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Packages/mafft/src/mafft-7.487-with-extensions/core/Galign11.c
starsareintherose eeb4358381 add mafft
2021-08-10 22:21:03 +08:00

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#include "mltaln.h"
#include "dp.h"
#define DEBUG 0
#define XXXXXXX 0
#define USE_PENALTY_EX 1
#define TERMGAPFAC 0.0
#define TERMGAPFAC_EX 0.0
#if 1
static void match_calc_mtx( double **mtx, double *match, char **s1, char **s2, int i1, int lgth2 )
{
char *seq2 = s2[0];
double *doubleptr = mtx[(unsigned char)s1[0][i1]];
while( lgth2-- )
*match++ = doubleptr[(unsigned char)*seq2++];
}
#else
static void match_calc( double *match, char **s1, char **s2, int i1, int lgth2 )
{
int j;
for( j=0; j<lgth2; j++ )
match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
}
#endif
static double Atracking( double *lasthorizontalw, double *lastverticalw,
char **seq1, char **seq2,
char **mseq1, char **mseq2,
int **ijp,
int tailgp,
int *warpis, int *warpjs, int warpbase )
{
int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
// char gap[] = "-";
char *gap;
gap = newgapstr;
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
double wm, g;
double fpenalty = (double)penalty;
double fpenalty_ex = (double)penalty_ex;
#if 0
for( i=0; i<lgth1; i++ )
{
fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
}
#endif
for( i=0; i<lgth1+1; i++ )
{
ijp[i][0] = i + 1;
}
for( j=0; j<lgth2+1; j++ )
{
ijp[0][j] = -( j + 1 );
}
// if( tailgp == 1 || ijp[lgth1][lgth2] >= warpbase )
if( tailgp == 1 )
;
else
{
#if 1
// reporterr( "lastverticalw[lgth1-1] = %f\n", lastverticalw[lgth1-1] );
// reporterr( "lasthorizontalw[lgth2-1] = %f\n", lasthorizontalw[lgth2-1] );
wm = lasthorizontalw[lgth2-1] - 1.0; // lasthorizontalw[lgth2-1] yori kanarazu chiisai.
for( j=lgth2-2; j>=0; j-- )
{
if( (g=lasthorizontalw[j]+ ( fpenalty * TERMGAPFAC + fpenalty_ex * (lgth2-1-j) * TERMGAPFAC_EX ) ) > wm )
{
wm = g;
iin = lgth1-1; jin = j;
ijp[lgth1][lgth2] = -( lgth2 - j );
}
}
for( i=lgth1-2; i>=0; i-- )
{
if( ( g=lastverticalw[i]+ ( fpenalty * TERMGAPFAC + fpenalty_ex * (lgth1-1-i) * TERMGAPFAC_EX ) ) > wm )
{
wm = g;
iin = i; jin = lgth2-1;
ijp[lgth1][lgth2] = +( lgth1 - i );
}
}
if( lasthorizontalw[lgth2-1] > wm ) // score ga onaji baai erabarenai
{
wm = lasthorizontalw[lgth2-1];
iin = lgth1-1; jin = lgth2-1;
ijp[lgth1][lgth2] = 0;
}
#else
wm = lastverticalw[0];
for( i=0; i<lgth1; i++ )
{
if( lastverticalw[i] >= wm )
{
wm = lastverticalw[i];
iin = i; jin = lgth2-1;
ijp[lgth1][lgth2] = +( lgth1 - i );
}
}
for( j=0; j<lgth2; j++ )
{
if( lasthorizontalw[j] >= wm )
{
wm = lasthorizontalw[j];
iin = lgth1-1; jin = j;
ijp[lgth1][lgth2] = -( lgth2 - j );
}
}
#endif
}
mseq1[0] += lgth1+lgth2;
*mseq1[0] = 0;
mseq2[0] += lgth1+lgth2;
*mseq2[0] = 0;
iin = lgth1; jin = lgth2;
limk = lgth1+lgth2 + 1;
for( k=0; k<limk; k++ )
{
if( ijp[iin][jin] >= warpbase )
{
// fprintf( stderr, "WARP!\n" );
ifi = warpis[ijp[iin][jin]-warpbase];
jfi = warpjs[ijp[iin][jin]-warpbase];
}
else 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;
}
if( ifi == -warpbase && jfi == -warpbase )
{
l = iin;
while( --l >= 0 )
{
*--mseq1[0] = seq1[0][l];
*--mseq2[0] = *gap;
k++;
}
l= jin;
while( --l >= 0 )
{
*--mseq1[0] = *gap;
*--mseq2[0] = seq2[0][l];
k++;
}
break;
}
else
{
l = iin - ifi;
while( --l > 0 )
{
*--mseq1[0] = seq1[0][ifi+l];
*--mseq2[0] = *gap;
k++;
}
l= jin - jfi;
while( --l > 0 )
{
*--mseq1[0] = *gap;
*--mseq2[0] = seq2[0][jfi+l];
k++;
}
}
if( iin <= 0 || jin <= 0 ) break;
*--mseq1[0] = seq1[0][ifi];
*--mseq2[0] = seq2[0][jfi];
k++;
iin = ifi; jin = jfi;
}
// fprintf( stderr, "%s\n", mseq1[0] );
// fprintf( stderr, "%s\n", mseq2[0] );
return( wm );
}
double G__align11( double **n_dynamicmtx, char **seq1, char **seq2, int alloclen, int headgp, int tailgp )
{
// int k;
register int i, j;
int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
int lastj;
int lgth1, lgth2;
int resultlen;
double wm, wmo; /* int ?????? */
double g;
double *currentw, *previousw;
double fpenalty = (double)penalty;
double fpenalty_shift = (double)penalty_shift;
double fpenalty_tmp;
#if USE_PENALTY_EX
double fpenalty_ex = (double)penalty_ex;
double fpenalty_ex_i;
#endif
#if 1
double *wtmp;
int *ijppt;
double *mjpt, *prept, *curpt;
int *mpjpt;
#endif
static TLS double mi = 0.0;
static TLS double *m = NULL;
static TLS int **ijp = NULL;
static TLS int mpi = 0;
static TLS int *mp = NULL;
static TLS double *w1 = NULL;
static TLS double *w2 = NULL;
static TLS double *match = NULL;
static TLS double *initverticalw = NULL; /* kufuu sureba iranai */
static TLS double *lastverticalw = NULL; /* kufuu sureba iranai */
static TLS char **mseq1 = NULL;
static TLS char **mseq2 = NULL;
static TLS char **mseq = NULL;
static TLS int **intwork = NULL;
static TLS double **doublework = NULL;
static TLS int orlgth1 = 0, orlgth2 = 0;
static TLS double **amino_dynamicmtx = NULL; // ??
int *warpis = NULL;
int *warpjs = NULL;
int *warpi = NULL;
int *warpj = NULL;
int *prevwarpi = NULL;
int *prevwarpj = NULL;
double *wmrecords = NULL;
double *prevwmrecords = NULL;
int warpn = 0;
int warpbase;
double curm = 0.0;
double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
int *warpipt, *warpjpt;
if( seq1 == NULL )
{
if( orlgth1 > 0 && orlgth2 > 0 )
{
orlgth1 = 0;
orlgth2 = 0;
if( mseq1 ) free( mseq1 ); mseq1 = NULL;
if( mseq2 ) free( mseq2 ); mseq2 = NULL;
if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
if( match ) FreeFloatVec( match ); match = NULL;
if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
if( m ) FreeFloatVec( m ); m = NULL;
if( mp ) FreeIntVec( mp ); mp = NULL;
if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
}
orlgth1 = 0;
orlgth2 = 0;
return( 0.0 );
}
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
warpbase = lgth1 + lgth2;
warpis = NULL;
warpjs = NULL;
warpn = 0;
if( trywarp )
{
// fprintf( stderr, "IN G__align11\n" );
if( headgp == 0 || tailgp == 0 )
{
fprintf( stderr, "At present, headgp and tailgp must be 1.\n" );
exit( 1 );
}
wmrecords = AllocateFloatVec( lgth2+1 );
warpi = AllocateIntVec( lgth2+1 );
warpj = AllocateIntVec( lgth2+1 );
prevwmrecords = AllocateFloatVec( lgth2+1 );
prevwarpi = AllocateIntVec( lgth2+1 );
prevwarpj = AllocateIntVec( lgth2+1 );
for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
}
#if 0
if( lgth1 <= 0 || lgth2 <= 0 )
{
fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
}
#endif
#if 1
if( lgth1 == 0 && lgth2 == 0 )
return( 0.0 );
if( lgth1 == 0 )
{
seq1[0][lgth2] = 0;
while( lgth2 ) seq1[0][--lgth2] = *newgapstr;
// fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
return( 0.0 );
}
if( lgth2 == 0 )
{
seq2[0][lgth1] = 0;
while( lgth1 ) seq2[0][--lgth1] = *newgapstr;
// fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
return( 0.0 );
}
#endif
wm = 0.0;
if( orlgth1 == 0 )
{
mseq1 = AllocateCharMtx( 2, 0 ); // 2020/Apr
mseq2 = AllocateCharMtx( 2, 0 ); // 2020/Apr
}
if( lgth1 > orlgth1 || lgth2 > orlgth2 )
{
int ll1, ll2;
if( orlgth1 > 0 && orlgth2 > 0 )
{
FreeFloatVec( w1 );
FreeFloatVec( w2 );
FreeFloatVec( match );
FreeFloatVec( initverticalw );
FreeFloatVec( lastverticalw );
FreeFloatVec( m );
FreeIntVec( mp );
FreeCharMtx( mseq );
FreeFloatMtx( doublework );
FreeIntMtx( intwork );
FreeDoubleMtx( amino_dynamicmtx );
}
ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
#if DEBUG
fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
#endif
w1 = AllocateFloatVec( ll2+2 );
w2 = AllocateFloatVec( ll2+2 );
match = AllocateFloatVec( ll2+2 );
initverticalw = AllocateFloatVec( ll1+2 );
lastverticalw = AllocateFloatVec( ll1+2 );
m = AllocateFloatVec( ll2+2 );
mp = AllocateIntVec( ll2+2 );
mseq = AllocateCharMtx( 2, ll1+ll2 ); // 2020/Apr
doublework = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
amino_dynamicmtx = AllocateDoubleMtx( 0x100, 0x100 );
#if DEBUG
fprintf( stderr, "succeeded\n" );
#endif
orlgth1 = ll1 - 100;
orlgth2 = ll2 - 100;
}
for( i=0; i<nalphabets; i++) for( j=0; j<nalphabets; j++ )
amino_dynamicmtx[(unsigned char)amino[i]][(unsigned char)amino[j]] = (double)n_dynamicmtx[i][j];
mseq1[0] = mseq[0];
mseq2[0] = mseq[1];
if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
{
int ll1, ll2;
if( commonAlloc1 && commonAlloc2 )
{
FreeIntMtx( commonIP );
}
ll1 = MAX( orlgth1, commonAlloc1 );
ll2 = MAX( orlgth2, commonAlloc2 );
#if DEBUG
fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
#endif
commonIP = AllocateIntMtx( ll1+10, ll2+10 );
#if DEBUG
fprintf( stderr, "succeeded\n\n" );
#endif
commonAlloc1 = ll1;
commonAlloc2 = ll2;
}
ijp = commonIP;
#if 0
for( i=0; i<lgth1; i++ )
fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
#endif
currentw = w1;
previousw = w2;
match_calc_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 );
if( headgp == 1 )
{
for( i=1; i<lgth1+1; i++ )
{
initverticalw[i] += fpenalty;
#if USE_PENALTY_EX
// initverticalw[i] += fpenalty_ex * i; // ato de fukkatsu
// reporterr( "added _ex\n" );
#endif
}
for( j=1; j<lgth2+1; j++ )
{
currentw[j] += fpenalty;
#if USE_PENALTY_EX
// currentw[j] += fpenalty_ex * j; // ato de fukkatsu
// reporterr( "added _ex\n" );
#endif
}
}
else
{
for( i=1; i<lgth1+1; i++ )
{
initverticalw[i] += fpenalty * TERMGAPFAC;
#if USE_PENALTY_EX // 2018/Apr/22
initverticalw[i] += fpenalty_ex * i * TERMGAPFAC_EX;
// reporterr( "added _ex\n" );
#endif
}
for( j=1; j<lgth2+1; j++ )
{
currentw[j] += fpenalty * TERMGAPFAC;
#if USE_PENALTY_EX // 2018/Apr/22
currentw[j] += fpenalty_ex * j * TERMGAPFAC_EX;
// reporterr( "added _ex\n" );
#endif
}
}
for( j=1; j<lgth2+1; ++j )
{
m[j] = currentw[j-1]; mp[j] = 0;
}
if( lgth2 == 0 )
lastverticalw[0] = 0.0; // lgth2==0 no toki error
else
lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
lastj = lgth2+1;
#if XXXXXXX
fprintf( stderr, "currentw = \n" );
for( i=0; i<lgth1+1; i++ )
{
fprintf( stderr, "%5.2f ", currentw[i] );
}
fprintf( stderr, "\n" );
fprintf( stderr, "initverticalw = \n" );
for( i=0; i<lgth2+1; i++ )
{
fprintf( stderr, "%5.2f ", initverticalw[i] );
}
fprintf( stderr, "\n" );
#endif
for( i=1; i<lasti; i++ )
{
wtmp = previousw;
previousw = currentw;
currentw = wtmp;
previousw[0] = initverticalw[i-1];
match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, i, lgth2 );
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
currentw[0] = initverticalw[i];
mi = previousw[0]; mpi = 0;
ijppt = ijp[i] + 1;
mjpt = m + 1;
prept = previousw;
curpt = currentw + 1;
mpjpt = mp + 1;
if( trywarp )
{
prevwmrecordspt = prevwmrecords;
wmrecordspt = wmrecords+1;
wmrecords1pt = wmrecords;
warpipt = warpi + 1;
warpjpt = warpj + 1;
}
if( i < lgth1 ) fpenalty_ex_i = fpenalty_ex;
else fpenalty_ex_i = 0.0; // 2018/May/11
for( j=1; j<lastj; j++ )
{
wm = *prept;
*ijppt = 0;
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=mi+fpenalty) > wm )
{
wm = g;
*ijppt = -( j - mpi );
}
if( (g=*prept) >= mi )
// if( (g=*prept) > mi )
{
mi = g;
mpi = j-1;
}
#if USE_PENALTY_EX
mi += fpenalty_ex_i;
// mi += fpenalty_ex;
#endif
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=*mjpt + fpenalty) > wm )
{
wm = g;
*ijppt = +( i - *mpjpt );
}
if( (g=*prept) >= *mjpt )
// if( (g=*prept) > *mjpt )
{
*mjpt = g;
*mpjpt = i-1;
}
#if USE_PENALTY_EX
if( j < lgth2 ) // 2018/May/11
m[j] += fpenalty_ex;
#endif
#if 1
if( trywarp )
{
fpenalty_tmp = fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] );
// fprintf( stderr, "fpenalty_shift = %f\n", fpenalty_tmp );
// fprintf( stderr, "\n\n\nwarp to %c-%c (%d-%d) from %c-%c (%d-%d) ? prevwmrecords[%d] = %f + %f <- wm = %f\n", seq1[0][prevwarpi[j-1]], seq2[0][prevwarpj[j-1]], prevwarpi[j-1], prevwarpj[j-1], seq1[0][i], seq2[0][j], i, j, j, prevwmrecords[j-1], fpenalty_tmp, wm );
// if( (g=prevwmrecords[j-1] + fpenalty_shift )> wm )
if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
{
// fprintf( stderr, "Yes! Warp!! from %d-%d (%c-%c) to %d-%d (%c-%c) fpenalty_tmp = %f! warpn = %d\n", i, j, seq1[0][i], seq2[0][j-1], prevwarpi[j-1], prevwarpj[j-1],seq1[0][prevwarpi[j-1]], seq2[0][prevwarpj[j-1]], fpenalty_tmp, warpn );
if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
{
*ijppt = warpbase + warpn - 1;
}
else
{
*ijppt = warpbase + warpn;
warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
warpis[warpn] = prevwarpi[j-1];
warpjs[warpn] = prevwarpj[j-1];
warpn++;
}
wm = g;
}
else
{
}
curm = *curpt + wm;
// fprintf( stderr, "###### curm = %f at %c-%c, i=%d, j=%d\n", curm, seq1[0][i], seq2[0][j], i, j );
// fprintf( stderr, "copy from i, j-1? %f > %f?\n", wmrecords[j-1], curm );
// if( wmrecords[j-1] > wmrecords[j] )
if( *wmrecords1pt > *wmrecordspt )
{
// fprintf( stderr, "yes\n" );
// wmrecords[j] = wmrecords[j-1];
*wmrecordspt = *wmrecords1pt;
// warpi[j] = warpi[j-1];
// warpj[j] = warpj[j-1];
*warpipt = *(warpipt-1);
*warpjpt = *(warpjpt-1);
// fprintf( stderr, "warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
}
// else
// {
// fprintf( stderr, "no\n" );
// }
// fprintf( stderr, " curm = %f at %c-%c\n", curm, seq1[0][i], seq2[0][j] );
// fprintf( stderr, " wmrecords[%d] = %f\n", j, wmrecords[j] );
// fprintf( stderr, "replace?\n" );
// if( curm > wmrecords[j] )
if( curm > *wmrecordspt )
{
// fprintf( stderr, "yes at %d-%d (%c-%c), replaced warp: warpi[j]=%d, warpj[j]=%d warpn=%d, wmrecords[j] = %f -> %f\n", i, j, seq1[0][i], seq2[0][j], i, j, warpn, wmrecords[j], curm );
// wmrecords[j] = curm;
*wmrecordspt = curm;
// warpi[j] = i;
// warpj[j] = j;
*warpipt = i;
*warpjpt = j;
}
// else
// {
// fprintf( stderr, "No! warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
// }
// fprintf( stderr, "%d-%d (%c-%c) curm = %5.0f, wmrecords[j]=%f\n", i, j, seq1[0][i], seq2[0][j], curm, wmrecords[j] );
wmrecordspt++;
wmrecords1pt++;
warpipt++;
warpjpt++;
}
#endif
*curpt++ += wm;
ijppt++;
mjpt++;
prept++;
mpjpt++;
}
lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
if( trywarp )
{
fltncpy( prevwmrecords, wmrecords, lastj );
intncpy( prevwarpi, warpi, lastj );
intncpy( prevwarpj, warpj, lastj );
}
}
if( trywarp )
{
// fprintf( stderr, "\nwm = %f\n", wm );
// fprintf( stderr, "warpn = %d\n", warpn );
free( wmrecords );
free( prevwmrecords );
free( warpi );
free( warpj );
free( prevwarpi );
free( prevwarpj );
}
wmo = Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, tailgp, warpis, warpjs, warpbase );
if( !tailgp ) wm = wmo;
// reporterr( "wm (after tracking) = %f\n", wm );
if( warpis ) free( warpis );
if( warpjs ) free( warpjs );
resultlen = strlen( mseq1[0] );
if( alloclen < resultlen || resultlen > N )
{
fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
ErrorExit( "LENGTH OVER!\n" );
}
strcpy( seq1[0], mseq1[0] );
strcpy( seq2[0], mseq2[0] );
#if 0
fprintf( stderr, "\n" );
fprintf( stderr, ">\n%s\n", mseq1[0] );
fprintf( stderr, ">\n%s\n", mseq2[0] );
fprintf( stderr, "wm = %f\n", wm );
#endif
return( wm );
}
double G__align11_noalign( double **n_dynamicmtx, int penal, int penal_ex, char **seq1, char **seq2, int alloclen )
/* warp mitaiou */
{
// int k;
register int i, j;
int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
int lgth1, lgth2;
// int resultlen;
double wm; /* int ?????? */
double g;
double *currentw, *previousw;
double fpenalty = (double)penal;
#if USE_PENALTY_EX
double fpenalty_ex = (double)penal_ex;
double fpenalty_ex_i;
#endif
#if 1
double *wtmp;
double *mjpt, *prept, *curpt;
// int *mpjpt;
#endif
static TLS double mi, *m;
static TLS double *w1, *w2;
static TLS double *match;
static TLS double *initverticalw; /* kufuu sureba iranai */
static TLS double *lastverticalw; /* kufuu sureba iranai */
static TLS int **intwork;
static TLS double **doublework;
static TLS int orlgth1 = 0, orlgth2 = 0;
static TLS double **amino_dynamicmtx;
if( seq1 == NULL )
{
if( orlgth1 > 0 && orlgth2 > 0 )
{
orlgth1 = 0;
orlgth2 = 0;
FreeFloatVec( w1 );
FreeFloatVec( w2 );
FreeFloatVec( match );
FreeFloatVec( initverticalw );
FreeFloatVec( lastverticalw );
free( m );
FreeFloatMtx( doublework );
FreeIntMtx( intwork );
FreeDoubleMtx( amino_dynamicmtx );
}
return( 0.0 );
}
wm = 0.0;
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
#if 0
if( lgth1 <= 0 || lgth2 <= 0 )
{
fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
}
#endif
if( lgth1 > orlgth1 || lgth2 > orlgth2 )
{
int ll1, ll2;
if( orlgth1 > 0 && orlgth2 > 0 )
{
FreeFloatVec( w1 );
FreeFloatVec( w2 );
FreeFloatVec( match );
FreeFloatVec( initverticalw );
FreeFloatVec( lastverticalw );
FreeFloatVec( m );
FreeFloatMtx( doublework );
FreeIntMtx( intwork );
FreeDoubleMtx( amino_dynamicmtx );
}
ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
#if DEBUG
fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
#endif
w1 = AllocateFloatVec( ll2+2 );
w2 = AllocateFloatVec( ll2+2 );
match = AllocateFloatVec( ll2+2 );
initverticalw = AllocateFloatVec( ll1+2 );
lastverticalw = AllocateFloatVec( ll1+2 );
m = AllocateFloatVec( ll2+2 );
doublework = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
// amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
amino_dynamicmtx = AllocateDoubleMtx( 0x100, 0x100 ); // 2017/Nov. constants.c no 'charsize' wo global hensuu nishita houga yoi?
#if DEBUG
fprintf( stderr, "succeeded\n" );
#endif
orlgth1 = ll1 - 100;
orlgth2 = ll2 - 100;
}
for( i=0; i<nalphabets; i++) for( j=0; j<nalphabets; j++ )
amino_dynamicmtx[(int)amino[i]][(int)amino[j]] = (double)n_dynamicmtx[i][j];
#if 0
for( i=0; i<lgth1; i++ )
fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
#endif
currentw = w1;
previousw = w2;
match_calc_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 );
if( 1 ) // tsuneni outgap-1
{
for( i=1; i<lgth1+1; i++ )
{
initverticalw[i] += fpenalty;
#if USE_PENALTY_EX // 2018/Apr/23
// initverticalw[i] += fpenalty_ex * i; // ato de fukkatsu
// reporterr( "added _ex\n" );
#endif
}
for( j=1; j<lgth2+1; j++ )
{
currentw[j] += fpenalty;
#if USE_PENALTY_EX // 2018/Apr/23
// currentw[j] += fpenalty_ex * j; // ato de fukkatsu
// reporterr( "added _ex\n" );
#endif
}
}
for( j=1; j<lgth2+1; ++j )
{
m[j] = currentw[j-1];
}
if( lgth2 == 0 )
lastverticalw[0] = 0.0; // lgth2==0 no toki error
else
lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap-1
#if XXXXXXX
fprintf( stderr, "currentw = \n" );
for( i=0; i<lgth1+1; i++ )
{
fprintf( stderr, "%5.2f ", currentw[i] );
}
fprintf( stderr, "\n" );
fprintf( stderr, "initverticalw = \n" );
for( i=0; i<lgth2+1; i++ )
{
fprintf( stderr, "%5.2f ", initverticalw[i] );
}
fprintf( stderr, "\n" );
#endif
for( i=1; i<lasti; i++ )
{
wtmp = previousw;
previousw = currentw;
currentw = wtmp;
previousw[0] = initverticalw[i-1];
match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, i, lgth2 );
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
currentw[0] = initverticalw[i];
mi = previousw[0];
mjpt = m + 1;
prept = previousw;
curpt = currentw + 1;
if( i < lgth1 ) fpenalty_ex_i = fpenalty_ex;
else fpenalty_ex_i = 0.0; // 2018/May/11
for( j=1; j<lgth2+1; j++ )
{
wm = *prept;
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=mi+fpenalty) > wm )
{
wm = g;
}
// if( (g=*prept) >= mi )
if( (g=*prept) > mi ) // onaji hazu
{
mi = g;
}
#if USE_PENALTY_EX
mi += fpenalty_ex_i;
#endif
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=*mjpt + fpenalty) > wm )
{
wm = g;
}
// if( (g=*prept) >= *mjpt )
if( (g=*prept) > *mjpt ) // onaji hazu
{
*mjpt = g;
}
#if USE_PENALTY_EX
if( j < lgth2 ) // 2018/May/11
m[j] += fpenalty_ex;
#endif
#if 0
fprintf( stderr, "%5.0f ", wm );
#endif
*curpt++ += wm;
mjpt++;
prept++;
}
lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
}
#if 0
fprintf( stderr, "\n" );
fprintf( stderr, ">\n%s\n", mseq1[0] );
fprintf( stderr, ">\n%s\n", mseq2[0] );
fprintf( stderr, "wm (noalign) = %f\n", wm );
#endif
return( wm );
}
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