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#include <seqan/sequence.h>
#include <seqan/file.h>
using namespace seqan2;
int main()
{
//![string_example]
String<char> myText; // A string of characters.
String<int> myNumbers; // A string of integers.
//![string_example]
//![simple_string_construction]
myText = "Hello SeqAn!";
//![simple_string_construction]
//![string_of_strings_example]
String<String<char> > myStringList; // A string of character strings.
//![string_of_strings_example]
//![special_types_example]
String<Dna> myGenome; // A string of nucleotides.
String<AminoAcid> myProtein; // A string of amino acids.
//![special_types_example]
//![shortcuts_example]
// Instead of String<Dna> dnaSeq we can also write:
DnaString dnaSeq = "TATA";
//![shortcuts_example]
//![specification_example]
String<Dna> myGenome1; // A default string of nucleotides.
String<Dna, Alloc<> > myGenome2; // The same type as above.
//![specification_example]
//![external_string_spec]
// Most of the string is stored on the disk.
String<Dna, External<> > myLargeGenome;
//![external_string_spec]
//![initialization_example]
String<Dna> myDnaGenome = "TATACGCG";
//![initialization_example]
Dna5String genome = "ATGGTTTCAACGTAATGCTGAACATGTCGCGT";
Dna5String read = "TGGTNTCA";
unsigned beginPosition = 1;
//![assignment5_code_to_change]
// We have to create a copy of the corresponding fragment of the genome, where the read aligns to
// Change this piece of code using an infix of the genome
Dna5String genomeFragment;
for (unsigned i = 0; i < length(read); ++i)
{
appendValue(genomeFragment, genome[beginPosition + i]);
}
//![assignment5_code_to_change]
}
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