void foldrna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *additionalpair )
{
int i, j;
// int ui, uj;
// int uiup, ujup;
int uido, ujdo;
static TLS char **useq1, **useq2;
static TLS char **oseq1, **oseq2, **oseq1r, **oseq2r, *odir1, *odir2;
static TLS RNApair **pairprob1, **pairprob2;
static TLS RNApair *pairpt1, *pairpt2;
int lgth1 = strlen( seq1[0] );
int lgth2 = strlen( seq2[0] );
static TLS float **impmtx2;
static TLS float **map;
// double lenfac;
float prob;
int **sgapmap1, **sgapmap2;
char *nogapdum;
float **tbppmtx;
// fprintf( stderr, "nseq1=%d, lgth1=%d\n", nseq1, lgth1 );
useq1 = AllocateCharMtx( nseq1, lgth1+10 );
useq2 = AllocateCharMtx( nseq2, lgth2+10 );
oseq1 = AllocateCharMtx( nseq1, lgth1+10 );
oseq2 = AllocateCharMtx( nseq2, lgth2+10 );
oseq1r = AllocateCharMtx( nseq1, lgth1+10 );
oseq2r = AllocateCharMtx( nseq2, lgth2+10 );
odir1 = AllocateCharVec( lgth1+10 );
odir2 = AllocateCharVec( lgth2+10 );
sgapmap1 = AllocateIntMtx( nseq1, lgth1+1 );
sgapmap2 = AllocateIntMtx( nseq2, lgth2+1 );
nogapdum = AllocateCharVec( MAX( lgth1, lgth2 ) );
pairprob1 = (RNApair **)calloc( lgth1, sizeof( RNApair *) );
pairprob2 = (RNApair **)calloc( lgth2, sizeof( RNApair *) );
map = AllocateFloatMtx( lgth1, lgth2 );
impmtx2 = AllocateFloatMtx( lgth1, lgth2 );
tbppmtx = AllocateFloatMtx( lgth1, lgth2 );
for( i=0; i<nseq1; i++ ) strcpy( useq1[i], seq1[i] );
for( i=0; i<nseq2; i++ ) strcpy( useq2[i], seq2[i] );
for( i=0; i<nseq1; i++ ) strcpy( oseq1[i], seq1[i] );
for( i=0; i<nseq2; i++ ) strcpy( oseq2[i], seq2[i] );
for( i=0; i<nseq1; i++ ) commongappick_record( 1, useq1+i, sgapmap1[i] );
for( i=0; i<nseq2; i++ ) commongappick_record( 1, useq2+i, sgapmap2[i] );
for( i=0; i<lgth1; i++ )
{
pairprob1[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
pairprob1[i][0].bestpos = -1;
pairprob1[i][0].bestscore = -1;
}
for( i=0; i<lgth2; i++ )
{
pairprob2[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
pairprob2[i][0].bestpos = -1;
pairprob2[i][0].bestscore = -1;
}
utot( nseq1, lgth1, oseq1 );
utot( nseq2, lgth2, oseq2 );
// fprintf( stderr, "folding group1\n" );
// rnalocal( oseq1, useq1, eff1, eff1, nseq1, nseq1, lgth1+10, pair1 );
/* base-pairing probability of group 1 */
if( rnaprediction == 'r' )
rnaalifoldcall( oseq1, nseq1, pairprob1 );
else
mccaskillextract( oseq1, useq1, nseq1, pairprob1, grouprna1, sgapmap1, eff1 );
// fprintf( stderr, "folding group2\n" );
// rnalocal( oseq2, useq2, eff2, eff2, nseq2, nseq2, lgth2+10, pair2 );
/* base-pairing probability of group 2 */
if( rnaprediction == 'r' )
rnaalifoldcall( oseq2, nseq2, pairprob2 );
else
mccaskillextract( oseq2, useq2, nseq2, pairprob2, grouprna2, sgapmap2, eff2 );
#if 0
makerseq( oseq1, oseq1r, odir1, pairprob1, nseq1, lgth1 );
makerseq( oseq2, oseq2r, odir2, pairprob2, nseq2, lgth2 );
fprintf( stderr, "%s\n", odir2 );
for( i=0; i<nseq1; i++ )
{
fprintf( stdout, ">ori\n%s\n", oseq1[0] );
fprintf( stdout, ">rev\n%s\n", oseq1r[0] );
}
#endif
/* similarity score */
Lalignmm_hmout( oseq1, oseq2, eff1, eff2, nseq1, nseq2, 10000, NULL, NULL, NULL, NULL, map );
if( 1 )
{
if( RNAscoremtx == 'n' )
{
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
{
// impmtx2[i][j] = osoiaveragescore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
impmtx2[i][j] = 0.0;
}
}
else if( RNAscoremtx == 'r' )
{
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
{
tbppmtx[i][j] = 1.0;
impmtx2[i][j] = 0.0;
}
for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
{
for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
{
uido = pairpt1->bestpos;
ujdo = pairpt2->bestpos;
prob = pairpt1->bestscore * pairpt2->bestscore;
if( uido > -1 && ujdo > -1 )
{
if( uido > i && j > ujdo )
{
impmtx2[i][j] += prob * pairedribosumscore53( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j, uido, ujdo ) * consweight_multi;
tbppmtx[i][j] -= prob;
}
else if( i < uido && j < ujdo )
{
impmtx2[i][j] += prob * pairedribosumscore35( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j, uido, ujdo ) * consweight_multi;
tbppmtx[i][j] -= prob;
}
}
}
}
for( i=0; i<lgth1; i++ )
{
for( j=0; j<lgth2; j++ )
{
impmtx2[i][j] += tbppmtx[i][j] * singleribosumscore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
}
}
}
/* four-way consistency */
for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
{
// if( pairprob1[i] == NULL ) continue;
for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
{
// fprintf( stderr, "i=%d, j=%d, pn1=%d, pn2=%d\n", i, j, pairpt1-pairprob1[i], pairpt2-pairprob2[j] );
// if( pairprob2[j] == NULL ) continue;
uido = pairpt1->bestpos;
ujdo = pairpt2->bestpos;
prob = pairpt1->bestscore * pairpt2->bestscore;
// prob = 1.0;
// fprintf( stderr, "i=%d->uido=%d, j=%d->ujdo=%d\n", i, uido, j, ujdo );
// fprintf( stderr, "impmtx2[%d][%d] = %f\n", i, j, impmtx2[i][j] );
// if( i < uido && j > ujdo ) continue;
// if( i > uido && j < ujdo ) continue;
// posdistj = abs( ujdo-j );
// if( uido > -1 && ujdo > -1 )
if( uido > -1 && ujdo > -1 && ( ( i > uido && j > ujdo ) || ( i < uido && j < ujdo ) ) )
{
{
impmtx2[i][j] += MAX( 0, map[uido][ujdo] ) * consweight_rna * 600 * prob; // osoi
}
}
}
}
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
{
impmtx[i][j] += impmtx2[i][j];
// fprintf( stderr, "fastathreshold=%f, consweight_multi=%f, consweight_rna=%f\n", fastathreshold, consweight_multi, consweight_rna );
// impmtx[i][j] *= 0.5;
}
// impmtx[0][0] += 10000.0;
// impmtx[lgth1-1][lgth2-1] += 10000.0;
#if 0
fprintf( stdout, "#impmtx2 = \n" );
for( i=0; i<lgth1; i++ )
{
for( j=0; j<lgth2; j++ )
{
fprintf( stdout, "%d %d %f\n", i, j, impmtx2[i][j] );
}
fprintf( stdout, "\n" );
}
exit( 1 );
#endif
}
FreeCharMtx( useq1 );
FreeCharMtx( useq2 );
FreeCharMtx( oseq1 );
FreeCharMtx( oseq2 );
FreeCharMtx( oseq1r );
FreeCharMtx( oseq2r );
free( odir1 );
free( odir2 );
FreeFloatMtx( impmtx2 );
FreeFloatMtx( map );
FreeIntMtx( sgapmap1 );
FreeIntMtx( sgapmap2 );
FreeFloatMtx( tbppmtx );
for( i=0; i<lgth1; i++ ) free( pairprob1[i] );
for( i=0; i<lgth2; i++ ) free( pairprob2[i] );
free( pairprob1 );
free( pairprob2 );
}
int main( int argc, char *argv[] )
{
static char com[10000];
static int *nlen;
int left, right;
int res;
static char **name, **seq, **nogap;
static int **gapmap;
static int *order;
int i, j;
FILE *infp;
RNApair ***pairprob;
RNApair **alnpairprob;
RNApair *pairprobpt;
RNApair *pt;
int *alnpairnum;
float prob;
int adpos;
arguments( argc, argv );
#ifndef enablemultithread
nthread = 0;
#endif
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
if( !whereismccaskillmea )
whereismccaskillmea = "";
getnumlen( infp );
rewind( infp );
if( dorp != 'd' )
{
fprintf( stderr, "nuc only\n" );
exit( 1 );
}
seq = AllocateCharMtx( njob, nlenmax*2+1 );
nogap = AllocateCharMtx( njob, nlenmax*2+1 );
gapmap = AllocateIntMtx( njob, nlenmax*2+1 );
order = AllocateIntVec( njob );
name = AllocateCharMtx( njob, B+1 );
nlen = AllocateIntVec( njob );
pairprob = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
alnpairprob = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
alnpairnum = AllocateIntVec( nlenmax );
for( i=0; i<nlenmax; i++ ) alnpairnum[i] = 0;
readData_pointer( infp, name, nlen, seq );
fclose( infp );
for( i=0; i<njob; i++ )
{
pairprob[i] = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
for( j=0; j<nlenmax; j++ )
{
pairprob[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
pairprob[i][j][0].bestpos = -1;
pairprob[i][j][0].bestscore = -1.0;
}
strcpy( nogap[i], seq[i] );
order[i] = i;
}
for( j=0; j<nlenmax; j++ )
{
alnpairprob[j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
alnpairprob[j][0].bestpos = -1;
alnpairprob[j][0].bestscore = -1.0;
}
constants( njob, seq );
if( alg == 'G' )
fprintf( stderr, "Running DAFS (Sato et al. 2012; http://www.ncrna.org/).\n" );
else
fprintf( stderr, "Running mxscarna with the mccaskill_mea mode.\n" );
#ifdef enablemultithread
if( nthread > 0 )
{
int jobpos;
pthread_t *handle;
pthread_mutex_t mutex;
thread_arg_t *targ;
jobpos = 0;
targ = calloc( nthread, sizeof( thread_arg_t ) );
handle = calloc( nthread, sizeof( pthread_t ) );
pthread_mutex_init( &mutex, NULL );
for( i=0; i<nthread; i++ )
{
targ[i].thread_no = i;
targ[i].njob = njob;
targ[i].jobpospt = &jobpos;
targ[i].gapmap = gapmap;
targ[i].nogap = nogap;
targ[i].nlenmax = nlenmax;
targ[i].pairprob = pairprob;
targ[i].mutex = &mutex;
// athread( targ );
pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
}
for( i=0; i<nthread; i++ )
{
pthread_join( handle[i], NULL );
}
pthread_mutex_destroy( &mutex );
for( i=0; i<njob; i++ )
{
fprintf( stdout, ">%d\n", i );
outmccaskill( stdout, pairprob[i], nlenmax );
}
}
else
#endif
{
for( i=0; i<njob; i++ )
{
fprintf( stderr, "%d / %d\n", i+1, njob );
commongappick_record( 1, nogap+i, gapmap[i] );
infp = fopen( "_mccaskillinorg", "w" );
// fprintf( infp, ">in\n%s\n", nogap[i] );
fprintf( infp, ">in\n" );
write1seq( infp, nogap[i] );
fclose( infp );
system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran
if( alg == 'G' )
sprintf( com, "env PATH=%s dafs --mafft-out _mccaskillout _mccaskillin > _dum1 2>_dum", whereismccaskillmea );
else
sprintf( com, "env PATH=%s mxscarnamod -m -writebpp _mccaskillin > _mccaskillout 2>_dum", whereismccaskillmea );
res = system( com );
if( res )
{
fprintf( stderr, "ERROR IN mccaskill_mea\n" );
exit( 1 );
}
infp = fopen( "_mccaskillout", "r" );
readrawmccaskill( infp, pairprob[i], nlenmax );
fclose( infp );
fprintf( stdout, ">%d\n", i );
outmccaskill( stdout, pairprob[i], nlenmax );
}
}
for( i=0; i<njob; i++ )
{
for( j=0; j<nlen[i]; j++ ) for( pairprobpt=pairprob[i][j]; pairprobpt->bestpos!=-1; pairprobpt++ )
{
left = gapmap[i][j];
right = gapmap[i][pairprobpt->bestpos];
prob = pairprobpt->bestscore;
for( pt=alnpairprob[left]; pt->bestpos!=-1; pt++ )
if( pt->bestpos == right ) break;
if( pt->bestpos == -1 )
{
alnpairprob[left] = (RNApair *)realloc( alnpairprob[left], (alnpairnum[left]+2) * sizeof( RNApair ) );
adpos = alnpairnum[left];
alnpairnum[left]++;
alnpairprob[left][adpos].bestscore = 0.0;
alnpairprob[left][adpos].bestpos = right;
alnpairprob[left][adpos+1].bestscore = -1.0;
alnpairprob[left][adpos+1].bestpos = -1;
pt = alnpairprob[left]+adpos;
}
else
adpos = pt-alnpairprob[left];
pt->bestscore += prob;
if( pt->bestpos != right )
{
fprintf( stderr, "okashii!\n" );
exit( 1 );
}
// fprintf( stderr, "adding %d-%d, %f\n", left, right, prob );
}
}
for( i=0; i<njob; i++ )
{
for( j=0; j<nlenmax; j++ ) free( pairprob[i][j] );
free( pairprob[i] );
}
free( pairprob );
for( j=0; j<nlenmax; j++ ) free( alnpairprob[j] );
free( alnpairprob );
free( alnpairnum );
fprintf( stderr, "%d thread(s)\n", nthread );
return( 0 );
#if 0
fprintf( stdout, "result=\n" );
for( i=0; i<nlenmax; i++ ) for( pairprobpt=alnpairprob[i]; pairprobpt->bestpos!=-1; pairprobpt++ )
{
pairprobpt->bestscore /= (float)njob;
left = i;
right = pairprobpt->bestpos;
prob = pairprobpt->bestscore;
fprintf( stdout, "%d-%d, %f\n", left, right, prob );
}
return( 0 );
#endif
}
static void *athread( void *arg )
{
thread_arg_t *targ = (thread_arg_t *)arg;
int thread_no = targ->thread_no;
int njob = targ->njob;
int *jobpospt = targ->jobpospt;
int **gapmap = targ->gapmap;
char **nogap = targ->nogap;
int nlenmax = targ->nlenmax;
RNApair ***pairprob = targ->pairprob;
int i, res;
FILE *infp;
char *com;
char *dirname;
dirname = calloc( 100, sizeof( char ) );
com = calloc( 1000, sizeof( char ) );
while( 1 )
{
pthread_mutex_lock( targ->mutex );
i = *jobpospt;
if( i == njob )
{
pthread_mutex_unlock( targ->mutex );
return( NULL );
}
*jobpospt = i+1;
pthread_mutex_unlock( targ->mutex );
sprintf( dirname, "_%d", i );
sprintf( com, "rm -rf %s", dirname );
system( com );
sprintf( com, "mkdir %s", dirname );
system( com );
fprintf( stderr, "%d / %d (by thread %4d)\n", i+1, njob, thread_no );
commongappick_record( 1, nogap+i, gapmap[i] );
sprintf( com, "%s/_mccaskillinorg", dirname );
infp = fopen( com, "w" );
// fprintf( infp, ">in\n%s\n", nogap[i] );
fprintf( infp, ">in\n" );
write1seq( infp, nogap[i] );
fclose( infp );
sprintf( com, "tr -d '\\r' < %s/_mccaskillinorg > %s/_mccaskillin", dirname, dirname );
system( com ); // for cygwin, wakaran
if( alg == 'G' )
sprintf( com, "cd %s; %s/dafs --mafft-out _mccaskillout _mccaskillin > _dum1 2>_dum", dirname, whereismccaskillmea );
else
sprintf( com, "cd %s; %s/mxscarnamod -m -writebpp _mccaskillin > _mccaskillout 2>_dum", dirname, whereismccaskillmea );
res = system( com );
if( res )
{
fprintf( stderr, "ERROR IN mccaskill_mea\n" );
exit( 1 );
}
sprintf( com, "%s/_mccaskillout", dirname );
infp = fopen( com, "r" );
readrawmccaskill( infp, pairprob[i], nlenmax );
fclose( infp );
sprintf( com, "rm -rf %s > /dev/null 2>&1", dirname );
if( system( com ) )
{
fprintf( stderr, "retrying to rmdir\n" );
// nanosleep( 100000 );
sleep( 1 );
system( com );
}
}
free( dirname );
free( com );
}
float Falign_localhom( char **seq1, char **seq2,
double *eff1, double *eff2,
int clus1, int clus2,
int alloclen,
LocalHom ***localhom, float *totalimpmatch,
int *gapmap1, int *gapmap2,
int *chudanpt, int chudanref, int *chudanres )
{
// tditeration.c deha alloclen ha huhen nanode
// prevalloclen ha iranai.
int i, j, k, l, m, maxk;
int nlen, nlen2, nlen4;
static TLS int crossscoresize = 0;
static TLS char **tmpseq1 = NULL;
static TLS char **tmpseq2 = NULL;
static TLS char **tmpptr1 = NULL;
static TLS char **tmpptr2 = NULL;
static TLS char **tmpres1 = NULL;
static TLS char **tmpres2 = NULL;
static TLS char **result1 = NULL;
static TLS char **result2 = NULL;
#if RND
static TLS char **rndseq1 = NULL;
static TLS char **rndseq2 = NULL;
#endif
static TLS Fukusosuu **seqVector1 = NULL;
static TLS Fukusosuu **seqVector2 = NULL;
static TLS Fukusosuu **naiseki = NULL;
static TLS Fukusosuu *naisekiNoWa = NULL;
static TLS double *soukan = NULL;
static TLS double **crossscore = NULL;
int nlentmp;
static TLS int *kouho = NULL;
static TLS Segment *segment = NULL;
static TLS Segment *segment1 = NULL;
static TLS Segment *segment2 = NULL;
static TLS Segment **sortedseg1 = NULL;
static TLS Segment **sortedseg2 = NULL;
static TLS int *cut1 = NULL;
static TLS int *cut2 = NULL;
static TLS char *sgap1, *egap1, *sgap2, *egap2;
static TLS int localalloclen = 0;
int lag;
int tmpint;
int count, count0;
int len1, len2;
int totallen;
float totalscore;
float impmatch;
extern Fukusosuu *AllocateFukusosuuVec();
extern Fukusosuu **AllocateFukusosuuMtx();
if( seq1 == NULL )
{
if( result1 )
{
// fprintf( stderr, "Freeing localarrays in Falign\n" );
localalloclen = 0;
mymergesort( 0, 0, NULL );
alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
fft( 0, NULL, 1 );
A__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
G__align11( NULL, NULL, 0, 0, 0 );
partA__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
if( crossscore ) FreeDoubleMtx( crossscore );
FreeCharMtx( result1 );
FreeCharMtx( result2 );
FreeCharMtx( tmpres1 );
FreeCharMtx( tmpres2 );
FreeCharMtx( tmpseq1 );
FreeCharMtx( tmpseq2 );
free( sgap1 );
free( egap1 );
free( sgap2 );
free( egap2 );
free( kouho );
free( cut1 );
free( cut2 );
free( tmpptr1 );
free( tmpptr2 );
free( segment );
free( segment1 );
free( segment2 );
free( sortedseg1 );
free( sortedseg2 );
if( !kobetsubunkatsu )
{
FreeFukusosuuMtx ( seqVector1 );
FreeFukusosuuMtx ( seqVector2 );
FreeFukusosuuVec( naisekiNoWa );
FreeFukusosuuMtx( naiseki );
FreeDoubleVec( soukan );
}
}
else
{
// fprintf( stderr, "Did not allocate localarrays in Falign\n" );
}
return( 0.0 );
}
len1 = strlen( seq1[0] );
len2 = strlen( seq2[0] );
nlentmp = MAX( len1, len2 );
nlen = 1;
while( nlentmp >= nlen ) nlen <<= 1;
#if 0
fprintf( stderr, "### nlen = %d\n", nlen );
#endif
nlen2 = nlen/2; nlen4 = nlen2 / 2;
#if DEBUG
fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
#endif
if( !localalloclen )
{
sgap1 = AllocateCharVec( njob );
egap1 = AllocateCharVec( njob );
sgap2 = AllocateCharVec( njob );
egap2 = AllocateCharVec( njob );
kouho = AllocateIntVec( NKOUHO );
cut1 = AllocateIntVec( MAXSEG );
cut2 = AllocateIntVec( MAXSEG );
tmpptr1 = AllocateCharMtx( njob, 0 );
tmpptr2 = AllocateCharMtx( njob, 0 );
result1 = AllocateCharMtx( njob, alloclen );
result2 = AllocateCharMtx( njob, alloclen );
tmpres1 = AllocateCharMtx( njob, alloclen );
tmpres2 = AllocateCharMtx( njob, alloclen );
// crossscore = AllocateDoubleMtx( MAXSEG, MAXSEG );
segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
segment1 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
segment2 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
sortedseg1 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
sortedseg2 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
if( !( segment && segment1 && segment2 && sortedseg1 && sortedseg2 ) )
ErrorExit( "Allocation error\n" );
if ( scoremtx == -1 ) n20or4or2 = 4;
else if( fftscore == 1 ) n20or4or2 = 2;
else n20or4or2 = 20;
}
if( localalloclen < nlen )
{
if( localalloclen )
{
#if 1
if( !kobetsubunkatsu )
{
FreeFukusosuuMtx ( seqVector1 );
FreeFukusosuuMtx ( seqVector2 );
FreeFukusosuuVec( naisekiNoWa );
FreeFukusosuuMtx( naiseki );
FreeDoubleVec( soukan );
}
FreeCharMtx( tmpseq1 );
FreeCharMtx( tmpseq2 );
#endif
#if RND
FreeCharMtx( rndseq1 );
FreeCharMtx( rndseq2 );
#endif
}
tmpseq1 = AllocateCharMtx( njob, nlen );
tmpseq2 = AllocateCharMtx( njob, nlen );
if( !kobetsubunkatsu )
{
naisekiNoWa = AllocateFukusosuuVec( nlen );
naiseki = AllocateFukusosuuMtx( n20or4or2, nlen );
seqVector1 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
seqVector2 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
soukan = AllocateDoubleVec( nlen+1 );
}
#if RND
rndseq1 = AllocateCharMtx( njob, nlen );
rndseq2 = AllocateCharMtx( njob, nlen );
for( i=0; i<njob; i++ )
{
generateRndSeq( rndseq1[i], nlen );
generateRndSeq( rndseq2[i], nlen );
}
#endif
localalloclen = nlen;
}
for( j=0; j<clus1; j++ ) strcpy( tmpseq1[j], seq1[j] );
for( j=0; j<clus2; j++ ) strcpy( tmpseq2[j], seq2[j] );
#if 0
fftfp = fopen( "input_of_Falign", "w" );
fprintf( fftfp, "nlen = %d\n", nlen );
fprintf( fftfp, "seq1: ( %d sequences ) \n", clus1 );
for( i=0; i<clus1; i++ )
fprintf( fftfp, "%s\n", seq1[i] );
fprintf( fftfp, "seq2: ( %d sequences ) \n", clus2 );
for( i=0; i<clus2; i++ )
fprintf( fftfp, "%s\n", seq2[i] );
fclose( fftfp );
system( "less input_of_Falign < /dev/tty > /dev/tty" );
#endif
if( !kobetsubunkatsu )
{
fprintf( stderr, "FFT ... " );
for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
if( fftscore && scoremtx != -1 )
{
for( i=0; i<clus1; i++ )
{
seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] );
}
}
else
{
#if 0
for( i=0; i<clus1; i++ ) for( j=0; j<n20or4or2; j++ )
seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] );
#else
for( i=0; i<clus1; i++ )
seq_vec_3( seqVector1, eff1[i], tmpseq1[i] );
#endif
}
#if RND
for( i=0; i<clus1; i++ )
{
vec_init2( seqVector1, rndseq1[i], eff1[i], len1, nlen );
}
#endif
#if 0
fftfp = fopen( "seqVec", "w" );
fprintf( fftfp, "before transform\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "nlen=%d\n", nlen );
fprintf( fftfp, "%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector1[k][l].R, seqVector1[k][l].I );
}
fclose( fftfp );
system( "less seqVec < /dev/tty > /dev/tty" );
#endif
for( j=0; j<n20or4or2; j++ ) vec_init( seqVector2[j], nlen );
if( fftscore && scoremtx != -1 )
{
for( i=0; i<clus2; i++ )
{
seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] );
}
}
else
{
#if 0
for( i=0; i<clus2; i++ ) for( j=0; j<n20or4or2; j++ )
seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] );
#else
for( i=0; i<clus2; i++ )
seq_vec_3( seqVector2, eff2[i], tmpseq2[i] );
#endif
}
#if RND
for( i=0; i<clus2; i++ )
{
vec_init2( seqVector2, rndseq2[i], eff2[i], len2, nlen );
}
#endif
#if 0
fftfp = fopen( "seqVec2", "w" );
fprintf( fftfp, "before fft\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
}
fclose( fftfp );
system( "less seqVec2 < /dev/tty > /dev/tty" );
#endif
for( j=0; j<n20or4or2; j++ )
{
fft( nlen, seqVector2[j], (j==0) );
fft( nlen, seqVector1[j], 0 );
}
#if 0
fftfp = fopen( "seqVec2", "w" );
fprintf( fftfp, "#after fft\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "#%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
}
fclose( fftfp );
system( "less seqVec2 < /dev/tty > /dev/tty" );
#endif
for( k=0; k<n20or4or2; k++ )
{
for( l=0; l<nlen; l++ )
calcNaiseki( naiseki[k]+l, seqVector1[k]+l, seqVector2[k]+l );
}
for( l=0; l<nlen; l++ )
{
naisekiNoWa[l].R = 0.0;
naisekiNoWa[l].I = 0.0;
for( k=0; k<n20or4or2; k++ )
{
naisekiNoWa[l].R += naiseki[k][l].R;
naisekiNoWa[l].I += naiseki[k][l].I;
}
}
#if 0
fftfp = fopen( "naisekiNoWa", "w" );
fprintf( fftfp, "#Before fft\n" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f %f\n", l, naisekiNoWa[l].R, naisekiNoWa[l].I );
fclose( fftfp );
system( "less naisekiNoWa < /dev/tty > /dev/tty " );
#endif
fft( -nlen, naisekiNoWa, 0 );
for( m=0; m<=nlen2; m++ )
soukan[m] = naisekiNoWa[nlen2-m].R;
for( m=nlen2+1; m<nlen; m++ )
soukan[m] = naisekiNoWa[nlen+nlen2-m].R;
#if 0
fftfp = fopen( "naisekiNoWa", "w" );
fprintf( fftfp, "#After fft\n" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f\n", l, naisekiNoWa[l].R );
fclose( fftfp );
fftfp = fopen( "list.plot", "w" );
fprintf( fftfp, "plot 'naisekiNoWa'\npause -1" );
fclose( fftfp );
system( "/usr/bin/gnuplot list.plot &" );
#endif
#if 0
fprintf( stderr, "frt write start\n" );
fftfp = fopen( "frt", "w" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f\n", l-nlen2, soukan[l] );
fclose( fftfp );
system( "less frt < /dev/tty > /dev/tty" );
#if 0
fftfp = fopen( "list.plot", "w" );
fprintf( fftfp, "plot 'frt'\n pause +1" );
fclose( fftfp );
system( "/usr/bin/gnuplot list.plot" );
#endif
#endif
getKouho( kouho, NKOUHO, soukan, nlen );
#if 0
for( i=0; i<NKOUHO; i++ )
{
fprintf( stderr, "kouho[%d] = %d\n", i, kouho[i] );
}
#endif
}
#if KEIKA
fprintf( stderr, "Searching anchors ... " );
#endif
count = 0;
#define CAND 0
#if CAND
fftfp = fopen( "cand", "w" );
fclose( fftfp );
#endif
if( kobetsubunkatsu )
{
maxk = 1;
kouho[0] = 0;
}
else
{
maxk = NKOUHO;
}
for( k=0; k<maxk; k++ )
{
lag = kouho[k];
zurasu2( lag, clus1, clus2, seq1, seq2, tmpptr1, tmpptr2 );
#if CAND
fftfp = fopen( "cand", "a" );
fprintf( fftfp, "Candidate No.%d lag = %d\n", k+1, lag );
fprintf( fftfp, "%s\n", tmpptr1[0] );
fprintf( fftfp, "%s\n", tmpptr2[0] );
fclose( fftfp );
#endif
tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
while( tmpint-- > 0 )
{
if( lag > 0 )
{
segment1[count].start = segment[count].start ;
segment1[count].end = segment[count].end ;
segment1[count].center = segment[count].center;
segment1[count].score = segment[count].score;
segment2[count].start = segment[count].start + lag;
segment2[count].end = segment[count].end + lag;
segment2[count].center = segment[count].center + lag;
segment2[count].score = segment[count].score ;
}
else
{
segment1[count].start = segment[count].start - lag;
segment1[count].end = segment[count].end - lag;
segment1[count].center = segment[count].center - lag;
segment1[count].score = segment[count].score ;
segment2[count].start = segment[count].start ;
segment2[count].end = segment[count].end ;
segment2[count].center = segment[count].center;
segment2[count].score = segment[count].score ;
}
#if 0
fftfp = fopen( "cand", "a" );
fprintf( fftfp, "Goukaku=%dko\n", tmpint );
fprintf( fftfp, "in 1 %d\n", segment1[count].center );
fprintf( fftfp, "in 2 %d\n", segment2[count].center );
fclose( fftfp );
#endif
segment1[count].pair = &segment2[count];
segment2[count].pair = &segment1[count];
count++;
#if 0
fprintf( stderr, "count=%d\n", count );
#endif
}
}
#if 1
if( !kobetsubunkatsu )
fprintf( stderr, "%d segments found\n", count );
#endif
if( !count && fftNoAnchStop )
ErrorExit( "Cannot detect anchor!" );
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT before sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( fftfp, "%d score = %f\n", segment2[l].center, segment1[l].score );
}
fclose( fftfp );
#endif
#if KEIKA
fprintf( stderr, "Aligning anchors ... " );
#endif
for( i=0; i<count; i++ )
{
sortedseg1[i] = &segment1[i];
sortedseg2[i] = &segment2[i];
}
#if 0
tmpsort( count, sortedseg1 );
tmpsort( count, sortedseg2 );
qsort( sortedseg1, count, sizeof( Segment * ), segcmp );
qsort( sortedseg2, count, sizeof( Segment * ), segcmp );
#else
mymergesort( 0, count-1, sortedseg1 );
mymergesort( 0, count-1, sortedseg2 );
#endif
for( i=0; i<count; i++ ) sortedseg1[i]->number = i;
for( i=0; i<count; i++ ) sortedseg2[i]->number = i;
if( kobetsubunkatsu )
{
for( i=0; i<count; i++ )
{
cut1[i+1] = sortedseg1[i]->center;
cut2[i+1] = sortedseg2[i]->center;
}
cut1[0] = 0;
cut2[0] = 0;
cut1[count+1] = len1;
cut2[count+1] = len2;
count += 2;
}
else
{
if( crossscoresize < count+2 )
{
crossscoresize = count+2;
#if 1
fprintf( stderr, "######allocating crossscore, size = %d\n", crossscoresize );
#endif
if( crossscore ) FreeDoubleMtx( crossscore );
crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
}
for( i=0; i<count+2; i++ ) for( j=0; j<count+2; j++ )
crossscore[i][j] = 0.0;
for( i=0; i<count; i++ )
{
crossscore[segment1[i].number+1][segment1[i].pair->number+1] = segment1[i].score;
cut1[i+1] = sortedseg1[i]->center;
cut2[i+1] = sortedseg2[i]->center;
}
#if DEBUG
fprintf( stderr, "AFTER SORT\n" );
for( i=0; i<count; i++ ) fprintf( stderr, "%d, %d\n", segment1[i].start, segment2[i].start );
#endif
crossscore[0][0] = 10000000.0;
cut1[0] = 0;
cut2[0] = 0;
crossscore[count+1][count+1] = 10000000.0;
cut1[count+1] = len1;
cut2[count+1] = len2;
count += 2;
count0 = count;
blockAlign2( cut1, cut2, sortedseg1, sortedseg2, crossscore, &count );
if( count0 > count )
{
#if 0
fprintf( stderr, "\7 REPEAT!? \n" );
#else
fprintf( stderr, "REPEAT!? \n" );
#endif
if( fftRepeatStop ) exit( 1 );
}
#if KEIKA
else fprintf( stderr, "done\n" );
#endif
}
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT after sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( fftfp, "%d\n", segment2[l].center );
}
fclose( fftfp );
#endif
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT after sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut : %d %d\n", cut1[l], cut2[l] );
}
fclose( fftfp );
#endif
#if KEIKA
fprintf( trap_g, "Devided to %d segments\n", count-1 );
fprintf( trap_g, "%d %d forg\n", MIN( clus1, clus2 ), count-1 );
#endif
totallen = 0;
for( j=0; j<clus1; j++ ) result1[j][0] = 0;
for( j=0; j<clus2; j++ ) result2[j][0] = 0;
totalscore = 0.0;
*totalimpmatch = 0.0;
for( i=0; i<count-1; i++ )
{
#if DEBUG
fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
#else
#if KEIKA
fprintf( stderr, "DP %03d / %03d\r", i+1, count-1 );
#endif
#endif
if( cut1[i] )
{
getkyokaigap( sgap1, seq1, cut1[i]-1, clus1 );
getkyokaigap( sgap2, seq2, cut2[i]-1, clus2 );
}
else
{
for( j=0; j<clus1; j++ ) sgap1[j] = 'o';
for( j=0; j<clus2; j++ ) sgap2[j] = 'o';
}
if( cut1[i+1] != len1 )
{
getkyokaigap( egap1, seq1, cut1[i+1], clus1 );
getkyokaigap( egap2, seq2, cut2[i+1], clus2 );
}
else
{
for( j=0; j<clus1; j++ ) egap1[j] = 'o';
for( j=0; j<clus2; j++ ) egap2[j] = 'o';
}
for( j=0; j<clus1; j++ )
{
strncpy( tmpres1[j], seq1[j]+cut1[i], cut1[i+1]-cut1[i] );
tmpres1[j][cut1[i+1]-cut1[i]] = 0;
}
if( kobetsubunkatsu ) commongappick_record( clus1, tmpres1, gapmap1 );
for( j=0; j<clus2; j++ )
{
strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
tmpres2[j][cut2[i+1]-cut2[i]] = 0;
}
if( kobetsubunkatsu ) commongappick_record( clus2, tmpres2, gapmap2 );
#if 0
fprintf( stderr, "count = %d\n", count );
fprintf( stderr, "### reg1 = %d-%d\n", cut1[i], cut1[i+1]-1 );
fprintf( stderr, "### reg2 = %d-%d\n", cut2[i], cut2[i+1]-1 );
#endif
switch( alg )
{
case( 'a' ):
totalscore += Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
break;
case( 'Q' ):
totalscore += partQ__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2 );
*totalimpmatch += impmatch;
// fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
break;
case( 'A' ):
totalscore += partA__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres );
*totalimpmatch += impmatch;
// fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
break;
default:
fprintf( stderr, "alg = %c\n", alg );
ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
break;
}
#ifdef enablemultithread
if( chudanres && *chudanres )
{
// fprintf( stderr, "\n\n## CHUUDAN!!! at Falign_localhom\n" );
return( -1.0 );
}
#endif
nlen = strlen( tmpres1[0] );
if( totallen + nlen > alloclen )
{
fprintf( stderr, "totallen=%d + nlen=%d > alloclen = %d\n", totallen, nlen, alloclen );
ErrorExit( "LENGTH OVER in Falign\n " );
}
for( j=0; j<clus1; j++ ) strcat( result1[j], tmpres1[j] );
for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] );
totallen += nlen;
#if 0
fprintf( stderr, "%4d\r", totallen );
fprintf( stderr, "\n\n" );
for( j=0; j<clus1; j++ )
{
fprintf( stderr, "%s\n", tmpres1[j] );
}
fprintf( stderr, "-------\n" );
for( j=0; j<clus2; j++ )
{
fprintf( stderr, "%s\n", tmpres2[j] );
}
#endif
}
#if KEIKA
fprintf( stderr, "DP ... done \n" );
#endif
for( j=0; j<clus1; j++ ) strcpy( seq1[j], result1[j] );
for( j=0; j<clus2; j++ ) strcpy( seq2[j], result2[j] );
#if 0
for( j=0; j<clus1; j++ )
{
fprintf( stderr, "%s\n", result1[j] );
}
fprintf( stderr, "- - - - - - - - - - -\n" );
for( j=0; j<clus2; j++ )
{
fprintf( stderr, "%s\n", result2[j] );
}
#endif
return( totalscore );
}
