OpenMS
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 
74 private:
77 
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 
A container for consensus elements.
Definition: ConsensusMap.h:92
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Helper class for peptide and protein quantification based on feature data annotated with IDs.
Definition: ProteinResolver.h:56
Merge files according to experimental design.
Definition: QuantitativeExperimentalDesign.h:58
void applyDesign2Resolver(ProteinResolver &resolver, TextFile &file, StringList &fileNames)
xxxxxxx
void findRelevantFilePaths_(std::map< String, StringList > &design2FileBaseName, std::map< String, StringList > &design2FilePath, StringList &filePaths)
void mapFiles2Design_(std::map< String, StringList > &experiments, TextFile &file)
helper class. which file name belongs to which experimental setting
void mergeConsensusMaps_(ConsensusMap &map, const String &experiment, StringList &file_paths)
QuantitativeExperimentalDesign & operator=(const QuantitativeExperimentalDesign &)
Not implemented.
void analyzeHeader_(UInt &expCol, UInt &fileCol, StringList &header)
Analyze header, which column represents filename and experimental setting.
QuantitativeExperimentalDesign(const QuantitativeExperimentalDesign &)
Not implemented.
void mergeIDFiles_(std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment, StringList &file_paths)
QuantitativeExperimentalDesign()
Default constructor.
void getSeparator_(String &separator)
Helper class to get separator of the experimental design text file.
A more convenient string class.
Definition: String.h:60
This class provides some basic file handling methods for text files.
Definition: TextFile.h:47
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48