| OpenMS 2.5.0

Public Member Functions | List of all members
MzQuantMLFile Class Reference
Format » File IO

File adapter for MzQuantML files. More...

`#include <OpenMS/FORMAT/MzQuantMLFile.h>`

Inheritance diagram for MzQuantMLFile:

## Public Member Functions

| MzQuantMLFile ()
| Default constructor. More...
| ~MzQuantMLFile () override
| Destructor. More...
void | load (const String &filename, MSQuantifications &msq)
| Loads a map from a MzQuantML file. More...
void | store (const String &filename, const MSQuantifications &cmsq) const
| Stores a map in a MzQuantML 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 String & | getVersion () const
| return the version of the schema More...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (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 () const
| Ends the progress display. More...
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_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

File adapter for MzQuantML files.

If a critical error occurs due to the missing functionality, Exception::NotImplemented is thrown.

## Constructor & Destructor Documentation

## ◆ MzQuantMLFile()

MzQuantMLFile | ( |  | ) |

Default constructor.

## ◆ ~MzQuantMLFile()

~MzQuantMLFile | ( |  | ) |

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

  filename | File name of the file to be checked.
  errors | Errors during the validation are returned in this output parameter.
  warnings | Warnings during the validation are returned in this output parameter.

Exceptions

  Exception::FileNotFound | is thrown if the file could not be opened

## ◆ load()

void load | ( | const String & | filename,
|  | MSQuantifications & | msq
| ) |  |

Loads a map from a MzQuantML file.

Exceptions

  Exception::FileNotFound | is thrown if the file could not be opened
  Exception::ParseError | is thrown if an error occurs during parsing

## ◆ store()

void store | ( | const String & | filename,
|  | const MSQuantifications & | cmsq
| ) |  | const

Stores a map in a MzQuantML file.

Exceptions

  Exception::UnableToCreateFile | is thrown if the file could not be created