binaries/src/mafft/core/partSalignmm.c.comment

   1 #include "mltaln.h"
   2 #include "dp.h"
   3
   4 #define MACHIGAI 0
   5 #define OUTGAP0TRY 1
   6 #define DEBUG 0
   7 #define XXXXXXX    0
   8 #define USE_PENALTY_EX  0
   9
  10 static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
  11 {
  12         int i, j, gc, gb;
  13         float feff;
  14
  15         for( i=0; i<len; i++ ) ogcp[i] = 0.0;
  16         for( j=0; j<clus; j++ )
  17         {
  18                 feff = (float)eff[j];
  19                 gc = 0;
  20                 for( i=0; i<len; i++ )
  21                 {
  22                         gb = gc;
  23                         gc = ( seq[j][i] == '-' );
  24                         {
  25                                 if( !gb *  gc ) ogcp[i] += feff;
  26                         }
  27                 }
  28         }
  29 }
  30
  31 static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
  32 {
  33         int i, j, gc, gb;
  34         float feff;
  35
  36         for( i=0; i<len; i++ ) fgcp[i] = 0.0;
  37         for( j=0; j<clus; j++ )
  38         {
  39                 feff = (float)eff[j];
  40                 gc = ( seq[j][0] == '-' );
  41                 for( i=1; i<len+1; i++ )
  42                 {
  43                         gb = gc;
  44                         gc = ( seq[j][i] == '-' );
  45                         {
  46                                 if( gb * !gc ) fgcp[i-1] += feff;
  47                         }
  48                 }
  49         }
  50 }
  51
  52
  53
  54
  55
  56 static int impalloclen = 0;
  57 static float **impmtx = NULL;
  58 float part_imp_match_out_sc( int i1, int j1 )
  59 {
  60 //      fprintf( stderr, "impalloclen = %d\n", impalloclen );
  61 //      fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] );
  62         return( impmtx[i1][j1] );
  63 #if 0
  64         if( i1 == l1 || j1 == l2 ) return( 0.0 );
  65         return( impmtx[i1+start1][j1+start2] );
  66 #endif
  67 }
  68 static void part_imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int start2, int *gapmap2 )
  69 {
  70         int j;
  71         for( j=0; j<lgth2; j++ )
  72         {
  73                 imp[j] += impmtx[i1][start2+gapmap2[j]];
  74         }
  75 }
  76
  77 void part_imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
  78 {
  79         int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
  80         double effij, effijx;
  81         char *pt, *pt1, *pt2;
  82         int allgap;
  83         LocalHom *tmpptr;
  84
  85         if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 )
  86         {
  87                 if( impmtx ) FreeFloatMtx( impmtx );
  88                 impalloclen = MAX( lgth1, lgth2 ) + 2;
  89                 impmtx = AllocateFloatMtx( impalloclen+100, impalloclen+100 );
  90         }
  91
  92
  93 #if 0
  94         fprintf( stderr, "eff1 in _init_strict = \n" );
  95         for( i=0; i<clus1; i++ )
  96                 fprintf( stderr, "eff1[] = %f\n", eff1[i] );
  97         for( i=0; i<clus2; i++ )
  98                 fprintf( stderr, "eff2[] = %f\n", eff2[i] );
  99 #endif
 100
 101         for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
 102                 impmtx[i][j] = 0.0;
 103         effijx = 1.0 * fastathreshold;
 104         for( i=0; i<clus1; i++ )
 105         {
 106                 for( j=0; j<clus2; j++ )
 107                 {
 108                         effij = eff1[i] * eff2[j] * effijx;
 109                         tmpptr = localhom[i][j];
 110                         while( tmpptr )
 111                         {
 112 //                              fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
 113 //                              fprintf( stderr, "end1   = %d\n", tmpptr->end1   );
 114 //                              fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
 115 //                              fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
 116                                 pt = seq1[i];
 117                                 tmpint = -1;
 118                                 while( *pt != 0 )
 119                                 {
 120                                         if( *pt++ != '-' ) tmpint++;
 121                                         if( tmpint == tmpptr->start1 ) break;
 122                                 }
 123                                 start1 = (int)( pt - seq1[i] ) - 1;
 124
 125                                 if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
 126                                 else
 127                                 {
 128 #if MACHIGAI
 129                                         while( *pt != 0 )
 130                                         {
 131                                                 if( tmpint == tmpptr->end1 ) break;
 132                                                 if( *pt++ != '-' ) tmpint++;
 133                                         }
 134                                         end1 = (int)( pt - seq1[i] ) - 1;
 135 #else
 136                                         while( *pt != 0 )
 137                                         {
 138 //                                              fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
 139                                                 if( *pt++ != '-' ) tmpint++;
 140                                                 if( tmpint == tmpptr->end1 ) break;
 141                                         }
 142                                         end1 = (int)( pt - seq1[i] ) - 1;
 143 #endif
 144                                 }
 145
 146                                 pt = seq2[j];
 147                                 tmpint = -1;
 148                                 while( *pt != 0 )
 149                                 {
 150                                         if( *pt++ != '-' ) tmpint++;
 151                                         if( tmpint == tmpptr->start2 ) break;
 152                                 }
 153                                 start2 = (int)( pt - seq2[j] ) - 1;
 154                                 if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
 155                                 else
 156                                 {
 157 #if MACHIGAI
 158                                         while( *pt != 0 )
 159                                         {
 160                                                 if( tmpint == tmpptr->end2 ) break;
 161                                                 if( *pt++ != '-' ) tmpint++;
 162                                         }
 163                                         end2 = (int)( pt - seq2[j] ) - 1;
 164 #else
 165                                         while( *pt != 0 )
 166                                         {
 167                                                 if( *pt++ != '-' ) tmpint++;
 168                                                 if( tmpint == tmpptr->end2 ) break;
 169                                         }
 170                                         end2 = (int)( pt - seq2[j] ) - 1;
 171 #endif
 172                                 }
 173 //                              fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
 174 //                              fprintf( stderr, "step 0\n" );
 175                                 if( end1 - start1 != end2 - start2 )
 176                                 {
 177 //                                      fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
 178                                 }
 179
 180                                 k1 = start1; k2 = start2;
 181                                 pt1 = seq1[i] + k1;
 182                                 pt2 = seq2[j] + k2;
 183                                 while( *pt1 && *pt2 )
 184                                 {
 185                                         if( *pt1 != '-' && *pt2 != '-' )
 186                                         {
 187 // ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
 188 //                                              impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
 189 //                                              impmtx[k1][k2] += tmpptr->importance * effij;
 190                                                 impmtx[k1][k2] += tmpptr->fimportance * effij;
 191 //                                              fprintf( stderr, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen );
 192 //                                              fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 193                                                 k1++; k2++;
 194                                                 pt1++; pt2++;
 195                                         }
 196                                         else if( *pt1 != '-' && *pt2 == '-' )
 197                                         {
 198 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 199                                                 k2++; pt2++;
 200                                         }
 201                                         else if( *pt1 == '-' && *pt2 != '-' )
 202                                         {
 203 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 204                                                 k1++; pt1++;
 205                                         }
 206                                         else if( *pt1 == '-' && *pt2 == '-' )
 207                                         {
 208 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 209                                                 k1++; pt1++;
 210                                                 k2++; pt2++;
 211                                         }
 212                                         if( k1 > end1 || k2 > end2 ) break;
 213                                 }
 214                                 tmpptr = tmpptr->next;
 215                         }
 216                 }
 217         }
 218 #if 1
 219         0printf( stderr, "impmtx = \n" );
 220         for( k2=0; k2<lgth2; k2++ )
 221                 fprintf( stderr, "%6.3f ", (double)k2 );
 222         fprintf( stderr, "\n" );
 223         for( k1=0; k1<lgth1; k1++ )
 224         {
 225                 fprintf( stderr, "%d", k1 );
 226                 for( k2=0; k2<lgth2; k2++ )
 227                         fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
 228                 fprintf( stderr, "\n" );
 229         }
 230         exit( 1 );
 231 #endif
 232 }
 233
 234 void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
 235 {
 236         int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
 237         static int impalloclen = 0;
 238         char *pt;
 239         int allgap;
 240         static char *nocount1 = NULL;
 241         static char *nocount2 = NULL;
 242
 243         if( impalloclen < lgth1 || impalloclen < lgth2 )
 244         {
 245                 if( impmtx ) FreeFloatMtx( impmtx );
 246                 if( nocount1 ) free( nocount1 );
 247                 if( nocount2 ) free( nocount2 );
 248                 impalloclen = MAX( lgth1, lgth2 ) + 2;
 249                 impmtx = AllocateFloatMtx( impalloclen, impalloclen );
 250                 nocount1 = AllocateCharVec( impalloclen );
 251                 nocount2 = AllocateCharVec( impalloclen );
 252                 impalloclen -= 2;
 253         }
 254
 255         for( i=0; i<lgth1; i++ )
 256         {
 257                 for( j=0; j<clus1; j++ )
 258                         if( seq1[j][i] == '-' ) break;
 259                 if( j != clus1 ) nocount1[i] = 1;
 260                 else                     nocount1[i] = 0;
 261         }
 262         for( i=0; i<lgth2; i++ )
 263         {
 264                 for( j=0; j<clus2; j++ )
 265                         if( seq2[j][i] == '-' ) break;
 266                 if( j != clus2 ) nocount2[i] = 1;
 267                 else                     nocount2[i] = 0;
 268         }
 269
 270 #if 0
 271 fprintf( stderr, "nocount2 =\n" );
 272 for( i = 0; i<impalloclen; i++ )
 273 {
 274         fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
 275 }
 276 #endif
 277
 278         for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
 279                 impmtx[i][j] = 0.0;
 280         for( i=0; i<clus1; i++ )
 281         {
 282                 fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
 283                 for( j=0; j<clus2; j++ )
 284                 {
 285                         fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
 286                         fprintf( stderr, "end1   = %d\n", localhom[i][j]->end1   );
 287                         fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
 288                         pt = seq1[i];
 289                         tmpint = -1;
 290                         while( *pt != 0 )
 291                         {
 292                                 if( *pt++ != '-' ) tmpint++;
 293                                 if( tmpint == localhom[i][j]->start1 ) break;
 294                         }
 295                         start1 = pt - seq1[i] - 1;
 296
 297                         while( *pt != 0 )
 298                         {
 299 //                              fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
 300                                 if( *pt++ != '-' ) tmpint++;
 301                                 if( tmpint == localhom[i][j]->end1 ) break;
 302                         }
 303                         end1 = pt - seq1[i] - 1;
 304
 305                         pt = seq2[j];
 306                         tmpint = -1;
 307                         while( *pt != 0 )
 308                         {
 309                                 if( *pt++ != '-' ) tmpint++;
 310                                 if( tmpint == localhom[i][j]->start2 ) break;
 311                         }
 312                         start2 = pt - seq2[j] - 1;
 313                         while( *pt != 0 )
 314                         {
 315                                 if( *pt++ != '-' ) tmpint++;
 316                                 if( tmpint == localhom[i][j]->end2 ) break;
 317                         }
 318                         end2 = pt - seq2[j] - 1;
 319 //                      fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
 320                         k1 = start1;
 321                         k2 = start2;
 322                         fprintf( stderr, "step 0\n" );
 323                         while( k1 <= end1 && k2 <= end2 )
 324                         {
 325 #if 0
 326                                 if( !nocount1[k1] && !nocount2[k2] )
 327                                         impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
 328                                 k1++; k2++;
 329 #else
 330                                 if( !nocount1[k1] && !nocount2[k2] )
 331                                         impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
 332                                 k1++; k2++;
 333 #endif
 334                         }
 335
 336                         dif = ( end1 - start1 ) - ( end2 - start2 );
 337                         fprintf( stderr, "dif = %d\n", dif );
 338                         if( dif > 0 )
 339                         {
 340                                 do
 341                                 {
 342                                         fprintf( stderr, "dif = %d\n", dif );
 343                                         k1 = start1;
 344                                         k2 = start2 - dif;
 345                                         while( k1 <= end1 && k2 <= end2 )
 346                                         {
 347                                                 if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
 348                                                         impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
 349                                                 k1++; k2++;
 350                                         }
 351                                 }
 352                                 while( dif-- );
 353                         }
 354                         else
 355                         {
 356                                 do
 357                                 {
 358                                         k1 = start1 + dif;
 359                                         k2 = start2;
 360                                         while( k1 <= end1 )
 361                                         {
 362                                                 if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
 363                                                         impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
 364                                                 k1++; k2++;
 365                                         }
 366                                 }
 367                                 while( dif++ );
 368                         }
 369                 }
 370         }
 371 #if 1
 372         fprintf( stderr, "impmtx = \n" );
 373         for( k2=0; k2<lgth2; k2++ )
 374                 fprintf( stderr, "%6.3f ", (double)k2 );
 375         fprintf( stderr, "\n" );
 376         for( k1=0; k1<lgth1; k1++ )
 377         {
 378                 fprintf( stderr, "%d", k1 );
 379                 for( k2=0; k2<lgth2; k2++ )
 380                         fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
 381                 fprintf( stderr, "\n" );
 382         }
 383         exit( 1 );
 384 #endif
 385 }
 386
 387 static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
 388 {
 389         int j, k, l;
 390         float scarr[26];
 391         float **cpmxpd = floatwork;
 392         int **cpmxpdn = intwork;
 393         int count = 0;
 394
 395         if( initialize )
 396         {
 397                 for( j=0; j<lgth2; j++ )
 398                 {
 399                         count = 0;
 400                         for( l=0; l<26; l++ )
 401                         {
 402                                 if( cpmx2[l][j] )
 403                                 {
 404                                         cpmxpd[count][j] = cpmx2[l][j];
 405                                         cpmxpdn[count][j] = l;
 406                                         count++;
 407                                 }
 408                         }
 409                         cpmxpdn[count][j] = -1;
 410                 }
 411         }
 412
 413         for( l=0; l<26; l++ )
 414         {
 415                 scarr[l] = 0.0;
 416                 for( k=0; k<26; k++ )
 417                         scarr[l] += n_dis[k][l] * cpmx1[k][i1];
 418         }
 419 #if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
 420         {
 421                 float *fpt, **fptpt, *fpt2;
 422                 int *ipt, **iptpt;
 423                 fpt2 = match;
 424                 iptpt = cpmxpdn;
 425                 fptpt = cpmxpd;
 426                 while( lgth2-- )
 427                 {
 428                         *fpt2 = 0.0;
 429                         ipt=*iptpt,fpt=*fptpt;
 430                         while( *ipt > -1 )
 431                                 *fpt2 += scarr[*ipt++] * *fpt++;
 432                         fpt2++,iptpt++,fptpt++;
 433                 }
 434         }
 435 #else
 436         for( j=0; j<lgth2; j++ )
 437         {
 438                 match[j] = 0.0;
 439                 for( k=0; cpmxpdn[k][j]>-1; k++ )
 440                         match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
 441         }
 442 #endif
 443 }
 444
 445 static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
 446                                                 char **seq1, char **seq2,
 447                         char **mseq1, char **mseq2,
 448                         float **cpmx1, float **cpmx2,
 449                         short **ijp, int icyc, int jcyc,
 450                                                 int start1, int end1, int start2, int end2,
 451                                                 int *gapmap1, int *gapmap2 )
 452 {
 453         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
 454         char gap[] = "-";
 455         float wm;
 456         lgth1 = strlen( seq1[0] );
 457         lgth2 = strlen( seq2[0] );
 458
 459 #if 0
 460         for( i=0; i<lgth1; i++ )
 461         {
 462                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 463         }
 464 #endif
 465
 466         if( outgap == 1 )
 467                 ;
 468         else
 469         {
 470                 wm = lastverticalw[0];
 471                 for( i=0; i<lgth1; i++ )
 472                 {
 473                         if( lastverticalw[i] >= wm )
 474                         {
 475                                 wm = lastverticalw[i];
 476                                 iin = i; jin = lgth2-1;
 477                                 ijp[lgth1][lgth2] = +( lgth1 - i );
 478                         }
 479                 }
 480                 for( j=0; j<lgth2; j++ )
 481                 {
 482                         if( lasthorizontalw[j] >= wm )
 483                         {
 484                                 wm = lasthorizontalw[j];
 485                                 iin = lgth1-1; jin = j;
 486                                 ijp[lgth1][lgth2] = -( lgth2 - j );
 487                         }
 488                 }
 489         }
 490
 491     for( i=0; i<lgth1+1; i++ )
 492     {
 493         ijp[i][0] = i + 1;
 494     }
 495     for( j=0; j<lgth2+1; j++ )
 496     {
 497         ijp[0][j] = -( j + 1 );
 498     }
 499
 500         for( i=0; i<icyc; i++ )
 501         {
 502                 mseq1[i] += lgth1+lgth2;
 503                 *mseq1[i] = 0;
 504         }
 505         for( j=0; j<jcyc; j++ )
 506         {
 507                 mseq2[j] += lgth1+lgth2;
 508                 *mseq2[j] = 0;
 509         }
 510         iin = lgth1; jin = lgth2;
 511         *impwmpt = 0.0;
 512         for( k=0; k<=lgth1+lgth2; k++ )
 513         {
 514                 if( ijp[iin][jin] < 0 )
 515                 {
 516                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 517                 }
 518                 else if( ijp[iin][jin] > 0 )
 519                 {
 520                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 521                 }
 522                 else
 523                 {
 524                         ifi = iin-1; jfi = jin-1;
 525                 }
 526                 l = iin - ifi;
 527                 while( --l )
 528                 {
 529                         for( i=0; i<icyc; i++ )
 530                                 *--mseq1[i] = seq1[i][ifi+l];
 531                         for( j=0; j<jcyc; j++ )
 532                                 *--mseq2[j] = *gap;
 533                         k++;
 534                 }
 535                 l= jin - jfi;
 536                 while( --l )
 537                 {
 538                         for( i=0; i<icyc; i++ )
 539                                 *--mseq1[i] = *gap;
 540                         for( j=0; j<jcyc; j++ )
 541                                 *--mseq2[j] = seq2[j][jfi+l];
 542                         k++;
 543                 }
 544                 if( iin != lgth1 && jin != lgth2 ) // ??
 545                 {
 546                         *impwmpt += part_imp_match_out_sc( gapmap1[iin]+start1, gapmap2[jin]+start2 );
 547 //                      fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
 548                 }
 549                 if( iin <= 0 || jin <= 0 ) break;
 550                 for( i=0; i<icyc; i++ )
 551                         *--mseq1[i] = seq1[i][ifi];
 552                 for( j=0; j<jcyc; j++ )
 553                         *--mseq2[j] = seq2[j][jfi];
 554                 k++;
 555                 iin = ifi; jin = jfi;
 556         }
 557 }
 558 static float Atracking( float *lasthorizontalw, float *lastverticalw,
 559                                                 char **seq1, char **seq2,
 560                         char **mseq1, char **mseq2,
 561                         float **cpmx1, float **cpmx2,
 562                         short **ijp, int icyc, int jcyc )
 563 {
 564         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk;
 565         char gap[] = "-";
 566         float wm = 0.0;
 567         lgth1 = strlen( seq1[0] );
 568         lgth2 = strlen( seq2[0] );
 569
 570 #if 0
 571         for( i=0; i<lgth1; i++ )
 572         {
 573                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 574         }
 575 #endif
 576
 577         if( outgap == 1 )
 578                 ;
 579         else
 580         {
 581                 wm = lastverticalw[0];
 582                 for( i=0; i<lgth1; i++ )
 583                 {
 584                         if( lastverticalw[i] >= wm )
 585                         {
 586                                 wm = lastverticalw[i];
 587                                 iin = i; jin = lgth2-1;
 588                                 ijp[lgth1][lgth2] = +( lgth1 - i );
 589                         }
 590                 }
 591                 for( j=0; j<lgth2; j++ )
 592                 {
 593                         if( lasthorizontalw[j] >= wm )
 594                         {
 595                                 wm = lasthorizontalw[j];
 596                                 iin = lgth1-1; jin = j;
 597                                 ijp[lgth1][lgth2] = -( lgth2 - j );
 598                         }
 599                 }
 600         }
 601
 602     for( i=0; i<lgth1+1; i++ )
 603     {
 604         ijp[i][0] = i + 1;
 605     }
 606     for( j=0; j<lgth2+1; j++ )
 607     {
 608         ijp[0][j] = -( j + 1 );
 609     }
 610
 611         for( i=0; i<icyc; i++ )
 612         {
 613                 mseq1[i] += lgth1+lgth2;
 614                 *mseq1[i] = 0;
 615         }
 616         for( j=0; j<jcyc; j++ )
 617         {
 618                 mseq2[j] += lgth1+lgth2;
 619                 *mseq2[j] = 0;
 620         }
 621         iin = lgth1; jin = lgth2;
 622         lastk = lgth1+lgth2;
 623         for( k=0; k<=lastk; k++ )
 624         {
 625                 if( ijp[iin][jin] < 0 )
 626                 {
 627                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 628                 }
 629                 else if( ijp[iin][jin] > 0 )
 630                 {
 631                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 632                 }
 633                 else
 634                 {
 635                         ifi = iin-1; jfi = jin-1;
 636                 }
 637                 l = iin - ifi;
 638                 while( --l )
 639                 {
 640                         for( i=0; i<icyc; i++ )
 641                                 *--mseq1[i] = seq1[i][ifi+l];
 642                         for( j=0; j<jcyc; j++ )
 643                                 *--mseq2[j] = *gap;
 644                         k++;
 645                 }
 646                 l= jin - jfi;
 647                 while( --l )
 648                 {
 649                         for( i=0; i<icyc; i++ )
 650                                 *--mseq1[i] = *gap;
 651                         for( j=0; j<jcyc; j++ )
 652                                 *--mseq2[j] = seq2[j][jfi+l];
 653                         k++;
 654                 }
 655                 if( iin <= 0 || jin <= 0 ) break;
 656                 for( i=0; i<icyc; i++ )
 657                         *--mseq1[i] = seq1[i][ifi];
 658                 for( j=0; j<jcyc; j++ )
 659                         *--mseq2[j] = seq2[j][jfi];
 660                 k++;
 661                 iin = ifi; jin = jfi;
 662         }
 663         return( 0.0 );
 664 }
 665
 666 float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2 )
 667 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 668 {
 669 //      int k;
 670         register int i, j;
 671         int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
 672         int lgth1, lgth2;
 673         int resultlen;
 674         float wm = 0.0;   /* int ?????? */
 675         float g;
 676         float *currentw, *previousw;
 677 #if 1
 678         float *wtmp;
 679         short *ijppt;
 680         float *mjpt, *prept, *curpt;
 681         int *mpjpt;
 682 #endif
 683         static float mi, *m;
 684         static short **ijp;
 685         static int mpi, *mp;
 686         static float *w1, *w2;
 687         static float *match;
 688         static float *initverticalw;    /* kufuu sureba iranai */
 689         static float *lastverticalw;    /* kufuu sureba iranai */
 690         static char **mseq1;
 691         static char **mseq2;
 692         static char **mseq;
 693         static float *ogcp1;
 694         static float *ogcp2;
 695         static float *fgcp1;
 696         static float *fgcp2;
 697         static float **cpmx1;
 698         static float **cpmx2;
 699         static int **intwork;
 700         static float **floatwork;
 701         static int orlgth1 = 0, orlgth2 = 0;
 702         float fpenalty = (float)penalty;
 703         float fpenalty_ex = (float)penalty_ex;
 704         float *fgcp2pt;
 705         float *ogcp2pt;
 706         float fgcp1va;
 707         float ogcp1va;
 708
 709
 710
 711 #if 0
 712         fprintf( stderr, "eff in SA+++align\n" );
 713         for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
 714 #endif
 715         if( orlgth1 == 0 )
 716         {
 717                 mseq1 = AllocateCharMtx( njob, 0 );
 718                 mseq2 = AllocateCharMtx( njob, 0 );
 719         }
 720
 721
 722         lgth1 = strlen( seq1[0] );
 723         lgth2 = strlen( seq2[0] );
 724
 725         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 726         {
 727                 int ll1, ll2;
 728
 729                 if( orlgth1 > 0 && orlgth2 > 0 )
 730                 {
 731                         FreeFloatVec( w1 );
 732                         FreeFloatVec( w2 );
 733                         FreeFloatVec( match );
 734                         FreeFloatVec( initverticalw );
 735                         FreeFloatVec( lastverticalw );
 736
 737                         FreeFloatVec( m );
 738                         FreeIntVec( mp );
 739
 740                         FreeCharMtx( mseq );
 741
 742                         FreeFloatVec( ogcp1 );
 743                         FreeFloatVec( ogcp2 );
 744                         FreeFloatVec( fgcp1 );
 745                         FreeFloatVec( fgcp2 );
 746
 747
 748                         FreeFloatMtx( cpmx1 );
 749                         FreeFloatMtx( cpmx2 );
 750
 751                         FreeFloatMtx( floatwork );
 752                         FreeIntMtx( intwork );
 753                 }
 754
 755                 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
 756                 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
 757
 758 #if DEBUG
 759                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
 760 #endif
 761
 762                 w1 = AllocateFloatVec( ll2+2 );
 763                 w2 = AllocateFloatVec( ll2+2 );
 764                 match = AllocateFloatVec( ll2+2 );
 765
 766                 initverticalw = AllocateFloatVec( ll1+2 );
 767                 lastverticalw = AllocateFloatVec( ll1+2 );
 768
 769                 m = AllocateFloatVec( ll2+2 );
 770                 mp = AllocateIntVec( ll2+2 );
 771
 772                 mseq = AllocateCharMtx( njob, ll1+ll2 );
 773
 774                 ogcp1 = AllocateFloatVec( ll1+2 );
 775                 ogcp2 = AllocateFloatVec( ll2+2 );
 776                 fgcp1 = AllocateFloatVec( ll1+2 );
 777                 fgcp2 = AllocateFloatVec( ll2+2 );
 778
 779                 cpmx1 = AllocateFloatMtx( 26, ll1+2 );
 780                 cpmx2 = AllocateFloatMtx( 26, ll2+2 );
 781
 782                 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
 783                 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
 784
 785 #if DEBUG
 786                 fprintf( stderr, "succeeded\n" );
 787 #endif
 788
 789                 orlgth1 = ll1 - 100;
 790                 orlgth2 = ll2 - 100;
 791         }
 792
 793
 794         for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
 795         for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
 796
 797
 798         if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
 799         {
 800                 int ll1, ll2;
 801
 802                 if( commonAlloc1 && commonAlloc2 )
 803                 {
 804                         FreeShortMtx( commonIP );
 805                 }
 806
 807                 ll1 = MAX( orlgth1, commonAlloc1 );
 808                 ll2 = MAX( orlgth2, commonAlloc2 );
 809
 810 #if DEBUG
 811                 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 812 #endif
 813
 814                 commonIP = AllocateShortMtx( ll1+10, ll2+10 );
 815
 816 #if DEBUG
 817                 fprintf( stderr, "succeeded\n\n" );
 818 #endif
 819
 820                 commonAlloc1 = ll1;
 821                 commonAlloc2 = ll2;
 822         }
 823         ijp = commonIP;
 824
 825         cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
 826         cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
 827
 828         OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
 829         OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
 830         FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
 831         FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
 832
 833         for( i=0; i<lgth1; i++ )
 834         {
 835                 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
 836                 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
 837         }
 838         for( i=0; i<lgth2; i++ )
 839         {
 840                 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
 841                 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
 842         }
 843 #if 0
 844         for( i=0; i<lgth1; i++ )
 845                 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
 846 #endif
 847
 848         currentw = w1;
 849         previousw = w2;
 850
 851
 852         match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
 853
 854
 855         match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
 856 #if 0 // -> tbfast.c
 857         if( localhom )
 858                 imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
 859
 860 #endif
 861
 862         if( outgap == 1 )
 863         {
 864                 for( i=1; i<lgth1+1; i++ )
 865                 {
 866                         initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
 867                 }
 868                 for( j=1; j<lgth2+1; j++ )
 869                 {
 870                         currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
 871                 }
 872         }
 873 #if OUTGAP0TRY
 874         else
 875         {
 876                 for( j=1; j<lgth2+1; j++ )
 877                         currentw[j] -= offset * j / 2.0;
 878                 for( i=1; i<lgth1+1; i++ )
 879                         initverticalw[i] -= offset * i / 2.0;
 880         }
 881 #endif
 882
 883         for( j=1; j<lgth2+1; ++j )
 884         {
 885                 m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
 886         }
 887
 888         lastverticalw[0] = currentw[lgth2-1];
 889
 890         if( outgap ) lasti = lgth1+1; else lasti = lgth1;
 891
 892 #if XXXXXXX
 893 fprintf( stderr, "currentw = \n" );
 894 for( i=0; i<lgth1+1; i++ )
 895 {
 896         fprintf( stderr, "%5.2f ", currentw[i] );
 897 }
 898 fprintf( stderr, "\n" );
 899 fprintf( stderr, "initverticalw = \n" );
 900 for( i=0; i<lgth2+1; i++ )
 901 {
 902         fprintf( stderr, "%5.2f ", initverticalw[i] );
 903 }
 904 fprintf( stderr, "\n" );
 905 fprintf( stderr, "fcgp\n" );
 906 for( i=0; i<lgth1; i++ )
 907         fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
 908 for( i=0; i<lgth2; i++ )
 909         fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
 910 #endif
 911
 912         for( i=1; i<lasti; i++ )
 913         {
 914                 wtmp = previousw;
 915                 previousw = currentw;
 916                 currentw = wtmp;
 917
 918                 previousw[0] = initverticalw[i-1];
 919
 920                 match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
 921 #if XXXXXXX
 922 fprintf( stderr, "\n" );
 923 fprintf( stderr, "i=%d\n", i );
 924 fprintf( stderr, "currentw = \n" );
 925 for( j=0; j<lgth2; j++ )
 926 {
 927         fprintf( stderr, "%5.2f ", currentw[j] );
 928 }
 929 fprintf( stderr, "\n" );
 930 #endif
 931                 if( localhom )
 932                 {
 933 //                      fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
 934 //                      imp_match_out_vead( currentw, i, lgth2 );
 935                         part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
 936                 }
 937 #if XXXXXXX
 938 fprintf( stderr, "\n" );
 939 fprintf( stderr, "i=%d\n", i );
 940 fprintf( stderr, "currentw = \n" );
 941 for( j=0; j<lgth2; j++ )
 942 {
 943         fprintf( stderr, "%5.2f ", currentw[j] );
 944 }
 945 fprintf( stderr, "\n" );
 946 #endif
 947                 currentw[0] = initverticalw[i];
 948
 949
 950                 mi = previousw[0] + ogcp2[1]; mpi = 0;
 951
 952                 ijppt = ijp[i] + 1;
 953                 mjpt = m + 1;
 954                 prept = previousw;
 955                 curpt = currentw + 1;
 956                 mpjpt = mp + 1;
 957                 fgcp2pt = fgcp2;
 958                 ogcp2pt = ogcp2+1;
 959                 fgcp1va = fgcp1[i-1];
 960                 ogcp1va = ogcp1[i];
 961                 for( j=1; j<lgth2+1; j++ )
 962                 {
 963                         wm = *prept;
 964                         *ijppt = 0;
 965
 966 #if 0
 967                         fprintf( stderr, "%5.0f->", wm );
 968 #endif
 969                         g = mi + *fgcp2pt;
 970 #if 0
 971                         fprintf( stderr, "%5.0f?", g );
 972 #endif
 973                         if( g > wm )
 974                         {
 975                                 wm = g;
 976                                 *ijppt = -( j - mpi );
 977                         }
 978                         g = *prept + *ogcp2pt;
 979                         if( g >= mi )
 980                         {
 981                                 mi = g;
 982                                 mpi = j-1;
 983                         }
 984 #if USE_PENALTY_EX
 985                         mi += fpenalty_ex;
 986 #endif
 987
 988                         g = *mjpt + fgcp1va;
 989 #if 0
 990                         fprintf( stderr, "%5.0f?", g );
 991 #endif
 992                         if( g > wm )
 993                         {
 994                                 wm = g;
 995                                 *ijppt = +( i - *mpjpt );
 996                         }
 997                         g = *prept + ogcp1va;
 998                         if( g >= *mjpt )
 999                         {
1000                                 *mjpt = g;
1001                                 *mpjpt = i-1;
1002                         }
1003 #if USE_PENALTY_EX
1004                         m[j] += fpenalty_ex;
1005 #endif
1006
1007 #if 0
1008                         fprintf( stderr, "%5.0f ", wm );
1009 #endif
1010                         *curpt += wm;
1011                         ijppt++;
1012                         mjpt++;
1013                         prept++;
1014                         mpjpt++;
1015                         curpt++;
1016                         fgcp2pt++;
1017                         ogcp2pt++;
1018                 }
1019                 lastverticalw[i] = currentw[lgth2-1];
1020         }
1021
1022 #if OUTGAP0TRY
1023         if( !outgap )
1024         {
1025                 for( j=1; j<lgth2+1; j++ )
1026                         currentw[j] -= offset * ( lgth2 - j ) / 2.0;
1027                 for( i=1; i<lgth1+1; i++ )
1028                         lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
1029         }
1030 #endif
1031
1032         /*
1033         fprintf( stderr, "\n" );
1034         for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
1035         fprintf( stderr, "#####\n" );
1036         for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
1037         fprintf( stderr, "====>" );
1038         for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
1039         for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
1040         */
1041         if( localhom )
1042         {
1043                 Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2 );
1044         }
1045         else
1046                 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1047
1048 //      fprintf( stderr, "### impmatch = %f\n", *impmatch );
1049
1050         resultlen = strlen( mseq1[0] );
1051         if( alloclen < resultlen || resultlen > N )
1052         {
1053                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
1054                 ErrorExit( "LENGTH OVER!\n" );
1055         }
1056
1057
1058         for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
1059         for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
1060         /*
1061         fprintf( stderr, "\n" );
1062         for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
1063         fprintf( stderr, "#####\n" );
1064         for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
1065         */
1066
1067
1068         return( wm );
1069 }
1070