[project @ 4]

[mussa.git] / mussa_gui_seq.cc

diff --git a/mussa_gui_seq.cc b/mussa_gui_seq.cc
index bf1afb3a2ef5fdec116493ef96cfdd4ee8c0235f..4cf34afc56b638e9fba46310075e205f75cc09f7 100644 (file)
--- a/mussa_gui_seq.cc
+++ b/mussa_gui_seq.cc
@@ -2,13 +2,12 @@
 
 
 void
-SeqView::setup(string name, int sq_num, int win_len, 
+SeqView::setup(string name, int sq_num, 
                vector<Sequence> *some_seqs,
-               Nway_Paths *some_paths, vector<int> some_lens)
+               list<vector<int> > some_paths, vector<int> some_lens)
 {
   ana_name = name;
   seq_num = sq_num;
-  base_window_len = win_len;
   S = some_seqs;
   P = some_paths;
   seq_lens = some_lens;
@@ -17,6 +16,8 @@ SeqView::setup(string name, int sq_num, int win_len,
 
   fl_font(FL_COURIER, 14);
   cout << fl_width('A') << endl;
+
+  align_offsets(0);
 }
 
 
@@ -34,9 +35,11 @@ SeqView::draw()
   int window_length, win_i;
   int rc_1 = 0; 
   int rc_2 = 0;
+  string sub_seq;
+  int offset1, offset2;
+  float center1, center2;
 
 
-  window_length = base_window_len;
   fl_font(FL_COURIER, 14);
   fl_color(FL_BLACK);
   //blatantly stolen from FR2
@@ -45,52 +48,149 @@ SeqView::draw()
   y_loc = 10;
   for(seq_i = seq_num-1; seq_i >= 0; --seq_i)
   {
-    //a_seq = a_seq;
-    fl_draw((*S)[seq_i].c_seq(), 0+x(), y_loc+y()); 
+    sub_seq = (*S)[seq_i].seq();
+    sub_seq = sub_seq.substr(seq_align_offsets[seq_i]);
+    fl_draw(sub_seq.c_str(), 0+x(), y_loc+y()); 
     y_loc += y_seq_incre;
   }
 
   fl_color(FL_RED);
   fl_line_style(FL_SOLID, 1, NULL);
-  //fl_line(x(),10+y(),20+x(),y_max/2 + y());
-
-      //fl_color(FL_RED);
-
 
-  for(pathz_i = P->pathz.begin(); pathz_i != P->pathz.end(); ++pathz_i)
+  for(pathz_i = P.begin(); pathz_i != P.end(); ++pathz_i)
   {
     a_path = *pathz_i;
     y_loc = 0;
-    for(i2 = seq_num - 1; i2 > 0; i2--)
+    window_length = a_path[0];
+    for(i2 = seq_num; i2 > 1; i2--)
     {
       // RC case handling
 
-      // ugh, and xor...only want black if one of the nodes is rc
+      // ugh, and xor...only want rc coloring if just one of the nodes is rc
       if ( ((a_path[i2] < 0) || (a_path[i2-1] < 0)) &&
            !((a_path[i2] < 0) && (a_path[i2-1] < 0)) )
         fl_color(FL_BLUE);
 
+      offset1 = seq_align_offsets[i2-1];
+      offset2 = seq_align_offsets[i2-2];
+      center1 = 0.5;
+      center2 = 0.5;
+
       // no matter the case, any RC node needs an offset
       if (a_path[i2] < 0)
+      {
         rc_1 = window_length;        
+        offset1 = -offset1;
+        center1 = -center1;
+      }
       if (a_path[i2-1] < 0)
+      {
         rc_2 = window_length;        
-      // normal case
+        offset2 = -offset2;
+        center2 = -center2;
+      }
+
+      // draw the line for each bp in this window that actually matches
       for(win_i = 0; win_i < window_length; win_i++)
-        fl_line(abs((int)((a_path[i2]-rc_1+win_i+x()+0.5)*ch_width)),
-                y_loc + 10+y(),
-                abs((int)((a_path[i2-1]-rc_2+win_i+x()+0.5)*ch_width)),
-                y_loc+y_seq_incre+y());
+      {
+        x_start = abs((int) (a_path[i2]-rc_1+win_i-offset1) );
+        x_end = abs((int) (a_path[i2-1]-rc_2+win_i-offset2) );
+        fl_line( (x_start+center1)*ch_width, y_loc + 10,
+                 (x_end+center2)*ch_width, y_loc+y_seq_incre );
+      }
       y_loc += y_seq_incre;
-      //if ((a_path[i2] < 0) || (a_path[i2-1] < 0))
-      //{
-        fl_color(FL_RED);
-        rc_1 = 0;
-        rc_2 = 0;
-        //}
+      fl_color(FL_RED);
+      rc_1 = 0;
+      rc_2 = 0;
     }
   }
 }
+
+void
+SeqView::debug_draw()
+{
+  int seq_i;
+  Sequence a_seq;
+  int i, y_loc;
+  vector<int> a_path;
+  list<vector<int> >::iterator pathz_i;
+  int i2;
+  int x_start, y_start, x_end, y_end;
+  double ch_width;
+  int window_length, win_i;
+  int rc_1 = 0; 
+  int rc_2 = 0;
+  string sub_seq;
+
+
+  cout << "debugging...\n";
+  y_loc = 10;
+  for(seq_i = seq_num-1; seq_i >= 0; --seq_i)
+  {
+    sub_seq = (*S)[seq_i].seq();
+    cout << sub_seq << endl;
+    sub_seq = sub_seq.substr(seq_align_offsets[seq_i]);
+    cout << sub_seq << endl;
+    //fl_draw(sub_seq.c_str(), 0+x(), y_loc+y());     
+    y_loc += y_seq_incre;
+  }
+}
+
+void
+SeqView::align_offsets(int align_num)
+{
+  list<vector<int> >::iterator pathz_i;
+  int i;
+
+
+  if (P.begin() == P.end())
+    cout << "crud....\n";
+  pathz_i = P.begin();
+  while(pathz_i != P.end())
+  {
+    //cout << (*pathz_i)[0] << endl;
+    ++pathz_i;
+  }
+
+  // find the path specified
+  i = 0;
+  pathz_i = P.begin();
+  cout << "fee\n";
+  while( (i < align_num) && (pathz_i != P.end()) )
+  {
+  cout << "fie\n";
+    ++i;
+    ++pathz_i;
+  }
+
+  cout << "foe\n";
+  // now set the alignment offsets - basically where the path starts
+  seq_align_offsets.clear();
+  for(i = 0; i < seq_num; i++)
+  {
+    cout << (*pathz_i)[i+1] << endl;
+    seq_align_offsets.push_back( (*pathz_i)[i+1] );
+  }
+  cout << "fum\n";
+}
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 /*
       x_start = (int) ();
       y_start = ;