///A tutorial about finding supermaximal repeats.
#include <iostream>
#include <seqan/index.h>

using namespace seqan;

int main ()
{
///We begin with a @Class.String@ to store our sequence.
	String<char> myString = "How many wood would a woodchuck chuck.";

///Then we create an @Class.Index@ of this @Class.StringSet@.
	typedef Index< String<char> > TMyIndex;
	TMyIndex myIndex(myString);

///To find supermaximal repeats, we use SeqAn's @Spec.SuperMaxRepeats Iterator@ 
///and set the minimum repeat length to 3.
	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 @Function.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;
}
