36 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
37 #define OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
90 void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > > & candidates,
const std::vector<DoubleReal> & spec);
102 void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > > & candidates,
const String & DTA_file);
120 void setNumberOfModifications(
Size number_of_mods)
const;
126 Size getNumberOfModifications()
const;
133 void setTags(
const std::vector<String> & tags);
139 const std::vector<String> & getTags();
145 void setUseTags(
bool use_tags);
158 void setModificationOutputMethod(
const String & s);
164 String getModificationOutputMethod();
168 String vToString_(std::vector<String> v);
180 #endif //OPENMS_EXAMPLES_SuffixArrayPeptideFinder_H
A more convenient string class.
Definition: String.h:56
String modification_output_method_
output method for modifications
Definition: SuffixArrayPeptideFinder.h:174
concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by defau...
Definition: BigString.h:50
std::pair< String, String > FASTAEntry
Definition: SuffixArrayPeptideFinder.h:59
BigString big_string_
bigString object holding all peptides of fasta file
Definition: SuffixArrayPeptideFinder.h:170
wrapper for easy use of sufArray
Definition: SuffixArrayPeptideFinder.h:50
SuffixArray * sa_
pointer to suffixarray
Definition: SuffixArrayPeptideFinder.h:172
WEIGHTMODE
Definition: WeightWrapper.h:55
Definition: WeightWrapper.h:55
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Encapsulated weight queries to simplify mono vs average weight computation.
Definition: WeightWrapper.h:50
abstract class for suffix array
Definition: SuffixArray.h:51