vector<FLPs> empty_FLP_vector;
FLPs dummy_comp;
+
+ //--------------------------------------------------------
+ // Load Muway
+ //--------------------------------------------------------
analysis_path = ana_file;
analysis_name = ana_path.leaf();
fs::path muway(analysis_name+".muway", fs::native);
threshold = the_paths.get_threshold();
soft_thres = threshold;
- int seq_num = the_paths.sequence_count();
+
+ //--------------------------------------------------------
+ // Load Sequence
+ //--------------------------------------------------------
+ //int seq_num = the_paths.sequence_count();
fs::path museq(analysis_name + ".museq", fs::native);
a_file_path = analysis_path / museq;
// this is a bit of a hack due to C++ not acting like it should with files
- for (i = 1; i <= seq_num; i++)
+ /*for (i = 1; i <= seq_num; i++)
{
boost::shared_ptr<Sequence> tmp_seq(new Sequence);
tmp_seq->load_museq(a_file_path, i);
the_seqs.push_back(tmp_seq);
+ }*/
+
+ i = 1;
+ //int seq_num = 0;
+ boost::filesystem::fstream load_museq_fs;
+ load_museq_fs.open(a_file_path, std::ios::in);
+ boost::shared_ptr<Sequence> tmp_seq;
+ while (1)
+ {
+ tmp_seq = Sequence::load_museq(load_museq_fs);
+
+ if (tmp_seq)
+ {
+ the_seqs.push_back(tmp_seq);
+ }
+ else
+ {
+ break;
+ }
+
+
+ //safe guard in case of an infinate loop.
+ //FIXME: If mussa can handle a comparison of 10000 sequences
+ // in the future, then this code should be fixed.
+ if (i == 10000)
+ {
+ throw mussa_load_error(" Run away sequence load!");
+ }
+ i++;
}
+ load_museq_fs.close();
+ //--------------------------------------------------------
+ // Load Motifs
+ //--------------------------------------------------------
fs::path mtl(analysis_name + ".mtl", fs::native);
fs::path motif_file = analysis_path / mtl;
if (fs::exists(motif_file)) {
load_motifs(motif_file);
}
+
+ vector<Sequence>::size_type seq_num = the_seqs.size();
empty_FLP_vector.clear();
for(i = 0; i < seq_num; i++)
{
all_comps[i].push_back(dummy_comp);
}
+
for(i = 0; i < seq_num; i++)
{
for(i2 = i+1; i2 < seq_num; i2++)