本文整理汇总了C++中Paths::path方法的典型用法代码示例。如果您正苦于以下问题：C++ Paths::path方法的具体用法？C++ Paths::path怎么用？C++ Paths::path使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Paths的用法示例。
在下文中一共展示了Paths::path方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: homogenize
void Homogenizer::homogenize(vg::VG* o_graph, xg::XG* xindex, gcsa::GCSA* gcsa_index, gcsa::LCPArray* lcp_index, Paths cached_paths, int kmer_size){
bool in_mem_path_only = true;
vector<id_t> tips = find_non_ref_tips(o_graph);
/* TODO filter by whether a read is on the ref path
// 2. Cache the reference path(s)
// (Not sure how to grab these, so for now just grab the first path in the graph)
map<string, list<Mapping> > cached_paths;
set<string> kept_paths;
*/
string ref_path = o_graph->paths.all_path_names()[0];
//o_graph->unchop();
/*
Paths p = o_graph->paths;
//
// 3. Remove all paths in the graph, except the reference
(o_graph->paths).keep_paths(kept_paths);
*/
/* Generate edges/nodes to add to graph */
//vector<MaximalExactMatch> find_smems(const string& seq);
Mapper* mapper;
mapper= new Mapper(xindex, gcsa_index, lcp_index);
map<vg::id_t, vector<MaximalExactMatch> > matches;
map<vg::id_t, string> ref_node_to_clip;
vector<string> seqs;
for (int i = 0; i < tips.size(); i++){
Node* n = o_graph->get_node(tips[i]);
if (n->sequence().length() < 4 || (o_graph->paths).has_node_mapping(n->id())){
continue;
}
vector<MaximalExactMatch> m = mapper->find_mems_simple(n->sequence().begin(),
n->sequence().end(),
200,
mapper->min_mem_length);
// Why >1? Because we need to match the node AND somewhere else in the graph.
if (m.size() > 1){
cerr << "POTENTIAL NEW EDGE" << endl;
matches[tips[i]] = m;
// map<id_t, map<string, set<Mapping*>>> node_mapping;
// Get paths of tip
set<string> paths_of_tip = cached_paths.of_node(tips[i]);
// Find the closest reference node to the tip
vg::id_t ref_node = -1;
for (auto m : paths_of_tip){
cerr << m << endl;
Path path_of_tip = cached_paths.path(m);
if (m == ref_path){
continue;
}
else{
bool on_ref = false;
for (int j = 0; j < path_of_tip.mapping_size(); j++){
Mapping nearby_mapping = path_of_tip.mapping(j);
Position pos = nearby_mapping.position();
vg::id_t n_id = pos.node_id();
if (o_graph->paths.has_node_mapping(n_id)){
ref_node = n_id;
on_ref = true;
}
else if (on_ref == false && n_id != tips[i]){
ref_node = n_id;
}
else{
continue;
}
}
}
}
if (ref_node != -1){
ref_node_to_clip[ref_node] = n->sequence();
}
}
}
cerr << ref_node_to_clip.size() << " candidate edges generated. Modifying graph" << endl;
//need to remove the tips sequences first.
//cut_tips(tips, o_graph);
vector<Path> new_p_vec;
for (auto x : ref_node_to_clip){
Alignment clip_aln;
cerr << "Length of softclip: " << x.second.size() << endl;
clip_aln = mapper->align(x.second);
if (clip_aln.score() < 30){
continue;
}
cerr << clip_aln.DebugString();
Path new_aln_p = clip_aln.path();
//new_p_vec.clear();
new_p_vec.push_back(new_aln_p);
//for (int i = 0; i < new_aln_p.mapping_size(); i++){
//vector<Translation> tras = o_graph->edit(new_p_vec);
//.........这里部分代码省略.........