OpenMS  2.7.0
Classes | Public Types | Static Public Member Functions | List of all members
FileTypes Struct Reference

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

#include <OpenMS/FORMAT/FileTypes.h>

Classes

class  FileTypeList
 holds a vector of known file types, e.g. as a way to specify supported input formats More...
 

Public Types

enum  Type {
  UNKNOWN , DTA , DTA2D , MZDATA ,
  MZXML , FEATUREXML , IDXML , CONSENSUSXML ,
  MGF , INI , TOPPAS , TRANSFORMATIONXML ,
  MZML , CACHEDMZML , MS2 , PEPXML ,
  PROTXML , MZIDENTML , MZQUANTML , QCML ,
  MZQC , GELML , TRAML , MSP ,
  OMSSAXML , MASCOTXML , PNG , XMASS ,
  TSV , MZTAB , PEPLIST , HARDKLOER ,
  KROENIK , FASTA , EDTA , CSV ,
  TXT , OBO , HTML , ANALYSISXML ,
  XSD , PSQ , MRM , SQMASS ,
  PQP , MS , OSW , PSMS ,
  PIN , PARAMXML , SPLIB , NOVOR ,
  XQUESTXML , SPECXML , JSON , RAW ,
  EXE , XML , BZ2 , GZ ,
  SIZE_OF_TYPE
}
 Actual file types enum. More...
 
enum class  Filter { COMPACT , ONE_BY_ONE , BOTH }
 

Static Public Member Functions

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

◆ Filter

enum Filter
strong
Enumerator
COMPACT 

make a single item, e.g. 'all readable files (*.mzML *.mzXML);;'

ONE_BY_ONE 

list all types individually, e.g. 'mzML files (*.mzML);;mzXML files (*.mzXML);;'

BOTH 

combine COMPACT and ONE_BY_ONE

◆ 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)

MZQC 

mzQC (HUPO PSI format) (.mzQC)

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

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)

XML 

any XML format

BZ2 

any BZ2 compressed file

GZ 

any Gzipped file

SIZE_OF_TYPE 

No file type. Simply stores the number of types.

Member Function Documentation

◆ nameToType()

static Type nameToType ( const String name)
static

Converts a file type name into a Type

Parameters
nameA case-insensitive name (e.g. FASTA or Fasta, etc.)

◆ typeToDescription()

static String typeToDescription ( Type  type)
static

Returns the human-readable explanation of the type. This may or may not add information, e.g. MZML becomes "mzML raw data file", but FEATUREXML becomes "OpenMS feature map"

◆ 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().