: color_mapper(new AnnotationColors)
{
clear();
- connect(&the_paths, SIGNAL(progress(const std::string&, int, int)),
- this, SIGNAL(progress(const std::string&, int, int)));
+ connect(&the_paths, SIGNAL(progress(const QString&, int, int)),
+ this, SIGNAL(progress(const QString&, int, int)));
}
Mussa::Mussa(const Mussa& m)
analysis_path(m.analysis_path),
dirty(m.dirty)
{
- connect(&the_paths, SIGNAL(progress(const std::string&, int, int)),
- this, SIGNAL(progress(const std::string&, int, int)));
+ connect(&the_paths, SIGNAL(progress(const QString&, int, int)),
+ this, SIGNAL(progress(const QString&, int, int)));
+}
+
+MussaRef Mussa::init()
+{
+ boost::shared_ptr<Mussa> m(new Mussa());
+ return m;
}
boost::filesystem::path Mussa::get_analysis_path() const
}
-const vector<boost::shared_ptr<Sequence> >&
+const vector<SequenceRef>&
Mussa::sequences() const
{
return the_seqs;
void Mussa::load_motifs(std::istream &in)
{
std::string data;
- const char *alphabet = Alphabet::nucleic_cstr;
+ const char *alphabet = Alphabet::dna_cstr;
motif_parser::ParsedMotifs parsed_motifs(motif_sequences, color_mapper);
// slurp our data into a string
{
// once we've loaded all the motifs from the file,
// lets attach them to the sequences
- for(vector<boost::shared_ptr<Sequence> >::iterator seq_i = the_seqs.begin();
+ for(vector<SequenceRef >::iterator seq_i = the_seqs.begin();
seq_i != the_seqs.end();
++seq_i)
{