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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 
36 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
37 #define OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
38 
39 #include <vector>
42 
43 namespace OpenMS
44 {
45  class String;
46  class SuffixArray;
50  class OPENMS_DLLAPI SuffixArrayPeptideFinder :
51  public WeightWrapper
52  {
53 
54 public:
55 
59  typedef std::pair<String, String> FASTAEntry;
60 
70  SuffixArrayPeptideFinder(const String & filename, const String & method, const WeightWrapper::WEIGHTMODE weight_mode = WeightWrapper::MONO);
71 
76 
80  virtual ~SuffixArrayPeptideFinder();
81 
90  void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > > & candidates, const std::vector<DoubleReal> & spec);
91 
102  void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > > & candidates, const String & DTA_file);
103 
108  void setTolerance(const DoubleReal t);
109 
114  DoubleReal getTolerance() const;
115 
120  void setNumberOfModifications(Size number_of_mods) const;
121 
126  Size getNumberOfModifications() const;
127 
133  void setTags(const std::vector<String> & tags);
134 
139  const std::vector<String> & getTags();
140 
145  void setUseTags(bool use_tags);
146 
151  bool getUseTags();
152 
158  void setModificationOutputMethod(const String & s);
159 
164  String getModificationOutputMethod();
165 
166 protected:
167 
168  String vToString_(std::vector<String> v);
169 
171 
173 
175 
176  };
177 
178 }
179 
180 #endif //OPENMS_EXAMPLES_SuffixArrayPeptideFinder_H
A more convenient string class.
Definition: String.h:56
String modification_output_method_
output method for modifications
Definition: SuffixArrayPeptideFinder.h:174
concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by defau...
Definition: BigString.h:50
std::pair< String, String > FASTAEntry
Definition: SuffixArrayPeptideFinder.h:59
BigString big_string_
bigString object holding all peptides of fasta file
Definition: SuffixArrayPeptideFinder.h:170
wrapper for easy use of sufArray
Definition: SuffixArrayPeptideFinder.h:50
SuffixArray * sa_
pointer to suffixarray
Definition: SuffixArrayPeptideFinder.h:172
WEIGHTMODE
Definition: WeightWrapper.h:55
Definition: WeightWrapper.h:55
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Encapsulated weight queries to simplify mono vs average weight computation.
Definition: WeightWrapper.h:50
abstract class for suffix array
Definition: SuffixArray.h:51

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:21 using doxygen 1.8.5