35 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H
36 #define OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H
116 void findSpec(std::vector<std::vector<std::pair<std::pair<SignedSize, SignedSize>,
double> > >& candidates,
const std::vector<double>& spec);
124 bool save(
const String& file_name);
131 bool open(
const String& file_name);
138 void setTolerance(
double t);
144 double getTolerance()
const;
152 bool isDigestingEnd(
const char aa1,
const char aa2)
const;
159 void setTags(
const std::vector<String>& tags);
165 const std::vector<String>& getTags();
171 void setUseTags(
bool use_tags);
183 void setNumberOfModifications(
Size number_of_mods);
189 Size getNumberOfModifications();
194 void printStatistic();
216 SignedSize getLCP_(
const std::pair<SignedSize, SignedSize>& last_point,
const std::pair<SignedSize, SignedSize>& current_point);
225 SignedSize findFirst_(
const std::vector<double>& spec,
double& m);
252 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);
266 std::vector<std::pair<SignedSize, SignedSize> >
indices_;
286 #endif //OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H
std::vector< SignedSize > lcp_
vector of ints with lcp values
Definition: SuffixArrayTrypticCompressed.h:268
A more convenient string class.
Definition: String.h:57
SignedSize progress_
Definition: SuffixArrayTrypticCompressed.h:282
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:128
std::vector< std::pair< SignedSize, SignedSize > > indices_
vector of pairs of ints describing all relevant suffixes
Definition: SuffixArrayTrypticCompressed.h:266
bool use_tags_
indicates whether tags are used or not
Definition: SuffixArrayTrypticCompressed.h:280
double tol_
mass tolerance for finding candidates
Definition: SuffixArrayTrypticCompressed.h:264
WEIGHTMODE
Definition: WeightWrapper.h:55
std::vector< String > tags_
all given tags
Definition: SuffixArrayTrypticCompressed.h:278
Size number_of_modifications_
number of allowed modifications
Definition: SuffixArrayTrypticCompressed.h:276
Definition: WeightWrapper.h:55
const String & s_
the string with which the suffix array is build
Definition: SuffixArrayTrypticCompressed.h:262
Encapsulated weight queries to simplify mono vs average weight computation.
Definition: WeightWrapper.h:50
String toString(T i)
toString functions (single argument)
Definition: StringUtils.h:68
std::vector< SignedSize > skip_
vector of ints with skip values
Definition: SuffixArrayTrypticCompressed.h:270
Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS...
Definition: SuffixArrayTrypticCompressed.h:63
abstract class for suffix array
Definition: SuffixArray.h:50