// add a function para new_thres defaults to -1 to later deal with
// reanalysis with higher thres - if statement whether to record base thres
// or new thres (ie if -1, then base)
- save_file << " thres=" << threshold << " >\n";
+ save_file << " thres=" << threshold << " soft_thres=" << soft_thres << " >\n";
path_i = refined_pathz.begin();
paths_end = refined_pathz.end();
//cout << a_path.size() << endl;
//first entry is the window length of the windows in the path
save_file << a_path.window_size << ":";
- for(size_t i = 0; i != sequence_count(); ++i)
+ for(size_type i = 0; i != sequence_count(); ++i)
{
save_file << a_path[i];
if (i != sequence_count())
}
-size_t
-NwayPaths::sequence_count()
+NwayPaths::size_type NwayPaths::sequence_count() const
{
if (refined_pathz.begin() == refined_pathz.end() )
return 0;
return refined_pathz.begin()->size();
}
+NwayPaths::size_type NwayPaths::size() const
+{
+ return pathz.size();
+}
void
NwayPaths::load(fs::path load_file_path)
data = file_data_line.substr(equal_split_i+1);
threshold = atoi (data.c_str());
file_data_line = file_data_line.substr(space_split_i+1);
-
+ // get cur_threshold
+ //std::cout << "file_data_line: " << file_data_line << "\n";
+ //std::cout << "find(\">\"): " << file_data_line.find(">") << "\n";
+ if (file_data_line.find(">") != 0)
+ {
+ space_split_i = file_data_line.find(" ");
+ header_data = file_data_line.substr(0,space_split_i);
+ equal_split_i = header_data.find("=");
+ data = file_data_line.substr(equal_split_i+1);
+ soft_thres = atoi (data.c_str());
+ file_data_line = file_data_line.substr(space_split_i+1);
+ }
+ else
+ {
+ soft_thres = threshold;
+ }
+ //std::cout << "nway_soft_thres: " << soft_thres << "\n";
//cout << "seq_num=" << species_num << " win=" << win_size;
//cout << " thres=" << threshold << endl;
// whats our window size?
path_width = file_data_line.substr(0,colon_split_i);
file_data_line = file_data_line.substr(colon_split_i+1);
- for(size_t i = 0; i < species_num; i++)
+ for(size_type i = 0; i < species_num; i++)
{
comma_split_i = file_data_line.find(",");
path_node = file_data_line.substr(0, comma_split_i);
void
-NwayPaths::path_search(vector<vector<FLPs> > all_comparisons, ConservedPath path, size_t depth)
+NwayPaths::path_search(vector<vector<FLPs> > all_comparisons, ConservedPath path, size_type depth)
{
list<int> new_nodes, trans_check_nodes;
list<int>::iterator new_nodes_i, new_nodes_end;
//cout << " * species " << depth << " node: " << *new_nodes_i << endl;
// check transitivity with previous nodes in path
trans_check_good = true;
- for(size_t i = 0; i < depth - 1; i++)
+ for(size_type i = 0; i < depth - 1; i++)
{
trans_check_nodes = all_comparisons[i][depth].match_locations(path[i]);
if ( (trans_check_nodes.end() == find(trans_check_nodes.begin(),
{
fs::fstream save_file;
list<ConservedPath >::iterator path_i, paths_end;
- size_t i;
+ size_type i;
save_file.open(save_file_path, ios::app);