| #include "mltaln.h" |
| #include "dp.h" |
| |
| #define DEBUG 0 |
| |
| static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize ) |
| { |
| int j, k, l; |
| float scarr[26]; |
| float **cpmxpd = floatwork; |
| int **cpmxpdn = intwork; |
| int count = 0; |
| |
| if( initialize ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| count = 0; |
| for( l=0; l<26; l++ ) |
| { |
| if( cpmx2[l][j] ) |
| { |
| cpmxpd[count][j] = cpmx2[l][j]; |
| cpmxpdn[count][j] = l; |
| count++; |
| } |
| } |
| cpmxpdn[count][j] = -1; |
| } |
| } |
| |
| for( l=0; l<26; l++ ) |
| { |
| scarr[l] = 0.0; |
| for( k=0; k<26; k++ ) |
| scarr[l] += n_dis[k][l] * cpmx1[k][i1]; |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| match[j] = 0; |
| for( k=0; cpmxpdn[k][j] > -1; k++ ) |
| match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j]; |
| } |
| } |
| |
| static float Atracking( float *lasthorizontalw, float *lastverticalw, |
| char **seq1, char **seq2, |
| char **mseq1, char **mseq2, |
| float **cpmx1, float **cpmx2, |
| int **ijp, int icyc, int jcyc ) |
| { |
| int i, j, k, l, iin, jin, ifi, jfi, lgth1, lgth2; |
| char gap[] = "-"; |
| float wm; |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| #if DEBUG |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] ); |
| } |
| #endif |
| |
| if( outgap == 1 ) |
| ; |
| else |
| { |
| wm = lastverticalw[0]; |
| for( i=0; i<lgth1; i++ ) |
| { |
| if( lastverticalw[i] >= wm ) |
| { |
| wm = lastverticalw[i]; |
| iin = i; jin = lgth2-1; |
| ijp[lgth1][lgth2] = +( lgth1 - i ); |
| } |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| if( lasthorizontalw[j] >= wm ) |
| { |
| wm = lasthorizontalw[j]; |
| iin = lgth1-1; jin = j; |
| ijp[lgth1][lgth2] = -( lgth2 - j ); |
| } |
| } |
| } |
| |
| for( i=0; i<lgth1+1; i++ ) |
| { |
| ijp[i][0] = i + 1; |
| } |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| ijp[0][j] = -( j + 1 ); |
| } |
| |
| for( i=0; i<icyc; i++ ) |
| { |
| mseq1[i] += lgth1+lgth2; |
| *mseq1[i] = 0; |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| mseq2[j] += lgth1+lgth2; |
| *mseq2[j] = 0; |
| } |
| iin = lgth1; jin = lgth2; |
| for( k=0; k<=lgth1+lgth2; k++ ) |
| { |
| if( ijp[iin][jin] < 0 ) |
| { |
| ifi = iin-1; jfi = jin+ijp[iin][jin]; |
| } |
| else if( ijp[iin][jin] > 0 ) |
| { |
| ifi = iin-ijp[iin][jin]; jfi = jin-1; |
| } |
| else |
| { |
| ifi = iin-1; jfi = jin-1; |
| } |
| l = iin - ifi; |
| while( --l ) |
| { |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = seq1[i][ifi+l]; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = *gap; |
| k++; |
| } |
| l= jin - jfi; |
| while( --l ) |
| { |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = *gap; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = seq2[j][jfi+l]; |
| k++; |
| } |
| if( iin <= 0 || jin <= 0 ) break; |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = seq1[i][ifi]; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = seq2[j][jfi]; |
| k++; |
| iin = ifi; jin = jfi; |
| } |
| return( 0.0 ); |
| } |
| |
| |
| float Aalign( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen ) |
| /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ |
| { |
| register int i, j; |
| int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */ |
| int lgth1, lgth2; |
| int resultlen; |
| float wm = 0.0; /* int ?????? */ |
| float g; |
| float x; |
| static float mi, *m; |
| static int **ijp; |
| static int mpi, *mp; |
| static float *currentw; |
| static float *previousw; |
| static float *match; |
| static float *initverticalw; /* kufuu sureba iranai */ |
| static float *lastverticalw; /* kufuu sureba iranai */ |
| static char **mseq1; |
| static char **mseq2; |
| static char **mseq; |
| static float **cpmx1; |
| static float **cpmx2; |
| static int **intwork; |
| static float **floatwork; |
| static int orlgth1 = 0, orlgth2 = 0; |
| |
| #if DEBUG |
| fprintf( stderr, "eff in SA+++align\n" ); |
| for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] ); |
| #endif |
| if( orlgth1 == 0 ) |
| { |
| mseq1 = AllocateCharMtx( njob, 1 ); |
| mseq2 = AllocateCharMtx( njob, 1 ); /* by J. Thompson */ |
| } |
| |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| if( lgth1 > orlgth1 || lgth2 > orlgth2 ) |
| { |
| int ll1, ll2; |
| |
| if( orlgth1 > 0 && orlgth2 > 0 ) |
| { |
| FreeFloatVec( currentw ); |
| FreeFloatVec( previousw ); |
| FreeFloatVec( match ); |
| FreeFloatVec( initverticalw ); |
| FreeFloatVec( lastverticalw ); |
| |
| FreeFloatVec( m ); |
| FreeIntVec( mp ); |
| |
| FreeCharMtx( mseq ); |
| |
| FreeFloatMtx( cpmx1 ); |
| FreeFloatMtx( cpmx2 ); |
| |
| FreeFloatMtx( floatwork ); |
| FreeIntMtx( intwork ); |
| } |
| |
| ll1 = MAX( (int)(1.1*lgth1), orlgth1 ) + 100; |
| ll2 = MAX( (int)(1.1*lgth2), orlgth2 ) + 100; |
| |
| fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 ); |
| |
| currentw = AllocateFloatVec( ll2+2 ); |
| previousw = AllocateFloatVec( ll2+2 ); |
| match = AllocateFloatVec( ll2+2 ); |
| |
| initverticalw = AllocateFloatVec( ll1+2 ); |
| lastverticalw = AllocateFloatVec( ll1+2 ); |
| |
| m = AllocateFloatVec( ll2+2 ); |
| mp = AllocateIntVec( ll2+2 ); |
| |
| mseq = AllocateCharMtx( njob, ll1+ll2 ); |
| |
| cpmx1 = AllocateFloatMtx( 26, ll1+2 ); |
| cpmx2 = AllocateFloatMtx( 26, ll2+2 ); |
| |
| floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); |
| intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 ); |
| |
| fprintf( stderr, "succeeded\n" ); |
| |
| orlgth1 = ll1; |
| orlgth2 = ll2; |
| } |
| |
| for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i]; |
| for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j]; |
| |
| |
| if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 ) |
| { |
| int ll1, ll2; |
| |
| if( commonAlloc1 && commonAlloc2 ) |
| { |
| FreeIntMtx( commonIP ); |
| } |
| |
| ll1 = MAX( orlgth1, commonAlloc1 ); |
| ll2 = MAX( orlgth2, commonAlloc2 ); |
| |
| fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 ); |
| |
| commonIP = AllocateIntMtx( ll1+10, ll2+10 ); |
| |
| fprintf( stderr, "succeeded\n\n" ); |
| |
| commonAlloc1 = ll1; |
| commonAlloc2 = ll2; |
| } |
| ijp = commonIP; |
| |
| cpmx_calc( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc ); |
| cpmx_calc( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc ); |
| |
| match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 ); |
| match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 ); |
| |
| if( outgap == 1 ) |
| { |
| for( i=1; i<lgth1+1; i++ ) |
| { |
| initverticalw[i] += penalty * 0.5; |
| } |
| for( j=1; j<lgth2+1; j++ ) |
| { |
| currentw[j] += penalty * 0.5; |
| } |
| } |
| |
| for( j=0; j<lgth2+1; ++j ) |
| { |
| m[j] = currentw[j-1] + penalty * 0.5; mp[j] = 0; |
| } |
| |
| lastverticalw[0] = currentw[lgth2-1]; |
| |
| if( outgap ) lasti = lgth1+1; else lasti = lgth1; |
| |
| for( i=1; i<lasti; i++ ) |
| { |
| |
| floatncpy( previousw, currentw, lgth2+1 ); |
| previousw[0] = initverticalw[i-1]; |
| |
| match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 ); |
| currentw[0] = initverticalw[i]; |
| |
| mi = previousw[0] + penalty * 0.5; mpi = 0; |
| for( j=1; j<lgth2+1; j++ ) |
| { |
| wm = previousw[j-1]; |
| ijp[i][j] = 0; |
| |
| g = penalty * 0.5; |
| x = mi + g; |
| if( x > wm ) |
| { |
| wm = x; |
| ijp[i][j] = -( j - mpi ); |
| } |
| g = penalty * 0.5; |
| x = previousw[j-1] + g; |
| if( mi <= x ) |
| { |
| mi = x; |
| mpi = j-1; |
| } |
| |
| g = penalty * 0.5; |
| x = m[j] + g; |
| if( x > wm ) |
| { |
| wm = x; |
| ijp[i][j] = +( i - mp[j] ); |
| } |
| g = penalty * 0.5; |
| x = previousw[j-1] + g; |
| if( m[j] <= x ) |
| { |
| m[j] = x; |
| mp[j] = i-1; |
| } |
| currentw[j] += wm; |
| } |
| lastverticalw[i] = currentw[lgth2-1]; |
| } |
| /* |
| fprintf( stderr, "\n" ); |
| for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] ); |
| fprintf( stderr, "#####\n" ); |
| for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] ); |
| fprintf( stderr, "====>" ); |
| for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] ); |
| for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] ); |
| */ |
| Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc ); |
| |
| resultlen = strlen( mseq1[0] ); |
| if( alloclen < resultlen || resultlen > N ) |
| { |
| fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N ); |
| ErrorExit( "LENGTH OVER!\n" ); |
| } |
| |
| for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] ); |
| for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] ); |
| /* |
| fprintf( stderr, "\n" ); |
| for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] ); |
| fprintf( stderr, "#####\n" ); |
| for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] ); |
| */ |
| return( wm ); |
| } |