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MzIdentMLHandler Class Reference

XML STREAM 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 writeMetaInfos_ (String &s, 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...
 
void writeEnyzme_ (String &s, ProteinIdentification::DigestionEnzyme enzy, UInt miss, UInt indent) const
 Helper method that writes a source file. More...
 
void writeModParam_ (String &s, const std::vector< String > &fixed, const std::vector< String > &variable, UInt indent) const
 Helper method that writes the modification search params. 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 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...
 
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...
 
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...
 
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)
 

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 ()
 
 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...
 
- Static Public Member Functions inherited from XMLHandler
static String writeXMLEscape (const String &to_escape)
 Escapes a string and returns the escaped string. More...
 

Detailed Description

XML STREAM handler for MzIdentMLFile.

In read-mode, this class will parse an MzIdentML XML file and append the input identifications to the provided PeptideIdentifications and ProteinIdentifications.

Note
Do not use this class. It is only needed in MzIdentMLFile.
DOM and STREAM handler for MzIdentML have the same interface for legacy id structures.

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
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.

void writeEnyzme_ ( String s,
ProteinIdentification::DigestionEnzyme  enzy,
UInt  miss,
UInt  indent 
) const
protected

Helper method that writes a source file.

Helper method that writes the Enzymes

void writeMetaInfos_ ( String s,
const MetaInfoInterface meta,
UInt  indent 
) const
protected

Writes user terms.

void writeModParam_ ( String s,
const std::vector< String > &  fixed,
const std::vector< String > &  variable,
UInt  indent 
) const
protected

Helper method that writes the modification search params.

virtual void writeTo ( std::ostream &  )
virtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

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 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:42 using doxygen 1.8.9.1