binaries/src/mafft/core/MSalign11.c.m

   1 #include "mltaln.h"
   2 #include "dp.h"
   3
   4 #define MEMSAVE 1
   5
   6 #define DEBUG 1
   7 #define USE_PENALTY_EX  0
   8 #define STOREWM 1
   9
  10 #define DPTANNI 10
  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 gap = '-';
 100         char *gaptable1, *gt1bk;
 101         char *gaptable2, *gt2bk;
 102         lgth1 = ien-ist+1;
 103         lgth2 = jen-jst+1;
 104
 105         gt1bk = AllocateCharVec( lgth1+lgth2+1 );
 106         gt2bk = AllocateCharVec( lgth1+lgth2+1 );
 107
 108 #if 0
 109         for( i=0; i<lgth1; i++ )
 110         {
 111                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
 112         }
 113 #endif
 114
 115
 116 //      fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
 117
 118     for( i=0; i<lgth1+1; i++ )
 119     {
 120         ijp[i][0] = i + 1;
 121     }
 122     for( j=0; j<lgth2+1; j++ )
 123     {
 124         ijp[0][j] = -( j + 1 );
 125     }
 126
 127
 128         gaptable1 = gt1bk + lgth1+lgth2;
 129         *gaptable1 = 0;
 130         gaptable2 = gt2bk + lgth1+lgth2;
 131         *gaptable2 = 0;
 132
 133 //      if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
 134
 135         iin = lgth1; jin = lgth2;
 136         klim = lgth1+lgth2;
 137         for( k=0; k<=klim; k++ )
 138         {
 139                 if( ijp[iin][jin] < 0 )
 140                 {
 141                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 142                 }
 143                 else if( ijp[iin][jin] > 0 )
 144                 {
 145                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 146                 }
 147                 else
 148                 {
 149                         ifi = iin-1; jfi = jin-1;
 150                 }
 151                 l = iin - ifi;
 152                 while( --l )
 153                 {
 154                         *--gaptable1 = 'o';
 155                         *--gaptable2 = '-';
 156                         k++;
 157                 }
 158                 l= jin - jfi;
 159                 while( --l )
 160                 {
 161                         *--gaptable1 = '-';
 162                         *--gaptable2 = 'o';
 163                         k++;
 164                 }
 165                 if( iin <= 0 || jin <= 0 ) break;
 166                 *--gaptable1 = 'o';
 167                 *--gaptable2 = 'o';
 168                 k++;
 169                 iin = ifi; jin = jfi;
 170
 171         }
 172
 173         for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 );
 174         for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 );
 175
 176         free( gt1bk );
 177         free( gt2bk );
 178
 179 //      fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
 180 //      fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
 181         return( 0.0 );
 182 }
 183
 184 static float MSalign11_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 )
 185 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 186 {
 187 //      int k;
 188         register int i, j;
 189         int ll1, ll2;
 190         int lasti, lastj;
 191         int resultlen;
 192         float wm = 0.0;   /* int ?????? */
 193         float g;
 194         float *currentw, *previousw;
 195         float fpenalty_ex = (float)penalty_ex;
 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         float dumfl;
 212         int lgth1, lgth2;
 213         float *ogcp1;
 214         float *fgcp1;
 215         float *ogcp2;
 216         float *fgcp2;
 217         char **aseq1;
 218         char **aseq2;
 219         char **aseq1bk, **aseq2bk;
 220
 221         ogcp1 = gapinfo[0] + ist;
 222         fgcp1 = gapinfo[1] + ist;
 223         ogcp2 = gapinfo[2] + jst;
 224         fgcp2 = gapinfo[3] + jst;
 225
 226 #if STOREWM
 227         char ttt1[10000], ttt2[10000];
 228 #endif
 229
 230
 231         lgth1 = ien-ist+1;
 232         lgth2 = jen-jst+1;
 233
 234 #if STOREWM
 235         strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
 236         strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
 237
 238         fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
 239         fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
 240         fprintf( stderr, "ttt1 = %s\n", ttt1 );
 241         fprintf( stderr, "ttt2 = %s\n", ttt2 );
 242 #endif
 243
 244
 245         ll1 = ( (int)(lgth1) ) + 100;
 246         ll2 = ( (int)(lgth2) ) + 100;
 247
 248 //      aseq1 = AllocateCharMtx( icyc, 0 );
 249 //      aseq2 = AllocateCharMtx( jcyc, 0 );
 250 //      aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
 251 //      aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
 252 //      for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
 253 //      for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
 254
 255         w1 = AllocateFloatVec( ll2+2 );
 256         w2 = AllocateFloatVec( ll2+2 );
 257
 258         initverticalw = AllocateFloatVec( ll1+2 );
 259         lastverticalw = AllocateFloatVec( ll1+2 );
 260
 261         m = AllocateFloatVec( ll2+2 );
 262         mp = AllocateIntVec( ll2+2 );
 263
 264         floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
 265         intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
 266
 267
 268         intmtx = AllocateIntMtx( ll1+1, ll2+1 );
 269
 270         ijp = intmtx;
 271
 272         currentw = w1;
 273         previousw = w2;
 274
 275         match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
 276
 277         match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
 278
 279         for( i=1; i<lgth1+1; i++ )
 280         {
 281                 initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
 282         }
 283         for( j=1; j<lgth2+1; j++ )
 284         {
 285                 currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
 286         }
 287
 288         for( j=1; j<lgth2+1; ++j )
 289         {
 290                 m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;;
 291         }
 292
 293         lastverticalw[0] = currentw[lgth2-1];
 294
 295
 296
 297         lasti = lgth1+1;
 298         for( i=1; i<lasti; i++ )
 299         {
 300
 301                 wtmp = previousw;
 302                 previousw = currentw;
 303                 currentw = wtmp;
 304
 305                 previousw[0] = initverticalw[i-1];
 306
 307                 match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
 308                 currentw[0] = initverticalw[i];
 309
 310                 mi = previousw[0] + ogcp2[1];
 311                 mpi = 0;
 312
 313                 ijppt = ijp[i] + 1;
 314                 mjpt = m + 1;
 315                 prept = previousw;
 316                 curpt = currentw + 1;
 317                 mpjpt = mp + 1;
 318                 lastj = lgth2+1;
 319                 for( j=1; j<lastj; j++ )
 320                 {
 321                         wm = *prept;
 322                         *ijppt = 0;
 323
 324 #if 0
 325                         fprintf( stderr, "%5.0f->", wm );
 326 #endif
 327                         g = mi + fgcp2[j-1];
 328 #if 0
 329                         fprintf( stderr, "%5.0f?", g );
 330 #endif
 331                         if( g > wm )
 332                         {
 333                                 wm = g;
 334                                 *ijppt = -( j - mpi );
 335                         }
 336                         g = *prept + ogcp2[j];
 337                         if( g >= mi )
 338                         {
 339                                 mi = g;
 340                                 mpi = j-1;
 341                         }
 342 #if USE_PENALTY_EX
 343                         mi += fpenalty_ex;
 344 #endif
 345
 346                         g = *mjpt + fgcp1[i-1];
 347 #if 0
 348                         fprintf( stderr, "%5.0f?", g );
 349 #endif
 350                         if( g > wm )
 351                         {
 352                                 wm = g;
 353                                 *ijppt = +( i - *mpjpt );
 354                         }
 355                         g = *prept + ogcp1[i];
 356                         if( g >= *mjpt )
 357                         {
 358                                 *mjpt = g;
 359                                 *mpjpt = i-1;
 360                         }
 361 #if USE_PENALTY_EX
 362                         m[j] += fpenalty_ex;
 363 #endif
 364
 365 #if 0
 366                         fprintf( stderr, "%5.0f ", wm );
 367 #endif
 368                         *curpt += wm;
 369
 370
 371                         ijppt++;
 372                         mjpt++;
 373                         prept++;
 374                         mpjpt++;
 375                         curpt++;
 376                 }
 377                 lastverticalw[i] = currentw[lgth2-1];
 378         }
 379
 380 //      fprintf( stderr, "wm = %f\n", wm );
 381
 382         Atracking( seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, ist, ien, jst, jen );
 383
 384 //      for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
 385 //      for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
 386
 387 //      fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
 388 //      fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
 389
 390         FreeFloatVec( w1 );
 391         FreeFloatVec( w2 );
 392         FreeFloatVec( initverticalw );
 393         FreeFloatVec( lastverticalw );
 394
 395         FreeFloatVec( m );
 396         FreeIntVec( mp );
 397
 398
 399         FreeFloatMtx( floatwork );
 400         FreeIntMtx( intwork );
 401
 402         FreeIntMtx( intmtx );
 403
 404 //      FreeCharMtx( aseq1bk );
 405 //      FreeCharMtx( aseq2bk );
 406
 407 //      free( aseq1 );
 408 //      free( aseq2 );
 409
 410         return( wm );
 411
 412 }
 413
 414 static float MSalign11_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 )
 415 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 416 {
 417 //      int k;
 418         int alnlen;
 419         float value = 0.0;
 420         register int i, j;
 421         char **aseq1, **aseq2;
 422         int ll1, ll2, l, len;
 423         int lasti, lastj, imid, jmid;
 424         int resultlen;
 425         float wm = 0.0;   /* int ?????? */
 426         float g;
 427         float *currentw, *previousw;
 428         float fpenalty_ex = (float)penalty_ex;
 429         float *wtmp;
 430 //      short *ijppt;
 431         int *mpjpt;
 432 //      short **ijp;
 433         int *mp;
 434         int mpi;
 435         float *mjpt, *prept, *curpt;
 436         float mi;
 437         float *m;
 438         float *w1, *w2;
 439 //      float *match;
 440         float *initverticalw;    /* kufuu sureba iranai */
 441         float *lastverticalw;    /* kufuu sureba iranai */
 442         int **intwork;
 443         float **floatwork;
 444 //      short **shortmtx;
 445 #if STOREWM
 446         float **WMMTX;
 447         float **WMMTX2;
 448 #endif
 449         float *midw;
 450         float *midm;
 451         float *midn;
 452         float dumfl;
 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; //muda
 461         int jumpi, jumpj;
 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 = MSalign11_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 1
 779         fprintf( stderr, "WMMTX (1) = \n" );
 780     for( i=0; i<lgth1; i++ )
 781     {
 782         for( j=0; j<lgth2; j++ )
 783         {
 784             fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
 785         }
 786         fprintf( stderr, "\n" );
 787     }
 788         fprintf( stderr, "\n" );
 789         fprintf( stderr, "WMMTX2 (1) = \n" );
 790     for( i=0; i<lgth1; i++ )
 791     {
 792         for( j=0; j<lgth2; j++ )
 793         {
 794             fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
 795         }
 796         fprintf( stderr, "\n" );
 797     }
 798         fprintf( stderr, "\n" );
 799 #endif
 800
 801 // gyakudp
 802
 803         match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
 804         match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
 805
 806         for( i=0; i<lgth1-1; i++ )
 807         {
 808                 initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
 809 //              initverticalw[i] += fpenalty;
 810         }
 811         for( j=0; j<lgth2-1; j++ )
 812         {
 813                 currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
 814 //              currentw[j] += fpenalty;
 815         }
 816
 817 #if STOREWM
 818         for( i=0; i<lgth1-1; i++ )
 819         {
 820                 WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
 821                 fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
 822         }
 823         for( j=0; j<lgth2-1; j++ )
 824         {
 825                 WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
 826                 fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
 827         }
 828 #endif
 829
 830
 831
 832
 833
 834
 835         for( j=lgth2-1; j>0; --j )
 836         {
 837                 m[j-1] = currentw[j] + fgcp2[lgth2-2];
 838 //              m[j-1] = currentw[j];
 839                 mp[j] = lgth1-1;
 840         }
 841
 842 //      for( j=0; j<lgth2; j++ ) m[j] = 0.0;
 843         // m[lgth2-1] ha irunoka?
 844
 845
 846 //      for( i=lgth1-2; i>=imid; i-- )
 847         firstm = -9999999.9;
 848         firstmp = lgth1-1;
 849         for( i=lgth1-2; i>-1; i-- )
 850         {
 851                 wtmp = previousw;
 852                 previousw = currentw;
 853                 currentw = wtmp;
 854                 previousw[lgth2-1] = initverticalw[i+1];
 855 //              match_calc( currentw, seq1, seq2, i, lgth2 );
 856                 match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
 857
 858                 currentw[lgth2-1] = initverticalw[i];
 859
 860 //              m[lgth2] = fgcp1[i];
 861 //              WMMTX2[i][lgth2] += m[lgth2];
 862 //              fprintf( stderr, "m[] = %f\n", m[lgth2] );
 863
 864                 mi = previousw[lgth2-1] + fgcp2[lgth2-2];
 865 //              mi = previousw[lgth2-1];
 866                 mpi = lgth2 - 1;
 867
 868                 mjpt = m + lgth2 - 2;
 869                 prept = previousw + lgth2 - 1;
 870                 curpt = currentw + lgth2 - 2;
 871                 mpjpt = mp + lgth2 - 2;
 872
 873
 874                 for( j=lgth2-2; j>-1; j-- )
 875                 {
 876                         wm = *prept;
 877                         ijpi = i+1;
 878                         ijpj = j+1;
 879
 880                         g = mi + ogcp2[j+1];
 881 //                      g = mi + fpenalty;
 882                         if( g > wm )
 883                         {
 884                                 wm = g;
 885                                 ijpj = mpi;
 886                                 ijpi = i+1;
 887                         }
 888
 889                         g = *prept + fgcp2[j];
 890 //                      g = *prept;
 891                         if( g >= mi )
 892                         {
 893 //                              fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
 894                                 mi = g;
 895                                 mpi = j + 1;
 896                         }
 897
 898 #if USE_PENALTY_EX
 899                         mi += fpenalty_ex;
 900 #endif
 901
 902 //                      fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
 903                         g = *mjpt + ogcp1[i+1];
 904 //                      g = *mjpt + fpenalty;
 905                         if( g > wm )
 906                         {
 907                                 wm = g;
 908                                 ijpi = *mpjpt;
 909                                 ijpj = j+1;
 910                         }
 911
 912 //                      if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
 913                         g = *prept + fgcp1[i];
 914 //                      g = *prept;
 915                         if( g >= *mjpt )
 916                         {
 917                                 *mjpt = g;
 918                                 *mpjpt = i + 1;
 919                         }
 920
 921 #if USE_PENALTY_EX
 922                         m[j] += fpenalty_ex;
 923 #endif
 924
 925                         if( i == jumpi || i == imid - 1 )
 926                         {
 927                                 jumpforwi[j] = ijpi; //muda
 928                                 jumpforwj[j] = ijpj; //muda
 929 //                              fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
 930 //                              fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
 931                         }
 932                         if( i == imid ) // muda
 933                         {
 934                                 midw[j] += wm;
 935 //                              midm[j+1] += *mjpt + fpenalty; //??????
 936                                 midm[j+1] += *mjpt; //??????
 937                         }
 938                         if( i == imid - 1 )
 939                         {
 940 //                              midn[j] += mi + fpenalty;  //????
 941                                 midn[j] += mi;  //????
 942                         }
 943 #if STOREWM
 944                         WMMTX[i][j] += wm;
 945 //                      WMMTX2[i][j+1] += *mjpt + fpenalty;
 946                         WMMTX2[i][j+1] += *mjpt;
 947 #endif
 948                         *curpt += wm;
 949
 950                         mjpt--;
 951                         prept--;
 952                         mpjpt--;
 953                         curpt--;
 954                 }
 955 //              fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
 956                 g = *prept + fgcp1[i];
 957                 if( firstm < g )
 958                 {
 959                         firstm = g;
 960                         firstmp = i + 1;
 961                 }
 962 #if STOREWM
 963                 WMMTX2[i][j+1] += firstm;
 964 #endif
 965                 if( i == imid ) midm[j+1] += firstm;
 966
 967                 if( i == imid - 1 )
 968                 {
 969                         maxwm = midw[1];
 970                         jmid = 0;
 971 //                      if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
 972                         for( j=2; j<lgth2-1; j++ )
 973                         {
 974                                 wm = midw[j];
 975                                 if( wm > maxwm )
 976                                 {
 977                                         jmid = j;
 978                                         maxwm = wm;
 979                                 }
 980 //                              if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
 981                         }
 982                         for( j=0; j<lgth2+1; j++ )
 983                         {
 984                                 wm = midm[j];
 985                                 if( wm > maxwm )
 986                                 {
 987                                         jmid = j;
 988                                         maxwm = wm;
 989                                 }
 990 //                              if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
 991                         }
 992
 993 //                      if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
 994
 995
 996 //                      fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
 997                         wm = midw[jmid];
 998                         jumpi = imid-1;
 999                         jumpj = jmid-1;
1000                         if( jmid > 0 && midn[jmid-1] > wm ) //060413
1001                         {
1002                                 jumpi = imid-1;
1003                                 jumpj = jumpbacki[jmid];
1004                                 wm = midn[jmid-1];
1005 //                              fprintf( stderr, "rejump (n)\n" );
1006                         }
1007                         if( midm[jmid] > wm )
1008                         {
1009                                 jumpi = jumpbackj[jmid];
1010                                 jumpj = jmid-1;
1011                                 wm = midm[jmid];
1012 //                              fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
1013                         }
1014
1015
1016 //                      fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
1017 //                      fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
1018 #if STOREWM
1019                         fprintf( stderr, "imid = %d\n", imid );
1020                         fprintf( stderr, "midn = \n" );
1021                         for( j=0; j<lgth2; j++ )
1022                         {
1023                                 fprintf( stderr, "% 7.1f ", midn[j] );
1024                         }
1025                         fprintf( stderr, "\n" );
1026                         fprintf( stderr, "midw = \n" );
1027                         for( j=0; j<lgth2; j++ )
1028                         {
1029                                 fprintf( stderr, "% 7.1f ", midw[j] );
1030                         }
1031                         fprintf( stderr, "\n" );
1032                         fprintf( stderr, "midm = \n" );
1033                         for( j=0; j<lgth2; j++ )
1034                         {
1035                                 fprintf( stderr, "% 7.1f ", midm[j] );
1036                         }
1037                         fprintf( stderr, "\n" );
1038 #endif
1039 //                      fprintf( stderr, "maxwm = %f\n", maxwm );
1040                 }
1041                 if( i == jumpi ) //saki?
1042                 {
1043 //                      fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
1044 //                      fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
1045                         if( jmid == 0 )
1046                         {
1047 //                              fprintf( stderr, "CHUI2!\n" );
1048                                 jumpj = 0; jmid = 1;
1049                                 jumpi = firstmp - 1;
1050                                 imid = firstmp;
1051                         }
1052
1053 #if 0
1054                         else if( jmid == lgth2 )
1055                         {
1056                                 fprintf( stderr, "CHUI1!\n" );
1057                                 jumpi=0; jumpj=0;
1058                                 imid=jumpforwi[0]; jmid=lgth2-1;
1059                         }
1060 #else // 060414
1061                         else if( jmid >= lgth2 )
1062                         {
1063 //                              fprintf( stderr, "CHUI1!\n" );
1064                                 jumpi=imid-1; jmid=lgth2;
1065                                 jumpj = lgth2-1;
1066                         }
1067 #endif
1068                         else
1069                         {
1070                                 imid = jumpforwi[jumpj];
1071                                 jmid = jumpforwj[jumpj];
1072                         }
1073 #if 0
1074                         fprintf( stderr, "jumpi -> %d\n", jumpi );
1075                         fprintf( stderr, "jumpj -> %d\n", jumpj );
1076                         fprintf( stderr, "imid -> %d\n", imid );
1077                         fprintf( stderr, "jmid -> %d\n", jmid );
1078 #endif
1079
1080 #if STOREWM
1081 //                      break;
1082 #else
1083                         break;
1084 #endif
1085                 }
1086         }
1087 #if 0
1088                 jumpi=0; jumpj=0;
1089                 imid=lgth1-1; jmid=lgth2-1;
1090         }
1091 #endif
1092
1093 //      fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
1094 //      fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
1095
1096 //      for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
1097 //      for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
1098 //      for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
1099 //      for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
1100
1101
1102 #if STOREWM
1103         fprintf( stderr, "WMMTX = \n" );
1104     for( i=0; i<lgth1; i++ )
1105     {
1106 //        fprintf( stderr, "%d ", i );
1107         for( j=0; j<lgth2; j++ )
1108         {
1109             fprintf( stderr, "%d %d % 10.2f\n", i, j, WMMTX[i][j] );
1110         }
1111         fprintf( stderr, "\n" );
1112     }
1113         fprintf( stderr, "WMMTX2 = \n" );
1114     for( i=0; i<lgth1; i++ )
1115     {
1116         fprintf( stderr, "%d ", i );
1117         for( j=0; j<lgth2+1; j++ )
1118         {
1119             fprintf( stderr, "% 10.2f", WMMTX2[i][j] );
1120         }
1121         fprintf( stderr, "\n" );
1122     }
1123
1124         fprintf( stderr, "jumpbacki = \n" );
1125         for( j=0; j<lgth2; j++ )
1126         {
1127                 fprintf( stderr, "% 7d ", jumpbacki[j] );
1128         }
1129         fprintf( stderr, "\n" );
1130         fprintf( stderr, "jumpbackj = \n" );
1131         for( j=0; j<lgth2; j++ )
1132         {
1133                 fprintf( stderr, "% 7d ", jumpbackj[j] );
1134         }
1135         fprintf( stderr, "\n" );
1136         fprintf( stderr, "jumpforwi = \n" );
1137         for( j=0; j<lgth2; j++ )
1138         {
1139                 fprintf( stderr, "% 7d ", jumpforwi[j] );
1140         }
1141         fprintf( stderr, "\n" );
1142         fprintf( stderr, "jumpforwj = \n" );
1143         for( j=0; j<lgth2; j++ )
1144         {
1145                 fprintf( stderr, "% 7d ", jumpforwj[j] );
1146         }
1147         fprintf( stderr, "\n" );
1148
1149
1150 #endif
1151
1152
1153 //      Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1154
1155 #if 0 // irukamo
1156         resultlen = strlen( mseq1[0] );
1157         if( alloclen < resultlen || resultlen > N )
1158         {
1159                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
1160                 ErrorExit( "LENGTH OVER!\n" );
1161         }
1162 #endif
1163
1164
1165
1166 #if 0
1167         fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
1168         fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
1169
1170         fprintf( stderr, "imid = %d\n", imid );
1171         fprintf( stderr, "jmid = %d\n", jmid );
1172 #endif
1173
1174
1175         FreeFloatVec( w1 );
1176         FreeFloatVec( w2 );
1177         FreeFloatVec( initverticalw );
1178         FreeFloatVec( lastverticalw );
1179         FreeFloatVec( midw );
1180         FreeFloatVec( midm );
1181         FreeFloatVec( midn );
1182
1183         FreeIntVec( jumpbacki );
1184         FreeIntVec( jumpbackj );
1185         FreeIntVec( jumpforwi );
1186         FreeIntVec( jumpforwj );
1187         FreeIntVec( jumpdummi );
1188         FreeIntVec( jumpdummj );
1189
1190         FreeFloatVec( m );
1191         FreeIntVec( mp );
1192
1193         FreeFloatMtx( floatwork );
1194         FreeIntMtx( intwork );
1195
1196 #if STOREWM
1197         FreeFloatMtx( WMMTX );
1198         FreeFloatMtx( WMMTX2 );
1199 #endif
1200
1201 //      fprintf( stderr, "==== calling myself (first)\n" );
1202
1203 #if 0
1204                 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
1205                 fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
1206 #endif
1207         value = MSalign11_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
1208 #if 0
1209                 fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
1210                 fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
1211 #endif
1212 #if MEMSAVE
1213 #else
1214         for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
1215         for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
1216 #endif
1217
1218 //      fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
1219 //      fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
1220
1221         len = strlen( mseq1[0] );
1222 //      fprintf( stderr, "len = %d\n", len );
1223         l = jmid - jumpj - 1;
1224 //      fprintf( stderr, "l=%d\n", l );
1225         if( l > 0 )
1226         {
1227                 for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
1228                 for( i=0; i<icyc; i++ )
1229                 {
1230                         strcat( mseq1[i], gaps );
1231                         mseq1[i][len+l] = 0;
1232                 }
1233                 for( j=0; j<jcyc; j++ )
1234                 {
1235                         strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
1236                         mseq2[j][len+l] = 0;
1237                 }
1238 //              fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
1239                 value +=  ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
1240 //              value += fpenalty;
1241         }
1242         len = strlen( mseq1[0] );
1243         l = imid - jumpi - 1;
1244 //      fprintf( stderr, "l=%d\n", l );
1245         if( l > 0 )
1246         {
1247                 for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
1248                 for( i=0; i<icyc; i++ )
1249                 {
1250                         strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
1251                         mseq1[i][len+l] = 0;
1252                 }
1253                 for( j=0; j<jcyc; j++ )
1254                 {
1255                         strcat( mseq2[j], gaps );
1256                         mseq2[j][len+l] = 0;
1257                 }
1258
1259 //              for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
1260 //              for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
1261
1262
1263 //              fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
1264                 value += ( ogcp1[jumpi+1] + fgcp1[imid-1] );
1265 //              value += fpenalty;
1266         }
1267 #if 0
1268         for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
1269         for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
1270 #endif
1271
1272 //      fprintf( stderr, "==== calling myself (second)\n" );
1273
1274 #if MEMSAVE
1275         alnlen = strlen( aseq1[0] );
1276         for( i=0; i<icyc; i++ ) aseq1[i] += alnlen;
1277         for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen;
1278 #endif
1279
1280 #if 0
1281                 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
1282                 fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
1283 #endif
1284         value += MSalign11_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
1285 #if 0
1286                 fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
1287                 fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
1288 #endif
1289
1290
1291
1292 #if DEBUG
1293         if( value - maxwm > 1 || maxwm - value > 1 )
1294         {
1295                 fprintf( stderr, "WARNING value  = %f, but maxwm = %f\n", value, maxwm );
1296                 for( i=0; i<icyc; i++ )
1297                 {
1298                         fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
1299                         fprintf( stderr, "%s\n", aseq1[i] );
1300                 }
1301                 for( i=0; i<jcyc; i++ )
1302                 {
1303                         fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
1304                         fprintf( stderr, "%s\n", aseq2[i] );
1305                 }
1306
1307 //              exit( 1 );
1308         }
1309         else
1310         {
1311                 fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
1312         }
1313 #endif
1314
1315 #if MEMSAVE
1316 #else
1317         for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
1318         for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
1319 #endif
1320
1321 //      fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
1322 //      fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
1323
1324         free( gaps );
1325 #if MEMSAVE
1326         free( aseq1 );
1327         free( aseq2 );
1328 #else
1329         FreeCharMtx( aseq1 );
1330         FreeCharMtx( aseq2 );
1331 #endif
1332
1333         return( value );
1334 }
1335
1336
1337
1338 float MSalign11( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2 )
1339 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
1340 {
1341 //      int k;
1342         int i, j;
1343         int ll1, ll2;
1344         int lgth1, lgth2;
1345         float wm = 0.0;   /* int ?????? */
1346         char **mseq1;
1347         char **mseq2;
1348         char **mseq;
1349         float *ogcp1;
1350         float *ogcp2;
1351         float *fgcp1;
1352         float *fgcp2;
1353         float **cpmx1;
1354         float **cpmx2;
1355         float **gapinfo;
1356         float fpenalty = (float)penalty;
1357         int nglen1, nglen2;
1358
1359 #if 0
1360         fprintf( stderr, "eff in SA+++align\n" );
1361         for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
1362 #endif
1363
1364         nglen1 = seqlen( seq1[0] );
1365         nglen2 = seqlen( seq2[0] );
1366
1367         lgth1 = strlen( seq1[0] );
1368         lgth2 = strlen( seq2[0] );
1369
1370         ll1 = ( (int)(lgth1) ) + 100;
1371         ll2 = ( (int)(lgth2) ) + 100;
1372
1373         mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
1374         mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
1375
1376         gapinfo = AllocateFloatMtx( 4, 0 );
1377         ogcp1 = AllocateFloatVec( ll1+2 );
1378         ogcp2 = AllocateFloatVec( ll2+2 );
1379         fgcp1 = AllocateFloatVec( ll1+2 );
1380         fgcp2 = AllocateFloatVec( ll2+2 );
1381
1382
1383         cpmx1 = AllocateFloatMtx( ll1+2, 27 );
1384         cpmx2 = AllocateFloatMtx( ll2+2, 27 );
1385
1386         for( i=0; i<icyc; i++ )
1387         {
1388                 if( strlen( seq1[i] ) != lgth1 )
1389                 {
1390                         fprintf( stderr, "i = %d / %d\n", i, icyc );
1391                         fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
1392                         exit( 1 );
1393                 }
1394         }
1395         for( j=0; j<jcyc; j++ )
1396         {
1397                 if( strlen( seq2[j] ) != lgth2 )
1398                 {
1399                         fprintf( stderr, "j = %d / %d\n", j, jcyc );
1400                         fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
1401                         exit( 1 );
1402                 }
1403         }
1404
1405         MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
1406         MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
1407
1408
1409 #if 1
1410
1411         if( sgap1 )
1412         {
1413                 new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
1414                 new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
1415                 new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
1416                 new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
1417         }
1418         else
1419         {
1420                 st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
1421                 st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
1422                 st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
1423                 st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
1424         }
1425
1426 #if 1
1427         for( i=0; i<lgth1; i++ )
1428         {
1429                 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
1430                 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
1431 //              fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
1432         }
1433         for( i=0; i<lgth2; i++ )
1434         {
1435                 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
1436                 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
1437 //              fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
1438         }
1439 #else
1440         for( i=0; i<lgth1; i++ )
1441         {
1442                 ogcp1[i] = 0.5 * fpenalty;
1443                 fgcp1[i] = 0.5 * fpenalty;
1444         }
1445         for( i=0; i<lgth2; i++ )
1446         {
1447                 ogcp2[i] = 0.5 * fpenalty;
1448                 fgcp2[i] = 0.5 * fpenalty;
1449         }
1450 #endif
1451
1452         gapinfo[0] = ogcp1;
1453         gapinfo[1] = fgcp1;
1454         gapinfo[2] = ogcp2;
1455         gapinfo[3] = fgcp2;
1456 #endif
1457
1458 #if 0
1459         fprintf( stdout, "in MSalign11.c\n" );
1460         for( i=0; i<icyc; i++ )
1461         {
1462                 fprintf( stdout, ">%d of GROUP1\n", i );
1463                 fprintf( stdout, "%s\n", seq1[i] );
1464         }
1465         for( i=0; i<jcyc; i++ )
1466         {
1467                 fprintf( stdout, ">%d of GROUP2\n", i );
1468                 fprintf( stdout, "%s\n", seq2[i] );
1469         }
1470         fflush( stdout );
1471 #endif
1472
1473         wm = MSalign11_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
1474 #if DEBUG
1475                 fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
1476                 fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
1477                 fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
1478                 fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
1479 #endif
1480
1481 //      fprintf( stderr, "wm = %f\n", wm );
1482
1483
1484         for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
1485         for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
1486
1487         if( seqlen( seq1[0] ) != nglen1 )
1488         {
1489                 fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
1490                 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
1491                 exit( 1 );
1492         }
1493         if( seqlen( seq2[0] ) != nglen2 )
1494         {
1495                 fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
1496                 exit( 1 );
1497         }
1498
1499         FreeFloatVec( ogcp1 );
1500         FreeFloatVec( ogcp2 );
1501         FreeFloatVec( fgcp1 );
1502         FreeFloatVec( fgcp2 );
1503         FreeFloatMtx( cpmx1 );
1504         FreeFloatMtx( cpmx2 );
1505         free( (void *)gapinfo );
1506
1507         FreeCharMtx( mseq1 );
1508         FreeCharMtx( mseq2 );
1509
1510         lgth1 = strlen( seq1[0] );
1511         lgth2 = strlen( seq2[0] );
1512         for( i=0; i<icyc; i++ )
1513         {
1514                 if( strlen( seq1[i] ) != lgth1 )
1515                 {
1516                         fprintf( stderr, "i = %d / %d\n", i, icyc );
1517                         fprintf( stderr, "hairetsu ga kowareta (end of MSalign11) !\n" );
1518                         exit( 1 );
1519                 }
1520         }
1521         for( j=0; j<jcyc; j++ )
1522         {
1523                 if( strlen( seq2[j] ) != lgth2 )
1524                 {
1525                         fprintf( stderr, "j = %d / %d\n", j, jcyc );
1526                         fprintf( stderr, "hairetsu ga kowareta (end of MSalign11) !\n" );
1527                         exit( 1 );
1528                 }
1529         }
1530
1531         return( wm );
1532 }