ProteinsAnchorsSamplingSpace read_protein_anchors_mapping(
multifit::ProteomicsData *prots, const std::string &anchors_prot_map_fn,
int max_paths) {
ProteinsAnchorsSamplingSpace ret(prots);
std::fstream in;
IMP_LOG_TERSE("FN:" << anchors_prot_map_fn << std::endl);
in.open(anchors_prot_map_fn.c_str(), std::fstream::in);
if (!in.good()) {
IMP_WARN(
"Problem opening file " << anchors_prot_map_fn
<< " for reading; returning empty mapping data"
<< std::endl);
in.close();
return ret;
}
std::string line;
// first line should be the anchors line
getline(in, line);
std::string anchors_fn =
get_relative_path(anchors_prot_map_fn, parse_anchors_line(line));
IMP_LOG_TERSE("FN:" << anchors_fn << std::endl);
multifit::AnchorsData anchors_data =
multifit::read_anchors_data(anchors_fn.c_str());
ret.set_anchors(anchors_data);
ret.set_anchors_filename(anchors_fn);
while (!in.eof()) {
if (!getline(in, line)) break;
IMP_LOG_VERBOSE("working on line:" << line);
IMP_USAGE_CHECK(is_protein_line(line), "the line should be a protein line");
boost::tuple<std::string, std::string, IntsList> prot_data =
parse_protein_line(anchors_prot_map_fn, line, max_paths);
ret.set_paths_for_protein(boost::get<0>(prot_data),
boost::get<2>(prot_data));
ret.set_paths_filename_for_protein(boost::get<0>(prot_data),
boost::get<1>(prot_data));
}
return ret;
}
ProteomicsData *read_proteomics_data(const char *prot_fn) {
std::fstream in;
IMP_NEW(ProteomicsData, data, ());
in.open(prot_fn, std::fstream::in);
if (! in.good()) {
IMP_WARN("Problem opening file " << prot_fn <<
" for reading; returning empty proteomics data" << std::endl);
in.close();
return data.release();
}
std::string line;
getline(in, line); //skip proteins header line
getline(in, line); //skip proteins header line
while ((!in.eof()) && (!is_interaction_header_line(line, data))){
parse_protein_line(line,data);
if (!getline(in, line)) break;
}
getline(in, line);
while ((!in.eof()) && (!is_xlink_header_line(line,data))){
parse_interaction_line(line,data);
if (!getline(in, line)) break;
}
getline(in, line);
while (!in.eof() && (!is_ev_header_line(line,data))){
parse_xlink_line(line,data);
if (!getline(in, line)) break;
}
getline(in, line);
while (!in.eof()) { //ev lines
parse_ev_line(line,data);
if (!getline(in, line)) break;
if (line.size()==0) break;
}
in.close();
return data.release();
}