move strand into seqspan

[mussa.git] / alg / motif_parser.cpp

diff --git a/alg/motif_parser.cpp b/alg/motif_parser.cpp
index d05f15bbd55410ec1b2e76c94ce5114b6cb85a68..5ba355028f5fc699c23d991bde0a9caf706bef8b 100644 (file)
--- a/alg/motif_parser.cpp
+++ b/alg/motif_parser.cpp
@@ -1,6 +1,7 @@
 #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>
@@ -56,7 +57,7 @@ void motif_parser::push_motif::operator()(
   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;
@@ -93,7 +94,7 @@ motif_parser::ParsedMotifs::ParsedMotifs(
 
 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;