website/archive/binaries/mac/src/mafft/core/suboptalign11.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 typedef struct _shuryoten
  10 {
  11         int i;
  12         int j;
  13         float wm;
  14         struct _shuryoten *next;
  15         struct _shuryoten *prev;
  16 } Shuryoten;
  17
  18
  19 static int localstop;
  20
  21 static int compshuryo( Shuryoten *s1_arg, Shuryoten *s2_arg )
  22 {
  23         Shuryoten *s1 = (Shuryoten *)s1_arg;
  24         Shuryoten *s2 = (Shuryoten *)s2_arg;
  25         if      ( s1->wm > s2->wm ) return( -1 );
  26         else if ( s1->wm < s2->wm ) return( 1 );
  27         else                        return( 0 );
  28 }
  29
  30 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
  31 {
  32         int j;
  33
  34         for( j=0; j<lgth2; j++ )
  35                 match[j] = amino_dis[(int)(*s1)[i1]][(int)(*s2)[j]];
  36 }
  37
  38 static float gentracking( int **used,
  39                                                 char **seq1, char **seq2,
  40                         char **mseq1, char **mseq2,
  41                         float **cpmx1, float **cpmx2,
  42                         int **ijpi, int **ijpj, int *off1pt, int *off2pt, int endi, int endj )
  43 {
  44         int l, iin, jin, lgth1, lgth2, k, limk;
  45         int ifi=0, jfi=0;
  46 //      char gap[] = "-";
  47         char *gap;
  48         gap = newgapstr;
  49         static char *res1 = NULL, *res2 = NULL;
  50         char *mspt1, *mspt2;
  51         if( res1 == NULL )
  52         {
  53                 res1 = (char *)calloc( N, sizeof( char ) );
  54                 res2 = (char *)calloc( N, sizeof( char ) );
  55         }
  56
  57         lgth1 = strlen( seq1[0] );
  58         lgth2 = strlen( seq2[0] );
  59
  60         mspt1 = res1 + lgth1+lgth2;
  61         *mspt1 = 0;
  62         mspt2 = res2 + lgth1+lgth2;
  63         *mspt2 = 0;
  64         iin = endi; jin = endj;
  65
  66         limk = lgth1+lgth2;
  67         if( used[iin][jin] ) return( -1.0 );
  68         for( k=0; k<=limk; k++ )
  69         {
  70                 ifi = ( ijpi[iin][jin] );
  71                 jfi = ( ijpj[iin][jin] );
  72
  73                 if( used[ifi][jfi] ) return( -1.0 );
  74
  75                 l = iin - ifi;
  76                 while( --l )
  77                 {
  78                         *--mspt1 = seq1[0][ifi+l];
  79                         *--mspt2 = *gap;
  80                         k++;
  81                 }
  82                 l= jin - jfi;
  83                 while( --l )
  84                 {
  85                         *--mspt1 = *gap;
  86                         *--mspt2 = seq2[0][jfi+l];
  87                         k++;
  88                 }
  89
  90                 if( iin <= 0 || jin <= 0 ) break;
  91                 *--mspt1 = seq1[0][ifi];
  92                 *--mspt2 = seq2[0][jfi];
  93                 if( ijpi[ifi][jfi] == localstop ) break;
  94                 if( ijpj[ifi][jfi] == localstop ) break;
  95                 k++;
  96                 iin = ifi; jin = jfi;
  97         }
  98         if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
  99         if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
 100
 101 //      fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
 102
 103         iin = endi; jin = endj;
 104         limk = lgth1+lgth2;
 105         for( k=0; k<=limk; k++ )
 106         {
 107                 ifi = ( ijpi[iin][jin] );
 108                 jfi = ( ijpj[iin][jin] );
 109
 110                 used[ifi][jfi] = 1;
 111                 if( iin <= 0 || jin <= 0 ) break;
 112                 if( ijpi[ifi][jfi] == localstop ) break;
 113                 if( ijpj[ifi][jfi] == localstop ) break;
 114
 115                 k++;
 116                 iin = ifi; jin = jfi;
 117         }
 118
 119
 120         strcpy( mseq1[0], mspt1 );
 121         strcpy( mseq2[0], mspt2 );
 122
 123         fprintf( stderr, "mseq1=%s\nmseq2=%s\n", mspt1, mspt2 );
 124
 125         return( 0.0 );
 126 }
 127
 128
 129 float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
 130 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 131 {
 132         int k;
 133         static int **used;
 134         register int i, j;
 135         int lasti, lastj;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
 136         int lgth1, lgth2;
 137         int resultlen;
 138         float wm = 0.0;   // by D.Mathog,
 139         float g;
 140         float *currentw, *previousw;
 141 #if 1
 142         float *wtmp;
 143         int *ijpipt;
 144         int *ijpjpt;
 145         float *mjpt, *Mjpt, *prept, *curpt;
 146         int *mpjpt, *Mpjpt;
 147 #endif
 148         static float mi, *m;
 149         static float Mi, *largeM;
 150         static int **ijpi;
 151         static int **ijpj;
 152         static int mpi, *mp;
 153         static int Mpi, *Mp;
 154         static float *w1, *w2;
 155 //      static float *match;
 156         static float *initverticalw;    /* kufuu sureba iranai */
 157         static float *lastverticalw;    /* kufuu sureba iranai */
 158         static char **mseq1;
 159         static char **mseq2;
 160         static float **cpmx1;
 161         static float **cpmx2;
 162         static int **intwork;
 163         static float **floatwork;
 164         static int orlgth1 = 0, orlgth2 = 0;
 165         float maxwm;
 166         float tbk;
 167         int tbki, tbkj;
 168         int endali, endalj;
 169 //      float localthr = 0.0;
 170 //      float localthr2 = 0.0;
 171         float fpenalty = (float)penalty;
 172         float fpenalty_OP = (float)penalty_OP;
 173         float fpenalty_ex = (float)penalty_ex;
 174 //      float fpenalty_EX = (float)penalty_EX;
 175         float foffset = (float)offset;
 176         float localthr = -foffset;
 177         float localthr2 = -foffset;
 178         static Shuryoten *shuryo = NULL;
 179         int numshuryo;
 180         float minshuryowm = 0.0; // by D.Mathog
 181         int minshuryopos = 0; // by D.Mathog
 182         float resf;
 183
 184
 185 //      fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
 186
 187         fprintf( stderr, "in suboptalign11\n" );
 188         if( !shuryo )
 189         {
 190                 shuryo = (Shuryoten *)calloc( 100, sizeof( Shuryoten ) );
 191         }
 192         for( i=0; i<100; i++ )
 193         {
 194                 shuryo[i].i = -1;
 195                 shuryo[i].j = -1;
 196                 shuryo[i].wm = 0.0;
 197         }
 198         numshuryo = 0;
 199
 200         if( orlgth1 == 0 )
 201         {
 202         }
 203
 204
 205         lgth1 = strlen( seq1[0] );
 206         lgth2 = strlen( seq2[0] );
 207
 208         fprintf( stderr, "in suboptalign11 step 1\n" );
 209
 210         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 211         {
 212                 int ll1, ll2;
 213
 214         fprintf( stderr, "in suboptalign11 step 1.3\n" );
 215                 if( orlgth1 > 0 && orlgth2 > 0 )
 216                 {
 217         fprintf( stderr, "in suboptalign11 step 1.4\n" );
 218                         FreeFloatVec( w1 );
 219                         FreeFloatVec( w2 );
 220 //                      FreeFloatVec( match );
 221                         FreeFloatVec( initverticalw );
 222                         FreeFloatVec( lastverticalw );
 223         fprintf( stderr, "in suboptalign11 step 1.5\n" );
 224
 225                         FreeFloatVec( m );
 226                         FreeIntVec( mp );
 227                         FreeFloatVec( largeM );
 228                         FreeIntVec( Mp );
 229         fprintf( stderr, "in suboptalign11 step 1.6\n" );
 230
 231
 232                         FreeFloatMtx( cpmx1 );
 233                         FreeFloatMtx( cpmx2 );
 234
 235         fprintf( stderr, "in suboptalign11 step 1.7\n" );
 236                         FreeFloatMtx( floatwork );
 237                         FreeIntMtx( intwork );
 238                 }
 239
 240                 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
 241                 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
 242
 243 #if DEBUG
 244                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
 245 #endif
 246
 247                 w1 = AllocateFloatVec( ll2+2 );
 248                 w2 = AllocateFloatVec( ll2+2 );
 249 //              match = AllocateFloatVec( ll2+2 );
 250
 251                 initverticalw = AllocateFloatVec( ll1+2 );
 252                 lastverticalw = AllocateFloatVec( ll1+2 );
 253
 254                 m = AllocateFloatVec( ll2+2 );
 255                 mp = AllocateIntVec( ll2+2 );
 256                 largeM = AllocateFloatVec( ll2+2 );
 257                 Mp = AllocateIntVec( ll2+2 );
 258
 259                 cpmx1 = AllocateFloatMtx( 26, ll1+2 );
 260                 cpmx2 = AllocateFloatMtx( 26, ll2+2 );
 261
 262                 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
 263                 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
 264
 265                 mseq1 = AllocateCharMtx( njob, ll1+ll2 );
 266                 mseq2 = AllocateCharMtx( njob, ll1+ll2 );
 267
 268 #if DEBUG
 269                 fprintf( stderr, "succeeded\n" );
 270 #endif
 271
 272                 orlgth1 = ll1 - 100;
 273                 orlgth2 = ll2 - 100;
 274         }
 275         fprintf( stderr, "in suboptalign11 step 1.6\n" );
 276
 277
 278
 279         fprintf( stderr, "in suboptalign11 step 2\n" );
 280
 281         if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
 282         {
 283                 int ll1, ll2;
 284
 285                 if( commonAlloc1 && commonAlloc2 )
 286                 {
 287                         FreeIntMtx( commonIP );
 288                         FreeIntMtx( commonJP );
 289                         FreeIntMtx( used );
 290                 }
 291
 292                 ll1 = MAX( orlgth1, commonAlloc1 );
 293                 ll2 = MAX( orlgth2, commonAlloc2 );
 294
 295 #if DEBUG
 296                 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 297 #endif
 298
 299                 used = AllocateIntMtx( ll1+10, ll2+10 );
 300                 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
 301                 commonJP = AllocateIntMtx( ll1+10, ll2+10 );
 302
 303 #if DEBUG
 304                 fprintf( stderr, "succeeded\n\n" );
 305 #endif
 306
 307                 commonAlloc1 = ll1;
 308                 commonAlloc2 = ll2;
 309         }
 310         ijpi = commonIP;
 311         ijpj = commonJP;
 312
 313
 314 #if 0
 315         for( i=0; i<lgth1; i++ )
 316                 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
 317 #endif
 318
 319         fprintf( stderr, "in suboptalign11 step 3\n" );
 320         currentw = w1;
 321         previousw = w2;
 322
 323         match_calc( initverticalw, seq2, seq1, 0, lgth1 );
 324
 325         match_calc( currentw, seq1, seq2, 0, lgth2 );
 326
 327
 328         lasti = lgth2+1;
 329         for( j=1; j<lasti; ++j )
 330         {
 331                 m[j] = currentw[j-1]; mp[j] = 0;
 332                 largeM[j] = currentw[j-1]; Mp[j] = 0;
 333         }
 334
 335         lastverticalw[0] = currentw[lgth2-1];
 336
 337
 338 #if 0
 339 fprintf( stderr, "currentw = \n" );
 340 for( i=0; i<lgth1+1; i++ )
 341 {
 342         fprintf( stderr, "%5.2f ", currentw[i] );
 343 }
 344 fprintf( stderr, "\n" );
 345 fprintf( stderr, "initverticalw = \n" );
 346 for( i=0; i<lgth2+1; i++ )
 347 {
 348         fprintf( stderr, "%5.2f ", initverticalw[i] );
 349 }
 350 fprintf( stderr, "\n" );
 351 #endif
 352 #if DEBUG2
 353         fprintf( stderr, "\n" );
 354         fprintf( stderr, "       " );
 355         for( j=0; j<lgth2+1; j++ )
 356                 fprintf( stderr, "%c     ", seq2[0][j] );
 357         fprintf( stderr, "\n" );
 358 #endif
 359
 360         localstop = lgth1+lgth2+1;
 361         maxwm = -999.9;
 362         endali = endalj = 0;
 363 #if DEBUG2
 364         fprintf( stderr, "\n" );
 365         fprintf( stderr, "%c   ", seq1[0][0] );
 366
 367         for( j=0; j<lgth2+1; j++ )
 368                 fprintf( stderr, "%5.0f ", currentw[j] );
 369         fprintf( stderr, "\n" );
 370 #endif
 371
 372         lasti = lgth1+1;
 373         for( i=1; i<lasti; i++ )
 374         {
 375                 wtmp = previousw;
 376                 previousw = currentw;
 377                 currentw = wtmp;
 378
 379                 previousw[0] = initverticalw[i-1];
 380
 381                 match_calc( currentw, seq1, seq2, i, lgth2 );
 382 #if DEBUG2
 383                 fprintf( stderr, "%c   ", seq1[0][i] );
 384                 fprintf( stderr, "%5.0f ", currentw[0] );
 385 #endif
 386
 387 #if XXXXXXX
 388 fprintf( stderr, "\n" );
 389 fprintf( stderr, "i=%d\n", i );
 390 fprintf( stderr, "currentw = \n" );
 391 for( j=0; j<lgth2; j++ )
 392 {
 393         fprintf( stderr, "%5.2f ", currentw[j] );
 394 }
 395 fprintf( stderr, "\n" );
 396 #endif
 397 #if XXXXXXX
 398 fprintf( stderr, "\n" );
 399 fprintf( stderr, "i=%d\n", i );
 400 fprintf( stderr, "currentw = \n" );
 401 for( j=0; j<lgth2; j++ )
 402 {
 403         fprintf( stderr, "%5.2f ", currentw[j] );
 404 }
 405 fprintf( stderr, "\n" );
 406 #endif
 407                 currentw[0] = initverticalw[i];
 408
 409                 mi = previousw[0]; mpi = 0;
 410                 Mi = previousw[0]; Mpi = 0;
 411
 412 #if 0
 413                 if( mi < localthr ) mi = localthr2;
 414 #endif
 415
 416                 ijpipt = ijpi[i] + 1;
 417                 ijpjpt = ijpj[i] + 1;
 418                 mjpt = m + 1;
 419                 Mjpt = largeM + 1;
 420                 prept = previousw;
 421                 curpt = currentw + 1;
 422                 mpjpt = mp + 1;
 423                 Mpjpt = Mp + 1;
 424                 tbk = -999999.9;
 425                 tbki = 0;
 426                 tbkj = 0;
 427                 lastj = lgth2+1;
 428                 for( j=1; j<lastj; j++ )
 429                 {
 430                         wm = *prept;
 431                         *ijpipt = i-1;
 432                         *ijpjpt = j-1;
 433
 434
 435 //                      fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
 436 //                      fprintf( stderr, "wm=%f\n", wm );
 437 #if 0
 438                         fprintf( stderr, "%5.0f->", wm );
 439 #endif
 440                         g = mi + fpenalty;
 441 #if 0
 442                         fprintf( stderr, "%5.0f?", g );
 443 #endif
 444                         if( g > wm )
 445                         {
 446                                 wm = g;
 447 //                              *ijpipt = i - 1;
 448                                 *ijpjpt = mpi;
 449                         }
 450                         g = *prept;
 451                         if( g > mi )
 452                         {
 453                                 mi = g;
 454                                 mpi = j-1;
 455                         }
 456
 457 #if USE_PENALTY_EX
 458                         mi += fpenalty_ex;
 459 #endif
 460
 461 #if 0
 462                         fprintf( stderr, "%5.0f->", wm );
 463 #endif
 464                         g = *mjpt + fpenalty;
 465 #if 0
 466                         fprintf( stderr, "m%5.0f?", g );
 467 #endif
 468                         if( g > wm )
 469                         {
 470                                 wm = g;
 471                                 *ijpipt = *mpjpt;
 472 //                              *ijpjpt = j - 1;
 473                         }
 474                         g = *prept;
 475                         if( g > *mjpt )
 476                         {
 477                                 *mjpt = g;
 478                                 *mpjpt = i-1;
 479                         }
 480 #if USE_PENALTY_EX
 481                         *mjpt += fpenalty_ex;
 482 #endif
 483
 484
 485                         g =  tbk + fpenalty_OP;
 486 //                      g =  tbk;
 487                         if( g > wm )
 488                         {
 489                                 wm = g;
 490                                 *ijpipt = tbki;
 491                                 *ijpjpt = tbkj;
 492 //                              fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
 493                         }
 494                         g = Mi;
 495                         if( g > tbk )
 496                         {
 497                                 tbk = g;
 498                                 tbki = i-1;
 499                                 tbkj = Mpi;
 500                         }
 501                         g = *Mjpt;
 502                         if( g > tbk )
 503                         {
 504                                 tbk = g;
 505                                 tbki = *Mpjpt;
 506                                 tbkj = j-1;
 507                         }
 508 //                      tbk += fpenalty_EX;// + foffset;
 509
 510                         g = *prept;
 511                         if( g > *Mjpt )
 512                         {
 513                                 *Mjpt = g;
 514                                 *Mpjpt = i-1;
 515                         }
 516 //                      *Mjpt += fpenalty_EX;// + foffset;
 517
 518                         g = *prept;
 519                         if( g > Mi )
 520                         {
 521                                 Mi = g;
 522                                 Mpi = j-1;
 523                         }
 524 //                      Mi += fpenalty_EX;// + foffset;
 525
 526
 527 //                      fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
 528 //                      fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );
 529
 530
 531                         if( maxwm < wm )
 532                         {
 533                                 maxwm = wm;
 534                                 endali = i;
 535                                 endalj = j;
 536                         }
 537
 538 #if 1
 539                         if( numshuryo < 100 )
 540                         {
 541                                 shuryo[numshuryo].i = i;
 542                                 shuryo[numshuryo].j = j;
 543                                 shuryo[numshuryo].wm = wm;
 544
 545                                 if( minshuryowm > wm )
 546                                 {
 547                                          minshuryowm = wm;
 548                                          minshuryopos = numshuryo;
 549                                 }
 550                                 numshuryo++;
 551                         }
 552                         else
 553                         {
 554                                 if( wm > minshuryowm )
 555                                 {
 556                                         shuryo[minshuryopos].i = i;
 557                                         shuryo[minshuryopos].j = j;
 558                                         shuryo[minshuryopos].wm = wm;
 559                                         minshuryowm = wm;
 560                                         for( k=0; k<100; k++ )    // muda
 561                                         {
 562                                                 if( shuryo[k].wm < minshuryowm )
 563                                                 {
 564                                                         minshuryowm = shuryo[k].wm;
 565                                                         minshuryopos = k;
 566                                                         break;
 567                                                 }
 568                                         }
 569                                 }
 570                         }
 571 #endif
 572 #if 1
 573                         if( wm < localthr )
 574                         {
 575 //                              fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
 576                                 *ijpipt = localstop;
 577 //                              *ijpjpt = localstop;
 578                                 wm = localthr2;
 579                         }
 580 #endif
 581 #if 0
 582                         fprintf( stderr, "%5.0f ", *curpt );
 583 #endif
 584 #if DEBUG2
 585                         fprintf( stderr, "%5.0f ", wm );
 586 //                      fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
 587 #endif
 588
 589                         *curpt += wm;
 590                         ijpipt++;
 591                         ijpjpt++;
 592                         mjpt++;
 593                         Mjpt++;
 594                         prept++;
 595                         mpjpt++;
 596                         Mpjpt++;
 597                         curpt++;
 598                 }
 599 #if DEBUG2
 600                 fprintf( stderr, "\n" );
 601 #endif
 602
 603                 lastverticalw[i] = currentw[lgth2-1];
 604         }
 605
 606         for( k=0; k<100; k++ )
 607         {
 608                 fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
 609         }
 610
 611
 612 #if 1
 613         fprintf( stderr, "maxwm = %f\n", maxwm );
 614         fprintf( stderr, "endali = %d\n", endali );
 615         fprintf( stderr, "endalj = %d\n", endalj );
 616 #endif
 617
 618         qsort( shuryo, 100, sizeof( Shuryoten ), (int (*)())compshuryo );
 619         for( k=0; k<100; k++ )
 620         {
 621                 fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
 622         }
 623
 624
 625         lasti = lgth1+1;
 626     for( i=0; i<lasti; i++ )
 627     {
 628         ijpi[i][0] = localstop;
 629         ijpj[i][0] = localstop;
 630     }
 631         lastj = lgth2+1;
 632     for( j=0; j<lastj; j++ )
 633     {
 634         ijpi[0][j] = localstop;
 635         ijpj[0][j] = localstop;
 636     }
 637
 638         for( i=0; i<lasti; i++ ) for( j=0; j<lastj; j++ ) used[i][j] = 0;
 639
 640         for( k=0; k<numshuryo; k++ )
 641         {
 642                 if( shuryo[k].wm < shuryo[0].wm * 0.3 ) break;
 643                 fprintf( stderr, "k=%d, shuryo[k].i,j,wm=%d,%d,%f go\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
 644                 resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shuryo[k].i, shuryo[k].j );
 645                 if( resf == -1.0 ) continue;
 646                 putlocalhom3( mseq1[0], mseq2[0], lhmpt, *off1pt, *off2pt, (int)shuryo[k].wm, strlen( mseq1[0] ) );
 647 #if 0
 648                 fprintf( stderr, "\n" );
 649                 fprintf( stderr, ">\n%s\n", mseq1[0] );
 650                 fprintf( stderr, ">\n%s\n", mseq2[0] );
 651 #endif
 652         }
 653         for( i=0; i<20; i++ )
 654         {
 655                 for( j=0; j<20; j++ )
 656                 {
 657                         fprintf( stderr, "%2d ", used[i][j] );
 658                 }
 659                 fprintf( stderr, "\n" );
 660         }
 661
 662
 663 //      fprintf( stderr, "### impmatch = %f\n", *impmatch );
 664
 665         resultlen = strlen( mseq1[0] );
 666         if( alloclen < resultlen || resultlen > N )
 667         {
 668                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
 669                 ErrorExit( "LENGTH OVER!\n" );
 670         }
 671
 672
 673
 674
 675
 676         return( wm );
 677 }
 678