dynprog.cpp 11.2 KB
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
/*
  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, Marc Duez

  "Vidjil" is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation, either version 3 of the License, or
  (at your option) any later version.

  "Vidjil" is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with "Vidjil". If not, see <http://www.gnu.org/licenses/>
*/

#include "dynprog.h"
#include "tools.h"
#include <cassert>
#include <list>
#include <cstdlib>
#include <string>

#define SUBST 0
#define INSER 1
#define DELET 2
#define HOMO2X 3
#define HOMO2Y 4
#define FIN 5
Mikaël Salson's avatar
Mikaël Salson committed
33
#define BACKSIZE 120
Mikaël Salson's avatar
Mikaël Salson committed
34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104

using namespace std;


Cost::Cost(int match, int mismatch, int indel, int del_end, int homopolymer)
{
  this -> match = match ;
  this -> mismatch = mismatch ;
  this -> insertion = indel ;
  this -> deletion = indel ;
  this -> deletion_end = del_end ;
  this -> homopolymer = (homopolymer == MINUS_INF ? indel: homopolymer);
}


ostream& operator<<(ostream& out, const Cost& cost)
{
  out << "(" << cost.match 
      << ", " << cost.mismatch
      << "/" << cost.insertion
      << "/" << cost.deletion
      << ", " << cost.deletion_end
      << ", " << cost.homopolymer
      << ")" ;
  return out;
}

Cost::Cost()
{
}

int Cost::substitution(char a, char b)
{
  return (a == b) ? match : mismatch ;
}

/*
int Cost::ins(char current, char next)
{
  return (next == current) ? homopolymer : insertion ;
}

int Cost::del(char current, char next)
{
  return (next == current) ? homopolymer : deletion ;
}
*/

int Cost::homo2(char xa, char xb, char y)
{
  return ((xa == xb) && (xb == y)) ? homopolymer : MINUS_INF ;
}


DynProg::DynProg(const string &x, const string &y, DynProgMode mode, const Cost& cost, const bool reverse_x, const bool reverse_y)
{
  this -> x = reverse_x ? reverse(x) : x ;
  this -> y = reverse_y ? reverse(y) : y ;

  this -> reverse_x = reverse_x ;
  this -> reverse_y = reverse_y ;

  m = x.size();
  n = y.size();
  // cout << "Dynprog " << x << "(" << m << ") / " << y << "(" << n << ")" << endl ;

  S = new int*[m+1];
  for (int i = 0; i <= m; i++) {
    S[i] = new int[n+1];
  }
  
105
  B = new backtrack_info*[m+1];
Mikaël Salson's avatar
Mikaël Salson committed
106
  for (int i = 0; i <= m; i++) {
107
    B[i] = new backtrack_info[n+1];
Mikaël Salson's avatar
Mikaël Salson committed
108
  }
Mikaël Salson's avatar
Mikaël Salson committed
109
  
Mikaël Salson's avatar
Mikaël Salson committed
110 111 112 113 114 115 116
  this -> mode = mode;
  this -> cost = cost;

  this -> best_i = -1 ;
  this -> best_j = -1 ;
  this -> first_i = -1 ;
  this -> first_j = -1 ;
Mikaël Salson's avatar
Mikaël Salson committed
117 118 119 120
  
  gap1=NULL;
  gap2=NULL;
  linkgap=NULL;
Mikaël Salson's avatar
Mikaël Salson committed
121 122 123 124 125 126 127 128 129 130 131 132 133 134

  init();
}

DynProg::~DynProg() {
  for (int i = 0; i <= m; i++) {
    delete [] S[i];
  }
  delete [] S;
  
  for (int i = 0; i <= m; i++) {
    delete [] B[i];
  }
  delete [] B;
Mikaël Salson's avatar
Mikaël Salson committed
135 136 137 138
  
  delete [] gap1;
  delete [] gap2;
  delete [] linkgap;
Mikaël Salson's avatar
Mikaël Salson committed
139 140 141 142 143 144 145
}

void DynProg::init()
{ 
  if (mode == Local || mode == LocalEndWithSomeDeletions)
    for (int i=0; i<=m; i++)
      S[i][0] = 0 ;
Mathieu Giraud's avatar
Mathieu Giraud committed
146 147 148 149 150
  else if (mode == GlobalButMostlyLocal)
    for (int i=0; i<=m; i++)
      S[i][0] = i * cost.insertion / 2 ;
  else // Global, SemiGlobal
    for (int i=0; i<=m; i++)
Mikaël Salson's avatar
Mikaël Salson committed
151 152 153 154 155
      S[i][0] = i * cost.insertion ;
   
  if (mode == SemiGlobal || mode == SemiGlobalTrans || mode == Local || mode == LocalEndWithSomeDeletions)
    for (int j=0; j<=n; j++)
      S[0][j] = 0 ;
Mathieu Giraud's avatar
Mathieu Giraud committed
156 157 158
  else if (mode == GlobalButMostlyLocal)
    for (int j=0; j<=n; j++)
      S[0][j] = j * cost.deletion / 2 ;
Mikaël Salson's avatar
Mikaël Salson committed
159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174
  else
    for (int j=0; j<=n; j++)
      S[0][j] = j * cost.deletion ;
}

int DynProg::compute()
{
  best_score = MINUS_INF ;

  for (int i=1; i<=m; i++)
    for (int j=1; j<=n; j++)
    {
      int subst = S[i-1][j-1] + cost.substitution(x[i-1], y[j-1]);

      int inser = S[i-1][j] + cost.insertion;
      int delet = S[i][j-1] + cost.deletion;
Mathieu Giraud's avatar
Mathieu Giraud committed
175
      
Mikaël Salson's avatar
Mikaël Salson committed
176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203
      // Also dealing with homopolymers (in a dirty way!)
      // int inser = S[i-1][j] + (i > 1 ? cost.ins(x[i-2], x[i-1]) : cost.ins(0,1));
      // int delet = S[i][j-1] + (j > 1 ? cost.del(y[j-2], y[j-1]) : cost.del(0,1));

      int best = max(max(subst, inser), delet);

      // Homopolymers (2 <-> 1)
      int homo2x = i > 1 ? S[i-2][j-1] + cost.homo2(x[i-2], x[i-1], y[j-1]) : MINUS_INF ;
      int homo2y = j > 1 ? S[i-1][j-2] + cost.homo2(y[j-2], y[j-1], x[i-1]) : MINUS_INF ;
      best = max(max(homo2x, homo2y), best);
      
      if (mode == Local || mode == LocalEndWithSomeDeletions)
	{
	  best = max(0, best); 

	  int tbest = best ;

	  if (mode == LocalEndWithSomeDeletions)
	    tbest += cost.deletion_end*(n-j);   
     
	  if (tbest > best_score)
	    {
	      best_score = tbest ;
	      best_i = i ;
	      best_j = j ;
	    }
	    
	  if (best == 0){
204
	    B[i][j].type = FIN;
Mikaël Salson's avatar
Mikaël Salson committed
205 206 207 208 209 210
	  }
	}
      
      S[i][j] = best ;
      
      if (best==subst){
211 212 213
	B[i][j].i = i-1 ;
	B[i][j].j = j-1 ;
	B[i][j].type = SUBST ;
Mikaël Salson's avatar
Mikaël Salson committed
214 215
      }
      if (best==inser){
216 217 218
	B[i][j].i = i-1 ;
	B[i][j].j = j ;
	B[i][j].type = INSER ;
Mikaël Salson's avatar
Mikaël Salson committed
219 220
      }
      if (best==delet){
221 222 223
	B[i][j].i = i ;
	B[i][j].j = j-1 ;
	B[i][j].type = DELET ;
Mikaël Salson's avatar
Mikaël Salson committed
224 225
      }
      if (best==homo2x){
226 227 228 229
	B[i][j].i = i-2 ;
	if (B[i][j].i < 0) B[i][j].i = 0 ;
	B[i][j].j = j-1 ;
	B[i][j].type = HOMO2X ;
Mikaël Salson's avatar
Mikaël Salson committed
230 231
      }
      if (best==homo2y){
232 233 234 235
	B[i][j].i = i-1 ;
	B[i][j].j = j-2 ;
	if (B[i][j].j < 0) B[i][j].j = 0 ;
	B[i][j].type = HOMO2Y ;
Mikaël Salson's avatar
Mikaël Salson committed
236
      }
Mikaël Salson's avatar
Mikaël Salson committed
237

Mikaël Salson's avatar
Mikaël Salson committed
238 239 240 241
      
      if (mode == Local || mode == LocalEndWithSomeDeletions)
	{
      	  if (best == 0){
242
	    B[i][j].type = FIN;
Mikaël Salson's avatar
Mikaël Salson committed
243 244 245 246 247 248 249 250
	  }
	}
      
    }

  if (mode == Local || mode == LocalEndWithSomeDeletions)
    {
      for (int i=0; i<=n; i++){
251
	B[0][i].type = FIN;
Mikaël Salson's avatar
Mikaël Salson committed
252 253
      }
      for (int i=0; i<=m; i++){
254
	B[i][0].type = FIN;
Mikaël Salson's avatar
Mikaël Salson committed
255 256 257 258 259 260 261 262 263 264 265 266 267 268
      }
      
    }
  if (mode == SemiGlobal)
    {
      best_i = m ;
      
      for (int j=1; j<=n; j++)
	if (S[m][j] > best_score)
	  {
	    best_score = S[m][j] ;
	    best_j = j ;
	  }
      for (int i=1; i<=n; i++){
269 270 271
	B[0][i].i = 0 ;
	B[0][i].j = i-1 ;
	B[0][i].type = DELET;
Mikaël Salson's avatar
Mikaël Salson committed
272 273
      }
      for (int i=0; i<=m; i++){
274
	B[i][0].type = FIN;
Mikaël Salson's avatar
Mikaël Salson committed
275 276 277 278 279 280 281 282 283 284 285 286 287 288 289
      }
    }

  if (mode == SemiGlobalTrans)
    {
      best_j = n ;
      
      for (int i=1; i<=m; i++)
	if (S[i][n] > best_score)
	  {
	    best_score = S[i][n] ;
	    best_i = i ;
	  }
	  
      for (int i=0; i<=n; i++){
290
	B[0][i].type = FIN;
Mikaël Salson's avatar
Mikaël Salson committed
291 292
      }
      for (int i=0; i<=m; i++){
293 294 295
	B[i][0].i = i-1 ;
	B[i][0].j = 0 ;
	B[i][0].type = INSER;
Mikaël Salson's avatar
Mikaël Salson committed
296 297 298 299
      }
    }


Mathieu Giraud's avatar
Mathieu Giraud committed
300
  if ((mode == Global) || (mode == GlobalButMostlyLocal))
Mikaël Salson's avatar
Mikaël Salson committed
301 302 303 304 305 306
    {
      best_i = m ;
      best_j = n ;
      best_score = S[m][n];

      for (int i=0; i<=m; i++){
307 308 309
	B[i][0].i = i-1 ;
	B[i][0].j = 0 ;
	B[i][0].type = INSER;
Mikaël Salson's avatar
Mikaël Salson committed
310 311
      }
      for (int i=1; i<=n; i++){
312 313 314
	B[0][i].i = 0 ;
	B[0][i].j = i-1 ;
	B[0][i].type = DELET;
Mikaël Salson's avatar
Mikaël Salson committed
315
      }
316
      B[0][0].type = FIN;
Mikaël Salson's avatar
Mikaël Salson committed
317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333
    }

  if (reverse_x)
    best_i = m - best_i + 1 ;

  if (reverse_y)
    best_j = n - best_j + 1;

  // In the matrix positions start at 1, but start positions may start at 0
  best_i -= 1;   
  best_j -= 1;

  return best_score ;
}

void DynProg::backtrack()
{
Mikaël Salson's avatar
Mikaël Salson committed
334 335 336 337
  gap1 = new int[x.size()+1];
  linkgap = new int[x.size()+1];
  gap2 = new int[y.size()+1];
      
338
  for (unsigned int i = 0; i <=x.size(); i++) {
Mikaël Salson's avatar
Mikaël Salson committed
339 340 341
    gap1[i] = 0;
    linkgap[i] = 0;
  }
342
  for (unsigned int i = 0; i <= y.size(); i++) {
Mikaël Salson's avatar
Mikaël Salson committed
343 344 345 346 347 348 349 350 351
    gap2[i] = 0;
  }
  
  
  int g1=x.size();
  int g2=y.size();
  
  int ti=best_i+1;
  int tj=best_j+1;
Mikaël Salson's avatar
Mikaël Salson committed
352 353 354 355 356 357 358 359 360 361 362 363 364
  int tmpi, tmpj;
  tmpi=ti;
  tmpj=tj;
  
  str_back = "";
  string str1, str2, str3;
  
  ostringstream back_s1;
  ostringstream back_s2;
  ostringstream back_tr;
  ostringstream back;
  
  
365
  while ( B[ti][tj].type != FIN ){
Mikaël Salson's avatar
Mikaël Salson committed
366
    
367 368
    tmpi=B[ti][tj].i;
    tmpj=B[ti][tj].j;
Mikaël Salson's avatar
Mikaël Salson committed
369

370
    if (B[ti][tj].type == SUBST ){
Mikaël Salson's avatar
Mikaël Salson committed
371
      linkgap[g1]=g2;
Mikaël Salson's avatar
Mikaël Salson committed
372
      back_s1 << x[ti-1];
Mikaël Salson's avatar
Mikaël Salson committed
373
      g1--;
Mikaël Salson's avatar
Mikaël Salson committed
374
      back_s2 << y[tj-1];
Mikaël Salson's avatar
Mikaël Salson committed
375 376
      g2--;

Mikaël Salson's avatar
Mikaël Salson committed
377 378 379 380 381
      if(x[ti-1]==y[tj-1]) {
	back_tr << "|";
      }else{
	back_tr << ":";
      }
Mikaël Salson's avatar
Mikaël Salson committed
382
      
Mikaël Salson's avatar
Mikaël Salson committed
383
    }
384
    if (B[ti][tj].type == INSER ){
Mikaël Salson's avatar
Mikaël Salson committed
385
      linkgap[g1]=g2;
Mikaël Salson's avatar
Mikaël Salson committed
386
      back_s1 << x[ti-1];
Mikaël Salson's avatar
Mikaël Salson committed
387
      g1--;
Mikaël Salson's avatar
Mikaël Salson committed
388
      back_s2 << " ";
Mikaël Salson's avatar
Mikaël Salson committed
389
      gap2[g2]++;
Mikaël Salson's avatar
Mikaël Salson committed
390
      back_tr << ".";
Mikaël Salson's avatar
Mikaël Salson committed
391
      
Mikaël Salson's avatar
Mikaël Salson committed
392
    }
393
    if (B[ti][tj].type == DELET){
Mikaël Salson's avatar
Mikaël Salson committed
394
    linkgap[g1]=g2;
Mikaël Salson's avatar
Mikaël Salson committed
395
      back_s1 << " ";
Mikaël Salson's avatar
Mikaël Salson committed
396
      gap1[g1]++;
Mikaël Salson's avatar
Mikaël Salson committed
397
      back_s2 << y[tj-1];
Mikaël Salson's avatar
Mikaël Salson committed
398
      g2--;
Mikaël Salson's avatar
Mikaël Salson committed
399
      back_tr << ".";
Mikaël Salson's avatar
Mikaël Salson committed
400
      
Mikaël Salson's avatar
Mikaël Salson committed
401
    }
402
    if (B[ti][tj].type == HOMO2X ){
Mikaël Salson's avatar
Mikaël Salson committed
403
      linkgap[g1]=g2;
Mikaël Salson's avatar
Mikaël Salson committed
404
      back_s1 << x[ti-1] << x[ti-2];
Mikaël Salson's avatar
Mikaël Salson committed
405 406 407
      g1--;
      linkgap[g1]=g2;
      g1--;
Mikaël Salson's avatar
Mikaël Salson committed
408
      back_s2  << " " << y[tj-1];
Mikaël Salson's avatar
Mikaël Salson committed
409 410 411
      gap2[g2]++;
      g2--;
      back_tr << " h";
Mikaël Salson's avatar
Mikaël Salson committed
412 413 414

    }
      
415
    if (B[ti][tj].type == HOMO2Y ){
Mikaël Salson's avatar
Mikaël Salson committed
416
    linkgap[g1]=g2;
Mikaël Salson's avatar
Mikaël Salson committed
417
      back_s1 << " " << x[ti-1] ;
Mikaël Salson's avatar
Mikaël Salson committed
418 419
      gap1[g1]++;
      g1--;
Mikaël Salson's avatar
Mikaël Salson committed
420
      back_s2 <<  y[tj-1] << y[tj-2] ;
Mikaël Salson's avatar
Mikaël Salson committed
421 422 423
      g2--;
      g2--;
      back_tr << " h";
Mikaël Salson's avatar
Mikaël Salson committed
424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450
    }
    
    ti=tmpi;
    tj=tmpj;
  }

  str1=back_s1.str();
  str1 =string (str1.rbegin(), str1.rend());
  str1 = str1;
  str2=back_tr.str();
  str2 = string (str2.rbegin(), str2.rend());
  str3=back_s2.str();
  str3 = string (str3.rbegin(), str3.rend());
  
  back << ti <<	"  >>	" << str1.substr(0, BACKSIZE-8) << endl;
  back << " diff	" << str2.substr(0, BACKSIZE-8) << endl;
  back << tj <<	"  >>	" << str3.substr(0, BACKSIZE-8) << endl << endl;
  for (size_t k=0 ; (BACKSIZE-8+k*BACKSIZE)< str1.length() ; k++){
    back << str1.substr(BACKSIZE-8+k*BACKSIZE, BACKSIZE) << endl;
    back << str2.substr(BACKSIZE-8+k*BACKSIZE, BACKSIZE) << endl;
    back << str3.substr(BACKSIZE-8+k*BACKSIZE, BACKSIZE) << endl << endl;
  }
  
  first_i=ti;
  first_j=tj;
  
  str_back=back.str();
Mathieu Giraud's avatar
Mathieu Giraud committed
451 452

  // cout << str_back << endl ;
Mikaël Salson's avatar
Mikaël Salson committed
453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536
}


float identity_percent(int score)
{
  int match = (score + IdentityDirty.match/2) / IdentityDirty.match ;

  int mismatch = (score - match * IdentityDirty.match) / IdentityDirty.mismatch ;

  float pcent = (100. * (float) match) / (match + mismatch) ;

  // cout << score << "  " << match << "  " << mismatch << "  " << pcent << endl ; 

  return pcent ;
}


ostream& operator<<(ostream& out, const DynProg& dp)
{
  out << "       " ;

  for (int j=0; j<dp.n; j++)
    out << setw(4) << dp.y[j] << " ";

  out << endl ;

  for (int i=0; i<=dp.m; i++)
    {
      if (i)
	out << dp.x[i-1] << " " ;
      else
	out << "  " ;

      for (int j=0; j<=dp.n; j++)
	out << setw(4) << dp.S[i][j] << " ";

      out << endl ;      
    }
  
  out << "best: " << dp.best_i << "," << dp.best_j << endl;

  return out ;
}


Cost strToCost(string str, Cost default_cost){

  if (str.length()!=0){
    string::size_type stTemp = str.find(',');
	  
    std::list<int> val;
    
    while(stTemp != string::npos)
    {
	  val.push_back(atoi(str.substr(0, stTemp).c_str() ) );
	  str = str.substr(stTemp + 1);
	  stTemp = str.find(',');
    }
    val.push_back(atoi(str.c_str() ) );

    if (val.size()==5){ 
      int val1=val.front();
      val.pop_front();
      int val2=val.front();
      val.pop_front();
      int val3=val.front();
      val.pop_front();
      int val4=val.front();
      val.pop_front();
      int val5=val.front();
      val.pop_front();
      Cost result = Cost(val1, val2, val3, val4, val5);
      cout << "use custom Cost "<< result << endl;
      return result;
    }
    
    cout << "incorrect Cost format, use default "<< default_cost<<endl;
  }
  
  return default_cost;
}