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OpenMS
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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 , 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 | FileProperties { READABLE , WRITEABLE , PROVIDES_SPECTRUM , PROVIDES_EXPERIMENT , PROVIDES_FEATURES , PROVIDES_CONSENSUSFEATURES , PROVIDES_IDENTIFICATIONS , PROVIDES_TRANSITIONS , PROVIDES_QUANTIFICATIONS , PROVIDES_TRANSFORMATIONS , PROVIDES_QC , SIZE_OF_FILEPROPERTIES } |
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... | |
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).
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strong |
| 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. |
Converts a file type name into a Type
| name | A case-insensitive name (e.g. FASTA or Fasta, etc.) |
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"
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().
1.9.1 
