+++ /dev/null
-#include "mltaln.h"
-
-//static FILE *fftfp;
-static TLS int n20or4or2;
-
-#define KEIKA 0
-#define RND 0
-#define DEBUG 0
-
-extern int fft( int, Fukusosuu *, int );
-
-
-#if 0
-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
-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 TLS 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;
- }
-}
-
-
-#if 0
-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 TLS int i, j, k, p;
- static TLS int allo = 0;
- static TLS Segment **work = NULL;
-
- if( seg == NULL )
- {
- free( work ); work = NULL;
- return;
- }
-
- 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++];
- }
-}
-
-
-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 );
-}
git://source.jalview.org / jabaws.git / blobdiff