blob: ff1d9567b3cb9328983ab1be5bec630c234664bf [file] [log] [blame]
#include "mltaln.h"
#if 0
static FILE *fftfp;
#endif
static int n20or4or2;
#define KEIKA 0
#define RND 0
#define DEBUG 0
#if RND // by D.Mathog
static void generateRndSeq( char *seq, int len )
{
while( len-- )
#if 1
*seq++ = (int)( rnd() * n20or4or2 );
#else
*seq++ = (int)1;
#endif
}
#endif
static void vec_init( Fukusosuu *result, int nlen )
{
while( nlen-- )
{
result->R = result->I = 0.0;
result++;
}
}
#if 0 // by D.Mathog
static void vec_init2( Fukusosuu **result, char *seq, double eff, int st, int ed )
{
int i;
for( i=st; i<ed; i++ )
result[(int)*seq++][i].R += eff;
}
#endif
static void seq_vec_2( Fukusosuu *result, double *score, double incr, char *seq )
{
static int n;
for( ; *seq; result++ )
{
n = amino_n[(int)*seq++];
if( n < 20 && n >= 0 ) result->R += incr * score[n];
#if 0
fprintf( stderr, "n=%d, score=%f, inc=%f R=%f\n",n, score[n], incr * score[n], result->R );
#endif
}
}
static void seq_vec_3( Fukusosuu **result, double incr, char *seq )
{
int i;
int n;
for( i=0; *seq; i++ )
{
n = amino_n[(int)*seq++];
if( n < n20or4or2 && n >= 0 ) result[n][i].R += incr;
}
}
static void seq_vec_5( Fukusosuu *result, double *score1, double *score2, double incr, char *seq )
{
int n;
for( ; *seq; result++ )
{
n = amino_n[(int)*seq++];
if( n > 20 ) continue;
result->R += incr * score1[n];
result->I += incr * score2[n];
#if 0
fprintf( stderr, "n=%d, score=%f, inc=%f R=%f\n",n, score[n], incr * score[n], result->R );
#endif
}
}
static void seq_vec_4( Fukusosuu *result, double incr, char *seq )
{
char s;
for( ; *seq; result++ )
{
s = *seq++;
if( s == 'a' )
result->R += incr;
else if( s == 't' )
result->R -= incr;
else if( s == 'g' )
result->I += incr;
else if( s == 'c' )
result->I -= incr;
}
}
#if 0 // by D.Mathog
static void seq_vec( Fukusosuu *result, char query, double incr, char *seq )
{
#if 0
int bk = nlen;
#endif
while( *seq )
{
if( *seq++ == query ) result->R += incr;
result++;
#if 0
fprintf( stderr, "i = %d result->R = %f\n", bk-nlen, (result-1)->R );
#endif
}
}
static int checkRepeat( int num, int *cutpos )
{
int tmp, buf;
buf = *cutpos;
while( num-- )
{
if( ( tmp = *cutpos++ ) < buf ) return( 1 );
buf = tmp;
}
return( 0 );
}
static int segcmp( void *ptr1, void *ptr2 )
{
int diff;
Segment **seg1 = (Segment **)ptr1;
Segment **seg2 = (Segment **)ptr2;
#if 0
return( (*seg1)->center - (*seg2)->center );
#else
diff = (*seg1)->center - (*seg2)->center;
if( diff ) return( diff );
diff = (*seg1)->start - (*seg2)->start;
if( diff ) return( diff );
diff = (*seg1)->end - (*seg2)->end;
if( diff ) return( diff );
fprintf( stderr, "USE STABLE SORT !!\n" );
exit( 1 );
return( 0 );
#endif
}
#endif
static void mymergesort( int first, int last, Segment **seg )
{
int middle;
static int i, j, k, p;
static int allo = 0;
static Segment **work = NULL;
if( last > allo )
{
allo = last;
if( work ) free( work );
work = (Segment **)calloc( allo / 2 + 1, sizeof( Segment *) );
}
if( first < last )
{
middle = ( first + last ) / 2;
mymergesort( first, middle, seg );
mymergesort( middle+1, last, seg );
p = 0;
for( i=first; i<=middle; i++ ) work[p++] = seg[i];
i = middle + 1; j = 0; k = first;
while( i <= last && j < p )
{
if( work[j]->center <= seg[i]->center )
seg[k++] = work[j++];
else
seg[k++] = seg[i++];
}
while( j < p ) seg[k++] = work[j++];
}
}
double Fgetlag( char **seq1, char **seq2,
double *eff1, double *eff2,
int clus1, int clus2,
int alloclen )
{
int i, j, k, l, m;
int nlen, nlen2, nlen4;
static int crossscoresize = 0;
static char **tmpseq1 = NULL;
static char **tmpseq2 = NULL;
static char **tmpptr1 = NULL;
static char **tmpptr2 = NULL;
static char **tmpres1 = NULL;
static char **tmpres2 = NULL;
static char **result1 = NULL;
static char **result2 = NULL;
#if RND
static char **rndseq1 = NULL;
static char **rndseq2 = NULL;
#endif
static Fukusosuu **seqVector1 = NULL;
static Fukusosuu **seqVector2 = NULL;
static Fukusosuu **naiseki = NULL;
static Fukusosuu *naisekiNoWa = NULL;
static double *soukan = NULL;
static double **crossscore = NULL;
int nlentmp;
static int *kouho = NULL;
static Segment *segment = NULL;
static Segment *segment1 = NULL;
static Segment *segment2 = NULL;
static Segment **sortedseg1 = NULL;
static Segment **sortedseg2 = NULL;
static int *cut1 = NULL;
static int *cut2 = NULL;
static int localalloclen = 0;
int lag;
int tmpint;
int count, count0;
int len1, len2;
int totallen;
float dumfl = 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 )
{
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
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 );
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( fftkeika ) 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( stdout, "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
for( k=0; k<NKOUHO; 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, ">Candidate No.%d lag = %d\n", k+1, lag );
fprintf( fftfp, "%s\n", tmpptr2[0] );
fprintf( fftfp, ">\n", k+1, lag );
fclose( fftfp );
#endif
tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
if( tmpint == 0 ) break; // 060430 iinoka ?
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
fprintf( stderr, "Goukaku=%dko\n", tmpint );
fprintf( stderr, "in 1 %d\n", segment1[count].center );
fprintf( stderr, "in 2 %d\n", segment2[count].center );
#endif
segment1[count].pair = &segment2[count];
segment2[count].pair = &segment1[count];
count++;
#if 0
fprintf( stderr, "count=%d\n", count );
#endif
}
}
#if 1
fprintf( stderr, "done. (%d anchors)\r", count );
#endif
if( !count && fftNoAnchStop )
ErrorExit( "Cannot detect anchor!" );
#if 0
fprintf( stdout, "RESULT before sort:\n" );
for( l=0; l<count+1; l++ )
{
fprintf( stdout, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( stdout, "%d score = %f\n", segment2[l].center, segment1[l].score );
}
exit( 1 );
#endif
#if KEIKA
fprintf( stderr, "Aligning anchors ... " );
#endif
for( i=0; i<count; i++ )
{
sortedseg1[i] = &segment1[i];
sortedseg2[i] = &segment2[i];
}
{
mymergesort( 0, count-1, sortedseg1 );
mymergesort( 0, count-1, sortedseg2 );
for( i=0; i<count; i++ ) sortedseg1[i]->number = i;
for( i=0; i<count; i++ ) sortedseg2[i]->number = i;
if( crossscoresize < count+2 )
{
crossscoresize = count+2;
fprintf( stderr, "####################################################################################################################################allocating crossscore, size = %d\n", crossscoresize );
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( fftkeika )
{
if( count0 > count )
{
fprintf( stderr, "REPEAT!? \n" );
if( fftRepeatStop ) exit( 1 );
}
#if KEIKA
else
fprintf( stderr, "done\n" );
fprintf( stderr, "done. (%d anchors)\n", count );
#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;
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
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;
}
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;
}
switch( alg )
{
case( 'a' ):
Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
break;
case( 'M' ):
MSalignmm( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL );
break;
case( 'A' ):
if( clus1 == 1 && clus2 == 1 )
G__align11( tmpres1, tmpres2, alloclen );
else
A__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
break;
case( 'H' ):
if( clus1 == 1 && clus2 == 1 )
G__align11( tmpres1, tmpres2, alloclen );
else
H__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
break;
case( 'Q' ):
if( clus1 == 1 && clus2 == 1 )
G__align11( tmpres1, tmpres2, alloclen );
else
Q__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
break;
default:
fprintf( stderr, "alg = %c\n", alg );
ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
break;
}
nlen = strlen( tmpres1[0] );
if( 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( 0.0 );
}
float Falign( char **seq1, char **seq2,
double *eff1, double *eff2,
int clus1, int clus2,
int alloclen, int *fftlog )
{
int i, j, k, l, m, maxk;
int nlen, nlen2, nlen4;
static int prevalloclen = 0;
static int crossscoresize = 0;
static char **tmpseq1 = NULL;
static char **tmpseq2 = NULL;
static char **tmpptr1 = NULL;
static char **tmpptr2 = NULL;
static char **tmpres1 = NULL;
static char **tmpres2 = NULL;
static char **result1 = NULL;
static char **result2 = NULL;
#if RND
static char **rndseq1 = NULL;
static char **rndseq2 = NULL;
#endif
static Fukusosuu **seqVector1 = NULL;
static Fukusosuu **seqVector2 = NULL;
static Fukusosuu **naiseki = NULL;
static Fukusosuu *naisekiNoWa = NULL;
static double *soukan = NULL;
static double **crossscore = NULL;
int nlentmp;
static int *kouho = NULL;
static Segment *segment = NULL;
static Segment *segment1 = NULL;
static Segment *segment2 = NULL;
static Segment **sortedseg1 = NULL;
static Segment **sortedseg2 = NULL;
static int *cut1 = NULL;
static int *cut2 = NULL;
static char *sgap1, *egap1, *sgap2, *egap2;
static int localalloclen = 0;
int lag;
int tmpint;
int count, count0;
int len1, len2;
int totallen;
float totalscore;
float dumfl = 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( prevalloclen != alloclen ) // Falign_noudp mo kaeru
{
if( prevalloclen )
{
FreeCharMtx( result1 );
FreeCharMtx( result2 );
FreeCharMtx( tmpres1 );
FreeCharMtx( tmpres2 );
}
// fprintf( stderr, "\n\n\nreallocating ...\n" );
result1 = AllocateCharMtx( njob, alloclen );
result2 = AllocateCharMtx( njob, alloclen );
tmpres1 = AllocateCharMtx( njob, alloclen );
tmpres2 = AllocateCharMtx( njob, alloclen );
prevalloclen = alloclen;
}
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 );
// 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 = 1;
else if( fftscore ) n20or4or2 = 1;
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 )
{
if( fftkeika ) fprintf( stderr, " FFT ... " );
for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
if( fftscore && scoremtx != -1 )
{
for( i=0; i<clus1; i++ )
{
#if 1
seq_vec_5( seqVector1[0], polarity, volume, eff1[i], tmpseq1[i] );
#else
seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] );
#endif
}
}
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++ )
{
#if 1
seq_vec_5( seqVector2[0], polarity, volume, eff2[i], tmpseq2[i] );
#else
seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] );
#endif
}
}
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, "soukan\n" );
for( l=0; l<nlen; l++ )
fprintf( stderr, "%d %f\n", l-nlen2, soukan[l] );
#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];
if( lag <= -len1 || len2 <= lag ) continue;
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, ">Candidate No.%d lag = %d\n", k+1, lag );
fprintf( fftfp, "%s\n", tmpptr2[0] );
fprintf( fftfp, ">\n", k+1, lag );
fclose( fftfp );
#endif
// fprintf( stderr, "lag = %d\n", lag );
tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
// if( lag == -50 ) exit( 1 );
if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
if( tmpint == 0 ) break; // 060430 iinoka ?
while( tmpint-- > 0 )
{
#if 0
if( segment[count].end - segment[count].start < fftWinSize )
{
count++;
continue;
}
#endif
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
fprintf( stderr, "in 1 %d\n", segment1[count].center );
fprintf( stderr, "in 2 %d\n", segment2[count].center );
#endif
segment1[count].pair = &segment2[count];
segment2[count].pair = &segment1[count];
count++;
}
}
#if 0
if( !kobetsubunkatsu && fftkeika )
fprintf( stderr, "%d anchors found\r", count );
#endif
if( !count && fftNoAnchStop )
ErrorExit( "Cannot detect anchor!" );
#if 0
fprintf( stderr, "RESULT before sort:\n" );
for( l=0; l<count+1; l++ )
{
fprintf( stderr, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( stderr, "%d score = %f\n", segment2[l].center, segment1[l].score );
}
#endif
#if KEIKA
fprintf( stderr, "done. (%d anchors)\n", count );
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
if( fftkeika ) 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 0
fprintf( stderr, "AFTER SORT\n" );
for( i=0; i<count+1; i++ ) fprintf( stderr, "%d, %d\n", cut1[i], cut2[i] );
fprintf( stderr, "crossscore = \n" );
for( i=0; i<count+1; i++ )
{
for( j=0; j<count+1; j++ )
fprintf( stderr, "%.0f ", crossscore[i][j] );
fprintf( stderr, "\n" );
}
#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( count-count0 )
// fprintf( stderr, "%d unused anchors\n", count0-count );
if( !kobetsubunkatsu && fftkeika )
fprintf( stderr, "%d anchors found\n", count );
if( fftkeika )
{
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
fprintf( stderr, "RESULT after blckalign:\n" );
for( l=0; l<count+1; l++ )
{
fprintf( stderr, "cut : %d %d\n", cut1[l], cut2[l] );
}
#endif
#if 0
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;
*fftlog = -1;
for( i=0; i<count-1; i++ )
{
*fftlog += 1;
if( cut1[i] ) // chuui
{
// getkyokaigap( sgap1, tmpres1, nlen-1, clus1 );
// getkyokaigap( sgap2, tmpres2, nlen-1, clus2 );
getkyokaigap( sgap1, tmpres1, nlen-1, clus1 );
getkyokaigap( sgap2, tmpres2, nlen-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 ) // chuui
{
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';
}
#if 0
{
fprintf( stderr, "kyokkaigap1(%d)=", cut1[i]-1 );
for( j=0; j<clus1; j++ )
fprintf( stderr, "%c", sgap1[j] );
fprintf( stderr, "=kyokkaigap1-start\n" );
}
{
fprintf( stderr, "kyokkaigap2(%d)=", cut2[i]-1 );
for( j=0; j<clus2; j++ )
fprintf( stderr, "%c", sgap2[j] );
fprintf( stderr, "=kyokkaigap2-start\n" );
}
{
fprintf( stderr, "kyokkaigap1(%d)=", cut1[i]-1 );
for( j=0; j<clus1; j++ )
fprintf( stderr, "%c", egap1[j] );
fprintf( stderr, "=kyokkaigap1-end\n" );
}
{
fprintf( stderr, "kyokkaigap2(%d)=", cut2[i]-1 );
for( j=0; j<clus2; j++ )
fprintf( stderr, "%c", egap2[j] );
fprintf( stderr, "=kyokkaigap2-end\n" );
}
#endif
#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
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 && fftkeika ) commongappick( clus1, tmpres1 ); //dvtditr に呼ばれたとき fftkeika=1
// if( kobetsubunkatsu ) commongappick( clus1, tmpres1 );
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 && fftkeika ) commongappick( clus2, tmpres2 ); //dvtditr に呼ばれたとき fftkeika=1
// if( kobetsubunkatsu ) commongappick( clus2, tmpres2 );
if( constraint )
{
fprintf( stderr, "Not supported\n" );
exit( 1 );
}
#if 0
fprintf( stderr, "i=%d, before alignment", i );
fprintf( stderr, "%4d\n", 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 0
fprintf( stdout, "writing input\n" );
for( j=0; j<clus1; j++ )
{
fprintf( stdout, ">%d of GROUP1\n", j );
fprintf( stdout, "%s\n", tmpres1[j] );
}
for( j=0; j<clus2; j++ )
{
fprintf( stdout, ">%d of GROUP2\n", j );
fprintf( stdout, "%s\n", tmpres2[j] );
}
fflush( stdout );
#endif
switch( alg )
{
case( 'a' ):
totalscore += Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
break;
case( 'M' ):
totalscore += MSalignmm( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2 );
break;
case( 'A' ):
if( clus1 == 1 && clus2 == 1 )
{
totalscore += G__align11( tmpres1, tmpres2, alloclen );
}
else
totalscore += A__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2 );
break;
case( 'H' ):
if( clus1 == 1 && clus2 == 1 )
{
totalscore += G__align11( tmpres1, tmpres2, alloclen );
}
else
totalscore += H__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2 );
break;
case( 'Q' ):
if( clus1 == 1 && clus2 == 1 )
{
totalscore += G__align11( tmpres1, tmpres2, alloclen );
}
else
totalscore += Q__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2 );
break;
default:
fprintf( stderr, "alg = %c\n", alg );
ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
break;
}
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, "i=%d", i );
fprintf( stderr, "%4d\n", 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 );
}
float Falign_noudp( char **seq1, char **seq2,
double *eff1, double *eff2,
int clus1, int clus2,
int alloclen, int *fftlog )
{
int i, j, k, l, m, maxk;
int nlen, nlen2, nlen4;
static int prevalloclen = 0;
// static int crossscoresize = 0;
static char **tmpseq1 = NULL;
static char **tmpseq2 = NULL;
static char **tmpptr1 = NULL;
static char **tmpptr2 = NULL;
static char **tmpres1 = NULL;
static char **tmpres2 = NULL;
static char **result1 = NULL;
static char **result2 = NULL;
#if RND
static char **rndseq1 = NULL;
static char **rndseq2 = NULL;
#endif
static Fukusosuu **seqVector1 = NULL;
static Fukusosuu **seqVector2 = NULL;
static Fukusosuu **naiseki = NULL;
static Fukusosuu *naisekiNoWa = NULL;
static double *soukan = NULL;
int nlentmp;
static int *kouho = NULL;
static Segment *segment = NULL;
static Segment *segment1 = NULL;
static Segment *segment2 = NULL;
static Segment **sortedseg1 = NULL;
static Segment **sortedseg2 = NULL;
static int *cut1 = NULL;
static int *cut2 = NULL;
static char *sgap1, *egap1, *sgap2, *egap2;
static int localalloclen = 0;
int lag;
int tmpint;
int count, count0;
int len1, len2;
int totallen;
float totalscore;
int nkouho;
// float dumfl = 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 0
fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
#endif
if( prevalloclen != alloclen ) // Falign_noudp mo kaeru
{
if( prevalloclen )
{
FreeCharMtx( result1 );
FreeCharMtx( result2 );
FreeCharMtx( tmpres1 );
FreeCharMtx( tmpres2 );
}
// fprintf( stderr, "\n\n\nreallocating ...\n" );
result1 = AllocateCharMtx( njob, alloclen );
result2 = AllocateCharMtx( njob, alloclen );
tmpres1 = AllocateCharMtx( njob, alloclen );
tmpres2 = AllocateCharMtx( njob, alloclen );
prevalloclen = alloclen;
}
if( !localalloclen )
{
sgap1 = AllocateCharVec( njob );
egap1 = AllocateCharVec( njob );
sgap2 = AllocateCharVec( njob );
egap2 = AllocateCharVec( njob );
kouho = AllocateIntVec( NKOUHO_LONG );
cut1 = AllocateIntVec( MAXSEG );
cut2 = AllocateIntVec( MAXSEG );
tmpptr1 = AllocateCharMtx( njob, 0 );
tmpptr2 = AllocateCharMtx( njob, 0 );
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 = 1;
else if( fftscore ) n20or4or2 = 1;
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, nlen+1 );
seqVector2 = AllocateFukusosuuMtx( n20or4or2, 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( scoremtx == -1 )
{
for( i=0; i<clus1; i++ )
seq_vec_4( seqVector1[0], eff1[i], tmpseq1[i] );
}
else if( fftscore )
{
for( i=0; i<clus1; i++ )
{
#if 0
seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] );
#else
seq_vec_5( seqVector1[0], polarity, volume, eff1[i], tmpseq1[i] );
#endif
}
}
else
{
for( i=0; i<clus1; i++ )
seq_vec_3( seqVector1, eff1[i], tmpseq1[i] );
}
#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( scoremtx == -1 )
{
for( i=0; i<clus2; i++ )
seq_vec_4( seqVector2[0], eff2[i], tmpseq2[i] );
}
else if( fftscore )
{
for( i=0; i<clus2; i++ )
{
#if 0
seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] );
#else
seq_vec_5( seqVector2[0], polarity, volume, eff2[i], tmpseq2[i] );
#endif
}
}
else
{
for( i=0; i<clus2; i++ )
seq_vec_3( seqVector2, eff2[i], tmpseq2[i] );
}
#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, "soukan\n" );
for( l=0; l<nlen; l++ )
fprintf( stderr, "%d %f\n", l-nlen2, soukan[l] );
#if 0
fftfp = fopen( "list.plot", "w" );
fprintf( fftfp, "plot 'frt'\n pause +1" );
fclose( fftfp );
system( "/usr/bin/gnuplot list.plot" );
#endif
#endif
nkouho = getKouho( kouho, NKOUHO_LONG, 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];
if( lag <= -len1 || len2 <= lag ) continue;
// fprintf( stderr, "k=%d, lag=%d\n", k, lag );
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, ">Candidate No.%d lag = %d\n", k+1, lag );
fprintf( fftfp, "%s\n", tmpptr2[0] );
fprintf( fftfp, ">\n", k+1, lag );
fclose( fftfp );
#endif
// fprintf( stderr, "lag = %d\n", lag );
tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
// fprintf( stderr, "lag = %d, %d found\n", lag, tmpint );
// if( lag == -50 ) exit( 1 );
if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
// fprintf( stderr, "##### k=%d / %d\n", k, maxk );
if( tmpint == 0 ) break; // 060430 iinoka ?
while( tmpint-- > 0 )
{
#if 0
if( segment[count].end - segment[count].start < fftWinSize )
{
count++;
continue;
}
#endif
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
fprintf( stderr, "##### k=%d / %d\n", k, maxk );
fprintf( stderr, "anchor %d, score = %f\n", count, segment1[count].score );
fprintf( stderr, "in 1 %d\n", segment1[count].center );
fprintf( stderr, "in 2 %d\n", segment2[count].center );
#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, "done. (%d anchors) ", count );
#endif
if( !count && fftNoAnchStop )
ErrorExit( "Cannot detect anchor!" );
#if 0
fprintf( stderr, "RESULT before sort:\n" );
for( l=0; l<count+1; l++ )
{
fprintf( stderr, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( stderr, "%d score = %f\n", segment2[l].center, segment1[l].score );
}
#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
{
cut1[0] = 0;
cut2[0] = 0;
count0 = 0;
for( i=0; i<count; i++ )
{
// fprintf( stderr, "i=%d, %d-%d ?\n", i, sortedseg1[i]->center, sortedseg1[i]->pair->center );
if( sortedseg1[i]->center > cut1[count0]
&& sortedseg1[i]->pair->center > cut2[count0] )
{
count0++;
cut1[count0] = sortedseg1[i]->center;
cut2[count0] = sortedseg1[i]->pair->center;
}
else
{
if( i && sortedseg1[i]->score > sortedseg1[i-1]->score )
{
if( sortedseg1[i]->center > cut1[count0-1]
&& sortedseg1[i]->pair->center > cut2[count0-1] )
{
cut1[count0] = sortedseg1[i]->center;
cut2[count0] = sortedseg1[i]->pair->center;
}
else
{
// count0--;
}
}
}
}
// if( count-count0 )
// fprintf( stderr, "%d anchors unused\n", count-count0 );
cut1[count0+1] = len1;
cut2[count0+1] = len2;
count = count0 + 2;
count0 = count;
}
// exit( 0 );
#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
fprintf( stderr, "RESULT after blckalign:\n" );
for( l=0; l<count+1; l++ )
{
fprintf( stderr, "cut : %d %d\n", cut1[l], cut2[l] );
}
#endif
#if 0
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;
*fftlog = -1;
for( i=0; i<count-1; i++ )
{
*fftlog += 1;
if( cut1[i] )
{
// getkyokaigap( sgap1, seq1, cut1[i]-1, clus1 );
// getkyokaigap( sgap2, seq2, cut2[i]-1, clus2 );
getkyokaigap( sgap1, tmpres1, nlen-1, clus1 );
getkyokaigap( sgap2, tmpres2, nlen-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';
}
#if DEBUG
fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
#else
#if 1
fprintf( stderr, "DP %05d / %05d \b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", i+1, count-1 );
#endif
#endif
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 && fftkeika ) commongappick( clus1, tmpres1 ); //dvtditr に呼ばれたとき fftkeika=1
// if( kobetsubunkatsu ) commongappick( clus1, tmpres1 );
for( j=0; j<clus2; j++ )
{
// fprintf( stderr, "### cut2[i+1]-cut2[i] = %d\n", cut2[i+1]-cut2[i] );
if( cut2[i+1]-cut2[i] <= 0 )
fprintf( stderr, "### cut2[i+1]=%d, cut2[i]=%d\n", cut2[i+1], cut2[i] );
strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
tmpres2[j][cut2[i+1]-cut2[i]] = 0;
}
if( kobetsubunkatsu && fftkeika ) commongappick( clus2, tmpres2 ); //dvtditr に呼ばれたとき fftkeika=1
// if( kobetsubunkatsu ) commongappick( clus2, tmpres2 );
if( constraint )
{
fprintf( stderr, "Not supported\n" );
exit( 1 );
}
#if 0
fprintf( stderr, "i=%d, before alignment", i );
fprintf( stderr, "%4d\n", 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 0
fprintf( stdout, "writing input\n" );
for( j=0; j<clus1; j++ )
{
fprintf( stdout, ">%d of GROUP1\n", j );
fprintf( stdout, "%s\n", tmpres1[j] );
}
for( j=0; j<clus2; j++ )
{
fprintf( stdout, ">%d of GROUP2\n", j );
fprintf( stdout, "%s\n", tmpres2[j] );
}
fflush( stdout );
#endif
switch( alg )
{
case( 'M' ):
totalscore += MSalignmm( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2 );
break;
default:
fprintf( stderr, "alg = %c\n", alg );
ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
break;
}
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, "i=%d", i );
fprintf( stderr, "%4d\n", 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 );
}
float Falign_udpari_long( char **seq1, char **seq2,
double *eff1, double *eff2,
int clus1, int clus2,
int alloclen, int *fftlog )
{
int i, j, k, l, m, maxk;
int nlen, nlen2, nlen4;
static int prevalloclen = 0;
static int crossscoresize = 0;
static char **tmpseq1 = NULL;
static char **tmpseq2 = NULL;
static char **tmpptr1 = NULL;
static char **tmpptr2 = NULL;
static char **tmpres1 = NULL;
static char **tmpres2 = NULL;
static char **result1 = NULL;
static char **result2 = NULL;
#if RND
static char **rndseq1 = NULL;
static char **rndseq2 = NULL;
#endif
static Fukusosuu **seqVector1 = NULL;
static Fukusosuu **seqVector2 = NULL;
static Fukusosuu **naiseki = NULL;
static Fukusosuu *naisekiNoWa = NULL;
static double *soukan = NULL;
static double **crossscore = NULL;
int nlentmp;
static int *kouho = NULL;
static Segment *segment = NULL;
static Segment *segment1 = NULL;
static Segment *segment2 = NULL;
static Segment **sortedseg1 = NULL;
static Segment **sortedseg2 = NULL;
static int *cut1 = NULL;
static int *cut2 = NULL;
static char *sgap1, *egap1, *sgap2, *egap2;
static int localalloclen = 0;
int lag;
int tmpint;
int count, count0;
int len1, len2;
int totallen;
float totalscore;
int nkouho;
// float dumfl = 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 0
fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
#endif
if( prevalloclen != alloclen ) // Falign_noudp mo kaeru
{
if( prevalloclen )
{
FreeCharMtx( result1 );
FreeCharMtx( result2 );
FreeCharMtx( tmpres1 );
FreeCharMtx( tmpres2 );
}
// fprintf( stderr, "\n\n\nreallocating ...\n" );
result1 = AllocateCharMtx( njob, alloclen );
result2 = AllocateCharMtx( njob, alloclen );
tmpres1 = AllocateCharMtx( njob, alloclen );
tmpres2 = AllocateCharMtx( njob, alloclen );
prevalloclen = alloclen;
}
if( !localalloclen )
{
sgap1 = AllocateCharVec( njob );
egap1 = AllocateCharVec( njob );
sgap2 = AllocateCharVec( njob );
egap2 = AllocateCharVec( njob );
kouho = AllocateIntVec( NKOUHO_LONG );
cut1 = AllocateIntVec( MAXSEG );
cut2 = AllocateIntVec( MAXSEG );
tmpptr1 = AllocateCharMtx( njob, 0 );
tmpptr2 = AllocateCharMtx( njob, 0 );
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 = 1;
else if( fftscore ) n20or4or2 = 1;
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, nlen+1 );
seqVector2 = AllocateFukusosuuMtx( n20or4or2, 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] );