Mac binaries
[jabaws.git] / website / archive / binaries / mac / src / mafft / core / Falign_localhom.c
diff --git a/website/archive/binaries/mac/src/mafft/core/Falign_localhom.c b/website/archive/binaries/mac/src/mafft/core/Falign_localhom.c
new file mode 100644 (file)
index 0000000..ba2dee3
--- /dev/null
@@ -0,0 +1,871 @@
+#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 );
+}