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SuffixArrayPeptideFinder.h
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31 // $Maintainer: Clemens Groepl,Andreas Bertsch$
32 // $Authors: Chris Bauer $
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34 
35 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
36 #define OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
37 
40 
41 #include <OpenMS/CONCEPT/Types.h>
43 #include <OpenMS/OpenMSConfig.h>
44 
45 #include <vector>
46 
47 namespace OpenMS
48 {
49  class SuffixArray;
50 
54  class OPENMS_DLLAPI SuffixArrayPeptideFinder :
55  public WeightWrapper
56  {
57  //@deprecated Deprecated in OpenMS 2.0 - only used by PILISIdentification (experimental TOPP tool)
58 public:
59 
63  typedef std::pair<String, String> FASTAEntry;
64 
74  SuffixArrayPeptideFinder(const String& filename, const String& method, const WeightWrapper::WEIGHTMODE weight_mode = WeightWrapper::MONO);
75 
80 
84  virtual ~SuffixArrayPeptideFinder();
85 
94  void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > >& candidates, const std::vector<double>& spec);
95 
106  void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > >& candidates, const String& DTA_file);
107 
112  void setTolerance(const double t);
113 
118  double getTolerance() const;
119 
124  void setNumberOfModifications(Size number_of_mods) const;
125 
130  Size getNumberOfModifications() const;
131 
137  void setTags(const std::vector<String>& tags);
138 
143  const std::vector<String>& getTags();
144 
149  void setUseTags(bool use_tags);
150 
155  bool getUseTags();
156 
162  void setModificationOutputMethod(const String& s);
163 
168  String getModificationOutputMethod();
169 
170 protected:
171 
172  String vToString_(std::vector<String> v);
173 
175 
177 
179 
180  };
181 
182 }
183 
184 #endif //OPENMS_EXAMPLES_SuffixArrayPeptideFinder_H
A more convenient string class.
Definition: String.h:57
String modification_output_method_
output method for modifications
Definition: SuffixArrayPeptideFinder.h:178
concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by defau...
Definition: BigString.h:52
std::pair< String, String > FASTAEntry
Definition: SuffixArrayPeptideFinder.h:63
BigString big_string_
bigString object holding all peptides of fasta file
Definition: SuffixArrayPeptideFinder.h:174
wrapper for easy use of sufArray
Definition: SuffixArrayPeptideFinder.h:54
SuffixArray * sa_
pointer to suffixarray
Definition: SuffixArrayPeptideFinder.h:176
WEIGHTMODE
Definition: WeightWrapper.h:55
Definition: WeightWrapper.h:55
Encapsulated weight queries to simplify mono vs average weight computation.
Definition: WeightWrapper.h:50
abstract class for suffix array
Definition: SuffixArray.h:50

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:42 using doxygen 1.8.5