binaries/src/mafft/core/Salignmm.c.fast

   1 #include "mltaln.h"
   2 #include "dp.h"
   3
   4 #define OUTGAP0TRY 1
   5 #define DEBUG 0
   6 #define XXXXXXX    0
   7 #define USE_PENALTY_EX  0
   8
   9 static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
  10 {
  11         int i, j, gc, gb;
  12         float feff;
  13
  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 //              totaleff+= eff[j];
  29         }
  30 //      for( i=0; i<len; i++ )
  31 //      {
  32 //              fprintf( stderr, "ogcp[%d] = %30.20f\n", i, ogcp[i] );
  33 //              ogcp[i] /= totaleff;
  34 //      }
  35 }
  36
  37 static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
  38 {
  39         int i, j, gc, gb;
  40         float feff;
  41
  42         for( i=0; i<len+1; i++ ) fgcp[i] = 0.0;
  43         for( j=0; j<clus; j++ )
  44         {
  45                 feff = (float)eff[j];
  46                 gc = ( seq[j][0] == '-' );
  47                 for( i=1; i<len+1; i++ )
  48                 {
  49                         gb = gc;
  50                         gc = ( seq[j][i] == '-' );
  51                         {
  52                                 if( gb * !gc ) fgcp[i-1] += feff;
  53                         }
  54                 }
  55 //              totaleff += eff[j];
  56 //              fprintf( stderr, "eff[%d] = %30.20f\n", j, eff[j] );
  57         }
  58 //      for( i=0; i<len; i++ )
  59 //      {
  60 //              fgcp[i] /= totaleff;
  61 //              fprintf( stderr, "fgcp[%d] = %30.20f\n", i, fgcp[i] );
  62 //      }
  63 }
  64 static float **impmtx = NULL;
  65 float imp_match_out_sc( int i1, int j1 )
  66 {
  67 //      fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
  68 //      fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
  69         return( impmtx[i1][j1] );
  70 }
  71 static void imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int *gapmap2 )
  72 {
  73         int j;
  74         float *pt = impmtx[i1];
  75         for( j=0; j<lgth2; j++ )
  76                 *imp++ += pt[gapmap2[j]];
  77 }
  78 static void imp_match_out_vead( float *imp, int i1, int lgth2 )
  79 {
  80         int j;
  81         float *pt = impmtx[i1];
  82         for( j=0; j<lgth2; j++ )
  83                 *imp++ += pt[j];
  84 }
  85
  86 void 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 )
  87 {
  88         int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
  89         static int impalloclen = 0;
  90         float effij;
  91         double effijx;
  92         char *pt, *pt1, *pt2;
  93         int allgap;
  94         static char *nocount1 = NULL;
  95         static char *nocount2 = NULL;
  96         LocalHom *tmpptr;
  97
  98         if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
  99         {
 100                 if( impmtx ) FreeFloatMtx( impmtx );
 101                 if( nocount1 ) free( nocount1 );
 102                 if( nocount2 ) free( nocount2 );
 103                 impalloclen = MAX( lgth1, lgth2 ) + 2;
 104                 impmtx = AllocateFloatMtx( impalloclen, impalloclen );
 105                 nocount1 = AllocateCharVec( impalloclen );
 106                 nocount2 = AllocateCharVec( impalloclen );
 107         }
 108
 109         for( i=0; i<lgth1; i++ )
 110         {
 111                 for( j=0; j<clus1; j++ )
 112                         if( seq1[j][i] == '-' ) break;
 113                 if( j != clus1 ) nocount1[i] = 1;
 114                 else                     nocount1[i] = 0;
 115         }
 116         for( i=0; i<lgth2; i++ )
 117         {
 118                 for( j=0; j<clus2; j++ )
 119                         if( seq2[j][i] == '-' ) break;
 120                 if( j != clus2 ) nocount2[i] = 1;
 121                 else                     nocount2[i] = 0;
 122         }
 123
 124 #if 0
 125 fprintf( stderr, "nocount2 =\n" );
 126 for( i = 0; i<impalloclen; i++ )
 127 {
 128         fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
 129 }
 130 #endif
 131
 132
 133
 134 #if 0
 135         fprintf( stderr, "eff1 in _init_strict = \n" );
 136         for( i=0; i<clus1; i++ )
 137                 fprintf( stderr, "eff1[] = %f\n", eff1[i] );
 138         for( i=0; i<clus2; i++ )
 139                 fprintf( stderr, "eff2[] = %f\n", eff2[i] );
 140 #endif
 141
 142         for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
 143                 impmtx[i][j] = 0.0;
 144         effijx =  fastathreshold;
 145         for( i=0; i<clus1; i++ )
 146         {
 147                 for( j=0; j<clus2; j++ )
 148                 {
 149                         effij = (float)( eff1[i] * eff2[j] * effijx );
 150                         tmpptr = localhom[i][j];
 151                         while( tmpptr )
 152                         {
 153 //                              fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
 154 //                              fprintf( stderr, "end1   = %d\n", tmpptr->end1   );
 155 //                              fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
 156 //                              fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
 157                                 pt = seq1[i];
 158                                 tmpint = -1;
 159                                 while( *pt != 0 )
 160                                 {
 161                                         if( *pt++ != '-' ) tmpint++;
 162                                         if( tmpint == tmpptr->start1 ) break;
 163                                 }
 164                                 start1 = pt - seq1[i] - 1;
 165
 166                                 while( *pt != 0 )
 167                                 {
 168 //                                      fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
 169                                         if( *pt++ != '-' ) tmpint++;
 170                                         if( tmpint == tmpptr->end1 ) break;
 171                                 }
 172                                 end1 = pt - seq1[i] - 1;
 173
 174                                 pt = seq2[j];
 175                                 tmpint = -1;
 176                                 while( *pt != 0 )
 177                                 {
 178                                         if( *pt++ != '-' ) tmpint++;
 179                                         if( tmpint == tmpptr->start2 ) break;
 180                                 }
 181                                 start2 = pt - seq2[j] - 1;
 182                                 while( *pt != 0 )
 183                                 {
 184                                         if( *pt++ != '-' ) tmpint++;
 185                                         if( tmpint == tmpptr->end2 ) break;
 186                                 }
 187                                 end2 = pt - seq2[j] - 1;
 188 //                              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] );
 189 //                              fprintf( stderr, "step 0\n" );
 190                                 if( end1 - start1 != end2 - start2 )
 191                                 {
 192 //                                      fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
 193                                 }
 194
 195 #if 1
 196                                 k1 = start1; k2 = start2;
 197                                 pt1 = seq1[i] + k1;
 198                                 pt2 = seq2[j] + k2;
 199                                 while( *pt1 && *pt2 )
 200                                 {
 201                                         if( *pt1 != '-' && *pt2 != '-' )
 202                                         {
 203 // ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
 204 //                                              impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
 205 //                                              impmtx[k1][k2] += tmpptr->importance * effij;
 206                                                 impmtx[k1][k2] += tmpptr->fimportance * effij;
 207 //                                              fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 208                                                 k1++; k2++;
 209                                                 pt1++; pt2++;
 210                                         }
 211                                         else if( *pt1 != '-' && *pt2 == '-' )
 212                                         {
 213 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 214                                                 k2++; pt2++;
 215                                         }
 216                                         else if( *pt1 == '-' && *pt2 != '-' )
 217                                         {
 218 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 219                                                 k1++; pt1++;
 220                                         }
 221                                         else if( *pt1 == '-' && *pt2 == '-' )
 222                                         {
 223 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 224                                                 k1++; pt1++;
 225                                                 k2++; pt2++;
 226                                         }
 227                                         if( k1 > end1 || k2 > end2 ) break;
 228                                 }
 229 #else
 230                                 while( k1 <= end1 && k2 <= end2 )
 231                                 {
 232                                         fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
 233                                         if( !nocount1[k1] && !nocount2[k2] )
 234                                         {
 235                                                 impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j]  * fastathreshold;
 236                                                 fprintf( stderr, "marked\n" );
 237                                         }
 238                                         else
 239                                                 fprintf( stderr, "no count\n" );
 240                                         k1++; k2++;
 241                                 }
 242 #endif
 243                                 tmpptr = tmpptr->next;
 244                         }
 245                 }
 246         }
 247 #if 0
 248         fprintf( stderr, "impmtx = \n" );
 249         for( k2=0; k2<lgth2; k2++ )
 250                 fprintf( stderr, "%6.3f ", (double)k2 );
 251         fprintf( stderr, "\n" );
 252         for( k1=0; k1<lgth1; k1++ )
 253         {
 254                 fprintf( stderr, "%d", k1 );
 255                 for( k2=0; k2<lgth2; k2++ )
 256                         fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
 257                 fprintf( stderr, "\n" );
 258         }
 259 #endif
 260 }
 261
 262 void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
 263 {
 264         int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
 265         static int impalloclen = 0;
 266         char *pt;
 267         int allgap;
 268         static char *nocount1 = NULL;
 269         static char *nocount2 = NULL;
 270
 271         if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
 272         {
 273                 if( impmtx ) FreeFloatMtx( impmtx );
 274                 if( nocount1 ) free( nocount1 );
 275                 if( nocount2 ) free( nocount2 );
 276                 impalloclen = MAX( lgth1, lgth2 ) + 2;
 277                 impmtx = AllocateFloatMtx( impalloclen, impalloclen );
 278                 nocount1 = AllocateCharVec( impalloclen );
 279                 nocount2 = AllocateCharVec( impalloclen );
 280         }
 281
 282         for( i=0; i<lgth1; i++ )
 283         {
 284                 for( j=0; j<clus1; j++ )
 285                         if( seq1[j][i] == '-' ) break;
 286                 if( j != clus1 ) nocount1[i] = 1;
 287                 else                     nocount1[i] = 0;
 288         }
 289         for( i=0; i<lgth2; i++ )
 290         {
 291                 for( j=0; j<clus2; j++ )
 292                         if( seq2[j][i] == '-' ) break;
 293                 if( j != clus2 ) nocount2[i] = 1;
 294                 else                     nocount2[i] = 0;
 295         }
 296
 297 #if 0
 298 fprintf( stderr, "nocount2 =\n" );
 299 for( i = 0; i<impalloclen; i++ )
 300 {
 301         fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
 302 }
 303 #endif
 304
 305         for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
 306                 impmtx[i][j] = 0;
 307         for( i=0; i<clus1; i++ )
 308         {
 309                 fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
 310                 for( j=0; j<clus2; j++ )
 311                 {
 312                         fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
 313                         fprintf( stderr, "end1   = %d\n", localhom[i][j]->end1   );
 314                         fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
 315                         pt = seq1[i];
 316                         tmpint = -1;
 317                         while( *pt != 0 )
 318                         {
 319                                 if( *pt++ != '-' ) tmpint++;
 320                                 if( tmpint == localhom[i][j]->start1 ) break;
 321                         }
 322                         start1 = pt - seq1[i] - 1;
 323
 324                         while( *pt != 0 )
 325                         {
 326 //                              fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
 327                                 if( *pt++ != '-' ) tmpint++;
 328                                 if( tmpint == localhom[i][j]->end1 ) break;
 329                         }
 330                         end1 = pt - seq1[i] - 1;
 331
 332                         pt = seq2[j];
 333                         tmpint = -1;
 334                         while( *pt != 0 )
 335                         {
 336                                 if( *pt++ != '-' ) tmpint++;
 337                                 if( tmpint == localhom[i][j]->start2 ) break;
 338                         }
 339                         start2 = pt - seq2[j] - 1;
 340                         while( *pt != 0 )
 341                         {
 342                                 if( *pt++ != '-' ) tmpint++;
 343                                 if( tmpint == localhom[i][j]->end2 ) break;
 344                         }
 345                         end2 = pt - seq2[j] - 1;
 346 //                      fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
 347                         k1 = start1;
 348                         k2 = start2;
 349                         fprintf( stderr, "step 0\n" );
 350                         while( k1 <= end1 && k2 <= end2 )
 351                         {
 352 #if 0
 353                                 if( !nocount1[k1] && !nocount2[k2] )
 354                                         impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
 355                                 k1++; k2++;
 356 #else
 357                                 if( !nocount1[k1] && !nocount2[k2] )
 358                                         impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
 359                                 k1++; k2++;
 360 #endif
 361                         }
 362
 363                         dif = ( end1 - start1 ) - ( end2 - start2 );
 364                         fprintf( stderr, "dif = %d\n", dif );
 365                         if( dif > 0 )
 366                         {
 367                                 do
 368                                 {
 369                                         fprintf( stderr, "dif = %d\n", dif );
 370                                         k1 = start1;
 371                                         k2 = start2 - dif;
 372                                         while( k1 <= end1 && k2 <= end2 )
 373                                         {
 374                                                 if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
 375                                                         impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
 376                                                 k1++; k2++;
 377                                         }
 378                                 }
 379                                 while( dif-- );
 380                         }
 381                         else
 382                         {
 383                                 do
 384                                 {
 385                                         k1 = start1 + dif;
 386                                         k2 = start2;
 387                                         while( k1 <= end1 )
 388                                         {
 389                                                 if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
 390                                                         impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
 391                                                 k1++; k2++;
 392                                         }
 393                                 }
 394                                 while( dif++ );
 395                         }
 396                 }
 397         }
 398 #if 0
 399         fprintf( stderr, "impmtx = \n" );
 400         for( k2=0; k2<lgth2; k2++ )
 401                 fprintf( stderr, "%6.3f ", (double)k2 );
 402         fprintf( stderr, "\n" );
 403         for( k1=0; k1<lgth1; k1++ )
 404         {
 405                 fprintf( stderr, "%d", k1 );
 406                 for( k2=0; k2<lgth2; k2++ )
 407                         fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
 408                 fprintf( stderr, "\n" );
 409         }
 410 #endif
 411 }
 412
 413 static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
 414 {
 415         int j, k, l;
 416         float scarr[26];
 417         float **cpmxpd = floatwork;
 418         int **cpmxpdn = intwork;
 419         int count = 0;
 420
 421         if( initialize )
 422         {
 423                 for( j=0; j<lgth2; j++ )
 424                 {
 425                         count = 0;
 426                         for( l=0; l<26; l++ )
 427                         {
 428                                 if( cpmx2[l][j] )
 429                                 {
 430                                         cpmxpd[count][j] = cpmx2[l][j];
 431                                         cpmxpdn[count][j] = l;
 432                                         count++;
 433                                 }
 434                         }
 435                         cpmxpdn[count][j] = -1;
 436                 }
 437         }
 438
 439         for( l=0; l<26; l++ )
 440         {
 441                 scarr[l] = 0.0;
 442                 for( k=0; k<26; k++ )
 443                         scarr[l] += n_dis[k][l] * cpmx1[k][i1];
 444         }
 445 #if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
 446         {
 447                 float *fpt, **fptpt, *fpt2;
 448                 int *ipt, **iptpt;
 449                 fpt2 = match;
 450                 iptpt = cpmxpdn;
 451                 fptpt = cpmxpd;
 452                 while( lgth2-- )
 453                 {
 454                         *fpt2 = 0.0;
 455                         ipt=*iptpt,fpt=*fptpt;
 456                         while( *ipt > -1 )
 457                                 *fpt2 += scarr[*ipt++] * *fpt++;
 458                         fpt2++,iptpt++,fptpt++;
 459                 }
 460         }
 461 #else
 462         for( j=0; j<lgth2; j++ )
 463         {
 464                 match[j] = 0.0;
 465                 for( k=0; cpmxpdn[k][j]>-1; k++ )
 466                         match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
 467         }
 468 #endif
 469 }
 470
 471 static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
 472                                                 char **seq1, char **seq2,
 473                         char **mseq1, char **mseq2,
 474                         float **cpmx1, float **cpmx2,
 475                         short **ijp, int icyc, int jcyc )
 476 {
 477         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
 478         char gap[] = "-";
 479         float wm;
 480         lgth1 = strlen( seq1[0] );
 481         lgth2 = strlen( seq2[0] );
 482
 483 #if 0
 484         for( i=0; i<lgth1; i++ )
 485         {
 486                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 487         }
 488 #endif
 489
 490         if( outgap == 1 )
 491                 ;
 492         else
 493         {
 494                 wm = lastverticalw[0];
 495                 for( i=0; i<lgth1; i++ )
 496                 {
 497                         if( lastverticalw[i] >= wm )
 498                         {
 499                                 wm = lastverticalw[i];
 500                                 iin = i; jin = lgth2-1;
 501                                 ijp[lgth1][lgth2] = +( lgth1 - i );
 502                         }
 503                 }
 504                 for( j=0; j<lgth2; j++ )
 505                 {
 506                         if( lasthorizontalw[j] >= wm )
 507                         {
 508                                 wm = lasthorizontalw[j];
 509                                 iin = lgth1-1; jin = j;
 510                                 ijp[lgth1][lgth2] = -( lgth2 - j );
 511                         }
 512                 }
 513         }
 514
 515     for( i=0; i<lgth1+1; i++ )
 516     {
 517         ijp[i][0] = i + 1;
 518     }
 519     for( j=0; j<lgth2+1; j++ )
 520     {
 521         ijp[0][j] = -( j + 1 );
 522     }
 523
 524         for( i=0; i<icyc; i++ )
 525         {
 526                 mseq1[i] += lgth1+lgth2;
 527                 *mseq1[i] = 0;
 528         }
 529         for( j=0; j<jcyc; j++ )
 530         {
 531                 mseq2[j] += lgth1+lgth2;
 532                 *mseq2[j] = 0;
 533         }
 534         iin = lgth1; jin = lgth2;
 535         *impwmpt = 0.0;
 536         for( k=0; k<=lgth1+lgth2; k++ )
 537         {
 538                 if( ijp[iin][jin] < 0 )
 539                 {
 540                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 541                 }
 542                 else if( ijp[iin][jin] > 0 )
 543                 {
 544                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 545                 }
 546                 else
 547                 {
 548                         ifi = iin-1; jfi = jin-1;
 549                 }
 550                 l = iin - ifi;
 551                 while( --l )
 552                 {
 553                         for( i=0; i<icyc; i++ )
 554                                 *--mseq1[i] = seq1[i][ifi+l];
 555                         for( j=0; j<jcyc; j++ )
 556                                 *--mseq2[j] = *gap;
 557                         k++;
 558                 }
 559                 l= jin - jfi;
 560                 while( --l )
 561                 {
 562                         for( i=0; i<icyc; i++ )
 563                                 *--mseq1[i] = *gap;
 564                         for( j=0; j<jcyc; j++ )
 565                                 *--mseq2[j] = seq2[j][jfi+l];
 566                         k++;
 567                 }
 568                 if( iin == lgth1 || jin == lgth2 )
 569                         ;
 570                 else
 571                 {
 572                         *impwmpt += imp_match_out_sc( iin, jin );
 573
 574 //              fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
 575                 }
 576                 if( iin <= 0 || jin <= 0 ) break;
 577                 for( i=0; i<icyc; i++ )
 578                         *--mseq1[i] = seq1[i][ifi];
 579                 for( j=0; j<jcyc; j++ )
 580                         *--mseq2[j] = seq2[j][jfi];
 581                 k++;
 582                 iin = ifi; jin = jfi;
 583         }
 584 }
 585 static void Atracking_localhom_gapmap( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
 586                                                 char **seq1, char **seq2,
 587                         char **mseq1, char **mseq2,
 588                         float **cpmx1, float **cpmx2,
 589                         short **ijp, int icyc, int jcyc,
 590                                                 int *gapmap1, int *gapmap2 )
 591 {
 592         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
 593         char gap[] = "-";
 594         float wm;
 595         lgth1 = strlen( seq1[0] );
 596         lgth2 = strlen( seq2[0] );
 597
 598 #if 0
 599         for( i=0; i<lgth1; i++ )
 600         {
 601                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 602         }
 603 #endif
 604
 605         if( outgap == 1 )
 606                 ;
 607         else
 608         {
 609                 wm = lastverticalw[0];
 610                 for( i=0; i<lgth1; i++ )
 611                 {
 612                         if( lastverticalw[i] >= wm )
 613                         {
 614                                 wm = lastverticalw[i];
 615                                 iin = i; jin = lgth2-1;
 616                                 ijp[lgth1][lgth2] = +( lgth1 - i );
 617                         }
 618                 }
 619                 for( j=0; j<lgth2; j++ )
 620                 {
 621                         if( lasthorizontalw[j] >= wm )
 622                         {
 623                                 wm = lasthorizontalw[j];
 624                                 iin = lgth1-1; jin = j;
 625                                 ijp[lgth1][lgth2] = -( lgth2 - j );
 626                         }
 627                 }
 628         }
 629
 630     for( i=0; i<lgth1+1; i++ )
 631     {
 632         ijp[i][0] = i + 1;
 633     }
 634     for( j=0; j<lgth2+1; j++ )
 635     {
 636         ijp[0][j] = -( j + 1 );
 637     }
 638
 639         for( i=0; i<icyc; i++ )
 640         {
 641                 mseq1[i] += lgth1+lgth2;
 642                 *mseq1[i] = 0;
 643         }
 644         for( j=0; j<jcyc; j++ )
 645         {
 646                 mseq2[j] += lgth1+lgth2;
 647                 *mseq2[j] = 0;
 648         }
 649         iin = lgth1; jin = lgth2;
 650         *impwmpt = 0.0;
 651         for( k=0; k<=lgth1+lgth2; k++ )
 652         {
 653                 if( ijp[iin][jin] < 0 )
 654                 {
 655                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 656                 }
 657                 else if( ijp[iin][jin] > 0 )
 658                 {
 659                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 660                 }
 661                 else
 662                 {
 663                         ifi = iin-1; jfi = jin-1;
 664                 }
 665                 l = iin - ifi;
 666                 while( --l )
 667                 {
 668                         for( i=0; i<icyc; i++ )
 669                                 *--mseq1[i] = seq1[i][ifi+l];
 670                         for( j=0; j<jcyc; j++ )
 671                                 *--mseq2[j] = *gap;
 672                         k++;
 673                 }
 674                 l= jin - jfi;
 675                 while( --l )
 676                 {
 677                         for( i=0; i<icyc; i++ )
 678                                 *--mseq1[i] = *gap;
 679                         for( j=0; j<jcyc; j++ )
 680                                 *--mseq2[j] = seq2[j][jfi+l];
 681                         k++;
 682                 }
 683                 if( iin == lgth1 || jin == lgth2 )
 684                         ;
 685                 else
 686                 {
 687                         *impwmpt += imp_match_out_sc( gapmap1[iin], gapmap2[jin] );
 688
 689 //              fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
 690                 }
 691                 if( iin <= 0 || jin <= 0 ) break;
 692                 for( i=0; i<icyc; i++ )
 693                         *--mseq1[i] = seq1[i][ifi];
 694                 for( j=0; j<jcyc; j++ )
 695                         *--mseq2[j] = seq2[j][jfi];
 696                 k++;
 697                 iin = ifi; jin = jfi;
 698         }
 699 }
 700 static float Atracking( float *lasthorizontalw, float *lastverticalw,
 701                                                 char **seq1, char **seq2,
 702                         char **mseq1, char **mseq2,
 703                         float **cpmx1, float **cpmx2,
 704                         short **ijp, int icyc, int jcyc )
 705 {
 706         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
 707         char gap[] = "-";
 708         float wm;
 709         lgth1 = strlen( seq1[0] );
 710         lgth2 = strlen( seq2[0] );
 711
 712 #if 0
 713         for( i=0; i<lgth1; i++ )
 714         {
 715                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 716         }
 717 #endif
 718
 719         if( outgap == 1 )
 720                 ;
 721         else
 722         {
 723                 wm = lastverticalw[0];
 724                 for( i=0; i<lgth1; i++ )
 725                 {
 726                         if( lastverticalw[i] >= wm )
 727                         {
 728                                 wm = lastverticalw[i];
 729                                 iin = i; jin = lgth2-1;
 730                                 ijp[lgth1][lgth2] = +( lgth1 - i );
 731                         }
 732                 }
 733                 for( j=0; j<lgth2; j++ )
 734                 {
 735                         if( lasthorizontalw[j] >= wm )
 736                         {
 737                                 wm = lasthorizontalw[j];
 738                                 iin = lgth1-1; jin = j;
 739                                 ijp[lgth1][lgth2] = -( lgth2 - j );
 740                         }
 741                 }
 742         }
 743
 744     for( i=0; i<lgth1+1; i++ )
 745     {
 746         ijp[i][0] = i + 1;
 747     }
 748     for( j=0; j<lgth2+1; j++ )
 749     {
 750         ijp[0][j] = -( j + 1 );
 751     }
 752
 753         for( i=0; i<icyc; i++ )
 754         {
 755                 mseq1[i] += lgth1+lgth2;
 756                 *mseq1[i] = 0;
 757         }
 758         for( j=0; j<jcyc; j++ )
 759         {
 760                 mseq2[j] += lgth1+lgth2;
 761                 *mseq2[j] = 0;
 762         }
 763         iin = lgth1; jin = lgth2;
 764         for( k=0; k<=lgth1+lgth2; k++ )
 765         {
 766                 if( ijp[iin][jin] < 0 )
 767                 {
 768                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 769                 }
 770                 else if( ijp[iin][jin] > 0 )
 771                 {
 772                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 773                 }
 774                 else
 775                 {
 776                         ifi = iin-1; jfi = jin-1;
 777                 }
 778                 l = iin - ifi;
 779                 while( --l )
 780                 {
 781                         for( i=0; i<icyc; i++ )
 782                                 *--mseq1[i] = seq1[i][ifi+l];
 783                         for( j=0; j<jcyc; j++ )
 784                                 *--mseq2[j] = *gap;
 785                         k++;
 786                 }
 787                 l= jin - jfi;
 788                 while( --l )
 789                 {
 790                         for( i=0; i<icyc; i++ )
 791                                 *--mseq1[i] = *gap;
 792                         for( j=0; j<jcyc; j++ )
 793                                 *--mseq2[j] = seq2[j][jfi+l];
 794                         k++;
 795                 }
 796                 if( iin <= 0 || jin <= 0 ) break;
 797                 for( i=0; i<icyc; i++ )
 798                         *--mseq1[i] = seq1[i][ifi];
 799                 for( j=0; j<jcyc; j++ )
 800                         *--mseq2[j] = seq2[j][jfi];
 801                 k++;
 802                 iin = ifi; jin = jfi;
 803         }
 804         return( 0.0 );
 805 }
 806
 807 float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch )
 808 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 809 {
 810 //      int k;
 811         register int i, j;
 812         int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
 813         int lgth1, lgth2;
 814         int resultlen;
 815         float wm;   /* int ?????? */
 816         float g;
 817         float *currentw, *previousw;
 818 //      float fpenalty = (float)penalty;
 819         float fpenalty_ex = (float)penalty_ex;
 820 #if 1
 821         float *wtmp;
 822         short *ijppt;
 823         float *mjpt, *prept, *curpt;
 824         int *mpjpt;
 825 #endif
 826         static float mi, *m;
 827         static short **ijp;
 828         static int mpi, *mp;
 829         static float *w1, *w2;
 830         static float *match;
 831         static float *initverticalw;    /* kufuu sureba iranai */
 832         static float *lastverticalw;    /* kufuu sureba iranai */
 833         static char **mseq1;
 834         static char **mseq2;
 835         static char **mseq;
 836         static float *ogcp1;
 837         static float *ogcp2;
 838         static float *fgcp1;
 839         static float *fgcp2;
 840         static float **cpmx1;
 841         static float **cpmx2;
 842         static int **intwork;
 843         static float **floatwork;
 844         static int orlgth1 = 0, orlgth2 = 0;
 845         float fpenalty = (float)penalty;
 846
 847
 848 #if 0
 849         fprintf( stderr, "eff in SA+++align\n" );
 850         for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
 851 #endif
 852         if( orlgth1 == 0 )
 853         {
 854                 mseq1 = AllocateCharMtx( njob, 0 );
 855                 mseq2 = AllocateCharMtx( njob, 0 );
 856         }
 857
 858
 859         lgth1 = strlen( seq1[0] );
 860         lgth2 = strlen( seq2[0] );
 861
 862         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 863         {
 864                 int ll1, ll2;
 865
 866                 if( orlgth1 > 0 && orlgth2 > 0 )
 867                 {
 868                         FreeFloatVec( w1 );
 869                         FreeFloatVec( w2 );
 870                         FreeFloatVec( match );
 871                         FreeFloatVec( initverticalw );
 872                         FreeFloatVec( lastverticalw );
 873
 874                         FreeFloatVec( m );
 875                         FreeIntVec( mp );
 876
 877                         FreeCharMtx( mseq );
 878
 879                         FreeFloatVec( ogcp1 );
 880                         FreeFloatVec( ogcp2 );
 881                         FreeFloatVec( fgcp1 );
 882                         FreeFloatVec( fgcp2 );
 883
 884
 885                         FreeFloatMtx( cpmx1 );
 886                         FreeFloatMtx( cpmx2 );
 887
 888                         FreeFloatMtx( floatwork );
 889                         FreeIntMtx( intwork );
 890                 }
 891
 892                 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
 893                 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
 894
 895 #if DEBUG
 896                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
 897 #endif
 898
 899                 w1 = AllocateFloatVec( ll2+2 );
 900                 w2 = AllocateFloatVec( ll2+2 );
 901                 match = AllocateFloatVec( ll2+2 );
 902
 903                 initverticalw = AllocateFloatVec( ll1+2 );
 904                 lastverticalw = AllocateFloatVec( ll1+2 );
 905
 906                 m = AllocateFloatVec( ll2+2 );
 907                 mp = AllocateIntVec( ll2+2 );
 908
 909                 mseq = AllocateCharMtx( njob, ll1+ll2 );
 910
 911                 ogcp1 = AllocateFloatVec( ll1+2 );
 912                 ogcp2 = AllocateFloatVec( ll2+2 );
 913                 fgcp1 = AllocateFloatVec( ll1+2 );
 914                 fgcp2 = AllocateFloatVec( ll2+2 );
 915
 916                 cpmx1 = AllocateFloatMtx( 26, ll1+2 );
 917                 cpmx2 = AllocateFloatMtx( 26, ll2+2 );
 918
 919                 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
 920                 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
 921
 922 #if DEBUG
 923                 fprintf( stderr, "succeeded\n" );
 924 #endif
 925
 926                 orlgth1 = ll1 - 100;
 927                 orlgth2 = ll2 - 100;
 928         }
 929
 930
 931         for( i=0; i<icyc; i++ )
 932         {
 933                 mseq1[i] = mseq[i];
 934                 seq1[i][lgth1] = 0;
 935         }
 936         for( j=0; j<jcyc; j++ )
 937         {
 938                 mseq2[j] = mseq[icyc+j];
 939                 seq2[j][lgth2] = 0;
 940         }
 941
 942
 943         if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
 944         {
 945                 int ll1, ll2;
 946
 947                 if( commonAlloc1 && commonAlloc2 )
 948                 {
 949                         FreeShortMtx( commonIP );
 950                 }
 951
 952                 ll1 = MAX( orlgth1, commonAlloc1 );
 953                 ll2 = MAX( orlgth2, commonAlloc2 );
 954
 955 #if DEBUG
 956                 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 957 #endif
 958
 959                 commonIP = AllocateShortMtx( ll1+10, ll2+10 );
 960
 961 #if DEBUG
 962                 fprintf( stderr, "succeeded\n\n" );
 963 #endif
 964
 965                 commonAlloc1 = ll1;
 966                 commonAlloc2 = ll2;
 967         }
 968         ijp = commonIP;
 969
 970 #if 0
 971         {
 972                 float t = 0.0;
 973                 for( i=0; i<icyc; i++ )
 974                         t += eff1[i];
 975         fprintf( stderr, "## totaleff = %f\n", t );
 976         }
 977 #endif
 978         cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
 979         cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
 980
 981         OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
 982         OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
 983         FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
 984         FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
 985
 986         for( i=0; i<lgth1; i++ )
 987         {
 988                 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
 989                 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
 990         }
 991         for( i=0; i<lgth2; i++ )
 992         {
 993                 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
 994                 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
 995         }
 996 #if 0
 997         for( i=0; i<lgth1; i++ )
 998                 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
 999 #endif
1000
1001         currentw = w1;
1002         previousw = w2;
1003
1004         match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
1005
1006         match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
1007 #if 0 // -> tbfast.c
1008         if( localhom )
1009                 imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
1010
1011 #endif
1012
1013         if( outgap == 1 )
1014         {
1015                 for( i=1; i<lgth1+1; i++ )
1016                 {
1017                         initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
1018                 }
1019                 for( j=1; j<lgth2+1; j++ )
1020                 {
1021                         currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
1022                 }
1023         }
1024 #if OUTGAP0TRY
1025         else
1026         {
1027                 for( j=1; j<lgth2+1; j++ )
1028                         currentw[j] -= offset * j / 2.0;
1029                 for( i=1; i<lgth1+1; i++ )
1030                         initverticalw[i] -= offset * i / 2.0;
1031         }
1032 #endif
1033
1034         for( j=1; j<lgth2+1; ++j )
1035         {
1036                 m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
1037         }
1038
1039         lastverticalw[0] = currentw[lgth2-1];
1040
1041         if( outgap ) lasti = lgth1+1; else lasti = lgth1;
1042
1043 #if XXXXXXX
1044 fprintf( stderr, "currentw = \n" );
1045 for( i=0; i<lgth1+1; i++ )
1046 {
1047         fprintf( stderr, "%5.2f ", currentw[i] );
1048 }
1049 fprintf( stderr, "\n" );
1050 fprintf( stderr, "initverticalw = \n" );
1051 for( i=0; i<lgth2+1; i++ )
1052 {
1053         fprintf( stderr, "%5.2f ", initverticalw[i] );
1054 }
1055 fprintf( stderr, "\n" );
1056 fprintf( stderr, "fcgp\n" );
1057 for( i=0; i<lgth1; i++ )
1058         fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
1059 for( i=0; i<lgth2; i++ )
1060         fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
1061 #endif
1062
1063         for( i=1; i<lasti; i++ )
1064         {
1065                 wtmp = previousw;
1066                 previousw = currentw;
1067                 currentw = wtmp;
1068
1069                 previousw[0] = initverticalw[i-1];
1070
1071                 match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
1072 #if XXXXXXX
1073 fprintf( stderr, "\n" );
1074 fprintf( stderr, "i=%d\n", i );
1075 fprintf( stderr, "currentw = \n" );
1076 for( j=0; j<lgth2; j++ )
1077 {
1078         fprintf( stderr, "%5.2f ", currentw[j] );
1079 }
1080 fprintf( stderr, "\n" );
1081 #endif
1082                 if( localhom )
1083                 {
1084 //                      fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
1085 #if  0
1086                         imp_match_out_vead( currentw, i, lgth2 );
1087 #else
1088                         imp_match_out_vead( currentw, i, lgth2 );
1089 #endif
1090                 }
1091 #if XXXXXXX
1092 fprintf( stderr, "\n" );
1093 fprintf( stderr, "i=%d\n", i );
1094 fprintf( stderr, "currentw = \n" );
1095 for( j=0; j<lgth2; j++ )
1096 {
1097         fprintf( stderr, "%5.2f ", currentw[j] );
1098 }
1099 fprintf( stderr, "\n" );
1100 #endif
1101                 currentw[0] = initverticalw[i];
1102
1103 #if 1
1104
1105                 mi = previousw[0] + ogcp2[1]; mpi = 0;
1106
1107                 ijppt = ijp[i] + 1;
1108                 mjpt = m + 1;
1109                 prept = previousw;
1110                 curpt = currentw + 1;
1111                 mpjpt = mp + 1;
1112                 for( j=1; j<lgth2+1; j++ )
1113                 {
1114                         wm = *prept;
1115                         *ijppt = 0;
1116
1117 #if 0
1118                         fprintf( stderr, "%5.0f->", wm );
1119 #endif
1120                         g = mi + fgcp2[j-1];
1121 #if 0
1122                         fprintf( stderr, "%5.0f?", g );
1123 #endif
1124                         if( g > wm )
1125                         {
1126                                 wm = g;
1127                                 *ijppt = -( j - mpi );
1128                         }
1129                         g = *prept + ogcp2[j];
1130                         if( g >= mi )
1131                         {
1132                                 mi = g;
1133                                 mpi = j-1;
1134                         }
1135 #if USE_PENALTY_EX
1136                         mi += fpenalty_ex;
1137 #endif
1138
1139                         g = *mjpt + fgcp1[i-1];
1140 #if 0
1141                         fprintf( stderr, "%5.0f?", g );
1142 #endif
1143                         if( g > wm )
1144                         {
1145                                 wm = g;
1146                                 *ijppt = +( i - *mpjpt );
1147                         }
1148                         g = *prept + ogcp1[i];
1149                         if( g >= *mjpt )
1150                         {
1151                                 *mjpt = g;
1152                                 *mpjpt = i-1;
1153                         }
1154 #if USE_PENALTY_EX
1155                         m[j] += fpenalty_ex;
1156 #endif
1157
1158 #if 0
1159                         fprintf( stderr, "%5.0f ", wm );
1160 #endif
1161                         *curpt += wm;
1162                         ijppt++;
1163                         mjpt++;
1164                         prept++;
1165                         mpjpt++;
1166                         curpt++;
1167                 }
1168                 lastverticalw[i] = currentw[lgth2-1];
1169 #else
1170         floatncpy( previousw, currentw, lgth2+1 );
1171         previousw[0] = initverticalw[i-1];
1172
1173
1174         match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
1175         currentw[0] = initverticalw[i];
1176
1177         mi = previousw[0] + ogcp2[1]; mpi = 0;
1178         for( j=1; j<lgth2+1; j++ )
1179         {
1180             wm = previousw[j-1];
1181             ijp[i][j] = 0;
1182
1183             g = fgcp2[j-1];
1184             if( mi + g > wm )
1185             {
1186                 wm = mi + g;
1187                 ijp[i][j] = -( j - mpi );
1188             }
1189             g = ogcp2[j];
1190             if( mi <= previousw[j-1] + g )
1191             {
1192                 mi = previousw[j-1] + g;
1193                 mpi = j-1;
1194             }
1195
1196             g = fgcp1[i-1];
1197             if( m[j] + g > wm )
1198             {
1199                 wm = m[j] + g;
1200                 ijp[i][j] = +( i - mp[j] );
1201             }
1202             g = ogcp1[i];
1203             if( m[j] <= previousw[j-1] + g )
1204             {
1205                 m[j] = previousw[j-1] + g ;
1206                 mp[j] = i-1;
1207             }
1208             currentw[j] += wm;
1209         }
1210         lastverticalw[i] = currentw[lgth2-1];
1211
1212 #endif
1213         }
1214
1215 //      fprintf( stderr, "wm = %f\n", wm );
1216
1217 #if OUTGAP0TRY
1218         if( !outgap )
1219         {
1220                 for( j=1; j<lgth2+1; j++ )
1221                         currentw[j] -= offset * ( lgth2 - j ) / 2.0;
1222                 for( i=1; i<lgth1+1; i++ )
1223                         lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
1224         }
1225 #endif
1226
1227         /*
1228         fprintf( stderr, "\n" );
1229         for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
1230         fprintf( stderr, "#####\n" );
1231         for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
1232         fprintf( stderr, "====>" );
1233         for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
1234         for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
1235         */
1236         if( localhom )
1237         {
1238                 Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1239         }
1240         else
1241                 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1242
1243 //      fprintf( stderr, "### impmatch = %f\n", *impmatch );
1244
1245         resultlen = strlen( mseq1[0] );
1246         if( alloclen < resultlen || resultlen > N )
1247         {
1248                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
1249                 ErrorExit( "LENGTH OVER!\n" );
1250         }
1251
1252
1253         for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
1254         for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
1255         /*
1256         fprintf( stderr, "\n" );
1257         for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
1258         fprintf( stderr, "#####\n" );
1259         for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
1260         */
1261
1262         fprintf( stderr, "wm = %f\n", wm );
1263
1264         return( wm );
1265 }
1266
1267 float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 )
1268 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
1269 {
1270 //      int k;
1271         register int i, j;
1272         int lasti, lastj;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
1273         int lgth1, lgth2;
1274         int resultlen;
1275         float wm;   /* int ?????? */
1276         float g;
1277         float *currentw, *previousw;
1278 //      float fpenalty = (float)penalty;
1279         float fpenalty_ex = (float)penalty_ex;
1280 #if 1
1281         float *wtmp;
1282         short *ijppt;
1283         float *mjpt, *prept, *curpt;
1284         int *mpjpt;
1285 #endif
1286         static float mi, *m;
1287         static short **ijp;
1288         static int mpi, *mp;
1289         static float *w1, *w2;
1290         static float *match;
1291         static float *initverticalw;    /* kufuu sureba iranai */
1292         static float *lastverticalw;    /* kufuu sureba iranai */
1293         static char **mseq1;
1294         static char **mseq2;
1295         static char **mseq;
1296         static float *ogcp1;
1297         static float *ogcp2;
1298         static float *fgcp1;
1299         static float *fgcp2;
1300         static float **cpmx1;
1301         static float **cpmx2;
1302         static int **intwork;
1303         static float **floatwork;
1304         static int orlgth1 = 0, orlgth2 = 0;
1305
1306
1307 #if 0
1308         fprintf( stderr, "eff in SA+++align\n" );
1309         for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
1310 #endif
1311         if( orlgth1 == 0 )
1312         {
1313                 mseq1 = AllocateCharMtx( njob, 0 );
1314                 mseq2 = AllocateCharMtx( njob, 0 );
1315         }
1316
1317
1318         lgth1 = strlen( seq1[0] );
1319         lgth2 = strlen( seq2[0] );
1320
1321         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
1322         {
1323                 int ll1, ll2;
1324
1325                 if( orlgth1 > 0 && orlgth2 > 0 )
1326                 {
1327                         FreeFloatVec( w1 );
1328                         FreeFloatVec( w2 );
1329                         FreeFloatVec( match );
1330                         FreeFloatVec( initverticalw );
1331                         FreeFloatVec( lastverticalw );
1332
1333                         FreeFloatVec( m );
1334                         FreeIntVec( mp );
1335
1336                         FreeCharMtx( mseq );
1337
1338                         FreeFloatVec( ogcp1 );
1339                         FreeFloatVec( ogcp2 );
1340                         FreeFloatVec( fgcp1 );
1341                         FreeFloatVec( fgcp2 );
1342
1343
1344                         FreeFloatMtx( cpmx1 );
1345                         FreeFloatMtx( cpmx2 );
1346
1347                         FreeFloatMtx( floatwork );
1348                         FreeIntMtx( intwork );
1349                 }
1350
1351                 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
1352                 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
1353
1354 #if DEBUG
1355                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
1356 #endif
1357
1358                 w1 = AllocateFloatVec( ll2+2 );
1359                 w2 = AllocateFloatVec( ll2+2 );
1360                 match = AllocateFloatVec( ll2+2 );
1361
1362                 initverticalw = AllocateFloatVec( ll1+2 );
1363                 lastverticalw = AllocateFloatVec( ll1+2 );
1364
1365                 m = AllocateFloatVec( ll2+2 );
1366                 mp = AllocateIntVec( ll2+2 );
1367
1368                 mseq = AllocateCharMtx( njob, ll1+ll2 );
1369
1370                 ogcp1 = AllocateFloatVec( ll1+2 );
1371                 ogcp2 = AllocateFloatVec( ll2+2 );
1372                 fgcp1 = AllocateFloatVec( ll1+2 );
1373                 fgcp2 = AllocateFloatVec( ll2+2 );
1374
1375                 cpmx1 = AllocateFloatMtx( 26, ll1+2 );
1376                 cpmx2 = AllocateFloatMtx( 26, ll2+2 );
1377
1378                 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
1379                 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
1380
1381 #if DEBUG
1382                 fprintf( stderr, "succeeded\n" );
1383 #endif
1384
1385                 orlgth1 = ll1 - 100;
1386                 orlgth2 = ll2 - 100;
1387         }
1388
1389
1390         for( i=0; i<icyc; i++ )
1391         {
1392                 mseq1[i] = mseq[i];
1393                 seq1[i][lgth1] = 0;
1394         }
1395         for( j=0; j<jcyc; j++ )
1396         {
1397                 mseq2[j] = mseq[icyc+j];
1398                 seq2[j][lgth2] = 0;
1399         }
1400
1401
1402         if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
1403         {
1404                 int ll1, ll2;
1405
1406                 if( commonAlloc1 && commonAlloc2 )
1407                 {
1408                         FreeShortMtx( commonIP );
1409                 }
1410
1411                 ll1 = MAX( orlgth1, commonAlloc1 );
1412                 ll2 = MAX( orlgth2, commonAlloc2 );
1413
1414 #if DEBUG
1415                 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
1416 #endif
1417
1418                 commonIP = AllocateShortMtx( ll1+10, ll2+10 );
1419
1420 #if DEBUG
1421                 fprintf( stderr, "succeeded\n\n" );
1422 #endif
1423
1424                 commonAlloc1 = ll1;
1425                 commonAlloc2 = ll2;
1426         }
1427         ijp = commonIP;
1428
1429         cpmx_calc_new( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
1430         cpmx_calc_new( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
1431
1432         OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1  );
1433         OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
1434         FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
1435         FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
1436
1437         for( i=0; i<lgth1; i++ )
1438         {
1439                 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
1440                 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
1441         }
1442         for( i=0; i<lgth2; i++ )
1443         {
1444                 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
1445                 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
1446         }
1447 #if 0
1448         for( i=0; i<lgth1; i++ )
1449                 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
1450 #endif
1451
1452         currentw = w1;
1453         previousw = w2;
1454
1455
1456         match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
1457
1458
1459         match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
1460 #if 0 // -> tbfast.c
1461         if( localhom )
1462                 imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
1463
1464 #endif
1465
1466         if( outgap == 1 )
1467         {
1468                 for( i=1; i<lgth1+1; i++ )
1469                 {
1470                         initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
1471                 }
1472                 for( j=1; j<lgth2+1; j++ )
1473                 {
1474                         currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
1475                 }
1476         }
1477 #if OUTGAP0TRY
1478         else
1479         {
1480                 for( j=1; j<lgth2+1; j++ )
1481                         currentw[j] -= offset * j / 2.0;
1482                 for( i=1; i<lgth1+1; i++ )
1483                         initverticalw[i] -= offset * i / 2.0;
1484         }
1485 #endif
1486
1487         for( j=1; j<lgth2+1; ++j )
1488         {
1489                 m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
1490         }
1491
1492         lastverticalw[0] = currentw[lgth2-1];
1493
1494         if( outgap ) lasti = lgth1+1; else lasti = lgth1;
1495
1496 #if XXXXXXX
1497 fprintf( stderr, "currentw = \n" );
1498 for( i=0; i<lgth1+1; i++ )
1499 {
1500         fprintf( stderr, "%5.2f ", currentw[i] );
1501 }
1502 fprintf( stderr, "\n" );
1503 fprintf( stderr, "initverticalw = \n" );
1504 for( i=0; i<lgth2+1; i++ )
1505 {
1506         fprintf( stderr, "%5.2f ", initverticalw[i] );
1507 }
1508 fprintf( stderr, "\n" );
1509 fprintf( stderr, "fcgp\n" );
1510 for( i=0; i<lgth1; i++ )
1511         fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
1512 for( i=0; i<lgth2; i++ )
1513         fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
1514 #endif
1515
1516         for( i=1; i<lasti; i++ )
1517         {
1518                 wtmp = previousw;
1519                 previousw = currentw;
1520                 currentw = wtmp;
1521
1522                 previousw[0] = initverticalw[i-1];
1523
1524                 match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
1525 #if XXXXXXX
1526 fprintf( stderr, "\n" );
1527 fprintf( stderr, "i=%d\n", i );
1528 fprintf( stderr, "currentw = \n" );
1529 for( j=0; j<lgth2; j++ )
1530 {
1531         fprintf( stderr, "%5.2f ", currentw[j] );
1532 }
1533 fprintf( stderr, "\n" );
1534 #endif
1535                 if( localhom )
1536                 {
1537 //                      fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
1538 #if  0
1539                         imp_match_out_vead( currentw, i, lgth2 );
1540 #else
1541                         imp_match_out_vead_gapmap( currentw, gapmap1[i], lgth2, gapmap2 );
1542 #endif
1543                 }
1544 #if XXXXXXX
1545 fprintf( stderr, "\n" );
1546 fprintf( stderr, "i=%d\n", i );
1547 fprintf( stderr, "currentw = \n" );
1548 for( j=0; j<lgth2; j++ )
1549 {
1550         fprintf( stderr, "%5.2f ", currentw[j] );
1551 }
1552 fprintf( stderr, "\n" );
1553 #endif
1554                 currentw[0] = initverticalw[i];
1555
1556 #if 1
1557
1558                 mi = previousw[0] + ogcp2[1]; mpi = 0;
1559
1560                 ijppt = ijp[i] + 1;
1561                 mjpt = m + 1;
1562                 prept = previousw;
1563                 curpt = currentw + 1;
1564                 mpjpt = mp + 1;
1565                 for( j=1; j<lgth2+1; j++ )
1566                 {
1567                         wm = *prept;
1568                         *ijppt = 0;
1569
1570 #if 0
1571                         fprintf( stderr, "%5.0f->", wm );
1572 #endif
1573                         g = mi + fgcp2[j-1];
1574 #if 0
1575                         fprintf( stderr, "%5.0f?", g );
1576 #endif
1577                         if( g > wm )
1578                         {
1579                                 wm = g;
1580                                 *ijppt = -( j - mpi );
1581                         }
1582                         g = *prept + ogcp2[j];
1583                         if( g >= mi )
1584                         {
1585                                 mi = g;
1586                                 mpi = j-1;
1587                         }
1588 #if USE_PENALTY_EX
1589                         mi += fpenalty_ex;
1590 #endif
1591
1592                         g = *mjpt + fgcp1[i-1];
1593 #if 0
1594                         fprintf( stderr, "%5.0f?", g );
1595 #endif
1596                         if( g > wm )
1597                         {
1598                                 wm = g;
1599                                 *ijppt = +( i - *mpjpt );
1600                         }
1601                         g = *prept + ogcp1[i];
1602                         if( g >= *mjpt )
1603                         {
1604                                 *mjpt = g;
1605                                 *mpjpt = i-1;
1606                         }
1607 #if USE_PENALTY_EX
1608                         m[j] += fpenalty_ex;
1609 #endif
1610
1611 #if 0
1612                         fprintf( stderr, "%5.0f ", wm );
1613 #endif
1614                         *curpt += wm;
1615                         ijppt++;
1616                         mjpt++;
1617                         prept++;
1618                         mpjpt++;
1619                         curpt++;
1620                 }
1621                 lastverticalw[i] = currentw[lgth2-1];
1622 #else
1623         floatncpy( previousw, currentw, lgth2+1 );
1624         previousw[0] = initverticalw[i-1];
1625
1626
1627         match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
1628         currentw[0] = initverticalw[i];
1629
1630         mi = previousw[0] + ogcp2[1]; mpi = 0;
1631                 lastj = lgth2+1;
1632         for( j=1; j<lastj; j++ )
1633         {
1634             wm = previousw[j-1];
1635             ijp[i][j] = 0;
1636
1637             g = fgcp2[j-1];
1638             if( mi + g > wm )
1639             {
1640                 wm = mi + g;
1641                 ijp[i][j] = -( j - mpi );
1642             }
1643             g = ogcp2[j];
1644             if( mi <= previousw[j-1] + g )
1645             {
1646                 mi = previousw[j-1] + g;
1647                 mpi = j-1;
1648             }
1649
1650             g = fgcp1[i-1];
1651             if( m[j] + g > wm )
1652             {
1653                 wm = m[j] + g;
1654                 ijp[i][j] = +( i - mp[j] );
1655             }
1656             g = ogcp1[i];
1657             if( m[j] <= previousw[j-1] + g )
1658             {
1659                 m[j] = previousw[j-1] + g ;
1660                 mp[j] = i-1;
1661             }
1662             currentw[j] += wm;
1663         }
1664         lastverticalw[i] = currentw[lgth2-1];
1665
1666 #endif
1667         }
1668
1669 #if OUTGAP0TRY
1670         if( !outgap )
1671         {
1672                 for( j=1; j<lgth2+1; j++ )
1673                         currentw[j] -= offset * ( lgth2 - j ) / 2.0;
1674                 for( i=1; i<lgth1+1; i++ )
1675                         lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
1676         }
1677 #endif
1678
1679         /*
1680         fprintf( stderr, "\n" );
1681         for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
1682         fprintf( stderr, "#####\n" );
1683         for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
1684         fprintf( stderr, "====>" );
1685         for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
1686         for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
1687         */
1688         if( localhom )
1689         {
1690                 Atracking_localhom_gapmap( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, gapmap1, gapmap2 );
1691         }
1692         else
1693                 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1694
1695 //      fprintf( stderr, "### impmatch = %f\n", *impmatch );
1696
1697         resultlen = strlen( mseq1[0] );
1698         if( alloclen < resultlen || resultlen > N )
1699         {
1700                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
1701                 ErrorExit( "LENGTH OVER!\n" );
1702         }
1703
1704
1705         for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
1706         for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
1707         /*
1708         fprintf( stderr, "\n" );
1709         for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
1710         fprintf( stderr, "#####\n" );
1711         for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
1712         */
1713
1714         fprintf( stderr, "wm = %f\n", wm );
1715
1716         return( wm );
1717 }
1718
1719 float translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, int clus1, int clus2, int alloclen )
1720 {
1721     int i;
1722     float wm;
1723     char **result;
1724     char *seq, **aseq;
1725     double *effarr;
1726     int nseq;
1727         int resultlen;
1728
1729     if     ( clus1 == 1 && clus2 != 1 )
1730     {
1731         seq = mseq1[0]; aseq = mseq2; effarr = effarr2; nseq = clus2+1;
1732 #if 0
1733                 printf( "effarr in transl... = \n" );
1734                 for( i=0; i<clus2; i++ ) printf( "%f ", effarr2[i] );
1735 #endif
1736     }
1737     else if( clus1 != 1 && clus2 == 1 )
1738     {
1739         seq = mseq2[0]; aseq = mseq1; effarr = effarr1; nseq = clus1+1;
1740     }
1741     else ErrorExit( "ERROR in translate_and_Calign" );
1742
1743     result = Calignm1( &wm, aseq, seq, effarr, nseq-2, 0 );
1744
1745         resultlen = strlen( result[0] );
1746         if( alloclen < resultlen || resultlen > N )
1747         {
1748                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
1749                 ErrorExit( "LENGTH OVER!\n" );
1750         }
1751     for( i=0; i<nseq-1; i++ ) strcpy( aseq[i], result[i] );
1752     strcpy( seq, result[nseq-1] );
1753
1754     return( 0.0 );
1755 }