| #include "mltaln.h" |
| #include "dp.h" |
| |
| #define DEBUG 0 |
| #define XXXXXXX 0 |
| #define USE_PENALTY_EX 1 |
| |
| |
| #if 1 |
| static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 ) |
| { |
| char *seq2 = s2[0]; |
| int *intptr = amino_dis[(int)s1[0][i1]]; |
| |
| while( lgth2-- ) |
| *match++ = intptr[(int)*seq2++]; |
| } |
| #else |
| static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 ) |
| { |
| int j; |
| |
| for( j=0; j<lgth2; j++ ) |
| match[j] = amino_dis[(*s1)[i1]][(*s2)[j]]; |
| } |
| #endif |
| |
| static float genGtracking( float *lasthorizontalw, float *lastverticalw, |
| char **seq1, char **seq2, |
| char **mseq1, char **mseq2, |
| float **cpmx1, float **cpmx2, |
| int **ijpi, int **ijpj ) |
| { |
| int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk; |
| char gap[] = "-"; |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] ); |
| } |
| #endif |
| |
| for( i=0; i<lgth1+1; i++ ) |
| { |
| ijpi[i][0] = -1; |
| ijpj[i][0] = -1; // ??? |
| } |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| ijpi[0][j] = -1; // ??? |
| ijpj[0][j] = -1; |
| } |
| |
| |
| mseq1[0] += lgth1+lgth2; |
| *mseq1[0] = 0; |
| mseq2[0] += lgth1+lgth2; |
| *mseq2[0] = 0; |
| iin = lgth1; jin = lgth2; |
| limk = lgth1+lgth2 + 1; |
| for( k=0; k<limk; k++ ) |
| { |
| ifi = ( ijpi[iin][jin] ); |
| jfi = ( ijpj[iin][jin] ); |
| l = iin - ifi; |
| while( --l ) |
| { |
| *--mseq1[0] = seq1[0][ifi+l]; |
| *--mseq2[0] = *gap; |
| k++; |
| } |
| l= jin - jfi; |
| while( --l ) |
| { |
| *--mseq1[0] = *gap; |
| *--mseq2[0] = seq2[0][jfi+l]; |
| k++; |
| } |
| if( iin <= 0 || jin <= 0 ) break; |
| *--mseq1[0] = seq1[0][ifi]; |
| *--mseq2[0] = seq2[0][jfi]; |
| |
| // fprintf( stdout, "mseq1 = %s\n", mseq1[0] ); |
| // fprintf( stdout, "mseq2 = %s\n", mseq2[0] ); |
| |
| k++; |
| iin = ifi; jin = jfi; |
| } |
| return( 0.0 ); |
| } |
| |
| |
| float genG__align11( char **seq1, char **seq2, int alloclen ) |
| /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ |
| { |
| // int k; |
| register int i, j; |
| int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */ |
| int lgth1, lgth2; |
| int resultlen; |
| float wm; /* int ?????? */ |
| float g; |
| float *currentw, *previousw; |
| float fpenalty = (float)penalty; |
| float fpenalty_OP = (float)penalty_OP; |
| #if USE_PENALTY_EX |
| float fpenalty_ex = (float)penalty_ex; |
| #endif |
| #if 1 |
| float *wtmp; |
| int *ijpipt; |
| int *ijpjpt; |
| float *mjpt, *Mjpt, *prept, *curpt; |
| int *mpjpt, *Mpjpt; |
| #endif |
| static float mi, *m; |
| static float Mi, *largeM; |
| static int **ijpi; |
| static int **ijpj; |
| static int mpi, *mp; |
| static int Mpi, *Mp; |
| static float *w1, *w2; |
| 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; |
| float tbk; |
| int tbki, tbkj; |
| |
| wm = 0.0; |
| |
| if( orlgth1 == 0 ) |
| { |
| mseq1 = AllocateCharMtx( njob, 0 ); |
| mseq2 = AllocateCharMtx( njob, 0 ); |
| } |
| |
| |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| |
| |
| if( lgth1 <= 0 || lgth2 <= 0 ) |
| { |
| fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 ); |
| } |
| |
| if( lgth1 > orlgth1 || lgth2 > orlgth2 ) |
| { |
| int ll1, ll2; |
| |
| if( orlgth1 > 0 && orlgth2 > 0 ) |
| { |
| FreeFloatVec( w1 ); |
| FreeFloatVec( w2 ); |
| FreeFloatVec( match ); |
| FreeFloatVec( initverticalw ); |
| FreeFloatVec( lastverticalw ); |
| |
| FreeFloatVec( m ); |
| FreeIntVec( mp ); |
| FreeFloatVec( largeM ); |
| FreeIntVec( Mp ); |
| |
| FreeCharMtx( mseq ); |
| |
| |
| FreeFloatMtx( cpmx1 ); |
| FreeFloatMtx( cpmx2 ); |
| |
| FreeFloatMtx( floatwork ); |
| FreeIntMtx( intwork ); |
| } |
| |
| ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100; |
| ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100; |
| |
| #if DEBUG |
| fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 ); |
| #endif |
| |
| w1 = AllocateFloatVec( ll2+2 ); |
| w2 = AllocateFloatVec( ll2+2 ); |
| match = AllocateFloatVec( ll2+2 ); |
| |
| initverticalw = AllocateFloatVec( ll1+2 ); |
| lastverticalw = AllocateFloatVec( ll1+2 ); |
| |
| m = AllocateFloatVec( ll2+2 ); |
| mp = AllocateIntVec( ll2+2 ); |
| largeM = 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 ); |
| |
| #if DEBUG |
| fprintf( stderr, "succeeded\n" ); |
| #endif |
| |
| orlgth1 = ll1 - 100; |
| orlgth2 = ll2 - 100; |
| } |
| |
| |
| mseq1[0] = mseq[0]; |
| mseq2[0] = mseq[1]; |
| |
| |
| if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 ) |
| { |
| int ll1, ll2; |
| |
| if( commonAlloc1 && commonAlloc2 ) |
| { |
| FreeIntMtx( commonIP ); |
| FreeIntMtx( commonJP ); |
| } |
| |
| ll1 = MAX( orlgth1, commonAlloc1 ); |
| ll2 = MAX( orlgth2, commonAlloc2 ); |
| |
| #if DEBUG |
| fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 ); |
| #endif |
| |
| commonIP = AllocateIntMtx( ll1+10, ll2+10 ); |
| commonJP = AllocateIntMtx( ll1+10, ll2+10 ); |
| |
| #if DEBUG |
| fprintf( stderr, "succeeded\n\n" ); |
| #endif |
| |
| commonAlloc1 = ll1; |
| commonAlloc2 = ll2; |
| } |
| ijpi = commonIP; |
| ijpj = commonJP; |
| |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] ); |
| #endif |
| |
| currentw = w1; |
| previousw = w2; |
| |
| |
| match_calc( initverticalw, seq2, seq1, 0, lgth1 ); |
| |
| |
| match_calc( currentw, seq1, seq2, 0, lgth2 ); |
| |
| if( outgap == 1 ) |
| { |
| for( i=1; i<lgth1+1; i++ ) |
| { |
| initverticalw[i] += fpenalty; |
| } |
| for( j=1; j<lgth2+1; j++ ) |
| { |
| currentw[j] += fpenalty; |
| } |
| } |
| |
| for( j=1; j<lgth2+1; ++j ) |
| { |
| m[j] = currentw[j-1]; mp[j] = 0; |
| largeM[j] = currentw[j-1]; Mp[j] = 0; |
| } |
| |
| if( lgth2 == 0 ) |
| lastverticalw[0] = 0.0; // lgth2==0 no toki error |
| else |
| lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error |
| |
| if( outgap ) lasti = lgth1+1; else lasti = lgth1; |
| |
| #if XXXXXXX |
| fprintf( stderr, "currentw = \n" ); |
| for( i=0; i<lgth1+1; i++ ) |
| { |
| fprintf( stderr, "%5.2f ", currentw[i] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "initverticalw = \n" ); |
| for( i=0; i<lgth2+1; i++ ) |
| { |
| fprintf( stderr, "%5.2f ", initverticalw[i] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| |
| for( i=1; i<lasti; i++ ) |
| { |
| wtmp = previousw; |
| previousw = currentw; |
| currentw = wtmp; |
| |
| previousw[0] = initverticalw[i-1]; |
| |
| match_calc( currentw, seq1, seq2, i, lgth2 ); |
| #if XXXXXXX |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "i=%d\n", i ); |
| fprintf( stderr, "currentw = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "%5.2f ", currentw[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| #if XXXXXXX |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "i=%d\n", i ); |
| fprintf( stderr, "currentw = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "%5.2f ", currentw[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| currentw[0] = initverticalw[i]; |
| |
| mi = previousw[0]; mpi = 0; |
| Mi = previousw[0]; Mpi = 0; |
| |
| ijpipt = ijpi[i] + 1; |
| ijpjpt = ijpj[i] + 1; |
| mjpt = m + 1; |
| Mjpt = largeM + 1; |
| prept = previousw; |
| curpt = currentw + 1; |
| mpjpt = mp + 1; |
| Mpjpt = Mp + 1; |
| tbk = -9999999.9; |
| tbki = 0; |
| tbkj = 0; |
| for( j=1; j<lgth2+1; j++ ) |
| { |
| wm = *prept; |
| *ijpipt = i-1; |
| *ijpjpt = j-1; |
| |
| #if 0 |
| fprintf( stderr, "%5.0f->", wm ); |
| #endif |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| if( (g=mi+fpenalty) > wm ) |
| { |
| wm = g; |
| // *ijpipt = i - 1; // iranai |
| *ijpjpt = mpi; |
| } |
| if( (g=*prept) >= mi ) |
| { |
| mi = g; |
| mpi = j-1; |
| } |
| #if USE_PENALTY_EX |
| mi += fpenalty_ex; |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| if( (g=*mjpt + fpenalty) > wm ) |
| { |
| wm = g; |
| *ijpipt = *mpjpt; |
| *ijpjpt = j - 1; //IRU! |
| } |
| if( (g=*prept) >= *mjpt ) |
| { |
| *mjpt = g; |
| *mpjpt = i-1; |
| } |
| #if USE_PENALTY_EX |
| m[j] += fpenalty_ex; |
| #endif |
| |
| #if 1 |
| g = tbk + fpenalty_OP; |
| if( g > wm ) |
| { |
| wm = g; |
| *ijpipt = tbki; |
| *ijpjpt = tbkj; |
| // fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt ); |
| } |
| if( Mi > tbk ) |
| { |
| tbk = Mi; //error desu. |
| tbki = i-1; |
| tbkj = Mpi; |
| } |
| if( *Mjpt > tbk ) |
| { |
| tbk = *Mjpt; |
| tbki = *Mpjpt; |
| tbkj = j-1; |
| } |
| |
| if( *prept > *Mjpt ) |
| { |
| *Mjpt = *prept; |
| *Mpjpt = i-1; |
| } |
| if( *prept > Mi ) |
| { |
| Mi = *prept; |
| Mpi = j-1; |
| } |
| |
| #endif |
| |
| |
| #if 0 |
| fprintf( stderr, "%5.0f ", wm ); |
| #endif |
| *curpt++ += wm; |
| ijpipt++; |
| ijpjpt++; |
| mjpt++; |
| Mjpt++; |
| prept++; |
| mpjpt++; |
| Mpjpt++; |
| } |
| lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error |
| } |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stdout, "i,j=%d,%d - ijpi,ijpj=%d,%d\n", i, j, ijpi[i][j], ijpj[i][j] ); |
| } |
| } |
| fflush( stdout ); |
| #endif |
| |
| genGtracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj ); |
| |
| 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" ); |
| } |
| |
| |
| strcpy( seq1[0], mseq1[0] ); |
| strcpy( seq2[0], mseq2[0] ); |
| #if 0 |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, ">\n%s\n", mseq1[0] ); |
| fprintf( stderr, ">\n%s\n", mseq2[0] ); |
| fprintf( stderr, "wm = %f\n", wm ); |
| #endif |
| |
| return( wm ); |
| } |
| |
