OpenMS
MascotXMLFile.h
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1 // Copyright (c) 2002-2023, 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: Nico Pfeifer $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
12 #include <OpenMS/FORMAT/XMLFile.h>
17 
18 
19 namespace OpenMS
20 {
21  class ProteinIdentification;
22 
31  class OPENMS_DLLAPI MascotXMLFile :
32  public Internal::XMLFile
33  {
34 public:
35 
38 
50  void load(const String& filename,
51  ProteinIdentification& protein_identification,
52  std::vector<PeptideIdentification>& id_data,
53  const SpectrumMetaDataLookup& lookup);
54 
67  void load(const String& filename,
68  ProteinIdentification& protein_identification,
69  std::vector<PeptideIdentification>& id_data,
70  std::map<String, std::vector<AASequence> >& peptides,
71  const SpectrumMetaDataLookup& lookup);
72 
80  static void initializeLookup(SpectrumMetaDataLookup& lookup, const PeakMap& experiment, const String& scan_regex = "");
81 
82  };
83 
84 } // namespace OpenMS
85 
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:23
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:46
Used to load Mascot XML files.
Definition: MascotXMLFile.h:33
void load(const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, std::map< String, std::vector< AASequence > > &peptides, const SpectrumMetaDataLookup &lookup)
Loads data from a Mascot XML file.
void load(const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, const SpectrumMetaDataLookup &lookup)
Loads data from a Mascot XML file.
MascotXMLFile()
Constructor.
static void initializeLookup(SpectrumMetaDataLookup &lookup, const PeakMap &experiment, const String &scan_regex="")
Initializes a helper object for looking up spectrum meta data (RT, m/z)
Representation of a protein identification run.
Definition: ProteinIdentification.h:50
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:117
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22