| OpenMS 2.5.0

Public Member Functions | Private Member Functions | List of all members
MzIdentMLValidator Class Reference

Semantically validates MzXML files. More...

`#include <OpenMS/FORMAT/VALIDATORS/MzIdentMLValidator.h>`

Inheritance diagram for MzIdentMLValidator:

## Public Member Functions

| MzIdentMLValidator (const CVMappings &mapping, const ControlledVocabulary &cv)
| Constructor. More...
| ~MzIdentMLValidator () 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 String & | getVersion () const
| return the version of the schema More...

## Private Member Functions

| MzIdentMLValidator ()
| Not implemented. More...
| MzIdentMLValidator (const MzIdentMLValidator &rhs)
| Not implemented. More...
MzIdentMLValidator & | operator= (const MzIdentMLValidator &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 }
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 String | getPath_ (UInt remove_from_end=0) const
| Returns the current element path. More...
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...
virtual void | handleTerm_ (const String &path, const CVTerm &parsed_term)
| Handling of the term. More...
Protected Member Functions inherited from XMLHandler
bool | equal_ (const XMLCh *a, const XMLCh *b) const
| Returns if two Xerces strings are equal. More...
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)
| Conversion of a String to an integer value. More...
Int | asInt_ (const XMLCh *in)
| Conversion of a Xerces string to an integer value. More...
UInt | asUInt_ (const String &in)
| Conversion of a String to an unsigned integer value. More...
double | asDouble_ (const String &in)
| Conversion of a String to a double value. More...
float | asFloat_ (const String &in)
| Conversion of a String to a float value. More...
bool | asBool_ (const String &in)
| Conversion of a string to a boolean value. More...
DateTime | asDateTime_ (String date_string)
| Conversion of a xs:datetime string to a DateTime value. More...
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...
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...
| ~XMLHandler () override
| Destructor. More...
void | reset ()
| Release internal memory used for parsing (call. More...
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...
String | errorString ()
| Returns the last error description. 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...
void | checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids)
void | fatalError (const xercesc::SAXParseException &exception) override
void | error (const xercesc::SAXParseException &exception) override
void | warning (const xercesc::SAXParseException &exception) override
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 String & | getVersion () const
| return the version of the schema More...
Static Protected Member Functions inherited from XMLHandler
static String | writeXMLEscape (const String &to_escape)
| Escapes a string and returns the escaped string. More...
Protected Attributes inherited from SemanticValidator
const CVMappings & | mapping_
| Reference to the mappings. More...
const ControlledVocabulary & | cv_
| Reference to the CVs. More...
StringList | errors_
| Validation errors. More...
StringList | warnings_
| Validation warnings. More...
StringList | open_tags_
| List of open tags. More...
Map< String, std::vector< CVMappingRule > > | rules_
| Rules (location => rule) More...
Map< String, Map< String, 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 | error_message_
| Error message of the last error. More...
String | file_
| File name. More...
String | version_
| Schema version. More...
StringManager | sm_
| Helper class for string conversion. More...
std::vector< String > | open_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...

## Detailed Description

Semantically validates MzXML files.

## Constructor & Destructor Documentation

## ◆ MzIdentMLValidator() [1/3]

MzIdentMLValidator | ( | const CVMappings & | mapping,
|  | const ControlledVocabulary & | cv
| ) |  |

Constructor.

Parameters

  mapping | The mapping rules
  cv | All controlled vocabularies required for the mapping

## ◆ ~MzIdentMLValidator()

~MzIdentMLValidator | ( |  | ) |

override

Destructor.

## ◆ MzIdentMLValidator() [2/3]

MzIdentMLValidator | ( |  | ) |

private

Not implemented.

## ◆ MzIdentMLValidator() [3/3]

MzIdentMLValidator | ( | const MzIdentMLValidator & | rhs | ) |

private

Not implemented.

## Member Function Documentation

## ◆ operator=()

MzIdentMLValidator& operator= | ( | const MzIdentMLValidator & | rhs | ) |

private

Not implemented.