Page Maximal Unique Matches

Example for using the Mums Iterator.

Given a set of sequences, a unique match is a match that occurs exactly once in each sequence. A maximal unique match (MUM) is a unique match that is not part of any longer unique match. The following example demonstrates how to iterate over all MUMs and output them.

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

using namespace seqan;

int main ()
    // We begin with a StringSet that stores multiple strings.
	StringSet< String<char> > mySet;
	resize(mySet, 3);
	mySet[0] = "SeqAn is a library for sequence analysis.";
	mySet[1] = "The String class is the fundamental sequence type in SeqAn.";
	mySet[2] = "Subsequences can be handled with SeqAn's Segment class.";

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

    // To find maximal unique matches (Mums), we use the Mums Iterator and set the minimum MUM length to 3.
	Iterator< TMyIndex, Mums >::Type myMUMiterator(myIndex, 3);
	String< SAValue<TMyIndex>::Type > occs;

	while (!atEnd(myMUMiterator)) {
        // A multiple match can be represented by the positions it occurs at in every sequence and its length. 
        // getOccurrences@ returns an unordered sequence of pairs (seqNo,seqOfs) the match occurs at.
		occs = getOccurrences(myMUMiterator);
        //To order them ascending according seqNo we use orderOccurrences.
		for(unsigned i = 0; i < length(occs); ++i)
			std::cout << getValueI2(occs[i]) << ", ";

        // repLength returns the length of the match.
		std::cout << repLength(myMUMiterator) << "   ";

        // The match string itself can be determined with representative.
		std::cout << "\t\"" << representative(myMUMiterator) << '\"' << std::endl;


	return 0;

The only maximal matches that occur in all 3 sequences are "SeqAn" and "sequence". They occur exactly once and thus are maximal unique matches.

weese@tanne:~/seqan$ cd demos
weese@tanne:~/seqan/demos$ make index_mums
weese@tanne:~/seqan/demos$ ./index_mums
0, 53, 33, 5    "SeqAn"
23, 36, 3, 8    "sequence"
weese@tanne:~/seqan/demos$ *