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SuffixArrayTrypticCompressed.h
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34 
35 
36 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H
37 #define OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H
38 
42 
43 namespace OpenMS
44 {
45  class String;
46 
54  class OPENMS_DLLAPI SuffixArrayTrypticCompressed :
55  public SuffixArray
56  , public WeightWrapper
57  {
58 
59 public:
60 
71  SuffixArrayTrypticCompressed(const String & st, const String & filename, const WeightWrapper::WEIGHTMODE weight_mode = WeightWrapper::MONO);
72 
77 
82 
86  String toString();
87 
97  void findSpec(std::vector<std::vector<std::pair<std::pair<SignedSize, SignedSize>, DoubleReal> > > & candidates, const std::vector<DoubleReal> & spec);
98 
105  bool save(const String & file_name);
112  bool open(const String & file_name);
113 
119  void setTolerance(DoubleReal t);
120 
125  DoubleReal getTolerance() const;
126 
133  bool isDigestingEnd(const char aa1, const char aa2) const;
134 
140  void setTags(const std::vector<String> & tags);
141 
146  const std::vector<String> & getTags();
147 
152  void setUseTags(bool use_tags);
153 
158  bool getUseTags();
159 
164  void setNumberOfModifications(Size number_of_mods);
165 
170  Size getNumberOfModifications();
171 
175  void printStatistic();
176 
177 protected:
178 
183 
189  SignedSize getNextSep_(const SignedSize p) const;
190 
197  SignedSize getLCP_(const std::pair<SignedSize, SignedSize> & last_point, const std::pair<SignedSize, SignedSize> & current_point);
198 
206  SignedSize findFirst_(const std::vector<DoubleReal> & spec, DoubleReal & m);
207 
217  SignedSize findFirst_(const std::vector<DoubleReal> & spec, DoubleReal & m, SignedSize start, SignedSize end);
218 
231  void parseTree_(SignedSize start_index, SignedSize stop_index, SignedSize depth, SignedSize walked_in, SignedSize edge_len, std::vector<std::pair<SignedSize, SignedSize> > & out_number, std::vector<std::pair<SignedSize, SignedSize> > & edge_length, std::vector<SignedSize> & leafe_depth);
232 
239  bool hasMoreOutgoings_(SignedSize start_index, SignedSize stop_index, SignedSize walked_in);
240 
241  const String & s_;
242 
244 
245  std::vector<std::pair<SignedSize, SignedSize> > indices_;
246 
247  std::vector<SignedSize> lcp_;
248 
249  std::vector<SignedSize> skip_;
250 
251  //const SignedSize getIndex_ (const String & s);
252 
253  DoubleReal masse_[256];
254 
256 
257  std::vector<String> tags_;
258 
259  bool use_tags_;
260 
262  };
263 }
264 
265 #endif //OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H
std::vector< SignedSize > lcp_
vector of ints with lcp values
Definition: SuffixArrayTrypticCompressed.h:247
A more convenient string class.
Definition: String.h:56
SignedSize progress_
Definition: SuffixArrayTrypticCompressed.h:261
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:151
std::vector< std::pair< SignedSize, SignedSize > > indices_
vector of pairs of ints describing all relevant sufices
Definition: SuffixArrayTrypticCompressed.h:245
bool use_tags_
indicates whether tags are used or not
Definition: SuffixArrayTrypticCompressed.h:259
WEIGHTMODE
Definition: WeightWrapper.h:55
std::vector< String > tags_
all given tags
Definition: SuffixArrayTrypticCompressed.h:257
Size number_of_modifications_
number of allowed modifications
Definition: SuffixArrayTrypticCompressed.h:255
Definition: WeightWrapper.h:55
DoubleReal tol_
mass tolerance for finding candidates
Definition: SuffixArrayTrypticCompressed.h:243
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
const String & s_
the string with which the suffix array is build
Definition: SuffixArrayTrypticCompressed.h:241
Encapsulated weight queries to simplify mono vs average weight computation.
Definition: WeightWrapper.h:50
std::vector< SignedSize > skip_
vector of ints with skip values
Definition: SuffixArrayTrypticCompressed.h:249
Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS...
Definition: SuffixArrayTrypticCompressed.h:54
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