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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Stephan Aiche $
// $Authors: Andreas Bertsch, Marc Sturm, Stephan Aiche $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_FILETYPES_H
#define OPENMS_FORMAT_FILETYPES_H
#include <OpenMS/config.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <string>
#include <map>
namespace OpenMS
{
/**
@brief 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).
@ingroup FileIO
*/
struct OPENMS_DLLAPI FileTypes
{
//NOTE: if you change/add something here, do not forget to change FileTyoes::initializeMap_
///Actual file types enum.
enum Type
{
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, ///< Tranformation description file (.trafoXML)
MZML, ///< MzML file (.mzML)
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, ///< mzQualityML (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, ///< msInspect file (.tsv)
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
SIZE_OF_TYPE ///< No file type. Simply stores the number of types
};
/// Returns the name/extension of the type.
static String typeToName(Type type);
/// Returns the mzML name (TODO: switch to accession since they are more stable!)
static String typeToMZML(Type type);
/// Converts a file type name into a Type
static Type nameToType(const String& name);
private:
/// Maps the FileType::Type to the preferred extension.
static const std::map<Type, String> name_of_types_;
/// Maps the FileType::Type to the preferred mzML CV name.
static const std::map<Type, String> name_of_MZMLtypes_;
/// Initializer for the file extension map.
static std::map<Type, String> initializeMap_();
/// Initializer for the file extension map.
static std::map<Type, String> initializeMZMLMap_();
};
} //namespace OpenMS
#endif //OPENMS_FORMAT_FILETYPES_H
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