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void | endElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override |
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void | startElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override |
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void | addProteinGroups_ (MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::unordered_map< std::string, UInt > &accession_to_id, XMLHandler::ActionMode mode) |
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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 |
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 DateTime value. More...
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bool | equal_ (const XMLCh *a, const XMLCh *b) const |
| Returns if two Xerces strings are equal. 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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String | 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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double | attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const |
| Converts an attribute to a double. 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_ (double &value, const xercesc::Attributes &a, const char *name) const |
| Assigns the attribute content to the double 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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String | 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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double | attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const |
| Converts an attribute to a double. 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_ (double &value, const xercesc::Attributes &a, const XMLCh *name) const |
| Assigns the attribute content to the double 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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| XMLHandler (const String &filename, const String &version) |
| Default constructor. More...
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| ~XMLHandler () override |
| Destructor. More...
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void | reset () |
| Release internal memory used for parsing (call. More...
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void | fatalError (const xercesc::SAXParseException &exception) override |
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void | error (const xercesc::SAXParseException &exception) override |
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void | warning (const xercesc::SAXParseException &exception) override |
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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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void | characters (const XMLCh *const chars, const XMLSize_t length) override |
| Parsing method for character data. More...
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void | startElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override |
| Parsing method for opening tags. More...
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void | endElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname) override |
| Parsing method for closing tags. 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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virtual LOADDETAIL | getLoadDetail () const |
| handler which support partial loading, implement this method More...
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virtual void | setLoadDetail (const LOADDETAIL d) |
| handler which support partial loading, implement this method More...
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void | checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) |
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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 | parseBuffer_ (const std::string &buffer, XMLHandler *handler) |
| Parses the in-memory buffer given by buffer 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...
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void | enforceEncoding_ (const String &encoding) |
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| 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) |
| 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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| ProgressLogger () |
| Constructor. More...
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| ~ProgressLogger () |
| Destructor. More...
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| ProgressLogger (const ProgressLogger &other) |
| Copy constructor. More...
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ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More...
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void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More...
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LogType | getLogType () const |
| Returns the type of progress log being used. More...
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void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More...
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void | setProgress (SignedSize value) const |
| Sets the current progress. More...
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void | endProgress () const |
| Ends the progress display. More...
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void | nextProgress () const |
| increment progress by 1 (according to range begin-end) 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 https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/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!