float genL__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt ) /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ { // int k; register int i, j; int lasti, lastj; int lgth1, lgth2; int resultlen; float wm = 0.0; /* int ?????? */ float g; float *currentw, *previousw; #if 1 float *wtmp; int *ijpipt; int *ijpjpt; float *mjpt, *Mjpt, *prept, *curpt; int *mpjpt, *Mpjpt; #endif static TLS float mi, *m; static TLS float Mi, *largeM; static TLS int **ijpi; static TLS int **ijpj; static TLS int mpi, *mp; static TLS int Mpi, *Mp; static TLS float *w1, *w2; static TLS float *match; static TLS float *initverticalw; /* kufuu sureba iranai */ static TLS float *lastverticalw; /* kufuu sureba iranai */ static TLS char **mseq1; static TLS char **mseq2; static TLS char **mseq; static TLS float **cpmx1; static TLS float **cpmx2; static TLS int **intwork; static TLS float **floatwork; static TLS int orlgth1 = 0, orlgth2 = 0; float maxwm; float tbk; int tbki, tbkj; int endali, endalj; // float localthr = 0.0; // float localthr2 = 0.0; float fpenalty = (float)penalty; float fpenalty_OP = (float)penalty_OP; float fpenalty_ex = (float)penalty_ex; // float fpenalty_EX = (float)penalty_EX; float foffset = (float)offset; float localthr = -foffset; float localthr2 = -foffset; if( seq1 == NULL ) { if( orlgth1 > 0 && orlgth2 > 0 ) { orlgth1 = 0; orlgth2 = 0; free( mseq1 ); free( mseq2 ); FreeFloatVec( w1 ); FreeFloatVec( w2 ); FreeFloatVec( match ); FreeFloatVec( initverticalw ); FreeFloatVec( lastverticalw ); FreeFloatVec( m ); FreeIntVec( mp ); free( largeM ); free( Mp ); FreeCharMtx( mseq ); FreeFloatMtx( cpmx1 ); FreeFloatMtx( cpmx2 ); FreeFloatMtx( floatwork ); FreeIntMtx( intwork ); } return( 0.0 ); } // fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty ); if( orlgth1 == 0 ) { mseq1 = AllocateCharMtx( njob, 0 ); mseq2 = AllocateCharMtx( njob, 0 ); } lgth1 = strlen( seq1[0] ); lgth2 = strlen( seq2[0] ); 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( nalphabets, ll1+2 ); cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 ); floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 ); intwork = AllocateIntMtx( nalphabets, 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 ); lasti = lgth2+1; for( j=1; j<lasti; ++j ) { m[j] = currentw[j-1]; mp[j] = 0; largeM[j] = currentw[j-1]; Mp[j] = 0; } lastverticalw[0] = currentw[lgth2-1]; #if 0 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 #if DEBUG2 fprintf( stderr, "\n" ); fprintf( stderr, " " ); for( j=0; j<lgth2+1; j++ ) fprintf( stderr, "%c ", seq2[0][j] ); fprintf( stderr, "\n" ); #endif localstop = lgth1+lgth2+1; maxwm = -999999999.9; endali = endalj = 0; #if DEBUG2 fprintf( stderr, "\n" ); fprintf( stderr, "%c ", seq1[0][0] ); for( j=0; j<lgth2+1; j++ ) fprintf( stderr, "%5.0f ", currentw[j] ); fprintf( stderr, "\n" ); #endif lasti = lgth1+1; 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 DEBUG2 fprintf( stderr, "%c ", seq1[0][i] ); fprintf( stderr, "%5.0f ", currentw[0] ); #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 #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; #if 0 if( mi < localthr ) mi = localthr2; #endif 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 = -999999.9; tbki = 0; tbkj = 0; lastj = lgth2+1; for( j=1; j<lastj; j++ ) { wm = *prept; *ijpipt = i-1; *ijpjpt = j-1; // fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] ); // fprintf( stderr, "wm=%f\n", wm ); #if 0 fprintf( stderr, "%5.0f->", wm ); #endif g = mi + fpenalty; #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( g > wm ) { wm = g; // *ijpipt = i - 1; *ijpjpt = mpi; } g = *prept; if( g > mi ) { mi = g; mpi = j-1; } #if USE_PENALTY_EX mi += fpenalty_ex; #endif #if 0 fprintf( stderr, "%5.0f->", wm ); #endif g = *mjpt + fpenalty; #if 0 fprintf( stderr, "m%5.0f?", g ); #endif if( g > wm ) { wm = g; *ijpipt = *mpjpt; *ijpjpt = j - 1; //IRU! } g = *prept; if( g > *mjpt ) { *mjpt = g; *mpjpt = i-1; } #if USE_PENALTY_EX *mjpt += fpenalty_ex; #endif g = tbk + fpenalty_OP; // g = tbk; 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 ); } // g = Mi; if( Mi > tbk ) { tbk = Mi; //error desu. tbki = i-1; tbkj = Mpi; } // g = *Mjpt; if( *Mjpt > tbk ) { tbk = *Mjpt; tbki = *Mpjpt; tbkj = j-1; } // tbk += fpenalty_EX;// + foffset; // g = *prept; if( *prept > *Mjpt ) { *Mjpt = *prept; *Mpjpt = i-1; } // *Mjpt += fpenalty_EX;// + foffset; // g = *prept; if( *prept > Mi ) { Mi = *prept; Mpi = j-1; } // Mi += fpenalty_EX;// + foffset; // fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt ); // fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] ); if( maxwm < wm ) { maxwm = wm; endali = i; endalj = j; } #if 1 if( wm < localthr ) { // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt ); *ijpipt = localstop; // *ijpjpt = localstop; wm = localthr2; } #endif #if 0 fprintf( stderr, "%5.0f ", *curpt ); #endif #if DEBUG2 fprintf( stderr, "%5.0f ", wm ); // fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop ); #endif *curpt += wm; ijpipt++; ijpjpt++; mjpt++; Mjpt++; prept++; mpjpt++; Mpjpt++; curpt++; } #if DEBUG2 fprintf( stderr, "\n" ); #endif lastverticalw[i] = currentw[lgth2-1]; } #if DEBUG2 fprintf( stderr, "maxwm = %f\n", maxwm ); fprintf( stderr, "endali = %d\n", endali ); fprintf( stderr, "endalj = %d\n", endalj ); #endif if( ijpi[endali][endalj] == localstop ) // && ijpj[endali][endalj] == localstop ) { strcpy( seq1[0], "" ); strcpy( seq2[0], "" ); *off1pt = *off2pt = 0; return( 0.0 ); } gentracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, endali, endalj ); // fprintf( stderr, "### impmatch = %f\n", *impmatch ); 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] ); #endif return( maxwm ); }
float G__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; #if USE_PENALTY_EX float fpenalty_ex = (float)penalty_ex; #endif #if 1 float *wtmp; int *ijppt; float *mjpt, *prept, *curpt; int *mpjpt; #endif static float mi, *m; static int **ijp; 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 int **intwork; static float **floatwork; static int orlgth1 = 0, orlgth2 = 0; 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 ); FreeCharMtx( mseq ); 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 ); mseq = AllocateCharMtx( njob, ll1+ll2 ); 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 ); } 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 ); #if DEBUG fprintf( stderr, "succeeded\n\n" ); #endif commonAlloc1 = ll1; commonAlloc2 = ll2; } ijp = commonIP; #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; } 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; ijppt = ijp[i] + 1; mjpt = m + 1; prept = previousw; curpt = currentw + 1; mpjpt = mp + 1; for( j=1; j<lgth2+1; j++ ) { wm = *prept; *ijppt = 0; #if 0 fprintf( stderr, "%5.0f->", wm ); #endif #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( (g=mi+fpenalty) > wm ) { wm = g; *ijppt = -( j - 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; *ijppt = +( i - *mpjpt ); } if( (g=*prept) >= *mjpt ) { *mjpt = g; *mpjpt = i-1; } #if USE_PENALTY_EX m[j] += fpenalty_ex; #endif #if 0 fprintf( stderr, "%5.0f ", wm ); #endif *curpt++ += wm; ijppt++; mjpt++; prept++; mpjpt++; } lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error } Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp ); 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 ); }
float MSalign11( 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, lastj; int iin = 0, jin = 0; // by Mathog, a guess int lgth1, lgth2; int resultlen; float wm = 0.0; /* int ?????? */ float g; float *currentw, *previousw; float fpenalty = (float)penalty; #if USE_PENALTY_EX float fpenalty_ex = (float)penalty_ex; #endif float *maxinw = NULL, *maxinwpt = NULL; // by D.Mathog, guess float *maxinh = NULL; // by D.Mathog, guess #if 1 float wmmax; float *wtmp; int *ijppt; float *mjpt, *prept, *curpt; int *mpjpt; #endif static float mi, *m; static int **ijp; 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 **WMMTX; static float **floatwork; static int orlgth1 = 0, orlgth2 = 0; if( orlgth1 == 0 ) { mseq1 = AllocateCharMtx( njob, 0 ); mseq2 = AllocateCharMtx( njob, 0 ); } lgth1 = strlen( seq1[0] ); lgth2 = strlen( seq2[0] ); if( lgth1 > orlgth1 || lgth2 > orlgth2 ) { int ll1, ll2; if( orlgth1 > 0 && orlgth2 > 0 ) { FreeFloatVec( w1 ); FreeFloatVec( w2 ); FreeFloatVec( match ); FreeFloatVec( initverticalw ); FreeFloatVec( lastverticalw ); FreeFloatVec( maxinw ); FreeFloatVec( maxinh ); FreeFloatVec( m ); 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 ); maxinw = AllocateFloatVec( ll1+2 ); m = AllocateFloatVec( ll2+2 ); mp = AllocateIntVec( ll2+2 ); maxinh = AllocateFloatVec( 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 ); FreeFloatMtx( WMMTX ); } 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 ); WMMTX = AllocateFloatMtx( ll1+10, ll2+10 ); #if DEBUG fprintf( stderr, "succeeded\n\n" ); #endif commonAlloc1 = ll1; commonAlloc2 = ll2; } ijp = commonIP; #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 ); WMMTX[0][0] = initverticalw[0]; maxinh[0] = initverticalw[0]; for( i=1; i<lgth1+1; i++ ) { initverticalw[i] += fpenalty; WMMTX[i][0] = initverticalw[i]; if( maxinh[0] < initverticalw[i] ) maxinh[0] = initverticalw[i]; } maxinw[0] = currentw[0]; for( j=1; j<lgth2+1; j++ ) { currentw[j] += fpenalty; WMMTX[0][j] = currentw[j]; if( maxinw[0] < currentw[j] ) maxinw[0] = currentw[j]; } for( j=1; j<lgth2+1; ++j ) { m[j] = currentw[j-1]; mp[j] = 0; } lastverticalw[0] = currentw[lgth2-1]; lasti = lgth1+1; for( i=1; i<lasti; i++ ) { wtmp = previousw; previousw = currentw; currentw = wtmp; previousw[0] = initverticalw[i-1]; match_calc( currentw, seq1, seq2, i, lgth2 ); currentw[0] = initverticalw[i]; mi = previousw[0]; mpi = 0; maxinwpt = maxinw + i; *maxinwpt = currentw[0]; fprintf( stderr, "currentw[0] = %f, *maxinwpt = %f\n", currentw[0], maxinw[i] ); ijppt = ijp[i] + 1; mjpt = m + 1; prept = previousw; curpt = currentw + 1; mpjpt = mp + 1; lastj = lgth2+1; for( j=1; j<lastj; j++ ) { wm = *prept; *ijppt = 0; #if 0 fprintf( stderr, "%5.0f->", wm ); #endif g = mi + fpenalty; #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( g > wm ) { wm = g; *ijppt = -( j - mpi ); } g = *prept; if( g >= mi ) { mi = g; mpi = j-1; } #if USE_PENALTY_EX mi += fpenalty_ex; #endif g = *mjpt + fpenalty; #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( g > wm ) { wm = g; *ijppt = +( i - *mpjpt ); } g = *prept; if( g >= *mjpt ) { *mjpt = g; *mpjpt = i-1; } #if USE_PENALTY_EX m[j] += fpenalty_ex; #endif #if 0 fprintf( stderr, "%5.0f ", wm ); #endif *curpt += wm; WMMTX[i][j] = *curpt; if( j<lgth2 && *maxinwpt < *curpt ) *maxinwpt = *curpt; if( j<lgth2 && maxinh[j] < *curpt ) maxinh[j] = *curpt; // fprintf( stderr, "maxintwpt = %f\n", *maxinwpt ); ijppt++; mjpt++; prept++; mpjpt++; curpt++; } lastverticalw[i] = currentw[lgth2-1]; } wmmax = -999.9; for( i=0; i<lgth1; i++ ) { g = lastverticalw[i]; if( g > wmmax ) { wmmax = g; iin = i; jin = lgth2-1; } } for( j=0; j<lgth2; j++ ) { g = currentw[j]; if( g > wmmax ) { wmmax = g; iin = lgth1-1; jin = j; } } for( i=0; i<lgth1; i++ ) fprintf( stderr, "maxinw[%d] = %f\n", i, maxinw[i] ); for( j=0; j<lgth2; j++ ) fprintf( stderr, "maxinh[%d] = %f\n", j, maxinh[j] ); fprintf( stderr, "wmmax = %f (%d,%d)\n", wmmax, iin, jin ); if( iin == lgth1 - 1 && jin == lgth2 - 1 ) ; else wmmax += fpenalty; fprintf( stderr, "wmmax = %f\n", wmmax ); #if 0 for( i=0; i<lgth1; i++ ) { for( j=0; j<lgth2; j++ ) { fprintf( stderr, "% 10.2f ", WMMTX[i][j] ); } fprintf( stderr, "\n" ); } #endif mseq1[0] += lgth1+lgth2; *mseq1[0] = 0; mseq2[0] += lgth1+lgth2; *mseq2[0] = 0; backdp( WMMTX, wmmax, maxinw, maxinh, lgth1, lgth2, alloclen, w1, w2, initverticalw, m, mp, iin, jin, seq1, seq2, mseq1, mseq2 ); fprintf( stderr, "\n" ); #if 1 fprintf( stderr, "\n" ); fprintf( stderr, ">MSres\n%s\n", mseq1[0] ); fprintf( stderr, ">MSres\n%s\n", mseq2[0] ); #endif #if 0 for( i=0; i<lgth1; i++ ) { for( j=0; j<lgth2; j++ ) { fprintf( stderr, "% 10.2f ", WMMTX[i][j] ); } fprintf( stderr, "\n" ); } #endif mseq1[0] = mseq[0]; mseq2[0] = mseq[1]; mseq1[0] += lgth1+lgth2; *mseq1[0] = 0; mseq2[0] += lgth1+lgth2; *mseq2[0] = 0; Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp ); 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 1 fprintf( stderr, "\n" ); fprintf( stderr, ">\n%s\n", mseq1[0] ); fprintf( stderr, ">\n%s\n", mseq2[0] ); #endif return( wm ); }
void backdp( float **WMMTX, float wmmax, float *maxinw, float *maxinh, int lgth1, int lgth2, int alloclen, float *w1, float *w2, float *initverticalw, float *m, int *mp, int iin, int jin, char **seq1, char **seq2, char **mseq1, char **mseq2 ) { register int i, j; int prevhiti, prevhitj; // int lasti, lastj; float g; float fpenalty = (float)penalty; #if USE_PENALTY_EX float fpenalty_ex = (float)penalty_ex; #endif float *currentw, *previousw, *wtmp; float mi; int mpi; int *mpjpt; float *mjpt, *prept, *curpt; float wm = 0.0; float forwwm; currentw = w1; previousw = w2; match_calc( initverticalw, seq2, seq1, lgth2-1, lgth1 ); match_calc( currentw, seq1, seq2, lgth1-1, lgth2 ); prevhiti = iin; prevhitj = jin; fprintf( stderr, "prevhiti = %d, lgth1 = %d\n", prevhiti, lgth1 ); fprintf( stderr, "prevhitj = %d, lgth2 = %d\n", prevhitj, lgth2 ); extendmseq( mseq1, mseq2, seq1, seq2, prevhiti, prevhitj, lgth1, lgth2 ); for( i=0; i<lgth1-1; i++ ) { initverticalw[i] += fpenalty; WMMTX[i][lgth2-1] += fpenalty; } for( j=0; j<lgth2-1; j++ ) { currentw[j] += fpenalty; WMMTX[lgth1-1][j] += fpenalty; } #if 0 fprintf( stderr, "initverticalw = \n" ); for( i=0; i<lgth1; i++ ) fprintf( stderr, "% 8.2f", initverticalw[i] ); fprintf( stderr, "\n" ); fprintf( stderr, "currentw = \n" ); for( i=0; i<lgth2; i++ ) fprintf( stderr, "% 8.2f", currentw[i] ); fprintf( stderr, "\n" ); #endif for( j=lgth2-1; j>0; --j ) { m[j-1] = currentw[j]; mp[j] = 0; // iranai } for( j=0; j<lgth2; j++ ) m[j] = 0.0; //m[lgth2-1] ga, irunoka iranainoka irahai. for( i=lgth1-2; i>-1; i-- ) { wtmp = previousw; previousw = currentw; currentw = wtmp; previousw[lgth2-1] = initverticalw[i+1]; match_calc( currentw, seq1, seq2, i, lgth2 ); #if 0 fprintf( stderr, "i=%d, currentw = \n", i ); for( j=0; j<lgth2; j++ ) fprintf( stderr, "% 8.2f", currentw[j] ); fprintf( stderr, "\n" ); #endif currentw[lgth2-1] = initverticalw[i]; mi = previousw[lgth2-1]; mpi = lgth2-1; //iranai mjpt = m + lgth2 - 2; prept = previousw + lgth2 - 1; curpt = currentw + lgth2 - 2; mpjpt = mp + lgth2 - 2; for( j=lgth2-2; j>-1; j-- ) { // fprintf( stderr, "i,j=%d,%d %c-%c ", i, j, seq1[0][i], seq2[0][j] ); wm = *prept; g = mi + fpenalty; #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( g > wm ) { wm = g; } g = *prept; if( g >= mi ) { mi = g; mpi = j+1; //iranai } #if USE_PENALTY_EX mi += fpenalty_ex; #endif g = *mjpt + fpenalty; #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( g > wm ) { wm = g; } g = *prept; if( g >= *mjpt ) { *mjpt = g; *mpjpt = i-1; //iranai } #if USE_PENALTY_EX m[j] += fpenalty_ex; #endif #if 0 fprintf( stderr, "*curpt = %5.0f \n", *curpt ); #endif // forwwm = wm + MIN( maxinw[i], maxinh[j] ); forwwm = wm + MIN( maxinw[i], maxinh[j] ); WMMTX[i][j] = forwwm; if( forwwm == wmmax && i<prevhiti && j<prevhitj ) { fprintf( stderr, "hit!\n" ); extendmseq( mseq1, mseq2, seq1, seq2, i, j, prevhiti, prevhitj ); if( forwwm == wmmax ) { *--mseq1[0] = 'u'; *--mseq2[0] = 'u'; } prevhiti = i; prevhitj = j; } *curpt += wm; mjpt--; prept--; mpjpt--; curpt--; } } extendmseq( mseq1, mseq2, seq1, seq2, -1, -1, prevhiti, prevhitj ); }
float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2 ) /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ { // int k; register int i, j; int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */ int lgth1, lgth2; int resultlen; float wm = 0.0; /* int ?????? */ float g; float *currentw, *previousw; #if 1 float *wtmp; int *ijppt; float *mjpt, *prept, *curpt; int *mpjpt; #endif static float mi, *m; static int **ijp; 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 *ogcp1; static float *ogcp2; static float *fgcp1; static float *fgcp2; static float **cpmx1; static float **cpmx2; static int **intwork; static float **floatwork; static int orlgth1 = 0, orlgth2 = 0; float fpenalty = (float)penalty; #if USE_PENALTY_EX float fpenalty_ex = (float)penalty_ex; #endif float *fgcp2pt; float *ogcp2pt; float fgcp1va; float ogcp1va; #if 0 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, 0 ); mseq2 = AllocateCharMtx( njob, 0 ); } lgth1 = strlen( seq1[0] ); lgth2 = strlen( seq2[0] ); 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 ); FreeCharMtx( mseq ); FreeFloatVec( ogcp1 ); FreeFloatVec( ogcp2 ); FreeFloatVec( fgcp1 ); FreeFloatVec( fgcp2 ); 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 ); mseq = AllocateCharMtx( njob, ll1+ll2 ); ogcp1 = AllocateFloatVec( ll1+2 ); ogcp2 = AllocateFloatVec( ll2+2 ); fgcp1 = AllocateFloatVec( ll1+2 ); fgcp2 = AllocateFloatVec( ll2+2 ); cpmx1 = AllocateFloatMtx( 26, ll1+2 ); cpmx2 = AllocateFloatMtx( 26, ll2+2 ); #if FASTMATCHCALC floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 ); intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 ); #else floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 ); #endif #if DEBUG fprintf( stderr, "succeeded\n" ); #endif orlgth1 = ll1 - 100; orlgth2 = ll2 - 100; } 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 ); #if DEBUG fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 ); #endif commonIP = AllocateIntMtx( ll1+10, ll2+10 ); #if DEBUG fprintf( stderr, "succeeded\n\n" ); #endif commonAlloc1 = ll1; commonAlloc2 = ll2; } ijp = commonIP; cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc ); if( sgap1 ) { new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 ); new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 ); new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 ); new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 ); } else { st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 ); st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 ); st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 ); st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 ); } for( i=0; i<lgth1; i++ ) { ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty; fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty; } for( i=0; i<lgth2; i++ ) { ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty; fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty; } #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, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 ); if( localhom ) part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 ); match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 ); if( localhom ) part_imp_match_out_vead_gapmap( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 ); #if 0 // -> tbfast.c if( localhom ) imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 ); #endif if( outgap == 1 ) { for( i=1; i<lgth1+1; i++ ) { initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ; } for( j=1; j<lgth2+1; j++ ) { currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ; } } #if OUTGAP0TRY else { for( j=1; j<lgth2+1; j++ ) currentw[j] -= offset * j / 2.0; for( i=1; i<lgth1+1; i++ ) initverticalw[i] -= offset * i / 2.0; } #endif for( j=1; j<lgth2+1; ++j ) { m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0; } lastverticalw[0] = currentw[lgth2-1]; if( outgap ) lasti = lgth1+1; else lasti = lgth1; lastj = lgth2+1; #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" ); fprintf( stderr, "fcgp\n" ); for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] ); for( i=0; i<lgth2; i++ ) fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] ); #endif for( i=1; i<lasti; i++ ) { wtmp = previousw; previousw = currentw; currentw = wtmp; previousw[0] = initverticalw[i-1]; match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 ); #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( localhom ) { // fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i ); // imp_match_out_vead( currentw, i, lgth2 ); part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 ); } #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] + ogcp2[1]; mpi = 0; ijppt = ijp[i] + 1; mjpt = m + 1; prept = previousw; curpt = currentw + 1; mpjpt = mp + 1; fgcp2pt = fgcp2; ogcp2pt = ogcp2+1; fgcp1va = fgcp1[i-1]; ogcp1va = ogcp1[i]; for( j=1; j<lastj; j++ ) { wm = *prept; *ijppt = 0; #if 0 fprintf( stderr, "%5.0f->", wm ); #endif g = mi + *fgcp2pt; #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( g > wm ) { wm = g; *ijppt = -( j - mpi ); } g = *prept + *ogcp2pt; if( g >= mi ) { mi = g; mpi = j-1; } #if USE_PENALTY_EX mi += fpenalty_ex; #endif g = *mjpt + fgcp1va; #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( g > wm ) { wm = g; *ijppt = +( i - *mpjpt ); } g = *prept + ogcp1va; if( g >= *mjpt ) { *mjpt = g; *mpjpt = i-1; } #if USE_PENALTY_EX m[j] += fpenalty_ex; #endif #if 0 fprintf( stderr, "%5.0f ", wm ); #endif *curpt += wm; ijppt++; mjpt++; prept++; mpjpt++; curpt++; fgcp2pt++; ogcp2pt++; } lastverticalw[i] = currentw[lgth2-1]; } #if OUTGAP0TRY if( !outgap ) { for( j=1; j<lgth2+1; j++ ) currentw[j] -= offset * ( lgth2 - j ) / 2.0; for( i=1; i<lgth1+1; i++ ) lastverticalw[i] -= offset * ( lgth1 - i / 2.0); } #endif /* 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] ); */ if( localhom ) { Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2 ); } else Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc ); // fprintf( stderr, "### impmatch = %f\n", *impmatch ); 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 ); }
float L__align11_noalign( char **seq1, char **seq2 ) /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ { // int k; register int i, j; int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */ int lgth1, lgth2; // int resultlen; float wm = 0.0; /* int ?????? */ float g; float *currentw, *previousw; #if 1 float *wtmp; // int *ijppt; float *mjpt, *prept, *curpt; // int *mpjpt; #endif static TLS float mi, *m; // static TLS int **ijp; // static TLS int mpi, *mp; static TLS float *w1, *w2; static TLS float *match; static TLS float *initverticalw; /* kufuu sureba iranai */ static TLS float *lastverticalw; /* kufuu sureba iranai */ // static TLS char **mseq1; // static TLS char **mseq2; // static TLS char **mseq; // static TLS int **intwork; // static TLS float **floatwork; static TLS int orlgth1 = 0, orlgth2 = 0; float maxwm; // int endali = 0, endalj = 0; // by D.Mathog, a guess // int endali, endalj; float localthr = -offset; float localthr2 = -offset; // float localthr = 100; // float localthr2 = 100; float fpenalty = (float)penalty; float fpenalty_ex = (float)penalty_ex; if( seq1 == NULL ) { if( orlgth1 > 0 && orlgth2 > 0 ) { orlgth1 = 0; orlgth2 = 0; // free( mseq1 ); // free( mseq2 ); FreeFloatVec( w1 ); FreeFloatVec( w2 ); FreeFloatVec( match ); FreeFloatVec( initverticalw ); FreeFloatVec( lastverticalw ); FreeFloatVec( m ); // FreeIntVec( mp ); // FreeCharMtx( mseq ); } return( 0.0 ); } // if( orlgth1 == 0 ) // { // mseq1 = AllocateCharMtx( njob, 0 ); // mseq2 = AllocateCharMtx( njob, 0 ); // } lgth1 = strlen( seq1[0] ); lgth2 = strlen( seq2[0] ); 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 ); // FreeCharMtx( mseq ); // 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 ); // mseq = AllocateCharMtx( njob, ll1+ll2 ); // 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 ); // } // // 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 ); #if DEBUG // fprintf( stderr, "succeeded\n\n" ); #endif // commonAlloc1 = ll1; // commonAlloc2 = ll2; // } // ijp = commonIP; #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 ); lasti = lgth2+1; for( j=1; j<lasti; ++j ) { m[j] = currentw[j-1]; // mp[j] = 0; #if 0 if( m[j] < localthr ) m[j] = localthr2; #endif } lastverticalw[0] = currentw[lgth2-1]; lasti = lgth1+1; #if 0 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 #if DEBUG2 fprintf( stderr, "\n" ); fprintf( stderr, " " ); for( j=0; j<lgth2; j++ ) fprintf( stderr, "%c ", seq2[0][j] ); fprintf( stderr, "\n" ); #endif localstop = lgth1+lgth2+1; maxwm = -999999999.9; #if DEBUG2 fprintf( stderr, "\n" ); fprintf( stderr, "%c ", seq1[0][0] ); for( j=0; j<lgth2+1; j++ ) fprintf( stderr, "%5.0f ", currentw[j] ); 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 DEBUG2 fprintf( stderr, "%c ", seq1[0][i] ); fprintf( stderr, "%5.0f ", currentw[0] ); #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 #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; #if 0 if( mi < localthr ) mi = localthr2; #endif // ijppt = ijp[i] + 1; mjpt = m + 1; prept = previousw; curpt = currentw + 1; // mpjpt = mp + 1; lastj = lgth2+1; for( j=1; j<lastj; j++ ) { wm = *prept; // *ijppt = 0; #if 0 fprintf( stderr, "%5.0f->", wm ); #endif #if 0 fprintf( stderr, "%5.0f?", g ); #endif if( (g=mi+fpenalty) > wm ) { wm = g; // *ijppt = -( j - mpi ); } if( *prept > mi ) { mi = *prept; // 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; // *ijppt = +( i - *mpjpt ); } if( *prept > *mjpt ) { *mjpt = *prept; // *mpjpt = i-1; } #if USE_PENALTY_EX *mjpt += fpenalty_ex; #endif if( maxwm < wm ) { maxwm = wm; // endali = i; // endalj = j; } #if 1 if( wm < localthr ) { // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt ); // *ijppt = localstop; wm = localthr2; } #endif #if 0 fprintf( stderr, "%5.0f ", *curpt ); #endif #if DEBUG2 fprintf( stderr, "%5.0f ", wm ); // fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop ); #endif *curpt++ += wm; // ijppt++; mjpt++; prept++; // mpjpt++; } #if DEBUG2 fprintf( stderr, "\n" ); #endif lastverticalw[i] = currentw[lgth2-1]; } #if 0 fprintf( stderr, "maxwm = %f\n", maxwm ); fprintf( stderr, "endali = %d\n", endali ); fprintf( stderr, "endalj = %d\n", endalj ); #endif #if 0 // IRUKAMO!!!! if( ijp[endali][endalj] == localstop ) { strcpy( seq1[0], "" ); strcpy( seq2[0], "" ); *off1pt = *off2pt = 0; fprintf( stderr, "maxwm <- 0.0 \n" ); return( 0.0 ); } #else if( maxwm < localthr ) { fprintf( stderr, "maxwm <- 0.0 \n" ); return( 0.0 ); } #endif // Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj ); // 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, "wm=%f\n", wm ); fprintf( stderr, ">\n%s\n", mseq1[0] ); fprintf( stderr, ">\n%s\n", mseq2[0] ); fprintf( stderr, "maxwm = %f\n", maxwm ); fprintf( stderr, " wm = %f\n", wm ); #endif return( maxwm ); }