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| | MascotXMLHandler (ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &identifications, const String &filename, std::map< String, std::vector< AASequence > > &peptides, const RTMapping &rt_mapping=RTMapping(), const String &scan_regex="") |
| | Constructor. More...
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| virtual | ~MascotXMLHandler () |
| | Destructor. More...
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| virtual void | endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname) |
| | Parsing method for closing tags. More...
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| virtual void | startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) |
| | Parsing method for opening tags. More...
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| virtual void | characters (const XMLCh *const chars, const XMLSize_t) |
| | Parsing method for character data. More...
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Public Member Functions inherited from XMLHandler |
| | XMLHandler (const String &filename, const String &version) |
| | Default constructor. More...
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| virtual | ~XMLHandler () |
| | Destructor. More...
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| void | reset () |
| | Release internal memory used for parsing (call. More...
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| void | fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const |
| | Fatal error handler. Throws a ParseError exception. More...
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| void | error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const |
| | Error handler for recoverable errors. More...
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| void | warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const |
| | Warning handler. More...
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| virtual void | writeTo (std::ostream &) |
| | Writes the contents to a stream. More...
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| String | errorString () |
| | Returns the last error description. More...
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| void | fatalError (const xercesc::SAXParseException &exception) |
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| void | error (const xercesc::SAXParseException &exception) |
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| void | warning (const xercesc::SAXParseException &exception) |
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Protected Member Functions inherited from XMLHandler |
| bool | equal_ (const XMLCh *a, const XMLCh *b) |
| | Returns if two xerces strings are equal. More...
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| void | writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const |
| | Writes the content of MetaInfoInterface to the file. More...
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| Int | asInt_ (const String &in) |
| | Conversion of a String to an integer value. More...
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| Int | asInt_ (const XMLCh *in) |
| | Conversion of a Xerces string to an integer value. More...
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| UInt | asUInt_ (const String &in) |
| | Conversion of a String to an unsigned integer value. More...
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| double | asDouble_ (const String &in) |
| | Conversion of a String to a double value. More...
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| float | asFloat_ (const String &in) |
| | Conversion of a String to a float value. More...
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| bool | asBool_ (const String &in) |
| | Conversion of a string to a boolean value. More...
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| DateTime | asDateTime_ (String date_string) |
| | Conversion of a xs:datetime string to a DataTime value. More...
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| char * | attributeAsString_ (const xercesc::Attributes &a, const char *name) const |
| | Converts an attribute to a String. More...
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| Int | attributeAsInt_ (const xercesc::Attributes &a, const char *name) const |
| | Converts an attribute to a Int. More...
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| DoubleReal | attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const |
| | Converts an attribute to a DoubleReal. More...
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| DoubleList | attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const |
| | Converts an attribute to a DoubleList. More...
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| IntList | attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const |
| | Converts an attribute to an IntList. More...
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| StringList | attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const |
| | Converts an attribute to an StringList. More...
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| bool | optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const char *name) const |
| | Assigns the attribute content to the String value if the attribute is present. More...
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| bool | optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const char *name) const |
| | Assigns the attribute content to the Int value if the attribute is present. More...
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| bool | optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const char *name) const |
| | Assigns the attribute content to the UInt value if the attribute is present. More...
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| bool | optionalAttributeAsDouble_ (DoubleReal &value, const xercesc::Attributes &a, const char *name) const |
| | Assigns the attribute content to the DoubleReal value if the attribute is present. More...
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| bool | optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const char *name) const |
| | Assigns the attribute content to the DoubleList value if the attribute is present. More...
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| bool | optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const char *name) const |
| | Assigns the attribute content to the StringList value if the attribute is present. More...
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| bool | optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const char *name) const |
| | Assigns the attribute content to the IntList value if the attribute is present. More...
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| char * | attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const |
| | Converts an attribute to a String. More...
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| Int | attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const |
| | Converts an attribute to a Int. More...
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| DoubleReal | attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const |
| | Converts an attribute to a DoubleReal. More...
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| DoubleList | attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const |
| | Converts an attribute to a DoubleList. More...
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| IntList | attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const |
| | Converts an attribute to a IntList. More...
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| StringList | attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const |
| | Converts an attribute to a StringList. More...
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| bool | optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const XMLCh *name) const |
| | Assigns the attribute content to the String value if the attribute is present. More...
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| bool | optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const XMLCh *name) const |
| | Assigns the attribute content to the Int value if the attribute is present. More...
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| bool | optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const XMLCh *name) const |
| | Assigns the attribute content to the UInt value if the attribute is present. More...
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| bool | optionalAttributeAsDouble_ (DoubleReal &value, const xercesc::Attributes &a, const XMLCh *name) const |
| | Assigns the attribute content to the DoubleReal value if the attribute is present. More...
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| bool | optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const |
| | Assigns the attribute content to the DoubleList value if the attribute is present. More...
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| bool | optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const XMLCh *name) const |
| | Assigns the attribute content to the IntList value if the attribute is present. More...
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| bool | optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const XMLCh *name) const |
| | Assigns the attribute content to the StringList value if the attribute is present. More...
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| SignedSize | cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0) |
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Protected Attributes inherited from XMLHandler |
| String | error_message_ |
| | Error message of the last error. More...
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| String | file_ |
| | File name. More...
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| String | version_ |
| | Schema version. More...
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| StringManager | sm_ |
| | Helper class for string conversion. More...
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| std::vector< String > | open_tags_ |
| | Stack of open XML tags. More...
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std::vector< std::vector
< String > > | cv_terms_ |
| | Array of CV term lists (one sublist denotes one term and it's children) More...
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Handler that is used for parsing MascotXML data.