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