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