binaries/src/mafft/core/Lalign11.c

   1 #include "mltaln.h"
   2 #include "dp.h"
   3
   4 #define DEBUG 0
   5 #define DEBUG2 0
   6 #define XXXXXXX    0
   7 #define USE_PENALTY_EX  1
   8
   9
  10 static TLS int localstop; // 060910
  11
  12 #if 1
  13 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
  14 {
  15         char *seq2 = s2[0];
  16         int *intptr;
  17
  18         intptr = amino_dis[(int)s1[0][i1]];
  19         while( lgth2-- )
  20                 *match++ = intptr[(int)*seq2++];
  21 }
  22 #else
  23 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
  24 {
  25         int j;
  26
  27         for( j=0; j<lgth2; j++ )
  28                 match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
  29 }
  30 #endif
  31
  32 #if 0
  33 static void match_calc_bk( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
  34 {
  35         int j, k, l;
  36         float scarr[26];
  37         float **cpmxpd = floatwork;
  38         int **cpmxpdn = intwork;
  39         int count = 0;
  40
  41         if( initialize )
  42         {
  43                 for( j=0; j<lgth2; j++ )
  44                 {
  45                         count = 0;
  46                         for( l=0; l<26; l++ )
  47                         {
  48                                 if( cpmx2[l][j] )
  49                                 {
  50                                         cpmxpd[count][j] = cpmx2[l][j];
  51                                         cpmxpdn[count][j] = l;
  52                                         count++;
  53                                 }
  54                         }
  55                         cpmxpdn[count][j] = -1;
  56                 }
  57         }
  58
  59         for( l=0; l<26; l++ )
  60         {
  61                 scarr[l] = 0.0;
  62                 for( k=0; k<26; k++ )
  63                         scarr[l] += n_dis[k][l] * cpmx1[k][i1];
  64         }
  65 #if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
  66         {
  67                 float *fpt, **fptpt, *fpt2;
  68                 int *ipt, **iptpt;
  69                 fpt2 = match;
  70                 iptpt = cpmxpdn;
  71                 fptpt = cpmxpd;
  72                 while( lgth2-- )
  73                 {
  74                         *fpt2 = 0.0;
  75                         ipt=*iptpt,fpt=*fptpt;
  76                         while( *ipt > -1 )
  77                                 *fpt2 += scarr[*ipt++] * *fpt++;
  78                         fpt2++,iptpt++,fptpt++;
  79                 }
  80         }
  81 #else
  82         for( j=0; j<lgth2; j++ )
  83         {
  84                 match[j] = 0.0;
  85                 for( k=0; cpmxpdn[k][j]>-1; k++ )
  86                         match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
  87         }
  88 #endif
  89 }
  90 #endif
  91
  92 static float Ltracking( float *lasthorizontalw, float *lastverticalw,
  93                                                 char **seq1, char **seq2,
  94                         char **mseq1, char **mseq2,
  95                         int **ijp, int *off1pt, int *off2pt, int endi, int endj )
  96 {
  97         int i, j, l, iin, jin, lgth1, lgth2, k, limk;
  98         int ifi=0, jfi=0; // by D.Mathog, a guess
  99 //      char gap[] = "-";
 100         char *gap;
 101         gap = newgapstr;
 102         lgth1 = strlen( seq1[0] );
 103         lgth2 = strlen( seq2[0] );
 104
 105 #if 0
 106         for( i=0; i<lgth1; i++ )
 107         {
 108                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 109         }
 110 #endif
 111
 112     for( i=0; i<lgth1+1; i++ )
 113     {
 114         ijp[i][0] = localstop;
 115     }
 116     for( j=0; j<lgth2+1; j++ )
 117     {
 118         ijp[0][j] = localstop;
 119     }
 120
 121         mseq1[0] += lgth1+lgth2;
 122         *mseq1[0] = 0;
 123         mseq2[0] += lgth1+lgth2;
 124         *mseq2[0] = 0;
 125         iin = endi; jin = endj;
 126         limk = lgth1+lgth2;
 127         for( k=0; k<=limk; k++ )
 128         {
 129                 if( ijp[iin][jin] < 0 )
 130                 {
 131                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 132                 }
 133                 else if( ijp[iin][jin] > 0 )
 134                 {
 135                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 136                 }
 137                 else
 138                 {
 139                         ifi = iin-1; jfi = jin-1;
 140                 }
 141                 l = iin - ifi;
 142                 while( --l )
 143                 {
 144                         *--mseq1[0] = seq1[0][ifi+l];
 145                         *--mseq2[0] = *gap;
 146                         k++;
 147                 }
 148                 l= jin - jfi;
 149                 while( --l )
 150                 {
 151                         *--mseq1[0] = *gap;
 152                         *--mseq2[0] = seq2[0][jfi+l];
 153                         k++;
 154                 }
 155
 156                 if( iin <= 0 || jin <= 0 ) break;
 157                 *--mseq1[0] = seq1[0][ifi];
 158                 *--mseq2[0] = seq2[0][jfi];
 159                 if( ijp[ifi][jfi] == localstop ) break;
 160                 k++;
 161                 iin = ifi; jin = jfi;
 162         }
 163         if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
 164         if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
 165
 166 //      fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
 167
 168
 169         return( 0.0 );
 170 }
 171
 172
 173 float L__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
 174 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 175 {
 176 //      int k;
 177         register int i, j;
 178         int lasti, lastj;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
 179         int lgth1, lgth2;
 180         int resultlen;
 181         float wm = 0.0;   /* int ?????? */
 182         float g;
 183         float *currentw, *previousw;
 184 #if 1
 185         float *wtmp;
 186         int *ijppt;
 187         float *mjpt, *prept, *curpt;
 188         int *mpjpt;
 189 #endif
 190         static TLS float mi, *m;
 191         static TLS int **ijp;
 192         static TLS int mpi, *mp;
 193         static TLS float *w1, *w2;
 194         static TLS float *match;
 195         static TLS float *initverticalw;    /* kufuu sureba iranai */
 196         static TLS float *lastverticalw;    /* kufuu sureba iranai */
 197         static TLS char **mseq1;
 198         static TLS char **mseq2;
 199         static TLS char **mseq;
 200 //      static TLS int **intwork;
 201 //      static TLS float **floatwork;
 202         static TLS int orlgth1 = 0, orlgth2 = 0;
 203         float maxwm;
 204         int endali = 0, endalj = 0; // by D.Mathog, a guess
 205 //      int endali, endalj;
 206         float localthr = -offset;
 207         float localthr2 = -offset;
 208 //      float localthr = 100;
 209 //      float localthr2 = 100;
 210         float fpenalty = (float)penalty;
 211         float fpenalty_ex = (float)penalty_ex;
 212
 213         if( seq1 == NULL )
 214         {
 215                 if( orlgth1 > 0 && orlgth2 > 0 )
 216                 {
 217                         orlgth1 = 0;
 218                         orlgth2 = 0;
 219                         free( mseq1 );
 220                         free( mseq2 );
 221                         FreeFloatVec( w1 );
 222                         FreeFloatVec( w2 );
 223                         FreeFloatVec( match );
 224                         FreeFloatVec( initverticalw );
 225                         FreeFloatVec( lastverticalw );
 226
 227                         FreeFloatVec( m );
 228                         FreeIntVec( mp );
 229
 230                         FreeCharMtx( mseq );
 231
 232                 }
 233                 return( 0.0 );
 234         }
 235
 236
 237         if( orlgth1 == 0 )
 238         {
 239                 mseq1 = AllocateCharMtx( njob, 0 );
 240                 mseq2 = AllocateCharMtx( njob, 0 );
 241         }
 242
 243
 244         lgth1 = strlen( seq1[0] );
 245         lgth2 = strlen( seq2[0] );
 246
 247         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 248         {
 249                 int ll1, ll2;
 250
 251                 if( orlgth1 > 0 && orlgth2 > 0 )
 252                 {
 253                         FreeFloatVec( w1 );
 254                         FreeFloatVec( w2 );
 255                         FreeFloatVec( match );
 256                         FreeFloatVec( initverticalw );
 257                         FreeFloatVec( lastverticalw );
 258
 259                         FreeFloatVec( m );
 260                         FreeIntVec( mp );
 261
 262                         FreeCharMtx( mseq );
 263
 264
 265
 266 //                      FreeFloatMtx( floatwork );
 267 //                      FreeIntMtx( intwork );
 268                 }
 269
 270                 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
 271                 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
 272
 273 #if DEBUG
 274                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
 275 #endif
 276
 277                 w1 = AllocateFloatVec( ll2+2 );
 278                 w2 = AllocateFloatVec( ll2+2 );
 279                 match = AllocateFloatVec( ll2+2 );
 280
 281                 initverticalw = AllocateFloatVec( ll1+2 );
 282                 lastverticalw = AllocateFloatVec( ll1+2 );
 283
 284                 m = AllocateFloatVec( ll2+2 );
 285                 mp = AllocateIntVec( ll2+2 );
 286
 287                 mseq = AllocateCharMtx( njob, ll1+ll2 );
 288
 289
 290 //              floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
 291 //              intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
 292
 293 #if DEBUG
 294                 fprintf( stderr, "succeeded\n" );
 295 #endif
 296
 297                 orlgth1 = ll1 - 100;
 298                 orlgth2 = ll2 - 100;
 299         }
 300
 301
 302         mseq1[0] = mseq[0];
 303         mseq2[0] = mseq[1];
 304
 305
 306         if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
 307         {
 308                 int ll1, ll2;
 309
 310                 if( commonAlloc1 && commonAlloc2 )
 311                 {
 312                         FreeIntMtx( commonIP );
 313                 }
 314
 315                 ll1 = MAX( orlgth1, commonAlloc1 );
 316                 ll2 = MAX( orlgth2, commonAlloc2 );
 317
 318 #if DEBUG
 319                 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 320 #endif
 321
 322                 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
 323
 324 #if DEBUG
 325                 fprintf( stderr, "succeeded\n\n" );
 326 #endif
 327
 328                 commonAlloc1 = ll1;
 329                 commonAlloc2 = ll2;
 330         }
 331         ijp = commonIP;
 332
 333
 334 #if 0
 335         for( i=0; i<lgth1; i++ )
 336                 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
 337 #endif
 338
 339         currentw = w1;
 340         previousw = w2;
 341
 342         match_calc( initverticalw, seq2, seq1, 0, lgth1 );
 343
 344         match_calc( currentw, seq1, seq2, 0, lgth2 );
 345
 346
 347         lasti = lgth2+1;
 348         for( j=1; j<lasti; ++j )
 349         {
 350                 m[j] = currentw[j-1]; mp[j] = 0;
 351 #if 0
 352                 if( m[j] < localthr ) m[j] = localthr2;
 353 #endif
 354         }
 355
 356         lastverticalw[0] = currentw[lgth2-1];
 357
 358         lasti = lgth1+1;
 359
 360 #if 0
 361 fprintf( stderr, "currentw = \n" );
 362 for( i=0; i<lgth1+1; i++ )
 363 {
 364         fprintf( stderr, "%5.2f ", currentw[i] );
 365 }
 366 fprintf( stderr, "\n" );
 367 fprintf( stderr, "initverticalw = \n" );
 368 for( i=0; i<lgth2+1; i++ )
 369 {
 370         fprintf( stderr, "%5.2f ", initverticalw[i] );
 371 }
 372 fprintf( stderr, "\n" );
 373 #endif
 374 #if DEBUG2
 375         fprintf( stderr, "\n" );
 376         fprintf( stderr, "       " );
 377         for( j=0; j<lgth2; j++ )
 378                 fprintf( stderr, "%c     ", seq2[0][j] );
 379         fprintf( stderr, "\n" );
 380 #endif
 381
 382         localstop = lgth1+lgth2+1;
 383         maxwm = -999999999.9;
 384 #if DEBUG2
 385         fprintf( stderr, "\n" );
 386         fprintf( stderr, "%c   ", seq1[0][0] );
 387
 388         for( j=0; j<lgth2+1; j++ )
 389                 fprintf( stderr, "%5.0f ", currentw[j] );
 390         fprintf( stderr, "\n" );
 391 #endif
 392
 393         for( i=1; i<lasti; i++ )
 394         {
 395                 wtmp = previousw;
 396                 previousw = currentw;
 397                 currentw = wtmp;
 398
 399                 previousw[0] = initverticalw[i-1];
 400
 401                 match_calc( currentw, seq1, seq2, i, lgth2 );
 402 #if DEBUG2
 403                 fprintf( stderr, "%c   ", seq1[0][i] );
 404                 fprintf( stderr, "%5.0f ", currentw[0] );
 405 #endif
 406
 407 #if XXXXXXX
 408 fprintf( stderr, "\n" );
 409 fprintf( stderr, "i=%d\n", i );
 410 fprintf( stderr, "currentw = \n" );
 411 for( j=0; j<lgth2; j++ )
 412 {
 413         fprintf( stderr, "%5.2f ", currentw[j] );
 414 }
 415 fprintf( stderr, "\n" );
 416 #endif
 417 #if XXXXXXX
 418 fprintf( stderr, "\n" );
 419 fprintf( stderr, "i=%d\n", i );
 420 fprintf( stderr, "currentw = \n" );
 421 for( j=0; j<lgth2; j++ )
 422 {
 423         fprintf( stderr, "%5.2f ", currentw[j] );
 424 }
 425 fprintf( stderr, "\n" );
 426 #endif
 427                 currentw[0] = initverticalw[i];
 428
 429                 mi = previousw[0]; mpi = 0;
 430
 431 #if 0
 432                 if( mi < localthr ) mi = localthr2;
 433 #endif
 434
 435                 ijppt = ijp[i] + 1;
 436                 mjpt = m + 1;
 437                 prept = previousw;
 438                 curpt = currentw + 1;
 439                 mpjpt = mp + 1;
 440                 lastj = lgth2+1;
 441                 for( j=1; j<lastj; j++ )
 442                 {
 443                         wm = *prept;
 444                         *ijppt = 0;
 445
 446 #if 0
 447                         fprintf( stderr, "%5.0f->", wm );
 448 #endif
 449 #if 0
 450                         fprintf( stderr, "%5.0f?", g );
 451 #endif
 452                         if( (g=mi+fpenalty) > wm )
 453                         {
 454                                 wm = g;
 455                                 *ijppt = -( j - mpi );
 456                         }
 457                         if( *prept > mi )
 458                         {
 459                                 mi = *prept;
 460                                 mpi = j-1;
 461                         }
 462
 463 #if USE_PENALTY_EX
 464                         mi += fpenalty_ex;
 465 #endif
 466
 467 #if 0
 468                         fprintf( stderr, "%5.0f?", g );
 469 #endif
 470                         if( (g=*mjpt+fpenalty) > wm )
 471                         {
 472                                 wm = g;
 473                                 *ijppt = +( i - *mpjpt );
 474                         }
 475                         if( *prept > *mjpt )
 476                         {
 477                                 *mjpt = *prept;
 478                                 *mpjpt = i-1;
 479                         }
 480 #if USE_PENALTY_EX
 481                         *mjpt += fpenalty_ex;
 482 #endif
 483
 484                         if( maxwm < wm )
 485                         {
 486                                 maxwm = wm;
 487                                 endali = i;
 488                                 endalj = j;
 489                         }
 490 #if 1
 491                         if( wm < localthr )
 492                         {
 493 //                              fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
 494                                 *ijppt = localstop;
 495                                 wm = localthr2;
 496                         }
 497 #endif
 498 #if 0
 499                         fprintf( stderr, "%5.0f ", *curpt );
 500 #endif
 501 #if DEBUG2
 502                         fprintf( stderr, "%5.0f ", wm );
 503 //                      fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
 504 #endif
 505
 506                         *curpt++ += wm;
 507                         ijppt++;
 508                         mjpt++;
 509                         prept++;
 510                         mpjpt++;
 511                 }
 512 #if DEBUG2
 513                 fprintf( stderr, "\n" );
 514 #endif
 515
 516                 lastverticalw[i] = currentw[lgth2-1];
 517         }
 518
 519
 520 #if 0
 521         fprintf( stderr, "maxwm = %f\n", maxwm );
 522         fprintf( stderr, "endali = %d\n", endali );
 523         fprintf( stderr, "endalj = %d\n", endalj );
 524 #endif
 525
 526         if( ijp[endali][endalj] == localstop )
 527         {
 528                 strcpy( seq1[0], "" );
 529                 strcpy( seq2[0], "" );
 530                 *off1pt = *off2pt = 0;
 531                 return( 0.0 );
 532         }
 533
 534         Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj );
 535
 536
 537         resultlen = strlen( mseq1[0] );
 538         if( alloclen < resultlen || resultlen > N )
 539         {
 540                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
 541                 ErrorExit( "LENGTH OVER!\n" );
 542         }
 543
 544
 545         strcpy( seq1[0], mseq1[0] );
 546         strcpy( seq2[0], mseq2[0] );
 547
 548 #if 0
 549         fprintf( stderr, "wm=%f\n", wm );
 550         fprintf( stderr, ">\n%s\n", mseq1[0] );
 551         fprintf( stderr, ">\n%s\n", mseq2[0] );
 552
 553         fprintf( stderr, "maxwm = %f\n", maxwm );
 554         fprintf( stderr, "   wm = %f\n",    wm );
 555 #endif
 556
 557         return( maxwm );
 558 }
 559