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MzIdentMLHandler Class Reference

XML handler for MzIdentMLFile. More...

#include <OpenMS/FORMAT/HANDLERS/MzIdentMLHandler.h>

Inheritance diagram for MzIdentMLHandler:
XMLHandler

Public Member Functions

virtual void endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname)
 Parsing method for closing tags. More...
 
virtual void startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes)
 Parsing method for opening tags. More...
 
virtual void characters (const XMLCh *const chars, const XMLSize_t length)
 Parsing method for character data. More...
 
virtual void writeTo (std::ostream &os)
 Writes the contents to a stream. More...
 
Constructors and destructor
 MzIdentMLHandler (const Identification &id, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a write-only handler. More...
 
 MzIdentMLHandler (const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a write-only handler for internal identification structures. More...
 
 MzIdentMLHandler (Identification &id, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a read-only handler. More...
 
 MzIdentMLHandler (std::vector< ProteinIdentification > &pro_id, std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
 Constructor for a read-only handler for internal identification structures. More...
 
virtual ~MzIdentMLHandler ()
 Destructor. More...
 
- Public Member Functions inherited from XMLHandler
 XMLHandler (const String &filename, const String &version)
 Default constructor. More...
 
virtual ~XMLHandler ()
 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...
 
String errorString ()
 Returns the last error description. More...
 
void fatalError (const xercesc::SAXParseException &exception)
 
void error (const xercesc::SAXParseException &exception)
 
void warning (const xercesc::SAXParseException &exception)
 

Protected Member Functions

void handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const String &accession, const xercesc::Attributes &attributes, const String &cv_ref)
 Handles CV terms. More...
 
void handleUserParam_ (const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
 Handles user terms. More...
 
void writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
 Writes user terms. More...
 
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...
 
- Protected Member Functions inherited from XMLHandler
bool equal_ (const XMLCh *a, const XMLCh *b)
 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 DataTime value. More...
 
char * 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...
 
DoubleReal attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
 Converts an attribute to a DoubleReal. 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_ (DoubleReal &value, const xercesc::Attributes &a, const char *name) const
 Assigns the attribute content to the DoubleReal 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...
 
char * 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...
 
DoubleReal attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
 Converts an attribute to a DoubleReal. 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_ (DoubleReal &value, const xercesc::Attributes &a, const XMLCh *name) const
 Assigns the attribute content to the DoubleReal 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)
 

Protected Attributes

const ProgressLoggerlogger_
 Progress logger. More...
 
ControlledVocabulary cv_
 Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More...
 
ControlledVocabulary unimod_
 Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo) More...
 
String tag_
 XML tag parse element. More...
 
Identificationid_
 Identification Item. More...
 
std::vector
< ProteinIdentification > * 
pro_id_
 internal Identification Item for proteins More...
 
std::vector
< PeptideIdentification > * 
pep_id_
 Identification Item for peptides. More...
 
const Identificationcid_
 
const std::vector
< ProteinIdentification > * 
cpro_id_
 
const std::vector
< PeptideIdentification > * 
cpep_id_
 
SpectrumIdentification current_spectrum_id_
 SpectrumIdentification Item. More...
 
IdentificationHit current_id_hit_
 IdentificationHit Item. More...
 
- 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< Stringopen_tags_
 Stack of open XML tags. More...
 
std::vector< std::vector
< String > > 
cv_terms_
 Array of CV term lists (one sublist denotes one term and it's children) More...
 

Private Member Functions

 MzIdentMLHandler ()
 Helper method that writes a source file. More...
 
 MzIdentMLHandler (const MzIdentMLHandler &rhs)
 
MzIdentMLHandleroperator= (const MzIdentMLHandler &rhs)
 

Private Attributes

Map< String, AASequencepep_sequences_
 
AASequence actual_peptide_
 
Int current_mod_location_
 
ProteinHit actual_protein_
 

Additional Inherited Members

- Public Types inherited from XMLHandler
enum  ActionMode { LOAD, STORE }
 Action to set the current mode (for error messages) More...
 

Detailed Description

XML handler for MzIdentMLFile.

Note
Do not use this class. It is only needed in MzIdentMLFile.

Constructor & Destructor Documentation

MzIdentMLHandler ( const Identification id,
const String filename,
const String version,
const ProgressLogger logger 
)

Constructor for a write-only handler.

MzIdentMLHandler ( const std::vector< ProteinIdentification > &  pro_id,
const std::vector< PeptideIdentification > &  pep_id,
const String filename,
const String version,
const ProgressLogger logger 
)

Constructor for a write-only handler for internal identification structures.

MzIdentMLHandler ( Identification id,
const String filename,
const String version,
const ProgressLogger logger 
)

Constructor for a read-only handler.

MzIdentMLHandler ( std::vector< ProteinIdentification > &  pro_id,
std::vector< PeptideIdentification > &  pep_id,
const String filename,
const String version,
const ProgressLogger logger 
)

Constructor for a read-only handler for internal identification structures.

virtual ~MzIdentMLHandler ( )
virtual

Destructor.

MzIdentMLHandler ( )
private

Helper method that writes a source file.

MzIdentMLHandler ( const MzIdentMLHandler rhs)
private

Member Function Documentation

virtual void characters ( const XMLCh *const  chars,
const XMLSize_t  length 
)
virtual

Parsing method for character data.

Reimplemented from XMLHandler.

virtual void endElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const  qname 
)
virtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

ControlledVocabulary::CVTerm getChildWithName_ ( const String parent_accession,
const String name 
) const
protected

Looks up a child CV term of parent_accession with the name name. If no such term is found, an empty term is returned.

void handleCVParam_ ( const String parent_parent_tag,
const String parent_tag,
const String accession,
const xercesc::Attributes &  attributes,
const String cv_ref 
)
protected

Handles CV terms.

void handleUserParam_ ( const String parent_parent_tag,
const String parent_tag,
const String name,
const String type,
const String value 
)
protected

Handles user terms.

MzIdentMLHandler& operator= ( const MzIdentMLHandler rhs)
private
virtual void startElement ( const XMLCh *  uri,
const XMLCh *  localname,
const XMLCh *const  qname,
const xercesc::Attributes &  attrs 
)
virtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

virtual void writeTo ( std::ostream &  )
virtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

void writeUserParam_ ( std::ostream &  os,
const MetaInfoInterface meta,
UInt  indent 
) const
protected

Writes user terms.

Member Data Documentation

AASequence actual_peptide_
private
ProteinHit actual_protein_
private
const Identification* cid_
protected
const std::vector<PeptideIdentification>* cpep_id_
protected
const std::vector<ProteinIdentification>* cpro_id_
protected
IdentificationHit current_id_hit_
protected
Int current_mod_location_
private
SpectrumIdentification current_spectrum_id_
protected
ControlledVocabulary cv_
protected

Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)

Identification* id_
protected
const ProgressLogger& logger_
protected

Progress logger.

std::vector<PeptideIdentification>* pep_id_
protected

Identification Item for peptides.

Map<String, AASequence> pep_sequences_
private
std::vector<ProteinIdentification>* pro_id_
protected

internal Identification Item for proteins

String tag_
protected

XML tag parse element.

ControlledVocabulary unimod_
protected

Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:37 using doxygen 1.8.5