OpenMS  2.4.0
QuantitativeExperimentalDesign.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Immanuel Luhn$
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34 
35 #pragma once
36 
39 #include <OpenMS/FORMAT/TextFile.h>
42 
43 //#include <vector>
44 
45 namespace OpenMS
46 {
56  class OPENMS_DLLAPI QuantitativeExperimentalDesign :
57  public DefaultParamHandler
58  {
59 public:
60 
63 
64  //Destructor
66 
72  void applyDesign2Resolver(ProteinResolver & resolver, TextFile & file, StringList & fileNames);
73 
79  void applyDesign2Quantifier(PeptideAndProteinQuant & quantifier, TextFile & file, StringList & fileNames);
80  //std::vector< std::pair<PeptideAndProteinQuant::PeptideData,PeptideAndProteinQuant::ProteinQuant> >& result);
81 
82 private:
85 
88 
89  void mergeFeatureMaps_(FeatureMap & map, const String & experiment, StringList & file_paths);
90 
91  void mergeConsensusMaps_(ConsensusMap & map, const String & experiment, StringList & file_paths);
92 
93  void mergeIDFiles_(std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides, const String & experiment, StringList & file_paths);
94 
95  void findRelevantFilePaths_(std::map<String, StringList> & design2FileBaseName, std::map<String, StringList> & design2FilePath, StringList & filePaths);
96 
98  void analyzeHeader_(UInt & expCol, UInt & fileCol, StringList & header);
99 
101  void getSeparator_(String & separator);
102 
104  void mapFiles2Design_(std::map<String, StringList> & experiments, TextFile & file);
105 
106 
107  };
108 
109 } // namespace OpenMS
110 
A more convenient string class.
Definition: String.h:57
Merge files according to experimental design.
Definition: QuantitativeExperimentalDesign.h:56
A container for features.
Definition: FeatureMap.h:93
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
A container for consensus elements.
Definition: ConsensusMap.h:75
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Helper class for peptide and protein quantification based on feature data annotated with IDs...
Definition: ProteinResolver.h:56
Helper class for peptide and protein quantification based on feature data annotated with IDs...
Definition: PeptideAndProteinQuant.h:52
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46