OpenMS
MzMLValidator Class Reference

Semantically validates MzXML files. More...

#include <OpenMS/FORMAT/VALIDATORS/MzMLValidator.h>

Inheritance diagram for MzMLValidator:
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Collaboration diagram for MzMLValidator:
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Public Member Functions

 MzMLValidator (const CVMappings &mapping, const ControlledVocabulary &cv)
 Constructor. More...
 
 ~MzMLValidator () override
 Destructor. More...
 
- Public Member Functions inherited from SemanticValidator
 SemanticValidator (const CVMappings &mapping, const ControlledVocabulary &cv)
 Constructor. More...
 
 ~SemanticValidator () override
 Destructor. More...
 
bool validate (const String &filename, StringList &errors, StringList &warnings)
 Semantically validates an XML file. More...
 
bool locateTerm (const String &path, const CVTerm &parsed_term) const
 Checks if a CVTerm is allowed in a given path. More...
 
void setTag (const String &tag)
 Sets the CV parameter tag name (default: 'cvParam') More...
 
void setAccessionAttribute (const String &accession)
 Sets the name of the attribute for accessions in the CV parameter tag name (default: 'accession') More...
 
void setNameAttribute (const String &name)
 Sets the name of the attribute for accessions in the CV parameter tag name (default: 'name') More...
 
void setValueAttribute (const String &value)
 Sets the name of the attribute for accessions in the CV parameter tag name (default: 'value') More...
 
void setCheckTermValueTypes (bool check)
 Set if CV term value types should be check (enabled by default) More...
 
void setCheckUnits (bool check)
 Set if CV term units should be check (disabled by default) More...
 
void setUnitAccessionAttribute (const String &accession)
 Sets the name of the unit accession attribute (default: 'unitAccession') More...
 
void setUnitNameAttribute (const String &name)
 Sets the name of the unit name attribute (default: 'unitName') More...
 
- Public Member Functions inherited from XMLFile
 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)
 Checks if a file validates against the XML schema. More...
 
const StringgetVersion () const
 return the version of the schema More...
 

Protected Member Functions

void startElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
 
String getPath_ (UInt remove_from_end=0) const override
 Returns the current element path. More...
 
void handleTerm_ (const String &path, const CVTerm &parsed_term) override
 Handling of the term. More...
 
- Protected Member Functions inherited from SemanticValidator
void startElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
 
void endElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
 
void characters (const XMLCh *const chars, const XMLSize_t) override
 
virtual void getCVTerm_ (const xercesc::Attributes &attributes, CVTerm &parsed_term)
 Parses the CV term accession (required), name (required) and value (optional) from the XML attributes. More...
 
- 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...
 
Int asInt_ (const String &in) const
 Conversion of a String to an integer value. More...
 
Int asInt_ (const XMLCh *in) const
 Conversion of a Xerces string to an integer value. More...
 
UInt asUInt_ (const String &in) const
 Conversion of a String to an unsigned integer value. More...
 
double asDouble_ (const String &in) const
 Conversion of a String to a double value. More...
 
float asFloat_ (const String &in) const
 Conversion of a String to a float value. More...
 
bool asBool_ (const String &in) const
 Conversion of a string to a boolean value. More...
 
DateTime asDateTime_ (String date_string) const
 Conversion of a xs:datetime string to a DateTime value. More...
 
bool equal_ (const XMLCh *a, const XMLCh *b) const
 Returns if two Xerces strings are equal. More...
 
SignedSize cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)
 
String attributeAsString_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a String. More...
 
Int attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a Int. More...
 
double attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a double. More...
 
DoubleList attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a DoubleList. More...
 
IntList attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to an IntList. More...
 
StringList attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to an StringList. More...
 
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...
 
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...
 
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...
 
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...
 
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...
 
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...
 
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...
 
String attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a String. More...
 
Int attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a Int. More...
 
double attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a double. More...
 
DoubleList attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a DoubleList. More...
 
IntList attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a IntList. More...
 
StringList attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a StringList. More...
 
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_ (double &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the double 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...
 
 XMLHandler (const String &filename, const String &version)
 Default constructor. More...
 
 ~XMLHandler () override
 Destructor. More...
 
void reset ()
 Release internal memory used for parsing (call. More...
 
void fatalError (const xercesc::SAXParseException &exception) override
 
void error (const xercesc::SAXParseException &exception) override
 
void warning (const xercesc::SAXParseException &exception) override
 
void fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Fatal error handler. Throws a ParseError exception. More...
 
void error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Error handler for recoverable errors. More...
 
void warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
 Warning handler. More...
 
void characters (const XMLCh *const chars, const XMLSize_t length) override
 Parsing method for character data. More...
 
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...
 
void endElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname) override
 Parsing method for closing tags. More...
 
virtual void writeTo (std::ostream &)
 Writes the contents to a stream. More...
 
virtual LOADDETAIL getLoadDetail () const
 handler which support partial loading, implement this method More...
 
virtual void setLoadDetail (const LOADDETAIL d)
 handler which support partial loading, implement this method More...
 
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...
 
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...
 
void checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const
 
- Protected Member Functions inherited from XMLFile
void parse_ (const String &filename, XMLHandler *handler)
 Parses the XML file given by filename using the handler given by handler. More...
 
void parseBuffer_ (const std::string &buffer, XMLHandler *handler)
 Parses the in-memory buffer given by buffer using the handler given by handler. More...
 
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)
 Checks if a file validates against the XML schema. More...
 
const StringgetVersion () const
 return the version of the schema More...
 

Protected Attributes

std::map< String, std::vector< CVTerm > > param_groups_
 CV terms which can have a value (term => value type) More...
 
String current_id_
 Current referenceableParamGroup identifier. More...
 
String binary_data_array_
 Binary data array name. More...
 
String binary_data_type_
 Binary data array type. More...
 
- Protected Attributes inherited from SemanticValidator
const CVMappingsmapping_
 Reference to the mappings. More...
 
const ControlledVocabularycv_
 Reference to the CVs. More...
 
StringList errors_
 Validation errors. More...
 
StringList warnings_
 Validation warnings. More...
 
StringList open_tags_
 List of open tags. More...
 
std::map< String, std::vector< CVMappingRule > > rules_
 Rules (location => rule) More...
 
std::map< String, std::map< String, std::map< String, UInt > > > fulfilled_
 
String cv_tag_
 
String accession_att_
 
String name_att_
 
String value_att_
 
String unit_accession_att_
 
String unit_name_att_
 
bool check_term_value_types_
 
bool check_units_
 
- Protected Attributes inherited from XMLHandler
String file_
 File name. More...
 
String version_
 Schema version. More...
 
StringManager sm_
 Helper class for string conversion. More...
 
std::vector< Stringopen_tags_
 Stack of open XML tags. More...
 
LOADDETAIL load_detail_
 parse only until total number of scans and chroms have been determined from attributes More...
 
std::vector< std::vector< String > > cv_terms_
 Array of CV term lists (one sublist denotes one term and it's children) More...
 
- Protected Attributes inherited from XMLFile
String schema_location_
 XML schema file location. More...
 
String schema_version_
 Version string. More...
 
String enforced_encoding_
 Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...
 

Private Member Functions

 MzMLValidator ()
 Not implemented. More...
 
 MzMLValidator (const MzMLValidator &rhs)
 Not implemented. More...
 
MzMLValidatoroperator= (const MzMLValidator &rhs)
 Not implemented. More...
 

Additional Inherited Members

- Protected Types inherited from XMLHandler
enum  ActionMode { LOAD , STORE }
 Action to set the current mode (for error messages) More...
 
enum  LOADDETAIL { LD_ALLDATA , LD_RAWCOUNTS , LD_COUNTS_WITHOPTIONS }
 
- Static Protected Member Functions inherited from XMLHandler
static String writeXMLEscape (const String &to_escape)
 Escapes a string and returns the escaped string. More...
 
static DataValue fromXSDString (const String &type, const String &value)
 Convert an XSD type (e.g. 'xsd:double') to a DataValue. More...
 

Detailed Description

Semantically validates MzXML files.

Constructor & Destructor Documentation

◆ MzMLValidator() [1/3]

MzMLValidator ( const CVMappings mapping,
const ControlledVocabulary cv 
)

Constructor.

Parameters
mappingThe mapping rules
cvAll controlled vocabularies required for the mapping

◆ ~MzMLValidator()

~MzMLValidator ( )
override

Destructor.

◆ MzMLValidator() [2/3]

MzMLValidator ( )
private

Not implemented.

◆ MzMLValidator() [3/3]

MzMLValidator ( const MzMLValidator rhs)
private

Not implemented.

Member Function Documentation

◆ getPath_()

String getPath_ ( UInt  remove_from_end = 0) const
overrideprotectedvirtual

Returns the current element path.

Reimplemented from SemanticValidator.

◆ handleTerm_()

void handleTerm_ ( const String path,
const CVTerm parsed_term 
)
overrideprotectedvirtual

Handling of the term.

Reimplemented from SemanticValidator.

◆ operator=()

MzMLValidator& operator= ( const MzMLValidator rhs)
private

Not implemented.

◆ startElement()

void startElement ( const XMLCh * const  ,
const XMLCh * const  ,
const XMLCh *const  qname,
const xercesc::Attributes &  attributes 
)
overrideprotected

Member Data Documentation

◆ binary_data_array_

String binary_data_array_
protected

Binary data array name.

◆ binary_data_type_

String binary_data_type_
protected

Binary data array type.

◆ current_id_

String current_id_
protected

Current referenceableParamGroup identifier.

◆ param_groups_

std::map<String, std::vector<CVTerm> > param_groups_
protected

CV terms which can have a value (term => value type)