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| TraMLHandler ()=delete |
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| TraMLHandler (const TraMLHandler &rhs)=delete |
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TraMLHandler & | operator= (const TraMLHandler &rhs)=delete |
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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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const ProgressLogger & | logger_ |
| Progress logger. More...
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ControlledVocabulary | cv_ |
| Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More...
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String | tag_ |
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TargetedExperiment * | exp_ |
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const TargetedExperiment * | cexp_ |
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TargetedExperiment::Publication | actual_publication_ |
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TargetedExperiment::Contact | actual_contact_ |
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TargetedExperiment::Instrument | actual_instrument_ |
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TargetedExperiment::Prediction | actual_prediction_ |
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Software | actual_software_ |
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TargetedExperiment::Protein | actual_protein_ |
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TargetedExperiment::RetentionTime | actual_rt_ |
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TargetedExperiment::Peptide | actual_peptide_ |
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TargetedExperiment::Compound | actual_compound_ |
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ReactionMonitoringTransition | actual_transition_ |
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IncludeExcludeTarget | actual_target_ |
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CVTermList | actual_validation_ |
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TargetedExperiment::Interpretation | actual_interpretation_ |
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std::vector< ReactionMonitoringTransition::Product > | actual_intermediate_products_ |
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ReactionMonitoringTransition::Product | actual_product_ |
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ReactionMonitoringTransition::Configuration | actual_configuration_ |
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SourceFile | actual_sourcefile_ |
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| TraMLHandler (const TargetedExperiment &exp, const String &filename, const String &version, const ProgressLogger &logger) |
| Constructor for a write-only handler. More...
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| TraMLHandler (TargetedExperiment &exp, const String &filename, const String &version, const ProgressLogger &logger) |
| Constructor for a read-only handler. More...
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| ~TraMLHandler () override |
| Destructor. 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 | writeTo (std::ostream &os) override |
| Writes the contents to a stream. More...
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void | handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const CVTerm &cv_term) |
| Handles CV terms. More...
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void | handleUserParam_ (const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value) |
| Handles user terms. More...
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void | writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent) const |
| Writes user terms. More...
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void | writeUserParams_ (std::ostream &os, const std::vector< MetaInfoInterface > &meta, UInt indent) const |
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void | writeCVParams_ (std::ostream &os, const CVTermList &cv_terms, UInt indent) const |
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void | writeCVParams_ (std::ostream &os, const CVTermListInterface &cv_terms, UInt indent) const |
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void | writeCVList_ (std::ostream &os, const std::map< String, std::vector< CVTerm >> &cv_terms, UInt indent) const |
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void | writeTarget_ (std::ostream &os, const std::vector< IncludeExcludeTarget >::const_iterator &it) const |
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void | writeRetentionTime_ (std::ostream &os, const TargetedExperimentHelper::RetentionTime &rt) const |
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void | writeProduct_ (std::ostream &os, const std::vector< ReactionMonitoringTransition::Product >::const_iterator &prod_it) const |
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void | writeConfiguration_ (std::ostream &os, const std::vector< ReactionMonitoringTransition::Configuration >::const_iterator &cit) const |
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ControlledVocabulary::CVTerm | getChildWithName_ (const String &parent_accession, const String &name) const |
| Looks up a child CV term of parent_accession with the name name . If no such term is found, an empty term is returned. More...
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Static Public Member Functions inherited from XMLHandler |
static String | writeXMLEscape (const String &to_escape) |
| Escapes a string and returns the escaped string. More...
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static DataValue | fromXSDString (const String &type, const String &value) |
| Convert an XSD type (e.g. 'xsd:double') to a DataValue. 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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Protected Attributes inherited from XMLHandler |
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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LOADDETAIL | load_detail_ |
| parse only until total number of scans and chroms have been determined from attributes 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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XML handler for TraMLFile.
- Note
- Do not use this class. It is only needed in TraMLFile.