OpenMS
MzIdentMLFile Class Reference

File adapter for MzIdentML files. More...

#include <OpenMS/FORMAT/MzIdentMLFile.h>

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

 MzIdentMLFile ()
 Default constructor. More...
 
 ~MzIdentMLFile () override
 Destructor. More...
 
void load (const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
 Loads the identifications from a MzIdentML file. More...
 
void store (const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
 Stores the identifications in a MzIdentML file. More...
 
void store (const String &filename, const Identification &id) const
 Stores the identifications in a MzIdentML file. More...
 
bool isSemanticallyValid (const String &filename, StringList &errors, StringList &warnings)
 Checks if a file is valid with respect to the mapping file and the controlled vocabulary. 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...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
virtual ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (const ProgressLogger &other)
 Assignment Operator. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress (UInt64 bytes_processed=0) const
 
void nextProgress () const
 increment progress by 1 (according to range begin-end) More...
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD , GUI , NONE }
 Possible log types. More...
 
- 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)
 
- Static Protected Member Functions inherited from ProgressLogger
static String logTypeToFactoryName_ (LogType type)
 Return the name of the factory product used for this log type. 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...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
time_t last_invoke_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

File adapter for MzIdentML files.

This file adapter exposes the internal MzIdentML processing capabilities to the library. The file adapter interface is kept the same as idXML file adapter for downward capability reasons. For now, read-in will be performed with DOM write-out with STREAM

Note
due to the limited capabilities of idXML/PeptideIdentification/ProteinIdentification not all MzIdentML features can be supported. Development for these structures will be discontinued, a new interface with appropriate structures will be provided.
If a critical error occurs due to the missing functionality, Exception::NotImplemented is thrown.
All PSM will be read into PeptideIdentification, even the passThreshold=false, threshold will be read into ProteinIdentification (i.e. one id run), considered at writing also will only be the threshold set in ProteinIdentification
All PSM will be read into PeptideIdentification, even the passThreshold=false

Constructor & Destructor Documentation

◆ MzIdentMLFile()

Default constructor.

◆ ~MzIdentMLFile()

~MzIdentMLFile ( )
override

Destructor.

Member Function Documentation

◆ isSemanticallyValid()

bool isSemanticallyValid ( const String filename,
StringList errors,
StringList warnings 
)

Checks if a file is valid with respect to the mapping file and the controlled vocabulary.

Parameters
filenameFile name of the file to be checked.
errorsErrors during the validation are returned in this output parameter.
warningsWarnings during the validation are returned in this output parameter.
Exceptions
Exception::FileNotFoundis thrown if the file could not be opened

◆ load()

void load ( const String filename,
std::vector< ProteinIdentification > &  poid,
std::vector< PeptideIdentification > &  peid 
)

Loads the identifications from a MzIdentML file.

Exceptions
Exception::FileNotFoundis thrown if the file could not be opened
Exception::ParseErroris thrown if an error occurs during parsing

Referenced by TOPPViewBase::addDataFile().

◆ store() [1/2]

void store ( const String filename,
const Identification id 
) const

Stores the identifications in a MzIdentML file.

Exceptions
Exception::UnableToCreateFileis thrown if the file could not be created

◆ store() [2/2]

void store ( const String filename,
const std::vector< ProteinIdentification > &  poid,
const std::vector< PeptideIdentification > &  peid 
) const

Stores the identifications in a MzIdentML file.

Exceptions
Exception::UnableToCreateFileis thrown if the file could not be created