binaries/src/mafft/core/MSalignmm.c

   1 #include "mltaln.h"
   2 #include "dp.h"
   3
   4 #define MEMSAVE 1
   5
   6 #define DEBUG 0
   7 #define USE_PENALTY_EX  0
   8 #define STOREWM 0
   9
  10 #define DPTANNI 100
  11
  12
  13 static int reccycle = 0;
  14
  15
  16 static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
  17 {
  18         int j, k, l;
  19         float scarr[26];
  20         float **cpmxpd = floatwork;
  21         int **cpmxpdn = intwork;
  22         int count = 0;
  23         float *matchpt;
  24         float **cpmxpdpt;
  25         int **cpmxpdnpt;
  26         int cpkd;
  27
  28         if( initialize )
  29         {
  30                 for( j=0; j<lgth2; j++ )
  31                 {
  32                         count = 0;
  33                         for( l=0; l<26; l++ )
  34                         {
  35                                 if( cpmx2[j][l] )
  36                                 {
  37                                         cpmxpd[j][count] = cpmx2[j][l];
  38                                         cpmxpdn[j][count] = l;
  39                                         count++;
  40                                 }
  41                         }
  42                         cpmxpdn[j][count] = -1;
  43                 }
  44         }
  45
  46         for( l=0; l<26; l++ )
  47         {
  48                 scarr[l] = 0.0;
  49                 for( k=0; k<26; k++ )
  50                 {
  51                         scarr[l] += n_dis[k][l] * cpmx1[i1][k];
  52                 }
  53         }
  54 #if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
  55         {
  56                 float *fpt, **fptpt, *fpt2;
  57                 int *ipt, **iptpt;
  58                 fpt2 = match;
  59                 iptpt = cpmxpdn;
  60                 fptpt = cpmxpd;
  61                 while( lgth2-- )
  62                 {
  63                         *fpt2 = 0.0;
  64                         ipt=*iptpt,fpt=*fptpt;
  65                         while( *ipt > -1 )
  66                                 *fpt2 += scarr[*ipt++] * *fpt++;
  67                         fpt2++,iptpt++,fptpt++;
  68                 }
  69         }
  70         for( j=0; j<lgth2; j++ )
  71         {
  72                 match[j] = 0.0;
  73                 for( k=0; cpmxpdn[j][k]>-1; k++ )
  74                         match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
  75         }
  76 #else
  77         matchpt = match;
  78         cpmxpdnpt = cpmxpdn;
  79         cpmxpdpt = cpmxpd;
  80         while( lgth2-- )
  81         {
  82                 *matchpt = 0.0;
  83                 for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
  84                         *matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
  85                 matchpt++;
  86                 cpmxpdnpt++;
  87                 cpmxpdpt++;
  88         }
  89 #endif
  90 }
  91
  92 static float Atracking(
  93                                                 char **seq1, char **seq2,
  94                         char **mseq1, char **mseq2,
  95                         int **ijp, int icyc, int jcyc,
  96                                                 int ist, int ien, int jst, int jen )
  97 {
  98         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
  99         char *gaptable1, *gt1bk;
 100         char *gaptable2, *gt2bk;
 101         lgth1 = ien-ist+1;
 102         lgth2 = jen-jst+1;
 103
 104         gt1bk = AllocateCharVec( lgth1+lgth2+1 );
 105         gt2bk = AllocateCharVec( lgth1+lgth2+1 );
 106
 107 #if 0
 108         for( i=0; i<lgth1; i++ )
 109         {
 110                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 111         }
 112 #endif
 113
 114
 115 //      fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
 116
 117     for( i=0; i<lgth1+1; i++ )
 118     {
 119         ijp[i][0] = i + 1;
 120     }
 121     for( j=0; j<lgth2+1; j++ )
 122     {
 123         ijp[0][j] = -( j + 1 );
 124     }
 125
 126
 127         gaptable1 = gt1bk + lgth1+lgth2;
 128         *gaptable1 = 0;
 129         gaptable2 = gt2bk + lgth1+lgth2;
 130         *gaptable2 = 0;
 131
 132 //      if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
 133
 134         iin = lgth1; jin = lgth2;
 135         klim = lgth1+lgth2;
 136         for( k=0; k<=klim; k++ )
 137         {
 138                 if( ijp[iin][jin] < 0 )
 139                 {
 140                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 141                 }
 142                 else if( ijp[iin][jin] > 0 )
 143                 {
 144                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 145                 }
 146                 else
 147                 {
 148                         ifi = iin-1; jfi = jin-1;
 149                 }
 150                 l = iin - ifi;
 151                 while( --l )
 152                 {
 153                         *--gaptable1 = 'o';
 154                         *--gaptable2 = '-';
 155                         k++;
 156                 }
 157                 l= jin - jfi;
 158                 while( --l )
 159                 {
 160                         *--gaptable1 = '-';
 161                         *--gaptable2 = 'o';
 162                         k++;
 163                 }
 164                 if( iin <= 0 || jin <= 0 ) break;
 165                 *--gaptable1 = 'o';
 166                 *--gaptable2 = 'o';
 167                 k++;
 168                 iin = ifi; jin = jfi;
 169
 170         }
 171
 172         for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 );
 173         for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 );
 174
 175         free( gt1bk );
 176         free( gt2bk );
 177
 178 //      fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
 179 //      fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
 180         return( 0.0 );
 181 }
 182
 183 static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float **gapinfo )
 184 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 185 {
 186 //      int k;
 187         register int i, j;
 188         int ll1, ll2;
 189         int lasti, lastj;
 190         float wm = 0.0;   /* int ?????? */
 191         float g;
 192         float *currentw, *previousw;
 193 #if USE_PENALTY_EX
 194         float fpenalty_ex = (float)penalty_ex;
 195 #endif
 196 #if 1
 197         float *wtmp;
 198         int *ijppt;
 199         float *mjpt, *prept, *curpt;
 200         int *mpjpt;
 201 #endif
 202         float mi, *m;
 203         int **ijp;
 204         int mpi, *mp;
 205         float *w1, *w2;
 206         float *initverticalw;    /* kufuu sureba iranai */
 207         float *lastverticalw;    /* kufuu sureba iranai */
 208         int **intwork;
 209         float **floatwork;
 210         int **intmtx;
 211         int lgth1, lgth2;
 212         float *ogcp1;
 213         float *fgcp1;
 214         float *ogcp2;
 215         float *fgcp2;
 216 //      char **aseq1;
 217 //      char **aseq2;
 218 //      char **aseq1bk, **aseq2bk;
 219
 220         ogcp1 = gapinfo[0] + ist;
 221         fgcp1 = gapinfo[1] + ist;
 222         ogcp2 = gapinfo[2] + jst;
 223         fgcp2 = gapinfo[3] + jst;
 224
 225 #if STOREWM
 226         char ttt1[10000], ttt2[10000];
 227 #endif
 228
 229
 230         lgth1 = ien-ist+1;
 231         lgth2 = jen-jst+1;
 232
 233 #if STOREWM
 234         strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
 235         strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
 236
 237         fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
 238         fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
 239         fprintf( stderr, "ttt1 = %s\n", ttt1 );
 240         fprintf( stderr, "ttt2 = %s\n", ttt2 );
 241 #endif
 242
 243
 244         ll1 = ( (int)(lgth1) ) + 100;
 245         ll2 = ( (int)(lgth2) ) + 100;
 246
 247 //      aseq1 = AllocateCharMtx( icyc, 0 );
 248 //      aseq2 = AllocateCharMtx( jcyc, 0 );
 249 //      aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
 250 //      aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
 251 //      for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
 252 //      for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
 253
 254         w1 = AllocateFloatVec( ll2+2 );
 255         w2 = AllocateFloatVec( ll2+2 );
 256
 257         initverticalw = AllocateFloatVec( ll1+2 );
 258         lastverticalw = AllocateFloatVec( ll1+2 );
 259
 260         m = AllocateFloatVec( ll2+2 );
 261         mp = AllocateIntVec( ll2+2 );
 262
 263         floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
 264         intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
 265
 266
 267         intmtx = AllocateIntMtx( ll1+1, ll2+1 );
 268
 269         ijp = intmtx;
 270
 271         currentw = w1;
 272         previousw = w2;
 273
 274         match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
 275
 276         match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
 277
 278         for( i=1; i<lgth1+1; i++ )
 279         {
 280                 initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
 281         }
 282         for( j=1; j<lgth2+1; j++ )
 283         {
 284                 currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
 285         }
 286
 287         for( j=1; j<lgth2+1; ++j )
 288         {
 289                 m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;;
 290         }
 291
 292         lastverticalw[0] = currentw[lgth2-1];
 293
 294
 295
 296         lasti = lgth1+1;
 297         for( i=1; i<lasti; i++ )
 298         {
 299
 300                 wtmp = previousw;
 301                 previousw = currentw;
 302                 currentw = wtmp;
 303
 304                 previousw[0] = initverticalw[i-1];
 305
 306                 match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
 307                 currentw[0] = initverticalw[i];
 308
 309                 mi = previousw[0] + ogcp2[1];
 310                 mpi = 0;
 311
 312                 ijppt = ijp[i] + 1;
 313                 mjpt = m + 1;
 314                 prept = previousw;
 315                 curpt = currentw + 1;
 316                 mpjpt = mp + 1;
 317                 lastj = lgth2+1;
 318                 for( j=1; j<lastj; j++ )
 319                 {
 320                         wm = *prept;
 321                         *ijppt = 0;
 322
 323 #if 0
 324                         fprintf( stderr, "%5.0f->", wm );
 325 #endif
 326                         g = mi + fgcp2[j-1];
 327 #if 0
 328                         fprintf( stderr, "%5.0f?", g );
 329 #endif
 330                         if( g > wm )
 331                         {
 332                                 wm = g;
 333                                 *ijppt = -( j - mpi );
 334                         }
 335                         g = *prept + ogcp2[j];
 336                         if( g >= mi )
 337                         {
 338                                 mi = g;
 339                                 mpi = j-1;
 340                         }
 341 #if USE_PENALTY_EX
 342                         mi += fpenalty_ex;
 343 #endif
 344
 345                         g = *mjpt + fgcp1[i-1];
 346 #if 0
 347                         fprintf( stderr, "%5.0f?", g );
 348 #endif
 349                         if( g > wm )
 350                         {
 351                                 wm = g;
 352                                 *ijppt = +( i - *mpjpt );
 353                         }
 354                         g = *prept + ogcp1[i];
 355                         if( g >= *mjpt )
 356                         {
 357                                 *mjpt = g;
 358                                 *mpjpt = i-1;
 359                         }
 360 #if USE_PENALTY_EX
 361                         m[j] += fpenalty_ex;
 362 #endif
 363
 364 #if 0
 365                         fprintf( stderr, "%5.0f ", wm );
 366 #endif
 367                         *curpt += wm;
 368
 369
 370                         ijppt++;
 371                         mjpt++;
 372                         prept++;
 373                         mpjpt++;
 374                         curpt++;
 375                 }
 376                 lastverticalw[i] = currentw[lgth2-1];
 377         }
 378
 379 //      fprintf( stderr, "wm = %f\n", wm );
 380
 381         Atracking( seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, ist, ien, jst, jen );
 382
 383 //      for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
 384 //      for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
 385
 386 //      fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
 387 //      fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
 388
 389         FreeFloatVec( w1 );
 390         FreeFloatVec( w2 );
 391         FreeFloatVec( initverticalw );
 392         FreeFloatVec( lastverticalw );
 393
 394         FreeFloatVec( m );
 395         FreeIntVec( mp );
 396
 397
 398         FreeFloatMtx( floatwork );
 399         FreeIntMtx( intwork );
 400
 401         FreeIntMtx( intmtx );
 402
 403 //      FreeCharMtx( aseq1bk );
 404 //      FreeCharMtx( aseq2bk );
 405
 406 //      free( aseq1 );
 407 //      free( aseq2 );
 408
 409         return( wm );
 410
 411 }
 412
 413 static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo )
 414 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 415 {
 416 //      int k;
 417         int alnlen;
 418         float value = 0.0;
 419         register int i, j;
 420         char **aseq1, **aseq2;
 421         int ll1, ll2, l, len;
 422         int lasti, lastj, imid;
 423         int jmid = 0; // by D.Mathog, a guess
 424         float wm = 0.0;   /* int ?????? */
 425         float g;
 426         float *currentw, *previousw;
 427 #if USE_PENALTY_EX
 428         float fpenalty_ex = (float)penalty_ex;
 429 #endif
 430         float *wtmp;
 431 //      short *ijppt;
 432         int *mpjpt;
 433 //      short **ijp;
 434         int *mp;
 435         int mpi;
 436         float *mjpt, *prept, *curpt;
 437         float mi;
 438         float *m;
 439         float *w1, *w2;
 440 //      float *match;
 441         float *initverticalw;    /* kufuu sureba iranai */
 442         float *lastverticalw;    /* kufuu sureba iranai */
 443         int **intwork;
 444         float **floatwork;
 445 //      short **shortmtx;
 446 #if STOREWM
 447         float **WMMTX;
 448         float **WMMTX2;
 449 #endif
 450         float *midw;
 451         float *midm;
 452         float *midn;
 453         int lgth1, lgth2;
 454         float maxwm;
 455         int *jumpforwi;
 456         int *jumpforwj;
 457         int *jumpbacki;
 458         int *jumpbackj;
 459         int *jumpdummi; //muda
 460         int *jumpdummj = NULL; // by D.Mathog, a guess
 461         int jumpi, jumpj = 0; // by D.Mathog, a guess
 462         char *gaps;
 463         int ijpi, ijpj;
 464         float *ogcp1;
 465         float *fgcp1;
 466         float *ogcp2;
 467         float *fgcp2;
 468         float firstm;
 469         int firstmp;
 470 #if STOREWM
 471         static char ttt1[50000];
 472         static char ttt2[50000];
 473 #endif
 474
 475         ogcp1 = gapinfo[0] + ist;
 476         fgcp1 = gapinfo[1] + ist;
 477         ogcp2 = gapinfo[2] + jst;
 478         fgcp2 = gapinfo[3] + jst;
 479
 480         depth++;
 481         reccycle++;
 482
 483         lgth1 = ien-ist+1;
 484         lgth2 = jen-jst+1;
 485
 486 //      if( lgth1 < 5 )
 487 //              fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
 488 //      if( lgth2 < 5 )
 489 //              fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
 490 //
 491
 492 #if STOREWM
 493         fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
 494         strncpy( ttt1, seq1[0]+ist, lgth1 );
 495         strncpy( ttt2, seq2[0]+jst, lgth2 );
 496         ttt1[lgth1] = 0;
 497         ttt2[lgth2] = 0;
 498         fprintf( stderr, "seq1 = %s\n", ttt1 );
 499         fprintf( stderr, "seq2 = %s\n", ttt2 );
 500 #endif
 501         if( lgth2 <= 0 ) // lgth1 <= 0 ha?
 502         {
 503 //              fprintf( stderr, "\n\n==== jimei\n\n" );
 504 //              exit( 1 );
 505                 for( i=0; i<icyc; i++ )
 506                 {
 507                         strncpy( mseq1[i], seq1[i]+ist, lgth1 );
 508                         mseq1[i][lgth1] = 0;
 509                 }
 510                 for( i=0; i<jcyc; i++ )
 511                 {
 512                         mseq2[i][0] = 0;
 513                         for( j=0; j<lgth1; j++ )
 514                                 strcat( mseq2[i], "-" );
 515                 }
 516
 517 //              fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
 518 //              fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
 519
 520                 return( 0.0 );
 521         }
 522
 523 #if MEMSAVE
 524         aseq1 = AllocateCharMtx( icyc, 0 );
 525         aseq2 = AllocateCharMtx( jcyc, 0 );
 526         for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
 527         for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
 528 #else
 529         aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
 530         aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
 531 #endif
 532
 533 //  if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai
 534 //    if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
 535     if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
 536         {
 537 //              fprintf( stderr, "==== Going to _tanni\n" );
 538
 539                 value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
 540
 541
 542 #if MEMSAVE
 543                 free( aseq1 );
 544                 free( aseq2 );
 545 #else
 546                 for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
 547                 for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
 548
 549                 FreeCharMtx( aseq1 );
 550                 FreeCharMtx( aseq2 );
 551 #endif
 552
 553 //              fprintf( stderr, "value = %f\n", value );
 554
 555                 return( value );
 556         }
 557 //      fprintf( stderr, "Trying to divide the mtx\n" );
 558
 559         ll1 = ( (int)(lgth1) ) + 100;
 560         ll2 = ( (int)(lgth2) ) + 100;
 561
 562 //      fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
 563
 564         w1 = AllocateFloatVec( ll2+2 );
 565         w2 = AllocateFloatVec( ll2+2 );
 566 //      match = AllocateFloatVec( ll2+2 );
 567         midw = AllocateFloatVec( ll2+2 );
 568         midn = AllocateFloatVec( ll2+2 );
 569         midm = AllocateFloatVec( ll2+2 );
 570         jumpbacki = AllocateIntVec( ll2+2 );
 571         jumpbackj = AllocateIntVec( ll2+2 );
 572         jumpforwi = AllocateIntVec( ll2+2 );
 573         jumpforwj = AllocateIntVec( ll2+2 );
 574         jumpdummi = AllocateIntVec( ll2+2 );
 575         jumpdummj = AllocateIntVec( ll2+2 );
 576
 577         initverticalw = AllocateFloatVec( ll1+2 );
 578         lastverticalw = AllocateFloatVec( ll1+2 );
 579
 580         m = AllocateFloatVec( ll2+2 );
 581         mp = AllocateIntVec( ll2+2 );
 582         gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
 583
 584         floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
 585         intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
 586
 587 #if DEBUG
 588         fprintf( stderr, "succeeded\n" );
 589 #endif
 590
 591 #if STOREWM
 592         WMMTX = AllocateFloatMtx( ll1, ll2 );
 593         WMMTX2 = AllocateFloatMtx( ll1, ll2 );
 594 #endif
 595 #if 0
 596         shortmtx = AllocateShortMtx( ll1, ll2 );
 597
 598 #if DEBUG
 599         fprintf( stderr, "succeeded\n\n" );
 600 #endif
 601
 602         ijp = shortmtx;
 603 #endif
 604
 605         currentw = w1;
 606         previousw = w2;
 607
 608         match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
 609
 610         match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
 611
 612         for( i=1; i<lgth1+1; i++ )
 613         {
 614                 initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
 615         }
 616         for( j=1; j<lgth2+1; j++ )
 617         {
 618                 currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
 619         }
 620
 621 #if STOREWM
 622         WMMTX[0][0] = initverticalw[0];
 623         for( i=1; i<lgth1+1; i++ )
 624         {
 625                 WMMTX[i][0] = initverticalw[i];
 626         }
 627         for( j=1; j<lgth2+1; j++ )
 628         {
 629                 WMMTX[0][j] = currentw[j];
 630         }
 631 #endif
 632
 633
 634         for( j=1; j<lgth2+1; ++j )
 635         {
 636                 m[j] = currentw[j-1] + ogcp1[1];
 637 //              m[j] = currentw[j-1];
 638                 mp[j] = 0;
 639         }
 640
 641         lastverticalw[0] = currentw[lgth2-1];
 642
 643         imid = lgth1 * 0.5;
 644
 645         jumpi = 0; // atode kawaru.
 646         lasti = lgth1+1;
 647 #if STOREWM
 648         for( i=1; i<lasti; i++ )
 649 #else
 650         for( i=1; i<=imid; i++ )
 651 #endif
 652         {
 653                 wtmp = previousw;
 654                 previousw = currentw;
 655                 currentw = wtmp;
 656
 657                 previousw[0] = initverticalw[i-1];
 658
 659                 match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
 660                 currentw[0] = initverticalw[i];
 661
 662                 m[0] = ogcp1[i];
 663 #if STOREM
 664                 WMMTX2[i][0] = m[0];
 665 #endif
 666                 if( i == imid ) midm[0] = m[0];
 667
 668                 mi = previousw[0] + ogcp2[1];
 669 //              mi = previousw[0];
 670                 mpi = 0;
 671
 672
 673 //              ijppt = ijp[i] + 1;
 674                 mjpt = m + 1;
 675                 prept = previousw;
 676                 curpt = currentw + 1;
 677                 mpjpt = mp + 1;
 678
 679
 680                 lastj = lgth2+1;
 681                 for( j=1; j<lastj; j++ )
 682                 {
 683
 684                         wm = *prept;
 685
 686 #if 0
 687                         fprintf( stderr, "%5.0f->", wm );
 688 #endif
 689                         g = mi + fgcp2[j-1];
 690 //                      g = mi + fpenalty;
 691 #if 0
 692                         fprintf( stderr, "%5.0f?", g );
 693 #endif
 694                         if( g > wm )
 695                         {
 696                                 wm = g;
 697 //                              *ijppt = -( j - mpi );
 698                         }
 699                         g = *prept + ogcp2[j];
 700 //                      g = *prept;
 701                         if( g >= mi )
 702                         {
 703                                 mi = g;
 704                                 mpi = j-1;
 705                         }
 706 #if USE_PENALTY_EX
 707                         mi += fpenalty_ex;
 708 #endif
 709
 710                         g = *mjpt + fgcp1[i-1];
 711 //                      g = *mjpt + fpenalty;
 712 #if 0
 713                         fprintf( stderr, "%5.0f?", g );
 714 #endif
 715                         if( g > wm )
 716                         {
 717                                 wm = g;
 718 //                              *ijppt = +( i - *mpjpt );
 719                         }
 720
 721
 722                         g = *prept + ogcp1[i];
 723 //                      g = *prept;
 724                         if( g >= *mjpt )
 725                         {
 726                                 *mjpt = g;
 727                                 *mpjpt = i-1;
 728                         }
 729 #if USE_PENALTY_EX
 730                         m[j] += fpenalty_ex;
 731 #endif
 732
 733 #if 0
 734                         fprintf( stderr, "%5.0f ", wm );
 735 #endif
 736                         *curpt += wm;
 737
 738 #if STOREWM
 739                         WMMTX[i][j] = *curpt;
 740                         WMMTX2[i][j] = *mjpt;
 741 #endif
 742
 743                         if( i == imid ) //muda
 744                         {
 745                                 jumpbackj[j] = *mpjpt; // muda atode matomeru
 746                                 jumpbacki[j] = mpi; // muda atode matomeru
 747 //                              fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
 748 //                              fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
 749                                 midw[j] = *curpt;
 750                                 midm[j] = *mjpt;
 751                                 midn[j] = mi;
 752                         }
 753
 754 //                      fprintf( stderr, "m[%d] = %f\n", j, m[j] );
 755                         mjpt++;
 756                         prept++;
 757                         mpjpt++;
 758                         curpt++;
 759
 760                 }
 761                 lastverticalw[i] = currentw[lgth2-1];
 762
 763 #if STOREWM
 764                 WMMTX2[i][lgth2] = m[lgth2-1];
 765 #endif
 766
 767 #if 0  // ue
 768                 if( i == imid )
 769                 {
 770                         for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
 771                         for( j=0; j<lgth2; j++ ) midm[j] = m[j];
 772                 }
 773 #endif
 774         }
 775 //      for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
 776 //      for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
 777
 778 #if 0
 779     for( i=0; i<lgth1; i++ )
 780     {
 781         for( j=0; j<lgth2; j++ )
 782         {
 783             fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
 784         }
 785         fprintf( stderr, "\n" );
 786     }
 787         fprintf( stderr, "\n" );
 788         fprintf( stderr, "WMMTX2 = \n" );
 789     for( i=0; i<lgth1; i++ )
 790     {
 791         for( j=0; j<lgth2; j++ )
 792         {
 793             fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
 794         }
 795         fprintf( stderr, "\n" );
 796     }
 797         fprintf( stderr, "\n" );
 798 #endif
 799
 800 // gyakudp
 801
 802         match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
 803         match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
 804
 805         for( i=0; i<lgth1-1; i++ )
 806         {
 807                 initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
 808 //              initverticalw[i] += fpenalty;
 809         }
 810         for( j=0; j<lgth2-1; j++ )
 811         {
 812                 currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
 813 //              currentw[j] += fpenalty;
 814         }
 815
 816 #if STOREWM
 817         for( i=0; i<lgth1-1; i++ )
 818         {
 819                 WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
 820                 fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
 821         }
 822         for( j=0; j<lgth2-1; j++ )
 823         {
 824                 WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
 825                 fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
 826         }
 827 #endif
 828
 829
 830
 831
 832
 833
 834         for( j=lgth2-1; j>0; --j )
 835         {
 836                 m[j-1] = currentw[j] + fgcp2[lgth2-2];
 837 //              m[j-1] = currentw[j];
 838                 mp[j] = lgth1-1;
 839         }
 840
 841 //      for( j=0; j<lgth2; j++ ) m[j] = 0.0;
 842         // m[lgth2-1] ha irunoka?
 843
 844
 845 //      for( i=lgth1-2; i>=imid; i-- )
 846         firstm = -9999999.9;
 847         firstmp = lgth1-1;
 848         for( i=lgth1-2; i>-1; i-- )
 849         {
 850                 wtmp = previousw;
 851                 previousw = currentw;
 852                 currentw = wtmp;
 853                 previousw[lgth2-1] = initverticalw[i+1];
 854 //              match_calc( currentw, seq1, seq2, i, lgth2 );
 855                 match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
 856
 857                 currentw[lgth2-1] = initverticalw[i];
 858
 859 //              m[lgth2] = fgcp1[i];
 860 //              WMMTX2[i][lgth2] += m[lgth2];
 861 //              fprintf( stderr, "m[] = %f\n", m[lgth2] );
 862
 863                 mi = previousw[lgth2-1] + fgcp2[lgth2-2];
 864 //              mi = previousw[lgth2-1];
 865                 mpi = lgth2 - 1;
 866
 867                 mjpt = m + lgth2 - 2;
 868                 prept = previousw + lgth2 - 1;
 869                 curpt = currentw + lgth2 - 2;
 870                 mpjpt = mp + lgth2 - 2;
 871
 872
 873                 for( j=lgth2-2; j>-1; j-- )
 874                 {
 875                         wm = *prept;
 876                         ijpi = i+1;
 877                         ijpj = j+1;
 878
 879                         g = mi + ogcp2[j+1];
 880 //                      g = mi + fpenalty;
 881                         if( g > wm )
 882                         {
 883                                 wm = g;
 884                                 ijpj = mpi;
 885                                 ijpi = i+1;
 886                         }
 887
 888                         g = *prept + fgcp2[j];
 889 //                      g = *prept;
 890                         if( g >= mi )
 891                         {
 892 //                              fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
 893                                 mi = g;
 894                                 mpi = j + 1;
 895                         }
 896
 897 #if USE_PENALTY_EX
 898                         mi += fpenalty_ex;
 899 #endif
 900
 901 //                      fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
 902                         g = *mjpt + ogcp1[i+1];
 903 //                      g = *mjpt + fpenalty;
 904                         if( g > wm )
 905                         {
 906                                 wm = g;
 907                                 ijpi = *mpjpt;
 908                                 ijpj = j+1;
 909                         }
 910
 911 //                      if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
 912                         g = *prept + fgcp1[i];
 913 //                      g = *prept;
 914                         if( g >= *mjpt )
 915                         {
 916                                 *mjpt = g;
 917                                 *mpjpt = i + 1;
 918                         }
 919
 920 #if USE_PENALTY_EX
 921                         m[j] += fpenalty_ex;
 922 #endif
 923
 924                         if( i == jumpi || i == imid - 1 )
 925                         {
 926                                 jumpforwi[j] = ijpi; //muda
 927                                 jumpforwj[j] = ijpj; //muda
 928 //                              fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
 929 //                              fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
 930                         }
 931                         if( i == imid ) // muda
 932                         {
 933                                 midw[j] += wm;
 934 //                              midm[j+1] += *mjpt + fpenalty; //??????
 935                                 midm[j+1] += *mjpt; //??????
 936                         }
 937                         if( i == imid - 1 )
 938                         {
 939 //                              midn[j] += mi + fpenalty;  //????
 940                                 midn[j] += mi;  //????
 941                         }
 942 #if STOREWM
 943                         WMMTX[i][j] += wm;
 944 //                      WMMTX2[i][j+1] += *mjpt + fpenalty;
 945                         WMMTX2[i][j+1] += *mjpt;
 946 #endif
 947                         *curpt += wm;
 948
 949                         mjpt--;
 950                         prept--;
 951                         mpjpt--;
 952                         curpt--;
 953                 }
 954 //              fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
 955                 g = *prept + fgcp1[i];
 956                 if( firstm < g )
 957                 {
 958                         firstm = g;
 959                         firstmp = i + 1;
 960                 }
 961 #if STOREWM
 962                 WMMTX2[i][j+1] += firstm;
 963 #endif
 964                 if( i == imid ) midm[j+1] += firstm;
 965
 966                 if( i == imid - 1 )
 967                 {
 968                         maxwm = midw[1];
 969                         jmid = 0;
 970 //                      if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
 971                         for( j=2; j<lgth2-1; j++ )
 972                         {
 973                                 wm = midw[j];
 974                                 if( wm > maxwm )
 975                                 {
 976                                         jmid = j;
 977                                         maxwm = wm;
 978                                 }
 979 //                              if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
 980                         }
 981                         for( j=0; j<lgth2+1; j++ )
 982                         {
 983                                 wm = midm[j];
 984                                 if( wm > maxwm )
 985                                 {
 986                                         jmid = j;
 987                                         maxwm = wm;
 988                                 }
 989 //                              if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
 990                         }
 991
 992 //                      if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
 993
 994
 995 //                      fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
 996                         wm = midw[jmid];
 997                         jumpi = imid-1;
 998                         jumpj = jmid-1;
 999                         if( jmid > 0 && midn[jmid-1] > wm ) //060413
1000                         {
1001                                 jumpi = imid-1;
1002                                 jumpj = jumpbacki[jmid];
1003                                 wm = midn[jmid-1];
1004 //                              fprintf( stderr, "rejump (n)\n" );
1005                         }
1006                         if( midm[jmid] > wm )
1007                         {
1008                                 jumpi = jumpbackj[jmid];
1009                                 jumpj = jmid-1;
1010                                 wm = midm[jmid];
1011 //                              fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
1012                         }
1013
1014
1015 //                      fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
1016 //                      fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
1017 #if STOREWM
1018                         fprintf( stderr, "imid = %d\n", imid );
1019                         fprintf( stderr, "midn = \n" );
1020                         for( j=0; j<lgth2; j++ )
1021                         {
1022                                 fprintf( stderr, "% 7.1f ", midn[j] );
1023                         }
1024                         fprintf( stderr, "\n" );
1025                         fprintf( stderr, "midw = \n" );
1026                         for( j=0; j<lgth2; j++ )
1027                         {
1028                                 fprintf( stderr, "% 7.1f ", midw[j] );
1029                         }
1030                         fprintf( stderr, "\n" );
1031                         fprintf( stderr, "midm = \n" );
1032                         for( j=0; j<lgth2; j++ )
1033                         {
1034                                 fprintf( stderr, "% 7.1f ", midm[j] );
1035                         }
1036                         fprintf( stderr, "\n" );
1037 #endif
1038 //                      fprintf( stderr, "maxwm = %f\n", maxwm );
1039                 }
1040                 if( i == jumpi ) //saki?
1041                 {
1042 //                      fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
1043 //                      fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
1044                         if( jmid == 0 )
1045                         {
1046 //                              fprintf( stderr, "CHUI2!\n" );
1047                                 jumpj = 0; jmid = 1;
1048                                 jumpi = firstmp - 1;
1049                                 imid = firstmp;
1050                         }
1051
1052 #if 0
1053                         else if( jmid == lgth2 )
1054                         {
1055                                 fprintf( stderr, "CHUI1!\n" );
1056                                 jumpi=0; jumpj=0;
1057                                 imid=jumpforwi[0]; jmid=lgth2-1;
1058                         }
1059 #else // 060414
1060                         else if( jmid >= lgth2 )
1061                         {
1062 //                              fprintf( stderr, "CHUI1!\n" );
1063                                 jumpi=imid-1; jmid=lgth2;
1064                                 jumpj = lgth2-1;
1065                         }
1066 #endif
1067                         else
1068                         {
1069                                 imid = jumpforwi[jumpj];
1070                                 jmid = jumpforwj[jumpj];
1071                         }
1072 #if 0
1073                         fprintf( stderr, "jumpi -> %d\n", jumpi );
1074                         fprintf( stderr, "jumpj -> %d\n", jumpj );
1075                         fprintf( stderr, "imid -> %d\n", imid );
1076                         fprintf( stderr, "jmid -> %d\n", jmid );
1077 #endif
1078
1079 #if STOREWM
1080                         break;
1081 #else
1082                         break;
1083 #endif
1084                 }
1085         }
1086 #if 0
1087                 jumpi=0; jumpj=0;
1088                 imid=lgth1-1; jmid=lgth2-1;
1089         }
1090 #endif
1091
1092 //      fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
1093 //      fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
1094
1095 //      for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
1096 //      for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
1097 //      for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
1098 //      for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
1099
1100
1101 #if STOREWM
1102         fprintf( stderr, "WMMTX = \n" );
1103     for( i=0; i<lgth1; i++ )
1104     {
1105         fprintf( stderr, "%d ", i );
1106         for( j=0; j<lgth2; j++ )
1107         {
1108             fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
1109         }
1110         fprintf( stderr, "\n" );
1111     }
1112 //      fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
1113     for( i=0; i<lgth1; i++ )
1114     {
1115         fprintf( stderr, "%d ", i );
1116         for( j=0; j<lgth2+1; j++ )
1117         {
1118             fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
1119         }
1120         fprintf( stderr, "\n" );
1121     }
1122
1123         fprintf( stderr, "jumpbacki = \n" );
1124         for( j=0; j<lgth2; j++ )
1125         {
1126                 fprintf( stderr, "% 7d ", jumpbacki[j] );
1127         }
1128         fprintf( stderr, "\n" );
1129         fprintf( stderr, "jumpbackj = \n" );
1130         for( j=0; j<lgth2; j++ )
1131         {
1132                 fprintf( stderr, "% 7d ", jumpbackj[j] );
1133         }
1134         fprintf( stderr, "\n" );
1135         fprintf( stderr, "jumpforwi = \n" );
1136         for( j=0; j<lgth2; j++ )
1137         {
1138                 fprintf( stderr, "% 7d ", jumpforwi[j] );
1139         }
1140         fprintf( stderr, "\n" );
1141         fprintf( stderr, "jumpforwj = \n" );
1142         for( j=0; j<lgth2; j++ )
1143         {
1144                 fprintf( stderr, "% 7d ", jumpforwj[j] );
1145         }
1146         fprintf( stderr, "\n" );
1147
1148
1149 #endif
1150
1151
1152 //      Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1153
1154 #if 0 // irukamo
1155         resultlen = strlen( mseq1[0] );
1156         if( alloclen < resultlen || resultlen > N )
1157         {
1158                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
1159                 ErrorExit( "LENGTH OVER!\n" );
1160         }
1161 #endif
1162
1163
1164
1165 #if 0
1166         fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
1167         fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
1168
1169         fprintf( stderr, "imid = %d\n", imid );
1170         fprintf( stderr, "jmid = %d\n", jmid );
1171 #endif
1172
1173
1174         FreeFloatVec( w1 );
1175         FreeFloatVec( w2 );
1176         FreeFloatVec( initverticalw );
1177         FreeFloatVec( lastverticalw );
1178         FreeFloatVec( midw );
1179         FreeFloatVec( midm );
1180         FreeFloatVec( midn );
1181
1182         FreeIntVec( jumpbacki );
1183         FreeIntVec( jumpbackj );
1184         FreeIntVec( jumpforwi );
1185         FreeIntVec( jumpforwj );
1186         FreeIntVec( jumpdummi );
1187         FreeIntVec( jumpdummj );
1188
1189         FreeFloatVec( m );
1190         FreeIntVec( mp );
1191
1192         FreeFloatMtx( floatwork );
1193         FreeIntMtx( intwork );
1194
1195 #if STOREWM
1196         FreeFloatMtx( WMMTX );
1197         FreeFloatMtx( WMMTX2 );
1198 #endif
1199
1200 //      fprintf( stderr, "==== calling myself (first)\n" );
1201
1202 #if 0
1203                 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
1204                 fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
1205 #endif
1206         value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
1207 #if 0
1208                 fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
1209                 fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
1210 #endif
1211 #if MEMSAVE
1212 #else
1213         for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
1214         for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
1215 #endif
1216
1217 //      fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
1218 //      fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
1219
1220         len = strlen( mseq1[0] );
1221 //      fprintf( stderr, "len = %d\n", len );
1222         l = jmid - jumpj - 1;
1223 //      fprintf( stderr, "l=%d\n", l );
1224         if( l > 0 )
1225         {
1226                 for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
1227                 for( i=0; i<icyc; i++ )
1228                 {
1229                         strcat( mseq1[i], gaps );
1230                         mseq1[i][len+l] = 0;
1231                 }
1232                 for( j=0; j<jcyc; j++ )
1233                 {
1234                         strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
1235                         mseq2[j][len+l] = 0;
1236                 }
1237 //              fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
1238                 value +=  ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
1239 //              value += fpenalty;
1240         }
1241         len = strlen( mseq1[0] );
1242         l = imid - jumpi - 1;
1243 //      fprintf( stderr, "l=%d\n", l );
1244         if( l > 0 )
1245         {
1246                 for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
1247                 for( i=0; i<icyc; i++ )
1248                 {
1249                         strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
1250                         mseq1[i][len+l] = 0;
1251                 }
1252                 for( j=0; j<jcyc; j++ )
1253                 {
1254                         strcat( mseq2[j], gaps );
1255                         mseq2[j][len+l] = 0;
1256                 }
1257
1258 //              for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
1259 //              for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
1260
1261
1262 //              fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
1263                 value += ( ogcp1[jumpi+1] + fgcp1[imid-1] );
1264 //              value += fpenalty;
1265         }
1266 #if 0
1267         for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
1268         for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
1269 #endif
1270
1271 //      fprintf( stderr, "==== calling myself (second)\n" );
1272
1273 #if MEMSAVE
1274         alnlen = strlen( aseq1[0] );
1275         for( i=0; i<icyc; i++ ) aseq1[i] += alnlen;
1276         for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen;
1277 #endif
1278
1279 #if 0
1280                 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
1281                 fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
1282 #endif
1283         value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
1284 #if 0
1285                 fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
1286                 fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
1287 #endif
1288
1289
1290
1291 #if DEBUG
1292         if( value - maxwm > 1 || maxwm - value > 1 )
1293         {
1294                 fprintf( stderr, "WARNING value  = %f, but maxwm = %f\n", value, maxwm );
1295                 for( i=0; i<icyc; i++ )
1296                 {
1297                         fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
1298                         fprintf( stderr, "%s\n", aseq1[i] );
1299                 }
1300                 for( i=0; i<jcyc; i++ )
1301                 {
1302                         fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
1303                         fprintf( stderr, "%s\n", aseq2[i] );
1304                 }
1305
1306 //              exit( 1 );
1307         }
1308         else
1309         {
1310                 fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
1311         }
1312 #endif
1313
1314 #if MEMSAVE
1315 #else
1316         for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
1317         for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
1318 #endif
1319
1320 //      fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
1321 //      fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
1322
1323         free( gaps );
1324 #if MEMSAVE
1325         free( aseq1 );
1326         free( aseq2 );
1327 #else
1328         FreeCharMtx( aseq1 );
1329         FreeCharMtx( aseq2 );
1330 #endif
1331
1332         return( value );
1333 }
1334
1335
1336
1337 float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2 )
1338 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
1339 {
1340 //      int k;
1341         int i, j;
1342         int ll1, ll2;
1343         int lgth1, lgth2;
1344         float wm = 0.0;   /* int ?????? */
1345         char **mseq1;
1346         char **mseq2;
1347         float *ogcp1;
1348         float *ogcp2;
1349         float *fgcp1;
1350         float *fgcp2;
1351         float **cpmx1;
1352         float **cpmx2;
1353         float **gapinfo;
1354         float fpenalty = (float)penalty;
1355         int nglen1, nglen2;
1356
1357 #if 0
1358         fprintf( stderr, "eff in SA+++align\n" );
1359         for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
1360 #endif
1361
1362         nglen1 = seqlen( seq1[0] );
1363         nglen2 = seqlen( seq2[0] );
1364
1365         lgth1 = strlen( seq1[0] );
1366         lgth2 = strlen( seq2[0] );
1367
1368         ll1 = ( (int)(lgth1) ) + 100;
1369         ll2 = ( (int)(lgth2) ) + 100;
1370
1371         mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
1372         mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
1373
1374         gapinfo = AllocateFloatMtx( 4, 0 );
1375         ogcp1 = AllocateFloatVec( ll1+2 );
1376         ogcp2 = AllocateFloatVec( ll2+2 );
1377         fgcp1 = AllocateFloatVec( ll1+2 );
1378         fgcp2 = AllocateFloatVec( ll2+2 );
1379
1380
1381         cpmx1 = AllocateFloatMtx( ll1+2, 27 );
1382         cpmx2 = AllocateFloatMtx( ll2+2, 27 );
1383
1384         for( i=0; i<icyc; i++ )
1385         {
1386                 if( strlen( seq1[i] ) != lgth1 )
1387                 {
1388                         fprintf( stderr, "i = %d / %d\n", i, icyc );
1389                         fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
1390                         exit( 1 );
1391                 }
1392         }
1393         for( j=0; j<jcyc; j++ )
1394         {
1395                 if( strlen( seq2[j] ) != lgth2 )
1396                 {
1397                         fprintf( stderr, "j = %d / %d\n", j, jcyc );
1398                         fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
1399                         exit( 1 );
1400                 }
1401         }
1402
1403         MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
1404         MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
1405
1406
1407 #if 1
1408
1409         if( sgap1 )
1410         {
1411                 new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
1412                 new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
1413                 new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
1414                 new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
1415         }
1416         else
1417         {
1418                 st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
1419                 st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
1420                 st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
1421                 st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
1422         }
1423
1424 #if 1
1425         for( i=0; i<lgth1; i++ )
1426         {
1427                 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
1428                 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
1429 //              fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
1430         }
1431         for( i=0; i<lgth2; i++ )
1432         {
1433                 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
1434                 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
1435 //              fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
1436         }
1437 #else
1438         for( i=0; i<lgth1; i++ )
1439         {
1440                 ogcp1[i] = 0.5 * fpenalty;
1441                 fgcp1[i] = 0.5 * fpenalty;
1442         }
1443         for( i=0; i<lgth2; i++ )
1444         {
1445                 ogcp2[i] = 0.5 * fpenalty;
1446                 fgcp2[i] = 0.5 * fpenalty;
1447         }
1448 #endif
1449
1450         gapinfo[0] = ogcp1;
1451         gapinfo[1] = fgcp1;
1452         gapinfo[2] = ogcp2;
1453         gapinfo[3] = fgcp2;
1454 #endif
1455
1456 #if 0
1457         fprintf( stdout, "in MSalignmm.c\n" );
1458         for( i=0; i<icyc; i++ )
1459         {
1460                 fprintf( stdout, ">%d of GROUP1\n", i );
1461                 fprintf( stdout, "%s\n", seq1[i] );
1462         }
1463         for( i=0; i<jcyc; i++ )
1464         {
1465                 fprintf( stdout, ">%d of GROUP2\n", i );
1466                 fprintf( stdout, "%s\n", seq2[i] );
1467         }
1468         fflush( stdout );
1469 #endif
1470
1471         wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
1472 #if DEBUG
1473                 fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
1474                 fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
1475                 fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
1476                 fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
1477 #endif
1478
1479 //      fprintf( stderr, "wm = %f\n", wm );
1480
1481
1482         for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
1483         for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
1484
1485         if( seqlen( seq1[0] ) != nglen1 )
1486         {
1487                 fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
1488                 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
1489                 exit( 1 );
1490         }
1491         if( seqlen( seq2[0] ) != nglen2 )
1492         {
1493                 fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
1494                 exit( 1 );
1495         }
1496
1497         FreeFloatVec( ogcp1 );
1498         FreeFloatVec( ogcp2 );
1499         FreeFloatVec( fgcp1 );
1500         FreeFloatVec( fgcp2 );
1501         FreeFloatMtx( cpmx1 );
1502         FreeFloatMtx( cpmx2 );
1503         free( (void *)gapinfo );
1504
1505         FreeCharMtx( mseq1 );
1506         FreeCharMtx( mseq2 );
1507
1508         lgth1 = strlen( seq1[0] );
1509         lgth2 = strlen( seq2[0] );
1510         for( i=0; i<icyc; i++ )
1511         {
1512                 if( strlen( seq1[i] ) != lgth1 )
1513                 {
1514                         fprintf( stderr, "i = %d / %d\n", i, icyc );
1515                         fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
1516                         exit( 1 );
1517                 }
1518         }
1519         for( j=0; j<jcyc; j++ )
1520         {
1521                 if( strlen( seq2[j] ) != lgth2 )
1522                 {
1523                         fprintf( stderr, "j = %d / %d\n", j, jcyc );
1524                         fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
1525                         exit( 1 );
1526                 }
1527         }
1528
1529         return( wm );
1530 }