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//![assignment1]
#include <seqan/sequence.h>
#include <seqan/index.h>
//![assignment1]
namespace seqan2{
//![SAValue]
template<>
struct SAValue<String<Dna> >
{
typedef unsigned Type;
};
//![SAValue]
//![SAValue2]
template<>
struct SAValue<StringSet<String<Dna> > >
{
typedef Pair<unsigned, unsigned> Type;
};
//![SAValue2]
//![SAValue3]
typedef Pair<unsigned char, unsigned> Type;
//![SAValue3]
}
//![assignment1]
using namespace seqan2;
int main()
{
//![assignment1]
//![save]
const char * tempFileName = SEQAN_TEMP_FILENAME();
//![save]
{
//![assignment1]
String<char> text = "This is the first example";
Index<String<char>, FMIndex<> > index(text);
//![assignment1]
//![esa]
//![finder]
String<Dna5> genome = "ACGTACGTACGTN";
Index<String<Dna5>, IndexEsa<> > esaIndex(genome);
//![esa]
//![finder]
//![fm]
StringSet<String<AminoAcid> > protein;
appendValue(protein, "VXLAGZ");
appendValue(protein, "GKTVXL");
appendValue(protein, "XLZ");
Index<StringSet<String<AminoAcid> >, FMIndex<> > fmIndex(protein);
//![fm]
//![finder]
Finder<Index<String<Dna5>, IndexEsa<> > > esaFinder(esaIndex);
//![finder]
//![finder_multiple]
find(esaFinder, "ACGT"); // first occurrence of "ACGT"
find(esaFinder, "ACGT"); // second occurrence of "ACGT"
find(esaFinder, "ACGT"); // third occurrence of "ACGT"
//![finder_multiple]
//![finder_position]
find(esaFinder, "ACGT"); // first occurrence of "ACGT"
position(esaFinder); // -> 0
find(esaFinder, "ACGT"); // second occurrence of "ACGT"
position(esaFinder); // -> 4
find(esaFinder, "ACGT"); // third occurrence of "ACGT"
position(esaFinder); // -> 8
//![finder_position]
//![save]
save(index, tempFileName);
//![save]
//![open]
open(index, tempFileName);
//![open]
//![require]
indexRequire(index, FibreSA());
//![require]
//![require2]
indexRequire(esaIndex, EsaSA());
indexRequire(esaIndex, EsaLcp());
indexRequire(esaIndex, EsaChildtab()); // for TopDown iterators
indexRequire(esaIndex, EsaBwt()); // for (Super-)MaxRepeats iterators
//![require2]
//![external]
Index<String<Dna, External<> >, IndexEsa<> > external_index;
//![external]
indexRequire(external_index, EsaSA());
save(external_index, tempFileName);
//![external]
open(external_index, tempFileName);
//![external]
StringSet<String<Dna> > set;
appendValue(set, "ACTG");
//![config]
typedef FMIndexConfig<void, unsigned> TConfig;
Index<StringSet<String<Dna> >, FMIndex<void, TConfig> > configIndex(set);
//![config]
}
// clean up tmp directory
ClassTest::_deleteTempFile(ClassTest::_stripFileName(tempFileName));
//![assignment1]
return 0;
}
//![assignment1]
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