OpenMS  2.5.0
MultiplexDeltaMassesGenerator.h
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31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
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34 
35 #pragma once
36 
42 
43 #include <vector>
44 #include <algorithm>
45 #include <iostream>
46 #include <ostream>
47 
48 
49 namespace OpenMS
50 {
61  class OPENMS_DLLAPI MultiplexDeltaMassesGenerator :
62  public DefaultParamHandler
63  {
64  public:
65 
69  struct OPENMS_DLLAPI Label
70  {
74  double delta_mass;
75 
76  Label(String sn, String ln, String d, double dm);
77  };
78 
83 
93  MultiplexDeltaMassesGenerator(String labels, int missed_cleavages, std::map<String,double> label_mass_shift);
94 
99  void generateKnockoutDeltaMasses();
100 
108  void printSamplesLabelsList(std::ostream &stream) const;
109 
122  void printDeltaMassesList(std::ostream &stream) const;
123 
129  std::vector<MultiplexDeltaMasses> getDeltaMassesList();
130 
134  const std::vector<MultiplexDeltaMasses>& getDeltaMassesList() const;
135 
143  std::vector<std::vector<String> > getSamplesLabelsList();
144 
152  const std::vector<std::vector<String> >& getSamplesLabelsList() const;
153 
159  String getLabelShort(String label);
160 
166  String getLabelLong(String label);
167 
176  MultiplexDeltaMasses::LabelSet extractLabelSet(AASequence sequence);
177 
178  private:
179 
184 
188  std::vector<String> labels_list_;
189 
193  std::vector<std::vector<String> > samples_labels_;
194 
199 
203  std::vector<MultiplexDeltaMasses> delta_masses_list_;
204 
208  std::vector<Label> label_master_list_;
209 
214  std::map<String, double> label_delta_mass_;
215 
220  std::map<String, String> label_short_long_;
221 
226  std::map<String, String> label_long_short_;
227 
231  void fillLabelMasterList_();
232  };
233 
234 }
235 
DefaultParamHandler.h
OpenMS::MultiplexDeltaMassesGenerator::Label::long_name
String long_name
Definition: MultiplexDeltaMassesGenerator.h:72
OpenMS::MultiplexDeltaMassesGenerator::Label::short_name
String short_name
Definition: MultiplexDeltaMassesGenerator.h:71
OpenMS::MultiplexDeltaMassesGenerator::labels_list_
std::vector< String > labels_list_
flat list of all occurring isotopic labels
Definition: MultiplexDeltaMassesGenerator.h:188
OpenMS::MultiplexDeltaMasses::LabelSet
std::multiset< String > LabelSet
set of labels associated with a mass shift
Definition: MultiplexDeltaMasses.h:73
OpenMS::MultiplexDeltaMassesGenerator::label_master_list_
std::vector< Label > label_master_list_
master list of all labels
Definition: MultiplexDeltaMassesGenerator.h:208
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MultiplexDeltaMassesGenerator::Label
complete label information
Definition: MultiplexDeltaMassesGenerator.h:69
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MultiplexDeltaMassesGenerator::label_long_short_
std::map< String, String > label_long_short_
mapping from a long label (as in PSI-MS name) to a short label (as in the user params) e....
Definition: MultiplexDeltaMassesGenerator.h:226
OpenMS::MultiplexDeltaMassesGenerator::labels_
String labels_
isotopic labels
Definition: MultiplexDeltaMassesGenerator.h:183
OpenMS::MultiplexDeltaMassesGenerator::missed_cleavages_
int missed_cleavages_
maximum number of missed cleavages
Definition: MultiplexDeltaMassesGenerator.h:198
OpenMS::MultiplexDeltaMassesGenerator::samples_labels_
std::vector< std::vector< String > > samples_labels_
list of samples with their corresponding labels
Definition: MultiplexDeltaMassesGenerator.h:193
OpenMS::MultiplexDeltaMassesGenerator::label_short_long_
std::map< String, String > label_short_long_
mapping from a short label (as in the user params) to a long label (as in PSI-MS name) e....
Definition: MultiplexDeltaMassesGenerator.h:220
MultiplexDeltaMasses.h
OpenMS::MultiplexDeltaMassesGenerator::Label::delta_mass
double delta_mass
Definition: MultiplexDeltaMassesGenerator.h:74
AASequence.h
OpenMS::MultiplexDeltaMassesGenerator::delta_masses_list_
std::vector< MultiplexDeltaMasses > delta_masses_list_
list of all possible mass shift patterns
Definition: MultiplexDeltaMassesGenerator.h:203
OpenMS::MultiplexDeltaMassesGenerator::Label::description
String description
Definition: MultiplexDeltaMassesGenerator.h:73
String.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::MultiplexDeltaMassesGenerator
generates complete list of all possible mass shifts due to isotopic labelling
Definition: MultiplexDeltaMassesGenerator.h:61
OpenMS::MultiplexDeltaMassesGenerator::label_delta_mass_
std::map< String, double > label_delta_mass_
mapping from single label to delta mass e.g. "Arg10" -> 10.0082686
Definition: MultiplexDeltaMassesGenerator.h:214
StandardTypes.h