1 // This file is part of the Mussa source distribution.
2 // http://mussa.caltech.edu/
3 // Contact author: Tristan De Buysscher, tristan@caltech.edu
5 // This program and all associated source code files are Copyright (C) 2005
6 // the California Institute of Technology, Pasadena, CA, 91125 USA. It is
7 // under the GNU Public License; please see the included LICENSE.txt
8 // file for more information, or contact Tristan directly.
11 // ----------------------------------------
12 // ---------- mussa_nway.cc -----------
13 // ----------------------------------------
15 #include <boost/filesystem/fstream.hpp>
16 namespace fs = boost::filesystem;
18 #include "alg/mussa_callback.hpp"
19 #include "alg/nway_paths.hpp"
20 #include "alg/conserved_path.hpp"
21 #include "mussa_exceptions.hpp"
28 NwayPaths::NwayPaths()
32 NwayPaths::NwayPaths(const NwayPaths &o)
34 refined_pathz(o.refined_pathz),
35 threshold(o.threshold),
37 soft_thres(o.soft_thres),
38 ent_thres(o.ent_thres),
39 c_sequences(o.c_sequences)
43 void NwayPaths::clear()
47 refined_pathz.clear();
51 NwayPaths::setup(int w, int t)
54 soft_thres = threshold;
58 //cout << "nway: thres = " << threshold
59 // << ", soft threo = " << soft_thres << endl;
63 NwayPaths::set_soft_threshold(int sft_thres)
65 soft_thres = sft_thres;
68 int NwayPaths::get_soft_threshold() const
73 int NwayPaths::get_threshold() const
78 int NwayPaths::get_window() const
83 // dumbly goes thru and combines path windows exactly adjacent (ie + 1 index)
84 // doesn't deal with interleaved adjacency
86 NwayPaths::simple_refine()
88 // ext_path remembers the first window set in an extending path
89 ConservedPath ext_path, new_path;
90 list<ConservedPath>::iterator cur_path, next_path;
91 list<ConservedPath>::iterator pathz_i;
93 bool extending, end = false;
95 refined_pathz.clear();
97 //cout << "path number is: " << pathz.size() << endl;
98 pathz_i = pathz.begin();
101 // only try to extend when pathz isn't empty.
102 if (pathz_i != pathz.end())
107 while(pathz_i != pathz.end())
109 // keep track of current path and advance to next path
114 if (pathz_i == pathz.end()) {
119 // if node for each seq is equal to the next node+1 then for all
120 // sequences then we are extending
121 extending = cur_path->nextTo(*next_path);
130 // add the extend window length as first element and add as refined
131 // now that we have the path to extend save it
133 new_path.extend(win_ext_len);
134 refined_pathz.push_back(new_path);
138 ext_path = *next_path;
141 if ((path_count % 100) == 0)
142 emit progress("refine", path_count-1, pathz.size());
145 // this mysterious call tells the dialog box that we're actually done
146 emit progress("refine", pathz.size(), pathz.size());
147 //cout << "r_path number is: " << refined_pathz.size() << endl;
151 NwayPaths::add_path(int threshold, vector<int>& loaded_path)
153 pathz.push_back(ConservedPath(threshold, 0.0, loaded_path));
157 NwayPaths::add_path(ConservedPath loaded_path)
159 pathz.push_back(loaded_path);
164 NwayPaths::save(fs::path save_file_path)
166 fs::fstream save_file;
167 list<ConservedPath >::iterator path_i, paths_end;
169 save_file.open(save_file_path, ios::out);
171 save_file << "<Mussa type=flp seq_count=" << sequence_count();
172 save_file << " win=" << win_size;
173 // add a function para new_thres defaults to -1 to later deal with
174 // reanalysis with higher thres - if statement whether to record base thres
175 // or new thres (ie if -1, then base)
176 save_file << " thres=" << threshold << " >\n";
178 path_i = refined_pathz.begin();
179 paths_end = refined_pathz.end();
180 //path_i = pathz.begin();
181 //paths_end = pathz.end();
182 while (path_i != paths_end)
184 ConservedPath& a_path = *path_i;
185 //cout << a_path.size() << endl;
186 //first entry is the window length of the windows in the path
187 save_file << a_path.window_size << ":";
188 for(size_t i = 0; i != sequence_count(); ++i)
190 save_file << a_path[i];
191 if (i != sequence_count())
198 save_file << "</Mussa>\n";
204 NwayPaths::sequence_count()
206 if (refined_pathz.begin() == refined_pathz.end() )
209 return refined_pathz.begin()->size();
214 NwayPaths::load(fs::path load_file_path)
216 fs::fstream load_file;
217 string file_data_line, header_data, data, path_node, path_width;
218 int space_split_i, equal_split_i, comma_split_i, colon_split_i;
219 vector<int> loaded_path;
221 load_file.open(load_file_path, ios::in);
225 throw mussa_load_error("Sequence File: " + load_file_path.string() + " not found");
230 // grab mussa tag - discard for now...maybe check in future...
231 getline(load_file,file_data_line);
232 space_split_i = file_data_line.find(" ");
233 file_data_line = file_data_line.substr(space_split_i+1);
234 // grab type tag - need in future to distinguish between flp and vlp paths
235 space_split_i = file_data_line.find(" ");
236 file_data_line = file_data_line.substr(space_split_i+1);
237 // get species/seq number
238 space_split_i = file_data_line.find(" ");
239 header_data = file_data_line.substr(0,space_split_i);
240 equal_split_i = header_data.find("=");
241 data = file_data_line.substr(equal_split_i+1);
242 unsigned int species_num = atoi (data.c_str());
243 file_data_line = file_data_line.substr(space_split_i+1);
245 space_split_i = file_data_line.find(" ");
246 header_data = file_data_line.substr(0,space_split_i);
247 equal_split_i = header_data.find("=");
248 data = file_data_line.substr(equal_split_i+1);
249 win_size = atoi (data.c_str());
250 file_data_line = file_data_line.substr(space_split_i+1);
251 // get threshold size
252 space_split_i = file_data_line.find(" ");
253 header_data = file_data_line.substr(0,space_split_i);
254 equal_split_i = header_data.find("=");
255 data = file_data_line.substr(equal_split_i+1);
256 threshold = atoi (data.c_str());
257 file_data_line = file_data_line.substr(space_split_i+1);
259 //cout << "seq_num=" << species_num << " win=" << win_size;
260 //cout << " thres=" << threshold << endl;
262 // clear out the current data
263 refined_pathz.clear();
267 getline(load_file,file_data_line);
268 while ( (!load_file.eof()) && (file_data_line != "</Mussa>") )
270 if (file_data_line != "")
273 colon_split_i = file_data_line.find(":");
274 // whats our window size?
275 path_width = file_data_line.substr(0,colon_split_i);
276 file_data_line = file_data_line.substr(colon_split_i+1);
277 for(size_t i = 0; i < species_num; i++)
279 comma_split_i = file_data_line.find(",");
280 path_node = file_data_line.substr(0, comma_split_i);
281 temp = atoi (path_node.c_str());
282 loaded_path.push_back(temp);
283 file_data_line = file_data_line.substr(comma_split_i+1);
285 assert (loaded_path.size() == species_num );
286 refined_pathz.push_back(ConservedPath(atoi(path_width.c_str()),
290 getline(load_file,file_data_line);
298 NwayPaths::path_search(vector<vector<FLPs> > all_comparisons, ConservedPath path, size_t depth)
300 list<int> new_nodes, trans_check_nodes;
301 list<int>::iterator new_nodes_i, new_nodes_end;
302 bool trans_check_good;
304 new_nodes = all_comparisons[depth - 1][depth].match_locations(path[depth-1]);
305 new_nodes_i = new_nodes.begin();
306 new_nodes_end = new_nodes.end();
307 while(new_nodes_i != new_nodes_end)
309 //cout << " * species " << depth << " node: " << *new_nodes_i << endl;
310 // check transitivity with previous nodes in path
311 trans_check_good = true;
312 for(size_t i = 0; i < depth - 1; i++)
314 trans_check_nodes = all_comparisons[i][depth].match_locations(path[i]);
315 if ( (trans_check_nodes.end() == find(trans_check_nodes.begin(),
316 trans_check_nodes.end(),
318 (trans_check_nodes.end() == find(trans_check_nodes.begin(),
319 trans_check_nodes.end(),
320 *new_nodes_i * -1) ) )
321 trans_check_good = false;
324 if (trans_check_good)
326 // this makes sure path nodes are recorded with RC status relative to
328 if ( path[depth-1] >= 0)
329 path.push_back(*new_nodes_i);
331 path.push_back(*new_nodes_i * -1);
333 if (depth < all_comparisons.size() - 1)
334 path_search(all_comparisons, path, depth + 1);
336 pathz.push_back(path);
342 /* use this if I ever get the friggin seqcomp match lists to sort...
343 if (binary_search(trans_check_nodes.begin(), trans_check_nodes.end(),
348 NwayPaths::find_paths_r(vector<vector<FLPs> > all_comparisons)
351 int win_i, window_num;
353 list<int>::iterator new_nodes_i, new_nodes_end;
356 window_num = all_comparisons[0][1].size();
357 // loop thru all windows in first species
358 for (win_i = 0; win_i < window_num; win_i++)
361 path.push_back(win_i);
362 new_nodes = all_comparisons[0][1].match_locations(path[0]);
363 new_nodes_i = new_nodes.begin();
364 new_nodes_end = new_nodes.end();
365 //if (new_nodes_i != new_nodes_end)
366 //cout << "* species 0 node: " << win_i << endl;
368 while(new_nodes_i != new_nodes_end)
370 //cout << " * species 1 node: " << *new_nodes_i << endl;
371 path[1] = *new_nodes_i;
372 path_search(all_comparisons, path, 2);
380 NwayPaths::save_old(fs::path save_file_path)
382 fs::fstream save_file;
383 list<ConservedPath >::iterator path_i, paths_end;
386 save_file.open(save_file_path, ios::app);
388 path_i = pathz.begin();
389 paths_end = pathz.end();
390 while(path_i != paths_end)
392 ConservedPath& a_path = *path_i;
393 //cout << a_path.size() << endl;
394 for(i = 0; i < path_i->size(); ++i)
395 save_file << i << "," << a_path[i] << " ";
405 NwayPaths::find_paths(vector<vector<FLPs> > all_comparisons)
408 vector<list<list<int> > > path_src_tree;
410 list<int>::iterator node_i, node_end;
411 <list<list<int> > >::iterator branch_i, branch_end;
414 path_src_tree.reserve(all_comparisons.size()- 1);
417 // loop thru all windows in first species
418 for (win_i = 0; win_i < window_num; win_i++)
420 // clear the path search tree
421 for(i = 0; i < all_comparisons.size(); i++)
422 path_src_tree[i].clear();
424 // top level kept empty even tho implicity has one entry of the first
425 // species at this window - why bother, adds a little speed
427 // get connection list for first species, creating a list of nodes
428 // of second species connected to the first species at this window
429 new_nodes = all_comparisons[0][1];
430 path_src_tree[1].push_back(new_nodes);
432 // loop thru rest of species for this window to see if any paths of matches
433 // go across all species
434 // if path search tree becomes empty, break out of loop, no reason to search further
436 while ((sp_i < all_comparisons.size()) && (path tree not empty))
438 branch_i = path_src_tree[1].begin();
439 branch_end = path_src_tree[1].end();
440 while (branch_i != branch_end)
442 node_i = branch_i->begin();
443 node_end = branch_i->end();
447 // loop over all current nodes
448 // get connection list for each node
449 // loop over each previous node in list
450 // get those nodes connection list
451 // intersect previous node connections with current
456 // insert any of the paths found into the master list of paths
458 // add no paths if tmp_pathz is empty...
462 void NwayPaths::refine()
468 void NwayPaths::print(list<vector<int> >& dump_path)
470 list<vector<int> >::iterator pathz_i;
471 vector<int>::iterator path_i;
473 cout << "printing list of lists\n";
474 for (pathz_i = dump_path.begin(); pathz_i != dump_path.end(); ++pathz_i)
476 for (path_i = pathz_i->begin(); path_i != pathz_i->end(); ++path_i)
477 cout << *path_i << " ";