| OpenMS 2.5.0

Public Types | Static Public Member Functions | Static Private Member Functions | Static Private Attributes | List of all members
FileTypes Struct Reference
Format » File IO

Centralizes the file types recognized by FileHandler. More...

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

## Public Types

enum | Type { UNKNOWN, DTA, DTA2D, MZDATA, MZXML, FEATUREXML, IDXML, CONSENSUSXML, MGF, INI, TOPPAS, TRANSFORMATIONXML, MZML, CACHEDMZML, MS2, PEPXML,
PROTXML, MZIDENTML, MZQUANTML, QCML,
GELML, TRAML, MSP, OMSSAXML,
MASCOTXML, PNG, XMASS, TSV,
MZTAB, PEPLIST, HARDKLOER, KROENIK,
FASTA, EDTA, CSV, TXT,
OBO, HTML, XML, ANALYSISXML,
XSD, PSQ, MRM, SQMASS,
PQP, MS, OSW, PSMS,
PIN, PARAMXML, SPLIB, NOVOR,
XQUESTXML, SPECXML, JSON, RAW,
EXE, SIZE_OF_TYPE
}
| Actual file types enum. More...

## Static Public Member Functions

static String | typeToName (Type type)
| Returns the name/extension of the type. More...
static String | typeToMZML (Type type)
| Returns the mzML name (TODO: switch to accession since they are more stable!) More...
static Type | nameToType (const String &name)
| Converts a file type name into a Type. More...

## Static Private Member Functions

static std::map< Type, String > | initializeMap_ ()
| Initializer for the file extension map. More...
static std::map< Type, String > | initializeMZMLMap_ ()
| Initializer for the file extension map. More...

## Static Private Attributes

static const std::map< Type, String > | name_of_types_
| Maps the FileType::Type to the preferred extension. More...
static const std::map< Type, String > | name_of_MZMLtypes_
| Maps the FileType::Type to the preferred mzML CV name. More...

## Detailed Description

Centralizes the file types recognized by FileHandler.

FileType separate from FileHandler to avoid circular inclusions by DocumentIdentifier, ExperimentalSettings and FileHandler and respective fileclasses (e.g. DTA2DFile).

## Member Enumeration Documentation

## ◆ Type

enum Type

Actual file types enum.

Enumerator
UNKNOWN | Unknown file extension.
DTA | DTA file (.dta)
DTA2D | DTA2D file (.dta2d)
MZDATA | MzData file (.mzData)
MZXML | MzXML file (.mzXML)
FEATUREXML | OpenMS feature file (.featureXML)
IDXML | OpenMS identification format (.idXML)
CONSENSUSXML | OpenMS consensus map format (.consensusXML)
MGF | Mascot Generic Format (.mgf)
INI | OpenMS parameters file (.ini)
TOPPAS | OpenMS parameters file with workflow information (.toppas)
TRANSFORMATIONXML | Transformation description file (.trafoXML)
MZML | MzML file (.mzML)
CACHEDMZML | CachedMzML file (.cachedmzML)
MS2 | MS2 file (.ms2)
PEPXML | TPP pepXML file (.pepXML)
PROTXML | TPP protXML file (.protXML)
MZIDENTML | mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
MZQUANTML | mzQuantML (HUPO PSI AnalysisXML followup format) (.mzq)
QCML | qcML (will undergo standardisation maybe) (.qcml)
GELML | GelML (HUPO PSI format) (.gelML)
TRAML | TraML (HUPO PSI format) for transitions (.traML)
MSP | NIST spectra library file format (.msp)
OMSSAXML | OMSSA XML file format for peptide identifications (.xml)
MASCOTXML | Mascot XML file format for peptide identifications (.xml)
PNG | Portable Network Graphics (.png)
XMASS | XMass Analysis file (fid)
TSV | any TSV file, for example msInspect file or OpenSWATH transition file (see TransitionTSVFile)
MZTAB | mzTab file (.mzTab)
PEPLIST | specArray file (.peplist)
HARDKLOER | hardkloer file (.hardkloer)
KROENIK | kroenik file (.kroenik)
FASTA | FASTA file (.fasta)
EDTA | enhanced comma separated files (RT, m/z, Intensity, [meta])
CSV | general comma separated files format (might also be tab or space separated!!!), data should be regular, i.e. matrix form
TXT | any text format, which has only loose definition of what it actually contains – thus it is usually hard to say where the file actually came from (e.g. PepNovo).
OBO | Controlled Vocabulary format.
HTML | any HTML format
XML | any XML format
ANALYSISXML | analysisXML format
XSD | XSD schema format.
PSQ | NCBI binary blast db.
MRM | SpectraST MRM List.
SQMASS | SqLite format for mass and chromatograms, see SqMassFile.
PQP | OpenSWATH Peptide Query Parameter (PQP) SQLite DB, see TransitionPQPFile.
MS | SIRIUS file format (.ms)
OSW | OpenSWATH OpenSWATH report (OSW) SQLite DB.
PSMS | Percolator tab-delimited output (PSM level)
PIN | Percolator tab-delimited input (PSM level)
PARAMXML | internal format for writing and reading parameters (also used as part of CTD)
SPLIB | SpectraST binary spectral library file (sptxt is the equivalent text-based format, similar to the MSP format)
NOVOR | Novor custom parameter file.
XQUESTXML | xQuest XML file format for protein-protein cross-link identifications (.xquest.xml)
SPECXML | xQuest XML file format for matched spectra for spectra visualization in the xQuest results manager (.spec.xml)
JSON | JavaScript Object Notation file (.json)
RAW | Thermo Raw File (.raw)
EXE | Executable (.exe)
SIZE_OF_TYPE | No file type. Simply stores the number of types.

## Member Function Documentation

## ◆ initializeMap_()

static std::map<Type, String> initializeMap_ | ( |  | ) |

static private

Initializer for the file extension map.

## ◆ initializeMZMLMap_()

static std::map<Type, String> initializeMZMLMap_ | ( |  | ) |

static private

Initializer for the file extension map.

## ◆ nameToType()

static Type nameToType | ( | const String & | name | ) |

static

Converts a file type name into a Type.

## ◆ typeToMZML()

static String typeToMZML | ( | Type | type | ) |

static

Returns the mzML name (TODO: switch to accession since they are more stable!)

## ◆ typeToName()

static String typeToName | ( | Type | type | ) |

static

Returns the name/extension of the type.

Referenced by TOPPViewBase::addDataFile(), and InspectOutfile::getExperiment().

## Member Data Documentation

## ◆ name_of_MZMLtypes_

const std::map<Type, String> name_of_MZMLtypes_

static private

Maps the FileType::Type to the preferred mzML CV name.

## ◆ name_of_types_

const std::map<Type, String> name_of_types_

static private

Maps the FileType::Type to the preferred extension.