| OpenMS 2.5.0

QuantitativeExperimentalDesign.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
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16 // For a full list of authors, refer to the file AUTHORS.
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Immanuel Luhn$
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/METADATA/PeptideIdentification.h>
39 #include <OpenMS/FORMAT/TextFile.h>
40 #include <OpenMS/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.h>
41 #include <OpenMS/ANALYSIS/QUANTITATION/ProteinResolver.h>
42
43 //#include <vector>
44
45 namespace OpenMS
46 {
56 class OPENMS_DLLAPI QuantitativeExperimentalDesign :
57 public DefaultParamHandler
58 {
59 public:
60
62 QuantitativeExperimentalDesign();
63
64 //Destructor
65 ~QuantitativeExperimentalDesign() override;
66
72 void applyDesign2Resolver(ProteinResolver & resolver, TextFile & file, StringList & fileNames);
73
74 private:
76 QuantitativeExperimentalDesign(const QuantitativeExperimentalDesign &);
77
79 QuantitativeExperimentalDesign & operator=(const QuantitativeExperimentalDesign &);
80
81 void mergeConsensusMaps_(ConsensusMap & map, const String & experiment, StringList & file_paths);
82
83 void mergeIDFiles_(std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides, const String & experiment, StringList & file_paths);
84
85 void findRelevantFilePaths_(std::map<String, StringList> & design2FileBaseName, std::map<String, StringList> & design2FilePath, StringList & filePaths);
86
88 void analyzeHeader_(UInt & expCol, UInt & fileCol, StringList & header);
89
91 void getSeparator_(String & separator);
92
94 void mapFiles2Design_(std::map<String, StringList> & experiments, TextFile & file);
95
96
97 };
98
99 } // namespace OpenMS
100
OpenMS::String
A more convenient string class.
Definition: String.h:58
PeptideAndProteinQuant.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::QuantitativeExperimentalDesign
Merge files according to experimental design.
Definition: QuantitativeExperimentalDesign.h:56
OpenMS::ProteinResolver
Helper class for peptide and protein quantification based on feature data annotated with IDs...
Definition: ProteinResolver.h:56
TextFile.h
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DefaultParamHandler.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
ProteinResolver.h