36 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H 
   37 #define OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICCOMPRESSED_H 
   97     void findSpec(std::vector<std::vector<std::pair<std::pair<SignedSize, SignedSize>, 
DoubleReal> > > & candidates, 
const std::vector<DoubleReal> & spec);
 
  105     bool save(
const String & file_name);
 
  112     bool open(
const String & file_name);
 
  133     bool isDigestingEnd(
const char aa1, 
const char aa2) 
const;
 
  140     void setTags(
const std::vector<String> & tags);
 
  146     const std::vector<String> & getTags();
 
  152     void setUseTags(
bool use_tags);
 
  164     void setNumberOfModifications(
Size number_of_mods);
 
  170     Size getNumberOfModifications();
 
  175     void printStatistic();
 
  197     SignedSize getLCP_(
const std::pair<SignedSize, SignedSize> & last_point, 
const std::pair<SignedSize, SignedSize> & current_point);
 
  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);
 
  245     std::vector<std::pair<SignedSize, SignedSize> > 
indices_; 
 
  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