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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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| |
| void | addProteinGroups_ (MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::map< String, UInt > &accession_to_id) |
| | Add data from ProteinGroups to a MetaInfoInterface. More...
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| |
| void | getProteinGroups_ (std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name) |
| | Read and store ProteinGroup data. 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...
|
| |
| 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...
|
| |
| 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...
|
| |
| 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...
|
| |
| 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...
|
| |
| 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...
|
| |
| 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...
|
| |
| 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...
|
| |
| 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...
|
| |
| virtual void | characters (const XMLCh *const chars, const XMLSize_t length) |
| | Parsing method for character data. More...
|
| |
| virtual void | writeTo (std::ostream &) |
| | Writes the contents to a stream. More...
|
| |
| String | errorString () |
| | Returns the last error description. More...
|
| |
| 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 filename using the handler given by handler. More...
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| |
| void | save_ (const String &filename, XMLHandler *handler) const |
| | Stores the contents of the XML handler given by handler in the file given by filename. More...
|
| |
| void | enforceEncoding_ (const String &encoding) |
| |
| | XMLFile () |
| | Default constructor. More...
|
| |
| | XMLFile (const String &schema_location, const String &version) |
| | Constructor that sets the schema location. More...
|
| |
| virtual | ~XMLFile () |
| | Destructor. More...
|
| |
| bool | isValid (const String &filename, std::ostream &os=std::cerr) |
| | Checks if a file validates against the XML schema. More...
|
| |
| const String & | getVersion () const |
| | return the version of the schema More...
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| |
Used to load and store idXML files.
This class is used to load and store documents that implement the schema of idXML files.
A documented schema for this format can be found at http://open-ms.sourceforge.net/schemas/.
One file can contain several ProteinIdentification runs. Each run consists of peptide hits stored in PeptideIdentification and (optional) protein hits stored in Identification. Peptide and protein hits are connected via a string identifier. We use the search engine and the date as identifier.
- Note
- This format will eventually be replaced by the HUPO-PSI (mzIdentML and mzQuantML)) AnalysisXML formats!