blob: 19f26ecf376261b5320d2caafc78216878e2b55d [file] [log] [blame]
#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