--- /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