X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Fmotif_parser.cpp;h=5ba355028f5fc699c23d991bde0a9caf706bef8b;hp=c59c2873e160d697ab46d2b08510d1d985f905cf;hb=75496e2c562d728af983c347527270eba360c6ee;hpb=b9755e1974201ff513c66b0fd684bde330c6fff6

diff --git a/alg/motif_parser.cpp b/alg/motif_parser.cpp
index c59c287..5ba3550 100644
--- a/alg/motif_parser.cpp
+++ b/alg/motif_parser.cpp
@@ -57,7 +57,7 @@ void motif_parser::push_motif::operator()(
   Iterator end) const
 {
   float red, green, blue, alpha;
-  Sequence seq(parsed->sequence, nucleic_alphabet);
+  Sequence seq(parsed->sequence, dna_alphabet, SeqSpan::PlusStrand);
   seq.set_fasta_header(parsed->name);
   
   alpha = 1.0;
@@ -94,7 +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;