35 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
36 #define OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H
94 void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > >& candidates,
const std::vector<double>& spec);
106 void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String> > >& candidates,
const String& DTA_file);
112 void setTolerance(
const double t);
118 double getTolerance()
const;
124 void setNumberOfModifications(
Size number_of_mods)
const;
130 Size getNumberOfModifications()
const;
137 void setTags(
const std::vector<String>& tags);
143 const std::vector<String>& getTags();
149 void setUseTags(
bool use_tags);
162 void setModificationOutputMethod(
const String& s);
168 String getModificationOutputMethod();
172 String vToString_(std::vector<String> v);
184 #endif //OPENMS_EXAMPLES_SuffixArrayPeptideFinder_H
A more convenient string class.
Definition: String.h:57
String modification_output_method_
output method for modifications
Definition: SuffixArrayPeptideFinder.h:178
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by defau...
Definition: BigString.h:52
std::pair< String, String > FASTAEntry
Definition: SuffixArrayPeptideFinder.h:63
BigString big_string_
bigString object holding all peptides of fasta file
Definition: SuffixArrayPeptideFinder.h:174
wrapper for easy use of sufArray
Definition: SuffixArrayPeptideFinder.h:54
SuffixArray * sa_
pointer to suffixarray
Definition: SuffixArrayPeptideFinder.h:176
WEIGHTMODE
Definition: WeightWrapper.h:55
Definition: WeightWrapper.h:55
Encapsulated weight queries to simplify mono vs average weight computation.
Definition: WeightWrapper.h:50
abstract class for suffix array
Definition: SuffixArray.h:50