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///A tutorial about finding supermaximal repeats.
//![includes]
#include <iostream>
#include <seqan/index.h>
using namespace seqan;
//![includes]
//![init]
int main()
{
String<char> myString = "How many wood would a woodchuck chuck.";
typedef Index<String<char> > TMyIndex;
TMyIndex myIndex(myString);
//![init]
//![iteration]
Iterator<TMyIndex, SuperMaxRepeats>::Type myRepeatIterator(myIndex, 3);
while (!atEnd(myRepeatIterator))
{
// A repeat can be represented by its length and positions it occurs at.
// Function getOccurrences returns an unordered sequence of these positions
// The length of this sequence, i.e. the repeat abundance can be obtained
// from countOccurrences.
for (unsigned i = 0; i < countOccurrences(myRepeatIterator); ++i)
std::cout << getOccurrences(myRepeatIterator)[i] << ", ";
// Function repLength returns the length of the repeat string.
std::cout << repLength(myRepeatIterator) << " ";
// The repeat string itself can be determined with function representative.
std::cout << "\t\"" << representative(myRepeatIterator) << '\"' << std::endl;
++myRepeatIterator;
}
return 0;
}
//![iteration]
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