website/archive/binaries/mac/src/mafft/core/Galign11.c

   1 #include "mltaln.h"
   2 #include "dp.h"
   3
   4 #define DEBUG 0
   5 #define XXXXXXX    0
   6 #define USE_PENALTY_EX  1
   7
   8
   9 #if 1
  10 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
  11 {
  12         char *seq2 = s2[0];
  13         int *intptr = amino_dis[(int)s1[0][i1]];
  14
  15         while( lgth2-- )
  16                 *match++ = intptr[(int)*seq2++];
  17 }
  18 static void match_calc_mtx( int mtx[0x80][0x80], float *match, char **s1, char **s2, int i1, int lgth2 )
  19 {
  20         char *seq2 = s2[0];
  21         int *intptr = mtx[(int)s1[0][i1]];
  22
  23         while( lgth2-- )
  24                 *match++ = intptr[(int)*seq2++];
  25 }
  26 #else
  27 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
  28 {
  29         int j;
  30
  31         for( j=0; j<lgth2; j++ )
  32                 match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
  33 }
  34 #endif
  35
  36 static float Atracking( float *lasthorizontalw, float *lastverticalw,
  37                                                 char **seq1, char **seq2,
  38                         char **mseq1, char **mseq2,
  39                         int **ijp,
  40                                                 int tailgp )
  41 {
  42         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
  43 //      char gap[] = "-";
  44         char *gap;
  45         gap = newgapstr;
  46         lgth1 = strlen( seq1[0] );
  47         lgth2 = strlen( seq2[0] );
  48         float wm;
  49
  50
  51 #if 0
  52         for( i=0; i<lgth1; i++ )
  53         {
  54                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
  55         }
  56 #endif
  57
  58     for( i=0; i<lgth1+1; i++ )
  59     {
  60         ijp[i][0] = i + 1;
  61     }
  62     for( j=0; j<lgth2+1; j++ )
  63     {
  64         ijp[0][j] = -( j + 1 );
  65     }
  66
  67         if( tailgp == 1 )
  68                 ;
  69         else
  70         {
  71                 wm = lastverticalw[0];
  72                 for( i=0; i<lgth1; i++ )
  73                 {
  74                         if( lastverticalw[i] >= wm )
  75                         {
  76                                 wm = lastverticalw[i];
  77                                 iin = i; jin = lgth2-1;
  78                                 ijp[lgth1][lgth2] = +( lgth1 - i );
  79                         }
  80                 }
  81                 for( j=0; j<lgth2; j++ )
  82                 {
  83                         if( lasthorizontalw[j] >= wm )
  84                         {
  85                                 wm = lasthorizontalw[j];
  86                                 iin = lgth1-1; jin = j;
  87                                 ijp[lgth1][lgth2] = -( lgth2 - j );
  88                         }
  89                 }
  90         }
  91
  92
  93
  94         mseq1[0] += lgth1+lgth2;
  95         *mseq1[0] = 0;
  96         mseq2[0] += lgth1+lgth2;
  97         *mseq2[0] = 0;
  98
  99
 100         iin = lgth1; jin = lgth2;
 101         limk = lgth1+lgth2 + 1;
 102         for( k=0; k<limk; k++ )
 103         {
 104                 if( ijp[iin][jin] < 0 )
 105                 {
 106                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 107                 }
 108                 else if( ijp[iin][jin] > 0 )
 109                 {
 110                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 111                 }
 112                 else
 113                 {
 114                         ifi = iin-1; jfi = jin-1;
 115                 }
 116                 l = iin - ifi;
 117                 while( --l )
 118                 {
 119                         *--mseq1[0] = seq1[0][ifi+l];
 120                         *--mseq2[0] = *gap;
 121                         k++;
 122                 }
 123                 l= jin - jfi;
 124                 while( --l )
 125                 {
 126                         *--mseq1[0] = *gap;
 127                         *--mseq2[0] = seq2[0][jfi+l];
 128                         k++;
 129                 }
 130                 if( iin <= 0 || jin <= 0 ) break;
 131                 *--mseq1[0] = seq1[0][ifi];
 132                 *--mseq2[0] = seq2[0][jfi];
 133                 k++;
 134                 iin = ifi; jin = jfi;
 135         }
 136         return( 0.0 );
 137 }
 138
 139
 140 float G__align11( char **seq1, char **seq2, int alloclen, int headgp, int tailgp )
 141 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 142 {
 143 //      int k;
 144         register int i, j;
 145         int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
 146         int lgth1, lgth2;
 147         int resultlen;
 148         float wm;   /* int ?????? */
 149         float g;
 150         float *currentw, *previousw;
 151         float fpenalty = (float)penalty;
 152 #if USE_PENALTY_EX
 153         float fpenalty_ex = (float)penalty_ex;
 154 #endif
 155 #if 1
 156         float *wtmp;
 157         int *ijppt;
 158         float *mjpt, *prept, *curpt;
 159         int *mpjpt;
 160 #endif
 161         static TLS float mi, *m;
 162         static TLS int **ijp;
 163         static TLS int mpi, *mp;
 164         static TLS float *w1, *w2;
 165         static TLS float *match;
 166         static TLS float *initverticalw;    /* kufuu sureba iranai */
 167         static TLS float *lastverticalw;    /* kufuu sureba iranai */
 168         static TLS char **mseq1;
 169         static TLS char **mseq2;
 170         static TLS char **mseq;
 171         static TLS int **intwork;
 172         static TLS float **floatwork;
 173         static TLS int orlgth1 = 0, orlgth2 = 0;
 174
 175         if( seq1 == NULL )
 176         {
 177                 if( orlgth1 > 0 && orlgth2 > 0 )
 178                 {
 179                         orlgth1 = 0;
 180                         orlgth2 = 0;
 181                         free( mseq1 );
 182                         free( mseq2 );
 183                         FreeFloatVec( w1 );
 184                         FreeFloatVec( w2 );
 185                         FreeFloatVec( match );
 186                         FreeFloatVec( initverticalw );
 187                         FreeFloatVec( lastverticalw );
 188
 189                         FreeFloatVec( m );
 190                         FreeIntVec( mp );
 191
 192                         FreeCharMtx( mseq );
 193
 194
 195
 196                         FreeFloatMtx( floatwork );
 197                         FreeIntMtx( intwork );
 198                 }
 199                 return( 0.0 );
 200         }
 201
 202         lgth1 = strlen( seq1[0] );
 203         lgth2 = strlen( seq2[0] );
 204
 205         if( lgth1 <= 0 || lgth2 <= 0 )
 206         {
 207                 fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
 208         }
 209
 210 #if 1
 211         if( lgth1 == 0 && lgth2 == 0 )
 212                 return( 0.0 );
 213
 214         if( lgth1 == 0 )
 215         {
 216                 seq1[0][lgth2] = 0;
 217                 while( lgth2 ) seq1[0][--lgth2] = '-';
 218 //              fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
 219                 return( 0.0 );
 220         }
 221
 222         if( lgth2 == 0 )
 223         {
 224                 seq2[0][lgth1] = 0;
 225                 while( lgth1 ) seq2[0][--lgth1] = '-';
 226 //              fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
 227                 return( 0.0 );
 228         }
 229 #endif
 230
 231
 232         wm = 0.0;
 233
 234         if( orlgth1 == 0 )
 235         {
 236                 mseq1 = AllocateCharMtx( njob, 0 );
 237                 mseq2 = AllocateCharMtx( njob, 0 );
 238         }
 239
 240
 241
 242         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 243         {
 244                 int ll1, ll2;
 245
 246                 if( orlgth1 > 0 && orlgth2 > 0 )
 247                 {
 248                         FreeFloatVec( w1 );
 249                         FreeFloatVec( w2 );
 250                         FreeFloatVec( match );
 251                         FreeFloatVec( initverticalw );
 252                         FreeFloatVec( lastverticalw );
 253
 254                         FreeFloatVec( m );
 255                         FreeIntVec( mp );
 256
 257                         FreeCharMtx( mseq );
 258
 259
 260
 261                         FreeFloatMtx( floatwork );
 262                         FreeIntMtx( intwork );
 263                 }
 264
 265                 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
 266                 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
 267
 268 #if DEBUG
 269                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
 270 #endif
 271
 272                 w1 = AllocateFloatVec( ll2+2 );
 273                 w2 = AllocateFloatVec( ll2+2 );
 274                 match = AllocateFloatVec( ll2+2 );
 275
 276                 initverticalw = AllocateFloatVec( ll1+2 );
 277                 lastverticalw = AllocateFloatVec( ll1+2 );
 278
 279                 m = AllocateFloatVec( ll2+2 );
 280                 mp = AllocateIntVec( ll2+2 );
 281
 282                 mseq = AllocateCharMtx( njob, ll1+ll2 );
 283
 284
 285                 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
 286                 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
 287
 288 #if DEBUG
 289                 fprintf( stderr, "succeeded\n" );
 290 #endif
 291
 292                 orlgth1 = ll1 - 100;
 293                 orlgth2 = ll2 - 100;
 294         }
 295
 296
 297         mseq1[0] = mseq[0];
 298         mseq2[0] = mseq[1];
 299
 300
 301         if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
 302         {
 303                 int ll1, ll2;
 304
 305                 if( commonAlloc1 && commonAlloc2 )
 306                 {
 307                         FreeIntMtx( commonIP );
 308                 }
 309
 310                 ll1 = MAX( orlgth1, commonAlloc1 );
 311                 ll2 = MAX( orlgth2, commonAlloc2 );
 312
 313 #if DEBUG
 314                 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 315 #endif
 316
 317                 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
 318
 319 #if DEBUG
 320                 fprintf( stderr, "succeeded\n\n" );
 321 #endif
 322
 323                 commonAlloc1 = ll1;
 324                 commonAlloc2 = ll2;
 325         }
 326         ijp = commonIP;
 327
 328
 329 #if 0
 330         for( i=0; i<lgth1; i++ )
 331                 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
 332 #endif
 333
 334         currentw = w1;
 335         previousw = w2;
 336
 337
 338         match_calc( initverticalw, seq2, seq1, 0, lgth1 );
 339
 340
 341         match_calc( currentw, seq1, seq2, 0, lgth2 );
 342
 343         if( headgp == 1 )
 344         {
 345                 for( i=1; i<lgth1+1; i++ )
 346                 {
 347                         initverticalw[i] += fpenalty;
 348                 }
 349                 for( j=1; j<lgth2+1; j++ )
 350                 {
 351                         currentw[j] += fpenalty;
 352                 }
 353         }
 354
 355         for( j=1; j<lgth2+1; ++j )
 356         {
 357                 m[j] = currentw[j-1]; mp[j] = 0;
 358         }
 359
 360         if( lgth2 == 0 )
 361                 lastverticalw[0] = 0.0;               // lgth2==0 no toki error
 362         else
 363                 lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
 364
 365         if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
 366
 367 #if XXXXXXX
 368 fprintf( stderr, "currentw = \n" );
 369 for( i=0; i<lgth1+1; i++ )
 370 {
 371         fprintf( stderr, "%5.2f ", currentw[i] );
 372 }
 373 fprintf( stderr, "\n" );
 374 fprintf( stderr, "initverticalw = \n" );
 375 for( i=0; i<lgth2+1; i++ )
 376 {
 377         fprintf( stderr, "%5.2f ", initverticalw[i] );
 378 }
 379 fprintf( stderr, "\n" );
 380 #endif
 381
 382         for( i=1; i<lasti; i++ )
 383         {
 384                 wtmp = previousw;
 385                 previousw = currentw;
 386                 currentw = wtmp;
 387
 388                 previousw[0] = initverticalw[i-1];
 389
 390                 match_calc( currentw, seq1, seq2, i, lgth2 );
 391 #if XXXXXXX
 392 fprintf( stderr, "\n" );
 393 fprintf( stderr, "i=%d\n", i );
 394 fprintf( stderr, "currentw = \n" );
 395 for( j=0; j<lgth2; j++ )
 396 {
 397         fprintf( stderr, "%5.2f ", currentw[j] );
 398 }
 399 fprintf( stderr, "\n" );
 400 #endif
 401 #if XXXXXXX
 402 fprintf( stderr, "\n" );
 403 fprintf( stderr, "i=%d\n", i );
 404 fprintf( stderr, "currentw = \n" );
 405 for( j=0; j<lgth2; j++ )
 406 {
 407         fprintf( stderr, "%5.2f ", currentw[j] );
 408 }
 409 fprintf( stderr, "\n" );
 410 #endif
 411                 currentw[0] = initverticalw[i];
 412
 413                 mi = previousw[0]; mpi = 0;
 414
 415                 ijppt = ijp[i] + 1;
 416                 mjpt = m + 1;
 417                 prept = previousw;
 418                 curpt = currentw + 1;
 419                 mpjpt = mp + 1;
 420                 for( j=1; j<lgth2+1; j++ )
 421                 {
 422                         wm = *prept;
 423                         *ijppt = 0;
 424
 425 #if 0
 426                         fprintf( stderr, "%5.0f->", wm );
 427 #endif
 428 #if 0
 429                         fprintf( stderr, "%5.0f?", g );
 430 #endif
 431                         if( (g=mi+fpenalty) > wm )
 432                         {
 433                                 wm = g;
 434                                 *ijppt = -( j - mpi );
 435                         }
 436                         if( (g=*prept) >= mi )
 437                         {
 438                                 mi = g;
 439                                 mpi = j-1;
 440                         }
 441 #if USE_PENALTY_EX
 442                         mi += fpenalty_ex;
 443 #endif
 444
 445 #if 0
 446                         fprintf( stderr, "%5.0f?", g );
 447 #endif
 448                         if( (g=*mjpt + fpenalty) > wm )
 449                         {
 450                                 wm = g;
 451                                 *ijppt = +( i - *mpjpt );
 452                         }
 453                         if( (g=*prept) >= *mjpt )
 454                         {
 455                                 *mjpt = g;
 456                                 *mpjpt = i-1;
 457                         }
 458 #if USE_PENALTY_EX
 459                         m[j] += fpenalty_ex;
 460 #endif
 461
 462 #if 0
 463                         fprintf( stderr, "%5.0f ", wm );
 464 #endif
 465                         *curpt++ += wm;
 466                         ijppt++;
 467                         mjpt++;
 468                         prept++;
 469                         mpjpt++;
 470                 }
 471                 lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
 472         }
 473
 474         Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, tailgp );
 475
 476         resultlen = strlen( mseq1[0] );
 477         if( alloclen < resultlen || resultlen > N )
 478         {
 479                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
 480                 ErrorExit( "LENGTH OVER!\n" );
 481         }
 482
 483
 484         strcpy( seq1[0], mseq1[0] );
 485         strcpy( seq2[0], mseq2[0] );
 486 #if 0
 487         fprintf( stderr, "\n" );
 488         fprintf( stderr, ">\n%s\n", mseq1[0] );
 489         fprintf( stderr, ">\n%s\n", mseq2[0] );
 490         fprintf( stderr, "wm = %f\n", wm );
 491 #endif
 492
 493         return( wm );
 494 }
 495
 496 float G__align11_noalign( int scoremtx[0x80][0x80], int penal, int penal_ex, char **seq1, char **seq2, int alloclen )
 497 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 498 {
 499 //      int k;
 500         register int i, j;
 501         int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
 502         int lgth1, lgth2;
 503 //      int resultlen;
 504         float wm;   /* int ?????? */
 505         float g;
 506         float *currentw, *previousw;
 507         float fpenalty = (float)penal;
 508 #if USE_PENALTY_EX
 509         float fpenalty_ex = (float)penal_ex;
 510 #endif
 511 #if 1
 512         float *wtmp;
 513         float *mjpt, *prept, *curpt;
 514 //      int *mpjpt;
 515 #endif
 516         static TLS float mi, *m;
 517         static TLS float *w1, *w2;
 518         static TLS float *match;
 519         static TLS float *initverticalw;    /* kufuu sureba iranai */
 520         static TLS float *lastverticalw;    /* kufuu sureba iranai */
 521         static TLS int **intwork;
 522         static TLS float **floatwork;
 523         static TLS int orlgth1 = 0, orlgth2 = 0;
 524
 525         if( seq1 == NULL )
 526         {
 527                 if( orlgth1 > 0 && orlgth2 > 0 )
 528                 {
 529                         orlgth1 = 0;
 530                         orlgth2 = 0;
 531                         FreeFloatVec( w1 );
 532                         FreeFloatVec( w2 );
 533                         FreeFloatVec( match );
 534                         FreeFloatVec( initverticalw );
 535                         FreeFloatVec( lastverticalw );
 536                         free( m );
 537
 538
 539                         FreeFloatMtx( floatwork );
 540                         FreeIntMtx( intwork );
 541                 }
 542                 return( 0.0 );
 543         }
 544
 545         wm = 0.0;
 546
 547
 548
 549         lgth1 = strlen( seq1[0] );
 550         lgth2 = strlen( seq2[0] );
 551
 552
 553
 554         if( lgth1 <= 0 || lgth2 <= 0 )
 555         {
 556                 fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
 557         }
 558
 559         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 560         {
 561                 int ll1, ll2;
 562
 563                 if( orlgth1 > 0 && orlgth2 > 0 )
 564                 {
 565                         FreeFloatVec( w1 );
 566                         FreeFloatVec( w2 );
 567                         FreeFloatVec( match );
 568                         FreeFloatVec( initverticalw );
 569                         FreeFloatVec( lastverticalw );
 570
 571                         FreeFloatVec( m );
 572
 573
 574
 575
 576                         FreeFloatMtx( floatwork );
 577                         FreeIntMtx( intwork );
 578                 }
 579
 580                 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
 581                 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
 582
 583 #if DEBUG
 584                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
 585 #endif
 586
 587                 w1 = AllocateFloatVec( ll2+2 );
 588                 w2 = AllocateFloatVec( ll2+2 );
 589                 match = AllocateFloatVec( ll2+2 );
 590
 591                 initverticalw = AllocateFloatVec( ll1+2 );
 592                 lastverticalw = AllocateFloatVec( ll1+2 );
 593
 594                 m = AllocateFloatVec( ll2+2 );
 595
 596
 597
 598                 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
 599                 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
 600
 601 #if DEBUG
 602                 fprintf( stderr, "succeeded\n" );
 603 #endif
 604
 605                 orlgth1 = ll1 - 100;
 606                 orlgth2 = ll2 - 100;
 607         }
 608
 609
 610
 611
 612
 613
 614 #if 0
 615         for( i=0; i<lgth1; i++ )
 616                 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
 617 #endif
 618
 619         currentw = w1;
 620         previousw = w2;
 621
 622
 623         match_calc_mtx( scoremtx, initverticalw, seq2, seq1, 0, lgth1 );
 624
 625
 626         match_calc_mtx( scoremtx, currentw, seq1, seq2, 0, lgth2 );
 627
 628         if( 1 ) // tsuneni outgap-1
 629         {
 630                 for( i=1; i<lgth1+1; i++ )
 631                 {
 632                         initverticalw[i] += fpenalty;
 633                 }
 634                 for( j=1; j<lgth2+1; j++ )
 635                 {
 636                         currentw[j] += fpenalty;
 637                 }
 638         }
 639
 640         for( j=1; j<lgth2+1; ++j )
 641         {
 642                 m[j] = currentw[j-1];
 643         }
 644
 645         if( lgth2 == 0 )
 646                 lastverticalw[0] = 0.0;               // lgth2==0 no toki error
 647         else
 648                 lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
 649
 650         if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap-1
 651
 652 #if XXXXXXX
 653 fprintf( stderr, "currentw = \n" );
 654 for( i=0; i<lgth1+1; i++ )
 655 {
 656         fprintf( stderr, "%5.2f ", currentw[i] );
 657 }
 658 fprintf( stderr, "\n" );
 659 fprintf( stderr, "initverticalw = \n" );
 660 for( i=0; i<lgth2+1; i++ )
 661 {
 662         fprintf( stderr, "%5.2f ", initverticalw[i] );
 663 }
 664 fprintf( stderr, "\n" );
 665 #endif
 666
 667         for( i=1; i<lasti; i++ )
 668         {
 669                 wtmp = previousw;
 670                 previousw = currentw;
 671                 currentw = wtmp;
 672
 673                 previousw[0] = initverticalw[i-1];
 674
 675                 match_calc_mtx( scoremtx, currentw, seq1, seq2, i, lgth2 );
 676 #if XXXXXXX
 677 fprintf( stderr, "\n" );
 678 fprintf( stderr, "i=%d\n", i );
 679 fprintf( stderr, "currentw = \n" );
 680 for( j=0; j<lgth2; j++ )
 681 {
 682         fprintf( stderr, "%5.2f ", currentw[j] );
 683 }
 684 fprintf( stderr, "\n" );
 685 #endif
 686 #if XXXXXXX
 687 fprintf( stderr, "\n" );
 688 fprintf( stderr, "i=%d\n", i );
 689 fprintf( stderr, "currentw = \n" );
 690 for( j=0; j<lgth2; j++ )
 691 {
 692         fprintf( stderr, "%5.2f ", currentw[j] );
 693 }
 694 fprintf( stderr, "\n" );
 695 #endif
 696                 currentw[0] = initverticalw[i];
 697
 698                 mi = previousw[0];
 699
 700                 mjpt = m + 1;
 701                 prept = previousw;
 702                 curpt = currentw + 1;
 703                 for( j=1; j<lgth2+1; j++ )
 704                 {
 705                         wm = *prept;
 706
 707 #if 0
 708                         fprintf( stderr, "%5.0f->", wm );
 709 #endif
 710 #if 0
 711                         fprintf( stderr, "%5.0f?", g );
 712 #endif
 713                         if( (g=mi+fpenalty) > wm )
 714                         {
 715                                 wm = g;
 716                         }
 717                         if( (g=*prept) >= mi )
 718                         {
 719                                 mi = g;
 720                         }
 721 #if USE_PENALTY_EX
 722                         mi += fpenalty_ex;
 723 #endif
 724
 725 #if 0
 726                         fprintf( stderr, "%5.0f?", g );
 727 #endif
 728                         if( (g=*mjpt + fpenalty) > wm )
 729                         {
 730                                 wm = g;
 731                         }
 732                         if( (g=*prept) >= *mjpt )
 733                         {
 734                                 *mjpt = g;
 735                         }
 736 #if USE_PENALTY_EX
 737                         m[j] += fpenalty_ex;
 738 #endif
 739
 740 #if 0
 741                         fprintf( stderr, "%5.0f ", wm );
 742 #endif
 743                         *curpt++ += wm;
 744                         mjpt++;
 745                         prept++;
 746                 }
 747                 lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
 748         }
 749
 750 #if 0
 751         fprintf( stderr, "\n" );
 752         fprintf( stderr, ">\n%s\n", mseq1[0] );
 753         fprintf( stderr, ">\n%s\n", mseq2[0] );
 754         fprintf( stderr, "wm = %f\n", wm );
 755 #endif
 756
 757         return( wm );
 758 }