+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- mussa_nway.cc -----------
// ----------------------------------------
{
species_num = sp_num;
threshold = t;
+ soft_thres = threshold;
win_size = w;
pathz.clear();
-}
-
-void
-Nway_Paths::path_search(vector<vector<FLPs> > all_comparisons, vector<int> path, int depth)
-{
- list<int> new_nodes, trans_check_nodes;
- list<int>::iterator new_nodes_i, new_nodes_end;
- int i;
- bool trans_check_good;
-
- new_nodes = all_comparisons[depth - 1][depth].matches(path[depth-1]);
- new_nodes_i = new_nodes.begin();
- new_nodes_end = new_nodes.end();
- while(new_nodes_i != new_nodes_end)
- {
- //cout << " * species " << depth << " node: " << *new_nodes_i << endl;
- // check transitivity with previous nodes in path
- for(i = 0; i < depth - 1; i++)
- {
- trans_check_good = true;
- trans_check_nodes = all_comparisons[i][depth].matches(path[i]);
- if ( (trans_check_nodes.end() == find(trans_check_nodes.begin(),
- trans_check_nodes.end(),
- *new_nodes_i) ) &&
- (trans_check_nodes.end() == find(trans_check_nodes.begin(),
- trans_check_nodes.end(),
- *new_nodes_i * -1) ) )
- trans_check_good = false;
- }
-
- if (trans_check_good)
- {
- // this makes sure path nodes are recorded with RC status relative to
- // the base species
- if ( path[depth-1] >= 0)
- path.push_back(*new_nodes_i);
- else
- path.push_back(*new_nodes_i * -1);
-
- if (depth < species_num - 1)
- path_search(all_comparisons, path, depth + 1);
- else
- pathz.push_back(path);
- path.pop_back();
- }
- ++new_nodes_i;
- }
+ cout << "nway: species_num = " << species_num << ", thres = " << threshold
+ << ", softo = " << soft_thres << endl;
}
-// cout << " ****I have the power...\n";
-
-/* use this if I ever get the friggin seqcomp match lists to sort...
- if (binary_search(trans_check_nodes.begin(), trans_check_nodes.end(),
- *new_nodes_i))
-*/
void
-Nway_Paths::find_paths_r(vector<vector<FLPs> > all_comparisons)
+Nway_Paths::set_soft_thres(int sft_thres)
{
- vector<int> path;
- int win_i, window_num;
- list<int> new_nodes;
- list<int>::iterator new_nodes_i, new_nodes_end;
-
- pathz.clear();
- window_num = all_comparisons[0][1].win_num();
- cout << window_num << endl;
- // loop thru all windows in first species
- for (win_i = 0; win_i < window_num; win_i++)
- {
- path.clear();
- path.push_back(win_i);
- new_nodes = all_comparisons[0][1].matches(path[0]);
- new_nodes_i = new_nodes.begin();
- new_nodes_end = new_nodes.end();
- //if (new_nodes_i != new_nodes_end)
- //cout << "* species 0 node: " << win_i << endl;
- // cout << "foookin hell\n";
- path.push_back(0);
- while(new_nodes_i != new_nodes_end)
- {
- //cout << " * species 1 node: " << *new_nodes_i << endl;
- path[1] = *new_nodes_i;
- path_search(all_comparisons, path, 2);
- ++new_nodes_i;
- }
- }
+ soft_thres = sft_thres;
}
+
// dumbly goes thru and combines path windows exactly adjacent (ie + 1 index)
// doesn't deal with interleaved adjacency
void
vector<int> ext_path, cur_path, next_path, new_path;
list<vector<int> >::iterator pathz_i;
int i2, win_ext_len = 0;
- bool extending;
+ bool extending, end = false;
+ int count_loop = 0;
refined_pathz.clear();
+ cout << "path number is: " << pathz.size() << endl;
pathz_i = pathz.begin();
- ext_path = *pathz_i;
+ ext_path = *pathz_i;
+
while(pathz_i != pathz.end())
{
+ //cout << "path number is: " << pathz.size() << endl;
+ //++count_loop;
+ //cout << "glorpagh!!!!!" << count_loop << endl;
+
// keep track of current path and advance to next path
cur_path = *pathz_i;
++pathz_i;
- next_path = *pathz_i;
+ if (pathz_i == pathz.end())
+ end = true;
+ else
+ next_path = *pathz_i;
+
+ //cout << "S\'Nork!\n";
- // if node for each seq is equal to the next node+1 then for all
- // sequences then we are extending
- extending = true;
- for(i2 = 0; i2 < species_num; i2++)
+ if (not end)
{
- //cout << cur_path[i2] << " vs " << next_path[i2] << endl;
- if (cur_path[i2] + 1 != next_path[i2])
- extending = false;
+ // if node for each seq is equal to the next node+1 then for all
+ // sequences then we are extending
+ extending = true;
+ for(i2 = 0; i2 < species_num; i2++)
+ {
+ //cout << cur_path[i2] << " vs " << endl;
+ //cout << next_path[i2] << endl;
+ if (cur_path[i2] + 1 != next_path[i2])
+ extending = false;
+ }
}
+ else
+ extending = false;
+
if (extending)
{
//cout << "Raaaawwwrrr! I am extending\n";
}
else
{
+ //cout << "Larfnarg?\n";
// add the extend window length as first element and add as refined
new_path = ext_path;
new_path.insert(new_path.begin(),win_size + win_ext_len);
for(i2 = 1; i2 <= species_num; i2++)
{
- if (new_path[i2] < 0)
- {
- //cout << "before: " << new_path[i2];
- new_path[i2] += win_ext_len;
- //cout << " after: " << new_path[i2] << endl;
- }
+ if (new_path[i2] < 0)
+ {
+ //cout << "before: " << new_path[i2];
+ new_path[i2] += win_ext_len;
+ //cout << " after: " << new_path[i2] << endl;
+ }
}
refined_pathz.push_back(new_path);
// reset stuff
ext_path = next_path;
}
}
+ cout << "r_path number is: " << refined_pathz.size() << endl;
}
+
+void
+Nway_Paths::path_search(vector<vector<FLPs> > all_comparisons, vector<int> path, int depth)
+{
+ list<int> new_nodes, trans_check_nodes;
+ list<int>::iterator new_nodes_i, new_nodes_end;
+ int i;
+ bool trans_check_good;
+
+ new_nodes = all_comparisons[depth - 1][depth].matches(path[depth-1]);
+ new_nodes_i = new_nodes.begin();
+ new_nodes_end = new_nodes.end();
+ while(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(i = 0; i < depth - 1; i++)
+ {
+ trans_check_nodes = all_comparisons[i][depth].matches(path[i]);
+ if ( (trans_check_nodes.end() == find(trans_check_nodes.begin(),
+ trans_check_nodes.end(),
+ *new_nodes_i) ) &&
+ (trans_check_nodes.end() == find(trans_check_nodes.begin(),
+ trans_check_nodes.end(),
+ *new_nodes_i * -1) ) )
+ trans_check_good = false;
+ }
+
+ if (trans_check_good)
+ {
+ // this makes sure path nodes are recorded with RC status relative to
+ // the base species
+ if ( path[depth-1] >= 0)
+ path.push_back(*new_nodes_i);
+ else
+ path.push_back(*new_nodes_i * -1);
+
+ if (depth < species_num - 1)
+ path_search(all_comparisons, path, depth + 1);
+ else
+ pathz.push_back(path);
+ path.pop_back();
+ }
+ ++new_nodes_i;
+ }
+}
+// cout << " ****I have the power...\n";
+
+/* use this if I ever get the friggin seqcomp match lists to sort...
+ if (binary_search(trans_check_nodes.begin(), trans_check_nodes.end(),
+ *new_nodes_i))
+*/
+
+void
+Nway_Paths::find_paths_r(vector<vector<FLPs> > all_comparisons)
+{
+ vector<int> path;
+ int win_i, window_num;
+ list<int> new_nodes;
+ list<int>::iterator new_nodes_i, new_nodes_end;
+
+ pathz.clear();
+ window_num = all_comparisons[0][1].win_num();
+ cout << window_num << endl;
+ // loop thru all windows in first species
+ for (win_i = 0; win_i < window_num; win_i++)
+ {
+ path.clear();
+ path.push_back(win_i);
+ new_nodes = all_comparisons[0][1].matches(path[0]);
+ new_nodes_i = new_nodes.begin();
+ new_nodes_end = new_nodes.end();
+ //if (new_nodes_i != new_nodes_end)
+ //cout << "* species 0 node: " << win_i << endl;
+ // cout << "foookin hell\n";
+ path.push_back(0);
+ while(new_nodes_i != new_nodes_end)
+ {
+ //cout << " * species 1 node: " << *new_nodes_i << endl;
+ path[1] = *new_nodes_i;
+ path_search(all_comparisons, path, 2);
+ ++new_nodes_i;
+ }
+ }
+}
+
+
void
Nway_Paths::save_old(string save_file_path)
{
projects / mussa.git / blobdiff