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