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 ,   OMS , 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)
OMS	OpenMS database file.
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

name	A 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().