| OpenMS 2.5.0

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

File adapter for HUPO PSI TraML files. More...

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

Inheritance diagram for TraMLFile:

## Public Member Functions

| TraMLFile ()
| Default constructor. More...
| ~TraMLFile () override
| Destructor. More...
void | load (const String &filename, TargetedExperiment &id)
| Loads a map from a TraML file. More...
void | store (const String &filename, const TargetedExperiment &id) const
| Stores a map in a TraML 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 HUPO PSI TraML files.

TraML files contain information about transitions used for targeted proteomics and metabolomics experiments:

Deutsch et al. "TraML--a standard format for exchange of selected reaction monitoring transition lists." Mol Cell Proteomics. 2012 Apr;11(4):R111.015040. doi: 10.1074/mcp.R111.015040.

In OpenMS, TraML files can be generated from TSV or CSV files using the TransitionTSVFile class or the TargetedFileConverter TOPP Tool. For more information on the TSV format required by the TOPP tool, see see also the documentation of TransitionTSVFile.

## Constructor & Destructor Documentation

## ◆ TraMLFile()

TraMLFile | ( |  | ) |

Default constructor.

## ◆ ~TraMLFile()

~TraMLFile | ( |  | ) |

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,
|  | TargetedExperiment & | id
| ) |  |

Loads a map from a TraML file.

Exceptions

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

Referenced by TOPPOpenSwathBase::loadTransitionList().

## ◆ store()

void store | ( | const String & | filename,
|  | const TargetedExperiment & | id
| ) |  | const

Stores a map in a TraML file.

Exceptions

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