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SuffixArray.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_SUFFIXARRAY_H
37 #define OPENMS_DATASTRUCTURES_SUFFIXARRAY_H
38 
39 #include <vector>
41 
42 
43 namespace OpenMS
44 {
45  class String;
46 
51  class OPENMS_DLLAPI SuffixArray
52  {
53 
54 public:
55 
63  SuffixArray(const String & st, const String & filename);
64 
68  SuffixArray(const SuffixArray & sa);
69 
73  virtual ~SuffixArray() = 0;
74 
78  virtual String toString() = 0;
79 
88  virtual void findSpec(std::vector<std::vector<std::pair<std::pair<SignedSize, SignedSize>, DoubleReal> > > & candidates, const std::vector<DoubleReal> & spec) = 0;
89 
96  virtual bool save(const String & filename) = 0;
103  virtual bool open(const String & filename) = 0;
104 
110  virtual void setTolerance(DoubleReal t) = 0;
111 
116  virtual DoubleReal getTolerance() const = 0;
117 
124  virtual bool isDigestingEnd(const char aa1, const char aa2) const = 0;
125 
131  virtual void setTags(const std::vector<String> & tags) = 0;
132 
137  virtual const std::vector<String> & getTags() = 0;
138 
143  virtual void setUseTags(bool use_tags) = 0;
144 
149  virtual bool getUseTags() = 0;
150 
155  virtual void setNumberOfModifications(Size number_of_mods) = 0;
156 
161  virtual Size getNumberOfModifications() = 0;
162 
166  virtual void printStatistic() = 0;
167 
171  SuffixArray();
172 
173 
174  };
175 }
176 
177 #endif //OPENMS_DATASTRUCTURES_SUFARRAY_H
A more convenient string class.
Definition: String.h:56
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
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