OpenMS
2.5.0
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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... | |
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).
enum Type |
Actual file types enum.
Enumerator | |
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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. |
Initializer for the file extension map.
Initializer for the file extension map.
Converts a file type name into a Type.
Referenced by TOPPXFDR::loadInputFile_().
Returns the mzML name (TODO: switch to accession since they are more stable!)
Returns the name/extension of the type.
Referenced by TOPPViewBase::addDataFile(), and InspectOutfile::getExperiment().
Maps the FileType::Type to the preferred mzML CV name.