This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation.
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| ConsensusXMLHandler (ConsensusMap &map, const String &filename) |
| Constructor. More...
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| ConsensusXMLHandler (const ConsensusMap &map, const String &filename) |
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| ~ConsensusXMLHandler () override |
| Destructor. More...
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PeakFileOptions & | getOptions () |
| Mutable access to the options for loading/storing. More...
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void | setOptions (const PeakFileOptions &) |
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const PeakFileOptions & | getOptions () const |
| Non-mutable access to the options for loading/storing. More...
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void | writeTo (std::ostream &os) override |
| Docu in base class XMLHandler::writeTo. 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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| ~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 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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DataValue | cvParamToValue (const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession) const |
| Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...
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DataValue | cvParamToValue (const ControlledVocabulary &cv, const CVTerm &raw_term) const |
| Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...
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void | checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const |
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| ProgressLogger () |
| Constructor. More...
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virtual | ~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 | setLogger (ProgressLoggerImpl *logger) |
| Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const |
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void | nextProgress () const |
| increment progress by 1 (according to range begin-end) More...
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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 | characters (const XMLCh *const chars, const XMLSize_t length) override |
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void | writePeptideIdentification_ (const String &filename, std::ostream &os, const PeptideIdentification &id, const String &tag_name, UInt indentation_level) |
| Writes a peptide identification to a stream (for assigned/unassigned peptide identifications) More...
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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, const String &runid, 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) const |
| Conversion of a String to an integer value. More...
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Int | asInt_ (const XMLCh *in) const |
| Conversion of a Xerces string to an integer value. More...
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UInt | asUInt_ (const String &in) const |
| Conversion of a String to an unsigned integer value. More...
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double | asDouble_ (const String &in) const |
| Conversion of a String to a double value. More...
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float | asFloat_ (const String &in) const |
| Conversion of a String to a float value. More...
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bool | asBool_ (const String &in) const |
| Conversion of a string to a boolean value. More...
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DateTime | asDateTime_ (String date_string) const |
| 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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This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation.
This class can be used to load the content of a consensusXML file into a ConsensusMap or to save the content of an ConsensusMap object into an XML file.
A documented schema for this format can be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS
- Todo:
- Take care that unique ids are assigned properly by TOPP tools before calling ConsensusXMLFile::store(). There will be a message on OPENMS_LOG_INFO but we will make no attempt to fix the problem in this class. (all developers)