|  | 
| void | resetMembers_ () | 
|  | reset members after reading/writing  More... 
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|  | 
| virtual void | endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname) | 
|  | Docu in base class.  More... 
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|  | 
| virtual void | startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) | 
|  | Docu in base class.  More... 
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|  | 
| void | registerProtein_ (const String &protein_name) | 
|  | Creates a new protein entry (if not already present) and appends it to the current group.  More... 
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|  | 
| void | matchModification_ (const DoubleReal mass, const String &origin, String &modification_description) | 
|  | find modification name given a modified AA mass  More... 
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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) | 
|  | 
|  | 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 | characters (const XMLCh *const chars, const XMLSize_t length) | 
|  | Parsing method for character data.  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) | 
|  | 
| void | error (const xercesc::SAXParseException &exception) | 
|  | 
| void | warning (const xercesc::SAXParseException &exception) | 
|  | 
| void | parse_ (const String &filename, XMLHandler *handler) | 
|  | Parses the XML file given by filenameusing the handler given byhandler.  More...
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|  | 
| void | save_ (const String &filename, XMLHandler *handler) const | 
|  | Stores the contents of the XML handler given by handlerin the file given byfilename.  More...
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|  | 
| void | enforceEncoding_ (const String &encoding) | 
|  | 
|  | XMLFile () | 
|  | Default constructor.  More... 
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|  | 
|  | XMLFile (const String &schema_location, const String &version) | 
|  | Constructor that sets the schema location.  More... 
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|  | 
| virtual | ~XMLFile () | 
|  | Destructor.  More... 
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|  | 
| bool | isValid (const String &filename, std::ostream &os=std::cerr) | 
|  | Checks if a file validates against the XML schema.  More... 
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|  | 
| const String & | getVersion () const | 
|  | return the version of the schema  More... 
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|  | 
Used to load (storing not supported, yet) ProtXML files. 
This class is used to load (storing not supported, yet) documents that implement the schema of ProtXML files.
A documented schema for this format comes with the TPP.
OpenMS can only read parts of the protein_summary subtree to extract protein-peptide associations. All other parts are silently ignored.
For protein groups, only the "group leader" (which is annotated with a probability and coverage) receives these attributes. All indistinguishable proteins of the same group only have an accession and score of -1.
- Note
- This format will eventually be replaced by the HUPO-PSI (mzIdentML and mzQuantML) AnalysisXML formats!
- Todo:
- Document which metavalues of Protein/PeptideHit are filled when reading ProtXML (Chris)