#include "mussa_exceptions.hpp"
-#include "alg/alphabet.hpp"
-#include "alg/motif_parser.hpp"
+#include "alphabet.hpp"
+#include "motif_parser.hpp"
+#include "seq.hpp"
#include <boost/spirit/core.hpp>
#include <boost/spirit/actor/push_back_actor.hpp>
Iterator end) const
{
float red, green, blue, alpha;
- Sequence seq(parsed->sequence, Sequence::nucleic_alphabet);
+ Sequence seq(parsed->sequence, dna_alphabet, SeqSpan::PlusStrand);
seq.set_fasta_header(parsed->name);
alpha = 1.0;
break;
}
Color c(red, green, blue, alpha);
- parsed->color_mapper->appendInstanceColor("motif", seq.c_str(), c);
+ std::string motif_subseq(seq.begin(), seq.end());
+ parsed->color_mapper->appendInstanceColor("motif", motif_subseq, c);
parsed->motifs.insert(seq);
parsed->sequence.clear();
void motif_parser::ParsedMotifs::parse(const std::string &data)
{
- const char *alphabet = Alphabet::nucleic_cstr;
+ const char *alphabet = Alphabet::dna_cstr;
// parse our string
spirit::parse_info<std::string::const_iterator> result;
motifs.clear();
throw motif_load_error(msg.str());
}
-}
\ No newline at end of file
+}