMLHandler | |
ConsensusXMLHandler(ConsensusMap< ConsensusElementType > &consensus_map, const String &filename, const String &version, bool load_elements_maps=true) | ConsensusXMLHandler | [inline] |
ConsensusXMLHandler(const StarAlignment< ConsensusElementType > &alignment, const String &filename, const String &version) | ConsensusXMLHandler | [inline] |
cv_terms_ | XMLHandler | [protected] |
cvStringToEnum_(UInt section, const String &term, const char *message) | XMLHandler | [inline, protected] |
ElementContainerType typedef | ConsensusXMLHandler | |
ElementType typedef | ConsensusXMLHandler | |
endElement(const XMLCh *const , const XMLCh *const , const XMLCh *const qname) | ConsensusXMLHandler | [inline, virtual] |
equal_(const XMLCh *a, const XMLCh *b) | XMLHandler | [inline, protected] |
error(const xercesc::SAXParseException &exception) | XMLHandler | |
error(const String &msg, UInt line=0, UInt column=0) const | XMLHandler | |
error_message_ | XMLHandler | [mutable, protected] |
errorString() | XMLHandler | |
fatalError(const xercesc::SAXParseException &exception) | XMLHandler | |
fatalError(const String &msg, UInt line=0, UInt column=0) const | XMLHandler | |
feature_map_flag_ | ConsensusXMLHandler | [protected] |
file_ | XMLHandler | [protected] |
it_ | ConsensusXMLHandler | [protected] |
it_range_ | ConsensusXMLHandler | [protected] |
load_elements_maps_ | ConsensusXMLHandler | [protected] |
loadFile_(const String &, UInt, const ConsensusElementT &) | ConsensusXMLHandler | [inline, protected] |
loadFile_(const String &file_name, UInt id, const ConsensusFeature< FeatureMap< > > &) | ConsensusXMLHandler | [inline] |
loadFile_(const String &file_name, UInt id, const ConsensusPeak< DPeakArray< Peak2D > > &) | ConsensusXMLHandler | [inline] |
loadFile_(const String &file_name, UInt id, const ConsensusFeature< ConsensusMap< ConsensusFeature< FeatureMap< > > > > &) | ConsensusXMLHandler | [inline] |
open_tags_ | XMLHandler | [protected] |
optionalAttributeAsDouble_(DoubleReal &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | [inline, protected] |
optionalAttributeAsDouble_(DoubleReal &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] |
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] |
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] |
pos_ | ConsensusXMLHandler | [protected] |
pos_range_ | ConsensusXMLHandler | [protected] |
PositionType typedef | ConsensusXMLHandler | |
sm_ | XMLHandler | [protected] |
startElement(const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) | ConsensusXMLHandler | [inline, virtual] |
version_ | XMLHandler | [protected] |
warning(const xercesc::SAXParseException &exception) | XMLHandler | |
warning(const String &msg, UInt line=0, UInt column=0) const | XMLHandler | |
writeCellList_(std::ostream &os, const Grid &grid) | ConsensusXMLHandler | [inline, protected] |
writeCVS_(std::ostream &os, DoubleReal value, const String &acc, const String &name, int indent=4) const | XMLHandler | [inline, protected] |
writeCVS_(std::ostream &os, const String &value, const String &acc, const String &name, int indent=4) const | XMLHandler | [inline, protected] |
writeCVS_(std::ostream &os, int value, int map, const String &acc, const String &name, int indent=4) | XMLHandler | [protected] |
writeTo(std::ostream &os) | ConsensusXMLHandler | [inline, virtual] |
writeUserParam_(std::ostream &os, const MetaInfoInterface &meta, int indent=4) | XMLHandler | [inline, protected] |
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const | XMLHandler | [protected] |
XMLHandler(const String &filename, const String &version) | XMLHandler | |
~ConsensusXMLHandler() | ConsensusXMLHandler | [inline, virtual] |
~XMLHandler() | XMLHandler | [virtual] |