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

   1 #include "mltaln.h"
   2
   3 //static FILE *fftfp;
   4 static TLS int n20or4or2;
   5
   6 #define KEIKA 0
   7 #define RND   0
   8 #define DEBUG 0
   9
  10 extern int fft( int, Fukusosuu *, int );
  11
  12
  13 #if 0
  14 static void generateRndSeq( char *seq, int len )
  15 {
  16         while( len-- )
  17 #if 1
  18                 *seq++ = (int)( rnd() * n20or4or2 );
  19 #else
  20                 *seq++ = (int)1;
  21 #endif
  22 }
  23 #endif
  24
  25 static void vec_init( Fukusosuu *result, int nlen )
  26 {
  27         while( nlen-- )
  28         {
  29                 result->R = result->I = 0.0;
  30                 result++;
  31         }
  32 }
  33
  34 #if 0
  35 static void vec_init2( Fukusosuu **result, char *seq, double eff, int st, int ed )
  36 {
  37         int i;
  38         for( i=st; i<ed; i++ )
  39                 result[(int)*seq++][i].R += eff;
  40 }
  41 #endif
  42
  43 static void seq_vec_2( Fukusosuu *result, double *score, double incr, char *seq )
  44 {
  45         static TLS int n;
  46         for( ; *seq; result++ )
  47         {
  48                 n = amino_n[(int)*seq++];
  49                 if( n < 20 && n >= 0 ) result->R += incr * score[n];
  50 #if 0
  51                 fprintf( stderr, "n=%d, score=%f, inc=%f R=%f\n",n,  score[n], incr * score[n], result->R );
  52 #endif
  53         }
  54 }
  55
  56 static void seq_vec_3( Fukusosuu **result, double incr, char *seq )
  57 {
  58         int i;
  59         int n;
  60         for( i=0; *seq; i++ )
  61         {
  62                 n = amino_n[(int)*seq++];
  63                 if( n < n20or4or2 && n >= 0 ) result[n][i].R += incr;
  64         }
  65 }
  66
  67
  68 #if 0
  69 static void seq_vec( Fukusosuu *result, char query, double incr, char *seq )
  70 {
  71 #if 0
  72         int bk = nlen;
  73 #endif
  74         while( *seq )
  75         {
  76                 if( *seq++ == query ) result->R += incr;
  77                 result++;
  78 #if 0
  79 fprintf( stderr, "i = %d result->R = %f\n", bk-nlen, (result-1)->R );
  80 #endif
  81         }
  82 }
  83
  84 static int checkRepeat( int num, int *cutpos )
  85 {
  86         int tmp, buf;
  87
  88         buf = *cutpos;
  89         while( num-- )
  90         {
  91                 if( ( tmp = *cutpos++ ) < buf ) return( 1 );
  92                 buf = tmp;
  93         }
  94         return( 0 );
  95 }
  96
  97 static int segcmp( void *ptr1, void *ptr2 )
  98 {
  99         int diff;
 100         Segment **seg1 = (Segment **)ptr1;
 101         Segment **seg2 = (Segment **)ptr2;
 102 #if 0
 103         return( (*seg1)->center - (*seg2)->center );
 104 #else
 105         diff = (*seg1)->center - (*seg2)->center;
 106         if( diff ) return( diff );
 107
 108         diff = (*seg1)->start - (*seg2)->start;
 109         if( diff ) return( diff );
 110
 111         diff = (*seg1)->end - (*seg2)->end;
 112         if( diff ) return( diff );
 113
 114         fprintf( stderr, "USE STABLE SORT !!\n" );
 115         exit( 1 );
 116         return( 0 );
 117 #endif
 118 }
 119
 120 #endif
 121
 122
 123 static void mymergesort( int first, int last, Segment **seg )
 124 {
 125         int middle;
 126         static TLS int i, j, k, p;
 127         static TLS int allo = 0;
 128         static TLS Segment **work = NULL;
 129
 130         if( seg == NULL )
 131         {
 132                 free( work ); work = NULL;
 133                 return;
 134         }
 135
 136         if( last > allo )
 137         {
 138                 allo = last;
 139                 if( work ) free( work );
 140                 work = (Segment **)calloc( allo / 2 + 1, sizeof( Segment *) );
 141         }
 142
 143         if( first < last )
 144         {
 145                 middle = ( first + last ) / 2;
 146                 mymergesort( first, middle, seg );
 147                 mymergesort( middle+1, last, seg );
 148                 p = 0;
 149                 for( i=first; i<=middle; i++ ) work[p++] = seg[i];
 150                 i = middle + 1; j = 0; k = first;
 151                 while( i <= last && j < p )
 152                 {
 153                         if( work[j]->center <= seg[i]->center )
 154                                 seg[k++] = work[j++];
 155                         else
 156                                 seg[k++] = seg[i++];
 157                 }
 158                 while( j < p ) seg[k++] = work[j++];
 159         }
 160 }
 161
 162
 163 float Falign_localhom( char  **seq1, char  **seq2,
 164                           double *eff1, double *eff2,
 165                           int    clus1, int    clus2,
 166                           int alloclen,
 167                            LocalHom ***localhom, float *totalimpmatch,
 168                            int *gapmap1, int *gapmap2,
 169                                 int *chudanpt, int chudanref, int *chudanres )
 170 {
 171    // tditeration.c deha alloclen ha huhen nanode
 172    // prevalloclen ha iranai.
 173         int i, j, k, l, m, maxk;
 174         int nlen, nlen2, nlen4;
 175         static TLS int crossscoresize = 0;
 176         static TLS char **tmpseq1 = NULL;
 177         static TLS char **tmpseq2 = NULL;
 178         static TLS char **tmpptr1 = NULL;
 179         static TLS char **tmpptr2 = NULL;
 180         static TLS char **tmpres1 = NULL;
 181         static TLS char **tmpres2 = NULL;
 182         static TLS char **result1 = NULL;
 183         static TLS char **result2 = NULL;
 184 #if RND
 185         static TLS char **rndseq1 = NULL;
 186         static TLS char **rndseq2 = NULL;
 187 #endif
 188         static TLS Fukusosuu **seqVector1 = NULL;
 189         static TLS Fukusosuu **seqVector2 = NULL;
 190         static TLS Fukusosuu **naiseki = NULL;
 191         static TLS Fukusosuu *naisekiNoWa = NULL;
 192         static TLS double *soukan = NULL;
 193         static TLS double **crossscore = NULL;
 194         int nlentmp;
 195         static TLS int *kouho = NULL;
 196         static TLS Segment *segment = NULL;
 197         static TLS Segment *segment1 = NULL;
 198         static TLS Segment *segment2 = NULL;
 199         static TLS Segment **sortedseg1 = NULL;
 200         static TLS Segment **sortedseg2 = NULL;
 201         static TLS int *cut1 = NULL;
 202         static TLS int *cut2 = NULL;
 203         static TLS char *sgap1, *egap1, *sgap2, *egap2;
 204         static TLS int localalloclen = 0;
 205         int lag;
 206         int tmpint;
 207         int count, count0;
 208         int len1, len2;
 209         int totallen;
 210         float totalscore;
 211         float impmatch;
 212
 213         extern Fukusosuu   *AllocateFukusosuuVec();
 214         extern Fukusosuu  **AllocateFukusosuuMtx();
 215
 216         if( seq1 == NULL )
 217         {
 218                 if( result1 )
 219                 {
 220 //                      fprintf( stderr, "Freeing localarrays in Falign\n" );
 221                         localalloclen = 0;
 222                         mymergesort( 0, 0, NULL );
 223                         alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
 224                         fft( 0, NULL, 1 );
 225                         A__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
 226                         G__align11( NULL, NULL, 0, 0, 0 );
 227                         partA__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
 228                         blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
 229                         if( crossscore ) FreeDoubleMtx( crossscore );
 230                         FreeCharMtx( result1 );
 231                         FreeCharMtx( result2 );
 232                         FreeCharMtx( tmpres1 );
 233                         FreeCharMtx( tmpres2 );
 234                         FreeCharMtx( tmpseq1 );
 235                         FreeCharMtx( tmpseq2 );
 236                         free( sgap1 );
 237                         free( egap1 );
 238                         free( sgap2 );
 239                         free( egap2 );
 240                         free( kouho );
 241                         free( cut1 );
 242                         free( cut2 );
 243                         free( tmpptr1 );
 244                         free( tmpptr2 );
 245                         free( segment );
 246                         free( segment1 );
 247                         free( segment2 );
 248                         free( sortedseg1 );
 249                         free( sortedseg2 );
 250                         if( !kobetsubunkatsu )
 251                         {
 252                                 FreeFukusosuuMtx ( seqVector1 );
 253                                 FreeFukusosuuMtx ( seqVector2 );
 254                                 FreeFukusosuuVec( naisekiNoWa );
 255                                 FreeFukusosuuMtx( naiseki );
 256                                 FreeDoubleVec( soukan );
 257                         }
 258                 }
 259                 else
 260                 {
 261 //                      fprintf( stderr, "Did not allocate localarrays in Falign\n" );
 262                 }
 263
 264                 return( 0.0 );
 265         }
 266
 267         len1 = strlen( seq1[0] );
 268         len2 = strlen( seq2[0] );
 269         nlentmp = MAX( len1, len2 );
 270
 271         nlen = 1;
 272         while( nlentmp >= nlen ) nlen <<= 1;
 273 #if 0
 274         fprintf( stderr, "###   nlen    = %d\n", nlen );
 275 #endif
 276
 277         nlen2 = nlen/2; nlen4 = nlen2 / 2;
 278
 279 #if DEBUG
 280         fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
 281         fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
 282 #endif
 283
 284         if( !localalloclen )
 285         {
 286                 sgap1 = AllocateCharVec( njob );
 287                 egap1 = AllocateCharVec( njob );
 288                 sgap2 = AllocateCharVec( njob );
 289                 egap2 = AllocateCharVec( njob );
 290                 kouho = AllocateIntVec( NKOUHO );
 291                 cut1 = AllocateIntVec( MAXSEG );
 292                 cut2 = AllocateIntVec( MAXSEG );
 293                 tmpptr1 = AllocateCharMtx( njob, 0 );
 294                 tmpptr2 = AllocateCharMtx( njob, 0 );
 295                 result1 = AllocateCharMtx( njob, alloclen );
 296                 result2 = AllocateCharMtx( njob, alloclen );
 297                 tmpres1 = AllocateCharMtx( njob, alloclen );
 298                 tmpres2 = AllocateCharMtx( njob, alloclen );
 299 //              crossscore = AllocateDoubleMtx( MAXSEG, MAXSEG );
 300                 segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
 301                 segment1 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
 302                 segment2 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
 303                 sortedseg1 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
 304                 sortedseg2 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
 305                 if( !( segment && segment1 && segment2 && sortedseg1 && sortedseg2 ) )
 306                         ErrorExit( "Allocation error\n" );
 307
 308                 if     ( scoremtx == -1 ) n20or4or2 = 4;
 309                 else if( fftscore == 1  ) n20or4or2 = 2;
 310                 else                      n20or4or2 = 20;
 311         }
 312         if( localalloclen < nlen )
 313         {
 314                 if( localalloclen )
 315                 {
 316 #if 1
 317                         if( !kobetsubunkatsu )
 318                         {
 319                                 FreeFukusosuuMtx ( seqVector1 );
 320                                 FreeFukusosuuMtx ( seqVector2 );
 321                                 FreeFukusosuuVec( naisekiNoWa );
 322                                 FreeFukusosuuMtx( naiseki );
 323                                 FreeDoubleVec( soukan );
 324                         }
 325                         FreeCharMtx( tmpseq1 );
 326                         FreeCharMtx( tmpseq2 );
 327 #endif
 328 #if RND
 329                         FreeCharMtx( rndseq1 );
 330                         FreeCharMtx( rndseq2 );
 331 #endif
 332                 }
 333
 334                 tmpseq1 = AllocateCharMtx( njob, nlen );
 335                 tmpseq2 = AllocateCharMtx( njob, nlen );
 336                 if( !kobetsubunkatsu )
 337                 {
 338                         naisekiNoWa = AllocateFukusosuuVec( nlen );
 339                         naiseki = AllocateFukusosuuMtx( n20or4or2, nlen );
 340                         seqVector1 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
 341                         seqVector2 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
 342                         soukan = AllocateDoubleVec( nlen+1 );
 343                 }
 344 #if RND
 345                 rndseq1 = AllocateCharMtx( njob, nlen );
 346                 rndseq2 = AllocateCharMtx( njob, nlen );
 347                 for( i=0; i<njob; i++ )
 348                 {
 349                         generateRndSeq( rndseq1[i], nlen );
 350                         generateRndSeq( rndseq2[i], nlen );
 351                 }
 352 #endif
 353                 localalloclen = nlen;
 354         }
 355
 356         for( j=0; j<clus1; j++ ) strcpy( tmpseq1[j], seq1[j] );
 357         for( j=0; j<clus2; j++ ) strcpy( tmpseq2[j], seq2[j] );
 358
 359 #if 0
 360 fftfp = fopen( "input_of_Falign", "w" );
 361 fprintf( fftfp, "nlen = %d\n", nlen );
 362 fprintf( fftfp, "seq1: ( %d sequences ) \n", clus1 );
 363 for( i=0; i<clus1; i++ )
 364         fprintf( fftfp, "%s\n", seq1[i] );
 365 fprintf( fftfp, "seq2: ( %d sequences ) \n", clus2 );
 366 for( i=0; i<clus2; i++ )
 367         fprintf( fftfp, "%s\n", seq2[i] );
 368 fclose( fftfp );
 369 system( "less input_of_Falign < /dev/tty > /dev/tty" );
 370 #endif
 371         if( !kobetsubunkatsu )
 372         {
 373                 fprintf( stderr,  "FFT ... " );
 374
 375                 for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
 376                 if( fftscore && scoremtx != -1 )
 377                 {
 378                         for( i=0; i<clus1; i++ )
 379                         {
 380                                 seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
 381                                 seq_vec_2( seqVector1[1], volume,   eff1[i], tmpseq1[i] );
 382                         }
 383                 }
 384                 else
 385                 {
 386 #if 0
 387                         for( i=0; i<clus1; i++ ) for( j=0; j<n20or4or2; j++ )
 388                                 seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] );
 389 #else
 390                         for( i=0; i<clus1; i++ )
 391                                 seq_vec_3( seqVector1, eff1[i], tmpseq1[i] );
 392 #endif
 393                 }
 394 #if RND
 395                 for( i=0; i<clus1; i++ )
 396                 {
 397                         vec_init2( seqVector1, rndseq1[i], eff1[i], len1, nlen );
 398                 }
 399 #endif
 400 #if 0
 401 fftfp = fopen( "seqVec", "w" );
 402 fprintf( fftfp, "before transform\n" );
 403 for( k=0; k<n20or4or2; k++ )
 404 {
 405    fprintf( fftfp, "nlen=%d\n", nlen );
 406    fprintf( fftfp, "%c\n", amino[k] );
 407    for( l=0; l<nlen; l++ )
 408    fprintf( fftfp, "%f %f\n", seqVector1[k][l].R, seqVector1[k][l].I );
 409 }
 410 fclose( fftfp );
 411 system( "less seqVec < /dev/tty > /dev/tty" );
 412 #endif
 413
 414                 for( j=0; j<n20or4or2; j++ ) vec_init( seqVector2[j], nlen );
 415                 if( fftscore && scoremtx != -1 )
 416                 {
 417                         for( i=0; i<clus2; i++ )
 418                         {
 419                                 seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
 420                                 seq_vec_2( seqVector2[1], volume,   eff2[i], tmpseq2[i] );
 421                         }
 422                 }
 423                 else
 424                 {
 425 #if 0
 426                         for( i=0; i<clus2; i++ ) for( j=0; j<n20or4or2; j++ )
 427                                 seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] );
 428 #else
 429                         for( i=0; i<clus2; i++ )
 430                                 seq_vec_3( seqVector2, eff2[i], tmpseq2[i] );
 431 #endif
 432                 }
 433 #if RND
 434                 for( i=0; i<clus2; i++ )
 435                 {
 436                         vec_init2( seqVector2, rndseq2[i], eff2[i], len2, nlen );
 437                 }
 438 #endif
 439
 440 #if 0
 441 fftfp = fopen( "seqVec2", "w" );
 442 fprintf( fftfp, "before fft\n" );
 443 for( k=0; k<n20or4or2; k++ )
 444 {
 445    fprintf( fftfp, "%c\n", amino[k] );
 446    for( l=0; l<nlen; l++ )
 447    fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
 448 }
 449 fclose( fftfp );
 450 system( "less seqVec2 < /dev/tty > /dev/tty" );
 451 #endif
 452
 453                 for( j=0; j<n20or4or2; j++ )
 454                 {
 455                         fft( nlen, seqVector2[j], (j==0) );
 456                         fft( nlen, seqVector1[j], 0 );
 457                 }
 458 #if 0
 459 fftfp = fopen( "seqVec2", "w" );
 460 fprintf( fftfp, "#after fft\n" );
 461 for( k=0; k<n20or4or2; k++ )
 462 {
 463    fprintf( fftfp, "#%c\n", amino[k] );
 464    for( l=0; l<nlen; l++ )
 465            fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
 466 }
 467 fclose( fftfp );
 468 system( "less seqVec2 < /dev/tty > /dev/tty" );
 469 #endif
 470
 471                 for( k=0; k<n20or4or2; k++ )
 472                 {
 473                         for( l=0; l<nlen; l++ )
 474                                 calcNaiseki( naiseki[k]+l, seqVector1[k]+l, seqVector2[k]+l );
 475                 }
 476                 for( l=0; l<nlen; l++ )
 477                 {
 478                         naisekiNoWa[l].R = 0.0;
 479                         naisekiNoWa[l].I = 0.0;
 480                         for( k=0; k<n20or4or2; k++ )
 481                         {
 482                                 naisekiNoWa[l].R += naiseki[k][l].R;
 483                                 naisekiNoWa[l].I += naiseki[k][l].I;
 484                         }
 485                 }
 486
 487 #if 0
 488         fftfp = fopen( "naisekiNoWa", "w" );
 489         fprintf( fftfp, "#Before fft\n" );
 490         for( l=0; l<nlen; l++ )
 491                 fprintf( fftfp, "%d  %f %f\n", l, naisekiNoWa[l].R, naisekiNoWa[l].I );
 492         fclose( fftfp );
 493         system( "less naisekiNoWa < /dev/tty > /dev/tty " );
 494 #endif
 495
 496                 fft( -nlen, naisekiNoWa, 0 );
 497
 498                 for( m=0; m<=nlen2; m++ )
 499                         soukan[m] = naisekiNoWa[nlen2-m].R;
 500                 for( m=nlen2+1; m<nlen; m++ )
 501                         soukan[m] = naisekiNoWa[nlen+nlen2-m].R;
 502
 503 #if 0
 504         fftfp = fopen( "naisekiNoWa", "w" );
 505         fprintf( fftfp, "#After fft\n" );
 506         for( l=0; l<nlen; l++ )
 507                 fprintf( fftfp, "%d  %f\n", l, naisekiNoWa[l].R );
 508         fclose( fftfp );
 509         fftfp = fopen( "list.plot", "w"  );
 510         fprintf( fftfp, "plot 'naisekiNoWa'\npause -1" );
 511         fclose( fftfp );
 512         system( "/usr/bin/gnuplot list.plot &" );
 513 #endif
 514 #if 0
 515         fprintf( stderr, "frt write start\n" );
 516         fftfp = fopen( "frt", "w" );
 517         for( l=0; l<nlen; l++ )
 518                 fprintf( fftfp, "%d  %f\n", l-nlen2, soukan[l] );
 519         fclose( fftfp );
 520         system( "less frt < /dev/tty > /dev/tty" );
 521 #if 0
 522         fftfp = fopen( "list.plot", "w"  );
 523         fprintf( fftfp, "plot 'frt'\n pause +1" );
 524         fclose( fftfp );
 525         system( "/usr/bin/gnuplot list.plot" );
 526 #endif
 527 #endif
 528
 529
 530                 getKouho( kouho, NKOUHO, soukan, nlen );
 531
 532 #if 0
 533                 for( i=0; i<NKOUHO; i++ )
 534                 {
 535                         fprintf( stderr, "kouho[%d] = %d\n", i, kouho[i] );
 536                 }
 537 #endif
 538         }
 539
 540 #if KEIKA
 541         fprintf( stderr, "Searching anchors ... " );
 542 #endif
 543         count = 0;
 544
 545
 546
 547 #define CAND 0
 548 #if CAND
 549         fftfp = fopen( "cand", "w" );
 550         fclose( fftfp );
 551 #endif
 552         if( kobetsubunkatsu )
 553         {
 554                 maxk = 1;
 555                 kouho[0] = 0;
 556         }
 557         else
 558         {
 559                 maxk = NKOUHO;
 560         }
 561
 562         for( k=0; k<maxk; k++ )
 563         {
 564                 lag = kouho[k];
 565                 zurasu2( lag, clus1, clus2, seq1, seq2, tmpptr1, tmpptr2 );
 566 #if CAND
 567                 fftfp = fopen( "cand", "a" );
 568                 fprintf( fftfp, "Candidate No.%d lag = %d\n", k+1, lag );
 569                 fprintf( fftfp, "%s\n", tmpptr1[0] );
 570                 fprintf( fftfp, "%s\n", tmpptr2[0] );
 571                 fclose( fftfp );
 572 #endif
 573                 tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
 574
 575                 if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
 576
 577
 578                 while( tmpint-- > 0 )
 579                 {
 580                         if( lag > 0 )
 581                         {
 582                                 segment1[count].start  = segment[count].start ;
 583                                 segment1[count].end    = segment[count].end   ;
 584                                 segment1[count].center = segment[count].center;
 585                                 segment1[count].score  = segment[count].score;
 586
 587                                 segment2[count].start  = segment[count].start  + lag;
 588                                 segment2[count].end    = segment[count].end    + lag;
 589                                 segment2[count].center = segment[count].center + lag;
 590                                 segment2[count].score  = segment[count].score       ;
 591                         }
 592                         else
 593                         {
 594                                 segment1[count].start  = segment[count].start  - lag;
 595                                 segment1[count].end    = segment[count].end    - lag;
 596                                 segment1[count].center = segment[count].center - lag;
 597                                 segment1[count].score  = segment[count].score       ;
 598
 599                                 segment2[count].start  = segment[count].start ;
 600                                 segment2[count].end    = segment[count].end   ;
 601                                 segment2[count].center = segment[count].center;
 602                                 segment2[count].score  = segment[count].score ;
 603                         }
 604 #if 0
 605                         fftfp = fopen( "cand", "a" );
 606                         fprintf( fftfp, "Goukaku=%dko\n", tmpint );
 607                         fprintf( fftfp, "in 1 %d\n", segment1[count].center );
 608                         fprintf( fftfp, "in 2 %d\n", segment2[count].center );
 609                         fclose( fftfp );
 610 #endif
 611                         segment1[count].pair = &segment2[count];
 612                         segment2[count].pair = &segment1[count];
 613                         count++;
 614 #if 0
 615                         fprintf( stderr, "count=%d\n", count );
 616 #endif
 617                 }
 618         }
 619 #if 1
 620         if( !kobetsubunkatsu )
 621                 fprintf( stderr, "%d segments found\n", count );
 622 #endif
 623         if( !count && fftNoAnchStop )
 624                 ErrorExit( "Cannot detect anchor!" );
 625 #if 0
 626         fftfp = fopen( "fft", "a" );
 627         fprintf( fftfp, "RESULT before sort:\n" );
 628         for( l=0; l<count; l++ )
 629         {
 630                 fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
 631                 fprintf( fftfp, "%d score = %f\n", segment2[l].center, segment1[l].score );
 632         }
 633         fclose( fftfp );
 634 #endif
 635
 636 #if KEIKA
 637         fprintf( stderr, "Aligning anchors ... " );
 638 #endif
 639         for( i=0; i<count; i++ )
 640         {
 641                 sortedseg1[i] = &segment1[i];
 642                 sortedseg2[i] = &segment2[i];
 643         }
 644 #if 0
 645         tmpsort( count, sortedseg1 );
 646         tmpsort( count, sortedseg2 );
 647         qsort( sortedseg1, count, sizeof( Segment * ), segcmp );
 648         qsort( sortedseg2, count, sizeof( Segment * ), segcmp );
 649 #else
 650         mymergesort( 0, count-1, sortedseg1 );
 651         mymergesort( 0, count-1, sortedseg2 );
 652 #endif
 653         for( i=0; i<count; i++ ) sortedseg1[i]->number = i;
 654         for( i=0; i<count; i++ ) sortedseg2[i]->number = i;
 655
 656
 657         if( kobetsubunkatsu )
 658         {
 659                 for( i=0; i<count; i++ )
 660             {
 661                         cut1[i+1] = sortedseg1[i]->center;
 662                         cut2[i+1] = sortedseg2[i]->center;
 663                 }
 664                 cut1[0] = 0;
 665                 cut2[0] = 0;
 666                 cut1[count+1] = len1;
 667                 cut2[count+1] = len2;
 668                 count += 2;
 669         }
 670         else
 671         {
 672                 if( crossscoresize < count+2 )
 673                 {
 674                         crossscoresize = count+2;
 675 #if 1
 676                         fprintf( stderr, "######allocating crossscore, size = %d\n", crossscoresize );
 677 #endif
 678                         if( crossscore ) FreeDoubleMtx( crossscore );
 679                         crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
 680                 }
 681                 for( i=0; i<count+2; i++ ) for( j=0; j<count+2; j++ )
 682                         crossscore[i][j] = 0.0;
 683                 for( i=0; i<count; i++ )
 684                 {
 685                         crossscore[segment1[i].number+1][segment1[i].pair->number+1] = segment1[i].score;
 686                         cut1[i+1] = sortedseg1[i]->center;
 687                         cut2[i+1] = sortedseg2[i]->center;
 688                 }
 689
 690 #if DEBUG
 691                 fprintf( stderr, "AFTER SORT\n" );
 692                 for( i=0; i<count; i++ ) fprintf( stderr, "%d, %d\n", segment1[i].start, segment2[i].start );
 693 #endif
 694
 695                 crossscore[0][0] = 10000000.0;
 696                 cut1[0] = 0;
 697                 cut2[0] = 0;
 698                 crossscore[count+1][count+1] = 10000000.0;
 699                 cut1[count+1] = len1;
 700                 cut2[count+1] = len2;
 701                 count += 2;
 702                 count0 = count;
 703
 704                 blockAlign2( cut1, cut2, sortedseg1, sortedseg2, crossscore, &count );
 705                 if( count0 > count )
 706                 {
 707 #if 0
 708                         fprintf( stderr, "\7 REPEAT!? \n" );
 709 #else
 710                         fprintf( stderr, "REPEAT!? \n" );
 711 #endif
 712                         if( fftRepeatStop ) exit( 1 );
 713                 }
 714 #if KEIKA
 715                 else fprintf( stderr, "done\n" );
 716 #endif
 717         }
 718
 719 #if 0
 720         fftfp = fopen( "fft", "a" );
 721         fprintf( fftfp, "RESULT after sort:\n" );
 722         for( l=0; l<count; l++ )
 723         {
 724                 fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
 725                 fprintf( fftfp, "%d\n", segment2[l].center );
 726         }
 727         fclose( fftfp );
 728 #endif
 729
 730 #if 0
 731         fftfp = fopen( "fft", "a" );
 732         fprintf( fftfp, "RESULT after sort:\n" );
 733         for( l=0; l<count; l++ )
 734         {
 735                 fprintf( fftfp, "cut : %d %d\n", cut1[l], cut2[l] );
 736         }
 737         fclose( fftfp );
 738 #endif
 739
 740 #if KEIKA
 741         fprintf( trap_g, "Devided to %d segments\n", count-1 );
 742         fprintf( trap_g, "%d  %d forg\n", MIN( clus1, clus2 ), count-1 );
 743 #endif
 744
 745         totallen = 0;
 746         for( j=0; j<clus1; j++ ) result1[j][0] = 0;
 747         for( j=0; j<clus2; j++ ) result2[j][0] = 0;
 748         totalscore = 0.0;
 749         *totalimpmatch = 0.0;
 750         for( i=0; i<count-1; i++ )
 751         {
 752 #if DEBUG
 753                 fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
 754 #else
 755 #if KEIKA
 756                 fprintf( stderr, "DP %03d / %03d\r", i+1, count-1 );
 757 #endif
 758 #endif
 759
 760                 if( cut1[i] )
 761                 {
 762                         getkyokaigap( sgap1, seq1, cut1[i]-1, clus1 );
 763                         getkyokaigap( sgap2, seq2, cut2[i]-1, clus2 );
 764                 }
 765                 else
 766                 {
 767                         for( j=0; j<clus1; j++ ) sgap1[j] = 'o';
 768                         for( j=0; j<clus2; j++ ) sgap2[j] = 'o';
 769                 }
 770                 if( cut1[i+1] != len1 )
 771                 {
 772                         getkyokaigap( egap1, seq1, cut1[i+1], clus1 );
 773                         getkyokaigap( egap2, seq2, cut2[i+1], clus2 );
 774                 }
 775                 else
 776                 {
 777                         for( j=0; j<clus1; j++ ) egap1[j] = 'o';
 778                         for( j=0; j<clus2; j++ ) egap2[j] = 'o';
 779                 }
 780
 781                 for( j=0; j<clus1; j++ )
 782                 {
 783                         strncpy( tmpres1[j], seq1[j]+cut1[i], cut1[i+1]-cut1[i] );
 784                         tmpres1[j][cut1[i+1]-cut1[i]] = 0;
 785                 }
 786                 if( kobetsubunkatsu ) commongappick_record( clus1, tmpres1, gapmap1 );
 787                 for( j=0; j<clus2; j++ )
 788                 {
 789                         strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
 790                         tmpres2[j][cut2[i+1]-cut2[i]] = 0;
 791                 }
 792                 if( kobetsubunkatsu ) commongappick_record( clus2, tmpres2, gapmap2 );
 793
 794 #if 0
 795                 fprintf( stderr, "count = %d\n", count );
 796                 fprintf( stderr, "### reg1 = %d-%d\n", cut1[i], cut1[i+1]-1 );
 797                 fprintf( stderr, "### reg2 = %d-%d\n", cut2[i], cut2[i+1]-1 );
 798 #endif
 799
 800                 switch( alg )
 801                 {
 802                         case( 'a' ):
 803                                 totalscore += Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
 804                                 break;
 805                         case( 'Q' ):
 806                                 totalscore += partQ__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2 );
 807                                 *totalimpmatch += impmatch;
 808 //                              fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
 809                                 break;
 810                         case( 'A' ):
 811                                 totalscore += partA__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres );
 812                                 *totalimpmatch += impmatch;
 813 //                              fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
 814
 815
 816                                 break;
 817                         default:
 818                                 fprintf( stderr, "alg = %c\n", alg );
 819                                 ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
 820                                 break;
 821                 }
 822 #ifdef enablemultithread
 823                 if( chudanres && *chudanres )
 824                 {
 825 //                      fprintf( stderr, "\n\n## CHUUDAN!!! at Falign_localhom\n" );
 826                         return( -1.0 );
 827                 }
 828 #endif
 829
 830                 nlen = strlen( tmpres1[0] );
 831                 if( totallen + nlen > alloclen )
 832                 {
 833                         fprintf( stderr, "totallen=%d +  nlen=%d > alloclen = %d\n", totallen, nlen, alloclen );
 834                         ErrorExit( "LENGTH OVER in Falign\n " );
 835                 }
 836                 for( j=0; j<clus1; j++ ) strcat( result1[j], tmpres1[j] );
 837                 for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] );
 838                 totallen += nlen;
 839 #if 0
 840                 fprintf( stderr, "%4d\r", totallen );
 841                 fprintf( stderr, "\n\n" );
 842                 for( j=0; j<clus1; j++ )
 843                 {
 844                         fprintf( stderr, "%s\n", tmpres1[j] );
 845                 }
 846                 fprintf( stderr, "-------\n" );
 847                 for( j=0; j<clus2; j++ )
 848                 {
 849                         fprintf( stderr, "%s\n", tmpres2[j] );
 850                 }
 851 #endif
 852         }
 853 #if KEIKA
 854         fprintf( stderr, "DP ... done   \n" );
 855 #endif
 856
 857         for( j=0; j<clus1; j++ ) strcpy( seq1[j], result1[j] );
 858         for( j=0; j<clus2; j++ ) strcpy( seq2[j], result2[j] );
 859 #if 0
 860         for( j=0; j<clus1; j++ )
 861         {
 862                 fprintf( stderr, "%s\n", result1[j] );
 863         }
 864         fprintf( stderr, "- - - - - - - - - - -\n" );
 865         for( j=0; j<clus2; j++ )
 866         {
 867                 fprintf( stderr, "%s\n", result2[j] );
 868         }
 869 #endif
 870         return( totalscore );
 871 }