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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 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAY_H
36 #define OPENMS_DATASTRUCTURES_SUFFIXARRAY_H
37 
38 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/OpenMSConfig.h>
40 
41 #include <vector>
42 
43 namespace OpenMS
44 {
45  class String;
46 
50  class OPENMS_DLLAPI SuffixArray
51  {
52 
53 public:
54 
62  SuffixArray(const String& st, const String& filename);
63 
67  SuffixArray(const SuffixArray& sa);
68 
72  virtual ~SuffixArray() = 0;
73 
77  virtual String toString() = 0;
78 
87  virtual void findSpec(std::vector<std::vector<std::pair<std::pair<SignedSize, SignedSize>, double> > >& candidates, const std::vector<double>& spec) = 0;
88 
95  virtual bool save(const String& filename) = 0;
102  virtual bool open(const String& filename) = 0;
103 
109  virtual void setTolerance(double t) = 0;
110 
115  virtual double getTolerance() const = 0;
116 
123  virtual bool isDigestingEnd(const char aa1, const char aa2) const = 0;
124 
130  virtual void setTags(const std::vector<String>& tags) = 0;
131 
136  virtual const std::vector<String>& getTags() = 0;
137 
142  virtual void setUseTags(bool use_tags) = 0;
143 
148  virtual bool getUseTags() = 0;
149 
154  virtual void setNumberOfModifications(Size number_of_mods) = 0;
155 
160  virtual Size getNumberOfModifications() = 0;
161 
165  virtual void printStatistic() = 0;
166 
170  SuffixArray();
171 
172 
173  };
174 }
175 
176 #endif //OPENMS_DATASTRUCTURES_SUFARRAY_H
A more convenient string class.
Definition: String.h:57
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
String toString(T i)
toString functions (single argument)
Definition: StringUtils.h:68
abstract class for suffix array
Definition: SuffixArray.h:50

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:53 using doxygen 1.8.9.1