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 #include "gui/SeqView.hpp"
16 #include <FL/fl_draw.H>
21 SeqView::setup(string name, int sq_num,
22 vector<Sequence> *some_seqs,
23 list<ConservedPath > some_paths, vector<int> some_lens,
24 vector<fltk_motif> *some_motifs)
33 the_motifs = some_motifs;
35 y_seq_incre = (y_max-10-10) / (seq_num - 1);
37 fl_font(FL_COURIER, 14);
38 cout << "font width: " << fl_width('A') << endl;
40 index_pad = 6 * (int) fl_width('A') + 5;
45 for(seq_i = 0; seq_i < seq_num; ++seq_i)
46 raw_sequence.push_back( (*S)[seq_i].get_seq() );
48 for(list<ConservedPath >::iterator pathz_i = P.begin();
52 show_aligns.push_back(true);
61 cout << x() << " " << y() << " " << w() << " " << h() << endl;
65 SeqView::resize(int new_x, int new_y, int new_w, int new_h)
72 // hmmm, why do I use these values on the the widgets inherent ones?
73 // I think there was a reason...once?
79 // things that need to be recalculated
80 y_seq_incre = (y_max-10-10) / (seq_num - 1);
90 // clear drawing area and set background to white
92 fl_rectf(x(), y(), w(), h());
94 fl_font(FL_COURIER, 14);
95 //blatantly stolen from FR2
96 ch_width = fl_width('A'); // monospaced: all characters are same width
101 int grey_box_num, grey_box_len;
103 // draw in some light grey boxes every 10bp to delineate for user
104 //fl_color(200,235,235);
105 fl_color(180,180,180);
106 grey_box_num = (((x_max - index_pad) / (int) ch_width) / 10) + 1;
107 grey_box_len = 10 * (int) ch_width;
108 for(i = 0; i < grey_box_num; i++)
110 fl_rectf(x()+index_pad-1 + (i * grey_box_len), y(), grey_box_len, h());
114 draw_motifs(ch_width);
116 draw_sequence(ch_width);
118 draw_match_lines(ch_width);
120 draw_indices(ch_width);
123 // draw some bounding boxes to visually separate things
124 fl_color(150,200,255);
125 fl_line_style(FL_SOLID, 2, NULL);
126 fl_rect(x(), y(), w(), h());
127 fl_rect(x()+index_pad-1, y(), w()-2*(index_pad-1), h());
131 SeqView::draw_motifs(double ch_width)
133 vector<fltk_motif>::iterator motif_i;
134 vector<int> some_motif_locs;
135 vector<int>::iterator i_locs;
136 int scale_len, motif_len, i2;
139 //fl_color(255,0,255);
140 fl_line_style(FL_SOLID, 10, NULL);
141 motif_i = the_motifs->begin();
142 while (motif_i != the_motifs->end())
144 fl_color(motif_i->color);
145 motif_len = motif_i->seq.length();
146 scale_len = (int) (motif_len * ch_width);
148 if (!motif_i->locations.empty())
149 for(i2 = 0; i2 < seq_num; i2++)
151 some_motif_locs = (*motif_i).locations[i2];
153 i_locs = some_motif_locs.begin();
154 while (i_locs != some_motif_locs.end())
156 x_start = (int) ((*i_locs +scroll_offset - seq_align_offsets[i2])
157 * ch_width) + index_pad + x();
159 //cout << *i_locs << ":" << x_start << " ";
160 // don't draw highlights outside of box range, they can wraparound past some boundry
161 if ((x_start > 0) && (x_start < w()))
162 fl_line(x_start,y_loc,x_start+scale_len,y_loc);
166 y_loc += y_seq_incre;
173 SeqView::draw_sequence(double ch_width)
178 int seq_len, sub_seq_start, sub_seq_len;
183 y_loc = y_min + 10 + 5;
185 for(seq_i = 0; seq_i < seq_num; seq_i++)
187 seq_len = raw_sequence[seq_i].length();
188 sub_seq_start = seq_align_offsets[seq_i] - scroll_offset;
189 sub_seq_len = (x_max - index_pad) / (int) ch_width;
190 //cout << x_max << " index_pad: " << index_pad << " y - ip: " << (x_max - index_pad) << endl;
192 // gotta check thru boundary conditions to make sure we're producing the
193 // right string for the current position (otherwise gonna crash due to
194 // illegal indexing into substr
195 if (sub_seq_start < 0)
197 sub_seq_len = sub_seq_len - sub_seq_start;
202 else if (sub_seq_start >= seq_len)
204 sub_seq_start = seq_len;
207 else if ((sub_seq_start + sub_seq_len) >= seq_len)
208 sub_seq_len = seq_len - sub_seq_start;
210 sub_seq = raw_sequence[seq_i].substr(sub_seq_start, sub_seq_len);
211 fl_draw(sub_seq.c_str(), index_pad, y_loc);
212 y_loc += y_seq_incre;
218 SeqView::draw_match_lines(double ch_width)
222 int x_start, y_start, x_end, y_end;
223 int window_length, win_i;
226 int offset1, offset2;
227 float center1, center2;
229 vector<bool> rc_list;
231 vector<bool> matched;
236 for(list<ConservedPath >::iterator pathz_i = P.begin();
240 if (show_aligns[align_counter])
242 ConservedPath& a_path = *pathz_i;
243 window_length = a_path.window_size;
244 // determine which parts of the path are RC relative to first species
245 rc_list = a_path.reverseComplimented();
247 // loop over each bp in the conserved region for all sequences
248 for(win_i = 0; win_i < window_length; win_i++)
250 // determine which exact base pairs match between the sequences
252 for(i2 = 0; i2 < a_path.size()-1; i2++)
254 // assume not rc as most likely, adjust below
257 // no matter the case, any RC node needs adjustments
259 rc_1 = window_length-1;
260 if (a_path[i2+1] < 0)
261 rc_2 = window_length-1;
263 x_start = (abs(a_path[i2]-rc_1+win_i));
264 x_end = (abs(a_path[i2+1]-rc_2+win_i));
267 // ugh, and xor...only want rc coloring if just one of the nodes is rc
268 // if both nodes are rc, then they are 'normal' relative to each other
269 if ( ( rc_list[i2] || rc_list[i2+1] ) &&
270 !(rc_list[i2] && rc_list[i2+1] ) )
271 { //the hideous rc matching logic - not complex, but annoying
272 if ( !( ( (raw_sequence[i2][x_start] == 'A') &&
273 (raw_sequence[i2+1][x_end] == 'T') ) ||
274 ( (raw_sequence[i2][x_start] == 'T') &&
275 (raw_sequence[i2+1][x_end] == 'A') ) ||
276 ( (raw_sequence[i2][x_start] == 'G') &&
277 (raw_sequence[i2+1][x_end] == 'C') ) ||
278 ( (raw_sequence[i2][x_start] == 'C') &&
279 (raw_sequence[i2+1][x_end] == 'G') ) ) )
284 if (!( (raw_sequence[i2][x_start] == raw_sequence[i2+1][x_end]) &&
285 (raw_sequence[i2][x_start] != 'N') &&
286 (raw_sequence[i2+1][x_end] != 'N') ) )
291 // draw for matches stretching across all sequences
294 fl_line_style(FL_SOLID, 1, NULL);
296 // now can draw the line for each bp in this window that matches
297 // grrr, need to ask if anyone cares if I switch the seq
301 for(i2 = 0; i2 < a_path.size()-1; i2++)
303 // assume not rc as most likely, adjust below
306 // this makes the lines start in the middle of the drawn char/bp
309 // no matter the case, any RC node needs adjustments
312 rc_1 = window_length;
317 rc_2 = window_length;
321 // set offset based on current alignment for which bp to show
322 offset1 = seq_align_offsets[i2];
323 offset2 = seq_align_offsets[i2+1];
325 if ( ( rc_list[i2] || rc_list[i2+1] ) &&
326 !(rc_list[i2] && rc_list[i2+1] ) )
331 // maybe shouldn't recalc these, but store values from first loop
332 x_start = (abs((int) (a_path[i2]-rc_1+win_i)));
333 x_end = (abs((int) (a_path[i2+1]-rc_2+win_i)));
335 fl_line( (int)((x_start+center1-offset1+scroll_offset)*ch_width)
336 + index_pad, y_loc + 10,
337 (int)((x_end+center2-offset2+scroll_offset)*ch_width)
338 + index_pad, y_loc+y_seq_incre );
339 y_loc += y_seq_incre;
349 SeqView::draw_indices(double ch_width)
354 ostringstream an_index;
358 // clear out space on sides to draw in index values
359 // I block out the sides rather than adding offsets to the drawing of seq
360 // and conservation lines since the lines need to draw off the 'edge'
362 fl_rectf(0, y_min, index_pad, h()+y_min);
363 fl_rectf(w()-index_pad, y_min, index_pad, h()+y_min);
365 // now can draw in the indices of the start and end of the shown sequence
367 y_loc = y_min + 10 + 5;
368 for(seq_i = 0; seq_i < seq_num; seq_i++)
371 an_index << (seq_align_offsets[seq_i]-scroll_offset);
372 fl_draw((an_index.str()).c_str(), 2, y_loc);
374 shown_seq_len = (w() - 2 * index_pad) / (int) ch_width;
376 an_index << (seq_align_offsets[seq_i]-scroll_offset+shown_seq_len);
377 fl_draw((an_index.str()).c_str(), w()-index_pad+2, y_loc);
378 y_loc += y_seq_incre;
384 SeqView::toggle_align(int align_num)
386 //cout << align_num << endl;
387 //cout << show_aligns[align_num] << endl;
388 show_aligns[align_num] = !show_aligns[align_num];
389 //cout << show_aligns[align_num] << endl;
394 SeqView::align_offsets(int align_num)
396 list<ConservedPath >::iterator pathz_i;
400 cout << "alignment: " << align_num << endl;
402 if (P.begin() == P.end())
403 cout << "crud....\n";
408 while(pathz_i != P.end())
411 // find the path specified
414 while( (i < align_num) && (pathz_i != P.end()) )
420 // now set the alignment offsets - basically where the path starts
421 seq_align_offsets.clear();
422 for(i = 0; i < seq_num ; i++)
424 //cout << (*pathz_i)[i+1] << endl;
425 seq_align_offsets.push_back( abs((*pathz_i).track_indexes[i]) );
426 // for testing purposes: to see everything in the short test sequences
427 //seq_align_offsets.push_back(0);
429 // reset any dragging done, otherwise might be hard to find selected align
437 SeqView::handle(int e)
441 // this empty string needs to be put on cout, otherwise the -O optimize
442 // compile option seems to throw this function away with the following:
443 // gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
449 if (Fl::event_button3())
451 cout << "menu menu menu!\n";
458 drag_change = Fl::event_x();
462 drag_change = Fl::event_x() - drag_change;
463 scroll_offset += drag_change;
464 drag_change = Fl::event_x();
470 //scroll_offset += Fl::event_x() - drag_start;
471 //scroll_dist = Fl::event_x() - drag_start;
472 //scroll_offset += scroll_dist;
473 //scroll_offset += scroll_pos;
480 return_value = Fl_Widget::handle(e);
487 SeqView::toggle_bars()
489 show_bars = !show_bars;
495 SeqView::toggle_motifs()
497 show_motifs = !show_motifs;
503 SeqView::reporter(string id, int value)
505 cout << id << " : " << value << endl;