| #include "mltaln.h" |
| #include "dp.h" |
| |
| #define MEMSAVE 1 |
| |
| #define DEBUG 0 |
| #define USE_PENALTY_EX 0 |
| #define STOREWM 1 |
| |
| #define DPTANNI 10 |
| |
| #define LOCAL 0 |
| |
| static int reccycle = 0; |
| |
| static float localthr; |
| |
| static void match_ribosum( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize ) |
| { |
| int j, k, l; |
| float scarr[38]; |
| float **cpmxpd = floatwork; |
| int **cpmxpdn = intwork; |
| int count = 0; |
| float *matchpt; |
| float **cpmxpdpt; |
| int **cpmxpdnpt; |
| int cpkd; |
| |
| if( initialize ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| count = 0; |
| for( l=0; l<37; l++ ) |
| { |
| if( cpmx2[j][l] ) |
| { |
| cpmxpd[j][count] = cpmx2[j][l]; |
| cpmxpdn[j][count] = l; |
| count++; |
| } |
| } |
| cpmxpdn[j][count] = -1; |
| } |
| } |
| |
| for( l=0; l<37; l++ ) |
| { |
| scarr[l] = 0.0; |
| for( k=0; k<37; k++ ) |
| { |
| scarr[l] += ribosumdis[k][l] * cpmx1[i1][k]; |
| } |
| } |
| #if 0 /* ¤³¤ì¤ò»È¤¦¤È¤¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */ |
| { |
| float *fpt, **fptpt, *fpt2; |
| int *ipt, **iptpt; |
| fpt2 = match; |
| iptpt = cpmxpdn; |
| fptpt = cpmxpd; |
| while( lgth2-- ) |
| { |
| *fpt2 = 0.0; |
| ipt=*iptpt,fpt=*fptpt; |
| while( *ipt > -1 ) |
| *fpt2 += scarr[*ipt++] * *fpt++; |
| fpt2++,iptpt++,fptpt++; |
| } |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| match[j] = 0.0; |
| for( k=0; cpmxpdn[j][k]>-1; k++ ) |
| match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k]; |
| } |
| #else |
| matchpt = match; |
| cpmxpdnpt = cpmxpdn; |
| cpmxpdpt = cpmxpd; |
| while( lgth2-- ) |
| { |
| *matchpt = 0.0; |
| for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ ) |
| *matchpt += scarr[cpkd] * (*cpmxpdpt)[k]; |
| matchpt++; |
| cpmxpdnpt++; |
| cpmxpdpt++; |
| } |
| #endif |
| } |
| |
| 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; |
| float *matchpt; |
| float **cpmxpdpt; |
| int **cpmxpdnpt; |
| int cpkd; |
| |
| if( initialize ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| count = 0; |
| for( l=0; l<26; l++ ) |
| { |
| if( cpmx2[j][l] ) |
| { |
| cpmxpd[j][count] = cpmx2[j][l]; |
| cpmxpdn[j][count] = l; |
| count++; |
| } |
| } |
| cpmxpdn[j][count] = -1; |
| } |
| } |
| |
| for( l=0; l<26; l++ ) |
| { |
| scarr[l] = 0.0; |
| for( k=0; k<26; k++ ) |
| { |
| scarr[l] += (n_dis[k][l]-RNAthr) * cpmx1[i1][k]; |
| } |
| } |
| #if 0 /* ¤³¤ì¤ò»È¤¦¤È¤¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */ |
| { |
| float *fpt, **fptpt, *fpt2; |
| int *ipt, **iptpt; |
| fpt2 = match; |
| iptpt = cpmxpdn; |
| fptpt = cpmxpd; |
| while( lgth2-- ) |
| { |
| *fpt2 = 0.0; |
| ipt=*iptpt,fpt=*fptpt; |
| while( *ipt > -1 ) |
| *fpt2 += scarr[*ipt++] * *fpt++; |
| fpt2++,iptpt++,fptpt++; |
| } |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| match[j] = 0.0; |
| for( k=0; cpmxpdn[j][k]>-1; k++ ) |
| match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k]; |
| } |
| #else |
| matchpt = match; |
| cpmxpdnpt = cpmxpdn; |
| cpmxpdpt = cpmxpd; |
| while( lgth2-- ) |
| { |
| *matchpt = 0.0; |
| for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ ) |
| *matchpt += scarr[cpkd] * (*cpmxpdpt)[k]; |
| matchpt++; |
| cpmxpdnpt++; |
| cpmxpdpt++; |
| } |
| #endif |
| } |
| |
| #if 0 |
| static void match_add( 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; |
| float *matchpt; |
| float **cpmxpdpt; |
| int **cpmxpdnpt; |
| int cpkd; |
| |
| |
| if( initialize ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| count = 0; |
| for( l=0; l<26; l++ ) |
| { |
| if( cpmx2[j][l] ) |
| { |
| cpmxpd[j][count] = cpmx2[j][l]; |
| cpmxpdn[j][count] = l; |
| count++; |
| } |
| } |
| cpmxpdn[j][count] = -1; |
| } |
| } |
| |
| for( l=0; l<26; l++ ) |
| { |
| scarr[l] = 0.0; |
| for( k=0; k<26; k++ ) |
| { |
| scarr[l] += n_dis[k][l] * cpmx1[i1][k]; |
| } |
| } |
| #if 0 /* ¤³¤ì¤ò»È¤¦¤È¤¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */ |
| { |
| float *fpt, **fptpt, *fpt2; |
| int *ipt, **iptpt; |
| fpt2 = match; |
| iptpt = cpmxpdn; |
| fptpt = cpmxpd; |
| while( lgth2-- ) |
| { |
| *fpt2 = 0.0; |
| ipt=*iptpt,fpt=*fptpt; |
| while( *ipt > -1 ) |
| *fpt2 += scarr[*ipt++] * *fpt++; |
| fpt2++,iptpt++,fptpt++; |
| } |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| match[j] = 0.0; |
| for( k=0; cpmxpdn[j][k]>-1; k++ ) |
| match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k]; |
| } |
| #else |
| matchpt = match; |
| cpmxpdnpt = cpmxpdn; |
| cpmxpdpt = cpmxpd; |
| while( lgth2-- ) |
| { |
| // *matchpt = 0.0; // add dakara |
| for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ ) |
| *matchpt += scarr[cpkd] * (*cpmxpdpt)[k]; |
| matchpt++; |
| cpmxpdnpt++; |
| cpmxpdpt++; |
| } |
| #endif |
| } |
| #endif |
| |
| #if 0 |
| static float Atracking( |
| char **seq1, char **seq2, |
| char **mseq1, char **mseq2, |
| int **ijp, int icyc, int jcyc, |
| int ist, int ien, int jst, int jen ) |
| { |
| int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim; |
| char *gaptable1, *gt1bk; |
| char *gaptable2, *gt2bk; |
| lgth1 = ien-ist+1; |
| lgth2 = jen-jst+1; |
| |
| gt1bk = AllocateCharVec( lgth1+lgth2+1 ); |
| gt2bk = AllocateCharVec( lgth1+lgth2+1 ); |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] ); |
| } |
| #endif |
| |
| |
| // fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 ); |
| |
| for( i=0; i<lgth1+1; i++ ) |
| { |
| ijp[i][0] = i + 1; |
| } |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| ijp[0][j] = -( j + 1 ); |
| } |
| |
| |
| gaptable1 = gt1bk + lgth1+lgth2; |
| *gaptable1 = 0; |
| gaptable2 = gt2bk + lgth1+lgth2; |
| *gaptable2 = 0; |
| |
| // if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] ); |
| |
| iin = lgth1; jin = lgth2; |
| klim = lgth1+lgth2; |
| for( k=0; k<=klim; 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 ) |
| { |
| *--gaptable1 = 'o'; |
| *--gaptable2 = '-'; |
| k++; |
| } |
| l= jin - jfi; |
| while( --l ) |
| { |
| *--gaptable1 = '-'; |
| *--gaptable2 = 'o'; |
| k++; |
| } |
| if( iin <= 0 || jin <= 0 ) break; |
| *--gaptable1 = 'o'; |
| *--gaptable2 = 'o'; |
| k++; |
| iin = ifi; jin = jfi; |
| |
| } |
| |
| for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 ); |
| for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 ); |
| |
| free( gt1bk ); |
| free( gt2bk ); |
| |
| // fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] ); |
| // fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] ); |
| return( 0.0 ); |
| } |
| #endif |
| |
| |
| static float MSalign2m2m_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo, float **map ) |
| /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ |
| { |
| float value = 0.0; |
| register int i, j; |
| char **aseq1, **aseq2; |
| int ll1, ll2; |
| int lasti, lastj, imid, jmid = 0; |
| float wm = 0.0; /* int ?????? */ |
| float g; |
| float *currentw, *previousw; |
| #if USE_PENALTY_EX |
| float fpenalty_ex = (float)penalty_ex; |
| #endif |
| // float fpenalty = (float)penalty; |
| float *wtmp; |
| // short *ijppt; |
| int *mpjpt; |
| // short **ijp; |
| int *mp; |
| int mpi; |
| float *mjpt, *prept, *curpt; |
| float mi; |
| float *m; |
| float *w1, *w2; |
| // float *match; |
| float *initverticalw; /* kufuu sureba iranai */ |
| float *lastverticalw; /* kufuu sureba iranai */ |
| int **intwork; |
| float **floatwork; |
| // short **shortmtx; |
| #if STOREWM |
| float **WMMTX; |
| float **WMMTX2; |
| #endif |
| float *midw; |
| float *midm; |
| float *midn; |
| int lgth1, lgth2; |
| float maxwm = 0.0; |
| int *jumpforwi; |
| int *jumpforwj; |
| int *jumpbacki; |
| int *jumpbackj; |
| int *jumpdummi; //muda |
| int *jumpdummj; //muda |
| int jumpi, jumpj = 0; |
| char *gaps; |
| int ijpi, ijpj; |
| float *ogcp1; |
| float *fgcp1; |
| float *ogcp2; |
| float *fgcp2; |
| float firstm; |
| int firstmp; |
| #if 0 |
| static char ttt1[50000]; |
| static char ttt2[50000]; |
| #endif |
| |
| localthr = -offset + 500; // 0? |
| |
| ogcp1 = gapinfo[0] + ist; |
| fgcp1 = gapinfo[1] + ist; |
| ogcp2 = gapinfo[2] + jst; |
| fgcp2 = gapinfo[3] + jst; |
| |
| depth++; |
| reccycle++; |
| |
| lgth1 = ien-ist+1; |
| lgth2 = jen-jst+1; |
| |
| // if( lgth1 < 5 ) |
| // fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 ); |
| // if( lgth2 < 5 ) |
| // fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 ); |
| // |
| |
| #if 0 |
| fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen ); |
| strncpy( ttt1, seq1[0]+ist, lgth1 ); |
| strncpy( ttt2, seq2[0]+jst, lgth2 ); |
| ttt1[lgth1] = 0; |
| ttt2[lgth2] = 0; |
| fprintf( stderr, "seq1 = %s\n", ttt1 ); |
| fprintf( stderr, "seq2 = %s\n", ttt2 ); |
| #endif |
| if( lgth2 <= 0 ) // lgth1 <= 0 ha? |
| { |
| // fprintf( stderr, "\n\n==== jimei\n\n" ); |
| // exit( 1 ); |
| for( i=0; i<icyc; i++ ) |
| { |
| strncpy( mseq1[i], seq1[i]+ist, lgth1 ); |
| mseq1[i][lgth1] = 0; |
| } |
| for( i=0; i<jcyc; i++ ) |
| { |
| mseq2[i][0] = 0; |
| for( j=0; j<lgth1; j++ ) |
| strcat( mseq2[i], "-" ); |
| } |
| |
| // fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] ); |
| // fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] ); |
| |
| return( 0.0 ); |
| } |
| |
| #if MEMSAVE |
| aseq1 = AllocateCharMtx( icyc, 0 ); |
| aseq2 = AllocateCharMtx( jcyc, 0 ); |
| for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i]; |
| for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i]; |
| #else |
| aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 ); |
| aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 ); |
| #endif |
| |
| // if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai |
| // if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari |
| if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka? |
| { |
| // fprintf( stderr, "==== Going to _tanni\n" ); |
| |
| // value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo ); |
| |
| |
| #if MEMSAVE |
| free( aseq1 ); |
| free( aseq2 ); |
| #else |
| for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] ); |
| for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] ); |
| |
| FreeCharMtx( aseq1 ); |
| FreeCharMtx( aseq2 ); |
| #endif |
| |
| // fprintf( stderr, "value = %f\n", value ); |
| |
| return( value ); |
| } |
| // fprintf( stderr, "Trying to divide the mtx\n" ); |
| |
| ll1 = ( (int)(lgth1) ) + 100; |
| ll2 = ( (int)(lgth2) ) + 100; |
| |
| // fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 ); |
| |
| w1 = AllocateFloatVec( ll2+2 ); |
| w2 = AllocateFloatVec( ll2+2 ); |
| // match = AllocateFloatVec( ll2+2 ); |
| midw = AllocateFloatVec( ll2+2 ); |
| midn = AllocateFloatVec( ll2+2 ); |
| midm = AllocateFloatVec( ll2+2 ); |
| jumpbacki = AllocateIntVec( ll2+2 ); |
| jumpbackj = AllocateIntVec( ll2+2 ); |
| jumpforwi = AllocateIntVec( ll2+2 ); |
| jumpforwj = AllocateIntVec( ll2+2 ); |
| jumpdummi = AllocateIntVec( ll2+2 ); |
| jumpdummj = AllocateIntVec( ll2+2 ); |
| |
| initverticalw = AllocateFloatVec( ll1+2 ); |
| lastverticalw = AllocateFloatVec( ll1+2 ); |
| |
| m = AllocateFloatVec( ll2+2 ); |
| mp = AllocateIntVec( ll2+2 ); |
| gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 ); |
| |
| floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 ); |
| intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 ); |
| |
| #if DEBUG |
| fprintf( stderr, "succeeded\n" ); |
| #endif |
| |
| #if STOREWM |
| WMMTX = AllocateFloatMtx( ll1, ll2 ); |
| WMMTX2 = AllocateFloatMtx( ll1, ll2 ); |
| #endif |
| #if 0 |
| shortmtx = AllocateShortMtx( ll1, ll2 ); |
| |
| #if DEBUG |
| fprintf( stderr, "succeeded\n\n" ); |
| #endif |
| |
| ijp = shortmtx; |
| #endif |
| |
| currentw = w1; |
| previousw = w2; |
| |
| match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 ); |
| |
| match_ribosum( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 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 STOREWM |
| WMMTX[0][0] = initverticalw[0]; |
| for( i=1; i<lgth1+1; i++ ) |
| { |
| WMMTX[i][0] = initverticalw[i]; |
| } |
| for( j=1; j<lgth2+1; j++ ) |
| { |
| WMMTX[0][j] = currentw[j]; |
| } |
| #endif |
| |
| |
| for( j=1; j<lgth2+1; ++j ) |
| { |
| m[j] = currentw[j-1] + ogcp1[1]; |
| // m[j] = currentw[j-1]; |
| mp[j] = 0; |
| } |
| |
| lastverticalw[0] = currentw[lgth2-1]; |
| |
| imid = lgth1 * 0.5; |
| |
| jumpi = 0; // atode kawaru. |
| lasti = lgth1+1; |
| #if STOREWM |
| for( i=1; i<lasti; i++ ) |
| #else |
| for( i=1; i<=imid; i++ ) |
| #endif |
| { |
| wtmp = previousw; |
| previousw = currentw; |
| currentw = wtmp; |
| |
| previousw[0] = initverticalw[i-1]; |
| |
| match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 ); |
| currentw[0] = initverticalw[i]; |
| |
| m[0] = ogcp1[i]; |
| #if STOREM |
| WMMTX2[i][0] = m[0]; |
| #endif |
| if( i == imid ) midm[0] = m[0]; |
| |
| mi = previousw[0] + ogcp2[1]; |
| // mi = previousw[0]; |
| mpi = 0; |
| |
| |
| // 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; |
| |
| #if 0 |
| fprintf( stderr, "%5.0f->", wm ); |
| #endif |
| g = mi + fgcp2[j-1]; |
| // g = mi + fpenalty; |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| if( g > wm ) |
| { |
| wm = g; |
| // *ijppt = -( j - mpi ); |
| } |
| g = *prept + ogcp2[j]; |
| // g = *prept; |
| if( g >= mi ) |
| { |
| mi = g; |
| mpi = j-1; |
| } |
| #if USE_PENALTY_EX |
| mi += fpenalty_ex; |
| #endif |
| |
| g = *mjpt + fgcp1[i-1]; |
| // g = *mjpt + fpenalty; |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| if( g > wm ) |
| { |
| wm = g; |
| // *ijppt = +( i - *mpjpt ); |
| } |
| |
| |
| g = *prept + ogcp1[i]; |
| // g = *prept; |
| if( g >= *mjpt ) |
| { |
| *mjpt = g; |
| *mpjpt = i-1; |
| } |
| #if USE_PENALTY_EX |
| m[j] += fpenalty_ex; |
| #endif |
| #if LOCAL |
| if( wm < localthr ) |
| { |
| // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt ); |
| wm = 0; |
| } |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "%5.0f ", wm ); |
| #endif |
| *curpt += wm; |
| |
| |
| #if STOREWM |
| WMMTX[i][j] = *curpt; |
| WMMTX2[i][j] = *mjpt; |
| #endif |
| |
| if( i == imid ) //muda |
| { |
| jumpbackj[j] = *mpjpt; // muda atode matomeru |
| jumpbacki[j] = mpi; // muda atode matomeru |
| // fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt ); |
| // fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi ); |
| midw[j] = *curpt; |
| midm[j] = *mjpt; |
| midn[j] = mi; |
| } |
| |
| // fprintf( stderr, "m[%d] = %f\n", j, m[j] ); |
| mjpt++; |
| prept++; |
| mpjpt++; |
| curpt++; |
| |
| } |
| lastverticalw[i] = currentw[lgth2-1]; |
| |
| #if STOREWM |
| WMMTX2[i][lgth2] = m[lgth2-1]; |
| #endif |
| |
| #if 0 // ue |
| if( i == imid ) |
| { |
| for( j=0; j<lgth2; j++ ) midw[j] = currentw[j]; |
| for( j=0; j<lgth2; j++ ) midm[j] = m[j]; |
| } |
| #endif |
| } |
| // for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j]; |
| // for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j]; |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 10.2f ", WMMTX[i][j] ); |
| } |
| fprintf( stderr, "\n" ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "WMMTX2 = \n" ); |
| for( i=0; i<lgth1; i++ ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 10.2f ", WMMTX2[i][j] ); |
| } |
| fprintf( stderr, "\n" ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| |
| // gyakudp |
| |
| match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 ); |
| match_ribosum( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 ); |
| |
| for( i=0; i<lgth1-1; i++ ) |
| { |
| initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] ); |
| // initverticalw[i] += fpenalty; |
| } |
| for( j=0; j<lgth2-1; j++ ) |
| { |
| currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] ); |
| // currentw[j] += fpenalty; |
| } |
| |
| #if STOREWM |
| for( i=0; i<lgth1-1; i++ ) |
| { |
| WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] ); |
| // fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] ); |
| } |
| for( j=0; j<lgth2-1; j++ ) |
| { |
| WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] ); |
| // fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] ); |
| } |
| #endif |
| |
| |
| |
| |
| |
| |
| for( j=lgth2-1; j>0; --j ) |
| { |
| m[j-1] = currentw[j] + fgcp2[lgth2-2]; |
| // m[j-1] = currentw[j]; |
| mp[j] = lgth1-1; |
| } |
| |
| // for( j=0; j<lgth2; j++ ) m[j] = 0.0; |
| // m[lgth2-1] ha irunoka? |
| |
| |
| // for( i=lgth1-2; i>=imid; i-- ) |
| firstm = -9999999.9; |
| firstmp = lgth1-1; |
| 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 ); |
| match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 ); |
| |
| currentw[lgth2-1] = initverticalw[i]; |
| |
| // m[lgth2] = fgcp1[i]; |
| // WMMTX2[i][lgth2] += m[lgth2]; |
| // fprintf( stderr, "m[] = %f\n", m[lgth2] ); |
| |
| mi = previousw[lgth2-1] + fgcp2[lgth2-2]; |
| // mi = previousw[lgth2-1]; |
| mpi = lgth2 - 1; |
| |
| mjpt = m + lgth2 - 2; |
| prept = previousw + lgth2 - 1; |
| curpt = currentw + lgth2 - 2; |
| mpjpt = mp + lgth2 - 2; |
| |
| |
| for( j=lgth2-2; j>-1; j-- ) |
| { |
| wm = *prept; |
| ijpi = i+1; |
| ijpj = j+1; |
| |
| g = mi + ogcp2[j+1]; |
| // g = mi + fpenalty; |
| if( g > wm ) |
| { |
| wm = g; |
| ijpj = mpi; |
| ijpi = i+1; |
| } |
| |
| g = *prept + fgcp2[j]; |
| // g = *prept; |
| if( g >= mi ) |
| { |
| // fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 ); |
| mi = g; |
| mpi = j + 1; |
| } |
| |
| #if USE_PENALTY_EX |
| mi += fpenalty_ex; |
| #endif |
| |
| // fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt ); |
| g = *mjpt + ogcp1[i+1]; |
| // g = *mjpt + fpenalty; |
| if( g > wm ) |
| { |
| wm = g; |
| ijpi = *mpjpt; |
| ijpj = j+1; |
| } |
| |
| // if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j ); |
| g = *prept + fgcp1[i]; |
| // g = *prept; |
| if( g >= *mjpt ) |
| { |
| *mjpt = g; |
| *mpjpt = i + 1; |
| } |
| |
| #if USE_PENALTY_EX |
| m[j] += fpenalty_ex; |
| #endif |
| |
| if( i == jumpi || i == imid - 1 ) |
| { |
| jumpforwi[j] = ijpi; //muda |
| jumpforwj[j] = ijpj; //muda |
| // fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi ); |
| // fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj ); |
| } |
| if( i == imid ) // muda |
| { |
| midw[j] += wm; |
| // midm[j+1] += *mjpt + fpenalty; //?????? |
| midm[j+1] += *mjpt; //?????? |
| } |
| if( i == imid - 1 ) |
| { |
| // midn[j] += mi + fpenalty; //???? |
| midn[j] += mi; //???? |
| } |
| #if LOCAL |
| if( wm < localthr ) |
| { |
| // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt ); |
| wm = 0; |
| } |
| #endif |
| |
| #if STOREWM |
| WMMTX[i][j] += wm; |
| // WMMTX2[i][j+1] += *mjpt + fpenalty; |
| WMMTX2[i][j] += *curpt; |
| #endif |
| *curpt += wm; |
| |
| mjpt--; |
| prept--; |
| mpjpt--; |
| curpt--; |
| } |
| // fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 ); |
| g = *prept + fgcp1[i]; |
| if( firstm < g ) |
| { |
| firstm = g; |
| firstmp = i + 1; |
| } |
| #if STOREWM |
| // WMMTX2[i][j+1] += firstm; |
| #endif |
| if( i == imid ) midm[j+1] += firstm; |
| |
| if( i == imid - 1 ) |
| { |
| maxwm = midw[1]; |
| jmid = 0; |
| // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm ); |
| for( j=2; j<lgth2-1; j++ ) |
| { |
| wm = midw[j]; |
| if( wm > maxwm ) |
| { |
| jmid = j; |
| maxwm = wm; |
| } |
| // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm ); |
| } |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| wm = midm[j]; |
| if( wm > maxwm ) |
| { |
| jmid = j; |
| maxwm = wm; |
| } |
| // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm ); |
| } |
| |
| // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm ); |
| |
| |
| // fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid ); |
| wm = midw[jmid]; |
| jumpi = imid-1; |
| jumpj = jmid-1; |
| if( jmid > 0 && midn[jmid-1] > wm ) //060413 |
| { |
| jumpi = imid-1; |
| jumpj = jumpbacki[jmid]; |
| wm = midn[jmid-1]; |
| // fprintf( stderr, "rejump (n)\n" ); |
| } |
| if( midm[jmid] > wm ) |
| { |
| jumpi = jumpbackj[jmid]; |
| jumpj = jmid-1; |
| wm = midm[jmid]; |
| // fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi ); |
| } |
| |
| |
| // fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid ); |
| // fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj ); |
| #if 0 |
| fprintf( stderr, "imid = %d\n", imid ); |
| fprintf( stderr, "midn = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7.1f ", midn[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "midw = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7.1f ", midw[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "midm = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7.1f ", midm[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| // fprintf( stderr, "maxwm = %f\n", maxwm ); |
| } |
| if( i == jumpi ) //saki? |
| { |
| // fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi ); |
| // fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj ); |
| if( jmid == 0 ) |
| { |
| // fprintf( stderr, "CHUI2!\n" ); |
| jumpj = 0; jmid = 1; |
| jumpi = firstmp - 1; |
| imid = firstmp; |
| } |
| |
| #if 0 |
| else if( jmid == lgth2 ) |
| { |
| fprintf( stderr, "CHUI1!\n" ); |
| jumpi=0; jumpj=0; |
| imid=jumpforwi[0]; jmid=lgth2-1; |
| } |
| #else // 060414 |
| else if( jmid >= lgth2 ) |
| { |
| // fprintf( stderr, "CHUI1!\n" ); |
| jumpi=imid-1; jmid=lgth2; |
| jumpj = lgth2-1; |
| } |
| #endif |
| else |
| { |
| imid = jumpforwi[jumpj]; |
| jmid = jumpforwj[jumpj]; |
| } |
| #if 0 |
| fprintf( stderr, "jumpi -> %d\n", jumpi ); |
| fprintf( stderr, "jumpj -> %d\n", jumpj ); |
| fprintf( stderr, "imid -> %d\n", imid ); |
| fprintf( stderr, "jmid -> %d\n", jmid ); |
| #endif |
| |
| #if STOREWM |
| // break; |
| #else |
| break; |
| #endif |
| } |
| } |
| #if 0 |
| jumpi=0; jumpj=0; |
| imid=lgth1-1; jmid=lgth2-1; |
| } |
| #endif |
| |
| // fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi ); |
| // fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj ); |
| |
| // for( j=0; j<lgth2; j++ ) midw[j] += currentw[j]; |
| // for( j=0; j<lgth2; j++ ) midm[j] += m[j+1]; |
| // for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j]; |
| // for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j]; |
| |
| |
| |
| for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ ) |
| map[i][j] = WMMTX[i][j] / maxwm; |
| // map[i][j] = WMMTX2[i][j] / maxwm; |
| |
| #if STOREWM |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| float maxpairscore = -9999.9; |
| float tmpscore; |
| |
| for( j=0; j<lgth2; j++ ) |
| { |
| if( maxpairscore < (tmpscore=WMMTX[i][j]) ) |
| { |
| map12[i].pos = j; |
| map12[i].score = tmpscore; |
| maxpairscore = tmpscore; |
| } |
| } |
| |
| for( k=0; k<lgth1; k++ ) |
| { |
| if( i == k ) continue; |
| if( map12[i].score <= WMMTX[k][map12[i].pos] ) |
| break; |
| } |
| if( k != lgth1 ) |
| { |
| map12[i].pos = -1; |
| map12[i].score = -1.0; |
| } |
| fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] ); |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| float maxpairscore = -9999.9; |
| float tmpscore; |
| |
| for( i=0; i<lgth1; i++ ) |
| { |
| if( maxpairscore < (tmpscore=WMMTX[i][j]) ) |
| { |
| map21[j].pos = i; |
| map21[j].score = tmpscore; |
| maxpairscore = tmpscore; |
| } |
| } |
| |
| for( k=0; k<lgth2; k++ ) |
| { |
| if( j == k ) continue; |
| if( map21[j].score <= WMMTX[map21[j].pos][k] ) |
| break; |
| } |
| if( k != lgth2 ) |
| { |
| map21[j].pos = -1; |
| map21[j].score = -1.0; |
| } |
| fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] ); |
| } |
| |
| for( i=0; i<lgth1; i++ ) |
| { |
| if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i ) |
| fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos ); |
| } |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "WMMTX = \n" ); |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "%d ", i ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7.2f ", WMMTX[i][j] ); |
| } |
| fprintf( stderr, "\n" ); |
| } |
| // fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty ); |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "%d ", i ); |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| fprintf( stderr, "% 7.2f ", WMMTX2[i][j] ); |
| } |
| fprintf( stderr, "\n" ); |
| } |
| #endif |
| |
| #if 0 |
| fprintf( stdout, "#WMMTX = \n" ); |
| for( i=0; i<lgth1; i++ ) |
| { |
| // fprintf( stdout, "%d ", i ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| // if( WMMTX[i][j] > amino_dis['a']['g'] -1 ) |
| fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] ); |
| if( WMMTX[i][j] == maxwm ) |
| fprintf( stdout, "selected \n" ); |
| else |
| fprintf( stdout, "\n" ); |
| } |
| fprintf( stdout, "\n" ); |
| } |
| #endif |
| |
| #if 0 |
| |
| fprintf( stderr, "jumpbacki = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7d ", jumpbacki[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "jumpbackj = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7d ", jumpbackj[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "jumpforwi = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7d ", jumpforwi[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "jumpforwj = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7d ", jumpforwj[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| |
| |
| #endif |
| |
| |
| // Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc ); |
| |
| #if 0 // irukamo |
| 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" ); |
| } |
| #endif |
| |
| |
| |
| #if 0 |
| fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid ); |
| fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid ); |
| |
| fprintf( stderr, "imid = %d\n", imid ); |
| fprintf( stderr, "jmid = %d\n", jmid ); |
| #endif |
| |
| |
| FreeFloatVec( w1 ); |
| FreeFloatVec( w2 ); |
| FreeFloatVec( initverticalw ); |
| FreeFloatVec( lastverticalw ); |
| FreeFloatVec( midw ); |
| FreeFloatVec( midm ); |
| FreeFloatVec( midn ); |
| |
| FreeIntVec( jumpbacki ); |
| FreeIntVec( jumpbackj ); |
| FreeIntVec( jumpforwi ); |
| FreeIntVec( jumpforwj ); |
| FreeIntVec( jumpdummi ); |
| FreeIntVec( jumpdummj ); |
| |
| FreeFloatVec( m ); |
| FreeIntVec( mp ); |
| |
| FreeFloatMtx( floatwork ); |
| FreeIntMtx( intwork ); |
| |
| #if STOREWM |
| FreeFloatMtx( WMMTX ); |
| FreeFloatMtx( WMMTX2 ); |
| #endif |
| |
| return( value ); |
| |
| } |
| static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo, float **map ) |
| /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ |
| { |
| int alnlen; |
| float value = 0.0; |
| register int i, j; |
| char **aseq1, **aseq2; |
| int ll1, ll2, l, len; |
| int lasti, lastj, imid, jmid=0; |
| float wm = 0.0; /* int ?????? */ |
| float g; |
| float *currentw, *previousw; |
| #if USE_PENALTY_EX |
| float fpenalty_ex = (float)RNApenalty_ex; |
| #endif |
| // float fpenalty = (float)penalty; |
| float *wtmp; |
| // short *ijppt; |
| int *mpjpt; |
| // short **ijp; |
| int *mp; |
| int mpi; |
| float *mjpt, *prept, *curpt; |
| float mi; |
| float *m; |
| float *w1, *w2; |
| // float *match; |
| float *initverticalw; /* kufuu sureba iranai */ |
| float *lastverticalw; /* kufuu sureba iranai */ |
| int **intwork; |
| float **floatwork; |
| // short **shortmtx; |
| #if STOREWM |
| float **WMMTX; |
| float **WMMTX2; |
| #endif |
| float *midw; |
| float *midm; |
| float *midn; |
| int lgth1, lgth2; |
| float maxwm = 0.0; |
| int *jumpforwi; |
| int *jumpforwj; |
| int *jumpbacki; |
| int *jumpbackj; |
| int *jumpdummi; //muda |
| int *jumpdummj; //muda |
| int jumpi, jumpj = 0; |
| char *gaps; |
| int ijpi, ijpj; |
| float *ogcp1; |
| float *fgcp1; |
| float *ogcp2; |
| float *fgcp2; |
| float firstm; |
| int firstmp; |
| #if 0 |
| static char ttt1[50000]; |
| static char ttt2[50000]; |
| #endif |
| |
| localthr = -offset + 500; // 0? |
| |
| ogcp1 = gapinfo[0] + ist; |
| fgcp1 = gapinfo[1] + ist; |
| ogcp2 = gapinfo[2] + jst; |
| fgcp2 = gapinfo[3] + jst; |
| |
| depth++; |
| reccycle++; |
| |
| lgth1 = ien-ist+1; |
| lgth2 = jen-jst+1; |
| |
| // if( lgth1 < 5 ) |
| // fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 ); |
| // if( lgth2 < 5 ) |
| // fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 ); |
| // |
| |
| #if 0 |
| fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen ); |
| strncpy( ttt1, seq1[0]+ist, lgth1 ); |
| strncpy( ttt2, seq2[0]+jst, lgth2 ); |
| ttt1[lgth1] = 0; |
| ttt2[lgth2] = 0; |
| fprintf( stderr, "seq1 = %s\n", ttt1 ); |
| fprintf( stderr, "seq2 = %s\n", ttt2 ); |
| #endif |
| if( lgth2 <= 0 ) // lgth1 <= 0 ha? |
| { |
| // fprintf( stderr, "\n\n==== jimei\n\n" ); |
| // exit( 1 ); |
| for( i=0; i<icyc; i++ ) |
| { |
| strncpy( mseq1[i], seq1[i]+ist, lgth1 ); |
| mseq1[i][lgth1] = 0; |
| } |
| for( i=0; i<jcyc; i++ ) |
| { |
| mseq2[i][0] = 0; |
| for( j=0; j<lgth1; j++ ) |
| strcat( mseq2[i], "-" ); |
| } |
| |
| // fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] ); |
| // fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] ); |
| |
| return( 0.0 ); |
| } |
| |
| #if MEMSAVE |
| aseq1 = AllocateCharMtx( icyc, 0 ); |
| aseq2 = AllocateCharMtx( jcyc, 0 ); |
| for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i]; |
| for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i]; |
| #else |
| aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 ); |
| aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 ); |
| #endif |
| |
| // if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai |
| // if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari |
| if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka? |
| { |
| // fprintf( stderr, "==== Going to _tanni\n" ); |
| |
| // value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo ); |
| |
| |
| #if MEMSAVE |
| free( aseq1 ); |
| free( aseq2 ); |
| #else |
| for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] ); |
| for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] ); |
| |
| FreeCharMtx( aseq1 ); |
| FreeCharMtx( aseq2 ); |
| #endif |
| |
| // fprintf( stderr, "value = %f\n", value ); |
| |
| return( value ); |
| } |
| // fprintf( stderr, "Trying to divide the mtx\n" ); |
| |
| ll1 = ( (int)(lgth1) ) + 100; |
| ll2 = ( (int)(lgth2) ) + 100; |
| |
| // fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 ); |
| |
| w1 = AllocateFloatVec( ll2+2 ); |
| w2 = AllocateFloatVec( ll2+2 ); |
| // match = AllocateFloatVec( ll2+2 ); |
| midw = AllocateFloatVec( ll2+2 ); |
| midn = AllocateFloatVec( ll2+2 ); |
| midm = AllocateFloatVec( ll2+2 ); |
| jumpbacki = AllocateIntVec( ll2+2 ); |
| jumpbackj = AllocateIntVec( ll2+2 ); |
| jumpforwi = AllocateIntVec( ll2+2 ); |
| jumpforwj = AllocateIntVec( ll2+2 ); |
| jumpdummi = AllocateIntVec( ll2+2 ); |
| jumpdummj = AllocateIntVec( ll2+2 ); |
| |
| initverticalw = AllocateFloatVec( ll1+2 ); |
| lastverticalw = AllocateFloatVec( ll1+2 ); |
| |
| m = AllocateFloatVec( ll2+2 ); |
| mp = AllocateIntVec( ll2+2 ); |
| gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 ); |
| |
| floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 ); |
| intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 ); |
| |
| #if DEBUG |
| fprintf( stderr, "succeeded\n" ); |
| #endif |
| |
| #if STOREWM |
| WMMTX = AllocateFloatMtx( ll1, ll2 ); |
| WMMTX2 = AllocateFloatMtx( ll1, ll2 ); |
| #endif |
| #if 0 |
| shortmtx = AllocateShortMtx( ll1, ll2 ); |
| |
| #if DEBUG |
| fprintf( stderr, "succeeded\n\n" ); |
| #endif |
| |
| ijp = shortmtx; |
| #endif |
| |
| currentw = w1; |
| previousw = w2; |
| |
| match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 ); |
| |
| match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 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 STOREWM |
| WMMTX[0][0] = initverticalw[0]; |
| for( i=1; i<lgth1+1; i++ ) |
| { |
| WMMTX[i][0] = initverticalw[i]; |
| } |
| for( j=1; j<lgth2+1; j++ ) |
| { |
| WMMTX[0][j] = currentw[j]; |
| } |
| #endif |
| |
| |
| for( j=1; j<lgth2+1; ++j ) |
| { |
| m[j] = currentw[j-1] + ogcp1[1]; |
| // m[j] = currentw[j-1]; |
| mp[j] = 0; |
| } |
| |
| lastverticalw[0] = currentw[lgth2-1]; |
| |
| imid = lgth1 * 0.5; |
| |
| jumpi = 0; // atode kawaru. |
| lasti = lgth1+1; |
| #if STOREWM |
| for( i=1; i<lasti; i++ ) |
| #else |
| for( i=1; i<=imid; i++ ) |
| #endif |
| { |
| wtmp = previousw; |
| previousw = currentw; |
| currentw = wtmp; |
| |
| previousw[0] = initverticalw[i-1]; |
| |
| match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 ); |
| currentw[0] = initverticalw[i]; |
| |
| m[0] = ogcp1[i]; |
| #if STOREM |
| WMMTX2[i][0] = m[0]; |
| #endif |
| if( i == imid ) midm[0] = m[0]; |
| |
| mi = previousw[0] + ogcp2[1]; |
| // mi = previousw[0]; |
| mpi = 0; |
| |
| |
| // 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; |
| |
| #if 0 |
| fprintf( stderr, "%5.0f->", wm ); |
| #endif |
| g = mi + fgcp2[j-1]; |
| // g = mi + fpenalty; |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| if( g > wm ) |
| { |
| wm = g; |
| // *ijppt = -( j - mpi ); |
| } |
| g = *prept + ogcp2[j]; |
| // g = *prept; |
| if( g >= mi ) |
| { |
| mi = g; |
| mpi = j-1; |
| } |
| #if USE_PENALTY_EX |
| mi += fpenalty_ex; |
| #endif |
| |
| g = *mjpt + fgcp1[i-1]; |
| // g = *mjpt + fpenalty; |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| if( g > wm ) |
| { |
| wm = g; |
| // *ijppt = +( i - *mpjpt ); |
| } |
| |
| |
| g = *prept + ogcp1[i]; |
| // g = *prept; |
| if( g >= *mjpt ) |
| { |
| *mjpt = g; |
| *mpjpt = i-1; |
| } |
| #if USE_PENALTY_EX |
| m[j] += fpenalty_ex; |
| #endif |
| #if LOCAL |
| if( wm < localthr ) |
| { |
| // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt ); |
| wm = 0; |
| } |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "%5.0f ", wm ); |
| #endif |
| *curpt += wm; |
| |
| |
| #if STOREWM |
| WMMTX[i][j] = *curpt; |
| WMMTX2[i][j] = *mjpt; |
| #endif |
| |
| if( i == imid ) //muda |
| { |
| jumpbackj[j] = *mpjpt; // muda atode matomeru |
| jumpbacki[j] = mpi; // muda atode matomeru |
| // fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt ); |
| // fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi ); |
| midw[j] = *curpt; |
| midm[j] = *mjpt; |
| midn[j] = mi; |
| } |
| |
| // fprintf( stderr, "m[%d] = %f\n", j, m[j] ); |
| mjpt++; |
| prept++; |
| mpjpt++; |
| curpt++; |
| |
| } |
| lastverticalw[i] = currentw[lgth2-1]; |
| |
| #if STOREWM |
| WMMTX2[i][lgth2] = m[lgth2-1]; |
| #endif |
| |
| #if 0 // ue |
| if( i == imid ) |
| { |
| for( j=0; j<lgth2; j++ ) midw[j] = currentw[j]; |
| for( j=0; j<lgth2; j++ ) midm[j] = m[j]; |
| } |
| #endif |
| } |
| // for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j]; |
| // for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j]; |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 10.2f ", WMMTX[i][j] ); |
| } |
| fprintf( stderr, "\n" ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "WMMTX2 = \n" ); |
| for( i=0; i<lgth1; i++ ) |
| { |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 10.2f ", WMMTX2[i][j] ); |
| } |
| fprintf( stderr, "\n" ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| |
| // gyakudp |
| |
| match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 ); |
| match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 ); |
| |
| for( i=0; i<lgth1-1; i++ ) |
| { |
| initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] ); |
| // initverticalw[i] += fpenalty; |
| } |
| for( j=0; j<lgth2-1; j++ ) |
| { |
| currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] ); |
| // currentw[j] += fpenalty; |
| } |
| |
| #if STOREWM |
| for( i=0; i<lgth1-1; i++ ) |
| { |
| WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] ); |
| // fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] ); |
| } |
| for( j=0; j<lgth2-1; j++ ) |
| { |
| WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] ); |
| // fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] ); |
| } |
| #endif |
| |
| |
| |
| |
| |
| |
| for( j=lgth2-1; j>0; --j ) |
| { |
| m[j-1] = currentw[j] + fgcp2[lgth2-2]; |
| // m[j-1] = currentw[j]; |
| mp[j] = lgth1-1; |
| } |
| |
| // for( j=0; j<lgth2; j++ ) m[j] = 0.0; |
| // m[lgth2-1] ha irunoka? |
| |
| |
| // for( i=lgth1-2; i>=imid; i-- ) |
| firstm = -9999999.9; |
| firstmp = lgth1-1; |
| 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 ); |
| match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 ); |
| |
| currentw[lgth2-1] = initverticalw[i]; |
| |
| // m[lgth2] = fgcp1[i]; |
| // WMMTX2[i][lgth2] += m[lgth2]; |
| // fprintf( stderr, "m[] = %f\n", m[lgth2] ); |
| |
| mi = previousw[lgth2-1] + fgcp2[lgth2-2]; |
| // mi = previousw[lgth2-1]; |
| mpi = lgth2 - 1; |
| |
| mjpt = m + lgth2 - 2; |
| prept = previousw + lgth2 - 1; |
| curpt = currentw + lgth2 - 2; |
| mpjpt = mp + lgth2 - 2; |
| |
| |
| for( j=lgth2-2; j>-1; j-- ) |
| { |
| wm = *prept; |
| ijpi = i+1; |
| ijpj = j+1; |
| |
| g = mi + ogcp2[j+1]; |
| // g = mi + fpenalty; |
| if( g > wm ) |
| { |
| wm = g; |
| ijpj = mpi; |
| ijpi = i+1; |
| } |
| |
| g = *prept + fgcp2[j]; |
| // g = *prept; |
| if( g >= mi ) |
| { |
| // fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 ); |
| mi = g; |
| mpi = j + 1; |
| } |
| |
| #if USE_PENALTY_EX |
| mi += fpenalty_ex; |
| #endif |
| |
| // fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt ); |
| g = *mjpt + ogcp1[i+1]; |
| // g = *mjpt + fpenalty; |
| if( g > wm ) |
| { |
| wm = g; |
| ijpi = *mpjpt; |
| ijpj = j+1; |
| } |
| |
| // if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j ); |
| g = *prept + fgcp1[i]; |
| // g = *prept; |
| if( g >= *mjpt ) |
| { |
| *mjpt = g; |
| *mpjpt = i + 1; |
| } |
| |
| #if USE_PENALTY_EX |
| m[j] += fpenalty_ex; |
| #endif |
| |
| if( i == jumpi || i == imid - 1 ) |
| { |
| jumpforwi[j] = ijpi; //muda |
| jumpforwj[j] = ijpj; //muda |
| // fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi ); |
| // fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj ); |
| } |
| if( i == imid ) // muda |
| { |
| midw[j] += wm; |
| // midm[j+1] += *mjpt + fpenalty; //?????? |
| midm[j+1] += *mjpt; //?????? |
| } |
| if( i == imid - 1 ) |
| { |
| // midn[j] += mi + fpenalty; //???? |
| midn[j] += mi; //???? |
| } |
| #if LOCAL |
| if( wm < localthr ) |
| { |
| // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt ); |
| wm = 0; |
| } |
| #endif |
| |
| #if STOREWM |
| WMMTX[i][j] += wm; |
| // WMMTX2[i][j+1] += *mjpt + fpenalty; |
| WMMTX2[i][j] += *curpt; |
| #endif |
| *curpt += wm; |
| |
| mjpt--; |
| prept--; |
| mpjpt--; |
| curpt--; |
| } |
| // fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 ); |
| g = *prept + fgcp1[i]; |
| if( firstm < g ) |
| { |
| firstm = g; |
| firstmp = i + 1; |
| } |
| #if STOREWM |
| // WMMTX2[i][j+1] += firstm; |
| #endif |
| if( i == imid ) midm[j+1] += firstm; |
| |
| if( i == imid - 1 ) |
| { |
| maxwm = midw[1]; |
| jmid = 0; |
| // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm ); |
| for( j=2; j<lgth2-1; j++ ) |
| { |
| wm = midw[j]; |
| if( wm > maxwm ) |
| { |
| jmid = j; |
| maxwm = wm; |
| } |
| // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm ); |
| } |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| wm = midm[j]; |
| if( wm > maxwm ) |
| { |
| jmid = j; |
| maxwm = wm; |
| } |
| // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm ); |
| } |
| |
| // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm ); |
| |
| |
| // fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid ); |
| wm = midw[jmid]; |
| jumpi = imid-1; |
| jumpj = jmid-1; |
| if( jmid > 0 && midn[jmid-1] > wm ) //060413 |
| { |
| jumpi = imid-1; |
| jumpj = jumpbacki[jmid]; |
| wm = midn[jmid-1]; |
| // fprintf( stderr, "rejump (n)\n" ); |
| } |
| if( midm[jmid] > wm ) |
| { |
| jumpi = jumpbackj[jmid]; |
| jumpj = jmid-1; |
| wm = midm[jmid]; |
| // fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi ); |
| } |
| |
| |
| // fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid ); |
| // fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj ); |
| #if 0 |
| fprintf( stderr, "imid = %d\n", imid ); |
| fprintf( stderr, "midn = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7.1f ", midn[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "midw = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7.1f ", midw[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "midm = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7.1f ", midm[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| // fprintf( stderr, "maxwm = %f\n", maxwm ); |
| } |
| if( i == jumpi ) //saki? |
| { |
| // fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi ); |
| // fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj ); |
| if( jmid == 0 ) |
| { |
| // fprintf( stderr, "CHUI2!\n" ); |
| jumpj = 0; jmid = 1; |
| jumpi = firstmp - 1; |
| imid = firstmp; |
| } |
| |
| #if 0 |
| else if( jmid == lgth2 ) |
| { |
| fprintf( stderr, "CHUI1!\n" ); |
| jumpi=0; jumpj=0; |
| imid=jumpforwi[0]; jmid=lgth2-1; |
| } |
| #else // 060414 |
| else if( jmid >= lgth2 ) |
| { |
| // fprintf( stderr, "CHUI1!\n" ); |
| jumpi=imid-1; jmid=lgth2; |
| jumpj = lgth2-1; |
| } |
| #endif |
| else |
| { |
| imid = jumpforwi[jumpj]; |
| jmid = jumpforwj[jumpj]; |
| } |
| #if 0 |
| fprintf( stderr, "jumpi -> %d\n", jumpi ); |
| fprintf( stderr, "jumpj -> %d\n", jumpj ); |
| fprintf( stderr, "imid -> %d\n", imid ); |
| fprintf( stderr, "jmid -> %d\n", jmid ); |
| #endif |
| |
| #if STOREWM |
| // break; |
| #else |
| break; |
| #endif |
| } |
| } |
| #if 0 |
| jumpi=0; jumpj=0; |
| imid=lgth1-1; jmid=lgth2-1; |
| } |
| #endif |
| |
| // fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi ); |
| // fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj ); |
| |
| // for( j=0; j<lgth2; j++ ) midw[j] += currentw[j]; |
| // for( j=0; j<lgth2; j++ ) midm[j] += m[j+1]; |
| // for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j]; |
| // for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j]; |
| |
| |
| |
| for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ ) |
| map[i][j] = WMMTX[i][j] / maxwm; |
| // map[i][j] = WMMTX2[i][j] / maxwm; |
| |
| #if STOREWM |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| float maxpairscore = -9999.9; |
| float tmpscore; |
| |
| for( j=0; j<lgth2; j++ ) |
| { |
| if( maxpairscore < (tmpscore=WMMTX[i][j]) ) |
| { |
| map12[i].pos = j; |
| map12[i].score = tmpscore; |
| maxpairscore = tmpscore; |
| } |
| } |
| |
| for( k=0; k<lgth1; k++ ) |
| { |
| if( i == k ) continue; |
| if( map12[i].score <= WMMTX[k][map12[i].pos] ) |
| break; |
| } |
| if( k != lgth1 ) |
| { |
| map12[i].pos = -1; |
| map12[i].score = -1.0; |
| } |
| fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] ); |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| float maxpairscore = -9999.9; |
| float tmpscore; |
| |
| for( i=0; i<lgth1; i++ ) |
| { |
| if( maxpairscore < (tmpscore=WMMTX[i][j]) ) |
| { |
| map21[j].pos = i; |
| map21[j].score = tmpscore; |
| maxpairscore = tmpscore; |
| } |
| } |
| |
| for( k=0; k<lgth2; k++ ) |
| { |
| if( j == k ) continue; |
| if( map21[j].score <= WMMTX[map21[j].pos][k] ) |
| break; |
| } |
| if( k != lgth2 ) |
| { |
| map21[j].pos = -1; |
| map21[j].score = -1.0; |
| } |
| fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] ); |
| } |
| |
| for( i=0; i<lgth1; i++ ) |
| { |
| if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i ) |
| fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos ); |
| } |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "WMMTX = \n" ); |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "%d ", i ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7.2f ", WMMTX[i][j] ); |
| } |
| fprintf( stderr, "\n" ); |
| } |
| // fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty ); |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "%d ", i ); |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| fprintf( stderr, "% 7.2f ", WMMTX2[i][j] ); |
| } |
| fprintf( stderr, "\n" ); |
| } |
| exit( 1 ); |
| #endif |
| |
| #if 0 |
| fprintf( stdout, "#WMMTX = \n" ); |
| for( i=0; i<lgth1; i++ ) |
| { |
| // fprintf( stdout, "%d ", i ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| // if( WMMTX[i][j] > amino_dis['a']['g'] -1 ) |
| fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] ); |
| if( WMMTX[i][j] == maxwm ) |
| fprintf( stdout, "selected \n" ); |
| else |
| fprintf( stdout, "\n" ); |
| } |
| fprintf( stdout, "\n" ); |
| } |
| exit( 1 ); |
| #endif |
| |
| #if 0 |
| |
| fprintf( stderr, "jumpbacki = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7d ", jumpbacki[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "jumpbackj = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7d ", jumpbackj[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "jumpforwi = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7d ", jumpforwi[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "jumpforwj = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "% 7d ", jumpforwj[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| |
| |
| #endif |
| |
| |
| // Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc ); |
| |
| #if 0 // irukamo |
| 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" ); |
| } |
| #endif |
| |
| |
| |
| #if 0 |
| fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid ); |
| fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid ); |
| |
| fprintf( stderr, "imid = %d\n", imid ); |
| fprintf( stderr, "jmid = %d\n", jmid ); |
| #endif |
| |
| |
| FreeFloatVec( w1 ); |
| FreeFloatVec( w2 ); |
| FreeFloatVec( initverticalw ); |
| FreeFloatVec( lastverticalw ); |
| FreeFloatVec( midw ); |
| FreeFloatVec( midm ); |
| FreeFloatVec( midn ); |
| |
| FreeIntVec( jumpbacki ); |
| FreeIntVec( jumpbackj ); |
| FreeIntVec( jumpforwi ); |
| FreeIntVec( jumpforwj ); |
| FreeIntVec( jumpdummi ); |
| FreeIntVec( jumpdummj ); |
| |
| FreeFloatVec( m ); |
| FreeIntVec( mp ); |
| |
| FreeFloatMtx( floatwork ); |
| FreeIntMtx( intwork ); |
| |
| #if STOREWM |
| FreeFloatMtx( WMMTX ); |
| FreeFloatMtx( WMMTX2 ); |
| #endif |
| |
| return( value ); |
| |
| // fprintf( stderr, "==== calling myself (first)\n" ); |
| |
| #if 0 |
| fprintf( stderr, "seq1[0] = %s\n", seq1[0] ); |
| fprintf( stderr, "seq2[0] = %s\n", seq2[0] ); |
| #endif |
| value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo, map ); |
| #if 0 |
| fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] ); |
| fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] ); |
| #endif |
| #if MEMSAVE |
| #else |
| for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] ); |
| for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] ); |
| #endif |
| |
| // fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien ); |
| // fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen ); |
| |
| len = strlen( mseq1[0] ); |
| // fprintf( stderr, "len = %d\n", len ); |
| l = jmid - jumpj - 1; |
| // fprintf( stderr, "l=%d\n", l ); |
| if( l > 0 ) |
| { |
| for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0; |
| for( i=0; i<icyc; i++ ) |
| { |
| strcat( mseq1[i], gaps ); |
| mseq1[i][len+l] = 0; |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| strncat( mseq2[j], seq2[j]+jst+jumpj+1, l ); |
| mseq2[j][len+l] = 0; |
| } |
| // fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 ); |
| value += ( ogcp2[jumpj+1] + fgcp2[jmid-1] ); |
| // value += fpenalty; |
| } |
| len = strlen( mseq1[0] ); |
| l = imid - jumpi - 1; |
| // fprintf( stderr, "l=%d\n", l ); |
| if( l > 0 ) |
| { |
| for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0; |
| for( i=0; i<icyc; i++ ) |
| { |
| strncat( mseq1[i], seq1[i]+ist+jumpi+1, l ); |
| mseq1[i][len+l] = 0; |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| strcat( mseq2[j], gaps ); |
| mseq2[j][len+l] = 0; |
| } |
| |
| // for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] ); |
| // for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] ); |
| |
| |
| // fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] ); |
| value += ( ogcp1[jumpi+1] + fgcp1[imid-1] ); |
| // value += fpenalty; |
| } |
| #if 0 |
| for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] ); |
| for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] ); |
| #endif |
| |
| // fprintf( stderr, "==== calling myself (second)\n" ); |
| |
| #if MEMSAVE |
| alnlen = strlen( aseq1[0] ); |
| for( i=0; i<icyc; i++ ) aseq1[i] += alnlen; |
| for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen; |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "seq1[0] = %s\n", seq1[0] ); |
| fprintf( stderr, "seq2[0] = %s\n", seq2[0] ); |
| #endif |
| value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo, map ); |
| #if 0 |
| fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] ); |
| fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] ); |
| #endif |
| |
| |
| |
| #if DEBUG |
| if( value - maxwm > 1 || maxwm - value > 1 ) |
| { |
| fprintf( stderr, "WARNING value = %f, but maxwm = %f\n", value, maxwm ); |
| for( i=0; i<icyc; i++ ) |
| { |
| fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] ); |
| fprintf( stderr, "%s\n", aseq1[i] ); |
| } |
| for( i=0; i<jcyc; i++ ) |
| { |
| fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] ); |
| fprintf( stderr, "%s\n", aseq2[i] ); |
| } |
| |
| // exit( 1 ); |
| } |
| else |
| { |
| fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm ); |
| } |
| #endif |
| |
| #if MEMSAVE |
| #else |
| for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] ); |
| for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] ); |
| #endif |
| |
| // fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien ); |
| // fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen ); |
| |
| free( gaps ); |
| #if MEMSAVE |
| free( aseq1 ); |
| free( aseq2 ); |
| #else |
| FreeCharMtx( aseq1 ); |
| FreeCharMtx( aseq2 ); |
| #endif |
| |
| return( value ); |
| } |
| |
| |
| |
| float Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, float **map ) |
| /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ |
| { |
| // int k; |
| int i, j; |
| int ll1, ll2; |
| int lgth1, lgth2; |
| float wm = 0.0; /* int ?????? */ |
| char **mseq1; |
| char **mseq2; |
| // char **mseq; |
| float *ogcp1; |
| float *ogcp2; |
| float *fgcp1; |
| float *fgcp2; |
| float **cpmx1; |
| float **cpmx2; |
| float **gapinfo; |
| // float fpenalty; |
| float fpenalty = (float)RNApenalty; |
| int nglen1, nglen2; |
| |
| |
| |
| |
| |
| #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 |
| |
| nglen1 = seqlen( seq1[0] ); |
| nglen2 = seqlen( seq2[0] ); |
| |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| ll1 = ( (int)(lgth1) ) + 100; |
| ll2 = ( (int)(lgth2) ) + 100; |
| |
| mseq1 = AllocateCharMtx( icyc, ll1+ll2 ); |
| mseq2 = AllocateCharMtx( jcyc, ll1+ll2 ); |
| |
| gapinfo = AllocateFloatMtx( 4, 0 ); |
| ogcp1 = AllocateFloatVec( ll1+2 ); |
| ogcp2 = AllocateFloatVec( ll2+2 ); |
| fgcp1 = AllocateFloatVec( ll1+2 ); |
| fgcp2 = AllocateFloatVec( ll2+2 ); |
| |
| |
| cpmx1 = AllocateFloatMtx( ll1+2, 27 ); |
| cpmx2 = AllocateFloatMtx( ll2+2, 27 ); |
| |
| for( i=0; i<icyc; i++ ) |
| { |
| if( strlen( seq1[i] ) != lgth1 ) |
| { |
| fprintf( stderr, "i = %d / %d\n", i, icyc ); |
| fprintf( stderr, "bug! hairetsu ga kowareta!\n" ); |
| exit( 1 ); |
| } |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| if( strlen( seq2[j] ) != lgth2 ) |
| { |
| fprintf( stderr, "j = %d / %d\n", j, jcyc ); |
| fprintf( stderr, "bug! hairetsu ga kowareta!\n" ); |
| exit( 1 ); |
| } |
| } |
| |
| MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); |
| MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc ); |
| |
| |
| #if 1 |
| |
| 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, egap2 ); |
| 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 ); |
| } |
| |
| #if 1 |
| for( i=0; i<lgth1; i++ ) |
| { |
| ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty; |
| fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty; |
| // fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] ); |
| } |
| for( i=0; i<lgth2; i++ ) |
| { |
| ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty; |
| fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty; |
| // fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] ); |
| } |
| #else |
| for( i=0; i<lgth1; i++ ) |
| { |
| ogcp1[i] = 0.5 * fpenalty; |
| fgcp1[i] = 0.5 * fpenalty; |
| } |
| for( i=0; i<lgth2; i++ ) |
| { |
| ogcp2[i] = 0.5 * fpenalty; |
| fgcp2[i] = 0.5 * fpenalty; |
| } |
| #endif |
| |
| gapinfo[0] = ogcp1; |
| gapinfo[1] = fgcp1; |
| gapinfo[2] = ogcp2; |
| gapinfo[3] = fgcp2; |
| #endif |
| |
| #if 0 |
| fprintf( stdout, "in MSalignmm.c\n" ); |
| for( i=0; i<icyc; i++ ) |
| { |
| fprintf( stdout, ">%d of GROUP1\n", i ); |
| fprintf( stdout, "%s\n", seq1[i] ); |
| } |
| for( i=0; i<jcyc; i++ ) |
| { |
| fprintf( stdout, ">%d of GROUP2\n", i ); |
| fprintf( stdout, "%s\n", seq2[i] ); |
| } |
| fflush( stdout ); |
| #endif |
| |
| wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map ); |
| #if DEBUG |
| fprintf( stderr, " seq1[0] = %s\n", seq1[0] ); |
| fprintf( stderr, " seq2[0] = %s\n", seq2[0] ); |
| fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] ); |
| fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] ); |
| #endif |
| |
| // fprintf( stderr, "wm = %f\n", wm ); |
| |
| #if 0 |
| |
| for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] ); |
| for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] ); |
| |
| if( seqlen( seq1[0] ) != nglen1 ) |
| { |
| fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 ); |
| fprintf( stderr, "seq1[0] = %s\n", seq1[0] ); |
| exit( 1 ); |
| } |
| if( seqlen( seq2[0] ) != nglen2 ) |
| { |
| fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 ); |
| exit( 1 ); |
| } |
| #endif |
| |
| FreeFloatVec( ogcp1 ); |
| FreeFloatVec( ogcp2 ); |
| FreeFloatVec( fgcp1 ); |
| FreeFloatVec( fgcp2 ); |
| FreeFloatMtx( cpmx1 ); |
| FreeFloatMtx( cpmx2 ); |
| free( (void *)gapinfo ); |
| |
| FreeCharMtx( mseq1 ); |
| FreeCharMtx( mseq2 ); |
| |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| for( i=0; i<icyc; i++ ) |
| { |
| if( strlen( seq1[i] ) != lgth1 ) |
| { |
| fprintf( stderr, "i = %d / %d\n", i, icyc ); |
| fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" ); |
| exit( 1 ); |
| } |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| if( strlen( seq2[j] ) != lgth2 ) |
| { |
| fprintf( stderr, "j = %d / %d\n", j, jcyc ); |
| fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" ); |
| exit( 1 ); |
| } |
| } |
| |
| return( wm ); |
| } |
| |
| float Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, float **map ) |
| /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ |
| { |
| // int k; |
| int i, j; |
| int ll1, ll2; |
| int lgth1, lgth2; |
| float wm = 0.0; /* int ?????? */ |
| char **mseq1; |
| char **mseq2; |
| float *ogcp1; |
| float *ogcp2; |
| float *fgcp1; |
| float *fgcp2; |
| float **cpmx1; |
| float **cpmx2; |
| float **gapinfo; |
| float fpenalty = (float)penalty; |
| int nglen1, nglen2; |
| |
| #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 |
| |
| nglen1 = seqlen( seq1[0] ); |
| nglen2 = seqlen( seq2[0] ); |
| |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| ll1 = ( (int)(lgth1) ) + 100; |
| ll2 = ( (int)(lgth2) ) + 100; |
| |
| mseq1 = AllocateCharMtx( icyc, ll1+ll2 ); |
| mseq2 = AllocateCharMtx( jcyc, ll1+ll2 ); |
| |
| gapinfo = AllocateFloatMtx( 4, 0 ); |
| ogcp1 = AllocateFloatVec( ll1+2 ); |
| ogcp2 = AllocateFloatVec( ll2+2 ); |
| fgcp1 = AllocateFloatVec( ll1+2 ); |
| fgcp2 = AllocateFloatVec( ll2+2 ); |
| |
| |
| cpmx1 = AllocateFloatMtx( ll1+2, 39 ); |
| cpmx2 = AllocateFloatMtx( ll2+2, 39 ); |
| |
| for( i=0; i<icyc; i++ ) |
| { |
| if( strlen( seq1[i] ) != lgth1 ) |
| { |
| fprintf( stderr, "i = %d / %d\n", i, icyc ); |
| fprintf( stderr, "bug! hairetsu ga kowareta!\n" ); |
| exit( 1 ); |
| } |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| if( strlen( seq2[j] ) != lgth2 ) |
| { |
| fprintf( stderr, "j = %d / %d\n", j, jcyc ); |
| fprintf( stderr, "bug! hairetsu ga kowareta!\n" ); |
| exit( 1 ); |
| } |
| } |
| |
| #if 0 |
| MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); |
| MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc ); |
| #else |
| cpmx_ribosum( seq1, seq1r, dir1, cpmx1, eff1, lgth1, icyc ); |
| cpmx_ribosum( seq2, seq2r, dir2, cpmx2, eff2, lgth2, jcyc ); |
| #endif |
| |
| |
| #if 1 |
| |
| 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, egap2 ); |
| 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 ); |
| } |
| |
| #if 1 |
| for( i=0; i<lgth1; i++ ) |
| { |
| ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty; |
| fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty; |
| // fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] ); |
| } |
| for( i=0; i<lgth2; i++ ) |
| { |
| ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty; |
| fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty; |
| // fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] ); |
| } |
| #else |
| for( i=0; i<lgth1; i++ ) |
| { |
| ogcp1[i] = 0.5 * fpenalty; |
| fgcp1[i] = 0.5 * fpenalty; |
| } |
| for( i=0; i<lgth2; i++ ) |
| { |
| ogcp2[i] = 0.5 * fpenalty; |
| fgcp2[i] = 0.5 * fpenalty; |
| } |
| #endif |
| |
| gapinfo[0] = ogcp1; |
| gapinfo[1] = fgcp1; |
| gapinfo[2] = ogcp2; |
| gapinfo[3] = fgcp2; |
| #endif |
| |
| #if 0 |
| fprintf( stdout, "in MSalignmm.c\n" ); |
| for( i=0; i<icyc; i++ ) |
| { |
| fprintf( stdout, ">%d of GROUP1\n", i ); |
| fprintf( stdout, "%s\n", seq1[i] ); |
| } |
| for( i=0; i<jcyc; i++ ) |
| { |
| fprintf( stdout, ">%d of GROUP2\n", i ); |
| fprintf( stdout, "%s\n", seq2[i] ); |
| } |
| fflush( stdout ); |
| #endif |
| |
| wm = MSalign2m2m_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map ); |
| #if DEBUG |
| fprintf( stderr, " seq1[0] = %s\n", seq1[0] ); |
| fprintf( stderr, " seq2[0] = %s\n", seq2[0] ); |
| fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] ); |
| fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] ); |
| #endif |
| |
| // fprintf( stderr, "wm = %f\n", wm ); |
| |
| #if 0 |
| |
| for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] ); |
| for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] ); |
| |
| if( seqlen( seq1[0] ) != nglen1 ) |
| { |
| fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 ); |
| fprintf( stderr, "seq1[0] = %s\n", seq1[0] ); |
| exit( 1 ); |
| } |
| if( seqlen( seq2[0] ) != nglen2 ) |
| { |
| fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 ); |
| exit( 1 ); |
| } |
| #endif |
| |
| FreeFloatVec( ogcp1 ); |
| FreeFloatVec( ogcp2 ); |
| FreeFloatVec( fgcp1 ); |
| FreeFloatVec( fgcp2 ); |
| FreeFloatMtx( cpmx1 ); |
| FreeFloatMtx( cpmx2 ); |
| free( (void *)gapinfo ); |
| |
| FreeCharMtx( mseq1 ); |
| FreeCharMtx( mseq2 ); |
| |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| for( i=0; i<icyc; i++ ) |
| { |
| if( strlen( seq1[i] ) != lgth1 ) |
| { |
| fprintf( stderr, "i = %d / %d\n", i, icyc ); |
| fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" ); |
| exit( 1 ); |
| } |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| if( strlen( seq2[j] ) != lgth2 ) |
| { |
| fprintf( stderr, "j = %d / %d\n", j, jcyc ); |
| fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" ); |
| exit( 1 ); |
| } |
| } |
| |
| return( wm ); |
| } |