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QuantitativeExperimentalDesign.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Immanuel Luhn$
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34 
35 #ifndef OPENMS_ANALYSIS_QUANTITATION_QUANTITATIVEEXPERIMENTALDESIGN_H
36 #define OPENMS_ANALYSIS_QUANTITATION_QUANTITATIVEEXPERIMENTALDESIGN_H
37 
40 #include <OpenMS/FORMAT/TextFile.h>
43 
44 //#include <vector>
45 
46 namespace OpenMS
47 {
57  class OPENMS_DLLAPI QuantitativeExperimentalDesign :
58  public DefaultParamHandler
59  {
60 public:
61 
64 
65  //Destructor
67 
73  void applyDesign2Resolver(ProteinResolver & resolver, TextFile & file, StringList & fileNames);
74 
80  void applyDesign2Quantifier(PeptideAndProteinQuant & quantifier, TextFile & file, StringList & fileNames);
81  //std::vector< std::pair<PeptideAndProteinQuant::PeptideData,PeptideAndProteinQuant::ProteinQuant> >& result);
82 
83 private:
86 
89 
90  void mergeFeatureMaps_(FeatureMap & map, const String & experiment, StringList & file_paths);
91 
92  void mergeConsensusMaps_(ConsensusMap & map, const String & experiment, StringList & file_paths);
93 
94  void mergeIDFiles_(std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides, const String & experiment, StringList & file_paths);
95 
96  void findRelevantFilePaths_(std::map<String, StringList> & design2FileBaseName, std::map<String, StringList> & design2FilePath, StringList & filePaths);
97 
99  void analyzeHeader_(UInt & expCol, UInt & fileCol, StringList & header);
100 
102  void getSeparator_(String & separator);
103 
105  void mapFiles2Design_(std::map<String, StringList> & experiments, TextFile & file);
106 
107 
108  };
109 
110 } // namespace OpenMS
111 
112 #endif // OPENMS_ANALYSIS_QUANTITATION_QUANTITATIVEEXPERIMENTALDESIGN_H
A more convenient string class.
Definition: String.h:57
Merge files according to experimental design.
Definition: QuantitativeExperimentalDesign.h:57
A container for features.
Definition: FeatureMap.h:94
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
A container for consensus elements.
Definition: ConsensusMap.h:72
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Helper class for peptide and protein quantification based on feature data annotated with IDs...
Definition: ProteinResolver.h:59
Helper class for peptide and protein quantification based on feature data annotated with IDs...
Definition: PeptideAndProteinQuant.h:53
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
This class provides some basic file handling methods for text files.
Definition: TextFile.h:47

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13