binaries/src/mafft/core/Halignmm.c

   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 #define FASTMATCHCALC 1
  10
  11 static TLS float **impmtx = NULL;
  12
  13 #if 0 // by D.Mathog
  14 static float countnocountxx( Gappat *pat1, float diaf1, Gappat *pat2, int offset1, int offset2 )
  15 {
  16 //      return( 0.0 );
  17         float gclose;
  18         float gmatch;
  19         Gappat *pat1bk = pat1;
  20         Gappat *pat2bk = pat2;
  21
  22         gmatch = 0.0;
  23         for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0
  24         {
  25                 if( pat2->len + offset2 == offset1 )
  26                 {
  27                         gmatch = diaf1 * pat2->freq;
  28                 }
  29         }
  30         for( pat1=pat1bk+1; pat1->len != 0; pat1++ ) // excl. len=0
  31         {
  32                 for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0
  33                 {
  34                         if( pat1->len + offset1 == pat2->len + offset2 )
  35                         {
  36                                 gmatch += pat1->freq * pat2->freq;
  37 //                              if( r ) fprintf( stderr, "match1!!, len=%d, gmatch=%f * %f\n", pat2->len, pat1->freq, pat2->freq );
  38                         }
  39                 }
  40         }
  41         return( gmatch );
  42 }
  43 #endif
  44
  45 static float countnocountmatchx( Gappat *pat1, Gappat *pat2, int offset1, int offset2, int r )
  46 {
  47         Gappat *pat1bk = pat1;
  48         Gappat *pat2bk = pat2;
  49         float val = 0.0;
  50         // pat1[][0] ha total gap.
  51         for( pat1=pat1bk+1; pat1->len != 0; pat1++ )
  52         {
  53                 for( pat2=pat2bk+1; pat2->len != 0; pat2++ )
  54                 {
  55                         if( pat1->len + offset1 == pat2->len + offset2 )
  56                         {
  57                                 val += pat1->freq * pat2->freq;
  58                                 if( r ) fprintf( stderr, "y %d-%d, len=%d,%d, val = %f\n", (int)(pat1-pat1bk), (int)(pat2-pat2bk), pat1->len, pat2->len, val ); // 070405
  59 //                              if( r ) fprintf( stderr, "y %d-%d, len=%d,%d, val = %f\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len, val );
  60                         }
  61                 }
  62         }
  63         if( r ) fprintf( stderr, "nocountmatch=%f\n", val );
  64         return( val );
  65 }
  66
  67 #if 0 // by D.Mathog
  68 static float countnocountmatch( Gappat *pat1, Gappat *pat2, int r )
  69 {
  70 //      return( 0.0 );
  71         Gappat *pat1bk = pat1;
  72         Gappat *pat2bk = pat2;
  73         float val = 0.0;
  74         // pat1[][0] ha total gap.
  75         for( pat1=pat1bk+1; pat1->len != 0; pat1++ )
  76         {
  77 //              if( r ) fprintf( stderr, "b %d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len );
  78                 for( pat2=pat2bk+1; pat2->len != 0; pat2++ )
  79                 {
  80                         if( pat1->len == pat2->len )
  81                         {
  82 //                              if( r ) fprintf( stderr, " x%d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len );
  83                                 val += pat1->freq * pat2->freq;
  84 //                              if( r ) fprintf( stderr, "y %d-%d, val = %f\n", pat1-pat1bk, pat2-pat2bk,val );
  85 //                              if( r ) fprintf( stderr, "z tsugi, %d-%d, len=%d,%d\n", pat1-pat1bk+1, pat2-pat2bk+1, (pat1+1)->len, (pat2+1)->len );
  86                         }
  87 //                      if( r ) fprintf( stderr, "a %d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len );
  88                 }
  89         }
  90 //      fprintf( stderr, "nocountmatch=%f\n", val );
  91         return( val );
  92 }
  93 #endif
  94
  95 static float countnocountx( Gappat *pat1, float diaf1, Gappat *pat2, int offset1, int r )
  96 {
  97 //      return( 0.0 );
  98         float gmatch;
  99         Gappat *pat1bk = pat1;
 100         Gappat *pat2bk = pat2;
 101
 102         gmatch = 0.0;
 103         for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0
 104         {
 105                 if( pat2->len == offset1 )
 106                 {
 107                         gmatch = diaf1 * pat2->freq;
 108 //                      if( r ) fprintf( stderr, "match0!!, len=%d, gmatch=%f * %f\n", pat2->len, diaf1, pat2->freq );
 109                 }
 110         }
 111         for( pat1=pat1bk+1; pat1->len != 0; pat1++ ) // excl. len=0
 112         {
 113                 for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0
 114                 {
 115                         if( pat1->len + offset1 == pat2->len )
 116                         {
 117                                 gmatch += pat1->freq * pat2->freq;
 118 //                              if( r ) fprintf( stderr, "match1!!, len=%d, gmatch=%f * %f\n", pat2->len, pat1->freq, pat2->freq );
 119                         }
 120                 }
 121         }
 122         return( gmatch );
 123 }
 124
 125 #if 0 // by D.Mathog
 126 static float countnocount( Gappat *pat1, Gappat *pat2, int offset1, int offset2 ) //osoi
 127 {
 128 //      return( 0.0 );
 129         Gappat *pat1bk = pat1;
 130         Gappat *pat2bk = pat2;
 131         float val = 0.0;
 132         // pat1[][0] ha total gap.
 133         for( pat1=pat1bk+1; pat1->len != -1; pat1++ )
 134         {
 135                 for( pat2=pat2bk+1; pat2->len != -1; pat2++ )
 136                 {
 137                         if( pat1->len+offset1 == pat2->len+offset2 )
 138                         {
 139                                 val += pat1->freq * pat2->freq;
 140                         }
 141                 }
 142         }
 143 //      fprintf( stderr, "nocount=%f\n", val );
 144         return( val );
 145 }
 146 #endif
 147
 148
 149
 150 #if 1 // tditeration
 151 float imp_match_out_scH( int i1, int j1 )
 152 {
 153 //      fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
 154 //      fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
 155         return( impmtx[i1][j1] );
 156 }
 157 #endif
 158
 159 static void imp_match_out_veadH( float *imp, int i1, int lgth2 )
 160 {
 161 #if FASTMATCHCALC
 162         float *pt = impmtx[i1];
 163         while( lgth2-- )
 164                 *imp++ += *pt++;
 165 #else
 166         int j;
 167         float *pt = impmtx[i1];
 168         for( j=0; j<lgth2; j++ )
 169                 *imp++ += pt[j];
 170 #endif
 171 }
 172 static void imp_match_out_vead_tateH( float *imp, int j1, int lgth1 )
 173 {
 174         int i;
 175         for( i=0; i<lgth1; i++ )
 176                 *imp++ += impmtx[i][j1];
 177 }
 178
 179 #if 1 // tbfast.c kara yobareru.
 180 void imp_match_init_strictH( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
 181 {
 182         int i, j, k1, k2, tmpint, start1, start2, end1, end2;
 183         static TLS int impalloclen = 0;
 184         float effij;
 185         double effijx;
 186         char *pt, *pt1, *pt2;
 187         static TLS char *nocount1 = NULL;
 188         static TLS char *nocount2 = NULL;
 189         LocalHom *tmpptr;
 190
 191         if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
 192         {
 193                 if( impmtx ) FreeFloatMtx( impmtx );
 194                 if( nocount1 ) free( nocount1 );
 195                 if( nocount2 ) free( nocount2 );
 196                 impalloclen = MAX( lgth1, lgth2 ) + 2;
 197                 impmtx = AllocateFloatMtx( impalloclen, impalloclen );
 198                 nocount1 = AllocateCharVec( impalloclen );
 199                 nocount2 = AllocateCharVec( impalloclen );
 200         }
 201
 202         for( i=0; i<lgth1; i++ )
 203         {
 204                 for( j=0; j<clus1; j++ )
 205                         if( seq1[j][i] == '-' ) break;
 206                 if( j != clus1 ) nocount1[i] = 1;
 207                 else                     nocount1[i] = 0;
 208         }
 209         for( i=0; i<lgth2; i++ )
 210         {
 211                 for( j=0; j<clus2; j++ )
 212                         if( seq2[j][i] == '-' ) break;
 213                 if( j != clus2 ) nocount2[i] = 1;
 214                 else                     nocount2[i] = 0;
 215         }
 216
 217 #if 0
 218 fprintf( stderr, "nocount2 =\n" );
 219 for( i = 0; i<impalloclen; i++ )
 220 {
 221         fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
 222 }
 223 #endif
 224
 225
 226
 227 #if 0
 228         fprintf( stderr, "eff1 in _init_strict = \n" );
 229         for( i=0; i<clus1; i++ )
 230                 fprintf( stderr, "eff1[] = %f\n", eff1[i] );
 231         for( i=0; i<clus2; i++ )
 232                 fprintf( stderr, "eff2[] = %f\n", eff2[i] );
 233 #endif
 234
 235         for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
 236                 impmtx[i][j] = 0.0;
 237         effijx =  fastathreshold;
 238         for( i=0; i<clus1; i++ )
 239         {
 240                 for( j=0; j<clus2; j++ )
 241                 {
 242                         effij = (float)( eff1[i] * eff2[j] * effijx );
 243                         tmpptr = localhom[i][j];
 244                         while( tmpptr )
 245                         {
 246 //                              fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
 247 //                              fprintf( stderr, "end1   = %d\n", tmpptr->end1   );
 248 //                              fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
 249 //                              fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
 250                                 pt = seq1[i];
 251                                 tmpint = -1;
 252                                 while( *pt != 0 )
 253                                 {
 254                                         if( *pt++ != '-' ) tmpint++;
 255                                         if( tmpint == tmpptr->start1 ) break;
 256                                 }
 257                                 start1 = pt - seq1[i] - 1;
 258
 259                                 if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
 260                                 else
 261                                 {
 262 #if MACHIGAI
 263                                         while( *pt != 0 )
 264                                         {
 265 //                                              fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
 266                                                 if( tmpint == tmpptr->end1 ) break;
 267                                                 if( *pt++ != '-' ) tmpint++;
 268                                         }
 269                                         end1 = pt - seq1[i] - 0;
 270 #else
 271                                         while( *pt != 0 )
 272                                         {
 273 //                                              fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
 274                                                 if( *pt++ != '-' ) tmpint++;
 275                                                 if( tmpint == tmpptr->end1 ) break;
 276                                         }
 277                                         end1 = pt - seq1[i] - 1;
 278 #endif
 279                                 }
 280
 281                                 pt = seq2[j];
 282                                 tmpint = -1;
 283                                 while( *pt != 0 )
 284                                 {
 285                                         if( *pt++ != '-' ) tmpint++;
 286                                         if( tmpint == tmpptr->start2 ) break;
 287                                 }
 288                                 start2 = pt - seq2[j] - 1;
 289                                 if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
 290                                 else
 291                                 {
 292 #if MACHIGAI
 293                                         while( *pt != 0 )
 294                                         {
 295                                                 if( tmpint == tmpptr->end2 ) break;
 296                                                 if( *pt++ != '-' ) tmpint++;
 297                                         }
 298                                         end2 = pt - seq2[j] - 0;
 299 #else
 300                                         while( *pt != 0 )
 301                                         {
 302                                                 if( *pt++ != '-' ) tmpint++;
 303                                                 if( tmpint == tmpptr->end2 ) break;
 304                                         }
 305                                         end2 = pt - seq2[j] - 1;
 306 #endif
 307                                 }
 308 //                              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] );
 309 //                              fprintf( stderr, "step 0\n" );
 310                                 if( end1 - start1 != end2 - start2 )
 311                                 {
 312 //                                      fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
 313                                 }
 314
 315 #if 1
 316                                 k1 = start1; k2 = start2;
 317                                 pt1 = seq1[i] + k1;
 318                                 pt2 = seq2[j] + k2;
 319                                 while( *pt1 && *pt2 )
 320                                 {
 321                                         if( *pt1 != '-' && *pt2 != '-' )
 322                                         {
 323 // ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
 324 //                                              impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
 325 //                                              impmtx[k1][k2] += tmpptr->importance * effij;
 326                                                 impmtx[k1][k2] += tmpptr->fimportance * effij;
 327 //                                              fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
 328 //                                              fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 329 //                                              fprintf( stderr, "%d (%c) - %d (%c)  - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
 330                                                 k1++; k2++;
 331                                                 pt1++; pt2++;
 332                                         }
 333                                         else if( *pt1 != '-' && *pt2 == '-' )
 334                                         {
 335 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 336                                                 k2++; pt2++;
 337                                         }
 338                                         else if( *pt1 == '-' && *pt2 != '-' )
 339                                         {
 340 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 341                                                 k1++; pt1++;
 342                                         }
 343                                         else if( *pt1 == '-' && *pt2 == '-' )
 344                                         {
 345 //                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
 346                                                 k1++; pt1++;
 347                                                 k2++; pt2++;
 348                                         }
 349                                         if( k1 > end1 || k2 > end2 ) break;
 350                                 }
 351 #else
 352                                 while( k1 <= end1 && k2 <= end2 )
 353                                 {
 354                                         fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
 355                                         if( !nocount1[k1] && !nocount2[k2] )
 356                                         {
 357                                                 impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j]  * fastathreshold;
 358                                                 fprintf( stderr, "marked\n" );
 359                                         }
 360                                         else
 361                                                 fprintf( stderr, "no count\n" );
 362                                         k1++; k2++;
 363                                 }
 364 #endif
 365                                 tmpptr = tmpptr->next;
 366                         }
 367                 }
 368         }
 369 #if 0
 370         if( clus1 == 1 && clus2 == 6 )
 371         {
 372                 fprintf( stderr, "\n" );
 373                 fprintf( stderr, "seq1[0] =  %s\n", seq1[0] );
 374                 fprintf( stderr, "seq2[0] =  %s\n", seq2[0] );
 375                 fprintf( stderr, "impmtx = \n" );
 376                 for( k2=0; k2<lgth2; k2++ )
 377                         fprintf( stderr, "%6.3f ", (double)k2 );
 378                 fprintf( stderr, "\n" );
 379                 for( k1=0; k1<lgth1; k1++ )
 380                 {
 381                         fprintf( stderr, "%d ", k1 );
 382                         for( k2=0; k2<3; k2++ )
 383                                 fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
 384                         fprintf( stderr, "\n" );
 385                 }
 386                 exit( 1 );
 387         }
 388 #endif
 389 }
 390 #endif
 391
 392
 393 static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
 394 {
 395 #if FASTMATCHCALC
 396         int j, l;
 397         float scarr[26];
 398         float **cpmxpd = floatwork;
 399         int **cpmxpdn = intwork;
 400         float *matchpt, *cpmxpdpt, **cpmxpdptpt;
 401         int *cpmxpdnpt, **cpmxpdnptpt;
 402         if( initialize )
 403         {
 404                 int count = 0;
 405                 for( j=0; j<lgth2; j++ )
 406                 {
 407                         count = 0;
 408                         for( l=0; l<26; l++ )
 409                         {
 410                                 if( cpmx2[l][j] )
 411                                 {
 412                                         cpmxpd[j][count] = cpmx2[l][j];
 413                                         cpmxpdn[j][count] = l;
 414                                         count++;
 415                                 }
 416                         }
 417                         cpmxpdn[j][count] = -1;
 418                 }
 419         }
 420
 421         {
 422                 for( l=0; l<26; l++ )
 423                 {
 424                         scarr[l] = 0.0;
 425                         for( j=0; j<26; j++ )
 426                                 scarr[l] += n_dis[j][l] * cpmx1[j][i1];
 427                 }
 428                 matchpt = match;
 429                 cpmxpdnptpt = cpmxpdn;
 430                 cpmxpdptpt = cpmxpd;
 431                 while( lgth2-- )
 432                 {
 433                         *matchpt = 0.0;
 434                         cpmxpdnpt = *cpmxpdnptpt++;
 435                         cpmxpdpt = *cpmxpdptpt++;
 436                         while( *cpmxpdnpt>-1 )
 437                                 *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
 438                         matchpt++;
 439                 }
 440         }
 441 #else
 442         int j, k, l;
 443         float scarr[26];
 444         float **cpmxpd = floatwork;
 445         int **cpmxpdn = intwork;
 446 // simple
 447         if( initialize )
 448         {
 449                 int count = 0;
 450                 for( j=0; j<lgth2; j++ )
 451                 {
 452                         count = 0;
 453                         for( l=0; l<26; l++ )
 454                         {
 455                                 if( cpmx2[l][j] )
 456                                 {
 457                                         cpmxpd[count][j] = cpmx2[l][j];
 458                                         cpmxpdn[count][j] = l;
 459                                         count++;
 460                                 }
 461                         }
 462                         cpmxpdn[count][j] = -1;
 463                 }
 464         }
 465         for( l=0; l<26; l++ )
 466         {
 467                 scarr[l] = 0.0;
 468                 for( k=0; k<26; k++ )
 469                         scarr[l] += n_dis[k][l] * cpmx1[k][i1];
 470         }
 471         for( j=0; j<lgth2; j++ )
 472         {
 473                 match[j] = 0.0;
 474                 for( k=0; cpmxpdn[k][j]>-1; k++ )
 475                         match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
 476         }
 477 #endif
 478 }
 479
 480 static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
 481                                                 char **seq1, char **seq2,
 482                         char **mseq1, char **mseq2,
 483                         float **cpmx1, float **cpmx2,
 484                         int **ijp, int icyc, int jcyc )
 485 {
 486         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
 487         float wm;
 488         char *gaptable1, *gt1bk;
 489         char *gaptable2, *gt2bk;
 490         lgth1 = strlen( seq1[0] );
 491         lgth2 = strlen( seq2[0] );
 492         gt1bk = AllocateCharVec( lgth1+lgth2+1 );
 493         gt2bk = AllocateCharVec( lgth1+lgth2+1 );
 494
 495 #if 0
 496         for( i=0; i<lgth1; i++ )
 497         {
 498                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 499         }
 500 #endif
 501
 502         if( outgap == 1 )
 503                 ;
 504         else
 505         {
 506                 wm = lastverticalw[0];
 507                 for( i=0; i<lgth1; i++ )
 508                 {
 509                         if( lastverticalw[i] >= wm )
 510                         {
 511                                 wm = lastverticalw[i];
 512                                 iin = i; jin = lgth2-1;
 513                                 ijp[lgth1][lgth2] = +( lgth1 - i );
 514                         }
 515                 }
 516                 for( j=0; j<lgth2; j++ )
 517                 {
 518                         if( lasthorizontalw[j] >= wm )
 519                         {
 520                                 wm = lasthorizontalw[j];
 521                                 iin = lgth1-1; jin = j;
 522                                 ijp[lgth1][lgth2] = -( lgth2 - j );
 523                         }
 524                 }
 525         }
 526
 527     for( i=0; i<lgth1+1; i++ )
 528     {
 529         ijp[i][0] = i + 1;
 530     }
 531     for( j=0; j<lgth2+1; j++ )
 532     {
 533         ijp[0][j] = -( j + 1 );
 534     }
 535
 536         gaptable1 = gt1bk + lgth1+lgth2;
 537         *gaptable1 = 0;
 538         gaptable2 = gt2bk + lgth1+lgth2;
 539         *gaptable2 = 0;
 540
 541         iin = lgth1; jin = lgth2;
 542         *impwmpt = 0.0;
 543         for( k=0; k<=lgth1+lgth2; k++ )
 544         {
 545                 if( ijp[iin][jin] < 0 )
 546                 {
 547                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 548                 }
 549                 else if( ijp[iin][jin] > 0 )
 550                 {
 551                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 552                 }
 553                 else
 554                 {
 555                         ifi = iin-1; jfi = jin-1;
 556                 }
 557                 l = iin - ifi;
 558                 while( --l )
 559                 {
 560                         *--gaptable1 = 'o';
 561                         *--gaptable2 = '-';
 562                         k++;
 563                 }
 564                 l= jin - jfi;
 565                 while( --l )
 566                 {
 567                         *--gaptable1 = '-';
 568                         *--gaptable2 = 'o';
 569                         k++;
 570                 }
 571                 if( iin == lgth1 || jin == lgth2 )
 572                         ;
 573                 else
 574                 {
 575                         *impwmpt += imp_match_out_scH( iin, jin );
 576
 577 //              fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
 578                 }
 579                 if( iin <= 0 || jin <= 0 ) break;
 580                 *--gaptable1 = 'o';
 581                 *--gaptable2 = 'o';
 582                 k++;
 583                 iin = ifi; jin = jfi;
 584         }
 585
 586         for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
 587         for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
 588
 589         free( gt1bk );
 590         free( gt2bk );
 591 }
 592
 593 static float Atracking( float *lasthorizontalw, float *lastverticalw,
 594                                                 char **seq1, char **seq2,
 595                         char **mseq1, char **mseq2,
 596                         float **cpmx1, float **cpmx2,
 597                         int **ijp, int icyc, int jcyc )
 598 {
 599         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
 600         float wm;
 601         char *gaptable1, *gt1bk;
 602         char *gaptable2, *gt2bk;
 603         lgth1 = strlen( seq1[0] );
 604         lgth2 = strlen( seq2[0] );
 605
 606         gt1bk = AllocateCharVec( lgth1+lgth2+1 );
 607         gt2bk = AllocateCharVec( lgth1+lgth2+1 );
 608
 609 #if 0
 610         for( i=0; i<lgth1; i++ )
 611         {
 612                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 613         }
 614 #endif
 615
 616         if( outgap == 1 )
 617                 ;
 618         else
 619         {
 620                 wm = lastverticalw[0];
 621                 for( i=0; i<lgth1; i++ )
 622                 {
 623                         if( lastverticalw[i] >= wm )
 624                         {
 625                                 wm = lastverticalw[i];
 626                                 iin = i; jin = lgth2-1;
 627                                 ijp[lgth1][lgth2] = +( lgth1 - i );
 628                         }
 629                 }
 630                 for( j=0; j<lgth2; j++ )
 631                 {
 632                         if( lasthorizontalw[j] >= wm )
 633                         {
 634                                 wm = lasthorizontalw[j];
 635                                 iin = lgth1-1; jin = j;
 636                                 ijp[lgth1][lgth2] = -( lgth2 - j );
 637                         }
 638                 }
 639         }
 640
 641     for( i=0; i<lgth1+1; i++ )
 642     {
 643         ijp[i][0] = i + 1;
 644     }
 645     for( j=0; j<lgth2+1; j++ )
 646     {
 647         ijp[0][j] = -( j + 1 );
 648     }
 649
 650         gaptable1 = gt1bk + lgth1+lgth2;
 651         *gaptable1 = 0;
 652         gaptable2 = gt2bk + lgth1+lgth2;
 653         *gaptable2 = 0;
 654
 655         iin = lgth1; jin = lgth2;
 656         for( k=0; k<=lgth1+lgth2; k++ )
 657         {
 658                 if( ijp[iin][jin] < 0 )
 659                 {
 660                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 661                 }
 662                 else if( ijp[iin][jin] > 0 )
 663                 {
 664                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 665                 }
 666                 else
 667                 {
 668                         ifi = iin-1; jfi = jin-1;
 669                 }
 670                 l = iin - ifi;
 671                 while( --l )
 672                 {
 673                         *--gaptable1 = 'o';
 674                         *--gaptable2 = '-';
 675                         k++;
 676                 }
 677                 l= jin - jfi;
 678                 while( --l )
 679                 {
 680                         *--gaptable1 = '-';
 681                         *--gaptable2 = 'o';
 682                         k++;
 683                 }
 684                 if( iin <= 0 || jin <= 0 ) break;
 685                 *--gaptable1 = 'o';
 686                 *--gaptable2 = 'o';
 687                 k++;
 688                 iin = ifi; jin = jfi;
 689         }
 690
 691         for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
 692         for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
 693
 694         free( gt1bk );
 695         free( gt2bk );
 696
 697         return( 0.0 );
 698 }
 699
 700 float H__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
 701 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 702 {
 703 //      int k;
 704         register int i, j;
 705         int lasti, lastj;      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
 706         int lgth1, lgth2;
 707         int resultlen;
 708         float wm = 0.0;   /* int ?????? */
 709         float g;
 710         float *currentw, *previousw;
 711 //      float fpenalty = (float)penalty;
 712 #if USE_PENALTY_EX
 713         float fpenalty_ex = (float)penalty_ex;
 714 #endif
 715 #if 1
 716         float *wtmp;
 717         int *ijppt;
 718         float *mjpt, *prept, *curpt;
 719         int *mpjpt;
 720 #endif
 721         static TLS float mi, *m;
 722         static TLS int **ijp;
 723         static TLS int mpi, *mp;
 724         static TLS float *w1, *w2;
 725         static TLS float *match;
 726         static TLS float *initverticalw;    /* kufuu sureba iranai */
 727         static TLS float *lastverticalw;    /* kufuu sureba iranai */
 728         static TLS char **mseq1;
 729         static TLS char **mseq2;
 730         static TLS char **mseq;
 731         static TLS Gappat **gappat1;
 732         static TLS Gappat **gappat2;
 733         static TLS float *digf1;
 734         static TLS float *digf2;
 735         static TLS float *diaf1;
 736         static TLS float *diaf2;
 737         static TLS float *gapz1;
 738         static TLS float *gapz2;
 739         static TLS float *gapf1;
 740         static TLS float *gapf2;
 741         static TLS float *ogcp1g;
 742         static TLS float *ogcp2g;
 743         static TLS float *fgcp1g;
 744         static TLS float *fgcp2g;
 745         static TLS float *ogcp1;
 746         static TLS float *ogcp2;
 747         static TLS float *fgcp1;
 748         static TLS float *fgcp2;
 749         static TLS float **cpmx1;
 750         static TLS float **cpmx2;
 751         static TLS int **intwork;
 752         static TLS float **floatwork;
 753         static TLS int orlgth1 = 0, orlgth2 = 0;
 754         float fpenalty = (float)penalty;
 755         float tmppenal;
 756         float cumpenal;
 757         float *fgcp2pt;
 758         float *ogcp2pt;
 759         float fgcp1va;
 760         float ogcp1va;
 761         int maegap;
 762
 763
 764
 765 #if 0
 766         fprintf( stderr, "####  eff in SA+++align\n" );
 767         fprintf( stderr, "####  seq1[0] = %s\n", seq1[0] );
 768         fprintf( stderr, "####  strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
 769         for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
 770 #endif
 771         if( orlgth1 == 0 )
 772         {
 773                 mseq1 = AllocateCharMtx( njob, 0 );
 774                 mseq2 = AllocateCharMtx( njob, 0 );
 775         }
 776
 777
 778         lgth1 = strlen( seq1[0] );
 779         lgth2 = strlen( seq2[0] );
 780 #if 0
 781         if( lgth1 == 0 || lgth2 == 0 )
 782         {
 783                 fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
 784         }
 785 #endif
 786
 787         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 788         {
 789                 int ll1, ll2;
 790
 791                 if( orlgth1 > 0 && orlgth2 > 0 )
 792                 {
 793                         FreeFloatVec( w1 );
 794                         FreeFloatVec( w2 );
 795                         FreeFloatVec( match );
 796                         FreeFloatVec( initverticalw );
 797                         FreeFloatVec( lastverticalw );
 798
 799                         FreeFloatVec( m );
 800                         FreeIntVec( mp );
 801
 802                         FreeCharMtx( mseq );
 803
 804                         free( gappat1 );
 805                         free( gappat2 );
 806                         FreeFloatVec( digf1 );
 807                         FreeFloatVec( digf2 );
 808                         FreeFloatVec( diaf1 );
 809                         FreeFloatVec( diaf2 );
 810                         FreeFloatVec( gapz1 );
 811                         FreeFloatVec( gapz2 );
 812                         FreeFloatVec( gapf1 );
 813                         FreeFloatVec( gapf2 );
 814                         FreeFloatVec( ogcp1 );
 815                         FreeFloatVec( ogcp2 );
 816                         FreeFloatVec( fgcp1 );
 817                         FreeFloatVec( fgcp2 );
 818                         FreeFloatVec( ogcp1g );
 819                         FreeFloatVec( ogcp2g );
 820                         FreeFloatVec( fgcp1g );
 821                         FreeFloatVec( fgcp2g );
 822
 823
 824                         FreeFloatMtx( cpmx1 );
 825                         FreeFloatMtx( cpmx2 );
 826
 827                         FreeFloatMtx( floatwork );
 828                         FreeIntMtx( intwork );
 829                 }
 830
 831                 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
 832                 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
 833
 834 #if DEBUG
 835                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
 836 #endif
 837
 838                 w1 = AllocateFloatVec( ll2+2 );
 839                 w2 = AllocateFloatVec( ll2+2 );
 840                 match = AllocateFloatVec( ll2+2 );
 841
 842                 initverticalw = AllocateFloatVec( ll1+2 );
 843                 lastverticalw = AllocateFloatVec( ll1+2 );
 844
 845                 m = AllocateFloatVec( ll2+2 );
 846                 mp = AllocateIntVec( ll2+2 );
 847
 848                 mseq = AllocateCharMtx( njob, ll1+ll2 );
 849
 850                 digf1 = AllocateFloatVec( ll1+2 );
 851                 digf2 = AllocateFloatVec( ll2+2 );
 852                 diaf1 = AllocateFloatVec( ll1+2 );
 853                 diaf2 = AllocateFloatVec( ll2+2 );
 854                 gappat1 = (Gappat **)calloc( ll1+2, sizeof( Gappat * ) );
 855                 gappat2 = (Gappat **)calloc( ll2+2, sizeof( Gappat * ) );
 856                 gapz1 = AllocateFloatVec( ll1+2 );
 857                 gapz2 = AllocateFloatVec( ll2+2 );
 858                 gapf1 = AllocateFloatVec( ll1+2 );
 859                 gapf2 = AllocateFloatVec( ll2+2 );
 860                 ogcp1 = AllocateFloatVec( ll1+2 );
 861                 ogcp2 = AllocateFloatVec( ll2+2 );
 862                 fgcp1 = AllocateFloatVec( ll1+2 );
 863                 fgcp2 = AllocateFloatVec( ll2+2 );
 864                 ogcp1g = AllocateFloatVec( ll1+2 );
 865                 ogcp2g = AllocateFloatVec( ll2+2 );
 866                 fgcp1g = AllocateFloatVec( ll1+2 );
 867                 fgcp2g = AllocateFloatVec( ll2+2 );
 868
 869                 cpmx1 = AllocateFloatMtx( 26, ll1+2 );
 870                 cpmx2 = AllocateFloatMtx( 26, ll2+2 );
 871
 872 #if FASTMATCHCALC
 873                 floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
 874                 intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
 875 #else
 876                 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
 877                 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
 878 #endif
 879
 880 #if DEBUG
 881                 fprintf( stderr, "succeeded\n" );
 882 #endif
 883
 884                 orlgth1 = ll1 - 100;
 885                 orlgth2 = ll2 - 100;
 886         }
 887
 888
 889         for( i=0; i<icyc; i++ )
 890         {
 891                 mseq1[i] = mseq[i];
 892                 seq1[i][lgth1] = 0;
 893         }
 894         for( j=0; j<jcyc; j++ )
 895         {
 896                 mseq2[j] = mseq[icyc+j];
 897                 seq2[j][lgth2] = 0;
 898         }
 899
 900
 901         if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
 902         {
 903                 int ll1, ll2;
 904
 905                 if( commonAlloc1 && commonAlloc2 )
 906                 {
 907                         FreeIntMtx( commonIP );
 908                 }
 909
 910                 ll1 = MAX( orlgth1, commonAlloc1 );
 911                 ll2 = MAX( orlgth2, commonAlloc2 );
 912
 913 #if DEBUG
 914                 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 915 #endif
 916
 917                 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
 918
 919 #if DEBUG
 920                 fprintf( stderr, "succeeded\n\n" );
 921 #endif
 922
 923                 commonAlloc1 = ll1;
 924                 commonAlloc2 = ll2;
 925         }
 926         ijp = commonIP;
 927
 928 #if 0
 929         {
 930                 float t = 0.0;
 931                 for( i=0; i<icyc; i++ )
 932                         t += eff1[i];
 933         fprintf( stderr, "## totaleff = %f\n", t );
 934         }
 935 #endif
 936
 937         cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
 938         cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
 939
 940         if( sgap1 )
 941         {
 942                 new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
 943                 new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap1 );
 944                 new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
 945                 new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap1, egap2 );
 946                 getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 ); // sgap1 ha iranai ?
 947                 getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 ); // sgap1 ha iranai ?
 948                 getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 ); // sgap1 ha iranai ?
 949                 getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap1, egap2 ); // sgap1 ha iranai ?
 950                 getgapfreq( gapf1, icyc, seq1, eff1, lgth1 ); // atode
 951                 getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 ); // atode
 952                 getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 ); // atode
 953                 getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 ); // atode
 954         }
 955         else
 956         {
 957                 st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
 958                 st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
 959                 st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
 960                 st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
 961                 st_getGapPattern( gappat1, icyc, seq1, eff1, lgth1 );
 962                 st_getGapPattern( gappat2, jcyc, seq2, eff2, lgth2 );
 963                 getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
 964                 getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
 965                 getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
 966                 getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
 967                 getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
 968                 getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
 969                 getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
 970                 getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
 971         }
 972
 973 #if 0
 974         for( i=0; i<lgth1; i++ )
 975                 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
 976 #endif
 977
 978         currentw = w1;
 979         previousw = w2;
 980
 981         match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
 982         if( localhom )
 983                 imp_match_out_vead_tateH( initverticalw, 0, lgth1 ); // 060306
 984
 985         match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
 986         if( localhom )
 987                 imp_match_out_veadH( currentw, 0, lgth2 ); // 060306
 988
 989
 990 #if 0 // -> tbfast.c
 991         if( localhom )
 992                 imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
 993
 994 #endif
 995
 996         if( outgap == 1 )
 997         {
 998 //              if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
 999 //              initverticalw[0] += g;
1000 //              currentw[0] += g;
1001
1002 //              if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
1003 //              initverticalw[0] += g;
1004 //              currentw[0] += g;
1005
1006                 for( i=1; i<lgth1+1; i++ )
1007                 {
1008 //                      initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
1009
1010                         tmppenal = 0.0;
1011 //                      tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
1012 //                      tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+0.0) + gapz2[0]*(1.0-digf1[0] - diaf1[0]) ) * 0.5 * fpenalty; // mada
1013 //                      tmppenal = ( (1.0-0.0)*(1.0-ogcp1g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada
1014 //                      tmppenal = 0.5 * fpenalty;
1015 //                      tmppenal -= ( (1.0-0.0) * (1.0-diaf1[0]) + 0.0 ) * 0.5 * fpenalty; // 0.
1016 //                      tmppenal -= ( (1.0-gapf2[j-1]) * ogcp1g[i] + gapf2[j-1] ) * 0.5 * fpenalty;
1017 //                      fprintf( stderr, "0,0<-%d,%d, tmppenal 1 = %f\n", i, 0, tmppenal );
1018                         initverticalw[i] += tmppenal;
1019
1020                         tmppenal = diaf1[i] * ( 1.0 - gapf2[0] ) * fpenalty;
1021                         if( gappat1[i][0].freq )
1022                         {
1023                                 tmppenal += ( gappat1[i][0].freq ) * ( 1.0 - gapf2[0] ) * fpenalty;
1024                                 tmppenal -= ( countnocountx( gappat2[0], diaf2[0], gappat1[i], i, 1 ) ) * fpenalty;
1025                         }
1026 //                      tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
1027 //                      tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapz2[1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
1028 //                      tmppenal = ( (1.0-gapf2[0])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[0]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
1029 //                      tmppenal = 0.5 * fpenalty;
1030 //                      tmppenal -= ( (1.0-gapf2[0]) * (1.0-diaf1[i]) + gapf2[0] ) * 0.5 * fpenalty;
1031 //                      tmppenal -= ( (1.0-gapf2[j]) * fgcp1g[i] + gapf2[j] ) * 0.5 * fpenalty;
1032                         initverticalw[i] += tmppenal;
1033 //                      fprintf( stderr, "0,0<-%d,%d, tmppenal 2 = %f, cumpenal=%f, fgcp1g[i]=%f, ogcp1g[i]=%f\n", i, 0, tmppenal, cumpenal, fgcp1g[i], ogcp1g[i] );
1034
1035                 }
1036                 cumpenal = 0.0;
1037                 for( j=1; j<lgth2+1; j++ )
1038                 {
1039 //                      currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
1040
1041                         tmppenal = 0.0;
1042 //                      tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapf1[i-1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
1043 //                      tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+0.0) + gapz1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
1044 //                      tmppenal = ( (1.0-0.0)*(1.0-ogcp2g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada
1045 //                      tmppenal = 0.5 * fpenalty;
1046 //                      tmppenal -= ( (1.0-0.0) * (1.0-diaf2[0]) + 0.0 ) * 0.5 * fpenalty; // 0.
1047 //                      tmppenal -= ( (1.0-gapf1[0]) * fgcp2g[j] + gapf1[0] ) * 0.5 * fpenalty;
1048 //                      fprintf( stderr, "0,0<-%d,%d, tmppenal 3 = %f\n", 0, j, tmppenal );
1049                         currentw[j] += tmppenal;
1050
1051                         tmppenal = diaf2[j] * ( 1.0 - gapf1[0] ) * fpenalty;
1052                         if( gappat2[j][0].freq )
1053                         {
1054                                 tmppenal += ( gappat2[j][0].freq ) * ( 1.0 - gapf1[0] ) * fpenalty;
1055                                 tmppenal -= ( countnocountx( gappat1[0], diaf1[0], gappat2[j], j, 1 ) ) * fpenalty;
1056                         }
1057 //                      tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
1058 //                      tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapz1[1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
1059 //                      tmppenal = ( (1.0-gapf1[0])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
1060 //                      tmppenal = 0.5 * fpenalty;
1061 //                      tmppenal -= ( (1.0-gapf1[0]) * (1.0-diaf2[j]) + gapf1[0] ) * 0.5 * fpenalty;
1062 //                      tmppenal -= ( (1.0-gapf1[0]) * ogcp2g[j] + gapf1[i-1] ) * 0.5 * fpenalty;
1063 //                      fprintf( stderr, "0,0<-%d,%d, tmppenal 4 = %f\n", 0, j, tmppenal );
1064                         currentw[j] += tmppenal;
1065                 }
1066         }
1067 #if OUTGAP0TRY
1068         else
1069         {
1070                 for( j=1; j<lgth2+1; j++ )
1071                         currentw[j] -= offset * j / 2.0;
1072                 for( i=1; i<lgth1+1; i++ )
1073                         initverticalw[i] -= offset * i / 2.0;
1074         }
1075 #endif
1076
1077         m[0] = 0.0; // iranai
1078         for( j=1; j<lgth2+1; ++j )
1079         {
1080 //              m[j] = currentw[j-1] + ogcp1[1];
1081                 mp[j] = 0;
1082
1083                 tmppenal = 0.0;
1084 //              tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[1]+fgcp1g[1]) + gapz2[j]*(1.0-digf1[1]-diaf1[1]) ) * 0.5 * fpenalty; // mada
1085 //              tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[1]+fgcp1g[1]) + gapf2[j-1]*(1.0-digf1[1]-diaf1[1]) ) * 0.5 * fpenalty; // mada
1086 //              tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
1087 //              tmppenal = 0.5 * fpenalty;
1088 //              tmppenal -= ( (1.0-0.0) * (1.0-0.0) + 0.0 ) * 0.5 * fpenalty;
1089 //              tmppenal -= ( (1.0-gapf2[-1]) * (1.0-diaf1[0]) + gapf2[-1] ) * 0.5 * fpenalty;
1090 //              if( tmppenal ) fprintf( stderr, "%c=%c, end j tmppenal=%f\n", seq1[0][0], seq2[0][j-1], tmppenal );
1091                 m[j] = currentw[j-1] + tmppenal + fpenalty * 10000;
1092 //              m[j] = currentw[j-1] + ogcp1[1];
1093         }
1094         if( lgth2 == 0 )
1095                 lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
1096         else
1097                 lastverticalw[0] = currentw[lgth2-1];
1098
1099         if( outgap ) lasti = lgth1+1; else lasti = lgth1;
1100
1101 #if XXXXXXX
1102 fprintf( stderr, "currentw = \n" );
1103 for( i=0; i<lgth1+1; i++ )
1104 {
1105         fprintf( stderr, "%5.2f ", currentw[i] );
1106 }
1107 fprintf( stderr, "\n" );
1108 fprintf( stderr, "initverticalw = \n" );
1109 for( i=0; i<lgth2+1; i++ )
1110 {
1111         fprintf( stderr, "%5.2f ", initverticalw[i] );
1112 }
1113 fprintf( stderr, "\n" );
1114 fprintf( stderr, "fcgp\n" );
1115 for( i=0; i<lgth1; i++ )
1116         fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
1117 for( i=0; i<lgth2; i++ )
1118         fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
1119 #endif
1120
1121         for( i=1; i<lasti; i++ )
1122         {
1123                 wtmp = previousw;
1124                 previousw = currentw;
1125                 currentw = wtmp;
1126
1127                 previousw[0] = initverticalw[i-1];
1128
1129                 match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
1130 #if XXXXXXX
1131 fprintf( stderr, "\n" );
1132 fprintf( stderr, "i=%d\n", i );
1133 fprintf( stderr, "currentw = \n" );
1134 for( j=0; j<lgth2; j++ )
1135 {
1136         fprintf( stderr, "%5.2f ", currentw[j] );
1137 }
1138 fprintf( stderr, "\n" );
1139 #endif
1140                 if( localhom )
1141                 {
1142 //                      fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
1143 #if  0
1144                         imp_match_out_veadH( currentw, i, lgth2 );
1145 #else
1146                         imp_match_out_veadH( currentw, i, lgth2 );
1147 #endif
1148                 }
1149 #if XXXXXXX
1150 fprintf( stderr, "\n" );
1151 fprintf( stderr, "i=%d\n", i );
1152 fprintf( stderr, "currentw = \n" );
1153 for( j=0; j<lgth2; j++ )
1154 {
1155         fprintf( stderr, "%5.2f ", currentw[j] );
1156 }
1157 fprintf( stderr, "\n" );
1158 #endif
1159                 currentw[0] = initverticalw[i];
1160
1161
1162 //              mi = previousw[0] + ogcp2[1];  // machigai
1163                 tmppenal = 0.0;
1164 //              tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[1]+fgcp2g[1]) + gapz1[i]*(1.0-digf2[1]-diaf2[1]) ) * 0.5 * fpenalty; // mada
1165 //              tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[1]+fgcp2g[1]) + gapf1[i-1]*(1.0-digf2[1]-diaf2[1]) ) * 0.5 * fpenalty; // mada
1166 //              fprintf( stderr, "%c=%c, end i tmppenal=%f, ogcp2g[1]=%f\n", seq1[0][i-1], seq2[0][0], tmppenal, ogcp2g[1] );
1167 //              mi = previousw[0] + tmppenal;
1168                 mi = previousw[0] + tmppenal + fpenalty * 10000;
1169
1170                 mpi = 0;
1171                 ijppt = ijp[i] + 1;
1172                 mjpt = m + 1;
1173                 prept = previousw;
1174                 curpt = currentw + 1;
1175                 mpjpt = mp + 1;
1176                 fgcp2pt = fgcp2;
1177                 ogcp2pt = ogcp2 + 1;
1178                 fgcp1va = fgcp1[i-1];
1179                 ogcp1va = ogcp1[i];
1180                 lastj = lgth2+1;
1181                 for( j=1; j<lastj; j++ )
1182                 {
1183                         wm = *prept;
1184
1185                         if( gappat2[j][0].freq )
1186                         {
1187                                 g = diaf1[i] * gappat2[j][0].freq * fpenalty;
1188 //                              if( seq1[0][i] == 'D' && seq2[0][j] == 'D' )
1189 //                              if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] );
1190                                 wm += g;
1191                         }
1192
1193                         if( gappat1[i][0].freq )
1194                         {
1195                                 g = diaf2[j] * gappat1[i][0].freq * fpenalty;
1196 //                              if( seq1[0][i] == 'D' && seq2[0][j] == 'D' )
1197 //                              if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] );
1198                                 wm += g;
1199                         }
1200                         {
1201                                 g = ( (gappat1[i][0].freq) * (gappat2[j][0].freq) ) * fpenalty;
1202 //                              if( seq1[0][i] == 'D' && seq2[0][j] == 'D' )
1203 //                              if( g ) fprintf( stderr, "match penal3=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] );
1204                                 wm += g;
1205                         }
1206                         if( 0 )
1207                         {
1208                                 maegap = ijp[i-1][j-1];
1209 //                              if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' )
1210 //                                      fprintf( stderr, "i,j=%d,%d, maegap=%d\n", i, j, maegap );
1211                                 maegap = 0;
1212
1213                                 if( maegap == 0 )
1214                                 {
1215                                         g = ( countnocountmatchx( gappat1[i], gappat2[j], 0, 0, 0 ) ) * fpenalty;
1216 //                                      if( seq1[0][i] == 'D' && seq2[0][j] == 'D' )
1217 //                                              fprintf( stderr, "kanwa0 %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 1 ) );
1218                                 }
1219 #if 0 // atta houga yoi hazu
1220                                 else if( maegap < 0 ) // i jump
1221                                 {
1222                                         g = ( countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 0 ) ) * fpenalty;
1223                                         if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' )
1224                                         {
1225                                                 fprintf( stderr, "i-jumped, offset1=%d\n", maegap );
1226                                                 fprintf( stderr, "kanwa1 %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 0 ) );
1227                                         }
1228                                 }
1229                                 else                  // j jump
1230                                 {
1231                                         g = ( countnocountmatchx( gappat1[i], gappat2[j], maegap, 0, 0 ) ) * fpenalty;
1232                                         if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' )
1233                                         {
1234                                                 fprintf( stderr, "j-jumped, offset1=%d\n", maegap );
1235                                                 fprintf( stderr, "kanwa2, %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 1 ) );
1236                                         }
1237                                 }
1238 #endif
1239                                 wm -= g;
1240                         }
1241
1242                         *ijppt = 0;
1243
1244 #if 0
1245                         fprintf( stderr, "%5.0f->", wm );
1246 #endif
1247 #if 0
1248                         fprintf( stderr, "%5.0f?", g );
1249 #endif
1250 //                      tmppenal = fpenalty;
1251                         tmppenal = diaf2[j] * ( 1.0 - gapf1[i] ) * fpenalty;
1252                         if( gappat2[j][0].freq )
1253                         {
1254                                 tmppenal += ( gappat2[j][0].freq ) * ( 1.0 - gapf1[i] ) * fpenalty;
1255 //                              tmppenal -= ( countnocountx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, 0 ) ) * fpenalty;
1256                                 maegap = ijp[i-1][mpi];
1257                                 maegap = 0;
1258                                 if( maegap == 0 )
1259                                 {
1260                                         tmppenal -= ( countnocountx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, 0 ) ) * fpenalty;
1261                                 }
1262 #if 0 // attahouga yoi hazu
1263                                 else if( maegap < 0 ) // i jump
1264                                 {
1265                                         maegap = -maegap;
1266                                         tmppenal -= ( countnocountxx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1+maegap, 0 ) ) * fpenalty;
1267                                 }
1268                                 else                  // j jump
1269                                 {
1270                                         tmppenal -= ( countnocountxx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, maegap ) ) * fpenalty;
1271                                 }
1272 #endif
1273                         }
1274                         if( (g=mi+tmppenal) > wm )
1275                         {
1276 //                              if( seq1[0][i] == 'A' && seq2[0][j] == 'A' ) fprintf( stderr, "jump i start=%f (i,j=%d,%d, *ijppt=%d, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, i, j, -(j-mpi), digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
1277                                 wm = g;
1278                                 *ijppt = -( j - mpi );
1279                         }
1280                         if( (g=*prept) >= mi )
1281                         {
1282 //                              fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
1283                                 mi = g;
1284                                 mpi = j-1;
1285                         }
1286                         else if( j != 1 )
1287                         {
1288 //                              mi += ( ogcp2g[j-0] + fgcp2g[j] ) * fpenalty * 0.5;
1289 //                              fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", '=', '=', seq2[0][j-1], seq2[0][j], ogcp2g[j-0] * fpenalty*0.5, fgcp2g[j] * fpenalty*0.5 );
1290                         }
1291 #if USE_PENALTY_EX
1292                                 mi += fpenalty_ex;
1293 #endif
1294
1295 #if 0
1296                         fprintf( stderr, "%5.0f?", g );
1297 #endif
1298
1299 //                      tmppenal = fpenalty;
1300                         tmppenal = diaf1[i] * ( 1.0 - gapf2[j] ) * fpenalty;
1301                         if( gappat1[i][0].freq )
1302                         {
1303                                 tmppenal += ( gappat1[i][0].freq ) * ( 1.0 - gapf2[j] ) * fpenalty;
1304 //                              tmppenal -= ( countnocountx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, 1 ) ) * fpenalty;
1305                                 maegap = ijp[*mpjpt][j-1];
1306                                 if( maegap == 0 )
1307                                 {
1308                                         tmppenal -= ( countnocountx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, 1 ) ) * fpenalty;
1309                                 }
1310 #if 0 // attahouga yoi hazu
1311                                 else if( maegap > 0 ) // j jump
1312                                 {
1313                                         tmppenal -= ( countnocountxx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1+maegap, 0 ) ) * fpenalty;
1314                                 }
1315                                 else                  // i jump
1316                                 {
1317                                         maegap = -maegap;
1318                                         tmppenal -= ( countnocountxx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, maegap ) ) * fpenalty;
1319                                 }
1320 #endif
1321                         }
1322                         if( (g=*mjpt+tmppenal) > wm )
1323                         {
1324 //                              if( seq1[0][i] == 'S' && seq2[0][j] == 'S' ) fprintf( stderr, "jump j start at %d, %d, g=%f, %c-%c\n", i, j, g-*mjpt, seq1[0][i], seq2[0][j] );
1325                                 wm = g;
1326                                 *ijppt = +( i - *mpjpt );
1327                         }
1328                         if( (g=*prept) >= *mjpt )
1329                         {
1330 //                              fprintf( stderr, "jump j end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
1331                                 *mjpt = g;
1332                                 *mpjpt = i-1;
1333                         }
1334                         else if( i != 1 )
1335                         {
1336 //                              m[j] += ( ogcp1g[i-0] + fgcp1g[i] ) * fpenalty * 0.5;
1337 //                              fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", seq1[0][i-1], seq1[0][i], '=', '=', ogcp1g[i-0] * fpenalty*0.5, fgcp1g[i] * fpenalty*0.5 );
1338                         }
1339 #if USE_PENALTY_EX
1340                         m[j] += fpenalty_ex;
1341 #endif
1342
1343 #if 0
1344                         fprintf( stderr, "%5.0f ", wm );
1345 #endif
1346                         *curpt++ += wm;
1347                         ijppt++;
1348                         mjpt++;
1349                         prept++;
1350                         mpjpt++;
1351                         fgcp2pt++;
1352                         ogcp2pt++;
1353                 }
1354                 lastverticalw[i] = currentw[lgth2-1];
1355         }
1356
1357 //      fprintf( stderr, "wm = %f\n", wm );
1358
1359 #if OUTGAP0TRY
1360         if( !outgap )
1361         {
1362                 for( j=1; j<lgth2+1; j++ )
1363                         currentw[j] -= offset * ( lgth2 - j ) / 2.0;
1364                 for( i=1; i<lgth1+1; i++ )
1365                         lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
1366         }
1367 #endif
1368
1369         /*
1370         fprintf( stderr, "\n" );
1371         for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
1372         fprintf( stderr, "#####\n" );
1373         for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
1374         fprintf( stderr, "====>" );
1375         for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
1376         for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
1377         */
1378         if( localhom )
1379         {
1380                 Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1381         }
1382         else
1383                 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1384
1385 //      fprintf( stderr, "### impmatch = %f\n", *impmatch );
1386
1387         resultlen = strlen( mseq1[0] );
1388         if( alloclen < resultlen || resultlen > N )
1389         {
1390                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
1391                 ErrorExit( "LENGTH OVER!\n" );
1392         }
1393
1394
1395         for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
1396         for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
1397         /*
1398         fprintf( stderr, "\n" );
1399         for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
1400         fprintf( stderr, "#####\n" );
1401         for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
1402         */
1403
1404         fprintf( stderr, "wm = %f\n", wm );
1405
1406         for( i=0; i<lgth1+1; i++ )
1407         {
1408                 free( gappat1[i] );
1409                 gappat1[i] = NULL;
1410         }
1411         for( i=0; i<lgth2+1; i++ )
1412         {
1413                 free( gappat2[i] );
1414                 gappat2[i] = NULL;
1415         }
1416
1417         return( wm );
1418 }
1419