binaries/src/mafft/core/SAalignmm.c

   1 #include "mltaln.h"
   2 #include "dp.h"
   3
   4 #define DEBUG 0
   5
   6 static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
   7 {
   8         int j, k, l;
   9         float scarr[26];
  10         float **cpmxpd = floatwork;
  11         int **cpmxpdn = intwork;
  12         int count = 0;
  13
  14         if( initialize )
  15         {
  16                 for( j=0; j<lgth2; j++ )
  17                 {
  18                         count = 0;
  19                         for( l=0; l<26; l++ )
  20                         {
  21                                 if( cpmx2[l][j] )
  22                                 {
  23                                         cpmxpd[count][j] = cpmx2[l][j];
  24                                         cpmxpdn[count][j] = l;
  25                                         count++;
  26                                 }
  27                         }
  28                         cpmxpdn[count][j] = -1;
  29                 }
  30         }
  31
  32         for( l=0; l<26; l++ )
  33         {
  34                 scarr[l] = 0.0;
  35                 for( k=0; k<26; k++ )
  36                         scarr[l] += n_dis[k][l] * cpmx1[k][i1];
  37         }
  38         for( j=0; j<lgth2; j++ )
  39         {
  40                 match[j] = 0;
  41                 for( k=0; cpmxpdn[k][j] > -1;  k++ )
  42                         match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
  43         }
  44 }
  45
  46 static float Atracking( float *lasthorizontalw, float *lastverticalw,
  47                                                 char **seq1, char **seq2,
  48                         char **mseq1, char **mseq2,
  49                         float **cpmx1, float **cpmx2,
  50                         int **ijp, int icyc, int jcyc )
  51 {
  52         int i, j, k, l, iin, jin, ifi, jfi, lgth1, lgth2;
  53 //      char gap[] = "-";
  54         char *gap;
  55         float wm;
  56         gap = newgapstr;
  57         lgth1 = strlen( seq1[0] );
  58         lgth2 = strlen( seq2[0] );
  59
  60 #if DEBUG
  61         for( i=0; i<lgth1; i++ )
  62         {
  63                 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
  64         }
  65 #endif
  66
  67         if( outgap == 1 )
  68                 ;
  69         else
  70         {
  71                 wm = lastverticalw[0];
  72                 for( i=0; i<lgth1; i++ )
  73                 {
  74                         if( lastverticalw[i] >= wm )
  75                         {
  76                                 wm = lastverticalw[i];
  77                                 iin = i; jin = lgth2-1;
  78                                 ijp[lgth1][lgth2] = +( lgth1 - i );
  79                         }
  80                 }
  81                 for( j=0; j<lgth2; j++ )
  82                 {
  83                         if( lasthorizontalw[j] >= wm )
  84                         {
  85                                 wm = lasthorizontalw[j];
  86                                 iin = lgth1-1; jin = j;
  87                                 ijp[lgth1][lgth2] = -( lgth2 - j );
  88                         }
  89                 }
  90         }
  91
  92     for( i=0; i<lgth1+1; i++ )
  93     {
  94         ijp[i][0] = i + 1;
  95     }
  96     for( j=0; j<lgth2+1; j++ )
  97     {
  98         ijp[0][j] = -( j + 1 );
  99     }
 100
 101         for( i=0; i<icyc; i++ )
 102         {
 103                 mseq1[i] += lgth1+lgth2;
 104                 *mseq1[i] = 0;
 105         }
 106         for( j=0; j<jcyc; j++ )
 107         {
 108                 mseq2[j] += lgth1+lgth2;
 109                 *mseq2[j] = 0;
 110         }
 111         iin = lgth1; jin = lgth2;
 112         for( k=0; k<=lgth1+lgth2; k++ )
 113         {
 114                 if( ijp[iin][jin] < 0 )
 115                 {
 116                         ifi = iin-1; jfi = jin+ijp[iin][jin];
 117                 }
 118                 else if( ijp[iin][jin] > 0 )
 119                 {
 120                         ifi = iin-ijp[iin][jin]; jfi = jin-1;
 121                 }
 122                 else
 123                 {
 124                         ifi = iin-1; jfi = jin-1;
 125                 }
 126                 l = iin - ifi;
 127                 while( --l )
 128                 {
 129                         for( i=0; i<icyc; i++ )
 130                                 *--mseq1[i] = seq1[i][ifi+l];
 131                         for( j=0; j<jcyc; j++ )
 132                                 *--mseq2[j] = *gap;
 133                         k++;
 134                 }
 135                 l= jin - jfi;
 136                 while( --l )
 137                 {
 138                         for( i=0; i<icyc; i++ )
 139                                 *--mseq1[i] = *gap;
 140                         for( j=0; j<jcyc; j++ )
 141                                 *--mseq2[j] = seq2[j][jfi+l];
 142                         k++;
 143                 }
 144                 if( iin <= 0 || jin <= 0 ) break;
 145                 for( i=0; i<icyc; i++ )
 146                         *--mseq1[i] = seq1[i][ifi];
 147                 for( j=0; j<jcyc; j++ )
 148                         *--mseq2[j] = seq2[j][jfi];
 149                 k++;
 150                 iin = ifi; jin = jfi;
 151         }
 152         return( 0.0 );
 153 }
 154
 155
 156 float Aalign( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
 157 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 158 {
 159         register int i, j;
 160         int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
 161         int lgth1, lgth2;
 162         int resultlen;
 163         float wm = 0.0;   /* int ?????? */
 164         float g;
 165         float x;
 166         static TLS float mi, *m;
 167         static TLS int **ijp;
 168         static TLS int mpi, *mp;
 169         static TLS float *currentw;
 170         static TLS float *previousw;
 171         static TLS float *match;
 172         static TLS float *initverticalw;    /* kufuu sureba iranai */
 173         static TLS float *lastverticalw;    /* kufuu sureba iranai */
 174         static TLS char **mseq1;
 175         static TLS char **mseq2;
 176         static TLS char **mseq;
 177         static TLS float **cpmx1;
 178         static TLS float **cpmx2;
 179         static TLS int **intwork;
 180         static TLS float **floatwork;
 181         static TLS int orlgth1 = 0, orlgth2 = 0;
 182
 183 #if DEBUG
 184         fprintf( stderr, "eff in SA+++align\n" );
 185         for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
 186 #endif
 187         if( orlgth1 == 0 )
 188         {
 189                 mseq1 = AllocateCharMtx( njob, 1 );
 190                 mseq2 = AllocateCharMtx( njob, 1 ); /* by J. Thompson */
 191         }
 192
 193         lgth1 = strlen( seq1[0] );
 194         lgth2 = strlen( seq2[0] );
 195
 196         if( lgth1 > orlgth1 || lgth2 > orlgth2 )
 197         {
 198                 int ll1, ll2;
 199
 200                 if( orlgth1 > 0 && orlgth2 > 0 )
 201                 {
 202                         FreeFloatVec( currentw );
 203                         FreeFloatVec( previousw );
 204                         FreeFloatVec( match );
 205                         FreeFloatVec( initverticalw );
 206                         FreeFloatVec( lastverticalw );
 207
 208                         FreeFloatVec( m );
 209                         FreeIntVec( mp );
 210
 211                         FreeCharMtx( mseq );
 212
 213                         FreeFloatMtx( cpmx1 );
 214                         FreeFloatMtx( cpmx2 );
 215
 216                         FreeFloatMtx( floatwork );
 217                         FreeIntMtx( intwork );
 218                 }
 219
 220                 ll1 = MAX( (int)(1.1*lgth1), orlgth1 ) + 100;
 221                 ll2 = MAX( (int)(1.1*lgth2), orlgth2 ) + 100;
 222
 223                 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
 224
 225                 currentw = AllocateFloatVec( ll2+2 );
 226                 previousw = AllocateFloatVec( ll2+2 );
 227                 match = AllocateFloatVec( ll2+2 );
 228
 229                 initverticalw = AllocateFloatVec( ll1+2 );
 230                 lastverticalw = AllocateFloatVec( ll1+2 );
 231
 232                 m = AllocateFloatVec( ll2+2 );
 233                 mp = AllocateIntVec( ll2+2 );
 234
 235                 mseq = AllocateCharMtx( njob, ll1+ll2 );
 236
 237                 cpmx1 = AllocateFloatMtx( 26, ll1+2 );
 238                 cpmx2 = AllocateFloatMtx( 26, ll2+2 );
 239
 240                 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
 241                 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
 242
 243                 fprintf( stderr, "succeeded\n" );
 244
 245                 orlgth1 = ll1;
 246                 orlgth2 = ll2;
 247         }
 248
 249         for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
 250         for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
 251
 252
 253         if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
 254         {
 255                 int ll1, ll2;
 256
 257                 if( commonAlloc1 && commonAlloc2 )
 258                 {
 259                         FreeIntMtx( commonIP );
 260                 }
 261
 262                 ll1 = MAX( orlgth1, commonAlloc1 );
 263                 ll2 = MAX( orlgth2, commonAlloc2 );
 264
 265                 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 266
 267                 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
 268
 269                 fprintf( stderr, "succeeded\n\n" );
 270
 271                 commonAlloc1 = ll1;
 272                 commonAlloc2 = ll2;
 273         }
 274         ijp = commonIP;
 275
 276         cpmx_calc( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
 277         cpmx_calc( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
 278
 279         match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
 280         match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
 281
 282         if( outgap == 1 )
 283         {
 284                 for( i=1; i<lgth1+1; i++ )
 285                 {
 286                         initverticalw[i] += penalty * 0.5;
 287                 }
 288                 for( j=1; j<lgth2+1; j++ )
 289                 {
 290                         currentw[j] += penalty * 0.5;
 291                 }
 292         }
 293
 294         for( j=0; j<lgth2+1; ++j )
 295         {
 296                 m[j] = currentw[j-1] + penalty * 0.5; mp[j] = 0;
 297         }
 298
 299         lastverticalw[0] = currentw[lgth2-1];
 300
 301         if( outgap ) lasti = lgth1+1; else lasti = lgth1;
 302
 303         for( i=1; i<lasti; i++ )
 304         {
 305
 306                 floatncpy( previousw, currentw, lgth2+1 );
 307                 previousw[0] = initverticalw[i-1];
 308
 309                 match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
 310                 currentw[0] = initverticalw[i];
 311
 312                 mi = previousw[0] + penalty * 0.5; mpi = 0;
 313                 for( j=1; j<lgth2+1; j++ )
 314                 {
 315                         wm = previousw[j-1];
 316                         ijp[i][j] = 0;
 317
 318                         g = penalty * 0.5;
 319                         x = mi + g;
 320                         if( x > wm )
 321                         {
 322                                 wm = x;
 323                                 ijp[i][j] = -( j - mpi );
 324                         }
 325                         g = penalty * 0.5;
 326                         x = previousw[j-1] + g;
 327                         if( mi <= x )
 328                         {
 329                                 mi = x;
 330                                 mpi = j-1;
 331                         }
 332
 333                         g = penalty * 0.5;
 334                         x = m[j] + g;
 335                         if( x > wm )
 336                         {
 337                                 wm = x;
 338                                 ijp[i][j] = +( i - mp[j] );
 339                         }
 340                         g = penalty * 0.5;
 341                         x = previousw[j-1] + g;
 342                         if( m[j] <= x )
 343                         {
 344                                 m[j] = x;
 345                                 mp[j] = i-1;
 346                         }
 347                         currentw[j] += wm;
 348                 }
 349                 lastverticalw[i] = currentw[lgth2-1];
 350         }
 351         /*
 352         fprintf( stderr, "\n" );
 353         for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
 354         fprintf( stderr, "#####\n" );
 355         for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
 356         fprintf( stderr, "====>" );
 357         for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
 358         for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
 359         */
 360         Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
 361
 362         resultlen = strlen( mseq1[0] );
 363         if( alloclen < resultlen || resultlen > N )
 364         {
 365                 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
 366                 ErrorExit( "LENGTH OVER!\n" );
 367         }
 368
 369         for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
 370         for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
 371         /*
 372         fprintf( stderr, "\n" );
 373         for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
 374         fprintf( stderr, "#####\n" );
 375         for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
 376         */
 377         return( wm );
 378 }