OpenMS
IBSpectraFile.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Stephan Aiche $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/config.h>
13 
14 // boost shared_ptr
15 #include <boost/shared_ptr.hpp>
16 
17 namespace OpenMS
18 {
19 
20  // forward declaration
21  class ConsensusMap;
22  class String;
23  class IsobaricQuantitationMethod;
24  class AASequence;
25 
30  class OPENMS_DLLAPI IBSpectraFile
31  {
32 public:
37 
42 
47 
56  void store(const String& filename, const ConsensusMap& cm);
57 private:
58 
64  boost::shared_ptr<IsobaricQuantitationMethod> guessExperimentType_(const ConsensusMap& cm);
65 
72 
79  String getModifString_(const AASequence& sequence);
80  };
81 
82 }
83 
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
A container for consensus elements.
Definition: ConsensusMap.h:66
Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantificatio...
Definition: IBSpectraFile.h:31
StringList constructHeader_(const IsobaricQuantitationMethod &quantMethod)
Constructs the matching file header for the given quantitation method.
boost::shared_ptr< IsobaricQuantitationMethod > guessExperimentType_(const ConsensusMap &cm)
Guesses the type of isobaric quantitation performed on the experiment.
IBSpectraFile()
Constructor.
IBSpectraFile & operator=(const IBSpectraFile &rhs)
Assignment operator.
String getModifString_(const AASequence &sequence)
Generates the modification string for the given AASequence.
void store(const String &filename, const ConsensusMap &cm)
Writes the contents of the ConsensusMap cm into the file named by filename.
IBSpectraFile(const IBSpectraFile &other)
Copy constructor.
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:32
A more convenient string class.
Definition: String.h:34
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19