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//![main]
#include <iostream>
#include <seqan/file.h>
#include <seqan/journaled_set.h>
using namespace seqan2;
int main()
{
typedef String<char, Journaled<Alloc<>, SortedArray, Alloc<> > > TJournalString;
typedef Host<TJournalString>::Type THost;
typedef StringSet<TJournalString, Owner<JournaledSet> > TJournaledSet;
TJournaledSet journaledSet;
THost reference = "DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE";
THost seq0 = "DPKKPRGKMVNSPPAFFVQTSREEHKKKHPDASVFSKKCSERWKTMSAKEKGKFEDMAKARYEREMKTTYIPKGETYIPPKGE";
THost seq1 = "DPHHPPKPRGKMVNSPPAFFVQTSREEHKPDASVFSKKCSERRMPNHHTMSAKEKGKFEDMAKARYEREMKTTYIPKGETYIPPKGE";
THost seq2 = "DPKKPRGKMSSYAFFVQTSREEHKKKHPKKCDEFSKKCSERWKTMSAKEKGKFEDARYEREMKTYIPPKGE";
//![main]
//![init]
setHost(journaledSet, reference);
appendValue(journaledSet, TJournalString(seq0));
appendValue(journaledSet, TJournalString(seq1));
appendValue(journaledSet, TJournalString(seq2));
//![init]
//![join]
join(journaledSet, 0, JoinConfig<GlobalAlign<JournaledManhatten> >()); // Simply inserts the
join(journaledSet, 1, JoinConfig<GlobalAlign<JournaledCompact> >()); // Uses default scoring scheme to compute compact journal.
JoinConfig<GlobalAlign<JournaledCompact> > joinConfig;
setScoringScheme(joinConfig, Score<int, BiAffine>(0, -1, -1)); // Note the mismatch score is forbidden internally when used in the context of journaling.
join(journaledSet, 2, joinConfig); // Compute journal using Levenshtein distance.
std::cout << "Reference: " << host(journaledSet) << std::endl;
for (unsigned i = 0; i < length(journaledSet); ++i)
std::cout << "Journaled Sequence " << i << ": " << value(journaledSet, i) << std::endl;
return 0;
}
//![join]
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