+//void
+//Sequence::load_museq(fs::path load_file_path, int seq_num)
+//{
+// fs::fstream load_file;
+// std::string file_data_line;
+// int seq_counter;
+// //annot an_annot;
+// int annot_begin;
+// int annot_end;
+// std::string annot_name;
+// std::string annot_type;
+//
+// std::string::size_type space_split_i;
+// std::string annot_value;
+//
+// annotation_list.reset(new SeqSpanRefList);
+//
+// load_file.open(load_file_path, std::ios::in);
+//
+// seq_counter = 0;
+// // search for the seq_num-th sequence
+// while ( (!load_file.eof()) && (seq_counter < seq_num) )
+// {
+// getline(load_file,file_data_line);
+// if (file_data_line == "<Sequence>")
+// seq_counter++;
+// }
+// getline(load_file, file_data_line);
+// // looks like the sequence is written as a single line
+// set_filtered_sequence(file_data_line, reduced_dna_alphabet, 0, file_data_line.size(), SeqSpan::PlusStrand);
+// getline(load_file, file_data_line);
+// getline(load_file, file_data_line);
+// if (file_data_line == "<Annotations>")
+// {
+// getline(load_file, file_data_line);
+// species = file_data_line;
+// while ( (!load_file.eof()) && (file_data_line != "</Annotations>") )
+// {
+// getline(load_file,file_data_line);
+// if ((file_data_line != "") && (file_data_line != "</Annotations>"))
+// {
+// // need to get 4 values...almost same code 4 times...
+// // get annot start index
+// space_split_i = file_data_line.find(" ");
+// annot_value = file_data_line.substr(0,space_split_i);
+// annot_begin = atoi (annot_value.c_str());
+// file_data_line = file_data_line.substr(space_split_i+1);
+// // get annot end index
+// space_split_i = file_data_line.find(" ");
+// annot_value = file_data_line.substr(0,space_split_i);
+// annot_end = atoi (annot_value.c_str());
+//
+// if (space_split_i == std::string::npos) // no entry for type or name
+// {
+// std::cout << "seq, annots - no type or name\n";
+// annot_name = "";
+// annot_type = "";
+// }
+// else // else get annot type
+// {
+// file_data_line = file_data_line.substr(space_split_i+1);
+// space_split_i = file_data_line.find(" ");
+// annot_value = file_data_line.substr(0,space_split_i);
+// //an_annot.type = annot_value;
+// annot_type = annot_value;
+// if (space_split_i == std::string::npos) // no entry for name
+// {
+// std::cout << "seq, annots - no name\n";
+// annot_name = "";
+// }
+// else // get annot name
+// {
+// file_data_line = file_data_line.substr(space_split_i+1);
+// space_split_i = file_data_line.find(" ");
+// annot_value = file_data_line.substr(0,space_split_i);
+// // this seems like its wrong?
+// annot_type = annot_value;
+// }
+// }
+// add_annotation(annot_name, annot_type, annot_begin, annot_end);
+// }
+// //std::cout << "seq, annots: " << an_annot.start << ", " << an_annot.end
+// // << "-->" << an_annot.type << "::" << an_annot.name << std::endl;
+// }
+// }
+// load_file.close();
+//}
+
+SequenceRef Sequence::load_museq(boost::filesystem::fstream& load_file)