--- /dev/null
+#define DEFAULTGOP_N -1530
+#define DEFAULTGEP_N 0
+#define DEFAULTOFS_N -123
+#define DEFAULTPAMN 200
+
+#define DEFAULTRNAGOP_N -1530
+#define DEFAULTRNAGEP_N 0
+#define DEFAULTRNATHR_N 0
+
+// -h 0.11150 -> all positive
+
+double ribosum4[4][4] =
+{
+// a g c t
+{ 2.22, -1.46, -1.86, -1.39, }, // a
+{ -1.46, 1.03, -2.48, -1.74, }, // g
+{ -1.86, -2.48, 1.16, -1.05, }, // c
+{ -1.39, -1.74, -1.05, 1.65, }, // t
+};
+
+double ribosum16[16][16] =
+{
+// aa ag ac at ga gg gc gt ca cg cc ct ta tg tc tt
+{ -2.49, -8.24, -7.04, -4.32, -6.86, -8.39, -5.03, -5.84, -8.84, -4.68, -14.37, -12.64, -4.01, -6.16, -11.32, -9.05, }, // aa
+{ -8.24, -0.80, -8.89, -5.13, -8.61, -5.38, -5.77, -6.60, -10.41, -4.57, -14.53, -10.14, -5.43, -5.94, -8.87, -11.07, }, // ag
+{ -7.04, -8.89, -2.11, -2.04, -9.73, -11.05, -3.81, -4.72, -9.37, -5.86, -9.08, -10.45, -5.33, -6.93, -8.67, -7.83, }, // ac
+{ -4.32, -5.13, -2.04, 4.49, -5.33, -5.61, 2.70, 0.59, -5.56, 1.67, -6.71, -5.17, 1.61, -0.51, -4.81, -2.98, }, // at
+{ -6.86, -8.61, -9.73, -5.33, -1.05, -8.67, -4.88, -6.10, -7.98, -6.00, -12.43, -7.71, -5.85, -7.55, -6.63, -11.54, }, // ga
+{ -8.39, -5.38, -11.05, -5.61, -8.67, -1.98, -4.13, -5.77, -11.36, -4.66, -12.58, -13.69, -5.75, -4.27, -12.01, -10.79, }, // gg
+{ -5.03, -5.77, -3.81, 2.70, -4.88, -4.13, 5.62, 1.21, -5.95, 2.11, -3.70, -5.84, 1.60, -0.08, -4.49, -3.90, }, // gc
+{ -5.84, -6.60, -4.72, 0.59, -6.10, -5.77, 1.21, 3.47, -7.93, -0.27, -7.88, -5.61, -0.57, -2.09, -5.30, -4.45, }, // gt
+{ -8.84, -10.41, -9.37, -5.56, -7.98, -11.36, -5.95, -7.93, -5.13, -3.57, -10.45, -8.49, -2.42, -5.63, -7.08, -8.39, }, // ca
+{ -4.68, -4.57, -5.86, 1.67, -6.00, -4.66, 2.11, -0.27, -3.57, 5.36, -5.71, -4.96, 2.75, 1.32, -4.91, -3.67, }, // cg
+{ -14.37, -14.53, -9.08, -6.71, -12.43, -12.58, -3.70, -7.88, -10.45, -5.71, -3.59, -5.77, -6.88, -8.41, -7.40, -5.41, }, // cc
+{ -12.64, -10.14, -10.45, -5.17, -7.71, -13.69, -5.84, -5.61, -8.49, -4.96, -5.77, -2.28, -4.72, -7.36, -3.83, -5.21, }, // ct
+{ -4.01, -5.43, -5.33, 1.61, -5.85, -5.75, 1.60, -0.57, -2.42, 2.75, -6.88, -4.72, 4.97, 1.14, -2.98, -3.39, }, // ta
+{ -6.16, -5.94, -6.93, -0.51, -7.55, -4.27, -0.08, -2.09, -5.63, 1.32, -8.41, -7.36, 1.14, 3.36, -4.76, -4.28, }, // tg
+{ -11.32, -8.87, -8.67, -4.81, -6.63, -12.01, -4.49, -5.30, -7.08, -4.91, -7.40, -3.83, -2.98, -4.76, -3.21, -5.97, }, // tc
+{ -9.05, -11.07, -7.83, -2.98, -11.54, -10.79, -3.90, -4.45, -8.39, -3.67, -5.41, -5.21, -3.39, -4.28, -5.97, -0.02, }, // tt
+};
+
+int locpenaltyn = -1750;
+char locaminon[] = "agctuAGCTUnNbdhkmnrsvwyx-O";
+char locgrpn[] =
+{
+ 0, 1, 2, 3, 3, 0, 1, 2, 3, 3,
+ 4, 4, 5, 5, 5, 5, 5, 5, 5, 5,
+ 5, 5, 5, 5, 5, 5
+};
+int exgpn = +00;
+int locn_disn[26][26] =
+/* u ha constants.c no nakade shori */
+/* 0 - 4 dake yomareru. */
+ {
+ {
+ 1000, 600, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 600, 1000, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 1000, 600, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 600, 1000, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 500, 500, 0, 0, 0, 500, 500, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, -500,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0,
+ },
+
+ {
+ -500, -500, -500, -500, -500, -500, -500, -500, -500, -500,
+ -500, -500, -500, -500, -500, -500, -500, -500, -500, -500,
+ -500, -500, -500, -500, 0, 500,
+ },
+ };
--- /dev/null
+#include "mltaln.h"
+
+#if 0
+static FILE *fftfp;
+#endif
+static TLS 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 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;
+ }
+}
+
+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 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++];
+ }
+}
+
+
+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 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 int localalloclen = 0;
+ int lag;
+ int tmpint;
+ int count, count0;
+ int len1, len2;
+ int totallen;
+ float dumfl = 0.0;
+ int headgp, tailgp;
+
+ 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], 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( i == 0 ) headgp = outgap; else headgp = 1;
+ if( i == count-2 ) tailgp = outgap; else tailgp = 1;
+
+#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, NULL, 0, NULL, headgp, tailgp );
+ break;
+ case( 'A' ):
+ if( clus1 == 1 && clus2 == 1 )
+ G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
+ else
+ A__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp );
+ break;
+ case( 'H' ):
+ if( clus1 == 1 && clus2 == 1 )
+ G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
+ 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, headgp, tailgp );
+ 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 *chudanpt, int chudanref, int *chudanres )
+{
+ int i, j, k, l, m, maxk;
+ int nlen, nlen2, nlen4;
+ static TLS int prevalloclen = 0;
+ 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 dumfl = 0.0;
+ int headgp, tailgp;
+
+
+ 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 );
+ 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( 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], 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( i == 0 ) headgp = outgap; else headgp = 1;
+ if( i == count-2 ) tailgp = outgap; else tailgp = 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 \e$B$K8F$P$l$?$H$-\e(B fftkeika=1
+// if( kobetsubunkatsu ) commongappick( clus1, tmpres1 );
+ for( j=0; j<clus2; j++ )
+ {
+ strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
+ tmpres2[j][cut2[i+1]-cut2[i]] = 0;
+ }
+ if( kobetsubunkatsu && fftkeika ) commongappick( clus2, tmpres2 ); //dvtditr \e$B$K8F$P$l$?$H$-\e(B 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, chudanpt, chudanref, chudanres, headgp, tailgp );
+ break;
+ case( 'A' ):
+ if( clus1 == 1 && clus2 == 1 )
+ {
+ totalscore += G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
+ }
+ else
+ totalscore += A__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+ break;
+ case( 'H' ):
+ if( clus1 == 1 && clus2 == 1 )
+ {
+ totalscore += G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
+ }
+ 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, headgp, tailgp );
+ }
+ 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;
+ }
+
+#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, "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 );
+}
+
+
+
+
+
+
+
+
+/*
+sakujo wo kentou (2010/10/05)
+*/
+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 TLS int prevalloclen = 0;
+ 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;
+ int nkouho = 0;
+ int headgp, tailgp;
+// 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], 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 ? // 090530 yameta
+ 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
+ {
+ if( count < 5000 )
+ {
+ 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;
+
+// fprintf( stderr, "\n\n\ncalling blockAlign2\n\n\n\n" );
+ 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
+ }
+ }
+
+
+ else
+ {
+ fprintf( stderr, "\nMany anchors were found. The upper-level DP is skipped.\n\n" );
+
+ 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( i == 0 ) headgp = outgap; else headgp = 1;
+ if( i == count-2 ) tailgp = outgap; else tailgp = 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 \e$B$K8F$P$l$?$H$-\e(B fftkeika=1
+// if( kobetsubunkatsu ) commongappick( clus1, tmpres1 );
+ for( j=0; j<clus2; j++ )
+ {
+// fprintf( stderr, "### cut2[i+1]-cut2[i] = %d\n", cut2[i+1]-cut2[i] );
+ if( cut2[i+1]-cut2[i] <= 0 )
+ fprintf( stderr, "### cut2[i+1]=%d, cut2[i]=%d\n", cut2[i+1], cut2[i] );
+ strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
+ tmpres2[j][cut2[i+1]-cut2[i]] = 0;
+ }
+ if( kobetsubunkatsu && fftkeika ) commongappick( clus2, tmpres2 ); //dvtditr \e$B$K8F$P$l$?$H$-\e(B 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, NULL, 0, NULL, headgp, tailgp );
+ 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 );
+}
--- /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 );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+
+#if 1
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char *seq2 = s2[0];
+ int *intptr = amino_dis[(int)s1[0][i1]];
+
+ while( lgth2-- )
+ *match++ = intptr[(int)*seq2++];
+}
+static void match_calc_mtx( int mtx[0x80][0x80], float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char *seq2 = s2[0];
+ int *intptr = mtx[(int)s1[0][i1]];
+
+ while( lgth2-- )
+ *match++ = intptr[(int)*seq2++];
+}
+#else
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ int j;
+
+ for( j=0; j<lgth2; j++ )
+ match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
+}
+#endif
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ int **ijp,
+ int tailgp )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ float wm;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ if( tailgp == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+
+
+ iin = lgth1; jin = lgth2;
+ limk = lgth1+lgth2 + 1;
+ for( k=0; k<limk; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--mseq1[0] = seq1[0][ifi+l];
+ *--mseq2[0] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mseq1[0] = seq1[0][ifi];
+ *--mseq2[0] = seq2[0][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ return( 0.0 );
+}
+
+
+float G__align11( char **seq1, char **seq2, int alloclen, int headgp, int tailgp )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ orlgth1 = 0;
+ orlgth2 = 0;
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+ return( 0.0 );
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 <= 0 || lgth2 <= 0 )
+ {
+ fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+
+#if 1
+ if( lgth1 == 0 && lgth2 == 0 )
+ return( 0.0 );
+
+ if( lgth1 == 0 )
+ {
+ seq1[0][lgth2] = 0;
+ while( lgth2 ) seq1[0][--lgth2] = '-';
+// fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ return( 0.0 );
+ }
+
+ if( lgth2 == 0 )
+ {
+ seq2[0][lgth1] = 0;
+ while( lgth1 ) seq2[0][--lgth1] = '-';
+// fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+ return( 0.0 );
+ }
+#endif
+
+
+ wm = 0.0;
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+ if( headgp == 1 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+ }
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+ }
+
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // lgth2==0 no toki error
+ else
+ lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
+
+ if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ for( j=1; j<lgth2+1; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ if( (g=*prept) >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt + fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ if( (g=*prept) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
+ }
+
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, tailgp );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+#if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+ fprintf( stderr, "wm = %f\n", wm );
+#endif
+
+ return( wm );
+}
+
+float G__align11_noalign( int scoremtx[0x80][0x80], int penal, int penal_ex, char **seq1, char **seq2, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+// int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penal;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penal_ex;
+#endif
+#if 1
+ float *wtmp;
+ float *mjpt, *prept, *curpt;
+// int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ orlgth1 = 0;
+ orlgth2 = 0;
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ free( m );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+ return( 0.0 );
+ }
+
+ wm = 0.0;
+
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+
+
+ if( lgth1 <= 0 || lgth2 <= 0 )
+ {
+ fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+
+
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+
+
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+
+
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+
+ match_calc_mtx( scoremtx, initverticalw, seq2, seq1, 0, lgth1 );
+
+
+ match_calc_mtx( scoremtx, currentw, seq1, seq2, 0, lgth2 );
+
+ if( 1 ) // tsuneni outgap-1
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+ }
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1];
+ }
+
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // lgth2==0 no toki error
+ else
+ lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
+
+ if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap-1
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc_mtx( scoremtx, currentw, seq1, seq2, i, lgth2 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0];
+
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ for( j=1; j<lgth2+1; j++ )
+ {
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+ }
+ if( (g=*prept) >= mi )
+ {
+ mi = g;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt + fpenalty) > wm )
+ {
+ wm = g;
+ }
+ if( (g=*prept) >= *mjpt )
+ {
+ *mjpt = g;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ mjpt++;
+ prept++;
+ }
+ lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
+ }
+
+#if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+ fprintf( stderr, "wm = %f\n", wm );
+#endif
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 1
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define FASTMATCHCALC 1
+
+static TLS float **impmtx = NULL;
+
+#if 0 // by D.Mathog
+static float countnocountxx( Gappat *pat1, float diaf1, Gappat *pat2, int offset1, int offset2 )
+{
+// return( 0.0 );
+ float gclose;
+ float gmatch;
+ Gappat *pat1bk = pat1;
+ Gappat *pat2bk = pat2;
+
+ gmatch = 0.0;
+ for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0
+ {
+ if( pat2->len + offset2 == offset1 )
+ {
+ gmatch = diaf1 * pat2->freq;
+ }
+ }
+ for( pat1=pat1bk+1; pat1->len != 0; pat1++ ) // excl. len=0
+ {
+ for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0
+ {
+ if( pat1->len + offset1 == pat2->len + offset2 )
+ {
+ gmatch += pat1->freq * pat2->freq;
+// if( r ) fprintf( stderr, "match1!!, len=%d, gmatch=%f * %f\n", pat2->len, pat1->freq, pat2->freq );
+ }
+ }
+ }
+ return( gmatch );
+}
+#endif
+
+static float countnocountmatchx( Gappat *pat1, Gappat *pat2, int offset1, int offset2, int r )
+{
+ Gappat *pat1bk = pat1;
+ Gappat *pat2bk = pat2;
+ float val = 0.0;
+ // pat1[][0] ha total gap.
+ for( pat1=pat1bk+1; pat1->len != 0; pat1++ )
+ {
+ for( pat2=pat2bk+1; pat2->len != 0; pat2++ )
+ {
+ if( pat1->len + offset1 == pat2->len + offset2 )
+ {
+ val += pat1->freq * pat2->freq;
+ if( r ) fprintf( stderr, "y %d-%d, len=%d,%d, val = %f\n", (int)(pat1-pat1bk), (int)(pat2-pat2bk), pat1->len, pat2->len, val ); // 070405
+// if( r ) fprintf( stderr, "y %d-%d, len=%d,%d, val = %f\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len, val );
+ }
+ }
+ }
+ if( r ) fprintf( stderr, "nocountmatch=%f\n", val );
+ return( val );
+}
+
+#if 0 // by D.Mathog
+static float countnocountmatch( Gappat *pat1, Gappat *pat2, int r )
+{
+// return( 0.0 );
+ Gappat *pat1bk = pat1;
+ Gappat *pat2bk = pat2;
+ float val = 0.0;
+ // pat1[][0] ha total gap.
+ for( pat1=pat1bk+1; pat1->len != 0; pat1++ )
+ {
+// if( r ) fprintf( stderr, "b %d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len );
+ for( pat2=pat2bk+1; pat2->len != 0; pat2++ )
+ {
+ if( pat1->len == pat2->len )
+ {
+// if( r ) fprintf( stderr, " x%d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len );
+ val += pat1->freq * pat2->freq;
+// if( r ) fprintf( stderr, "y %d-%d, val = %f\n", pat1-pat1bk, pat2-pat2bk,val );
+// if( r ) fprintf( stderr, "z tsugi, %d-%d, len=%d,%d\n", pat1-pat1bk+1, pat2-pat2bk+1, (pat1+1)->len, (pat2+1)->len );
+ }
+// if( r ) fprintf( stderr, "a %d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len );
+ }
+ }
+// fprintf( stderr, "nocountmatch=%f\n", val );
+ return( val );
+}
+#endif
+
+static float countnocountx( Gappat *pat1, float diaf1, Gappat *pat2, int offset1, int r )
+{
+// return( 0.0 );
+ float gmatch;
+ Gappat *pat1bk = pat1;
+ Gappat *pat2bk = pat2;
+
+ gmatch = 0.0;
+ for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0
+ {
+ if( pat2->len == offset1 )
+ {
+ gmatch = diaf1 * pat2->freq;
+// if( r ) fprintf( stderr, "match0!!, len=%d, gmatch=%f * %f\n", pat2->len, diaf1, pat2->freq );
+ }
+ }
+ for( pat1=pat1bk+1; pat1->len != 0; pat1++ ) // excl. len=0
+ {
+ for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0
+ {
+ if( pat1->len + offset1 == pat2->len )
+ {
+ gmatch += pat1->freq * pat2->freq;
+// if( r ) fprintf( stderr, "match1!!, len=%d, gmatch=%f * %f\n", pat2->len, pat1->freq, pat2->freq );
+ }
+ }
+ }
+ return( gmatch );
+}
+
+#if 0 // by D.Mathog
+static float countnocount( Gappat *pat1, Gappat *pat2, int offset1, int offset2 ) //osoi
+{
+// return( 0.0 );
+ Gappat *pat1bk = pat1;
+ Gappat *pat2bk = pat2;
+ float val = 0.0;
+ // pat1[][0] ha total gap.
+ for( pat1=pat1bk+1; pat1->len != -1; pat1++ )
+ {
+ for( pat2=pat2bk+1; pat2->len != -1; pat2++ )
+ {
+ if( pat1->len+offset1 == pat2->len+offset2 )
+ {
+ val += pat1->freq * pat2->freq;
+ }
+ }
+ }
+// fprintf( stderr, "nocount=%f\n", val );
+ return( val );
+}
+#endif
+
+
+
+#if 1 // tditeration
+float imp_match_out_scH( int i1, int j1 )
+{
+// fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
+// fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
+ return( impmtx[i1][j1] );
+}
+#endif
+
+static void imp_match_out_veadH( float *imp, int i1, int lgth2 )
+{
+#if FASTMATCHCALC
+ float *pt = impmtx[i1];
+ while( lgth2-- )
+ *imp++ += *pt++;
+#else
+ int j;
+ float *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[j];
+#endif
+}
+static void imp_match_out_vead_tateH( float *imp, int j1, int lgth1 )
+{
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[i][j1];
+}
+
+#if 1 // tbfast.c kara yobareru.
+void imp_match_init_strictH( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
+{
+ int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ static TLS int impalloclen = 0;
+ float effij;
+ double effijx;
+ char *pt, *pt1, *pt2;
+ static TLS char *nocount1 = NULL;
+ static TLS char *nocount2 = NULL;
+ LocalHom *tmpptr;
+
+ if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ if( nocount1 ) free( nocount1 );
+ if( nocount2 ) free( nocount2 );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+ nocount1 = AllocateCharVec( impalloclen );
+ nocount2 = AllocateCharVec( impalloclen );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<clus1; j++ )
+ if( seq1[j][i] == '-' ) break;
+ if( j != clus1 ) nocount1[i] = 1;
+ else nocount1[i] = 0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ if( seq2[j][i] == '-' ) break;
+ if( j != clus2 ) nocount2[i] = 1;
+ else nocount2[i] = 0;
+ }
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+ fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "eff1 in _init_strict = \n" );
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "eff1[] = %f\n", eff1[i] );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "eff2[] = %f\n", eff2[i] );
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ effijx = fastathreshold;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ effij = (float)( eff1[i] * eff2[j] * effijx );
+ tmpptr = localhom[i][j];
+ while( tmpptr )
+ {
+// fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
+// fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
+// fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
+// fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start1 ) break;
+ }
+ start1 = pt - seq1[i] - 1;
+
+ if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( tmpint == tmpptr->end1 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end1 = pt - seq1[i] - 0;
+#else
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end1 ) break;
+ }
+ end1 = pt - seq1[i] - 1;
+#endif
+ }
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start2 ) break;
+ }
+ start2 = pt - seq2[j] - 1;
+ if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end2 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end2 = pt - seq2[j] - 0;
+#else
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end2 ) break;
+ }
+ end2 = pt - seq2[j] - 1;
+#endif
+ }
+// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
+// fprintf( stderr, "step 0\n" );
+ if( end1 - start1 != end2 - start2 )
+ {
+// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ }
+
+#if 1
+ k1 = start1; k2 = start2;
+ pt1 = seq1[i] + k1;
+ pt2 = seq2[j] + k2;
+ while( *pt1 && *pt2 )
+ {
+ if( *pt1 != '-' && *pt2 != '-' )
+ {
+// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
+// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
+// impmtx[k1][k2] += tmpptr->importance * effij;
+ impmtx[k1][k2] += tmpptr->fimportance * effij;
+// fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
+// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+// fprintf( stderr, "%d (%c) - %d (%c) - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
+ k1++; k2++;
+ pt1++; pt2++;
+ }
+ else if( *pt1 != '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k2++; pt2++;
+ }
+ else if( *pt1 == '-' && *pt2 != '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ }
+ else if( *pt1 == '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ k2++; pt2++;
+ }
+ if( k1 > end1 || k2 > end2 ) break;
+ }
+#else
+ while( k1 <= end1 && k2 <= end2 )
+ {
+ fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
+ if( !nocount1[k1] && !nocount2[k2] )
+ {
+ impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j] * fastathreshold;
+ fprintf( stderr, "marked\n" );
+ }
+ else
+ fprintf( stderr, "no count\n" );
+ k1++; k2++;
+ }
+#endif
+ tmpptr = tmpptr->next;
+ }
+ }
+ }
+#if 0
+ if( clus1 == 1 && clus2 == 6 )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d ", k1 );
+ for( k2=0; k2<3; k2++ )
+ fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+ }
+#endif
+}
+#endif
+
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+ int j, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<26; j++ )
+ scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+#else
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+// simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin == lgth1 || jin == lgth2 )
+ ;
+ else
+ {
+ *impwmpt += imp_match_out_scH( iin, jin );
+
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+
+ return( 0.0 );
+}
+
+float H__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+// float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS Gappat **gappat1;
+ static TLS Gappat **gappat2;
+ static TLS float *digf1;
+ static TLS float *digf2;
+ static TLS float *diaf1;
+ static TLS float *diaf2;
+ static TLS float *gapz1;
+ static TLS float *gapz2;
+ static TLS float *gapf1;
+ static TLS float *gapf2;
+ static TLS float *ogcp1g;
+ static TLS float *ogcp2g;
+ static TLS float *fgcp1g;
+ static TLS float *fgcp2g;
+ static TLS float *ogcp1;
+ static TLS float *ogcp2;
+ static TLS float *fgcp1;
+ static TLS float *fgcp2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float fpenalty = (float)penalty;
+ float tmppenal;
+ float cumpenal;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fgcp1va;
+ float ogcp1va;
+ int maegap;
+
+
+
+#if 0
+ fprintf( stderr, "#### eff in SA+++align\n" );
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ free( gappat1 );
+ free( gappat2 );
+ FreeFloatVec( digf1 );
+ FreeFloatVec( digf2 );
+ FreeFloatVec( diaf1 );
+ FreeFloatVec( diaf2 );
+ FreeFloatVec( gapz1 );
+ FreeFloatVec( gapz2 );
+ FreeFloatVec( gapf1 );
+ FreeFloatVec( gapf2 );
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatVec( ogcp1g );
+ FreeFloatVec( ogcp2g );
+ FreeFloatVec( fgcp1g );
+ FreeFloatVec( fgcp2g );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ digf1 = AllocateFloatVec( ll1+2 );
+ digf2 = AllocateFloatVec( ll2+2 );
+ diaf1 = AllocateFloatVec( ll1+2 );
+ diaf2 = AllocateFloatVec( ll2+2 );
+ gappat1 = (Gappat **)calloc( ll1+2, sizeof( Gappat * ) );
+ gappat2 = (Gappat **)calloc( ll2+2, sizeof( Gappat * ) );
+ gapz1 = AllocateFloatVec( ll1+2 );
+ gapz2 = AllocateFloatVec( ll2+2 );
+ gapf1 = AllocateFloatVec( ll1+2 );
+ gapf2 = AllocateFloatVec( ll2+2 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+ ogcp1g = AllocateFloatVec( ll1+2 );
+ ogcp2g = AllocateFloatVec( ll2+2 );
+ fgcp1g = AllocateFloatVec( ll1+2 );
+ fgcp2g = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] = mseq[i];
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] = mseq[icyc+j];
+ seq2[j][lgth2] = 0;
+ }
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+#if 0
+ {
+ float t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap1 );
+ new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap1, egap2 );
+ getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 ); // sgap1 ha iranai ?
+ getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 ); // sgap1 ha iranai ?
+ getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 ); // sgap1 ha iranai ?
+ getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap1, egap2 ); // sgap1 ha iranai ?
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 ); // atode
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 ); // atode
+ getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 ); // atode
+ getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 ); // atode
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
+ st_getGapPattern( gappat1, icyc, seq1, eff1, lgth1 );
+ st_getGapPattern( gappat2, jcyc, seq2, eff2, lgth2 );
+ getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
+ getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
+ getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
+ getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
+ getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ if( localhom )
+ imp_match_out_vead_tateH( initverticalw, 0, lgth1 ); // 060306
+
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ if( localhom )
+ imp_match_out_veadH( currentw, 0, lgth2 ); // 060306
+
+
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+ if( outgap == 1 )
+ {
+// if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+// initverticalw[0] += g;
+// currentw[0] += g;
+
+// if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+// initverticalw[0] += g;
+// currentw[0] += g;
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+// initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+
+ tmppenal = 0.0;
+// tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+0.0) + gapz2[0]*(1.0-digf1[0] - diaf1[0]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-0.0)*(1.0-ogcp1g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-0.0) * (1.0-diaf1[0]) + 0.0 ) * 0.5 * fpenalty; // 0.
+// tmppenal -= ( (1.0-gapf2[j-1]) * ogcp1g[i] + gapf2[j-1] ) * 0.5 * fpenalty;
+// fprintf( stderr, "0,0<-%d,%d, tmppenal 1 = %f\n", i, 0, tmppenal );
+ initverticalw[i] += tmppenal;
+
+ tmppenal = diaf1[i] * ( 1.0 - gapf2[0] ) * fpenalty;
+ if( gappat1[i][0].freq )
+ {
+ tmppenal += ( gappat1[i][0].freq ) * ( 1.0 - gapf2[0] ) * fpenalty;
+ tmppenal -= ( countnocountx( gappat2[0], diaf2[0], gappat1[i], i, 1 ) ) * fpenalty;
+ }
+// tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapz2[1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[0])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[0]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[0]) * (1.0-diaf1[i]) + gapf2[0] ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[j]) * fgcp1g[i] + gapf2[j] ) * 0.5 * fpenalty;
+ initverticalw[i] += tmppenal;
+// fprintf( stderr, "0,0<-%d,%d, tmppenal 2 = %f, cumpenal=%f, fgcp1g[i]=%f, ogcp1g[i]=%f\n", i, 0, tmppenal, cumpenal, fgcp1g[i], ogcp1g[i] );
+
+ }
+ cumpenal = 0.0;
+ for( j=1; j<lgth2+1; j++ )
+ {
+// currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+
+ tmppenal = 0.0;
+// tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapf1[i-1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+0.0) + gapz1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-0.0)*(1.0-ogcp2g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-0.0) * (1.0-diaf2[0]) + 0.0 ) * 0.5 * fpenalty; // 0.
+// tmppenal -= ( (1.0-gapf1[0]) * fgcp2g[j] + gapf1[0] ) * 0.5 * fpenalty;
+// fprintf( stderr, "0,0<-%d,%d, tmppenal 3 = %f\n", 0, j, tmppenal );
+ currentw[j] += tmppenal;
+
+ tmppenal = diaf2[j] * ( 1.0 - gapf1[0] ) * fpenalty;
+ if( gappat2[j][0].freq )
+ {
+ tmppenal += ( gappat2[j][0].freq ) * ( 1.0 - gapf1[0] ) * fpenalty;
+ tmppenal -= ( countnocountx( gappat1[0], diaf1[0], gappat2[j], j, 1 ) ) * fpenalty;
+ }
+// tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapz1[1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf1[0])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf1[0]) * (1.0-diaf2[j]) + gapf1[0] ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf1[0]) * ogcp2g[j] + gapf1[i-1] ) * 0.5 * fpenalty;
+// fprintf( stderr, "0,0<-%d,%d, tmppenal 4 = %f\n", 0, j, tmppenal );
+ currentw[j] += tmppenal;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ m[0] = 0.0; // iranai
+ for( j=1; j<lgth2+1; ++j )
+ {
+// m[j] = currentw[j-1] + ogcp1[1];
+ mp[j] = 0;
+
+ tmppenal = 0.0;
+// tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[1]+fgcp1g[1]) + gapz2[j]*(1.0-digf1[1]-diaf1[1]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[1]+fgcp1g[1]) + gapf2[j-1]*(1.0-digf1[1]-diaf1[1]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-0.0) * (1.0-0.0) + 0.0 ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[-1]) * (1.0-diaf1[0]) + gapf2[-1] ) * 0.5 * fpenalty;
+// if( tmppenal ) fprintf( stderr, "%c=%c, end j tmppenal=%f\n", seq1[0][0], seq2[0][j-1], tmppenal );
+ m[j] = currentw[j-1] + tmppenal + fpenalty * 10000;
+// m[j] = currentw[j-1] + ogcp1[1];
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_veadH( currentw, i, lgth2 );
+#else
+ imp_match_out_veadH( currentw, i, lgth2 );
+#endif
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+
+// mi = previousw[0] + ogcp2[1]; // machigai
+ tmppenal = 0.0;
+// tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[1]+fgcp2g[1]) + gapz1[i]*(1.0-digf2[1]-diaf2[1]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[1]+fgcp2g[1]) + gapf1[i-1]*(1.0-digf2[1]-diaf2[1]) ) * 0.5 * fpenalty; // mada
+// fprintf( stderr, "%c=%c, end i tmppenal=%f, ogcp2g[1]=%f\n", seq1[0][i-1], seq2[0][0], tmppenal, ogcp2g[1] );
+// mi = previousw[0] + tmppenal;
+ mi = previousw[0] + tmppenal + fpenalty * 10000;
+
+ mpi = 0;
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fgcp2pt = fgcp2;
+ ogcp2pt = ogcp2 + 1;
+ fgcp1va = fgcp1[i-1];
+ ogcp1va = ogcp1[i];
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+
+ if( gappat2[j][0].freq )
+ {
+ g = diaf1[i] * gappat2[j][0].freq * fpenalty;
+// if( seq1[0][i] == 'D' && seq2[0][j] == 'D' )
+// if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] );
+ wm += g;
+ }
+
+ if( gappat1[i][0].freq )
+ {
+ g = diaf2[j] * gappat1[i][0].freq * fpenalty;
+// if( seq1[0][i] == 'D' && seq2[0][j] == 'D' )
+// if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] );
+ wm += g;
+ }
+ {
+ g = ( (gappat1[i][0].freq) * (gappat2[j][0].freq) ) * fpenalty;
+// if( seq1[0][i] == 'D' && seq2[0][j] == 'D' )
+// if( g ) fprintf( stderr, "match penal3=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] );
+ wm += g;
+ }
+ if( 0 )
+ {
+ maegap = ijp[i-1][j-1];
+// if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' )
+// fprintf( stderr, "i,j=%d,%d, maegap=%d\n", i, j, maegap );
+ maegap = 0;
+
+ if( maegap == 0 )
+ {
+ g = ( countnocountmatchx( gappat1[i], gappat2[j], 0, 0, 0 ) ) * fpenalty;
+// if( seq1[0][i] == 'D' && seq2[0][j] == 'D' )
+// fprintf( stderr, "kanwa0 %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 1 ) );
+ }
+#if 0 // atta houga yoi hazu
+ else if( maegap < 0 ) // i jump
+ {
+ g = ( countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 0 ) ) * fpenalty;
+ if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' )
+ {
+ fprintf( stderr, "i-jumped, offset1=%d\n", maegap );
+ fprintf( stderr, "kanwa1 %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 0 ) );
+ }
+ }
+ else // j jump
+ {
+ g = ( countnocountmatchx( gappat1[i], gappat2[j], maegap, 0, 0 ) ) * fpenalty;
+ if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' )
+ {
+ fprintf( stderr, "j-jumped, offset1=%d\n", maegap );
+ fprintf( stderr, "kanwa2, %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 1 ) );
+ }
+ }
+#endif
+ wm -= g;
+ }
+
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+// tmppenal = fpenalty;
+ tmppenal = diaf2[j] * ( 1.0 - gapf1[i] ) * fpenalty;
+ if( gappat2[j][0].freq )
+ {
+ tmppenal += ( gappat2[j][0].freq ) * ( 1.0 - gapf1[i] ) * fpenalty;
+// tmppenal -= ( countnocountx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, 0 ) ) * fpenalty;
+ maegap = ijp[i-1][mpi];
+ maegap = 0;
+ if( maegap == 0 )
+ {
+ tmppenal -= ( countnocountx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, 0 ) ) * fpenalty;
+ }
+#if 0 // attahouga yoi hazu
+ else if( maegap < 0 ) // i jump
+ {
+ maegap = -maegap;
+ tmppenal -= ( countnocountxx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1+maegap, 0 ) ) * fpenalty;
+ }
+ else // j jump
+ {
+ tmppenal -= ( countnocountxx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, maegap ) ) * fpenalty;
+ }
+#endif
+ }
+ if( (g=mi+tmppenal) > wm )
+ {
+// if( seq1[0][i] == 'A' && seq2[0][j] == 'A' ) fprintf( stderr, "jump i start=%f (i,j=%d,%d, *ijppt=%d, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, i, j, -(j-mpi), digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ if( (g=*prept) >= mi )
+ {
+// fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
+ mi = g;
+ mpi = j-1;
+ }
+ else if( j != 1 )
+ {
+// mi += ( ogcp2g[j-0] + fgcp2g[j] ) * fpenalty * 0.5;
+// fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", '=', '=', seq2[0][j-1], seq2[0][j], ogcp2g[j-0] * fpenalty*0.5, fgcp2g[j] * fpenalty*0.5 );
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+
+// tmppenal = fpenalty;
+ tmppenal = diaf1[i] * ( 1.0 - gapf2[j] ) * fpenalty;
+ if( gappat1[i][0].freq )
+ {
+ tmppenal += ( gappat1[i][0].freq ) * ( 1.0 - gapf2[j] ) * fpenalty;
+// tmppenal -= ( countnocountx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, 1 ) ) * fpenalty;
+ maegap = ijp[*mpjpt][j-1];
+ if( maegap == 0 )
+ {
+ tmppenal -= ( countnocountx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, 1 ) ) * fpenalty;
+ }
+#if 0 // attahouga yoi hazu
+ else if( maegap > 0 ) // j jump
+ {
+ tmppenal -= ( countnocountxx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1+maegap, 0 ) ) * fpenalty;
+ }
+ else // i jump
+ {
+ maegap = -maegap;
+ tmppenal -= ( countnocountxx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, maegap ) ) * fpenalty;
+ }
+#endif
+ }
+ if( (g=*mjpt+tmppenal) > wm )
+ {
+// if( seq1[0][i] == 'S' && seq2[0][j] == 'S' ) fprintf( stderr, "jump j start at %d, %d, g=%f, %c-%c\n", i, j, g-*mjpt, seq1[0][i], seq2[0][j] );
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ if( (g=*prept) >= *mjpt )
+ {
+// fprintf( stderr, "jump j end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+ else if( i != 1 )
+ {
+// m[j] += ( ogcp1g[i-0] + fgcp1g[i] ) * fpenalty * 0.5;
+// fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", seq1[0][i-1], seq1[0][i], '=', '=', ogcp1g[i-0] * fpenalty*0.5, fgcp1g[i] * fpenalty*0.5 );
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+ fprintf( stderr, "wm = %f\n", wm );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ free( gappat1[i] );
+ gappat1[i] = NULL;
+ }
+ for( i=0; i<lgth2+1; i++ )
+ {
+ free( gappat2[i] );
+ gappat2[i] = NULL;
+ }
+
+ return( wm );
+}
+
--- /dev/null
+#if 0
+#include "mltaln.h"
+#endif
+#define DEFAULTGOP_J -1530
+#define DEFAULTGEP_J -00
+#define DEFAULTOFS_J -123 /* +10 -- -50 teido ka ? */
+#define DEFAULTPAMN 200
+
+void JTTmtx( double **rsr, double *freq, char locamino[26], char locgrp[26], int isTM )
+{
+ int i, j;
+ double r[20][20];
+// char locamino0[] = "ARNDCQEGHILKMFPSTWYVBZX.-U";
+ char locamino0[] = "ARNDCQEGHILKMFPSTWYVBZX.-J";
+ char locgrp0[] =
+ {
+ 0, 3, 2, 2, 5, 2, 2, 0, 3, 1, 1, 3, 1, 4, 0, 0, 0, 4, 4, 1, 2, 2,
+ 6, 6, 6, 1,
+ };
+
+ double freq0[20] =
+ {
+ 0.077,
+ 0.051,
+ 0.043,
+ 0.052,
+ 0.020,
+ 0.041,
+ 0.062,
+ 0.074,
+ 0.023,
+ 0.052,
+ 0.091,
+ 0.059,
+ 0.024,
+ 0.040,
+ 0.051,
+ 0.069,
+ 0.059,
+ 0.014,
+ 0.032,
+ 0.066,
+ };
+ double freq0_TM[20] =
+ {
+ 0.1051,
+ 0.0157,
+ 0.0185,
+ 0.0089,
+ 0.0219,
+ 0.0141,
+ 0.0097,
+ 0.0758,
+ 0.0168,
+ 0.1188,
+ 0.1635,
+ 0.0112,
+ 0.0333,
+ 0.0777,
+ 0.0260,
+ 0.0568,
+ 0.0523,
+ 0.0223,
+ 0.0324,
+ 0.1195,
+ };
+
+ /* Lower triangular is JTT's Accepted point mutations */
+ r[ 1][ 0]= 247;
+
+ r[ 2][ 0]= 216; r[ 2][ 1]= 116;
+
+ r[ 3][ 0]= 386; r[ 3][ 1]= 48; r[ 3][ 2]= 1433;
+
+ r[ 4][ 0]= 106; r[ 4][ 1]= 125; r[ 4][ 2]= 32; r[ 4][ 3]= 13;
+
+ r[ 5][ 0]= 208; r[ 5][ 1]= 750; r[ 5][ 2]= 159; r[ 5][ 3]= 130;
+ r[ 5][ 4]= 9;
+
+ r[ 6][ 0]= 600; r[ 6][ 1]= 119; r[ 6][ 2]= 180; r[ 6][ 3]= 2914;
+ r[ 6][ 4]= 8; r[ 6][ 5]= 1027;
+
+ r[ 7][ 0]= 1183; r[ 7][ 1]= 614; r[ 7][ 2]= 291; r[ 7][ 3]= 577;
+ r[ 7][ 4]= 98; r[ 7][ 5]= 84; r[ 7][ 6]= 610;
+
+ r[ 8][ 0]= 46; r[ 8][ 1]= 446; r[ 8][ 2]= 466; r[ 8][ 3]= 144;
+ r[ 8][ 4]= 40; r[ 8][ 5]= 635; r[ 8][ 6]= 41; r[ 8][ 7]= 41;
+
+ r[ 9][ 0]= 173; r[ 9][ 1]= 76; r[ 9][ 2]= 130; r[ 9][ 3]= 37;
+ r[ 9][ 4]= 19; r[ 9][ 5]= 20; r[ 9][ 6]= 43; r[ 9][ 7]= 25;
+ r[ 9][ 8]= 26;
+
+ r[10][ 0]= 257; r[10][ 1]= 205; r[10][ 2]= 63; r[10][ 3]= 34;
+ r[10][ 4]= 36; r[10][ 5]= 314; r[10][ 6]= 65; r[10][ 7]= 56;
+ r[10][ 8]= 134; r[10][ 9]= 1324;
+
+ r[11][ 0]= 200; r[11][ 1]= 2348; r[11][ 2]= 758; r[11][ 3]= 102;
+ r[11][ 4]= 7; r[11][ 5]= 858; r[11][ 6]= 754; r[11][ 7]= 142;
+ r[11][ 8]= 85; r[11][ 9]= 75; r[11][10]= 94;
+
+ r[12][ 0]= 100; r[12][ 1]= 61; r[12][ 2]= 39; r[12][ 3]= 27;
+ r[12][ 4]= 23; r[12][ 5]= 52; r[12][ 6]= 30; r[12][ 7]= 27;
+ r[12][ 8]= 21; r[12][ 9]= 704; r[12][10]= 974; r[12][11]= 103;
+
+ r[13][ 0]= 51; r[13][ 1]= 16; r[13][ 2]= 15; r[13][ 3]= 8;
+ r[13][ 4]= 66; r[13][ 5]= 9; r[13][ 6]= 13; r[13][ 7]= 18;
+ r[13][ 8]= 50; r[13][ 9]= 196; r[13][10]= 1093; r[13][11]= 7;
+ r[13][12]= 49;
+
+ r[14][ 0]= 901; r[14][ 1]= 217; r[14][ 2]= 31; r[14][ 3]= 39;
+ r[14][ 4]= 15; r[14][ 5]= 395; r[14][ 6]= 71; r[14][ 7]= 93;
+ r[14][ 8]= 157; r[14][ 9]= 31; r[14][10]= 578; r[14][11]= 77;
+ r[14][12]= 23; r[14][13]= 36;
+
+ r[15][ 0]= 2413; r[15][ 1]= 413; r[15][ 2]= 1738; r[15][ 3]= 244;
+ r[15][ 4]= 353; r[15][ 5]= 182; r[15][ 6]= 156; r[15][ 7]= 1131;
+ r[15][ 8]= 138; r[15][ 9]= 172; r[15][10]= 436; r[15][11]= 228;
+ r[15][12]= 54; r[15][13]= 309; r[15][14]= 1138;
+
+ r[16][ 0]= 2440; r[16][ 1]= 230; r[16][ 2]= 693; r[16][ 3]= 151;
+ r[16][ 4]= 66; r[16][ 5]= 149; r[16][ 6]= 142; r[16][ 7]= 164;
+ r[16][ 8]= 76; r[16][ 9]= 930; r[16][10]= 172; r[16][11]= 398;
+ r[16][12]= 343; r[16][13]= 39; r[16][14]= 412; r[16][15]= 2258;
+
+ r[17][ 0]= 11; r[17][ 1]= 109; r[17][ 2]= 2; r[17][ 3]= 5;
+ r[17][ 4]= 38; r[17][ 5]= 12; r[17][ 6]= 12; r[17][ 7]= 69;
+ r[17][ 8]= 5; r[17][ 9]= 12; r[17][10]= 82; r[17][11]= 9;
+ r[17][12]= 8; r[17][13]= 37; r[17][14]= 6; r[17][15]= 36;
+ r[17][16]= 8;
+
+ r[18][ 0]= 41; r[18][ 1]= 46; r[18][ 2]= 114; r[18][ 3]= 89;
+ r[18][ 4]= 164; r[18][ 5]= 40; r[18][ 6]= 15; r[18][ 7]= 15;
+ r[18][ 8]= 514; r[18][ 9]= 61; r[18][10]= 84; r[18][11]= 20;
+ r[18][12]= 17; r[18][13]= 850; r[18][14]= 22; r[18][15]= 164;
+ r[18][16]= 45; r[18][17]= 41;
+
+ r[19][ 0]= 1766; r[19][ 1]= 69; r[19][ 2]= 55; r[19][ 3]= 127;
+ r[19][ 4]= 99; r[19][ 5]= 58; r[19][ 6]= 226; r[19][ 7]= 276;
+ r[19][ 8]= 22; r[19][ 9]= 3938; r[19][10]= 1261; r[19][11]= 58;
+ r[19][12]= 559; r[19][13]= 189; r[19][14]= 84; r[19][15]= 219;
+ r[19][16]= 526; r[19][17]= 27; r[19][18]= 42;
+
+
+ /* Upper triangular is JTT's Accepted point mutations for transmembrane */
+ r[ 0][ 1]= 21; r[ 0][ 2]= 2; r[ 0][ 3]= 7; r[ 0][ 4]= 13;
+ r[ 0][ 5]= 4; r[ 0][ 6]= 6; r[ 0][ 7]= 160; r[ 0][ 8]= 6;
+ r[ 0][ 9]= 44; r[ 0][10]= 43; r[ 0][11]= 5; r[ 0][12]= 10;
+ r[ 0][13]= 21; r[ 0][14]= 34; r[ 0][15]= 198; r[ 0][16]= 202;
+ r[ 0][17]= 0; r[ 0][18]= 1; r[ 0][19]= 292;
+
+ r[ 1][ 2]= 0; r[ 1][ 3]= 1; r[ 1][ 4]= 2; r[ 1][ 5]= 21;
+ r[ 1][ 6]= 3; r[ 1][ 7]= 22; r[ 1][ 8]= 21; r[ 1][ 9]= 4;
+ r[ 1][10]= 8; r[ 1][11]= 53; r[ 1][12]= 19; r[ 1][13]= 0;
+ r[ 1][14]= 1; r[ 1][15]= 5; r[ 1][16]= 5; r[ 1][17]= 28;
+ r[ 1][18]= 0; r[ 1][19]= 0;
+
+ r[ 2][ 3]= 14; r[ 2][ 4]= 1; r[ 2][ 5]= 7; r[ 2][ 6]= 0;
+ r[ 2][ 7]= 0; r[ 2][ 8]= 8; r[ 2][ 9]= 4; r[ 2][10]= 5;
+ r[ 2][11]= 11; r[ 2][12]= 3; r[ 2][13]= 1; r[ 2][14]= 2;
+ r[ 2][15]= 32; r[ 2][16]= 19; r[ 2][17]= 1; r[ 2][18]= 1;
+ r[ 2][19]= 2;
+
+ r[ 3][ 4]= 0; r[ 3][ 5]= 0; r[ 3][ 6]= 12; r[ 3][ 7]= 15;
+ r[ 3][ 8]= 4; r[ 3][ 9]= 1; r[ 3][10]= 0; r[ 3][11]= 2;
+ r[ 3][12]= 1; r[ 3][13]= 0; r[ 3][14]= 1; r[ 3][15]= 0;
+ r[ 3][16]= 6; r[ 3][17]= 0; r[ 3][18]= 1; r[ 3][19]= 4;
+
+ r[ 4][ 5]= 0; r[ 4][ 6]= 0; r[ 4][ 7]= 13; r[ 4][ 8]= 2;
+ r[ 4][ 9]= 4; r[ 4][10]= 11; r[ 4][11]= 0; r[ 4][12]= 1;
+ r[ 4][13]= 34; r[ 4][14]= 0; r[ 4][15]= 48; r[ 4][16]= 13;
+ r[ 4][17]= 8; r[ 4][18]= 23; r[ 4][19]= 47;
+
+ r[ 5][ 6]= 16; r[ 5][ 7]= 1; r[ 5][ 8]= 26; r[ 5][ 9]= 1;
+ r[ 5][10]= 16; r[ 5][11]= 6; r[ 5][12]= 3; r[ 5][13]= 0;
+ r[ 5][14]= 5; r[ 5][15]= 7; r[ 5][16]= 2; r[ 5][17]= 0;
+ r[ 5][18]= 0; r[ 5][19]= 0;
+
+ r[ 6][ 7]= 21; r[ 6][ 8]= 0; r[ 6][ 9]= 0; r[ 6][10]= 0;
+ r[ 6][11]= 0; r[ 6][12]= 0; r[ 6][13]= 0; r[ 6][14]= 0;
+ r[ 6][15]= 4; r[ 6][16]= 2; r[ 6][17]= 0; r[ 6][18]= 0;
+ r[ 6][19]= 7;
+
+ r[ 7][ 8]= 1; r[ 7][ 9]= 10; r[ 7][10]= 0; r[ 7][11]= 0;
+ r[ 7][12]= 3; r[ 7][13]= 4; r[ 7][14]= 7; r[ 7][15]= 64;
+ r[ 7][16]= 12; r[ 7][17]= 5; r[ 7][18]= 0; r[ 7][19]= 53;
+
+ r[ 8][ 9]= 3; r[ 8][10]= 2; r[ 8][11]= 0; r[ 8][12]= 1;
+ r[ 8][13]= 0; r[ 8][14]= 0; r[ 8][15]= 0; r[ 8][16]= 4;
+ r[ 8][17]= 0; r[ 8][18]= 29; r[ 8][19]= 2;
+
+ r[ 9][10]= 273; r[ 9][11]= 0; r[ 9][12]= 161; r[ 9][13]= 66;
+ r[ 9][14]= 4; r[ 9][15]= 22; r[ 9][16]= 150; r[ 9][17]= 1;
+ r[ 9][18]= 4; r[ 9][19]= 883;
+
+ r[10][11]= 1; r[10][12]= 153; r[10][13]= 251; r[10][14]= 37;
+ r[10][15]= 43; r[10][16]= 26; r[10][17]= 20; r[10][18]= 6;
+ r[10][19]= 255;
+
+ r[11][12]= 4; r[11][13]= 0; r[11][14]= 0; r[11][15]= 1;
+ r[11][16]= 2; r[11][17]= 0; r[11][18]= 5; r[11][19]= 1;
+
+ r[12][13]= 8; r[12][14]= 0; r[12][15]= 1; r[12][16]= 32;
+ r[12][17]= 1; r[12][18]= 5; r[12][19]= 89;
+
+ r[13][14]= 0; r[13][15]= 32; r[13][16]= 9; r[13][17]= 2;
+ r[13][18]= 54; r[13][19]= 37;
+
+ r[14][15]= 9; r[14][16]= 10; r[14][17]= 0; r[14][18]= 1;
+ r[14][19]= 1;
+
+ r[15][16]= 134; r[15][17]= 1; r[15][18]= 22; r[15][19]= 13;
+
+ r[16][17]= 1; r[16][18]= 3; r[16][19]= 48;
+
+ r[17][18]= 2; r[17][19]= 18;
+
+ r[18][19]= 2;
+
+
+
+ for (i = 0; i < 20; i++) r[i][i] = 0.0;
+ if( isTM )
+ {
+ for (i = 1; i < 20; i++) for (j = 0; j < i; j++)
+ {
+ r[j][i] /= 400.0 * freq0_TM[i] * freq0_TM[j];
+ r[i][j] = r[j][i];
+ }
+ for( i=0; i<20; i++ ) freq[i] = freq0_TM[i];
+ }
+ else
+ {
+ for (i = 1; i < 20; i++) for (j = 0; j < i; j++)
+ {
+ r[i][j] /= 400.0 * freq0[i] * freq0[j];
+ r[j][i] = r[i][j];
+ }
+ for( i=0; i<20; i++ ) freq[i] = freq0[i];
+ }
+
+ for( i=0; i<26; i++ ) locamino[i] = locamino0[i];
+ for( i=0; i<26; i++ ) locgrp[(int)locamino[i]] = locgrp0[i];
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ ) rsr[i][j] = r[i][j];
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define DEBUG2 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+
+static TLS int localstop; // 060910
+
+#if 1
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char *seq2 = s2[0];
+ int *intptr;
+
+ intptr = amino_dis[(int)s1[0][i1]];
+ while( lgth2-- )
+ *match++ = intptr[(int)*seq2++];
+}
+#else
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ int j;
+
+ for( j=0; j<lgth2; j++ )
+ match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
+}
+#endif
+
+#if 0
+static void match_calc_bk( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+#endif
+
+static float Ltracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ int **ijp, int *off1pt, int *off2pt, int endi, int endj )
+{
+ int i, j, l, iin, jin, lgth1, lgth2, k, limk;
+ int ifi=0, jfi=0; // by D.Mathog, a guess
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = localstop;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = localstop;
+ }
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+ iin = endi; jin = endj;
+ limk = lgth1+lgth2;
+ for( k=0; k<=limk; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--mseq1[0] = seq1[0][ifi+l];
+ *--mseq2[0] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][jfi+l];
+ k++;
+ }
+
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mseq1[0] = seq1[0][ifi];
+ *--mseq2[0] = seq2[0][jfi];
+ if( ijp[ifi][jfi] == localstop ) break;
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
+ if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
+
+// fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
+
+
+ return( 0.0 );
+}
+
+
+float L__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+// static TLS int **intwork;
+// static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float maxwm;
+ int endali = 0, endalj = 0; // by D.Mathog, a guess
+// int endali, endalj;
+ float localthr = -offset;
+ float localthr2 = -offset;
+// float localthr = 100;
+// float localthr2 = 100;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ orlgth1 = 0;
+ orlgth2 = 0;
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ }
+ return( 0.0 );
+ }
+
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+
+// FreeFloatMtx( floatwork );
+// FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+
+// floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+// intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+
+ lasti = lgth2+1;
+ for( j=1; j<lasti; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+#if 0
+ if( m[j] < localthr ) m[j] = localthr2;
+#endif
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ lasti = lgth1+1;
+
+#if 0
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, " " );
+ for( j=0; j<lgth2; j++ )
+ fprintf( stderr, "%c ", seq2[0][j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ localstop = lgth1+lgth2+1;
+ maxwm = -999999999.9;
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "%c ", seq1[0][0] );
+
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if DEBUG2
+ fprintf( stderr, "%c ", seq1[0][i] );
+ fprintf( stderr, "%5.0f ", currentw[0] );
+#endif
+
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+#if 0
+ if( mi < localthr ) mi = localthr2;
+#endif
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ if( *prept > mi )
+ {
+ mi = *prept;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt+fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ if( *prept > *mjpt )
+ {
+ *mjpt = *prept;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ *mjpt += fpenalty_ex;
+#endif
+
+ if( maxwm < wm )
+ {
+ maxwm = wm;
+ endali = i;
+ endalj = j;
+ }
+#if 1
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ *ijppt = localstop;
+ wm = localthr2;
+ }
+#endif
+#if 0
+ fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if DEBUG2
+ fprintf( stderr, "%5.0f ", wm );
+// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ }
+#if DEBUG2
+ fprintf( stderr, "\n" );
+#endif
+
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+
+#if 0
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, "endali = %d\n", endali );
+ fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+ if( ijp[endali][endalj] == localstop )
+ {
+ strcpy( seq1[0], "" );
+ strcpy( seq2[0], "" );
+ *off1pt = *off2pt = 0;
+ return( 0.0 );
+ }
+
+ Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj );
+
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+
+#if 0
+ fprintf( stderr, "wm=%f\n", wm );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, " wm = %f\n", wm );
+#endif
+
+ return( maxwm );
+}
+
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define DEBUG2 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+static short localstop;
+
+#if 1
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char *seq2 = s2[0];
+ int *intptr;
+
+ intptr = amino_dis[s1[0][i1]];
+ while( lgth2-- )
+ *match++ = intptr[*seq2++];
+}
+#else
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ int j;
+
+ for( j=0; j<lgth2; j++ )
+ match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
+}
+#endif
+
+static void match_calc_bk( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+
+static float Ltracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ short **ijp, int *off1pt, int *off2pt, int endi, int endj )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+ char gap[] = "-";
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = localstop;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = localstop;
+ }
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+ iin = endi; jin = endj;
+ limk = lgth1+lgth2;
+ for( k=0; k<=limk; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--mseq1[0] = seq1[0][ifi+l];
+ *--mseq2[0] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][jfi+l];
+ k++;
+ }
+
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mseq1[0] = seq1[0][ifi];
+ *--mseq2[0] = seq2[0][jfi];
+ if( ijp[ifi][jfi] == localstop ) break;
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
+ if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
+
+// fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
+
+
+ return( 0.0 );
+}
+
+
+float L__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static float mi, *m;
+ static short **ijp;
+ static int mpi, *mp;
+ static float *w1, *w2;
+ static float *match;
+ static float *initverticalw; /* kufuu sureba iranai */
+ static float *lastverticalw; /* kufuu sureba iranai */
+ static char **mseq1;
+ static char **mseq2;
+ static char **mseq;
+ static float **cpmx1;
+ static float **cpmx2;
+ static int **intwork;
+ static float **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+ float maxwm;
+ int endali, endalj;
+ float localthr = -offset;
+ float localthr2 = -offset;
+// float localthr = 100;
+// float localthr2 = 100;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeShortMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateShortMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+
+ lasti = lgth2+1;
+ for( j=1; j<lasti; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+#if 0
+ if( m[j] < localthr ) m[j] = localthr2;
+#endif
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ lasti = lgth1+1;
+
+#if 0
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, " " );
+ for( j=0; j<lgth2; j++ )
+ fprintf( stderr, "%c ", seq2[0][j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ localstop = lgth1+lgth2+1;
+ maxwm = -999.9;
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "%c ", seq1[0][0] );
+
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if DEBUG2
+ fprintf( stderr, "%c ", seq1[0][i] );
+ fprintf( stderr, "%5.0f ", currentw[0] );
+#endif
+
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+#if 0
+ if( mi < localthr ) mi = localthr2;
+#endif
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ if( *prept > mi )
+ {
+ mi = *prept;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt+fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ if( *prept > *mjpt )
+ {
+ *mjpt = *prept;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ *mjpt += fpenalty_ex;
+#endif
+
+ if( maxwm < wm )
+ {
+ maxwm = wm;
+ endali = i;
+ endalj = j;
+ }
+#if 1
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ *ijppt = localstop;
+ wm = localthr2;
+ }
+#endif
+#if 0
+ fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if DEBUG2
+ fprintf( stderr, "%5.0f ", wm );
+// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ }
+#if DEBUG2
+ fprintf( stderr, "\n" );
+#endif
+
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+
+#if DEBUG2
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, "endali = %d\n", endali );
+ fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+ Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, off1pt, off2pt, endali, endalj );
+
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+
+#if 0
+ fprintf( stderr, "wm=%f\n", wm );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+
+
+ return( wm );
+}
+
+float L__align11_noalign( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static float mi, *m;
+ static short **ijp;
+ static int mpi, *mp;
+ static float *w1, *w2;
+ static float *match;
+ static float *initverticalw; /* kufuu sureba iranai */
+ static float *lastverticalw; /* kufuu sureba iranai */
+ static char **mseq1;
+ static char **mseq2;
+ static char **mseq;
+ static float **cpmx1;
+ static float **cpmx2;
+ static int **intwork;
+ static float **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+ float maxwm;
+ int endali, endalj;
+ float localthr = -offset;
+ float localthr2 = -offset;
+// float localthr = 100;
+// float localthr2 = 100;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+#if 0
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeShortMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateShortMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+#endif
+// ijp = commonIP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+
+ lasti = lgth2+1;
+ for( j=1; j<lasti; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+#if 0
+ if( m[j] < localthr ) m[j] = localthr2;
+#endif
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ lasti = lgth1+1;
+
+#if 0
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, " " );
+ for( j=0; j<lgth2; j++ )
+ fprintf( stderr, "%c ", seq2[0][j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ localstop = lgth1+lgth2+1;
+ maxwm = -999.9;
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "%c ", seq1[0][0] );
+
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if DEBUG2
+ fprintf( stderr, "%c ", seq1[0][i] );
+ fprintf( stderr, "%5.0f ", currentw[0] );
+#endif
+
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+#if 0
+ if( mi < localthr ) mi = localthr2;
+#endif
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+// mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+// *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ if( *prept > mi )
+ {
+ mi = *prept;
+// mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt+fpenalty) > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+ if( *prept > *mjpt )
+ {
+ *mjpt = *prept;
+// *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ *mjpt += fpenalty_ex;
+#endif
+
+ if( maxwm < wm )
+ {
+ maxwm = wm;
+ endali = i;
+ endalj = j;
+ }
+#if 1
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+// *ijppt = localstop;
+ wm = localthr2;
+ }
+#endif
+#if 0
+ fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if DEBUG2
+ fprintf( stderr, "%5.0f ", wm );
+// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+
+ *curpt++ += wm;
+// ijppt++;
+ mjpt++;
+ prept++;
+// mpjpt++;
+ }
+#if DEBUG2
+ fprintf( stderr, "\n" );
+#endif
+
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+
+#if DEBUG2
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, "endali = %d\n", endali );
+ fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+#if 0
+
+ Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, off1pt, off2pt, endali, endalj );
+
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+
+ fprintf( stderr, "wm=%f\n", wm );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define DEBUG2 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+
+#if 1
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char *seq2 = s2[0];
+ int *intptr;
+
+ intptr = amino_dis[(int)s1[0][i1]];
+ while( lgth2-- )
+ *match++ = intptr[(int)*seq2++];
+}
+#else
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ int j;
+
+ for( j=0; j<lgth2; j++ )
+ match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
+}
+#endif
+
+#if 0
+static void match_calc_bk( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+#endif
+
+static float Ltracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ int **ijp, int *off1pt, int *off2pt, int endi, int endj, int localstop )
+{
+ int i, j, l, iin, jin, lgth1, lgth2, k, limk;
+ int ifi=0, jfi=0; // by D.Mathog, a guess
+ char gap[] = "-";
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = localstop;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = localstop;
+ }
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+ iin = endi; jin = endj;
+ limk = lgth1+lgth2;
+ for( k=0; k<=limk; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--mseq1[0] = seq1[0][ifi+l];
+ *--mseq2[0] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][jfi+l];
+ k++;
+ }
+
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mseq1[0] = seq1[0][ifi];
+ *--mseq2[0] = seq2[0][jfi];
+ if( ijp[ifi][jfi] == localstop ) break;
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
+ if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
+
+// fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
+
+
+ return( 0.0 );
+}
+
+
+float L__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ int **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ char **mseq1;
+ char **mseq2;
+ char **mseq;
+// int **intwork;
+// float **floatwork;
+ float maxwm;
+ int endali = 0, endalj = 0; // by D.Mathog, a guess
+// int endali, endalj;
+ float localthr = -offset;
+ float localthr2 = -offset;
+// float localthr = 100;
+// float localthr2 = 100;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+ int **localIP = NULL;
+ int localAlloc1 = 0, localAlloc2 = 0;
+ int localstop; // 060910
+
+
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ {
+ int ll1, ll2;
+
+
+ ll1 = (int)(1.3*lgth1) + 100;
+ ll2 = (int)(1.3*lgth2) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+
+// floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+// intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+ {
+ int ll1, ll2;
+
+
+ ll1 = (int)(1.3*lgth1) + 100;
+ ll2 = (int)(1.3*lgth2) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ localIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ localAlloc1 = ll1;
+ localAlloc2 = ll2;
+ }
+ ijp = localIP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+
+ lasti = lgth2+1;
+ for( j=1; j<lasti; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+#if 0
+ if( m[j] < localthr ) m[j] = localthr2;
+#endif
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ lasti = lgth1+1;
+
+#if 0
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, " " );
+ for( j=0; j<lgth2; j++ )
+ fprintf( stderr, "%c ", seq2[0][j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ localstop = lgth1+lgth2+1;
+ maxwm = -999999999.9;
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "%c ", seq1[0][0] );
+
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if DEBUG2
+ fprintf( stderr, "%c ", seq1[0][i] );
+ fprintf( stderr, "%5.0f ", currentw[0] );
+#endif
+
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+#if 0
+ if( mi < localthr ) mi = localthr2;
+#endif
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ if( *prept > mi )
+ {
+ mi = *prept;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt+fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ if( *prept > *mjpt )
+ {
+ *mjpt = *prept;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ *mjpt += fpenalty_ex;
+#endif
+
+ if( maxwm < wm )
+ {
+ maxwm = wm;
+ endali = i;
+ endalj = j;
+ }
+#if 1
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ *ijppt = localstop;
+ wm = localthr2;
+ }
+#endif
+#if 0
+ fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if DEBUG2
+ fprintf( stderr, "%5.0f ", wm );
+// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ }
+#if DEBUG2
+ fprintf( stderr, "\n" );
+#endif
+
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+
+#if 0
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, "endali = %d\n", endali );
+ fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+ if( ijp[endali][endalj] == localstop )
+ {
+ strcpy( seq1[0], "" );
+ strcpy( seq2[0], "" );
+ *off1pt = *off2pt = 0;
+ return( 0.0 );
+ }
+
+ Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj, localstop );
+
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+
+#if 0
+ fprintf( stderr, "wm=%f\n", wm );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, " wm = %f\n", wm );
+#endif
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+
+// FreeFloatMtx( floatwork );
+// FreeIntMtx( intwork );
+
+ FreeIntMtx( localIP );
+
+ return( maxwm );
+}
+
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MEMSAVE 1
+
+#define DEBUG 0
+#define USE_PENALTY_EX 0
+#define STOREWM 1
+
+#define DPTANNI 10
+
+#define LOCAL 0
+
+static int reccycle = 0;
+
+static float localthr;
+
+static void match_ribosum( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[38];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+ float *matchpt;
+ float **cpmxpdpt;
+ int **cpmxpdnpt;
+ int cpkd;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<37; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<37; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<37; k++ )
+ {
+ scarr[l] += ribosumdis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#else
+ matchpt = match;
+ cpmxpdnpt = cpmxpdn;
+ cpmxpdpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
+ *matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
+ matchpt++;
+ cpmxpdnpt++;
+ cpmxpdpt++;
+ }
+#endif
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+ float *matchpt;
+ float **cpmxpdpt;
+ int **cpmxpdnpt;
+ int cpkd;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += (n_dis[k][l]-RNAthr) * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#else
+ matchpt = match;
+ cpmxpdnpt = cpmxpdn;
+ cpmxpdpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
+ *matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
+ matchpt++;
+ cpmxpdnpt++;
+ cpmxpdpt++;
+ }
+#endif
+}
+
+#if 0
+static void match_add( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+ float *matchpt;
+ float **cpmxpdpt;
+ int **cpmxpdnpt;
+ int cpkd;
+
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#else
+ matchpt = match;
+ cpmxpdnpt = cpmxpdn;
+ cpmxpdpt = cpmxpd;
+ while( lgth2-- )
+ {
+// *matchpt = 0.0; // add dakara
+ for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
+ *matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
+ matchpt++;
+ cpmxpdnpt++;
+ cpmxpdpt++;
+ }
+#endif
+}
+#endif
+
+#if 0
+static float Atracking(
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ int **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+#endif
+
+
+static float MSalign2m2m_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo, float **map )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+ float value = 0.0;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2;
+ int lasti, lastj, imid, jmid = 0;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+// float fpenalty = (float)penalty;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+ float **WMMTX;
+ float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ int lgth1, lgth2;
+ float maxwm = 0.0;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj; //muda
+ int jumpi, jumpj = 0;
+ char *gaps;
+ int ijpi, ijpj;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ float firstm;
+ int firstmp;
+#if 0
+ static char ttt1[50000];
+ static char ttt2[50000];
+#endif
+
+ localthr = -offset + 500; // 0?
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// if( lgth1 < 5 )
+// fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
+// if( lgth2 < 5 )
+// fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
+//
+
+#if 0
+ fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+ strncpy( ttt1, seq1[0]+ist, lgth1 );
+ strncpy( ttt2, seq2[0]+jst, lgth2 );
+ ttt1[lgth1] = 0;
+ ttt2[lgth2] = 0;
+ fprintf( stderr, "seq1 = %s\n", ttt1 );
+ fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+ if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+ {
+// fprintf( stderr, "\n\n==== jimei\n\n" );
+// exit( 1 );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( 0.0 );
+ }
+
+#if MEMSAVE
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
+#else
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+#endif
+
+// if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai
+// if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+// value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+#if MEMSAVE
+ free( aseq1 );
+ free( aseq2 );
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+#endif
+
+// fprintf( stderr, "value = %f\n", value );
+
+ return( value );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_ribosum( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1];
+// m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 * 0.5;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+#if STOREWM
+ for( i=1; i<lasti; i++ )
+#else
+ for( i=1; i<=imid; i++ )
+#endif
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ m[0] = ogcp1[i];
+#if STOREM
+ WMMTX2[i][0] = m[0];
+#endif
+ if( i == imid ) midm[0] = m[0];
+
+ mi = previousw[0] + ogcp2[1];
+// mi = previousw[0];
+ mpi = 0;
+
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fgcp2[j-1];
+// g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ g = *prept + ogcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fgcp1[i-1];
+// g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+ g = *prept + ogcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+#if LOCAL
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ wm = 0;
+ }
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+// fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+ WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_ribosum( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+ }
+#endif
+
+
+
+
+
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j] + fgcp2[lgth2-2];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+
+// for( i=lgth1-2; i>=imid; i-- )
+ firstm = -9999999.9;
+ firstmp = lgth1-1;
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// m[lgth2] = fgcp1[i];
+// WMMTX2[i][lgth2] += m[lgth2];
+// fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+ mi = previousw[lgth2-1] + fgcp2[lgth2-2];
+// mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+ g = mi + ogcp2[j+1];
+// g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ ijpi = i+1;
+ }
+
+ g = *prept + fgcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + ogcp1[i+1];
+// g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ ijpj = j+1;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+ g = *prept + fgcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+// midm[j+1] += *mjpt + fpenalty; //??????
+ midm[j+1] += *mjpt; //??????
+ }
+ if( i == imid - 1 )
+ {
+// midn[j] += mi + fpenalty; //????
+ midn[j] += mi; //????
+ }
+#if LOCAL
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ wm = 0;
+ }
+#endif
+
+#if STOREWM
+ WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ WMMTX2[i][j] += *curpt;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+// fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+ g = *prept + fgcp1[i];
+ if( firstm < g )
+ {
+ firstm = g;
+ firstmp = i + 1;
+ }
+#if STOREWM
+// WMMTX2[i][j+1] += firstm;
+#endif
+ if( i == imid ) midm[j+1] += firstm;
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 0;
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ for( j=2; j<lgth2-1; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+// fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ if( jmid > 0 && midn[jmid-1] > wm ) //060413
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ wm = midn[jmid-1];
+// fprintf( stderr, "rejump (n)\n" );
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ wm = midm[jmid];
+// fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+ }
+
+
+// fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+// fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if 0
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+// fprintf( stderr, "maxwm = %f\n", maxwm );
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+ if( jmid == 0 )
+ {
+// fprintf( stderr, "CHUI2!\n" );
+ jumpj = 0; jmid = 1;
+ jumpi = firstmp - 1;
+ imid = firstmp;
+ }
+
+#if 0
+ else if( jmid == lgth2 )
+ {
+ fprintf( stderr, "CHUI1!\n" );
+ jumpi=0; jumpj=0;
+ imid=jumpforwi[0]; jmid=lgth2-1;
+ }
+#else // 060414
+ else if( jmid >= lgth2 )
+ {
+// fprintf( stderr, "CHUI1!\n" );
+ jumpi=imid-1; jmid=lgth2;
+ jumpj = lgth2-1;
+ }
+#endif
+ else
+ {
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+ }
+#if 0
+ fprintf( stderr, "jumpi -> %d\n", jumpi );
+ fprintf( stderr, "jumpj -> %d\n", jumpj );
+ fprintf( stderr, "imid -> %d\n", imid );
+ fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+
+#if STOREWM
+// break;
+#else
+ break;
+#endif
+ }
+ }
+#if 0
+ jumpi=0; jumpj=0;
+ imid=lgth1-1; jmid=lgth2-1;
+ }
+#endif
+
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ map[i][j] = WMMTX[i][j] / maxwm;
+// map[i][j] = WMMTX2[i][j] / maxwm;
+
+#if STOREWM
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ float maxpairscore = -9999.9;
+ float tmpscore;
+
+ for( j=0; j<lgth2; j++ )
+ {
+ if( maxpairscore < (tmpscore=WMMTX[i][j]) )
+ {
+ map12[i].pos = j;
+ map12[i].score = tmpscore;
+ maxpairscore = tmpscore;
+ }
+ }
+
+ for( k=0; k<lgth1; k++ )
+ {
+ if( i == k ) continue;
+ if( map12[i].score <= WMMTX[k][map12[i].pos] )
+ break;
+ }
+ if( k != lgth1 )
+ {
+ map12[i].pos = -1;
+ map12[i].score = -1.0;
+ }
+ fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] );
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ float maxpairscore = -9999.9;
+ float tmpscore;
+
+ for( i=0; i<lgth1; i++ )
+ {
+ if( maxpairscore < (tmpscore=WMMTX[i][j]) )
+ {
+ map21[j].pos = i;
+ map21[j].score = tmpscore;
+ maxpairscore = tmpscore;
+ }
+ }
+
+ for( k=0; k<lgth2; k++ )
+ {
+ if( j == k ) continue;
+ if( map21[j].score <= WMMTX[map21[j].pos][k] )
+ break;
+ }
+ if( k != lgth2 )
+ {
+ map21[j].pos = -1;
+ map21[j].score = -1.0;
+ }
+ fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i )
+ fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos );
+ }
+#endif
+
+#if 0
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+// fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+#if 0
+ fprintf( stdout, "#WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+// fprintf( stdout, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+// if( WMMTX[i][j] > amino_dis['a']['g'] -1 )
+ fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] );
+ if( WMMTX[i][j] == maxwm )
+ fprintf( stdout, "selected \n" );
+ else
+ fprintf( stdout, "\n" );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+#if 0
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+
+#endif
+
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+
+ return( value );
+
+}
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo, float **map )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+ int alnlen;
+ float value = 0.0;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid, jmid=0;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)RNApenalty_ex;
+#endif
+// float fpenalty = (float)penalty;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+ float **WMMTX;
+ float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ int lgth1, lgth2;
+ float maxwm = 0.0;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj; //muda
+ int jumpi, jumpj = 0;
+ char *gaps;
+ int ijpi, ijpj;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ float firstm;
+ int firstmp;
+#if 0
+ static char ttt1[50000];
+ static char ttt2[50000];
+#endif
+
+ localthr = -offset + 500; // 0?
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// if( lgth1 < 5 )
+// fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
+// if( lgth2 < 5 )
+// fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
+//
+
+#if 0
+ fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+ strncpy( ttt1, seq1[0]+ist, lgth1 );
+ strncpy( ttt2, seq2[0]+jst, lgth2 );
+ ttt1[lgth1] = 0;
+ ttt2[lgth2] = 0;
+ fprintf( stderr, "seq1 = %s\n", ttt1 );
+ fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+ if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+ {
+// fprintf( stderr, "\n\n==== jimei\n\n" );
+// exit( 1 );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( 0.0 );
+ }
+
+#if MEMSAVE
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
+#else
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+#endif
+
+// if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai
+// if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+// value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+#if MEMSAVE
+ free( aseq1 );
+ free( aseq2 );
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+#endif
+
+// fprintf( stderr, "value = %f\n", value );
+
+ return( value );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1];
+// m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 * 0.5;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+#if STOREWM
+ for( i=1; i<lasti; i++ )
+#else
+ for( i=1; i<=imid; i++ )
+#endif
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ m[0] = ogcp1[i];
+#if STOREM
+ WMMTX2[i][0] = m[0];
+#endif
+ if( i == imid ) midm[0] = m[0];
+
+ mi = previousw[0] + ogcp2[1];
+// mi = previousw[0];
+ mpi = 0;
+
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fgcp2[j-1];
+// g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ g = *prept + ogcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fgcp1[i-1];
+// g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+ g = *prept + ogcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+#if LOCAL
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ wm = 0;
+ }
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+// fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+ WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+ }
+#endif
+
+
+
+
+
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j] + fgcp2[lgth2-2];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+
+// for( i=lgth1-2; i>=imid; i-- )
+ firstm = -9999999.9;
+ firstmp = lgth1-1;
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// m[lgth2] = fgcp1[i];
+// WMMTX2[i][lgth2] += m[lgth2];
+// fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+ mi = previousw[lgth2-1] + fgcp2[lgth2-2];
+// mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+ g = mi + ogcp2[j+1];
+// g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ ijpi = i+1;
+ }
+
+ g = *prept + fgcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + ogcp1[i+1];
+// g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ ijpj = j+1;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+ g = *prept + fgcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+// midm[j+1] += *mjpt + fpenalty; //??????
+ midm[j+1] += *mjpt; //??????
+ }
+ if( i == imid - 1 )
+ {
+// midn[j] += mi + fpenalty; //????
+ midn[j] += mi; //????
+ }
+#if LOCAL
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ wm = 0;
+ }
+#endif
+
+#if STOREWM
+ WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ WMMTX2[i][j] += *curpt;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+// fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+ g = *prept + fgcp1[i];
+ if( firstm < g )
+ {
+ firstm = g;
+ firstmp = i + 1;
+ }
+#if STOREWM
+// WMMTX2[i][j+1] += firstm;
+#endif
+ if( i == imid ) midm[j+1] += firstm;
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 0;
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ for( j=2; j<lgth2-1; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+// fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ if( jmid > 0 && midn[jmid-1] > wm ) //060413
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ wm = midn[jmid-1];
+// fprintf( stderr, "rejump (n)\n" );
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ wm = midm[jmid];
+// fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+ }
+
+
+// fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+// fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if 0
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+// fprintf( stderr, "maxwm = %f\n", maxwm );
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+ if( jmid == 0 )
+ {
+// fprintf( stderr, "CHUI2!\n" );
+ jumpj = 0; jmid = 1;
+ jumpi = firstmp - 1;
+ imid = firstmp;
+ }
+
+#if 0
+ else if( jmid == lgth2 )
+ {
+ fprintf( stderr, "CHUI1!\n" );
+ jumpi=0; jumpj=0;
+ imid=jumpforwi[0]; jmid=lgth2-1;
+ }
+#else // 060414
+ else if( jmid >= lgth2 )
+ {
+// fprintf( stderr, "CHUI1!\n" );
+ jumpi=imid-1; jmid=lgth2;
+ jumpj = lgth2-1;
+ }
+#endif
+ else
+ {
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+ }
+#if 0
+ fprintf( stderr, "jumpi -> %d\n", jumpi );
+ fprintf( stderr, "jumpj -> %d\n", jumpj );
+ fprintf( stderr, "imid -> %d\n", imid );
+ fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+
+#if STOREWM
+// break;
+#else
+ break;
+#endif
+ }
+ }
+#if 0
+ jumpi=0; jumpj=0;
+ imid=lgth1-1; jmid=lgth2-1;
+ }
+#endif
+
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ map[i][j] = WMMTX[i][j] / maxwm;
+// map[i][j] = WMMTX2[i][j] / maxwm;
+
+#if STOREWM
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ float maxpairscore = -9999.9;
+ float tmpscore;
+
+ for( j=0; j<lgth2; j++ )
+ {
+ if( maxpairscore < (tmpscore=WMMTX[i][j]) )
+ {
+ map12[i].pos = j;
+ map12[i].score = tmpscore;
+ maxpairscore = tmpscore;
+ }
+ }
+
+ for( k=0; k<lgth1; k++ )
+ {
+ if( i == k ) continue;
+ if( map12[i].score <= WMMTX[k][map12[i].pos] )
+ break;
+ }
+ if( k != lgth1 )
+ {
+ map12[i].pos = -1;
+ map12[i].score = -1.0;
+ }
+ fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] );
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ float maxpairscore = -9999.9;
+ float tmpscore;
+
+ for( i=0; i<lgth1; i++ )
+ {
+ if( maxpairscore < (tmpscore=WMMTX[i][j]) )
+ {
+ map21[j].pos = i;
+ map21[j].score = tmpscore;
+ maxpairscore = tmpscore;
+ }
+ }
+
+ for( k=0; k<lgth2; k++ )
+ {
+ if( j == k ) continue;
+ if( map21[j].score <= WMMTX[map21[j].pos][k] )
+ break;
+ }
+ if( k != lgth2 )
+ {
+ map21[j].pos = -1;
+ map21[j].score = -1.0;
+ }
+ fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i )
+ fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos );
+ }
+#endif
+
+#if 0
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+// fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+#endif
+
+#if 0
+ fprintf( stdout, "#WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+// fprintf( stdout, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+// if( WMMTX[i][j] > amino_dis['a']['g'] -1 )
+ fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] );
+ if( WMMTX[i][j] == maxwm )
+ fprintf( stdout, "selected \n" );
+ else
+ fprintf( stdout, "\n" );
+ }
+ fprintf( stdout, "\n" );
+ }
+ exit( 1 );
+#endif
+
+#if 0
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+
+#endif
+
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+
+ return( value );
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+#if 0
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+#endif
+ value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo, map );
+#if 0
+ fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
+ fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
+#endif
+#if MEMSAVE
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+#endif
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+// fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
+ value += ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
+// value += fpenalty;
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+
+
+// fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
+ value += ( ogcp1[jumpi+1] + fgcp1[imid-1] );
+// value += fpenalty;
+ }
+#if 0
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+#if MEMSAVE
+ alnlen = strlen( aseq1[0] );
+ for( i=0; i<icyc; i++ ) aseq1[i] += alnlen;
+ for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen;
+#endif
+
+#if 0
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+#endif
+ value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo, map );
+#if 0
+ fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
+ fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
+#endif
+
+
+
+#if DEBUG
+ if( value - maxwm > 1 || maxwm - value > 1 )
+ {
+ fprintf( stderr, "WARNING value = %f, but maxwm = %f\n", value, maxwm );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
+ fprintf( stderr, "%s\n", aseq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
+ fprintf( stderr, "%s\n", aseq2[i] );
+ }
+
+// exit( 1 );
+ }
+ else
+ {
+ fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
+ }
+#endif
+
+#if MEMSAVE
+#else
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+#endif
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ free( gaps );
+#if MEMSAVE
+ free( aseq1 );
+ free( aseq2 );
+#else
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+#endif
+
+ return( value );
+}
+
+
+
+float Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, float **map )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm = 0.0; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+// char **mseq;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float **gapinfo;
+// float fpenalty;
+ float fpenalty = (float)RNApenalty;
+ int nglen1, nglen2;
+
+
+
+
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+ nglen1 = seqlen( seq1[0] );
+ nglen2 = seqlen( seq2[0] );
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 4, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 27 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+
+ for( i=0; i<icyc; i++ )
+ {
+ if( strlen( seq1[i] ) != lgth1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, icyc );
+ fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ if( strlen( seq2[j] ) != lgth2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, jcyc );
+ fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+ exit( 1 );
+ }
+ }
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+ new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+ new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
+ new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * fpenalty;
+ fgcp1[i] = 0.5 * fpenalty;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * fpenalty;
+ fgcp2[i] = 0.5 * fpenalty;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map );
+#if DEBUG
+ fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
+ fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+#endif
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if 0
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+ if( seqlen( seq1[0] ) != nglen1 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ exit( 1 );
+ }
+ if( seqlen( seq2[0] ) != nglen2 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
+ exit( 1 );
+ }
+#endif
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ for( i=0; i<icyc; i++ )
+ {
+ if( strlen( seq1[i] ) != lgth1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, icyc );
+ fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ if( strlen( seq2[j] ) != lgth2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, jcyc );
+ fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+ exit( 1 );
+ }
+ }
+
+ return( wm );
+}
+
+float Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, float **map )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm = 0.0; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float **gapinfo;
+ float fpenalty = (float)penalty;
+ int nglen1, nglen2;
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+ nglen1 = seqlen( seq1[0] );
+ nglen2 = seqlen( seq2[0] );
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 4, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 39 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 39 );
+
+ for( i=0; i<icyc; i++ )
+ {
+ if( strlen( seq1[i] ) != lgth1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, icyc );
+ fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ if( strlen( seq2[j] ) != lgth2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, jcyc );
+ fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+ exit( 1 );
+ }
+ }
+
+#if 0
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+#else
+ cpmx_ribosum( seq1, seq1r, dir1, cpmx1, eff1, lgth1, icyc );
+ cpmx_ribosum( seq2, seq2r, dir2, cpmx2, eff2, lgth2, jcyc );
+#endif
+
+
+#if 1
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+ new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+ new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
+ new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * fpenalty;
+ fgcp1[i] = 0.5 * fpenalty;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * fpenalty;
+ fgcp2[i] = 0.5 * fpenalty;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalign2m2m_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map );
+#if DEBUG
+ fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
+ fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+#endif
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if 0
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+ if( seqlen( seq1[0] ) != nglen1 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ exit( 1 );
+ }
+ if( seqlen( seq2[0] ) != nglen2 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
+ exit( 1 );
+ }
+#endif
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ for( i=0; i<icyc; i++ )
+ {
+ if( strlen( seq1[i] ) != lgth1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, icyc );
+ fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ if( strlen( seq2[j] ) != lgth2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, jcyc );
+ fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+ exit( 1 );
+ }
+ }
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+
+static void extendmseq( char **mseq1, char **mseq2, char **seq1, char **seq2, int i, int j, int prevhiti, int prevhitj )
+{
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ int l;
+
+ fprintf( stderr, "i=%d, prevhiti=%d\n", i, prevhiti );
+ fprintf( stderr, "j=%d, prevhitj=%d\n", j, prevhitj );
+ l = prevhiti - i - 1;
+ fprintf( stderr, "l=%d\n", l );
+ while( l>0 )
+ {
+ *--mseq1[0] = seq1[0][i+l--];
+ *--mseq2[0] = *gap;
+ }
+ l= prevhitj - j - 1;
+ fprintf( stderr, "l=%d\n", l );
+ while( l>0 )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][j+l--];
+ }
+ if( i < 0 || j < 0 ) return;
+ *--mseq1[0] = seq1[0][i];
+ *--mseq2[0] = seq2[0][j];
+ fprintf( stderr, "added %c to mseq1, mseq1 = %s \n", seq1[0][i], mseq1[0] );
+ fprintf( stderr, "added %c to mseq2, mseq2 = %s \n", seq2[0][j], mseq2[0] );
+}
+
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char tmpc = s1[0][i1];
+ char *seq2 = s2[0];
+
+ while( lgth2-- )
+ *match++ = amino_dis[(int)tmpc][(int)*seq2++];
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+ iin = lgth1; jin = lgth2;
+ limk = lgth1+lgth2 + 1;
+ for( k=0; k<limk; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--mseq1[0] = seq1[0][ifi+l];
+ *--mseq2[0] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mseq1[0] = seq1[0][ifi];
+ *--mseq2[0] = seq2[0][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ return( 0.0 );
+}
+
+void backdp( float **WMMTX, float wmmax, float *maxinw, float *maxinh, int lgth1, int lgth2, int alloclen, float *w1, float *w2, float *initverticalw, float *m, int *mp, int iin, int jin, char **seq1, char **seq2, char **mseq1, char **mseq2 )
+{
+ register int i, j;
+ int prevhiti, prevhitj;
+// int lasti, lastj;
+ float g;
+ float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+ float *currentw, *previousw, *wtmp;
+ float mi;
+ int mpi;
+ int *mpjpt;
+ float *mjpt, *prept, *curpt;
+ float wm = 0.0;
+ float forwwm;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, lgth2-1, lgth1 );
+ match_calc( currentw, seq1, seq2, lgth1-1, lgth2 );
+
+
+ prevhiti = iin;
+ prevhitj = jin;
+ fprintf( stderr, "prevhiti = %d, lgth1 = %d\n", prevhiti, lgth1 );
+ fprintf( stderr, "prevhitj = %d, lgth2 = %d\n", prevhitj, lgth2 );
+ extendmseq( mseq1, mseq2, seq1, seq2, prevhiti, prevhitj, lgth1, lgth2 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ WMMTX[i][lgth2-1] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += fpenalty;
+ WMMTX[lgth1-1][j] += fpenalty;
+ }
+
+
+#if 0
+ fprintf( stderr, "initverticalw = \n" );
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "% 8.2f", initverticalw[i] );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "currentw = \n" );
+ for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "% 8.2f", currentw[i] );
+ fprintf( stderr, "\n" );
+#endif
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j];
+ mp[j] = 0; // iranai
+ }
+
+ for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ //m[lgth2-1] ga, irunoka iranainoka irahai.
+
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[lgth2-1] = initverticalw[i+1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+
+#if 0
+ fprintf( stderr, "i=%d, currentw = \n", i );
+ for( j=0; j<lgth2; j++ ) fprintf( stderr, "% 8.2f", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ currentw[lgth2-1] = initverticalw[i];
+
+ mi = previousw[lgth2-1];
+ mpi = lgth2-1; //iranai
+
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+
+// fprintf( stderr, "i,j=%d,%d %c-%c ", i, j, seq1[0][i], seq2[0][j] );
+ wm = *prept;
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ }
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j+1; //iranai
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ }
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1; //iranai
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "*curpt = %5.0f \n", *curpt );
+#endif
+
+// forwwm = wm + MIN( maxinw[i], maxinh[j] );
+ forwwm = wm + MIN( maxinw[i], maxinh[j] );
+ WMMTX[i][j] = forwwm;
+ if( forwwm == wmmax && i<prevhiti && j<prevhitj )
+ {
+ fprintf( stderr, "hit!\n" );
+ extendmseq( mseq1, mseq2, seq1, seq2, i, j, prevhiti, prevhitj );
+ if( forwwm == wmmax )
+ {
+ *--mseq1[0] = 'u';
+ *--mseq2[0] = 'u';
+ }
+ prevhiti = i;
+ prevhitj = j;
+ }
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+ }
+ extendmseq( mseq1, mseq2, seq1, seq2, -1, -1, prevhiti, prevhitj );
+}
+
+
+float MSalign11( char **seq1, char **seq2, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj;
+ int iin = 0, jin = 0; // by Mathog, a guess
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+ float *maxinw = NULL, *maxinwpt = NULL; // by D.Mathog, guess
+ float *maxinh = NULL; // by D.Mathog, guess
+#if 1
+ float wmmax;
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static float mi, *m;
+ static int **ijp;
+ static int mpi, *mp;
+ static float *w1, *w2;
+ static float *match;
+ static float *initverticalw; /* kufuu sureba iranai */
+ static float *lastverticalw; /* kufuu sureba iranai */
+ static char **mseq1;
+ static char **mseq2;
+ static char **mseq;
+ static float **cpmx1;
+ static float **cpmx2;
+ static int **intwork;
+ static float **WMMTX;
+ static float **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( maxinw );
+ FreeFloatVec( maxinh );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+ maxinw = AllocateFloatVec( ll1+2 );
+
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ maxinh = AllocateFloatVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ FreeFloatMtx( WMMTX );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+ WMMTX = AllocateFloatMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+ WMMTX[0][0] = initverticalw[0];
+
+ maxinh[0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ WMMTX[i][0] = initverticalw[i];
+ if( maxinh[0] < initverticalw[i] ) maxinh[0] = initverticalw[i];
+ }
+ maxinw[0] = currentw[0];
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+ WMMTX[0][j] = currentw[j];
+ if( maxinw[0] < currentw[j] ) maxinw[0] = currentw[j];
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ lasti = lgth1+1;
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+ maxinwpt = maxinw + i;
+ *maxinwpt = currentw[0];
+
+ fprintf( stderr, "currentw[0] = %f, *maxinwpt = %f\n", currentw[0], maxinw[i] );
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+ WMMTX[i][j] = *curpt;
+
+
+ if( j<lgth2 && *maxinwpt < *curpt ) *maxinwpt = *curpt;
+ if( j<lgth2 && maxinh[j] < *curpt ) maxinh[j] = *curpt;
+// fprintf( stderr, "maxintwpt = %f\n", *maxinwpt );
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+ wmmax = -999.9;
+ for( i=0; i<lgth1; i++ )
+ {
+ g = lastverticalw[i];
+ if( g > wmmax )
+ {
+ wmmax = g;
+ iin = i;
+ jin = lgth2-1;
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ g = currentw[j];
+ if( g > wmmax )
+ {
+ wmmax = g;
+ iin = lgth1-1;
+ jin = j;
+ }
+ }
+
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "maxinw[%d] = %f\n", i, maxinw[i] );
+ for( j=0; j<lgth2; j++ )
+ fprintf( stderr, "maxinh[%d] = %f\n", j, maxinh[j] );
+
+ fprintf( stderr, "wmmax = %f (%d,%d)\n", wmmax, iin, jin );
+ if( iin == lgth1 - 1 && jin == lgth2 - 1 )
+ ;
+ else
+ wmmax += fpenalty;
+
+ fprintf( stderr, "wmmax = %f\n", wmmax );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+
+ backdp( WMMTX, wmmax, maxinw, maxinh, lgth1, lgth2, alloclen, w1, w2, initverticalw, m, mp, iin, jin, seq1, seq2, mseq1, mseq2 );
+
+ fprintf( stderr, "\n" );
+#if 1
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">MSres\n%s\n", mseq1[0] );
+ fprintf( stderr, ">MSres\n%s\n", mseq2[0] );
+#endif
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp );
+
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+#if 1
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+
+
+ return( wm );
+}
+
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MEMSAVE 1
+
+#define DEBUG 0
+#define USE_PENALTY_EX 0
+#define STOREWM 0
+
+#define DPTANNI 100
+
+
+static TLS int reccycle = 0;
+
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+ float *matchpt;
+ float **cpmxpdpt;
+ int **cpmxpdnpt;
+ int cpkd;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#else
+ matchpt = match;
+ cpmxpdnpt = cpmxpdn;
+ cpmxpdpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
+ *matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
+ matchpt++;
+ cpmxpdnpt++;
+ cpmxpdpt++;
+ }
+#endif
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ int **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen,
+ int fulllen1, int fulllen2, int tailgp )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ float wm;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, tailgp=%d, ien=%d, fulllen1=%d, jen=%d, fulllen2=%d\n", tailgp, ien, fulllen1, jen, fulllen2 );
+
+ if( tailgp == 1 )
+ ;
+ else if( ien == fulllen1-1 || jen == fulllen2-1 )
+ {
+// fprintf( stderr, "searching lasthorizontalw and lasthorizontalw\n" );
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+#if 0
+ else if( jen == fulllen2-1 )
+ {
+ fprintf( stderr, "searching lastverticalw\n" );
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ }
+ else if( ien == fulllen1-1 )
+ {
+ fprintf( stderr, "searching lasthorizontalw\n" );
+ wm = lasthorizontalw[0];
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, float **gapinfo, int headgp, int tailgp )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ int **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ int **intmtx;
+ int lgth1, lgth2;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+// char **aseq1;
+// char **aseq2;
+// char **aseq1bk, **aseq2bk;
+
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+#if STOREWM
+ char ttt1[10000], ttt2[10000];
+#endif
+
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if STOREWM
+ strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+ strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+
+ fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+ fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+ fprintf( stderr, "ttt1 = %s\n", ttt1 );
+ fprintf( stderr, "ttt2 = %s\n", ttt2 );
+#endif
+
+#if 0
+ fprintf( stderr, "in _tanni ist,ien = %d,%d, fulllen1=%d\n", ist, ien, fulllen1 );
+ fprintf( stderr, "in _tanni jst,jen = %d,%d, fulllen2=%d\n", jst, jen, fulllen2 );
+ fprintf( stderr, "in _tanni seq1[0] = %-*.*s\n", ien-ist+1, ien-ist+1, seq1[0]+ist );
+ fprintf( stderr, "in _tanni seq2[0] = %-*.*s\n", jen-jst+1, jen-jst+1, seq2[0]+jst );
+#endif
+
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+// aseq1 = AllocateCharMtx( icyc, 0 );
+// aseq2 = AllocateCharMtx( jcyc, 0 );
+// aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+// aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+// for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+// for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+
+
+ intmtx = AllocateIntMtx( ll1+1, ll2+1 );
+
+ ijp = intmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ if( headgp || ist != 0 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ }
+ }
+ if( headgp || jst != 0 )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ }
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+
+ if( tailgp || jen != fulllen2-1 ) lasti = lgth1+1; else lasti = lgth1;
+// if( 1 ) lasti = lgth1+1; else lasti = lgth1;
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + ogcp2[1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+// if( tailgp && jen != fulllen2-1 ) lastj = lgth2+1; else lastj = lgth2;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fgcp2[j-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + ogcp2[j];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fgcp1[i-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + ogcp1[i];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, ist, ien, jst, jen, fulllen1, fulllen2, tailgp );
+#if 0
+ fprintf( stderr, "res in _tanni mseq1[0] = %s\n", mseq1[0] );
+ fprintf( stderr, "res in _tanni mseq2[0] = %s\n", mseq2[0] );
+#endif
+
+// for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+// for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeIntMtx( intmtx );
+
+
+// FreeCharMtx( aseq1bk );
+// FreeCharMtx( aseq2bk );
+
+// free( aseq1 );
+// free( aseq2 );
+
+ return( wm );
+
+}
+
+static void freearrays_rec1(
+ float *w1, float *w2, float *initverticalw, float *lastverticalw,
+ float *midw, float *midm, float *midn,
+ int *jumpbacki, int *jumpbackj, int *jumpforwi, int *jumpforwj, int *jumpdummi, int *jumpdummj,
+ float *m, int *mp,
+ float **floatwork, int **intwork
+#if STOREWM
+ , float **WMMTX, float **WMMTX2
+#endif
+)
+{
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+}
+
+static void freearrays_rec2( char *gaps, char **aseq1, char **aseq2 )
+{
+ free( gaps );
+#if MEMSAVE
+ free( aseq1 );
+ free( aseq2 );
+#else
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+#endif
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, int depth, float **gapinfo, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int alnlen;
+ float value = 0.0;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid;
+ int jmid = 0; // by D.Mathog, a guess
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+ float **WMMTX;
+ float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ int lgth1, lgth2;
+ float maxwm;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj = NULL; // by D.Mathog, a guess
+ int jumpi, jumpj = 0; // by D.Mathog, a guess
+ char *gaps;
+ int ijpi, ijpj;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ float firstm;
+ int firstmp;
+#if STOREWM
+ static TLS char ttt1[50000];
+ static TLS char ttt2[50000];
+#endif
+
+#if 0
+ int nglen1, nglen2;
+ nglen1 = seqlen( seq1[0] );
+ nglen2 = seqlen( seq2[0] );
+#endif
+
+// fprintf( stderr, "fulllen1 = %d, fulllen2 = %d, headgp = %d, tailgp = %d\n", fulllen1, fulllen2, headgp, tailgp );
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// if( lgth1 < 5 )
+// fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
+// if( lgth2 < 5 )
+// fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
+//
+
+
+#if STOREWM
+ fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+ strncpy( ttt1, seq1[0]+ist, lgth1 );
+ strncpy( ttt2, seq2[0]+jst, lgth2 );
+ ttt1[lgth1] = 0;
+ ttt2[lgth2] = 0;
+ fprintf( stderr, "seq1 = %s\n", ttt1 );
+ fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+ if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+ {
+// fprintf( stderr, "\n\n==== jimei\n\n" );
+// exit( 1 );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( 0.0 );
+ }
+
+#if MEMSAVE
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
+#else
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+#endif
+
+// fprintf( stderr, "####(s) seq1[0] (%d) = \n%-*.*s\n (a%d-a%d)\n", depth, ien-ist+1, ien-ist+1, seq1[0]+ist, ist, ien );
+// fprintf( stderr, "####(s) seq2[0] (%d) = \n%-*.*s\n (b%d-b%d)\n", depth, jen-jst+1, jen-jst+1, seq2[0]+jst, jst, jen );
+
+// if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai
+// if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, gapinfo, headgp, tailgp );
+
+
+#if MEMSAVE
+ free( aseq1 );
+ free( aseq2 );
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+#endif
+
+// fprintf( stderr, "value = %f\n", value );
+
+ return( value );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1];
+// m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 * 0.5;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+#if STOREWM
+ for( i=1; i<lasti; i++ )
+#else
+ for( i=1; i<=imid; i++ )
+#endif
+ {
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! zenhan\n" );
+ *chudanres = 1;
+ freearrays_rec1
+ (
+ w1, w2, initverticalw, lastverticalw, midw, midm, midn,
+ jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
+ m, mp,
+ floatwork, intwork
+#if STOREWM
+ , WMMTX, WMMTX2
+#endif
+ );
+ freearrays_rec2( gaps, aseq1, aseq2 );
+ return( -1.0 );
+ }
+#endif
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ m[0] = ogcp1[i];
+#if STOREM
+ WMMTX2[i][0] = m[0];
+#endif
+ if( i == imid ) midm[0] = m[0];
+
+ mi = previousw[0] + ogcp2[1];
+// mi = previousw[0];
+ mpi = 0;
+
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fgcp2[j-1];
+// g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ g = *prept + ogcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fgcp1[i-1];
+// g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+ g = *prept + ogcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+// fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+ WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+ fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+ }
+#endif
+
+
+
+
+
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j] + fgcp2[lgth2-2];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+
+// for( i=lgth1-2; i>=imid; i-- )
+ firstm = -9999999.9;
+// firstmp = lgth1-1;
+ firstmp = lgth1;
+ for( i=lgth1-2; i>-1; i-- )
+ {
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! kouhan\n" );
+ *chudanres = 1;
+ freearrays_rec1
+ (
+ w1, w2, initverticalw, lastverticalw, midw, midm, midn,
+ jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
+ m, mp,
+ floatwork, intwork
+#if STOREWM
+ , WMMTX, WMMTX2
+#endif
+ );
+ freearrays_rec2( gaps, aseq1, aseq2 );
+ return( -1.0 );
+ }
+#endif
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// m[lgth2] = fgcp1[i];
+// WMMTX2[i][lgth2] += m[lgth2];
+// fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+ mi = previousw[lgth2-1] + fgcp2[lgth2-2];
+// mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+ g = mi + ogcp2[j+1];
+// g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ ijpi = i+1;
+ }
+
+ g = *prept + fgcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + ogcp1[i+1];
+// g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ ijpj = j+1;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+ g = *prept + fgcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+// midm[j+1] += *mjpt + fpenalty; //??????
+ midm[j+1] += *mjpt; //??????
+ }
+ if( i == imid - 1 )
+ {
+// midn[j] += mi + fpenalty; //????
+ midn[j] += mi; //????
+ }
+#if STOREWM
+ WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ WMMTX2[i][j+1] += *mjpt;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+// fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+ g = *prept + fgcp1[i];
+ if( firstm < g )
+ {
+ firstm = g;
+ firstmp = i + 1;
+ }
+#if STOREWM
+ WMMTX2[i][j+1] += firstm;
+#endif
+ if( i == imid ) midm[j+1] += firstm;
+
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 0;
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ for( j=2; j<lgth2-1; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+// fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ if( jmid > 0 && midn[jmid-1] > wm ) //060413
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ wm = midn[jmid-1];
+// fprintf( stderr, "rejump (n)\n" );
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ wm = midm[jmid];
+// fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+ }
+
+
+// fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+// fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if STOREWM
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+// fprintf( stderr, "maxwm = %f\n", maxwm );
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "#### FIRST i=%d, jumpi<imid=%d<%d, ist=%d, ien=%d, firstmp=%d, lgth1=%d\n", i, jumpi, imid, ist, ien, firstmp, lgth1 );
+// fprintf( stderr, "#### mark 1\n" );
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+
+ if( jmid == 0 )
+ {
+// fprintf( stderr, "#### CHUI2!\n" );
+ jumpj = 0; jmid = 1;
+#if 0 // v6.823 made
+ jumpi = firstmp-1;
+ imid = firstmp;
+#endif
+#if 0
+ jumpi = 0;
+ imid = 1;
+#else
+// if( 1 || firstmp > 100 ) // naze 100
+ if( imid < firstmp-1 ) // naze 100
+ {
+ jumpi = firstmp;
+ imid = firstmp+1;
+ }
+#if 0
+ else
+ {
+ jumpi = 0;
+ imid = 1;
+ }
+#endif
+#endif
+ }
+
+#if 0
+ else if( jmid == lgth2 )
+ {
+ fprintf( stderr, "CHUI1!\n" );
+ jumpi=0; jumpj=0;
+ imid=jumpforwi[0]; jmid=lgth2-1;
+ }
+#else // 060414
+ else if( jmid >= lgth2 )
+ {
+// fprintf( stderr, "CHUI1!\n" );
+ jumpi=imid-1; jmid=lgth2;
+ jumpj = lgth2-1;
+ }
+#endif
+ else
+ {
+// fprintf( stderr, "#### CHUI3!\n" );
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+ if( imid == jumpi ) jumpi = imid-1;
+ }
+#if 0
+ fprintf( stderr, "jumpi -> %d\n", jumpi );
+ fprintf( stderr, "jumpj -> %d\n", jumpj );
+ fprintf( stderr, "imid -> %d\n", imid );
+ fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+// fprintf( stderr, "#### FINAL i=%d, jumpi<imid=%d<%d, ist=%d, ien=%d, firstmp=%d\n", i, jumpi, imid, ist, ien, firstmp );
+
+#if STOREWM
+ break;
+#else
+ break;
+#endif
+ }
+ }
+
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if STOREWM
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+// fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+
+
+#endif
+
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+ freearrays_rec1
+ (
+ w1, w2, initverticalw, lastverticalw, midw, midm, midn,
+ jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
+ m, mp,
+ floatwork, intwork
+#if STOREWM
+ , WMMTX, WMMTX2
+#endif
+ );
+
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+ value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp ); // chudan mada
+#if 0
+ fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
+ fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
+#endif
+#if MEMSAVE
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+#endif
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+// fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
+ value += ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
+// value += fpenalty;
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+
+
+// fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
+ value += ( ogcp1[jumpi+1] + fgcp1[imid-1] );
+// value += fpenalty;
+ }
+#if 0
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+#if MEMSAVE
+ alnlen = strlen( aseq1[0] );
+ for( i=0; i<icyc; i++ ) aseq1[i] += alnlen;
+ for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen;
+#endif
+
+ value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp ); // chudan mada
+#if 0
+ fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
+ fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
+#endif
+
+
+
+#if DEBUG
+ if( value - maxwm > 1 || maxwm - value > 1 )
+ {
+ fprintf( stderr, "WARNING value = %f, but maxwm = %f\n", value, maxwm );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
+ fprintf( stderr, "%s\n", aseq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
+ fprintf( stderr, "%s\n", aseq2[i] );
+ }
+
+// exit( 1 );
+ }
+ else
+ {
+ fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
+ }
+#endif
+
+#if MEMSAVE
+#else
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+#endif
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = \n%s\n (a%d-a%d)\n", depth, mseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = \n%s\n (b%d-b%d)\n", depth, mseq2[0], jst, jen );
+
+ freearrays_rec2( gaps, aseq1, aseq2 );
+
+#if 0
+ if( seqlen( seq1[0] ) != nglen1 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ exit( 1 );
+ }
+ else
+ fprintf( stderr, "nglen1 is ok in _rec\n" );
+ if( seqlen( seq2[0] ) != nglen2 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
+ exit( 1 );
+ }
+ else
+ fprintf( stderr, "nglen2 is ok in _rec\n" );
+#endif
+
+ return( value );
+}
+
+static void freearrays(
+ float *ogcp1,
+ float *ogcp2,
+ float *fgcp1,
+ float *fgcp2,
+ float **cpmx1,
+ float **cpmx2,
+ float **gapinfo,
+ char **mseq1,
+ char **mseq2
+)
+{
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+}
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm = 0.0; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float **gapinfo;
+ float fpenalty = (float)penalty;
+ int nglen1, nglen2;
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+ nglen1 = seqlen( seq1[0] );
+ nglen2 = seqlen( seq2[0] );
+
+#if 0
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "seq1[%d] at root = %s\n", i, seq1[i] );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "seq2[%d] at root = %s\n", j, seq2[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 4, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 27 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+
+ for( i=0; i<icyc; i++ )
+ {
+ if( strlen( seq1[i] ) != lgth1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, icyc );
+ fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ if( strlen( seq2[j] ) != lgth2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, jcyc );
+ fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+ exit( 1 );
+ }
+ }
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+ new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+ new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
+ new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * fpenalty;
+ fgcp1[i] = 0.5 * fpenalty;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * fpenalty;
+ fgcp2[i] = 0.5 * fpenalty;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, lgth1, lgth2, mseq1, mseq2, 0, gapinfo, chudanpt, chudanref, chudanres, headgp, tailgp );
+#ifdef enablemultithread
+ if( chudanres && *chudanres )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! relay\n" );
+ *chudanres = 1;
+ freearrays( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1, cpmx2, gapinfo, mseq1, mseq2 );
+ return( -1.0 );
+ }
+#endif
+
+#if DEBUG
+ fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
+ fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+#endif
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+ if( seqlen( seq1[0] ) != nglen1 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ exit( 1 );
+ }
+ if( seqlen( seq2[0] ) != nglen2 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
+ exit( 1 );
+ }
+
+
+ freearrays( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1, cpmx2, gapinfo, mseq1, mseq2 );
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ for( i=0; i<icyc; i++ )
+ {
+ if( strlen( seq1[i] ) != lgth1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, icyc );
+ fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ if( strlen( seq2[j] ) != lgth2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, jcyc );
+ fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+ exit( 1 );
+ }
+ }
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define STOREWM 0
+
+#define DPTANNI 1000
+
+
+static reccycle = 0;
+
+static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = 0;
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ }
+// totaleff+= eff[j];
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "ogcp[%d] = %30.20f\n", i, ogcp[i] );
+// ogcp[i] /= totaleff;
+// }
+}
+
+static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len+1; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = ( seq[j][0] == '-' );
+ for( i=1; i<len+1; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc ) fgcp[i-1] += feff;
+ }
+ }
+// totaleff += eff[j];
+// fprintf( stderr, "eff[%d] = %30.20f\n", j, eff[j] );
+ }
+// for( i=0; i<len; i++ )
+// {
+// fgcp[i] /= totaleff;
+// fprintf( stderr, "fgcp[%d] = %30.20f\n", i, fgcp[i] );
+// }
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#endif
+}
+
+static float Atracking(
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ short **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char gap[] = "-";
+ float wm;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi];
+ k++;
+ iin = ifi; jin = jfi;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ }
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float dumfl;
+ int lgth1, lgth2;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ char **aseq1;
+ char **aseq2;
+ char **aseq1bk, **aseq2bk;
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+// char ttt1[10000], ttt2[10000];
+
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+// strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+//
+// fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+// fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+// fprintf( stderr, "ttt1 = %s\n", ttt1 );
+// fprintf( stderr, "ttt2 = %s\n", ttt2 );
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+
+
+ shortmtx = AllocateShortMtx( ll1+1, ll2+1 );
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + fpenalty * ogcp1[i];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ Atracking( seq1, seq2, aseq1, aseq2, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+
+ FreeCharMtx( aseq1bk );
+ FreeCharMtx( aseq2bk );
+
+ free( aseq1 );
+ free( aseq2 );
+
+ return( wm );
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid, jmid;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+// float **WMMTX;
+// float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ float dumfl;
+ int lgth1, lgth2;
+ float maxwm;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj; //muda
+ int jumpi, jumpj;
+ char *gaps;
+ int ijpi, ijpj;
+// float *ogcp1 = gapinfo[0];
+// float *fgcp1 = gapinfo[1];
+// float *ogcp2 = gapinfo[2];
+// float *fgcp2 = gapinfo[3];
+// static char ttt1[50000];
+// static char ttt2[50000];
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+// strncpy( ttt1, seq1[0]+ist, lgth1 );
+// strncpy( ttt2, seq2[0]+jst, lgth2 );
+// ttt1[lgth1] = 0;
+// ttt2[lgth2] = 0;
+// fprintf( stderr, "seq1 = %s\n", ttt1 );
+// fprintf( stderr, "seq2 = %s\n", ttt2 );
+ if( lgth2 <= 0 )
+ {
+ fprintf( stderr, "==== jimei\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( (float)offset * lgth1 );
+ }
+
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI )
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ wm = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+// fprintf( stderr, "freeing aseq\n" );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( wm );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+// initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+// currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+// m[j] = currentw[j-1] + fpenalty * ogcp1[1];
+ m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 / 2;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+// for( i=1; i<lasti; i++ )
+ for( i=1; i<=imid; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+
+// mi = previousw[0] + fpenalty * ogcp2[1];
+ mi = previousw[0];
+ mpi = 0;
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+// *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+// g = *prept + fpenalty * ogcp2[j];
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// g = *mjpt + fpenalty * fgcp1[i-1];
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+// g = *prept + fpenalty * ogcp1[i];
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+// initverticalw[i] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+// currentw[j] += fpenalty * ( fgcp2[lgth1-1] + ogcp2[j+1] );
+ currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += fpenalty;
+ }
+#endif
+
+ for( j=lgth2-1; j>0; --j )
+ {
+// m[j-1] = currentw[j] + fpenalty * fgcp2[lgth2-2];
+ m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+// for( i=lgth1-2; i>=imid; i-- )
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// mi = previousw[lgth2-1] + fpenalty * fgcp2[lgth2-2];
+ mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+// g = mi + fpenalty * ogcp2[j+1];
+ g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ }
+
+// g = *prept + fpenalty + fgcp2[j];
+ g = *prept;
+ if( g > mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+// g = *mjpt + fpenalty * ogcp1[i+1];
+ g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+// g = *prept + fpenalty * fgcp1[i];
+ g = *prept;
+ if( g > *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+ midm[j+1] += *mjpt + fpenalty; //??????
+ }
+ if( i == imid - 1 )
+ {
+ midn[j] += mi + fpenalty; //????
+ }
+#if STOREWM
+ WMMTX[i][j] += wm;
+ WMMTX2[i][j+1] += *mjpt + fpenalty;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 1;
+ for( j=2; j<lgth2; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+ }
+// fprintf( stderr, "imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ {
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ }
+ if( midn[jmid-1] >= wm )
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ }
+#if 0
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+// fprintf( stderr, "imid -> %d\n", imid );
+// fprintf( stderr, "jmid -> %d\n", jmid );
+ break;
+ }
+ }
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if 0
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+
+
+#endif
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+ MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+ }
+#if DEBUG
+ fprintf( stderr, "after gapfill mseq1[0]=%s\n", mseq1[0] );
+ fprintf( stderr, "after gapfill mseq2[0]=%s\n", mseq2[0] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+ MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
+
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ free( gaps );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( wm );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+ char **mseq;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float **gapinfo;
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 4, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 27 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+
+ for( i=0; i<icyc; i++ )
+ {
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ seq2[j][lgth2] = 0;
+ }
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+ OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 1.0;
+ fgcp1[i] = 1.0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 1.0;
+ fgcp2[i] = 1.0;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define STOREWM 0
+
+#define DPTANNI 1000
+
+
+static reccycle = 0;
+
+static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = 0;
+// gc = ( gappat[j] == '-' );
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ }
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "ogcp[%d] = %30.20f\n", i, ogcp[i] );
+// }
+}
+
+static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+// gc = ( seq[j][0] == '-' );
+ gc = 0;
+ for( i=1; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc )
+ {
+ fgcp[i-1] += feff;
+ }
+ }
+ }
+ {
+ gb = gc;
+ gc = 0;
+ {
+// fprintf( stderr, "changed gc=%d, gb=%d\n", gc, gb );
+ if( gb * !gc ) fgcp[i-1] += feff;
+ }
+ }
+// fprintf( stderr, "eff[%d] = %30.20f\n", j, eff[j] );
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "fgcp[%d] = %30.20f\n", i, fgcp[i] );
+// }
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#endif
+}
+
+static float Atracking(
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ short **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char gap[] = "-";
+ float wm;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi];
+ k++;
+ iin = ifi; jin = jfi;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ }
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float dumfl;
+ int lgth1, lgth2;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ char **aseq1;
+ char **aseq2;
+ char **aseq1bk, **aseq2bk;
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+#if STOREWM
+ char ttt1[10000], ttt2[10000];
+#endif
+
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if STOREWM
+ strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+ strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+
+ fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+ fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+ fprintf( stderr, "ttt1 = %s\n", ttt1 );
+ fprintf( stderr, "ttt2 = %s\n", ttt2 );
+#endif
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+
+
+ shortmtx = AllocateShortMtx( ll1+1, ll2+1 );
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + fpenalty * ogcp1[i];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ Atracking( seq1, seq2, aseq1, aseq2, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+
+ FreeCharMtx( aseq1bk );
+ FreeCharMtx( aseq2bk );
+
+ free( aseq1 );
+ free( aseq2 );
+
+ return( wm );
+
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ float value = 0.0;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid, jmid;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+ float **WMMTX;
+ float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ float dumfl;
+ int lgth1, lgth2;
+ float maxwm;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj; //muda
+ int jumpi, jumpj;
+ char *gaps;
+ int ijpi, ijpj;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ float firstm;
+ int firstmp;
+#if STOREWM
+ static char ttt1[50000];
+ static char ttt2[50000];
+#endif
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+
+#if STOREWM
+ fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+ strncpy( ttt1, seq1[0]+ist, lgth1 );
+ strncpy( ttt2, seq2[0]+jst, lgth2 );
+ ttt1[lgth1] = 0;
+ ttt2[lgth2] = 0;
+ fprintf( stderr, "seq1 = %s\n", ttt1 );
+ fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+ if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+ {
+ fprintf( stderr, "\n\n==== jimei\n\n" );
+// exit( 1 );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+ fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+ fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( 0.0 );
+ }
+
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI )
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+// fprintf( stderr, "freeing aseq\n" );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+// fprintf( stderr, "value = %f\n", value );
+
+ return( value );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1];
+// m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 * 0.5;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+#if STOREWM
+ for( i=1; i<lasti; i++ )
+#else
+ for( i=1; i<=imid; i++ )
+#endif
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ m[0] = fpenalty * ogcp1[i];
+#if STOREM
+ WMMTX2[i][0] = m[0];
+#endif
+ if( i == imid ) midm[0] = m[0];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+// mi = previousw[0];
+ mpi = 0;
+
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+// g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+// g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+ g = *prept + fpenalty * ogcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+// fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+ WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+ fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+ }
+#endif
+
+
+
+
+
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j] + fpenalty * fgcp2[lgth2-2];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+
+// for( i=lgth1-2; i>=imid; i-- )
+ firstm = -9999999.9;
+ firstmp = lgth1-1;
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// m[lgth2] = fpenalty * fgcp1[i];
+// WMMTX2[i][lgth2] += m[lgth2];
+// fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+ mi = previousw[lgth2-1] + fpenalty * fgcp2[lgth2-2];
+// mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+ g = mi + fpenalty * ogcp2[j+1];
+// g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ ijpi = i+1;
+ }
+
+ g = *prept + fpenalty * fgcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + fpenalty * ogcp1[i+1];
+// g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ ijpj = j+1;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+ g = *prept + fpenalty * fgcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+// midm[j+1] += *mjpt + fpenalty; //??????
+ midm[j+1] += *mjpt; //??????
+ }
+ if( i == imid - 1 )
+ {
+// midn[j] += mi + fpenalty; //????
+ midn[j] += mi; //????
+ }
+#if STOREWM
+ WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ WMMTX2[i][j+1] += *mjpt;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+// fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+ g = *prept + fpenalty * fgcp1[i];
+ if( firstm < g )
+ {
+ firstm = g;
+ firstmp = i + 1;
+ }
+#if STOREWM
+ WMMTX2[i][j+1] += firstm;
+#endif
+ if( i == imid ) midm[j+1] += firstm;
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 0;
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ for( j=2; j<lgth2-1; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+// fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ if( midn[jmid-1] > wm )
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ wm = midn[jmid-1];
+// fprintf( stderr, "rejump (n)\n" );
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ wm = midm[jmid];
+// fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+ }
+
+
+// fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+// fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if STOREWM
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+// fprintf( stderr, "maxwm = %f\n", maxwm );
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+ if( jmid == 0 )
+ {
+// fprintf( stderr, "CHUI2!\n" );
+ jumpj = 0; jmid = 1;
+ jumpi = firstmp - 1;
+ imid = firstmp;
+ }
+ else if( jmid == lgth2 )
+ {
+// fprintf( stderr, "CHUI1!\n" );
+ jumpi=0; jumpj=0;
+ imid=jumpforwi[0]; jmid=lgth2-1;
+ }
+ else
+ {
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+ }
+#if 0
+ fprintf( stderr, "jumpi -> %d\n", jumpi );
+ fprintf( stderr, "jumpj -> %d\n", jumpj );
+ fprintf( stderr, "imid -> %d\n", imid );
+ fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+
+#if STOREWM
+ break;
+#else
+ break;
+#endif
+ }
+ }
+#if 0
+ jumpi=0; jumpj=0;
+ imid=lgth1-1; jmid=lgth2-1;
+ }
+#endif
+
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if STOREWM
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+
+
+#endif
+
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+// fprintf( stderr, "jumpi = %d\n", jumpi );
+ value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+// fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
+ value += fpenalty * ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
+// value += fpenalty;
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+
+
+// fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
+ value += fpenalty * ( ogcp1[jumpi+1] + fgcp1[imid-1] );
+// value += fpenalty;
+ }
+#if 0
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+ value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
+
+
+
+#if DEBUG
+ if( value - maxwm > 1 || maxwm - value > 1 )
+ {
+ fprintf( stderr, "WARNING value = %f, but maxwm = %f penalty = %f\n", value, maxwm, fpenalty );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
+ fprintf( stderr, "%s\n", aseq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
+ fprintf( stderr, "%s\n", aseq2[i] );
+ }
+
+// exit( 1 );
+ }
+ else
+ {
+ fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
+ }
+#endif
+
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ free( gaps );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( value );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+ char **mseq;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float **gapinfo;
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 4, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 27 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+
+ for( i=0; i<icyc; i++ )
+ {
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ seq2[j][lgth2] = 0;
+ }
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+
+ OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5;
+ fgcp1[i] = 0.5;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5;
+ fgcp2[i] = 0.5;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define STOREWM 0
+
+#define DPTANNI 1000
+
+
+static reccycle = 0;
+
+static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = 0;
+// gc = ( gappat[j] == '-' );
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ }
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "ogcp[%d] = %30.20f\n", i, ogcp[i] );
+// }
+}
+
+static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+// gc = ( seq[j][0] == '-' );
+ gc = 0;
+ for( i=1; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc )
+ {
+ fgcp[i-1] += feff;
+ }
+ }
+ }
+ {
+ gb = gc;
+ gc = 0;
+ {
+// fprintf( stderr, "changed gc=%d, gb=%d\n", gc, gb );
+ if( gb * !gc ) fgcp[i-1] += feff;
+ }
+ }
+// fprintf( stderr, "eff[%d] = %30.20f\n", j, eff[j] );
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "fgcp[%d] = %30.20f\n", i, fgcp[i] );
+// }
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#endif
+}
+
+static float Atracking(
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ short **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char gap[] = "-";
+ float wm;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi];
+ k++;
+ iin = ifi; jin = jfi;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ }
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float dumfl;
+ int lgth1, lgth2;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ char **aseq1;
+ char **aseq2;
+ char **aseq1bk, **aseq2bk;
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+#if STOREWM
+ char ttt1[10000], ttt2[10000];
+#endif
+
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if STOREWM
+ strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+ strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+
+ fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+ fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+ fprintf( stderr, "ttt1 = %s\n", ttt1 );
+ fprintf( stderr, "ttt2 = %s\n", ttt2 );
+#endif
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+
+
+ shortmtx = AllocateShortMtx( ll1+1, ll2+1 );
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + fpenalty * ogcp1[i];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ Atracking( seq1, seq2, aseq1, aseq2, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+
+ FreeCharMtx( aseq1bk );
+ FreeCharMtx( aseq2bk );
+
+ free( aseq1 );
+ free( aseq2 );
+
+ return( wm );
+
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ float value = 0.0;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid, jmid;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+ float **WMMTX;
+ float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ float dumfl;
+ int lgth1, lgth2;
+ float maxwm;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj; //muda
+ int jumpi, jumpj;
+ char *gaps;
+ int ijpi, ijpj;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ float firstm;
+ int firstmp;
+#if STOREWM
+ static char ttt1[50000];
+ static char ttt2[50000];
+#endif
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+
+#if STOREWM
+ fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+ strncpy( ttt1, seq1[0]+ist, lgth1 );
+ strncpy( ttt2, seq2[0]+jst, lgth2 );
+ ttt1[lgth1] = 0;
+ ttt2[lgth2] = 0;
+ fprintf( stderr, "seq1 = %s\n", ttt1 );
+ fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+ if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+ {
+ fprintf( stderr, "==== jimei\n" );
+// exit( 1 );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+ fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+ fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( 0.0 );
+ }
+
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI )
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+// fprintf( stderr, "freeing aseq\n" );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+// fprintf( stderr, "value = %f\n", value );
+
+ return( value );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1];
+// m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 * 0.5;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+#if STOREWM
+ for( i=1; i<lasti; i++ )
+#else
+ for( i=1; i<=imid; i++ )
+#endif
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ m[0] = fpenalty * ogcp1[i];
+#if STOREM
+ WMMTX2[i][0] = m[0];
+#endif
+ if( i == imid ) midm[0] = m[0];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+// mi = previousw[0];
+ mpi = 0;
+
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+// g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+// g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+ g = *prept + fpenalty * ogcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+// fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+ WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+ fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+ }
+#endif
+
+
+
+
+
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j] + fpenalty * fgcp2[lgth2-2];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+
+// for( i=lgth1-2; i>=imid; i-- )
+ firstm = -9999999.9;
+ firstmp = lgth1-1;
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// m[lgth2] = fpenalty * fgcp1[i];
+// WMMTX2[i][lgth2] += m[lgth2];
+// fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+ mi = previousw[lgth2-1] + fpenalty * fgcp2[lgth2-2];
+// mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+ g = mi + fpenalty * ogcp2[j+1];
+// g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ ijpi = i+1;
+ }
+
+ g = *prept + fpenalty * fgcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + fpenalty * ogcp1[i+1];
+// g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ ijpj = j+1;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+ g = *prept + fpenalty * fgcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+// midm[j+1] += *mjpt + fpenalty; //??????
+ midm[j+1] += *mjpt; //??????
+ }
+ if( i == imid - 1 )
+ {
+// midn[j] += mi + fpenalty; //????
+ midn[j] += mi; //????
+ }
+#if STOREWM
+ WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ WMMTX2[i][j+1] += *mjpt;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+// fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+ g = *prept + fpenalty * fgcp1[i];
+ if( firstm < g )
+ {
+ firstm = g;
+ firstmp = i + 1;
+ }
+#if STOREWM
+ WMMTX2[i][j+1] += firstm;
+#endif
+ if( i == imid ) midm[j+1] += firstm;
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 0;
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ for( j=2; j<lgth2-1; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+// fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ if( midn[jmid-1] > wm )
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ wm = midn[jmid-1];
+// fprintf( stderr, "rejump (n)\n" );
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ wm = midm[jmid];
+// fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+ }
+
+
+// fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+// fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if STOREWM
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+// fprintf( stderr, "maxwm = %f\n", maxwm );
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+ if( jmid == 0 )
+ {
+// fprintf( stderr, "CHUI2!\n" );
+ jumpj = 0; jmid = 1;
+ jumpi = firstmp - 1;
+ imid = firstmp;
+ }
+ else if( jmid == lgth2 )
+ {
+// fprintf( stderr, "CHUI1!\n" );
+ jumpi=0; jumpj=0;
+ imid=jumpforwi[0]; jmid=lgth2-1;
+ }
+ else
+ {
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+ }
+#if 0
+ fprintf( stderr, "jumpi -> %d\n", jumpi );
+ fprintf( stderr, "jumpj -> %d\n", jumpj );
+ fprintf( stderr, "imid -> %d\n", imid );
+ fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+
+#if STOREWM
+ break;
+#else
+ break;
+#endif
+ }
+ }
+#if 0
+ jumpi=0; jumpj=0;
+ imid=lgth1-1; jmid=lgth2-1;
+ }
+#endif
+
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if STOREWM
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+
+
+#endif
+
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+// fprintf( stderr, "jumpi = %d\n", jumpi );
+ value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+// fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
+ value += fpenalty * ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
+// value += fpenalty;
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+
+
+// fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
+ value += fpenalty * ( ogcp1[jumpi+1] + fgcp1[imid-1] );
+// value += fpenalty;
+ }
+#if 0
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+ value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
+
+
+
+#if DEBUG
+ if( value - maxwm > 1 || maxwm - value > 1 )
+ {
+ fprintf( stderr, "WARNING value = %f, but maxwm = %f penalty = %f\n", value, maxwm, fpenalty );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
+ fprintf( stderr, "%s\n", aseq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
+ fprintf( stderr, "%s\n", aseq2[i] );
+ }
+
+// exit( 1 );
+ }
+ else
+ {
+ fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
+ }
+#endif
+
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ free( gaps );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( value );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+ char **mseq;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float **gapinfo;
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 4, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 27 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+
+ for( i=0; i<icyc; i++ )
+ {
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ seq2[j][lgth2] = 0;
+ }
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+
+ OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5;
+ fgcp1[i] = 0.5;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5;
+ fgcp2[i] = 0.5;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define STOREWM 0
+
+#define DPTANNI 50
+
+
+static reccycle = 0;
+
+static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff )
+{
+ int i, j, gc, gb;
+ int len = strlen( seq[0] );
+ float totaleff = 0.0;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ gc = 0;
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += eff[j];
+ }
+ }
+ totaleff+= eff[j];
+ }
+ for( i=0; i<len; i++ )
+ ogcp[i] /= totaleff;
+}
+
+static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff )
+{
+ int i, j, gc, gb;
+ int len = strlen( seq[0] );
+ float totaleff = 0.0;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ gc = ( seq[j][0] == '-' );
+ for( i=1; i<len+1; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc ) fgcp[i-1] += eff[j];
+ }
+ }
+ totaleff += eff[j];
+ }
+ for( i=0; i<len; i++ )
+ fgcp[i] /= totaleff;
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#endif
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ short **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char gap[] = "-";
+ float wm;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi];
+ k++;
+ iin = ifi; jin = jfi;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ }
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float *gapinfo[4] )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float dumfl;
+ int lgth1, lgth2;
+ float *ogcp1 = gapinfo[0];
+ float *fgcp1 = gapinfo[1];
+ float *ogcp2 = gapinfo[2];
+ float *fgcp2 = gapinfo[3];
+ static char **aseq1 = NULL;
+ static char **aseq2 = NULL;
+ static char **aseq1bk, **aseq2bk;
+
+// char ttt1[10000], ttt2[10000];
+
+ if( !aseq1 )
+ {
+ aseq1 = AllocateCharMtx( njob, 0 );
+ aseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+// strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+//
+// fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+// fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+// fprintf( stderr, "ttt1 = %s\n", ttt1 );
+// fprintf( stderr, "ttt2 = %s\n", ttt2 );
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+
+ shortmtx = AllocateShortMtx( ll1+1, ll2+1 );
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + fpenalty * ogcp1[i];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+
+ Atracking( currentw, lastverticalw, seq1, seq2, aseq1, aseq2, cpmx1+ist, cpmx2+jst, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+
+ FreeCharMtx( aseq1bk );
+ FreeCharMtx( aseq2bk );
+
+ return( wm );
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float *gapinfo[4] )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid, jmid;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+// float **WMMTX;
+// float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ float dumfl;
+ int lgth1, lgth2;
+ float maxwm;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj; //muda
+ int jumpi, jumpj;
+ char *gaps;
+ int ijpi, ijpj;
+// float *ogcp1 = gapinfo[0];
+// float *fgcp1 = gapinfo[1];
+// float *ogcp2 = gapinfo[2];
+// float *fgcp2 = gapinfo[3];
+// static char ttt1[50000];
+// static char ttt2[50000];
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+// strncpy( ttt1, seq1[0]+ist, lgth1 );
+// strncpy( ttt2, seq2[0]+jst, lgth2 );
+// ttt1[lgth1] = 0;
+// ttt2[lgth2] = 0;
+// fprintf( stderr, "seq1 = %s\n", ttt1 );
+// fprintf( stderr, "seq2 = %s\n", ttt2 );
+ if( lgth2 <= 0 )
+ {
+ fprintf( stderr, "==== jimei\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( (float)offset * lgth1 );
+ }
+
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI )
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ wm = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+// fprintf( stderr, "freeing aseq\n" );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( wm );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+// initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+// currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+// m[j] = currentw[j-1] + fpenalty * ogcp1[1];
+ m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 / 2;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+// for( i=1; i<lasti; i++ )
+ for( i=1; i<=imid; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+
+// mi = previousw[0] + fpenalty * ogcp2[1];
+ mi = previousw[0];
+ mpi = 0;
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+// *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+// g = *prept + fpenalty * ogcp2[j];
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// g = *mjpt + fpenalty * fgcp1[i-1];
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+// g = *prept + fpenalty * ogcp1[i];
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+// initverticalw[i] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+// currentw[j] += fpenalty * ( fgcp2[lgth1-1] + ogcp2[j+1] );
+ currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += fpenalty;
+ }
+#endif
+
+ for( j=lgth2-1; j>0; --j )
+ {
+// m[j-1] = currentw[j] + fpenalty * fgcp2[lgth2-2];
+ m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+// for( i=lgth1-2; i>=imid; i-- )
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// mi = previousw[lgth2-1] + fpenalty * fgcp2[lgth2-2];
+ mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+// g = mi + fpenalty * ogcp2[j+1];
+ g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ }
+
+// g = *prept + fpenalty + fgcp2[j];
+ g = *prept;
+ if( g > mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+// g = *mjpt + fpenalty * ogcp1[i+1];
+ g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+// g = *prept + fpenalty * fgcp1[i];
+ g = *prept;
+ if( g > *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+ midm[j+1] += *mjpt + fpenalty; //??????
+ }
+ if( i == imid - 1 )
+ {
+ midn[j] += mi + fpenalty; //????
+ }
+#if STOREWM
+ WMMTX[i][j] += wm;
+ WMMTX2[i][j+1] += *mjpt + fpenalty;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 1;
+ for( j=2; j<lgth2; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+ }
+// fprintf( stderr, "imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ {
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ }
+ if( midn[jmid-1] >= wm )
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ }
+#if 0
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+// fprintf( stderr, "imid -> %d\n", imid );
+// fprintf( stderr, "jmid -> %d\n", jmid );
+ break;
+ }
+ }
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if 0
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+
+
+#endif
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+ MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+ }
+#if DEBUG
+ fprintf( stderr, "after gapfill mseq1[0]=%s\n", mseq1[0] );
+ fprintf( stderr, "after gapfill mseq2[0]=%s\n", mseq2[0] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+ MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
+
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ free( gaps );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( wm );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm; /* int ?????? */
+ static char **mseq1 = NULL;
+ static char **mseq2 = NULL;
+ char **mseq;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float *gapinfo[4];
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+ if( mseq1 == NULL )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 26 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 26 );
+
+ for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
+ for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+#if 1
+ OpeningGapCount( ogcp1, icyc, seq1, eff1 );
+ OpeningGapCount( ogcp2, jcyc, seq2, eff2 );
+ FinalGapCount( fgcp1, icyc, seq1, eff1 );
+ FinalGapCount( fgcp2, jcyc, seq2, eff2 );
+
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+ }
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeCharMtx( mseq );
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 1
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+
+#define DPTANNI 100
+
+static void OpeningGapCount( double *ogcp, int clus, char **seq, double *eff )
+{
+ int i, j, gc, gb;
+ int len = strlen( seq[0] );
+ double totaleff = 0.0;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ gc = 0;
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += eff[j];
+ }
+ }
+ totaleff+= eff[j];
+ }
+ for( i=0; i<len; i++ )
+ ogcp[i] /= totaleff;
+}
+
+static void FinalGapCount( double *fgcp, int clus, char **seq, double *eff )
+{
+ int i, j, gc, gb;
+ int len = strlen( seq[0] );
+ double totaleff = 0.0;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ gc = ( seq[j][0] == '-' );
+ for( i=1; i<len+1; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc ) fgcp[i-1] += eff[j];
+ }
+ }
+ totaleff += eff[j];
+ }
+ for( i=0; i<len; i++ )
+ fgcp[i] /= totaleff;
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#endif
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ short **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char gap[] = "-";
+ float wm;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi];
+ k++;
+ iin = ifi; jin = jfi;
+
+ fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ }
+ fprintf( stderr, "in Atracking (owari), mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float **WMMTX;
+ float dumfl;
+ int lgth1, lgth2;
+ static char **aseq1 = NULL;
+ static char **aseq2 = NULL;
+ static char **aseq1bk, **aseq2bk;
+
+ if( !aseq1 )
+ {
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ }
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+ fprintf( stderr, "seq1[0]+ist = %s\n", seq1[0]+ist );
+ fprintf( stderr, "seq2[0]+jst = %s\n", seq2[0]+jst );
+
+ fprintf( stderr, "ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+ fprintf( stderr, "jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ fprintf( stderr, "calling match_calc\n" );
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+ WMMTX[0][j] = currentw[j];
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1];
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ fprintf( stderr, "entering to loop\n" );
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+
+ fprintf( stderr, "i=%d\n", i );
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ fprintf( stderr, "calling match_calc, ist=%d, lgth2=%d\n", ist, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ fprintf( stderr, "done\n" );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ fprintf( stderr, "j=%d\n", j );
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+ WMMTX[i][j] = *curpt;
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ fprintf( stderr, "j=%d end\n", j );
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ fprintf( stderr, "i=%d end\n", i );
+ }
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+ Atracking( currentw, lastverticalw, seq1, seq2, aseq1, aseq2, cpmx1+ist, cpmx2+jst, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+ fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+ fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+ FreeFloatMtx( WMMTX );
+
+ FreeCharMtx( aseq1bk );
+ FreeCharMtx( aseq2bk );
+
+ return( wm );
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2;
+ int lasti, lastj, imid, jmid;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float **WMMTX;
+ float dumfl;
+ int lgth1, lgth2;
+ float maxwm;
+
+ depth++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+ fprintf( stderr, "==== MSalign (%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, ist, ien, jst, jen );
+ if( lgth2 <= 0 )
+ {
+ fprintf( stderr, "==== Jimei\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+ fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+ fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( (float)offset * lgth1 );
+ }
+
+
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+
+ if( lgth1 < DPTANNI )
+ {
+ fprintf( stderr, "==== Going to _tanni\n" );
+ wm = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2 );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+ fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+ fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ fprintf( stderr, "freeing aseq\n" );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( wm );
+ }
+ fprintf( stderr, "Trying to divide the mtx\n" );
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+ WMMTX[0][j] = currentw[j];
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1];
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 / 2;
+
+ lasti = lgth1+1;
+// for( i=1; i<lasti; i++ )
+ for( i=1; i<=imid; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+ WMMTX[i][j] = *curpt;
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ WMMTX[i][lgth2-1] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += fpenalty;
+ WMMTX[lgth1-1][j] += fpenalty;
+ }
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j];
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+ for( i=lgth1-2; i>=imid; i-- )
+// for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+ mi = previousw[lgth2-1];
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ g = mi + fpenalty;
+ if( g > wm ) wm = g;
+
+ g = *prept;
+ if( g >= mi ) mi = g;
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty;
+ if( g > wm ) wm = g;
+
+ g = *prept;
+ if( g >= *mjpt ) *mjpt = g;
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ WMMTX[i][j] += wm;
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+ }
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+ maxwm = -999999999.9;
+ jmid = -100;
+ for( j=0; j<lgth2; j++ )
+ {
+ wm = WMMTX[imid][j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+ }
+ // gap no tochu de kirrareru kanousei ari.
+
+ fprintf( stderr, "wm = %f\n", wm );
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+ FreeFloatMtx( WMMTX );
+
+
+ fprintf( stderr, "==== calling myself (first)\n" );
+ MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+imid, jst, jst+jmid, alloclen, aseq1, aseq2, depth );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+ fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+ fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+
+ fprintf( stderr, "==== calling myself (second)\n" );
+ MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid+1, ien, jst+jmid+1, jen, alloclen, aseq1, aseq2, depth );
+
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+
+ fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+ fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+ fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( wm );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm; /* int ?????? */
+ static char **mseq1 = NULL;
+ static char **mseq2 = NULL;
+ char **mseq;
+ double *ogcp1;
+ double *ogcp2;
+ double *fgcp1;
+ double *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+
+#if 1
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+ if( mseq1 == NULL )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ ogcp1 = AllocateDoubleVec( ll1+2 );
+ ogcp2 = AllocateDoubleVec( ll2+2 );
+ fgcp1 = AllocateDoubleVec( ll1+2 );
+ fgcp2 = AllocateDoubleVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 26 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 26 );
+
+ for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
+ for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
+
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
+
+#if 0
+ OpeningGapCount( ogcp1, icyc, seq1, eff1 );
+ OpeningGapCount( ogcp2, jcyc, seq2, eff2 );
+ FinalGapCount( fgcp1, icyc, seq1, eff1 );
+ FinalGapCount( fgcp2, jcyc, seq2, eff2 );
+
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 1.0 - ogcp1[i];
+ fgcp1[i] = 1.0 - fgcp1[i];
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 1.0 - ogcp2[i];
+ fgcp2[i] = 1.0 - fgcp2[i];
+ }
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0 );
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+ FreeDoubleVec( ogcp1 );
+ FreeDoubleVec( ogcp2 );
+ FreeDoubleVec( fgcp1 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ FreeDoubleVec( fgcp2 );
+
+ FreeCharMtx( mseq );
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define STOREWM 0
+
+#define DPTANNI 10
+
+
+static reccycle = 0;
+
+static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = 0;
+// gc = ( gappat[j] == '-' );
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ }
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "ogcp[%d] = %30.20f\n", i, ogcp[i] );
+// }
+}
+
+static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+// gc = ( seq[j][0] == '-' );
+ gc = 0;
+ for( i=1; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc )
+ {
+ fgcp[i-1] += feff;
+ }
+ }
+ }
+ {
+ gb = gc;
+ gc = 0;
+ {
+// fprintf( stderr, "changed gc=%d, gb=%d\n", gc, gb );
+ if( gb * !gc ) fgcp[i-1] += feff;
+ }
+ }
+// fprintf( stderr, "eff[%d] = %30.20f\n", j, eff[j] );
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "fgcp[%d] = %30.20f\n", i, fgcp[i] );
+// }
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#endif
+}
+
+static float Atracking(
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ short **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char gap[] = "-";
+ float wm;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi];
+ k++;
+ iin = ifi; jin = jfi;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ }
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float dumfl;
+ int lgth1, lgth2;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ char **aseq1;
+ char **aseq2;
+ char **aseq1bk, **aseq2bk;
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+#if STOREWM
+ char ttt1[10000], ttt2[10000];
+#endif
+
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if STOREWM
+ strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+ strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+
+ fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+ fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+ fprintf( stderr, "ttt1 = %s\n", ttt1 );
+ fprintf( stderr, "ttt2 = %s\n", ttt2 );
+#endif
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+
+
+ shortmtx = AllocateShortMtx( ll1+1, ll2+1 );
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + fpenalty * ogcp1[i];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ Atracking( seq1, seq2, aseq1, aseq2, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+
+ FreeCharMtx( aseq1bk );
+ FreeCharMtx( aseq2bk );
+
+ free( aseq1 );
+ free( aseq2 );
+
+ return( wm );
+
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ float value = 0.0;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid, jmid;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+ float **WMMTX;
+ float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ float dumfl;
+ int lgth1, lgth2;
+ float maxwm;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj; //muda
+ int jumpi, jumpj;
+ char *gaps;
+ int ijpi, ijpj;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+#if STOREWM
+ static char ttt1[50000];
+ static char ttt2[50000];
+#endif
+
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+
+#if STOREWM
+ fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+ strncpy( ttt1, seq1[0]+ist, lgth1 );
+ strncpy( ttt2, seq2[0]+jst, lgth2 );
+ ttt1[lgth1] = 0;
+ ttt2[lgth2] = 0;
+ fprintf( stderr, "seq1 = %s\n", ttt1 );
+ fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+ if( lgth2 <= 0 )
+ {
+ fprintf( stderr, "==== jimei\n" );
+// exit( 1 );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( (float)offset * lgth1 );
+ }
+
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI )
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+// fprintf( stderr, "freeing aseq\n" );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+// fprintf( stderr, "value = %f\n", value );
+
+ return( value );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1];
+// m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 * 0.5;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+#if STOREWM
+ for( i=1; i<lasti; i++ )
+#else
+ for( i=1; i<=imid; i++ )
+#endif
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+// mi = previousw[0];
+ mpi = 0;
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+// g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+// g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+ g = *prept + fpenalty * ogcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+ fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+ }
+#endif
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j] + fpenalty * fgcp2[lgth2-2];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+// for( i=lgth1-2; i>=imid; i-- )
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+ mi = previousw[lgth2-1] + fpenalty * fgcp2[lgth2-2];
+// mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+ g = mi + fpenalty * ogcp2[j+1];
+// g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ }
+
+ g = *prept + fpenalty * fgcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + fpenalty * ogcp1[i+1];
+// g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+ g = *prept + fpenalty * fgcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+// midm[j+1] += *mjpt + fpenalty; //??????
+ midm[j+1] += *mjpt; //??????
+ }
+ if( i == imid - 1 )
+ {
+// midn[j] += mi + fpenalty; //????
+ midn[j] += mi; //????
+ }
+#if STOREWM
+ WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ WMMTX2[i][j+1] += *mjpt;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ for( j=2; j<lgth2-1; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=1; j<lgth2; j++ )
+ {
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=2; j<lgth2; j++ )
+ {
+ wm = midn[j-1];
+ if( wm > maxwm )
+ {
+ jmid = j-1;
+ maxwm = wm;
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+
+ if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+#if 0
+ fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ if( midn[jmid-1] > wm )
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ wm = midn[jmid-1];
+ fprintf( stderr, "rejump (n)\n" );
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ wm = midm[jmid];
+ fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+ }
+#endif
+
+ fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+ fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if STOREWM
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+// fprintf( stderr, "maxwm = %f\n", maxwm );
+ }
+
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+ fprintf( stderr, "imid -> %d\n", imid );
+ fprintf( stderr, "jmid -> %d\n", jmid );
+#if STOREWM
+#else
+ break;
+#endif
+ }
+ }
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if STOREWM
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+
+
+#endif
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+ fprintf( stderr, "jumpi = %d\n", jumpi );
+ value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+ fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
+ value += fpenalty * ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
+// value += fpenalty;
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+
+
+ fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
+ value += fpenalty * ( ogcp1[jumpi+1] + fgcp1[imid-1] );
+// value += fpenalty;
+ }
+#if 0
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+ value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
+
+
+
+ if( value - maxwm > 1 || maxwm - value > 1 )
+ {
+ fprintf( stderr, "WARNING value = %f, but maxwm = %f penalty = %f\n", value, maxwm, fpenalty );
+#if 1
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
+ fprintf( stderr, "%s\n", aseq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
+ fprintf( stderr, "%s\n", aseq2[i] );
+ }
+#endif
+
+// exit( 1 );
+ }
+ else
+ {
+ fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
+ }
+
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ free( gaps );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( value );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+ char **mseq;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float **gapinfo;
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 4, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 27 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+
+ for( i=0; i<icyc; i++ )
+ {
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ seq2[j][lgth2] = 0;
+ }
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+
+ OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5;
+ fgcp1[i] = 0.5;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5;
+ fgcp2[i] = 0.5;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MEMSAVE 1
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define STOREWM 0
+
+#define DPTANNI 1000
+
+
+static reccycle = 0;
+
+static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = 0;
+// gc = ( gappat[j] == '-' );
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ }
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "ogcp[%d] = %30.20f\n", i, ogcp[i] );
+// }
+}
+
+static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+// gc = ( seq[j][0] == '-' );
+ gc = 0;
+ for( i=1; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc )
+ {
+ fgcp[i-1] += feff;
+ }
+ }
+ }
+ {
+ gb = gc;
+ gc = 0;
+ {
+// fprintf( stderr, "changed gc=%d, gb=%d\n", gc, gb );
+ if( gb * !gc ) fgcp[i-1] += feff;
+ }
+ }
+// fprintf( stderr, "eff[%d] = %30.20f\n", j, eff[j] );
+ }
+// for( i=0; i<len; i++ )
+// {
+// fprintf( stderr, "fgcp[%d] = %30.20f\n", i, fgcp[i] );
+// }
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#endif
+}
+
+static float Atracking(
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ short **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char gap[] = "-";
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi];
+ k++;
+ iin = ifi; jin = jfi;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ }
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float dumfl;
+ int lgth1, lgth2;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ char **aseq1;
+ char **aseq2;
+ char **aseq1bk, **aseq2bk;
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+#if STOREWM
+ char ttt1[10000], ttt2[10000];
+#endif
+
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if STOREWM
+ strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+ strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+
+ fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+ fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+ fprintf( stderr, "ttt1 = %s\n", ttt1 );
+ fprintf( stderr, "ttt2 = %s\n", ttt2 );
+#endif
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+
+
+ shortmtx = AllocateShortMtx( ll1+1, ll2+1 );
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + fpenalty * ogcp1[i];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ Atracking( seq1, seq2, aseq1, aseq2, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+
+ FreeCharMtx( aseq1bk );
+ FreeCharMtx( aseq2bk );
+
+ free( aseq1 );
+ free( aseq2 );
+
+ return( wm );
+
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int alnlen;
+ float value = 0.0;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid, jmid;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+#if STOREWM
+ float **WMMTX;
+ float **WMMTX2;
+#endif
+ float *midw;
+ float *midm;
+ float *midn;
+ float dumfl;
+ int lgth1, lgth2;
+ float maxwm;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj; //muda
+ int jumpi, jumpj;
+ char *gaps;
+ int ijpi, ijpj;
+ float *ogcp1;
+ float *fgcp1;
+ float *ogcp2;
+ float *fgcp2;
+ float firstm;
+ int firstmp;
+#if STOREWM
+ static char ttt1[50000];
+ static char ttt2[50000];
+#endif
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+
+#if STOREWM
+ fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+ strncpy( ttt1, seq1[0]+ist, lgth1 );
+ strncpy( ttt2, seq2[0]+jst, lgth2 );
+ ttt1[lgth1] = 0;
+ ttt2[lgth2] = 0;
+ fprintf( stderr, "seq1 = %s\n", ttt1 );
+ fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+ if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+ {
+// fprintf( stderr, "\n\n==== jimei\n\n" );
+// exit( 1 );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( 0.0 );
+ }
+
+#if MEMSAVE
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
+#else
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+#endif
+
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI )
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+#if MEMSAVE
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+#endif
+
+// fprintf( stderr, "value = %f\n", value );
+
+ return( value );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1];
+// m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 * 0.5;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+#if STOREWM
+ for( i=1; i<lasti; i++ )
+#else
+ for( i=1; i<=imid; i++ )
+#endif
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ m[0] = fpenalty * ogcp1[i];
+#if STOREM
+ WMMTX2[i][0] = m[0];
+#endif
+ if( i == imid ) midm[0] = m[0];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+// mi = previousw[0];
+ mpi = 0;
+
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+// g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+// g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+ g = *prept + fpenalty * ogcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+// fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+ WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+// initverticalw[i] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+// currentw[j] += fpenalty;
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+ fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+ }
+#endif
+
+
+
+
+
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j] + fpenalty * fgcp2[lgth2-2];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+
+// for( i=lgth1-2; i>=imid; i-- )
+ firstm = -9999999.9;
+ firstmp = lgth1-1;
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// m[lgth2] = fpenalty * fgcp1[i];
+// WMMTX2[i][lgth2] += m[lgth2];
+// fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+ mi = previousw[lgth2-1] + fpenalty * fgcp2[lgth2-2];
+// mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+ g = mi + fpenalty * ogcp2[j+1];
+// g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ ijpi = i+1;
+ }
+
+ g = *prept + fpenalty * fgcp2[j];
+// g = *prept;
+ if( g >= mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + fpenalty * ogcp1[i+1];
+// g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ ijpj = j+1;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+ g = *prept + fpenalty * fgcp1[i];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+// midm[j+1] += *mjpt + fpenalty; //??????
+ midm[j+1] += *mjpt; //??????
+ }
+ if( i == imid - 1 )
+ {
+// midn[j] += mi + fpenalty; //????
+ midn[j] += mi; //????
+ }
+#if STOREWM
+ WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ WMMTX2[i][j+1] += *mjpt;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+// fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+ g = *prept + fpenalty * fgcp1[i];
+ if( firstm < g )
+ {
+ firstm = g;
+ firstmp = i + 1;
+ }
+#if STOREWM
+ WMMTX2[i][j+1] += firstm;
+#endif
+ if( i == imid ) midm[j+1] += firstm;
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 0;
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ for( j=2; j<lgth2-1; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+// fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ if( jmid > 0 && midn[jmid-1] > wm ) //060413
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ wm = midn[jmid-1];
+// fprintf( stderr, "rejump (n)\n" );
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ wm = midm[jmid];
+// fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+ }
+
+
+// fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+// fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if STOREWM
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+// fprintf( stderr, "maxwm = %f\n", maxwm );
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+ if( jmid == 0 )
+ {
+// fprintf( stderr, "CHUI2!\n" );
+ jumpj = 0; jmid = 1;
+ jumpi = firstmp - 1;
+ imid = firstmp;
+ }
+
+#if 0
+ else if( jmid == lgth2 )
+ {
+ fprintf( stderr, "CHUI1!\n" );
+ jumpi=0; jumpj=0;
+ imid=jumpforwi[0]; jmid=lgth2-1;
+ }
+#else // 060414
+ else if( jmid >= lgth2 )
+ {
+ fprintf( stderr, "CHUI1!\n" );
+ jumpi=imid-1; jmid=lgth2;
+ jumpj = lgth2-1;
+ }
+#endif
+ else
+ {
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+ }
+#if 0
+ fprintf( stderr, "jumpi -> %d\n", jumpi );
+ fprintf( stderr, "jumpj -> %d\n", jumpj );
+ fprintf( stderr, "imid -> %d\n", imid );
+ fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+
+#if STOREWM
+ break;
+#else
+ break;
+#endif
+ }
+ }
+#if 0
+ jumpi=0; jumpj=0;
+ imid=lgth1-1; jmid=lgth2-1;
+ }
+#endif
+
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if STOREWM
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+
+
+#endif
+
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+// fprintf( stderr, "jumpi = %d\n", jumpi );
+ value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
+#if MEMSAVE
+ alnlen = strlen( aseq1[0] );
+ for( i=0; i<icyc; i++ ) aseq1[i] += alnlen;
+ for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen;
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+#endif
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+// fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
+ value += fpenalty * ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
+// value += fpenalty;
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+
+
+// fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
+ value += fpenalty * ( ogcp1[jumpi+1] + fgcp1[imid-1] );
+// value += fpenalty;
+ }
+#if 0
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+
+ value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
+
+
+
+#if DEBUG
+ if( value - maxwm > 1 || maxwm - value > 1 )
+ {
+ fprintf( stderr, "WARNING value = %f, but maxwm = %f penalty = %f\n", value, maxwm, fpenalty );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
+ fprintf( stderr, "%s\n", aseq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
+ fprintf( stderr, "%s\n", aseq2[i] );
+ }
+
+// exit( 1 );
+ }
+ else
+ {
+ fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
+ }
+#endif
+
+#if MEMSAVE
+#else
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+#endif
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ free( gaps );
+#if MEMSAVE
+#else
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+#endif
+
+ return( value );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm = 0.0; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+ char **mseq;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float **gapinfo;
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 4, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 27 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+
+ for( i=0; i<icyc; i++ )
+ {
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ seq2[j][lgth2] = 0;
+ }
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+
+ OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5;
+ fgcp1[i] = 0.5;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5;
+ fgcp2[i] = 0.5;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+
+#define DPTANNI 1000
+
+
+static reccycle = 0;
+
+static void OpeningGapCount( float *ogcp, int clus, char **seq, double *eff )
+{
+ int i, j, gc, gb;
+ int len = strlen( seq[0] );
+ float totaleff = 0.0;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ gc = 0;
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += eff[j];
+ }
+ }
+ totaleff+= eff[j];
+ }
+ for( i=0; i<len; i++ )
+ ogcp[i] /= totaleff;
+}
+
+static void FinalGapCount( float *fgcp, int clus, char **seq, double *eff )
+{
+ int i, j, gc, gb;
+ int len = strlen( seq[0] );
+ float totaleff = 0.0;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ gc = ( seq[j][0] == '-' );
+ for( i=1; i<len+1; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc ) fgcp[i-1] += eff[j];
+ }
+ }
+ totaleff += eff[j];
+ }
+ for( i=0; i<len; i++ )
+ fgcp[i] /= totaleff;
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ {
+ scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#endif
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ short **ijp, int icyc, int jcyc,
+ int ist, int ien, int jst, int jen )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+ char gap[] = "-";
+ float wm;
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+
+// fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+ iin = lgth1; jin = lgth2;
+ klim = lgth1+lgth2;
+ for( k=0; k<=klim; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ist+ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jst+jfi];
+ k++;
+ iin = ifi; jin = jfi;
+
+// if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+ }
+// fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+ return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float *gapinfo[4] )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int ll1, ll2;
+ int lasti, lastj;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+#if 1
+ float *wtmp;
+ short *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ float mi, *m;
+ short **ijp;
+ int mpi, *mp;
+ float *w1, *w2;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+ short **shortmtx;
+ float dumfl;
+ int lgth1, lgth2;
+ float *ogcp1 = gapinfo[0];
+ float *fgcp1 = gapinfo[1];
+ float *ogcp2 = gapinfo[2];
+ float *fgcp2 = gapinfo[3];
+ static char **aseq1 = NULL;
+ static char **aseq2 = NULL;
+ static char **aseq1bk, **aseq2bk;
+
+// char ttt1[10000], ttt2[10000];
+
+ if( !aseq1 )
+ {
+ aseq1 = AllocateCharMtx( njob, 0 );
+ aseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+// strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+
+// fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+// fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+// fprintf( stderr, "ttt1 = %s\n", ttt1 );
+// fprintf( stderr, "ttt2 = %s\n", ttt2 );
+
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+
+ shortmtx = AllocateShortMtx( ll1+1, ll2+1 );
+
+ ijp = shortmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + fpenalty * ogcp1[1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + fpenalty * ogcp2[1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty * fgcp2[j-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + fpenalty * ogcp2[j];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty * fgcp1[i-1];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + fpenalty * ogcp1[i];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+
+ Atracking( currentw, lastverticalw, seq1, seq2, aseq1, aseq2, cpmx1+ist, cpmx2+jst, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ FreeShortMtx( shortmtx );
+
+ FreeCharMtx( aseq1bk );
+ FreeCharMtx( aseq2bk );
+
+ return( wm );
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float *gapinfo[4] )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid, jmid;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_ex = (float)penalty_ex;
+ float *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ float *mjpt, *prept, *curpt;
+ float mi;
+ float *m;
+ float *w1, *w2;
+// float *match;
+ float *initverticalw; /* kufuu sureba iranai */
+ float *lastverticalw; /* kufuu sureba iranai */
+ int **intwork;
+ float **floatwork;
+// short **shortmtx;
+// float **WMMTX;
+// float **WMMTX2;
+ float *midw;
+ float *midm;
+ float dumfl;
+ int lgth1, lgth2;
+ float maxwm;
+ int *jumpforw;
+ int *jumpback;
+ int *jumpdumm; //muda
+ int *jumppt;
+ int jumpi;
+ int jumpj;
+ char *gaps;
+// static char ttt1[50000];
+// static char ttt2[50000];
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+// strncpy( ttt1, seq1[0]+ist, lgth1 );
+// strncpy( ttt2, seq2[0]+jst, lgth2 );
+// fprintf( stderr, "seq1 = %s\n", ttt1 );
+// fprintf( stderr, "seq2 = %s\n", ttt2 );
+ if( lgth2 <= 0 )
+ {
+// fprintf( stderr, "==== jimei\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+ strcat( mseq2[i], "-" );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( (float)offset * lgth1 );
+ }
+
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+
+ if( lgth1 < DPTANNI )
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ wm = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+// fprintf( stderr, "freeing aseq\n" );
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( wm );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpback = AllocateIntVec( ll2+2 );
+ jumpforw = AllocateIntVec( ll2+2 );
+ jumpdumm = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+#if 0
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+// WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+// WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+// WMMTX[0][j] = currentw[j];
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1];
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 / 2;
+
+ lasti = lgth1+1;
+// for( i=1; i<lasti; i++ )
+ for( i=1; i<=imid; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+
+ mi = previousw[0];
+ mpi = 0;
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ if( i == imid ) jumppt = jumpback+1;
+ else jumppt = jumpdumm+1;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *jumppt = 0; // muda atode saishukai dake matomeru
+// *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *jumppt = +mpi; // muda atode matomeru
+// *ijppt = -( j - mpi );
+ }
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt (f)= %d\n", i, j, *mpjpt );
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ *jumppt = -*mpjpt; // muda atode matomeru
+ }
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+// WMMTX[i][j] = *curpt;
+// WMMTX2[i][j] = *mjpt;
+
+ if( i == imid ) //muda
+ {
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ }
+
+// ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ jumppt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+ match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+// WMMTX[i][lgth2-1] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += fpenalty;
+// WMMTX[lgth1-1][j] += fpenalty;
+ }
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+ for( i=lgth1-2; i>=imid; i-- )
+// for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+// match_calc( currentw, seq1, seq2, i, lgth2 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+ currentw[lgth2-1] = initverticalw[i];
+
+ mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+ if( i == imid ) jumppt = jumpforw + lgth2 - 2;
+ else jumppt = jumpdumm + lgth2 - 2;
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ *jumppt = 0; //muda
+
+ g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ *jumppt = +mpi; //muda
+ }
+
+ g = *prept;
+ if( g > mi )
+ {
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ *jumppt = -*mpjpt; //muda
+ }
+
+ g = *prept;
+ if( g > *mjpt )
+ {
+// fprintf( stderr, "mjpt: %f->%f (%d,%d)\n", *mjpt, g, i, j );
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+ midm[j+1] += *mjpt + fpenalty;
+ }
+// WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+// mpjpt--;
+ curpt--;
+ jumppt--;
+ }
+ }
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+#if 0
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpback = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpback[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10d ", jumpforw[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+#endif
+
+
+ maxwm = -999999999.9;
+ jmid = -100;
+ for( j=0; j<lgth2; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+ }
+#if 0
+ fprintf( stderr, "jmid=%d, maxwm = %f\n", jmid, maxwm );
+ fprintf( stderr, "jumpforw[%d] = %d\n", jmid, jumpforw[jmid] );
+ fprintf( stderr, "jumpback[%d] = %d\n", jmid, jumpback[jmid] );
+
+ if( jumpback[jmid] == 0 )
+ {
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ }
+ else if( jumpback[jmid] < 0 )
+ {
+ jumpi = - jumpback[jmid];
+ jumpj = jmid-1;
+ }
+ else
+ {
+ jumpi = imid-1;
+ jumpj = jumpback[jmid];
+ }
+
+ if( jumpforw[jmid] == 0 )
+ {
+ ;
+ }
+ else if( jumpforw[jmid] < 0 )
+ {
+ imid = - jumpforw[jmid];
+ fprintf( stderr, "XXXX imid = %d", imid );
+ }
+ else
+ {
+ fprintf( stderr, "OXOXO" );
+ jmid = jumpforw[jmid];
+ }
+#else
+ jumpi = imid-1;
+ jumpj = jmid-1;
+#endif
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+// FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+
+ FreeIntVec( jumpback );
+ FreeIntVec( jumpforw );
+ FreeIntVec( jumpdumm );
+ free( gaps );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+// FreeShortMtx( shortmtx );
+// FreeFloatMtx( WMMTX );
+// FreeFloatMtx( WMMTX2 );
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+ MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+#if 1
+ if( l > 0 )
+ {
+ fprintf( stderr, "l=%d\n", l );
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+ }
+ l = imid - jumpi - 1;
+ if( l > 0 )
+ {
+ fprintf( stderr, "l=%d\n", l );
+ for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+ }
+#endif
+// fprintf( stderr, "after gapfill mseq1[0]=%s\n", mseq1[0] );
+// fprintf( stderr, "after gapfill mseq2[0]=%s\n", mseq2[0] );
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+ MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );
+
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+
+ return( wm );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int i, j;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ float wm; /* int ?????? */
+ static char **mseq1 = NULL;
+ static char **mseq2 = NULL;
+ char **mseq;
+ float *ogcp1;
+ float *ogcp2;
+ float *fgcp1;
+ float *fgcp2;
+ float **cpmx1;
+ float **cpmx2;
+ float *gapinfo[4];
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+ if( mseq1 == NULL )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(1.3*lgth1) ) + 100;
+ ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( ll1+2, 26 );
+ cpmx2 = AllocateFloatMtx( ll2+2, 26 );
+
+ for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
+ for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
+
+ MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+#if 1
+ OpeningGapCount( ogcp1, icyc, seq1, eff1 );
+ OpeningGapCount( ogcp2, jcyc, seq2, eff2 );
+ FinalGapCount( fgcp1, icyc, seq1, eff1 );
+ FinalGapCount( fgcp2, jcyc, seq2, eff2 );
+
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+ }
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeCharMtx( mseq );
+
+ return( wm );
+}
--- /dev/null
+PREFIX = /usr/local
+LIBDIR = $(PREFIX)/libexec/mafft
+BINDIR = $(PREFIX)/bin
+MANDIR = $(PREFIX)/share/man/man1
+
+#MNO_CYGWIN = -mno-cygwin
+
+#ENABLE_MULTITHREAD = -Denablemultithread
+#Uncomment this to enable multithreading (linux only)
+
+CC = gcc
+CFLAGS = -O3
+#CFLAGS = -O0 -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3
+
+MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS)
+
+ifeq ($(ENABLE_MULTITHREAD),-Denablemultithread)
+LIBS = -lm -lpthread
+else
+LIBS = -lm
+endif
+
+INSTALL = install
+
+PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
+ pair2hat3s multi2hat3s rnatest pairash \
+ splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \
+ seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu
+SCRIPTS = mafft mafft-homologs.rb
+OBJREPLACEU = mtxutl.o io.o replaceu.o defs.o mltaln9.o
+OBJRESTOREU = mtxutl.o io.o restoreu.o defs.o mltaln9.o
+OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.o
+OBJSEQ2REGTABLE = mtxutl.o io.o seq2regtable.o defs.o
+OBJCOUNTLEN = mtxutl.o io.o countlen.o defs.o
+OBJF2CL = mtxutl.o io.o f2cl.o constants.o defs.o
+OBJMCCASKILLWRAP = mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o
+OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o
+OBJMULTI2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
+ multi2hat3s.o defs.o fft.o fftFunctions.o
+OBJPAIR2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
+ pair2hat3s.o defs.o fft.o fftFunctions.o
+OBJRNATEST = mtxutl.o io.o mltaln9.o tddis.o constants.o Lalignmm.o \
+ rna.o rnatest.o defs.o fft.o fftFunctions.o
+OBJPAIRASH = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
+ pairash.o defs.o fft.o fftFunctions.o
+OBJPAIRLOCALALIGN = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o \
+ pairlocalalign.o defs.o fft.o fftFunctions.o
+OBJDUMMY = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+ disttbfast_dummy.o dummy.o defs.o fft.o fftFunctions.o
+OBJSPLITFROMALN = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+ Lalign11.o splitfromaln.o defs.o fft.o fftFunctions.o
+OBJSPLITTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+ Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o
+OBJSPLITTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+ Lalign11.o splittbfast2.o defs.o fft.o fftFunctions.o
+OBJSPLITTBFASTP = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+ Lalign11.o defs.o fft.o fftFunctions.o
+OBJDISTTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+ disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o
+OBJTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
+ tbfast.o defs.o fft.o fftFunctions.o addfunctions.o
+OBJTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o MSalignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
+ tbfast2.o defs.o fft.o fftFunctions.o
+OBJSETCORE = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+ setcore.o defs.o fft.o fftFunctions.o
+OBJTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o fftFunctions.o fft.o \
+ tditeration.o tditr.o defs.o SAalignmm.o treeOperation.o
+OBJDVTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o \
+ tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o
+OBJGETLAG = mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+ getlag.o defs.o fft.o fftFunctions.o
+OBJGAPFILL = mtxutl.o io.o constants.o gapfill.o defs.o
+OBJDNDFAST5 = dndfast5.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
+OBJDNDBLAST = dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
+OBJDNDFAST7 = dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
+OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
+OBJDNDFAST4 = dndfast4.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
+OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
+OBJSEXTET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o
+OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o
+OBJTRIPLET6 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet6.o defs.o
+OBJTRIPLET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet5.o defs.o
+OBJOCTET4 = io.o constants.o mtxutl.o mltaln9.o tddis.o octet4.o defs.o
+OBJDNDPRE = dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o
+OBJDNDPRESCORE = dndpre2.o io.o constants.o mtxutl.o mltaln9.o defs.o
+OBJGALN = io.o mtxutl.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o \
+ SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o
+OBJSCORE = io.o mtxutl.o mltaln9.o score.o constants.o defs.o
+
+HEADER = mltaln.h mtxutl.h
+FFTHEADER = fft.h
+
+MANPAGES = mafft.1 mafft-homologs.1
+
+
+
+all : $(PROGS) $(SCRIPTS)
+ cp $(SCRIPTS) ../scripts
+ chmod 755 ../scripts/*
+ cp $(PROGS) ../binaries
+ chmod 755 ../binaries/*
+ cp $(MANPAGES) ../binaries
+ @echo done.
+
+univscript: univscript.tmpl Makefile
+ sed "s:_PROGS:$(PROGS):" univscript.tmpl > univscript
+
+mafft: mafft.tmpl
+ sed "s:_LIBDIR:$(LIBDIR):" mafft.tmpl > mafft
+
+mafft-homologs.rb: mafft-homologs.tmpl
+# cp mafft-homologs.tmpl mafft-homologs.rb
+ sed "s:_BINDIR:$(BINDIR):" mafft-homologs.tmpl > mafft-homologs.rb
+
+mltaln.h : functions.h
+ touch mltaln.h
+
+tbfast : $(OBJTBFAST)
+ $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS)
+
+tbfast2 : $(OBJTBFAST2)
+ $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS)
+
+disttbfast : $(OBJDISTTBFAST)
+ $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS)
+
+splittbfast : $(OBJSPLITTBFAST)
+ $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS)
+
+splitfromaln : $(OBJSPLITFROMALN)
+ $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS)
+
+splittbfast2 : $(OBJSPLITTBFAST2)
+ $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS)
+
+dummy : $(OBJDUMMY)
+ $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS)
+
+setcore : $(OBJSETCORE)
+ $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS)
+
+countlen : $(OBJCOUNTLEN)
+ $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS)
+
+seq2regtable : $(OBJSEQ2REGTABLE)
+ $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS)
+
+regtable2seq : $(OBJREGTABLE2SEQ)
+ $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS)
+
+replaceu : $(OBJREPLACEU)
+ $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS)
+
+restoreu : $(OBJRESTOREU)
+ $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS)
+
+f2cl : $(OBJF2CL)
+ $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS)
+
+mccaskillwrap : $(OBJMCCASKILLWRAP)
+ $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS)
+
+contrafoldwrap : $(OBJCONTRAFOLDWRAP)
+ $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS)
+
+pairlocalalign : $(OBJPAIRLOCALALIGN)
+ $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS)
+
+pairash : $(OBJPAIRASH)
+ $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS)
+
+rnatest : $(OBJRNATEST)
+ $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS)
+
+pair2hat3s : $(OBJPAIR2HAT3S)
+ $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS)
+
+multi2hat3s : $(OBJMULTI2HAT3S)
+ $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS)
+
+getlag : $(OBJGETLAG)
+ $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS)
+
+tditr : $(OBJTDITR)
+ $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS)
+
+dvtditr : $(OBJDVTDITR)
+ $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS)
+
+mafft-profile : $(OBJGALN)
+ $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS)
+
+gapfill : $(OBJGAPFILL)
+ $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS)
+
+dndfast4 : $(OBJDNDFAST4)
+ $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS)
+
+dndfast5 : $(OBJDNDFAST5)
+ $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS)
+
+dndfast6 : $(OBJDNDFAST6)
+ $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS)
+
+dndfast7 : $(OBJDNDFAST7)
+ $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS)
+
+dndblast : $(OBJDNDBLAST)
+ $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS)
+
+dndfast3 : $(OBJDNDFAST3)
+ $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS)
+
+triplet : $(OBJTRIPLET)
+ $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS)
+
+triplet3 : $(OBJTRIPLET3)
+ $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS)
+
+sextet3 : $(OBJSEXTET3)
+ $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS)
+
+sextet4 : $(OBJSEXTET4)
+ $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS)
+
+sextet5 : $(OBJSEXTET5)
+ $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS)
+
+mafft-distance : $(OBJDISTANCE)
+ $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS)
+
+triplet5 : $(OBJTRIPLET5)
+ $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS)
+
+triplet6 : $(OBJTRIPLET6)
+ $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS)
+
+octet4 : $(OBJOCTET4)
+ $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS)
+
+dndpre : $(OBJDNDPRE)
+ $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS)
+
+dndpre2 : $(OBJDNDPRESCORE)
+ $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS)
+
+score : $(OBJSCORE)
+ $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS)
+
+genMtx : $(OBJGENMTX)
+ $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS)
+
+gapfill.o : gapfill.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c gapfill.c
+
+mltaln9.o : mltaln9.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c mltaln9.c
+
+tddis.o : tddis.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c tddis.c
+
+constants.o : constants.c miyata.h miyata5.h blosum.c DNA.h JTT.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c constants.c
+
+defs.o : defs.c
+ $(CC) $(MYCFLAGS) -c defs.c
+
+#A+++alignmm.o : SA+++alignmm.c $(HEADER)
+# $(CC) $(MYCFLAGS) -c SA+++alignmm.c -o A+++alignmm.o
+
+Salignmm.o : Salignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c Salignmm.c
+
+Halignmm.o : Halignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c Halignmm.c
+
+Ralignmm.o : Ralignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c Ralignmm.c
+
+Qalignmm.o : Qalignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c Qalignmm.c
+
+MSalignmm.o : MSalignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c MSalignmm.c
+
+partSalignmm.o : partSalignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c partSalignmm.c
+
+partQalignmm.o : partQalignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c partQalignmm.c
+
+Lalign11.o : Lalign11.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c Lalign11.c
+
+genalign11.o : genalign11.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c genalign11.c
+
+genGalign11.o : genGalign11.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c genGalign11.c
+
+suboptalign11.o : suboptalign11.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c suboptalign11.c
+
+Galign11.o : Galign11.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c Galign11.c
+
+MSalign11.o : MSalign11.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c MSalign11.c
+
+SAalignmm.o : SAalignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c SAalignmm.c -o SAalignmm.o
+
+Lalignmm.o : Lalignmm.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c Lalignmm.c
+
+rna.o : rna.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c rna.c
+
+disttbfast.o : disttbfast.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c disttbfast.c
+
+splitfromaln.o : splitfromaln.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c splitfromaln.c
+
+splittbfast.o : splittbfast.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c splittbfast.c
+
+splittbfast2.o : splittbfast2.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c splittbfast2.c
+
+disttbfast_dummy.o : disttbfast_dummy.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c disttbfast_dummy.c
+
+dummy.o : dummy.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c dummy.c
+
+tbfast.o : tbfast.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c tbfast.c
+
+tbfast2.o : tbfast2.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c tbfast2.c
+
+setcore.o : setcore.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c setcore.c
+
+getlag.o : getlag.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c getlag.c
+
+tditr.o : tditr.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c tditr.c
+
+dvtditr.o : dvtditr.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c dvtditr.c
+
+tditeration.o : tditeration.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c tditeration.c
+
+mafft-profile.o : mafft-profile.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c mafft-profile.c
+
+dndfast4.o : dndfast4.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c dndfast4.c
+
+dndfast5.o : dndfast5.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c dndfast5.c
+
+dndfast6.o : dndfast6.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c dndfast6.c
+
+dndfast7.o : dndfast7.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c dndfast7.c
+
+dndblast.o : dndblast.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c dndblast.c
+
+dndfast3.o : dndfast3.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c dndfast3.c
+
+dndpre.o : dndpre.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c dndpre.c
+
+countlen.o : countlen.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c countlen.c
+
+seq2regtable.o : seq2regtable.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c seq2regtable.c
+
+regtable2seq.o : regtable2seq.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c regtable2seq.c
+
+f2cl.o : f2cl.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c f2cl.c
+
+replaceu.o : replaceu.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c replaceu.c
+
+restoreu.o : restoreu.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c restoreu.c
+
+mccaskillwrap.o : mccaskillwrap.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c mccaskillwrap.c
+
+contrafoldwrap.o : contrafoldwrap.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c contrafoldwrap.c
+
+pairlocalalign.o : pairlocalalign.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c pairlocalalign.c
+
+pairash.o : pairash.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c pairash.c
+
+rnatest.o : rnatest.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c rnatest.c
+
+multi2hat3s.o : multi2hat3s.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c multi2hat3s.c
+
+pair2hat3s.o : pair2hat3s.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c pair2hat3s.c
+
+dndpre2.o : dndpre2.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c dndpre2.c
+
+io.o : io.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c io.c
+
+nj.o : nj.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c nj.c
+
+treeOperation.o : treeOperation.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c treeOperation.c
+
+sextet5.o : sextet5.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c sextet5.c
+
+mafft-distance.o : mafft-distance.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c mafft-distance.c
+
+triplet5.o : triplet5.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c triplet5.c
+
+triplet6.o : triplet6.c $(HEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c triplet6.c
+
+fft.o : fft.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c fft.c
+
+fftFunctions.o : fftFunctions.c $(HEADER) $(FFTHEADER)
+ $(CC) $(MYCFLAGS) -c fftFunctions.c
+
+Falign.o : Falign.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c Falign.c
+
+Falign_localhom.o : Falign_localhom.c $(HEADER) $(FFTHEADER) $(MTXHEADER)
+ $(CC) $(MYCFLAGS) -c Falign_localhom.c
+
+mtxutl.o : mtxutl.c
+ $(CC) $(MYCFLAGS) -c mtxutl.c
+
+addfunctions.o : addfunctions.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c addfunctions.c
+
+score.o : score.c $(HEADER)
+ $(CC) $(MYCFLAGS) -c score.c
+
+clean :
+ rm -f *.o *.a *.exe *~ $(PROGS) $(SCRIPTS)
+# rm -f ../binaries/* ../scripts/*
+
+install : all
+ mkdir -p $(LIBDIR)
+ chmod 755 $(LIBDIR)
+ mkdir -p $(BINDIR)
+ chmod 755 $(BINDIR)
+ chmod 755 $(SCRIPTS)
+ $(INSTALL) $(SCRIPTS) $(BINDIR)
+ chmod 755 $(PROGS)
+ $(INSTALL) $(PROGS) $(LIBDIR)
+ $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR)
+
+ ( cd $(BINDIR); \
+rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
+rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \
+ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
+ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
+ln -s mafft einsi; \
+ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
+ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
+ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
+rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \
+rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . )
+
+ mkdir -p $(MANDIR)
+ chmod 755 $(MANDIR)
+ $(INSTALL) -m 644 $(MANPAGES) $(MANDIR)
+# remove incorrectly installed manpages by previous versions
+# rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 1
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define FASTMATCHCALC 1
+
+
+
+static TLS float **impmtx = NULL;
+static TLS int impalloclen = 0;
+#if 1 // tditeration to naiveQscore_imp de tsukawareru.
+float imp_match_out_scQ( int i1, int j1 )
+{
+// fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
+// fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
+ return( impmtx[i1][j1] );
+}
+#endif
+
+static void imp_match_out_veadQ_gapmap( float *imp, int i1, int lgth2, int *gapmap2 )
+{
+#if FASTMATCHCALC
+ float *pt = impmtx[i1];
+ int *gapmappt = gapmap2;
+ while( lgth2-- )
+ *imp++ += pt[*gapmappt++];
+#else
+ int j;
+ float *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[gapmap2[j]];
+#endif
+}
+
+
+static void imp_match_out_vead_tateQ_gapmap( float *imp, int j1, int lgth1, int *gapmap1 )
+{
+#if FASTMATCHCALC
+ int *gapmappt = gapmap1;
+ while( lgth1-- )
+ *imp++ += impmtx[*gapmappt++][j1];
+#else
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[gapmap1[i]][j1];
+#endif
+}
+
+
+static void imp_match_out_veadQ( float *imp, int i1, int lgth2 )
+{
+#if FASTMATCHCALC
+ float *pt = impmtx[i1];
+ while( lgth2-- )
+ *imp++ += *pt++;
+#else
+ int j;
+ float *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[j];
+#endif
+}
+static void imp_match_out_vead_tateQ( float *imp, int j1, int lgth1 )
+{
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[i][j1];
+}
+
+void imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *additionalpair )
+{
+ foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, additionalpair );
+}
+
+#if 1 // tbfast.c kara yobareru.
+void imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
+{
+ int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ float effij;
+ double effijx;
+ char *pt, *pt1, *pt2;
+ static TLS char *nocount1 = NULL;
+ static TLS char *nocount2 = NULL;
+ LocalHom *tmpptr;
+
+ if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ if( nocount1 ) free( nocount1 );
+ if( nocount2 ) free( nocount2 );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+ nocount1 = AllocateCharVec( impalloclen );
+ nocount2 = AllocateCharVec( impalloclen );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<clus1; j++ )
+ if( seq1[j][i] == '-' ) break;
+ if( j != clus1 ) nocount1[i] = 1;
+ else nocount1[i] = 0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ if( seq2[j][i] == '-' ) break;
+ if( j != clus2 ) nocount2[i] = 1;
+ else nocount2[i] = 0;
+ }
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+ fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "eff1 in _init_strict = \n" );
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "eff1[] = %f\n", eff1[i] );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "eff2[] = %f\n", eff2[i] );
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ effijx = fastathreshold;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ effij = (float)( eff1[i] * eff2[j] * effijx );
+ tmpptr = localhom[i][j];
+ while( tmpptr )
+ {
+// fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
+// fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
+// fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
+// fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start1 ) break;
+ }
+ start1 = pt - seq1[i] - 1;
+
+ if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( tmpint == tmpptr->end1 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end1 = pt - seq1[i] - 0;
+#else
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end1 ) break;
+ }
+ end1 = pt - seq1[i] - 1;
+#endif
+ }
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start2 ) break;
+ }
+ start2 = pt - seq2[j] - 1;
+ if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end2 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end2 = pt - seq2[j] - 0;
+#else
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end2 ) break;
+ }
+ end2 = pt - seq2[j] - 1;
+#endif
+ }
+// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
+// fprintf( stderr, "step 0\n" );
+ if( end1 - start1 != end2 - start2 )
+ {
+// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ }
+
+#if 1
+ k1 = start1; k2 = start2;
+ pt1 = seq1[i] + k1;
+ pt2 = seq2[j] + k2;
+ while( *pt1 && *pt2 )
+ {
+ if( *pt1 != '-' && *pt2 != '-' )
+ {
+// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
+// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
+// impmtx[k1][k2] += tmpptr->importance * effij;
+ impmtx[k1][k2] += tmpptr->fimportance * effij;
+// fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
+// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+// fprintf( stderr, "%d (%c) - %d (%c) - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
+ k1++; k2++;
+ pt1++; pt2++;
+ }
+ else if( *pt1 != '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k2++; pt2++;
+ }
+ else if( *pt1 == '-' && *pt2 != '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ }
+ else if( *pt1 == '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ k2++; pt2++;
+ }
+ if( k1 > end1 || k2 > end2 ) break;
+ }
+#else
+ while( k1 <= end1 && k2 <= end2 )
+ {
+ fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
+ if( !nocount1[k1] && !nocount2[k2] )
+ {
+ impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j] * fastathreshold;
+ fprintf( stderr, "marked\n" );
+ }
+ else
+ fprintf( stderr, "no count\n" );
+ k1++; k2++;
+ }
+#endif
+ tmpptr = tmpptr->next;
+ }
+ }
+ }
+#if 0
+ if( clus1 == 1 && clus2 == 6 )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d ", k1 );
+ for( k2=0; k2<3; k2++ )
+ fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+ }
+#endif
+}
+#endif
+
+
+static void clearvec( float *match, int lgth )
+{
+ while( lgth-- ) *match++ = 0.0;
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+ int j, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<26; j++ )
+ scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+// scarr[l] *= consweight_multi;
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+#else
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+// simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+// scarr[l] *= consweight_multi;
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+
+static void Atracking_localhom_gapmap( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc,
+ int *gapmap1, int *gapmap2 )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+// char gap[] = "-";
+ char *gap;
+ float wm;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi+l];
+ k++;
+ }
+ if( iin != lgth1 && jin != lgth2 ) // ??
+ {
+ *impwmpt += imp_match_out_scQ( gapmap1[iin], gapmap2[jin] );
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+}
+
+#if 0
+static void Atracking_localhom_gapmap_bk( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc,
+ int *gapmap1, int *gapmap2 )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin == lgth1 || jin == lgth2 )
+ ;
+ else
+ {
+ *impwmpt += imp_match_out_scQ( gapmap1[iin], gapmap2[jin] );
+
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = '-';
+ *--gaptable2 = '-';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
+ fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+
+
+ free( gt1bk );
+ free( gt2bk );
+}
+
+#endif
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin == lgth1 || jin == lgth2 )
+ ;
+ else
+ {
+ *impwmpt += imp_match_out_scQ( iin, jin );
+
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+}
+
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+
+ return( 0.0 );
+}
+
+float Q__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+// float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+ fprintf( stderr, "fpenalty_ex = %f\n", fpenalty_ex );
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *digf1;
+ static TLS float *digf2;
+ static TLS float *diaf1;
+ static TLS float *diaf2;
+ static TLS float *gapz1;
+ static TLS float *gapz2;
+ static TLS float *gapf1;
+ static TLS float *gapf2;
+ static TLS float *ogcp1g;
+ static TLS float *ogcp2g;
+ static TLS float *fgcp1g;
+ static TLS float *fgcp2g;
+ static TLS float *og_h_dg_n1_p;
+ static TLS float *og_h_dg_n2_p;
+ static TLS float *fg_h_dg_n1_p;
+ static TLS float *fg_h_dg_n2_p;
+ static TLS float *og_t_fg_h_dg_n1_p;
+ static TLS float *og_t_fg_h_dg_n2_p;
+ static TLS float *fg_t_og_h_dg_n1_p;
+ static TLS float *fg_t_og_h_dg_n2_p;
+ static TLS float *gapz_n1;
+ static TLS float *gapz_n2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float tmppenal;
+ float *fg_t_og_h_dg_n2_p_pt;
+ float *og_t_fg_h_dg_n2_p_pt;
+ float *og_h_dg_n2_p_pt;
+ float *fg_h_dg_n2_p_pt;
+ float *gapz_n2_pt0;
+ float *gapz_n2_pt1;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fg_t_og_h_dg_n1_p_va;
+ float og_t_fg_h_dg_n1_p_va;
+ float og_h_dg_n1_p_va;
+ float fg_h_dg_n1_p_va;
+ float gapz_n1_va0;
+ float gapz_n1_va1;
+ float fgcp1va;
+ float ogcp1va;
+ float kyokaipenal;
+#if 1
+ float fpenalty = (float)penalty;
+#else
+ float fpenalty;
+ if( RNAscoremtx != 'r' ) fpenalty = (float)penalty;
+ else fpenalty = (float)penalty * 10;
+#endif
+
+#if 0
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+#endif
+
+
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( digf1 );
+ FreeFloatVec( digf2 );
+ FreeFloatVec( diaf1 );
+ FreeFloatVec( diaf2 );
+ FreeFloatVec( gapz1 );
+ FreeFloatVec( gapz2 );
+ FreeFloatVec( gapf1 );
+ FreeFloatVec( gapf2 );
+ FreeFloatVec( ogcp1g );
+ FreeFloatVec( ogcp2g );
+ FreeFloatVec( fgcp1g );
+ FreeFloatVec( fgcp2g );
+ FreeFloatVec( og_h_dg_n1_p );
+ FreeFloatVec( og_h_dg_n2_p );
+ FreeFloatVec( fg_h_dg_n1_p );
+ FreeFloatVec( fg_h_dg_n2_p );
+ FreeFloatVec( og_t_fg_h_dg_n1_p );
+ FreeFloatVec( og_t_fg_h_dg_n2_p );
+ FreeFloatVec( fg_t_og_h_dg_n1_p );
+ FreeFloatVec( fg_t_og_h_dg_n2_p );
+ FreeFloatVec( gapz_n1 );
+ FreeFloatVec( gapz_n2 );
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ digf1 = AllocateFloatVec( ll1+2 );
+ digf2 = AllocateFloatVec( ll2+2 );
+ diaf1 = AllocateFloatVec( ll1+2 );
+ diaf2 = AllocateFloatVec( ll2+2 );
+ gapz1 = AllocateFloatVec( ll1+2 );
+ gapz2 = AllocateFloatVec( ll2+2 );
+ gapf1 = AllocateFloatVec( ll1+2 );
+ gapf2 = AllocateFloatVec( ll2+2 );
+ ogcp1g = AllocateFloatVec( ll1+2 );
+ ogcp2g = AllocateFloatVec( ll2+2 );
+ fgcp1g = AllocateFloatVec( ll1+2 );
+ fgcp2g = AllocateFloatVec( ll2+2 );
+ og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ og_t_fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_t_fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_t_og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_t_og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ gapz_n1 = AllocateFloatVec( ll1+2 );
+ gapz_n2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] = mseq[i];
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] = mseq[icyc+j];
+ seq2[j][lgth2] = 0;
+ }
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+#if 0
+ {
+ float t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
+ getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
+ getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
+ getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
+ getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
+ getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
+ getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 1
+ lastj = lgth2+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n2_p[i] = ( 1.0-ogcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ fg_h_dg_n2_p[i] = ( 1.0-fgcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n2_p[i] = (1.0-ogcp2g[i]+fgcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n2_p[i] = (1.0-fgcp2g[i]+ogcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ gapz_n2[i] = (1.0-gapz2[i]);
+ }
+ lastj = lgth1+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n1_p[i] = ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ fg_h_dg_n1_p[i] = ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n1_p[i] = (1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n1_p[i] = (1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ gapz_n1[i] = (1.0-gapz1[i]);
+ }
+#endif
+
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ if( RNAscoremtx != 'r' )
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ else
+ clearvec( initverticalw, lgth1 );
+ if( localhom )
+ imp_match_out_vead_tateQ( initverticalw, 0, lgth1 ); // 060306
+
+ if( RNAscoremtx != 'r' )
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ else
+ clearvec( currentw, lgth2 );
+ if( localhom )
+ imp_match_out_veadQ( currentw, 0, lgth2 ); // 060306
+
+
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+
+
+ kyokaipenal = 0.0;
+ if( outgap == 1 )
+ {
+ g = 0.0;
+
+ g += ogcp1g[0] * og_h_dg_n2_p[0];
+// g += ogcp1g[0] * ( 1.0-ogcp2g[0]-digf2[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += ogcp2g[0] * og_h_dg_n1_p[0];
+// g += ogcp2g[0] * ( 1.0-ogcp1g[0]-digf1[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += fgcp1g[0] * fg_h_dg_n2_p[0];
+// g += fgcp1g[0] * ( 1.0-fgcp2g[0]-digf2[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ g += fgcp2g[0] * fg_h_dg_n1_p[0];
+// g += fgcp2g[0] * ( 1.0-fgcp1g[0]-digf1[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ kyokaipenal = g;
+ initverticalw[0] += g;
+ currentw[0] += g;
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ tmppenal = gapz_n2[0]*og_t_fg_h_dg_n1_p[0];
+// tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+fgcp1g[0]-digf1[0]) ) * 0.5 * fpenalty; // mada
+ initverticalw[i] += tmppenal;
+
+ tmppenal = gapz_n2[1]*fg_t_og_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ initverticalw[i] += tmppenal;
+
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ tmppenal = gapz_n1[0]*og_t_fg_h_dg_n2_p[0];
+// tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+fgcp2g[0]-digf2[0]) ) * 0.5 * fpenalty; // mada
+ currentw[j] += tmppenal;
+
+ tmppenal = gapz_n1[1]*fg_t_og_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ currentw[j] += tmppenal;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ m[0] = 0.0; // iranai
+ for( j=1; j<lgth2+1; ++j )
+ {
+ mp[j] = 0;
+ m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ if( RNAscoremtx != 'r' )
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+ else
+ clearvec( currentw, lgth2 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_veadQ( currentw, i, lgth2 );
+#else
+ imp_match_out_veadQ( currentw, i, lgth2 );
+#endif
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mpi = 0;
+ mi = previousw[0] + 10000 * fpenalty;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fg_t_og_h_dg_n2_p_pt = fg_t_og_h_dg_n2_p + 1;
+ og_t_fg_h_dg_n2_p_pt = og_t_fg_h_dg_n2_p + 1;
+ og_h_dg_n2_p_pt = og_h_dg_n2_p + 1;
+ fg_h_dg_n2_p_pt = fg_h_dg_n2_p + 1;
+ gapz_n2_pt0 = gapz_n2 + 1;
+ gapz_n2_pt1 = gapz_n2 + 2;
+ fgcp2pt = fgcp2g + 1;
+ ogcp2pt = ogcp2g + 1;
+
+ fg_t_og_h_dg_n1_p_va = fg_t_og_h_dg_n1_p[i];
+ og_t_fg_h_dg_n1_p_va = og_t_fg_h_dg_n1_p[i];
+ og_h_dg_n1_p_va = og_h_dg_n1_p[i];
+ fg_h_dg_n1_p_va = fg_h_dg_n1_p[i];
+ gapz_n1_va0 = gapz_n1[i];
+ gapz_n1_va1 = gapz_n1[i+1];
+ fgcp1va = fgcp1g[i];
+ ogcp1va = ogcp1g[i];
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+
+ g = ogcp1va * *og_h_dg_n2_p_pt;
+// g = ogcp1g[i] * og_h_dg_n2_p[j];
+// g = ogcp1g[i] * ( 1.0-ogcp2g[j]-digf2[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = *ogcp2pt * og_h_dg_n1_p_va;
+// g = ogcp2g[j] * og_h_dg_n1_p[i];
+// g = ogcp2g[j] * ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = fgcp1va * *fg_h_dg_n2_p_pt;
+// g = fgcp1g[i] * fg_h_dg_n2_p[j];
+// g = fgcp1g[i] * ( 1.0-fgcp2g[j]-digf2[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal3=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = *fgcp2pt * fg_h_dg_n1_p_va;
+// g = fgcp2g[j] * fg_h_dg_n1_p[i];
+// g = fgcp2g[j] * ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal4=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ tmppenal = gapz_n1_va1 * *fg_t_og_h_dg_n2_p_pt;
+// tmppenal = gapz_n1[i+1] * fg_t_og_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ if( (g=mi+tmppenal) > wm )
+ {
+// fprintf( stderr, "jump i start=%f (j=%d, fgcp2g[j]=%f, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, j, fgcp2g[j], digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ tmppenal = gapz_n1_va0 * *og_t_fg_h_dg_n2_p_pt;
+// tmppenal = gapz_n1[i] * og_t_fg_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ if( (g=*prept+tmppenal) >= mi )
+ {
+// fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
+ mi = g;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ tmppenal = *gapz_n2_pt1 * fg_t_og_h_dg_n1_p_va;
+// tmppenal = gapz_n2[j+1] * fg_t_og_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ if( (g=*mjpt+tmppenal) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ tmppenal = *gapz_n2_pt0 * og_t_fg_h_dg_n1_p_va;
+// tmppenal = gapz_n2[j] * og_t_fg_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ if( (g=*prept+tmppenal) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+
+
+
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fg_t_og_h_dg_n2_p_pt++;
+ og_t_fg_h_dg_n2_p_pt++;
+ og_h_dg_n2_p_pt++;
+ fg_h_dg_n2_p_pt++;
+ gapz_n2_pt0++;
+ gapz_n2_pt1++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+
+ return( wm );
+}
+
+float Q__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *gapmap1, int *gapmap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+// float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+ fprintf( stderr, "fpenalty_ex = %f\n", fpenalty_ex );
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *digf1;
+ static TLS float *digf2;
+ static TLS float *diaf1;
+ static TLS float *diaf2;
+ static TLS float *gapz1;
+ static TLS float *gapz2;
+ static TLS float *gapf1;
+ static TLS float *gapf2;
+ static TLS float *ogcp1g;
+ static TLS float *ogcp2g;
+ static TLS float *fgcp1g;
+ static TLS float *fgcp2g;
+ static TLS float *og_h_dg_n1_p;
+ static TLS float *og_h_dg_n2_p;
+ static TLS float *fg_h_dg_n1_p;
+ static TLS float *fg_h_dg_n2_p;
+ static TLS float *og_t_fg_h_dg_n1_p;
+ static TLS float *og_t_fg_h_dg_n2_p;
+ static TLS float *fg_t_og_h_dg_n1_p;
+ static TLS float *fg_t_og_h_dg_n2_p;
+ static TLS float *gapz_n1;
+ static TLS float *gapz_n2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float tmppenal;
+ float *fg_t_og_h_dg_n2_p_pt;
+ float *og_t_fg_h_dg_n2_p_pt;
+ float *og_h_dg_n2_p_pt;
+ float *fg_h_dg_n2_p_pt;
+ float *gapz_n2_pt0;
+ float *gapz_n2_pt1;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fg_t_og_h_dg_n1_p_va;
+ float og_t_fg_h_dg_n1_p_va;
+ float og_h_dg_n1_p_va;
+ float fg_h_dg_n1_p_va;
+ float gapz_n1_va0;
+ float gapz_n1_va1;
+ float fgcp1va;
+ float ogcp1va;
+ float kyokaipenal;
+ float fpenalty = (float)penalty;
+
+#if 0
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+#endif
+
+
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( digf1 );
+ FreeFloatVec( digf2 );
+ FreeFloatVec( diaf1 );
+ FreeFloatVec( diaf2 );
+ FreeFloatVec( gapz1 );
+ FreeFloatVec( gapz2 );
+ FreeFloatVec( gapf1 );
+ FreeFloatVec( gapf2 );
+ FreeFloatVec( ogcp1g );
+ FreeFloatVec( ogcp2g );
+ FreeFloatVec( fgcp1g );
+ FreeFloatVec( fgcp2g );
+ FreeFloatVec( og_h_dg_n1_p );
+ FreeFloatVec( og_h_dg_n2_p );
+ FreeFloatVec( fg_h_dg_n1_p );
+ FreeFloatVec( fg_h_dg_n2_p );
+ FreeFloatVec( og_t_fg_h_dg_n1_p );
+ FreeFloatVec( og_t_fg_h_dg_n2_p );
+ FreeFloatVec( fg_t_og_h_dg_n1_p );
+ FreeFloatVec( fg_t_og_h_dg_n2_p );
+ FreeFloatVec( gapz_n1 );
+ FreeFloatVec( gapz_n2 );
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ digf1 = AllocateFloatVec( ll1+2 );
+ digf2 = AllocateFloatVec( ll2+2 );
+ diaf1 = AllocateFloatVec( ll1+2 );
+ diaf2 = AllocateFloatVec( ll2+2 );
+ gapz1 = AllocateFloatVec( ll1+2 );
+ gapz2 = AllocateFloatVec( ll2+2 );
+ gapf1 = AllocateFloatVec( ll1+2 );
+ gapf2 = AllocateFloatVec( ll2+2 );
+ ogcp1g = AllocateFloatVec( ll1+2 );
+ ogcp2g = AllocateFloatVec( ll2+2 );
+ fgcp1g = AllocateFloatVec( ll1+2 );
+ fgcp2g = AllocateFloatVec( ll2+2 );
+ og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ og_t_fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_t_fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_t_og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_t_og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ gapz_n1 = AllocateFloatVec( ll1+2 );
+ gapz_n2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] = mseq[i];
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] = mseq[icyc+j];
+ seq2[j][lgth2] = 0;
+ }
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+#if 0
+ {
+ float t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
+ getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
+ getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
+ getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
+ getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
+ getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
+ getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 1
+ lastj = lgth2+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n2_p[i] = ( 1.0-ogcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ fg_h_dg_n2_p[i] = ( 1.0-fgcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n2_p[i] = (1.0-ogcp2g[i]+fgcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n2_p[i] = (1.0-fgcp2g[i]+ogcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ gapz_n2[i] = (1.0-gapz2[i]);
+ }
+ lastj = lgth1+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n1_p[i] = ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ fg_h_dg_n1_p[i] = ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n1_p[i] = (1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n1_p[i] = (1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ gapz_n1[i] = (1.0-gapz1[i]);
+ }
+#endif
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ if( RNAscoremtx != 'r' )
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ else
+ clearvec( initverticalw, lgth1 );
+ if( localhom )
+ imp_match_out_vead_tateQ_gapmap( initverticalw, gapmap2[0], lgth1, gapmap1 ); // 060306
+
+ if( RNAscoremtx != 'r' )
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ else
+ clearvec( currentw, lgth2 );
+ if( localhom )
+ imp_match_out_veadQ_gapmap( currentw, gapmap1[0], lgth2, gapmap2 ); // 060306
+
+
+
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+
+
+ kyokaipenal = 0.0;
+ if( outgap == 1 )
+ {
+ g = 0.0;
+
+ g += ogcp1g[0] * og_h_dg_n2_p[0];
+// g += ogcp1g[0] * ( 1.0-ogcp2g[0]-digf2[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += ogcp2g[0] * og_h_dg_n1_p[0];
+// g += ogcp2g[0] * ( 1.0-ogcp1g[0]-digf1[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += fgcp1g[0] * fg_h_dg_n2_p[0];
+// g += fgcp1g[0] * ( 1.0-fgcp2g[0]-digf2[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ g += fgcp2g[0] * fg_h_dg_n1_p[0];
+// g += fgcp2g[0] * ( 1.0-fgcp1g[0]-digf1[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ kyokaipenal = g;
+ initverticalw[0] += g;
+ currentw[0] += g;
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ tmppenal = gapz_n2[0]*og_t_fg_h_dg_n1_p[0];
+// tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+fgcp1g[0]-digf1[0]) ) * 0.5 * fpenalty; // mada
+ initverticalw[i] += tmppenal;
+
+ tmppenal = gapz_n2[1]*fg_t_og_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ initverticalw[i] += tmppenal;
+
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ tmppenal = gapz_n1[0]*og_t_fg_h_dg_n2_p[0];
+// tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+fgcp2g[0]-digf2[0]) ) * 0.5 * fpenalty; // mada
+ currentw[j] += tmppenal;
+
+ tmppenal = gapz_n1[1]*fg_t_og_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ currentw[j] += tmppenal;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ m[0] = 0.0; // iranai
+ for( j=1; j<lgth2+1; ++j )
+ {
+ mp[j] = 0;
+ m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ if( RNAscoremtx != 'r' )
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+ else
+ clearvec( currentw, lgth2 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_veadQ( currentw, i, lgth2 );
+#else
+ imp_match_out_veadQ_gapmap( currentw, gapmap1[i], lgth2, gapmap2 );
+#endif
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mpi = 0;
+ mi = previousw[0] + 10000 * fpenalty;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fg_t_og_h_dg_n2_p_pt = fg_t_og_h_dg_n2_p + 1;
+ og_t_fg_h_dg_n2_p_pt = og_t_fg_h_dg_n2_p + 1;
+ og_h_dg_n2_p_pt = og_h_dg_n2_p + 1;
+ fg_h_dg_n2_p_pt = fg_h_dg_n2_p + 1;
+ gapz_n2_pt0 = gapz_n2 + 1;
+ gapz_n2_pt1 = gapz_n2 + 2;
+ fgcp2pt = fgcp2g + 1;
+ ogcp2pt = ogcp2g + 1;
+
+ fg_t_og_h_dg_n1_p_va = fg_t_og_h_dg_n1_p[i];
+ og_t_fg_h_dg_n1_p_va = og_t_fg_h_dg_n1_p[i];
+ og_h_dg_n1_p_va = og_h_dg_n1_p[i];
+ fg_h_dg_n1_p_va = fg_h_dg_n1_p[i];
+ gapz_n1_va0 = gapz_n1[i];
+ gapz_n1_va1 = gapz_n1[i+1];
+ fgcp1va = fgcp1g[i];
+ ogcp1va = ogcp1g[i];
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+
+ g = ogcp1va * *og_h_dg_n2_p_pt;
+// g = ogcp1g[i] * og_h_dg_n2_p[j];
+// g = ogcp1g[i] * ( 1.0-ogcp2g[j]-digf2[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = *ogcp2pt * og_h_dg_n1_p_va;
+// g = ogcp2g[j] * og_h_dg_n1_p[i];
+// g = ogcp2g[j] * ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = fgcp1va * *fg_h_dg_n2_p_pt;
+// g = fgcp1g[i] * fg_h_dg_n2_p[j];
+// g = fgcp1g[i] * ( 1.0-fgcp2g[j]-digf2[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal3=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = *fgcp2pt * fg_h_dg_n1_p_va;
+// g = fgcp2g[j] * fg_h_dg_n1_p[i];
+// g = fgcp2g[j] * ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal4=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ tmppenal = gapz_n1_va1 * *fg_t_og_h_dg_n2_p_pt;
+// tmppenal = gapz_n1[i+1] * fg_t_og_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ if( (g=mi+tmppenal) > wm )
+ {
+// fprintf( stderr, "jump i start=%f (j=%d, fgcp2g[j]=%f, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, j, fgcp2g[j], digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ tmppenal = gapz_n1_va0 * *og_t_fg_h_dg_n2_p_pt;
+// tmppenal = gapz_n1[i] * og_t_fg_h_dg_n2_p[j];
+// tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ if( (g=*prept+tmppenal) >= mi )
+ {
+// fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
+ mi = g;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ tmppenal = *gapz_n2_pt1 * fg_t_og_h_dg_n1_p_va;
+// tmppenal = gapz_n2[j+1] * fg_t_og_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ if( (g=*mjpt+tmppenal) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ tmppenal = *gapz_n2_pt0 * og_t_fg_h_dg_n1_p_va;
+// tmppenal = gapz_n2[j] * og_t_fg_h_dg_n1_p[i];
+// tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ if( (g=*prept+tmppenal) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+
+
+
+
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fg_t_og_h_dg_n2_p_pt++;
+ og_t_fg_h_dg_n2_p_pt++;
+ og_h_dg_n2_p_pt++;
+ fg_h_dg_n2_p_pt++;
+ gapz_n2_pt0++;
+ gapz_n2_pt1++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom_gapmap( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, gapmap1, gapmap2 );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+
+ return( wm );
+}
+
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 1
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define FASTMATCHCALC 1
+
+
+static TLS float **impmtx = NULL;
+#if 1 // tditeration to naiveRscore_imp de tsukawareru.
+float imp_match_out_scR( int i1, int j1 )
+{
+// fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
+// fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
+ return( impmtx[i1][j1] );
+}
+#endif
+
+static void imp_match_out_veadR( float *imp, int i1, int lgth2 )
+{
+#if FASTMATCHCALC
+ float *pt = impmtx[i1];
+ while( lgth2-- )
+ *imp++ += *pt++;
+#else
+ int j;
+ float *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[j];
+#endif
+}
+static void imp_match_out_vead_tateR( float *imp, int j1, int lgth1 )
+{
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[i][j1];
+}
+
+#if 1 // tbfast.c kara yobareru.
+void imp_match_init_strictR( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
+{
+ int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ static TLS int impalloclen = 0;
+ float effij;
+ double effijx;
+ char *pt, *pt1, *pt2;
+ static TLS char *nocount1 = NULL;
+ static char *nocount2 = NULL;
+ LocalHom *tmpptr;
+
+ if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ if( nocount1 ) free( nocount1 );
+ if( nocount2 ) free( nocount2 );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+ nocount1 = AllocateCharVec( impalloclen );
+ nocount2 = AllocateCharVec( impalloclen );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<clus1; j++ )
+ if( seq1[j][i] == '-' ) break;
+ if( j != clus1 ) nocount1[i] = 1;
+ else nocount1[i] = 0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ if( seq2[j][i] == '-' ) break;
+ if( j != clus2 ) nocount2[i] = 1;
+ else nocount2[i] = 0;
+ }
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+ fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "eff1 in _init_strict = \n" );
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "eff1[] = %f\n", eff1[i] );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "eff2[] = %f\n", eff2[i] );
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ effijx = fastathreshold;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ effij = (float)( eff1[i] * eff2[j] * effijx );
+ tmpptr = localhom[i][j];
+ while( tmpptr )
+ {
+// fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
+// fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
+// fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
+// fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start1 ) break;
+ }
+ start1 = pt - seq1[i] - 1;
+
+ if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( tmpint == tmpptr->end1 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end1 = pt - seq1[i] - 0;
+#else
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end1 ) break;
+ }
+ end1 = pt - seq1[i] - 1;
+#endif
+ }
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start2 ) break;
+ }
+ start2 = pt - seq2[j] - 1;
+ if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end2 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end2 = pt - seq2[j] - 0;
+#else
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end2 ) break;
+ }
+ end2 = pt - seq2[j] - 1;
+#endif
+ }
+// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
+// fprintf( stderr, "step 0\n" );
+ if( end1 - start1 != end2 - start2 )
+ {
+// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ }
+
+#if 1
+ k1 = start1; k2 = start2;
+ pt1 = seq1[i] + k1;
+ pt2 = seq2[j] + k2;
+ while( *pt1 && *pt2 )
+ {
+ if( *pt1 != '-' && *pt2 != '-' )
+ {
+// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
+// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
+// impmtx[k1][k2] += tmpptr->importance * effij;
+ impmtx[k1][k2] += tmpptr->fimportance * effij;
+// fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
+// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+// fprintf( stderr, "%d (%c) - %d (%c) - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
+ k1++; k2++;
+ pt1++; pt2++;
+ }
+ else if( *pt1 != '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k2++; pt2++;
+ }
+ else if( *pt1 == '-' && *pt2 != '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ }
+ else if( *pt1 == '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ k2++; pt2++;
+ }
+ if( k1 > end1 || k2 > end2 ) break;
+ }
+#else
+ while( k1 <= end1 && k2 <= end2 )
+ {
+ fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
+ if( !nocount1[k1] && !nocount2[k2] )
+ {
+ impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j] * fastathreshold;
+ fprintf( stderr, "marked\n" );
+ }
+ else
+ fprintf( stderr, "no count\n" );
+ k1++; k2++;
+ }
+#endif
+ tmpptr = tmpptr->next;
+ }
+ }
+ }
+#if 0
+ if( clus1 == 1 && clus2 == 6 )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d ", k1 );
+ for( k2=0; k2<3; k2++ )
+ fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+ }
+#endif
+}
+#endif
+
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+ int j, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<26; j++ )
+ scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+#else
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+// simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin == lgth1 || jin == lgth2 )
+ ;
+ else
+ {
+ *impwmpt += imp_match_out_scR( iin, jin );
+
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+
+ return( 0.0 );
+}
+
+float R__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+// float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *digf1;
+ static TLS float *digf2;
+ static TLS float *diaf1;
+ static TLS float *diaf2;
+ static TLS float *gapz1;
+ static TLS float *gapz2;
+ static TLS float *gapf1;
+ static TLS float *gapf2;
+ static TLS float *ogcp1g;
+ static TLS float *ogcp2g;
+ static TLS float *fgcp1g;
+ static TLS float *fgcp2g;
+ static TLS float *ogcp1;
+ static TLS float *ogcp2;
+ static TLS float *fgcp1;
+ static TLS float *fgcp2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float fpenalty = (float)penalty;
+ float tmppenal;
+ float cumpenal;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fgcp1va;
+ float ogcp1va;
+ float kyokaipenal;
+
+
+
+#if 0
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( digf1 );
+ FreeFloatVec( digf2 );
+ FreeFloatVec( diaf1 );
+ FreeFloatVec( diaf2 );
+ FreeFloatVec( gapz1 );
+ FreeFloatVec( gapz2 );
+ FreeFloatVec( gapf1 );
+ FreeFloatVec( gapf2 );
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatVec( ogcp1g );
+ FreeFloatVec( ogcp2g );
+ FreeFloatVec( fgcp1g );
+ FreeFloatVec( fgcp2g );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ digf1 = AllocateFloatVec( ll1+2 );
+ digf2 = AllocateFloatVec( ll2+2 );
+ diaf1 = AllocateFloatVec( ll1+2 );
+ diaf2 = AllocateFloatVec( ll2+2 );
+ gapz1 = AllocateFloatVec( ll1+2 );
+ gapz2 = AllocateFloatVec( ll2+2 );
+ gapf1 = AllocateFloatVec( ll1+2 );
+ gapf2 = AllocateFloatVec( ll2+2 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+ ogcp1g = AllocateFloatVec( ll1+2 );
+ ogcp2g = AllocateFloatVec( ll2+2 );
+ fgcp1g = AllocateFloatVec( ll1+2 );
+ fgcp2g = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] = mseq[i];
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] = mseq[icyc+j];
+ seq2[j][lgth2] = 0;
+ }
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+#if 0
+ {
+ float t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
+ getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
+ getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
+ getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
+ getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
+ getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
+ getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ if( localhom )
+ imp_match_out_vead_tateR( initverticalw, 0, lgth1 ); // 060306
+
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ if( localhom )
+ imp_match_out_veadR( currentw, 0, lgth2 ); // 060306
+
+
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+
+
+ kyokaipenal = 0.0;
+ if( outgap == 1 )
+ {
+ g = 0.0;
+
+ g += ogcp1g[0] * ( 1.0-ogcp2g[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += ogcp2g[0] * ( 1.0-ogcp1g[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
+
+ g += fgcp1g[0] * ( 1.0-fgcp2g[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ g += fgcp2g[0] * ( 1.0-fgcp1g[0] ) * fpenalty * 0.5;
+// if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+
+ kyokaipenal = g;
+ initverticalw[0] += g;
+ currentw[0] += g;
+
+ cumpenal = 0.0;
+ for( i=1; i<lgth1+1; i++ )
+ {
+// initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+
+// Q tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+fgcp1g[0]-digf1[0]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+ tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+0.0) + gapz2[0]*(1.0-digf1[0] - diaf1[0]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-0.0)*(1.0-ogcp1g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-0.0) * (1.0-diaf1[0]) + 0.0 ) * 0.5 * fpenalty; // 0.
+// tmppenal -= ( (1.0-gapf2[j-1]) * ogcp1g[i] + gapf2[j-1] ) * 0.5 * fpenalty;
+// fprintf( stderr, "0,0<-%d,%d, tmppenal 1 = %f\n", i, 0, tmppenal );
+ initverticalw[i] += tmppenal;
+
+// Q tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+ tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapz2[1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[0])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[0]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[0]) * (1.0-diaf1[i]) + gapf2[0] ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[j]) * fgcp1g[i] + gapf2[j] ) * 0.5 * fpenalty;
+ initverticalw[i] += tmppenal;
+ cumpenal += ( ogcp1g[i-0] + fgcp1g[i] ) * fpenalty * 0.5;
+ initverticalw[i] += cumpenal - fgcp1g[i] * fpenalty * 0.5; // honto ha iru
+// fprintf( stderr, "0,0<-%d,%d, tmppenal 2 = %f, cumpenal=%f, fgcp1g[i]=%f, ogcp1g[i]=%f\n", i, 0, tmppenal, cumpenal, fgcp1g[i], ogcp1g[i] );
+
+ }
+ cumpenal = 0.0;
+ for( j=1; j<lgth2+1; j++ )
+ {
+// currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+
+// tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+fgcp2g[0]-digf2[0]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapf1[i-1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+ tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+0.0) + gapz1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-0.0)*(1.0-ogcp2g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-0.0) * (1.0-diaf2[0]) + 0.0 ) * 0.5 * fpenalty; // 0.
+// tmppenal -= ( (1.0-gapf1[0]) * fgcp2g[j] + gapf1[0] ) * 0.5 * fpenalty;
+// fprintf( stderr, "0,0<-%d,%d, tmppenal 3 = %f\n", 0, j, tmppenal );
+ currentw[j] += tmppenal;
+
+// tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+ tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapz1[1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf1[0])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf1[0]) * (1.0-diaf2[j]) + gapf1[0] ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf1[0]) * ogcp2g[j] + gapf1[i-1] ) * 0.5 * fpenalty;
+// fprintf( stderr, "0,0<-%d,%d, tmppenal 4 = %f\n", 0, j, tmppenal );
+ currentw[j] += tmppenal;
+ cumpenal += ( ogcp2g[j-0] + fgcp2g[j] ) * fpenalty * 0.5;
+ currentw[j] += cumpenal - fgcp2g[j] * fpenalty * 0.5; // honto ha iru
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ m[0] = 0.0; // iranai
+ for( j=1; j<lgth2+1; ++j )
+ {
+ mp[j] = 0;
+ m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_veadR( currentw, i, lgth2 );
+#else
+ imp_match_out_veadR( currentw, i, lgth2 );
+#endif
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mpi = 0;
+ mi = previousw[0] + 10000 * fpenalty;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fgcp2pt = fgcp2;
+ ogcp2pt = ogcp2 + 1;
+ fgcp1va = fgcp1[i-1];
+ ogcp1va = ogcp1[i];
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+
+ g = ogcp1g[i] * ( 1.0-ogcp2g[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = ogcp2g[j] * ( 1.0-ogcp1g[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = fgcp1g[i] * ( 1.0-fgcp2g[j] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal3=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+ g = fgcp2g[j] * ( 1.0-fgcp1g[i] ) * fpenalty * 0.5;
+// if( g && i==j ) fprintf( stderr, "match penal4=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm += g;
+
+#if 0
+ g = fgcp2g[j] * ogcp1g[i] * fpenalty * 0.5;
+ if( g ) fprintf( stderr, "match m-penal5=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm -= g;
+
+ g = fgcp1g[i] * ogcp2g[j] * fpenalty * 0.5;
+ if( g ) fprintf( stderr, "match m-penal6=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
+ wm -= g;
+#endif
+
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+// tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+ tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapz1[i+1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf1[i])*(1.0-diaf2[j]) + gapf1[i] ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf1[i])*fgcp2g[j] + gapf1[i] ) * 0.5 * fpenalty;
+// tmppenal = *fgcp2pt-fpenalty*0.5*gapf1[i];
+// tmppenal = *fgcp2pt;
+ if( (g=mi+tmppenal) > wm )
+ {
+// fprintf( stderr, "jump i start=%f (j=%d, fgcp2g[j]=%f, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, j, fgcp2g[j], digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+// tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
+ tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapz1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapf1[i-1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
+// tmppenal = *ogcp2pt-fpenalty*0.5*(gapf2[j-1]+gapf1[i-1]);
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf1[i-1])*(1.0-diaf2[j]) + gapf1[i-1] ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf1[i-1])*ogcp2g[j] + gapf1[i-1] ) * 0.5 * fpenalty;
+// tmppenal = *prept+*ogcp2pt;
+ if( (g=*prept+tmppenal) >= mi )
+ {
+// fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
+ mi = g;
+ mpi = j-1;
+ }
+ else if( j != 1 )
+ {
+ mi += ( ogcp2g[j-0] + fgcp2g[j] ) * fpenalty * 0.5; // CHUUI honto ha iru
+// fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", '=', '=', seq2[0][j-1], seq2[0][j], ogcp2g[j-0] * fpenalty*0.5, fgcp2g[j] * fpenalty*0.5 );
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+// tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapz2[j+1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[j])*(1.0-diaf1[i]) + gapf2[j] ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[j])*fgcp1g[i] + gapf2[j] ) * 0.5 * fpenalty;
+// tmppenal = fgcp1va-fpenalty*0.5*gapf2[j];
+// tmppenal = fgcp1va;
+ if( (g=*mjpt+tmppenal) > wm )
+ {
+// if( seq1[0][i] == 'Y' && seq2[0][j] == 'B' )
+// fprintf( stderr, "jump j start=%f, %c-%c\n", g-*mjpt, seq1[0][i], seq2[0][j] );
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+// tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
+ tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapz2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
+// tmppenal = ogcp1va-fpenalty*0.5*(gapf1[i-1]+gapf2[j-1]);
+// tmppenal = 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[j-1]) * (1.0-diaf1[i]) + gapf2[j-1] ) * 0.5 * fpenalty;
+// tmppenal -= ( (1.0-gapf2[j-1]) * ogcp1g[i] + gapf2[j-1] ) * 0.5 * fpenalty;
+// tmppenal = 0.5 * fpenalty - ( (1.0-gapf2[j-1]) * (ogcp1g[i]) + gapf2[j-1] ) * ( 0.5 * fpenalty );
+// tmppenal = ogcp1va-fpenalty*0.5*gapf2[j-1];
+// tmppenal = ogcp1va;
+ if( (g=*prept+tmppenal) >= *mjpt )
+ {
+// if( seq1[0][i] == 'T' && seq2[0][j] == 'T' )
+// fprintf( stderr, "jump j end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+ else if( i != 1 )
+ {
+ m[j] += ( ogcp1g[i-0] + fgcp1g[i] ) * fpenalty * 0.5; // CHUUI honto ha iru
+// fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", seq1[0][i-1], seq1[0][i], '=', '=', ogcp1g[i-0] * fpenalty*0.5, fgcp1g[i] * fpenalty*0.5 );
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+ fprintf( stderr, "wm = %f\n", wm );
+
+
+ return( wm );
+}
+
+
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0;
+ for( k=0; cpmxpdn[k][j] > -1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, k, l, iin, jin, ifi, jfi, lgth1, lgth2;
+// char gap[] = "-";
+ char *gap;
+ float wm;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if DEBUG
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+ iin = lgth1; jin = lgth2;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ return( 0.0 );
+}
+
+
+float Aalign( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+ register int i, j;
+ int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float x;
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *currentw;
+ static TLS float *previousw;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+
+#if DEBUG
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 1 );
+ mseq2 = AllocateCharMtx( njob, 1 ); /* by J. Thompson */
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( currentw );
+ FreeFloatVec( previousw );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.1*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.1*lgth2), orlgth2 ) + 100;
+
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+
+ currentw = AllocateFloatVec( ll2+2 );
+ previousw = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+ fprintf( stderr, "succeeded\n" );
+
+ orlgth1 = ll1;
+ orlgth2 = ll2;
+ }
+
+ for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
+ for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+ fprintf( stderr, "succeeded\n\n" );
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+ cpmx_calc( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
+ cpmx_calc( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
+
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+
+ if( outgap == 1 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += penalty * 0.5;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += penalty * 0.5;
+ }
+ }
+
+ for( j=0; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + penalty * 0.5; mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+ for( i=1; i<lasti; i++ )
+ {
+
+ floatncpy( previousw, currentw, lgth2+1 );
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + penalty * 0.5; mpi = 0;
+ for( j=1; j<lgth2+1; j++ )
+ {
+ wm = previousw[j-1];
+ ijp[i][j] = 0;
+
+ g = penalty * 0.5;
+ x = mi + g;
+ if( x > wm )
+ {
+ wm = x;
+ ijp[i][j] = -( j - mpi );
+ }
+ g = penalty * 0.5;
+ x = previousw[j-1] + g;
+ if( mi <= x )
+ {
+ mi = x;
+ mpi = j-1;
+ }
+
+ g = penalty * 0.5;
+ x = m[j] + g;
+ if( x > wm )
+ {
+ wm = x;
+ ijp[i][j] = +( i - mp[j] );
+ }
+ g = penalty * 0.5;
+ x = previousw[j-1] + g;
+ if( m[j] <= x )
+ {
+ m[j] = x;
+ mp[j] = i-1;
+ }
+ currentw[j] += wm;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+ return( wm );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 0
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define FASTMATCHCALC 1
+
+
+static TLS float **impmtx = NULL;
+static TLS int impalloclen = 0;
+float imp_match_out_sc( int i1, int j1 )
+{
+// fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
+// fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
+ return( impmtx[i1][j1] );
+}
+static void imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int *gapmap2 )
+{
+#if FASTMATCHCALC
+ float *pt = impmtx[i1];
+ int *gapmappt = gapmap2;
+ while( lgth2-- )
+ *imp++ += pt[*gapmappt++];
+#else
+ int j;
+ float *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[gapmap2[j]];
+#endif
+}
+
+
+static void imp_match_out_vead_tate_gapmap( float *imp, int j1, int lgth1, int *gapmap1 )
+{
+#if FASTMATCHCALC
+ int *gapmappt = gapmap1;
+ while( lgth1-- )
+ *imp++ += impmtx[*gapmappt++][j1];
+#else
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[gapmap1[i]][j1];
+#endif
+}
+
+static void imp_match_out_vead( float *imp, int i1, int lgth2 )
+{
+#if FASTMATCHCALC
+ float *pt = impmtx[i1];
+ while( lgth2-- )
+ *imp++ += *pt++;
+#else
+ int j;
+ float *pt = impmtx[i1];
+ for( j=0; j<lgth2; j++ )
+ *imp++ += pt[j];
+#endif
+}
+static void imp_match_out_vead_tate( float *imp, int j1, int lgth1 )
+{
+ int i;
+ for( i=0; i<lgth1; i++ )
+ *imp++ += impmtx[i][j1];
+}
+
+void imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *pair )
+{
+ foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, pair );
+}
+
+
+void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore )
+{
+ int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ float effij;
+ float effij_kozo;
+ double effijx;
+ char *pt, *pt1, *pt2;
+ static TLS char *nocount1 = NULL;
+ static TLS char *nocount2 = NULL;
+ LocalHom *tmpptr;
+
+ if( seq1 == NULL )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ impmtx = NULL;
+ if( nocount1 ) free( nocount1 );
+ nocount1 = NULL;
+ if( nocount2 ) free( nocount2 );
+ nocount2 = NULL;
+
+ return;
+ }
+
+ if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ if( nocount1 ) free( nocount1 );
+ if( nocount2 ) free( nocount2 );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+ nocount1 = AllocateCharVec( impalloclen );
+ nocount2 = AllocateCharVec( impalloclen );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<clus1; j++ )
+ if( seq1[j][i] == '-' ) break;
+ if( j != clus1 ) nocount1[i] = 1;
+ else nocount1[i] = 0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ if( seq2[j][i] == '-' ) break;
+ if( j != clus2 ) nocount2[i] = 1;
+ else nocount2[i] = 0;
+ }
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+ fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "eff1 in _init_strict = \n" );
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "eff1[] = %f\n", eff1[i] );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "eff2[] = %f\n", eff2[i] );
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ effijx = fastathreshold;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ effij = (float)( eff1[i] * eff2[j] * effijx );
+ effij_kozo = (float)( eff1_kozo[i] * eff2_kozo[j] * effijx );
+ tmpptr = localhom[i][j];
+ while( tmpptr )
+ {
+// fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
+// fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
+// fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
+// fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start1 ) break;
+ }
+ start1 = pt - seq1[i] - 1;
+
+ if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( tmpint == tmpptr->end1 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end1 = pt - seq1[i] - 0;
+#else
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end1 ) break;
+ }
+ end1 = pt - seq1[i] - 1;
+#endif
+ }
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start2 ) break;
+ }
+ start2 = pt - seq2[j] - 1;
+ if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end2 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end2 = pt - seq2[j] - 0;
+#else
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end2 ) break;
+ }
+ end2 = pt - seq2[j] - 1;
+#endif
+ }
+// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
+// fprintf( stderr, "step 0\n" );
+ if( end1 - start1 != end2 - start2 )
+ {
+// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ }
+
+#if 1
+ k1 = start1; k2 = start2;
+ pt1 = seq1[i] + k1;
+ pt2 = seq2[j] + k2;
+ while( *pt1 && *pt2 )
+ {
+ if( *pt1 != '-' && *pt2 != '-' )
+ {
+// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
+// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
+// impmtx[k1][k2] += tmpptr->importance * effij;
+// impmtx[k1][k2] += tmpptr->fimportance * effij;
+ if( tmpptr->korh == 'k' )
+ impmtx[k1][k2] += tmpptr->fimportance * effij_kozo;
+ else
+ impmtx[k1][k2] += tmpptr->fimportance * effij;
+
+// fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
+// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+// fprintf( stderr, "%d (%c) - %d (%c) - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
+ k1++; k2++;
+ pt1++; pt2++;
+ }
+ else if( *pt1 != '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k2++; pt2++;
+ }
+ else if( *pt1 == '-' && *pt2 != '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ }
+ else if( *pt1 == '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ k2++; pt2++;
+ }
+ if( k1 > end1 || k2 > end2 ) break;
+ }
+#else
+ while( k1 <= end1 && k2 <= end2 )
+ {
+ fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
+ if( !nocount1[k1] && !nocount2[k2] )
+ {
+ impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j] * fastathreshold;
+ fprintf( stderr, "marked\n" );
+ }
+ else
+ fprintf( stderr, "no count\n" );
+ k1++; k2++;
+ }
+#endif
+ tmpptr = tmpptr->next;
+ }
+ }
+ }
+
+#if 0
+ if( clus1 == 1 && clus2 == 1 )
+ {
+ fprintf( stderr, "writing impmtx\n" );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d ", k1 );
+ for( k2=0; k2<30; k2++ )
+ fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+// exit( 1 );
+ }
+#endif
+}
+
+#if 0
+void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
+{
+ int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ static TLS int impalloclen = 0;
+ char *pt;
+ int allgap;
+ static TLS char *nocount1 = NULL;
+ static TLS char *nocount2 = NULL;
+
+ if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ if( nocount1 ) free( nocount1 );
+ if( nocount2 ) free( nocount2 );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+ nocount1 = AllocateCharVec( impalloclen );
+ nocount2 = AllocateCharVec( impalloclen );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<clus1; j++ )
+ if( seq1[j][i] == '-' ) break;
+ if( j != clus1 ) nocount1[i] = 1;
+ else nocount1[i] = 0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ if( seq2[j][i] == '-' ) break;
+ if( j != clus2 ) nocount2[i] = 1;
+ else nocount2[i] = 0;
+ }
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+ fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0;
+ for( i=0; i<clus1; i++ )
+ {
+ fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
+ for( j=0; j<clus2; j++ )
+ {
+ fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
+ fprintf( stderr, "end1 = %d\n", localhom[i][j]->end1 );
+ fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->start1 ) break;
+ }
+ start1 = pt - seq1[i] - 1;
+
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->end1 ) break;
+ }
+ end1 = pt - seq1[i] - 1;
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->start2 ) break;
+ }
+ start2 = pt - seq2[j] - 1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->end2 ) break;
+ }
+ end2 = pt - seq2[j] - 1;
+// fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ k1 = start1;
+ k2 = start2;
+ fprintf( stderr, "step 0\n" );
+ while( k1 <= end1 && k2 <= end2 )
+ {
+#if 0
+ if( !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+#else
+ if( !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+#endif
+ }
+
+ dif = ( end1 - start1 ) - ( end2 - start2 );
+ fprintf( stderr, "dif = %d\n", dif );
+ if( dif > 0 )
+ {
+ do
+ {
+ fprintf( stderr, "dif = %d\n", dif );
+ k1 = start1;
+ k2 = start2 - dif;
+ while( k1 <= end1 && k2 <= end2 )
+ {
+ if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+ }
+ }
+ while( dif-- );
+ }
+ else
+ {
+ do
+ {
+ k1 = start1 + dif;
+ k2 = start2;
+ while( k1 <= end1 )
+ {
+ if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+ }
+ }
+ while( dif++ );
+ }
+ }
+ }
+#if 0
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d", k1 );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+#endif
+}
+#endif
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+ int j, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<26; j++ )
+// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+ scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+#else
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+// simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin == lgth1 || jin == lgth2 )
+ ;
+ else
+ {
+ *impwmpt += imp_match_out_sc( iin, jin );
+
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+}
+static void Atracking_localhom_gapmap( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc,
+ int *gapmap1, int *gapmap2 )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin == lgth1 || jin == lgth2 )
+ ;
+ else
+ {
+ *impwmpt += imp_match_out_sc( gapmap1[iin], gapmap2[jin] );
+
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = '-';
+ *--gaptable2 = '-';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+}
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc,
+ int tailgp )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ float wm;
+ char *gaptable1, *gt1bk;
+ char *gaptable2, *gt2bk;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+ gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( tailgp == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ gaptable1 = gt1bk + lgth1+lgth2;
+ *gaptable1 = 0;
+ gaptable2 = gt2bk + lgth1+lgth2;
+ *gaptable2 = 0;
+
+ iin = lgth1; jin = lgth2;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--gaptable1 = 'o';
+ *--gaptable2 = 'o';
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+ free( gt1bk );
+ free( gt2bk );
+
+ return( 0.0 );
+}
+
+float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+// float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *ogcp1;
+ static TLS float *ogcp2;
+ static TLS float *fgcp1;
+ static TLS float *fgcp2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float fpenalty = (float)penalty;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fgcp1va;
+ float ogcp1va;
+
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 )
+ {
+// fprintf( stderr, "## Freeing local arrays in A__align\n" );
+ orlgth1 = 0;
+ orlgth2 = 0;
+
+ imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
+
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ }
+ else
+ {
+// fprintf( stderr, "## Not allocated\n" );
+ }
+ return( 0.0 );
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 1
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+ if( lgth1 == 0 && lgth2 == 0 )
+ return( 0.0 );
+
+ if( lgth1 == 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ {
+ j = lgth2;
+ seq1[i][j] = 0;
+ while( j ) seq1[i][--j] = '-';
+// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+ }
+ return( 0.0 );
+ }
+
+ if( lgth2 == 0 )
+ {
+ for( i=0; i<jcyc; i++ )
+ {
+ j = lgth1;
+ seq2[i][j] = 0;
+ while( j ) seq2[i][--j] = '-';
+// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+ }
+ return( 0.0 );
+ }
+#endif
+
+
+#if 0
+ fprintf( stderr, "#### eff in SA+++align\n" );
+ fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "#### strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "#### strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] = mseq[i];
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] = mseq[icyc+j];
+ seq2[j][lgth2] = 0;
+ }
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+#if 0
+ {
+ float t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+ new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+ new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
+ new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+ }
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ if( localhom )
+ imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
+
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ if( localhom )
+ imp_match_out_vead( currentw, 0, lgth2 ); // 060306
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+ if( headgp == 1 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_vead( currentw, i, lgth2 );
+#else
+ imp_match_out_vead( currentw, i, lgth2 );
+#endif
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+
+ mi = previousw[0] + ogcp2[1]; mpi = 0;
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fgcp2pt = fgcp2;
+ ogcp2pt = ogcp2 + 1;
+ fgcp1va = fgcp1[i-1];
+ ogcp1va = ogcp1[i];
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+#ifdef xxxenablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+*fgcp2pt) > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ if( (g=*prept+*ogcp2pt) >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt+fgcp1va) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ if( (g=*prept+ogcp1va) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, tailgp );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+#if 0
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+#endif
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ return( wm );
+}
+
+float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+// float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *ogcp1;
+ static TLS float *ogcp2;
+ static TLS float *fgcp1;
+ static TLS float *fgcp2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fgcp1va;
+ float ogcp1va;
+
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 0
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalign_gapmap): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 27, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] = mseq[i];
+ seq1[i][lgth1] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] = mseq[icyc+j];
+ seq2[j][lgth2] = 0;
+ }
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+ cpmx_calc_new( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
+
+ st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+ }
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ if( localhom )
+ imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0], lgth1, gapmap1 ); // 060306
+
+
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ if( localhom )
+ imp_match_out_vead_gapmap( currentw, gapmap1[0], lgth2, gapmap2 ); // 060306
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+ if( 1 ) // tsuneni outgap=1
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+ }
+
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0;
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap=1
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if 0
+ imp_match_out_vead( currentw, i, lgth2 );
+#else
+ imp_match_out_vead_gapmap( currentw, gapmap1[i], lgth2, gapmap2 );
+#endif
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+
+ mi = previousw[0] + ogcp2[1]; mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fgcp2pt = fgcp2;
+ ogcp2pt = ogcp2 + 1;
+ fgcp1va = fgcp1[i-1];
+ ogcp1va = ogcp1[i];
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + *fgcp2pt;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + *ogcp2pt;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fgcp1va;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + ogcp1va;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom_gapmap( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, gapmap1, gapmap2 );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, 1 );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ return( wm );
+}
+
--- /dev/null
+#include "mltaln.h"
+
+void profilealignment( int n0, int n1, int n2, char **aln0, char **aln1, char **aln2, int alloclen, char alg ) // n1 ha allgap
+{
+ int i, newlen;
+ double *effarr0, *effarr2;
+ float dumfl;
+ double eff;
+ effarr0 = AllocateDoubleVec( n0 );
+ effarr2 = AllocateDoubleVec( n2 );
+
+ commongappick( n0, aln0 );
+ commongappick( n2, aln2 );
+
+
+ eff = 1.0 / (double)n0; for( i=0; i<n0; i++ ) effarr0[i] = eff;
+ eff = 1.0 / (double)n2; for( i=0; i<n2; i++ ) effarr2[i] = eff;
+
+ if( alg == 'M' )
+ MSalignmm( aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 ); //outgap=1??
+ else
+ A__align( aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 ); //outgap=1??
+
+ newlen = strlen( aln0[0] );
+
+ for( i=0; i<newlen; i++ ) aln1[0][i] = '-';
+ aln1[0][i] = 0;
+ for( i=1; i<n1; i++ ) strcpy( aln1[i], aln1[0] );
+
+
+ free( effarr0 );
+ free( effarr2 );
+}
+
+void eq2dash( char *s )
+{
+ while( *s )
+ {
+ if( *s == '=' ) *s = '-';
+ s++;
+ }
+}
+
+void findnewgaps( int n, char **seq, int *gaplen )
+{
+ int i, pos, len;
+ len = strlen( seq[0] );
+
+// fprintf( stderr, "seq[0] = %s\n", seq[0] );
+ for( i=0; i<len; i++ ) gaplen[i] = 0;
+
+ pos = 0;
+ for( i=0; i<len; i++ )
+ {
+ if( seq[0][i] == '=' )
+ {
+// fprintf( stderr, "Newgap! pos = %d\n", pos );
+ gaplen[pos]++;
+ }
+ else
+ pos++;
+ }
+}
+
+void findcommongaps( int n, char **seq, int *gaplen )
+{
+ int i, j, pos, len, len1;
+ len = strlen( seq[0] );
+ len1 = len+1;
+
+// fprintf( stderr, "seq[0] = %s\n", seq[0] );
+ for( i=0; i<len1; i++ ) gaplen[i] = 0;
+
+ pos = 0;
+ for( i=0; i<len; i++ )
+ {
+ for( j=0; j<n; j++ )
+ if( seq[j][i] != '-' ) break;
+
+ if( j == n ) gaplen[pos]++;
+ else
+ pos++;
+ }
+#if 0
+ for( i=0; i<pos; i++ )
+ {
+ fprintf( stderr, "vec[%d] = %d\n", i, gaplen[i] );
+ }
+#endif
+}
+
+void adjustgapmap( int newlen, int *gapmap, char *seq )
+{
+ int j;
+ int pos;
+ int newlen1 = newlen+1;
+ int *tmpmap;
+
+ tmpmap = AllocateIntVec( newlen+2 );
+ j = 0;
+ pos = 0;
+ while( *seq )
+ {
+// fprintf( stderr, "j=%d *seq = %c\n", j, *seq );
+ if( *seq++ == '=' )
+ tmpmap[j++] = 0;
+ else
+ {
+ tmpmap[j++] = gapmap[pos++];
+ }
+ }
+ tmpmap[j++] = gapmap[pos];
+
+ for(j=0; j<newlen1; j++)
+ gapmap[j] = tmpmap[j];
+
+ free( tmpmap );
+}
+
+void insertnewgaps( int njob, int *alreadyaligned, char **seq, int *ex1, int *ex2, int *gaplen, int *gapmap, int alloclen, char alg )
+{
+ int *mar;
+ char *gaps;
+ char *cptr;
+ int i, j, k, len, rep, len0;
+ char **mseq2, **mseq0, **mseq1;
+ char **aseq;
+ int ngroup2, ngroup0, ngroup1;
+ int *list0, *list1, *list2;
+ int posin12, gapshift, newpos;
+
+ mar = calloc( njob, sizeof( int ) );
+ list0 = calloc( njob, sizeof( int ) );
+ list1 = calloc( njob, sizeof( int ) );
+ list2 = calloc( njob, sizeof( int ) );
+
+ for( i=0; i<njob; i++ ) mar[i] = 0;
+ for( i=0; i<njob; i++ )
+ {
+ if( alreadyaligned[i]==0 ) mar[i] = 3;
+ }
+ for( i=0; (k=ex1[i])>-1; i++ )
+ {
+ mar[k] = 1;
+// fprintf( stderr, "excluding %d\n", ex1[i] );
+ }
+ for( i=0; (k=ex2[i])>-1; i++ )
+ {
+ mar[k] = 2;
+// fprintf( stderr, "excluding %d\n", ex2[i] );
+ }
+
+ ngroup2 = ngroup1 = ngroup0 = 0;
+ for( i=0; i<njob; i++ )
+ {
+ if( mar[i] == 2 )
+ {
+ list2[ngroup2] = i;
+ ngroup2++;
+ }
+ if( mar[i] == 1 )
+ {
+ list1[ngroup1] = i;
+ ngroup1++;
+ }
+ if( mar[i] == 0 )
+ {
+ list0[ngroup0] = i;
+ ngroup0++;
+ }
+ }
+ list0[ngroup0] = list1[ngroup1] = list2[ngroup2] = -1;
+ if( ngroup0 == 0 )
+ {
+ fprintf( stderr, "Nothing to do\n" );
+ free( mar );
+ free( list0 );
+ free( list1 );
+ free( list2 );
+ return;
+ }
+
+ for( i=0; i<njob; i++ ) if( mar[i] == 0 ) break;
+ rep = i;
+ len = strlen( seq[rep] );
+ len0 = len+1;
+
+//
+// if( i == njob )
+// {
+//// fprintf( stderr, "Nothing to do\n" );
+// free( mar );
+// return;
+// }
+
+ mseq2 = AllocateCharMtx( ngroup2, alloclen );
+ mseq1 = AllocateCharMtx( ngroup1, alloclen );
+ mseq0 = AllocateCharMtx( ngroup0, alloclen );
+ aseq = AllocateCharMtx( njob, alloclen );
+ gaps = calloc( alloclen, sizeof( char ) );
+
+ for( i=0; i<njob; i++ ) aseq[i][0] = 0;
+ posin12 = 0;
+ for( j=0; j<len0; j++ )
+ {
+ if( gaplen[j] )
+ {
+ for( i=0; i<ngroup0; i++ ) mseq0[i][0] = 0;
+ for( i=0; i<ngroup1; i++ ) mseq1[i][0] = 0;
+ for( i=0; i<ngroup2; i++ ) mseq2[i][0] = 0;
+
+ gapshift = gaplen[j];
+ cptr = gaps;
+ while( gapshift-- ) *cptr++ = '-';
+ *cptr = 0;
+ gapshift = gaplen[j];
+
+ for( i=0; i<ngroup0; i++ ) strncat( mseq0[i], gaps, gapshift );
+ for( i=0; i<ngroup1; i++ ) strncat( mseq1[i], seq[list1[i]]+posin12, gapshift );
+ for( i=0; i<ngroup2; i++ ) strncat( mseq2[i], seq[list2[i]]+posin12, gapshift );
+ posin12 += gapshift;
+
+ gapshift = gapmap[posin12];
+// fprintf( stderr, "gapmap[%d] kouho = %d\n", posin12, gapmap[posin12] );
+
+
+ for( i=0; i<ngroup0; i++ ) strncat( mseq0[i], seq[list0[i]]+j, gapshift );
+ for( i=0; i<ngroup1; i++ ) strncat( mseq1[i], seq[list1[i]]+posin12, gapshift );
+ for( i=0; i<ngroup2; i++ ) strncat( mseq2[i], seq[list2[i]]+posin12, gapshift );
+#if 0
+ for( i=0; i<ngroup0; i++ ) fprintf( stderr, "### mseq0[%d] = %s\n", i, mseq0[i] );
+ for( i=0; i<ngroup1; i++ ) fprintf( stderr, "### mseq1[%d] = %s\n", i, mseq1[i] );
+ for( i=0; i<ngroup2; i++ ) fprintf( stderr, "### mseq2[%d] = %s\n", i, mseq2[i] );
+#endif
+
+ if( gapshift ) profilealignment( ngroup0, ngroup1, ngroup2, mseq0, mseq1, mseq2, alloclen, alg );
+
+ j += gapshift;
+ posin12 += gapshift;
+
+ for( i=0; i<ngroup0; i++ ) strcat( aseq[list0[i]], mseq0[i] );
+ for( i=0; i<ngroup1; i++ ) strcat( aseq[list1[i]], mseq1[i] );
+ for( i=0; i<ngroup2; i++ ) strcat( aseq[list2[i]], mseq2[i] );
+ }
+
+ newpos = strlen( aseq[rep] );
+ for( i=0; i<ngroup0; i++ ) aseq[list0[i]][newpos] = seq[list0[i]][j];
+ for( i=0; i<ngroup1; i++ ) aseq[list1[i]][newpos] = seq[list1[i]][posin12];
+ for( i=0; i<ngroup2; i++ ) aseq[list2[i]][newpos] = seq[list2[i]][posin12];
+ for( i=0; i<ngroup0; i++ ) aseq[list0[i]][newpos+1] = 0;
+ for( i=0; i<ngroup1; i++ ) aseq[list1[i]][newpos+1] = 0;
+ for( i=0; i<ngroup2; i++ ) aseq[list2[i]][newpos+1] = 0;
+
+ posin12++;
+ }
+
+// for( i=0; i<njob; i++ ) if( mar[i] != 3 ) strcpy( seq[i], aseq[i] );
+ for( i=0; i<ngroup0; i++ ) strcpy( seq[list0[i]], aseq[list0[i]] );
+ for( i=0; i<ngroup1; i++ ) strcpy( seq[list1[i]], aseq[list1[i]] );
+ for( i=0; i<ngroup2; i++ ) strcpy( seq[list2[i]], aseq[list2[i]] );
+
+ free( mar );
+ free( gaps );
+ free( list0 );
+ free( list1 );
+ free( list2 );
+ FreeCharMtx( mseq2 );
+ FreeCharMtx( mseq0 );
+}
+
+
+void restorecommongaps( int njob, char **seq, int *ex1, int *ex2, int *gaplen, int alloclen )
+{
+ int *mar;
+ char *tmpseq;
+ char *cptr;
+ int *iptr;
+ int *tmpgaplen;
+ int i, j, k, len, rep, len1;
+
+ mar = calloc( njob, sizeof( int ) );
+ tmpseq = calloc( alloclen, sizeof( char ) );
+ tmpgaplen = calloc( alloclen, sizeof( int ) );
+// tmpseq = calloc( alloclen+2, sizeof( char ) );
+// tmpgaplen = calloc( alloclen+2, sizeof( int ) );
+
+
+ for( i=0; i<njob; i++ ) mar[i] = 0;
+ for( i=0; (k=ex1[i])>-1; i++ )
+ {
+ mar[k] = 1;
+// fprintf( stderr, "excluding %d\n", ex1[i] );
+ }
+ for( i=0; (k=ex2[i])>-1; i++ )
+ {
+ mar[k] = 1;
+// fprintf( stderr, "excluding %d\n", ex2[i] );
+ }
+
+ for( i=0; i<njob; i++ )
+ if( mar[i] ) break;
+
+ if( i == njob )
+ {
+// fprintf( stderr, "Nothing to do\n" );
+ free( mar );
+ free( tmpseq );
+ free( tmpgaplen );
+ return;
+ }
+ rep = i;
+ len = strlen( seq[rep] );
+ len1 = len+1;
+
+
+ for( i=0; i<njob; i++ )
+ {
+ if( mar[i] == 0 ) continue;
+ cptr = tmpseq;
+ for( j=0; j<len1; j++ )
+ {
+ for( k=0; k<gaplen[j]; k++ )
+ *(cptr++) = '-';
+ *(cptr++) = seq[i][j];
+ }
+ *cptr = 0;
+ strcpy( seq[i], tmpseq );
+ }
+
+ iptr = tmpgaplen;
+ for( j=0; j<len1; j++ )
+ {
+ *(iptr++) = gaplen[j];
+ for( k=0; k<gaplen[j]; k++ )
+ *(iptr++) = 0;
+ }
+ *iptr = -1;
+
+ iptr = tmpgaplen;
+ while( *iptr != -1 ) *gaplen++ = *iptr++;
+
+ free( mar );
+ free( tmpseq );
+ free( tmpgaplen );
+}
+
+#if 0
+int samemember( int *mem, int *cand )
+{
+ int i, j;
+
+#if 0
+ fprintf( stderr, "mem = " );
+ for( i=0; mem[i]>-1; i++ ) fprintf( stderr, "%d ", mem[i] );
+ fprintf( stderr, "\n" );
+
+ fprintf( stderr, "cand = " );
+ for( i=0; cand[i]>-1; i++ ) fprintf( stderr, "%d ", cand[i] );
+ fprintf( stderr, "\n" );
+#endif
+
+ for( i=0, j=0; mem[i]>-1; )
+ {
+ if( mem[i++] != cand[j++] ) return( 0 );
+ }
+
+ if( cand[j] == -1 )
+ {
+ return( 1 );
+ }
+ else
+ {
+ return( 0 );
+ }
+}
+#else
+int samemember( int *mem, int *cand )
+{
+ int i, j;
+ int nm, nc;
+#if 0
+ fprintf( stderr, "mem = " );
+ for( i=0; mem[i]>-1; i++ ) fprintf( stderr, "%d ", mem[i] );
+ fprintf( stderr, "\n" );
+
+ fprintf( stderr, "cand = " );
+ for( i=0; cand[i]>-1; i++ ) fprintf( stderr, "%d ", cand[i] );
+ fprintf( stderr, "\n" );
+#endif
+
+ nm = 0; for( i=0; mem[i]>-1; i++ ) nm++;
+ nc = 0; for( i=0; cand[i]>-1; i++ ) nc++;
+
+ if( nm != nc ) return( 0 );
+
+ for( i=0; mem[i]>-1; i++ )
+ {
+ for( j=0; cand[j]>-1; j++ )
+ if( mem[i] == cand[j] ) break;
+ if( cand[j] == -1 ) return( 0 );
+ }
+
+ if( mem[i] == -1 )
+ {
+ return( 1 );
+ }
+ else
+ {
+ return( 0 );
+ }
+}
+#endif
+
+
+int includemember( int *mem, int *cand ) // mem in cand
+{
+ int i, j;
+
+#if 0
+ fprintf( stderr, "mem = " );
+ for( i=0; mem[i]>-1; i++ ) fprintf( stderr, "%d ", mem[i] );
+ fprintf( stderr, "\n" );
+
+ fprintf( stderr, "cand = " );
+ for( i=0; cand[i]>-1; i++ ) fprintf( stderr, "%d ", cand[i] );
+ fprintf( stderr, "\n" );
+#endif
+
+ for( i=0; mem[i]>-1; i++ )
+ {
+ for( j=0; cand[j]>-1; j++ )
+ if( mem[i] == cand[j] ) break;
+ if( cand[j] == -1 ) return( 0 );
+ }
+// fprintf( stderr, "INCLUDED! mem[0]=%d\n", mem[0] );
+ return( 1 );
+}
--- /dev/null
+#define DEFAULTGOP_B -1530
+#define DEFAULTGEP_B -00
+#define DEFAULTOFS_B -123 /* +10 -- -50 teido ka ? */
+
+void BLOSUMmtx( int n, double **matrix, double *freq, char *amino, char *amino_grp )
+{
+ /*
+ char locaminod[26] = "GASTPLIMVDNEQFYWKRHCXXX.-U";
+ */
+// char locaminod[] = "ARNDCQEGHILKMFPSTWYVBZX.-U";
+ char locaminod[] = "ARNDCQEGHILKMFPSTWYVBZX.-J";
+ char locgrpd[] =
+ {
+ 0, 3, 2, 2, 5, 2, 2, 0, 3, 1, 1, 3, 1, 4, 0, 0, 0, 4, 4, 1, 2, 2,
+ 6, 6, 6, 1,
+ };
+ double freqd[20] =
+ {
+ 0.077,
+ 0.051,
+ 0.043,
+ 0.052,
+ 0.020,
+ 0.041,
+ 0.062,
+ 0.074,
+ 0.023,
+ 0.052,
+ 0.091,
+ 0.059,
+ 0.024,
+ 0.040,
+ 0.051,
+ 0.069,
+ 0.059,
+ 0.014,
+ 0.032,
+ 0.066,
+ };
+
+ double tmpmtx30[] =
+ {
+ 4,
+ -1, 8,
+ 0, -2, 8,
+ 0, -1, 1, 9,
+ -3, -2, -1, -3, 17,
+ 1, 3, -1, -1, -2, 8,
+ 0, -1, -1, 1, 1, 2, 6,
+ 0, -2, 0, -1, -4, -2, -2, 8,
+ -2, -1, -1, -2, -5, 0, 0, -3, 14,
+ 0, -3, 0, -4, -2, -2, -3, -1, -2, 6,
+ -1, -2, -2, -1, 0, -2, -1, -2, -1, 2, 4,
+ 0, 1, 0, 0, -3, 0, 2, -1, -2, -2, -2, 4,
+ 1, 0, 0, -3, -2, -1, -1, -2, 2, 1, 2, 2, 6,
+ -2, -1, -1, -5, -3, -3, -4, -3, -3, 0, 2, -1, -2, 10,
+ -1, -1, -3, -1, -3, 0, 1, -1, 1, -3, -3, 1, -4, -4, 11,
+ 1, -1, 0, 0, -2, -1, 0, 0, -1, -1, -2, 0, -2, -1, -1, 4,
+ 1, -3, 1, -1, -2, 0, -2, -2, -2, 0, 0, -1, 0, -2, 0, 2, 5,
+ -5, 0, -7, -4, -2, -1, -1, 1, -5, -3, -2, -2, -3, 1, -3, -3, -5, 20,
+ -4, 0, -4, -1, -6, -1, -2, -3, 0, -1, 3, -1, -1, 3, -2, -2, -1, 5, 9,
+ 1, -1, -2, -2, -2, -3, -3, -3, -3, 4, 1, -2, 0, 1, -4, -1, 1, -3, 1, 5,
+ 0, -2, 4, 5, -2, -1, 0, 0, -2, -2, -1, 0, -2, -3, -2, 0, 0, -5, -3, -2, 5,
+ 0, 0, -1, 0, 0, 4, 5, -2, 0, -3, -1, 1, -1, -4, 0, -1, -1, -1, -2, -3, 0, 4,
+ 0, -1, 0, -1, -2, 0, -1, -1, -1, 0, 0, 0, 0, -1, -1, 0, 0, -2, -1, 0, -1, 0, -1,
+ };
+
+ double tmpmtx45[] =
+ {
+ 5,
+ -2, 7,
+ -1, 0, 6,
+ -2, -1, 2, 7,
+ -1, -3, -2, -3, 12,
+ -1, 1, 0, 0, -3, 6,
+ -1, 0, 0, 2, -3, 2, 6,
+ 0, -2, 0, -1, -3, -2, -2, 7,
+ -2, 0, 1, 0, -3, 1, 0, -2, 10,
+ -1, -3, -2, -4, -3, -2, -3, -4, -3, 5,
+ -1, -2, -3, -3, -2, -2, -2, -3, -2, 2, 5,
+ -1, 3, 0, 0, -3, 1, 1, -2, -1, -3, -3, 5,
+ -1, -1, -2, -3, -2, 0, -2, -2, 0, 2, 2, -1, 6,
+ -2, -2, -2, -4, -2, -4, -3, -3, -2, 0, 1, -3, 0, 8,
+ -1, -2, -2, -1, -4, -1, 0, -2, -2, -2, -3, -1, -2, -3, 9,
+ 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -3, -1, -2, -2, -1, 4,
+ 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, 2, 5,
+ -2, -2, -4, -4, -5, -2, -3, -2, -3, -2, -2, -2, -2, 1, -3, -4, -3, 15,
+ -2, -1, -2, -2, -3, -1, -2, -3, 2, 0, 0, -1, 0, 3, -3, -2, -1, 3, 8,
+ 0, -2, -3, -3, -1, -3, -3, -3, -3, 3, 1, -2, 1, 0, -3, -1, 0, -3, -1, 5,
+ };
+ double tmpmtx50[] =
+ {
+ 5,
+ -2, 7,
+ -1, -1, 7,
+ -2, -2, 2, 8,
+ -1, -4, -2, -4, 13,
+ -1, 1, 0, 0, -3, 7,
+ -1, 0, 0, 2, -3, 2, 6,
+ 0, -3, 0, -1, -3, -2, -3, 8,
+ -2, 0, 1, -1, -3, 1, 0, -2, 10,
+ -1, -4, -3, -4, -2, -3, -4, -4, -4, 5,
+ -2, -3, -4, -4, -2, -2, -3, -4, -3, 2, 5,
+ -1, 3, 0, -1, -3, 2, 1, -2, 0, -3, -3, 6,
+ -1, -2, -2, -4, -2, 0, -2, -3, -1, 2, 3, -2, 7,
+ -3, -3, -4, -5, -2, -4, -3, -4, -1, 0, 1, -4, 0, 8,
+ -1, -3, -2, -1, -4, -1, -1, -2, -2, -3, -4, -1, -3, -4, 10,
+ 1, -1, 1, 0, -1, 0, -1, 0, -1, -3, -3, 0, -2, -3, -1, 5,
+ 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 2, 5,
+ -3, -3, -4, -5, -5, -1, -3, -3, -3, -3, -2, -3, -1, 1, -4, -4, -3, 15,
+ -2, -1, -2, -3, -3, -1, -2, -3, 2, -1, -1, -2, 0, 4, -3, -2, -2, 2, 8,
+ 0, -3, -3, -4, -1, -3, -3, -4, -4, 4, 1, -3, 1, -1, -3, -2, 0, -3, -1, 5,
+ };
+ double tmpmtx62[] =
+ {
+ 6,
+ -2, 8,
+ -2, -1, 8,
+ -3, -2, 2, 9,
+ -1, -5, -4, -5, 13,
+ -1, 1, 0, 0, -4, 8,
+ -1, 0, 0, 2, -5, 3, 7,
+ 0, -3, -1, -2, -4, -3, -3, 8,
+ -2, 0, 1, -2, -4, 1, 0, -3, 11,
+ -2, -4, -5, -5, -2, -4, -5, -6, -5, 6,
+ -2, -3, -5, -5, -2, -3, -4, -5, -4, 2, 6,
+ -1, 3, 0, -1, -5, 2, 1, -2, -1, -4, -4, 7,
+ -1, -2, -3, -5, -2, -1, -3, -4, -2, 2, 3, -2, 8,
+ -3, -4, -4, -5, -4, -5, -5, -5, -2, 0, 1, -5, 0, 9,
+ -1, -3, -3, -2, -4, -2, -2, -3, -3, -4, -4, -2, -4, -5, 11,
+ 2, -1, 1, 0, -1, 0, 0, 0, -1, -4, -4, 0, -2, -4, -1, 6,
+ 0, -2, 0, -2, -1, -1, -1, -2, -3, -1, -2, -1, -1, -3, -2, 2, 7,
+ -4, -4, -6, -6, -3, -3, -4, -4, -4, -4, -2, -4, -2, 1, -5, -4, -4, 16,
+ -3, -3, -3, -5, -4, -2, -3, -5, 3, -2, -2, -3, -1, 4, -4, -3, -2, 3, 10,
+ 0, -4, -4, -5, -1, -3, -4, -5, -5, 4, 1, -3, 1, -1, -4, -2, 0, -4, -2, 6,
+ };
+ double tmpmtx80[] =
+ {
+ 7,
+ -3, 9,
+ -3, -1, 9,
+ -3, -3, 2, 10,
+ -1, -6, -5, -7, 13,
+ -2, 1, 0, -1, -5, 9,
+ -2, -1, -1, 2, -7, 3, 8,
+ 0, -4, -1, -3, -6, -4, -4, 9,
+ -3, 0, 1, -2, -7, 1, 0, -4, 12,
+ -3, -5, -6, -7, -2, -5, -6, -7, -6, 7,
+ -3, -4, -6, -7, -3, -4, -6, -7, -5, 2, 6,
+ -1, 3, 0, -2, -6, 2, 1, -3, -1, -5, -4, 8,
+ -2, -3, -4, -6, -3, -1, -4, -5, -4, 2, 3, -3, 9,
+ -4, -5, -6, -6, -4, -5, -6, -6, -2, -1, 0, -5, 0, 10,
+ -1, -3, -4, -3, -6, -3, -2, -5, -4, -5, -5, -2, -4, -6, 12,
+ 2, -2, 1, -1, -2, -1, -1, -1, -2, -4, -4, -1, -3, -4, -2, 7,
+ 0, -2, 0, -2, -2, -1, -2, -3, -3, -2, -3, -1, -1, -4, -3, 2, 8,
+ -5, -5, -7, -8, -5, -4, -6, -6, -4, -5, -4, -6, -3, 0, -7, -6, -5, 16,
+ -4, -4, -4, -6, -5, -3, -5, -6, 3, -3, -2, -4, -3, 4, -6, -3, -3, 3, 11,
+ -1, -4, -5, -6, -2, -4, -4, -6, -5, 4, 1, -4, 1, -2, -4, -3, 0, -5, -3, 7,
+ };
+ double tmpmtx0[] =
+ {
+ 2.4,
+ -0.6, 4.7,
+ -0.3, 0.3, 3.8,
+ -0.3, -0.3, 2.2, 4.7,
+ 0.5, -2.2, -1.8, -3.2, 11.5,
+ -0.2, 1.5, 0.7, 0.9, -2.4, 2.7,
+ 0.0, 0.4, 0.9, 2.7, -3.0, 1.7, 3.6,
+ 0.5, -1.0, 0.4, 0.1, -2.0, -1.0, -0.8, 6.6,
+ -0.8, 0.6, 1.2, 0.4, -1.3, 1.2, 0.4, -1.4, 6.0,
+ -0.8, -2.4, -2.8, -3.8, -1.1, -1.9, -2.7, -4.5, -2.2, 4.0,
+ -1.2, -2.2, -3.0, -4.0, -1.5, -1.6, -2.8, -4.4, -1.9, 2.8, 4.0,
+ -0.4, 2.7, 0.8, 0.5, -2.8, 1.5, 1.2, -1.1, 0.6, -2.1, -2.1, 3.2,
+ -0.7, -1.7, -2.2, -3.0, -0.9, -1.0, -2.0, -3.5, -1.3, 2.5, 2.8, -1.4, 4.3,
+ -2.3, -3.2, -3.1, -4.5, -0.8, -2.6, -3.9, -5.2, -0.1, 1.0, 2.0, -3.3, 1.6, 7.0,
+ 0.3, -0.9, -0.9, -0.7, -3.1, -0.2, -0.5, -1.6, -1.1, -2.6, -2.3, -0.6, -2.4, -3.8, 7.6,
+ 1.1, -0.2, 0.9, 0.5, 0.1, 0.2, 0.2, 0.4, -0.2, -1.8, -2.1, 0.1, -1.4, -2.8, 0.4, 2.2,
+ 0.6, -0.2, 0.5, 0.0, -0.5, 0.0, -0.1, -1.1, -0.3, -0.6, -1.3, 0.1, -0.6, -2.2, 0.1, 1.5, 2.5,
+ -3.6, -1.6, -3.6, -5.2, -1.0, -2.7, -4.3, -4.0, -0.8, -1.8, -0.7, -3.5, -1.0, 3.6, -5.0, -3.3, -3.5, 14.2,
+ -2.2, -1.8, -1.4, -2.8, -0.5, -1.7, -2.7, -4.0, 2.2, -0.7, 0.0, -2.1, -0.2, 5.1, -3.1, -1.9, -1.9, 4.1, 7.8,
+ 0.1, -2.0, -2.2, -2.9, 0.0, -1.5, -1.9, -3.3, -2.0, 3.1, 1.8, -1.7, 1.6, 0.1, -1.8, -1.0, 0.0, -2.6, -1.1, 3.4,
+ };
+
+ int i, j, count;
+ double av;
+ double *tmpmtx;
+
+ if( n == 30 ) tmpmtx = tmpmtx30;
+ else if( n == 45 ) tmpmtx = tmpmtx45;
+ else if( n == 50 ) tmpmtx = tmpmtx50;
+ else if( n == 62 ) tmpmtx = tmpmtx62;
+ else if( n == 80 ) tmpmtx = tmpmtx80;
+ else if( n == 0 ) tmpmtx = tmpmtx0;
+ else if( n == -1 ) tmpmtx = loadaamtx();
+ else
+ {
+ fprintf( stderr, "blosum %d ?\n", n );
+ exit( 1 );
+ }
+
+ count = 0;
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ matrix[i][j] = matrix[j][i] = (double)tmpmtx[count++];
+ }
+ }
+ if( n == -1 && tmpmtx[400] != -1.0 )
+ {
+ for( i=0; i<20; i++ ) freq[i] = tmpmtx[400+i];
+ av = 0.0;
+ for( i=0; i<20; i++ ) av += freq[i];
+ for( i=0; i<20; i++ ) freq[i] /= av;
+ }
+ else
+ for( i=0; i<20; i++ ) freq[i] = freqd[i];
+
+#if 0
+ av = 0.0;
+ for( i=0; i<20; i++ )
+ av += matrix[i][i];
+ av /= 20;
+ fprintf( stdout, "av = %f\n", av );
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ matrix[i][j] /= av;
+
+ av = wav = 0;
+ count = 0;
+ wcount = 0.0;
+ tmptmp = 0.0;
+ for( i=0; i<20; i++ )
+ {
+ fprintf( stdout, "freq[%d] = %f\n", i, freq[i] );
+ tmptmp += freq[i];
+ for( j=0; j<20; j++ )
+ {
+ av += matrix[i][j];
+ wav += freq[i] * freq[j] * matrix[i][j];
+ count++;
+ wcount += freq[i] * freq[j];
+ }
+ }
+
+ av /= count;
+ wav /= wcount;
+ fprintf( stdout, "av = %f\n", av );
+ fprintf( stdout, "wav = %f\n", wav );
+ fprintf( stdout, "wcount = %f\n", wcount );
+ fprintf( stdout, "tmptmp = %f\n", tmptmp );
+
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stderr, "## %d-%d, %f\n", i, j, matrix[i][j] );
+ }
+ }
+
+ exit( 1 );
+#endif
+
+ for( i=0; i<26; i++ ) amino[i] = locaminod[i];
+ for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpd[i];
+}
--- /dev/null
+/*
+int locpenaltyd = -2400;
+int locoffsetd = -60;
+char locaminod[26] = "GASTPLIMVDNEQFYWKRHCXXX.-U";
+char locaminod[] = "ARNDCQEGHILKMFPSTWYVBZX.-U";
+char locgrpd[] =
+{
+ 0, 3, 2, 2, 5, 2, 2, 0, 3, 1, 1, 3, 1, 4, 0, 0, 0, 4, 4, 1, 2, 2,
+ 6, 6, 6, 6,
+};
+*/
--- /dev/null
+#include "mltaln.h"
+#include "miyata.h"
+#include "miyata5.h"
+#include "DNA.h"
+
+#include "JTT.c"
+#include "blosum.c"
+
+#define DEBUG 0
+#define TEST 0
+
+#define NORMALIZE1 1
+
+static int shishagonyuu( double in )
+{
+ int out;
+ if ( in > 0.0 ) out = ( (int)( in + 0.5 ) );
+ else if( in == 0.0 ) out = ( 0 );
+ else if( in < 0.0 ) out = ( (int)( in - 0.5 ) );
+ else out = 0;
+ return( out );
+}
+
+static void calcfreq_nuc( int nseq, char **seq, double *datafreq )
+{
+ int i, j, l;
+ int aan;
+ double total;
+ for( i=0; i<4; i++ )
+ datafreq[i] = 0.0;
+ total = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ l = strlen( seq[i] );
+ for( j=0; j<l; j++ )
+ {
+ aan = amino_n[(int)seq[i][j]];
+ if( aan == 4 ) aan = 3;
+ if( aan >= 0 && aan < 4 )
+ {
+ datafreq[aan] += 1.0;
+ total += 1.0;
+ }
+ }
+ }
+ for( i=0; i<4; i++ )
+ if( datafreq[i] < 0.0001 ) datafreq[i] = 0.0001;
+
+
+ total = 0.0; for( i=0; i<4; i++ ) total += datafreq[i];
+// fprintf( stderr, "total = %f\n", total );
+ for( i=0; i<4; i++ ) datafreq[i] /= (double)total;
+
+#if 0
+ fprintf( stderr, "\ndatafreq = " );
+ for( i=0; i<4; i++ )
+ fprintf( stderr, "%10.5f ", datafreq[i] );
+ fprintf( stderr, "\n" );
+ exit( 1 );
+#endif
+}
+
+static void calcfreq( int nseq, char **seq, double *datafreq )
+{
+ int i, j, l;
+ int aan;
+ double total;
+ for( i=0; i<20; i++ )
+ datafreq[i] = 0.0;
+ total = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ l = strlen( seq[i] );
+ for( j=0; j<l; j++ )
+ {
+ aan = amino_n[(int)seq[i][j]];
+ if( aan >= 0 && aan < 20 )
+ {
+ datafreq[aan] += 1.0;
+ total += 1.0;
+ }
+ }
+ }
+ for( i=0; i<20; i++ )
+ if( datafreq[i] < 0.0001 ) datafreq[i] = 0.0001;
+
+ fprintf( stderr, "datafreq = \n" );
+ for( i=0; i<20; i++ )
+ fprintf( stderr, "%f\n", datafreq[i] );
+
+ total = 0.0; for( i=0; i<20; i++ ) total += datafreq[i];
+ fprintf( stderr, "total = %f\n", total );
+ for( i=0; i<20; i++ ) datafreq[i] /= (double)total;
+}
+
+void constants( int nseq, char **seq )
+{
+ int i, j, x;
+// double tmp;
+
+ if( dorp == 'd' ) /* DNA */
+ {
+ int k, m;
+ double average;
+ double **pamx = AllocateDoubleMtx( 11,11 );
+ double **pam1 = AllocateDoubleMtx( 4, 4 );
+ double *freq = AllocateDoubleVec( 4 );
+
+
+ scoremtx = -1;
+ if( RNAppenalty == NOTSPECIFIED ) RNAppenalty = DEFAULTRNAGOP_N;
+ if( RNAppenalty_ex == NOTSPECIFIED ) RNAppenalty_ex = DEFAULTRNAGEP_N;
+ if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_N;
+ if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_N;
+ if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_N;
+ if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_N;
+ if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_N;
+ if( RNApthr == NOTSPECIFIED ) RNApthr = DEFAULTRNATHR_N;
+ if( pamN == NOTSPECIFIED ) pamN = DEFAULTPAMN;
+ if( kimuraR == NOTSPECIFIED ) kimuraR = 2;
+
+ RNApenalty = (int)( 3 * 600.0 / 1000.0 * RNAppenalty + 0.5 );
+ RNApenalty_ex = (int)( 3 * 600.0 / 1000.0 * RNAppenalty_ex + 0.5 );
+// fprintf( stderr, "DEFAULTRNAGOP_N = %d\n", DEFAULTRNAGOP_N );
+// fprintf( stderr, "RNAppenalty = %d\n", RNAppenalty );
+// fprintf( stderr, "RNApenalty = %d\n", RNApenalty );
+
+
+ RNAthr = (int)( 3 * 600.0 / 1000.0 * RNApthr + 0.5 );
+ penalty = (int)( 3 * 600.0 / 1000.0 * ppenalty + 0.5);
+ penalty_OP = (int)( 3 * 600.0 / 1000.0 * ppenalty_OP + 0.5);
+ penalty_ex = (int)( 3 * 600.0 / 1000.0 * ppenalty_ex + 0.5);
+ penalty_EX = (int)( 3 * 600.0 / 1000.0 * ppenalty_EX + 0.5);
+ offset = (int)( 3 * 600.0 / 1000.0 * poffset + 0.5);
+ offsetFFT = (int)( 3 * 600.0 / 1000.0 * (-0) + 0.5);
+ offsetLN = (int)( 3 * 600.0 / 1000.0 * 100 + 0.5);
+ penaltyLN = (int)( 3 * 600.0 / 1000.0 * -2000 + 0.5);
+ penalty_exLN = (int)( 3 * 600.0 / 1000.0 * -100 + 0.5);
+ sprintf( modelname, "%s%d (%d), %6.3f (%6.3f), %6.3f (%6.3f)", rnakozo?"RNA":"DNA", pamN, kimuraR,
+ -(double)ppenalty*0.001, -(double)ppenalty*0.003, -(double)poffset*0.001, -(double)poffset*0.003 );
+
+ if( kimuraR == 9999 )
+ {
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] = (double)locn_disn[i][j];
+#if NORMALIZE1
+ average = 0.0;
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ average += pamx[i][j];
+ average /= 16.0;
+
+ if( disp )
+ fprintf( stderr, "average = %f\n", average );
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] -= average;
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] *= 600.0 / average;
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] -= offset;
+#endif
+ }
+ else
+ {
+ double f = 0.99;
+ double s = (double)kimuraR / ( 2 + kimuraR ) * 0.01;
+ double v = (double)1 / ( 2 + kimuraR ) * 0.01;
+ pam1[0][0] = f; pam1[0][1] = s; pam1[0][2] = v; pam1[0][3] = v;
+ pam1[1][0] = s; pam1[1][1] = f; pam1[1][2] = v; pam1[1][3] = v;
+ pam1[2][0] = v; pam1[2][1] = v; pam1[2][2] = f; pam1[2][3] = s;
+ pam1[3][0] = v; pam1[3][1] = v; pam1[3][2] = s; pam1[3][3] = f;
+
+ fprintf( stderr, "generating %dPAM scoring matrix for nucleotides ... ", pamN );
+
+ if( disp )
+ {
+ fprintf( stderr, " TPM \n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pam1[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+
+ MtxuntDouble( pamx, 4 );
+ for( x=0; x < pamN; x++ ) MtxmltDouble( pamx, pam1, 4 );
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] /= 1.0 / 4.0;
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ {
+ if( pamx[i][j] == 0.0 )
+ {
+ fprintf( stderr, "WARNING: pamx[i][j] = 0.0 ?\n" );
+ pamx[i][j] = 0.00001; /* by J. Thompson */
+ }
+ pamx[i][j] = log10( pamx[i][j] ) * 1000.0;
+ }
+
+ if( disp )
+ {
+ fprintf( stderr, " after log\n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pamx[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+
+// ?????
+ for( i=0; i<26; i++ ) amino[i] = locaminon[i];
+ for( i=0; i<0x80; i++ ) amino_n[i] = -1;
+ for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
+ if( fmodel == 1 )
+ calcfreq_nuc( nseq, seq, freq );
+ else
+ {
+ freq[0] = 0.25;
+ freq[1] = 0.25;
+ freq[2] = 0.25;
+ freq[3] = 0.25;
+ }
+// fprintf( stderr, "a, freq[0] = %f\n", freq[0] );
+// fprintf( stderr, "g, freq[1] = %f\n", freq[1] );
+// fprintf( stderr, "c, freq[2] = %f\n", freq[2] );
+// fprintf( stderr, "t, freq[3] = %f\n", freq[3] );
+
+
+ average = 0.0;
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ average += pamx[i][j] * freq[i] * freq[j];
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] -= average;
+
+ average = 0.0;
+ for( i=0; i<4; i++ )
+ average += pamx[i][i] * 1.0 / 4.0;
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] *= 600.0 / average;
+
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] -= offset; /* extending gap cost */
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] = shishagonyuu( pamx[i][j] );
+
+ if( disp )
+ {
+ fprintf( stderr, " after shishagonyuu\n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pamx[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "done\n" );
+ }
+
+ for( i=0; i<5; i++ )
+ {
+ pamx[4][i] = pamx[3][i];
+ pamx[i][4] = pamx[i][3];
+ }
+
+ for( i=5; i<10; i++ ) for( j=5; j<10; j++ )
+ {
+ pamx[i][j] = pamx[i-5][j-5];
+ }
+
+ if( disp )
+ {
+ fprintf( stderr, " before dis\n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pamx[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ if( disp )
+ {
+ fprintf( stderr, " score matrix \n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pamx[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ for( i=0; i<26; i++ ) amino[i] = locaminon[i];
+ for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpn[i];
+ for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
+ for( i=0; i<10; i++ ) for( j=0; j<10; j++ ) n_dis[i][j] = shishagonyuu( pamx[i][j] );
+ if( disp )
+ {
+ fprintf( stderr, " score matrix \n" );
+ for( i=0; i<26; i++ )
+ {
+ for( j=0; j<26; j++ )
+ fprintf( stderr, "%+6d", n_dis[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+// RIBOSUM
+#if 1
+ average = 0.0;
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ average += ribosum4[i][j] * freq[i] * freq[j];
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ ribosum4[i][j] -= average;
+
+ average = 0.0;
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ ) for( k=0; k<4; k++ ) for( m=0; m<4; m++ )
+ {
+// if( i%4==0&&j%4==3 || i%4==3&&j%4==0 || i%4==1&&j%4==2 || i%4==2&&j%4==1 || i%4==1&&j%4==3 || i%4==3&&j%4==1 )
+// if( k%4==0&&m%4==3 || k%4==3&&m%4==0 || k%4==1&&m%4==2 || k%4==2&&m%4==1 || k%4==1&&m%4==3 || k%4==3&&m%4==1 )
+ average += ribosum16[i*4+j][k*4+m] * freq[i] * freq[j] * freq[k] * freq[m];
+ }
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
+ ribosum16[i][j] -= average;
+
+ average = 0.0;
+ for( i=0; i<4; i++ )
+ average += ribosum4[i][i] * freq[i];
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ ribosum4[i][j] *= 600.0 / average;
+
+ average = 0.0;
+ average += ribosum16[0*4+3][0*4+3] * freq[0] * freq[3]; // AU
+ average += ribosum16[3*4+0][3*4+0] * freq[3] * freq[0]; // UA
+ average += ribosum16[1*4+2][1*4+2] * freq[1] * freq[2]; // CG
+ average += ribosum16[2*4+1][2*4+1] * freq[2] * freq[1]; // GC
+ average += ribosum16[1*4+3][1*4+3] * freq[1] * freq[3]; // GU
+ average += ribosum16[3*4+1][3*4+1] * freq[3] * freq[1]; // UG
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
+ ribosum16[i][j] *= 600.0 / average;
+
+
+#if 1
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ ribosum4[i][j] -= offset; /* extending gap cost ?????*/
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
+ ribosum16[i][j] -= offset; /* extending gap cost ?????*/
+#endif
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ ribosum4[i][j] = shishagonyuu( ribosum4[i][j] );
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
+ ribosum16[i][j] = shishagonyuu( ribosum16[i][j] );
+
+ if( disp )
+ {
+ fprintf( stderr, "ribosum after shishagonyuu\n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", ribosum4[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "ribosum16 after shishagonyuu\n" );
+ for( i=0; i<16; i++ )
+ {
+ for( j=0; j<16; j++ )
+ fprintf( stderr, "%+#7.0f", ribosum16[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "done\n" );
+
+#if 1
+ for( i=0; i<37; i++ ) for( j=0; j<37; j++ ) ribosumdis[i][j] = 0.0; //iru
+ for( m=0; m<9; m++ ) for( i=0; i<4; i++ ) // loop
+ for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = ribosum4[i][j]; // loop-loop
+// for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = n_dis[i][j]; // loop-loop
+
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ ) ribosumdis[i+4][j+4] = ribosum16[i][j]; // stem5-stem5
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ ) ribosumdis[i+20][j+20] = ribosum16[i][j]; // stem5-stem5
+#else // do not use ribosum
+ for( i=0; i<37; i++ ) for( j=0; j<37; j++ ) ribosumdis[i][j] = 0.0; //iru
+ for( m=0; m<9; m++ ) for( i=0; i<4; i++ ) // loop
+ for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = n_dis[i][j]; // loop-loop
+#endif
+
+ if( disp )
+ {
+ fprintf( stderr, "ribosumdis\n" );
+ for( i=0; i<37; i++ )
+ {
+ for( j=0; j<37; j++ )
+ fprintf( stderr, "%+5d", ribosumdis[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "done\n" );
+#endif
+
+ FreeDoubleMtx( pam1 );
+ FreeDoubleMtx( pamx );
+ free( freq );
+
+ }
+ else if( dorp == 'p' && scoremtx == 1 ) /* Blosum */
+ {
+ double *freq;
+ double *freq1;
+ double *datafreq;
+ double average;
+// double tmp;
+ double **n_distmp;
+
+ n_distmp = AllocateDoubleMtx( 20, 20 );
+ datafreq = AllocateDoubleVec( 20 );
+ freq = AllocateDoubleVec( 20 );
+
+ if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_B;
+ if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_B;
+ if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_B;
+ if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_B;
+ if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_B;
+ if( pamN == NOTSPECIFIED ) pamN = 0;
+ if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
+ penalty = (int)( 600.0 / 1000.0 * ppenalty + 0.5 );
+ penalty_OP = (int)( 600.0 / 1000.0 * ppenalty_OP + 0.5 );
+ penalty_ex = (int)( 600.0 / 1000.0 * ppenalty_ex + 0.5 );
+ penalty_EX = (int)( 600.0 / 1000.0 * ppenalty_EX + 0.5 );
+ offset = (int)( 600.0 / 1000.0 * poffset + 0.5 );
+ offsetFFT = (int)( 600.0 / 1000.0 * (-0) + 0.5);
+ offsetLN = (int)( 600.0 / 1000.0 * 100 + 0.5);
+ penaltyLN = (int)( 600.0 / 1000.0 * -2000 + 0.5);
+ penalty_exLN = (int)( 600.0 / 1000.0 * -100 + 0.5);
+
+ BLOSUMmtx( nblosum, n_distmp, freq, amino, amino_grp );
+ if( nblosum == -1 )
+ sprintf( modelname, "User-defined, %6.3f, %+6.3f, %+6.3f", -(double)ppenalty/1000, -(double)poffset/1000, -(double)ppenalty_ex/1000 );
+ else
+ sprintf( modelname, "BLOSUM%d, %6.3f, %+6.3f, %+6.3f", nblosum, -(double)ppenalty/1000, -(double)poffset/1000, -(double)ppenalty_ex/1000 );
+#if 0
+ for( i=0; i<26; i++ ) amino[i] = locaminod[i];
+ for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpd[i];
+ for( i=0; i<0x80; i++ ) amino_n[i] = 0;
+ for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
+#endif
+ for( i=0; i<0x80; i++ )amino_n[i] = -1;
+ for( i=0; i<26; i++) amino_n[(int)amino[i]] = i;
+ if( fmodel == 1 )
+ {
+ calcfreq( nseq, seq, datafreq );
+ freq1 = datafreq;
+ }
+ else
+ freq1 = freq;
+#if TEST
+ fprintf( stderr, "raw scoreing matrix : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%6.2f", n_distmp[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+ if( fmodel == -1 )
+ average = 0.0;
+ else
+ {
+ for( i=0; i<20; i++ )
+#if TEST
+ fprintf( stdout, "freq[%c] = %f, datafreq[%c] = %f, freq1[] = %f\n", amino[i], freq[i], amino[i], datafreq[i], freq1[i] );
+#endif
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += n_distmp[i][j] * freq1[i] * freq1[j];
+ }
+#if TEST
+ fprintf( stdout, "####### average2 = %f\n", average );
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ n_distmp[i][j] -= average;
+#if TEST
+ fprintf( stdout, "average2 = %f\n", average );
+ fprintf( stdout, "after average substruction : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%6.2f", n_distmp[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ average = 0.0;
+ for( i=0; i<20; i++ )
+ average += n_distmp[i][i] * freq1[i];
+#if TEST
+ fprintf( stdout, "####### average1 = %f\n", average );
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ n_distmp[i][j] *= 600.0 / average;
+#if TEST
+ fprintf( stdout, "after average division : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stdout, "%7.1f", n_distmp[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ n_distmp[i][j] -= offset;
+#if TEST
+ fprintf( stdout, "after offset substruction (offset = %d): \n", offset );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stdout, "%7.1f", n_distmp[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+#if 0
+/* Ãí°Õ ¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª */
+ penalty -= offset;
+#endif
+
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ n_distmp[i][j] = shishagonyuu( n_distmp[i][j] );
+
+ if( disp )
+ {
+ fprintf( stdout, " scoring matrix \n" );
+ for( i=0; i<20; i++ )
+ {
+ fprintf( stdout, "%c ", amino[i] );
+ for( j=0; j<20; j++ )
+ fprintf( stdout, "%5.0f", n_distmp[i][j] );
+ fprintf( stdout, "\n" );
+ }
+ fprintf( stdout, " " );
+ for( i=0; i<20; i++ )
+ fprintf( stdout, " %c", amino[i] );
+
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += n_distmp[i][j] * freq1[i] * freq1[j];
+ fprintf( stdout, "average = %f\n", average );
+
+ average = 0.0;
+ for( i=0; i<20; i++ )
+ average += n_distmp[i][i] * freq1[i];
+ fprintf( stdout, "itch average = %f\n", average );
+ fprintf( stderr, "parameters: %d, %d, %d\n", penalty, penalty_ex, offset );
+
+
+ exit( 1 );
+ }
+
+ for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ ) n_dis[i][j] = (int)n_distmp[i][j];
+
+ FreeDoubleMtx( n_distmp );
+ FreeDoubleVec( datafreq );
+ FreeDoubleVec( freq );
+
+ fprintf( stderr, "done.\n" );
+
+ }
+ else if( dorp == 'p' && scoremtx == 2 ) /* Miyata-Yasunaga */
+ {
+ fprintf( stderr, "Not supported\n" );
+ exit( 1 );
+ for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = locn_dism[i][j];
+ for( i=0; i<26; i++ ) if( i != 24 ) n_dis[i][24] = n_dis[24][i] = exgpm;
+ n_dis[24][24] = 0;
+ if( ppenalty == NOTSPECIFIED ) ppenalty = locpenaltym;
+ if( poffset == NOTSPECIFIED ) poffset = -20;
+ if( pamN == NOTSPECIFIED ) pamN = 0;
+ if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
+
+ penalty = ppenalty;
+ offset = poffset;
+
+ sprintf( modelname, "Miyata-Yasunaga, %6.3f, %6.3f", -(double)ppenalty/1000, -(double)poffset/1000 );
+ for( i=0; i<26; i++ ) amino[i] = locaminom[i];
+ for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpm[i];
+#if DEBUG
+ fprintf( stdout, "scoreing matrix : \n" );
+ for( i=0; i<26; i++ )
+ {
+ for( j=0; j<26; j++ )
+ {
+ fprintf( stdout, "%#5d", n_dis[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+ }
+ else /* JTT */
+ {
+ double **rsr;
+ double **pam1;
+ double **pamx;
+ double *freq;
+ double *freq1;
+ double *mutab;
+ double *datafreq;
+ double average;
+ double tmp;
+ double delta;
+
+ rsr = AllocateDoubleMtx( 20, 20 );
+ pam1 = AllocateDoubleMtx( 20, 20 );
+ pamx = AllocateDoubleMtx( 20, 20 );
+ freq = AllocateDoubleVec( 20 );
+ mutab = AllocateDoubleVec( 20 );
+ datafreq = AllocateDoubleVec( 20 );
+
+ if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_J;
+ if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_J;
+ if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_J;
+ if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_J;
+ if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_J;
+ if( pamN == NOTSPECIFIED ) pamN = DEFAULTPAMN;
+ if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
+
+ penalty = (int)( 600.0 / 1000.0 * ppenalty + 0.5 );
+ penalty_OP = (int)( 600.0 / 1000.0 * ppenalty_OP + 0.5 );
+ penalty_ex = (int)( 600.0 / 1000.0 * ppenalty_ex + 0.5 );
+ penalty_EX = (int)( 600.0 / 1000.0 * ppenalty_EX + 0.5 );
+ offset = (int)( 600.0 / 1000.0 * poffset + 0.5 );
+ offsetFFT = (int)( 600.0 / 1000.0 * (-0) + 0.5 );
+ offsetLN = (int)( 600.0 / 1000.0 * 100 + 0.5);
+ penaltyLN = (int)( 600.0 / 1000.0 * -2000 + 0.5);
+ penalty_exLN = (int)( 600.0 / 1000.0 * -100 + 0.5);
+
+ sprintf( modelname, "%s %dPAM, %6.3f, %6.3f", (TMorJTT==TM)?"Transmembrane":"JTT", pamN, -(double)ppenalty/1000, -(double)poffset/1000 );
+
+ JTTmtx( rsr, freq, amino, amino_grp, (int)(TMorJTT==TM) );
+
+#if TEST
+ fprintf( stdout, "rsr = \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%9.2f ", rsr[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ for( i=0; i<0x80; i++ ) amino_n[i] = -1;
+ for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
+
+ if( fmodel == 1 )
+ {
+ calcfreq( nseq, seq, datafreq );
+ freq1 = datafreq;
+ }
+ else
+ freq1 = freq;
+
+ fprintf( stderr, "generating %dPAM %s scoring matrix for amino acids ... ", pamN, (TMorJTT==TM)?"Transmembrane":"JTT" );
+
+ tmp = 0.0;
+ for( i=0; i<20; i++ )
+ {
+ mutab[i] = 0.0;
+ for( j=0; j<20; j++ )
+ mutab[i] += rsr[i][j] * freq[j];
+ tmp += mutab[i] * freq[i];
+ }
+#if TEST
+ fprintf( stdout, "mutability = \n" );
+ for( i=0; i<20; i++ )
+ fprintf( stdout, "%5.3f\n", mutab[i] );
+
+ fprintf( stdout, "tmp = %f\n", tmp );
+#endif
+ delta = 0.01 / tmp;
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ if( i != j )
+ pam1[i][j] = delta * rsr[i][j] * freq[i];
+ else
+ pam1[i][j] = 1.0 - delta * mutab[i];
+ }
+ }
+
+ if( disp )
+ {
+ fprintf( stdout, "pam1 = \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%9.6f ", pam1[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+ }
+
+ MtxuntDouble( pamx, 20 );
+ for( x=0; x < pamN; x++ ) MtxmltDouble( pamx, pam1, 20 );
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] /= freq[j];
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ {
+ if( pamx[i][j] == 0.0 )
+ {
+ fprintf( stderr, "WARNING: pamx[%d][%d] = 0.0?\n", i, j );
+ pamx[i][j] = 0.00001; /* by J. Thompson */
+ }
+ pamx[i][j] = log10( pamx[i][j] ) * 1000.0;
+ }
+
+#if TEST
+ fprintf( stdout, "raw scoring matrix : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+ average = tmp = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ {
+ average += pamx[i][j] * freq1[i] * freq1[j];
+ tmp += freq1[i] * freq1[j];
+ }
+ average /= tmp;
+ fprintf( stdout, "Zenbu average = %f, tmp = %f \n", average, tmp );
+ average = tmp = 0.0;
+ for( i=0; i<20; i++ ) for( j=i; j<20; j++ )
+ {
+ average += pamx[i][j] * freq1[i] * freq1[j];
+ tmp += freq1[i] * freq1[j];
+ }
+ average /= tmp;
+ fprintf( stdout, "Zenbu average2 = %f, tmp = %f \n", average, tmp );
+ average = tmp = 0.0;
+ for( i=0; i<20; i++ )
+ {
+ average += pamx[i][i] * freq1[i];
+ tmp += freq1[i];
+ }
+ average /= tmp;
+ fprintf( stdout, "Itch average = %f, tmp = %f \n", average, tmp );
+#endif
+
+#if NORMALIZE1
+ if( fmodel == -1 )
+ average = 0.0;
+ else
+ {
+#if TEST
+ for( i=0; i<20; i++ )
+ fprintf( stdout, "freq[%c] = %f, datafreq[%c] = %f, freq1[] = %f\n", amino[i], freq[i], amino[i], datafreq[i], freq1[i] );
+#endif
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += pamx[i][j] * freq1[i] * freq1[j];
+ }
+#if TEST
+ fprintf( stdout, "####### average2 = %f\n", average );
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] -= average;
+#if TEST
+ fprintf( stdout, "average2 = %f\n", average );
+ fprintf( stdout, "after average substruction : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ average = 0.0;
+ for( i=0; i<20; i++ )
+ average += pamx[i][i] * freq1[i];
+#if TEST
+ fprintf( stdout, "####### average1 = %f\n", average );
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] *= 600.0 / average;
+#if TEST
+ fprintf( stdout, "after average division : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] -= offset;
+#if TEST
+ fprintf( stdout, "after offset substruction (offset = %d): \n", offset );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+#if 0
+/* Ãí°Õ ¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª */
+ penalty -= offset;
+#endif
+
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] = shishagonyuu( pamx[i][j] );
+
+#else
+
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += pamx[i][j];
+ average /= 400.0;
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ {
+ pamx[i][j] -= average;
+ pamx[i][j] = shishagonyuu( pamx[i][j] );
+ }
+#endif
+ if( disp )
+ {
+ fprintf( stdout, " scoring matrix \n" );
+ for( i=0; i<20; i++ )
+ {
+ fprintf( stdout, "%c ", amino[i] );
+ for( j=0; j<20; j++ )
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ fprintf( stdout, "\n" );
+ }
+ fprintf( stdout, " " );
+ for( i=0; i<20; i++ )
+ fprintf( stdout, " %c", amino[i] );
+
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += pamx[i][j] * freq1[i] * freq1[j];
+ fprintf( stdout, "average = %f\n", average );
+
+ average = 0.0;
+ for( i=0; i<20; i++ )
+ average += pamx[i][i] * freq1[i];
+ fprintf( stdout, "itch average = %f\n", average );
+ fprintf( stderr, "parameters: %d, %d, %d\n", penalty, penalty_ex, offset );
+
+
+ exit( 1 );
+ }
+
+ for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ ) n_dis[i][j] = (int)pamx[i][j];
+
+ fprintf( stderr, "done.\n" );
+ FreeDoubleMtx( rsr );
+ FreeDoubleMtx( pam1 );
+ FreeDoubleMtx( pamx );
+ FreeDoubleVec( freq );
+ FreeDoubleVec( mutab );
+ FreeDoubleVec( datafreq );
+ }
+ fprintf( stderr, "scoremtx = %d\n", scoremtx );
+
+#if DEBUG
+ fprintf( stderr, "scoremtx = %d\n", scoremtx );
+ fprintf( stderr, "amino[] = %s\n", amino );
+#endif
+
+ for( i=0; i<0x80; i++ )amino_n[i] = -1;
+ for( i=0; i<26; i++) amino_n[(int)amino[i]] = i;
+ for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_dis[i][j] = 0;
+ for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_disLN[i][j] = 0;
+ for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_dis_consweight_multi[i][j] = 0.0;
+ for( i=0; i<26; i++) for( j=0; j<26; j++ )
+ {
+ amino_dis[(int)amino[i]][(int)amino[j]] = n_dis[i][j];
+ n_dis_consweight_multi[i][j] = (float)n_dis[i][j] * consweight_multi;
+ amino_dis_consweight_multi[(int)amino[i]][(int)amino[j]] = (double)n_dis[i][j] * consweight_multi;
+ }
+
+ if( dorp == 'd' ) /* DNA */
+ {
+ for( i=0; i<5; i++) for( j=0; j<5; j++ )
+ amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
+ for( i=5; i<10; i++) for( j=5; j<10; j++ )
+ amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
+ for( i=0; i<5; i++) for( j=0; j<5; j++ )
+ n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
+ for( i=5; i<10; i++) for( j=5; j<10; j++ )
+ n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
+ }
+ else // protein
+ {
+ for( i=0; i<20; i++) for( j=0; j<20; j++ )
+ amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
+ for( i=0; i<20; i++) for( j=0; j<20; j++ )
+ n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
+ }
+
+#if 0
+ fprintf( stderr, "amino_dis (offset = %d): \n", offset );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stderr, "%5d", amino_dis[(int)amino[i]][(int)amino[j]] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "amino_disLN (offsetLN = %d): \n", offsetLN );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stderr, "%5d", amino_disLN[(int)amino[i]][(int)amino[j]] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "n_dis (offset = %d): \n", offset );
+ for( i=0; i<26; i++ )
+ {
+ for( j=0; j<26; j++ )
+ {
+ fprintf( stderr, "%5d", n_dis[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "n_disFFT (offsetFFT = %d): \n", offsetFFT );
+ for( i=0; i<26; i++ )
+ {
+ for( j=0; j<26; j++ )
+ {
+ fprintf( stderr, "%5d", n_disFFT[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+exit( 1 );
+#endif
+
+
+ ppid = 0;
+
+
+ if( fftThreshold == NOTSPECIFIED )
+ {
+ fftThreshold = FFT_THRESHOLD;
+ }
+ if( fftWinSize == NOTSPECIFIED )
+ {
+ if( dorp == 'd' )
+ fftWinSize = FFT_WINSIZE_D;
+ else
+ fftWinSize = FFT_WINSIZE_P;
+ }
+
+
+ if( fftscore )
+ {
+ double av, sd;
+
+ for( i=0; i<20; i++ ) polarity[i] = polarity_[i];
+ for( av=0.0, i=0; i<20; i++ ) av += polarity[i];
+ av /= 20.0;
+ for( sd=0.0, i=0; i<20; i++ ) sd += ( polarity[i]-av ) * ( polarity[i]-av );
+ sd /= 20.0; sd = sqrt( sd );
+ for( i=0; i<20; i++ ) polarity[i] -= av;
+ for( i=0; i<20; i++ ) polarity[i] /= sd;
+
+ for( i=0; i<20; i++ ) volume[i] = volume_[i];
+ for( av=0.0, i=0; i<20; i++ ) av += volume[i];
+ av /= 20.0;
+ for( sd=0.0, i=0; i<20; i++ ) sd += ( volume[i]-av ) * ( volume[i]-av );
+ sd /= 20.0; sd = sqrt( sd );
+ for( i=0; i<20; i++ ) volume[i] -= av;
+ for( i=0; i<20; i++ ) volume[i] /= sd;
+
+#if 0
+ for( i=0; i<20; i++ ) fprintf( stdout, "amino=%c, pol = %f<-%f, vol = %f<-%f\n", amino[i], polarity[i], polarity_[i], volume[i], volume_[i] );
+ for( i=0; i<20; i++ ) fprintf( stdout, "%c %+5.3f %+5.3f\n", amino[i], volume[i], polarity[i] );
+#endif
+ }
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+static char *whereiscontrafold;
+
+void unknown_n( char *out, char *in )
+{
+ while( *in )
+ {
+ if( *in == 'a' || *in == 'A' )
+ *out = 'A';
+ else if( *in == 't' || *in == 'T' || *in == 'u' || *in == 'U' )
+ *out = 'U';
+ else if( *in == 'g' || *in == 'G' )
+ *out = 'G';
+ else if( *in == 'c' || *in == 'C' )
+ *out = 'C';
+ else if( *in == '-' )
+ *out = '-';
+ else
+ *out = 'N';
+
+ out++;
+ in++;
+ }
+ *out = 0;
+}
+
+void outcontrafold( FILE *fp, RNApair **pairprob, int length )
+{
+ int i;
+ RNApair *pt;
+ for( i=0; i<length; i++ ) for( pt=pairprob[i]; pt->bestpos!=-1; pt++ )
+ {
+ if( pt->bestpos > i )
+ fprintf( fp, "%d %d %f\n", i, pt->bestpos, pt->bestscore );
+ }
+}
+
+#if 1
+static void readcontrafold( FILE *fp, RNApair **pairprob, int length )
+{
+ char gett[10000];
+ int *pairnum;
+ char *pt;
+ int i;
+ int left, right;
+ float prob;
+
+ pairnum = (int *)calloc( length, sizeof( int ) );
+ for( i=0; i<length; i++ ) pairnum[i] = 0;
+
+ while( 1 )
+ {
+ if( feof( fp ) ) break;
+ fgets( gett, 9999, fp );
+
+// fprintf( stderr, "gett=%s\n", gett );
+
+ pt = gett;
+
+ sscanf( gett, "%d ", &left );
+ left--;
+
+// fprintf( stderr, "left=%d\n", left );
+ pt = strchr( pt, ' ' ) + 1;
+// fprintf( stderr, "pt=%s\n", pt );
+
+ while( (pt = strchr( pt, ' ' ) ) )
+ {
+ pt++;
+// fprintf( stderr, "pt=%s\n", pt );
+ sscanf( pt, "%d:%f", &right, &prob );
+ right--;
+
+// fprintf( stderr, "%d-%d, %f\n", left, right, prob );
+
+ pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
+ pairprob[left][pairnum[left]].bestscore = prob;
+ pairprob[left][pairnum[left]].bestpos = right;
+ pairnum[left]++;
+ pairprob[left][pairnum[left]].bestscore = -1.0;
+ pairprob[left][pairnum[left]].bestpos = -1;
+// fprintf( stderr, "%d-%d, %f\n", left, right, prob );
+
+ pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
+ pairprob[right][pairnum[right]].bestscore = prob;
+ pairprob[right][pairnum[right]].bestpos = left;
+ pairnum[right]++;
+ pairprob[right][pairnum[right]].bestscore = -1.0;
+ pairprob[right][pairnum[right]].bestpos = -1;
+// fprintf( stderr, "%d-%d, %f\n", right, left, prob );
+ }
+ }
+ free( pairnum );
+}
+#endif
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+ inputfile = NULL;
+ dorp = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ whereiscontrafold = NULL;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'd':
+ whereiscontrafold = *++argv;
+ fprintf( stderr, "whereiscontrafold = %s\n", whereiscontrafold );
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static char com[10000];
+ static int *nlen;
+ int left, right;
+ int res;
+ static char **name, **seq, **nogap;
+ static int **gapmap;
+ static int *order;
+ int i, j;
+ FILE *infp;
+ RNApair ***pairprob;
+ RNApair **alnpairprob;
+ RNApair *pairprobpt;
+ RNApair *pt;
+ int *alnpairnum;
+ float prob;
+ int adpos;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ if( !whereiscontrafold )
+ whereiscontrafold = "";
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( dorp != 'd' )
+ {
+ fprintf( stderr, "nuc only\n" );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*2+1 );
+ nogap = AllocateCharMtx( njob, nlenmax*2+1 );
+ gapmap = AllocateIntMtx( njob, nlenmax*2+1 );
+ order = AllocateIntVec( njob );
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+ pairprob = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ alnpairprob = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
+ alnpairnum = AllocateIntVec( nlenmax );
+
+ for( i=0; i<nlenmax; i++ ) alnpairnum[i] = 0;
+
+ readData_pointer( infp, name, nlen, seq );
+ fclose( infp );
+
+ for( i=0; i<njob; i++ )
+ {
+ pairprob[i] = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
+ for( j=0; j<nlenmax; j++ )
+ {
+ pairprob[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+ pairprob[i][j][0].bestpos = -1;
+ pairprob[i][j][0].bestscore = -1.0;
+ }
+ unknown_n( nogap[i], seq[i] );
+ order[i] = i;
+ }
+ for( j=0; j<nlenmax; j++ )
+ {
+ alnpairprob[j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+ alnpairprob[j][0].bestpos = -1;
+ alnpairprob[j][0].bestscore = -1.0;
+ }
+
+
+ constants( njob, seq );
+
+ fprintf( stderr, "running contrafold\n" );
+ for( i=0; i<njob; i++ )
+ {
+ fprintf( stderr, "%d / %d\n", i+1, njob );
+ commongappick_record( 1, nogap+i, gapmap[i] );
+ infp = fopen( "_contrafoldin", "w" );
+ fprintf( infp, ">in\n%s\n", nogap[i] );
+ fclose( infp );
+#if 0 // contrafold v1
+ sprintf( com, "env PATH=%s contrafold predict _contrafoldin --posteriors 0.01 > _contrafoldout", whereiscontrafold );
+#else // contrafold v2
+ sprintf( com, "env PATH=%s contrafold predict _contrafoldin --posteriors 0.01 _contrafoldout", whereiscontrafold );
+#endif
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "error in contrafold\n" );
+ fprintf( stderr, "=================================================================\n" );
+ fprintf( stderr, "=================================================================\n" );
+ fprintf( stderr, "==\n" );
+ fprintf( stderr, "== This version of MAFFT supports CONTRAfold v2.02.\n" );
+ fprintf( stderr, "== If you have a lower version of CONTRAfold installed in the\n" );
+ fprintf( stderr, "== %s directory,\n", whereiscontrafold );
+ fprintf( stderr, "== please update it!\n" );
+ fprintf( stderr, "==\n" );
+ fprintf( stderr, "=================================================================\n" );
+ fprintf( stderr, "=================================================================\n" );
+ exit( 1 );
+ }
+
+
+ infp = fopen( "_contrafoldout", "r" );
+ readcontrafold( infp, pairprob[i], nlenmax );
+ fclose( infp );
+ fprintf( stdout, ">%d\n", i );
+ outcontrafold( stdout, pairprob[i], nlenmax );
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ for( j=0; j<nlen[i]; j++ ) for( pairprobpt=pairprob[i][j]; pairprobpt->bestpos!=-1; pairprobpt++ )
+ {
+ left = gapmap[i][j];
+ right = gapmap[i][pairprobpt->bestpos];
+ prob = pairprobpt->bestscore;
+
+ for( pt=alnpairprob[left]; pt->bestpos!=-1; pt++ )
+ if( pt->bestpos == right ) break;
+
+ if( pt->bestpos == -1 )
+ {
+ alnpairprob[left] = (RNApair *)realloc( alnpairprob[left], (alnpairnum[left]+2) * sizeof( RNApair ) );
+ adpos = alnpairnum[left];
+ alnpairnum[left]++;
+ alnpairprob[left][adpos].bestscore = 0.0;
+ alnpairprob[left][adpos].bestpos = right;
+ alnpairprob[left][adpos+1].bestscore = -1.0;
+ alnpairprob[left][adpos+1].bestpos = -1;
+ pt = alnpairprob[left]+adpos;
+ }
+ else
+ adpos = pt-alnpairprob[left];
+
+ pt->bestscore += prob;
+ if( pt->bestpos != right )
+ {
+ fprintf( stderr, "okashii!\n" );
+ exit( 1 );
+ }
+// fprintf( stderr, "adding %d-%d, %f\n", left, right, prob );
+ }
+ }
+ return( 0 );
+
+#if 0
+ fprintf( stdout, "result=\n" );
+
+ for( i=0; i<nlenmax; i++ ) for( pairprobpt=alnpairprob[i]; pairprobpt->bestpos!=-1; pairprobpt++ )
+ {
+ pairprobpt->bestscore /= (float)njob;
+ left = i;
+ right = pairprobpt->bestpos;
+ prob = pairprobpt->bestscore;
+ fprintf( stdout, "%d-%d, %f\n", left, right, prob );
+ }
+
+ return( 0 );
+#endif
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+
+int main( int argc, char *argv[] )
+{
+ FILE *infp;
+ int nlenmin;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ dorp = NOTSPECIFIED;
+ getnumlen_nogap( infp, &nlenmin );
+
+ fprintf( stdout, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
+ return( 0 );
+}
--- /dev/null
+#include <stdio.h>
+#include "dp.h"
+#include "mltaln.h"
+
+int TLS commonAlloc1 = 0;
+int TLS commonAlloc2 = 0;
+int TLS **commonIP = NULL;
+int TLS **commonJP = NULL;
+int nthread = 1;
+int randomseed = 0;
+int parallelizationstrategy = BAATARI1;
+
+
+char modelname[100];
+int njob, nlenmax;
+int amino_n[0x80];
+char amino_grp[0x80];
+int amino_dis[0x80][0x80];
+int amino_disLN[0x80][0x80];
+double amino_dis_consweight_multi[0x80][0x80];
+int n_dis[26][26];
+int n_disFFT[26][26];
+float n_dis_consweight_multi[26][26];
+char amino[26];
+double polarity[20];
+double volume[20];
+int ribosumdis[37][37];
+
+int ppid;
+double thrinter;
+double fastathreshold;
+int pslocal, ppslocal;
+int constraint;
+int divpairscore;
+int fmodel; // 1-> fmodel 0->default -1->raw
+int nblosum; // 45, 50, 62, 80
+int kobetsubunkatsu;
+int bunkatsu;
+int dorp;
+int niter;
+int contin;
+int calledByXced;
+int devide;
+int scmtd;
+int weight;
+int utree;
+int tbutree;
+int refine;
+int check;
+double cut;
+int cooling;
+int penalty, ppenalty, penaltyLN;
+int RNApenalty, RNAppenalty;
+int RNApenalty_ex, RNAppenalty_ex;
+int penalty_ex, ppenalty_ex, penalty_exLN;
+int penalty_EX, ppenalty_EX;
+int penalty_OP, ppenalty_OP;
+int RNAthr, RNApthr;
+int offset, poffset, offsetLN, offsetFFT;
+int scoremtx;
+int TMorJTT;
+char use_fft;
+char force_fft;
+int nevermemsave;
+int fftscore;
+int fftWinSize;
+int fftThreshold;
+int fftRepeatStop;
+int fftNoAnchStop;
+int divWinSize;
+int divThreshold;
+int disp;
+int outgap = 1;
+char alg;
+int cnst;
+int mix;
+int tbitr;
+int tbweight;
+int tbrweight;
+int disopt;
+int pamN;
+int checkC;
+float geta2;
+int treemethod;
+int kimuraR;
+char *swopt;
+int fftkeika;
+int score_check;
+int makedistmtx;
+char *inputfile;
+char *addfile;
+int addprofile = 1;
+int rnakozo;
+char rnaprediction;
+int scoreout = 0;
+int outnumber = 0;
+
+char *signalSM;
+FILE *prep_g;
+FILE *trap_g;
+char **seq_g;
+char **res_g;
+
+float consweight_multi = 1.0;
+float consweight_rna = 0.0;
+char RNAscoremtx = 'n';
+
+char *newgapstr = "-";
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+#define END_OF_VEC -1
+
+static int nadd;
+static int treein;
+static int topin;
+static int treeout;
+static int noalign;
+static int distout;
+static float lenfaca, lenfacb, lenfacc, lenfacd;
+#if 0
+#define PLENFACA 0.0123
+#define PLENFACB 10252
+#define PLENFACC 10822
+#define PLENFACD 0.5
+#define DLENFACA 0.01
+#define DLENFACB 2445
+#define DLENFACC 2412
+#define DLENFACD 0.1
+#else
+#define PLENFACA 0.01
+#define PLENFACB 10000
+#define PLENFACC 10000
+#define PLENFACD 0.1
+#define DLENFACA 0.01
+#define DLENFACB 2500
+#define DLENFACC 2500
+#define DLENFACD 0.1
+#endif
+
+#ifdef enablemultithread
+typedef struct _treebasethread_arg
+{
+ int thread_no;
+ int njob;
+ int *nrunpt;
+ int *nlen;
+ int *jobpospt;
+ int ***topol;
+ Treedep *dep;
+ char **aseq;
+ double *effarr;
+ int *alloclenpt;
+ int *fftlog;
+ pthread_mutex_t *mutex;
+ pthread_cond_t *treecond;
+} treebasethread_arg_t;
+
+typedef struct _distancematrixthread_arg
+{
+ int thread_no;
+ int njob;
+ int *jobpospt;
+ int **pointt;
+ float **mtx;
+ pthread_mutex_t *mutex;
+} distancematrixthread_arg_t;
+#endif
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ nthread = 1;
+ outnumber = 0;
+ topin = 0;
+ treein = 0;
+ treeout = 0;
+ distout = 0;
+ noalign = 0;
+ nevermemsave = 0;
+ inputfile = NULL;
+ nadd = 0;
+ addprofile = 1;
+ fftkeika = 0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ force_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'X';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = -1530;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = -123;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ TMorJTT = JTT;
+ scoreout = 0;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'I':
+ nadd = atoi( *++argv );
+ fprintf( stderr, "nadd = %d\n", nadd );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+// fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+// fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+ fprintf( stderr, "kappa = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+// fprintf( stderr, "blosum %d / kimura 200 \n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt/kimura %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "tm %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'C':
+ nthread = atoi( *++argv );
+ fprintf( stderr, "nthread = %d\n", nthread );
+ --argc;
+ goto nextoption;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'K':
+ addprofile = 0;
+ break;
+ case 'y':
+ distout = 1;
+ break;
+ case 't':
+ treeout = 1;
+ break;
+ case 'T':
+ noalign = 1;
+ break;
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+#if 0
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+#endif
+ case 'n' :
+ outnumber = 1;
+ break;
+ case 's':
+ treemethod = 's';
+ break;
+ case 'X':
+ treemethod = 'X'; // mix
+ break;
+ case 'E':
+ treemethod = 'E'; // upg (average)
+ break;
+ case 'q':
+ treemethod = 'q'; // minimum
+ break;
+#if 0
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'R':
+ alg = 'R';
+ break;
+ case 'Q':
+ alg = 'Q';
+ break;
+ case 'H':
+ alg = 'H';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'N':
+ nevermemsave = 1;
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'S':
+ scoreout = 1;
+ break;
+ case 'B':
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'G':
+ use_fft = 1;
+ force_fft = 1;
+ break;
+ case 'V':
+ topin = 1;
+ break;
+ case 'U':
+ treein = 1;
+ break;
+ case 'u':
+ weight = 0;
+ tbrweight = 0;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'd':
+ disp = 1;
+ break;
+#if 1
+ case 'O':
+ outgap = 0;
+ break;
+#else
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#endif
+ case 'J':
+ tbutree = 0;
+ break;
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'Z':
+ checkC = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+}
+
+
+
+
+static int maxl;
+static int tsize;
+
+void seq_grp_nuc( int *grp, char *seq )
+{
+ int tmp;
+ int *grpbk = grp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 4 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+ if( grp - grpbk < 6 )
+ {
+// fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
+// exit( 1 );
+ *grpbk = -1;
+ }
+}
+
+void seq_grp( int *grp, char *seq )
+{
+ int tmp;
+ int *grpbk = grp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 6 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+ if( grp - grpbk < 6 )
+ {
+// fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
+// exit( 1 );
+ *grpbk = -1;
+ }
+}
+
+void makecompositiontable_p( short *table, int *pointt )
+{
+ int point;
+
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ table[point]++;
+}
+
+int commonsextet_p( short *table, int *pointt )
+{
+ int value = 0;
+ short tmp;
+ int point;
+ static TLS short *memo = NULL;
+ static TLS int *ct = NULL;
+ static TLS int *cp;
+
+ if( table == NULL )
+ {
+ if( memo ) free( memo );
+ if( ct ) free( ct );
+ return( 0 );
+ }
+
+ if( *pointt == -1 )
+ return( 0 );
+
+ if( !memo )
+ {
+ memo = (short *)calloc( tsize, sizeof( short ) );
+ if( !memo ) ErrorExit( "Cannot allocate memo\n" );
+ ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) );
+ if( !ct ) ErrorExit( "Cannot allocate memo\n" );
+ }
+
+ cp = ct;
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ {
+ tmp = memo[point]++;
+ if( tmp < table[point] )
+ value++;
+ if( tmp == 0 ) *cp++ = point;
+ }
+ *cp = END_OF_VEC;
+
+ cp = ct;
+ while( *cp != END_OF_VEC )
+ memo[*cp++] = 0;
+
+ return( value );
+}
+
+void makepointtable_nuc( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ if( *n == -1 )
+ {
+ *pointt = -1;
+ return;
+ }
+
+ p = n;
+ point = *n++ * 1024;
+ point += *n++ * 256;
+ point += *n++ * 64;
+ point += *n++ * 16;
+ point += *n++ * 4;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 1024;
+ point *= 4;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+void makepointtable( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ if( *n == -1 )
+ {
+ *pointt = -1;
+ return;
+ }
+
+ p = n;
+ point = *n++ * 7776;
+ point += *n++ * 1296;
+ point += *n++ * 216;
+ point += *n++ * 36;
+ point += *n++ * 6;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 7776;
+ point *= 6;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+#ifdef enablemultithread
+static void *distancematrixthread( void *arg )
+{
+ distancematrixthread_arg_t *targ = (distancematrixthread_arg_t *)arg;
+ int thread_no = targ->thread_no;
+ int njob = targ->njob;
+ int *jobpospt = targ->jobpospt;
+ int **pointt = targ->pointt;
+ float **mtx = targ->mtx;
+
+ short *table1;
+ int i, j;
+
+ while( 1 )
+ {
+ pthread_mutex_lock( targ->mutex );
+ i = *jobpospt;
+ if( i == njob )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ commonsextet_p( NULL, NULL );
+ return( NULL );
+ }
+ *jobpospt = i+1;
+ pthread_mutex_unlock( targ->mutex );
+
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "\r% 5d / %d (thread %4d)", i+1, njob, thread_no );
+ }
+ makecompositiontable_p( table1, pointt[i] );
+
+ for( j=i; j<njob; j++ )
+ {
+ mtx[i][j-i] = (float)commonsextet_p( table1, pointt[j] );
+ }
+ free( table1 );
+ }
+}
+
+
+static void *treebasethread( void *arg )
+{
+ treebasethread_arg_t *targ = (treebasethread_arg_t *)arg;
+ int thread_no = targ->thread_no;
+ int *nrunpt = targ->nrunpt;
+ int njob = targ->njob;
+ int *nlen = targ->nlen;
+ int *jobpospt = targ->jobpospt;
+ int ***topol = targ->topol;
+ Treedep *dep = targ->dep;
+ char **aseq = targ->aseq;
+ double *effarr = targ->effarr;
+ int *alloclen = targ->alloclenpt;
+ int *fftlog = targ->fftlog;
+
+ char **mseq1, **mseq2;
+ char **localcopy;
+ int i, j, l;
+ int len1, len2;
+ int clus1, clus2;
+ float pscore, tscore;
+ char *indication1, *indication2;
+ double *effarr1 = NULL;
+ double *effarr2 = NULL;
+ float dumfl = 0.0;
+ int ffttry;
+ int m1, m2;
+#if 0
+ int i, j;
+#endif
+
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ localcopy = calloc( njob, sizeof( char * ) );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+// for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ while( 1 )
+ {
+ pthread_mutex_lock( targ->mutex );
+ l = *jobpospt;
+ if( l == njob-1 )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonIP = NULL;
+ Falign( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
+ free( mseq1 );
+ free( mseq2 );
+ free( localcopy );
+ free( effarr1 );
+ free( effarr2 );
+ free( indication1 );
+ free( indication2 );
+ return( NULL );
+ }
+ *jobpospt = l+1;
+
+ if( dep[l].child0 != -1 )
+ {
+ while( dep[dep[l].child0].done == 0 )
+ pthread_cond_wait( targ->treecond, targ->mutex );
+ }
+ if( dep[l].child1 != -1 )
+ {
+ while( dep[dep[l].child1].done == 0 )
+ pthread_cond_wait( targ->treecond, targ->mutex );
+ }
+ while( *nrunpt >= nthread )
+ pthread_cond_wait( targ->treecond, targ->mutex );
+ (*nrunpt)++;
+
+ m1 = topol[l][0][0];
+ m2 = topol[l][1][0];
+
+ len1 = strlen( aseq[m1] );
+ len2 = strlen( aseq[m2] );
+ if( *alloclen <= len1 + len2 )
+ {
+ fprintf( stderr, "\nReallocating.." );
+ *alloclen = ( len1 + len2 ) + 1000;
+ ReallocateCharMtx( aseq, njob, *alloclen + 10 );
+ fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
+ }
+
+ for( i=0; (j=topol[l][0][i])!=-1; i++ )
+ {
+ localcopy[j] = calloc( *alloclen, sizeof( char ) );
+ strcpy( localcopy[j], aseq[j] );
+ }
+ for( i=0; (j=topol[l][1][i])!=-1; i++ )
+ {
+ localcopy[j] = calloc( *alloclen, sizeof( char ) );
+ strcpy( localcopy[j], aseq[j] );
+ }
+ pthread_mutex_unlock( targ->mutex );
+
+#if 1 // CHUUI@@@@
+ clus1 = fastconjuction_noname( topol[l][0], localcopy, mseq1, effarr1, effarr, indication1 );
+ clus2 = fastconjuction_noname( topol[l][1], localcopy, mseq2, effarr2, effarr, indication2 );
+#else
+ clus1 = fastconjuction_noweight( topol[l][0], localcopy, mseq1, effarr1, indication1 );
+ clus2 = fastconjuction_noweight( topol[l][1], localcopy, mseq2, effarr2, indication2 );
+#endif
+
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ {
+ if( strlen( mseq1[i] ) != len1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, clus1 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after conjuction) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<clus2; j++ )
+ {
+ if( strlen( mseq2[j] ) != len2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, clus2 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after conjuction) !\n" );
+ exit( 1 );
+ }
+ }
+#endif
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ {
+ if( strlen( mseq1[i] ) != len1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, clus1 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after free topol) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<clus2; j++ )
+ {
+ if( strlen( mseq2[j] ) != len2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, clus2 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after free topol) !\n" );
+ exit( 1 );
+ }
+ }
+#endif
+
+
+// fprintf( trap_g, "\nSTEP-%d\n", l );
+// fprintf( trap_g, "group1 = %s\n", indication1 );
+// fprintf( trap_g, "group2 = %s\n", indication2 );
+
+// fprintf( stderr, "\rSTEP % 5d / %d %d-%d", l+1, njob-1, clus1, clus2 );
+ fprintf( stderr, "\rSTEP % 5d / %d (thread %4d)", l+1, njob-1, thread_no );
+
+#if 0
+ fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+#endif
+
+/*
+ fprintf( stderr, "before align all\n" );
+ display( aseq, njob );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+
+ if( !nevermemsave && ( alg != 'M' && ( len1 > 30000 || len2 > 30000 ) ) )
+ {
+ fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode\n", len1, len2 );
+ alg = 'M';
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonAlloc1 = 0;
+ commonAlloc2 = 0;
+ }
+
+// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
+ if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000);
+ else ffttry = 0;
+// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000); // v6.708
+// fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
+
+ if( force_fft || ( use_fft && ffttry ) )
+ {
+ fprintf( stderr, "f" );
+ if( alg == 'M' )
+ {
+ fprintf( stderr, "m" );
+ pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
+ }
+ else
+ {
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
+ }
+ }
+ else
+ {
+ fprintf( stderr, "d" );
+ fftlog[m1] = 0;
+ switch( alg )
+ {
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
+ break;
+ case( 'M' ):
+ fprintf( stderr, "m" );
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'Q' ):
+ if( clus1 == 1 && clus2 == 1 && 0 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+ pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ break;
+ case( 'R' ):
+ pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ case( 'H' ):
+ pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ case( 'A' ):
+ if( clus1 == 1 && clus2 == 1 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+ break;
+ default:
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f\n", pscore );
+#endif
+ tscore += pscore;
+ nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
+
+
+ if( disp ) display( localcopy, njob );
+
+ pthread_mutex_lock( targ->mutex );
+ dep[l].done = 1;
+ (*nrunpt)--;
+ pthread_cond_broadcast( targ->treecond );
+
+ for( i=0; (j=topol[l][0][i])!=-1; i++ )
+ strcpy( aseq[j], localcopy[j] );
+ for( i=0; (j=topol[l][1][i])!=-1; i++ )
+ strcpy( aseq[j], localcopy[j] );
+ pthread_mutex_unlock( targ->mutex );
+
+ for( i=0; (j=topol[l][0][i])!=-1; i++ )
+ free( localcopy[j] );
+ for( i=0; (j=topol[l][1][i])!=-1; i++ )
+ free( localcopy[j] );
+ free( topol[l][0] );
+ free( topol[l][1] );
+ free( topol[l] );
+
+
+// fprintf( stderr, "\n" );
+ }
+#if SCOREOUT
+ fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
+#endif
+}
+#endif
+
+static void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mseq2, int ***topol, double *effarr, int *alloclen )
+{
+ int l, len1, len2, i, m;
+ int len1nocommongap, len2nocommongap;
+ int clus1, clus2;
+ float pscore, tscore;
+ static char *indication1, *indication2;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ static int *fftlog; // fixed at 2006/07/26
+ float dumfl = 0.0;
+ int ffttry;
+ int m1, m2;
+ static int *gaplen;
+ static int *gapmap;
+ static int *alreadyaligned;
+#if 0
+ int i, j;
+#endif
+
+ if( effarr1 == NULL )
+ {
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+ fftlog = AllocateIntVec( njob );
+ gaplen = AllocateIntVec( *alloclen+10 );
+ gapmap = AllocateIntVec( *alloclen+10 );
+ alreadyaligned = AllocateIntVec( njob );
+ }
+ for( i=0; i<njob-nadd; i++ ) alreadyaligned[i] = 1;
+ for( i=njob-nadd; i<njob; i++ ) alreadyaligned[i] = 0;
+
+ for( l=0; l<njob; l++ ) fftlog[l] = 1;
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+// for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ tscore = 0.0;
+ for( l=0; l<njob-1; l++ )
+ {
+ if( mergeoralign[l] == 'n' )
+ {
+// fprintf( stderr, "SKIP!\n" );
+ free( topol[l][0] );
+ free( topol[l][1] );
+ free( topol[l] );
+ continue;
+ }
+
+ m1 = topol[l][0][0];
+ m2 = topol[l][1][0];
+ len1 = strlen( aseq[m1] );
+ len2 = strlen( aseq[m2] );
+ if( *alloclen < len1 + len2 )
+ {
+ fprintf( stderr, "\nReallocating.." );
+ *alloclen = ( len1 + len2 ) + 1000;
+ ReallocateCharMtx( aseq, njob, *alloclen + 10 );
+ gaplen = realloc( gaplen, ( *alloclen + 10 ) * sizeof( int ) );
+ if( gaplen == NULL )
+ {
+ fprintf( stderr, "Cannot realloc gaplen\n" );
+ exit( 1 );
+ }
+ gapmap = realloc( gapmap, ( *alloclen + 10 ) * sizeof( int ) );
+ if( gapmap == NULL )
+ {
+ fprintf( stderr, "Cannot realloc gapmap\n" );
+ exit( 1 );
+ }
+ fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
+ }
+
+#if 1 // CHUUI@@@@
+ clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2 );
+#else
+ clus1 = fastconjuction_noweight( topol[l][0], aseq, mseq1, effarr1, indication1 );
+ clus2 = fastconjuction_noweight( topol[l][1], aseq, mseq2, effarr2, indication2 );
+#endif
+ if( mergeoralign[l] == '1' || mergeoralign[l] == '2' )
+ {
+ newgapstr = "=";
+ }
+ else
+ newgapstr = "-";
+
+ len1nocommongap = len1;
+ len2nocommongap = len2;
+ if( mergeoralign[l] == '1' ) // nai
+ {
+ findcommongaps( clus2, mseq2, gapmap );
+ commongappick( clus2, mseq2 );
+ len2nocommongap = strlen( mseq2[0] );
+ }
+ else if( mergeoralign[l] == '2' )
+ {
+ findcommongaps( clus1, mseq1, gapmap );
+ commongappick( clus1, mseq1 );
+ len1nocommongap = strlen( mseq1[0] );
+ }
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ {
+ if( strlen( mseq1[i] ) != len1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, clus1 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after conjuction) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<clus2; j++ )
+ {
+ if( strlen( mseq2[j] ) != len2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, clus2 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after conjuction) !\n" );
+ exit( 1 );
+ }
+ }
+#endif
+
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ {
+ if( strlen( mseq1[i] ) != len1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, clus1 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after free topol) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<clus2; j++ )
+ {
+ if( strlen( mseq2[j] ) != len2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, clus2 );
+ fprintf( stderr, "hairetsu ga kowareta (in treebase, after free topol) !\n" );
+ exit( 1 );
+ }
+ }
+#endif
+
+
+// fprintf( trap_g, "\nSTEP-%d\n", l );
+// fprintf( trap_g, "group1 = %s\n", indication1 );
+// fprintf( trap_g, "group2 = %s\n", indication2 );
+
+// fprintf( stderr, "\rSTEP % 5d / %d %d-%d", l+1, njob-1, clus1, clus2 );
+ fprintf( stderr, "\rSTEP % 5d / %d ", l+1, njob-1 );
+ fflush( stderr );
+
+#if 0
+ fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+#endif
+
+/*
+ fprintf( stderr, "before align all\n" );
+ display( aseq, njob );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+
+ if( !nevermemsave && ( alg != 'M' && ( len1 > 30000 || len2 > 30000 ) ) )
+ {
+ fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode\n", len1, len2 );
+ alg = 'M';
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonAlloc1 = 0;
+ commonAlloc2 = 0;
+ }
+
+// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
+ if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000);
+ else ffttry = 0;
+// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000); // v6.708
+// fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
+
+ if( force_fft || ( use_fft && ffttry ) )
+ {
+ fprintf( stderr, "f" );
+ if( alg == 'M' )
+ {
+ fprintf( stderr, "m" );
+ pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
+ }
+ else
+ {
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
+ }
+ }
+ else
+ {
+ fprintf( stderr, "d" );
+ fftlog[m1] = 0;
+ switch( alg )
+ {
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
+ break;
+ case( 'M' ):
+ fprintf( stderr, "m" );
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'Q' ):
+ if( clus1 == 1 && clus2 == 1 && 0 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+ pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ break;
+ case( 'R' ):
+ pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ case( 'H' ):
+ pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ case( 'A' ):
+ if( clus1 == 1 && clus2 == 1 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+ break;
+ default:
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f\n", pscore );
+#endif
+ tscore += pscore;
+ nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ if( disp ) display( aseq, njob );
+// fprintf( stderr, "\n" );
+
+ if( mergeoralign[l] == '1' ) // jissainiha nai. atarashii hairetsu ha saigo dakara.
+ {
+ adjustgapmap( strlen( mseq2[0] )-len2nocommongap+len2, gapmap, mseq2[0] );
+ restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen );
+ findnewgaps( clus2, mseq2, gaplen );
+ insertnewgaps( njob, alreadyaligned, aseq, topol[l][1], topol[l][0], gaplen, gapmap, *alloclen, alg );
+ for( i=0; i<njob; i++ ) eq2dash( aseq[i] );
+ for( i=0; (m=topol[l][0][i])>-1; i++ ) alreadyaligned[m] = 1;
+ }
+ if( mergeoralign[l] == '2' )
+ {
+ adjustgapmap( strlen( mseq1[0] )-len1nocommongap+len1, gapmap, mseq1[0] );
+// fprintf( stderr, ">STEP1 mseq1[0] = \n%s\n", mseq1[0] );
+// fprintf( stderr, ">STEP1 mseq2[0] = \n%s\n", mseq2[0] );
+ restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen );
+// fprintf( stderr, "STEP2 mseq1[0] = %s\n", mseq1[0] );
+// fprintf( stderr, "STEP2 mseq2[0] = %s\n", mseq2[0] );
+ findnewgaps( clus1, mseq1, gaplen );
+ insertnewgaps( njob, alreadyaligned, aseq, topol[l][0], topol[l][1], gaplen, gapmap, *alloclen, alg );
+// fprintf( stderr, "STEP3 mseq1[0] = %s\n", mseq1[0] );
+// fprintf( stderr, "STEP3 mseq2[0] = %s\n", mseq2[0] );
+ for( i=0; i<njob; i++ ) eq2dash( aseq[i] );
+ for( i=0; (m=topol[l][1][i])>-1; i++ ) alreadyaligned[m] = 1;
+ }
+
+ free( topol[l][0] );
+ free( topol[l][1] );
+ free( topol[l] );
+ }
+#if SCOREOUT
+ fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
+#endif
+}
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( treemethod == 'X' )
+ fprintf( fp, "Tree = UPGMA (mix).\n" );
+ else if( treemethod == 'E' )
+ fprintf( fp, "Tree = UPGMA (average).\n" );
+ else if( treemethod == 'q' )
+ fprintf( fp, "Tree = Minimum linkage.\n" );
+ else
+ fprintf( fp, "Unknown tree.\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int *nlen;
+ static int *nogaplen;
+ static char **name, **seq;
+ static char **mseq1, **mseq2;
+ static char **bseq;
+ static double *eff;
+ int i, j;
+ static int ***topol;
+ static int *addmem;
+ static Treedep *dep;
+ static float **len;
+ FILE *infp;
+// FILE *adfp;
+ char c;
+ int alloclen;
+ float longer, shorter;
+ float lenfac;
+ float bunbo;
+
+ FILE *orderfp, *hat2p;
+ int *grpseq;
+ char *tmpseq;
+ int **pointt;
+ float **mtx = NULL; // by D. Mathog
+ static short *table1;
+ char b[B];
+ int ien;
+ double unweightedspscore;
+ int alignmentlength;
+ char *mergeoralign;
+ int foundthebranch;
+
+ arguments( argc, argv );
+#ifndef enablemultithread
+ nthread = 0;
+#endif
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( njob > 20000 )
+ {
+ fprintf( stderr, "The number of sequences must be < %d\n", 20000 );
+ fprintf( stderr, "Please try the --parttree option for such large data.\n" );
+ exit( 1 );
+ }
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*1+1 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+
+ topol = AllocateIntCub( njob, 2, 0 );
+ len = AllocateFloatMtx( njob, 2 );
+ eff = AllocateDoubleVec( njob );
+ mergeoralign = AllocateCharVec( njob );
+
+ dep = (Treedep *)calloc( njob, sizeof( Treedep ) );
+
+ if( nadd ) addmem = AllocateIntVec( nadd+1 );
+
+#if 0
+ Read( name, nlen, seq );
+ readData( infp, name, nlen, seq );
+#else
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+ nogaplen = AllocateIntVec( njob );
+ readData_pointer( infp, name, nlen, seq );
+ fclose( infp );
+#endif
+
+ constants( njob, seq );
+
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illegal character %c\n", c );
+ exit( 1 );
+ }
+
+ fprintf( stderr, "\n" );
+
+ if( !treein )
+ {
+ fprintf( stderr, "\n\nMaking a distance matrix ..\n" );
+ fflush( stderr );
+
+ tmpseq = AllocateCharVec( nlenmax+1 );
+ grpseq = AllocateIntVec( nlenmax+1 );
+ pointt = AllocateIntMtx( njob, nlenmax+1 );
+ mtx = AllocateFloatHalfMtx( njob );
+ if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
+ else tsize = (int)pow( 6, 6 );
+
+ if( dorp == 'd' )
+ {
+ lenfaca = DLENFACA;
+ lenfacb = DLENFACB;
+ lenfacc = DLENFACC;
+ lenfacd = DLENFACD;
+ }
+ else
+ {
+ lenfaca = PLENFACA;
+ lenfacb = PLENFACB;
+ lenfacc = PLENFACC;
+ lenfacd = PLENFACD;
+ }
+
+ maxl = 0;
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( tmpseq, seq[i] );
+ nogaplen[i] = strlen( tmpseq );
+ if( nogaplen[i] < 6 )
+ {
+// fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nogaplen[i] );
+// fprintf( stderr, "Please use mafft-ginsi, mafft-linsi or mafft-ginsi\n\n\n" );
+// exit( 1 );
+ }
+ if( nogaplen[i] > maxl ) maxl = nogaplen[i];
+ if( dorp == 'd' ) /* nuc */
+ {
+ seq_grp_nuc( grpseq, tmpseq );
+ makepointtable_nuc( pointt[i], grpseq );
+ }
+ else /* amino */
+ {
+ seq_grp( grpseq, tmpseq );
+ makepointtable( pointt[i], grpseq );
+ }
+ }
+#ifdef enablemultithread
+ if( nthread > 0 )
+ {
+ distancematrixthread_arg_t *targ;
+ int jobpos;
+ pthread_t *handle;
+ pthread_mutex_t mutex;
+
+ jobpos = 0;
+ targ = calloc( nthread, sizeof( distancematrixthread_arg_t ) );
+ handle = calloc( nthread, sizeof( pthread_t ) );
+ pthread_mutex_init( &mutex, NULL );
+
+ for( i=0; i<nthread; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].njob = njob;
+ targ[i].jobpospt = &jobpos;
+ targ[i].pointt = pointt;
+ targ[i].mtx = mtx;
+ targ[i].mutex = &mutex;
+
+ pthread_create( handle+i, NULL, distancematrixthread, (void *)(targ+i) );
+ }
+
+ for( i=0; i<nthread; i++ )
+ {
+ pthread_join( handle[i], NULL );
+ }
+ pthread_mutex_destroy( &mutex );
+ free( handle );
+ free( targ );
+ }
+ else
+#endif
+ {
+ for( i=0; i<njob; i++ )
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "\r% 5d / %d", i+1, njob );
+ fflush( stderr );
+ }
+ makecompositiontable_p( table1, pointt[i] );
+
+ for( j=i; j<njob; j++ )
+ {
+ mtx[i][j-i] = (float)commonsextet_p( table1, pointt[j] );
+ }
+ free( table1 );
+ }
+ }
+ fprintf( stderr, "\ndone.\n\n" );
+ fflush( stderr );
+ ien = njob-1;
+
+ for( i=0; i<ien; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ if( nogaplen[i] > nogaplen[j] )
+ {
+ longer=(float)nogaplen[i];
+ shorter=(float)nogaplen[j];
+ }
+ else
+ {
+ longer=(float)nogaplen[j];
+ shorter=(float)nogaplen[i];
+ }
+// lenfac = 3.0 / ( LENFACA + LENFACB / ( longer + LENFACC ) + shorter / longer * LENFACD );
+ lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
+// lenfac = 1.0;
+// fprintf( stderr, "lenfac = %f (%.0f,%.0f)\n", lenfac, longer, shorter );
+ bunbo = MIN( mtx[i][0], mtx[j][0] );
+ if( bunbo == 0.0 )
+ mtx[i][j-i] = 1.0;
+ else
+ mtx[i][j-i] = ( 1.0 - mtx[i][j-i] / bunbo ) * lenfac;
+// fprintf( stdout, "##### mtx = %f, mtx[i][0]=%f, mtx[j][0]=%f, bunbo=%f\n", mtx[i][j-i], mtx[i][0], mtx[j][0], bunbo );
+ }
+ }
+ if( disopt )
+ {
+ for( i=0; i<njob; i++ )
+ {
+ sprintf( b, "=lgth = %04d", nogaplen[i] );
+ strins( b, name[i] );
+ }
+ }
+ free( grpseq );
+ free( tmpseq );
+ FreeIntMtx( pointt );
+
+#if 1 // writehat2 wo kakinaosu
+ if( distout )
+ {
+ hat2p = fopen( "hat2", "w" );
+ WriteFloatHat2_pointer_halfmtx( hat2p, njob, name, mtx );
+ fclose( hat2p );
+ }
+#endif
+
+ }
+ else {
+#if 0 // readhat2 wo kakinaosu
+ fprintf( stderr, "Loading 'hat2' ... " );
+ prep = fopen( "hat2", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat2." );
+ readhat2_float( prep, njob, name, mtx ); // name chuui
+ fclose( prep );
+ fprintf( stderr, "done.\n" );
+#endif
+ }
+
+ if( treein )
+ {
+ fprintf( stderr, "Loading a tree ... " );
+ loadtree( njob, topol, len, name, nogaplen, dep );
+ }
+ else if( topin )
+ {
+ fprintf( stderr, "Loading a topology ... " );
+ loadtop( njob, mtx, topol, len );
+ FreeFloatHalfMtx( mtx, njob );
+ }
+ else if( treeout )
+ {
+ fprintf( stderr, "Constructing a UPGMA tree ... " );
+
+ fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( njob, mtx, topol, len, name, nogaplen, dep );
+// veryfastsupg_float_realloc_nobk_halfmtx_treeout( njob, mtx, topol, len, name, nogaplen );
+
+
+ FreeFloatHalfMtx( mtx, njob );
+ }
+ else
+ {
+ fprintf( stderr, "Constructing a UPGMA tree ... " );
+ fixed_musclesupg_float_realloc_nobk_halfmtx( njob, mtx, topol, len, dep );
+ FreeFloatHalfMtx( mtx, njob );
+ }
+// else
+// ErrorExit( "Incorrect tree\n" );
+ fprintf( stderr, "\ndone.\n\n" );
+ fflush( stderr );
+
+ orderfp = fopen( "order", "w" );
+ if( !orderfp )
+ {
+ fprintf( stderr, "Cannot open 'order'\n" );
+ exit( 1 );
+ }
+ for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
+ {
+ fprintf( orderfp, "%d\n", j );
+ }
+ for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
+ {
+ fprintf( orderfp, "%d\n", j );
+ }
+ fclose( orderfp );
+
+ if( ( treeout || distout ) && noalign )
+ {
+ writeData_pointer( stdout, njob, name, nlen, seq );
+ fprintf( stderr, "\n" );
+ SHOWVERSION;
+ return( 0 );
+ }
+
+
+ if( tbrweight )
+ {
+ weight = 3;
+#if 0
+ utree = 0; counteff( njob, topol, len, eff ); utree = 1;
+#else
+ counteff_simple_float( njob, topol, len, eff );
+#endif
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+ }
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stdout, "eff[%d] = %20.16f\n", i, eff[i] );
+ exit( 1 );
+#endif
+
+
+ FreeFloatMtx( len );
+
+ bseq = AllocateCharMtx( njob, nlenmax*2+1 );
+ alloclen = nlenmax*2+1;
+
+
+ if( nadd )
+ {
+ alignmentlength = strlen( seq[0] );
+ for( i=0; i<njob-nadd; i++ )
+ {
+ if( alignmentlength != strlen( seq[i] ) )
+ {
+ fprintf( stderr, "#################################################################################\n" );
+ fprintf( stderr, "# ERROR! #\n" );
+ fprintf( stderr, "# The original%4d sequences must be aligned #\n", njob-nadd );
+ fprintf( stderr, "#################################################################################\n" );
+ exit( 1 );
+ }
+ }
+ if( addprofile )
+ {
+ alignmentlength = strlen( seq[njob-nadd] );
+ for( i=njob-nadd; i<njob; i++ )
+ {
+ if( alignmentlength != strlen( seq[i] ) )
+ {
+ fprintf( stderr, "###############################################################################\n" );
+ fprintf( stderr, "# ERROR! #\n" );
+ fprintf( stderr, "# The%4d additional sequences must be aligned #\n", nadd );
+ fprintf( stderr, "# Otherwise, try the '--add' option, instead of '--addprofile' option. #\n" );
+ fprintf( stderr, "###############################################################################\n" );
+ exit( 1 );
+ }
+ }
+ for( i=0; i<nadd; i++ ) addmem[i] = njob-nadd+i;
+ addmem[nadd] = -1;
+ foundthebranch = 0;
+ for( i=0; i<njob-1; i++ )
+ {
+ if( samemember( topol[i][0], addmem ) ) // jissainiha nai
+ {
+ mergeoralign[i] = '1';
+ foundthebranch = 1;
+ }
+ else if( samemember( topol[i][1], addmem ) )
+ {
+ mergeoralign[i] = '2';
+ foundthebranch = 1;
+ }
+ else
+ {
+ mergeoralign[i] = 'n';
+ }
+ }
+ if( !foundthebranch )
+ {
+ fprintf( stderr, "###############################################################################\n" );
+ fprintf( stderr, "# ERROR! #\n" );
+ fprintf( stderr, "# There is no appropriate position to add the%4d sequences in the guide tree.#\n", nadd );
+ fprintf( stderr, "# Check whether the%4d sequences form a monophyletic cluster. #\n", nadd );
+ fprintf( stderr, "# If not, try the '--add' option, instead of the '--addprofile' option. #\n" );
+ fprintf( stderr, "############################################################################### \n" );
+ exit( 1 );
+ }
+ commongappick( nadd, seq+njob-nadd );
+ for( i=njob-nadd; i<njob; i++ ) strcpy( bseq[i], seq[i] );
+ }
+ else
+ {
+ for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'n';
+ for( j=njob-nadd; j<njob; j++ )
+ {
+ addmem[0] = j;
+ addmem[1] = -1;
+ for( i=0; i<njob-1; i++ )
+ {
+ if( samemember( topol[i][0], addmem ) ) // arieru
+ {
+// fprintf( stderr, "HIT!\n" );
+ if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
+ else mergeoralign[i] = '1';
+ }
+ else if( samemember( topol[i][1], addmem ) )
+ {
+// fprintf( stderr, "HIT!\n" );
+ if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
+ else mergeoralign[i] = '2';
+ }
+ }
+ }
+
+ for( i=0; i<nadd; i++ ) addmem[i] = njob-nadd+i;
+ addmem[nadd] = -1;
+ for( i=0; i<njob-1; i++ )
+ {
+ if( includemember( topol[i][0], addmem ) && includemember( topol[i][1], addmem ) )
+ {
+ mergeoralign[i] = 'w';
+ }
+ else if( includemember( topol[i][0], addmem ) )
+ {
+ mergeoralign[i] = '1';
+ }
+ else if( includemember( topol[i][1], addmem ) )
+ {
+ mergeoralign[i] = '2';
+ }
+ }
+#if 0
+ for( i=0; i<njob-1; i++ )
+ {
+ fprintf( stderr, "mem0 = " );
+ for( j=0; topol[i][0][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][0][j] );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "mem1 = " );
+ for( j=0; topol[i][1][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][1][j] );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "i=%d, mergeoralign[] = %c\n", i, mergeoralign[i] );
+ }
+#endif
+ for( i=njob-nadd; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+ }
+
+ commongappick( njob-nadd, seq );
+ for( i=0; i<njob-nadd; i++ ) strcpy( bseq[i], seq[i] );
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+ for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'a';
+ }
+
+ fprintf( stderr, "Progressive alignment ... \n" );
+
+#ifdef enablemultithread
+ if( nthread > 0 && nadd == 0 )
+ {
+ treebasethread_arg_t *targ;
+ int jobpos;
+ pthread_t *handle;
+ pthread_mutex_t mutex;
+ pthread_cond_t treecond;
+ int *fftlog;
+ int nrun;
+ int nthread_yoyu;
+
+ nthread_yoyu = nthread * 1;
+ nrun = 0;
+ jobpos = 0;
+ targ = calloc( nthread_yoyu, sizeof( treebasethread_arg_t ) );
+ fftlog = AllocateIntVec( njob );
+ handle = calloc( nthread_yoyu, sizeof( pthread_t ) );
+ pthread_mutex_init( &mutex, NULL );
+ pthread_cond_init( &treecond, NULL );
+
+ for( i=0; i<njob; i++ ) dep[i].done = 0;
+ for( i=0; i<njob; i++ ) fftlog[i] = 1;
+
+ for( i=0; i<nthread_yoyu; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].njob = njob;
+ targ[i].nrunpt = &nrun;
+ targ[i].nlen = nlen;
+ targ[i].jobpospt = &jobpos;
+ targ[i].topol = topol;
+ targ[i].dep = dep;
+ targ[i].aseq = bseq;
+ targ[i].effarr = eff;
+ targ[i].alloclenpt = &alloclen;
+ targ[i].fftlog = fftlog;
+ targ[i].mutex = &mutex;
+ targ[i].treecond = &treecond;
+
+ pthread_create( handle+i, NULL, treebasethread, (void *)(targ+i) );
+ }
+
+ for( i=0; i<nthread_yoyu; i++ )
+ {
+ pthread_join( handle[i], NULL );
+ }
+ pthread_mutex_destroy( &mutex );
+ pthread_cond_destroy( &treecond );
+ free( handle );
+ free( targ );
+ free( fftlog );
+ }
+ else
+#endif
+ {
+ treebase( nlen, bseq, nadd, mergeoralign, mseq1, mseq2, topol, eff, &alloclen );
+ }
+ fprintf( stderr, "\ndone.\n\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+ if( scoreout )
+ {
+ unweightedspscore = plainscore( njob, bseq );
+ fprintf( stderr, "\nSCORE %s = %.0f, ", "(treebase)", unweightedspscore );
+ fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
+ fprintf( stderr, "\n\n" );
+ }
+
+ free( mergeoralign );
+// writePre( njob, name, nlen, aseq, !contin );
+#if DEBUG
+ fprintf( stderr, "writing alignment to stdout\n" );
+#endif
+ writeData_pointer( stdout, njob, name, nlen, bseq );
+#if 0
+ writeData( stdout, njob, name, nlen, bseq );
+#endif
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
+
--- /dev/null
+#include "mltaln.h"
+#include <sys/types.h>
+#include <unistd.h>
+#define DEBUG 0
+#define TEST 0
+
+
+int howmanyx( char *s )
+{
+ int val = 0;
+ if( scoremtx == -1 )
+ {
+ do
+ {
+ if( !strchr( "atgcuATGCU", *s ) ) val++;
+ } while( *++s );
+ }
+ else
+ {
+ do
+ {
+ if( !strchr( "ARNDCQEGHILKMFPSTWYV", *s ) ) val++;
+ } while( *++s );
+ }
+ return( val );
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ inputfile = NULL;
+ disopt = 0;
+ divpairscore = 0;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'I':
+ disopt = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: -i\n" );
+ exit( 1 );
+ }
+}
+
+int main( int argc, char *argv[] )
+{
+ int ktuple;
+ int i, j;
+ FILE *infp;
+ FILE *hat2p;
+ FILE *hat3p;
+ char **seq = NULL; // by D.Mathog
+ char **seq1;
+ static char name[M][B];
+ static char name1[M][B];
+ static int nlen1[M];
+ double **mtx;
+ double **mtx2;
+ static int nlen[M];
+ char b[B];
+ double max;
+ char com[1000];
+ int opt[M];
+ int res;
+ char *home;
+ char queryfile[B];
+ char datafile[B];
+ char fastafile[B];
+ char hat2file[B];
+ int pid = (int)getpid();
+ LocalHom **localhomtable, *tmpptr;
+#if 1
+ home = getenv( "HOME" );
+#else /* $HOME wo tsukau to fasta ni watasu hikisuu ga afureru */
+ home = NULL;
+#endif
+
+#if DEBUG
+ if( home ) fprintf( stderr, "home = %s\n", home );
+#endif
+ if( !home ) home = "";
+ sprintf( queryfile, "%s/tmp/query-%d", home, pid );
+ sprintf( datafile, "%s/tmp/data-%d", home, pid );
+ sprintf( fastafile, "%s/tmp/fasta-%d", home, pid );
+ sprintf( hat2file, "hat2-%d", pid );
+
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+#if 0
+ PreRead( infp, &njob, &nlenmax );
+#else
+ dorp = NOTSPECIFIED;
+ getnumlen( infp );
+#endif
+
+ if( dorp == 'd' )
+ {
+ scoremtx = -1;
+ pamN = NOTSPECIFIED;
+ }
+ else
+ {
+ nblosum = 62;
+ scoremtx = 1;
+ }
+ constants( njob, seq );
+
+ rewind( infp );
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ seq1 = AllocateCharMtx( 2, nlenmax+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+ mtx2 = AllocateDoubleMtx( njob, njob );
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+
+ }
+ }
+
+#if 0
+ FRead( infp, name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ if( scoremtx == -1 ) ktuple = 6;
+ else ktuple = 1;
+
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( seq1[0], seq[i] );
+ strcpy( seq[i], seq1[0] );
+ }
+ for( j=0; j<njob; j++ )
+ {
+ sprintf( name1[j], "+==========+%d ", j );
+ nlen1[j] = nlen[j];
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+// fprintf( stderr, "### i = %d\n", i );
+
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "formatting .. " );
+ hat2p = fopen( datafile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open datafile." );
+ WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
+ fclose( hat2p );
+
+ if( scoremtx == -1 )
+ sprintf( com, "formatdb -p f -i %s -o F", datafile );
+ else
+ sprintf( com, "formatdb -i %s -o F", datafile );
+ system( com );
+ fprintf( stderr, "done.\n" );
+ }
+
+ hat2p = fopen( queryfile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open queryfile." );
+ WriteForFasta( hat2p, 1, name1+i, nlen+i, seq+i );
+ fclose( hat2p );
+
+
+ if( scoremtx == -1 )
+ sprintf( com, "blastall -e 1e10 -p blastn -m 7 -i %s -d %s > %s", queryfile, datafile, fastafile );
+ else
+ sprintf( com, "blastall -G 10 -E 1 -e 1e10 -p blastp -m 7 -i %s -d %s > %s", queryfile, datafile, fastafile );
+ res = system( com );
+ if( res ) ErrorExit( "error in fasta" );
+
+
+ hat2p = fopen( fastafile, "r" );
+ if( hat2p == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+ res = ReadBlastm7( hat2p, mtx[i], i, name1, localhomtable[i] );
+ fclose( hat2p );
+
+#if 0
+ for( j=0; j<njob; j++ )
+ {
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+// fprintf( stderr, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
+ }
+ }
+#endif
+
+ if( res < njob-i+i%10 )
+ {
+ fprintf( stderr, "WARNING: count (blast) = %d < %d\n", res, njob-i+i%10 );
+ }
+
+
+#if 0
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
+ fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
+ }
+#endif
+ fprintf( stderr, "query : %4d / %d\n", i+1, njob );
+ }
+
+#if 1
+ fprintf( stderr, "##### writing hat3\n" );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ )
+ {
+// fprintf( stderr, "mtx[%d][%d] = %f, mtx[%d][%d] = %f\n", i, j, mtx[i][j], j, i, mtx[j][i] );
+ if( i == j ) continue;
+ if( mtx[i][j] == mtx[j][i] && i > j ) continue;
+ if( mtx[j][i] > mtx[i][j] ) continue;
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
+ }
+ }
+ fclose( hat3p );
+#endif
+
+ for( i=0; i<njob; i++ )
+ {
+// fprintf( stderr, "### i = %d\n", i );
+ hat2p = fopen( datafile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open datafile." );
+ WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
+ fclose( hat2p );
+
+// seq1[0] = seq[i];
+// nlen1[0] = nlen[i];
+
+ hat2p = fopen( queryfile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open queryfile." );
+ WriteForFasta( hat2p, 1, name1+i, nlen+i, seq+i );
+ fclose( hat2p );
+
+
+ if( scoremtx == -1 )
+ sprintf( com, "fasta34 -z3 -m10 -n -Q -b%d -E%d -d%d %s %s %d > %s", M, M, 0, queryfile, datafile, ktuple, fastafile );
+ else
+ sprintf( com, "fasta34 -z3 -m10 -Q -b%d -E%d -d%d %s %s %d > %s", M, M, 0, queryfile, datafile, ktuple, fastafile );
+ res = system( com );
+ if( res ) ErrorExit( "error in fasta" );
+
+
+ hat2p = fopen( fastafile, "r" );
+ if( hat2p == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+ res = ReadFasta34noalign( hat2p, mtx[i], i, name1, localhomtable[i] );
+ fclose( hat2p );
+ if( res < njob - i )
+ {
+ fprintf( stderr, "count (fasta34 -z 3) = %d\n", res );
+ exit( 1 );
+ }
+
+
+ if( i == 0 )
+ for( j=0; j<njob; j++ ) opt[j] = (int)mtx[0][j];
+
+
+#if 0
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
+ fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
+ }
+#endif
+ fprintf( stderr, "query : %4d\r", i+1 );
+ }
+
+
+
+
+ for( i=0; i<njob; i++ )
+ {
+ max = mtx[i][i];
+ if( max == 0.0 )
+ {
+ for( j=0; j<njob; j++ )
+ mtx2[i][j] = 2.0;
+ }
+ else
+ {
+ for( j=0; j<njob; j++ )
+ {
+ mtx2[i][j] = ( max - mtx[MIN(i,j)][MAX(i,j)] ) / max * 2.0;
+// fprintf( stdout, "max = %f, mtx[%d][%d] = %f -> %f\n", max, i+1, j+1, mtx[i][j], mtx2[i][j] );
+ }
+ }
+ }
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+// fprintf( stdout, "mtx2[%d][%d] = %f, %f\n", i+1, j+1, mtx2[i][j], mtx2[j][i] );
+ mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
+ }
+
+#if 0
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i+1; jj<njob; jj++ )
+ fprintf( stderr, "mtx2[][] = %f\n", mtx2[i][jj] );
+ }
+#endif
+
+ for( i=0; i<njob; i++ ) name[i][0] = '=';
+
+ if( disopt )
+ {
+ strcpy( b, name[0] );
+ sprintf( name[0], "=query====lgth=%04d-%04d %.*s", nlen[0], howmanyx( seq[0] ), B-30, b );
+#if 0
+ strins( b, name[0] );
+#endif
+ for( i=1; i<njob; i++ )
+ {
+ strcpy( b, name[i] );
+ sprintf( name[i], "=opt=%04d=lgth=%04d-%04d %.*s", opt[i], nlen[i], howmanyx( seq[i] ), B-30, b );
+#if 0
+ strins( b, name[i] );
+#endif
+ }
+ }
+
+ hat2p = fopen( hat2file, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( hat2p, njob, name, mtx2 );
+ fclose( hat2p );
+
+
+ sprintf( com, "/bin/rm %s %s %s", queryfile, datafile, fastafile );
+ system( com );
+
+#if 0
+ sprintf( com, ALNDIR "/supgsdl < %s", hat2file );
+ res = system( com );
+ if( res ) ErrorExit( "error in spgsdl" );
+#endif
+
+ sprintf( com, "mv %s hat2", hat2file );
+ res = system( com );
+ if( res ) ErrorExit( "error in mv" );
+
+ SHOWVERSION;
+ exit( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+#include <sys/types.h>
+#include <unistd.h>
+#define DEBUG 0
+#define TEST 0
+
+
+int howmanyx( char *s )
+{
+ int val = 0;
+ if( scoremtx == -1 )
+ {
+ do
+ {
+ if( !strchr( "atgcuATGCU", *s ) ) val++;
+ } while( *++s );
+ }
+ else
+ {
+ do
+ {
+ if( !strchr( "ARNDCQEGHILKMFPSTWYV", *s ) ) val++;
+ } while( *++s );
+ }
+ return( val );
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ disopt = 0;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ while ( c = *++argv[0] )
+ switch( c )
+ {
+ case 'i':
+ disopt = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: -i\n" );
+ exit( 1 );
+ }
+}
+
+int main( int argc, char *argv[] )
+{
+ int ktuple;
+ int i, j;
+ FILE *hat2p;
+ char **seq;
+ char **seq1;
+ static char name[M][B];
+ static char name1[M][B];
+ static int nlen1[M];
+ double **mtx;
+ double **mtx2;
+ static int nlen[M];
+ char b[B];
+ double max;
+ char com[B];
+ int opt[M];
+ int res;
+ char *home;
+ char queryfile[B];
+ char datafile[B];
+ char fastafile[B];
+ char hat2file[B];
+ int pid = (int)getpid();
+#if 0
+ home = getenv( "HOME" );
+#else /* $HOME wo tsukau to fasta ni watasu hikisuu ga afureru */
+ home = NULL;
+#endif
+
+#if DEBUG
+ if( home ) fprintf( stderr, "home = %s\n", home );
+#endif
+ if( !home ) home = "";
+ sprintf( queryfile, "%s/tmp/query-%d\0", home, pid );
+ sprintf( datafile, "%s/tmp/data-%d\0", home, pid );
+ sprintf( fastafile, "%s/tmp/fasta-%d\0", home, pid );
+ sprintf( hat2file, "hat2-%d\0", pid );
+
+ arguments( argc, argv );
+#if 0
+ PreRead( stdin, &njob, &nlenmax );
+#else
+ getnumlen( stdin );
+#endif
+ rewind( stdin );
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ seq1 = AllocateCharMtx( 2, nlenmax+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+ mtx2 = AllocateDoubleMtx( njob, njob );
+
+#if 0
+ FRead( stdin, name, nlen, seq );
+#else
+ readData( stdin, name, nlen, seq );
+#endif
+ if( scoremtx == -1 ) ktuple = 6;
+ else ktuple = 1;
+
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( seq1[0], seq[i] );
+ strcpy( seq[i], seq1[0] );
+ }
+ for( j=0; j<njob; j++ )
+ {
+ sprintf( name1[j], "+==========+%d \0", j );
+ nlen1[j] = nlen[j];
+ }
+ hat2p = fopen( datafile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open datafile." );
+ WriteForFasta( hat2p, njob, name1, nlen1, seq );
+ fclose( hat2p );
+
+ for( i=0; i<njob; i++ )
+ {
+
+ hat2p = fopen( datafile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open datafile." );
+ WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
+ fclose( hat2p );
+
+
+ seq1[0] = seq[i];
+ nlen1[0] = nlen[i];
+
+ hat2p = fopen( queryfile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open queryfile." );
+ WriteForFasta( hat2p, 1, name1+i, nlen1, seq1 );
+ fclose( hat2p );
+
+ if( scoremtx == -1 )
+ sprintf( com, "fasta3 -n -Q -h -b%d -E%d -d%d %s %s %d > %s\0", M, M, 0, queryfile, datafile, ktuple, fastafile );
+ else
+ sprintf( com, "fasta3 -Q -h -b%d -E%d -d%d %s %s %d > %s\0", M, M, 0, queryfile, datafile, ktuple, fastafile );
+ res = system( com );
+ if( res ) ErrorExit( "error in fasta" );
+
+ hat2p = fopen( fastafile, "r" );
+ if( hat2p == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+ ReadFasta3( hat2p, mtx[i], njob-i, name1 );
+
+ if( i == 0 )
+ for( j=0; j<njob; j++ ) opt[j] = (int)mtx[0][j];
+
+ fclose( hat2p );
+
+#if 1
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
+ fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
+ }
+#endif
+ fprintf( stderr, "query : %#4d\n", i+1 );
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ max = mtx[i][i];
+ if( max == 0.0 )
+ {
+ for( j=0; j<njob; j++ )
+ mtx2[i][j] = 2.0;
+ }
+ else
+ {
+ for( j=0; j<njob; j++ )
+ {
+ mtx2[i][j] = ( max - mtx[MIN(i,j)][MAX(i,j)] ) / max * 2.0;
+// fprintf( stdout, "max = %f, mtx[%d][%d] = %f -> %f\n", max, i+1, j+1, mtx[i][j], mtx2[i][j] );
+ }
+ }
+ }
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+// fprintf( stdout, "mtx2[%d][%d] = %f, %f\n", i+1, j+1, mtx2[i][j], mtx2[j][i] );
+ mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
+ }
+#if 0
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i+1; jj<njob; jj++ )
+ fprintf( stderr, "mtx2[][] = %f\n", mtx2[i][jj] );
+ }
+#endif
+
+ for( i=0; i<njob; i++ ) name[i][0] = '=';
+
+ if( disopt )
+ {
+ strcpy( b, name[0] );
+ sprintf( name[0], "=query====lgth=%#04d-%04d %.*s\0", nlen[0], howmanyx( seq[0] ), B-30, b );
+#if 0
+ strins( b, name[0] );
+#endif
+ for( i=1; i<njob; i++ )
+ {
+ strcpy( b, name[i] );
+ sprintf( name[i], "=opt=%#04d=lgth=%#04d-%04d %.*s\0", opt[i], nlen[i], howmanyx( seq[i] ), B-30, b );
+#if 0
+ strins( b, name[i] );
+#endif
+ }
+ }
+
+ hat2p = fopen( hat2file, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( hat2p, njob, name, mtx2 );
+ fclose( hat2p );
+
+ sprintf( com, "/bin/rm %s %s %s", queryfile, datafile, fastafile );
+ system( com );
+
+#if 0
+ sprintf( com, ALNDIR "/supgsdl < %s\0", hat2file );
+ res = system( com );
+ if( res ) ErrorExit( "error in spgsdl" );
+#endif
+
+ sprintf( com, "mv %s hat2", hat2file );
+ res = system( com );
+ if( res ) ErrorExit( "error in mv" );
+
+ SHOWVERSION;
+ exit( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+#include <sys/types.h>
+#include <unistd.h>
+#define DEBUG 0
+#define TEST 0
+
+
+int howmanyx( char *s )
+{
+ int val = 0;
+ if( scoremtx == -1 )
+ {
+ do
+ {
+ if( !strchr( "atgcuATGCU", *s ) ) val++;
+ } while( *++s );
+ }
+ else
+ {
+ do
+ {
+ if( !strchr( "ARNDCQEGHILKMFPSTWYV", *s ) ) val++;
+ } while( *++s );
+ }
+ return( val );
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ inputfile = NULL;
+ disopt = 0;
+ divpairscore = 0;
+ swopt = "";
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'I':
+ disopt = 1;
+ break;
+ case 'A':
+ swopt = "-A";
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: -i\n" );
+ exit( 1 );
+ }
+}
+
+int main( int argc, char *argv[] )
+{
+ int ktuple;
+ int i, j;
+ FILE *hat2p;
+ FILE *hat3p;
+ FILE *infp;
+ char **seq = NULL; // by D.Mathog
+ char **seq1;
+ static char name[M][B];
+ static char name1[M][B];
+ static int nlen1[M];
+ double **mtx;
+ double **mtx2;
+ static int nlen[M];
+ char b[B];
+ double max;
+ char com[1000];
+ int opt[M];
+ int res;
+ char *home;
+ char *fastapath;
+ char queryfile[B];
+ char datafile[B];
+ char fastafile[B];
+ char hat2file[B];
+ int pid = (int)getpid();
+ LocalHom **localhomtable, *tmpptr;
+#if 0
+ home = getenv( "HOME" );
+#else /* $HOME wo tsukau to fasta ni watasu hikisuu ga afureru */
+ home = NULL;
+#endif
+ fastapath = getenv( "FASTA_4_MAFFT" );
+ if( !fastapath )
+ fastapath = "fasta34";
+
+#if DEBUG
+ if( home ) fprintf( stderr, "home = %s\n", home );
+#endif
+ if( !home ) home = "";
+ sprintf( queryfile, "%s/tmp/query-%d", home, pid );
+ sprintf( datafile, "%s/tmp/data-%d", home, pid );
+ sprintf( fastafile, "%s/tmp/fasta-%d", home, pid );
+ sprintf( hat2file, "hat2-%d", pid );
+
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+
+
+#if 0
+ PreRead( stdin, &njob, &nlenmax );
+#else
+ dorp = NOTSPECIFIED;
+ getnumlen( infp );
+#endif
+
+ if( dorp == 'd' )
+ {
+ scoremtx = -1;
+ pamN = NOTSPECIFIED;
+ }
+ else
+ {
+ nblosum = 62;
+ scoremtx = 1;
+ }
+ constants( njob, seq );
+
+ rewind( infp );
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ seq1 = AllocateCharMtx( 2, nlenmax+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+ mtx2 = AllocateDoubleMtx( njob, njob );
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+ }
+ }
+
+#if 0
+ FRead( infp, name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ if( scoremtx == -1 ) ktuple = 6;
+ else ktuple = 1;
+
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( seq1[0], seq[i] );
+ strcpy( seq[i], seq1[0] );
+ }
+ for( j=0; j<njob; j++ )
+ {
+ sprintf( name1[j], "+==========+%d ", j );
+ nlen1[j] = nlen[j];
+ }
+ hat2p = fopen( datafile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open datafile." );
+ WriteForFasta( hat2p, njob, name1, nlen1, seq );
+ fclose( hat2p );
+
+ for( i=0; i<njob; i++ )
+ {
+// fprintf( stderr, "### i = %d\n", i );
+ hat2p = fopen( datafile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open datafile." );
+ WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
+ fclose( hat2p );
+
+ seq1[0] = seq[i];
+ nlen1[0] = nlen[i];
+
+ hat2p = fopen( queryfile, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open queryfile." );
+ WriteForFasta( hat2p, 1, name1+i, nlen1, seq1 );
+ fclose( hat2p );
+
+
+ if( scoremtx == -1 )
+ sprintf( com, "%s %s -z3 -m10 -n -Q -b%d -E%d -d%d %s %s %d > %s", fastapath, swopt, M, M, M, queryfile, datafile, ktuple, fastafile );
+ else
+ sprintf( com, "%s %s -z3 -m10 -Q -b%d -E%d -d%d %s %s %d > %s", fastapath, swopt, M, M, M, queryfile, datafile, ktuple, fastafile );
+ res = system( com );
+ if( res ) ErrorExit( "error in fasta" );
+
+
+
+ hat2p = fopen( fastafile, "r" );
+ if( hat2p == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+ if( scoremtx == -1 )
+ res = ReadFasta34m10_nuc( hat2p, mtx[i], i, name1, localhomtable[i] );
+ else
+ res = ReadFasta34m10( hat2p, mtx[i], i, name1, localhomtable[i] );
+ fclose( hat2p );
+
+ if( res < njob - i )
+ {
+ fprintf( stderr, "count (fasta34 -z 3) = %d\n", res );
+ exit( 1 );
+ }
+
+
+ if( i == 0 )
+ for( j=0; j<njob; j++ ) opt[j] = (int)mtx[0][j];
+
+
+#if 0
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
+ fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
+ }
+#endif
+ fprintf( stderr, "query : %4d / %5d\r", i+1, njob );
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ max = mtx[i][i];
+ if( max == 0.0 )
+ {
+ for( j=0; j<njob; j++ )
+ mtx2[i][j] = 2.0;
+ }
+ else
+ {
+ for( j=0; j<njob; j++ )
+ {
+// fprintf( stderr, "##### mtx[%d][%d] = %f\n", i, j, mtx[i][j] );
+ mtx2[i][j] = ( max - mtx[MIN(i,j)][MAX(i,j)] ) / max * 2.0;
+// fprintf( stdout, "max = %f, mtx[%d][%d] = %f -> %f\n", max, i+1, j+1, mtx[i][j], mtx2[i][j] );
+ }
+ }
+ }
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+// fprintf( stdout, "mtx2[%d][%d] = %f, %f\n", i+1, j+1, mtx2[i][j], mtx2[j][i] );
+ mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
+ }
+
+#if 0
+ {
+ int ii, jj;
+ if( i < njob-1 ) for( jj=i+1; jj<njob; jj++ )
+ fprintf( stderr, "mtx2[][] = %f\n", mtx2[i][jj] );
+ }
+#endif
+
+ for( i=0; i<njob; i++ ) name[i][0] = '=';
+
+ if( disopt )
+ {
+ strcpy( b, name[0] );
+ sprintf( name[0], "=query====lgth=%04d-%04d %.*s", nlen[0], howmanyx( seq[0] ), B-30, b );
+#if 0
+ strins( b, name[0] );
+#endif
+ for( i=1; i<njob; i++ )
+ {
+ strcpy( b, name[i] );
+ sprintf( name[i], "=opt=%04d=lgth=%04d-%04d %.*s", opt[i], nlen[i], howmanyx( seq[i] ), B-30, b );
+#if 0
+ strins( b, name[i] );
+#endif
+ }
+ }
+
+ hat2p = fopen( hat2file, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( hat2p, njob, name, mtx2 );
+ fclose( hat2p );
+
+#if 1
+ fprintf( stderr, "##### writing hat3\n" );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
+ }
+ }
+ fclose( hat3p );
+#endif
+
+ sprintf( com, "/bin/rm %s %s %s", queryfile, datafile, fastafile );
+ system( com );
+
+#if 0
+ sprintf( com, ALNDIR "/supgsdl < %s", hat2file );
+ res = system( com );
+ if( res ) ErrorExit( "error in spgsdl" );
+#endif
+
+ sprintf( com, "mv %s hat2", hat2file );
+ res = system( com );
+ if( res ) ErrorExit( "error in mv" );
+
+ SHOWVERSION;
+ exit( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define TEST 0
+
+static int treeout = 0;
+
+#ifdef enablemultithread
+typedef struct _jobtable
+{
+ int i;
+ int j;
+} Jobtable;
+
+typedef struct _thread_arg
+{
+ int njob;
+ int thread_no;
+ float *selfscore;
+ double **mtx;
+ char **seq;
+ Jobtable *jobpospt;
+ pthread_mutex_t *mutex;
+} thread_arg_t;
+
+void *athread( void *arg )
+{
+ thread_arg_t *targ = (thread_arg_t *)arg;
+ int njob = targ->njob;
+ int thread_no = targ->thread_no;
+ float *selfscore = targ->selfscore;
+ double **mtx = targ->mtx;
+ char **seq = targ->seq;
+ Jobtable *jobpospt = targ->jobpospt;
+
+ int i, j;
+ float ssi, ssj, bunbo;
+
+ while( 1 )
+ {
+ pthread_mutex_lock( targ->mutex );
+ j = jobpospt->j;
+ i = jobpospt->i;
+ j++;
+ if( j == njob )
+ {
+ fprintf( stderr, "%4d/%4d (thread %4d), dndpre\r", i+1, njob, thread_no );
+ i++;
+ j = i + 1;
+ if( i == njob-1 )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ return( NULL );
+ }
+ }
+ jobpospt->j = j;
+ jobpospt->i = i;
+ pthread_mutex_unlock( targ->mutex );
+
+ ssi = selfscore[i];
+ ssj = selfscore[j];
+
+ bunbo = MIN( ssi, ssj );
+ if( bunbo == 0.0 )
+ mtx[i][j] = 1.0;
+ else
+ mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
+ }
+}
+
+#endif
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ nthread = 1;
+ alg = 'X';
+ fmodel = 0;
+ treeout = 0;
+ scoremtx = 1;
+ nblosum = 62;
+ dorp = NOTSPECIFIED;
+ inputfile = NULL;
+ ppenalty = NOTSPECIFIED; //?
+ ppenalty_ex = NOTSPECIFIED; //?
+ poffset = NOTSPECIFIED; //?
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 't':
+ treeout = '1';
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'a':
+ fmodel = 1;
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'C':
+ nthread = atoi( *++argv );
+ fprintf( stderr, "nthread = %d\n", nthread );
+ --argc;
+ goto nextoption;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+int main( int argc, char **argv )
+{
+ int i, j;
+ char **seq;
+ static char **name;
+ static int nlen[M];
+ float *selfscore;
+ double **mtx;
+ FILE *fp;
+ FILE *infp;
+ float ssi, ssj, bunbo;
+
+
+ arguments( argc, argv );
+#ifndef enablemultithread
+ nthread = 0;
+#endif
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+#if 0
+ PreRead( stdin, &njob, &nlenmax );
+#else
+ getnumlen( infp );
+#endif
+ rewind( infp );
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ name = AllocateCharMtx( njob, B+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+ selfscore = AllocateFloatVec( njob );
+
+#if 0
+ FRead( stdin, name, nlen, seq );
+#else
+ readData_pointer( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ constants( njob, seq );
+
+#if 0
+ for( i=0; i<njob-1; i++ )
+ {
+ fprintf( stderr, "%4d/%4d\r", i+1, njob );
+ for( j=i+1; j<njob; j++ )
+ mtx[i][j] = (double)substitution_hosei( seq[i], seq[j] );
+// fprintf( stderr, "i=%d,j=%d, l=%d &&& %f\n", i, j, nlen[0], mtx[i][j] );
+ }
+#else // 061003
+ for( i=0; i<njob; i++ )
+ {
+ selfscore[i] = (float)naivepairscore11( seq[i], seq[i], penalty );
+
+ }
+#ifdef enablemultithread
+ if( nthread > 0 )
+ {
+ thread_arg_t *targ;
+ Jobtable jobpos;
+ pthread_t *handle;
+ pthread_mutex_t mutex;
+
+ jobpos.i = 0;
+ jobpos.j = 0;
+
+ targ = calloc( nthread, sizeof( thread_arg_t ) );
+ handle = calloc( nthread, sizeof( pthread_t ) );
+ pthread_mutex_init( &mutex, NULL );
+
+ for( i=0; i<nthread; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].njob = njob;
+ targ[i].selfscore = selfscore;
+ targ[i].mtx = mtx;
+ targ[i].seq = seq;
+ targ[i].jobpospt = &jobpos;
+ targ[i].mutex = &mutex;
+
+ pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
+ }
+
+ for( i=0; i<nthread; i++ )
+ {
+ pthread_join( handle[i], NULL );
+ }
+ pthread_mutex_destroy( &mutex );
+ }
+ else
+#endif
+ {
+ for( i=0; i<njob-1; i++ )
+ {
+ ssi = selfscore[i];
+ fprintf( stderr, "%4d/%4d\r", i+1, njob );
+ for( j=i+1; j<njob; j++ )
+ {
+ ssj = selfscore[j];
+ bunbo = MIN( ssi, ssj );
+ if( bunbo == 0.0 )
+ mtx[i][j] = 1.0;
+ else
+ mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
+// mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / MIN( selfscore[i], selfscore[j] );
+// fprintf( stderr, "i=%d,j=%d, l=%d### %f, score = %d\n", i, j, nlen[0], mtx[i][j], naivepairscore11( seq[i], seq[j], penalty ) );
+ }
+ }
+ }
+#endif
+
+#if TEST
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
+#endif
+
+ fp = fopen( "hat2", "w" );
+ WriteHat2_pointer( fp, njob, name, mtx );
+ fclose( fp );
+#if 0
+ if( treeout )
+ {
+ int ***topol;
+ double **len;
+
+ topol = AllocateIntCub( njob, 2, njob );
+ len = AllocateDoubleMtx( njob, njob );
+ veryfastsupg_double_outtree( njob, mtx, topol, len );
+ }
+#endif
+ SHOWVERSION;
+ exit( 0 );
+/*
+ res = system( ALNDIR "/spgsdl < hat2" );
+ if( res ) exit( 1 );
+ else exit( 0 );
+*/
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 1
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ scoremtx = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+ fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+ fprintf( stderr, "blosum %d\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ fmodel = 1;
+ break;
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+int main( int argc, char *argv[] )
+{
+ static int nlen[M];
+ static char name[M][B], **seq;
+ int i, j, alloclen, c;
+ double **mtx;
+ double *self;
+ double tmpdouble;
+ FILE *fp;
+
+ arguments( argc, argv );
+
+ getnumlen( stdin );
+ rewind( stdin );
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*9+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+ self = AllocateDoubleVec( njob );
+ alloclen = nlenmax*9;
+
+ readData( stdin, name, nlen, seq );
+ constants( njob, seq );
+
+
+
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illeagal character %c\n", c );
+ exit( 1 );
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ self[i] = (double)substitution_nid( seq[i], seq[i] );
+// fprintf( stdout, "self[%d] = %f\n", i, self[i] );
+ }
+
+ for( i=0; i<njob-1; i++ )
+ for( j=i+1; j<njob; j++ )
+ {
+ tmpdouble = (double)substitution_score( seq[i], seq[j] );
+// fprintf( stdout, "tmpdouble = %f\n", tmpdouble );
+ mtx[i][j] = ( 1.0 - tmpdouble / MIN( self[i], self[j] ) );
+ if( mtx[i][j] < 0.95 )
+ mtx[i][j] = - log( 1.0 - mtx[i][j] );
+ else
+ mtx[i][j] = 3.0;
+ }
+
+#if TEST
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
+#endif
+
+ fp = fopen( "hat2", "w" );
+ WriteHat2( fp, njob, name, mtx );
+ fclose( fp );
+ exit( 0 );
+
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define TEST 0
+
+int main()
+{
+ int i, j;
+ char **seq;
+ static char name[M][B];
+ static int nlen[M];
+ double **mtx;
+ FILE *fp;
+ int res;
+
+ scoremtx = NOTSPECIFIED;
+
+#if 0
+ PreRead( stdin, &njob, &nlenmax );
+#else
+ getnumlen( stdin );
+#endif
+ rewind( stdin );
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+
+#if 0
+ FRead( stdin, name, nlen, seq );
+#else
+ readData( stdin, name, nlen, seq );
+#endif
+
+ for( i=0; i<njob-1; i++ )
+ {
+ fprintf( stderr, "%4d/%4d\r", i+1, njob );
+ for( j=i+1; j<njob; j++ )
+ mtx[i][j] = (double)substitution_score( seq[i], seq[j] );
+ }
+
+#if TEST
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
+#endif
+
+ fp = fopen( "hat2", "w" );
+ WriteHat2( fp, njob, name, mtx );
+ fclose( fp );
+ exit( 0 );
+/*
+ res = system( ALNDIR "/spgsdl < hat2" );
+ if( res ) exit( 1 );
+ else exit( 0 );
+*/
+}
--- /dev/null
+#ifdef enablemultithread
+#define TLS __thread
+#else
+#define TLS
+#endif
+
+extern TLS int commonAlloc1;
+extern TLS int commonAlloc2;
+extern TLS int **commonIP;
+extern TLS int **commonJP;
--- /dev/null
+ /* Tree-dependent-iteration */
+ /* Devide to segments */
+
+#include "mltaln.h"
+
+extern char **seq_g;
+extern char **res_g;
+
+static int intop;
+static int intree;
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+ char *argkey;
+
+ outnumber = 0;
+ nthread = 1;
+ randomseed = 0;
+ scoreout = 0;
+ parallelizationstrategy = BAATARI1;
+ intop = 0;
+ intree = 0;
+ inputfile = NULL;
+ rnakozo = 0;
+ rnaprediction = 'm';
+ nevermemsave = 0;
+ score_check = 1;
+ fftkeika = 1;
+ constraint = 0;
+ fmodel = 0;
+ kobetsubunkatsu = 1;
+ bunkatsu = 1;
+ nblosum = 62;
+ niter = 100;
+ calledByXced = 0;
+ devide = 1;
+ divWinSize = 20; /* 70 */
+ divThreshold = 65;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ scmtd = 5;
+ cooling = 1;
+ weight = 4;
+ utree = 1;
+ refine = 1;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ use_fft = 0; // CHUUI dochira demo mafft.tmpl deha F
+ force_fft = 0;
+ alg = 'A'; /* chuui */
+ mix = 0;
+ checkC = 0;
+ tbitr = 0;
+ treemethod = 'X';
+ scoremtx = 1;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ RNAppenalty = NOTSPECIFIED;
+ RNAppenalty_ex = NOTSPECIFIED;
+ RNApthr = NOTSPECIFIED;
+ TMorJTT = JTT;
+ consweight_multi = 1.0;
+ consweight_rna = 0.0;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'I':
+ niter = atoi( *++argv );
+ fprintf( stderr, "niter = %d\n", niter );
+ --argc;
+ goto nextoption;
+ case 'e':
+ RNApthr = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'o':
+ RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+// fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+// fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+ fprintf( stderr, "kappa = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+ fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt/kimura %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "tm %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'l':
+ fastathreshold = atof( *++argv );
+ constraint = 2;
+ --argc;
+ goto nextoption;
+ case 'r':
+ consweight_rna = atof( *++argv );
+ rnakozo = 1;
+ --argc;
+ goto nextoption;
+ case 'c':
+ consweight_multi = atof( *++argv );
+ --argc;
+ goto nextoption;
+ case 'C':
+ nthread = atoi( *++argv );
+ fprintf( stderr, "nthread = %d\n", nthread );
+ --argc;
+ goto nextoption;
+ case 't':
+ randomseed = atoi( *++argv );
+ fprintf( stderr, "randomseed = %d\n", randomseed );
+ --argc;
+ goto nextoption;
+ case 'p':
+ argkey = *++argv;
+ if( !strcmp( argkey, "BESTFIRST" ) ) parallelizationstrategy = BESTFIRST;
+ else if( !strcmp( argkey, "BAATARI0" ) ) parallelizationstrategy = BAATARI0;
+ else if( !strcmp( argkey, "BAATARI1" ) ) parallelizationstrategy = BAATARI1;
+ else if( !strcmp( argkey, "BAATARI2" ) ) parallelizationstrategy = BAATARI2;
+ else
+ {
+ fprintf( stderr, "Unknown parallelization strategy, %s\n", argkey );
+ exit( 1 );
+ }
+// exit( 1 );
+ --argc;
+ goto nextoption;
+ case 'S' :
+ scoreout = 1;
+ break;
+ case 's' :
+ RNAscoremtx = 'r';
+ break;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'N':
+ nevermemsave = 1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'Q':
+ alg = 'Q';
+ break;
+ case 'R':
+ rnaprediction = 'r';
+ break;
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#if 0
+ case 'e':
+ fftscore = 0;
+ break;
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+#endif
+ case 'T':
+ kobetsubunkatsu = 0;
+ break;
+ case 'B':
+ bunkatsu = 0;
+ break;
+#if 0
+ case 'c':
+ cooling = 1;
+ break;
+ case 'a':
+ alg = 'a';
+ break;
+ case 's' :
+ treemethod = 's';
+ break;
+#endif
+ case 'H':
+ alg = 'H';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+#if 0
+ case 't':
+ weight = 4;
+ break;
+#endif
+ case 'u':
+ weight = 0;
+ break;
+ case 'U':
+ intree = 1;
+ break;
+ case 'V':
+ intop = 1;
+ break;
+ case 'J':
+ utree = 0;
+ break;
+ case 'd':
+ disp = 1;
+ break;
+ case 'Z':
+ score_check = 0;
+ break;
+ case 'Y':
+ score_check = 2;
+ break;
+#if 0
+ case 'n' :
+ treemethod = 'n';
+ break;
+#endif
+ case 'n' :
+ outnumber = 1;
+ break;
+ case 'X' :
+ treemethod = 'X';
+ break;
+ case 'E' :
+ treemethod = 'E';
+ break;
+ case 'q' :
+ treemethod = 'q';
+ break;
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options : Check source file!\n" );
+ exit( 1 );
+ }
+#if 0
+ if( alg == 'A' && weight == 0 )
+ ErrorExit( "ERROR : Algorithm A+ and un-weighted\n" );
+#endif
+}
+
+
+int main( int argc, char *argv[] )
+{
+ int identity;
+ static int nlen[M];
+ static char **name, **seq, **aseq, **bseq;
+ static Segment *segment = NULL;
+ static int anchors[MAXSEG];
+ int i, j;
+ int iseg, nseg;
+ int ***topol;
+ double **len;
+ double **eff;
+ FILE *prep;
+ FILE *infp;
+ int alloclen;
+ int returnvalue;
+ char c;
+ int ocut;
+ char **seq_g_bk;
+ LocalHom **localhomtable = NULL; // by D.Mathog
+ RNApair ***singlerna;
+ int nogaplen;
+ static char **nogap1seq;
+ static char *kozoarivec;
+ int nkozo;
+
+ arguments( argc, argv );
+#ifndef enablemultithread
+ nthread = 0;
+#endif
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+#if 0
+ PreRead( stdin, &njob, &nlenmax );
+#else
+ getnumlen( infp );
+#endif
+ rewind( infp );
+
+ nkozo = 0;
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ ocut = cut;
+
+ segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
+// if( treemethod == 'X' || treemethod == 'E' || treemethod == 'q' )
+ topol = AllocateIntCub( njob, 2, njob );
+ len = AllocateDoubleMtx( njob, 2 );
+ eff = AllocateDoubleMtx( njob, njob );
+ seq = AllocateCharMtx( njob, nlenmax*9+1 );
+ name = AllocateCharMtx( njob, B+1 );
+ seq_g = AllocateCharMtx( njob, nlenmax*9+1 );
+ res_g = AllocateCharMtx( njob, nlenmax*9+1 );
+ aseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ nogap1seq = AllocateCharMtx( 1, nlenmax*1+1 );
+ alloclen = nlenmax * 9;
+ seq_g_bk = AllocateCharMtx( njob, 0 );
+ for( i=0; i<njob; i++ ) seq_g_bk[i] = seq_g[i];
+ kozoarivec = AllocateCharVec( njob );
+
+ if( constraint )
+ {
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].overlapaa = -1.0;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].importance = -1.0;
+ localhomtable[i][j].next = NULL;
+ localhomtable[i][j].nokori = 0;
+ localhomtable[i][j].extended = -1;
+ localhomtable[i][j].last = localhomtable[i]+j;
+ localhomtable[i][j].korh = 'h';
+ }
+ }
+ fprintf( stderr, "Loading 'hat3' ... " );
+ fflush( stderr );
+ prep = fopen( "hat3", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat3." );
+ readlocalhomtable2( prep, njob, localhomtable, kozoarivec );
+ fclose( prep );
+// for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+// fprintf( stdout, "%d %d %d %d %d %d %d\n", i, j, localhomtable[i][j].opt, localhomtable[i][j].start1, localhomtable[i][j].end1, localhomtable[i][j].start2, localhomtable[i][j].end2 );
+ fprintf( stderr, "done.\n" );
+ fflush( stderr );
+#if 0
+ fprintf( stderr, "Extending localhom ... " );
+ extendlocalhom( njob, localhomtable );
+ fprintf( stderr, "done.\n" );
+#endif
+ nkozo = 0;
+ for( i=0; i<njob; i++ ) if( kozoarivec[i] ) nkozo++;
+ }
+
+
+// if( nlenmax > 30000 )
+ if( nlenmax > 50000 ) // version >= 6.823
+ {
+#if 0
+ if( constraint )
+ {
+ fprintf( stderr, "\nnlenmax=%d, nagasugi!\n", nlenmax );
+ exit( 1 );
+ }
+ if( nevermemsave )
+ {
+ fprintf( stderr, "\nnevermemsave=1, nlenmax=%d, nagasugi!\n", nlenmax );
+ exit( 1 );
+ }
+#endif
+ if( !constraint && !nevermemsave && alg != 'M' )
+ {
+ fprintf( stderr, "\nnlenmax=%d, Switching to the memsave mode\n", nlenmax );
+ alg = 'M';
+ }
+ }
+
+#if 0
+ Read( name, nlen, seq_g );
+#else
+ readData_pointer( infp, name, nlen, seq_g );
+#endif
+ fclose( infp );
+
+
+ for( i=0; i<njob; i++ )
+ {
+ res_g[i][0] = 0;
+ }
+
+ identity = 1;
+ for( i=0; i<njob; i++ )
+ {
+ identity *= ( nlen[i] == nlen[0] );
+ }
+ if( !identity )
+ {
+ fprintf( stderr, "Input pre-aligned data\n" );
+ exit( 1 );
+ }
+ constants( njob, seq_g );
+
+#if 0
+ fprintf( stderr, "penalty = %d\n", penalty );
+ fprintf( stderr, "penalty_ex = %d\n", penalty_ex );
+ fprintf( stderr, "offset = %d\n", offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+#if 0
+ if( njob == 2 )
+ {
+ writePre( njob, name, nlen, seq_g, 1 );
+ SHOWVERSION;
+ return( 0 );
+ }
+#else
+ if( njob == 2 )
+ {
+ weight = 0;
+ niter = 1;
+ }
+#endif
+
+ c = seqcheck( seq_g );
+ if( c )
+ {
+ fprintf( stderr, "Illegal character %c\n", c );
+ exit( 1 );
+ }
+ commongappick( njob, seq_g );
+
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ singlerna = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ prep = fopen( "hat4", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat4 using mccaskill." );
+ fprintf( stderr, "Loading 'hat4' ... " );
+ fflush( stderr );
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( nogap1seq[0], seq_g[i] );
+ nogaplen = strlen( nogap1seq[0] );
+ singlerna[i] = (RNApair **)calloc( nogaplen, sizeof( RNApair * ) );
+ for( j=0; j<nogaplen; j++ )
+ {
+ singlerna[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+ singlerna[i][j][0].bestpos = -1;
+ singlerna[i][j][0].bestscore = -1.0;
+ }
+ readmccaskill( prep, singlerna[i], nogaplen );
+ }
+ fclose( prep );
+ fprintf( stderr, "\ndone.\n" );
+ fflush( stderr );
+ }
+ else
+ singlerna = NULL;
+
+
+
+ if( utree )
+ {
+ prep = fopen( "hat2", "r" );
+ if( !prep ) ErrorExit( "Make hat2." );
+ readhat2_pointer( prep, njob, name, eff );
+ fclose( prep );
+#if DEBUG
+ for( i=0; i<njob-1; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ printf( " %f", eff[i][j] );
+ }
+ printf( "\n" );
+ }
+#endif
+ if( intree )
+ veryfastsupg_double_loadtree( njob, eff, topol, len );
+ else if( intop ) // v6.528 deha if( intop ) dattanode intree ga mukou datta.
+ veryfastsupg_double_loadtop( njob, eff, topol, len );
+ else if( treemethod == 'X' || treemethod == 'E' || treemethod == 'q' )
+// veryfastsupg_double_outtree( njob, eff, topol, len, name );
+ fixed_musclesupg_double_treeout( njob, eff, topol, len, name );
+ else if( treemethod == 'n' )
+ nj( njob, eff, topol, len );
+ else if( treemethod == 's' )
+ spg( njob, eff, topol, len );
+ else if( treemethod == 'p' )
+ upg2( njob, eff, topol, len );
+ else ErrorExit( "Incorrect treemethod.\n" );
+ }
+#if DEBUG
+ printf( "utree = %d\n", utree );
+#endif
+
+
+ fprintf( stderr, "\n" );
+ if( ( !utree && kobetsubunkatsu ) || constraint || !bunkatsu )
+ {
+ nseg = 0;
+ anchors[0] =0;
+ anchors[1] =strlen( seq_g[0] );
+ nseg += 2;
+ }
+ else
+ {
+ nseg = searchAnchors( njob, seq_g, segment );
+#if 0
+ fprintf( stderr, "### nseg = %d\n", nseg );
+ fprintf( stderr, "### seq_g[0] = %s\n", seq_g[0] );
+ fprintf( stderr, "### nlenmax = %d\n", nlenmax );
+ fprintf( stderr, "### len = %d\n", strlen( seq_g[0] ) );
+
+#endif
+
+ anchors[0] = 0;
+ for( i=0; i<nseg; i++ ) anchors[i+1] = segment[i].center;
+ anchors[nseg+1] = strlen( seq_g[0] );
+ nseg +=2;
+
+#if 0
+ for( i=0; i<nseg; i++ )
+ fprintf( stderr, "anchor[%d] = %d\n", i, anchors[i] );
+#endif
+ }
+
+ for( i=0; i<njob; i++ ) res_g[i][0] = 0;
+
+ for( iseg=0; iseg<nseg-1; iseg++ )
+ {
+ int tmplen = anchors[iseg+1]-anchors[iseg];
+ int pos = strlen( res_g[0] );
+ for( j=0; j<njob; j++ )
+ {
+ strncpy( seq[j], seq_g[j], tmplen );
+ seq[j][tmplen]= 0;
+ seq_g[j] += tmplen;
+
+ }
+ fprintf( stderr, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
+ fflush( stderr );
+ fprintf( trap_g, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
+
+ cut = ocut;
+ returnvalue = TreeDependentIteration( njob, name, nlen, seq, bseq, topol, len, alloclen, localhomtable, singlerna, nkozo, kozoarivec );
+
+ for( i=0; i<njob; i++ )
+ strcat( res_g[i], bseq[i] );
+ }
+ FreeCharMtx( seq_g_bk );
+ FreeIntCub( topol );
+ FreeDoubleMtx( len );
+ FreeDoubleMtx( eff );
+ if( constraint ) FreeLocalHomTable( localhomtable, njob );
+
+#if 0
+ Write( stdout, njob, name, nlen, bseq );
+#endif
+
+ fprintf( stderr, "done\n" );
+ fprintf( trap_g, "done\n" );
+ fclose( trap_g );
+
+
+ devide = 0;
+ writePre( njob, name, nlen, res_g, 1 );
+#if 0
+ writeData( stdout, njob, name, nlen, res_g, 1 );
+#endif
+
+
+ SHOWVERSION;
+ return( 0 );
+}
+
+#if 0
+signed int main( int argc, char *argv[] )
+{
+ int i, nlen[M];
+ char b[B];
+ char a[] = "=";
+ int value;
+
+ gets( b ); njob = atoi( b );
+
+/*
+ scoremtx = 0;
+ if( strstr( b, "ayhoff" ) ) scoremtx = 1;
+ else if( strstr( b, "dna" ) || strstr( b, "DNA" ) ) scoremtx = -1;
+ else if( strstr( b, "M-Y" ) || strstr( b, "iyata" ) ) scoremtx = 2;
+ else scoremtx = 0;
+*/
+ if( strstr( b, "constraint" ) ) cnst = 1;
+
+ nlenmax = 0;
+ i = 0;
+ while( i<njob )
+ {
+ gets( b );
+ if( !strncmp( b, a, 1 ) )
+ {
+ gets( b ); nlen[i] = atoi( b );
+ if( nlen[i] > nlenmax ) nlenmax = nlen[i];
+ i++;
+ }
+ }
+ if( nlenmax > N || njob > M )
+ {
+ fprintf( stderr, "ERROR in main\n" );
+ exit( 1 );
+ }
+ /*
+ nlenmax = Na;
+ */
+ rewind( stdin );
+ value = main1( nlen, argc, argv );
+ exit( 0 );
+}
+#endif
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+
+static char *comment;
+static char *orderfile;
+static int format;
+static int namelen;
+
+static void fillspace( char *seq, int lenmax )
+{
+ int len = strlen( seq );
+ seq += len;
+ lenmax -= len;
+ while( lenmax-- ) *seq++ = ' ';
+ *seq = 0;
+}
+
+void setmark_clustal( int nlen, int nseq, char **seq, char *mark )
+{
+ int i, j, k;
+
+ char *strong[] = {
+ "STA",
+ "NEQK",
+ "NHQK",
+ "NDEQ",
+ "QHRK",
+ "MILV",
+ "MILF",
+ "HY",
+ "FYW",
+ };
+ int nstrong = 9;
+ char *weaker[] = {
+ "CSA",
+ "ATV",
+ "SAG",
+ "STNK",
+ "STPA",
+ "SGND",
+ "SNDEQK",
+ "NDEQHK",
+ "NEQHRK",
+ "FVLIM",
+ "HFY",
+ };
+ int nweaker = 11;
+
+ for( i=0; i<nlen; i++ )
+ {
+ mark[i] = ' ';
+ for( j=0; j<nseq; j++ )
+ if( '-' == seq[j][i] ) break;
+ if( j != nseq )
+ {
+ continue;
+ }
+ for( j=0; j<nseq; j++ )
+ if( toupper( seq[0][i] ) != toupper( seq[j][i] ) ) break;
+ if( j == nseq )
+ {
+ mark[i] = '*';
+ continue;
+ }
+ for( k=0; k<nstrong; k++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ if( !strchr( strong[k], toupper( seq[j][i] ) ) ) break;
+ }
+ if( j == nseq ) break;
+ }
+ if( k < nstrong )
+ {
+ mark[i] = ':';
+ continue;
+ }
+ for( k=0; k<nweaker; k++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ if( !strchr( weaker[k], toupper( seq[j][i] ) ) ) break;
+ }
+ if( j == nseq ) break;
+ }
+ if( k < nweaker )
+ {
+ mark[i] = '.';
+ continue;
+ }
+ }
+ mark[nlen] = 0;
+}
+
+void setmark( int nlen, int nseq, char **seq, char *mark )
+{
+ int i, j;
+
+ for( i=0; i<nlen; i++ )
+ {
+ mark[i] = ' ';
+ for( j=0; j<nseq; j++ )
+ if( '-' == seq[j][i] ) break;
+ if( j != nseq )
+ {
+ continue;
+ }
+ for( j=0; j<nseq; j++ )
+ if( seq[0][i] != seq[j][i] ) break;
+ if( j == nseq )
+ {
+ mark[i] = '*';
+ continue;
+ }
+ for( j=0; j<nseq; j++ )
+ if( amino_grp[(int)seq[0][i]] != amino_grp[(int)seq[j][i]] ) break;
+ if( j == nseq )
+ {
+ mark[i] = '.';
+ continue;
+ }
+ }
+ mark[nlen] = 0;
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+ namelen = 15;
+ scoremtx = 1;
+ nblosum = 62;
+ dorp = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ inputfile = NULL;
+ comment = NULL;
+ orderfile = NULL;
+ format = 'c';
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'c':
+ comment = *++argv;
+ fprintf( stderr, "comment = %s\n", comment );
+ --argc;
+ goto nextoption;
+ case 'r':
+ orderfile = *++argv;
+ fprintf( stderr, "orderfile = %s\n", orderfile );
+ --argc;
+ goto nextoption;
+ case 'n':
+ namelen = atoi( *++argv );
+ fprintf( stderr, "namelen = %d\n", namelen );
+ --argc;
+ goto nextoption;
+ case 'f':
+ format = 'f';
+ break;
+ case 'y':
+ format = 'y';
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int *nlen;
+ static char **name, **seq, *mark;
+ static int *order;
+ int i;
+ FILE *infp;
+ FILE *orderfp;
+ char gett[B];
+ int nlenmin;
+
+ arguments( argc, argv );
+
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen_casepreserve( infp, &nlenmin );
+ rewind( infp );
+
+ seq = AllocateCharMtx( njob, nlenmax*2+1 );
+ mark = AllocateCharVec( nlenmax*2+1 );
+ order = AllocateIntVec( njob );
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+
+
+ if( orderfile )
+ {
+ orderfp = fopen( orderfile, "r" );
+ if( !orderfile )
+ {
+ fprintf( stderr, "Cannot open %s\n", orderfile );
+ exit( 1 );
+ }
+ for( i=0; i<njob; i++ )
+ {
+ fgets( gett, B-1, orderfp );
+ order[i] = atoi( gett );
+ }
+ fclose( orderfp );
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) order[i] = i;
+ }
+
+ readData_pointer_casepreserve( infp, name, nlen, seq );
+ fclose( infp );
+
+ if( format == 'c' || format == 'y' ) for( i=0; i<njob; i++ ) fillspace( seq[i], nlenmax );
+ constants( njob, seq );
+
+// initSignalSM();
+
+// initFiles();
+
+
+
+// setmark( nlenmax, njob, seq, mark );
+ setmark_clustal( nlenmax, njob, seq, mark );
+
+ if( format == 'f' )
+ writeData_reorder_pointer( stdout, njob, name, nlen, seq, order );
+ else if( format == 'c' )
+ clustalout_pointer( stdout, njob, nlenmax, seq, name, mark, comment, order, namelen );
+ else if( format == 'y' )
+ phylipout_pointer( stdout, njob, nlenmax, seq, name, order );
+ else
+ fprintf( stderr, "Unknown format\n" );
+
+// SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+#include "mtxutl.h"
+
+/*
+ from "C gengo niyoru saishin algorithm jiten" ISBN4-87408-414-1 Haruhiko Okumura
+*/
+static void make_sintbl(int n, float sintbl[])
+{
+ int i, n2, n4, n8;
+ double c, s, dc, ds, t;
+
+ n2 = n / 2; n4 = n / 4; n8 = n / 8;
+ t = sin(PI / n);
+ dc = 2 * t * t; ds = sqrt(dc * (2 - dc));
+ t = 2 * dc; c = sintbl[n4] = 1; s = sintbl[0] = 0;
+ for (i = 1; i < n8; i++) {
+ c -= dc; dc += t * c;
+ s += ds; ds -= t * s;
+ sintbl[i] = s; sintbl[n4 - i] = c;
+ }
+ if (n8 != 0) sintbl[n8] = sqrt(0.5);
+ for (i = 0; i < n4; i++)
+ sintbl[n2 - i] = sintbl[i];
+ for (i = 0; i < n2 + n4; i++)
+ sintbl[i + n2] = - sintbl[i];
+}
+/*
+ {\tt fft()}.
+*/
+static void make_bitrev(int n, int bitrev[])
+{
+ int i, j, k, n2;
+
+ n2 = n / 2; i = j = 0;
+ for ( ; ; ) {
+ bitrev[i] = j;
+ if (++i >= n) break;
+ k = n2;
+ while (k <= j) { j -= k; k /= 2; }
+ j += k;
+ }
+}
+/*
+*/
+int fft(int n, Fukusosuu *x, int freeflag)
+{
+ static TLS int last_n = 0; /* {\tt n} */
+ static TLS int *bitrev = NULL; /* */
+ static TLS float *sintbl = NULL; /* */
+ int i, j, k, ik, h, d, k2, n4, inverse;
+ float t, s, c, dR, dI;
+
+ if (freeflag)
+ {
+ if (bitrev) free(bitrev);
+ if (sintbl) free(sintbl);
+ return( 0 );
+ }
+
+ /* */
+ if (n < 0) {
+ n = -n; inverse = 1; /* */
+ } else inverse = 0;
+ n4 = n / 4;
+ if (n != last_n || n == 0) {
+ last_n = n;
+#if 0
+ if (sintbl != NULL) {
+ free(sintbl);
+ sintbl = NULL;
+ }
+ if (bitrev != NULL) {
+ free(bitrev);
+ bitrev = NULL;
+ }
+ if (n == 0) return 0; /* */
+ sintbl = (float *)malloc((n + n4) * sizeof(float));
+ bitrev = (int *)malloc(n * sizeof(int));
+#else /* by T. Nishiyama */
+ sintbl = realloc(sintbl, (n + n4) * sizeof(float));
+ bitrev = realloc(bitrev, n * sizeof(int));
+#endif
+ if (sintbl == NULL || bitrev == NULL) {
+ fprintf(stderr, "\n"); return 1;
+ }
+ make_sintbl(n, sintbl);
+ make_bitrev(n, bitrev);
+ }
+ for (i = 0; i < n; i++) { /* */
+ j = bitrev[i];
+ if (i < j) {
+ t = x[i].R; x[i].R = x[j].R; x[j].R = t;
+ t = x[i].I; x[i].I = x[j].I; x[j].I = t;
+ }
+ }
+ for (k = 1; k < n; k = k2) { /* */
+#if 0
+ fprintf( stderr, "%d / %d\n", k, n );
+#endif
+ h = 0; k2 = k + k; d = n / k2;
+ for (j = 0; j < k; j++) {
+#if 0
+ if( j % 1 == 0 )
+ fprintf( stderr, "%d / %d\r", j, k );
+#endif
+ c = sintbl[h + n4];
+ if (inverse) s = - sintbl[h];
+ else s = sintbl[h];
+ for (i = j; i < n; i += k2) {
+#if 0
+ if( k>=4194000 ) fprintf( stderr, "in loop %d - %d < %d, k2=%d\r", j, i, n, k2 );
+#endif
+ ik = i + k;
+ dR = s * x[ik].I + c * x[ik].R;
+ dI = c * x[ik].I - s * x[ik].R;
+ x[ik].R = x[i].R - dR; x[i].R += dR;
+ x[ik].I = x[i].I - dI; x[i].I += dI;
+ }
+ h += d;
+ }
+ }
+ if (! inverse) /* n */
+ for (i = 0; i < n; i++) { x[i].R /= n; x[i].I /= n; }
+ return 0; /* */
+}
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <stddef.h>
+#include <math.h>
+#include "mtxutl.h"
+
+#define PI 3.14159265358979323846
+#define END_OF_VEC -1
+
+#define NKOUHO 20
+#define NKOUHO_LONG 500
+
+#define MAX(X,Y) ( ((X)>(Y))?(X):(Y) )
+#define MIN(X,Y) ( ((X)<(Y))?(X):(Y) )
+
--- /dev/null
+#include "mltaln.h"
+
+#define SEGMENTSIZE 150
+#define TMPTMPTMP 0
+
+#define DEBUG 0
+
+void keika( char *str, int current, int all )
+{
+ if( current == 0 )
+ fprintf( stderr, "%s : ", str );
+
+ fprintf( stderr, "\b\b\b\b\b\b\b\b" );
+ fprintf( stderr, "%3d /%3d", current+1, all+1 );
+
+ if( current+1 == all )
+ fprintf( stderr, "\b\b\b\b\b\b\b\bdone. \n" );
+}
+
+double maxItch( double *soukan, int size )
+{
+ int i;
+ double value = 0.0;
+ double cand;
+ for( i=0; i<size; i++ )
+ if( ( cand = soukan[i] ) > value ) value = cand;
+ return( value );
+}
+
+void calcNaiseki( Fukusosuu *value, Fukusosuu *x, Fukusosuu *y )
+{
+ value->R = x->R * y->R + x->I * y->I;
+ value->I = -x->R * y->I + x->I * y->R;
+}
+
+Fukusosuu *AllocateFukusosuuVec( int l1 )
+{
+ Fukusosuu *value;
+ value = (Fukusosuu *)calloc( l1, sizeof( Fukusosuu ) );
+ if( !value )
+ {
+ fprintf( stderr, "Cannot allocate %d FukusosuuVec\n", l1 );
+ return( NULL );
+ }
+ return( value );
+}
+
+Fukusosuu **AllocateFukusosuuMtx( int l1, int l2 )
+{
+ Fukusosuu **value;
+ int j;
+// fprintf( stderr, "allocating %d x %d FukusosuuMtx\n", l1, l2 );
+ value = (Fukusosuu **)calloc( l1+1, sizeof( Fukusosuu * ) );
+ if( !value )
+ {
+ fprintf( stderr, "Cannot allocate %d x %d FukusosuuVecMtx\n", l1, l2 );
+ exit( 1 );
+ }
+ for( j=0; j<l1; j++ )
+ {
+ value[j] = AllocateFukusosuuVec( l2 );
+ if( !value[j] )
+ {
+ fprintf( stderr, "Cannot allocate %d x %d FukusosuuVecMtx\n", l1, l2 );
+ exit( 1 );
+ }
+ }
+ value[l1] = NULL;
+ return( value );
+}
+
+Fukusosuu ***AllocateFukusosuuCub( int l1, int l2, int l3 )
+{
+ Fukusosuu ***value;
+ int i;
+ value = calloc( l1+1, sizeof( Fukusosuu ** ) );
+ if( !value ) ErrorExit( "Cannot allocate Fukusosuu" );
+ for( i=0; i<l1; i++ ) value[i] = AllocateFukusosuuMtx( l2, l3 );
+ value[l1] = NULL;
+ return( value );
+}
+
+void FreeFukusosuuVec( Fukusosuu *vec )
+{
+ free( (void *)vec );
+}
+
+void FreeFukusosuuMtx( Fukusosuu **mtx )
+{
+ int i;
+
+ for( i=0; mtx[i]; i++ )
+ free( (void *)mtx[i] );
+ free( (void *)mtx );
+}
+
+int getKouho( int *kouho, int nkouho, double *soukan, int nlen2 )
+{
+ int i, j;
+ int nlen4 = nlen2 / 2;
+ double max;
+ double tmp;
+ int ikouho = 0; // by D.Mathog, iinoka?
+ for( j=0; j<nkouho; j++ )
+ {
+ max = -9999.9;
+ for( i=0; i<nlen2; i++ )
+ {
+ if( ( tmp = soukan[i] ) > max )
+ {
+ ikouho = i;
+ max = tmp;
+ }
+ }
+#if 0
+ if( max < 0.15 )
+ {
+ break;
+ }
+#endif
+#if 0
+ fprintf( stderr, "Kouho No.%d, pos=%d, score=%f, lag=%d\n", j, ikouho, soukan[ikouho], ikouho-nlen4 );
+#endif
+ soukan[ikouho] = -9999.9;
+ kouho[j] = ( ikouho - nlen4 );
+ }
+ return( j );
+}
+
+void zurasu2( int lag, int clus1, int clus2,
+ char **seq1, char **seq2,
+ char **aseq1, char **aseq2 )
+{
+ int i;
+#if 0
+ fprintf( stderr, "### lag = %d\n", lag );
+#endif
+ if( lag > 0 )
+ {
+ for( i=0; i<clus1; i++ ) aseq1[i] = seq1[i];
+ for( i=0; i<clus2; i++ ) aseq2[i] = seq2[i]+lag;
+ }
+ else
+ {
+ for( i=0; i<clus1; i++ ) aseq1[i] = seq1[i]-lag;
+ for( i=0; i<clus2; i++ ) aseq2[i] = seq2[i];
+ }
+}
+
+void zurasu( int lag, int clus1, int clus2,
+ char **seq1, char **seq2,
+ char **aseq1, char **aseq2 )
+{
+ int i;
+#if DEBUG
+ fprintf( stderr, "lag = %d\n", lag );
+#endif
+ if( lag > 0 )
+ {
+ for( i=0; i<clus1; i++ ) strcpy( aseq1[i], seq1[i] );
+ for( i=0; i<clus2; i++ ) strcpy( aseq2[i], seq2[i]+lag );
+ }
+ else
+ {
+ for( i=0; i<clus1; i++ ) strcpy( aseq1[i], seq1[i]-lag );
+ for( i=0; i<clus2; i++ ) strcpy( aseq2[i], seq2[i] );
+ }
+}
+
+
+int alignableReagion( int clus1, int clus2,
+ char **seq1, char **seq2,
+ double *eff1, double *eff2,
+ Segment *seg )
+{
+ int i, j, k;
+ int status, starttmp = 0; // by D.Mathog, a gess
+ double score;
+ int value = 0;
+ int len, maxlen;
+ int length = 0; // by D.Mathog, a gess
+ static TLS double *stra = NULL;
+ static TLS int alloclen = 0;
+ double totaleff;
+ double cumscore;
+ static TLS double threshold;
+ static TLS double *prf1 = NULL;
+ static TLS double *prf2 = NULL;
+ static TLS int *hat1 = NULL;
+ static TLS int *hat2 = NULL;
+ int pre1, pre2;
+#if 0
+ char **seq1pt;
+ char **seq2pt;
+ double *eff1pt;
+ double *eff2pt;
+#endif
+
+#if 0
+ fprintf( stderr, "### In alignableRegion, clus1=%d, clus2=%d \n", clus1, clus2 );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "eff1[0] = %f\n", eff1[0] );
+ fprintf( stderr, "eff2[0] = %f\n", eff2[0] );
+#endif
+
+ if( clus1 == 0 )
+ {
+ FreeDoubleVec( stra ); stra = NULL;
+ FreeDoubleVec( prf1 ); prf1 = NULL;
+ FreeDoubleVec( prf2 ); prf2 = NULL;
+ FreeIntVec( hat1 ); hat1 = NULL;
+ FreeIntVec( hat2 ); hat2 = NULL;
+ return( 0 );
+ }
+
+ if( prf1 == NULL )
+ {
+ prf1 = AllocateDoubleVec( 26 );
+ prf2 = AllocateDoubleVec( 26 );
+ hat1 = AllocateIntVec( 27 );
+ hat2 = AllocateIntVec( 27 );
+ }
+
+ len = MIN( strlen( seq1[0] ), strlen( seq2[0] ) );
+ maxlen = MAX( strlen( seq1[0] ), strlen( seq2[0] ) ) + fftWinSize;
+ if( alloclen < maxlen )
+ {
+ if( alloclen )
+ {
+ FreeDoubleVec( stra );
+ }
+ else
+ {
+ threshold = (int)fftThreshold / 100.0 * 600.0 * fftWinSize;
+ }
+ stra = AllocateDoubleVec( maxlen );
+ alloclen = maxlen;
+ }
+
+
+ totaleff = 0.0;
+ for( i=0; i<clus1; i++ ) for( j=0; j<clus2; j++ ) totaleff += eff1[i] * eff2[j];
+ for( i=0; i<len; i++ )
+ {
+ /* make prfs */
+ for( j=0; j<26; j++ )
+ {
+ prf1[j] = 0.0;
+ prf2[j] = 0.0;
+ }
+#if 0
+ seq1pt = seq1;
+ eff1pt = eff1;
+ j = clus1;
+ while( j-- ) prf1[amino_n[(*seq1pt++)[i]]] += *eff1pt++;
+#else
+ for( j=0; j<clus1; j++ ) prf1[amino_n[(int)seq1[j][i]]] += eff1[j];
+#endif
+ for( j=0; j<clus2; j++ ) prf2[amino_n[(int)seq2[j][i]]] += eff2[j];
+
+ /* make hats */
+ pre1 = pre2 = 26;
+ for( j=25; j>=0; j-- )
+ {
+ if( prf1[j] )
+ {
+ hat1[pre1] = j;
+ pre1 = j;
+ }
+ if( prf2[j] )
+ {
+ hat2[pre2] = j;
+ pre2 = j;
+ }
+ }
+ hat1[pre1] = -1;
+ hat2[pre2] = -1;
+
+ /* make site score */
+ stra[i] = 0.0;
+ for( k=hat1[26]; k!=-1; k=hat1[k] )
+ for( j=hat2[26]; j!=-1; j=hat2[j] )
+// stra[i] += n_dis[k][j] * prf1[k] * prf2[j];
+ stra[i] += n_disFFT[k][j] * prf1[k] * prf2[j];
+ stra[i] /= totaleff;
+ }
+
+ (seg+0)->skipForeward = 0;
+ (seg+1)->skipBackward = 0;
+ status = 0;
+ cumscore = 0.0;
+ score = 0.0;
+ for( j=0; j<fftWinSize; j++ ) score += stra[j];
+
+ for( i=1; i<len-fftWinSize; i++ )
+ {
+ score = score - stra[i-1] + stra[i+fftWinSize-1];
+#if TMPTMPTMP
+ fprintf( stderr, "%d %10.0f ? %10.0f\n", i, score, threshold );
+#endif
+
+ if( score > threshold )
+ {
+#if 0
+ seg->start = i;
+ seg->end = i;
+ seg->center = ( seg->start + seg->end + fftWinSize ) / 2 ;
+ seg->score = score;
+ status = 0;
+ value++;
+#else
+ if( !status )
+ {
+ status = 1;
+ starttmp = i;
+ length = 0;
+ cumscore = 0.0;
+ }
+ length++;
+ cumscore += score;
+#endif
+ }
+ if( score <= threshold || length > SEGMENTSIZE )
+ {
+ if( status )
+ {
+ if( length > fftWinSize )
+ {
+ seg->start = starttmp;
+ seg->end = i;
+ seg->center = ( seg->start + seg->end + fftWinSize ) / 2 ;
+ seg->score = cumscore;
+#if 0
+ fprintf( stderr, "%d-%d length = %d, score = %f, value = %d\n", seg->start, seg->end, length, cumscore, value );
+#endif
+ if( length > SEGMENTSIZE )
+ {
+ (seg+0)->skipForeward = 1;
+ (seg+1)->skipBackward = 1;
+ }
+ else
+ {
+ (seg+0)->skipForeward = 0;
+ (seg+1)->skipBackward = 0;
+ }
+ value++;
+ seg++;
+ }
+ length = 0;
+ cumscore = 0.0;
+ status = 0;
+ starttmp = i;
+ if( value > MAXSEG - 3 ) ErrorExit( "TOO MANY SEGMENTS!");
+ }
+ }
+ }
+ if( status && length > fftWinSize )
+ {
+ seg->end = i;
+ seg->start = starttmp;
+ seg->center = ( starttmp + i + fftWinSize ) / 2 ;
+ seg->score = cumscore;
+#if 0
+fprintf( stderr, "%d-%d length = %d\n", seg->start, seg->end, length );
+#endif
+ value++;
+ }
+#if TMPTMPTMP
+ exit( 0 );
+#endif
+// fprintf( stderr, "returning %d\n", value );
+ return( value );
+}
+
+
+static int permit( Segment *seg1, Segment *seg2 )
+{
+ return( 0 );
+ if( seg1->end >= seg2->start ) return( 0 );
+ if( seg1->pair->end >= seg2->pair->start ) return( 0 );
+ else return( 1 );
+}
+
+void blockAlign2( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut )
+{
+ int i, j, k, shift, cur1, cur2, count, klim;
+ static TLS int crossscoresize = 0;
+ static TLS int *result1 = NULL;
+ static TLS int *result2 = NULL;
+ static TLS int *ocut1 = NULL;
+ static TLS int *ocut2 = NULL;
+ double maximum;
+ static TLS double **crossscore = NULL;
+ static TLS int **track = NULL;
+ static TLS double maxj, maxi;
+ static TLS int pointj, pointi;
+
+ if( cut1 == NULL)
+ {
+ if( result1 )
+ {
+ free( result1 );
+ free( result2 );
+ free( ocut1 );
+ free( ocut2 );
+ FreeIntMtx( track );
+ FreeDoubleMtx( crossscore );
+ }
+ return;
+ }
+
+ if( result1 == NULL )
+ {
+ result1 = AllocateIntVec( MAXSEG );
+ result2 = AllocateIntVec( MAXSEG );
+ ocut1 = AllocateIntVec( MAXSEG );
+ ocut2 = AllocateIntVec( MAXSEG );
+ }
+
+ if( crossscoresize < *ncut+2 )
+ {
+ crossscoresize = *ncut+2;
+ if( fftkeika ) fprintf( stderr, "allocating crossscore and track, size = %d\n", crossscoresize );
+ if( track ) FreeIntMtx( track );
+ if( crossscore ) FreeDoubleMtx( crossscore );
+ track = AllocateIntMtx( crossscoresize, crossscoresize );
+ crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
+ }
+
+#if 0
+ for( i=0; i<*ncut-2; i++ )
+ fprintf( stderr, "%d.start = %d, score = %f\n", i, seg1[i]->start, seg1[i]->score );
+
+ for( i=0; i<*ncut; i++ )
+ fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
+ for( i=0; i<*ncut; i++ )
+ {
+ for( j=0; j<*ncut; j++ )
+ fprintf( stderr, "%#4.0f ", ocrossscore[i][j] );
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+ for( i=0; i<*ncut; i++ ) for( j=0; j<*ncut; j++ ) /* mudadanaa */
+ crossscore[i][j] = ocrossscore[i][j];
+ for( i=0; i<*ncut; i++ )
+ {
+ ocut1[i] = cut1[i];
+ ocut2[i] = cut2[i];
+ }
+
+ for( i=1; i<*ncut; i++ )
+ {
+#if 0
+ fprintf( stderr, "### i=%d/%d\n", i,*ncut );
+#endif
+ for( j=1; j<*ncut; j++ )
+ {
+ pointi = 0; maxi = 0.0;
+ klim = j-2;
+ for( k=0; k<klim; k++ )
+ {
+/*
+ fprintf( stderr, "k=%d, i=%d\n", k, i );
+*/
+ if( k && k<*ncut-1 && j<*ncut-1 && !permit( seg1[k-1], seg1[j-1] ) ) continue;
+ if( crossscore[i-1][k] > maxj )
+ {
+ pointi = k;
+ maxi = crossscore[i-1][k];
+ }
+ }
+
+ pointj = 0; maxj = 0.0;
+ klim = i-2;
+ for( k=0; k<klim; k++ )
+ {
+ if( k && k<*ncut-1 && i<*ncut-1 && !permit( seg2[k-1], seg2[i-1] ) ) continue;
+ if( crossscore[k][j-1] > maxj )
+ {
+ pointj = k;
+ maxj = crossscore[k][j-1];
+ }
+ }
+
+ maxi += penalty;
+ maxj += penalty;
+
+ maximum = crossscore[i-1][j-1];
+ track[i][j] = 0;
+
+ if( maximum < maxi )
+ {
+ maximum = maxi ;
+ track[i][j] = j - pointi;
+ }
+
+ if( maximum < maxj )
+ {
+ maximum = maxj ;
+ track[i][j] = pointj - i;
+ }
+
+ crossscore[i][j] += maximum;
+ }
+ }
+#if 0
+ for( i=0; i<*ncut; i++ )
+ {
+ for( j=0; j<*ncut; j++ )
+ fprintf( stderr, "%3d ", track[i][j] );
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+
+ result1[MAXSEG-1] = *ncut-1;
+ result2[MAXSEG-1] = *ncut-1;
+
+ for( i=MAXSEG-1; i>=1; i-- )
+ {
+ cur1 = result1[i];
+ cur2 = result2[i];
+ if( cur1 == 0 || cur2 == 0 ) break;
+ shift = track[cur1][cur2];
+ if( shift == 0 )
+ {
+ result1[i-1] = cur1 - 1;
+ result2[i-1] = cur2 - 1;
+ continue;
+ }
+ else if( shift > 0 )
+ {
+ result1[i-1] = cur1 - 1;
+ result2[i-1] = cur2 - shift;
+ }
+ else if( shift < 0 )
+ {
+ result1[i-1] = cur1 + shift;
+ result2[i-1] = cur2 - 1;
+ }
+ }
+
+ count = 0;
+ for( j=i; j<MAXSEG; j++ )
+ {
+ if( ocrossscore[result1[j]][result2[j]] == 0.0 ) continue;
+
+ if( result1[j] == result1[j-1] || result2[j] == result2[j-1] )
+ if( ocrossscore[result1[j]][result2[j]] > ocrossscore[result1[j-1]][result2[j-1]] )
+ count--;
+
+ cut1[count] = ocut1[result1[j]];
+ cut2[count] = ocut2[result2[j]];
+
+ count++;
+ }
+
+ *ncut = count;
+#if 0
+ for( i=0; i<*ncut; i++ )
+ fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
+#endif
+}
+
+void blockAlign3( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut )
+// memory complexity = O(n^3), time complexity = O(n^2)
+{
+ int i, j, shift, cur1, cur2, count;
+ static TLS int crossscoresize = 0;
+ static TLS int jumpposi, *jumppos;
+ static TLS double jumpscorei, *jumpscore;
+ static TLS int *result1 = NULL;
+ static TLS int *result2 = NULL;
+ static TLS int *ocut1 = NULL;
+ static TLS int *ocut2 = NULL;
+ double maximum;
+ static TLS double **crossscore = NULL;
+ static TLS int **track = NULL;
+
+ if( result1 == NULL )
+ {
+ result1 = AllocateIntVec( MAXSEG );
+ result2 = AllocateIntVec( MAXSEG );
+ ocut1 = AllocateIntVec( MAXSEG );
+ ocut2 = AllocateIntVec( MAXSEG );
+ }
+ if( crossscoresize < *ncut+2 )
+ {
+ crossscoresize = *ncut+2;
+ if( fftkeika ) fprintf( stderr, "allocating crossscore and track, size = %d\n", crossscoresize );
+ if( track ) FreeIntMtx( track );
+ if( crossscore ) FreeDoubleMtx( crossscore );
+ if( jumppos ) FreeIntVec( jumppos );
+ if( jumpscore ) FreeDoubleVec( jumpscore );
+ track = AllocateIntMtx( crossscoresize, crossscoresize );
+ crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
+ jumppos = AllocateIntVec( crossscoresize );
+ jumpscore = AllocateDoubleVec( crossscoresize );
+ }
+
+#if 0
+ for( i=0; i<*ncut-2; i++ )
+ fprintf( stderr, "%d.start = %d, score = %f\n", i, seg1[i]->start, seg1[i]->score );
+
+ for( i=0; i<*ncut; i++ )
+ fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
+ for( i=0; i<*ncut; i++ )
+ {
+ for( j=0; j<*ncut; j++ )
+ fprintf( stderr, "%#4.0f ", ocrossscore[i][j] );
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+ for( i=0; i<*ncut; i++ ) for( j=0; j<*ncut; j++ ) /* mudadanaa */
+ crossscore[i][j] = ocrossscore[i][j];
+ for( i=0; i<*ncut; i++ )
+ {
+ ocut1[i] = cut1[i];
+ ocut2[i] = cut2[i];
+ }
+ for( j=0; j<*ncut; j++ )
+ {
+ jumpscore[j] = -999.999;
+ jumppos[j] = -1;
+ }
+
+ for( i=1; i<*ncut; i++ )
+ {
+
+ jumpscorei = -999.999;
+ jumpposi = -1;
+
+ for( j=1; j<*ncut; j++ )
+ {
+#if 1
+ fprintf( stderr, "in blockalign3, ### i=%d, j=%d\n", i, j );
+#endif
+
+
+#if 0
+ for( k=0; k<j-2; k++ )
+ {
+/*
+ fprintf( stderr, "k=%d, i=%d\n", k, i );
+*/
+ if( k && k<*ncut-1 && j<*ncut-1 && !permit( seg1[k-1], seg1[j-1] ) ) continue;
+ if( crossscore[i-1][k] > maxj )
+ {
+ pointi = k;
+ maxi = crossscore[i-1][k];
+ }
+ }
+
+ pointj = 0; maxj = 0.0;
+ for( k=0; k<i-2; k++ )
+ {
+ if( k && k<*ncut-1 && i<*ncut-1 && !permit( seg2[k-1], seg2[i-1] ) ) continue;
+ if( crossscore[k][j-1] > maxj )
+ {
+ pointj = k;
+ maxj = crossscore[k][j-1];
+ }
+ }
+
+
+ maxi += penalty;
+ maxj += penalty;
+#endif
+ maximum = crossscore[i-1][j-1];
+ track[i][j] = 0;
+
+ if( maximum < jumpscorei && permit( seg1[jumpposi], seg1[i] ) )
+ {
+ maximum = jumpscorei;
+ track[i][j] = j - jumpposi;
+ }
+
+ if( maximum < jumpscore[j] && permit( seg2[jumppos[j]], seg2[j] ) )
+ {
+ maximum = jumpscore[j];
+ track[i][j] = jumpscore[j] - i;
+ }
+
+ crossscore[i][j] += maximum;
+
+ if( jumpscorei < crossscore[i-1][j] )
+ {
+ jumpscorei = crossscore[i-1][j];
+ jumpposi = j;
+ }
+
+ if( jumpscore[j] < crossscore[i][j-1] )
+ {
+ jumpscore[j] = crossscore[i][j-1];
+ jumppos[j] = i;
+ }
+ }
+ }
+#if 0
+ for( i=0; i<*ncut; i++ )
+ {
+ for( j=0; j<*ncut; j++ )
+ fprintf( stderr, "%3d ", track[i][j] );
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+
+ result1[MAXSEG-1] = *ncut-1;
+ result2[MAXSEG-1] = *ncut-1;
+
+ for( i=MAXSEG-1; i>=1; i-- )
+ {
+ cur1 = result1[i];
+ cur2 = result2[i];
+ if( cur1 == 0 || cur2 == 0 ) break;
+ shift = track[cur1][cur2];
+ if( shift == 0 )
+ {
+ result1[i-1] = cur1 - 1;
+ result2[i-1] = cur2 - 1;
+ continue;
+ }
+ else if( shift > 0 )
+ {
+ result1[i-1] = cur1 - 1;
+ result2[i-1] = cur2 - shift;
+ }
+ else if( shift < 0 )
+ {
+ result1[i-1] = cur1 + shift;
+ result2[i-1] = cur2 - 1;
+ }
+ }
+
+ count = 0;
+ for( j=i; j<MAXSEG; j++ )
+ {
+ if( ocrossscore[result1[j]][result2[j]] == 0.0 ) continue;
+
+ if( result1[j] == result1[j-1] || result2[j] == result2[j-1] )
+ if( ocrossscore[result1[j]][result2[j]] > ocrossscore[result1[j-1]][result2[j-1]] )
+ count--;
+
+ cut1[count] = ocut1[result1[j]];
+ cut2[count] = ocut2[result2[j]];
+
+ count++;
+ }
+
+ *ncut = count;
+#if 0
+ for( i=0; i<*ncut; i++ )
+ fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
+#endif
+}
+
--- /dev/null
+extern int intlen( int *num );
+extern char seqcheck( char **seq );
+extern void scmx_calc( int icyc, char **aseq, double *effarr, float **scmx );
+extern void exitall( char arr[] );
+extern void display( char **seq, int nseq );
+extern void intergroup_score( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
+extern void intergroup_score_gapnomi( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
+extern void intergroup_score_new( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
+extern double score_calc5( char **seq, int s, double **eff, int ex );
+extern double score_calc4( char **seq, int s, double **eff, int ex );
+extern void upg2( int nseq, double **eff, int ***topol, double **len );
+//extern void veryfastsupg_float_realloc_nobk_halfmtx( int njob, float **mtx, int ***topol, float **len );
+//extern void veryfastsupg_float_realloc_nobk( int njob, float **mtx, int ***topol, float **len );
+extern void veryfastsupg_int_realloc_nobk( int njob, int **mtx, int ***topol, double **len );
+extern void veryfastsupg( int nseq, double **oeff, int ***topol, double **len );
+extern void veryfastsupg_double( int nseq, double **oeff, int ***topol, double **len );
+extern void veryfastsupg_double_loadtree( int nseq, double **oeff, int ***topol, double **len );
+extern void veryfastsupg_double_loadtop( int nseq, double **oeff, int ***topol, double **len );
+extern void veryfastsupg_int( int nseq, int **oeff, int ***topol, double **len );
+extern void fastsupg( int nseq, double **oeff, int ***topol, double **len );
+extern void supg( int nseq, double **oeff, int ***topol, double **len );
+extern void spg( int nseq, double **oeff, int ***topol, double **len );
+extern double ipower( double x, int n );
+extern void countnode( int nseq, int ***topol, double **node );
+extern void countnode_int( int nseq, int ***topol, int **node );
+extern void counteff_simple( int nseq, int ***topol, double **len, double *node );
+extern void counteff_simple_float( int nseq, int ***topol, float **len, double *node );
+extern void counteff( int nseq, int ***topol, double **len, double **node );
+extern float score_calc1( char *seq1, char *seq2 );
+extern float score_calcp( char *seq1, char *seq2, int len );
+extern float substitution_nid( char *seq1, char *seq2 );
+extern float substitution_score( char *seq1, char *seq2 );
+extern float substitution_hosei( char *seq1, char *seq2 );
+extern float substitution( char *seq1, char *seq2 );
+extern void treeconstruction( char **seq, int nseq, int ***topol, double **len, double **eff );
+extern float bscore_calc( char **seq, int s, double **eff );
+extern void AllocateTmpSeqs( char ***mseq2pt, char **mseq1pt, int locnlenmax );
+extern void FreeTmpSeqs( char **mseq2, char *mseq1 );
+extern void gappick_samestring( char *aseq );
+extern void gappick0( char *aseq, char *seq );
+extern void gappick( int nseq, int s, char **aseq, char **mseq2,
+ double **eff, double *effarr );
+extern void commongappick_record( int nseq, char **seq, int *map );
+extern void commongappick( int nseq, char **seq );
+extern double score_calc0( char **seq, int s, double **eff, int ex );
+extern void strins( char *str1, char *str2 );
+extern int isaligned( int nseq, char **seq );
+extern double score_calc_for_score( int nseq, char **seq );
+extern void floatncpy( float *vec1, float *vec2, int len );
+extern float score_calc_a( char **seq, int s, double **eff );
+extern float score_calc_s( char **seq, int s, double **eff );
+extern double score_calc_for_score_s( int s, char **seq );
+extern double SSPscore( int s, char **seq );
+extern double DSPscore( int s, char **seq );
+extern int searchAnchors( int nseq, char **seq, Segment *seg );
+extern char *progName( char *str );
+extern void dontcalcimportance( int nseq, double *eff, char **seq, LocalHom **localhom );
+extern void calcimportance( int nseq, double *eff, char **seq, LocalHom **localhom );
+extern void weightimportance2( int nseq, double *eff, LocalHom **localhom );
+extern void weightimportance4( int clus1, int clus2, double *eff1, double *eff2, LocalHom ***localhom );
+extern void extendlocalhom( int nseq, LocalHom **localhom );
+extern void extendlocalhom2( int nseq, LocalHom **localhom, double **mtx );
+extern int makelocal( char *s1, char *s2, int thr );
+extern void mdfymtx( char **pair, int s1, double **partialmtx, double **mtx );
+extern float score_calc( char **seq, int s );
+extern void cpmx_calc( char **seq, float **cpmx, double *eff, int lgth, int clus );
+extern void cpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus );
+extern void MScpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus );
+extern void mseqcat( char **seq1, char **seq2, double **eff, double *effarr1, double *effarr2, char name1[M][B], char name2[M][B], int clus1, int clus2 );
+extern void strnbcat( char *s1, char *s2, int m );
+extern int conjuctionforgaln( int s0, int s1, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d );
+extern int fastconjuction( int *memlist, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], char *d );
+extern int fastconjuction_noname_kozo( int *memlist, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d );
+extern int fastconjuction_noname( int *memlist, char **seq, char **aseq, double *peff, double *eff, char *d );
+extern int fastconjuction_noweight( int *memlist, char **seq, char **aseq, double *peff, char *d );
+extern int conjuctionfortbfast( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char *d );
+extern int conjuctionfortbfast_kozo( double *tmptmp, char **pair, int s, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d );
+extern int conjuction( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d );
+extern void floatdelete( float **cpmx, int d, int len );
+extern void chardelete( char *seq, int d );
+extern int RootBranchNode( int nseq, int ***topol, int step, int branch );
+extern void BranchLeafNode( int nseq, int ***topol, int *node, int step, int branch );
+extern void RootLeafNode( int nseq, int ***topol, int *node );
+extern void nodeFromABranch( int nseq, int *result, int **pairwisenode, int ***topol, double **len, int step, int num );
+extern void OneClusterAndTheOther( int locnjob, char **pair, int *s1, int *s2, int ***topol, int step, int branch );
+extern void makeEffMtx( int nseq, double **mtx, double *vec );
+extern void node_eff( int nseq, double *eff, int *node );
+extern int shrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink );
+extern int msshrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink );
+extern int fastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink );
+extern int msfastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink );
+extern int TreeDependentIteration( int locnjob, char **name, int nlen[M], char **aseq, char **bseq, int ***topol, double **len, int alloclen, LocalHom **localhomtable, RNApair ***single, int nkozo, char *kozoarivec );
+extern void checkMinusLength( int nseq, double **len );
+extern void negativeMember2( int *mem, int *query, int locnseq );
+extern int *negativeMember( int *query, int locnseq );
+extern int IntExistsInVec( int query, int *vector );
+extern NodeInCub searchParent( int top, int ***topol, int Start, int End );
+extern void stopolInit( int n, Node *stopol );
+extern void treeCnv( Node *stopol, int locnseq, int ***topol, double **len, double **bw );
+extern int isLeaf( Node node );
+extern double syntheticLength( Node *ob, Node *oppositeNode );
+extern double calcW( Node *ob, Node *op );
+extern void calcBranchWeight( double **bw, int locnseq, Node *stopol, int ***topol, double **len );
+extern void branchWeightToPairWeight( int locnseq, int ***topol, double **pw, double **bw );
+extern void weightFromABranch_rec( double *result, Node *ob, Node *op );
+extern void weightFromABranch( int nseq, double *result, Node *stopol, int ***topol, int step, int LorR );
+extern void keika( char *str, int current, int all );
+extern double maxItch( double *soukan, int size );
+extern void calcNaiseki( Fukusosuu *value, Fukusosuu *x, Fukusosuu *y );
+extern Fukusosuu *AllocateFukusosuuVec( int l1 );
+extern Fukusosuu **AllocateFukusosuuMtx( int l1, int l2 );
+extern Fukusosuu ***AllocateFukusosuuCub( int l1, int l2, int l3 );
+extern void FreeFukusosuuVec( Fukusosuu *vec );
+extern void FreeFukusosuuMtx( Fukusosuu **mtx );
+extern int getKouho( int *kouho, int nkouho, double *soukan, int nlen2 );
+extern void zurasu2( int lag, int clus1, int clus2, char **seq1, char **seq2, char **aseq1, char **aseq2 );
+extern void zurasu( int lag, int clus1, int clus2, char **seq1, char **seq2, char **aseq1, char **aseq2 );
+extern int alignableReagion( int clus1, int clus2, char **seq1, char **seq2, double *eff1, double *eff2, Segment *seg );
+extern void blockAlign( int *cut1, int *cut2, double **ocrossscore, int *ncut );
+extern void blockAlign2( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut );
+extern void blockAlign3( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut );
+extern float A__align11( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch );
+extern float imp_match_out_scH( int i1, int j1 );
+extern void imp_match_init_strictH( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
+extern float imp_match_out_scQ( int i1, int j1 );
+extern float imp_match_out_scR( int i1, int j1 );
+extern void imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
+extern void imp_match_init_strictR( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
+extern void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom );
+extern float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, int *, int, int *, int headgp, int tailgp );
+extern float Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, float **map );
+extern float Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, float **map );
+extern float MSalign11( char **seq1, char **seq2, int alloclen );
+//extern float rnalocal( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, RNApair **pair );
+extern float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *, int, int *, int headgp, int tailgp );
+extern float H__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
+extern float Q__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
+extern float Q__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *gapmap1, int *gapmap2 );
+extern float R__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
+extern float R__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
+extern float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 );
+extern float D__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 );
+extern float translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, int clus1, int clus2, int alloclen );
+extern double Fgetlag( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen );
+extern float Falign( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen, int *fftlog, int *, int, int * );
+extern float Falign_udpari_long( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen, int *fftlog );
+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 );
+extern float part_imp_match_out_sc( int i1, int j1 );
+extern float part_imp_match_out_scQ( int i1, int j1 );
+extern void part_imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore );
+extern void part_imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
+extern void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom );
+extern float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *, char *, char *, char *, int *, int, int * );
+extern float partQ__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *, char *, char *, char *);
+extern float G__align11( char **seq1, char **seq2, int alloclen, int headgp, int tailgp );
+extern float G__align11_noalign( int mtx[0x80][0x80], int penal, int penal_ex, char **seq1, char **seq2, int alloclen );
+extern float L__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
+extern float genL__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
+extern float genG__align11( char **seq1, char **seq2, int alloclen );
+extern float VAalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt );
+extern float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
+;
+extern int fft(int n, Fukusosuu *x, int dum);
+extern void topolcpy( int s1[], int s2[], int *mpt1, int *mpt2 );
+extern void topolcat( int s1[], int s2[], int *mpt1, int *mpt2 );
+extern void topolsort( int m, int s[] );
+extern void topolswap( int s1[], int s2[], int *mpt1, int *mpt2 );
+extern void reduc( double **mtx, int nseq, int im, int jm );
+extern void nj( int nseq, double **omtx, int ***topol, double **dis );
+extern void JTTmtx( double **rsr, double *freq, char locamino[26], char locgrp[26], int isTM );
+extern void BLOSUMmtx( int n, double **matrix, double *freq, char *amino, char *amino_grp );
+extern void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
+extern void putlocalhom_str( char *al1, char *al2, double *equiv, double scale, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
+extern void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
+extern void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
+extern void putlocalhom( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
+extern char *cutal( char *al, int al_display_start, int start, int end );
+extern void ErrorExit( char *message );
+extern void strncpy_caseC( char *str1, char *str2, int len );
+extern void seqUpper( int nseq, char **seq );
+extern void seqLower( int nseq, char **seq );
+extern int getaline_fp_eof( char *s, int l, FILE *fp );
+extern int getaline_fp_eof_new(char s[], int l, FILE *fp);
+extern int myfgets(char s[], int l, FILE *fp);
+extern float input_new( FILE *fp, int d );
+extern void PreRead( FILE *fp, int *locnjob, int *locnlenmax );
+extern int allSpace( char *str );
+extern void Read( char name[M][B], int nlen[M], char **seq );
+extern void FRead( FILE *fp, char name[][B], int nlen[], char **seq );
+extern void kake2hiku( char *str );
+extern void readDataforgaln( FILE *fp, char **name, int *nlen, char **seq );
+extern void readData( FILE *fp, char name[][B], int nlen[], char **seq );
+extern void readData_pointer_casepreserve( FILE *fp, char **name, int *nlen, char **seq );
+extern void readData_pointer( FILE *fp, char **name, int *nlen, char **seq );
+extern void readData_pointer2( FILE *fp, int nseq, char **name, int *nlen, char **seq );
+extern void readData_varlen( FILE *fp, char **name, int *nlen, char **seq );
+extern int countATGC( char *s, int *total );
+extern void getnumlen( FILE *fp );
+extern void getnumlen_casepreserve( FILE *fp, int *nlenmin );
+extern void getnumlen_nogap( FILE *fp, int *nlenmin );
+extern void WriteGapFill( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq );
+extern void writeDataforgaln( FILE *fp, int locnjob, char **name, int *nlen, char **aseq );
+extern void writeData( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq );
+extern void writeData_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq );
+extern void readhat2_floathalf( FILE *fp, int nseq, char name[M][B], float **mtx );
+extern void readhat2_floathalf_pointer( FILE *fp, int nseq, char **name, float **mtx );
+extern void readhat2_float( FILE *fp, int nseq, char name[M][B], float **mtx );
+extern void readhat2_int( FILE *fp, int nseq, char name[M][B], int **mtx );
+extern void readhat2_pointer( FILE *fp, int nseq, char **name, double **mtx );
+extern void readhat2( FILE *fp, int nseq, char name[M][B], double **mtx );
+extern void WriteFloatHat2_pointer_halfmtx( FILE *hat2p, int locnjob, char **name, float **mtx );
+extern void WriteFloatHat2( FILE *hat2p, int locnjob, char name[M][B], float **mtx );
+extern void WriteHat2_int( FILE *hat2p, int locnjob, char name[M][B], int **mtx );
+extern void WriteHat2( FILE *hat2p, int locnjob, char name[M][B], double **mtx );
+extern void WriteHat2_pointer( FILE *hat2p, int locnjob, char **name, double **mtx );
+extern int ReadFasta_sub( FILE *fp, double *dis, int nseq, char name[M][B] );
+extern int ReadSsearch( FILE *fp, double *dis, int nseq, char name[M][B] );
+extern int ReadBlastm7( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
+extern int ReadBlastm7_scoreonly( FILE *fp, double *dis, int nin );
+extern int ReadBlastm7_avscore( FILE *fp, double *dis, int nin );
+extern int ReadFasta34noalign( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
+extern int ReadFasta34m10_nuc( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
+extern int ReadFasta34m10( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
+extern int ReadFasta34m10_scoreonly_nuc( FILE *fp, double *dis, int nin );
+extern int ReadFasta34m10_scoreonly( FILE *fp, double *dis, int nin );
+extern int ReadFasta34( FILE *fp, double *dis, int nseq, char name[M][B], LocalHom *localhomlist );
+extern int ReadFasta3( FILE *fp, double *dis, int nseq, char name[M][B] );
+extern int ReadFasta( FILE *fp, double *dis, int nseq, char name[M][B] );
+extern int ReadOpt( FILE *fp, int opt[M], int nseq, char name[M][B] );
+extern int ReadOpt2( FILE *fp, int opt[M], int nseq, char name[M][B] );
+extern int writePre( int nseq, char **name, int nlen[M], char **aseq, int force );
+extern void readOtherOptions( int *ppidptr, int *fftThresholdptr, int *fftWinSizeptr );
+extern void initSignalSM( void );
+extern void initFiles( void );
+extern void WriteForFasta( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq );
+extern void readlocalhomtable( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec );
+extern void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec );
+extern void outlocalhom( LocalHom **localhom, int nseq );
+extern void outlocalhompt( LocalHom ***localhom, int n1, int n2 );
+extern void FreeLocalHomTable( LocalHom **localhomtable, int n ) ;
+extern void constants( int nseq, char **seq );
+extern void clustalout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, char *mark, char *comment, int *order, int namelen );
+extern void phylipout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, int *order );
+extern void writeData_reorder( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq, int *order );
+extern void writeData_reorder_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq, int *order );
+
+extern void resetlocalhom( int, LocalHom ** );
+extern int load1SeqWithoutName_new( FILE *fpp, char *cbuf );
+extern char *load1SeqWithoutName_realloc( FILE *fpp );
+extern char *load1SeqWithoutName_realloc_casepreserve( FILE *fpp );
+extern int disttbfast( char **in, int nlen[M], char name[M][B] );
+extern void searchKUorWA( FILE *fp );
+extern void gapireru( char *res, char *ori, char *gt );
+extern int seqlen( char *seq );
+extern void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len );
+extern void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len );
+extern void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len );
+extern void st_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len );
+extern void getdiaminofreq_x( float *freq, int clus, char **seq, double *eff, int len );
+extern void new_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len, char *s, char *e );
+extern void new_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len, char *g );
+extern void new_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len, char *g );
+extern void new_OpeningGapCount_zure( float *ogcp, int clus, char **seq, double *eff, int len, char *s, char *e );
+extern void getGapPattern( float *fgcp, int clus, char **seq, double *eff, int len, char *g );
+extern void getgapfreq( float *freq, int clus, char **seq, double *eff, int len );
+extern void getgapfreq_zure( float *freq, int clus, char **seq, double *eff, int len );
+//extern void getgapfreq_zure_part( float *freq, int clus, char **seq, double *eff, int len, char *s );
+extern void getgapfreq_zure_part( float *freq, int clus, char **seq, double *eff, int len, char *s );
+extern void getdiaminofreq_part( float *freq, int clus, char **seq, double *eff, int len, char *s, char *e );
+extern void getdigapfreq_part( float *freq, int clus, char **seq, double *eff, int len, char *s, char *e );
+extern void getdiaminofreq_st( float *freq, int clus, char **seq, double *eff, int len );
+extern void getdigapfreq_st( float *freq, int clus, char **seq, double *eff, int len );
+extern void st_getGapPattern( Gappat **gpat, int clus, char **seq, double *eff, int len );
+extern void getkyokaigap( char *g, char **s, int pos, int n );
+extern double *loadaamtx( void );
+extern float naivepairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
+extern float naivepairscore11( char *seq1, char *seq2, int penal );
+extern float naiveQpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
+extern float naiveRpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
+extern float naiveHpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
+extern void foldrna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *pair );
+extern void foldrna_gappick( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *pair );
+extern void imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
+extern void imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
+extern void part_imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
+extern void part_imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
+extern void imp_rnaQ_gappick( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
+extern void foldalignedrna( int clus1, int clus2, char **mseq1, char **mseq2, double *effarr1, double *effarr2, RNApair *rnapairboth );
+void readmccaskill( FILE *fp, RNApair **pairprob, int length );
+void makegrouprna( RNApair ***group, RNApair ***all, int *memlist );
+void makegrouprnait( RNApair ***group, RNApair ***all, char **pair, int s );
+extern void fixed_musclesupg_float_realloc_nobk_halfmtx( int nseq, float **eff, int ***topol, float **len, Treedep * );
+extern void loadtree( int nseq, int ***topol, float **len, char **name, int *nlen, Treedep * );
+extern void loadtop( int nseq, float **eff, int ***topol, float **len );
+extern void fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( int nseq, float **eff, int ***topol, float **len, char **name, int *nlen, Treedep * );
+extern void fixed_musclesupg_double_treeout( int nseq, double **eff, int ***topol, double **len, char **name );
+extern void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1kozo, double*eff2kozo, LocalHom ***localhom, int forscore );
+extern void miyataout_reorder_pointer( FILE *fp, int locnjob, int nlenmax, char **name, int *nlen, char **aseq, int *order );
+extern void veryfastsupg_double_outtree( int nseq, double **eff, int ***topol, double **len, char **name );
+extern void cpmx_ribosum( char **seq, char **seqr, char *dir, float **cpmx, double *eff, int lgth, int clus );
+extern void rnaalifoldcall( char **seq, int nseq, RNApair **pairprob );
+extern void readpairfoldalign( FILE *fp, char *seq1, char *seq2, char *aln1, char *aln2, int q1, int q2, int *of1, int *of2, int sumlen );
+extern void write1seq( FILE *fp, char *aseq );
+extern void assignstrweight( int nseq, double *strweight, Node *stopol, int ***topol, int step, int LorR, char *kozoari, double *seqweight );
+extern void cutData( FILE *, int **, char **, int * );
+extern void cutAlignment( FILE *, int **, char **, int *, char **, char ** );
+extern void catData( FILE * );
+extern void getnumlen_nogap_outallreg_web( FILE *fp, FILE *ofp, int *nlenminpt, int *isalignedpt );
+extern void getnumlen_nogap_outallreg( FILE *fp, int *nlenminpt );
+extern double plainscore( int nseq, char **seq );
+extern void eq2dash( char *s );
+extern void findnewgaps( int n, char **seq, int *gaplen );
+extern void findcommongaps( int, char **, int * );
+extern void adjustgapmap( int, int *, char * );
+extern void insertnewgaps( int njob, int *alreadyaligned, char **seq, int *ex1, int *ex2, int *gaplen, int *gapmap, int alloclen, char alg );
+extern void restorecommongaps( int n, char **seq, int *top0, int *top1, int *gaplen, int alloclen );
+extern int samemember( int *mem, int *cand );
+extern int includemember( int *mem, int *cand );
+extern void profilealignment( int n0, int n1, int n2, char **aln0, char **aln1, char **aln2, int alloclen, char alg );
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+
+#if 1
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char *seq2 = s2[0];
+ int *intptr = amino_dis[(int)s1[0][i1]];
+
+ while( lgth2-- )
+ *match++ = intptr[(int)*seq2++];
+}
+#else
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ int j;
+
+ for( j=0; j<lgth2; j++ )
+ match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
+}
+#endif
+
+static float genGtracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijpi, int **ijpj )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijpi[i][0] = -1;
+ ijpj[i][0] = -1; // ???
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijpi[0][j] = -1; // ???
+ ijpj[0][j] = -1;
+ }
+
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+ iin = lgth1; jin = lgth2;
+ limk = lgth1+lgth2 + 1;
+ for( k=0; k<limk; k++ )
+ {
+ ifi = ( ijpi[iin][jin] );
+ jfi = ( ijpj[iin][jin] );
+ l = iin - ifi;
+ while( --l )
+ {
+ *--mseq1[0] = seq1[0][ifi+l];
+ *--mseq2[0] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mseq1[0] = seq1[0][ifi];
+ *--mseq2[0] = seq2[0][jfi];
+
+// fprintf( stdout, "mseq1 = %s\n", mseq1[0] );
+// fprintf( stdout, "mseq2 = %s\n", mseq2[0] );
+
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ return( 0.0 );
+}
+
+
+float genG__align11( char **seq1, char **seq2, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_OP = (float)penalty_OP;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijpipt;
+ int *ijpjpt;
+ float *mjpt, *Mjpt, *prept, *curpt;
+ int *mpjpt, *Mpjpt;
+#endif
+ static float mi, *m;
+ static float Mi, *largeM;
+ static int **ijpi;
+ static int **ijpj;
+ static int mpi, *mp;
+ static int Mpi, *Mp;
+ static float *w1, *w2;
+ static float *match;
+ static float *initverticalw; /* kufuu sureba iranai */
+ static float *lastverticalw; /* kufuu sureba iranai */
+ static char **mseq1;
+ static char **mseq2;
+ static char **mseq;
+ static float **cpmx1;
+ static float **cpmx2;
+ static int **intwork;
+ static float **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+ float tbk;
+ int tbki, tbkj;
+
+ wm = 0.0;
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+
+
+ if( lgth1 <= 0 || lgth2 <= 0 )
+ {
+ fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+ FreeFloatVec( largeM );
+ FreeIntVec( Mp );
+
+ FreeCharMtx( mseq );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ largeM = AllocateFloatVec( ll2+2 );
+ Mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ FreeIntMtx( commonJP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+ commonJP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijpi = commonIP;
+ ijpj = commonJP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+ if( outgap == 1 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+ }
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+ largeM[j] = currentw[j-1]; Mp[j] = 0;
+ }
+
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // lgth2==0 no toki error
+ else
+ lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+ Mi = previousw[0]; Mpi = 0;
+
+ ijpipt = ijpi[i] + 1;
+ ijpjpt = ijpj[i] + 1;
+ mjpt = m + 1;
+ Mjpt = largeM + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ Mpjpt = Mp + 1;
+ tbk = -9999999.9;
+ tbki = 0;
+ tbkj = 0;
+ for( j=1; j<lgth2+1; j++ )
+ {
+ wm = *prept;
+ *ijpipt = i-1;
+ *ijpjpt = j-1;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+// *ijpipt = i - 1; // iranai
+ *ijpjpt = mpi;
+ }
+ if( (g=*prept) >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt + fpenalty) > wm )
+ {
+ wm = g;
+ *ijpipt = *mpjpt;
+ *ijpjpt = j - 1; //IRU!
+ }
+ if( (g=*prept) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 1
+ g = tbk + fpenalty_OP;
+ if( g > wm )
+ {
+ wm = g;
+ *ijpipt = tbki;
+ *ijpjpt = tbkj;
+// fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
+ }
+ if( Mi > tbk )
+ {
+ tbk = Mi; //error desu.
+ tbki = i-1;
+ tbkj = Mpi;
+ }
+ if( *Mjpt > tbk )
+ {
+ tbk = *Mjpt;
+ tbki = *Mpjpt;
+ tbkj = j-1;
+ }
+
+ if( *prept > *Mjpt )
+ {
+ *Mjpt = *prept;
+ *Mpjpt = i-1;
+ }
+ if( *prept > Mi )
+ {
+ Mi = *prept;
+ Mpi = j-1;
+ }
+
+#endif
+
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ ijpipt++;
+ ijpjpt++;
+ mjpt++;
+ Mjpt++;
+ prept++;
+ mpjpt++;
+ Mpjpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
+ }
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stdout, "i,j=%d,%d - ijpi,ijpj=%d,%d\n", i, j, ijpi[i][j], ijpj[i][j] );
+ }
+ }
+ fflush( stdout );
+#endif
+
+ genGtracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+#if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+ fprintf( stderr, "wm = %f\n", wm );
+#endif
+
+ return( wm );
+}
+
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define DEBUG2 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+static TLS int localstop;
+
+#if 1
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char tmpc = s1[0][i1];
+ char *seq2 = s2[0];
+
+ while( lgth2-- )
+ *match++ = amino_dis[(int)tmpc][(int)*seq2++];
+}
+#else
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ int j;
+
+ for( j=0; j<lgth2; j++ )
+ match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
+}
+#endif
+
+#if 0
+static void match_calc_bk( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ int count = 0;
+
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+#if 0
+ {
+ float *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+#else
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+#endif
+
+static float gentracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijpi, int **ijpj, int *off1pt, int *off2pt, int endi, int endj )
+{
+ int i, j, l, iin, jin, lgth1, lgth2, k, limk;
+ int ifi=0, jfi=0; // by D.Mathog
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijpi[i][0] = localstop;
+ ijpj[i][0] = localstop;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijpi[0][j] = localstop;
+ ijpj[0][j] = localstop;
+ }
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+ iin = endi; jin = endj;
+ limk = lgth1+lgth2;
+ for( k=0; k<=limk; k++ )
+ {
+
+ ifi = ( ijpi[iin][jin] );
+ jfi = ( ijpj[iin][jin] );
+ l = iin - ifi;
+// if( ijpi[iin][jin] < 0 || ijpj[iin][jin] < 0 )
+// {
+// fprintf( stderr, "skip! %d-%d\n", ijpi[iin][jin], ijpj[iin][jin] );
+// fprintf( stderr, "1: %c-%c\n", seq1[0][iin], seq1[0][ifi] );
+// fprintf( stderr, "2: %c-%c\n", seq2[0][jin], seq2[0][jfi] );
+// }
+ while( --l )
+ {
+ *--mseq1[0] = seq1[0][ifi+l];
+ *--mseq2[0] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][jfi+l];
+ k++;
+ }
+
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mseq1[0] = seq1[0][ifi];
+ *--mseq2[0] = seq2[0][jfi];
+
+ if( ijpi[ifi][jfi] == localstop ) break;
+ if( ijpj[ifi][jfi] == localstop ) break;
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
+ if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
+
+// fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
+
+
+ return( 0.0 );
+}
+
+
+float genL__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj;
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if 1
+ float *wtmp;
+ int *ijpipt;
+ int *ijpjpt;
+ float *mjpt, *Mjpt, *prept, *curpt;
+ int *mpjpt, *Mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS float Mi, *largeM;
+ static TLS int **ijpi;
+ static TLS int **ijpj;
+ static TLS int mpi, *mp;
+ static TLS int Mpi, *Mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float maxwm;
+ float tbk;
+ int tbki, tbkj;
+ int endali, endalj;
+// float localthr = 0.0;
+// float localthr2 = 0.0;
+ float fpenalty = (float)penalty;
+ float fpenalty_OP = (float)penalty_OP;
+ float fpenalty_ex = (float)penalty_ex;
+// float fpenalty_EX = (float)penalty_EX;
+ float foffset = (float)offset;
+ float localthr = -foffset;
+ float localthr2 = -foffset;
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ orlgth1 = 0;
+ orlgth2 = 0;
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+ free( largeM );
+ free( Mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ }
+ return( 0.0 );
+ }
+
+
+
+// fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+ FreeFloatVec( largeM );
+ FreeIntVec( Mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ largeM = AllocateFloatVec( ll2+2 );
+ Mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ FreeIntMtx( commonJP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+ commonJP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijpi = commonIP;
+ ijpj = commonJP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+
+ lasti = lgth2+1;
+ for( j=1; j<lasti; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+ largeM[j] = currentw[j-1]; Mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+#if 0
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, " " );
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%c ", seq2[0][j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ localstop = lgth1+lgth2+1;
+ maxwm = -999999999.9;
+ endali = endalj = 0;
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "%c ", seq1[0][0] );
+
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if DEBUG2
+ fprintf( stderr, "%c ", seq1[0][i] );
+ fprintf( stderr, "%5.0f ", currentw[0] );
+#endif
+
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+ Mi = previousw[0]; Mpi = 0;
+
+#if 0
+ if( mi < localthr ) mi = localthr2;
+#endif
+
+ ijpipt = ijpi[i] + 1;
+ ijpjpt = ijpj[i] + 1;
+ mjpt = m + 1;
+ Mjpt = largeM + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ Mpjpt = Mp + 1;
+ tbk = -999999.9;
+ tbki = 0;
+ tbkj = 0;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijpipt = i-1;
+ *ijpjpt = j-1;
+
+
+// fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
+// fprintf( stderr, "wm=%f\n", wm );
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijpipt = i - 1;
+ *ijpjpt = mpi;
+ }
+ g = *prept;
+ if( g > mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "m%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijpipt = *mpjpt;
+ *ijpjpt = j - 1; //IRU!
+ }
+ g = *prept;
+ if( g > *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ *mjpt += fpenalty_ex;
+#endif
+
+
+ g = tbk + fpenalty_OP;
+// g = tbk;
+ if( g > wm )
+ {
+ wm = g;
+ *ijpipt = tbki;
+ *ijpjpt = tbkj;
+// fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
+ }
+// g = Mi;
+ if( Mi > tbk )
+ {
+ tbk = Mi; //error desu.
+ tbki = i-1;
+ tbkj = Mpi;
+ }
+// g = *Mjpt;
+ if( *Mjpt > tbk )
+ {
+ tbk = *Mjpt;
+ tbki = *Mpjpt;
+ tbkj = j-1;
+ }
+// tbk += fpenalty_EX;// + foffset;
+
+// g = *prept;
+ if( *prept > *Mjpt )
+ {
+ *Mjpt = *prept;
+ *Mpjpt = i-1;
+ }
+// *Mjpt += fpenalty_EX;// + foffset;
+
+// g = *prept;
+ if( *prept > Mi )
+ {
+ Mi = *prept;
+ Mpi = j-1;
+ }
+// Mi += fpenalty_EX;// + foffset;
+
+
+// fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
+// fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );
+
+
+ if( maxwm < wm )
+ {
+ maxwm = wm;
+ endali = i;
+ endalj = j;
+ }
+#if 1
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ *ijpipt = localstop;
+// *ijpjpt = localstop;
+ wm = localthr2;
+ }
+#endif
+#if 0
+ fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if DEBUG2
+ fprintf( stderr, "%5.0f ", wm );
+// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+
+ *curpt += wm;
+ ijpipt++;
+ ijpjpt++;
+ mjpt++;
+ Mjpt++;
+ prept++;
+ mpjpt++;
+ Mpjpt++;
+ curpt++;
+ }
+#if DEBUG2
+ fprintf( stderr, "\n" );
+#endif
+
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+
+#if DEBUG2
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, "endali = %d\n", endali );
+ fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+ if( ijpi[endali][endalj] == localstop ) // && ijpj[endali][endalj] == localstop )
+ {
+ strcpy( seq1[0], "" );
+ strcpy( seq2[0], "" );
+ *off1pt = *off2pt = 0;
+ return( 0.0 );
+ }
+
+
+ gentracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, endali, endalj );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+
+#if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+
+
+ return( maxwm );
+}
+
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'C';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ scoremtx = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'D':
+ scoremtx = -1;
+ break;
+ case 'P':
+ scoremtx = 0;
+ break;
+ case 'i':
+ contin = 1;
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+ case 'Q':
+ calledByXced = 1;
+ break;
+ case 's':
+ treemethod = 's';
+ break;
+ case 'x':
+ treemethod = 'x';
+ break;
+ case 'p':
+ treemethod = 'p';
+ break;
+ case 'a':
+ alg = 'a';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'S':
+ alg = 'S';
+ break;
+ case 'C':
+ alg = 'C';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'd':
+ disp = 1;
+ break;
+ case 'o':
+ outgap = 0;
+ break;
+/* Modified 01/08/27, default: user tree */
+ case 'J':
+ tbutree = 0;
+ break;
+/* modification end. */
+ case 'Z':
+ checkC = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+ readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
+}
+
+
+void treebase( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double **mtx, int ***topol, double **len, double **eff, int alloclen )
+{
+ int i, j, l;
+ int clus1, clus2;
+ int s1, s2, r1, r2;
+ float pscore;
+ static char *indication1, *indication2;
+ static char **name1, **name2;
+ static double **partialmtx = NULL;
+ static int ***partialtopol = NULL;
+ static double **partiallen = NULL;
+ static double **partialeff = NULL;
+ static double *effarr = NULL;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+#if 0
+ char pair[njob][njob];
+#else
+ static char **pair;
+#endif
+ if( partialtopol == NULL )
+ {
+ partialmtx = AllocateDoubleMtx( njob, njob );
+ partialtopol = AllocateIntCub( njob, 2, njob );
+ partialeff = AllocateDoubleMtx( njob, njob );
+ partiallen = AllocateDoubleMtx( njob, 2 );
+ effarr = AllocateDoubleVec( njob );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( njob*3+100 );
+ indication2 = AllocateCharVec( njob*3+100 );
+ name1 = AllocateCharMtx( njob, B+1 );
+ name2 = AllocateCharMtx( njob, B+1 );
+#if 0
+#else
+ pair = AllocateCharMtx( njob, njob );
+#endif
+ }
+
+ if( checkC )
+ for( i=0; i<njob; i++ ) fprintf( stderr, "eff in tb-%d %f\n", i, eff[i][i] );
+
+ for( i=0; i<njob; i++ ) effarr[i] = eff[i][i];
+ for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
+
+ if( checkC )
+ for( i=0; i<njob; i++ ) fprintf( stderr, "effarr for aseq-%d %f\n", i, effarr[i] );
+
+ writePre( njob, name, nlen, aseq, 0 );
+
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
+ for( i=0; i<njob; i++ ) pair[i][i] = 1;
+ for( l=0; l<njob-1; l++ )
+ {
+ s1 = topol[l][0][0];
+ for( i=0; (r1=topol[l][0][i])>-1; i++ )
+ if( pair[s1][r1] != 1 ) exit( 1 );
+ s2 = topol[l][1][0];
+ for( i=0; (r2=topol[l][1][i])>-1; i++ )
+ if( pair[s2][r2] != 1 ) exit( 1 );
+
+ clus1 = conjuction( pair, s1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
+ clus2 = conjuction( pair, s2, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
+ fprintf( trap_g, "\nSTEP-%d\n", l );
+ fprintf( trap_g, "group1 = %s\n", indication1 );
+ fprintf( trap_g, "group2 = %s\n", indication2 );
+
+ fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+
+ if( checkC )
+ for( i=0; i<clus1; i++ ) fprintf( stderr, "STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
+/*
+ fprintf( stderr, "before align all\n" );
+ display( aseq, njob );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+ pscore = Fgetlag( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+
+ for( i=0; (r2=topol[l][1][i])>-1; i++ )
+ {
+ pair[s1][r2] = 1;
+ pair[s2][r2] = 0;
+ }
+
+ writePre( njob, name, nlen, aseq, 0 );
+
+ if( disp ) display( aseq, njob );
+ fprintf( stderr, "\n" );
+
+ }
+}
+
+static void WriteOptions( FILE *fp )
+{
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );
+
+ if( scoremtx == 0 || scoremtx == -1 )
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ else
+ fprintf( fp, "Gap Penalty = %+5.2f\n", (double)ppenalty/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Apgorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( treemethod == 'x' )
+ fprintf( fp, "Tree = UPGMA (3).\n" );
+ else if( treemethod == 's' )
+ fprintf( fp, "Tree = UPGMA (2).\n" );
+ else if( treemethod == 'p' )
+ fprintf( fp, "Tree = UPGMA (1).\n" );
+ else
+ fprintf( fp, "Unknown tree.\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( scoremtx == -1 )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int nlen[M];
+ static char **name, **seq;
+ static char **mseq1, **mseq2;
+ static char **aseq;
+ static char **bseq;
+ static double **pscore;
+ static double **eff;
+ static double **node0, **node1;
+ int i, j;
+ static int ***topol;
+ static double **len;
+ FILE *prep;
+ char c;
+ int alloclen;
+
+ arguments( argc, argv );
+ getnumlen( stdin );
+ rewind( stdin );
+
+ name = AllocateCharMtx( njob, B+1 );
+ seq = AllocateCharMtx( njob, nlenmax*5+1 );
+ aseq = AllocateCharMtx( njob, nlenmax*5+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*5+1 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ alloclen = nlenmax*5;
+
+ topol = AllocateIntCub( njob, 2, njob );
+ len = AllocateDoubleMtx( njob, 2 );
+ pscore = AllocateDoubleMtx( njob, njob );
+ eff = AllocateDoubleMtx( njob, njob );
+ node0 = AllocateDoubleMtx( njob, njob );
+ node1 = AllocateDoubleMtx( njob, njob );
+
+#if 0
+ Read( name, nlen, seq );
+#else
+ readData_pointer( stdin, name, nlen, seq );
+#endif
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illeagal character %c\n", c );
+ exit( 1 );
+ }
+
+ writePre( njob, name, nlen, seq, 0 );
+
+ if( tbutree == 0 )
+ {
+ for( i=1; i<njob; i++ )
+ {
+ if( nlen[i] != nlen[0] )
+ {
+ fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
+ exit( 1 );
+ }
+ }
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+ /*
+ pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
+ */
+ pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
+ }
+ }
+ else
+ {
+ fprintf( stderr, "Loading 'hat2' ... " );
+ prep = fopen( "hat2", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat2." );
+ readhat2_pointer( prep, njob, name, pscore );
+ fclose( prep );
+ fprintf( stderr, "done.\n" );
+
+#if 0
+ prep = fopen( "hat2_check", "w" );
+ WriteHat2( prep, njob, name, pscore );
+ fclose( prep );
+#endif
+
+ }
+
+ fprintf( stderr, "Constructing dendrogram ... " );
+ if( treemethod == 'x' )
+ supg( njob, pscore, topol, len );
+ else if( treemethod == 's' )
+ spg( njob, pscore, topol, len );
+ else if( treemethod == 'p' )
+ upg2( njob, pscore, topol, len );
+ else
+ ErrorExit( "Incorrect tree\n" );
+ fprintf( stderr, "done.\n" );
+
+ countnode( njob, topol, node0 );
+ if( tbrweight )
+ {
+ weight = 3;
+ utree = 0; counteff( njob, topol, len, eff ); utree = 1;
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) eff[i][i] = 1.0;
+ }
+
+
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+ treebase( name, nlen, bseq, aseq, mseq1, mseq2, pscore, topol, len, eff, alloclen );
+
+ fprintf( trap_g, "done\n" );
+ fclose( trap_g );
+
+ writePre( njob, name, nlen, aseq, !contin );
+ writeData_pointer( stdout, njob, name, nlen, aseq );
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+static int upperCase = 0;
+
+#define DEBUG 0
+#define IODEBUG 0
+
+char creverse( char f )
+{
+ static char *table = NULL;
+ if( table == NULL )
+ {
+ table = AllocateCharVec(0x80);
+ table['a'] = 't';
+ table['c'] = 'g';
+ table['g'] = 'c';
+ table['t'] = 'a';
+ table['u'] = 'a';
+ table['m'] = 'k';
+ table['r'] = 'y';
+ table['w'] = 'w';
+ table['s'] = 's';
+ table['y'] = 'r';
+ table['k'] = 'm';
+ table['v'] = 'b';
+ table['h'] = 'd';
+ table['d'] = 'h';
+ table['b'] = 'v';
+ table['n'] = 'n';
+ table['-'] = '-';
+ table['.'] = '.';
+ table['*'] = '*';
+ }
+ return( table[(int)f] );
+}
+
+void sreverse( char *r, char *s )
+{
+ r += strlen( s );
+ *r-- = 0;
+ while( *s )
+ *r-- = creverse( *s++ );
+// *r-- = ( *s++ );
+}
+
+void gappick_samestring( char *seq )
+{
+ char *aseq = seq;
+
+ for( ; *seq != 0; seq++ )
+ {
+ if( *seq != '-' )
+ *aseq++ = *seq;
+ }
+ *aseq = 0;
+}
+
+#if 0
+
+static int addlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, int skip )
+{
+ int pos1, pos2, start1, start2, end1, end2;
+ char *pt1, *pt2;
+ int iscore;
+ int isumscore;
+ int sumoverlap;
+ LocalHom *tmppt;
+ int st;
+ int nlocalhom = 0;
+ pt1 = al1; pt2 = al2;
+ pos1 = off1; pos2 = off2;
+
+ isumscore = 0;
+ sumoverlap = 0;
+
+#if 0
+ fprintf( stderr, "nlocalhom = %d in addlocalhom\n", nlocalhom );
+ fprintf( stderr, "al1 = %s, al2 = %s\n", al1, al2 );
+ fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
+ fprintf( stderr, "localhopt = %p, skip = %d\n", localhompt, skip );
+ fprintf( stderr, "pt1 = \n%s\n, pt2 = \n%s\n", pt1, pt2 );
+#endif
+
+ if( skip )
+ {
+ while( --skip > 0 ) localhompt = localhompt->next;
+ localhompt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ localhompt = localhompt->next;
+// fprintf( stderr, "tmppt = %p, localhompt = %p\n", tmppt, localhompt );
+ }
+ tmppt = localhompt;
+
+ st = 0;
+ iscore = 0;
+ while( *pt1 != 0 )
+ {
+// fprintf( stderr, "In in while loop\n" );
+// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+ if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+ {
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ isumscore += iscore;
+ sumoverlap += end2-start2+1;
+#else
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = iscore * 5.8 / 600;
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "iscore (1)= %d\n", iscore );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ iscore = 0;
+ st = 0;
+ }
+ else if( *pt1 != '-' && *pt2 != '-' )
+ {
+ if( st == 0 )
+ {
+ start1 = pos1; start2 = pos2;
+ st = 1;
+ }
+ iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]];
+// fprintf( stderr, "%c-%c, score(0) = %d\n", *pt1, *pt2, iscore );
+ }
+ if( *pt1++ != '-' ) pos1++;
+ if( *pt2++ != '-' ) pos2++;
+ }
+
+ if( st )
+ {
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ isumscore += iscore;
+ sumoverlap += end2-start2+1;
+#else
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = (double)iscore * 5.8 / 600;
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+#if 0
+ fprintf( stderr, "score (2)= %d\n", iscore );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ }
+
+ for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+ {
+ tmppt->overlapaa = sumoverlap;
+ tmppt->opt = (double)sumscore * 5.8 / 600 / sumoverlap;
+ }
+ return( nlocalhom );
+}
+
+#endif
+
+
+
+static int addlocalhom_r( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, int skip )
+{
+ int pos1, pos2, start1, start2, end1, end2;
+ char *pt1, *pt2;
+ double score;
+ double sumscore;
+ int sumoverlap;
+ LocalHom *tmppt = NULL; // by D.Mathog, a guess
+ int st;
+ int nlocalhom = 0;
+ pt1 = al1; pt2 = al2;
+ pos1 = off1; pos2 = off2;
+
+ sumscore = 0.0;
+ sumoverlap = 0;
+ start1 = 0; // by D.Mathog, a guess
+ start2 = 0; // by D.Mathog, a guess
+
+#if 0
+ fprintf( stderr, "nlocalhom = %d in addlocalhom\n", nlocalhom );
+ fprintf( stderr, "al1 = %s, al2 = %s\n", al1, al2 );
+ fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
+ fprintf( stderr, "localhopt = %p, skip = %d\n", localhompt, skip );
+#endif
+ fprintf( stderr, "pt1 = \n%s\n, pt2 = \n%s\n", pt1, pt2 );
+
+ if( skip )
+ {
+ while( --skip > 0 ) localhompt = localhompt->next;
+ localhompt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ localhompt = localhompt->next;
+ fprintf( stderr, "tmppt = %p, localhompt = %p\n", (void *)tmppt, (void *)localhompt );
+ }
+ tmppt = localhompt;
+
+ st = 0;
+ score = 0.0;
+ while( *pt1 != 0 )
+ {
+ fprintf( stderr, "In in while loop\n" );
+ fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+ if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+ {
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ sumscore += score;
+ sumoverlap += end2-start2+1;
+#else
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = score * 5.8 / 600;
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+ fprintf( stderr, "score (1)= %f\n", score );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+ score = 0.0;
+ st = 0;
+ }
+ else if( *pt1 != '-' && *pt2 != '-' )
+ {
+ if( st == 0 )
+ {
+ start1 = pos1; start2 = pos2;
+ st = 1;
+ }
+ score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]];
+// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
+ }
+ if( *pt1++ != '-' ) pos1++;
+ if( *pt2++ != '-' ) pos2++;
+ }
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ sumscore += score;
+ sumoverlap += end2-start2+1;
+#else
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = score * 5.8 / 600;
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+ fprintf( stderr, "score (2)= %f\n", score );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+
+ for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+ {
+ tmppt->overlapaa = sumoverlap;
+ tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
+ }
+ return( nlocalhom );
+}
+void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+ int pos1, pos2, start1, start2, end1, end2;
+ char *pt1, *pt2;
+ double score;
+ double sumscore;
+ int sumoverlap;
+ LocalHom *tmppt;
+ LocalHom *subnosento;
+ int st;
+ int saisho;
+
+ pt1 = al1; pt2 = al2;
+ pos1 = off1; pos2 = off2;
+
+ sumscore = 0.0;
+ sumoverlap = 0;
+ start1 = 0; // by Mathog, a guess
+ start2 = 0; // by Mathog, a guess
+
+ subnosento = localhompt;
+ while( subnosento->next ) subnosento = subnosento->next;
+ tmppt = subnosento;
+
+ saisho = ( localhompt->nokori == 0 );
+
+ fprintf( stderr, "localhompt = %p\n", (void *)localhompt );
+ fprintf( stderr, "tmppt = %p\n", (void *)tmppt );
+ fprintf( stderr, "subnosento = %p\n", (void *)subnosento );
+
+ st = 0;
+ score = 0.0;
+ while( *pt1 != 0 )
+ {
+// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+ if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+ {
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+
+ if( localhompt->nokori++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ if( divpairscore )
+ {
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+ }
+ else
+ {
+ sumscore += score;
+ sumoverlap += end2-start2+1;
+ }
+#else
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "score (1)= %f\n", score );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ score = 0.0;
+ st = 0;
+ }
+ else if( *pt1 != '-' && *pt2 != '-' )
+ {
+ if( st == 0 )
+ {
+ start1 = pos1; start2 = pos2;
+ st = 1;
+ }
+ score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
+// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
+ }
+ if( *pt1++ != '-' ) pos1++;
+ if( *pt2++ != '-' ) pos2++;
+ }
+ if( *(pt1-1) != '-' && *(pt2-1) != '-' )
+ {
+ if( localhompt->nokori++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+
+#if 1
+ if( divpairscore )
+ {
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+ }
+ else
+ {
+ sumscore += score;
+ sumoverlap += end2-start2+1;
+ }
+#else
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "score (2)= %f\n", score );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ }
+
+ fprintf( stderr, "sumscore = %f\n", sumscore );
+ if( !divpairscore )
+ {
+
+ if( !saisho ) subnosento = subnosento->next;
+ for( tmppt=subnosento; tmppt; tmppt=tmppt->next )
+ {
+ tmppt->overlapaa = sumoverlap;
+ tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
+ fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+ }
+ }
+}
+void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+ int pos1, pos2, start1, start2, end1, end2;
+ char *pt1, *pt2;
+ int iscore;
+ int isumscore;
+ int sumoverlap;
+ LocalHom *tmppt = localhompt;
+ int nlocalhom = 0;
+ int st;
+ pt1 = al1; pt2 = al2;
+ pos1 = off1; pos2 = off2;
+
+
+ isumscore = 0;
+ sumoverlap = 0;
+ start1 = 0; // by D.Mathog, a guess
+ start2 = 0; // by D.Mathog, a guess
+
+ st = 0;
+ iscore = 0;
+ while( *pt1 != 0 )
+ {
+// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+ if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+ {
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ if( divpairscore )
+ {
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ }
+ else
+ {
+ isumscore += iscore;
+ sumoverlap += end2-start2+1;
+ }
+#else
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "iscore (1)= %d\n", iscore );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ iscore = 0;
+ st = 0;
+ }
+ else if( *pt1 != '-' && *pt2 != '-' )
+ {
+ if( st == 0 )
+ {
+ start1 = pos1; start2 = pos2;
+ st = 1;
+ }
+ iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
+// fprintf( stderr, "%c-%c, iscore(0) = %d\n", *pt1, *pt2, iscore );
+ }
+ if( *pt1++ != '-' ) pos1++;
+ if( *pt2++ != '-' ) pos2++;
+ }
+ if( *(pt1-1) != '-' && *(pt2-1) != '-' )
+ {
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ if( divpairscore )
+ {
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ }
+ else
+ {
+ isumscore += iscore;
+ sumoverlap += end2-start2+1;
+ }
+#else
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "iscore (2)= %d\n", iscore );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ }
+
+ if( !divpairscore )
+ {
+ for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+ {
+ tmppt->overlapaa = sumoverlap;
+// tmppt->opt = (double)isumscore * 5.8 / ( 600 * sumoverlap );
+ tmppt->opt = (double)600 * 5.8 / 600;
+// fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+ }
+ }
+}
+
+void putlocalhom_str( char *al1, char *al2, double *equiv, double scale, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+ int posinaln, pos1, pos2, start1, start2, end1, end2;
+ char *pt1, *pt2;
+ int isumscore;
+ int sumoverlap;
+ LocalHom *tmppt = localhompt;
+ int nlocalhom = 0;
+// int st;
+ pt1 = al1; pt2 = al2;
+ pos1 = off1; pos2 = off2;
+
+ isumscore = 0;
+ sumoverlap = 0;
+ start1 = 0; // by D.Mathog, a guess
+ start2 = 0; // by D.Mathog, a guess
+
+ posinaln = 0;
+ while( *pt1 != 0 )
+ {
+ if( *pt1 != '-' && *pt2 != '-' && equiv[posinaln] > 0.0 )
+ {
+ start1 = end1 = pos1; start2 = end2 = pos2;
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ... (posinaln=%d)\n", posinaln );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+ tmppt->overlapaa = 1;
+// tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ tmppt->opt = equiv[posinaln] * scale;
+// fprintf( stdout, "*pt1=%c, *pt2=%c, equiv=%f\n", *pt1, *pt2, equiv[posinaln] );
+
+ }
+ if( *pt1++ != '-' ) pos1++;
+ if( *pt2++ != '-' ) pos2++;
+ posinaln++;
+ }
+}
+
+void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+ int pos1, pos2, start1, start2, end1, end2;
+ char *pt1, *pt2;
+ int iscore;
+ int isumscore;
+ int sumoverlap;
+ LocalHom *tmppt = localhompt;
+ int nlocalhom = 0;
+ int st;
+ pt1 = al1; pt2 = al2;
+ pos1 = off1; pos2 = off2;
+
+
+ isumscore = 0;
+ sumoverlap = 0;
+ start1 = 0; // by D.Mathog, a guess
+ start2 = 0; // by D.Mathog, a guess
+
+ st = 0;
+ iscore = 0;
+ while( *pt1 != 0 )
+ {
+// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+ if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+ {
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ if( divpairscore )
+ {
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ }
+ else
+ {
+ isumscore += iscore;
+ sumoverlap += end2-start2+1;
+ }
+#else
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "iscore (1)= %d\n", iscore );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ iscore = 0;
+ st = 0;
+ }
+ else if( *pt1 != '-' && *pt2 != '-' )
+ {
+ if( st == 0 )
+ {
+ start1 = pos1; start2 = pos2;
+ st = 1;
+ }
+ iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
+// fprintf( stderr, "%c-%c, iscore(0) = %d\n", *pt1, *pt2, iscore );
+ }
+ if( *pt1++ != '-' ) pos1++;
+ if( *pt2++ != '-' ) pos2++;
+ }
+ if( *(pt1-1) != '-' && *(pt2-1) != '-' )
+ {
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ if( divpairscore )
+ {
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+ }
+ else
+ {
+ isumscore += iscore;
+ sumoverlap += end2-start2+1;
+ }
+#else
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "iscore (2)= %d\n", iscore );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ }
+
+ if( !divpairscore )
+ {
+ for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+ {
+ tmppt->overlapaa = sumoverlap;
+ tmppt->opt = (double)isumscore * 5.8 / ( 600 * sumoverlap );
+// fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+ }
+ }
+}
+void putlocalhom( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+ int pos1, pos2, start1, start2, end1, end2;
+ char *pt1, *pt2;
+ double score;
+ double sumscore;
+ int sumoverlap;
+ LocalHom *tmppt = localhompt;
+ int nlocalhom = 0;
+ int st;
+ pt1 = al1; pt2 = al2;
+ pos1 = off1; pos2 = off2;
+
+
+ sumscore = 0.0;
+ sumoverlap = 0;
+ start1 = 0; // by D.Mathog, a guess
+ start2 = 0; // by D.Mathog, a guess
+
+ st = 0;
+ score = 0.0;
+ while( *pt1 != 0 )
+ {
+// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+ if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+ {
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ if( divpairscore )
+ {
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+ }
+ else
+ {
+ sumscore += score;
+ sumoverlap += end2-start2+1;
+ }
+#else
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "score (1)= %f\n", score );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+ score = 0.0;
+ st = 0;
+ }
+ else if( *pt1 != '-' && *pt2 != '-' )
+ {
+ if( st == 0 )
+ {
+ start1 = pos1; start2 = pos2;
+ st = 1;
+ }
+ score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
+// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
+ }
+ if( *pt1++ != '-' ) pos1++;
+ if( *pt2++ != '-' ) pos2++;
+ }
+ if( nlocalhom++ > 0 )
+ {
+// fprintf( stderr, "reallocating ...\n" );
+ tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+// fprintf( stderr, "done\n" );
+ tmppt = tmppt->next;
+ tmppt->next = NULL;
+ }
+ end1 = pos1 - 1;
+ end2 = pos2 - 1;
+ tmppt->start1 = start1;
+ tmppt->start2 = start2;
+ tmppt->end1 = end1 ;
+ tmppt->end2 = end2 ;
+
+#if 1
+ if( divpairscore )
+ {
+ tmppt->overlapaa = end2-start2+1;
+ tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+ }
+ else
+ {
+ sumscore += score;
+ sumoverlap += end2-start2+1;
+ }
+#else
+ tmppt->overlapaa = overlapaa;
+ tmppt->opt = (double)opt;
+#endif
+
+#if 0
+ fprintf( stderr, "score (2)= %f\n", score );
+ fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+ fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+
+ if( !divpairscore )
+ {
+ for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+ {
+ tmppt->overlapaa = sumoverlap;
+ tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
+// fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+ }
+ }
+}
+
+char *cutal( char *al, int al_display_start, int start, int end )
+{
+ int pos;
+ char *pt = al;
+ char *val = NULL;
+
+ pos = al_display_start;
+ do
+ {
+ if( start == pos ) val = pt;
+ if( end == pos ) break;
+// fprintf( stderr, "pos=%d, *pt=%c, val=%p\n", pos, *pt, val );
+ if( *pt != '-' ) pos++;
+ } while( *pt++ != 0 );
+ *(pt+1) = 0;
+ return( val );
+}
+
+void ErrorExit( char *message )
+{
+ fprintf( stderr, "%s\n", message );
+ exit( 1 );
+}
+
+void strncpy_caseC( char *str1, char *str2, int len )
+{
+ if( dorp == 'd' && upperCase > 0 )
+ {
+ while( len-- )
+ *str1++ = toupper( *str2++ );
+ }
+ else strncpy( str1, str2, len );
+}
+
+void seqUpper( int nseq, char **seq ) /* not used */
+{
+ int i, j, len;
+ for( i=0; i<nseq; i++ )
+ {
+ len = strlen( seq[i] );
+ for( j=0; j<len; j++ )
+ seq[i][j] = toupper( seq[i][j] );
+ }
+}
+
+void seqLower( int nseq, char **seq )
+{
+ int i, j, len;
+ for( i=0; i<nseq; i++ )
+ {
+ len = strlen( seq[i] );
+ for( j=0; j<len; j++ )
+ seq[i][j] = tolower( seq[i][j] );
+ }
+}
+
+int getaline_fp_eof( char *s, int l, FILE *fp ) /* end of file -> return 1 */
+{
+ int c, i = 0 ;
+ int noteofflag = 0;
+ for( i=0; i<l && ( noteofflag = ( (c=getc(fp)) != EOF ) ) && c != '\n'; i++ )
+ *s++ = c;
+ *s = '\0' ;
+ return( !noteofflag );
+}
+
+int getaline_fp_eof_new(s, l, fp) /* end of file -> return 1 */
+char s[] ; int l ; FILE *fp ;
+{
+ int c = 0, i = 0 ;
+ int noteofflag = 0;
+
+ if( feof( fp ) ) return( 1 );
+
+ for( i=0; i<l && ( noteofflag = ( (c=getc(fp)) != EOF ) ) && c != '\n'; i++ )
+ { *s++ = c ; }
+ *s = '\0' ;
+ if( c != '\n' && c != EOF ) while( getc(fp) != '\n' )
+ ;
+ return( !noteofflag );
+}
+
+int myfgets(s, l, fp) /* l°Ê¾å¤Ï¡¢¹ÔËö¤Þ¤ÇÆɤßÈô¤Ð¤¹ */
+char s[] ; int l ; FILE *fp ;
+{
+ int c = 0, i = 0 ;
+
+ if( feof( fp ) ) return( 1 );
+
+ for( i=0; i<l && ( c=getc( fp ) ) != '\n'; i++ )
+ *s++ = c;
+ *s = '\0' ;
+ if( c != '\n' )
+ while( getc(fp) != '\n' )
+ ;
+ return( 0 );
+}
+
+float input_new( FILE *fp, int d )
+{
+ char mojiretsu[10];
+ int i, c;
+
+ c = getc( fp );
+ if( c != '\n' )
+ ungetc( c, fp );
+
+ for( i=0; i<d; i++ )
+ mojiretsu[i] = getc( fp );
+ mojiretsu[i] = 0;
+
+ return( atof( mojiretsu ) );
+}
+
+
+void PreRead( FILE *fp, int *locnjob, int *locnlenmax )
+{
+ int i, nleni;
+ char b[B];
+
+ fgets( b, B-1, fp ); *locnjob = atoi( b );
+ *locnlenmax = 0;
+ i=0;
+ while( i<*locnjob )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( b, "=", 1 ) )
+ {
+ i++;
+ fgets( b, B-1, fp ); nleni = atoi( b );
+ if( nleni > *locnlenmax ) *locnlenmax = nleni;
+ }
+ }
+ if( *locnlenmax > N )
+ {
+ fprintf( stderr, "TOO LONG SEQUENCE!\n" );
+ exit( 1 );
+ }
+ if( njob > M )
+ {
+ fprintf( stderr, "TOO MANY SEQUENCE!\n" );
+ fprintf( stderr, "%d > %d\n", njob, M );
+ exit( 1 );
+ }
+}
+
+int allSpace( char *str )
+{
+ int value = 1;
+ while( *str ) value *= ( !isdigit( *str++ ) );
+ return( value );
+}
+
+void Read( char name[M][B], int nlen[M], char **seq )
+{
+ extern void FRead( FILE *x, char y[M][B], int z[M], char **w );
+ FRead( stdin, name, nlen, seq );
+}
+
+
+void FRead( FILE *fp, char name[][B], int nlen[], char **seq )
+{
+ int i, j;
+ char b[B];
+
+ fgets( b, B-1, fp );
+#if DEBUG
+ fprintf( stderr, "b = %s\n", b );
+#endif
+
+ if( strstr( b, "onnet" ) ) scoremtx = 1;
+ else if( strstr( b, "DnA" ) )
+ {
+ scoremtx = -1;
+ upperCase = -1;
+ }
+ else if( strstr( b, "dna" ) )
+ {
+ scoremtx = -1;
+ upperCase = 0;
+ }
+ else if( strstr( b, "DNA" ) )
+ {
+ scoremtx = -1;
+ upperCase = 1;
+ }
+ else if( strstr( b, "M-Y" ) || strstr( b, "iyata" ) ) scoremtx = 2;
+ else scoremtx = 0;
+#if DEBUG
+ fprintf( stderr, " %s->scoremtx = %d\n", b, scoremtx );
+#endif
+
+ geta2 = GETA2;
+
+#if 0
+ if( strlen( b ) >=25 )
+ {
+ b[25] = 0;
+ #if DEBUG
+ fprintf( stderr, "kimuraR = %s\n", b+20 );
+ #endif
+ kimuraR = atoi( b+20 );
+
+ if( kimuraR < 0 || 20 < kimuraR ) ErrorExit( "Illeagal kimuraR value.\n" );
+ if( allSpace( b+20 ) ) kimuraR = NOTSPECIFIED;
+ }
+ else kimuraR = NOTSPECIFIED;
+ #if DEBUG
+ fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ #endif
+
+ if( strlen( b ) >=20 )
+ {
+ b[20] = 0;
+ #if DEBUG
+ fprintf( stderr, "pamN = %s\n", b+15 );
+ #endif
+ pamN = atoi( b+15 );
+ if( pamN < 0 || 400 < pamN ) ErrorExit( "Illeagal pam value.\n" );
+ if( allSpace( b+15 ) ) pamN = NOTSPECIFIED;
+ }
+ else pamN = NOTSPECIFIED;
+
+ if( strlen( b ) >= 15 )
+ {
+ b[15] = 0;
+ #if DEBUG
+ fprintf( stderr, "poffset = %s\n", b+10 );
+ #endif
+ poffset = atoi( b+10 );
+ if( poffset > 500 ) ErrorExit( "Illegal extending gap ppenalty\n" );
+ if( allSpace( b+10 ) ) poffset = NOTSPECIFIED;
+ }
+ else poffset = NOTSPECIFIED;
+
+ if( strlen( b ) >= 10 )
+ {
+ b[10] = 0;
+ #if DEBUG
+ fprintf( stderr, "ppenalty = %s\n", b+5 );
+ #endif
+ ppenalty = atoi( b+5 );
+ if( ppenalty > 0 ) ErrorExit( "Illegal opening gap ppenalty\n" );
+ if( allSpace( b+5 ) ) ppenalty = NOTSPECIFIED;
+ }
+ else ppenalty = NOTSPECIFIED;
+#endif
+
+ for( i=0; i<njob; i++ )
+ {
+ getaline_fp_eof_new( b, B-1, fp );
+ strcpy( name[i], b );
+#if DEBUG
+ fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+ fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */
+ seq[i][0] = 0;
+ if( nlen[i] ) for( j=0; j <= (nlen[i]-1)/C; j++ )
+ {
+ getaline_fp_eof_new( b, B-1, fp );
+ /* b[C] = 0; */
+ strcat( seq[i], b );
+ }
+ seq[i][nlen[i]] = 0;
+ }
+ if( scoremtx == -1 && upperCase != -1 ) seqLower( njob, seq );
+}
+
+
+static int countKUorWA( FILE *fp )
+{
+ int value;
+ int c, b;
+
+ value= 0;
+ b = '\n';
+ while( ( c = getc( fp ) ) != EOF )
+ {
+ if( b == '\n' && ( c == '>' ) )
+ value++;
+ b = c;
+ }
+ rewind( fp );
+ return( value );
+}
+
+void searchKUorWA( FILE *fp )
+{
+ int c, b;
+ b = '\n';
+ while( !( ( ( c = getc( fp ) ) == '>' || c == EOF ) && b == '\n' ) )
+ b = c;
+ ungetc( c, fp );
+}
+
+static int onlyGraph( char *str )
+{
+ char tmp;
+ char *res = str;
+ char *bk = str;
+
+// while( (tmp=*str++) ) if( isgraph( tmp ) ) *res++ = tmp;
+ while( (tmp=*str++) )
+ {
+ if( 0x20 < tmp && tmp < 0x7f ) *res++ = tmp;
+ if( tmp == '>' )
+ {
+ fprintf( stderr, "========================================================\n" );
+ fprintf( stderr, "========================================================\n" );
+ fprintf( stderr, "=== \n" );
+ fprintf( stderr, "=== ERROR!! \n" );
+ fprintf( stderr, "=== In the '--anysymbol' and '--preservecase' modes, \n" );
+ fprintf( stderr, "=== '>' in sequence is unacceptable.\n" );
+ fprintf( stderr, "=== \n" );
+ fprintf( stderr, "========================================================\n" );
+ fprintf( stderr, "========================================================\n" );
+ exit( 1 );
+ }
+ }
+ *res = 0;
+ return( res - bk );
+}
+
+static int onlyAlpha_lower( char *str )
+{
+ char tmp;
+ char *res = str;
+ char *bk = str;
+
+ while( (tmp=*str++) )
+ if( isalpha( tmp ) || tmp == '-' || tmp == '*' || tmp == '.' )
+ *res++ = tolower( tmp );
+ *res = 0;
+ return( res - bk );
+}
+static int onlyAlpha_upper( char *str )
+{
+ char tmp;
+ char *res = str;
+ char *bk = str;
+
+ while( (tmp=*str++) )
+ if( isalpha( tmp ) || tmp == '-' || tmp == '*' || tmp == '.' )
+ *res++ = toupper( tmp );
+ *res = 0;
+ return( res - bk );
+}
+
+void kake2hiku( char *str )
+{
+ do
+ if( *str == '*' ) *str = '-';
+ while( *str++ );
+}
+
+char *load1SeqWithoutName_realloc_casepreserve( FILE *fpp )
+{
+ int c, b;
+ char *cbuf;
+ int size = N;
+ char *val;
+
+ val = malloc( (size+1) * sizeof( char ) );
+ cbuf = val;
+
+ b = '\n';
+ while( ( c = getc( fpp ) ) != EOF &&
+ !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+ {
+ *cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
+ if( cbuf - val == size )
+ {
+ size += N;
+ fprintf( stderr, "reallocating...\n" );
+ val = (char *)realloc( val, (size+1) * sizeof( char ) );
+ if( !val )
+ {
+ fprintf( stderr, "Allocation error in load1SeqWithoutName_realloc \n" );
+ exit( 1 );
+ }
+ fprintf( stderr, "done.\n" );
+ cbuf = val + size-N;
+ }
+ b = c;
+ }
+ ungetc( c, fpp );
+ *cbuf = 0;
+ onlyGraph( val );
+// kake2hiku( val );
+ return( val );
+}
+
+char *load1SeqWithoutName_realloc( FILE *fpp )
+{
+ int c, b;
+ char *cbuf;
+ int size = N;
+ char *val;
+
+ val = malloc( (size+1) * sizeof( char ) );
+ cbuf = val;
+
+ b = '\n';
+ while( ( c = getc( fpp ) ) != EOF &&
+ !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+ {
+ *cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
+ if( cbuf - val == size )
+ {
+ size += N;
+ fprintf( stderr, "reallocating...\n" );
+ val = (char *)realloc( val, (size+1) * sizeof( char ) );
+ if( !val )
+ {
+ fprintf( stderr, "Allocation error in load1SeqWithoutName_realloc \n" );
+ exit( 1 );
+ }
+ fprintf( stderr, "done.\n" );
+ cbuf = val + size-N;
+ }
+ b = c;
+ }
+ ungetc( c, fpp );
+ *cbuf = 0;
+ if( dorp == 'd' )
+ onlyAlpha_lower( val );
+ else
+ onlyAlpha_upper( val );
+ kake2hiku( val );
+ return( val );
+}
+
+int load1SeqWithoutName_new( FILE *fpp, char *cbuf )
+{
+ int c, b;
+ char *bk = cbuf;
+
+ b = '\n';
+ while( ( c = getc( fpp ) ) != EOF && /* by T. Nishiyama */
+ !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+ {
+ *cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
+ b = c;
+ }
+ ungetc( c, fpp );
+ *cbuf = 0;
+ if( dorp == 'd' )
+ onlyAlpha_lower( bk );
+ else
+ onlyAlpha_upper( bk );
+ kake2hiku( bk );
+ return( 0 );
+}
+
+
+void readDataforgaln( FILE *fp, char **name, int *nlen, char **seq )
+{
+ int i;
+ static char *tmpseq = NULL;
+
+#if 0
+ if( !tmpseq )
+ {
+ tmpseq = AllocateCharVec( N );
+ }
+#endif
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+ for( i=0; i<njob; i++ )
+ {
+ name[i][0] = '='; getc( fp );
+#if 0
+ fgets( name[i]+1, B-2, fp );
+ j = strlen( name[i] );
+ if( name[i][j-1] != '\n' )
+ ErrorExit( "Too long name\n" );
+ name[i][j-1] = 0;
+#else
+ myfgets( name[i]+1, B-2, fp );
+#endif
+#if 0
+ fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ strcpy( seq[i], tmpseq );
+ nlen[i] = strlen( seq[i] );
+ free( tmpseq );
+ }
+ if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
+#if 0
+ free( tmpseq );
+#endif
+}
+
+void readData_varlen( FILE *fp, char **name, int *nlen, char **seq )
+{
+ int i;
+ static char *tmpseq = NULL;
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+ for( i=0; i<njob; i++ )
+ {
+ name[i][0] = '='; getc( fp );
+#if 0
+ fgets( name[i]+1, B-2, fp );
+ j = strlen( name[i] );
+ if( name[i][j-1] != '\n' )
+ ErrorExit( "Too long name\n" );
+ name[i][j-1] = 0;
+#else
+ myfgets( name[i]+1, B-2, fp );
+#endif
+#if 0
+ fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ nlen[i] = strlen( tmpseq );
+// fprintf( stderr, "nlen[%d] = %d\n", i+1, nlen[i] );
+ seq[i] = calloc( nlen[i]+1, sizeof( char ) );
+ strcpy( seq[i], tmpseq );
+ free( tmpseq );
+ }
+ if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
+#if 0
+ free( tmpseq );
+#endif
+}
+
+void readData_pointer2( FILE *fp, int nseq, char **name, int *nlen, char **seq )
+{
+ int i;
+ static char *tmpseq = NULL;
+
+#if 0
+ if( !tmpseq )
+ {
+ tmpseq = AllocateCharVec( N );
+ }
+#endif
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+ for( i=0; i<nseq; i++ )
+ {
+ name[i][0] = '='; getc( fp );
+#if 0
+ fgets( name[i]+1, B-2, fp );
+ j = strlen( name[i] );
+ if( name[i][j-1] != '\n' )
+ ErrorExit( "Too long name\n" );
+ name[i][j-1] = 0;
+#else
+ myfgets( name[i]+1, B-2, fp );
+#endif
+#if 0
+ fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ strcpy( seq[i], tmpseq );
+ free( tmpseq );
+ nlen[i] = strlen( seq[i] );
+ }
+ if( dorp == 'd' && upperCase != -1 ) seqLower( nseq, seq );
+#if 0
+ free( tmpseq );
+#endif
+ if( outnumber )
+ {
+ char *namebuf;
+ char *cptr;
+ namebuf = calloc( B+100, sizeof( char ) );
+ for( i=0; i<nseq; i++ )
+ {
+ namebuf[0] = '=';
+ cptr = strstr( name[i], "_numo_e_" );
+ if( cptr )
+ sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, cptr+8 );
+ else
+ sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, name[i]+1 );
+ strncpy( name[i], namebuf, B );
+ name[i][B-1] = 0;
+ }
+ free( namebuf );
+// exit( 1 );
+ }
+}
+
+
+void readData_pointer_casepreserve( FILE *fp, char **name, int *nlen, char **seq )
+{
+ int i;
+ static char *tmpseq = NULL;
+
+#if 0
+ if( !tmpseq )
+ {
+ tmpseq = AllocateCharVec( N );
+ }
+#endif
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+ for( i=0; i<njob; i++ )
+ {
+ name[i][0] = '='; getc( fp );
+#if 0
+ fgets( name[i]+1, B-2, fp );
+ j = strlen( name[i] );
+ if( name[i][j-1] != '\n' )
+ ErrorExit( "Too long name\n" );
+ name[i][j-1] = 0;
+#else
+ myfgets( name[i]+1, B-2, fp );
+#endif
+#if 0
+ fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+ tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+ strcpy( seq[i], tmpseq );
+ free( tmpseq );
+ nlen[i] = strlen( seq[i] );
+ }
+}
+
+
+void readData_pointer( FILE *fp, char **name, int *nlen, char **seq )
+{
+ int i;
+ static char *tmpseq = NULL;
+
+#if 0
+ if( !tmpseq )
+ {
+ tmpseq = AllocateCharVec( N );
+ }
+#endif
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+ for( i=0; i<njob; i++ )
+ {
+ name[i][0] = '='; getc( fp );
+#if 0
+ fgets( name[i]+1, B-2, fp );
+ j = strlen( name[i] );
+ if( name[i][j-1] != '\n' )
+ ErrorExit( "Too long name\n" );
+ name[i][j-1] = 0;
+#else
+ myfgets( name[i]+1, B-2, fp );
+#endif
+#if 0
+ fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ strcpy( seq[i], tmpseq );
+ free( tmpseq );
+ nlen[i] = strlen( seq[i] );
+ }
+ if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
+#if 0
+ free( tmpseq );
+#endif
+ if( outnumber )
+ {
+ char *namebuf;
+ char *cptr;
+ namebuf = calloc( B+100, sizeof( char ) );
+ for( i=0; i<njob; i++ )
+ {
+ namebuf[0] = '=';
+ cptr = strstr( name[i], "_numo_e_" );
+ if( cptr )
+ sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, cptr+8 );
+ else
+ sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, name[i]+1 );
+ strncpy( name[i], namebuf, B );
+ name[i][B-1] = 0;
+ }
+ free( namebuf );
+// exit( 1 );
+ }
+}
+
+void readData( FILE *fp, char name[][B], int nlen[], char **seq )
+{
+ int i;
+ static char *tmpseq = NULL;
+
+#if 0
+ if( !tmpseq )
+ {
+ tmpseq = AllocateCharVec( N );
+ }
+#endif
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+ for( i=0; i<njob; i++ )
+ {
+ name[i][0] = '='; getc( fp );
+#if 0
+ fgets( name[i]+1, B-2, fp );
+ j = strlen( name[i] );
+ if( name[i][j-1] != '\n' )
+ ErrorExit( "Too long name\n" );
+ name[i][j-1] = 0;
+#else
+ myfgets( name[i]+1, B-2, fp );
+#endif
+#if 0
+ fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ strcpy( seq[i], tmpseq );
+ nlen[i] = strlen( seq[i] );
+ free( tmpseq );
+ }
+ if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
+#if 0
+ free( tmpseq );
+#endif
+}
+
+void cutAlignment( FILE *fp, int **regtable, char **revtable, int *outtable, char **name, char **outseq )
+{
+ int i, j;
+ int outlen;
+ static char *tmpseq = NULL;
+ static char *dumname = NULL;
+ char *fs, *rs;
+ int npos, lpos;
+ int startpos, endpos, seqlen;
+
+ if( dumname == NULL )
+ {
+ dumname = AllocateCharVec( N );
+ }
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+
+ npos = 0;
+ for( i=0; i<njob; i++ )
+ {
+ dumname[0] = '>'; getc( fp );
+ myfgets( dumname+1, B-1, fp );
+ tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+
+ if( outtable[i] )
+ {
+// putc( '>', stdout );
+// puts( dumname+1 );
+
+
+ strncat( name[npos], dumname, B-1 );
+ name[npos][B-1] = 0;
+
+ if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
+ seqlen = strlen( tmpseq );
+ lpos = 0;
+ for( j=0; j<5; j++ )
+ {
+ if( regtable[0][j*2] == -1 && regtable[0][j*2+1] == -1 ) continue;
+
+ startpos = regtable[0][j*2];
+ endpos = regtable[0][j*2+1];
+ if( startpos > endpos )
+ {
+ endpos = regtable[0][j*2];
+ startpos = regtable[0][j*2+1];
+ }
+
+ if( startpos < 0 ) startpos = 0;
+ if( endpos < 0 ) endpos = 0;
+ if( endpos >= seqlen ) endpos = seqlen-1;
+ if( startpos >= seqlen ) startpos = seqlen-1;
+
+// fprintf( stderr, "startpos = %d, endpos = %d\n", startpos, endpos );
+
+ outlen = endpos - startpos+1;
+ if( revtable[0][j] == 'f' )
+ {
+// fprintf( stderr, "regtable[%d][st] = %d\n", i, regtable[0][j*2+0] );
+// fprintf( stderr, "regtable[%d][en] = %d\n", i, regtable[0][j*2+1] );
+// fprintf( stderr, "outlen = %d\n", outlen );
+// fprintf( stdout, "%.*s\n", outlen, tmpseq+regtable[0][j*2] );
+ strncpy( outseq[npos] + lpos, tmpseq+startpos, outlen );
+ lpos += outlen;
+ }
+ else
+ {
+ fs = AllocateCharVec( outlen+1 );
+ rs = AllocateCharVec( outlen+1 );
+
+ fs[outlen] = 0;
+ strncpy( fs, tmpseq+startpos, outlen );
+ sreverse( rs, fs );
+// fprintf( stdout, "%s\n", rs );
+ strncpy( outseq[npos] + lpos, rs, outlen );
+ lpos += outlen;
+ free( fs );
+ free( rs );
+ }
+ outseq[npos][lpos] = 0;
+ }
+ npos++;
+ }
+ free( tmpseq );
+ }
+}
+
+void cutData( FILE *fp, int **regtable, char **revtable, int *outtable )
+{
+ int i, j;
+ int outlen, seqlen, startpos, endpos;
+ static char *tmpseq = NULL;
+ static char *dumname = NULL;
+ char *fs, *rs;
+
+ if( dumname == NULL )
+ {
+ dumname = AllocateCharVec( N );
+ }
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+ for( i=0; i<njob; i++ )
+ {
+ dumname[0] = '='; getc( fp );
+ myfgets( dumname+1, B-2, fp );
+ tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+
+ if( outtable[i] )
+ {
+ gappick_samestring( tmpseq );
+ putc( '>', stdout );
+ puts( dumname+1 );
+
+ seqlen = strlen( tmpseq );
+
+ if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
+ for( j=0; j<5; j++ )
+ {
+ if( regtable[i][j*2] == -1 && regtable[i][j*2+1] == -1 ) continue;
+
+ startpos = regtable[i][j*2];
+ endpos = regtable[i][j*2+1];
+
+ if( startpos > endpos )
+ {
+ endpos = regtable[i][j*2];
+ startpos = regtable[i][j*2+1];
+ }
+
+ if( startpos < 0 ) startpos = 0;
+ if( endpos < 0 ) endpos = 0;
+ if( endpos >= seqlen ) endpos = seqlen-1;
+ if( startpos >= seqlen ) startpos = seqlen-1;
+
+ outlen = endpos - startpos + 1;
+ if( revtable[i][j] == 'f' )
+ {
+ fprintf( stderr, "startpos = %d\n", startpos );
+ fprintf( stderr, "endpos = %d\n", endpos );
+ fprintf( stderr, "outlen = %d\n", outlen );
+ fprintf( stdout, "%.*s\n", outlen, tmpseq+startpos );
+ }
+ else
+ {
+ fs = AllocateCharVec( outlen+1 );
+ rs = AllocateCharVec( outlen+1 );
+
+ fs[outlen] = 0;
+ strncpy( fs, tmpseq+startpos, outlen );
+ sreverse( rs, fs );
+ fprintf( stdout, "%s\n", rs );
+ free( fs );
+ free( rs );
+ }
+ }
+ }
+ free( tmpseq );
+ }
+}
+
+void catData( FILE *fp )
+{
+ int i;
+ static char *tmpseq = NULL;
+ static char *dumname = NULL;
+// char *cptr;
+
+ if( dumname == NULL )
+ {
+ dumname = AllocateCharVec( N );
+ }
+
+ rewind( fp );
+ searchKUorWA( fp );
+
+ for( i=0; i<njob; i++ )
+ {
+ dumname[0] = '='; getc( fp );
+ myfgets( dumname+1, B-2, fp );
+ if( outnumber )
+ {
+ fprintf( stdout, ">_numo_s_%08d_numo_e_", i+1 );
+ }
+ else
+ {
+ putc( '>', stdout );
+ }
+ puts( dumname+1 );
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
+ puts( tmpseq );
+ free( tmpseq );
+ }
+}
+
+int countATGC( char *s, int *total )
+{
+ int nATGC;
+ int nChar;
+ char c;
+ nATGC = nChar = 0;
+
+ if( *s == 0 )
+ {
+ total = 0;
+ return( 0 );
+ }
+
+ do
+ {
+ c = tolower( *s );
+ if( isalpha( c ) )
+ {
+ nChar++;
+ if( c == 'a' || c == 't' || c == 'g' || c == 'c' || c == 'u' || c == 'n' )
+ nATGC++;
+ }
+ }
+ while( *++s );
+
+ *total = nChar;
+ return( nATGC );
+}
+
+double countATGCbk( char *s )
+{
+ int nATGC;
+ int nChar;
+ char c;
+ nATGC = nChar = 0;
+
+ do
+ {
+ c = tolower( *s );
+ if( isalpha( c ) )
+ {
+ nChar++;
+ if( c == 'a' || c == 't' || c == 'g' || c == 'c' || c == 'u' || c == 'n' )
+ nATGC++;
+ }
+ }
+ while( *++s );
+ return( (double)nATGC / nChar );
+}
+
+
+int countnogaplen( char *seq )
+{
+ int val = 0;
+ while( *seq )
+ if( *seq++ != '-' ) val++;
+ return( val );
+}
+
+void getnumlen_casepreserve( FILE *fp, int *nlenminpt )
+{
+ int total;
+ int nsite = 0;
+ int atgcnum;
+ int i, tmp;
+ char *tmpseq, *tmpname;
+ double atgcfreq;
+ tmpname = AllocateCharVec( N );
+ njob = countKUorWA( fp );
+ searchKUorWA( fp );
+ nlenmax = 0;
+ *nlenminpt = 99999999;
+ atgcnum = 0;
+ total = 0;
+ for( i=0; i<njob; i++ )
+ {
+ myfgets( tmpname, N-1, fp );
+ tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+ tmp = strlen( tmpseq );
+ if( tmp > nlenmax ) nlenmax = tmp;
+ if( tmp < *nlenminpt ) *nlenminpt = tmp;
+ atgcnum += countATGC( tmpseq, &nsite );
+ total += nsite;
+ free( tmpseq );
+ }
+ free( tmpname );
+ atgcfreq = (double)atgcnum / total;
+// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+ if( dorp == NOTSPECIFIED )
+ {
+ if( atgcfreq > 0.75 )
+ {
+ dorp = 'd';
+ upperCase = -1;
+ }
+ else
+ {
+ dorp = 'p';
+ upperCase = 0;
+ }
+ }
+}
+
+void getnumlen_nogap( FILE *fp, int *nlenminpt )
+{
+ int total;
+ int nsite = 0;
+ int atgcnum;
+ int i, tmp;
+ char *tmpseq, *tmpname;
+ double atgcfreq;
+ tmpname = AllocateCharVec( N );
+ njob = countKUorWA( fp );
+ searchKUorWA( fp );
+ nlenmax = 0;
+ *nlenminpt = 99999999;
+ atgcnum = 0;
+ total = 0;
+ for( i=0; i<njob; i++ )
+ {
+ myfgets( tmpname, N-1, fp );
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ tmp = countnogaplen( tmpseq );
+ if( tmp > nlenmax ) nlenmax = tmp;
+ if( tmp < *nlenminpt ) *nlenminpt = tmp;
+ atgcnum += countATGC( tmpseq, &nsite );
+ total += nsite;
+ free( tmpseq );
+ }
+ free( tmpname );
+ atgcfreq = (double)atgcnum / total;
+ fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+ if( dorp == NOTSPECIFIED )
+ {
+ if( atgcfreq > 0.75 )
+ {
+ dorp = 'd';
+ upperCase = -1;
+ }
+ else
+ {
+ dorp = 'p';
+ upperCase = 0;
+ }
+ }
+}
+
+
+void getnumlen_nogap_outallreg( FILE *fp, int *nlenminpt )
+{
+ int total;
+ int nsite = 0;
+ int atgcnum;
+ int i, tmp;
+ char *tmpseq, *tmpname;
+ double atgcfreq;
+ tmpname = AllocateCharVec( N );
+ njob = countKUorWA( fp );
+ searchKUorWA( fp );
+ nlenmax = 0;
+ *nlenminpt = 99999999;
+ atgcnum = 0;
+ total = 0;
+ for( i=0; i<njob; i++ )
+ {
+ myfgets( tmpname, N-1, fp );
+ fprintf( stdout, "%s\n", tmpname );
+ tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+ tmp = countnogaplen( tmpseq );
+ fprintf( stdout, "%d\n", tmp );
+ if( tmp > nlenmax ) nlenmax = tmp;
+ if( tmp < *nlenminpt ) *nlenminpt = tmp;
+ atgcnum += countATGC( tmpseq, &nsite );
+ total += nsite;
+ free( tmpseq );
+ }
+ free( tmpname );
+ atgcfreq = (double)atgcnum / total;
+ fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+ if( dorp == NOTSPECIFIED )
+ {
+ if( atgcfreq > 0.75 )
+ {
+ dorp = 'd';
+ upperCase = -1;
+ }
+ else
+ {
+ dorp = 'p';
+ upperCase = 0;
+ }
+ }
+}
+
+void getnumlen_nogap_outallreg_web( FILE *fp, FILE *ofp, int *nlenminpt, int *isalignedpt )
+{
+ int total;
+ int nsite = 0;
+ int atgcnum;
+ int alnlen = 0, alnlen_prev;
+ int i, tmp;
+ char *tmpseq, *tmpname;
+ double atgcfreq;
+ tmpname = AllocateCharVec( N );
+ njob = countKUorWA( fp );
+ searchKUorWA( fp );
+ nlenmax = 0;
+ *nlenminpt = 99999999;
+ atgcnum = 0;
+ total = 0;
+ alnlen_prev = -1;
+ *isalignedpt = 1;
+ for( i=0; i<njob; i++ )
+ {
+ myfgets( tmpname, N-1, fp );
+// fprintf( stdout, "%s\n", tmpname );
+ tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+ tmp = countnogaplen( tmpseq );
+// fprintf( stdout, "%d\n", tmp );
+ if( tmp > nlenmax ) nlenmax = tmp;
+ if( tmp < *nlenminpt ) *nlenminpt = tmp;
+ atgcnum += countATGC( tmpseq, &nsite );
+ total += nsite;
+
+ alnlen = strlen( tmpseq );
+// fprintf( stdout, "##### alnlen, alnlen_prev = %d, %d\n", alnlen, alnlen_prev );
+ if( i>0 && alnlen_prev != alnlen ) *isalignedpt = 0;
+ alnlen_prev = alnlen;
+
+ free( tmpseq );
+ atgcfreq = (double)atgcnum / total;
+// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+// if( dorp == NOTSPECIFIED ) // you kentou
+ {
+ if( atgcfreq > 0.75 )
+ {
+ dorp = 'd';
+ upperCase = -1;
+ }
+ else
+ {
+ dorp = 'p';
+ upperCase = 0;
+ }
+ }
+
+
+
+
+ fprintf( ofp, " <label for='s%d'><input type='checkbox' id='s%d' name='s%d' checked>%s</label>\n", i, i, i, tmpname );
+ fprintf( ofp, "<span id='t%d-0' style='display:none'>", i );
+ fprintf( ofp, " <a href='javascript:void(0)' onclick='ddcycle(this.form,\"t%d\")'>+reg</a>", i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-0' size='8' value='1'> End:<input type='text' name='e%d-0' size='8' value='%d'>", i, i, tmp );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-0'><input type='checkbox' name='r%d-0' id='r%d-0'>Reverse</label>", i, i, i );
+ fprintf( ofp, " Sequence Length:<input type='text' name='l%d' size='8' value='%d' readonly='readonly'>", i, tmp );
+ fprintf( ofp, "\n</span>" );
+ fprintf( ofp, "<span id='t%d-1' style='display:none'>", i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-1' size='8' value=''> End:<input type='text' name='e%d-1' size='8' value=''>", i, i );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-1'><input type='checkbox' name='r%d-1' id='r%d-1'>Reverse</label>", i, i, i );
+ fprintf( ofp, "\n</span>" );
+ fprintf( ofp, "<span id='t%d-2' style='display:none'>", i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-2' size='8' value=''> End:<input type='text' name='e%d-2' size='8' value=''>", i, i );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-2'><input type='checkbox' name='r%d-2' id='r%d-2'>Reverse</label>", i, i, i );
+ fprintf( ofp, "\n</span>" );
+ fprintf( ofp, "<span id='t%d-3' style='display:none'>", i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-3' size='8' value=''> End:<input type='text' name='e%d-3' size='8' value=''>", i, i );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-3'><input type='checkbox' name='r%d-3' id='r%d-3'>Reverse</label>", i, i, i );
+ fprintf( ofp, "\n</span>" );
+ fprintf( ofp, "<span id='t%d-4' style='display:none'>", i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-4' size='8' value=''> End:<input type='text' name='e%d-4' size='8' value=''>", i, i );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-4'><input type='checkbox' name='r%d-4' id='r%d-4'>Reverse</label>", i, i, i );
+ fprintf( ofp, "\n</span>" );
+ }
+ free( tmpname );
+ atgcfreq = (double)atgcnum / total;
+ fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+// if( dorp == NOTSPECIFIED ) // you kentou
+ {
+ if( atgcfreq > 0.75 )
+ {
+ dorp = 'd';
+ upperCase = -1;
+ }
+ else
+ {
+ dorp = 'p';
+ upperCase = 0;
+ }
+ }
+ if( *isalignedpt )
+ {
+ fprintf( ofp, "\n" );
+ fprintf( ofp, "<span id='tall-0' style='display:none'>" );
+ fprintf( ofp, "Cut the alignment\n" );
+ fprintf( ofp, " <a href='javascript:void(0)' onclick='ddcycle(this.form,\"tall\")'>+reg</a>" );
+ fprintf( ofp, " Begin:<input type='text' name='ball-0' size='8' value='1'> End:<input type='text' name='eall-0' size='8' value='%d'>", alnlen );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='rall-0'><input type='checkbox' name='rall-0' id='rall-0'>Reverse</label>" );
+ fprintf( ofp, " Alignment length:<input type='text' name='lall' size='8' value='%d' readonly='readonly'>", alnlen );
+ fprintf( ofp, "\n</span>" );
+ fprintf( ofp, "<span id='tall-1' style='display:none'>" );
+ fprintf( ofp, " Begin:<input type='text' name='ball-1' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='rall-1'><input type='checkbox' name='rall-1' id='rall-1'>Reverse</label>" );
+ fprintf( ofp, "\n</span>" );
+ fprintf( ofp, "<span id='tall-2' style='display:none'>" );
+ fprintf( ofp, " Begin:<input type='text' name='ball-2' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='rall-2'><input type='checkbox' name='rall-2' id='rall-2'>Reverse</label>" );
+ fprintf( ofp, "\n</span>" );
+ fprintf( ofp, "<span id='tall-3' style='display:none'>" );
+ fprintf( ofp, " Begin:<input type='text' name='ball-3' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='rall-3'><input type='checkbox' name='rall-3' id='rall-3'>Reverse</label>" );
+ fprintf( ofp, "\n</span>" );
+ fprintf( ofp, "<span id='tall-4' style='display:none'>" );
+ fprintf( ofp, " Begin:<input type='text' name='ball-4' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
+ if( dorp == 'd' ) fprintf( ofp, " <label for='rall-4'><input type='checkbox' name='rall-4' id='rall-4'>Reverse</label>" );
+ fprintf( ofp, "\n</span>" );
+ }
+
+}
+
+void getnumlen( FILE *fp )
+{
+ int total;
+ int nsite = 0;
+ int atgcnum;
+ int i, tmp;
+ char *tmpseq;
+ char *tmpname;
+ double atgcfreq;
+ tmpname = AllocateCharVec( N );
+ njob = countKUorWA( fp );
+ searchKUorWA( fp );
+ nlenmax = 0;
+ atgcnum = 0;
+ total = 0;
+ for( i=0; i<njob; i++ )
+ {
+ myfgets( tmpname, N-1, fp );
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ tmp = strlen( tmpseq );
+ if( tmp > nlenmax ) nlenmax = tmp;
+ atgcnum += countATGC( tmpseq, &nsite );
+ total += nsite;
+// fprintf( stderr, "##### total = %d\n", total );
+ free( tmpseq );
+ }
+
+ atgcfreq = (double)atgcnum / total;
+// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+ if( dorp == NOTSPECIFIED )
+ {
+ if( atgcfreq > 0.75 )
+ {
+ dorp = 'd';
+ upperCase = -1;
+ }
+ else
+ {
+ dorp = 'p';
+ upperCase = 0;
+ }
+ }
+ free( tmpname );
+}
+
+
+
+void WriteGapFill( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq )
+{
+ static char b[N];
+ int i, j;
+ int nalen[M];
+ static char gap[N];
+ static char buff[N];
+
+#if IODEBUG
+ fprintf( stderr, "IMAKARA KAKU\n" );
+#endif
+ nlenmax = 0;
+ for( i=0; i<locnjob; i++ )
+ {
+ int len = strlen( aseq[i] );
+ if( nlenmax < len ) nlenmax = len;
+ }
+
+ for( i=0; i<nlenmax; i++ ) gap[i] = '-';
+ gap[nlenmax] = 0;
+
+ fprintf( fp, "%5d", locnjob );
+ fprintf( fp, "\n" );
+
+ for( i=0; i<locnjob; i++ )
+ {
+ strcpy( buff, aseq[i] );
+ strncat( buff, gap, nlenmax-strlen( aseq[i] ) );
+ buff[nlenmax] = 0;
+ nalen[i] = strlen( buff );
+ fprintf( fp, "%s\n", name[i] );
+ fprintf( fp, "%5d\n", nalen[i] );
+ for( j=0; j<nalen[i]; j=j+C )
+ {
+ strncpy_caseC( b, buff+j, C ); b[C] = 0;
+ fprintf( fp, "%s\n",b );
+ }
+ }
+#if DEBUG
+ fprintf( stderr, "nalen[0] = %d\n", nalen[0] );
+#endif
+#if IODEBUG
+ fprintf( stderr, "KAKIOWATTA\n" );
+#endif
+}
+
+void writeDataforgaln( FILE *fp, int locnjob, char **name, int *nlen, char **aseq )
+{
+ int i, j;
+ int nalen;
+
+ for( i=0; i<locnjob; i++ )
+ {
+ nalen = strlen( aseq[i] );
+ fprintf( fp, ">%s\n", name[i]+1 );
+ for( j=0; j<nalen; j=j+C )
+ {
+#if 0
+ strncpy( b, aseq[i]+j, C ); b[C] = 0;
+ fprintf( fp, "%s\n",b );
+#else
+ fprintf( fp, "%.*s\n", C, aseq[i]+j );
+#endif
+ }
+ }
+}
+
+void writeData_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq )
+{
+ int i, j;
+ int nalen;
+
+ for( i=0; i<locnjob; i++ )
+ {
+#if DEBUG
+ fprintf( stderr, "i = %d in writeData\n", i );
+#endif
+ nalen = strlen( aseq[i] );
+ fprintf( fp, ">%s\n", name[i]+1 );
+ for( j=0; j<nalen; j=j+C )
+ {
+#if 0
+ strncpy( b, aseq[i]+j, C ); b[C] = 0;
+ fprintf( fp, "%s\n",b );
+#else
+ fprintf( fp, "%.*s\n", C, aseq[i]+j );
+#endif
+ }
+ }
+}
+
+void writeData( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq )
+{
+ int i, j;
+ int nalen;
+
+ for( i=0; i<locnjob; i++ )
+ {
+#if DEBUG
+ fprintf( stderr, "i = %d in writeData\n", i );
+#endif
+ nalen = strlen( aseq[i] );
+ fprintf( fp, ">%s\n", name[i]+1 );
+ for( j=0; j<nalen; j=j+C )
+ {
+#if 0
+ strncpy( b, aseq[i]+j, C ); b[C] = 0;
+ fprintf( fp, "%s\n",b );
+#else
+ fprintf( fp, "%.*s\n", C, aseq[i]+j );
+#endif
+ }
+ }
+}
+
+
+void write1seq( FILE *fp, char *aseq )
+{
+ int j;
+ int nalen;
+
+ nalen = strlen( aseq );
+ for( j=0; j<nalen; j=j+C )
+ fprintf( fp, "%.*s\n", C, aseq+j );
+}
+
+
+
+void readhat2_floathalf_pointer( FILE *fp, int nseq, char **name, float **mtx )
+{
+ int i, j, nseq0;
+ char b[B];
+
+ fgets( b, B, fp );
+ fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+ fgets( b, B, fp );
+ for( i=0; i<nseq; i++ )
+ {
+#if 0
+ getaline_fp_eof( b, B, fp );
+#else
+ myfgets( b, B-2, fp );
+#endif
+#if 0
+ j = MIN( strlen( b+6 ), 10 );
+ if( strncmp( name[i], b+6 , j ) )
+ {
+ fprintf( stderr, "Error in hat2\n" );
+ fprintf( stderr, "%s != %s\n", b, name[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ mtx[i][j-i] = ( input_new( fp, D ) );
+ }
+}
+void readhat2_floathalf( FILE *fp, int nseq, char name[M][B], float **mtx )
+{
+ int i, j, nseq0;
+ char b[B];
+
+ fgets( b, B, fp );
+ fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+ fgets( b, B, fp );
+ for( i=0; i<nseq; i++ )
+ {
+#if 0
+ getaline_fp_eof( b, B, fp );
+#else
+ myfgets( b, B-2, fp );
+#endif
+#if 0
+ j = MIN( strlen( b+6 ), 10 );
+ if( strncmp( name[i], b+6 , j ) )
+ {
+ fprintf( stderr, "Error in hat2\n" );
+ fprintf( stderr, "%s != %s\n", b, name[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ mtx[i][j-i] = ( input_new( fp, D ) );
+ }
+}
+void readhat2_float( FILE *fp, int nseq, char name[M][B], float **mtx )
+{
+ int i, j, nseq0;
+ char b[B];
+
+ fgets( b, B, fp );
+ fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+ fgets( b, B, fp );
+ for( i=0; i<nseq; i++ )
+ {
+#if 0
+ getaline_fp_eof( b, B, fp );
+#else
+ myfgets( b, B-2, fp );
+#endif
+#if 0
+ j = MIN( strlen( b+6 ), 10 );
+ if( strncmp( name[i], b+6 , j ) )
+ {
+ fprintf( stderr, "Error in hat2\n" );
+ fprintf( stderr, "%s != %s\n", b, name[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ mtx[i][j] = ( input_new( fp, D ) );
+ }
+}
+void readhat2_int( FILE *fp, int nseq, char name[M][B], int **mtx )
+{
+ int i, j, nseq0;
+ char b[B];
+
+ fgets( b, B, fp );
+ fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+ fgets( b, B, fp );
+ for( i=0; i<nseq; i++ )
+ {
+#if 0
+ getaline_fp_eof( b, B, fp );
+#else
+ myfgets( b, B-2, fp );
+#endif
+#if 0
+ j = MIN( strlen( b+6 ), 10 );
+ if( strncmp( name[i], b+6 , j ) )
+ {
+ fprintf( stderr, "Error in hat2\n" );
+ fprintf( stderr, "%s != %s\n", b, name[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ mtx[i][j] = (int)( input_new( fp, D ) * INTMTXSCALE + 0.5 );
+ }
+}
+
+void readhat2_pointer( FILE *fp, int nseq, char **name, double **mtx )
+{
+ int i, j, nseq0;
+ char b[B];
+
+ fgets( b, B, fp );
+ fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+ fgets( b, B, fp );
+ for( i=0; i<nseq; i++ )
+ {
+#if 0
+ getaline_fp_eof( b, B, fp );
+#else
+ myfgets( b, B-2, fp );
+#endif
+#if 0
+ j = MIN( strlen( b+6 ), 10 );
+ if( strncmp( name[i], b+6 , j ) )
+ {
+ fprintf( stderr, "Error in hat2\n" );
+ fprintf( stderr, "%s != %s\n", b, name[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ mtx[i][j] = (double)input_new( fp, D);
+ }
+}
+void readhat2( FILE *fp, int nseq, char name[M][B], double **mtx )
+{
+ int i, j, nseq0;
+ char b[B];
+
+ fgets( b, B, fp );
+ fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+ fgets( b, B, fp );
+ for( i=0; i<nseq; i++ )
+ {
+#if 0
+ getaline_fp_eof( b, B, fp );
+#else
+ myfgets( b, B-2, fp );
+#endif
+#if 0
+ j = MIN( strlen( b+6 ), 10 );
+ if( strncmp( name[i], b+6 , j ) )
+ {
+ fprintf( stderr, "Error in hat2\n" );
+ fprintf( stderr, "%s != %s\n", b, name[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ mtx[i][j] = (double)input_new( fp, D);
+ }
+}
+
+void WriteFloatHat2_pointer_halfmtx( FILE *hat2p, int locnjob, char **name, float **mtx )
+{
+ int i, j, ijsa;
+ double max = 0.0;
+ for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+ fprintf( hat2p, "%5d\n", 1 );
+ fprintf( hat2p, "%5d\n", locnjob );
+ fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+ for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+ for( i=0; i<locnjob; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ fprintf( hat2p, "%#6.3f", mtx[i][j-i] );
+ ijsa = j-i;
+ if( ijsa % 12 == 0 || ijsa == locnjob-i-1 ) fprintf( hat2p, "\n" );
+ }
+ }
+}
+
+void WriteFloatHat2_pointer( FILE *hat2p, int locnjob, char **name, float **mtx )
+{
+ int i, j;
+ double max = 0.0;
+ for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+ fprintf( hat2p, "%5d\n", 1 );
+ fprintf( hat2p, "%5d\n", locnjob );
+ fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+ for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+ for( i=0; i<locnjob; i++ )
+ {
+ for( j=1; j<locnjob-i; j++ )
+ {
+ fprintf( hat2p, "%#6.3f", mtx[i][j] );
+ if( j % 12 == 0 || j == locnjob-i-1 ) fprintf( hat2p, "\n" );
+ }
+ }
+}
+
+void WriteFloatHat2( FILE *hat2p, int locnjob, char name[M][B], float **mtx )
+{
+ int i, j;
+ double max = 0.0;
+ for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+ fprintf( hat2p, "%5d\n", 1 );
+ fprintf( hat2p, "%5d\n", locnjob );
+ fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+ for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+ for( i=0; i<locnjob; i++ )
+ {
+ for( j=1; j<locnjob-i; j++ )
+ {
+ fprintf( hat2p, "%#6.3f", mtx[i][j] );
+ if( j % 12 == 0 || j == locnjob-i-1 ) fprintf( hat2p, "\n" );
+ }
+ }
+}
+
+void WriteHat2_int( FILE *hat2p, int locnjob, char name[M][B], int **mtx )
+{
+ int i, j;
+ double max = 0.0;
+ for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+ max /= INTMTXSCALE;
+
+ fprintf( hat2p, "%5d\n", 1 );
+ fprintf( hat2p, "%5d\n", locnjob );
+ fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+ for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+ for( i=0; i<locnjob-1; i++ )
+ {
+ for( j=i+1; j<locnjob; j++ )
+ {
+ fprintf( hat2p, "%#6.3f", (float)mtx[i][j] / INTMTXSCALE );
+ if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
+ }
+ }
+}
+void WriteHat2_pointer( FILE *hat2p, int locnjob, char **name, double **mtx )
+{
+ int i, j;
+ double max = 0.0;
+ for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+ fprintf( hat2p, "%5d\n", 1 );
+ fprintf( hat2p, "%5d\n", locnjob );
+ fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+ for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+ for( i=0; i<locnjob-1; i++ )
+ {
+ for( j=i+1; j<locnjob; j++ )
+ {
+ fprintf( hat2p, "%#6.3f", mtx[i][j] );
+ if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
+ }
+ }
+}
+void WriteHat2( FILE *hat2p, int locnjob, char name[M][B], double **mtx )
+{
+ int i, j;
+ double max = 0.0;
+ for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+ fprintf( hat2p, "%5d\n", 1 );
+ fprintf( hat2p, "%5d\n", locnjob );
+ fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+ for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+ for( i=0; i<locnjob-1; i++ )
+ {
+ for( j=i+1; j<locnjob; j++ )
+ {
+ fprintf( hat2p, "%#6.3f", mtx[i][j] );
+ if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
+ }
+ }
+}
+
+#if 0
+void WriteHat2plain( FILE *hat2p, int locnjob, double **mtx )
+{
+ int i, j, ilim;
+
+ ilim = locnjob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ fprintf( hat2p, "%d-%d d=%.3f\n", i+1, i+1, 0.0 );
+ for( j=i+1; j<locnjob; j++ )
+ {
+ fprintf( hat2p, "%d-%d d=%.3f\n", i+1, j+1, mtx[i][j] );
+ }
+ }
+}
+#endif
+
+int ReadFasta_sub( FILE *fp, double *dis, int nseq, char name[M][B] )
+{
+ int i, count=0;
+ char b[B];
+ int junban[M];
+
+ count = 0;
+ for( i=0; i<10000000 && count<nseq; i++ )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+ count++;
+ }
+ }
+
+ for( i=0; i<nseq; i++ ) dis[i] = 0.0;
+ count = 0;
+ for( i=0; i<100000 && count<nseq; i++ )
+ {
+ if( fgets( b, B-1, fp ) ) break;
+ if( !strncmp( name[junban[count]], b, 20 ) )
+ {
+ fgets( b, B-1, fp );
+ dis[junban[count]] = atof( b );
+ count++;
+ }
+ }
+ return 0;
+}
+
+
+int ReadSsearch( FILE *fp, double *dis, int nseq, char name[M][B] )
+{
+ int i, count=0;
+ char b[B];
+ int junban[M];
+ int opt;
+
+ count = 0;
+ for( i=0; i<10000000 && count<nseq; i++ )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+ sscanf( b+75, "%d", &opt );
+ dis[junban[count]] = (double)opt;
+ count++;
+ }
+ }
+
+/*
+ count = 0;
+ for( i=0; i<100000 && count<nseq; i++ )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( name[junban[count]], b, 20 ) )
+ {
+ dis[junban[count]] = atof( b+65 );
+ count++;
+ }
+ }
+*/
+ return 0;
+}
+
+int ReadBlastm7_avscore( FILE *fp, double *dis, int nin )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ int *junban;
+ double score, sumscore;
+ double len, sumlen;
+ int qstart, qend, tstart, tend;
+ double scorepersite;
+ static char qal[N], tal[N], al[N];
+ int nlocalhom;
+
+ junban = calloc( nin, sizeof( int ) );
+
+ count = 0;
+ sumscore = 0.0;
+ sumlen = 0.0;
+ score = 0.0;
+ len = 0.0;
+ scorepersite = 0.0; // by D.Mathog, a guess
+ while( 1 )
+ {
+
+ if( feof( fp ) ) break;
+
+ while( fgets( b, B-1, fp ) )
+ {
+ if( !strncmp( " <Hit_def>", b, 19 ) || !strncmp( " <Hsp_num>", b, 23 ) ) break;
+ }
+
+ if( !strncmp( " <Hit_def>", b, 19 ) )
+ {
+ junban[count] = atoi( b+31 );
+ nlocalhom = 0;
+ }
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_score>", b, 25 ) ) break;
+ pt = b + 25;
+ score = atof( pt );
+ sumscore += score;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_query-from>", b, 30 ) ) break;
+ pt = b + 30;
+ qstart = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_query-to>", b, 28 ) ) break;
+ pt = b + 28;
+ qend = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_hit-from>", b, 28 ) ) break;
+ pt = b + 28;
+ tstart = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_hit-to>", b, 26 ) ) break;
+ pt = b + 26;
+ tend = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_align-len>", b, 29 ) ) break;
+ pt = b + 29;
+ len = atoi( pt );
+ sumlen += len;
+
+
+ while( fgets( al, N-100, fp ) )
+ if( !strncmp( " <Hsp_qseq>", al, 24 ) ) break;
+
+ strcpy( qal, al+24 );
+ pt = qal;
+ while( *++pt != '<' )
+ ;
+ *pt = 0;
+
+
+ while( fgets( al, N-100, fp ) )
+ if( !strncmp( " <Hsp_hseq>", al, 24 ) ) break;
+
+ strcpy( tal, al+24 );
+ pt = tal;
+ while( *++pt != '<' )
+ ;
+ *pt = 0;
+
+
+// fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " </Hsp>:", b, 18 ) ) break;
+
+
+ fgets( b, B-1, fp );
+
+
+ if( !strncmp( " </Hit_hsps>", b, 21 ) )
+ {
+ dis[junban[count++]] = sumscore;
+ sumscore = 0.0;
+ fgets( b, B-1, fp );
+ fgets( b, B-1, fp );
+ scorepersite = sumscore / sumlen;
+ if( scorepersite != (int)scorepersite )
+ {
+ fprintf( stderr, "ERROR! sumscore=%f, sumlen=%f, and scorepersite=%f\n", sumscore, sumlen, scorepersite );
+ exit( 1 );
+ }
+
+ if( !strncmp( " </Iteration_hits>", b, 23 ) ) break;
+ }
+ }
+
+ free( junban );
+
+ return (int)scorepersite;
+}
+int ReadBlastm7_scoreonly( FILE *fp, double *dis, int nin )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ int *junban;
+ int overlapaa;
+ double score, sumscore;
+ int qstart, qend, tstart, tend;
+ static char qal[N], tal[N], al[N];
+ int nlocalhom;
+
+ junban = calloc( nin, sizeof( int ) );
+
+ count = 0;
+ sumscore = 0.0;
+ score = 0.0;
+ while( 1 )
+ {
+
+ if( feof( fp ) ) break;
+
+ while( fgets( b, B-1, fp ) )
+ {
+ if( !strncmp( " <Hit_def>", b, 19 ) || !strncmp( " <Hsp_num>", b, 23 ) ) break;
+ }
+
+ if( !strncmp( " <Hit_def>", b, 19 ) )
+ {
+ junban[count] = atoi( b+31 );
+ nlocalhom = 0;
+ }
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_score>", b, 25 ) ) break;
+ pt = b + 25;
+ score = atof( pt );
+ sumscore += score;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_query-from>", b, 30 ) ) break;
+ pt = b + 30;
+ qstart = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_query-to>", b, 28 ) ) break;
+ pt = b + 28;
+ qend = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_hit-from>", b, 28 ) ) break;
+ pt = b + 28;
+ tstart = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_hit-to>", b, 26 ) ) break;
+ pt = b + 26;
+ tend = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_align-len>", b, 29 ) ) break;
+ pt = b + 29;
+ overlapaa = atoi( pt );
+
+
+ while( fgets( al, N-100, fp ) )
+ if( !strncmp( " <Hsp_qseq>", al, 24 ) ) break;
+
+ strcpy( qal, al+24 );
+ pt = qal;
+ while( *++pt != '<' )
+ ;
+ *pt = 0;
+
+
+ while( fgets( al, N-100, fp ) )
+ if( !strncmp( " <Hsp_hseq>", al, 24 ) ) break;
+
+ strcpy( tal, al+24 );
+ pt = tal;
+ while( *++pt != '<' )
+ ;
+ *pt = 0;
+
+
+// fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
+
+// nlocalhom += addlocalhom_r( qal, tal, localhomlist+junban[count], qstart, tstart, score, overlapaa, nlocalhom );
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " </Hsp>:", b, 18 ) ) break;
+
+
+ fgets( b, B-1, fp );
+
+
+ if( !strncmp( " </Hit_hsps>", b, 21 ) )
+ {
+ dis[junban[count++]] = sumscore;
+ sumscore = 0.0;
+ fgets( b, B-1, fp );
+ fgets( b, B-1, fp );
+ if( !strncmp( " </Iteration_hits>", b, 23 ) ) break;
+ }
+ }
+
+ free( junban );
+
+ return count;
+}
+
+int ReadBlastm7( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ static int junban[M];
+ int overlapaa;
+ double score, sumscore;
+ int qstart, qend, tstart, tend;
+ static char qal[N], tal[N], al[N];
+ int nlocalhom;
+
+
+
+ count = 0;
+ sumscore = 0.0;
+ score = 0.0;
+ nlocalhom = 0;
+ while( 1 )
+ {
+
+ if( feof( fp ) ) break;
+
+ while( fgets( b, B-1, fp ) )
+ {
+ if( !strncmp( " <Hit_def>", b, 19 ) || !strncmp( " <Hsp_num>", b, 23 ) ) break;
+ }
+
+ if( !strncmp( " <Hit_def>", b, 19 ) )
+ {
+ junban[count] = atoi( b+31 );
+ nlocalhom = 0;
+ }
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_score>", b, 25 ) ) break;
+ pt = b + 25;
+ score = atof( pt );
+ sumscore += score;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_query-from>", b, 30 ) ) break;
+ pt = b + 30;
+ qstart = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_query-to>", b, 28 ) ) break;
+ pt = b + 28;
+ qend = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_hit-from>", b, 28 ) ) break;
+ pt = b + 28;
+ tstart = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_hit-to>", b, 26 ) ) break;
+ pt = b + 26;
+ tend = atoi( pt ) - 1;
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " <Hsp_align-len>", b, 29 ) ) break;
+ pt = b + 29;
+ overlapaa = atoi( pt );
+
+
+ while( fgets( al, N-100, fp ) )
+ if( !strncmp( " <Hsp_qseq>", al, 24 ) ) break;
+
+ strcpy( qal, al+24 );
+ pt = qal;
+ while( *++pt != '<' )
+ ;
+ *pt = 0;
+
+
+ while( fgets( al, N-100, fp ) )
+ if( !strncmp( " <Hsp_hseq>", al, 24 ) ) break;
+
+ strcpy( tal, al+24 );
+ pt = tal;
+ while( *++pt != '<' )
+ ;
+ *pt = 0;
+
+
+// fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
+
+ nlocalhom += addlocalhom_r( qal, tal, localhomlist+junban[count], qstart, tstart, score, overlapaa, nlocalhom );
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( " </Hsp>:", b, 18 ) ) break;
+
+
+ fgets( b, B-1, fp );
+
+
+ if( !strncmp( " </Hit_hsps>", b, 21 ) )
+ {
+ dis[junban[count++]] = sumscore;
+ sumscore = 0.0;
+ fgets( b, B-1, fp );
+ fgets( b, B-1, fp );
+ if( !strncmp( " </Iteration_hits>", b, 23 ) ) break;
+ }
+ }
+ return count;
+}
+
+int ReadFasta34noalign( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ static int junban[M];
+ int opt;
+ double z, bits;
+
+
+ count = 0;
+#if 0
+ for( i=0; i<10000000 && count<nseq; i++ )
+#else
+ while( !feof( fp ) )
+#endif
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+
+ pt = strchr( b, ')' ) + 1;
+ sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
+ dis[junban[count]] = (double)opt;
+ count++;
+
+ }
+ }
+
+ return count;
+}
+int ReadFasta34m10_nuc( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ static int junban[M];
+ int overlapaa;
+ int opt, qstart, qend, tstart, tend;
+ double z, bits;
+ int qal_display_start, tal_display_start;
+ static char qal[N], tal[N];
+ char *qal2, *tal2;
+ int c;
+
+
+ count = 0;
+#if 0
+ for( i=0; i<10000000 && count<nseq; i++ )
+#else
+ while( !feof( fp ) )
+#endif
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+
+ if( strchr( b, 'r' ) ) continue;
+
+ pt = strchr( b, ']' ) + 1;
+ sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
+ dis[junban[count]] = (double)opt;
+ count++;
+
+ }
+ else if( 0 == strncmp( ">>+==========+", b, 14 ) )
+ {
+ break;
+ }
+
+ }
+ if( !count ) return -1;
+
+ count = 0;
+ while( 1 )
+ {
+ if( strncmp( ">>+==========+", b, 14 ) )
+ {
+ fgets( b, B-1, fp );
+ if( feof( fp ) ) break;
+ continue;
+ }
+ junban[count++] = atoi( b+14 );
+// fprintf( stderr, "t = %d\n", atoi( b+14 ) );
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "; fa_opt:", b, 9 ) || !strncmp( "; sw_s-w opt:", b, 13 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ opt = atoi( pt );
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_overlap:", b+4, 9 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ overlapaa = atoi( pt );
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_start:", b+4, 7 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ qstart = atoi( pt ) - 1;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_stop:", b+4, 6 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ qend = atoi( pt ) - 1;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_display_start:", b+4, 15 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ qal_display_start = atoi( pt ) - 1;
+
+ pt = qal;
+ while( (c = fgetc( fp )) )
+ {
+ if( c == '>' )
+ {
+ ungetc( c, fp );
+ break;
+ }
+ if( isalpha( c ) || c == '-' )
+ *pt++ = c;
+ }
+ *pt = 0;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_start:", b+4, 7 ) ) break;
+ pt = strstr( b, ":" ) + 1;
+ tstart = atoi( pt ) - 1;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_stop:", b+4, 6 ) ) break;
+ pt = strstr( b, ":" ) + 1;
+ tend = atoi( pt ) - 1;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_display_start:", b+4, 15 ) ) break;
+ pt = strstr( b, ":" ) + 1;
+ tal_display_start = atoi( pt ) - 1;
+
+ pt = tal;
+ while( ( c = fgetc( fp ) ) )
+ {
+ if( c == '>' )
+ {
+ ungetc( c, fp );
+ break;
+ }
+ if( isalpha( c ) || c == '-' )
+ *pt++ = c;
+ }
+ *pt = 0;
+
+// fprintf( stderr, "(%d-%d:%d-%d)\n", qstart, qend, tstart, tend );
+// fprintf( stderr, "qal_display_start = %d, tal_display_start = %d\n", qal_display_start, tal_display_start );
+
+// fprintf( stderr, "qal = %s\n", qal );
+// fprintf( stderr, "tal = %s\n", tal );
+
+ qal2 = cutal( qal, qal_display_start, qstart, qend );
+ tal2 = cutal( tal, tal_display_start, tstart, tend );
+
+// fprintf( stderr, "qal2 = %s\n", qal2 );
+// fprintf( stderr, "tal2 = %s\n", tal2 );
+
+// fprintf( stderr, "putting %d - %d, opt = %d\n", qmem, junban[count-1], opt );
+ putlocalhom( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa );
+ }
+// fprintf( stderr, "count = %d\n", count );
+ return count;
+}
+int ReadFasta34m10( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ static int junban[M];
+ int overlapaa;
+ int opt, qstart, qend, tstart, tend;
+ double z, bits;
+ int qal_display_start, tal_display_start;
+ static char qal[N], tal[N];
+ char *qal2, *tal2;
+ int c;
+
+
+ count = 0;
+#if 0
+ for( i=0; i<10000000 && count<nseq; i++ )
+#else
+ while( !feof( fp ) )
+#endif
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+
+ pt = strchr( b, ')' ) + 1;
+ sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
+ dis[junban[count]] = (double)opt;
+ count++;
+
+ }
+ else if( 0 == strncmp( ">>+==========+", b, 14 ) )
+ {
+ break;
+ }
+
+ }
+ if( !count ) return -1;
+
+ count = 0;
+ while( 1 )
+ {
+ if( strncmp( ">>+==========+", b, 14 ) )
+ {
+ fgets( b, B-1, fp );
+ if( feof( fp ) ) break;
+ continue;
+ }
+ junban[count++] = atoi( b+14 );
+// fprintf( stderr, "t = %d\n", atoi( b+14 ) );
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "; fa_opt:", b, 9 ) || !strncmp( "; sw_s-w opt:", b, 13 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ opt = atoi( pt );
+
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_overlap:", b+4, 9 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ overlapaa = atoi( pt );
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_start:", b+4, 7 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ qstart = atoi( pt ) - 1;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_stop:", b+4, 6 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ qend = atoi( pt ) - 1;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_display_start:", b+4, 15 ) ) break;
+ pt = strstr( b, ":" ) +1;
+ qal_display_start = atoi( pt ) - 1;
+
+ pt = qal;
+ while( (c = fgetc( fp )) )
+ {
+ if( c == '>' )
+ {
+ ungetc( c, fp );
+ break;
+ }
+ if( isalpha( c ) || c == '-' )
+ *pt++ = c;
+ }
+ *pt = 0;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_start:", b+4, 7 ) ) break;
+ pt = strstr( b, ":" ) + 1;
+ tstart = atoi( pt ) - 1;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_stop:", b+4, 6 ) ) break;
+ pt = strstr( b, ":" ) + 1;
+ tend = atoi( pt ) - 1;
+
+ while( fgets( b, B-1, fp ) )
+ if( !strncmp( "_display_start:", b+4, 15 ) ) break;
+ pt = strstr( b, ":" ) + 1;
+ tal_display_start = atoi( pt ) - 1;
+
+ pt = tal;
+ while( ( c = fgetc( fp ) ) )
+ {
+ if( c == '>' )
+ {
+ ungetc( c, fp );
+ break;
+ }
+ if( isalpha( c ) || c == '-' )
+ *pt++ = c;
+ }
+ *pt = 0;
+
+// fprintf( stderr, "(%d-%d:%d-%d)\n", qstart, qend, tstart, tend );
+// fprintf( stderr, "qal_display_start = %d, tal_display_start = %d\n", qal_display_start, tal_display_start );
+
+// fprintf( stderr, "qal = %s\n", qal );
+// fprintf( stderr, "tal = %s\n", tal );
+
+ qal2 = cutal( qal, qal_display_start, qstart, qend );
+ tal2 = cutal( tal, tal_display_start, tstart, tend );
+
+// fprintf( stderr, "qal2 = %s\n", qal2 );
+// fprintf( stderr, "tal2 = %s\n", tal2 );
+
+// fprintf( stderr, "putting %d - %d, opt = %d\n", qmem, junban[count-1], opt );
+ putlocalhom( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa );
+ }
+// fprintf( stderr, "count = %d\n", count );
+ return count;
+}
+int ReadFasta34m10_scoreonly_nucbk( FILE *fp, double *dis, int nin )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ int pos;
+ int opt;
+ double z, bits;
+
+ count = 0;
+ while( !feof( fp ) )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+===========+", b, 13 ) )
+ {
+ pos = atoi( b+13 );
+
+ if( strchr( b, 'r' ) ) continue;
+
+// pt = strchr( b, ')' ) + 1;
+ pt = strchr( b, ']' ) + 1;
+ sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
+ dis[pos] += (double)opt;
+ count++;
+#if 0
+ fprintf( stderr, "b=%s\n", b );
+ fprintf( stderr, "opt=%d\n", opt );
+ fprintf( stderr, "pos=%d\n", pos );
+ fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
+#endif
+
+ }
+ else if( 0 == strncmp( ">>><<<", b, 6 ) )
+ {
+ break;
+ }
+
+ }
+ if( !count ) return -1;
+
+ return count;
+}
+
+int ReadFasta34m10_scoreonly_nuc( FILE *fp, double *dis, int nin )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ int pos;
+ int opt;
+ double z, bits;
+ int c;
+ int *yonda;
+
+
+ yonda = AllocateIntVec( nin );
+ for( c=0; c<nin; c++ ) yonda[c] = 0;
+ for( c=0; c<nin; c++ ) dis[c] = 0.0;
+
+ count = 0;
+ while( !feof( fp ) )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+===========+", b, 13 ) )
+ {
+ pos = atoi( b+13 );
+
+ if( strchr( b, 'r' ) ) continue;
+
+// pt = strchr( b, ')' ) + 1;
+ pt = strchr( b, ']' ) + 1;
+ sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
+ if( yonda[pos] == 0 )
+ {
+ dis[pos] += (double)opt;
+ yonda[pos] = 1;
+ }
+ count++;
+#if 0
+ fprintf( stderr, "b=%s\n", b );
+ fprintf( stderr, "opt=%d\n", opt );
+ fprintf( stderr, "pos=%d\n", pos );
+ fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
+#endif
+
+ }
+ else if( !strncmp( ">>>", b, 3 ) )
+ {
+ for( c=0; c<nin; c++ ) yonda[c] = 0;
+ }
+ else if( 0 == strncmp( ">>><<<", b, 6 ) )
+ {
+ break;
+ }
+
+ }
+
+ free( yonda );
+
+ if( !count ) return -1;
+
+ return count;
+}
+
+int ReadFasta34m10_scoreonly( FILE *fp, double *dis, int nin )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ int pos;
+ int opt;
+ double z, bits;
+ int c;
+ int *yonda;
+
+
+ yonda = AllocateIntVec( nin );
+ for( c=0; c<nin; c++ ) yonda[c] = 0;
+ for( c=0; c<nin; c++ ) dis[c] = 0.0;
+
+ count = 0;
+ while( !feof( fp ) )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+===========+", b, 13 ) )
+ {
+ pos = atoi( b+13 );
+
+ pt = strchr( b, ')' ) + 1;
+ sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
+ if( yonda[pos] == 0 )
+ {
+ dis[pos] += (double)opt;
+ yonda[pos] = 1;
+ }
+ count++;
+#if 0
+ fprintf( stderr, "b=%s\n", b );
+ fprintf( stderr, "opt=%d\n", opt );
+ fprintf( stderr, "pos=%d\n", pos );
+ fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
+#endif
+
+ }
+ else if( !strncmp( ">>>", b, 3 ) )
+ {
+ for( c=0; c<nin; c++ ) yonda[c] = 0;
+ }
+ else if( 0 == strncmp( ">>><<<", b, 6 ) )
+ {
+ break;
+ }
+
+ }
+
+ free( yonda );
+
+ if( !count ) return -1;
+
+ return count;
+}
+int ReadFasta34( FILE *fp, double *dis, int nseq, char name[M][B], LocalHom *localhomlist )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ static int junban[M];
+ int overlapaa;
+ int opt, qstart, qend, tstart, tend;
+ double z, bits;
+
+
+ count = 0;
+#if 0
+ for( i=0; i<10000000 && count<nseq; i++ )
+#else
+ while( !feof( fp ) )
+#endif
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+
+ pt = strchr( b, ')' ) + 1;
+ sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
+ dis[junban[count]] = (double)opt;
+ count++;
+
+ }
+ else if( 0 == strncmp( ">>+==========+", b, 14 ) )
+ {
+ break;
+ }
+
+ }
+ if( !count ) return -1;
+
+ count = 0;
+ while( !feof( fp ) )
+ {
+ if( !strncmp(">>+==========+", b, 14 ) )
+ {
+ junban[count] = atoi( b+14 );
+ count++;
+ fgets( b, B-1, fp ); // initn:
+ pt = strstr( b, "opt: " ) + 5;
+ localhomlist[junban[count-1]].opt = atof( pt );
+ fgets( b, B-1, fp ); // Smith-Waterman score
+ pt = strstr( b, "ungapped) in " ) + 13;
+ sscanf( pt, "%d", &overlapaa );
+ fprintf( stderr, "pt = %s, overlapaa = %d\n", pt, overlapaa );
+ pt = strstr( b, "overlap (" ) + 8;
+ sscanf( pt, "(%d-%d:%d-%d)", &qstart, &qend, &tstart, &tend );
+ localhomlist[junban[count-1]].overlapaa = overlapaa;
+ localhomlist[junban[count-1]].start1 = qstart-1;
+ localhomlist[junban[count-1]].end1 = qend-1;
+ localhomlist[junban[count-1]].start2 = tstart-1;
+ localhomlist[junban[count-1]].end2 = tend-1;
+ }
+ fgets( b, B-1, fp );
+ }
+ fprintf( stderr, "count = %d\n", count );
+ return count;
+}
+
+int ReadFasta3( FILE *fp, double *dis, int nseq, char name[M][B] )
+{
+ int count=0;
+ char b[B];
+ char *pt;
+ int junban[M];
+ int initn, init1, opt;
+ double z;
+
+ count = 0;
+#if 0
+ for( i=0; i<10000000 && count<nseq; i++ )
+#else
+ while( !feof( fp ) )
+#endif
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+
+ pt = strchr( b, ')' ) + 1;
+ sscanf( pt, "%d %d %d %lf", &initn, &init1, &opt, &z );
+ dis[junban[count]] = (double)opt;
+ count++;
+ }
+ }
+ return 0;
+}
+
+int ReadFasta( FILE *fp, double *dis, int nseq, char name[M][B] )
+{
+ int i, count=0;
+ char b[B];
+ int junban[M];
+ int initn, init1, opt;
+
+ count = 0;
+ for( i=0; i<nseq; i++ ) dis[i] = 0.0;
+ for( i=0; !feof( fp ) && count<nseq; i++ )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+
+ sscanf( b+50, "%d %d %d", &initn, &init1, &opt );
+ dis[junban[count]] = (double)opt;
+ count++;
+ }
+ }
+
+/*
+ count = 0;
+ for( i=0; i<100000 && count<nseq; i++ )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( name[junban[count]], b, 20 ) )
+ {
+ dis[junban[count]] = atof( b+65 );
+ count++;
+ }
+ }
+*/
+ return 0;
+}
+
+
+int ReadOpt( FILE *fp, int opt[M], int nseq, char name[M][B] )
+{
+ int i, count=0;
+ char b[B];
+ int junban[M];
+ int optt, initn, init1;
+
+ count = 0;
+ for( i=0; i<10000000 && count<nseq; i++ )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+ sscanf( b+50, "%d %d %d", &initn, &init1, &optt );
+ opt[junban[count]] = (double)optt;
+ count++;
+ }
+ }
+ return 0;
+}
+
+int ReadOpt2( FILE *fp, int opt[M], int nseq, char name[M][B] )
+{
+ int i, count=0;
+ char b[B];
+ int junban[M];
+
+ count = 0;
+ for( i=0; i<10000000 && count<nseq; i++ )
+ {
+ fgets( b, B-1, fp );
+ if( !strncmp( "+==========+", b, 12 ) )
+ {
+ junban[count] = atoi( b+12 );
+ opt[junban[count]] = atoi( b+65 );
+ count++;
+ }
+ }
+ return 0;
+}
+
+
+
+int writePre( int nseq, char **name, int nlen[M], char **aseq, int force )
+{
+#if USE_XCED
+ int i, value;
+ if( !signalSM )
+ {
+ if( force )
+ {
+ rewind( prep_g );
+ if( devide ) dvWrite( prep_g, nseq, name, nlen, aseq );
+#if 0
+ else WriteGapFill( prep_g, nseq, name, nlen, aseq );
+#else
+ else writeData( prep_g, nseq, name, nlen, aseq );
+#endif
+ }
+ return( 0 );
+ }
+ for( i=0; i<10; i++ )
+ {
+#if IODEBUG
+ fprintf( stderr, "SEMAPHORE = %d\n", signalSM[SEMAPHORE] );
+#endif
+ if( signalSM[SEMAPHORE]-- > 0 )
+ {
+#if 0 /* /tmp/pre ¤Î´Ø·¸¤Ç¤Ï¤º¤·¤¿ */
+ if( ferror( prep_g ) ) prep_g = fopen( "pre", "w" );
+ if( !prep_g ) ErrorExit( "Cannot re-open pre." );
+#endif
+ rewind( prep_g );
+ signalSM[STATUS] = IMA_KAITERU;
+#if IODEBUG
+ if( force ) fprintf( stderr, "FINAL " );
+#endif
+ if( devide ) dvWrite( prep_g, nseq, name, nlen, aseq );
+ else WriteGapFill( prep_g, nseq, name, nlen, aseq );
+ /*
+ fprintf( prep_g, '\EOF' );
+ */
+ fflush( prep_g );
+ if( force ) signalSM[STATUS] = OSHIMAI;
+ else signalSM[STATUS] = KAKIOWATTA;
+ value = 1;
+ signalSM[SEMAPHORE]++;
+#if IODEBUG
+ fprintf( stderr, "signalSM[STATUS] = %c\n", signalSM[STATUS] );
+#endif
+ break;
+ }
+ else
+ {
+#if IODEBUG
+ fprintf( stderr, "YONDERUKARA_AKIRAMERU\n" );
+#endif
+ value = 0;
+ signalSM[SEMAPHORE]++;
+ if( !force ) break;
+#if IODEBUG
+ fprintf( stderr, "MATSU\n" );
+#endif
+ sleep( 1 );
+ }
+ }
+ if( force && !value ) ErrorExit( "xced ga pre wo hanasanai \n" );
+ return( value );
+#else
+ if( force )
+ {
+ rewind( prep_g );
+ writeData_pointer( prep_g, nseq, name, nlen, aseq );
+ }
+#endif
+ return( 0 );
+}
+
+
+void readOtherOptions( int *ppidptr, int *fftThresholdptr, int *fftWinSizeptr )
+{
+ if( calledByXced )
+ {
+ FILE *fp = fopen( "pre", "r" );
+ char b[B];
+ if( !fp ) ErrorExit( "Cannot open pre.\n" );
+ fgets( b, B-1, fp );
+ sscanf( b, "%d %d %d", ppidptr, fftThresholdptr, fftWinSizeptr );
+ fclose( fp );
+#if IODEBUG
+ fprintf( stderr, "b = %s\n", b );
+ fprintf( stderr, "ppid = %d\n", ppid );
+ fprintf( stderr, "fftThreshold = %d\n", fftThreshold );
+ fprintf( stderr, "fftWinSize = %d\n", fftWinSize );
+#endif
+ }
+ else
+ {
+ *ppidptr = 0;
+ *fftThresholdptr = FFT_THRESHOLD;
+ if( dorp == 'd' )
+ *fftWinSizeptr = FFT_WINSIZE_D;
+ else
+ *fftWinSizeptr = FFT_WINSIZE_P;
+ }
+#if 0
+ fprintf( stderr, "fftThresholdptr=%d\n", *fftThresholdptr );
+ fprintf( stderr, "fftWinSizeptr=%d\n", *fftWinSizeptr );
+#endif
+}
+
+void initSignalSM( void )
+{
+// int signalsmid;
+
+#if IODEBUG
+ if( ppid ) fprintf( stderr, "PID of xced = %d\n", ppid );
+#endif
+ if( !ppid )
+ {
+ signalSM = NULL;
+ return;
+ }
+
+#if 0
+ signalsmid = shmget( (key_t)ppid, 3, IPC_ALLOC | 0666 );
+ if( signalsmid == -1 ) ErrorExit( "Cannot get Shared memory for signal.\n" );
+ signalSM = shmat( signalsmid, 0, 0 );
+ if( (int)signalSM == -1 ) ErrorExit( "Cannot attatch Shared Memory for signal!\n" );
+ signalSM[STATUS] = IMA_KAITERU;
+ signalSM[SEMAPHORE] = 1;
+#endif
+}
+
+void initFiles( void )
+{
+ char pname[100];
+ if( ppid )
+ sprintf( pname, "/tmp/pre.%d", ppid );
+ else
+ sprintf( pname, "pre" );
+ prep_g = fopen( pname, "w" );
+ if( !prep_g ) ErrorExit( "Cannot open pre" );
+
+ trap_g = fopen( "trace", "w" );
+ if( !trap_g ) ErrorExit( "cannot open trace" );
+ fprintf( trap_g, "PID = %d\n", getpid() );
+ fflush( trap_g );
+}
+
+
+void WriteForFasta( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq )
+{
+ static char b[N];
+ int i, j;
+ int nalen[M];
+
+ for( i=0; i<locnjob; i++ )
+ {
+ nalen[i] = strlen( aseq[i] );
+ fprintf( fp, ">%s\n", name[i] );
+ for( j=0; j<nalen[i]; j=j+C )
+ {
+ strncpy( b, aseq[i]+j, C ); b[C] = 0;
+ fprintf( fp, "%s\n",b );
+ }
+ }
+}
+
+void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+{
+ double opt;
+ static char buff[B];
+ char infor[100];
+ int i, j, overlapaa, start1, end1, start2, end2;
+ LocalHom *tmpptr1, *tmpptr2;
+
+// for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+
+ while ( NULL != fgets( buff, B-1, fp ) )
+ {
+// fprintf( stderr, "\n" );
+ sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+ if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
+
+#if 0
+ if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+// if( i < j )
+ {
+ if( localhomtable[i][j].nokori++ > 0 )
+ {
+ tmpptr1 = localhomtable[i][j].last;
+// fprintf( stderr, "reallocating, localhomtable[%d][%d].nokori = %d\n", i, j, localhomtable[i][j].nokori );
+ tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr1 = tmpptr1->next;
+ tmpptr1->extended = -1;
+ tmpptr1->next = NULL;
+ localhomtable[i][j].last = tmpptr1;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j].nokori );
+ }
+ else
+ {
+ tmpptr1 = localhomtable[i]+j;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j].nokori );
+ }
+
+ tmpptr1->start1 = start1;
+ tmpptr1->start2 = start2;
+ tmpptr1->end1 = end1;
+ tmpptr1->end2 = end2;
+// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr1->opt = opt;
+ tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr1->overlapaa = overlapaa;
+ tmpptr1->korh = *infor;
+ }
+// else
+ {
+ if( localhomtable[j][i].nokori++ > 0 )
+ {
+ tmpptr2 = localhomtable[j][i].last;
+ tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr2 = tmpptr2->next;
+ tmpptr2->extended = -1;
+ tmpptr2->next = NULL;
+ localhomtable[j][i].last = tmpptr2;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", j, i, localhomtable[j][i].nokori );
+ }
+ else
+ {
+ tmpptr2 = localhomtable[j]+i;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", j, i, localhomtable[j][i].nokori );
+ }
+
+ tmpptr2->start2 = start1;
+ tmpptr2->start1 = start2;
+ tmpptr2->end2 = end1;
+ tmpptr2->end1 = end2;
+// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr2->opt = opt;
+ tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr2->overlapaa = overlapaa;
+ tmpptr2->korh = *infor;
+
+// fprintf( stderr, "i=%d, j=%d, st1=%d, en1=%d, opt = %f\n", i, j, tmpptr1->start1, tmpptr1->end1, opt );
+ }
+
+ }
+}
+void readlocalhomtable( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+{
+ double opt;
+ static char buff[B];
+ char infor[100];
+ int i, j, overlapaa, start1, end1, start2, end2;
+ int **nlocalhom = NULL;
+ LocalHom *tmpptr1=NULL, *tmpptr2=NULL; // by D.Mathog, a guess
+
+ nlocalhom = AllocateIntMtx( njob, njob );
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+
+ while ( NULL != fgets( buff, B-1, fp ) )
+ {
+// fprintf( stderr, "\n" );
+ sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+ if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
+
+#if 0
+ if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+
+// if( i < j )
+ {
+ if( nlocalhom[i][j]++ > 0 )
+ {
+// fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr1 = tmpptr1->next;
+ tmpptr1->next = NULL;
+ }
+ else
+ {
+ tmpptr1 = localhomtable[i]+j;
+// fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ }
+
+ tmpptr1->start1 = start1;
+ tmpptr1->start2 = start2;
+ tmpptr1->end1 = end1;
+ tmpptr1->end2 = end2;
+// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr1->opt = opt;
+ tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr1->overlapaa = overlapaa;
+ tmpptr1->korh = *infor;
+
+// fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
+ }
+// else
+ {
+ if( nlocalhom[j][i]++ > 0 )
+ {
+ tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr2 = tmpptr2->next;
+ tmpptr2->next = NULL;
+ }
+ else
+ tmpptr2 = localhomtable[j]+i;
+
+ tmpptr2->start2 = start1;
+ tmpptr2->start1 = start2;
+ tmpptr2->end2 = end1;
+ tmpptr2->end1 = end2;
+// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr2->opt = opt;
+ tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr2->overlapaa = overlapaa;
+ tmpptr2->korh = *infor;
+ }
+
+ }
+ FreeIntMtx( nlocalhom );
+}
+
+void outlocalhom( LocalHom **localhom, int nseq )
+{
+ int i, j;
+ LocalHom *tmpptr;
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+ {
+ tmpptr = localhom[i]+j;
+ fprintf( stderr, "%d-%d\n", i, j );
+ do
+ {
+ fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt );
+ }
+ while( (tmpptr=tmpptr->next) );
+ }
+}
+
+void outlocalhompt( LocalHom ***localhom, int n1, int n2 )
+{
+ int i, j;
+ LocalHom *tmpptr;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ tmpptr = localhom[i][j];
+ fprintf( stderr, "%d-%d\n", i, j );
+ do
+ {
+ fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f, wimp=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt, tmpptr->wimportance );
+ }
+ while( (tmpptr=tmpptr->next) );
+ }
+}
+
+void FreeLocalHomTable( LocalHom **localhomtable, int n )
+{
+ int i, j;
+ LocalHom *ppp, *tmpptr;
+ for( i=0; i<n; i++ )
+ {
+ for( j=0; j<n; j++ )
+ {
+ tmpptr=localhomtable[i]+j;
+ ppp = tmpptr->next;
+ for( ; tmpptr; tmpptr=ppp )
+ {
+#if DEBUG
+ fprintf( stderr, "i=%d, j=%d\n", i, j );
+#endif
+ ppp = tmpptr->next;
+ if( tmpptr!=localhomtable[i]+j )
+ {
+#if DEBUG
+ fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+ free( tmpptr );
+ }
+ }
+ }
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+ free( localhomtable[i] );
+ }
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable\n" );
+#endif
+ free( localhomtable );
+#if DEBUG
+ fprintf( stderr, "freed\n" );
+#endif
+}
+
+char *progName( char *str )
+{
+ char *value;
+ if( ( value = strrchr( str, '/' ) ) != NULL )
+ return( value+1 );
+ else
+ return( str );
+}
+
+static void tabtospace( char *str )
+{
+ char *p;
+// fprintf( stderr, "before = %s\n", str );
+ while( NULL != ( p = strchr( str , '\t' ) ) )
+ {
+ *p = ' ';
+ }
+// fprintf( stderr, "after = %s\n", str );
+}
+
+static char *extractfirstword( char *str )
+{
+ char *val = str;
+
+ tabtospace( str );
+ while( *str )
+ {
+ if( val == str && *str == ' ' )
+ {
+ val++; str++;
+ }
+ else if( *str != ' ' )
+ {
+ str++;
+ }
+ else if( *str == ' ' )
+ {
+ *str = 0;
+ }
+ }
+ return( val );
+}
+
+void phylipout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, int *order )
+{
+ int pos, pos2, j;
+ pos = 0;
+
+ fprintf( fp, " %d %d\n", nseq, maxlen );
+
+ while( pos < maxlen )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ if( pos == 0 )
+ fprintf( fp, "%-10.10s", extractfirstword( name[order[j]]+1 ) );
+ else
+ fprintf( fp, " " );
+
+ pos2 = pos;
+ while( pos2 < pos+41 && pos2 < maxlen )
+ {
+ fprintf( fp, " %.10s", seq[order[j]]+pos2 );
+ pos2 += 10;
+ }
+ fprintf( fp, "\n" );
+ }
+ fprintf( fp, "\n" );
+ pos += 50;
+ }
+}
+
+void clustalout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, char *mark, char *comment, int *order, int namelen )
+{
+ int pos, j;
+ pos = 0;
+ if( comment == NULL )
+ fprintf( fp, "CLUSTAL format alignment by MAFFT (v%s)\n\n", VERSION );
+ else
+ fprintf( fp, "CLUSTAL format alignment by MAFFT %s (v%s)\n\n", comment, VERSION );
+
+ while( pos < maxlen )
+ {
+ fprintf( fp, "\n" );
+ for( j=0; j<nseq; j++ )
+ {
+ fprintf( fp, "%-*.*s ", namelen, namelen, extractfirstword( name[order[j]]+1 ) );
+ fprintf( fp, "%.60s\n", seq[order[j]]+pos ); // Ťµ¤¬°ã¤¦¤È¤À¤á¡£
+ }
+ if( mark )
+ {
+ fprintf( fp, "%-*.*s ", namelen, namelen, "" );
+ fprintf( fp, "%.60s\n", mark + pos ); // Ťµ¤¬°ã¤¦¤È¤À¤á¡£
+ }
+ pos += 60;
+ }
+}
+
+
+void writeData_reorder_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq, int *order )
+{
+ int i, j, k;
+ int nalen;
+
+ for( i=0; i<locnjob; i++ )
+ {
+ k = order[i];
+#if DEBUG
+ fprintf( stderr, "i = %d in writeData\n", i );
+#endif
+ nalen = strlen( aseq[k] );
+ fprintf( fp, ">%s\n", name[k]+1 );
+ for( j=0; j<nalen; j=j+C )
+ {
+#if 0
+ strncpy( b, aseq[k]+j, C ); b[C] = 0;
+ fprintf( fp, "%s\n",b );
+#else
+ fprintf( fp, "%.*s\n", C, aseq[k]+j );
+#endif
+ }
+ }
+}
+void writeData_reorder( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq, int *order )
+{
+ int i, j, k;
+ int nalen;
+
+ for( i=0; i<locnjob; i++ )
+ {
+ k = order[i];
+#if DEBUG
+ fprintf( stderr, "i = %d in writeData\n", i );
+#endif
+ nalen = strlen( aseq[k] );
+ fprintf( fp, ">%s\n", name[k]+1 );
+ for( j=0; j<nalen; j=j+C )
+ {
+#if 0
+ strncpy( b, aseq[k]+j, C ); b[C] = 0;
+ fprintf( fp, "%s\n",b );
+#else
+ fprintf( fp, "%.*s\n", C, aseq[k]+j );
+#endif
+ }
+ }
+}
+static void showaamtxexample()
+{
+ fprintf( stderr, "Format error in aa matrix\n" );
+ fprintf( stderr, "# Example:\n" );
+ fprintf( stderr, "# comment\n" );
+ fprintf( stderr, " A R N D C Q E G H I L K M F P S T W Y V\n" );
+ fprintf( stderr, "A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0\n" );
+ fprintf( stderr, "R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3\n" );
+ fprintf( stderr, "...\n" );
+ fprintf( stderr, "V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4\n" );
+ fprintf( stderr, "frequency 0.07 0.05 0.04 0.05 0.02 .. \n" );
+ fprintf( stderr, "# Example end\n" );
+ fprintf( stderr, "Only the lower half is loaded\n" );
+ fprintf( stderr, "The last line (frequency) is optional.\n" );
+ exit( 1 );
+}
+
+double *loadaamtx( void )
+{
+ int i, j, k, ii, jj;
+ double *val;
+ double **raw;
+ int *map;
+ char *aaorder = "ARNDCQEGHILKMFPSTWYV";
+ char *inorder;
+ char *line;
+ char *ptr1;
+ char *ptr2;
+ char *mtxfname = "_aamtx";
+ FILE *mf;
+
+ raw = AllocateDoubleMtx( 21, 20 );
+ val = AllocateDoubleVec( 420 );
+ map = AllocateIntVec( 20 );
+
+ if( dorp != 'p' )
+ {
+ fprintf( stderr, "User-defined matrix is not supported for DNA\n" );
+ exit( 1 );
+ }
+
+ mf = fopen( mtxfname, "r" );
+ if( mf == NULL )
+ {
+ fprintf( stderr, "Cannot open the _aamtx file\n" );
+ exit( 1 );
+ }
+
+ inorder = calloc( 1000, sizeof( char ) );
+ line = calloc( 1000, sizeof( char ) );
+
+
+ while( !feof( mf ) )
+ {
+ fgets( inorder, 999, mf );
+ if( inorder[0] != '#' ) break;
+ }
+ ptr1 = ptr2 = inorder;
+ while( *ptr2 )
+ {
+ if( isalpha( *ptr2 ) )
+ {
+ *ptr1 = toupper( *ptr2 );
+ ptr1++;
+ }
+ ptr2++;
+ }
+ inorder[20] = 0;
+
+ for( i=0; i<20; i++ )
+ {
+ ptr2 = strchr( inorder, aaorder[i] );
+ if( ptr2 == NULL )
+ {
+ fprintf( stderr, "%c: not found in the first 20 letters.\n", aaorder[i] );
+ showaamtxexample();
+ }
+ else
+ {
+ map[i] = ptr2 - inorder;
+ }
+ }
+
+ i = 0;
+ while( !feof( mf ) )
+ {
+ fgets( line, 999, mf );
+// fprintf( stderr, "line = %s\n", line );
+ if( line[0] == '#' ) continue;
+ ptr1 = line;
+// fprintf( stderr, "line = %s\n", line );
+ for( j=0; j<=i; j++ )
+ {
+ while( !isdigit( *ptr1 ) && *ptr1 != '-' && *ptr1 != '.' )
+ ptr1++;
+
+ raw[i][j] = atof( ptr1 );
+// fprintf( stderr, "raw[][]=%f, %c-%c %d-%d\n", raw[i][j], inorder[i], inorder[j], i, j );
+ ptr1 = strchr( ptr1, ' ' );
+ if( ptr1 == NULL && j<i) showaamtxexample();
+ }
+ i++;
+ if( i > 19 ) break;
+ }
+
+ for( i=0; i<20; i++ ) raw[20][i] = -1.0;
+ while( !feof( mf ) )
+ {
+ fgets( line, 999, mf );
+ if( line[0] == 'f' )
+ {
+// fprintf( stderr, "line = %s\n", line );
+ ptr1 = line;
+ for( j=0; j<20; j++ )
+ {
+ while( !isdigit( *ptr1 ) && *ptr1 != '-' && *ptr1 != '.' )
+ ptr1++;
+
+ raw[20][j] = atof( ptr1 );
+// fprintf( stderr, "raw[20][]=%f, %c %d\n", raw[20][j], inorder[i], j );
+ ptr1 = strchr( ptr1, ' ' );
+ if( ptr1 == NULL && j<19) showaamtxexample();
+ }
+ break;
+ }
+ }
+
+ k = 0;
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ if( i != j )
+ {
+ ii = MAX( map[i], map[j] );
+ jj = MIN( map[i], map[j] );
+ }
+ else ii = jj = map[i];
+ val[k++] = raw[ii][jj];
+// fprintf( stderr, "%c-%c, %f\n", aaorder[i], aaorder[j], val[k-1] );
+ }
+ }
+ for( i=0; i<20; i++ ) val[400+i] = raw[20][map[i]];
+
+ fprintf( stderr, "inorder = %s\n", inorder );
+ fclose( mf );
+ free( inorder );
+ free( line );
+ FreeDoubleMtx( raw );
+ free( map );
+ return( val );
+}
+
+
+void readmccaskill( FILE *fp, RNApair **pairprob, int length )
+{
+ char gett[1000];
+ int *pairnum;
+ int i;
+ int left, right;
+ float prob;
+ int c;
+
+ pairnum = (int *)calloc( length, sizeof( int ) );
+ for( i=0; i<length; i++ ) pairnum[i] = 0;
+
+ c = getc( fp );
+ {
+ if( c != '>' )
+ {
+ fprintf( stderr, "format error in hat4\n" );
+ exit( 1 );
+ }
+ }
+ fgets( gett, 999, fp );
+ while( 1 )
+ {
+ if( feof( fp ) ) break;
+ c = getc( fp );
+ ungetc( c, fp );
+ if( c == '>' )
+ {
+ break;
+ }
+ fgets( gett, 999, fp );
+// fprintf( stderr, "gett = %s\n", gett );
+ sscanf( gett, "%d %d %f", &left, &right, &prob );
+
+ if( left >= length || right >= length )
+ {
+ fprintf( stderr, "format error in hat4\n" );
+ exit( 1 );
+ }
+
+ if( prob < 0.01 ) continue; // 080607, mafft ni dake eikyou
+
+ if( left != right && prob > 0.0 )
+ {
+ pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
+ pairprob[left][pairnum[left]].bestscore = prob;
+ pairprob[left][pairnum[left]].bestpos = right;
+ pairnum[left]++;
+ pairprob[left][pairnum[left]].bestscore = -1.0;
+ pairprob[left][pairnum[left]].bestpos = -1;
+// fprintf( stderr, "%d-%d, %f\n", left, right, prob );
+
+ pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
+ pairprob[right][pairnum[right]].bestscore = prob;
+ pairprob[right][pairnum[right]].bestpos = left;
+ pairnum[right]++;
+ pairprob[right][pairnum[right]].bestscore = -1.0;
+ pairprob[right][pairnum[right]].bestpos = -1;
+// fprintf( stderr, "%d-%d, %f\n", right, left, prob );
+ }
+ }
+ free( pairnum );
+}
+
+void readpairfoldalign( FILE *fp, char *s1, char *s2, char *aln1, char *aln2, int q1, int q2, int *of1, int *of2, int sumlen )
+{
+ char gett[1000];
+ int *maptoseq1;
+ int *maptoseq2;
+ char dumc;
+ int dumi;
+ char sinseq[100], sinaln[100];
+ int posinseq, posinaln;
+ int alnlen;
+ int i;
+ int pos1, pos2;
+ char *pa1, *pa2;
+ char qstr[1000];
+
+ *of1 = -1;
+ *of2 = -1;
+
+ maptoseq1 = AllocateIntVec( sumlen+1 );
+ maptoseq2 = AllocateIntVec( sumlen+1 );
+
+ posinaln = 0; // foldalign ga alingment wo kaesanaitok no tame.
+
+ while( !feof( fp ) )
+ {
+ fgets( gett, 999, fp );
+ if( !strncmp( gett, "; ALIGNING", 10 ) ) break;
+ }
+ sprintf( qstr, "; ALIGNING %d against %d\n", q1+1, q2+1 );
+ if( strcmp( gett, qstr ) )
+ {
+ fprintf( stderr, "Error in FOLDALIGN\n" );
+ fprintf( stderr, "qstr = %s, but gett = %s\n", qstr, gett );
+ exit( 1 );
+ }
+
+ while( !feof( fp ) )
+ {
+ fgets( gett, 999, fp );
+ if( !strncmp( gett, "; --------", 10 ) ) break;
+ }
+
+
+ while( !feof( fp ) )
+ {
+ fgets( gett, 999, fp );
+ if( !strncmp( gett, "; ********", 10 ) ) break;
+// fprintf( stderr, "gett = %s\n", gett );
+ sscanf( gett, "%c %c %s %s %d %d", &dumc, &dumc, sinseq, sinaln, &dumi, &dumi );
+ posinaln = atoi( sinaln );
+ posinseq = atoi( sinseq );
+// fprintf( stderr, "posinseq = %d\n", posinseq );
+// fprintf( stderr, "posinaln = %d\n", posinaln );
+ maptoseq1[posinaln-1] = posinseq-1;
+ }
+ alnlen = posinaln;
+
+ while( !feof( fp ) )
+ {
+ fgets( gett, 999, fp );
+ if( !strncmp( gett, "; --------", 10 ) ) break;
+ }
+
+ while( !feof( fp ) )
+ {
+ fgets( gett, 999, fp );
+ if( !strncmp( gett, "; ********", 10 ) ) break;
+// fprintf( stderr, "gett = %s\n", gett );
+ sscanf( gett, "%c %c %s %s %d %d", &dumc, &dumc, sinseq, sinaln, &dumi, &dumi );
+ posinaln = atof( sinaln );
+ posinseq = atof( sinseq );
+// fprintf( stderr, "posinseq = %d\n", posinseq );
+// fprintf( stderr, "posinaln = %d\n", posinaln );
+ maptoseq2[posinaln-1] = posinseq-1;
+ }
+ if( alnlen != posinaln )
+ {
+ fprintf( stderr, "Error in foldalign?\n" );
+ exit( 1 );
+ }
+
+ pa1 = aln1;
+ pa2 = aln2;
+ for( i=0; i<alnlen; i++ )
+ {
+ pos1 = maptoseq1[i];
+ pos2 = maptoseq2[i];
+
+ if( pos1 > -1 )
+ *pa1++ = s1[pos1];
+ else
+ *pa1++ = '-';
+
+ if( pos2 > -1 )
+ *pa2++ = s2[pos2];
+ else
+ *pa2++ = '-';
+ }
+ *pa1 = 0;
+ *pa2 = 0;
+
+ *of1 = 0;
+ for( i=0; i<alnlen; i++ )
+ {
+ *of1 = maptoseq1[i];
+ if( *of1 > -1 ) break;
+ }
+ *of2 = 0;
+ for( i=0; i<alnlen; i++ )
+ {
+ *of2 = maptoseq2[i];
+ if( *of2 > -1 ) break;
+ }
+
+// fprintf( stderr, "*of1=%d, aln1 = :%s:\n", *of1, aln1 );
+// fprintf( stderr, "*of2=%d, aln2 = :%s:\n", *of2, aln2 );
+
+ free( maptoseq1 );
+ free( maptoseq2 );
+}
--- /dev/null
+ /* iteration ( algorithm C ) */
+#include "mltaln.h"
+
+#define DEBUG 0
+
+static void Writeoptions( FILE *fp )
+{
+ if( scoremtx == 1 )
+ fprintf( fp, "Dayhoff( ... )\n" );
+ else if( scoremtx == -1 )
+ fprintf( fp, "DNA\n" );
+ else if( scoremtx == 2 )
+ fprintf( fp, "Miyata-Yasunaga\n" );
+ else
+ fprintf( fp, "JTT %dPAM\n", pamN );
+
+ if( scoremtx == 0 )
+ fprintf( fp, "Gap Penalty = %+d, %+d\n", penalty, offset );
+ else
+ fprintf( fp, "Gap Penalty = %+d\n", penalty );
+
+ fprintf( fp, "marginal score to search : best - %f\n", cut );
+ if( scmtd == 3 )
+ fprintf( fp, "score of rnd or sco\n" );
+ else if( scmtd == 4 )
+ fprintf( fp, "score = sigma( score for a pair of homologous amino acids ) / ( number of amino acids pairs )\n" );
+ else if( scmtd == 5 )
+ fprintf( fp, "score : SP\n" );
+ if( mix )
+ fprintf( fp, "?\n" );
+ else
+ {
+ if( weight == 2 )
+ fprintf( fp, "weighted, geta2 = %f\n", geta2 );
+ else if( weight == 3 )
+ {
+ if( scmtd == 4 )
+ fprintf( fp, "reversely weighted in function 'align', unweighted in function 'score_calc'\n" );
+ else
+ fprintf( fp, "weighted like ClustalW," );
+ }
+ else
+ fprintf( fp, "unweighted\n" );
+ }
+ if( weight && utree )
+ {
+ fprintf( fp, "using tree defined by the file hat2 with simplified UPG method\n" );
+ }
+ if( weight && !utree )
+ fprintf( fp, "using temporary tree by simplified UPG method\n" );
+ fprintf( fp, "Algorithm %c\n", alg );
+}
+
+
+
+
+char **align0( float *wm, char **aseq, char *seq, double effarr[M], int icyc, int ex )
+{
+ char **result;
+
+ if( alg == 'B' )
+ {
+ ErrorExit( "Sorry!" );
+ /*
+ if( outgap == 0 )
+ {
+ result = alignm1_o( wm, aseq, seq, scmx, effarr, icyc, ex );
+ }
+ if( outgap == 1 )
+ {
+ result = alignm1( wm, aseq, seq, scmx, effarr, icyc, ex );
+ }
+ */
+ }
+ else if( alg == 'C' )
+ {
+ result = Calignm1( wm, aseq, seq, effarr, icyc, ex );
+ }
+ return( result );
+}
+
+
+double score_m_1_0( char **aseq, int locnjob, int s, double **eff, double effarr[M] )
+{
+ double x;
+
+ if( alg == 'B' )
+ {
+ ErrorExit( "Sorry!" );
+ }
+ if( alg == 'C' )
+ {
+ x = Cscore_m_1( aseq, locnjob, s, eff );
+ }
+ fprintf( stderr, "in score_m_1_0 %f\n", x );
+ return( x );
+}
+
+int iteration( int locnjob, char name[M][B], int nlen[M], char **aseq, char **bseq, int ***topol, double **len, double **eff )
+{
+ double tscore, mscore;
+ int identity;
+ static char *mseq1, **mseq2 = NULL;
+ static char **result;
+ int i, l;
+ static double effarr[M];
+ int s;
+ int sss[2];
+ char ou;
+ int alloclen;
+ int resultlen;
+ int nlenmax0 = nlenmax;
+ FILE *prep;
+ char sai[M];
+ char sai1[M];
+ char sai2[M];
+#if 0
+ double his[2][M][MAXITERATION/locnjob+1];
+#else
+ double ***his;
+#endif
+ int cyc[2];
+ char shindou = 0;
+ float wm;
+ int returnvalue;
+
+ for( i=0; i<locnjob; i++ )
+ {
+ sai[i] = 1;
+ sai1[i] = 1;
+ sai2[i] = 2;
+ }
+ sai[locnjob] = sai1[locnjob] = sai2[locnjob] = 0;
+
+
+ Writeoptions( trap_g );
+
+ his = AllocateDoubleCub( 2, M, MAXITERATION/locnjob+1 );
+
+ if( mseq2 == NULL )
+ {
+ alloclen = nlenmax * 2.0;
+ AllocateTmpSeqs( &mseq2, &mseq1, alloclen );
+ }
+
+ if( !tbitr && !tbweight )
+ {
+ writePre( locnjob, name, nlen, aseq, 0 );
+
+#if 0
+ prep = fopen( "best", "w" );
+ Write( prep, locnjob, name, nlen, aseq );
+ fclose( prep );
+#endif
+ }
+
+
+
+
+ treeconstruction( aseq, locnjob, topol, len, eff );
+ tscore = score_calc0( aseq, locnjob, eff, 0 );
+
+#if DEBUG
+ fprintf( stderr, "eff mtx in iteration\n" );
+ for( i=0; i<locnjob; i++ )
+ {
+ for( j=0; j<locnjob; j++ )
+ {
+ fprintf( stderr, "%5.3f ", eff[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+ fprintf( stderr, "\n" );
+ if( disp )
+ {
+ fprintf( stderr, "aseq(initial)\n" );
+ display( aseq, locnjob );
+ }
+ fprintf( stderr, "initial score = %f \n", tscore );
+ fprintf( stderr, "\n" );
+ for( i=0; i<locnjob; i++ ) strcpy( bseq[i], aseq[i] );
+ mscore = tscore;
+ srand( time(NULL) );
+
+ sss[1] = 0;
+ sss[0] = locnjob-1;
+/*
+ sss[0] = (int)( (float)locnjob/2.0 );
+*/
+ ou = 1;
+ cyc[0] = 0; cyc[1] = 0;
+
+ for( s=-1, l=0; l<MAXITERATION; l++ )
+ {
+ int ss;
+ double tmpscore, tmpscore1;
+
+ if( strlen( aseq[0] ) > nlenmax )
+ nlenmax = strlen( aseq[0] );
+
+ /*
+ s = ( int )( rnd() * locnjob );
+ s++;
+ if( s == locnjob ) s = 0;
+ ou = 0;
+ */
+ if( ou == 0 )
+ {
+ ou = 1;
+ s = sss[0];
+ /*
+ sss[0]++;
+ if( sss[0] == locnjob )
+ {
+ sss[0] = 0;
+ cyc[0]++;
+ }
+ */
+ sss[0]--;
+ if( sss[0] == -1 )
+ {
+ sss[0] = locnjob-1;
+ cyc[0]++;
+ }
+ }
+ else
+ {
+ ou = 0;
+ s = sss[1];
+ sss[1]++;
+ if( sss[1] == locnjob )
+ {
+ sss[1] = 0;
+ cyc[1]++;
+ }
+ }
+ fprintf( trap_g, "%d ", weight );
+
+/*
+ for( i=0, count=0; i<strlen( aseq[s] ); i++ )
+ {
+ if( aseq[s][i] != '-' )
+ {
+ mseq1[count] = aseq[s][i];
+ count++;
+ }
+ }
+ mseq1[count] = 0;
+*/
+ gappick0( mseq1, aseq[s] );
+
+ if( checkC )
+ tmpscore = score_m_1_0( aseq, locnjob, s, eff, effarr );
+
+ gappick( locnjob, s, aseq, mseq2, eff, effarr );
+
+ result = align0( &wm, mseq2, mseq1, effarr, locnjob-2, s );
+ resultlen = strlen( result[0] );
+ if( resultlen > alloclen )
+ {
+ if( resultlen > nlenmax0*3 || resultlen > N )
+ {
+ fprintf(stderr, "Error in main1\n");
+ exit( 1 );
+ }
+ FreeTmpSeqs( mseq2, mseq1 );
+ alloclen = strlen( result[0] ) * 2.0;
+ fprintf( stderr, "\n\ntrying to allocate TmpSeqs\n\n" );
+ AllocateTmpSeqs( &mseq2, &mseq1, alloclen );
+ }
+ for( i=0; i<locnjob; i++ ) strcpy( mseq2[i], result[i] );
+
+ if( checkC )
+ fprintf( stderr, "wm in iteration == %f\n", wm );
+
+ strcpy( mseq1, mseq2[locnjob-1] );
+/*
+ Write( stdout, locnjob, name, nlen, mseq2 );
+*/
+ for( i=locnjob-2; i>=s; i-- ) strcpy( mseq2[i+1], mseq2[i] );
+ strcpy( mseq2[s], mseq1 );
+ if( checkC )
+ {
+ tmpscore1= score_m_1_0( mseq2, locnjob, s, eff, effarr );
+ fprintf( stderr, "pick up %d, before ALIGNM1 score_m_1_0 = %f\n", s+1, tmpscore );
+ fprintf( stderr, "pick up %d, after ALIGNM1 score_m_1_0 = %f\n", s+1, tmpscore1 );
+ if( tmpscore1 < tmpscore )
+ {
+ fprintf( stderr, "\7" );
+ fprintf( trap_g, ">>>>>>>n\n" );
+ }
+ if( fabs( wm - tmpscore1 ) / wm > 0.001 )
+ {
+ fprintf( stderr, "\7sorry\n" );
+ exit( 1 );
+ }
+ }
+
+ identity = !strcmp( mseq2[s], aseq[s] );
+ if( s == locnjob - 1 ) ss = 0; else ss=s+1;
+
+ identity *= !strcmp( mseq2[ss], aseq[ss] );
+
+ if( !identity )
+ {
+ tmpscore = score_calc0( mseq2, locnjob, eff, s );
+ }
+ else tmpscore = tscore;
+
+ if( disp )
+ {
+ fprintf( stderr, "% 3d % 3d / the rest \n", l+1, s+1 );
+ display( mseq2, locnjob );
+ }
+ fprintf( stderr, "% 3d % 3d / the rest \n", l+1, s+1 );
+ fprintf( stderr, "score = %f mscore = %f ", tmpscore, mscore );
+
+ fprintf( trap_g, "%#4d %#4d / the rest ", l+1, s+1 );
+ fprintf( trap_g, "score = %f mscore = %f ", tmpscore, mscore );
+
+ if( identity )
+ {
+ fprintf( stderr, "( identical )\n" );
+ fprintf( trap_g, "( identical )\n" );
+ sai[s] = 2;
+ }
+
+ else if( tmpscore > mscore - cut )
+ {
+ fprintf( stderr, "accepted\n" );
+ fprintf( trap_g, "accepted\n" );
+ for( i=0; i<locnjob; i++ ) strcpy( aseq[i], mseq2[i] );
+ strcpy( sai, sai1 ); /* kokoka ? */
+ if( !tbitr && !tbweight )
+ {
+ writePre( locnjob, name, nlen, aseq, 0 );
+ }
+ strcpy( sai, sai1 );
+ tscore = tmpscore;
+ /*
+ tscore = tmpscore = score_calc0( aseq, locnjob, eff, s ); * ? *
+ */
+ if( tmpscore > mscore )
+ {
+ for( i=0; i<locnjob; i++ ) strcpy( bseq[i], mseq2[i] );
+ treeconstruction( bseq, locnjob, topol, len, eff );
+ tscore = mscore = score_calc0( bseq, locnjob, eff, s );
+ fprintf( trap_g, " -> %f\n", mscore );
+ strcpy( sai, sai1 ); /* kokoka ? */
+#if 0
+ if( !tbitr && !tbweight )
+ { prep = fopen( "best", "w" );
+ Write( prep, locnjob, name, nlen, bseq );
+ fclose( prep );
+ }
+#endif
+ }
+ }
+
+ else
+ {
+ if( tmpscore == tscore )
+ {
+ fprintf( stderr, "occational coincidence \n" );
+ fprintf( trap_g, "occational coincidence\n" );
+ }
+ else
+ {
+ fprintf( stderr, "rejected\n" );
+ fprintf( trap_g, "rejected\n" );
+ }
+ for( i=0; i<locnjob; i++ ) strcpy( aseq[i], bseq[i] );
+ tscore = mscore;
+ sai[s] = 2;
+ }
+
+/*
+ prep = fopen( "cur", "w" );
+ Write( prep, locnjob, name, nlen, mseq2 );
+ fclose( prep );
+*/
+
+ his[ou][s][cyc[ou]] = tmpscore;
+ if( !strcmp( sai, sai2 ) )
+ {
+ returnvalue = 0;
+ fprintf( trap_g, "converged\n" );
+ break;
+ }
+ for( i=cyc[ou]-1; i>0; i-- )
+ {
+ if( tmpscore == his[ou][s][i] )
+ {
+ shindou = 1;
+ break;
+ }
+ }
+ fprintf( stderr, "\n" );
+ if( shindou == 1 )
+ {
+ returnvalue = -1;
+ fprintf( trap_g, "oscillating\n" );
+ break;
+ }
+ }
+ if( l == MAXITERATION ) returnvalue = -2;
+ FreeDoubleCub( his );
+ return( returnvalue );
+}
+
--- /dev/null
+#include "mltaln.h"
+#include "mtxutl.h"
+
+#define DEBUG 0
+#define TEST 0
+
+#define END_OF_VEC -1
+
+static int maxl;
+static int tsize;
+static char outputformat;
+static float lenfaca, lenfacb, lenfacc, lenfacd;
+#define PLENFACA 0.01
+#define PLENFACB 10000
+#define PLENFACC 10000
+#define PLENFACD 0.1
+#define DLENFACA 0.01
+#define DLENFACB 2500
+#define DLENFACC 2500
+#define DLENFACD 0.1
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ inputfile = NULL;
+ outputformat = 's';
+ scoremtx = 1;
+ nblosum = 62;
+ dorp = NOTSPECIFIED;
+ alg = 'X';
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'p':
+ outputformat = 'p';
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( inputfile == NULL )
+ {
+ argc--;
+ inputfile = *argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "Usage: mafft-distance [-PD] [-i inputfile] inputfile > outputfile\n" );
+ exit( 1 );
+ }
+}
+
+void seq_grp_nuc( int *grp, char *seq )
+{
+ int tmp;
+ int *grpbk = grp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 4 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+ if( grp - grpbk < 6 )
+ {
+ fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
+// exit( 1 );
+ *grpbk = -1;
+ }
+}
+
+void seq_grp( int *grp, char *seq )
+{
+ int tmp;
+ int *grpbk = grp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 6 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+ if( grp - grpbk < 6 )
+ {
+ fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
+// exit( 1 );
+ *grpbk = -1;
+ }
+}
+
+void makecompositiontable_p( short *table, int *pointt )
+{
+ int point;
+
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ table[point]++;
+}
+
+int commonsextet_p( short *table, int *pointt )
+{
+ int value = 0;
+ short tmp;
+ int point;
+ static short *memo = NULL;
+ static int *ct = NULL;
+ static int *cp;
+
+ if( *pointt == -1 )
+ return( 0 );
+
+ if( !memo )
+ {
+ memo = (short *)calloc( tsize, sizeof( short ) );
+ if( !memo ) ErrorExit( "Cannot allocate memo\n" );
+ ct = (int *)calloc( MIN( maxl, tsize)+1, sizeof( int ) );
+ if( !ct ) ErrorExit( "Cannot allocate memo\n" );
+ }
+
+ cp = ct;
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ {
+ tmp = memo[point]++;
+ if( tmp < table[point] )
+ value++;
+ if( tmp == 0 ) *cp++ = point;
+// fprintf( stderr, "cp - ct = %d (tsize = %d)\n", cp - ct, tsize );
+ }
+ *cp = END_OF_VEC;
+
+ cp = ct;
+ while( *cp != END_OF_VEC )
+ memo[*cp++] = 0;
+
+ return( value );
+}
+
+void makepointtable_nuc( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ if( *n == -1 )
+ {
+ *pointt = -1;
+ return;
+ }
+
+ p = n;
+ point = *n++ * 1024;
+ point += *n++ * 256;
+ point += *n++ * 64;
+ point += *n++ * 16;
+ point += *n++ * 4;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 1024;
+ point *= 4;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+void makepointtable( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ if( *n == -1 )
+ {
+ *pointt = -1;
+ return;
+ }
+
+ p = n;
+ point = *n++ * 7776;
+ point += *n++ * 1296;
+ point += *n++ * 216;
+ point += *n++ * 36;
+ point += *n++ * 6;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 7776;
+ point *= 6;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+int main( int argc, char **argv )
+{
+ int i, j, initj;
+ FILE *infp;
+ char **seq;
+ int *grpseq;
+ char *tmpseq;
+ int **pointt;
+ static char **name;
+ static int *nlen;
+ double *mtxself;
+ float score;
+ static short *table1;
+ float longer, shorter;
+ float lenfac;
+ float bunbo;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+#if 0
+ PreRead( stdin, &njob, &nlenmax );
+#else
+ getnumlen( infp );
+#endif
+ rewind( infp );
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ tmpseq = AllocateCharVec( nlenmax+1 );
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ grpseq = AllocateIntVec( nlenmax+1 );
+ pointt = AllocateIntMtx( njob, nlenmax+1 );
+ mtxself = AllocateDoubleVec( njob );
+ pamN = NOTSPECIFIED;
+ name = AllocateCharMtx( njob, B );
+ nlen = AllocateIntVec( njob );
+
+#if 0
+ FRead( infp, name, nlen, seq );
+#else
+ readData_pointer( infp, name, nlen, seq );
+#endif
+
+ fclose( infp );
+
+ constants( njob, seq );
+
+ if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
+ else tsize = (int)pow( 6, 6 );
+
+ if( dorp == 'd' )
+ {
+ lenfaca = DLENFACA;
+ lenfacb = DLENFACB;
+ lenfacc = DLENFACC;
+ lenfacd = DLENFACD;
+ }
+ else
+ {
+ lenfaca = PLENFACA;
+ lenfacb = PLENFACB;
+ lenfacc = PLENFACC;
+ lenfacd = PLENFACD;
+ }
+
+ maxl = 0;
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( tmpseq, seq[i] );
+ nlen[i] = strlen( tmpseq );
+// if( nlen[i] < 6 )
+// {
+// fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
+// exit( 1 );
+// }
+ if( nlen[i] > maxl ) maxl = nlen[i];
+ if( dorp == 'd' ) /* nuc */
+ {
+ seq_grp_nuc( grpseq, tmpseq );
+ makepointtable_nuc( pointt[i], grpseq );
+ }
+ else /* amino */
+ {
+ seq_grp( grpseq, tmpseq );
+ makepointtable( pointt[i], grpseq );
+ }
+ }
+ fprintf( stderr, "\nCalculating i-i scores ... " );
+ for( i=0; i<njob; i++ )
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ makecompositiontable_p( table1, pointt[i] );
+
+ score = commonsextet_p( table1, pointt[i] );
+ mtxself[i] = score;
+ free( table1 );
+ }
+
+ fprintf( stderr, "done.\n" );
+ fprintf( stderr, "\nCalculating i-j scores ... \n" );
+ if( outputformat == 'p' ) fprintf( stdout, "%-5d", njob );
+ for( i=0; i<njob; i++ )
+ {
+ if( outputformat == 'p' ) fprintf( stdout, "\n%-9d ", i+1 );
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "%4d / %4d\r", i+1, njob );
+ }
+ makecompositiontable_p( table1, pointt[i] );
+
+
+ if( outputformat == 'p' ) initj = 0;
+ else initj = i+1;
+ for( j=initj; j<njob; j++ )
+ {
+ if( nlen[i] > nlen[j] )
+ {
+ longer=(float)nlen[i];
+ shorter=(float)nlen[j];
+ }
+ else
+ {
+ longer=(float)nlen[j];
+ shorter=(float)nlen[i];
+ }
+// lenfac = 3.0 / ( LENFACA + LENFACB / ( longer + LENFACC ) + shorter / longer * LENFACD );
+ lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
+// lenfac = 1.0;
+// fprintf( stderr, "lenfac = %f (%.0f,%.0f)\n", lenfac, longer, shorter );
+ score = commonsextet_p( table1, pointt[j] );
+ bunbo = MIN( mtxself[i], mtxself[j] );
+ if( outputformat == 'p' )
+ {
+ if( bunbo == 0.0 )
+ fprintf( stdout, " %8.6f", 1.0 );
+ else
+ fprintf( stdout, " %8.6f", ( 1.0 - score / bunbo ) * lenfac );
+ if( j % 7 == 6 ) fprintf( stdout, "\n" );
+ }
+ else
+ {
+ if( bunbo == 0.0 )
+ fprintf( stdout, "%d-%d d=%4.2f l=%d,%d\n", i+1, j+1, 1.0, nlen[i], nlen[j] );
+ else
+ fprintf( stdout, "%d-%d d=%4.2f l=%d,%d\n", i+1, j+1, ( 1.0 - score / bunbo ) * lenfac, nlen[i], nlen[j] );
+ }
+// fprintf( stderr, "##### mtx = %f, mtx[i][0]=%f, mtx[j][0]=%f, bunbo=%f\n", mtx[i][j-i], mtx[i][0], mtx[j][0], bunbo );
+// score = (double)commonsextet_p( table1, pointt[j] );
+// fprintf( stdout, "%d-%d d=%4.2f l=%d,%d\n", i+1, j+1, ( 1.0 - score / MIN( mtxself[i], mtxself[j] ) ) * 3, nlen[i], nlen[j] );
+
+
+ }
+ free( table1 );
+ }
+
+ fprintf( stderr, "\n" );
+ if( outputformat == 'p' ) fprintf( stdout, "\n" );
+ SHOWVERSION;
+ exit( 0 );
+}
--- /dev/null
+.\" Title: MAFFT-HOMOLOGS
+.\" Author: Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
+.\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
+.\" Date: 2007-08-14
+.\" Manual: Mafft Manual
+.\" Source: mafft-homologs 2.1
+.\"
+.TH "MAFFT\-HOMOLOGS" "1" "2007\-06\-09" "mafft\-homologs 2.1" "Mafft Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+.RS 0
+mafft\-homologs \- aligns sequences together with homologues automatically collected from SwissProt via NCBI BLAST
+.RE
+.SH "SYNOPSIS"
+.RS 0
+\fBmafft\-homologs\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.SH "DESCRIPTION"
+.RS 0
+The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs. The reason for the improvement is probably the same as that for PSI\-BLAST. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs. According to Katoh et al. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences. Mafft\-homologs in a mafft server works like this:
+.sp
+.RS 4
+\h'-04' 1.\h'+02'Collect a number (50 by default) of close homologs (E=1e\-10 by default) of the input sequences.
+.RE
+.sp
+.RS 4
+\h'-04' 2.\h'+02'Align the input sequences and homologs all together using the L\-INS\-i strategy.
+.RE
+.sp
+.RS 4
+\h'-04' 3.\h'+02'Remove the homologs.
+.RE
+.RE
+.SH "OPTIONS"
+.RS 0
+.PP
+\fB\-a\fR \fI\fIn\fR\fR
+.RS 4
+The number of collected sequences (default: 50).
+.RE
+.PP
+\fB\-e\fR \fI\fIn\fR\fR
+.RS 4
+Threshold value (default: 1e\-10).
+.RE
+.PP
+\fB\-o\fR \fI\fIxxx\fR\fR
+.RS 4
+Options for mafft (default: " \-\-op 1.53 \-\-ep 0.123 \-\-maxiterate 1000 --localpair --reorder").
+.RE
+.PP
+\fB\-l\fR
+.RS 4
+Locally carries out BLAST searches instead of NCBI BLAST (requires locally installed BLAST and a database).
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+Outputs collected homologues also (default: off).
+.RE
+.PP
+\fB\-w\fR
+.RS 4
+entire sequences are subjected to BLAST search (default: well\-aligned region only)
+.RE
+.RE
+.SH "REQUIREMENTS"
+.RS 0
+.PP
+MAFFT version > 5.58.
+.PP
+Either of
+.RS 4
+.PP
+lynx (when remote BLAST server is used)
+.PP
+BLAST and a protein sequence database (when local BLAST is used)
+.RE
+.RE
+.SH "REFERENCES"
+.RS 0
+.PP
+Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment.
+.RE
+.SH "SEE ALSO"
+.RS 0
+.PP
+\fBmafft\fR(1)
+.RE
+.SH "AUTHORS"
+.RS 0
+.PP
+\fBKazutaka Katoh\fR <\&katoh_at_bioreg.kyushu\-u.ac.jp.\&>
+.sp -1n
+.IP "" 4
+Wrote Mafft.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.
+.RE
+.SH "COPYRIGHT"
+.RS 0
+Copyright \(co 2002\-2007 Kazutaka Katoh (mafft)
+.br
+Copyright \(co 2007 Charles Plessy (this manpage)
+.br
+.PP
+Mafft and its manpage are offered under the following conditions:
+.PP
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+.sp
+.RS 4
+\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+.RE
+.sp
+.RS 4
+\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+.RE
+.sp
+.RS 4
+\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.
+.RE
+.PP
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+.br
+.RE
--- /dev/null
+#!/usr/bin/env ruby
+
+localdb = "sp"
+# database name from which homologues are collected
+# by locally installed blast. Leave this if you do
+# not use the '-l' option.
+
+mafftpath = "_BINDIR/mafft"
+# path of mafft. "/usr/local/bin/mafft"
+# if mafft is in your command path, "mafft" is ok.
+
+blastpath = "blastall"
+# path of blastall.
+# if blastall is in your command path, "blastall" is ok.
+
+# mafft-homologs.rb v. 2.1 aligns sequences together with homologues
+# automatically collected from SwissProt via NCBI BLAST.
+#
+# mafft > 5.58 is required
+#
+# Usage:
+# mafft-homologs.rb [options] input > output
+# Options:
+# -a # the number of collected sequences (default: 50)
+# -e # threshold value (default: 1e-10)
+# -o "xxx" options for mafft
+# (default: " --op 1.53 --ep 0.123 --maxiterate 1000")
+# -l locally carries out blast searches instead of NCBI blast
+# (requires locally installed blast and a database)
+# -f outputs collected homologues also (default: off)
+# -w entire sequences are subjected to BLAST search
+# (default: well-aligned region only)
+
+require 'getopts'
+require 'tempfile'
+
+# mktemp
+GC.disable
+temp_vf = Tempfile.new("_vf").path
+temp_if = Tempfile.new("_if").path
+temp_pf = Tempfile.new("_pf").path
+temp_af = Tempfile.new("_af").path
+temp_qf = Tempfile.new("_qf").path
+temp_bf = Tempfile.new("_bf").path
+temp_rid = Tempfile.new("_rid").path
+temp_res = Tempfile.new("_res").path
+
+
+system( mafftpath + " --help > #{temp_vf} 2>&1" )
+pfp = File.open( "#{temp_vf}", 'r' )
+while pfp.gets
+ break if $_ =~ /MAFFT v/
+end
+pfp.close
+if( $_ ) then
+ mafftversion = sub( /^\D*/, "" ).split(" ").slice(0).strip.to_s
+else
+ mafftversion = "0"
+end
+if( mafftversion < "5.58" ) then
+ puts ""
+ puts "======================================================"
+ puts "Install new mafft (v. >= 5.58)"
+ puts "======================================================"
+ puts ""
+ exit
+end
+
+srand ( 0 )
+
+def readfasta( fp, name, seq )
+ nseq = 0
+ tmpseq = ""
+ while fp.gets
+ if $_ =~ /^>/ then
+ name.push( $_.sub(/>/,"").strip )
+ seq.push( tmpseq ) if nseq > 0
+ nseq += 1
+ tmpseq = ""
+ else
+ tmpseq += $_.strip
+ end
+ end
+ seq.push( tmpseq )
+ return nseq
+end
+
+nadd = 50
+eval = 1e-10
+local = 0
+fullout = 0
+entiresearch = 0
+corewin = 50
+corethr = 0.3
+mafftopt = " --op 1.53 --ep 0.123 --localpair --maxiterate 1000 --reorder "
+if getopts( "s", "f", "w", "l", "h", "e:", "a:", "o:", "c:", "d:" ) == nil || ARGV.length == 0 || $OPT_h then
+ puts "Usage: #{$0} [-h -l -e# -a# -o\"[options for mafft]\"] input_file"
+ exit
+end
+
+if $OPT_c then
+ corewin = $OPT_c.to_i
+end
+if $OPT_d then
+ corethr = $OPT_d.to_f
+end
+if $OPT_w
+ entiresearch = 1
+end
+if $OPT_f
+ fullout = 1
+end
+if $OPT_s
+ fullout = 0
+end
+if $OPT_l
+ local = 1
+end
+if $OPT_e then
+ eval = $OPT_e.to_f
+end
+if $OPT_a then
+ nadd = $OPT_a.to_i
+end
+if $OPT_o then
+ mafftopt += " " + $OPT_o + " "
+end
+
+system "cat " + ARGV.to_s + " > #{temp_if}"
+ar = mafftopt.split(" ")
+nar = ar.length
+for i in 0..(nar-1)
+ if ar[i] == "--seed" then
+ system "cat #{ar[i+1]} >> #{temp_if}"
+ end
+end
+
+nseq = 0
+ifp = File.open( "#{temp_if}", 'r' )
+ while ifp.gets
+ nseq += 1 if $_ =~ /^>/
+ end
+ifp.close
+
+if nseq >= 100 then
+ STDERR.puts "The number of input sequences must be <100."
+ exit
+elsif nseq == 1 then
+ system( "cp #{temp_if}" + " #{temp_pf}" )
+else
+ STDERR.puts "Performing preliminary alignment .. "
+ if entiresearch == 1 then
+# system( mafftpath + " --maxiterate 1000 --localpair #{temp_if} > #{temp_pf}" )
+ system( mafftpath + " --maxiterate 0 --retree 2 #{temp_if} > #{temp_pf}" )
+ else
+ system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} #{temp_if} > #{temp_pf}" )
+ end
+end
+
+pfp = File.open( "#{temp_pf}", 'r' )
+inname = []
+inseq = []
+slen = []
+act = []
+nin = 0
+nin = readfasta( pfp, inname, inseq )
+for i in 0..(nin-1)
+ slen.push( inseq[i].gsub(/-/,"").length )
+ act.push( 1 )
+end
+pfp.close
+
+pfp = File.open( "#{temp_if}", 'r' )
+orname = []
+orseq = []
+nin = 0
+nin = readfasta( pfp, orname, orseq )
+pfp.close
+
+allen = inseq[0].length
+for i in 0..(nin-2)
+ for j in (i+1)..(nin-1)
+ next if act[i] == 0
+ next if act[j] == 0
+ pid = 0.0
+ total = 0
+ for a in 0..(allen-1)
+ next if inseq[i][a,1] == "-" || inseq[j][a,1] == "-"
+ total += 1
+ pid += 1.0 if inseq[i][a,1] == inseq[j][a,1]
+ end
+ pid /= total
+# puts "#{i.to_s}, #{j.to_s}, #{pid.to_s}"
+ if pid > 0.5 then
+ if slen[i] < slen[j]
+ act[i] = 0
+ else
+ act[j] = 0
+ end
+ end
+ end
+end
+#p act
+
+
+afp = File.open( "#{temp_af}", 'w' )
+
+STDERR.puts "Searching .. \n"
+ids = []
+add = []
+sco = []
+for i in 0..(nin-1)
+ inseq[i].gsub!(/-/,"")
+ afp.puts ">" + orname[i]
+ afp.puts orseq[i]
+
+# afp.puts ">" + inname[i]
+# afp.puts inseq[i]
+
+ STDERR.puts "Query (#{i+1}/#{nin})\n" + inname[i]
+ if act[i] == 0 then
+ STDERR.puts "Skip.\n\n"
+ next
+ end
+
+ if local == 0 then
+ command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > #{temp_rid}"
+ system command
+
+ ridp = File.open( "#{temp_rid}", 'r' )
+ while ridp.gets
+ break if $_ =~ / RID = (.*)/
+ end
+ ridp.close
+ rid = $1.strip
+ STDERR.puts "Submitted to NCBI. rid = " + rid
+
+ STDERR.printf "Waiting "
+ while 1
+ STDERR.printf "."
+ sleep 10
+ command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > #{temp_res}"
+ system command
+ resp = File.open( "#{temp_res}", 'r' )
+# resp.gets
+# if $_ =~ /WAITING/ then
+# resp.close
+# next
+# end
+ while( resp.gets )
+ break if $_ =~ /QBlastInfoBegin/
+ end
+ resp.gets
+ if $_ =~ /WAITING/ then
+ resp.close
+ next
+ else
+ resp.close
+ break
+ end
+ end
+ else
+# puts "Not supported"
+# exit
+ qfp = File.open( "#{temp_qf}", 'w' )
+ qfp.puts "> "
+ qfp.puts inseq[i]
+ qfp.close
+ command = blastpath + " -p blastp -e #{eval} -b 1000 -m 7 -i #{temp_qf} -d #{localdb} > #{temp_res}"
+ system command
+ resp = File.open( "#{temp_res}", 'r' )
+ end
+ STDERR.puts " Done.\n\n"
+
+ resp = File.open( "#{temp_res}", 'r' )
+ while 1
+ while resp.gets
+ break if $_ =~ /<Hit_id>(.*)<\/Hit_id>/ || $_ =~ /(<Iteration_stat>)/
+ end
+ id = $1
+ break if $_ =~ /<Iteration_stat>/
+# p id
+ while resp.gets
+ break if $_ =~ /<Hsp_bit-score>(.*)<\/Hsp_bit-score>/
+ end
+ score = $1.to_f
+# p score
+
+ known = ids.index( id )
+ if known != nil then
+ if sco[known] >= score then
+ next
+ else
+ ids.delete_at( known )
+ add.delete_at( known )
+ sco.delete_at( known )
+ end
+ end
+ while resp.gets
+ break if $_ =~ /<Hsp_hseq>(.*)<\/Hsp_hseq>/
+ end
+# break if $1 == nil
+ target = $1.sub( /-/, "" ).sub( /U/, "X" )
+# p target
+# STDERR.puts "adding 1 seq"
+ ids.push( id )
+ sco.push( score )
+ add.push( target )
+ end
+ resp.close
+end
+
+n = ids.length
+
+outnum = 0
+while n > 0 && outnum < nadd
+ m = rand( n )
+ afp.puts ">_addedbymaffte_" + ids[m]
+ afp.puts add[m]
+ ids.delete_at( m )
+ add.delete_at( m )
+ n -= 1
+ outnum += 1
+end
+afp.close
+
+STDERR.puts "Performing alignment .. "
+system( mafftpath + mafftopt + " #{temp_af} > #{temp_bf}" )
+STDERR.puts "done."
+
+bfp = File.open( "#{temp_bf}", 'r' )
+outseq = []
+outnam = []
+readfasta( bfp, outnam, outseq )
+bfp.close
+
+outseq2 = []
+outnam2 = []
+
+len = outseq.length
+for i in 0..(len-1)
+# p outnam[i]
+ if fullout == 0 && outnam[i] =~ /_addedbymaffte_/ then
+ next
+ end
+ outseq2.push( outseq[i] )
+ outnam2.push( outnam[i].sub( /_addedbymaffte_/, "_ho_" ) )
+end
+
+nout = outseq2.length
+len = outseq[0].length
+p = len
+while p>0
+ p -= 1
+ allgap = 1
+ for j in 0..(nout-1)
+ if outseq2[j][p,1] != "-" then
+ allgap = 0
+ break
+ end
+ end
+ if allgap == 1 then
+ for j in 0..(nout-1)
+ outseq2[j][p,1] = ""
+ end
+ end
+end
+for i in 0..(nout-1)
+ puts ">" + outnam2[i]
+ puts outseq2[i].gsub( /.{1,60}/, "\\0\n" )
+end
+
+
+system( "rm -rf #{temp_if} #{temp_vf} #{temp_af} #{temp_bf} #{temp_pf} #{temp_qf} #{temp_res} #{temp_rid}" )
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+#if DEBUG
+#include <time.h>
+#include <sys/time.h>
+#include <sys/resource.h>
+double getrusage_sec()
+{
+ struct rusage t;
+ struct timeval tv;
+ getrusage(RUSAGE_SELF, &t);
+ tv = t.ru_utime;
+ return tv.tv_sec + (double)tv.tv_usec*1e-6;
+}
+#endif
+
+
+int intcmp( int *str1, int *str2 )
+{
+ while( *str1 != -1 && *str2 != -1 )
+ if( *str1++ != *str2++ ) return( 1 );
+ if( *str1 != *str2 ) return( 1 );
+ return( 0 );
+}
+
+char **arguments( int argc, char *argv[] )
+{
+ int c = 0;
+
+ fmodel = 0;
+ nblosum = 62;
+ calledByXced = 0;
+ devide = 0;
+ fftscore = 1;
+ use_fft = 1;
+ alg = 'A';
+ weight = 0;
+ utree = 1;
+ tbutree = 0;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 0;
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ scoremtx = 1;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = 0; // chokusetsu yobareru kara
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ TMorJTT = JTT;
+ treemethod = 'x';
+
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'N':
+ use_fft = 0;
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+ case 'Q':
+ alg = 'Q';
+ break;
+ case 'H':
+ alg = 'H';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'd':
+ disp = 1;
+ break;
+ case 'O':
+ outgap = 0;
+ break;
+ case 'a':
+ fmodel = 1;
+ break;
+ case 'u':
+ tbrweight = 0;
+ break;
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'Z':
+ checkC = 1;
+ break;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+ fprintf( stderr, "kappa = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+ fprintf( stderr, "blosum %d\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "tm %d\n", pamN );
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 2 )
+ {
+ fprintf( stderr, "options: Check source file ! %c ?\n", c );
+ exit( 1 );
+ }
+ fprintf( stderr, "tbitr = %d, tbrweight = %d, tbweight = %d\n", tbitr, tbrweight, tbweight );
+// readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
+ return( argv );
+
+}
+
+void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, double **len, double *eff, int alloclen )
+{
+ int i;
+ int clus1, clus2;
+ int s1, s2;
+ float pscore;
+ static char **name1, **name2;
+ double *effarr = eff;
+ double *effarr1 = NULL;
+ double *effarr2 = NULL;
+ static char *indication1, *indication2;
+ float dumfl = 0.0;
+ int intdum;
+#if DEBUG
+ double time1, time2;
+#endif
+
+
+// fprintf( stderr, "in GroupAlign fftWinSize = %d\n", fftWinSize );
+// fprintf( stderr, "in GroupAlign fftThreshold = %d\n", fftThreshold );
+
+ if( effarr1 == NULL )
+ {
+ name1 = AllocateCharMtx( nseq1, B );
+ name2 = AllocateCharMtx( nseq2, B );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+#if 0
+#else
+#endif
+ }
+
+ for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
+
+
+
+ s1 = 0;
+ s2 = nseq1;
+// fprintf( stdout, "nseq1 = %d\n", nseq1 );
+
+
+
+ clus1 = conjuctionforgaln( 0, nseq1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
+ clus2 = conjuctionforgaln( nseq1, njob, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
+/*
+ fprintf( stderr, "before align all\n" );
+ display( aseq, njob );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+ if( alg == 'Q' )
+ fprintf( stderr, "before realignment, score = %f\n", naiveQpairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
+ else if( alg == 'H' )
+ fprintf( stderr, "before realignment, score = %f\n", naivepairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
+
+ commongappick( nseq1, mseq1 );
+ commongappick( nseq2, mseq2 );
+
+
+#if DEBUG
+ time1 = getrusage_sec();
+ fprintf( stderr, "entering Falign\n" );
+#endif
+ if( use_fft )
+ {
+ if( alg == 'M' )
+ pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum );
+ else
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
+ }
+ else
+ {
+ if( alg == 'M' )
+ pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ else if( alg == 'H' )
+ pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ else if( alg == 'Q' )
+ pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ else
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+#if DEBUG
+ time2 = getrusage_sec();
+ fprintf( stdout, "### %d - %d, %f\n", clus1, clus2, time2-time1 );
+ fflush( stdout );
+#endif
+
+ if( alg == 'H' )
+ fprintf( stderr, "before realignment, score = %f\n", naivepairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
+ else if( alg == 'Q' )
+ fprintf( stderr, "after realignment, score = %f\n", naiveQpairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
+
+
+/*
+ fprintf( stderr, "after align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "after align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+ fprintf( stderr, "group-to-group %s /%s %f\n", indication1, indication2, pscore );
+ if( disp ) display( aseq, njob );
+ fprintf( stderr, "\n" );
+
+/*
+ trap = fopen( "pre", "r+" );
+ if( !trap ) ErrorExit( 1 );
+ WriteGapFill( trap, njob, name, nlen, aseq );
+ fclose( trap );
+ fprintf( stdout, "nseq1 = %d\n", nseq1 );
+*/
+}
+
+static void WriteOptions( FILE *fp )
+{
+ fprintf( fp, "tree-base method\n" );
+ if( tbweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbweight == 3 ) fprintf( fp, "reversely weighted\n" );
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );
+
+ if( scoremtx )
+ fprintf( fp, "Gap Penalty = %d, %d\n", penalty, offset );
+ else
+ fprintf( fp, "Gap Penalty = %d\n", penalty );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ char **argv2;
+ static int *nlen;
+ static char **name, **seq;
+ static char **seq1, **seq2;
+ static char **mseq1, **mseq2;
+ static char **aseq;
+ static char **bseq;
+ static double **pscore;
+ static double *eff;
+ int i, j, len1, len2;
+ static int ***topol;
+ static double **len;
+ FILE *gp1, *gp2;
+ char c;
+ int nlenmax1, nlenmax2, nseq1, nseq2;
+ int alloclen;
+
+ argv2 = arguments( argc, argv );
+
+ fprintf( stderr, "####### in galn\n" );
+
+ initFiles();
+
+ fprintf( stderr, "file1 = %s\n", argv2[0] );
+ fprintf( stderr, "file2 = %s\n", argv2[1] );
+
+ gp1 = fopen( argv2[0], "r" ); if( !gp1 ) ErrorExit( "cannot open file1" );
+ gp2 = fopen( argv2[1], "r" ); if( !gp2 ) ErrorExit( "cannot open file2" );
+
+#if 0
+ PreRead( gp1, &nseq1, &nlenmax1 );
+ PreRead( gp2, &nseq2, &nlenmax2 );
+#else
+ getnumlen( gp1 );
+ nseq1 = njob; nlenmax1 = nlenmax;
+ getnumlen( gp2 );
+ nseq2 = njob; nlenmax2 = nlenmax;
+#endif
+
+ njob = nseq1 + nseq2;
+ nlenmax = MAX( nlenmax1, nlenmax2 );
+
+ rewind( gp1 );
+ rewind( gp2 );
+
+
+ name = AllocateCharMtx( njob, B );
+ nlen = AllocateIntVec( njob );
+ seq1 = AllocateCharMtx( nseq1, nlenmax*3 );
+ seq2 = AllocateCharMtx( nseq2, nlenmax*3 );
+ seq = AllocateCharMtx( njob, 1 );
+ aseq = AllocateCharMtx( njob, nlenmax*3 );
+ bseq = AllocateCharMtx( njob, nlenmax*3 );
+ mseq1 = AllocateCharMtx( njob, 1 );
+ mseq2 = AllocateCharMtx( njob, 1 );
+ alloclen = nlenmax * 3;
+
+ topol = AllocateIntCub( njob, 2, njob );
+ len = AllocateDoubleMtx( njob, 2 );
+ pscore = AllocateDoubleMtx( njob, njob );
+ eff = AllocateDoubleVec( njob );
+
+#if 0
+ njob=nseq2; FRead( gp2, name+nseq1, nlen+nseq1, seq2 );
+ njob=nseq1; FRead( gp1, name, nlen, seq1 );
+#else
+ njob=nseq2; readDataforgaln( gp2, name+nseq1, nlen+nseq1, seq2 );
+ njob=nseq1; readDataforgaln( gp1, name, nlen, seq1 );
+#endif
+ njob = nseq1 + nseq2;
+
+
+#if 0 // CHUUI
+ commongappick( nseq1, seq1 );
+ commongappick( nseq2, seq2 );
+#endif
+
+ for( i=0; i<nseq1; i++ ) seq[i] = seq1[i];
+ for( i=nseq1; i<njob; i++ ) seq[i] = seq2[i-nseq1];
+/*
+ Write( stdout, njob, name, nlen, seq );
+*/
+
+ constants( njob, seq );
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illeagal character %c\n", c );
+ exit( 1 );
+ }
+ for( i=1; i<nseq1; i++ )
+ {
+ if( nlen[i] != nlen[0] )
+ ErrorExit( "group1 is not aligned." );
+ }
+ for( i=nseq1+1; i<njob; i++ )
+ {
+ if( nlen[i] != nlen[nseq1] )
+ ErrorExit( "group2 is not aligned." );
+ }
+ if( tbutree == 0 )
+ {
+ for( i=0; i<nseq1; i++ )
+ {
+ for( j=i+1; j<nseq1; j++ )
+ {
+ pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
+// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
+ }
+ for( j=nseq1; j<njob; j++ )
+ {
+ pscore[i][j] = 3.0;
+// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
+ }
+ }
+ for( i=nseq1; i<njob-1; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
+// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
+ }
+ }
+// fprintf( stderr, "\n" );
+
+
+ }
+ else
+ {
+ fprintf( stderr, "Not supported\n" );
+ exit( 1 );
+#if 0
+ prep = fopen( "hat2", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat2." );
+ readhat2( prep, njob, name, pscore );
+ fclose( prep );
+#endif
+ }
+ fprintf( stderr, "Constructing dendrogram ... " );
+ if( treemethod == 'x' )
+ veryfastsupg( njob, pscore, topol, len );
+ else
+ ErrorExit( "Incorrect tree\n" );
+ fprintf( stderr, "done.\n" );
+
+ if( tbrweight )
+ {
+ weight = 3;
+ counteff_simple( njob, topol, len, eff );
+// for( i=0; i<njob; i++ ) fprintf( stderr, "eff[%d] = %f\n", i, eff[i] );
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+ }
+
+ len1 = strlen( seq[0] );
+ len2 = strlen( seq[nseq1] );
+ if( len1 > 30000 || len2 > 30000 )
+ {
+ fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
+ alg = 'M';
+ }
+
+
+
+
+ GroupAlign( nseq1, nseq2, name, nlen, seq, aseq, mseq1, mseq2, topol, len, eff, alloclen );
+
+#if 0
+ writePre( njob, name, nlen, aseq, 1 );
+#else
+ writeDataforgaln( stdout, njob, name, nlen, aseq );
+#endif
+
+ SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+.\" Title: MAFFT
+.\" Author: Kazutaka Katoh <kazutaka.katoh@aist.go.jp>
+.\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
+.\" Date: 2007-08-14
+.\" Manual: Mafft Manual
+.\" Source: mafft 6.240
+.\"
+.TH "MAFFT" "1" "2007\-06\-09" "mafft 6.240" "Mafft Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "THIS MANUAL IS FOR V6.2XX (2007)"
+Recent versions (v6.8xx; 2010 Nov.) have more features than those described below.
+See also the tips page at
+http://mafft.cbrc.jp/alignment/software/tips0.html
+.SH "NAME"
+.RS 0
+.sp
+mafft \- Multiple alignment program for amino acid or nucleotide sequences
+.RE
+.SH "SYNOPSIS"
+.RS 0
+.HP 6
+\fBmafft\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 7
+\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 5
+\fBnwns\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBnwnsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 14
+\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR]
+.HP
+.sp
+\fIinput\fR, \fIgroup1\fR and \fIgroup2\fR must be in FASTA format.
+.RE
+.SH "DESCRIPTION"
+.RS 0
+\fBMAFFT\fR is a multiple sequence alignment program for unix\-like operating systems. It offers a range of multiple alignment methods.
+.SS "Accuracy\-oriented methods:"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'L\-INS\-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
+.HP 6
+\fBmafft\fR \fB\-\-localpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'G\-INS\-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
+.HP 6
+\fBmafft\fR \fB\-\-globalpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'E\-INS\-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
+.HP 6
+\fBmafft\fR \fB\-\-ep\fR\ \fI0\fR \fB\-\-genafpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.br
+
+For E\-INS\-i, the
+\fB\-\-ep\fR
+\fI0\fR
+option is recommended to allow large gaps.
+.RE
+.SS "Speed\-oriented methods:"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; two cycles only):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 7
+\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; max. 1000 iterations):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'FFT\-NS\-2 (fast; progressive method):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'FFT\-NS\-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'NW\-NS\-i (iterative refinement method without FFT approximation; two cycles only):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fB\-\-nofft\fR\ \fIinput\fR [>\ \fIoutput\fR]
+.HP 7
+\fBnwnsi\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'NW\-NS\-2 (fast; progressive method without the FFT approximation):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-nofft\fR\ \fIinput\fR [>\ \fIoutput\fR]
+.HP 6
+\fBnwns\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'NW\-NS\-PartTree\-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
+.HP 6
+\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-nofft\fR\ \fB\-\-parttree\fR \fIinput\fR [>\ \fIoutput\fR]
+.RE
+.SS "Group\-to\-group alignments"
+.HP 6
+.RS 4
+\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR]
+.sp
+or:
+.sp
+\fBmafft\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fB\-\-seed\fR\ \fIgroup1\fR \fB\-\-seed\fR\ \fIgroup2\fR /dev/null [>\ \fIoutput\fR]
+.RE
+.RE
+.RE
+.SH "OPTIONS"
+.SS "Algorithm"
+.RS 0
+.PP
+\fB\-\-auto\fR
+.RS 4
+Automatically selects an appropriate strategy from L\-INS\-i, FFT\-NS\-i and FFT\-NS\-2, according to data
+size. Default: off (always FFT\-NS\-2)
+.RE
+.PP
+\fB\-\-6merpair\fR
+.RS 4
+Distance is calculated based on the number of shared 6mers. Default: on
+.RE
+.PP
+\fB\-\-globalpair\fR
+.RS 4
+All pairwise alignments are computed with the Needleman\-Wunsch
+algorithm. More accurate but slower
+than \-\-6merpair. Suitable for a set of
+globally alignable sequences. Applicable to
+up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (G\-INS\-i). Default: off (6mer distance is used)
+.RE
+.PP
+\fB\-\-localpair\fR
+.RS 4
+All pairwise alignments are computed with the Smith\-Waterman
+algorithm. More accurate but slower
+than \-\-6merpair. Suitable for a set of
+locally alignable sequences. Applicable to
+up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (L\-INS\-i). Default: off (6mer distance is used)
+.RE
+.PP
+\fB\-\-genafpair\fR
+.RS 4
+All pairwise alignments are computed with a local
+algorithm with the generalized affine gap cost
+(Altschul 1998). More accurate but slower
+than \-\-6merpair. Suitable when large internal gaps
+are expected. Applicable to
+up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (E\-INS\-i). Default: off (6mer distance is used)
+.RE
+.\".PP
+.\"\fB\-\-fastswpair\fR
+.\".RS 4
+.\"Distance is calculated based on a FASTA alignment.
+.\"FASTA is required. Default: off (6mer distance is used)
+.\".RE
+.PP
+\fB\-\-fastapair\fR
+.RS 4
+All pairwise alignments are computed with FASTA (Pearson and Lipman 1988).
+FASTA is required. Default: off (6mer distance is used)
+.RE
+.\".PP
+.\"\fB\-\-blastpair\fR
+.\".RS 4
+.\"Distance is calculated based on a BLAST alignment. BLAST is
+.\"required. Default: off (6mer distance is used)
+.\".RE
+.PP
+\fB\-\-weighti\fR \fInumber\fR
+.RS 4
+Weighting factor for the consistency term calculated from pairwise alignments. Valid when
+either of \-\-globalpair, \-\-localpair, \-\-genafpair, \-\-fastapair or
+\-\-blastpair is selected. Default: 2.7
+.RE
+.PP
+\fB\-\-retree\fR \fInumber\fR
+.RS 4
+Guide tree is built \fInumber\fR times in the
+progressive stage. Valid with 6mer distance. Default: 2
+.RE
+.PP
+\fB\-\-maxiterate\fR \fInumber\fR
+.RS 4
+\fInumber\fR cycles of iterative refinement are performed. Default: 0
+.RE
+.PP
+\fB\-\-fft\fR
+.RS 4
+Use FFT approximation in group\-to\-group alignment. Default: on
+.RE
+.PP
+\fB\-\-nofft\fR
+.RS 4
+Do not use FFT approximation in group\-to\-group alignment. Default: off
+.RE
+.PP
+\fB\-\-noscore\fR
+.RS 4
+Alignment score is not checked in the iterative refinement stage. Default: off (score is checked)
+.RE
+.PP
+\fB\-\-memsave\fR
+.RS 4
+Use the Myers\-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt).
+.RE
+.PP
+\fB\-\-parttree\fR
+.RS 4
+Use a fast tree\-building method (PartTree, Katoh and Toh 2007) with
+the 6mer distance. Recommended for a large number (> ~10,000)
+of sequences are input. Default: off
+.RE
+.PP
+\fB\-\-dpparttree\fR
+.RS 4
+The PartTree algorithm is used with distances based on DP. Slightly
+more accurate and slower than \-\-parttree. Recommended for a large
+number (> ~10,000) of sequences are input. Default: off
+.RE
+.PP
+\fB\-\-fastaparttree\fR
+.RS 4
+The PartTree algorithm is used with distances based on FASTA. Slightly more accurate and slower than \-\-parttree. Recommended for a large number (> ~10,000) of sequences are input. FASTA is required. Default: off
+.RE
+.PP
+\fB\-\-partsize\fR \fInumber\fR
+.RS 4
+The number of partitions in the PartTree algorithm. Default: 50
+.RE
+.PP
+\fB\-\-groupsize\fR \fInumber\fR
+.RS 4
+Do not make alignment larger than \fInumber\fR sequences. Valid only with the \-\-*parttree options. Default: the number of input sequences
+.RE
+.RE
+.SS "Parameter"
+.RS 0
+.PP
+\fB\-\-op\fR \fInumber\fR
+.RS 4
+Gap opening penalty at group\-to\-group alignment. Default: 1.53
+.RE
+.PP
+\fB\-\-ep\fR \fInumber\fR
+.RS 4
+Offset value, which works like gap extension penalty, for
+group\-to\-group alignment. Default: 0.123
+.RE
+.PP
+\fB\-\-lop\fR \fInumber\fR
+.RS 4
+Gap opening penalty at local pairwise
+alignment. Valid when
+the \-\-localpair or \-\-genafpair option is selected. Default: \-2.00
+.RE
+.PP
+\fB\-\-lep\fR \fInumber\fR
+.RS 4
+Offset value at local pairwise alignment. Valid when
+the \-\-localpair or \-\-genafpair option is selected. Default: 0.1
+.RE
+.PP
+\fB\-\-lexp\fR \fInumber\fR
+.RS 4
+Gap extension penalty at local pairwise alignment. Valid when
+the \-\-localpair or \-\-genafpair option is selected. Default: \-0.1
+.RE
+.PP
+\fB\-\-LOP\fR \fInumber\fR
+.RS 4
+Gap opening penalty to skip the alignment. Valid when the
+\-\-genafpair option is selected. Default: \-6.00
+.RE
+.PP
+\fB\-\-LEXP\fR \fInumber\fR
+.RS 4
+Gap extension penalty to skip the alignment. Valid when the
+\-\-genafpair option is selected. Default: 0.00
+.RE
+.PP
+\fB\-\-bl\fR \fInumber\fR
+.RS 4
+BLOSUM \fInumber\fR matrix (Henikoff and Henikoff 1992) is used. \fInumber\fR=30, 45, 62 or 80. Default: 62
+.RE
+.PP
+\fB\-\-jtt\fR \fInumber\fR
+.RS 4
+JTT PAM \fInumber\fR (Jones et al. 1992) matrix is used. \fInumber\fR>0. Default: BLOSUM62
+.RE
+.PP
+\fB\-\-tm\fR \fInumber\fR
+.RS 4
+Transmembrane PAM \fInumber\fR (Jones et al. 1994) matrix is used. \fInumber\fR>0. Default: BLOSUM62
+.RE
+.PP
+\fB\-\-aamatrix\fR \fImatrixfile\fR
+.RS 4
+Use a user\-defined AA scoring matrix. The format of \fImatrixfile\fR is
+the same to that of BLAST. Ignored when nucleotide sequences are input. Default: BLOSUM62
+.RE
+.PP
+\fB\-\-fmodel\fR
+.RS 4
+Incorporate the AA/nuc composition information into
+the scoring matrix. Default: off
+.RE
+.RE
+.SS "Output"
+.RS 0
+.PP
+\fB\-\-clustalout\fR
+.RS 4
+Output format: clustal format. Default: off (fasta format)
+.RE
+.PP
+\fB\-\-inputorder\fR
+.RS 4
+Output order: same as input. Default: on
+.RE
+.PP
+\fB\-\-reorder\fR
+.RS 4
+Output order: aligned. Default: off (inputorder)
+.RE
+.PP
+\fB\-\-treeout\fR
+.RS 4
+Guide tree is output to the \fIinput\fR.tree file. Default: off
+.RE
+.PP
+\fB\-\-quiet\fR
+.RS 4
+Do not report progress. Default: off
+.RE
+.RE
+.SS "Input"
+.RS 0
+.PP
+\fB\-\-nuc\fR
+.RS 4
+Assume the sequences are nucleotide. Default: auto
+.RE
+.PP
+\fB\-\-amino\fR
+.RS 4
+Assume the sequences are amino acid. Default: auto
+.RE
+.PP
+\fB\-\-seed\fR \fIalignment1\fR [\fB--seed\fR \fIalignment2\fR \fB--seed\fR \fIalignment3\fR ...]
+.RS 4
+Seed alignments given in \fIalignment_n\fR (fasta format) are aligned with
+sequences in \fIinput\fR. The alignment within every seed is preserved.
+.RE
+.RE
+.SH "FILES"
+.RS 0
+.PP
+Mafft stores the input sequences and other files in a temporary directory, which by default is located in
+\fI/tmp\fR.
+.RE
+.SH "ENVIONMENT"
+.RS 0
+.PP
+\fBMAFFT_BINARIES\fR
+.RS 4
+Indicates the location of the binary files used by mafft. By default, they are searched in
+\fI/usr/local/lib/mafft\fR, but on Debian systems, they are searched in
+\fI/usr/lib/mafft\fR.
+.RE
+.PP
+\fBFASTA_4_MAFFT\fR
+.RS 4
+This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH.
+.RE
+.RE
+.SH "SEE ALSO"
+.RS 0
+.PP
+
+\fBmafft\-homologs\fR(1)
+.RE
+.SH "REFERENCES"
+.RS 0
+.SS "In English"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh and Toh (Bioinformatics 23:372\-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm).
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G\-INS\-i, L\-INS\-i and E\-INS\-i strategies)
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res. 30:3059\-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT\-NS\-1, FFT\-NS\-2 and FFT\-NS\-i strategies)
+.RE
+.SS "In Japanese"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh and Misawa (Seibutsubutsuri 46:312\-317, 2006) Multiple Sequence Alignments: the Next Generation
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Katoh and Kuma (Kagaku to Seibutsu 44:102\-108, 2006) Jissen\-teki Multiple Alignment
+.RE
+.RE
+.SH "AUTHORS"
+.RS 0
+.PP
+\fBKazutaka Katoh\fR <\&kazutaka.katoh_at_aist.go.jp\&>
+.sp -1n
+.IP "" 4
+Wrote Mafft.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam_at_plessy.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.
+.RE
+.SH "COPYRIGHT"
+.RS 0
+Copyright \(co 2002\-2007 Kazutaka Katoh (mafft)
+.br
+Copyright \(co 2007 Charles Plessy (this manpage)
+.br
+.PP
+Mafft and its manpage are offered under the following conditions:
+.PP
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+.sp
+.RS 4
+\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+.RE
+.sp
+.RS 4
+\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+.RE
+.sp
+.RS 4
+\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.
+.RE
+.PP
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+.br
+.RE
--- /dev/null
+@echo off\r
+\r
+setlocal\r
+\r
+if not "x%PROCESSOR_ARCHITECTURE%" == "xAMD64" goto _NotX64\r
+set COMSPEC=%WINDIR%\SysWOW64\cmd.exe\r
+%COMSPEC% /c %0 %*\r
+goto EOF\r
+:_NotX64\r
+\r
+set ROOTDIR="%~d0%~p0\ms"\r
+set PATH=/bin/\r
+set MAFFT_BINARIES=/lib/mafft\r
+\r
+%ROOTDIR%\bin\sh %ROOTDIR%\bin\mafft %*\r
+\r
+:EOF\r
--- /dev/null
+#! /bin/sh
+
+
+er=0;
+myself=`dirname "$0"`/`basename "$0"`; export myself
+version="v6.857b (2011/05/30)"; export version
+LANG=C; export LANG
+os=`uname`
+progname=`basename "$0"`
+if [ `echo $os | grep -i cygwin` ]; then
+ os="cygwin"
+elif [ `echo $os | grep -i darwin` ]; then
+ os="darwin"
+elif [ `echo $os | grep -i sunos` ]; then
+ os="sunos"
+elif [ `echo $os | grep -i linux` ]; then
+ os="linux"
+else
+ os="unix"
+fi
+export os
+
+if [ "$MAFFT_BINARIES" ]; then
+ prefix="$MAFFT_BINARIES"
+else
+ prefix=_LIBDIR
+fi
+export prefix
+
+if [ $# -gt 0 ]; then
+ if [ "$1" = "--man" ]; then
+ man "$prefix/mafft.1"
+ exit 0;
+ fi
+fi
+
+if [ ! -x "$prefix/tbfast" ]; then
+ echo "" 1>&2
+ echo "correctly installed?" 1>&2
+ echo "mafft binaries have to be installed in \$MAFFT_BINARIES" 1>&2
+ echo "or the $prefix directory". 1>&2
+ echo "" 1>&2
+ exit 1
+ er=1
+fi
+
+defaultiterate=0
+defaultcycle=2
+defaultgop="1.53"
+#defaultaof="0.123"
+defaultaof="0.000"
+defaultlaof="0.100"
+defaultlgop="-2.00"
+defaultfft=1
+defaultrough=0
+defaultdistance="sixtuples"
+#defaultdistance="local"
+defaultweighti="2.7"
+defaultweightr="0.0"
+defaultweightm="1.0"
+defaultmccaskill=0
+defaultcontrafold=0
+defaultalgopt=" "
+defaultalgoptit=" "
+defaultsbstmodel=" -b 62 "
+defaultfmodel=" "
+defaultkappa=" "
+if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
+ defaultfft=1
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="scarna"
+ defaultweighti="3.2"
+ defaultweightr="8.0"
+ defaultweightm="2.0"
+ defaultmccaskill=1
+ defaultcontrafold=0
+ defaultalgopt=" -A "
+ defaultalgoptit=" -AB " ## chui
+ defaultaof="0.0"
+ defaultsbstmodel=" -b 62 "
+ defaultkappa=" "
+ defaultfmodel=" -a "
+elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
+ defaultfft=1
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="global"
+ defaultweighti="3.2"
+ defaultweightr="8.0"
+ defaultweightm="2.0"
+ defaultmccaskill=1
+ defaultcontrafold=0
+ defaultalgopt=" -A "
+ defaultalgoptit=" -AB " ## chui
+ defaultaof="0.0"
+ defaultsbstmodel=" -b 62 "
+ defaultkappa=" "
+ defaultfmodel=" -a "
+elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
+ defaultfft=0
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="local"
+elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
+ defaultfft=1
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="global"
+elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
+ defaultfft=0
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="localgenaf"
+elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
+ defaultfft=1
+ defaultcycle=2
+ defaultdistance="sixtuples"
+elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
+ defaultfft=1
+ defaultcycle=2
+ defaultiterate=2
+ defaultdistance="sixtuples"
+elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
+ defaultfft=0
+ defaultcycle=2
+ defaultdistance="sixtuples"
+elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
+ defaultfft=0
+ defaultcycle=2
+ defaultiterate=2
+ defaultdistance="sixtuples"
+fi
+outputfile=""
+namelength=15
+anysymbol=0
+parallelizationstrategy="BAATARI2"
+kappa=$defaultkappa
+sbstmodel=$defaultsbstmodel
+fmodel=$defaultfmodel
+gop=$defaultgop
+aof=$defaultaof
+cycle=$defaultcycle
+iterate=$defaultiterate
+fft=$defaultfft
+rough=$defaultrough
+distance=$defaultdistance
+forcefft=0
+memopt=" "
+weightopt=" "
+GGOP="-6.00"
+LGOP="-6.00"
+LEXP="-0.000"
+GEXP="-0.000"
+lgop=$defaultlgop
+lexp="-0.100"
+laof=$defaultlaof
+pggop="-2.00"
+pgexp="-0.10"
+pgaof="0.10"
+rgop="-1.530"
+rgep="-0.000"
+seqtype=" "
+weighti=$defaultweighti
+weightr=$defaultweightr
+weightm=$defaultweightm
+rnaalifold=0
+mccaskill=$defaultmccaskill
+contrafold=$defaultcontrafold
+quiet=0
+debug=0
+sw=0
+algopt=$defaultalgopt
+algoptit=$defaultalgoptit
+scorecalcopt=" "
+coreout=0
+corethr="0.5"
+corewin="100"
+coreext=" "
+outputformat="pir"
+outorder="input"
+seed="x"
+seedtable="x"
+auto=0
+groupsize=-1
+partsize=50
+partdist="sixtuples"
+partorderopt=" -x "
+treeout=0
+distout=0
+treein=0
+topin=0
+treeinopt=" "
+seedfiles="/dev/null"
+seedtablefile="/dev/null"
+aamatrix="/dev/null"
+treeinfile="/dev/null"
+rnascoremtx=" "
+laraparams="/dev/null"
+foldalignopt=" "
+treealg=" -X "
+scoreoutarg=" "
+numthreads=0
+randomseed=0
+addfile="/dev/null"
+addarg0=" "
+outnum=" "
+if [ $# -gt 0 ]; then
+ while [ $# -gt 1 ];
+ do
+ if [ "$1" = "--auto" ]; then
+ auto=1
+ elif [ "$1" = "--anysymbol" ]; then
+ anysymbol=1
+ elif [ "$1" = "--preservecase" ]; then
+ anysymbol=1
+ elif [ "$1" = "--clustalout" ]; then
+ outputformat="clustal"
+ elif [ "$1" = "--phylipout" ]; then
+ outputformat="phylip"
+ elif [ "$1" = "--reorder" ]; then
+ outorder="aligned"
+ partorderopt=" "
+ elif [ "$1" = "--inputorder" ]; then
+ outorder="input"
+ partorderopt=" -x "
+ elif [ "$1" = "--unweight" ]; then
+ weightopt=" -u "
+ elif [ "$1" = "--algq" ]; then
+ algopt=" -Q "
+ algoptit=" -QB "
+ elif [ "$1" = "--namelength" ]; then
+ shift
+ namelength=`expr "$1" - 0`
+ elif [ "$1" = "--groupsize" ]; then
+ shift
+ groupsize=`expr "$1" - 0`
+ elif [ "$1" = "--partsize" ]; then
+ shift
+ partsize=`expr "$1" - 0`
+ elif [ "$1" = "--parttree" ]; then
+ distance="parttree"
+ partdist="sixtuples"
+ elif [ "$1" = "--dpparttree" ]; then
+ distance="parttree"
+ partdist="localalign"
+ elif [ "$1" = "--fastaparttree" ]; then
+ distance="parttree"
+ partdist="fasta"
+ elif [ "$1" = "--treeout" ]; then
+ treeout=1
+ elif [ "$1" = "--distout" ]; then
+ distout=1
+ elif [ "$1" = "--fastswpair" ]; then
+ distance="fasta"
+ sw=1
+ elif [ "$1" = "--fastapair" ]; then
+ distance="fasta"
+ sw=0
+ elif [ "$1" = "--averagelinkage" ]; then
+ treealg=" -E "
+ elif [ "$1" = "--minimumlinkage" ]; then
+ treealg=" -q "
+ elif [ "$1" = "--noscore" ]; then
+ scorecalcopt=" -Z "
+ elif [ "$1" = "--6merpair" ]; then
+ distance="sixtuples"
+ elif [ "$1" = "--blastpair" ]; then
+ distance="blast"
+ elif [ "$1" = "--globalpair" ]; then
+ distance="global"
+ elif [ "$1" = "--localpair" ]; then
+ distance="local"
+ elif [ "$1" = "--scarnapair" ]; then
+ distance="scarna"
+ elif [ "$1" = "--larapair" ]; then
+ distance="lara"
+ elif [ "$1" = "--slarapair" ]; then
+ distance="slara"
+ elif [ "$1" = "--foldalignpair" ]; then
+ distance="foldalignlocal"
+ elif [ "$1" = "--foldalignlocalpair" ]; then
+ distance="foldalignlocal"
+ elif [ "$1" = "--foldalignglobalpair" ]; then
+ distance="foldalignglobal"
+ elif [ "$1" = "--globalgenafpair" ]; then
+ distance="globalgenaf"
+ elif [ "$1" = "--localgenafpair" ]; then
+ distance="localgenaf"
+ elif [ "$1" = "--genafpair" ]; then
+ distance="localgenaf"
+ elif [ "$1" = "--memsave" ]; then
+ memopt=" -M -B " # -B (bunkatsunashi no riyu ga omoidasenai)
+ elif [ "$1" = "--nomemsave" ]; then
+ memopt=" -N "
+ elif [ "$1" = "--nuc" ]; then
+ seqtype=" -D "
+ elif [ "$1" = "--amino" ]; then
+ seqtype=" -P "
+ elif [ "$1" = "--fft" ]; then
+ fft=1
+ forcefft=1
+ elif [ "$1" = "--nofft" ]; then
+ fft=0
+ elif [ "$1" = "--quiet" ]; then
+ quiet=1
+ elif [ "$1" = "--debug" ]; then
+ debug=1
+ elif [ "$1" = "--coreext" ]; then
+ coreext=" -c "
+ elif [ "$1" = "--core" ]; then
+ coreout=1
+ elif [ "$1" = "--out" ]; then
+ shift
+ outputfile="$1"
+ elif [ "$1" = "--thread" ]; then
+ shift
+ numthreads=`expr "$1" - 0`
+ elif [ "$1" = "--randomseed" ]; then
+ shift
+ randomseed=`expr "$1" - 0`
+ elif [ "$1" = "--bestfirst" ]; then
+ parallelizationstrategy="BESTFIRST"
+ elif [ "$1" = "--adhoc0" ]; then
+ parallelizationstrategy="BAATARI0"
+ elif [ "$1" = "--adhoc1" ]; then
+ parallelizationstrategy="BAATARI1"
+ elif [ "$1" = "--adhoc2" ]; then
+ parallelizationstrategy="BAATARI2"
+ elif [ "$1" = "--simplehillclimbing" ]; then
+ parallelizationstrategy="BAATARI2"
+ elif [ "$1" = "--scoreout" ]; then
+ scoreoutarg="-S -B"
+ elif [ "$1" = "--outnum" ]; then
+ scoreoutarg="-n"
+ elif [ "$1" = "--addprofile" ]; then
+ shift
+ addarg0="-I"
+ addfile="$1"
+ elif [ "$1" = "--add" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
+ elif [ "$1" = "--maxiterate" ]; then
+ shift
+ iterate=`expr "$1" - 0`
+ elif [ "$1" = "--retree" ]; then
+ shift
+ cycle=`expr "$1" - 0`
+ elif [ "$1" = "--aamatrix" ]; then
+ shift
+ sbstmodel=" -b -1 "
+ aamatrix="$1"
+ elif [ "$1" = "--treein" ]; then
+ shift
+ treeinopt=" -U "
+ treein=1
+ treeinfile="$1"
+ elif [ "$1" = "--topin" ]; then
+ shift
+ treeinopt=" -V "
+ treein=1
+ treeinfile="$1"
+ echo "The --topin option has been disabled." 1>&2
+ echo "There was a bug in version < 6.530." 1>&2
+ echo "This bug has not yet been fixed." 1>&2
+ exit 1
+ elif [ "$1" = "--kappa" ]; then
+ shift
+ kappa=" -k $1 "
+ elif [ "$1" = "--fmodel" ]; then
+ fmodel=" -a "
+ elif [ "$1" = "--jtt" ]; then
+ shift
+ sbstmodel=" -j $1"
+ elif [ "$1" = "--kimura" ]; then
+ shift
+ sbstmodel=" -j $1"
+ elif [ "$1" = "--tm" ]; then
+ shift
+ sbstmodel=" -m $1"
+ elif [ "$1" = "--bl" ]; then
+ shift
+ sbstmodel=" -b $1"
+ elif [ "$1" = "--weighti" ]; then
+ shift
+ weighti="$1"
+ elif [ "$1" = "--weightr" ]; then
+ shift
+ weightr="$1"
+ elif [ "$1" = "--weightm" ]; then
+ shift
+ weightm="$1"
+ elif [ "$1" = "--rnaalifold" ]; then
+ rnaalifold=1
+ elif [ "$1" = "--mccaskill" ]; then
+ mccaskill=1
+ contrafold=0
+ elif [ "$1" = "--contrafold" ]; then
+ mccaskill=0
+ contrafold=1
+ elif [ "$1" = "--ribosum" ]; then
+ rnascoremtx=" -s "
+ elif [ "$1" = "--op" ]; then
+ shift
+ gop="$1"
+ elif [ "$1" = "--ep" ]; then
+ shift
+ aof="$1"
+ elif [ "$1" = "--rop" ]; then
+ shift
+ rgop="$1"
+ elif [ "$1" = "--rep" ]; then
+ shift
+ rgep="$1"
+ elif [ "$1" = "--lop" ]; then
+ shift
+ lgop="$1"
+ elif [ "$1" = "--LOP" ]; then
+ shift
+ LGOP="$1"
+ elif [ "$1" = "--lep" ]; then
+ shift
+ laof="$1"
+ elif [ "$1" = "--lexp" ]; then
+ shift
+ lexp="$1"
+ elif [ "$1" = "--LEXP" ]; then
+ shift
+ LEXP="$1"
+ elif [ "$1" = "--GEXP" ]; then
+ shift
+ GEXP="$1"
+ elif [ "$1" = "--GOP" ]; then
+ shift
+ GGOP="$1"
+ elif [ "$1" = "--gop" ]; then
+ shift
+ pggop="$1"
+ elif [ "$1" = "--gep" ]; then
+ shift
+ pgaof="$1"
+ elif [ "$1" = "--gexp" ]; then
+ shift
+ pgexp="$1"
+ elif [ "$1" = "--laraparams" ]; then
+ shift
+ laraparams="$1"
+ elif [ "$1" = "--corethr" ]; then
+ shift
+ corethr="$1"
+ elif [ "$1" = "--corewin" ]; then
+ shift
+ corewin="$1"
+ elif [ "$1" = "--seedtable" ]; then
+ shift
+ seedtable="y"
+ seedtablefile="$1"
+ elif [ "$1" = "--seed" ]; then
+ shift
+ seed="m"
+ seedfiles="$seedfiles $1"
+ elif [ $progname = "fftns" -o $progname = "nwns" ]; then
+ if [ "$1" -gt 0 ]; then
+ cycle=`expr "$1" - 0`
+ fi
+ else
+ echo "Unknown option: $1" 1>&2
+ er=1;
+ fi
+ shift
+ done;
+
+
+
+# TMPFILE=/tmp/$progname.$$
+ TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`
+ if [ $? -ne 0 ]; then
+ echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
+ TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX`
+ fi
+ umask 077
+# mkdir $TMPFILE || er=1
+ if [ $debug -eq 1 ]; then
+ trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0
+ else
+ trap "rm -rf $TMPFILE " 0
+ fi
+ if [ $# -eq 1 ]; then
+ if [ -r "$1" -o "$1" = - ]; then
+
+ if [ -r "$addfile" ]; then
+ printf '';
+ else
+ echo "$0": Cannot open "$addfile". 1>&2
+ exit 1;
+ fi
+
+ cat "$1" | tr "\r" "\n" > $TMPFILE/infile
+ echo "" >> $TMPFILE/infile
+ cat "$addfile" | tr "\r" "\n" | grep -v "^$" >> $TMPFILE/infile
+ cat "$addfile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_addfile
+ cat "$aamatrix" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_aamtx
+ cat "$treeinfile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_guidetree
+ cat "$seedtablefile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_seedtablefile
+ cat "$laraparams" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_lara.params
+# echo $seedfiles
+ infilename="$1"
+ seedfilesintmp="/dev/null"
+ seednseq="0"
+ set $seedfiles > /dev/null
+ while [ $# -gt 1 ];
+ do
+ shift
+ if [ -r "$1" ]; then
+ cat "$1" | tr "\r" "\n" > $TMPFILE/seed$#
+ else
+ echo "$0": Cannot open "$1". 1>&2
+ exit 1;
+ fi
+ seednseq=$seednseq" "`grep -c '^[>|=]' $TMPFILE/seed$#`
+ seedfilesintmp=$seedfilesintmp" "seed$#
+ done
+# ls $TMPFILE
+# echo $seedfilesintmp
+# echo $seednseq
+
+
+ else
+ echo "$0": Cannot open "$1". 1>&2
+ er=1
+# exit 1;
+ fi
+ else
+ echo '$#'"=$#" 1>&2
+ er=1
+ fi
+
+
+ if [ $os != "linux" ]; then
+ numthreads=0
+ fi
+
+ if [ $numthreads -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
+ echo 'Impossible' 1>&2;
+ exit 1;
+ fi
+
+ if [ $auto -eq 1 ]; then
+ "$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size
+ nseq=`awk '{print $1}' $TMPFILE/size`
+ nlen=`awk '{print $3}' $TMPFILE/size`
+ if [ $nlen -lt 2000 -a $nseq -lt 100 ]; then
+ distance="local"
+ iterate=1000
+ elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
+ distance="sixtuples"
+ iterate=2
+ else
+ distance="sixtuples"
+ iterate=0
+ fi
+ if [ $quiet -eq 0 ]; then
+ echo "nseq = " $nseq 1>&2
+ echo "nlen = " $nlen 1>&2
+ echo "distance = " $distance 1>&2
+ echo "iterate = " $iterate 1>&2
+ fi
+ fi
+
+ if [ $parallelizationstrategy = "BESTFIRST" -o $parallelizationstrategy = "BAATARI0" ]; then
+ iteratelimit=254
+ else
+ iteratelimit=16
+ fi
+ if [ $iterate -gt $iteratelimit ]; then #??
+ iterate=$iteratelimit
+ fi
+
+ if [ $rnaalifold -eq 1 ]; then
+ rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx "
+# rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R "
+ rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R "
+ elif [ $mccaskill -eq 1 -o $contrafold -eq 1 ]; then
+ rnaopt=" -o $rgop -c $weightm -r $weightr "
+# rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx "
+ rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx "
+ else
+ rnaopt=" "
+ rnaoptit=" -F "
+ fi
+
+ model="$sbstmodel $kappa $fmodel"
+
+ if [ $er -eq 1 ]; then
+ echo "------------------------------------------------------------------------------" 1>&2
+ echo " MAFFT" $version 1>&2
+# echo "" 1>&2
+# echo " Input format: fasta" 1>&2
+# echo "" 1>&2
+# echo " Usage: `basename $0` [options] inputfile > outputfile" 1>&2
+ echo " http://mafft.cbrc.jp/alignment/software/" 1>&2
+ echo " NAR 30:3059-3066 (2002), Briefings in Bioinformatics 9:286-298 (2008)" 1>&2
+# echo "------------------------------------------------------------------------------" 1>&2
+# echo " % mafft in > out" 1>&2
+ echo "------------------------------------------------------------------------------" 1>&2
+# echo "" 1>&2
+ echo "High speed:" 1>&2
+ echo " % mafft in > out" 1>&2
+ echo " % mafft --retree 1 in > out (fast)" 1>&2
+ echo "" 1>&2
+ echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2
+ echo " % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)" 1>&2
+ echo " % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)" 1>&2
+ echo " % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2
+ echo "" 1>&2
+ echo "If unsure which option to use:" 1>&2
+ echo " % mafft --auto in > out" 1>&2
+ echo "" 1>&2
+# echo "Other options:" 1>&2
+ echo "--op # : Gap opening penalty, default: 1.53" 1>&2
+ echo "--ep # : Offset (works like gap extension penalty), default: 0.0" 1>&2
+ echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2
+ echo "--clustalout : Output: clustal format, default: fasta" 1>&2
+ echo "--reorder : Outorder: aligned, default: input order" 1>&2
+ echo "--quiet : Do not report progress" 1>&2
+ echo "--thread # : Number of threads. (# must be <= number of physical cores - 1)" 1>&2
+# echo "" 1>&2
+# echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
+# echo " most accurate in many cases, assumes only one alignable domain" 1>&2
+# echo "" 1>&2
+# echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
+# echo " works well if many unalignable residues exist between alignable domains" 1>&2
+# echo "" 1>&2
+# echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
+# echo " suitable for globally alignable sequences " 1>&2
+# echo "" 1>&2
+# echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
+# echo " accurate and slow, iterative refinement method " 1>&2
+# echo "" 1>&2
+# echo "If the input sequences are long (~1,000,000nt)," 1>&2
+# echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
+# echo "" 1>&2
+# echo "If many (~5,000) sequences are to be aligned," 1>&2
+# echo "" 1>&2
+# echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
+# echo "" 1>&2
+# echo " --localpair : All pairwise local alignment information is included" 1>&2
+# echo " to the objective function, default: off" 1>&2
+# echo " --globalpair : All pairwise global alignment information is included" 1>&2
+# echo " to the objective function, default: off" 1>&2
+# echo " --op # : Gap opening penalty, default: $defaultgop " 1>&2
+# echo " --ep # : Offset (works like gap extension penalty), default: $defaultaof " 1>&2
+# echo " --bl #, --jtt # : Scoring matrix, default: BLOSUM62" 1>&2
+# echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
+# echo " or JTT (--jtt) # PAM. " 1>&2
+# echo " --nuc or --amino : Sequence type, default: auto" 1>&2
+# echo " --retree # : The number of tree building in progressive method " 1>&2
+# echo " (see the paper for detail), default: $defaultcycle " 1>&2
+# echo " --maxiterate # : Maximum number of iterative refinement, default: $defaultiterate " 1>&2
+# if [ $defaultfft -eq 1 ]; then
+# echo " --fft or --nofft: FFT is enabled or disabled, default: enabled" 1>&2
+# else
+# echo " --fft or --nofft: FFT is enabled or disabled, default: disabled" 1>&2
+# fi
+# echo " --memsave: Memory saving mode" 1>&2
+# echo " (for long genomic sequences), default: off" 1>&2
+# echo " --clustalout : Output: clustal format, default: fasta" 1>&2
+# echo " --reorder : Outorder: aligned, default: input order" 1>&2
+# echo " --quiet : Do not report progress" 1>&2
+# echo "-----------------------------------------------------------------------------" 1>&2
+ exit 1;
+ fi
+ if [ $sw -eq 1 ]; then
+ swopt=" -A "
+ else
+ swopt=" "
+ fi
+
+ if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+ if [ ! "$FASTA_4_MAFFT" ]; then
+ FASTA_4_MAFFT=`which fasta34`
+ fi
+
+ if [ ! -x "$FASTA_4_MAFFT" ]; then
+ echo "" 1>&2
+ echo "== Install FASTA ========================================================" 1>&2
+ echo "This option requires the fasta34 program (FASTA version x.xx or higher)" 1>&2
+ echo "installed in your PATH. If you have the fasta34 program but have renamed" 1>&2
+ echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
+ echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $distance = "lara" -o $distance = "slara" ]; then
+ if [ ! -x "$prefix/mafft_lara" ]; then
+ echo "" 1>&2
+ echo "== Install LaRA =========================================================" 1>&2
+ echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)." 1>&2
+ echo "The executable have to be renamed to 'mafft_lara' and installed into " 1>&2
+ echo "the $prefix directory. " 1>&2
+ echo "A configuration file of LaRA also have to be given" 1>&2
+ echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2
+ echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ if [ ! -s "$laraparams" ]; then
+ echo "" 1>&2
+ echo "== Configure LaRA =======================================================" 1>&2
+ echo "A configuration file of LaRA have to be given" 1>&2
+ echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2
+ echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
+ if [ ! -x "$prefix/foldalign210" ]; then
+ echo "" 1>&2
+ echo "== Install FOLDALIGN ====================================================" 1>&2
+ echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
+ echo "The executable have to be renamed to 'foldalign210' and installed into " 1>&2
+ echo "the $prefix directory. " 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $distance = "scarna" ]; then
+ if [ ! -x "$prefix/mxscarnamod" ]; then
+ echo "" 1>&2
+ echo "== Install MXSCARNA ======================================================" 1>&2
+ echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required." 1>&2
+ echo "Please 'make' at the 'extensions' directory of the MAFFT source package," 1>&2
+ echo "which contains the modified version of MXSCARNA." 1>&2
+ echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html " 1>&2
+ echo "==========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $mccaskill -eq 1 ]; then
+ if [ ! -x "$prefix/mxscarnamod" ]; then
+ echo "" 1>&2
+ echo "== Install MXSCARNA ======================================================" 1>&2
+ echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required." 1>&2
+ echo "Please 'make' at the 'extensions' directory of the MAFFT source package," 1>&2
+ echo "which contains the modified version of MXSCARNA." 1>&2
+ echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html " 1>&2
+ echo "==========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+ if [ $contrafold -eq 1 ]; then
+ if [ ! -x "$prefix/contrafold" ]; then
+ echo "" 1>&2
+ echo "== Install CONTRAfold ===================================================" 1>&2
+ echo "This option requires CONTRAfold" 1>&2
+ echo "(Do et al. http://contra.stanford.edu/contrafold/)." 1>&2
+ echo "The executable 'contrafold' have to be installed into " 1>&2
+ echo "the $prefix directory. " 1>&2
+ echo "=========================================================================" 1>&2
+ echo "" 1>&2
+ exit 1
+ fi
+ fi
+
+#old
+# if [ $treeout -eq 1 ]; then
+# parttreeoutopt="-t"
+# if [ $cycle -eq 0 ]; then
+# treeoutopt="-t -T"
+# groupsize=1
+# iterate=0
+# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+# distance="distonly"
+# fi
+# else
+# treeoutopt="-t"
+# fi
+# else
+# parttreeoutopt=" "
+# if [ $cycle -eq 0 ]; then
+# treeoutopt="-t -T"
+# iterate=0
+# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+# distance="distonly"
+# fi
+# else
+# treeoutopt=" "
+# fi
+# fi
+
+#new
+ if [ $cycle -eq 0 ]; then
+ treeoutopt="-t -T"
+ iterate=0
+ if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+ distance="distonly"
+ fi
+ if [ $treeout -eq 1 ]; then
+ parttreeoutopt="-t"
+ groupsize=1
+ else
+ parttreeoutopt=" "
+ fi
+ if [ $distout -eq 1 ]; then
+ distoutopt="-y -T"
+ fi
+ else
+ if [ $treeout -eq 1 ]; then
+ parttreeoutopt="-t"
+ treeoutopt="-t"
+ else
+ parttreeoutopt=" "
+ treeoutopt=" "
+ fi
+ if [ $distout -eq 1 ]; then
+ distoutopt="-y"
+ fi
+ fi
+#
+
+ formatcheck=`grep -c '^[[:blank:]]\+>' $TMPFILE/infile | head -1 `
+ if [ $formatcheck -gt 0 ]; then
+ echo "The first character of a description line must be " 1>&2
+ echo "the greater-than (>) symbol, not a blank." 1>&2
+ echo "Please check the format around the following line(s):" 1>&2
+ grep -n '^[[:blank:]]\+>' $TMPFILE/infile 1>&2
+ exit 1
+ fi
+
+ nseq=`grep -c '^[>|=]' $TMPFILE/infile | head -1 `
+ if [ $nseq -eq 2 ]; then
+ cycle=1
+ fi
+ if [ $cycle -gt 3 ]; then
+ cycle=3
+ fi
+
+ if [ $nseq -gt 4000 -a $iterate -gt 1 ]; then
+ echo "Too many sequences to perform iterative refinement!" 1>&2
+ echo "Please use a progressive method." 1>&2
+ exit 1
+ fi
+
+
+ if [ $distance = "sixtuples" -a \( $seed = "x" -a $seedtable = "x" \) ]; then
+ localparam=" "
+ elif [ $distance = "sixtuples" -a \( $seed != "x" -o $seedtable != "x" \) ]; then
+ if [ $cycle -lt 2 ]; then
+ cycle=2 # nazeda
+ fi
+ if [ $iterate -lt 2 ]; then
+ echo "############################################################################" 1>&2
+ echo "# Warning:" 1>&2
+ echo "# Progressive alignment method is incompatible with the --seed option." 1>&2
+ echo "# Automatically switched to the iterative refinement method." 1>&2
+ echo "# " 1>&2
+ echo "# Also consider using the '--add' option, which is compatible with" 1>&2
+ echo "# the progressive method and FASTER than the '--seed' option." 1>&2
+ echo "# Usage is:" 1>&2
+ echo "# % mafft --add newSequences existingAlignment > output" 1>&2
+ echo "############################################################################" 1>&2
+ iterate=2
+ fi
+ localparam="-l "$weighti
+ elif [ $distance = "parttree" ]; then
+ localparam=" "
+ if [ $groupsize -gt -1 ]; then
+ cycle=1
+ fi
+ else
+ localparam=" -l "$weighti
+ if [ $cycle -gt 1 ]; then # 09/01/08
+ cycle=1
+ fi
+ fi
+
+ if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+ aof="0.000"
+ fi
+
+ if [ "$memopt" = " -M -B " -a "$distance" != "sixtuples" ]; then
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+#exit
+
+ if [ $distance = "parttree" ]; then
+ if [ $seed != "x" -o $seedtable != "x" ]; then
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ if [ $iterate -gt 1 ]; then
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ if [ $outorder = "aligned" ]; then
+ outorder="input"
+ fi
+ outorder="input" # partorder ga kiku
+ if [ $partdist = "localalign" ]; then
+ splitopt=" -L " # -L -l -> fast
+ elif [ $partdist = "fasta" ]; then
+ splitopt=" -S "
+ else
+ splitopt=" "
+ fi
+ fi
+
+
+# if [ $nseq -gt 5000 ]; then
+# fft=0
+# fi
+ if [ $forcefft -eq 1 ]; then
+ param_fft=" -G "
+ fft=1
+ elif [ $fft -eq 1 ]; then
+ param_fft=" -F "
+ else
+ param_fft=" "
+ fi
+
+ if [ $seed != "x" -a $seedtable != "x" ]; then
+ echo 'Use either one of seedtable and seed. Not both.' 1>&2
+ exit 1
+ fi
+# if [ $seedtable != "x" -a $anysymbol -gt 0 ]; then
+# echo 'The combination of --seedtable and --anysymbol is not supported.' 1>&2
+# exit 1
+# fi
+
+ if [ $treein -eq 1 ]; then
+# if [ $iterate -gt 0 ]; then
+# echo 'Not supported yet.' 1>&2
+# exit 1
+# fi
+ cycle=1
+ fi
+
+ if [ "$addarg0" != " " ]; then
+ "$prefix/countlen" < $TMPFILE/_addfile > $TMPFILE/addsize
+ nadd=`awk '{print $1}' $TMPFILE/addsize`
+ if [ $nadd -eq "0" ]; then
+ echo Check $addfile 1>&2
+ exit 1;
+ fi
+ addarg="$addarg0 $nadd"
+ cycle=1
+ iterate=0
+ if [ $seed != "x" -o $seedtable != "x" ]; then
+ echo 'Impossible' 1>&2;
+ echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2
+ exit 1;
+ fi
+ fi
+
+ if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+ if [ $distance = "sixtuples" ]; then
+ echo 'Not supported.' 1>&2
+ echo 'Please add --globalpair, --localpair, --scarnapair,' 1>&2
+ echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
+ exit 1
+ fi
+ fi
+
+ if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+ if [ $distance = "scarna" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
+ strategy="X-I"
+ elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
+ strategy="Q-I"
+ fi
+ elif [ $distance = "fasta" -a $sw -eq 0 ]; then
+ strategy="F-I"
+ elif [ $distance = "fasta" -a $sw -eq 1 ]; then
+ strategy="H-I"
+ elif [ $distance = "blast" ]; then
+ strategy="B-I"
+ elif [ $distance = "global" -o $distance = "distonly" ]; then
+ strategy="G-I"
+ elif [ $distance = "local" ]; then
+ strategy="L-I"
+ elif [ $distance = "localgenaf" ]; then
+ strategy="E-I"
+ elif [ $distance = "globalgenaf" ]; then
+ strategy="K-I"
+ elif [ $fft -eq 1 ]; then
+ strategy="FFT-"
+ else
+ strategy="NW-"
+ fi
+ strategy=$strategy"NS-"
+ if [ $iterate -gt 0 ]; then
+ strategy=$strategy"i"
+ elif [ $distance = "parttree" ]; then
+ if [ $partdist = "fasta" ]; then
+ strategy=$strategy"FastaPartTree-"$cycle
+ elif [ $partdist = "localalign" ]; then
+ strategy=$strategy"DPPartTree-"$cycle
+ else
+ strategy=$strategy"PartTree-"$cycle
+ fi
+ else
+ strategy=$strategy$cycle
+ fi
+
+ explanation='?'
+ performance='Not tested.'
+ if [ $strategy = "F-INS-i" ]; then
+ explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
+ performance='Most accurate, but very slow'
+ elif [ $strategy = "L-INS-i" ]; then
+ explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
+ performance='Probably most accurate, very slow'
+ elif [ $strategy = "E-INS-i" ]; then
+ explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
+ performance='Suitable for sequences with long unalignable regions, very slow'
+ elif [ $strategy = "G-INS-i" ]; then
+ explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
+ performance='Suitable for sequences of similar lengths, very slow'
+ elif [ $strategy = "X-INS-i" ]; then
+ explanation='RNA secondary structure information is taken into account.'
+ performance='For short RNA sequences only, extremely slow'
+ elif [ $strategy = "F-INS-1" ]; then
+ explanation='Progressive method incorporating LOCAL pairwise alignment information'
+ elif [ $strategy = "L-INS-1" ]; then
+ explanation='Progressive method incorporating LOCAL pairwise alignment information'
+ elif [ $strategy = "G-INS-1" ]; then
+ explanation='Progressive method incorporating GLOBAL pairwise alignment information'
+ elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
+ explanation='Iterative refinement method (max. '$iterate' iterations)'
+ if [ $iterate -gt 2 ]; then
+ performance='Accurate but slow'
+ else
+ performance='Standard'
+ fi
+ elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
+ explanation='Progressive method (guide trees were built '$cycle' times.)'
+ performance='Fast but rough'
+ elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
+ explanation='Progressive method (rough guide tree was used.)'
+ performance='Very fast but very rough'
+ fi
+
+ if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
+ outputopt=" -c $strategy -r $TMPFILE/order "
+ elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
+ outputopt=" -c $strategy "
+ elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
+ outputopt=" -y -r $TMPFILE/order "
+ elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
+ outputopt=" -y "
+ elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
+ outputopt=" -f -r $TMPFILE/order "
+ else
+ outputopt="null"
+ fi
+
+ (
+ cd $TMPFILE;
+
+ if [ $quiet -gt 0 ]; then
+
+ if [ $anysymbol -eq 1 ]; then
+ mv infile orig
+ "$prefix/replaceu" -i orig > infile 2>/dev/null || exit 1
+ fi
+
+ if [ $seed != "x" ]; then
+ mv infile infile2
+ if [ $anysymbol -eq 1 ]; then
+ mv orig orig2
+ cat /dev/null > orig
+ fi
+ cat /dev/null > infile
+ cat /dev/null > hat3.seed
+ seedoffset=0
+# echo "seednseq="$seednseq
+# echo "seedoffset="$seedoffset
+ set $seednseq > /dev/null
+# echo $#
+ while [ $# -gt 1 ]
+ do
+ shift
+# echo "num="$#
+
+ if [ $anysymbol -eq 1 ]; then
+ cat seed$# >> orig
+ "$prefix/replaceu" -i seed$# -o $seedoffset > clean 2>/dev/null || exit 1
+ mv clean seed$#
+ fi
+ "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>/dev/null || exit 1
+ cat hat3 >> hat3.seed
+# echo "$1"
+ seedoffset=`expr $seedoffset + $1`
+# echo "$1"
+# echo "seedoffset="$seedoffset
+ done;
+# echo "seedoffset="$seedoffset
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/replaceu" -i orig2 -o $seedoffset >> infile 2>/dev/null || exit 1 # yarinaoshi
+ cat orig2 >> orig
+ else
+ cat infile2 >> infile
+ fi
+ elif [ $seedtable != "x" ]; then
+ cat _seedtablefile > hat3.seed
+ else
+ cat /dev/null > hat3.seed
+ fi
+# cat hat3.seed
+
+
+ if [ $mccaskill -eq 1 ]; then
+ "$prefix/mccaskillwrap" -C $numthreads -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
+ elif [ $contrafold -eq 1 ]; then
+ "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
+ fi
+ if [ $distance = "fasta" ]; then
+ "$prefix/dndfast7" $swopt < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "blast" ]; then
+ "$prefix/dndblast" < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "foldalignlocal" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "foldalignglobal" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "slara" ]; then
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -T -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "lara" ]; then
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -B -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "scarna" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -s -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "global" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -F < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "local" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof -L < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "globalgenaf" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -O $GGOP -E $GEXP -K < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "localgenaf" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null 2>&1 || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "distonly" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -t < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "parttree" ]; then
+ "$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft -p $partsize -s $groupsize $treealg -i infile > pre 2>/dev/null || exit 1
+ mv hat3.seed hat3
+ else
+ "$prefix/disttbfast" -O $outnum $addarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $algopt $treealg $scoreoutarg < infile > pre 2>/dev/null || exit 1
+ mv hat3.seed hat3
+ fi
+ while [ $cycle -gt 1 ]
+ do
+ if [ $distance = "parttree" ]; then
+ mv pre infile
+ "$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft -p $partsize -s $groupsize $treealg -i infile > pre 2>/dev/null || exit 1
+ else
+ "$prefix/tbfast" -O $outnum -C $numthreads $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>&1 || exit 1
+ fi
+ cycle=`expr $cycle - 1`
+ done
+ if [ $iterate -gt 0 ]; then
+ if [ $distance = "sixtuples" ]; then
+ "$prefix/dndpre" -C $numthreads < pre > /dev/null 2>&1 || exit 1
+ fi
+ "$prefix/dvtditr" -C $numthreads -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg < pre > /dev/null 2>&1 || exit 1
+ fi
+ else
+
+ if [ $anysymbol -eq 1 ]; then
+ mv infile orig
+ "$prefix/replaceu" -i orig > infile || exit 1
+ fi
+
+ if [ $seed != "x" ]; then
+ mv infile infile2
+ if [ $anysymbol -eq 1 ]; then
+ mv orig orig2
+ cat /dev/null > orig
+ fi
+ cat /dev/null > infile
+ cat /dev/null > hat3.seed
+ seedoffset=0
+# echo "seednseq="$seednseq
+# echo "seedoffset="$seedoffset
+ set $seednseq > /dev/null
+# echo $#
+ while [ $# -gt 1 ]
+ do
+ shift
+# echo "num="$#
+
+ if [ $anysymbol -eq 1 ]; then
+ cat seed$# >> orig
+ "$prefix/replaceu" -i seed$# -o $seedoffset > clean || exit 1
+ mv clean seed$#
+ fi
+ "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile || exit 1
+ cat hat3 >> hat3.seed
+# echo "$1"
+ seedoffset=`expr $seedoffset + $1`
+# echo "$1"
+# echo "seedoffset="$seedoffset
+ done;
+# echo "seedoffset="$seedoffset
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/replaceu" -i orig2 -o $seedoffset >> infile || exit 1 # yarinaoshi
+ cat orig2 >> orig
+ else
+ cat infile2 >> infile
+ fi
+ elif [ $seedtable != "x" ]; then
+ cat _seedtablefile > hat3.seed
+ else
+ cat /dev/null > hat3.seed
+ fi
+# cat hat3.seed
+
+ if [ $mccaskill -eq 1 ]; then
+ "$prefix/mccaskillwrap" -C $numthreads -d "$prefix" -i infile > hat4 || exit 1
+ elif [ $contrafold -eq 1 ]; then
+ "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 || exit 1
+ fi
+ if [ $distance = "fasta" ]; then
+ "$prefix/dndfast7" $swopt < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
+ elif [ $distance = "blast" ]; then
+ "$prefix/dndblast" < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
+ elif [ $distance = "foldalignlocal" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "foldalignglobal" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "slara" ]; then
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -T -d "$prefix" < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "lara" ]; then
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -B -d "$prefix" < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "scarna" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -s -d "$prefix" < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "global" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -F < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
+ elif [ $distance = "local" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof -L < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
+ elif [ $distance = "globalgenaf" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -O $GGOP -E $GEXP -K < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
+ elif [ $distance = "localgenaf" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
+ elif [ $distance = "distonly" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -t < infile > /dev/null || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
+ elif [ $distance = "parttree" ]; then
+ "$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft -p $partsize -s $groupsize $treealg -i infile > pre || exit 1
+ mv hat3.seed hat3
+ else
+ "$prefix/disttbfast" -O $outnum $addarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $algopt $treealg $scoreoutarg < infile > pre || exit 1
+ mv hat3.seed hat3
+ fi
+
+ while [ $cycle -gt 1 ]
+ do
+ if [ $distance = "parttree" ]; then
+ mv pre infile
+ "$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft -p $partsize -s $groupsize $treealg -i infile > pre || exit 1
+ else
+ "$prefix/tbfast" -O $outnum -C $numthreads $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null || exit 1
+ fi
+ cycle=`expr $cycle - 1`
+ done
+ if [ $iterate -gt 0 ]; then
+ if [ $distance = "sixtuples" ]; then
+ "$prefix/dndpre" -C $numthreads < pre > /dev/null 2>&1 || exit 1
+ fi
+ "$prefix/dvtditr" -C $numthreads -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg < pre > /dev/null || exit 1
+ fi
+ fi
+
+ if [ $coreout -eq 1 ]; then
+ "$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2
+ mv pre2 pre
+ elif [ $anysymbol -eq 1 ]; then
+ "$prefix/restoreu" -a pre -i orig > restored || exit 1
+ mv restored pre
+ fi
+
+ if [ $quiet -eq 0 ]; then
+ echo '' 1>&2
+ if [ $mccaskill -eq 1 ]; then
+ echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>&2
+ echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>&2
+ echo "incorporated in the iterative alignment process (4)." 1>&2
+ echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>&2
+ echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>&2
+ echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>&2
+ echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
+ echo "" 1>&2
+ elif [ $contrafold -eq 1 ]; then
+ echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>&2
+ echo "and then incorporated in the iterative alignment process (4)." 1>&2
+ echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>&2
+ echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
+ echo "" 1>&2
+ fi
+ if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+ echo "Pairwise alignments were computed by FASTA" 1>&2
+ echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>&2
+ fi
+ if [ $distance = "blast" ]; then
+ echo "Pairwise alignments were computed by BLAST" 1>&2
+ echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>&2
+ fi
+ if [ $distance = "scarna" ]; then
+ echo "Pairwise alignments were computed by MXSCARNA" 1>&2
+ echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>&2
+ fi
+ if [ $distance = "lara" -o $distance = "slara" ]; then
+ echo "Pairwise alignments were computed by LaRA" 1>&2
+ echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>&2
+ fi
+ if [ $distance = "foldalignlocal" ]; then
+ echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>&2
+ echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
+ fi
+ if [ $distance = "foldalignglobal" ]; then
+ echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
+ echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
+ fi
+ printf "\n" 1>&2
+ echo 'Strategy:' 1>&2
+ printf ' '$strategy 1>&2
+ echo ' ('$performance')' 1>&2
+ echo ' '$explanation 1>&2
+ echo '' 1>&2
+ echo "If unsure which option to use, try 'mafft --auto input > output'." 1>&2
+# echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>&2
+ echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>&2
+ echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>&2
+ echo '' 1>&2
+ fi
+ )
+
+ if [ "$outputfile" = "" ]; then
+ if [ "$outputopt" = "null" ]; then
+ cat < $TMPFILE/pre || exit 1
+ else
+ "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre || exit 1
+ fi
+ else
+ if [ "$outputopt" = "null" ]; then
+ cat < $TMPFILE/pre > "$outputfile" || exit 1
+ else
+ "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre > "$outputfile" || exit 1
+ fi
+ fi
+
+ if [ $treeout -eq 1 ]; then
+ cp $TMPFILE/infile.tree "$infilename.tree"
+ fi
+
+ if [ $distout -eq 1 ]; then
+ cp $TMPFILE/hat2 "$infilename.hat2"
+ fi
+
+ exit 0;
+fi
+
+prog="awk"
+
+tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
+if [ -x "$tmpawk" ]; then
+ prog="$tmpawk"
+fi
+
+tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
+if [ -x "$tmpawk" ]; then
+ prog="$tmpawk"
+fi
+
+#echo "prog="$prog 1>&2
+
+umask 077
+(
+$prog '
+BEGIN {
+ prefix = ENVIRON["prefix"];
+ version = ENVIRON["version"];
+ myself = ENVIRON["myself"];
+ while( 1 )
+ {
+ options = ""
+ printf( "\n" ) > "/dev/tty";
+ printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+ printf( " MAFFT %s\n", version ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+ printf( " Copyright (c) 2011 Kazutaka Katoh\n" ) > "/dev/tty";
+ printf( " NAR 30:3059-3066, NAR 33:511-518\n" ) > "/dev/tty";
+ printf( " http://mafft.cbrc.jp/alignment/software/\n" ) > "/dev/tty";
+ printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+
+ while( 1 )
+ {
+ printf( "\n" ) > "/dev/tty";
+ printf( "Input file? (fasta format)\n@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" )
+ if( res == 0 || NF == 0 )
+ continue;
+ infile = sprintf( "%s", $0 );
+
+ res = getline < infile;
+ close( infile );
+ if( res == -1 )
+ {
+ printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
+ printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/dev/tty";
+ }
+ else if( res == 0 )
+ printf( "%s: Empty.\n", infile ) > "/dev/tty";
+ else
+ {
+ printf( "OK. infile = %s\n\n", infile ) > "/dev/tty";
+ break;
+ }
+ }
+ nseq = 0;
+
+ while( 1 )
+ {
+ printf( "\n" ) > "/dev/tty";
+ printf( "Output file?\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 || NF == 0 )
+ continue;
+ else
+ {
+ outfile = sprintf( "%s", $0 );
+ printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
+ break;
+ }
+ }
+
+ while( 1 )
+ {
+ outargs = "";
+ printf( "\n" ) > "/dev/tty";
+ printf( "Output format?\n" ) > "/dev/tty";
+ printf( " 1. Clustal format / Sorted\n" ) > "/dev/tty";
+ printf( " 2. Clustal format / Input order\n" ) > "/dev/tty";
+ printf( " 3. Fasta format / Sorted\n" ) > "/dev/tty";
+ printf( " 4. Fasta format / Input order\n" ) > "/dev/tty";
+ printf( " 5. Phylip format / Sorted\n" ) > "/dev/tty";
+ printf( " 6. Phylip format / Input order\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+# printf( "res=%d, NF=%d\n", res, NF );
+
+ resnum = 0 + $1;
+# printf( "resnum=%d\n", resnum );
+
+ if( resnum < 1 || 6 < resnum )
+ continue;
+ else
+ {
+ if( resnum == 1 )
+ outargs = "--clustalout --reorder";
+ else if( resnum == 2 )
+ outargs = "--clustalout --inputorder";
+ else if( resnum == 3 )
+ outargs = "--reorder";
+ else if( resnum == 4 )
+ outargs = "--inputorder";
+ else if( resnum == 5 )
+ outargs = "--phylipout --reorder";
+ else if( resnum == 6 )
+ outargs = "--phylipout --inputorder";
+ else
+ continue;
+ printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty";
+ break;
+ }
+ }
+
+ while( 1 )
+ {
+ arguments = "";
+ printf( "\n" ) > "/dev/tty";
+ printf( "Strategy?\n" ) > "/dev/tty";
+ printf( " 1. --auto\n" ) > "/dev/tty";
+ printf( " 2. FFT-NS-1 (fast)\n" ) > "/dev/tty";
+ printf( " 3. FFT-NS-2 (default)\n" ) > "/dev/tty";
+ printf( " 4. G-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( " 5. L-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( " 6. E-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+# printf( "res=%d, NF=%d\n", res, NF );
+
+ resnum = 0 + $1;
+# printf( "resnum=%d\n", resnum );
+
+ if( resnum < 1 || 6 < resnum )
+ continue;
+ else
+ {
+ if( resnum == 1 )
+ arguments = "--auto";
+ else if( resnum == 2 )
+ arguments = "--retree 1";
+ else if( resnum == 3 )
+ arguments = "--retree 2";
+ else if( resnum == 4 )
+ arguments = "--globalpair --maxiterate 16";
+ else if( resnum == 5 )
+ arguments = "--localpair --maxiterate 16";
+ else if( resnum == 6 )
+ arguments = "--genafpair --maxiterate 16";
+ else
+ arguments = sprintf( "%s", $0 );
+ printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty";
+ break;
+ }
+ }
+
+
+ while( 1 )
+ {
+ printf( "\n" ) > "/dev/tty";
+ printf( "Additional arguments? (--ep #, --op #, --kappa #, etc)\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 || NF == 0 )
+ {
+ break;
+ }
+ else
+ {
+ addargs = sprintf( "%s", $0 );
+ printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
+ break;
+ }
+ }
+
+ arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
+
+ print ""
+ command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
+ gsub( /\\/, "/", command );
+
+
+ printf( "command=\n%s\n", command ) > "/dev/tty";
+
+
+ while( 1 )
+ {
+ go = 0;
+ printf( "OK?\n" ) > "/dev/tty";
+ printf( "@ [Y] " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 0 || $0 ~ /^[Yy]/ )
+ {
+ go=1;
+ break;
+ }
+ else
+ break;
+ }
+ if( go ) break;
+ printf( "\n" ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+ }
+ system( command );
+ command = sprintf( "less \"%s\"", outfile );
+ system( command );
+ printf( "Press Enter to exit." ) > "/dev/tty";
+ res = getline < "/dev/tty";
+}
+'
+)
+exit 0;
--- /dev/null
+#! /bin/sh
+er=0;
+myself=`dirname $0`/`basename $0`; export myself
+version="version 6.00 (2005/05/01)"; export version
+LANG=C; export LANG
+os=`uname`
+progname=`basename $0`
+if [ `echo $os | grep -i cygwin` ]; then
+ os="cygwin"
+elif [ `echo $os | grep -i darwin` ]; then
+ os="darwin"
+elif [ `echo $os | grep -i sunos` ]; then
+ os="sunos"
+else
+ os="unix"
+fi
+export os
+
+if [ $MAFFT_BINARIES ]; then
+ prefix=$MAFFT_BINARIES
+else
+ prefix=_PREFIX
+fi
+export prefix
+if [ ! -x $prefix/tbfast ]; then
+ echo ""
+ echo "correctly installed?" 2>&1
+ echo "mafft binaries have to be installed in" $prefix.
+ echo ""
+ exit 1
+ er=1
+fi
+
+defaultiterate=0
+defaultcycle=2
+defaultmodel=" -b 62 "
+defaultgop="1.53"
+defaultaof="0.123"
+defaultfft=1
+defaultrough=0
+defaultdistance="sixtuples"
+if [ $progname = "linsi" ]; then
+ defaultfft=0
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="local"
+elif [ $progname = "ginsi" ]; then
+ defaultfft=1
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="global"
+elif [ $progname = "einsi" ]; then
+ defaultfft=0
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="genaf"
+elif [ $progname = "fftns" ]; then
+ defaultfft=1
+ defaultcycle=2
+elif [ $progname = "fftnsi" ]; then
+ defaultfft=1
+ defaultcycle=2
+ defaultiterate=2
+elif [ $progname = "nwns" ]; then
+ defaultfft=0
+ defaultcycle=2
+elif [ $progname = "nwnsi" ]; then
+ defaultfft=0
+ defaultcycle=2
+ defaultiterate=2
+fi
+model=$defaultmodel
+gop=$defaultgop
+aof=$defaultaof
+cycle=$defaultcycle
+iterate=$defaultiterate
+fft=$defaultfft
+rough=$defaultrough
+distance=$defaultdistance
+LGOP="-6.00"
+LEXP="-0.000"
+lgop="-2.00"
+lexp="-0.100"
+laof="0.100"
+seqtype=" "
+param_it=" -x "
+weighti="2.7"
+quiet=0
+sw=0
+scorecalcopt=" "
+coreout=0
+corethr="0.5"
+corewin="100"
+coreext=" "
+outputformat="pir"
+outorder="input"
+if [ $# -gt 0 ]; then
+ while [ $# -gt 1 ];
+ do
+ if [ $1 = "--clustalout" ]; then
+ outputformat="clustal"
+ elif [ $1 = "--reorder" ]; then
+ outorder="aligned"
+ elif [ $1 = "--rough" ]; then
+ rough=1
+ elif [ $1 = "--noscore" ]; then
+ scorecalcopt=" -Z "
+ elif [ $1 = "--fastswpair" ]; then
+ distance="fasta"
+ sw=1
+ elif [ $1 = "--fastapair" ]; then
+ distance="fasta"
+ sw=0
+ elif [ $1 = "--suboptpair" ]; then
+ distance="subopt"
+ elif [ $1 = "--blastpair" ]; then
+ distance="blast"
+ elif [ $1 = "--globalpair" ]; then
+ distance="global"
+ elif [ $1 = "--localpair" ]; then
+ distance="local"
+ elif [ $1 = "--genafpair" ]; then
+ distance="genaf"
+ elif [ $1 = "--nuc" ]; then
+ seqtype=" -D "
+ elif [ $1 = "--amino" ]; then
+ seqtype=" -P "
+ elif [ $1 = "--fft" ]; then
+ fft=1
+ elif [ $1 = "--nofft" ]; then
+ fft=0
+ elif [ $1 = "--quiet" ]; then
+ quiet=1
+ elif [ $1 = "--nj" ]; then
+ param_it=" -n "
+ elif [ $1 = "--coreext" ]; then
+ coreext=" -c "
+ elif [ $1 = "--core" ]; then
+ coreout=1
+ elif [ $1 = "--maxiterate" ]; then
+ shift
+ iterate=`expr $1 - 0`
+ elif [ $1 = "--retree" ]; then
+ shift
+ cycle=`expr $1 - 0` || er=1
+ elif [ $1 = "--jtt" ]; then
+ shift
+ model=" -j "$1
+ elif [ $1 = "--tm" ]; then
+ shift
+ model=" -m "$1
+ elif [ $1 = "--bl" ]; then
+ shift
+ model=" -b "$1
+ elif [ $1 = "--weighti" ]; then
+ shift
+ weighti=$1
+ elif [ $1 = "--op" ]; then
+ shift
+ gop=$1
+ elif [ $1 = "--ep" ]; then
+ shift
+ aof=$1
+ elif [ $1 = "--lop" ]; then
+ shift
+ lgop=$1
+ elif [ $1 = "--LOP" ]; then
+ shift
+ LGOP=$1
+ elif [ $1 = "--lep" ]; then
+ shift
+ laof=$1
+ elif [ $1 = "--lexp" ]; then
+ shift
+ lexp=$1
+ elif [ $1 = "--LEXP" ]; then
+ shift
+ LEXP=$1
+ elif [ $1 = "--corethr" ]; then
+ shift
+ corethr=$1
+ elif [ $1 = "--corewin" ]; then
+ shift
+ corewin=$1
+ elif [ $1 -gt 0 -a $progname = "fftns" -o $1 -gt 0 -a $progname = "nwns" ]; then
+ cycle=`expr $1 - 0`
+ else
+ echo "Unknown option: " $1 2>&1
+ er=1;
+ fi
+ shift
+ done;
+ if [ $fft -eq 1 ]; then
+ param_fft=" -F "
+ else
+ param_fft=" "
+ fi
+ if [ $sw -eq 1 ]; then
+ swopt=" -A "
+ else
+ swopt=" "
+ fi
+
+ if [ $distance = "fasta" ]; then
+ if [ ! $FASTA_4_MAFFT ]; then
+ FASTA_4_MAFFT=`which fasta34`
+ fi
+
+ if [ ! -x $FASTA_4_MAFFT ]; then
+ echo ""
+ echo "== Install FASTA ========================================================"
+ echo "This option requires the fasta34 program (FASTA version x.xx or higher)"
+ echo "installed in your PATH. If you have the fasta34 program but have renamed"
+ echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable"
+ echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)."
+ echo "========================================================================="
+ echo ""
+ exit
+ fi
+ fi
+ if [ $distance = "sixtuples" ]; then
+ localparam=" "
+ else
+ cycle=1
+ localparam=" -l "$weighti
+ fi
+
+ if [ $distance = "fasta" -a $sw -eq 0 ]; then
+ strategy="F-I"
+ elif [ $distance = "fasta" -a $sw -eq 1 ]; then
+ strategy="H-I"
+ elif [ $distance = "subopt" ]; then
+ strategy="S-I"
+ elif [ $distance = "blast" ]; then
+ strategy="B-I"
+ elif [ $distance = "global" ]; then
+ strategy="G-I"
+ elif [ $distance = "local" ]; then
+ strategy="L-I"
+ elif [ $distance = "genaf" ]; then
+ strategy="E-I"
+ elif [ $fft -eq 1 ]; then
+ strategy="FFT-"
+ else
+ strategy="NW-"
+ fi
+ strategy=$strategy"NS-"
+ if [ $iterate -gt 0 ]; then
+ strategy=$strategy"i"
+ elif [ $rough -eq 1 ]; then
+ strategy=$strategy"ROUGH"
+ else
+ strategy=$strategy$cycle
+ fi
+
+ explanation='?'
+ performance='Not tested.'
+ if [ $strategy = "F-INS-i" ]; then
+ explanation='Iterative refinement method incorporating LOCAL pairwise alignment information'
+ performance='Most accurate, but very slow'
+ elif [ $strategy = "L-INS-i" ]; then
+ explanation='Iterative refinement method incorporating LOCAL pairwise alignment information'
+ performance='Probably most accurate, very slow'
+ elif [ $strategy = "E-INS-i" ]; then
+ explanation='Iterative refinement method incorporating LOCAL pairwise alignment with generalized affine gap costs (Altshul 1998)'
+ performance='Suitable for sequences with long unalignable regions, very slow'
+ elif [ $strategy = "G-INS-i" ]; then
+ explanation='Iterative refinement method incorporating GLOBAL pairwise alignment information'
+ performance='Suitable for sequences of similar lengths, very slow'
+ elif [ $strategy = "F-INS-1" ]; then
+ explanation='Progressive method incorporating LOCAL pairwise alignment information'
+ elif [ $strategy = "L-INS-1" ]; then
+ explanation='Progressive method incorporating LOCAL pairwise alignment information'
+ elif [ $strategy = "G-INS-1" ]; then
+ explanation='Progressive method incorporating GLOBAL pairwise alignment information'
+ elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
+ explanation='Iterative refinement method (max. '$iterate' iterations)'
+ if [ $iterate -gt 2 ]; then
+ performance='Accurate but slow'
+ else
+ performance='Standard'
+ fi
+ elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
+ explanation='Progressive method (guide trees were built '$cycle' times.)'
+ performance='Fast but rough'
+ elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
+ explanation='Progressive method (rough guide tree was used.)'
+ performance='Very fast but very rough'
+ fi
+
+ if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
+ outputcommand="$prefix/f2cl -c $strategy -r order "
+ elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
+ outputcommand="$prefix/f2cl -c $strategy "
+ elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
+ outputcommand="$prefix/f2cl -f -r order "
+ else
+ outputcommand=" cat "
+ fi
+
+ TMPFILE=/tmp/`basename $0`.`whoami`.$$.`date +%y%m%d%H%M%S`
+ TMPFILE=/tmp/$progname.$$
+ umask 077
+ mkdir $TMPFILE || er=1
+ trap "rm -r $TMPFILE " 0
+ if [ $# -eq 1 ]; then
+ if [ -s "$1" -o "$1" = - ]; then
+ cat "$1" | tr "\r" "\n" > $TMPFILE/infile
+ else
+ echo "Cannot open $1." 2>&1
+ er=1
+ fi
+ else
+ echo '$#'"=$#" 2>&1
+ er=1
+ fi
+
+
+ if [ $er -eq 1 ]; then
+ echo "" 2>&1
+ echo "MAFFT" $version 2>&1
+ echo "" 2>&1
+ echo " References: " 2>&1
+ echo " Katoh et al., 2002, NAR 30: 3059-3066" 2>&1
+ echo " Katoh et al., 2005, NAR 33: 511-518" 2>&1
+ echo " http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft" 2>&1
+ echo "" 2>&1
+# echo "Usage: `basename $0` [options] inputfile > outputfile" 2>&1
+ echo " Options: " 2>&1
+ echo " --globalpair : All pairwise global alignment information is included." 2>&1
+ echo " default: off" 2>&1
+ echo " --localpair : All pairwise local alignment information is included." 2>&1
+ echo " default: off" 2>&1
+ echo " --op # : Gap opening penalty (>0). default: $defaultgop " 2>&1
+ echo " --ep # : Offset (>0, works like gap extension penalty). " 2>&1
+ echo " default: $defaultaof " 2>&1
+ echo " --bl #, --jtt # : Scoring matrix. default: BLOSUM62" 2>&1
+ echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 2>&1
+ echo " or JTT (--jtt) # PAM. " 2>&1
+ echo " --nuc or --amino : Sequence type. default: auto" 2>&1
+ echo " --retree # : The number of tree building in progressive method " 2>&1
+ echo " (see the paper for detail). default: $defaultcycle " 2>&1
+ echo " --maxiterate # : Maximum number of iterative refinement. default: $defaultiterate " 2>&1
+ echo " --nj : Tree dependent iterative refinement is performed" 2>&1
+ echo " on an NJ tree. default: UPG tree" 2>&1
+ if [ $defaultfft -eq 1 ]; then
+ echo " --fft or --nofft: FFT is enabled or disabled. default: enabled" 2>&1
+ else
+ echo " --fft or --nofft: FFT is enabled or disabled. default: disabled" 2>&1
+ fi
+# if [ $defaultrough -eq 1 ]; then
+# echo " --rough : Rough alignment, for >1,000 sequences. default: enabled" 2>&1
+# else
+# echo " --rough : Rough alignment, for >1,000 sequences. default: disabled" 2>&1
+# i
+ echo " --clustalout: Output: clustal format (not tested). default: fasta" 2>&1
+ echo " --reorder: Outorder: aligned (not tested). default: input order" 2>&1
+ echo " --quiet : Do not report progress." 2>&1
+ echo "" 2>&1
+ echo " Input format: fasta format" 2>&1
+ echo "" 2>&1
+ echo " Typical usages:" 2>&1
+ echo " % mafft --maxiterate 1000 --localpair input > output" 2>&1
+ echo " L-INS-i (most accurate and very slow, iterative refinement" 2>&1
+ echo " method incorporating LOCAL alignment information)" 2>&1
+ echo "" 2>&1
+ echo " % mafft --maxiterate 1000 --globalpair input > output" 2>&1
+ echo " G-INS-i (slightly less accurate than L-INS-i and very slow," 2>&1
+ echo " iterative refinement method incorporating GLOBAL alignment" 2>&1
+ echo " information, suitable for sequences of similar lengths) " 2>&1
+ echo "" 2>&1
+ echo " % mafft --maxiterate 1000 input > output" 2>&1
+ echo " FFT-NS-i (accurate and slow, iterative refinement method)" 2>&1
+ echo "" 2>&1
+ echo " % mafft --retree 2 input > output (DEFAULT; same as mafft input > output)" 2>&1
+ echo " FFT-NS-2 (rough and fast, default, progressive method)" 2>&1
+ echo "" 2>&1
+ echo " % mafft --retree 1 input > output" 2>&1
+ echo " FFT-NS-1 (very rough and very fast, progressive method with" 2>&1
+ echo " a rough guide tree)" 2>&1
+ echo "" 2>&1
+ exit 1;
+ fi
+
+ (
+ cd $TMPFILE;
+ if [ $rough -gt 0 ]; then
+ $prefix/splitseq infile 500
+ for spfile in sp-[0-9]*[0-9]
+ do
+ echo $spfile > /dev/tty
+ nseq=`grep -c '^[>|=]' $spfile`
+ echo $nseq > /dev/tty
+ if [ $nseq -eq 1 ]; then
+ cp $spfile $spfile.aln
+ else
+ $prefix/sextet5 $seqtype < $spfile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < $spfile > /dev/null 2>&1 || exit 1
+ cat pre > $spfile.aln
+ fi
+ done
+ ngroup=0
+ for alfile in sp-[0-9]*[0-9].aln
+ do
+ ngroup=`expr $ngroup + 1`
+ echo $alfile > /dev/tty
+ if [ $ngroup -eq 1 ]; then
+ cp $alfile alall
+ else
+ $prefix/galn -A alall $alfile > altmp
+ mv altmp alall
+ fi
+ done
+ cat alall
+ else
+ if [ $quiet -gt 0 ]; then
+ if [ $distance = "subopt" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -S < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "fasta" ]; then
+ $prefix/dndfast7 $swopt < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "blast" ]; then
+ $prefix/dndblast < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "global" ]; then
+ $prefix/pairlocalalign $seqtype $model -f "-"$gop -h "-"$aof -F < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "local" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -L < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "genaf" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ else
+ $prefix/disttbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < infile > pre 2>/dev/null || exit 1
+ fi
+ while [ $cycle -gt 1 ]
+ do
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -JAx < pre > /dev/null 2>&1 || exit 1
+ cycle=`expr $cycle - 1`
+ done
+ if [ $iterate -gt 0 ]; then
+ if [ $distance == "sixtuples" ]; then
+ $prefix/dndpre < pre > /dev/null 2>&1 || exit 1
+ fi
+ $prefix/dvtditr $scorecalcopt $localparam -F -z 50 $seqtype $model -f "-"$gop -h "-"$aof -A -c -I $iterate $param_it < pre > /dev/null 2>&1 || exit 1
+ fi
+ else
+ if [ $distance = "subopt" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -S < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "fasta" ]; then
+ $prefix/dndfast7 $swopt < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "blast" ]; then
+ $prefix/dndblast < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "global" ]; then
+ $prefix/pairlocalalign $seqtype $model -f "-"$gop -h "-"$aof -F < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "local" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -L < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "genaf" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ else
+ $prefix/disttbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < infile > pre || exit 1
+ fi
+ while [ $cycle -gt 1 ]
+ do
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -JAx < pre > /dev/null || exit 1
+ cycle=`expr $cycle - 1`
+ done
+ if [ $iterate -gt 0 ]; then
+ if [ $distance = "sixtuples" ]; then
+ $prefix/dndpre < pre > /dev/null 2>&1 || exit 1
+ fi
+ $prefix/dvtditr $scorecalcopt $localparam -F -z 50 $seqtype $model -f "-"$gop -h "-"$aof -A -c -I $iterate $param_it < pre > /dev/null || exit 1
+ fi
+ fi
+# cat < pre || exit 1
+ if [ $coreout -eq 0 ]; then
+ $outputcommand < pre || exit 1
+ else
+ $prefix/setcore -w $corewin -i $corethr $coreext < pre > pre2
+ $outputcommand < pre2 || exit 1
+ fi
+ fi
+ )
+ echo '' >/dev/tty
+ if [ $distance = "fasta" ]; then
+ echo "Pairwise alignments were computed by FASTA" >/dev/tty
+ echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" >/dev/tty
+ fi
+ if [ $distance = "blast" ]; then
+ echo "Pairwise alignments were computed by BLAST">/dev/tty
+ echo "(Altschul et al., 1997, NAR 25:3389-3402)">/dev/tty
+ fi
+ printf "\n" >/dev/tty
+ echo 'Strategy:' >/dev/tty
+ printf ' '$strategy >/dev/tty
+ echo ' ('$performance')' >/dev/tty
+ echo ' '$explanation >/dev/tty
+ echo '' >/dev/tty
+ echo "Type '$0 --help' for other options." >/dev/tty
+ echo '' >/dev/tty
+ exit 0;
+fi
+
+prog="awk"
+
+if [ $os != "darwin" ]; then
+ echo "checking nawk"
+ tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
+ if [ -x $tmpawk ]; then
+ prog=$tmpawk
+ fi
+
+ echo "checking gawk"
+ tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
+ if [ -x $tmpawk ]; then
+ prog=$tmpawk
+ fi
+fi
+
+echo "prog="$prog
+
+umask 077
+export defaultaof
+export defaultgop
+export defaultfft
+export defaultcycle
+export defaultiterate
+(
+$prog '
+BEGIN {
+ prefix = ENVIRON["prefix"];
+ version = ENVIRON["version"];
+ myself = ENVIRON["myself"];
+ defaultgop = ENVIRON["defaultgop"]
+ defaultaof = ENVIRON["defaultaof"]
+ defaultfft = ENVIRON["defaultfft"]
+ defaultcycle = ENVIRON["defaultcycle"]
+ defaultiterate = ENVIRON["defaultiterate"]
+ while( 1 )
+ {
+ options = ""
+ printf( "\n" ) > "/dev/tty";
+ printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+ printf( " MAFFT %s\n", version ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+ printf( " K. Katoh, K. Misawa, K. Kuma and T. Miyata (2002)\n" ) > "/dev/tty";
+ printf( " Nucleic Acids Research 30: 3059-3066.\n" ) > "/dev/tty";
+ printf( " http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft\n" ) > "/dev/tty";
+ printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
+ printf( "\n" );
+
+ while( 1 )
+ {
+ printf( "\n" ) > "/dev/tty";
+ printf( "Input file? (fasta format)\n@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" )
+ if( res == 0 || NF == 0 )
+ continue;
+ infile0 = sprintf( "%s", $1 );
+ infile = sprintf( "%s", $1 );
+
+ res = getline < infile;
+ close( infile );
+ if( res == -1 )
+ printf( "%s: No such file.\n\n", infile );
+ else if( res == 0 )
+ printf( "%s: Empty.\n", infile );
+ else
+ {
+ printf( "OK. infile = %s\n\n", infile );
+ break;
+ }
+ }
+ nseq = 0;
+
+ while( 1 )
+ {
+ printf( "\n" ) > "/dev/tty";
+ printf( "Output file?\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 || NF == 0 )
+ continue;
+ else
+ {
+ outfile = sprintf( "%s", $1 );
+ printf( "OK. outfile = %s\n\n", outfile );
+ break;
+ }
+ }
+
+
+ while( 1 )
+ {
+ retree = defaultcycle
+ printf( "\n" );
+ printf( "Number of tree-rebuilding?\n" ) > "/dev/tty";
+ printf( "@ [%d] ", retree ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 0 )
+ ;
+ else
+ retree = 0 + $1;
+ if( retree < 1 || 10 < retree )
+ ;
+ else
+ {
+ printf( "OK. %d\n\n", retree );
+ break;
+ }
+ }
+
+ while( 1 )
+ {
+ niterate = defaultiterate;
+ printf( "\n" );
+ printf( "Maximum number of iterations?\n" ) > "/dev/tty";
+ printf( "@ [%d] ", niterate ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 0 )
+ ;
+ else
+ niterate = 0 + $1;
+ if( niterate < 0 || 1000 < niterate )
+ ;
+ else
+ {
+ printf( "OK. %d\n\n", niterate );
+ break;
+ }
+ }
+
+ while( 1 )
+ {
+ fft = defaultfft;
+ printf( "\n" );
+ printf( "Use fft?\n" ) > "/dev/tty";
+ printf( "@ [%s] ", fft?"Yes":"No" ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 0 )
+ {
+ break;
+ }
+ else if( NF == 0 || $0 ~ /^[Yy]/ )
+ {
+ fft = 1;
+ break;
+ }
+ else if( NF == 0 || $0 ~ /^[Nn]/ )
+ {
+ fft = 0;
+ break;
+ }
+ }
+ if( fft )
+ {
+ printf( "OK. FFT is enabled.\n\n" );
+ fftparam = " --fft ";
+ }
+ else
+ {
+ printf( "OK. FFT is disabled.\n\n" );
+ fftparam = " --nofft ";
+ }
+
+ while( 1 )
+ {
+ scoringmatrix = 3;
+ printf( "\n" );
+ printf( "Scoring matrix? (ignored when DNA sequence is input.)\n" ) > "/dev/tty";
+ printf( " 1. BLOSUM 30\n" ) > "/dev/tty";
+ printf( " 2. BLOSUM 45\n" ) > "/dev/tty";
+ printf( " 3. BLOSUM 62\n" ) > "/dev/tty";
+ printf( " 4. BLOSUM 80\n" ) > "/dev/tty";
+ printf( " 5. JTT 200\n" ) > "/dev/tty";
+ printf( " 6. JTT 100\n" ) > "/dev/tty";
+ printf( "@ [%d] ", scoringmatrix ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 0 )
+ ;
+ else
+ scoringmatrix = 0 + $1;
+ if( scoringmatrix < 1 || 6 < scoringmatrix )
+ ;
+ else
+ {
+ break;
+ }
+ }
+ if( scoringmatrix == 1 )
+ scoringparam = " --bl 30 ";
+ else if( scoringmatrix == 2 )
+ scoringparam = " --bl 45 ";
+ else if( scoringmatrix == 3 )
+ scoringparam = " --bl 62 ";
+ else if( scoringmatrix == 4 )
+ scoringparam = " --bl 80 ";
+ else if( scoringmatrix == 5 )
+ scoringparam = " --jtt 200 ";
+ else if( scoringmatrix == 6 )
+ scoringparam = " --jtt 100 ";
+ printf( "OK. %s\n\n",scoringparam );
+
+ while( 1 )
+ {
+ penalty = 0.0 + defaultgop;
+ offset = 0.0 + defaultaof;
+ printf( "\n" );
+ printf( "Parameters (gap opening penalty, offset)?\n", penalty, offset ) > "/dev/tty";
+ printf( "@ [%5.3f, %5.3f] ", penalty, offset ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 2 )
+ {
+ penalty = 0.0 + $1;
+ offset = 0.0 + $2;
+ }
+ else if( NF == 0 )
+ ;
+ else
+ continue;
+ if( penalty <= 0.0 || 10.0 < penalty )
+ ;
+ else if( offset <= 0.0 || 10.0 < offset )
+ ;
+ else
+ {
+ printf( "OK. %5.3f %5.3f\n\n", penalty, offset );
+ break;
+ }
+ }
+
+ command = sprintf( "%s %s --retree %d --maxiterate %d %s --op %f --ep %f %s > %s", myself, fftparam, retree, niterate, scoringparam, penalty, offset, infile, outfile );
+ printf( "%s\n\n", command );
+
+
+ while( 1 )
+ {
+ go = 0;
+ printf( "\n" );
+ printf( "OK?\n" );
+ printf( "@ [Y] " ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 0 || $0 ~ /^[Yy]/ )
+ {
+ go=1;
+ break;
+ }
+ else
+ break;
+ }
+ if( go ) break;
+ printf( "\n" );
+ printf( "\n" );
+ }
+ system( command );
+}
+'
+)
+exit 0;
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+static char *whereismccaskillmea;
+
+#ifdef enablemultithread
+typedef struct _thread_arg
+{
+ int thread_no;
+ int njob;
+ int *jobpospt;
+ int **gapmap;
+ char **nogap;
+ int nlenmax;
+ RNApair ***pairprob;
+ pthread_mutex_t *mutex;
+} thread_arg_t;
+#endif
+
+void outmccaskill( FILE *fp, RNApair **pairprob, int length )
+{
+ int i;
+ RNApair *pt;
+ for( i=0; i<length; i++ ) for( pt=pairprob[i]; pt->bestpos!=-1; pt++ )
+ {
+ if( pt->bestpos > i )
+ fprintf( fp, "%d %d %50.40f\n", i, pt->bestpos, pt->bestscore );
+ }
+}
+
+#if 1
+static void readrawmccaskill( FILE *fp, RNApair **pairprob, int length )
+{
+ char gett[1000];
+ int *pairnum;
+ int i;
+ int left, right;
+ float prob;
+
+ pairnum = (int *)calloc( length, sizeof( int ) );
+ for( i=0; i<length; i++ ) pairnum[i] = 0;
+
+ while( 1 )
+ {
+ fgets( gett, 999, fp );
+ if( feof( fp ) ) break;
+ if( gett[0] == '>' ) continue;
+ sscanf( gett, "%d %d %f", &left, &right, &prob );
+ if( prob < 0.01 ) continue; // mxscarna to mafft ryoho ni eikyou
+//fprintf( stderr, "gett = %s\n", gett );
+
+ if( left != right && prob > 0.0 )
+ {
+ pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
+ pairprob[left][pairnum[left]].bestscore = prob;
+ pairprob[left][pairnum[left]].bestpos = right;
+ pairnum[left]++;
+ pairprob[left][pairnum[left]].bestscore = -1.0;
+ pairprob[left][pairnum[left]].bestpos = -1;
+// fprintf( stderr, "%d-%d, %f\n", left, right, prob );
+
+ pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
+ pairprob[right][pairnum[right]].bestscore = prob;
+ pairprob[right][pairnum[right]].bestpos = left;
+ pairnum[right]++;
+ pairprob[right][pairnum[right]].bestscore = -1.0;
+ pairprob[right][pairnum[right]].bestpos = -1;
+// fprintf( stderr, "%d-%d, %f\n", right, left, prob );
+ }
+ }
+ free( pairnum );
+}
+#endif
+
+#ifdef enablemultithread
+static void *athread( void *arg )
+{
+ thread_arg_t *targ = (thread_arg_t *)arg;
+ int thread_no = targ->thread_no;
+ int njob = targ->njob;
+ int *jobpospt = targ->jobpospt;
+ int **gapmap = targ->gapmap;
+ char **nogap = targ->nogap;
+ int nlenmax = targ->nlenmax;
+ RNApair ***pairprob = targ->pairprob;
+
+ int i, res;
+ FILE *infp;
+ char *com;
+ char *dirname;
+
+ dirname = calloc( 100, sizeof( char ) );
+ com = calloc( 1000, sizeof( char ) );
+
+
+ while( 1 )
+ {
+ pthread_mutex_lock( targ->mutex );
+ i = *jobpospt;
+ if( i == njob )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ return( NULL );
+ }
+ *jobpospt = i+1;
+ pthread_mutex_unlock( targ->mutex );
+
+
+ sprintf( dirname, "_%d", i );
+ sprintf( com, "rm -rf %s", dirname );
+ system( com );
+ sprintf( com, "mkdir %s", dirname );
+ system( com );
+
+ fprintf( stderr, "%d / %d (by thread %4d)\n", i+1, njob, thread_no );
+ commongappick_record( 1, nogap+i, gapmap[i] );
+ sprintf( com, "%s/_mccaskillinorg", dirname );
+ infp = fopen( com, "w" );
+// fprintf( infp, ">in\n%s\n", nogap[i] );
+ fprintf( infp, ">in\n" );
+ write1seq( infp, nogap[i] );
+ fclose( infp );
+
+ sprintf( com, "tr -d '\\r' < %s/_mccaskillinorg > %s/_mccaskillin", dirname, dirname );
+ system( com ); // for cygwin, wakaran
+ sprintf( com, "cd %s; %s/mxscarnamod -m -writebpp _mccaskillin > _mccaskillout 2>_dum", dirname, whereismccaskillmea );
+ res = system( com );
+
+ if( res )
+ {
+ fprintf( stderr, "ERROR IN mccaskill_mea\n" );
+ exit( 1 );
+ }
+
+ sprintf( com, "%s/_mccaskillout", dirname );
+ infp = fopen( com, "r" );
+ readrawmccaskill( infp, pairprob[i], nlenmax );
+ fclose( infp );
+
+ sprintf( com, "rm -rf %s > /dev/null 2>&1", dirname );
+ if( system( com ) )
+ {
+ fprintf( stderr, "retrying to rmdir\n" );
+// nanosleep( 100000 );
+ sleep( 1 );
+ system( com );
+ }
+ }
+ free( dirname );
+ free( com );
+}
+#endif
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+ nthread = 1;
+ inputfile = NULL;
+ dorp = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ whereismccaskillmea = NULL;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'd':
+ whereismccaskillmea = *++argv;
+ fprintf( stderr, "whereismccaskillmea = %s\n", whereismccaskillmea );
+ --argc;
+ goto nextoption;
+ case 'C':
+ nthread = atoi( *++argv );
+ fprintf( stderr, "nthread = %d\n", nthread );
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static char com[10000];
+ static int *nlen;
+ int left, right;
+ int res;
+ static char **name, **seq, **nogap;
+ static int **gapmap;
+ static int *order;
+ int i, j;
+ FILE *infp;
+ RNApair ***pairprob;
+ RNApair **alnpairprob;
+ RNApair *pairprobpt;
+ RNApair *pt;
+ int *alnpairnum;
+ float prob;
+ int adpos;
+
+ arguments( argc, argv );
+#ifndef enablemultithread
+ nthread = 0;
+#endif
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ if( !whereismccaskillmea )
+ whereismccaskillmea = "";
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( dorp != 'd' )
+ {
+ fprintf( stderr, "nuc only\n" );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*2+1 );
+ nogap = AllocateCharMtx( njob, nlenmax*2+1 );
+ gapmap = AllocateIntMtx( njob, nlenmax*2+1 );
+ order = AllocateIntVec( njob );
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+ pairprob = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ alnpairprob = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
+ alnpairnum = AllocateIntVec( nlenmax );
+
+ for( i=0; i<nlenmax; i++ ) alnpairnum[i] = 0;
+
+ readData_pointer( infp, name, nlen, seq );
+ fclose( infp );
+
+ for( i=0; i<njob; i++ )
+ {
+ pairprob[i] = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
+ for( j=0; j<nlenmax; j++ )
+ {
+ pairprob[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+ pairprob[i][j][0].bestpos = -1;
+ pairprob[i][j][0].bestscore = -1.0;
+ }
+ strcpy( nogap[i], seq[i] );
+ order[i] = i;
+ }
+ for( j=0; j<nlenmax; j++ )
+ {
+ alnpairprob[j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+ alnpairprob[j][0].bestpos = -1;
+ alnpairprob[j][0].bestscore = -1.0;
+ }
+
+
+ constants( njob, seq );
+
+ fprintf( stderr, "Running mxscarna with the mccaskill_mea mode.\n" );
+#ifdef enablemultithread
+ if( nthread > 0 )
+ {
+ int jobpos;
+ pthread_t *handle;
+ pthread_mutex_t mutex;
+ thread_arg_t *targ;
+ jobpos = 0;
+
+ targ = calloc( nthread, sizeof( thread_arg_t ) );
+ handle = calloc( nthread, sizeof( pthread_t ) );
+ pthread_mutex_init( &mutex, NULL );
+
+ for( i=0; i<nthread; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].njob = njob;
+ targ[i].jobpospt = &jobpos;
+ targ[i].gapmap = gapmap;
+ targ[i].nogap = nogap;
+ targ[i].nlenmax = nlenmax;
+ targ[i].pairprob = pairprob;
+ targ[i].mutex = &mutex;
+
+// athread( targ );
+ pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
+
+ }
+
+ for( i=0; i<nthread; i++ )
+ {
+ pthread_join( handle[i], NULL );
+ }
+ pthread_mutex_destroy( &mutex );
+
+
+ for( i=0; i<njob; i++ )
+ {
+ fprintf( stdout, ">%d\n", i );
+ outmccaskill( stdout, pairprob[i], nlenmax );
+ }
+ }
+ else
+#endif
+ {
+ for( i=0; i<njob; i++ )
+ {
+ fprintf( stderr, "%d / %d\n", i+1, njob );
+ commongappick_record( 1, nogap+i, gapmap[i] );
+ infp = fopen( "_mccaskillinorg", "w" );
+// fprintf( infp, ">in\n%s\n", nogap[i] );
+ fprintf( infp, ">in\n" );
+ write1seq( infp, nogap[i] );
+ fclose( infp );
+
+ system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran
+ sprintf( com, "env PATH=%s mxscarnamod -m -writebpp _mccaskillin > _mccaskillout 2>_dum", whereismccaskillmea );
+ res = system( com );
+
+ if( res )
+ {
+ fprintf( stderr, "ERROR IN mccaskill_mea\n" );
+ exit( 1 );
+ }
+
+ infp = fopen( "_mccaskillout", "r" );
+ readrawmccaskill( infp, pairprob[i], nlenmax );
+ fclose( infp );
+ fprintf( stdout, ">%d\n", i );
+ outmccaskill( stdout, pairprob[i], nlenmax );
+ }
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ for( j=0; j<nlen[i]; j++ ) for( pairprobpt=pairprob[i][j]; pairprobpt->bestpos!=-1; pairprobpt++ )
+ {
+ left = gapmap[i][j];
+ right = gapmap[i][pairprobpt->bestpos];
+ prob = pairprobpt->bestscore;
+
+ for( pt=alnpairprob[left]; pt->bestpos!=-1; pt++ )
+ if( pt->bestpos == right ) break;
+
+ if( pt->bestpos == -1 )
+ {
+ alnpairprob[left] = (RNApair *)realloc( alnpairprob[left], (alnpairnum[left]+2) * sizeof( RNApair ) );
+ adpos = alnpairnum[left];
+ alnpairnum[left]++;
+ alnpairprob[left][adpos].bestscore = 0.0;
+ alnpairprob[left][adpos].bestpos = right;
+ alnpairprob[left][adpos+1].bestscore = -1.0;
+ alnpairprob[left][adpos+1].bestpos = -1;
+ pt = alnpairprob[left]+adpos;
+ }
+ else
+ adpos = pt-alnpairprob[left];
+
+ pt->bestscore += prob;
+ if( pt->bestpos != right )
+ {
+ fprintf( stderr, "okashii!\n" );
+ exit( 1 );
+ }
+// fprintf( stderr, "adding %d-%d, %f\n", left, right, prob );
+ }
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ for( j=0; j<nlenmax; j++ ) free( pairprob[i][j] );
+ free( pairprob[i] );
+ }
+ free( pairprob );
+ for( j=0; j<nlenmax; j++ ) free( alnpairprob[j] );
+ free( alnpairprob );
+ free( alnpairnum );
+ fprintf( stderr, "%d thread(s)\n", nthread );
+ return( 0 );
+
+#if 0
+ fprintf( stdout, "result=\n" );
+
+ for( i=0; i<nlenmax; i++ ) for( pairprobpt=alnpairprob[i]; pairprobpt->bestpos!=-1; pairprobpt++ )
+ {
+ pairprobpt->bestscore /= (float)njob;
+ left = i;
+ right = pairprobpt->bestpos;
+ prob = pairprobpt->bestscore;
+ fprintf( stdout, "%d-%d, %f\n", left, right, prob );
+ }
+
+ return( 0 );
+#endif
+}
--- /dev/null
+#!/usr/bin/env bash
+make clean
+make
+rm -rf binaries32
+mkdir binaries32
+mv ../binaries/* binaries32/
+
+export PATH=/MinGW64/mingw-w64-1.0-bin_i686-mingw_20100702/bin:$PATH
+export C_INCLUDE_PATH=/MinGW64/mingw-w64-1.0-bin_i686-mingw_20100702/include
+export LIBRARY_PATH=/MinGW64/mingw-w64-1.0-bin_i686-mingw_20100702/lib
+make clean
+make
+rm -rf binaries64
+mkdir binaries64
+mv ../binaries/* binaries64/
--- /dev/null
+double polarity_[] =
+{
+ 8.1, /* A */
+ 10.5, /* R */
+ 11.6, /* N */
+ 13.0, /* D */
+ 5.5, /* C */
+ 10.5, /* Q */
+ 12.3, /* E */
+ 9.0, /* G */
+ 10.4, /* H */
+ 5.2, /* I */
+ 4.9, /* L */
+ 11.3, /* K */
+ 5.7, /* M */
+ 5.2, /* F */
+ 8.0, /* P */
+ 9.2, /* S */
+ 8.6, /* T */
+ 5.4, /* W */
+ 6.2, /* Y */
+ 5.9, /* V */
+};
+
+double volume_[] =
+{
+ 31.0, /* A */
+ 124.0, /* R */
+ 56.0, /* N */
+ 54.0, /* D */
+ 55.0, /* C */
+ 85.0, /* Q */
+ 83.0, /* E */
+ 3.0, /* G */
+ 96.0, /* H */
+ 111.0, /* I */
+ 111.0, /* L */
+ 119.0, /* K */
+ 105.0, /* M */
+ 132.0, /* F */
+ 32.5, /* P */
+ 32.0, /* S */
+ 61.0, /* T */
+ 170.0, /* W */
+ 136.0, /* Y */
+ 84.0, /* V */
+};
--- /dev/null
+int locpenaltym = -1440;
+int exgpm = +0; /* != 0 nisuruto kowareru. exgp ha constants.c de kurikomu */
+char locaminom[] = "ARNDCQEGHILKMFPSTWYVBZX.-J";
+char locgrpm[] =
+{
+ 0, 3, 2, 2, 5, 2, 2, 0, 3, 1, 1, 3, 1, 4, 0, 0, 0, 4, 4, 1, 2, 2,
+ 6, 6, 6, 1,
+};
+int locn_dism[26][26] =
+ {
+ {
+ 600, -235, 91, -78, 202, 51, -103, 340, -21, -169,
+ -189, -246, -92, -323, 582, 454, 342, -400, -309, 71,
+ 7, -26, -15, -400, 0,-1400,
+ },
+
+ {
+ -235, 600, 17, -69, -275, 277, 185, -400, 365, -112,
+ -149, 485, -55, -106, -229, -183, 20, -178, 22, -95,
+ -26, 231, -15, -400, 0,-1400,
+ },
+
+ {
+ 91, 17, 600, 414, -209, 317, 357, 39, 231, -363,
+ -398, 74, -280, -400, 85, 225, 200, -400, -378, -189,
+ 507, 337, -15, -400, 0,-1400,
+ },
+
+ {
+ -78, -69, 414, 600, -395, 179, 342, -78, 108, -400,
+ -400, 14, -400, -400, -86, 65, 14, -400, -400, -372,
+ 507, 261, -15, -400, 0,-1400,
+ },
+
+ {
+ 202, -275, -209, -395, 600, -109, -332, -35, -132, 134,
+ 128, -335, 182, -40, 220, 74, 185, -355, -81, 354,
+ -302, -220, -15, -400, 0,-1400,
+ },
+
+ {
+ 51, 277, 317, 179, -109, 600, 360, -109, 508, -135,
+ -172, 297, -58, -203, 51, 128, 280, -378, -109, -9,
+ 248, 480, -15, -400, 0,-1400,
+ },
+
+ {
+ -103, 185, 357, 342, -332, 360, 600, -195, 325, -369,
+ -400, 274, -295, -400, -109, 11, 77, -400, -321, -249,
+ 350, 480, -15, -400, 0,-1400,
+ },
+
+ {
+ 340, -400, 39, -78, -35, -109, -195, 600, -195, -400,
+ -400, -400, -355, -400, 322, 357, 114, -400, -400, -189,
+ -19, -152, -15, -400, 0,-1400,
+ },
+
+ {
+ -21, 365, 231, 108, -132, 508, 325, -195, 600, -100,
+ -141, 374, -26, -152, -15, 45, 222, -303, -49, -3,
+ 169, 417, -15, -400, 0,-1400,
+ },
+
+ {
+ -169, -112, -363, -400, 134, -135, -369, -400, -100, 600,
+ 560, -212, 517, 425, -149, -243, -12, 108, 354, 357,
+ -400, -252, -15, -400, 0,-1400,
+ },
+
+ {
+ -189, -149, -398, -400, 128, -172, -400, -400, -141, 560,
+ 600, -252, 482, 420, -172, -269, -43, 105, 331, 340,
+ -400, -290, -15, -400, 0,-1400,
+ },
+
+ {
+ -246, 485, 74, 14, -335, 297, 274, -400, 374, -212,
+ -252, 600, -152, -215, -240, -175, -1, -289, -92, -172,
+ 44, 285, -15, -400, 0,-1400,
+ },
+
+ {
+ -92, -55, -280, -400, 182, -58, -295, -355, -26, 517,
+ 482, -152, 600, 365, -75, -163, 68, 59, 334, 422,
+ -368, -176, -15, -400, 0,-1400,
+ },
+
+ {
+ -323, -106, -400, -400, -40, -203, -400, -400, -152, 425,
+ 420, -215, 365, 600, -306, -386, -143, 282, 462, 191,
+ -400, -315, -15, -400, 0,-1400,
+ },
+
+ {
+ 582, -229, 85, -86, 220, 51, -109, 322, -15, -149,
+ -172, -240, -75, -306, 600, 440, 351, -400, -292, 88,
+ 0, -29, -15, -400, 0,-1400,
+ },
+
+ {
+ 454, -183, 225, 65, 74, 128, 11, 357, 45, -243,
+ -269, -175, -163, -386, 440, 600, 345, -400, -352, -15,
+ 145, 70, -15, -400, 0,-1400,
+ },
+
+ {
+ 342, 20, 200, 14, 185, 280, 77, 114, 222, -12,
+ -43, -1, 68, -143, 351, 345, 600, -400, -100, 194,
+ 107, 178, -15, -400, 0,-1400,
+ },
+
+ {
+ -400, -178, -400, -400, -355, -378, -400, -400, -303, 108,
+ 105, -289, 59, 282, -400, -400, -400, 600, 297, -118,
+ -400, -400, -15, -400, 0,-1400,
+ },
+
+ {
+ -309, 22, -378, -400, -81, -109, -321, -400, -49, 354,
+ 331, -92, 334, 462, -292, -352, -100, 297, 600, 165,
+ -400, -215, -15, -400, 0,-1400,
+ },
+
+ {
+ 71, -95, -189, -372, 354, -9, -249, -189, -3, 357,
+ 340, -172, 422, 191, 88, -15, 194, -118, 165, 600,
+ -280, -129, -15, -400, 0,-1400,
+ },
+
+ {
+ 7, -26, 507, 507, -302, 248, 350, -19, 169, -400,
+ -400, 44, -368, -400, 0, 145, 107, -400, -400, -280,
+ 507, 299, -400, -400, 0,-1400,
+ },
+
+ {
+ -26, 231, 337, 261, -220, 480, 480, -152, 417, -252,
+ -290, 285, -176, -315, -29, 70, 178, -400, -215, -129,
+ 299, 480, -400, -400, 0,-1400,
+ },
+
+ {
+ -15, -15, -15, -15, -15, -15, -15, -15, -15, -15,
+ -15, -15, -15, -15, -15, -15, -15, -15, -15, -15,
+ -400, -400, -400, -400, 0,-1400,
+ },
+
+ {
+ -400, -400, -400, -400, -400, -400, -400, -400, -400, -400,
+ -400, -400, -400, -400, -400, -400, -400, -400, -400, -400,
+ -400, -400, -400, -400, 0,-1400,
+ },
+
+ {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0,
+ },
+
+ {
+-1400,-1400,-1400,-1400,-1400,-1400,-1400,-1400,-1400,-1400,
+-1400,-1400,-1400,-1400,-1400,-1400,-1400,-1400,-1400,-1400,
+-1400,-1400,-1400,-1400, 0, 1600,
+ },
+ };
--- /dev/null
+#define USE_XCED 0
+
+#if USE_XCED
+#include "config.h"
+#include "share.h"
+#else
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <stddef.h>
+#include <sys/types.h>
+#include <string.h>
+#include <unistd.h>
+#include <math.h>
+#include <ctype.h>
+#include "mtxutl.h"
+#include <float.h>
+#ifdef enablemultithread
+#include <pthread.h>
+#endif
+
+#define VERSION "6.857b"
+#define SHOWVERSION fprintf( stderr, "%s (%s) Version " VERSION " alg=%c, model=%s\n%d thread(s)\n", progName( argv[0] ), (dorp=='d')?"nuc":"aa", alg, modelname, nthread )
+
+#define FFT_THRESHOLD 80
+#define FFT_WINSIZE_P 20
+#define FFT_WINSIZE_D 100
+#define DISPSEQF 60
+#define DISPSITEI 0
+#define MAXITERATION 500
+#define M 50000 /* njob no saidaiti */
+#define N 5000000 /* nlen no saidaiti */
+#define MAXSEG 100000
+#define B 256
+#define C 60 /* 1 gyou no mojisuu */
+#define D 6
+#define rnd() ( ( 1.0 / ( RAND_MAX + 1.0 ) ) * rand() )
+#define MAX(X,Y) ( ((X)>(Y))?(X):(Y) )
+#define MIN(X,Y) ( ((X)<(Y))?(X):(Y) )
+#define G(X) ( ((X)>(0))?(X):(0) )
+#define BEFF 1.0 /* 0.6 ni suruto zureru */
+#define WIN 3
+#define SGAPP -1000
+#define GETA2 0.001
+#define GETA3 0.001
+#define NOTSPECIFIED 100009
+#define SUEFF 0.1 /* upg/(spg+upg) -> sueff.sed */
+#define DIVLOCAL 0
+#define INTMTXSCALE 1000000.0
+#define JTT 201
+#define TM 202
+
+extern char modelname[100];
+extern int njob, nlenmax;
+extern int amino_n[0x80];
+extern char amino_grp[0x80];
+extern int amino_dis[0x80][0x80];
+extern int amino_disLN[0x80][0x80];
+extern double amino_dis_consweight_multi[0x80][0x80];
+extern int n_dis[26][26];
+extern int n_disFFT[26][26];
+extern float n_dis_consweight_multi[26][26];
+extern char amino[26];
+extern double polarity[20];
+extern double volume[20];
+extern int ribosumdis[37][37];
+
+extern int ppid;
+extern double thrinter;
+extern double fastathreshold;
+extern int pslocal, ppslocal;
+extern int constraint;
+extern int divpairscore;
+extern int fmodel; // 1-> fmodel 0->default -1->raw
+extern int nblosum; // 45, 50, 62, 80
+extern int kobetsubunkatsu;
+extern int bunkatsu;
+extern int dorp;
+extern int niter;
+extern int contin;
+extern int calledByXced;
+extern int devide;
+extern int scmtd;
+extern int weight;
+extern int utree;
+extern int tbutree;
+extern int refine;
+extern int check;
+extern double cut;
+extern int cooling;
+extern int penalty, ppenalty, penaltyLN;
+extern int RNApenalty, RNAppenalty;
+extern int RNApenalty_ex, RNAppenalty_ex;
+extern int penalty_ex, ppenalty_ex, penalty_exLN;
+extern int penalty_EX, ppenalty_EX;
+extern int penalty_OP, ppenalty_OP;
+extern int offset, poffset, offsetLN, offsetFFT;
+extern int RNAthr, RNApthr;
+extern int scoremtx;
+extern int TMorJTT;
+extern char use_fft;
+extern char force_fft;
+extern int nevermemsave;
+extern int fftscore;
+extern int fftWinSize;
+extern int fftThreshold;
+extern int fftRepeatStop;
+extern int fftNoAnchStop;
+extern int divWinSize;
+extern int divThreshold;
+extern int disp;
+extern int outgap;
+extern char alg;
+extern int cnst;
+extern int mix;
+extern int tbitr;
+extern int tbweight;
+extern int tbrweight;
+extern int disopt;
+extern int pamN;
+extern int checkC;
+extern float geta2;
+extern int treemethod;
+extern int kimuraR;
+extern char *swopt;
+extern int fftkeika;
+extern int score_check;
+extern char *inputfile;
+extern char *addfile;
+extern int addprofile;
+extern float consweight_multi;
+extern float consweight_rna;
+extern char RNAscoremtx;
+
+extern char *signalSM;
+extern FILE *prep_g;
+extern FILE *trap_g;
+extern char **seq_g;
+extern char **res_g;
+extern int rnakozo;
+extern char rnaprediction;
+
+/* sengen no ichi ha koko dake de ha nai */
+extern void constants();
+extern char **Calignm1();
+extern char **Dalignm1();
+extern char **align0();
+extern double Cscore_m_1( char **, int, int, double ** );
+extern double score_m_1( char **, int, int, double ** );
+extern double score_calc0( char **, int, double **, int );
+extern char seqcheck( char ** );
+extern float substitution( char *, char * );
+extern float substitution_score( char *, char * );
+extern float substitution_nid( char *, char * );
+extern float substitution_hosei( char *, char * );
+extern double ipower( double, int );
+extern float translate_and_Calign();
+extern float A__align();
+extern float A__align11();
+extern float A__align_gapmap();
+extern float partA__align();
+extern float L__align11();
+extern float G__align11();
+extern float Falign();
+extern float Falign_localhom();
+extern float Conalign();
+extern float Aalign();
+extern float imp_match_out_sc( int, int );
+extern float part_imp_match_out_sc( int, int );
+extern void ErrorExit();
+extern void cpmx_calc();
+extern void intergroup_score( char **, char **, double *, double *, int, int, int, double * );
+extern int conjuctionfortbfast();
+extern int fastconjuction();
+extern char seqcheck( char ** );
+
+typedef struct _LocalHom
+{
+ int nokori;
+ struct _LocalHom *next;
+ struct _LocalHom *last;
+ int start1;
+ int end1;
+ int start2;
+ int end2;
+ double opt;
+ int overlapaa;
+ int extended;
+ double importance;
+ float fimportance;
+ double wimportance;
+ char korh;
+} LocalHom;
+
+typedef struct _NodeInCub
+{
+ int step;
+ int LorR;
+} NodeInCub;
+
+typedef struct _Node
+{
+ struct _Node *children[3];
+ int tmpChildren[3];
+ double length[3];
+ double *weightptr[3];
+ int top[3];
+ int *members[3];
+} Node;
+
+typedef struct _Segment
+{
+ int start;
+ int end;
+ int center;
+ double score;
+ int skipForeward;
+ int skipBackward;
+ struct _Segment *pair;
+ int number;
+} Segment;
+
+typedef struct _Segments
+{
+ Segment group1;
+ Segment group2;
+ int number1;
+ int number2;
+} Segments;
+
+typedef struct _Bchain
+{
+ struct _Bchain *next;
+ struct _Bchain *prev;
+ int pos;
+} Bchain;
+
+typedef struct _Achain
+{
+ int next;
+ int prev;
+// int curr;
+} Achain;
+
+
+typedef struct _Fukusosuu
+{
+ double R;
+ double I;
+} Fukusosuu;
+
+typedef struct _Gappattern
+{
+ int len;
+ float freq;
+} Gappat;
+
+typedef struct _RNApair
+{
+ int uppos;
+ float upscore;
+ int downpos;
+ float downscore;
+ int bestpos;
+ float bestscore;
+} RNApair;
+
+typedef struct _Treedep
+{
+ int child0;
+ int child1;
+ int done;
+} Treedep;
+
+
+#include "fft.h"
+#include "dp.h"
+#include "functions.h"
+
+#ifdef enablemultithread
+#define TLS __thread
+#else
+#define TLS
+#endif
+
+extern TLS int commonAlloc1;
+extern TLS int commonAlloc2;
+extern TLS int **commonIP;
+extern TLS int **commonJP;
+extern int nthread;
+extern int randomseed;
+extern int parallelizationstrategy;
+#define BESTFIRST 0
+#define BAATARI0 1
+#define BAATARI1 2
+#define BAATARI2 3
+
+extern int scoreout;
+extern int outnumber;
+
+extern char *newgapstr;
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+#if 0
+int seqlen( char *seq )
+{
+ int val = 0;
+ while( *seq )
+ if( *seq++ != '-' ) val++;
+ return( val );
+}
+#else
+int seqlen( char *seq )
+{
+ int val = 0;
+ if( *newgapstr == '-' )
+ {
+ while( *seq )
+ if( *seq++ != '-' ) val++;
+ }
+ else
+ {
+ while( *seq )
+ {
+ if( *seq != '-' && *seq != *newgapstr ) val++;
+ seq++;
+ }
+ }
+ return( val );
+}
+#endif
+
+int intlen( int *num )
+{
+ int value = 0;
+ while( *num++ != -1 ) value++;
+ return( value );
+}
+
+char seqcheck( char **seq )
+{
+ int i, len;
+ char **seqbk = seq;
+ while( *seq )
+ {
+ len = strlen( *seq );
+ for( i=0; i<len; i++ )
+ {
+ if( amino_n[(int)(*seq)[i]] == -1 )
+ {
+
+ fprintf( stderr, "========================================================================= \n" );
+ fprintf( stderr, "========================================================================= \n" );
+ fprintf( stderr, "=== \n" );
+ fprintf( stderr, "=== Alphabet '%c' is unknown.\n", (*seq)[i] );
+ fprintf( stderr, "=== Please check site %d in sequence %d.\n", i+1, (int)(seq-seqbk+1) );
+ fprintf( stderr, "=== \n" );
+ fprintf( stderr, "=== To make an alignment having unusual characters (U, @, #, etc), try\n" );
+ fprintf( stderr, "=== %% mafft --anysymbol input > output\n" );
+ fprintf( stderr, "=== \n" );
+ fprintf( stderr, "========================================================================= \n" );
+ fprintf( stderr, "========================================================================= \n" );
+ return( (int)(*seq)[i] );
+ }
+ }
+ seq++;
+ }
+ return( 0 );
+}
+
+void scmx_calc( int icyc, char **aseq, double *effarr, float **scmx )
+{
+ int i, j, lgth;
+
+ lgth = strlen( aseq[0] );
+ for( j=0; j<lgth; j++ )
+ {
+ for( i=0; i<26; i++ )
+ {
+ scmx[i][j] = 0;
+ }
+ }
+ for( i=0; i<icyc+1; i++ )
+ {
+ int id;
+ id = amino_n[(int)aseq[i][0]];
+ scmx[id][0] += (float)effarr[i];
+ }
+ for( j=1; j<lgth-1; j++ )
+ {
+ for( i=0; i<icyc+1; i++ )
+ {
+ int id;
+ id = amino_n[(int)aseq[i][j]];
+ scmx[id][j] += (float)effarr[i];
+ }
+ }
+ for( i=0; i<icyc+1; i++ )
+ {
+ int id;
+ id = amino_n[(int)aseq[i][lgth-1]];
+ scmx[id][lgth-1] += (float)effarr[i];
+ }
+}
+
+void exitall( char arr[] )
+{
+ fprintf( stderr, "%s\n", arr );
+ exit( 1 );
+}
+
+void display( char **seq, int nseq )
+{
+ int i, imax;
+ char b[121];
+
+ if( !disp ) return;
+ if( nseq > DISPSEQF ) imax = DISPSEQF;
+ else imax = nseq;
+ fprintf( stderr, " ....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+\n" );
+ for( i=0; i<+imax; i++ )
+ {
+ strncpy( b, seq[i]+DISPSITEI, 120 );
+ b[120] = 0;
+ fprintf( stderr, "%3d %s\n", i+1, b );
+ }
+}
+#if 0
+double intergroup_score( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len )
+{
+ int i, j, k;
+ double score;
+ double tmpscore;
+ char *mseq1, *mseq2;
+ double efficient;
+ char xxx[100];
+
+// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
+// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
+
+ score = 0.0;
+ for( i=0; i<clus1; i++ ) for( j=0; j<clus2; j++ )
+ {
+ efficient = eff1[i] * eff2[j];
+ mseq1 = seq1[i];
+ mseq2 = seq2[j];
+ tmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+
+ if( mseq1[k] == '-' )
+ {
+ tmpscore += penalty;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ while( mseq1[++k] == '-' )
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ k--;
+ if( k >len-2 ) break;
+ continue;
+ }
+ if( mseq2[k] == '-' )
+ {
+ tmpscore += penalty;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ while( mseq2[++k] == '-' )
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ }
+ score += (double)tmpscore * efficient;
+#if 1
+ sprintf( xxx, "%f", score );
+// fprintf( stderr, "## score in intergroup_score = %f\n", score );
+#endif
+ }
+#if 0
+ fprintf( stderr, "###score = %f\n", score );
+#endif
+#if 0
+ fprintf( stderr, "## score in intergroup_score = %f\n", score );
+#endif
+ return( score );
+}
+#endif
+
+void intergroup_score_consweight( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value )
+{
+ int i, j, k;
+ int len2 = len - 2;
+ int ms1, ms2;
+ double tmpscore;
+ char *mseq1, *mseq2;
+ double efficient;
+
+// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
+// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
+
+
+
+ *value = 0.0;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ efficient = eff1[i] * eff2[j]; /* \e$B$J$<$+G[Ns$r;H$o$J$$$H$*$+$7$/$J$k\e(B, \e$BB?J,%P%0\e(B */
+ mseq1 = seq1[i];
+ mseq2 = seq2[j];
+ tmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ ms1 = (int)mseq1[k];
+ ms2 = (int)mseq2[k];
+ if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
+ tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+
+ if( ms1 == (int)'-' )
+ {
+ tmpscore += (double)penalty;
+ tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+ while( (ms1=(int)mseq1[++k]) == (int)'-' )
+ ;
+// tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+ k--;
+ if( k >len2 ) break;
+ continue;
+ }
+ if( ms2 == (int)'-' )
+ {
+ tmpscore += (double)penalty;
+ tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+ while( (ms2=(int)mseq2[++k]) == (int)'-' )
+ ;
+// tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+ k--;
+ if( k > len2 ) break;
+ continue;
+ }
+ }
+ *value += (double)tmpscore * (double)efficient;
+// fprintf( stderr, "val in _gapnomi = %f\n", *value );
+ }
+ }
+#if 0
+ fprintf( stdout, "###score = %f\n", score );
+#endif
+#if DEBUG
+ fprintf( stderr, "score in intergroup_score = %f\n", score );
+#endif
+// return( score );
+}
+void intergroup_score_gapnomi( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value )
+{
+ int i, j, k;
+ int len2 = len - 2;
+ int ms1, ms2;
+ double tmpscore;
+ char *mseq1, *mseq2;
+ double efficient;
+
+// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
+// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
+
+
+
+ *value = 0.0;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ efficient = eff1[i] * eff2[j]; /* \e$B$J$<$+G[Ns$r;H$o$J$$$H$*$+$7$/$J$k\e(B, \e$BB?J,%P%0\e(B */
+ mseq1 = seq1[i];
+ mseq2 = seq2[j];
+ tmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ ms1 = (int)mseq1[k];
+ ms2 = (int)mseq2[k];
+ if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
+// tmpscore += (double)amino_dis[ms1][ms2];
+
+ if( ms1 == (int)'-' )
+ {
+ tmpscore += (double)penalty;
+// tmpscore += (double)amino_dis[ms1][ms2];
+ while( (ms1=(int)mseq1[++k]) == (int)'-' )
+ ;
+// tmpscore += (double)amino_dis[ms1][ms2];
+ k--;
+ if( k >len2 ) break;
+ continue;
+ }
+ if( ms2 == (int)'-' )
+ {
+ tmpscore += (double)penalty;
+// tmpscore += (double)amino_dis[ms1][ms2];
+ while( (ms2=(int)mseq2[++k]) == (int)'-' )
+ ;
+// tmpscore += (double)amino_dis[ms1][ms2];
+ k--;
+ if( k > len2 ) break;
+ continue;
+ }
+ }
+ *value += (double)tmpscore * (double)efficient;
+// fprintf( stderr, "val in _gapnomi = %f\n", *value );
+ }
+ }
+#if 0
+ fprintf( stdout, "###score = %f\n", score );
+#endif
+#if DEBUG
+ fprintf( stderr, "score in intergroup_score = %f\n", score );
+#endif
+// return( score );
+}
+
+void intergroup_score( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value )
+{
+ int i, j, k;
+ int len2 = len - 2;
+ int ms1, ms2;
+ double tmpscore;
+ char *mseq1, *mseq2;
+ double efficient;
+
+ double gaptmpscore;
+ double gapscore = 0.0;
+
+// fprintf( stderr, "#### in intergroup_score\n" );
+
+// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
+// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
+
+ *value = 0.0;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ efficient = eff1[i] * eff2[j]; /* \e$B$J$<$+G[Ns$r;H$o$J$$$H$*$+$7$/$J$k\e(B, \e$BB?J,%P%0\e(B */
+ mseq1 = seq1[i];
+ mseq2 = seq2[j];
+ tmpscore = 0.0;
+ gaptmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ ms1 = (int)mseq1[k];
+ ms2 = (int)mseq2[k];
+ if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
+// tmpscore += (double)amino_dis[ms1][ms2];
+ tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+
+ if( ms1 == (int)'-' )
+ {
+ tmpscore += (double)penalty;
+ gaptmpscore += (double)penalty;
+// tmpscore += (double)amino_dis[ms1][ms2];
+ tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+ while( (ms1=(int)mseq1[++k]) == (int)'-' )
+// tmpscore += (double)amino_dis[ms1][ms2];
+ tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+ k--;
+ if( k >len2 ) break;
+ continue;
+ }
+ if( ms2 == (int)'-' )
+ {
+ tmpscore += (double)penalty;
+ gaptmpscore += (double)penalty;
+// tmpscore += (double)amino_dis[ms1][ms2];
+ tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+ while( (ms2=(int)mseq2[++k]) == (int)'-' )
+// tmpscore += (double)amino_dis[ms1][ms2];
+ tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
+ k--;
+ if( k > len2 ) break;
+ continue;
+ }
+ }
+ *value += (double)tmpscore * (double)efficient;
+ gapscore += (double)gaptmpscore * (double)efficient;
+ }
+ }
+#if 0
+ fprintf( stderr, "###gapscore = %f\n", gapscore );
+#endif
+#if DEBUG
+ fprintf( stderr, "score in intergroup_score = %f\n", score );
+#endif
+// return( score );
+}
+void intergroup_score_new( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value )
+{
+ int i, j, k;
+ int len2 = len - 2;
+ int ms1, ms2;
+ double tmpscore;
+ char *mseq1, *mseq2;
+ static double efficient[1];
+
+// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
+// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
+
+ *value = 0.0;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ *efficient = eff1[i] * eff2[j]; /* \e$B$J$<$+G[Ns$r;H$o$J$$$H$*$+$7$/$J$k\e(B, \e$BB?J,%P%0\e(B */
+ mseq1 = seq1[i];
+ mseq2 = seq2[j];
+ tmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ ms1 = (int)mseq1[k];
+ ms2 = (int)mseq2[k];
+ if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
+ tmpscore += (double)amino_dis[ms1][ms2];
+
+ if( ms1 == (int)'-' )
+ {
+ tmpscore += (double)penalty;
+ tmpscore += (double)amino_dis[ms1][ms2];
+ while( (ms1=(int)mseq1[++k]) == (int)'-' )
+ tmpscore += (double)amino_dis[ms1][ms2];
+ k--;
+ if( k >len2 ) break;
+ continue;
+ }
+ if( ms2 == (int)'-' )
+ {
+ tmpscore += (double)penalty;
+ tmpscore += (double)amino_dis[ms1][ms2];
+ while( (ms2=(int)mseq2[++k]) == (int)'-' )
+ tmpscore += (double)amino_dis[ms1][ms2];
+ k--;
+ if( k > len2 ) break;
+ continue;
+ }
+ }
+ *value += (double)tmpscore * (double)*efficient;
+ }
+ }
+#if 0
+ fprintf( stdout, "###score = %f\n", score );
+#endif
+#if DEBUG
+ fprintf( stderr, "score in intergroup_score = %f\n", score );
+#endif
+// return( score );
+}
+
+
+double score_calc5( char **seq, int s, double **eff, int ex ) /* method 3 deha nai */
+{
+ int i, j, k;
+ double c;
+ int len = strlen( seq[0] );
+ double score;
+ double tmpscore;
+ char *mseq1, *mseq2;
+ double efficient;
+#if DEBUG
+ FILE *fp;
+#endif
+
+ score = 0.0;
+ c = 0.0;
+
+ for( i=0; i<s; i++ )
+ {
+
+ if( i == ex ) continue;
+ efficient = eff[i][ex];
+ mseq1 = seq[i];
+ mseq2 = seq[ex];
+ tmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+
+ if( mseq1[k] == '-' )
+ {
+ tmpscore += penalty;
+ while( mseq1[++k] == '-' )
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ if( mseq2[k] == '-' )
+ {
+ tmpscore += penalty;
+ while( mseq2[++k] == '-' )
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ }
+ score += (double)tmpscore * efficient;
+/*
+ fprintf( stdout, "%d-%d tmpscore = %f, eff = %f, tmpscore*eff = %f\n", i, ex, tmpscore, efficient, tmpscore*efficient );
+*/
+ }
+ /*
+ fprintf( stdout, "total score = %f\n", score );
+ */
+
+ for( i=0; i<s-1; i++ )
+ {
+ for( j=i+1; j<s; j++ )
+ {
+ if( i == ex || j == ex ) continue;
+
+ efficient = eff[i][j];
+ mseq1 = seq[i];
+ mseq2 = seq[j];
+ tmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+
+ if( mseq1[k] == '-' )
+ {
+ tmpscore += penalty;
+ while( mseq1[++k] == '-' )
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ if( mseq2[k] == '-' )
+ {
+ tmpscore += penalty;
+ while( mseq2[++k] == '-' )
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ }
+ score += (double)tmpscore * efficient;
+ }
+ }
+/*
+ fprintf( stderr, "score in score_calc5 = %f\n", score );
+*/
+ return( (double)score );
+/*
+
+fprintf( trap_g, "score by fast = %f\n", (float)score );
+
+tmpscore = score = 0.0;
+ for( i=0; i<s; i++ )
+ {
+ if( i == ex ) continue;
+ tmpscore = Cscore_m_1( seq, i, eff );
+ fprintf( stdout, "%d %f\n", i, tmpscore );
+
+ score += tmpscore;
+ }
+ tmpscore = Cscore_m_1( seq, ex, eff );
+ fprintf( stdout, "ex%d %f\n", i, tmpscore );
+ score += tmpscore;
+
+ return( score );
+*/
+}
+
+
+
+double score_calc4( char **seq, int s, double **eff, int ex ) /* method 3 deha nai */
+{
+ int i, j, k;
+ double c;
+ int len = strlen( seq[0] );
+ double score;
+ long tmpscore;
+ char *mseq1, *mseq2;
+ double efficient;
+
+ score = 0.0;
+ c = 0.0;
+/*
+ printf( "in score_calc4\n" );
+ for( i=0; i<s; i++ )
+ {
+ for( j=0; j<s; j++ )
+ {
+ printf( "% 5.3f", eff[i][j] );
+ }
+ printf( "\n" );
+
+ }
+*/
+ for( i=0; i<s-1; i++ )
+ {
+ for( j=i+1; j<s; j++ )
+ {
+ efficient = eff[i][j];
+ if( mix == 1 ) efficient = 1.0;
+ /*
+ printf( "weight for %d v.s. %d = %f\n", i, j, efficient );
+ */
+ mseq1 = seq[i];
+ mseq2 = seq[j];
+ tmpscore = 0;
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]] + 400 * !scoremtx ;
+
+ c += efficient;
+
+ if( mseq1[k] == '-' )
+ {
+ tmpscore += penalty - n_dis[24][0];
+ while( mseq1[++k] == '-' )
+ ;
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ if( mseq2[k] == '-' )
+ {
+ tmpscore += penalty - n_dis[24][0];
+ while( mseq2[++k] == '-' )
+ ;
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ }
+ /*
+ if( x == 65 ) printf( "i=%d j=%d tmpscore=%d l=%d\n", i, j, tmpscore, len );
+ */
+ score += (double)tmpscore * efficient;
+ }
+ }
+ score /= c;
+ return( (double)score );
+}
+
+
+
+void upg2( int nseq, double **eff, int ***topol, double **len )
+{
+ int i, j, k;
+ double tmplen[M];
+
+ static char **pair = NULL;
+
+ if( !pair )
+ {
+ pair = AllocateCharMtx( njob, njob );
+ }
+
+ for( i=0; i<nseq; i++ ) tmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) pair[i][j] = 0;
+ for( i=0; i<nseq; i++ ) pair[i][i] = 1;
+
+ for( k=0; k<nseq-1; k++ )
+ {
+ float minscore = 9999.0;
+ int im = -1, jm = -1;
+ int count;
+
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ if( eff[i][j] < minscore )
+ {
+ minscore = eff[i][j];
+ im = i; jm = j;
+ }
+ }
+ for( i=0, count=0; i<nseq; i++ )
+ if( pair[im][i] > 0 )
+ {
+ topol[k][0][count] = i;
+ count++;
+ }
+ topol[k][0][count] = -1;
+ for( i=0, count=0; i<nseq; i++ )
+ if( pair[jm][i] > 0 )
+ {
+ topol[k][1][count] = i;
+ count++;
+ }
+ topol[k][1][count] = -1;
+
+ len[k][0] = minscore / 2.0 - tmplen[im];
+ len[k][1] = minscore / 2.0 - tmplen[jm];
+
+ tmplen[im] = minscore / 2.0;
+
+ for( i=0; i<nseq; i++ ) pair[im][i] += ( pair[jm][i] > 0 );
+ for( i=0; i<nseq; i++ ) pair[jm][i] = 0;
+
+ for( i=0; i<nseq; i++ )
+ {
+ if( i != im && i != jm )
+ {
+ eff[MIN(i,im)][MAX(i,im)] =
+ ( eff[MIN(i,im)][MAX(i,im)] + eff[MIN(i,jm)][MAX(i,jm)] ) / 2.0;
+ eff[MIN(i,jm)][MAX(i,jm)] = 9999.0;
+ }
+ eff[im][jm] = 9999.0;
+ }
+#if DEBUG
+ printf( "STEP-%03d:\n", k+1 );
+ printf( "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) printf( " %03d", topol[k][0][i] );
+ printf( "\n" );
+ printf( "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) printf( " %03d", topol[k][1][i] );
+ printf( "\n" );
+#endif
+ }
+}
+
+static void setnearest( int nseq, Bchain *acpt, float **eff, float *mindisfrompt, int *nearestpt, int pos )
+{
+ int j;
+ float tmpfloat;
+ float **effptpt;
+ Bchain *acptj;
+
+ *mindisfrompt = 999.9;
+ *nearestpt = -1;
+
+// if( (acpt+pos)->next ) effpt = eff[pos]+(acpt+pos)->next->pos-pos;
+
+// for( j=pos+1; j<nseq; j++ )
+ for( acptj=(acpt+pos)->next; acptj!=NULL; acptj=acptj->next )
+ {
+ j = acptj->pos;
+// if( (tmpfloat=*effpt++) < *mindisfrompt )
+ if( (tmpfloat=eff[pos][j-pos]) < *mindisfrompt )
+ {
+ *mindisfrompt = tmpfloat;
+ *nearestpt = j;
+ }
+ }
+ effptpt = eff;
+// for( j=0; j<pos; j++ )
+ for( acptj=acpt; (acptj&&acptj->pos!=pos); acptj=acptj->next )
+ {
+ j = acptj->pos;
+// if( (tmpfloat=(*effptpt++)[pos-j]) < *mindisfrompt )
+ if( (tmpfloat=eff[j][pos-j]) < *mindisfrompt )
+ {
+ *mindisfrompt = tmpfloat;
+ *nearestpt = j;
+ }
+ }
+}
+
+static void setnearest_double_fullmtx( int nseq, Bchain *acpt, double **eff, double *mindisfrompt, int *nearestpt, int pos )
+{
+ int j;
+ double tmpfloat;
+ double **effptpt;
+ Bchain *acptj;
+
+ *mindisfrompt = 999.9;
+ *nearestpt = -1;
+
+// if( (acpt+pos)->next ) effpt = eff[pos]+(acpt+pos)->next->pos-pos;
+
+// for( j=pos+1; j<nseq; j++ )
+ for( acptj=(acpt+pos)->next; acptj!=NULL; acptj=acptj->next )
+ {
+ j = acptj->pos;
+// if( (tmpfloat=*effpt++) < *mindisfrompt )
+ if( (tmpfloat=eff[pos][j]) < *mindisfrompt )
+ {
+ *mindisfrompt = tmpfloat;
+ *nearestpt = j;
+ }
+ }
+ effptpt = eff;
+// for( j=0; j<pos; j++ )
+ for( acptj=acpt; (acptj&&acptj->pos!=pos); acptj=acptj->next )
+ {
+ j = acptj->pos;
+// if( (tmpfloat=(*effptpt++)[pos-j]) < *mindisfrompt )
+ if( (tmpfloat=eff[j][pos]) < *mindisfrompt )
+ {
+ *mindisfrompt = tmpfloat;
+ *nearestpt = j;
+ }
+ }
+}
+
+
+
+static void loadtreeoneline( int *ar, float *len, FILE *fp )
+{
+ static char gett[1000];
+
+ fgets( gett, 999, fp );
+
+// fprintf( stderr, "gett=%s\n", gett );
+
+
+ sscanf( gett, "%d %d %f %f", ar, ar+1, len, len+1 );
+
+ ar[0]--;
+ ar[1]--;
+
+ if( ar[0] >= ar[1] )
+ {
+ fprintf( stderr, "Incorrect guide tree\n" );
+ exit( 1 );
+ }
+
+
+// fprintf( stderr, "ar[0] = %d, ar[1] = %d\n", ar[0], ar[1] );
+// fprintf( stderr, "len[0] = %f, len[1] = %f\n", len[0], len[1] );
+}
+
+void loadtree( int nseq, int ***topol, float **len, char **name, int *nlen, Treedep *dep )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ static int *hist = NULL;
+ static Bchain *ac = NULL;
+ int im = -1, jm = -1;
+ Bchain *acjmnext, *acjmprev;
+ int prevnode;
+ Bchain *acpti;
+ int *pt1, *pt2, *pt11, *pt22;
+ static int *nmemar;
+ int nmemim, nmemjm;
+ float minscore;
+ int *nearest = NULL; // by D.Mathog, a guess
+ float *mindisfrom = NULL; // by D.Mathog, a guess
+ static char **tree;
+ static char *treetmp;
+ static char *nametmp;
+ FILE *fp;
+ int node[2];
+
+ fp = fopen( "_guidetree", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "cannot open _guidetree\n" );
+ exit( 1 );
+ }
+
+ if( !hist )
+ {
+ hist = AllocateIntVec( njob );
+ ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
+ nmemar = AllocateIntVec( njob );
+ mindisfrom = AllocateFloatVec( njob );
+ nearest = AllocateIntVec( njob );
+ treetmp = AllocateCharVec( njob*50 );
+ nametmp = AllocateCharVec( 31 );
+ tree = AllocateCharMtx( njob, njob*50 );
+ }
+
+
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<30; j++ ) nametmp[j] = 0;
+ for( j=0; j<30; j++ )
+ {
+ if( isalnum( name[i][j] ) )
+ nametmp[j] = name[i][j];
+ else
+ nametmp[j] = '_';
+ }
+ nametmp[30] = 0;
+// sprintf( tree[i], "%d_l=%d_%.20s", i+1, nlen[i], nametmp+1 );
+ sprintf( tree[i], "%d_%.20s", i+1, nametmp+1 );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = ac+i+1;
+ ac[i].prev = ac+i-1;
+ ac[i].pos = i;
+ }
+ ac[nseq-1].next = NULL;
+
+
+ for( i=0; i<nseq; i++ )
+ {
+ hist[i] = -1;
+ nmemar[i] = 1;
+ }
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
+#if 0
+ minscore = 999.9;
+ for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+// fprintf( stderr, "k=%d i=%d\n", k, i );
+ if( mindisfrom[i] < minscore ) // muscle
+ {
+ im = i;
+ minscore = mindisfrom[i];
+ }
+ }
+ jm = nearest[im];
+ if( jm < im )
+ {
+ j=jm; jm=im; im=j;
+ }
+#else
+ minscore = 0.0;
+ len[k][0] = len[k][1] = -1.0;
+ loadtreeoneline( node, len[k], fp );
+ im = node[0];
+ jm = node[1];
+
+ if( len[k][0] == -1.0 || len[k][1] == -1.0 )
+ {
+ fprintf( stderr, "\n\nERROR: Branch length is not given.\n" );
+ exit( 1 );
+ }
+
+ if( len[k][0] < 0.0 ) len[k][0] = 0.0;
+ if( len[k][1] < 0.0 ) len[k][1] = 0.0;
+
+#endif
+
+ prevnode = hist[im];
+ if( dep ) dep[k].child0 = prevnode;
+ nmemim = nmemar[im];
+
+// fprintf( stderr, "prevnode = %d, nmemim = %d\n", prevnode, nmemim );
+
+ intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+
+ nmemjm = nmemar[jm];
+ prevnode = hist[jm];
+ if( dep ) dep[k].child1 = prevnode;
+
+// fprintf( stderr, "prevnode = %d, nmemjm = %d\n", prevnode, nmemjm );
+
+ intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
+ if( !intpt )
+ {
+ fprintf( stderr, "Cannot reallocate topol\n" );
+ exit( 1 );
+ }
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+// len[k][0] = ( minscore - tmptmplen[im] );
+// len[k][1] = ( minscore - tmptmplen[jm] );
+// len[k][0] = -1;
+// len[k][1] = -1;
+
+
+ hist[im] = k;
+ nmemar[im] = nmemim + nmemjm;
+
+ mindisfrom[im] = 999.9;
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ }
+ }
+
+ sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
+ strcpy( tree[im], treetmp );
+
+// fprintf( stderr, "im,jm=%d,%d\n", im, jm );
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ acjmprev->next = acjmnext;
+ if( acjmnext != NULL )
+ acjmnext->prev = acjmprev;
+// free( (void *)eff[jm] ); eff[jm] = NULL;
+
+#if 0 // muscle seems to miss this.
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( nearest[i] == im )
+ {
+// fprintf( stderr, "calling setnearest\n" );
+// setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i );
+ }
+ }
+#endif
+
+
+#if 0
+ fprintf( stdout, "vSTEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
+ fprintf( stdout, "\n" );
+#endif
+ }
+ fclose( fp );
+ fp = fopen( "infile.tree", "w" );
+ fprintf( fp, "%s\n", treetmp );
+ fprintf( fp, "#by loadtree\n" );
+ fclose( fp );
+
+ FreeCharMtx( tree );
+ free( treetmp );
+ free( nametmp );
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+ free( (void *)nmemar ); nmemar = NULL;
+ free( mindisfrom );
+ free( nearest );
+
+
+}
+
+static float sueff1, sueff05;
+static double sueff1_double, sueff05_double;
+
+static float cluster_mix_float( float d1, float d2 )
+{
+ return( MIN( d1, d2 ) * sueff1 + ( d1 + d2 ) * sueff05 );
+}
+static float cluster_average_float( float d1, float d2 )
+{
+ return( ( d1 + d2 ) * 0.5 );
+}
+static float cluster_minimum_float( float d1, float d2 )
+{
+ return( MIN( d1, d2 ) );
+}
+static double cluster_mix_double( double d1, double d2 )
+{
+ return( MIN( d1, d2 ) * sueff1_double + ( d1 + d2 ) * sueff05_double );
+}
+static double cluster_average_double( double d1, double d2 )
+{
+ return( ( d1 + d2 ) * 0.5 );
+}
+static double cluster_minimum_double( double d1, double d2 )
+{
+ return( MIN( d1, d2 ) );
+}
+
+void loadtop( int nseq, float **eff, int ***topol, float **len ) // computes branch length BUG!!
+{
+ int i, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ static Bchain *ac = NULL;
+ float eff1, eff0;
+ static float *tmptmplen = NULL;
+ static int *hist = NULL;
+ int im = -1, jm = -1;
+ Bchain *acjmnext, *acjmprev;
+ int prevnode;
+ Bchain *acpti;
+ int *pt1, *pt2, *pt11, *pt22;
+ static int *nmemar;
+ int nmemim, nmemjm;
+ float minscore;
+ static char **tree;
+ static char *treetmp;
+ FILE *fp;
+ int node[2];
+ float dumfl[2];
+ float (*clusterfuncpt[1])(float,float);
+
+
+ sueff1 = 1 - SUEFF;
+ sueff05 = SUEFF * 0.5;
+ if ( treemethod == 'X' )
+ clusterfuncpt[0] = cluster_mix_float;
+ else if ( treemethod == 'E' )
+ clusterfuncpt[0] = cluster_average_float;
+ else if ( treemethod == 'q' )
+ clusterfuncpt[0] = cluster_minimum_float;
+ else
+ {
+ fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
+ exit( 1 );
+ }
+
+ fp = fopen( "_guidetree", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "cannot open _guidetree\n" );
+ exit( 1 );
+ }
+
+ if( !hist )
+ {
+ treetmp = AllocateCharVec( njob*50 );
+ tree = AllocateCharMtx( njob, njob*50 );
+ hist = AllocateIntVec( njob );
+ tmptmplen = AllocateFloatVec( njob );
+ ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
+ nmemar = AllocateIntVec( njob );
+ }
+
+ for( i=0; i<nseq; i++ ) sprintf( tree[i], "%d", i+1 );
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = ac+i+1;
+ ac[i].prev = ac+i-1;
+ ac[i].pos = i;
+ }
+ ac[nseq-1].next = NULL;
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ hist[i] = -1;
+ nmemar[i] = 1;
+ }
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
+
+#if 0
+ minscore = 99999.9;
+ for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
+ {
+ effpt = eff[i=acpti->pos];
+// i = acpti->pos;
+ for( acptj=acpti->next; acptj!=NULL; acptj=acptj->next )
+ {
+// j=acptj->pos;
+// tmpfloat = eff[i][j-i];
+// if( tmpfloat < minscore )
+ if( (tmpfloat= effpt[(j=acptj->pos)-i]) < minscore )
+ {
+ minscore = tmpfloat;
+ im = i; jm = j;
+ }
+ }
+ }
+
+// fprintf( stderr, "im=%d, jm=%d, minscore = %f\n", im, jm, minscore );
+#else
+ dumfl[0] = dumfl[1] = -1.0;
+ loadtreeoneline( node, dumfl, fp );
+ im = node[0];
+ jm = node[1];
+ minscore = eff[im][jm-im];
+
+// fprintf( stderr, "im=%d, jm=%d, minscore = %f\n", im, jm, minscore );
+
+
+ if( dumfl[0] != -1.0 || dumfl[1] != -1.0 )
+ {
+ fprintf( stderr, "\n\nERROR: Branch length should not be given.\n" );
+ exit( 1 );
+ }
+
+#endif
+
+
+ prevnode = hist[im];
+ nmemim = nmemar[im];
+ intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ prevnode = hist[jm];
+ nmemjm = nmemar[jm];
+ intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
+ if( !intpt )
+ {
+ fprintf( stderr, "Cannot reallocate topol\n" );
+ exit( 1 );
+ }
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+ len[k][0] = ( minscore - tmptmplen[im] );
+ len[k][1] = ( minscore - tmptmplen[jm] );
+
+ if( len[k][0] < 0.0 ) len[k][0] = 0.0;
+ if( len[k][1] < 0.0 ) len[k][1] = 0.0;
+
+ tmptmplen[im] = minscore;
+
+ hist[im] = k;
+ nmemar[im] = nmemim + nmemjm;
+
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim-miniim];
+ eff1 = eff[minijm][maxijm-minijm];
+#if 0
+ eff[miniim][maxiim-miniim] =
+ MIN( eff0, eff1 ) * sueff1 + ( eff0 + eff1 ) * sueff05;
+#else
+ eff[miniim][maxiim-miniim] =
+ (clusterfuncpt[0])( eff0, eff1 );
+#endif
+ }
+ }
+// sprintf( treetmp, "(%s,%s)", tree[im], tree[jm] );
+ sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
+ strcpy( tree[im], treetmp );
+
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ acjmprev->next = acjmnext;
+ if( acjmnext != NULL )
+ acjmnext->prev = acjmprev;
+ free( (void *)eff[jm] ); eff[jm] = NULL;
+#if 0
+ fprintf( stdout, "vSTEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
+ fprintf( stdout, "\n" );
+#endif
+ }
+#if 1
+ fclose( fp );
+ fp = fopen( "infile.tree", "w" );
+ fprintf( fp, "%s\n", treetmp );
+ fprintf( fp, "by loadtop\n" );
+ fclose( fp );
+#endif
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+ free( (void *)nmemar ); nmemar = NULL;
+
+}
+
+
+void fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( int nseq, float **eff, int ***topol, float **len, char **name, int *nlen, Treedep *dep )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ float tmpfloat;
+ float eff1, eff0;
+ static float *tmptmplen = NULL;
+ static int *hist = NULL;
+ static Bchain *ac = NULL;
+ int im = -1, jm = -1;
+ Bchain *acjmnext, *acjmprev;
+ int prevnode;
+ Bchain *acpti;
+ int *pt1, *pt2, *pt11, *pt22;
+ static int *nmemar;
+ int nmemim, nmemjm;
+ float minscore;
+ int *nearest = NULL; // by D.Mathog, a guess
+ float *mindisfrom = NULL; // by D.Mathog, a guess
+ static char **tree;
+ static char *treetmp;
+ static char *nametmp, *nameptr, *tmpptr;
+ FILE *fp;
+ float (*clusterfuncpt[1])(float,float);
+
+
+ sueff1 = 1 - SUEFF;
+ sueff05 = SUEFF * 0.5;
+ if ( treemethod == 'X' )
+ clusterfuncpt[0] = cluster_mix_float;
+ else if ( treemethod == 'E' )
+ clusterfuncpt[0] = cluster_average_float;
+ else if ( treemethod == 'q' )
+ clusterfuncpt[0] = cluster_minimum_float;
+ else
+ {
+ fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
+ exit( 1 );
+ }
+
+ if( !hist )
+ {
+ hist = AllocateIntVec( njob );
+ tmptmplen = AllocateFloatVec( njob );
+ ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
+ nmemar = AllocateIntVec( njob );
+ mindisfrom = AllocateFloatVec( njob );
+ nearest = AllocateIntVec( njob );
+ treetmp = AllocateCharVec( njob*150 );
+ nametmp = AllocateCharVec( 130 );
+ tree = AllocateCharMtx( njob, njob*150 );
+ }
+
+
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<130; j++ ) nametmp[j] = 0;
+ for( j=0; j<130; j++ )
+ {
+ if( name[i][j] == 0 )
+ break;
+ else if( isalnum( name[i][j] ) )
+ nametmp[j] = name[i][j];
+ else
+ nametmp[j] = '_';
+ }
+ nametmp[129] = 0;
+// sprintf( tree[i], "%d_l=%d_%.20s", i+1, nlen[i], nametmp+1 );
+ if( outnumber )
+ nameptr = strstr( nametmp, "_numo_e" ) + 8;
+ else
+ nameptr = nametmp + 1;
+
+ if( (tmpptr=strstr( nameptr, "_oripos__" )) ) nameptr = tmpptr + 9; // = -> _ no tame
+
+ sprintf( tree[i], "%d_%.60s", i+1, nameptr );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = ac+i+1;
+ ac[i].prev = ac+i-1;
+ ac[i].pos = i;
+ }
+ ac[nseq-1].next = NULL;
+
+ for( i=0; i<nseq; i++ ) setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i ); // muscle
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ hist[i] = -1;
+ nmemar[i] = 1;
+ }
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
+
+ minscore = 999.9;
+ for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+// fprintf( stderr, "k=%d i=%d\n", k, i );
+ if( mindisfrom[i] < minscore ) // muscle
+ {
+ im = i;
+ minscore = mindisfrom[i];
+ }
+ }
+ jm = nearest[im];
+ if( jm < im )
+ {
+ j=jm; jm=im; im=j;
+ }
+
+
+ prevnode = hist[im];
+ if( dep ) dep[k].child0 = prevnode;
+ nmemim = nmemar[im];
+ intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ prevnode = hist[jm];
+ if( dep ) dep[k].child1 = prevnode;
+ nmemjm = nmemar[jm];
+ intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
+ if( !intpt )
+ {
+ fprintf( stderr, "Cannot reallocate topol\n" );
+ exit( 1 );
+ }
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+ len[k][0] = ( minscore - tmptmplen[im] );
+ len[k][1] = ( minscore - tmptmplen[jm] );
+
+ tmptmplen[im] = minscore;
+
+ hist[im] = k;
+ nmemar[im] = nmemim + nmemjm;
+
+ mindisfrom[im] = 999.9;
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim-miniim];
+ eff1 = eff[minijm][maxijm-minijm];
+#if 0
+ tmpfloat = eff[miniim][maxiim-miniim] =
+ MIN( eff0, eff1 ) * sueff1 + ( eff0 + eff1 ) * sueff05;
+#else
+ tmpfloat = eff[miniim][maxiim-miniim] =
+ (clusterfuncpt[0])( eff0, eff1 );
+#endif
+ if( tmpfloat < mindisfrom[i] )
+ {
+ mindisfrom[i] = tmpfloat;
+ nearest[i] = im;
+ }
+ if( tmpfloat < mindisfrom[im] )
+ {
+ mindisfrom[im] = tmpfloat;
+ nearest[im] = i;
+ }
+ if( nearest[i] == jm )
+ {
+ nearest[i] = im;
+ }
+ }
+ }
+
+ sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
+ strcpy( tree[im], treetmp );
+
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ acjmprev->next = acjmnext;
+ if( acjmnext != NULL )
+ acjmnext->prev = acjmprev;
+ free( (void *)eff[jm] ); eff[jm] = NULL;
+
+#if 1 // muscle seems to miss this.
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( nearest[i] == im )
+ {
+// fprintf( stderr, "calling setnearest\n" );
+ setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i );
+ }
+ }
+#endif
+
+
+#if 0
+ fprintf( stdout, "vSTEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
+ fprintf( stdout, "\n" );
+#endif
+ }
+ fp = fopen( "infile.tree", "w" );
+ fprintf( fp, "%s\n", treetmp );
+ fclose( fp );
+
+ FreeCharMtx( tree );
+ free( treetmp );
+ free( nametmp );
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+ free( (void *)nmemar ); nmemar = NULL;
+ free( mindisfrom );
+ free( nearest );
+
+}
+
+//void veryfastsupg_double_outtree( int nseq, double **eff, int ***topol, double **len, char **name )
+void fixed_musclesupg_double_treeout( int nseq, double **eff, int ***topol, double **len, char **name )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ double tmpfloat;
+ double eff1, eff0;
+ static double *tmptmplen = NULL;
+ static int *hist = NULL;
+ static Bchain *ac = NULL;
+ int im = -1, jm = -1;
+ Bchain *acjmnext, *acjmprev;
+ int prevnode;
+ Bchain *acpti;
+ int *pt1, *pt2, *pt11, *pt22;
+ static int *nmemar;
+ int nmemim, nmemjm;
+ double minscore;
+ int *nearest = NULL; // by D.Mathog, a guess
+ double *mindisfrom = NULL; // by D.Mathog, a guess
+ static char **tree;
+ static char *treetmp;
+ static char *nametmp, *nameptr, *tmpptr;
+ FILE *fp;
+ double (*clusterfuncpt[1])(double,double);
+
+
+ sueff1_double = 1 - SUEFF;
+ sueff05_double = SUEFF * 0.5;
+ if ( treemethod == 'X' )
+ clusterfuncpt[0] = cluster_mix_double;
+ else if ( treemethod == 'E' )
+ clusterfuncpt[0] = cluster_average_double;
+ else if ( treemethod == 'q' )
+ clusterfuncpt[0] = cluster_minimum_double;
+ else
+ {
+ fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
+ exit( 1 );
+ }
+
+ if( !hist )
+ {
+ hist = AllocateIntVec( njob );
+ tmptmplen = AllocateDoubleVec( njob );
+ ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
+ nmemar = AllocateIntVec( njob );
+ mindisfrom = AllocateDoubleVec( njob );
+ nearest = AllocateIntVec( njob );
+ treetmp = AllocateCharVec( njob*150 );
+ nametmp = AllocateCharVec( 91 );
+ tree = AllocateCharMtx( njob, njob*150 );
+ }
+
+
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<90; j++ ) nametmp[j] = 0;
+ for( j=0; j<90; j++ )
+ {
+ if( name[i][j] == 0 )
+ break;
+ else if( isalnum( name[i][j] ) )
+ nametmp[j] = name[i][j];
+ else
+ nametmp[j] = '_';
+ }
+ nametmp[90] = 0;
+// sprintf( tree[i], "%d_%.60s", i+1, nametmp+1 );
+ if( outnumber )
+ nameptr = strstr( nametmp, "_numo_e" ) + 8;
+ else
+ nameptr = nametmp + 1;
+
+ if( (tmpptr=strstr( nameptr, "_oripos__" )) ) nameptr = tmpptr + 9; // = -> _ no tame
+
+ sprintf( tree[i], "%d_%.60s", i+1, nameptr );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = ac+i+1;
+ ac[i].prev = ac+i-1;
+ ac[i].pos = i;
+ }
+ ac[nseq-1].next = NULL;
+
+ for( i=0; i<nseq; i++ ) setnearest_double_fullmtx( nseq, ac, eff, mindisfrom+i, nearest+i, i ); // muscle
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ hist[i] = -1;
+ nmemar[i] = 1;
+ }
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
+
+ minscore = 999.9;
+ for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+// fprintf( stderr, "k=%d i=%d\n", k, i );
+ if( mindisfrom[i] < minscore ) // muscle
+ {
+ im = i;
+ minscore = mindisfrom[i];
+ }
+ }
+ jm = nearest[im];
+ if( jm < im )
+ {
+ j=jm; jm=im; im=j;
+ }
+
+
+ prevnode = hist[im];
+ nmemim = nmemar[im];
+// intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
+ intpt = topol[k][0];
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ prevnode = hist[jm];
+ nmemjm = nmemar[jm];
+// intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
+ intpt = topol[k][1];
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+ len[k][0] = ( minscore - tmptmplen[im] );
+ len[k][1] = ( minscore - tmptmplen[jm] );
+
+
+ tmptmplen[im] = minscore;
+
+ hist[im] = k;
+ nmemar[im] = nmemim + nmemjm;
+
+ mindisfrom[im] = 999.9;
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+#if 0
+ tmpfloat = eff[miniim][maxiim] =
+ MIN( eff0, eff1 ) * sueff1 + ( eff0 + eff1 ) * sueff05;
+#else
+ tmpfloat = eff[miniim][maxiim] =
+ (clusterfuncpt[0])( eff0, eff1 );
+#endif
+ if( tmpfloat < mindisfrom[i] )
+ {
+ mindisfrom[i] = tmpfloat;
+ nearest[i] = im;
+ }
+ if( tmpfloat < mindisfrom[im] )
+ {
+ mindisfrom[im] = tmpfloat;
+ nearest[im] = i;
+ }
+ if( nearest[i] == jm )
+ {
+ nearest[i] = im;
+ }
+ }
+ }
+
+ sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
+ strcpy( tree[im], treetmp );
+
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ acjmprev->next = acjmnext;
+ if( acjmnext != NULL )
+ acjmnext->prev = acjmprev;
+// free( (void *)eff[jm] ); eff[jm] = NULL;
+
+#if 1 // muscle seems to miss this.
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( nearest[i] == im )
+ {
+// fprintf( stderr, "calling setnearest\n" );
+ setnearest_double_fullmtx( nseq, ac, eff, mindisfrom+i, nearest+i, i );
+ }
+ }
+#endif
+
+
+#if 0
+ fprintf( stdout, "vSTEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
+ fprintf( stdout, "\n" );
+#endif
+ }
+ fp = fopen( "infile.tree", "w" );
+ fprintf( fp, "%s\n", treetmp );
+ fclose( fp );
+
+ FreeCharMtx( tree );
+ free( treetmp );
+ free( nametmp );
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+ free( (void *)nmemar ); nmemar = NULL;
+ free( mindisfrom );
+ free( nearest );
+}
+
+
+void fixed_musclesupg_float_realloc_nobk_halfmtx( int nseq, float **eff, int ***topol, float **len, Treedep *dep )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ float tmpfloat;
+ float eff1, eff0;
+ static float *tmptmplen = NULL;
+ static int *hist = NULL;
+ static Bchain *ac = NULL;
+ int im = -1, jm = -1;
+ Bchain *acjmnext, *acjmprev;
+ int prevnode;
+ Bchain *acpti;
+ int *pt1, *pt2, *pt11, *pt22;
+ static int *nmemar;
+ int nmemim, nmemjm;
+ float minscore;
+// float sueff1 = 1 - SUEFF;
+// float sueff05 = SUEFF * 0.5;
+ int *nearest = NULL; // by Mathog, a guess
+ float *mindisfrom = NULL; // by Mathog, a guess
+ float (*clusterfuncpt[1])(float,float);
+
+
+ sueff1 = 1 - SUEFF;
+ sueff05 = SUEFF * 0.5;
+ if ( treemethod == 'X' )
+ clusterfuncpt[0] = cluster_mix_float;
+ else if ( treemethod == 'E' )
+ clusterfuncpt[0] = cluster_average_float;
+ else if ( treemethod == 'q' )
+ clusterfuncpt[0] = cluster_minimum_float;
+ else
+ {
+ fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
+ exit( 1 );
+ }
+
+ if( !hist )
+ {
+ hist = AllocateIntVec( njob );
+ tmptmplen = AllocateFloatVec( njob );
+ ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
+ nmemar = AllocateIntVec( njob );
+ mindisfrom = AllocateFloatVec( njob );
+ nearest = AllocateIntVec( njob );
+ }
+
+
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = ac+i+1;
+ ac[i].prev = ac+i-1;
+ ac[i].pos = i;
+ }
+ ac[nseq-1].next = NULL;
+
+ for( i=0; i<nseq; i++ ) setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i ); // muscle
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ hist[i] = -1;
+ nmemar[i] = 1;
+ }
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
+
+ minscore = 999.9;
+ for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+// fprintf( stderr, "k=%d i=%d\n", k, i );
+ if( mindisfrom[i] < minscore ) // muscle
+ {
+ im = i;
+ minscore = mindisfrom[i];
+ }
+ }
+ jm = nearest[im];
+ if( jm < im )
+ {
+ j=jm; jm=im; im=j;
+ }
+
+
+ prevnode = hist[im];
+ if( dep ) dep[k].child0 = prevnode;
+ nmemim = nmemar[im];
+ intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ prevnode = hist[jm];
+ if( dep ) dep[k].child1 = prevnode;
+ nmemjm = nmemar[jm];
+ intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
+ if( !intpt )
+ {
+ fprintf( stderr, "Cannot reallocate topol\n" );
+ exit( 1 );
+ }
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+ len[k][0] = ( minscore - tmptmplen[im] );
+ len[k][1] = ( minscore - tmptmplen[jm] );
+
+ tmptmplen[im] = minscore;
+
+ hist[im] = k;
+ nmemar[im] = nmemim + nmemjm;
+
+ mindisfrom[im] = 999.9;
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim-miniim];
+ eff1 = eff[minijm][maxijm-minijm];
+ tmpfloat = eff[miniim][maxiim-miniim] =
+#if 0
+ MIN( eff0, eff1 ) * sueff1 + ( eff0 + eff1 ) * sueff05;
+#else
+ (clusterfuncpt[0])( eff0, eff1 );
+#endif
+ if( tmpfloat < mindisfrom[i] )
+ {
+ mindisfrom[i] = tmpfloat;
+ nearest[i] = im;
+ }
+ if( tmpfloat < mindisfrom[im] )
+ {
+ mindisfrom[im] = tmpfloat;
+ nearest[im] = i;
+ }
+ if( nearest[i] == jm )
+ {
+ nearest[i] = im;
+ }
+ }
+ }
+
+// fprintf( stderr, "im,jm=%d,%d\n", im, jm );
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ acjmprev->next = acjmnext;
+ if( acjmnext != NULL )
+ acjmnext->prev = acjmprev;
+ free( (void *)eff[jm] ); eff[jm] = NULL;
+
+#if 1 // muscle seems to miss this.
+ for( acpti=ac; acpti!=NULL; acpti=acpti->next )
+ {
+ i = acpti->pos;
+ if( nearest[i] == im )
+ {
+// fprintf( stderr, "calling setnearest\n" );
+ setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i );
+ }
+ }
+#endif
+
+
+#if 0
+ fprintf( stdout, "vSTEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
+ fprintf( stdout, "\n" );
+#endif
+ }
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+ free( (void *)nmemar ); nmemar = NULL;
+ free( mindisfrom );
+ free( nearest );
+}
+
+
+
+
+
+
+
+
+void veryfastsupg_double_loadtop( int nseq, double **eff, int ***topol, double **len ) // BUG!!!
+{
+ int i, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ double eff1, eff0;
+ static double *tmptmplen = NULL;
+ static int *hist = NULL;
+ static Achain *ac = NULL;
+ double minscore;
+ static char **tree;
+ static char *treetmp;
+ int im = -1, jm = -1;
+ int prevnode, acjmnext, acjmprev;
+ int *pt1, *pt2, *pt11, *pt22;
+ FILE *fp;
+ int node[2];
+ float dumfl[2];
+
+ fp = fopen( "_guidetree", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "cannot open _guidetree\n" );
+ exit( 1 );
+ }
+
+ if( !hist )
+ {
+ treetmp = AllocateCharVec( njob*50 );
+ tree = AllocateCharMtx( njob, njob*50 );
+ hist = AllocateIntVec( njob );
+ tmptmplen = (double *)malloc( njob * sizeof( double ) );
+ ac = (Achain *)malloc( njob * sizeof( Achain ) );
+ }
+ for( i=0; i<nseq; i++ ) sprintf( tree[i], "%d", i+1 );
+
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = i+1;
+ ac[i].prev = i-1;
+// ac[i].curr = i;
+ }
+ ac[nseq-1].next = -1;
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) hist[i] = -1;
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
+
+#if 0
+ minscore = 99999.9;
+ for( i=0; ac[i].next!=-1; i=ac[i].next )
+ {
+ for( j=ac[i].next; j!=-1; j=ac[j].next )
+ {
+ tmpdouble = eff[i][j];
+ if( tmpdouble < minscore )
+ {
+ minscore = tmpdouble;
+ im = i; jm = j;
+ }
+ }
+ }
+#else
+ dumfl[0] = dumfl[1] = -1.0;
+ loadtreeoneline( node, dumfl, fp );
+ im = node[0];
+ jm = node[1];
+ minscore = eff[im][jm];
+
+// fprintf( stderr, "im=%d, jm=%d, minscore = %f\n", im, jm, minscore );
+
+
+ if( dumfl[0] != -1.0 || dumfl[1] != -1.0 )
+ {
+ fprintf( stderr, "\n\nBranch length should not given.\n" );
+ exit( 1 );
+ }
+#endif
+
+// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
+
+ intpt = topol[k][0];
+ prevnode = hist[im];
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ intpt = topol[k][1];
+ prevnode = hist[jm];
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+ len[k][0] = minscore - tmptmplen[im];
+ len[k][1] = minscore - tmptmplen[jm];
+
+ if( len[k][0] < 0.0 ) len[k][0] = 0.0;
+ if( len[k][1] < 0.0 ) len[k][1] = 0.0;
+
+ tmptmplen[im] = minscore;
+
+ hist[im] = k;
+
+ for( i=0; i!=-1; i=ac[i].next )
+ {
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+ eff[miniim][maxiim] =
+ MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
+ ( eff0 + eff1 ) * 0.5 * SUEFF;
+ }
+ }
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ ac[acjmprev].next = acjmnext;
+ if( acjmnext != -1 )
+ ac[acjmnext].prev = acjmprev;
+
+ sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
+ strcpy( tree[im], treetmp );
+#if 0
+ fprintf( stdout, "STEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
+ fprintf( stdout, "\n" );
+#endif
+ }
+ fclose( fp );
+
+ fp = fopen( "infile.tree", "w" );
+ fprintf( fp, "%s\n", treetmp );
+// fprintf( fp, "by veryfastsupg_double_loadtop\n" );
+ fclose( fp );
+
+#if 1
+ fprintf( stderr, "\n" );
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+ FreeCharMtx( tree );
+ free( treetmp );
+#endif
+}
+
+void veryfastsupg_double_loadtree( int nseq, double **eff, int ***topol, double **len )
+{
+ int i, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ double eff1, eff0;
+ static double *tmptmplen = NULL;
+ static int *hist = NULL;
+ static Achain *ac = NULL;
+ double minscore;
+ static char **tree;
+ static char *treetmp;
+ int im = -1, jm = -1;
+ int prevnode, acjmnext, acjmprev;
+ int *pt1, *pt2, *pt11, *pt22;
+ FILE *fp;
+ int node[2];
+ float lenfl[2];
+
+ fp = fopen( "_guidetree", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "cannot open _guidetree\n" );
+ exit( 1 );
+ }
+
+ if( !hist )
+ {
+ treetmp = AllocateCharVec( njob*50 );
+ tree = AllocateCharMtx( njob, njob*50 );
+ hist = AllocateIntVec( njob );
+ tmptmplen = (double *)malloc( njob * sizeof( double ) );
+ ac = (Achain *)malloc( njob * sizeof( Achain ) );
+ }
+
+ for( i=0; i<nseq; i++ ) sprintf( tree[i], "%d", i+1 );
+
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = i+1;
+ ac[i].prev = i-1;
+// ac[i].curr = i;
+ }
+ ac[nseq-1].next = -1;
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) hist[i] = -1;
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
+
+#if 0
+ minscore = 99999.9;
+ for( i=0; ac[i].next!=-1; i=ac[i].next )
+ {
+ for( j=ac[i].next; j!=-1; j=ac[j].next )
+ {
+ tmpdouble = eff[i][j];
+ if( tmpdouble < minscore )
+ {
+ minscore = tmpdouble;
+ im = i; jm = j;
+ }
+ }
+ }
+#else
+ lenfl[0] = lenfl[1] = -1.0;
+ loadtreeoneline( node, lenfl, fp );
+ im = node[0];
+ jm = node[1];
+ minscore = eff[im][jm];
+
+// fprintf( stderr, "im=%d, jm=%d, minscore = %f\n", im, jm, minscore );
+
+
+ if( lenfl[0] == -1.0 || lenfl[1] == -1.0 )
+ {
+ fprintf( stderr, "\n\nWARNING: Branch length is not given.\n" );
+ exit( 1 );
+ }
+
+ if( lenfl[0] < 0.0 ) lenfl[0] = 0.0;
+ if( lenfl[1] < 0.0 ) lenfl[1] = 0.0;
+#endif
+
+// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
+
+ intpt = topol[k][0];
+ prevnode = hist[im];
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ intpt = topol[k][1];
+ prevnode = hist[jm];
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+#if 0
+ len[k][0] = minscore - tmptmplen[im];
+ len[k][1] = minscore - tmptmplen[jm];
+#else
+ len[k][0] = lenfl[0];
+ len[k][1] = lenfl[1];
+#endif
+
+ tmptmplen[im] = minscore;
+
+ hist[im] = k;
+
+ for( i=0; i!=-1; i=ac[i].next )
+ {
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+ eff[miniim][maxiim] =
+ MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
+ ( eff0 + eff1 ) * 0.5 * SUEFF;
+ }
+ }
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ ac[acjmprev].next = acjmnext;
+ if( acjmnext != -1 )
+ ac[acjmnext].prev = acjmprev;
+
+ sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
+ strcpy( tree[im], treetmp );
+
+#if 0
+ fprintf( stdout, "STEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
+ fprintf( stdout, "\n" );
+#endif
+ }
+ fclose( fp );
+
+
+ fp = fopen( "infile.tree", "w" );
+ fprintf( fp, "%s\n", treetmp );
+// fprintf( fp, "by veryfastsupg_double_loadtree\n" );
+ fclose( fp );
+
+#if 1
+ fprintf( stderr, "\n" );
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+ FreeCharMtx( tree );
+ free( treetmp );
+#endif
+
+
+}
+
+#if 0
+void veryfastsupg_double( int nseq, double **eff, int ***topol, double **len )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ double tmpdouble;
+ double eff1, eff0;
+ static double *tmptmplen = NULL;
+ static int *hist = NULL;
+ static Achain *ac = NULL;
+ double minscore;
+ int im = -1, jm = -1;
+ int prevnode, acjmnext, acjmprev;
+ int *pt1, *pt2, *pt11, *pt22;
+ if( !hist )
+ {
+ hist = AllocateIntVec( njob );
+ tmptmplen = (double *)malloc( njob * sizeof( double ) );
+ ac = (Achain *)malloc( njob * sizeof( Achain ) );
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = i+1;
+ ac[i].prev = i-1;
+// ac[i].curr = i;
+ }
+ ac[nseq-1].next = -1;
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) hist[i] = -1;
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
+
+ minscore = 99999.9;
+ for( i=0; ac[i].next!=-1; i=ac[i].next )
+ {
+ for( j=ac[i].next; j!=-1; j=ac[j].next )
+ {
+ tmpdouble = eff[i][j];
+ if( tmpdouble < minscore )
+ {
+ minscore = tmpdouble;
+ im = i; jm = j;
+ }
+ }
+ }
+
+// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
+
+ intpt = topol[k][0];
+ prevnode = hist[im];
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ intpt = topol[k][1];
+ prevnode = hist[jm];
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+ len[k][0] = minscore - tmptmplen[im];
+ len[k][1] = minscore - tmptmplen[jm];
+
+ tmptmplen[im] = minscore;
+
+ hist[im] = k;
+
+ for( i=0; i!=-1; i=ac[i].next )
+ {
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+ eff[miniim][maxiim] =
+ MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
+ ( eff0 + eff1 ) * 0.5 * SUEFF;
+ }
+ }
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ ac[acjmprev].next = acjmnext;
+ if( acjmnext != -1 )
+ ac[acjmnext].prev = acjmprev;
+#if 0
+ fprintf( stdout, "STEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
+ fprintf( stdout, "\n" );
+#endif
+ }
+#if 1
+ fprintf( stderr, "\n" );
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+#endif
+}
+#endif
+
+void veryfastsupg_double_outtree( int nseq, double **eff, int ***topol, double **len, char **name )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ double tmpdouble;
+ double eff1, eff0;
+ static double *tmptmplen = NULL;
+ static int *hist = NULL;
+ static Achain *ac = NULL;
+ double minscore;
+ static char **tree;
+ static char *treetmp;
+ static char *nametmp;
+ FILE *fpout;
+ int im = -1, jm = -1;
+ int prevnode, acjmnext, acjmprev;
+ int *pt1, *pt2, *pt11, *pt22;
+ double (*clusterfuncpt[1])(double,double);
+
+
+ sueff1_double = 1 - SUEFF;
+ sueff05_double = SUEFF * 0.5;
+ if ( treemethod == 'X' )
+ clusterfuncpt[0] = cluster_mix_double;
+ else if ( treemethod == 'E' )
+ clusterfuncpt[0] = cluster_average_double;
+ else if ( treemethod == 'q' )
+ clusterfuncpt[0] = cluster_minimum_double;
+ else
+ {
+ fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
+ exit( 1 );
+ }
+
+ if( !hist )
+ {
+ treetmp = AllocateCharVec( njob*50 );
+ tree = AllocateCharMtx( njob, njob*50 );
+ hist = AllocateIntVec( njob );
+ tmptmplen = (double *)malloc( njob * sizeof( double ) );
+ ac = (Achain *)malloc( njob * sizeof( Achain ) );
+ nametmp = AllocateCharVec( 31 );
+ }
+
+// for( i=0; i<nseq; i++ ) sprintf( tree[i], "%d", i+1 );
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<30; j++ ) nametmp[j] = 0;
+ for( j=0; j<30; j++ )
+ {
+ if( isalnum( name[i][j] ) )
+ nametmp[j] = name[i][j];
+ else
+ nametmp[j] = '_';
+ }
+ nametmp[30] = 0;
+ sprintf( tree[i], "%d_%.20s", i+1, nametmp+1 );
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = i+1;
+ ac[i].prev = i-1;
+// ac[i].curr = i;
+ }
+ ac[nseq-1].next = -1;
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) hist[i] = -1;
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
+
+ minscore = 99999.9;
+ for( i=0; ac[i].next!=-1; i=ac[i].next )
+ {
+ for( j=ac[i].next; j!=-1; j=ac[j].next )
+ {
+ tmpdouble = eff[i][j];
+ if( tmpdouble < minscore )
+ {
+ minscore = tmpdouble;
+ im = i; jm = j;
+ }
+ }
+ }
+
+// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
+
+ intpt = topol[k][0];
+ prevnode = hist[im];
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ intpt = topol[k][1];
+ prevnode = hist[jm];
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+ len[k][0] = minscore - tmptmplen[im];
+ len[k][1] = minscore - tmptmplen[jm];
+
+ tmptmplen[im] = minscore;
+
+ hist[im] = k;
+
+ for( i=0; i!=-1; i=ac[i].next )
+ {
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+#if 0
+ eff[miniim][maxiim] =
+ MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
+ ( eff0 + eff1 ) * 0.5 * SUEFF;
+#else
+ eff[miniim][maxiim] =
+ (clusterfuncpt[0])( eff0, eff1 );
+#endif
+ }
+ }
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ ac[acjmprev].next = acjmnext;
+ if( acjmnext != -1 )
+ ac[acjmnext].prev = acjmprev;
+
+ sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
+ strcpy( tree[im], treetmp );
+#if 0
+ fprintf( stdout, "STEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
+ fprintf( stdout, "\n" );
+#endif
+ }
+ fpout = fopen( "infile.tree", "w" );
+ fprintf( fpout, "%s\n", treetmp );
+// fprintf( fpout, "by veryfastsupg_double_outtree\n" );
+ fclose( fpout );
+#if 1
+ fprintf( stderr, "\n" );
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+ FreeCharMtx( tree );
+ free( treetmp );
+ free( nametmp );
+#endif
+}
+
+void veryfastsupg( int nseq, double **oeff, int ***topol, double **len )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ int tmpint;
+ int eff1, eff0;
+ static double *tmptmplen = NULL;
+ static int **eff = NULL;
+ static int *hist = NULL;
+ static Achain *ac = NULL;
+ int minscore;
+ double minscoref;
+ int im = -1, jm = -1;
+ int prevnode, acjmnext, acjmprev;
+ int *pt1, *pt2, *pt11, *pt22;
+ if( !eff )
+ {
+ eff = AllocateIntMtx( njob, njob );
+ hist = AllocateIntVec( njob );
+ tmptmplen = (double *)malloc( njob * sizeof( double ) );
+ ac = (Achain *)malloc( njob * sizeof( Achain ) );
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ eff[i][j] = (int)( oeff[i][j] * INTMTXSCALE + 0.5 );
+ }
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = i+1;
+ ac[i].prev = i-1;
+// ac[i].curr = i;
+ }
+ ac[nseq-1].next = -1;
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) hist[i] = -1;
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
+
+ minscore = INTMTXSCALE*4;
+ for( i=0; ac[i].next!=-1; i=ac[i].next )
+ {
+ for( j=ac[i].next; j!=-1; j=ac[j].next )
+ {
+ tmpint = eff[i][j];
+ if( tmpint < minscore )
+ {
+ minscore = tmpint;
+ im = i; jm = j;
+ }
+ }
+ }
+ minscoref = (double)minscore * 0.5 / ( INTMTXSCALE );
+
+// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
+
+#if 1
+ intpt = topol[k][0];
+ prevnode = hist[im];
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ intpt = topol[k][1];
+ prevnode = hist[jm];
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+#else
+ intpt = topol[k][0];
+ for( i=0; i<nseq; i++ )
+ if( pair[im][i] > -2 )
+ *intpt++ = i;
+ *intpt = -1;
+
+ intpt = topol[k][1];
+ for( i=0; i<nseq; i++ )
+ if( pair[jm][i] > -2 )
+ *intpt++ = i;
+ *intpt = -1;
+#endif
+
+ len[k][0] = minscoref - tmptmplen[im];
+ len[k][1] = minscoref - tmptmplen[jm];
+
+ tmptmplen[im] = minscoref;
+
+ hist[im] = k;
+
+ for( i=0; i!=-1; i=ac[i].next )
+ {
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+ eff[miniim][maxiim] =
+ MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
+ ( eff0 + eff1 ) * 0.5 * SUEFF;
+ }
+ }
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ ac[acjmprev].next = acjmnext;
+ if( acjmnext != -1 )
+ ac[acjmnext].prev = acjmprev;
+#if 0
+ fprintf( stdout, "STEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
+ fprintf( stdout, "\n" );
+#endif
+ }
+#if 1
+ FreeIntMtx( eff ); eff = NULL;
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+#endif
+}
+void veryfastsupg_int( int nseq, int **oeff, int ***topol, double **len )
+/* len\e$B$O!"\e(B oeff\e$B$,@0?t!#\e(Blen\e$B$b<B$O@0?t!#\e(B
+ \e$BI,MW$K1~$8$F3d$C$F;H$&!#\e(B */
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+ int *intpt, *intpt2;
+ int tmpint;
+ int eff1, eff0;
+ static int *tmptmplen = NULL;
+ static int **eff = NULL;
+ static int *hist = NULL;
+ static Achain *ac = NULL;
+ int minscore;
+ int im = -1, jm = -1;
+ int prevnode, acjmnext, acjmprev;
+ int *pt1, *pt2, *pt11, *pt22;
+
+
+ if( !eff )
+ {
+ eff = AllocateIntMtx( njob, njob );
+ hist = AllocateIntVec( njob );
+ tmptmplen = AllocateIntVec( njob );
+ ac = (Achain *)malloc( njob * sizeof( Achain ) );
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ eff[i][j] = ( oeff[i][j] );
+ }
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = i+1;
+ ac[i].prev = i-1;
+// ac[i].curr = i;
+ }
+ ac[nseq-1].next = -1;
+
+ for( i=0; i<nseq; i++ ) tmptmplen[i] = 0;
+ for( i=0; i<nseq; i++ ) hist[i] = -1;
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
+
+ minscore = INTMTXSCALE*4;
+ for( i=0; ac[i].next!=-1; i=ac[i].next )
+ {
+ for( j=ac[i].next; j!=-1; j=ac[j].next )
+ {
+ tmpint = eff[i][j];
+ if( tmpint < minscore )
+ {
+ minscore = tmpint;
+ im = i; jm = j;
+ }
+ }
+ }
+
+// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
+
+ intpt = topol[k][0];
+ prevnode = hist[im];
+ if( prevnode == -1 )
+ {
+ *intpt++ = im;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ intpt = topol[k][1];
+ prevnode = hist[jm];
+ if( prevnode == -1 )
+ {
+ *intpt++ = jm;
+ *intpt = -1;
+ }
+ else
+ {
+ pt1 = topol[prevnode][0];
+ pt2 = topol[prevnode][1];
+ if( *pt1 > *pt2 )
+ {
+ pt11 = pt2;
+ pt22 = pt1;
+ }
+ else
+ {
+ pt11 = pt1;
+ pt22 = pt2;
+ }
+ for( intpt2=pt11; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ for( intpt2=pt22; *intpt2!=-1; )
+ *intpt++ = *intpt2++;
+ *intpt = -1;
+ }
+
+ minscore *= 0.5;
+
+ len[k][0] = (double)( minscore - tmptmplen[im] );
+ len[k][1] = (double)( minscore - tmptmplen[jm] );
+
+ tmptmplen[im] = minscore;
+
+#if 0
+ free( tmptmplen );
+ tmptmplen = AllocateIntVec( nseq );
+#endif
+
+
+ hist[im] = k;
+
+ for( i=0; i!=-1; i=ac[i].next )
+ {
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+ eff[miniim][maxiim] =
+ (int) ( (float)MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) + (float)( eff0 + eff1 ) * 0.5 * SUEFF );
+ }
+ }
+ acjmprev = ac[jm].prev;
+ acjmnext = ac[jm].next;
+ ac[acjmprev].next = acjmnext;
+ if( acjmnext != -1 )
+ ac[acjmnext].prev = acjmprev;
+#if 0
+ fprintf( stdout, "STEP-%03d:\n", k+1 );
+ fprintf( stdout, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
+ fprintf( stdout, "\n" );
+ fprintf( stdout, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
+ fprintf( stdout, "\n" );
+#endif
+ }
+ FreeIntMtx( eff ); eff = NULL;
+ free( (void *)tmptmplen ); tmptmplen = NULL;
+ free( hist ); hist = NULL;
+ free( (char *)ac ); ac = NULL;
+}
+void fastsupg( int nseq, double **oeff, int ***topol, double **len )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+#if 0
+ double eff[nseq][nseq];
+ char pair[njob][njob];
+#else
+ static float *tmplen;
+ int *intpt;
+ float tmpfloat;
+ float eff1, eff0;
+ static float **eff = NULL;
+ static char **pair = NULL;
+ static Achain *ac;
+ float minscore;
+ int im = -1, jm = -1;
+ if( !eff )
+ {
+ eff = AllocateFloatMtx( njob, njob );
+ pair = AllocateCharMtx( njob, njob );
+ tmplen = AllocateFloatVec( njob );
+ ac = (Achain *)calloc( njob, sizeof( Achain ) );
+ }
+#endif
+
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ eff[i][j] = (float)oeff[i][j];
+ }
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ ac[i].next = i+1;
+ ac[i].prev = i-1;
+// ac[i].curr = i;
+ }
+ ac[nseq-1].next = -1;
+
+ for( i=0; i<nseq; i++ ) tmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) pair[i][j] = 0;
+ for( i=0; i<nseq; i++ ) pair[i][i] = 1;
+
+ fprintf( stderr, "\n" );
+ for( k=0; k<nseq-1; k++ )
+ {
+ if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
+
+ minscore = 9999.0;
+ for( i=0; ac[i].next!=-1; i=ac[i].next )
+// for( i=0; i<nseq-1; i++ )
+ {
+ for( j=ac[i].next; j!=-1; j=ac[j].next )
+// for( j=i+1; j<nseq; j++ )
+ {
+ tmpfloat = eff[i][j];
+ if( tmpfloat < minscore )
+ {
+ minscore = tmpfloat;
+ im = i; jm = j;
+ }
+ }
+ }
+
+// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
+
+ intpt = topol[k][0];
+ for( i=0; i<nseq; i++ )
+ if( pair[im][i] > 0 )
+ *intpt++ = i;
+ *intpt = -1;
+
+ intpt = topol[k][1];
+ for( i=0; i<nseq; i++ )
+ if( pair[jm][i] > 0 )
+ *intpt++ = i;
+ *intpt = -1;
+
+ minscore /= 2.0;
+
+ len[k][0] = (double)minscore - tmplen[im];
+ len[k][1] = (double)minscore - tmplen[jm];
+
+ tmplen[im] = (double)minscore;
+
+ for( i=0; i<nseq; i++ ) pair[im][i] += ( pair[jm][i] > 0 );
+ for( i=0; i<nseq; i++ ) pair[jm][i] = 0;
+
+// for( i=0; i<nseq; i++ )
+ for( i=0; i!=-1; i=ac[i].next )
+ {
+ if( i != im && i != jm )
+ {
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+ eff[miniim][maxiim] =
+ MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
+ ( eff0 + eff1 ) * 0.5 * SUEFF;
+// eff[minijm][maxijm] = 9999.0;
+ }
+ }
+ ac[ac[jm].prev].next = ac[jm].next;
+ ac[ac[jm].next].prev = ac[jm].prev;
+// eff[im][jm] = 9999.0;
+#if 0
+ fprintf( stderr, "STEP-%03d:\n", k+1 );
+ fprintf( stderr, "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stderr, " %03d", topol[k][0][i] );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stderr, " %03d", topol[k][1][i] );
+ fprintf( stderr, "\n" );
+#endif
+ }
+ fprintf( stderr, "\n" );
+
+// FreeFloatMtx( eff );
+// FreeCharMtx( pair );
+// FreeFloatVec( tmplen );
+// free( ac );
+}
+void supg( int nseq, double **oeff, int ***topol, double **len )
+{
+ int i, j, k, miniim, maxiim, minijm, maxijm;
+#if 0
+ double eff[nseq][nseq];
+ char pair[njob][njob];
+#else
+ static float *tmplen;
+ int *intpt;
+ float **floatptpt;
+ float *floatpt;
+ float tmpfloat;
+ float eff1, eff0;
+ static float **eff = NULL;
+ static char **pair = NULL;
+ if( !eff )
+ {
+ eff = AllocateFloatMtx( njob, njob );
+ pair = AllocateCharMtx( njob, njob );
+ tmplen = AllocateFloatVec( njob );
+ }
+#endif
+
+
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ eff[i][j] = (float)oeff[i][j];
+ }
+ }
+ for( i=0; i<nseq; i++ ) tmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) pair[i][j] = 0;
+ for( i=0; i<nseq; i++ ) pair[i][i] = 1;
+
+ for( k=0; k<nseq-1; k++ )
+ {
+ float minscore = 9999.0;
+ int im = -1, jm = -1;
+
+
+ floatptpt = eff;
+ for( i=0; i<nseq-1; i++ )
+ {
+ floatpt = *floatptpt++ + i + 1;
+ for( j=i+1; j<nseq; j++ )
+ {
+ tmpfloat = *floatpt++;
+ if( tmpfloat < minscore )
+ {
+ minscore = tmpfloat;
+ im = i; jm = j;
+ }
+ }
+ }
+ intpt = topol[k][0];
+ for( i=0; i<nseq; i++ )
+ if( pair[im][i] > 0 )
+ *intpt++ = i;
+ *intpt = -1;
+
+ intpt = topol[k][1];
+ for( i=0; i<nseq; i++ )
+ if( pair[jm][i] > 0 )
+ *intpt++ = i;
+ *intpt = -1;
+
+ len[k][0] = (double)minscore / 2.0 - tmplen[im];
+ len[k][1] = (double)minscore / 2.0 - tmplen[jm];
+
+ tmplen[im] = (double)minscore / 2.0;
+
+ for( i=0; i<nseq; i++ ) pair[im][i] += ( pair[jm][i] > 0 );
+ for( i=0; i<nseq; i++ ) pair[jm][i] = 0;
+
+ for( i=0; i<nseq; i++ )
+ {
+ if( i != im && i != jm )
+ {
+#if 1
+ if( i < im )
+ {
+ miniim = i;
+ maxiim = im;
+ minijm = i;
+ maxijm = jm;
+ }
+ else if( i < jm )
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = i;
+ maxijm = jm;
+ }
+ else
+ {
+ miniim = im;
+ maxiim = i;
+ minijm = jm;
+ maxijm = i;
+ }
+#else
+ miniim = MIN( i, im );
+ maxiim = MAX( i, im );
+ minijm = MIN( i, jm );
+ maxijm = MAX( i, jm );
+#endif
+#if 1
+ eff0 = eff[miniim][maxiim];
+ eff1 = eff[minijm][maxijm];
+ eff[miniim][maxiim] =
+ MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
+ ( eff0 + eff1 ) * 0.5 * SUEFF;
+#else
+ MIN( eff[miniim][maxiim], eff[minijm][maxijm] ) * ( 1.0 - SUEFF ) +
+ ( eff[miniim][maxiim] + eff[minijm][maxijm] ) * 0.5 * SUEFF;
+#endif
+ eff[minijm][maxijm] = 9999.0;
+ eff[im][jm] = 9999.0;
+ }
+ }
+#if DEBUG
+ printf( "STEP-%03d:\n", k+1 );
+ printf( "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) printf( " %03d", topol[k][0][i] );
+ printf( "\n" );
+ printf( "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) printf( " %03d", topol[k][1][i] );
+ printf( "\n" );
+#endif
+ }
+}
+
+void spg( int nseq, double **oeff, int ***topol, double **len )
+{
+ int i, j, k;
+ double tmplen[M];
+#if 0
+ double eff[nseq][nseq];
+ char pair[njob][njob];
+#else
+ double **eff = NULL;
+ char **pair = NULL;
+ if( !eff )
+ {
+ eff = AllocateDoubleMtx( njob, njob );
+ pair = AllocateCharMtx( njob, njob );
+ }
+#endif
+
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) eff[i][j] = oeff[i][j];
+ for( i=0; i<nseq; i++ ) tmplen[i] = 0.0;
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) pair[i][j] = 0;
+ for( i=0; i<nseq; i++ ) pair[i][i] = 1;
+
+ for( k=0; k<nseq-1; k++ )
+ {
+ float minscore = 9999.0;
+ int im = -1, jm = -1;
+ int count;
+
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ if( eff[i][j] < minscore )
+ {
+ minscore = eff[i][j];
+ im = i; jm = j;
+ }
+ }
+ for( i=0, count=0; i<nseq; i++ )
+ if( pair[im][i] > 0 )
+ {
+ topol[k][0][count] = i;
+ count++;
+ }
+ topol[k][0][count] = -1;
+ for( i=0, count=0; i<nseq; i++ )
+ if( pair[jm][i] > 0 )
+ {
+ topol[k][1][count] = i;
+ count++;
+ }
+ topol[k][1][count] = -1;
+
+ len[k][0] = minscore / 2.0 - tmplen[im];
+ len[k][1] = minscore / 2.0 - tmplen[jm];
+
+ tmplen[im] = minscore / 2.0;
+
+ for( i=0; i<nseq; i++ ) pair[im][i] += ( pair[jm][i] > 0 );
+ for( i=0; i<nseq; i++ ) pair[jm][i] = 0;
+
+ for( i=0; i<nseq; i++ )
+ {
+ if( i != im && i != jm )
+ {
+ eff[MIN(i,im)][MAX(i,im)] =
+ MIN( eff[MIN(i,im)][MAX(i,im)], eff[MIN(i,jm)][MAX(i,jm)] );
+ eff[MIN(i,jm)][MAX(i,jm)] = 9999.0;
+ }
+ eff[im][jm] = 9999.0;
+ }
+#if DEBUG
+ printf( "STEP-%03d:\n", k+1 );
+ printf( "len0 = %f\n", len[k][0] );
+ for( i=0; topol[k][0][i]>-1; i++ ) printf( " %03d", topol[k][0][i] );
+ printf( "\n" );
+ printf( "len1 = %f\n", len[k][1] );
+ for( i=0; topol[k][1][i]>-1; i++ ) printf( " %03d", topol[k][1][i] );
+ printf( "\n" );
+#endif
+ }
+}
+
+double ipower( double x, int n ) /* n > 0 */
+{
+ double r;
+
+ r = 1;
+ while( n != 0 )
+ {
+ if( n & 1 ) r *= x;
+ x *= x; n >>= 1;
+ }
+ return( r );
+}
+
+void countnode( int nseq, int ***topol, double **node ) /* node[j][i] != node[i][j] */
+{
+ int i, j, k, s1, s2;
+ static double rootnode[M];
+
+ if( nseq-2 < 0 )
+ {
+ fprintf( stderr, "Too few sequence for countnode: nseq = %d\n", nseq );
+ exit( 1 );
+ }
+
+ for( i=0; i<nseq; i++ ) rootnode[i] = 0;
+ for( i=0; i<nseq-2; i++ )
+ {
+ for( j=0; topol[i][0][j]>-1; j++ )
+ rootnode[topol[i][0][j]]++;
+ for( j=0; topol[i][1][j]>-1; j++ )
+ rootnode[topol[i][1][j]]++;
+ for( j=0; topol[i][0][j]>-1; j++ )
+ {
+ s1 = topol[i][0][j];
+ for( k=0; topol[i][1][k]>-1; k++ )
+ {
+ s2 = topol[i][1][k];
+ node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2] - 1;
+ }
+ }
+ }
+ for( j=0; topol[nseq-2][0][j]>-1; j++ )
+ {
+ s1 = topol[nseq-2][0][j];
+ for( k=0; topol[nseq-2][1][k]>-1; k++ )
+ {
+ s2 = topol[nseq-2][1][k];
+ node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2];
+ }
+ }
+}
+
+void countnode_int( int nseq, int ***topol, int **node ) /* node[i][j] == node[j][i] */
+{
+ int i, j, k, s1, s2;
+ int rootnode[M];
+
+ for( i=0; i<nseq; i++ ) rootnode[i] = 0;
+ for( i=0; i<nseq-2; i++ )
+ {
+ for( j=0; topol[i][0][j]>-1; j++ )
+ rootnode[topol[i][0][j]]++;
+ for( j=0; topol[i][1][j]>-1; j++ )
+ rootnode[topol[i][1][j]]++;
+ for( j=0; topol[i][0][j]>-1; j++ )
+ {
+ s1 = topol[i][0][j];
+ for( k=0; topol[i][1][k]>-1; k++ )
+ {
+ s2 = topol[i][1][k];
+ node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2] - 1;
+ }
+ }
+ }
+ for( j=0; topol[nseq-2][0][j]>-1; j++ )
+ {
+ s1 = topol[nseq-2][0][j];
+ for( k=0; topol[nseq-2][1][k]>-1; k++ )
+ {
+ s2 = topol[nseq-2][1][k];
+ node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2];
+ }
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ node[j][i] = node[i][j];
+#if DEBUG
+ fprintf( stderr, "node[][] in countnode_int" );
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ fprintf( stderr, "%#3d", node[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+}
+
+void counteff_simple_float( int nseq, int ***topol, float **len, double *node )
+{
+ int i, j, s1, s2;
+ double total;
+ static double rootnode[M];
+ static double eff[M];
+
+#if DEBUG
+ for( i=0; i<nseq; i++ ){
+ fprintf( stderr, "len0 = %f\n", len[i][0] );
+ fprintf( stderr, "len1 = %f\n", len[i][1] );
+ }
+#endif
+ for( i=0; i<nseq; i++ )
+ {
+ rootnode[i] = 0.0;
+ eff[i] = 1.0;
+/*
+ rootnode[i] = 1.0;
+*/
+ }
+ for( i=0; i<nseq-1; i++ )
+ {
+ for( j=0; (s1=topol[i][0][j]) > -1; j++ )
+ {
+ rootnode[s1] += (double)len[i][0] * eff[s1];
+ eff[s1] *= 0.5;
+/*
+ rootnode[s1] *= 0.5;
+*/
+
+ }
+ for( j=0; (s2=topol[i][1][j]) > -1; j++ )
+ {
+ rootnode[s2] += (double)len[i][1] * eff[s2];
+ eff[s2] *= 0.5;
+/*
+ rootnode[s2] *= 0.5;
+*/
+
+ }
+ }
+ for( i=0; i<nseq; i++ )
+ {
+#if 1 /* 97.9.29 */
+ rootnode[i] += GETA3;
+#endif
+#if 0
+ fprintf( stderr, "### rootnode for %d = %f\n", i, rootnode[i] );
+#endif
+ }
+#if 1
+ total = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ total += rootnode[i];
+ }
+#else
+ total = 1.0;
+#endif
+
+ for( i=0; i<nseq; i++ )
+ {
+ node[i] = rootnode[i] / total;
+ }
+
+#if 0
+ fprintf( stderr, "weight array in counteff_simple\n" );
+ for( i=0; i<nseq; i++ )
+ fprintf( stderr, "%f\n", node[i] );
+ printf( "\n" );
+ exit( 1 );
+#endif
+}
+
+void counteff_simple( int nseq, int ***topol, double **len, double *node )
+{
+ int i, j, s1, s2;
+ double total;
+ static double rootnode[M];
+ static double eff[M];
+
+#if DEBUG
+ for( i=0; i<nseq; i++ ){
+ fprintf( stderr, "len0 = %f\n", len[i][0] );
+ fprintf( stderr, "len1 = %f\n", len[i][1] );
+ }
+#endif
+ for( i=0; i<nseq; i++ )
+ {
+ rootnode[i] = 0.0;
+ eff[i] = 1.0;
+/*
+ rootnode[i] = 1.0;
+*/
+ }
+ for( i=0; i<nseq-1; i++ )
+ {
+ for( j=0; (s1=topol[i][0][j]) > -1; j++ )
+ {
+ rootnode[s1] += len[i][0] * eff[s1];
+ eff[s1] *= 0.5;
+/*
+ rootnode[s1] *= 0.5;
+*/
+
+ }
+ for( j=0; (s2=topol[i][1][j]) > -1; j++ )
+ {
+ rootnode[s2] += len[i][1] * eff[s2];
+ eff[s2] *= 0.5;
+/*
+ rootnode[s2] *= 0.5;
+*/
+
+ }
+ }
+ for( i=0; i<nseq; i++ )
+ {
+#if 1 /* 97.9.29 */
+ rootnode[i] += GETA3;
+#endif
+#if 0
+ fprintf( stderr, "### rootnode for %d = %f\n", i, rootnode[i] );
+#endif
+ }
+#if 1
+ total = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ total += rootnode[i];
+ }
+#else
+ total = 1.0;
+#endif
+
+ for( i=0; i<nseq; i++ )
+ {
+ node[i] = rootnode[i] / total;
+ }
+
+#if 0
+ fprintf( stderr, "weight array in counteff_simple\n" );
+ for( i=0; i<nseq; i++ )
+ fprintf( stderr, "%f\n", node[i] );
+ printf( "\n" );
+ exit( 1 );
+#endif
+}
+
+
+void counteff( int nseq, int ***topol, double **len, double **node )
+{
+ int i, j, k, s1, s2;
+ double rootnode[M];
+ double eff[M];
+
+ if( mix )
+ {
+ switch( weight )
+ {
+ case( 2 ):
+ weight = 3;
+ break;
+ case( 3 ):
+ weight = 2;
+ break;
+ default:
+ ErrorExit( "mix error" );
+ break;
+ }
+ }
+
+ if( weight == 2 )
+ {
+ for( i=0; i<nseq; i++ ) rootnode[i] = 0;
+ for( i=0; i<nseq-2; i++ )
+ {
+ for( j=0; topol[i][0][j]>-1; j++ )
+ rootnode[topol[i][0][j]]++;
+ for( j=0; topol[i][1][j]>-1; j++ )
+ rootnode[topol[i][1][j]]++;
+ for( j=0; topol[i][0][j]>-1; j++ )
+ {
+ s1 = topol[i][0][j];
+ for( k=0; topol[i][1][k]>-1; k++ )
+ {
+ s2 = topol[i][1][k];
+ node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2] - 1;
+ }
+ }
+ }
+ for( j=0; topol[nseq-2][0][j]>-1; j++ )
+ {
+ s1 = topol[nseq-2][0][j];
+ for( k=0; topol[nseq-2][1][k]>-1; k++ )
+ {
+ s2 = topol[nseq-2][1][k];
+ node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2];
+ }
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ node[i][j] = ipower( 0.5, (int)node[i][j] ) + geta2;
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ node[j][i] = node[i][j];
+ }
+
+ if( weight == 3 )
+ {
+#if DEBUG
+ for( i=0; i<nseq; i++ ){
+ fprintf( stderr, "len0 = %f\n", len[i][0] );
+ fprintf( stderr, "len1 = %f\n", len[i][1] );
+ }
+#endif
+ for( i=0; i<nseq; i++ )
+ {
+ rootnode[i] = 0.0;
+ eff[i] = 1.0;
+/*
+ rootnode[i] = 1.0;
+*/
+ }
+ for( i=0; i<nseq-1; i++ )
+ {
+ for( j=0; (s1=topol[i][0][j]) > -1; j++ )
+ {
+ rootnode[s1] += len[i][0] * eff[s1];
+ eff[s1] *= 0.5;
+/*
+ rootnode[s1] *= 0.5;
+*/
+
+ }
+ for( j=0; (s2=topol[i][1][j]) > -1; j++ )
+ {
+ rootnode[s2] += len[i][1] * eff[s2];
+ eff[s2] *= 0.5;
+/*
+ rootnode[s2] *= 0.5;
+*/
+
+ }
+ }
+ for( i=0; i<nseq; i++ )
+ {
+#if 1 /* 97.9.29 */
+ rootnode[i] += GETA3;
+#endif
+#if DEBUG
+ fprintf( stderr, "rootnode for %d = %f\n", i, rootnode[i] );
+#endif
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ if( j != i )
+ node[i][j] = (double)rootnode[i] * rootnode[j];
+ else node[i][i] = rootnode[i];
+ }
+ }
+
+#if 0
+ printf( "weight matrix in counteff\n" );
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ printf( "%f ", node[i][j] );
+ }
+ printf( "\n" );
+ }
+#endif
+}
+
+float score_calcp( char *seq1, char *seq2, int len )
+{
+ int k;
+ int ms1, ms2;
+ float tmpscore;
+ int len2 = len - 2;
+
+ tmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ ms1 = (int)seq1[k];
+ ms2 = (int)seq2[k];
+ if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
+ tmpscore += (float)amino_dis[ms1][ms2];
+
+ if( ms1 == (int)'-' )
+ {
+ tmpscore += (float)penalty;
+ tmpscore += (float)amino_dis[ms1][ms2];
+ while( (ms1=(int)seq1[++k]) == (int)'-' )
+ tmpscore += (float)amino_dis[ms1][ms2];
+ k--;
+ if( k >len2 ) break;
+ continue;
+ }
+ if( ms2 == (int)'-' )
+ {
+ tmpscore += (float)penalty;
+ tmpscore += (float)amino_dis[ms1][ms2];
+ while( (ms2=(int)seq2[++k]) == (int)'-' )
+ tmpscore += (float)amino_dis[ms1][ms2];
+ k--;
+ if( k > len2 ) break;
+ continue;
+ }
+ }
+ return( tmpscore );
+}
+
+float score_calc1( char *seq1, char *seq2 ) /* method 1 */
+{
+ int k;
+ float score = 0.0;
+ int count = 0;
+ int len = strlen( seq1 );
+
+ for( k=0; k<len; k++ )
+ {
+ if( seq1[k] != '-' && seq2[k] != '-' )
+ {
+ score += (float)amino_dis[(int)seq1[k]][(int)seq2[k]];
+ count++;
+ }
+ }
+ if( count ) score /= (float)count;
+ else score = 1.0;
+ return( score );
+}
+
+float substitution_nid( char *seq1, char *seq2 )
+{
+ int k;
+ float s12;
+ int len = strlen( seq1 );
+
+ s12 = 0.0;
+ for( k=0; k<len; k++ )
+ if( seq1[k] != '-' && seq2[k] != '-' )
+ s12 += ( seq1[k] == seq2[k] );
+
+// fprintf( stdout, "s12 = %f\n", s12 );
+ return( s12 );
+}
+
+float substitution_score( char *seq1, char *seq2 )
+{
+ int k;
+ float s12;
+ int len = strlen( seq1 );
+
+ s12 = 0.0;
+ for( k=0; k<len; k++ )
+ if( seq1[k] != '-' && seq2[k] != '-' )
+ s12 += amino_dis[(int)seq1[k]][(int)seq2[k]];
+
+// fprintf( stdout, "s12 = %f\n", s12 );
+ return( s12 );
+}
+
+float substitution_hosei( char *seq1, char *seq2 ) /* method 1 */
+#if 0
+{
+ int k;
+ float score = 0.0;
+ int count = 0;
+ int len = strlen( seq1 );
+
+ for( k=0; k<len; k++ )
+ {
+ if( seq1[k] != '-' && seq2[k] != '-' )
+ {
+ score += (float)( seq1[k] != seq2[k] );
+ count++;
+ }
+ }
+ if( count ) score /= (float)count;
+ else score = 1.0;
+ if( score < 0.95 ) score = - log( 1.0 - score );
+ else score = 3.0;
+ return( score );
+}
+#else
+{
+ int count = 0;
+ float score;
+ int iscore = 0;
+ char s1, s2;
+
+ while( (s1=*seq1++) )
+ {
+ s2 = *seq2++;
+ if( s1 == '-' ) continue;
+ if( s2 == '-' ) continue;
+ iscore += ( s1 != s2 );
+ count++;
+ }
+ if( count ) score = (float)iscore / count;
+ else score = 1.0;
+ if( score < 0.95 ) score = - log( 1.0 - score );
+ else score = 3.0;
+ return( score );
+}
+#endif
+
+float substitution( char *seq1, char *seq2 ) /* method 1 */
+{
+ int k;
+ float score = 0.0;
+ int count = 0;
+ int len = strlen( seq1 );
+
+ for( k=0; k<len; k++ )
+ {
+ if( seq1[k] != '-' && seq2[k] != '-' )
+ {
+ score += (float)( seq1[k] != seq2[k] );
+ count++;
+ }
+ }
+ if( count ) score /= (float)count;
+ else score = 1.0;
+ return( score );
+}
+
+
+void treeconstruction( char **seq, int nseq, int ***topol, double **len, double **eff )
+{
+ int i, j;
+
+ if( weight > 1 )
+ {
+ if( utree == 0 )
+ {
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+/*
+ eff[i][j] = (double)score_calc1( seq[i], seq[j] );
+*/
+ eff[i][j] = (double)substitution_hosei( seq[i], seq[j] );
+ /*
+ fprintf( stderr, "%f\n", eff[i][j] );
+ */
+ }
+/*
+ fprintf( stderr, "distance matrix\n" );
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ fprintf( stderr, "%f ", eff[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+*/
+/*
+ upg( nseq, eff, topol, len );
+ upg2( nseq, eff, topol, len );
+*/
+ spg( nseq, eff, topol, len );
+ counteff( nseq, topol, len, eff );
+ }
+ }
+ else
+ {
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+ eff[i][j] = 1.0;
+ }
+/*
+fprintf( stderr, "weight matrix\n" );
+for( i=0; i<nseq; i++ )
+{
+ for( j=0; j<nseq; j++ )
+ {
+ fprintf( stderr, "%f ", eff[i][j] );
+ }
+ fprintf( stderr, "\n" );
+}
+*/
+}
+
+float bscore_calc( char **seq, int s, double **eff ) /* algorithm B */
+{
+ int i, j, k;
+ int gb1, gb2, gc1, gc2;
+ int cob;
+ int nglen;
+ int len = strlen( seq[0] );
+ long score;
+
+ score = 0;
+ nglen = 0;
+ for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
+ {
+ double efficient = eff[i][j];
+
+ gc1 = 0;
+ gc2 = 0;
+ for( k=0; k<len; k++ )
+ {
+ gb1 = gc1;
+ gb2 = gc2;
+
+ gc1 = ( seq[i][k] == '-' );
+ gc2 = ( seq[j][k] == '-' );
+
+ cob =
+ !gb1 * gc1
+ * !gb2 * !gc2
+
+ + !gb1 * !gc1
+ * !gb2 * gc2
+
+ + !gb1 * gc1
+ * gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * gc2
+
+ + gb1 * !gc1
+ * gb2 * gc2 *BEFF
+
+ + gb1 * gc1
+ * gb2 * !gc2 *BEFF
+ ;
+ score += (long)cob * penalty * efficient;
+ score += (long)amino_dis[(int)seq[i][k]][(int)seq[j][k]] * efficient;
+ nglen += ( !gc1 * !gc2 );
+ }
+ }
+ return( (float)score / nglen + 400.0 * !scoremtx );
+}
+
+void AllocateTmpSeqs( char ***mseq2pt, char **mseq1pt, int locnlenmax )
+{
+ *mseq2pt = AllocateCharMtx( njob, locnlenmax+1 );
+ *mseq1pt = AllocateCharVec( locnlenmax+1 );
+}
+
+void FreeTmpSeqs( char **mseq2, char *mseq1 )
+{
+ FreeCharMtx( mseq2 );
+ free( (char *)mseq1 );
+}
+
+
+void gappick0( char *aseq, char *seq )
+{
+ for( ; *seq != 0; seq++ )
+ {
+ if( *seq != '-' )
+ *aseq++ = *seq;
+ }
+ *aseq = 0;
+
+}
+
+void gappick( int nseq, int s, char **aseq, char **mseq2,
+ double **eff, double *effarr )
+{
+ int i, j, count, countjob, len, allgap;
+ len = strlen( aseq[0] );
+ for( i=0, count=0; i<len; i++ )
+ {
+ allgap = 1;
+ for( j=0; j<nseq; j++ ) if( j != s ) allgap *= ( aseq[j][i] == '-' );
+ if( allgap == 0 )
+ {
+ for( j=0, countjob=0; j<nseq; j++ )
+ {
+ if( j != s )
+ {
+ mseq2[countjob][count] = aseq[j][i];
+ countjob++;
+ }
+ }
+ count++;
+ }
+ }
+ for( i=0; i<nseq-1; i++ ) mseq2[i][count] = 0;
+
+ for( i=0, countjob=0; i<nseq; i++ )
+ {
+ if( i != s )
+ {
+ effarr[countjob] = eff[s][i];
+ countjob++;
+ }
+ }
+/*
+fprintf( stdout, "effarr in gappick s = %d\n", s+1 );
+for( i=0; i<countjob; i++ )
+ fprintf( stdout, " %f", effarr[i] );
+printf( "\n" );
+*/
+}
+
+void commongappick_record( int nseq, char **seq, int *map )
+{
+ int i, j, count;
+ int len = strlen( seq[0] );
+
+
+ for( i=0, count=0; i<=len; i++ )
+ {
+ /*
+ allgap = 1;
+ for( j=0; j<nseq; j++ )
+ allgap *= ( seq[j][i] == '-' );
+ if( !allgap )
+ */
+ for( j=0; j<nseq; j++ )
+ if( seq[j][i] != '-' ) break;
+ if( j != nseq )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ seq[j][count] = seq[j][i];
+ }
+ map[count] = i;
+ count++;
+ }
+ }
+}
+
+void commongappick( int nseq, char **seq )
+{
+ int i, j, count;
+ int len = strlen( seq[0] );
+
+ for( i=0, count=0; i<=len; i++ )
+ {
+ /*
+ allgap = 1;
+ for( j=0; j<nseq; j++ )
+ allgap *= ( seq[j][i] == '-' );
+ if( !allgap )
+ */
+ for( j=0; j<nseq; j++ )
+ if( seq[j][i] != '-' ) break;
+ if( j != nseq )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ seq[j][count] = seq[j][i];
+ }
+ count++;
+ }
+ }
+}
+
+double score_calc0( char **seq, int s, double **eff, int ex )
+{
+ double tmp;
+
+ if( scmtd == 4 ) tmp = score_calc4( seq, s, eff, ex );
+ if( scmtd == 5 ) tmp = score_calc5( seq, s, eff, ex );
+ else tmp = score_calc5( seq, s, eff, ex );
+
+ return( tmp );
+
+}
+
+/*
+float score_m_1( char **seq, int ex, double **eff )
+{
+ int i, j, k;
+ int len = strlen( seq[0] );
+ int gb1, gb2, gc1, gc2;
+ int cob;
+ int nglen;
+ double score;
+
+ score = 0.0;
+ nglen = 0;
+ for( i=0; i<njob; i++ )
+ {
+ double efficient = eff[MIN(i,ex)][MAX(i,ex)];
+ if( i == ex ) continue;
+
+ gc1 = 0;
+ gc2 = 0;
+ for( k=0; k<len; k++ )
+ {
+ gb1 = gc1;
+ gb2 = gc2;
+
+ gc1 = ( seq[i][k] == '-' );
+ gc2 = ( seq[ex][k] == '-' );
+
+ cob =
+ !gb1 * gc1
+ * !gb2 * !gc2
+
+ + !gb1 * !gc1
+ * !gb2 * gc2
+
+ + !gb1 * gc1
+ * gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * gc2
+
+ + gb1 * !gc1
+ * gb2 * gc2 *BEFF
+
+ + gb1 * gc1
+ * gb2 * !gc2 *BEFF
+ ;
+ score += (double)cob * penalty * efficient;
+ score += (double)amino_dis[seq[i][k]][seq[ex][k]] * efficient;
+ *
+ nglen += ( !gc1 * !gc2 );
+ *
+ if( !gc1 && !gc2 ) fprintf( stdout, "%f\n", score );
+ }
+ }
+ return( (float)score / nglen + 400.0 * !scoremtx );
+}
+*/
+
+#if 0
+void sitescore( char **seq, double **eff, char sco1[], char sco2[], char sco3[] )
+{
+ int i, j, k;
+ int len = strlen( seq[0] );
+ double tmp;
+ double count;
+ int ch;
+ double sco[N];
+
+ for( i=0; i<len; i++ )
+ {
+ tmp = 0.0; count = 0;
+ for( j=0; j<njob-1; j++ ) for( k=j+1; k<njob; k++ )
+ {
+ /*
+ if( seq[j][i] != '-' && seq[k][i] != '-' )
+ */
+ {
+ tmp += amino_dis[seq[j][i]][seq[k][i]] + 400 * !scoremtx;
+ count++;
+ }
+ }
+ if( count > 0.0 ) tmp /= count;
+ else( tmp = 0.0 );
+ ch = (int)( tmp/100.0 - 0.000001 );
+ sprintf( sco1+i, "%c", ch+0x61 );
+ }
+ sco1[len] = 0;
+
+ for( i=0; i<len; i++ )
+ {
+ tmp = 0.0; count = 0;
+ for( j=0; j<njob-1; j++ ) for( k=j+1; k<njob; k++ )
+ {
+ /*
+ if( seq[j][i] != '-' && seq[k][i] != '-' )
+ */
+ {
+ tmp += eff[j][k] * ( amino_dis[seq[j][i]][seq[k][i]] + 400 * !scoremtx );
+ count += eff[j][k];
+ }
+ }
+ if( count > 0.0 ) tmp /= count;
+ else( tmp = 0.0 );
+ tmp = ( tmp - 400 * !scoremtx ) * 2;
+ if( tmp < 0 ) tmp = 0;
+ ch = (int)( tmp/100.0 - 0.000001 );
+ sprintf( sco2+i, "%c", ch+0x61 );
+ sco[i] = tmp;
+ }
+ sco2[len] = 0;
+
+ for( i=WIN; i<len-WIN; i++ )
+ {
+ tmp = 0.0;
+ for( j=i-WIN; j<=i+WIN; j++ )
+ {
+ tmp += sco[j];
+ }
+ for( j=0; j<njob; j++ )
+ {
+ if( seq[j][i] == '-' )
+ {
+ tmp = 0.0;
+ break;
+ }
+ }
+ tmp /= WIN * 2 + 1;
+ ch = (int)( tmp/100.0 - 0.0000001 );
+ sprintf( sco3+i, "%c", ch+0x61 );
+ }
+ for( i=0; i<WIN; i++ ) sco3[i] = '-';
+ for( i=len-WIN; i<len; i++ ) sco3[i] = '-';
+ sco3[len] = 0;
+}
+#endif
+
+void strins( char *str1, char *str2 )
+{
+ char *bk;
+ int len1 = strlen( str1 );
+ int len2 = strlen( str2 );
+
+ bk = str2;
+ str2 += len1+len2;
+ str1 += len1-1;
+
+ while( str2 >= bk+len1 ) { *str2 = *(str2-len1); str2--;} // by D.Mathog
+ while( str2 >= bk ) { *str2-- = *str1--; }
+}
+
+int isaligned( int nseq, char **seq )
+{
+ int i;
+ int len = strlen( seq[0] );
+ for( i=1; i<nseq; i++ )
+ {
+ if( strlen( seq[i] ) != len ) return( 0 );
+ }
+ return( 1 );
+}
+
+double score_calc_for_score( int nseq, char **seq )
+{
+ int i, j, k, c;
+ int len = strlen( seq[0] );
+ double score;
+ double tmpscore;
+ char *mseq1, *mseq2;
+
+ score = 0.0;
+ for( i=0; i<nseq-1; i++ )
+ {
+ for( j=i+1; j<nseq; j++ )
+ {
+ mseq1 = seq[i];
+ mseq2 = seq[j];
+ tmpscore = 0.0;
+ c = 0;
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ c++;
+ if( mseq1[k] == '-' )
+ {
+ tmpscore += penalty - n_dis[0][24];
+ while( mseq1[++k] == '-' )
+ ;
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ if( mseq2[k] == '-' )
+ {
+ tmpscore += penalty - n_dis[0][24];
+ while( mseq2[++k] == '-' )
+ ;
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ }
+ score += (double)tmpscore / (double)c;
+#if DEBUG
+ printf( "tmpscore in mltaln9.c = %f\n", tmpscore );
+ printf( "tmpscore / c = %f\n", tmpscore/(double)c );
+#endif
+ }
+ }
+ fprintf( stderr, "raw score = %f\n", score );
+ score /= (double)nseq * ( nseq-1.0 ) / 2.0;
+ score += 400.0;
+#if DEBUG
+ printf( "score in mltaln9.c = %f\n", score );
+#endif
+ return( (double)score );
+}
+
+void floatncpy( float *vec1, float *vec2, int len )
+{
+ while( len-- )
+ *vec1++ = *vec2++;
+}
+
+float score_calc_a( char **seq, int s, double **eff ) /* algorithm A+ */
+{
+ int i, j, k;
+ int gb1, gb2, gc1, gc2;
+ int cob;
+ int nglen;
+ int len = strlen( seq[0] );
+ float score;
+
+ score = 0;
+ nglen = 0;
+ for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
+ {
+ double efficient = eff[i][j];
+
+ gc1 = 0;
+ gc2 = 0;
+ for( k=0; k<len; k++ )
+ {
+ gb1 = gc1;
+ gb2 = gc2;
+
+ gc1 = ( seq[i][k] == '-' );
+ gc2 = ( seq[j][k] == '-' );
+
+ cob =
+ !gb1 * gc1
+ * !gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * !gc2
+
+ + !gb1 * !gc1
+ * !gb2 * gc2
+
+ + !gb1 * !gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * gc2
+
+ + gb1 * !gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * !gb2 * gc2
+ ;
+ score += 0.5 * (float)cob * penalty * efficient;
+ score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]] * (float)efficient;
+ nglen += ( !gc1 * !gc2 );
+ }
+ }
+ return( (float)score / nglen + 400.0 * !scoremtx );
+}
+
+
+float score_calc_s( char **seq, int s, double **eff ) /* algorithm S, not used */
+{
+ int i, j, k;
+ int gb1, gb2, gc1, gc2;
+ int cob;
+ int nglen;
+ int len = strlen( seq[0] );
+ float score;
+
+ score = 0;
+ nglen = 0;
+ for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
+ {
+ double efficient = eff[i][j];
+
+ gc1 = 0;
+ gc2 = 0;
+ for( k=0; k<len; k++ )
+ {
+ gb1 = gc1;
+ gb2 = gc2;
+
+ gc1 = ( seq[i][k] == '-' );
+ gc2 = ( seq[j][k] == '-' );
+
+ cob =
+ !gb1 * gc1
+ * !gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * !gc2
+
+ + !gb1 * !gc1
+ * !gb2 * gc2
+
+ + !gb1 * !gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * gc2
+
+#if 0
+ + gb1 * !gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * !gb2 * gc2
+#endif
+ ;
+ score += 0.5 * (float)cob * penalty * efficient;
+ score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]] * (float)efficient;
+ nglen += ( !gc1 * !gc2 );
+ }
+ }
+ return( (float)score / nglen + 400.0 );
+}
+
+double score_calc_for_score_s( int s, char **seq ) /* algorithm S */
+{
+ int i, j, k;
+ int gb1, gb2, gc1, gc2;
+ int cob;
+ int nglen;
+ int len = strlen( seq[0] );
+ float score;
+
+ score = 0;
+ nglen = 0;
+ for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
+ {
+
+ gc1 = 0;
+ gc2 = 0;
+ for( k=0; k<len; k++ )
+ {
+ gb1 = gc1;
+ gb2 = gc2;
+
+ gc1 = ( seq[i][k] == '-' );
+ gc2 = ( seq[j][k] == '-' );
+
+ cob =
+ !gb1 * gc1
+ * !gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * !gc2
+
+ + !gb1 * !gc1
+ * !gb2 * gc2
+
+ + !gb1 * !gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * gc2
+
+#if 0
+ + gb1 * !gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * !gb2 * gc2
+#endif
+ ;
+ score += 0.5 * (float)cob * penalty;
+ score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]];
+ nglen += ( !gc1 * !gc2 );
+ }
+#if 0
+ fprintf( stderr, "i = %d, j=%d\n", i+1, j+1 );
+ fprintf( stderr, "score = %f\n", score );
+#endif
+ }
+ return( (double)score / nglen + 400.0 );
+}
+
+double SSPscore___( int s, char **seq, int ex ) /* algorithm S */
+{
+ int i, j, k;
+ int gb1, gb2, gc1, gc2;
+ int cob;
+ int nglen;
+ int len = strlen( seq[0] );
+ float score;
+
+ score = 0;
+ nglen = 0;
+ i=ex; for( j=0; j<s; j++ )
+ {
+
+ if( j == ex ) continue;
+
+ gc1 = 0;
+ gc2 = 0;
+ for( k=0; k<len; k++ )
+ {
+ gb1 = gc1;
+ gb2 = gc2;
+
+ gc1 = ( seq[i][k] == '-' );
+ gc2 = ( seq[j][k] == '-' );
+
+ cob =
+ !gb1 * gc1
+ * !gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * !gc2
+
+ + !gb1 * !gc1
+ * !gb2 * gc2
+
+ + !gb1 * !gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * !gc2 * 2.0
+
+ + gb1 * !gc1
+ * !gb2 * gc2 * 2.0
+
+#if 0
+ + gb1 * !gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * !gb2 * gc2
+#endif
+ ;
+ score += 0.5 * (float)cob * penalty;
+ score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]];
+ nglen += ( !gc1 * !gc2 ); /* tsukawanai */
+ }
+#if 0
+ fprintf( stderr, "i = %d, j=%d\n", i+1, j+1 );
+ fprintf( stderr, "score = %f\n", score );
+#endif
+ }
+ return( (double)score );
+}
+
+double SSPscore( int s, char **seq ) /* algorithm S */
+{
+ int i, j, k;
+ int gb1, gb2, gc1, gc2;
+ int cob;
+ int nglen;
+ int len = strlen( seq[0] );
+ float score;
+
+ score = 0;
+ nglen = 0;
+ for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
+ {
+
+ gc1 = 0;
+ gc2 = 0;
+ for( k=0; k<len; k++ )
+ {
+ gb1 = gc1;
+ gb2 = gc2;
+
+ gc1 = ( seq[i][k] == '-' );
+ gc2 = ( seq[j][k] == '-' );
+
+ cob =
+ !gb1 * gc1
+ * !gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * !gc2
+
+ + !gb1 * !gc1
+ * !gb2 * gc2
+
+ + !gb1 * !gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * !gc2
+
+ + gb1 * !gc1
+ * !gb2 * gc2
+
+#if 0
+ + gb1 * !gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * gb2 * !gc2
+
+ + !gb1 * gc1
+ * gb2 * gc2
+
+ + gb1 * gc1
+ * !gb2 * gc2
+#endif
+ ;
+ score += 0.5 * (float)cob * penalty;
+ score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]];
+ nglen += ( !gc1 * !gc2 ); /* tsukawanai */
+ }
+#if 0
+ fprintf( stderr, "i = %d, j=%d\n", i+1, j+1 );
+ fprintf( stderr, "score = %f\n", score );
+#endif
+ }
+ return( (double)score );
+}
+
+
+
+double DSPscore( int s, char **seq ) /* method 3 deha nai */
+{
+ int i, j, k;
+ double c;
+ int len = strlen( seq[0] );
+ double score;
+ double tmpscore;
+ char *mseq1, *mseq2;
+#if DEBUG
+ FILE *fp;
+#endif
+
+ score = 0.0;
+ c = 0.0;
+
+ for( i=0; i<s-1; i++ )
+ {
+ for( j=i+1; j<s; j++ )
+ {
+ mseq1 = seq[i];
+ mseq2 = seq[j];
+ tmpscore = 0.0;
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+
+ if( mseq1[k] == '-' )
+ {
+ tmpscore += penalty;
+ while( mseq1[++k] == '-' )
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ if( mseq2[k] == '-' )
+ {
+ tmpscore += penalty;
+ while( mseq2[++k] == '-' )
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ }
+ score += (double)tmpscore;
+ }
+ }
+
+ return( score );
+}
+
+
+#define SEGMENTSIZE 150
+
+int searchAnchors( int nseq, char **seq, Segment *seg )
+{
+ int i, j, k, kcyc;
+ int status;
+ double score;
+ int value = 0;
+ int len;
+ int length;
+ static double *stra = NULL;
+ static int alloclen = 0;
+ double cumscore;
+ static double threshold;
+
+ len = strlen( seq[0] );
+ if( alloclen < len )
+ {
+ if( alloclen )
+ {
+ FreeDoubleVec( stra );
+ }
+ else
+ {
+ threshold = (int)divThreshold / 100.0 * 600.0 * divWinSize;
+ }
+ stra = AllocateDoubleVec( len );
+ alloclen = len;
+ }
+
+ for( i=0; i<len; i++ )
+ {
+#if 0
+ /* make prf */
+ for( j=0; j<26; j++ )
+ {
+ prf[j] = 0.0;
+ }
+ for( j=0; j<nseq; j++ ) prf[amino_n[seq[j][i]]] += 1.0;
+
+ /* make hat */
+ pre = 26;
+ for( j=25; j>=0; j-- )
+ {
+ if( prf[j] )
+ {
+ hat[pre] = j;
+ pre = j;
+ }
+ }
+ hat[pre] = -1;
+
+ /* make site score */
+ stra[i] = 0.0;
+ for( k=hat[26]; k!=-1; k=hat[k] )
+ for( j=hat[26]; j!=-1; j=hat[j] )
+ stra[i] += n_dis[k][j] * prf[k] * prf[j];
+#else
+ stra[i] = 0.0;
+ kcyc = nseq-1;
+ for( k=0; k<kcyc; k++ ) for( j=k+1; j<nseq; j++ )
+ stra[i] += n_dis[(int)amino_n[(int)seq[k][i]]][(int)amino_n[(int)seq[j][i]]];
+ stra[i] /= (double)nseq * ( nseq-1 ) / 2;
+#endif
+ }
+
+ (seg+0)->skipForeward = 0;
+ (seg+1)->skipBackward = 0;
+ status = 0;
+ cumscore = 0.0;
+ score = 0.0;
+ length = 0; /* modified at 01/09/11 */
+ for( j=0; j<divWinSize; j++ ) score += stra[j];
+ for( i=1; i<len-divWinSize; i++ )
+ {
+ score = score - stra[i-1] + stra[i+divWinSize-1];
+#if DEBUG
+ fprintf( stderr, "%d %f ? %f", i, score, threshold );
+ if( score > threshold ) fprintf( stderr, "YES\n" );
+ else fprintf( stderr, "NO\n" );
+#endif
+
+ if( score > threshold )
+ {
+ if( !status )
+ {
+ status = 1;
+ seg->start = i;
+ length = 0;
+ cumscore = 0.0;
+ }
+ length++;
+ cumscore += score;
+ }
+ if( score <= threshold || length > SEGMENTSIZE )
+ {
+ if( status )
+ {
+ seg->end = i;
+ seg->center = ( seg->start + seg->end + divWinSize ) / 2 ;
+ seg->score = cumscore;
+#if DEBUG
+ fprintf( stderr, "%d-%d length = %d\n", seg->start, seg->end, length );
+#endif
+ if( length > SEGMENTSIZE )
+ {
+ (seg+0)->skipForeward = 1;
+ (seg+1)->skipBackward = 1;
+ }
+ else
+ {
+ (seg+0)->skipForeward = 0;
+ (seg+1)->skipBackward = 0;
+ }
+ length = 0;
+ cumscore = 0.0;
+ status = 0;
+ value++;
+ seg++;
+ if( value > MAXSEG - 3 ) ErrorExit( "TOO MANY SEGMENTS!");
+ }
+ }
+ }
+ if( status )
+ {
+ seg->end = i;
+ seg->center = ( seg->start + seg->end + divWinSize ) / 2 ;
+ seg->score = cumscore;
+#if DEBUG
+fprintf( stderr, "%d-%d length = %d\n", seg->start, seg->end, length );
+#endif
+ value++;
+ }
+ return( value );
+}
+
+void dontcalcimportance( int nseq, double *eff, char **seq, LocalHom **localhom )
+{
+ int i, j;
+ LocalHom *ptr;
+ static int *nogaplen = NULL;
+
+ if( nogaplen == NULL )
+ {
+ nogaplen = AllocateIntVec( nseq );
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ nogaplen[i] = seqlen( seq[i] );
+// fprintf( stderr, "nogaplen[%d] = %d\n", i, nogaplen[i] );
+ }
+
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ for( ptr=localhom[i]+j; ptr; ptr=ptr->next )
+ {
+// fprintf( stderr, "i,j=%d,%d,ptr=%p\n", i, j, ptr );
+#if 1
+ ptr->importance = ptr->opt / ptr->overlapaa;
+ ptr->fimportance = (float)ptr->importance;
+#else
+ ptr->importance = ptr->opt / MIN( nogaplen[i], nogaplen[j] );
+#endif
+ }
+ }
+ }
+}
+
+void calcimportance( int nseq, double *eff, char **seq, LocalHom **localhom )
+{
+ int i, j, pos, len;
+ static double *importance;
+ double tmpdouble;
+ static int *nogaplen = NULL;
+ LocalHom *tmpptr;
+
+ if( importance == NULL )
+ {
+ importance = AllocateDoubleVec( nlenmax );
+ nogaplen = AllocateIntVec( nseq );
+ }
+
+
+ for( i=0; i<nseq; i++ )
+ {
+ nogaplen[i] = seqlen( seq[i] );
+// fprintf( stderr, "nogaplen[] = %d\n", nogaplen[i] );
+ }
+
+#if 0
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+ {
+ tmpptr = localhom[i]+j;
+ fprintf( stderr, "%d-%d\n", i, j );
+ do
+ {
+ fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->opt );
+ } while( tmpptr=tmpptr->next );
+ }
+#endif
+
+
+ for( i=0; i<nseq; i++ )
+ {
+// fprintf( stderr, "i = %d\n", i );
+ for( pos=0; pos<nlenmax; pos++ )
+ importance[pos] = 0.0;
+ for( j=0; j<nseq; j++ )
+ {
+ if( i == j ) continue;
+ tmpptr = localhom[i]+j;
+ for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1 ) continue;
+ for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
+#if 1
+ importance[pos] += eff[j];
+#else
+ importance[pos] += eff[j] * tmpptr->opt / MIN( nogaplen[i], nogaplen[j] );
+ importance[pos] += eff[j] * tmpptr->opt / tmpptr->overlapaa;
+#endif
+ }
+ }
+#if 0
+ fprintf( stderr, "position specific importance of seq %d:\n", i );
+ for( pos=0; pos<nlenmax; pos++ )
+ fprintf( stderr, "%d: %f\n", pos, importance[pos] );
+ fprintf( stderr, "\n" );
+#endif
+ for( j=0; j<nseq; j++ )
+ {
+// fprintf( stderr, "i=%d, j=%d\n", i, j );
+ if( i == j ) continue;
+ if( localhom[i][j].opt == -1.0 ) continue;
+#if 1
+ for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ tmpdouble = 0.0;
+ len = 0;
+ for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
+ {
+ tmpdouble += importance[pos];
+ len++;
+ }
+ tmpdouble /= (double)len;
+
+ tmpptr->importance = tmpdouble * tmpptr->opt;
+ tmpptr->fimportance = (float)tmpptr->importance;
+ }
+#else
+ tmpdouble = 0.0;
+ len = 0;
+ for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
+ {
+ tmpdouble += importance[pos];
+ len++;
+ }
+ }
+
+ tmpdouble /= (double)len;
+
+ for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ tmpptr->importance = tmpdouble * tmpptr->opt;
+// tmpptr->importance = tmpptr->opt / tmpptr->overlapaa; //\e$B$J$+$C$?$3$H$K$9$k\e(B
+ }
+#endif
+
+// fprintf( stderr, "importance of match between %d - %d = %f\n", i, j, tmpdouble );
+ }
+ }
+
+#if 0
+ fprintf( stderr, "before averaging:\n" );
+
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+ {
+ fprintf( stderr, "%d-%d\n", i, j );
+ for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f -> %f opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->opt / tmpptr->overlapaa, eff[i] * tmpptr->importance, tmpptr->opt );
+ }
+ }
+#endif
+
+#if 1
+// fprintf( stderr, "average?\n" );
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ double imp;
+ LocalHom *tmpptr1, *tmpptr2;
+
+// fprintf( stderr, "i=%d, j=%d\n", i, j );
+
+ tmpptr1 = localhom[i]+j; tmpptr2 = localhom[j]+i;
+ for( ; tmpptr1 && tmpptr2; tmpptr1 = tmpptr1->next, tmpptr2 = tmpptr2->next)
+ {
+ if( tmpptr1->opt == -1.0 || tmpptr2->opt == -1.0 )
+ {
+// fprintf( stderr, "WARNING: i=%d, j=%d, tmpptr1->opt=%f, tmpptr2->opt=%f\n", i, j, tmpptr1->opt, tmpptr2->opt );
+ continue;
+ }
+// fprintf( stderr, "## importances = %f, %f\n", tmpptr1->importance, tmpptr2->importance );
+ imp = 0.5 * ( tmpptr1->importance + tmpptr2->importance );
+ tmpptr1->importance = tmpptr2->importance = imp;
+ tmpptr1->fimportance = tmpptr2->fimportance = (float)imp;
+
+// fprintf( stderr, "## importance = %f\n", tmpptr1->importance );
+
+ }
+
+#if 1
+ if( ( tmpptr1 && !tmpptr2 ) || ( !tmpptr1 && tmpptr2 ) )
+ {
+ fprintf( stderr, "ERROR: i=%d, j=%d\n", i, j );
+ exit( 1 );
+ }
+#endif
+ }
+#endif
+#if 0
+ fprintf( stderr, "after averaging:\n" );
+
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+ {
+ fprintf( stderr, "%d-%d\n", i, j );
+ for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f -> %f opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->opt / tmpptr->overlapaa, tmpptr->importance, tmpptr->opt );
+ }
+ }
+#endif
+}
+
+
+#if 0
+void weightimportance( int nseq, double **eff, LocalHom **localhom )
+{
+ int i, j, pos, len;
+ static double *importance;
+ double tmpdouble;
+ LocalHom *tmpptr, *tmpptr1, *tmpptr2;
+ if( importance == NULL )
+ importance = AllocateDoubleVec( nlenmax );
+
+
+ fprintf( stderr, "effmtx = :\n" );
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ fprintf( stderr, "%6.3f ", eff[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ for( pos=0; pos<nlenmax; pos++ )
+ importance[pos] = 0.0;
+ for( j=0; j<nseq; j++ )
+ {
+
+ if( i == j ) continue;
+ tmpptr = localhom[i]+j;
+ while( 1 )
+ {
+ fprintf( stderr, "i=%d, j=%d\n", i, j );
+ for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
+// importance[pos] += eff[i][j] * tmpptr->importance;
+ importance[pos] += eff[i][j] / (double)nseq * tmpptr->importance / 1.0;
+ fprintf( stderr, "eff[][] = %f, localhom[i][j].importance = %f \n", eff[i][j], tmpptr->importance );
+ tmpptr = tmpptr->next;
+ if( tmpptr == NULL ) break;
+ }
+
+ }
+#if 0
+ fprintf( stderr, "position specific importance of seq %d:\n", i );
+ for( pos=0; pos<nlenmax; pos++ )
+ fprintf( stderr, "%d: %f\n", pos, importance[pos] );
+ fprintf( stderr, "\n" );
+#endif
+ for( j=0; j<nseq; j++ )
+ {
+ fprintf( stderr, "i=%d, j=%d\n", i, j );
+ if( i == j ) continue;
+ tmpptr = localhom[i]+j;
+ do
+ {
+ tmpdouble = 0.0;
+ len = 0;
+ for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
+ {
+ tmpdouble += importance[pos];
+ len++;
+ }
+ tmpdouble /= (double)len;
+ tmpptr->importance = tmpdouble;
+ fprintf( stderr, "importance of match between %d - %d = %f\n", i, j, tmpdouble );
+ tmpptr = tmpptr->next;
+ } while( tmpptr );
+ }
+ }
+#if 1
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ fprintf( stderr, "i = %d, j=%d\n", i, j );
+ tmpptr1 = localhom[i]+j;
+ tmpptr2 = localhom[j]+i;
+ while( tmpptr1 && tmpptr2 )
+ {
+ tmpptr1->importance += tmpptr2->importance;
+ tmpptr1->importance *= 0.5;
+ tmpptr2->importance *= tmpptr1->importance;
+ fprintf( stderr, "%d-%d: s1=%d, e1=%d, s2=%d, e2=%d, importance=%f\n", i, j, tmpptr1->start1, tmpptr1->end1, tmpptr1->start2, tmpptr1->end2, tmpptr1->importance );
+ tmpptr1 = tmpptr1->next;
+ tmpptr2 = tmpptr2->next;
+ fprintf( stderr, "tmpptr1 = %p, tmpptr2 = %p\n", tmpptr1, tmpptr2 );
+ }
+ }
+#endif
+}
+
+void weightimportance2( int nseq, double *eff, LocalHom **localhom )
+{
+ int i, j, pos, len;
+ static double *wimportance;
+ double tmpdouble;
+ if( wimportance == NULL )
+ wimportance = AllocateDoubleVec( nlenmax );
+
+
+ fprintf( stderr, "effmtx = :\n" );
+ for( i=0; i<nseq; i++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ fprintf( stderr, "%6.3f ", eff[i] * eff[j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ fprintf( stderr, "i = %d\n", i );
+ for( pos=0; pos<nlenmax; pos++ )
+ wimportance[pos] = 0.0;
+ for( j=0; j<nseq; j++ )
+ {
+ if( i == j ) continue;
+ for( pos=localhom[i][j].start1; pos<=localhom[i][j].end1; pos++ )
+// wimportance[pos] += eff[i][j];
+ wimportance[pos] += eff[i] * eff[j] / (double)nseq * localhom[i][j].importance / 1.0;
+ }
+#if 0
+ fprintf( stderr, "position specific wimportance of seq %d:\n", i );
+ for( pos=0; pos<nlenmax; pos++ )
+ fprintf( stderr, "%d: %f\n", pos, wimportance[pos] );
+ fprintf( stderr, "\n" );
+#endif
+ for( j=0; j<nseq; j++ )
+ {
+ if( i == j ) continue;
+ tmpdouble = 0.0;
+ len = 0;
+ for( pos=localhom[i][j].start1; pos<=localhom[i][j].end1; pos++ )
+ {
+ tmpdouble += wimportance[pos];
+ len++;
+ }
+ tmpdouble /= (double)len;
+ localhom[i][j].wimportance = tmpdouble;
+ fprintf( stderr, "wimportance of match between %d - %d = %f\n", i, j, tmpdouble );
+ }
+ }
+#if 1
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ localhom[i][j].wimportance += localhom[j][i].wimportance;
+ localhom[i][j].wimportance = 0.5 * ( localhom[i][j].wimportance );
+ }
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ localhom[j][i].wimportance = localhom[i][j].wimportance;
+ }
+#endif
+}
+
+void weightimportance4( int clus1, int clus2, double *eff1, double *eff2, LocalHom ***localhom )
+{
+ int i, j, pos, len;
+ static double *wimportance;
+ LocalHom *tmpptr, *tmpptr1, *tmpptr2;
+ if( wimportance == NULL )
+ wimportance = AllocateDoubleVec( nlenmax );
+
+
+#if 0
+ fprintf( stderr, "effarr1 = :\n" );
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "%6.3f\n", eff1[i] );
+ fprintf( stderr, "effarr2 = :\n" );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "%6.3f\n", eff2[i] );
+#endif
+
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+// fprintf( stderr, "i=%d, j=%d\n", i, j );
+ tmpptr = localhom[i][j];
+ do
+ {
+ tmpptr->wimportance = tmpptr->importance * eff1[i] * eff2[j];
+ tmpptr = tmpptr->next;
+ } while( tmpptr );
+ }
+ }
+}
+
+static void addlocalhom_e( LocalHom *localhom, int start1, int start2, int end1, int end2, double opt )
+{
+ LocalHom *tmpptr;
+ tmpptr = localhom;
+
+ fprintf( stderr, "adding localhom\n" );
+ while( tmpptr->next )
+ tmpptr = tmpptr->next;
+ fprintf( stderr, "allocating localhom\n" );
+ tmpptr->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ fprintf( stderr, "done\n" );
+ tmpptr = tmpptr->next;
+
+ tmpptr->start1 = start1;
+ tmpptr->start2 = start2;
+ tmpptr->end1 = end1;
+ tmpptr->end2 = end2;
+ tmpptr->opt = opt;
+
+ fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+}
+
+#if 0
+#endif
+
+
+
+void extendlocalhom( int nseq, LocalHom **localhom )
+{
+ int i, j, k, pos0, pos1, pos2, st;
+ int start1, start2, end1, end2;
+ static int *tmpint1 = NULL;
+ static int *tmpint2 = NULL;
+ static int *tmpdouble1 = NULL;
+ static int *tmpdouble2 = NULL;
+ double opt;
+ LocalHom *tmpptr;
+ if( tmpint1 == NULL )
+ {
+ tmpint1 = AllocateIntVec( nlenmax );
+ tmpint2 = AllocateIntVec( nlenmax );
+ tmpdouble1 = AllocateIntVec( nlenmax );
+ tmpdouble2 = AllocateIntVec( nlenmax );
+ }
+
+
+ for( k=0; k<nseq; k++ )
+ {
+ for( i=0; i<nseq-1; i++ )
+ {
+ if( i == k ) continue;
+ for( pos0=0; pos0<nlenmax; pos0++ )
+ tmpint1[pos0] = -1;
+
+ tmpptr=localhom[k]+i;
+ do
+ {
+ pos0 = tmpptr->start1;
+ pos1 = tmpptr->start2;
+ while( pos0<=tmpptr->end1 )
+ {
+ tmpint1[pos0] = pos1++;
+ tmpdouble1[pos0] = tmpptr->opt;
+ pos0++;
+ }
+ } while( tmpptr = tmpptr->next );
+
+
+ for( j=i+1; j<nseq; j++ )
+ {
+ if( j == k ) continue;
+ for( pos1=0; pos1<nlenmax; pos1++ ) tmpint2[pos1] = -1;
+ tmpptr=localhom[k]+j;
+ do
+ {
+ pos0 = tmpptr->start1;
+ pos2 = tmpptr->start2;
+ while( pos0<=tmpptr->end1 )
+ {
+ tmpint2[pos0] = pos2++;
+ tmpdouble2[pos0++] = tmpptr->opt;
+ }
+ } while( tmpptr = tmpptr->next );
+
+#if 0
+
+ fprintf( stderr, "i,j=%d,%d\n", i, j );
+
+ for( pos0=0; pos0<nlenmax; pos0++ )
+ fprintf( stderr, "%d ", tmpint1[pos0] );
+ fprintf( stderr, "\n" );
+
+ for( pos0=0; pos0<nlenmax; pos0++ )
+ fprintf( stderr, "%d ", tmpint2[pos0] );
+ fprintf( stderr, "\n" );
+#endif
+
+
+ st = 0;
+ for( pos0=0; pos0<nlenmax; pos0++ )
+ {
+// fprintf( stderr, "pos0 = %d/%d, st = %d, tmpint1[pos0] = %d, tmpint2[pos0] = %d\n", pos0, nlenmax, st, tmpint1[pos0], tmpint2[pos0] );
+ if( tmpint1[pos0] >= 0 && tmpint2[pos0] >= 0 )
+ {
+ if( st == 0 )
+ {
+ st = 1;
+ start1 = tmpint1[pos0];
+ start2 = tmpint2[pos0];
+ opt = MIN( tmpdouble1[pos0], tmpdouble2[pos0] );
+ }
+ else if( tmpint1[pos0-1] != tmpint1[pos0]-1 || tmpint2[pos0-1] != tmpint2[pos0]-1 )
+ {
+ addlocalhom_e( localhom[i]+j, start1, start2, tmpint1[pos0-1], tmpint2[pos0-1], opt );
+ addlocalhom_e( localhom[j]+i, start2, start1, tmpint2[pos0-1], tmpint1[pos0-1], opt );
+ start1 = tmpint1[pos0];
+ start2 = tmpint2[pos0];
+ opt = MIN( tmpdouble1[pos0], tmpdouble2[pos0] );
+ }
+ }
+ if( tmpint1[pos0] == -1 || tmpint2[pos0] == -1 )
+ {
+ if( st == 1 )
+ {
+ st = 0;
+ addlocalhom_e( localhom[i]+j, start1, start2, tmpint1[pos0-1], tmpint2[pos0-1], opt );
+ addlocalhom_e( localhom[j]+i, start2, start1, tmpint2[pos0-1], tmpint1[pos0-1], opt );
+ }
+ }
+ }
+ }
+ }
+ }
+}
+#endif
+
+static void addlocalhom2_e( LocalHom *pt, LocalHom *lh, int sti, int stj, int eni, int enj, double opt, int overlp, int interm )
+{
+// dokka machigatteru
+ if( pt != lh ) // susumeru
+ {
+ pt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ pt = pt->next;
+ pt->next = NULL;
+ lh->last = pt;
+ }
+ else // sonomamatsukau
+ {
+ lh->last = pt;
+ }
+ lh->nokori++;
+// fprintf( stderr, "in addlocalhom2_e, pt = %p, pt->next = %p, interm=%d, sti-eni-stj-enj=%d %d %d %d\n", pt, pt->next, interm, sti, eni, stj, enj );
+
+ pt->start1 = sti;
+ pt->start2 = stj;
+ pt->end1 = eni;
+ pt->end2 = enj;
+ pt->opt = opt;
+ pt->extended = interm;
+ pt->overlapaa = overlp;
+#if 0
+ fprintf( stderr, "i: %d-%d\n", sti, eni );
+ fprintf( stderr, "j: %d-%d\n", stj, enj );
+ fprintf( stderr, "opt=%f\n", opt );
+ fprintf( stderr, "overlp=%d\n", overlp );
+#endif
+}
+
+void extendlocalhom2( int nseq, LocalHom **localhom, double **dist )
+{
+ int overlp, plim;
+ int i, j, k;
+ int pi, pj, pk, len;
+ int status, sti, stj;
+ int *ipt;
+ int co;
+ static int *ini = NULL;
+ static int *inj = NULL;
+ LocalHom *pt;
+
+ sti = 0; // by D.Mathog, a guess
+ stj = 0; // by D.Mathog, a guess
+
+ if( ini == NULL )
+ {
+ ini = AllocateIntVec( nlenmax+1 );
+ inj = AllocateIntVec( nlenmax+1 );
+ }
+
+
+ for( i=0; i<nseq-1; i++ )
+ {
+ for( j=i+1; j<nseq; j++ )
+ {
+#if 0
+ for( k=0; k<nseq; k++ ) sai[k] = 0;
+ numint = ncons;
+ while( 1 )
+ {
+ k = (int)( rnd() * nseq );
+ if( k == i || k == j ) continue; // mou yatta nomo habuita hoga ii
+ if( numint-- == 0 ) break;
+ if( sai[k] ) continue;
+ sai[k] = 1;
+#else
+ for( k=0; k<nseq; k++ )
+ {
+#endif
+// fprintf( stderr, "i=%d, j=%d, k=%d, dists = %f,%f,%f thrinter=%f\n", i, j, k, dist[i][j], dist[MIN(i,k)][MAX(i,k)], dist[MIN(j,k)][MAX(j,k)], thrinter );
+ if( k == i || k == j ) continue; // mou yatta nomo habuita hoga ii
+ if( dist[MIN(i,k)][MAX(i,k)] > dist[i][j] * thrinter || dist[MIN(j,k)][MAX(j,k)] > dist[i][j] * thrinter ) continue;
+ ipt = ini; co = nlenmax+1;
+ while( co-- ) *ipt++ = -1;
+ ipt = inj; co = nlenmax+1;
+ while( co-- ) *ipt++ = -1;
+ overlp = 0;
+
+ {
+ for( pt=localhom[i]+k; pt; pt=pt->next )
+ {
+// fprintf( stderr, "i=%d,k=%d,st1:st2=%d:%d,pt=%p,extended=%p\n", i, k, pt->start1, pt->start2, pt, pt->extended );
+ if( pt->opt == -1 )
+ {
+ fprintf( stderr, "opt kainaide tbfast.c = %f\n", pt->opt );
+ }
+ if( pt->extended > -1 ) break;
+ pi = pt->start1;
+ pk = pt->start2;
+ len = pt->end1 - pt->start1 + 1;
+ ipt = ini + pk;
+ while( len-- ) *ipt++ = pi++;
+ }
+ }
+
+ {
+ for( pt=localhom[j]+k; pt; pt=pt->next )
+ {
+ if( pt->opt == -1 )
+ {
+ fprintf( stderr, "opt kainaide tbfast.c = %f\n", pt->opt );
+ }
+ if( pt->extended > -1 ) break;
+ pj = pt->start1;
+ pk = pt->start2;
+ len = pt->end1 - pt->start1 + 1;
+ ipt = inj + pk;
+ while( len-- ) *ipt++ = pj++;
+ }
+ }
+#if 0
+ fprintf( stderr, "i=%d,j=%d,k=%d\n", i, j, k );
+ overlp = 0;
+ for( pk = 0; pk < nlenmax; pk++ )
+ {
+ if( ini[pk] != -1 && inj[pk] != -1 ) overlp++;
+ fprintf( stderr, " %d", inj[pk] );
+ }
+ fprintf( stderr, "\n" );
+
+ fprintf( stderr, "i=%d,j=%d,k=%d\n", i, j, k );
+ overlp = 0;
+ for( pk = 0; pk < nlenmax; pk++ )
+ {
+ if( ini[pk] != -1 && inj[pk] != -1 ) overlp++;
+ fprintf( stderr, " %d", ini[pk] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+ overlp = 0;
+ plim = nlenmax+1;
+ for( pk = 0; pk < plim; pk++ )
+ if( ini[pk] != -1 && inj[pk] != -1 ) overlp++;
+
+
+ status = 0;
+ plim = nlenmax+1;
+ for( pk=0; pk<plim; pk++ )
+ {
+// fprintf( stderr, "%d %d: %d-%d\n", i, j, ini[pk], inj[pk] );
+ if( status )
+ {
+ if( ini[pk] == -1 || inj[pk] == -1 || ini[pk-1] != ini[pk] - 1 || inj[pk-1] != inj[pk] - 1 ) // saigonoshori
+ {
+ status = 0;
+// fprintf( stderr, "end here!\n" );
+
+ pt = localhom[i][j].last;
+// fprintf( stderr, "in ex (ba), pt = %p, nokori=%d, i,j,k=%d,%d,%d\n", pt, localhom[i][j].nokori, i, j, k );
+ addlocalhom2_e( pt, localhom[i]+j, sti, stj, ini[pk-1], inj[pk-1], MIN( localhom[i][k].opt, localhom[j][k].opt ) * 1.0, overlp, k );
+// fprintf( stderr, "in ex, pt = %p, pt->next = %p, pt->next->next = %p\n", pt, pt->next, pt->next->next );
+
+ pt = localhom[j][i].last;
+// fprintf( stderr, "in ex (ba), pt = %p, pt->next = %p\n", pt, pt->next );
+// fprintf( stderr, "in ex (ba), pt = %p, pt->next = %p, k=%d\n", pt, pt->next, k );
+ addlocalhom2_e( pt, localhom[j]+i, stj, sti, inj[pk-1], ini[pk-1], MIN( localhom[i][k].opt, localhom[j][k].opt ) * 1.0, overlp, k );
+// fprintf( stderr, "in ex, pt = %p, pt->next = %p, pt->next->next = %p\n", pt, pt->next, pt->next->next );
+ }
+ }
+ if( !status ) // else deha arimasenn.
+ {
+ if( ini[pk] == -1 || inj[pk] == -1 ) continue;
+ sti = ini[pk];
+ stj = inj[pk];
+// fprintf( stderr, "start here!\n" );
+ status = 1;
+ }
+ }
+// if( status ) fprintf( stderr, "end here\n" );
+
+// exit( 1 );
+// fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
+ }
+#if 0
+ for( pt=localhomtable[i]+j; pt; pt=pt->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
+ }
+#endif
+ }
+ }
+}
+
+int makelocal( char *s1, char *s2, int thr )
+{
+ int start, maxstart, maxend;
+ char *pt1, *pt2;
+ double score;
+ double maxscore;
+
+ pt1 = s1;
+ pt2 = s2;
+
+ maxend = 0; // by D.Mathog, a guess
+
+// fprintf( stderr, "thr = %d, \ns1 = %s\ns2 = %s\n", thr, s1, s2 );
+ maxscore = 0.0;
+ score = 0.0;
+ start = 0;
+ maxstart = 0;
+ while( *pt1 )
+ {
+// fprintf( stderr, "*pt1 = %c*pt2 = %c\n", *pt1, *pt2 );
+ if( *pt1 == '-' || *pt2 == '-' )
+ {
+// fprintf( stderr, "penalty = %d\n", penalty );
+ score += penalty;
+ while( *pt1 == '-' || *pt2 == '-' )
+ {
+ pt1++; pt2++;
+ }
+ continue;
+ }
+
+ score += ( amino_dis[(int)*pt1++][(int)*pt2++] - thr );
+// score += ( amino_dis[(int)*pt1++][(int)*pt2++] );
+ if( score > maxscore )
+ {
+// fprintf( stderr, "score = %f\n", score );
+ maxscore = score;
+ maxstart = start;
+// fprintf( stderr, "## max! maxstart = %d, start = %d\n", maxstart, start );
+ }
+ if( score < 0.0 )
+ {
+// fprintf( stderr, "## resetting, start = %d, maxstart = %d\n", start, maxstart );
+ if( start == maxstart )
+ {
+ maxend = pt1 - s1;
+// fprintf( stderr, "maxend = %d\n", maxend );
+ }
+ score = 0.0;
+ start = pt1 - s1;
+ }
+ }
+ if( start == maxstart )
+ maxend = pt1 - s1 - 1;
+
+// fprintf( stderr, "maxstart = %d, maxend = %d, maxscore = %f\n", maxstart, maxend, maxscore );
+ s1[maxend+1] = 0;
+ s2[maxend+1] = 0;
+ return( maxstart );
+}
+
+void resetlocalhom( int nseq, LocalHom **lh )
+{
+ int i, j;
+ LocalHom *pt;
+
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ for( pt=lh[i]+j; pt; pt=pt->next )
+ pt->opt = 1.0;
+ }
+
+}
+
+void gapireru( char *res, char *ori, char *gt )
+{
+ char g;
+ while( (g = *gt++) )
+ {
+ if( g == '-' )
+ {
+ *res++ = *newgapstr;
+ }
+ else
+ {
+ *res++ = *ori++;
+ }
+ }
+ *res = 0;
+}
+
+void getkyokaigap( char *g, char **s, int pos, int n )
+{
+// char *bk = g;
+// while( n-- ) *g++ = '-';
+ while( n-- ) *g++ = (*s++)[pos];
+
+// fprintf( stderr, "bk = %s\n", bk );
+}
+
+void new_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len, char *sgappat )
+#if 0
+{
+ int i, j, gc, gb;
+ float feff;
+
+
+ for( i=0; i<len+1; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = ( sgappat[j] == '-' );
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ }
+}
+#else
+{
+ int i, j, gc, gb;
+ float feff;
+ float *fpt;
+ char *spt;
+
+ fpt = ogcp;
+ i = len;
+ while( i-- ) *fpt++ = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ spt = seq[j];
+ fpt = ogcp;
+ gc = ( sgappat[j] == '-' );
+ i = len;
+ while( i-- )
+ {
+ gb = gc;
+ gc = ( *spt++ == '-' );
+ {
+ if( !gb * gc ) *fpt += feff;
+ fpt++;
+ }
+ }
+ }
+}
+#endif
+void new_OpeningGapCount_zure( float *ogcp, int clus, char **seq, double *eff, int len, char *sgappat, char *egappat )
+#if 0
+{
+ int i, j, gc, gb;
+ float feff;
+
+
+ for( i=0; i<len+1; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = ( sgappat[j] == '-' );
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ {
+ gb = gc;
+ gc = ( egappat[j] == '-' );
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ }
+}
+#else
+{
+ int i, j, gc, gb;
+ float feff;
+ float *fpt;
+ char *spt;
+
+ fpt = ogcp;
+ i = len+2;
+ while( i-- ) *fpt++ = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ spt = seq[j];
+ fpt = ogcp;
+ gc = ( sgappat[j] == '-' );
+ i = len;
+ while( i-- )
+ {
+ gb = gc;
+ gc = ( *spt++ == '-' );
+ {
+ if( !gb * gc ) *fpt += feff;
+ fpt++;
+ }
+ }
+ {
+ gb = gc;
+ gc = ( egappat[j] == '-' );
+ if( !gb * gc ) *fpt += feff;
+ }
+ }
+}
+#endif
+
+void new_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len, char *sgappat, char *egappat )
+#if 0
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len+1; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = ( sgappat[j] == '-' );
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc ) fgcp[i] += feff;
+ }
+ }
+ {
+ gb = gc;
+ gc = ( egappat[j] == '-' );
+ {
+ if( gb * !gc ) fgcp[len] += feff;
+ }
+ }
+ }
+}
+#else
+{
+ int i, j, gc, gb;
+ float feff;
+ float *fpt;
+ char *spt;
+
+ fpt = fgcp;
+ i = len+2;
+ while( i-- ) *fpt++ = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ fpt = fgcp;
+ spt = seq[j];
+ gc = ( sgappat[j] == '-' );
+ i = len;
+ while( i-- )
+ {
+ gb = gc;
+ gc = ( *spt++ == '-' );
+ {
+ if( gb * !gc ) *fpt += feff;
+ fpt++;
+ }
+ }
+ {
+ gb = gc;
+ gc = ( egappat[j] == '-' );
+ {
+ if( gb * !gc ) *fpt += feff;
+ }
+ }
+ }
+}
+#endif
+void new_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len, char *egappat )
+#if 0
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = ( seq[j][0] == '-' );
+ for( i=1; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc ) fgcp[i-1] += feff;
+ }
+ }
+ {
+ gb = gc;
+ gc = ( egappat[j] == '-' );
+ {
+ if( gb * !gc ) fgcp[len-1] += feff;
+ }
+ }
+ }
+}
+#else
+{
+ int i, j, gc, gb;
+ float feff;
+ float *fpt;
+ char *spt;
+
+ fpt = fgcp;
+ i = len;
+ while( i-- ) *fpt++ = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ fpt = fgcp;
+ spt = seq[j];
+ gc = ( *spt == '-' );
+ i = len;
+ while( i-- )
+ {
+ gb = gc;
+ gc = ( *++spt == '-' );
+ {
+ if( gb * !gc ) *fpt += feff;
+ fpt++;
+ }
+ }
+ {
+ gb = gc;
+ gc = ( egappat[j] == '-' );
+ {
+ if( gb * !gc ) *fpt += feff;
+ }
+ }
+ }
+}
+#endif
+
+void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+ float *fpt;
+ char *spt;
+
+ fpt = ogcp;
+ i = len;
+ while( i-- ) *fpt++ = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ spt = seq[j];
+ fpt = ogcp;
+ gc = 0;
+// gc = 1;
+ i = len;
+ while( i-- )
+ {
+ gb = gc;
+ gc = ( *spt++ == '-' );
+ {
+ if( !gb * gc ) *fpt += feff;
+ fpt++;
+ }
+ }
+ }
+ ogcp[len] = 0.0;
+}
+
+void st_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+ float *fpt;
+ char *spt;
+
+ fpt = fgcp;
+ i = len+1;
+ while( i-- ) *fpt++ = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ fpt = fgcp+1;
+ spt = seq[j];
+ gc = ( *spt == '-' );
+ i = len;
+// for( i=1; i<len; i++ )
+ while( i-- )
+ {
+ gb = gc;
+ gc = ( *++spt == '-' );
+ {
+ if( gb * !gc ) *fpt += feff;
+ fpt++;
+ }
+ }
+ {
+ gb = gc;
+ gc = 0;
+// gc = 1;
+ {
+ if( gb * !gc ) *fpt += feff;
+ }
+ }
+ }
+}
+
+void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+ float *fpt;
+ char *spt;
+
+ fpt = fgcp;
+ i = len;
+ while( i-- ) *fpt++ = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ fpt = fgcp;
+ spt = seq[j];
+ gc = ( *spt == '-' );
+ i = len;
+// for( i=1; i<len; i++ )
+ while( i-- )
+ {
+ gb = gc;
+ gc = ( *++spt == '-' );
+ {
+ if( gb * !gc ) *fpt += feff;
+ fpt++;
+ }
+ }
+ {
+ gb = gc;
+ gc = 0;
+// gc = 1;
+ {
+ if( gb * !gc ) *fpt += feff;
+ }
+ }
+ }
+}
+
+void getGapPattern( float *fgcp, int clus, char **seq, double *eff, int len, char *xxx )
+{
+ int i, j, gc, gb;
+ float feff;
+ float *fpt;
+ char *spt;
+
+ fpt = fgcp;
+ i = len+1;
+ while( i-- ) *fpt++ = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ fpt = fgcp;
+ spt = seq[j];
+ gc = ( *spt == '-' );
+ i = len+1;
+ while( i-- )
+ {
+ gb = gc;
+ gc = ( *++spt == '-' );
+ {
+ if( gb * !gc ) *fpt += feff;
+ fpt++;
+ }
+ }
+#if 0
+ {
+ gb = gc;
+ gc = ( egappat[j] == '-' );
+ {
+ if( gb * !gc ) *fpt += feff;
+ }
+ }
+#endif
+ }
+ for( j=0; j<len; j++ )
+ {
+ fprintf( stderr, "%d, %f\n", j, fgcp[j] );
+ }
+}
+
+void getdigapfreq_st( float *freq, int clus, char **seq, double *eff, int len )
+{
+ int i, j;
+ float feff;
+ for( i=0; i<len+1; i++ ) freq[i] = 0.0;
+ for( i=0; i<clus; i++ )
+ {
+ feff = eff[i];
+ if( 0 && seq[i][0] == '-' ) // machigai kamo
+ freq[0] += feff;
+ for( j=1; j<len; j++ )
+ {
+ if( seq[i][j] == '-' && seq[i][j-1] == '-' )
+ freq[j] += feff;
+ }
+ if( 0 && seq[i][len-1] == '-' )
+ freq[len] += feff;
+ }
+// fprintf( stderr, "\ndigapf = \n" );
+// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
+}
+
+void getdiaminofreq_x( float *freq, int clus, char **seq, double *eff, int len )
+{
+ int i, j;
+ float feff;
+ for( i=0; i<len+2; i++ ) freq[i] = 0.0;
+ for( i=0; i<clus; i++ )
+ {
+ feff = eff[i];
+ if( seq[i][0] != '-' ) // tadashii
+ freq[0] += feff;
+ for( j=1; j<len; j++ )
+ {
+ if( seq[i][j] != '-' && seq[i][j-1] != '-' )
+ freq[j] += feff;
+ }
+ if( 1 && seq[i][len-1] != '-' ) // xxx wo tsukawanaitoki [len-1] nomi
+ freq[len] += feff;
+ }
+// fprintf( stderr, "\ndiaaf = \n" );
+// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
+}
+
+void getdiaminofreq_st( float *freq, int clus, char **seq, double *eff, int len )
+{
+ int i, j;
+ float feff;
+ for( i=0; i<len+1; i++ ) freq[i] = 0.0;
+ for( i=0; i<clus; i++ )
+ {
+ feff = eff[i];
+ if( seq[i][0] != '-' )
+ freq[0] += feff;
+ for( j=1; j<len; j++ )
+ {
+ if( seq[i][j] != '-' && seq[i][j-1] != '-' )
+ freq[j] += feff;
+ }
+// if( 1 && seq[i][len-1] != '-' ) // xxx wo tsukawanaitoki [len-1] nomi
+ freq[len] += feff;
+ }
+// fprintf( stderr, "\ndiaaf = \n" );
+// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
+}
+
+void getdigapfreq_part( float *freq, int clus, char **seq, double *eff, int len, char *sgappat, char *egappat )
+{
+ int i, j;
+ float feff;
+ for( i=0; i<len+2; i++ ) freq[i] = 0.0;
+ for( i=0; i<clus; i++ )
+ {
+ feff = eff[i];
+// if( seq[i][0] == '-' )
+ if( seq[i][0] == '-' && sgappat[i] == '-' )
+ freq[0] += feff;
+ for( j=1; j<len; j++ )
+ {
+ if( seq[i][j] == '-' && seq[i][j-1] == '-' )
+ freq[j] += feff;
+ }
+// if( seq[i][len] == '-' && seq[i][len-1] == '-' ) // xxx wo tsukawanaitoki arienai
+ if( egappat[i] == '-' && seq[i][len-1] == '-' )
+ freq[len] += feff;
+ }
+// fprintf( stderr, "\ndigapf = \n" );
+// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
+}
+
+void getdiaminofreq_part( float *freq, int clus, char **seq, double *eff, int len, char *sgappat, char *egappat )
+{
+ int i, j;
+ float feff;
+ for( i=0; i<len+2; i++ ) freq[i] = 0.0;
+ for( i=0; i<clus; i++ )
+ {
+ feff = eff[i];
+ if( seq[i][0] != '-' && sgappat[i] != '-' )
+ freq[0] += feff;
+ for( j=1; j<len; j++ )
+ {
+ if( seq[i][j] != '-' && seq[i][j-1] != '-' )
+ freq[j] += feff;
+ }
+// if( 1 && seq[i][len-1] != '-' ) // xxx wo tsukawanaitoki [len-1] nomi
+ if( egappat[i] != '-' && seq[i][len-1] != '-' ) // xxx wo tsukawanaitoki [len-1] nomi
+ freq[len] += feff;
+ }
+// fprintf( stderr, "\ndiaaf = \n" );
+// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
+}
+
+void getgapfreq_zure_part( float *freq, int clus, char **seq, double *eff, int len, char *sgap )
+{
+ int i, j;
+ float feff;
+ for( i=0; i<len+2; i++ ) freq[i] = 0.0;
+ for( i=0; i<clus; i++ )
+ {
+ feff = eff[i];
+ if( sgap[i] == '-' )
+ freq[0] += feff;
+ for( j=0; j<len; j++ )
+ {
+ if( seq[i][j] == '-' )
+ freq[j+1] += feff;
+ }
+// if( egap[i] == '-' )
+// freq[len+1] += feff;
+ }
+// fprintf( stderr, "\ngapf = \n" );
+// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
+}
+
+void getgapfreq_zure( float *freq, int clus, char **seq, double *eff, int len )
+{
+ int i, j;
+ float feff;
+ for( i=0; i<len+1; i++ ) freq[i] = 0.0;
+ for( i=0; i<clus; i++ )
+ {
+ feff = eff[i];
+ for( j=0; j<len; j++ )
+ {
+ if( seq[i][j] == '-' )
+ freq[j+1] += feff;
+ }
+ }
+ freq[len+1] = 0.0;
+// fprintf( stderr, "\ngapf = \n" );
+// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
+}
+
+void getgapfreq( float *freq, int clus, char **seq, double *eff, int len )
+{
+ int i, j;
+ float feff;
+ for( i=0; i<len+1; i++ ) freq[i] = 0.0;
+ for( i=0; i<clus; i++ )
+ {
+ feff = eff[i];
+ for( j=0; j<len; j++ )
+ {
+ if( seq[i][j] == '-' )
+ freq[j] += feff;
+ }
+ }
+ freq[len] = 0.0;
+// fprintf( stderr, "\ngapf = \n" );
+// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
+}
+
+void st_getGapPattern( Gappat **pat, int clus, char **seq, double *eff, int len )
+{
+ int i, j, k, gb, gc;
+ int known;
+ float feff;
+ Gappat **fpt;
+ char *spt;
+ int gaplen;
+
+ fpt = pat;
+ i = len+1;
+ while( i-- )
+ {
+ if( *fpt ) free( *fpt );
+ *fpt++ = NULL;
+ }
+
+ for( j=0; j<clus; j++ )
+ {
+// fprintf( stderr, "seq[%d] = %s\n", j, seq[j] );
+ feff = (float)eff[j];
+
+ fpt = pat;
+ *fpt = NULL; // Falign.c kara yobareru tokiha chigau.
+ spt = seq[j];
+ gc = 0;
+ gaplen = 0;
+
+ for( i=0; i<len+1; i++ )
+// while( i-- )
+ {
+// fprintf( stderr, "i=%d, gaplen = %d\n", i, gaplen );
+ gb = gc;
+ gc = ( i != len && *spt++ == '-' );
+ if( gc )
+ gaplen++;
+ else
+ {
+ if( gb && gaplen )
+ {
+ k = 1;
+ known = 0;
+ if( *fpt ) for( ; (*fpt)[k].len != -1; k++ )
+ {
+ if( (*fpt)[k].len == gaplen )
+ {
+// fprintf( stderr, "known\n" );
+ known = 1;
+ break;
+ }
+ }
+
+ if( known == 0 )
+ {
+ *fpt = (Gappat *)realloc( *fpt, (k+3) * sizeof( Gappat ) ); // mae1 (total), ato2 (len0), term
+ if( !*fpt )
+ {
+ fprintf( stderr, "Cannot allocate gappattern!'n" );
+ fprintf( stderr, "Use an approximate method, with the --mafft5 option.\n" );
+ exit( 1 );
+ }
+ (*fpt)[k].freq = 0.0;
+ (*fpt)[k].len = gaplen;
+ (*fpt)[k+1].len = -1;
+ (*fpt)[k+1].freq = 0.0; // iranai
+// fprintf( stderr, "gaplen=%d, Unknown, %f\n", gaplen, (*fpt)[k].freq );
+ }
+
+// fprintf( stderr, "adding pos %d, len=%d, k=%d, freq=%f->", i, gaplen, k, (*fpt)[k].freq );
+ (*fpt)[k].freq += feff;
+// fprintf( stderr, "%f\n", (*fpt)[k].freq );
+ gaplen = 0;
+ }
+ }
+ fpt++;
+ }
+ }
+#if 1
+ for( j=0; j<len+1; j++ )
+ {
+ if( pat[j] )
+ {
+// fprintf( stderr, "j=%d\n", j );
+// for( i=1; pat[j][i].len!=-1; i++ )
+// fprintf( stderr, "pos=%d, i=%d, len=%d, freq=%f\n", j, i, pat[j][i].len, pat[j][i].freq );
+
+ pat[j][0].len = 0; // iminashi
+ pat[j][0].freq = 0.0;
+ for( i=1; pat[j][i].len!=-1;i++ )
+ {
+ pat[j][0].freq += pat[j][i].freq;
+// fprintf( stderr, "totaling, i=%d, result = %f\n", i, pat[j][0].freq );
+ }
+// fprintf( stderr, "totaled, result = %f\n", pat[j][0].freq );
+
+ pat[j][i].freq = 1.0 - pat[j][0].freq;
+ pat[j][i].len = 0; // imiari
+ pat[j][i+1].len = -1;
+ }
+ else
+ {
+ pat[j] = (Gappat *)calloc( 3, sizeof( Gappat ) );
+ pat[j][0].freq = 0.0;
+ pat[j][0].len = 0; // iminashi
+
+ pat[j][1].freq = 1.0 - pat[j][0].freq;
+ pat[j][1].len = 0; // imiari
+ pat[j][2].len = -1;
+ }
+ }
+#endif
+}
+
+static void commongappickpair( char *r1, char *r2, char *i1, char *i2 )
+{
+// strcpy( r1, i1 );
+// strcpy( r2, i2 );
+// return; // not SP
+ while( *i1 )
+ {
+ if( *i1 == '-' && *i2 == '-' )
+ {
+ i1++;
+ i2++;
+ }
+ else
+ {
+ *r1++ = *i1++;
+ *r2++ = *i2++;
+ }
+ }
+ *r1 = 0;
+ *r2 = 0;
+}
+
+float naiveRpairscore( int n1, int n2, char **seq1, char **seq2, double *eff1, double *eff2, int penal )
+{
+// return( 0 );
+ int i, j;
+ float val;
+ float valf;
+ int pv;
+ double deff;
+ char *p1, *p2, *p1p, *p2p;
+ val = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ deff = eff1[i] * eff2[j];
+// fprintf( stderr, "feff %d-%d = %f\n", i, j, feff );
+// fprintf( stderr, "i1 = %s\n", seq1[i] );
+// fprintf( stderr, "i2 = %s\n", seq2[j] );
+// fprintf( stderr, "s1 = %s\n", s1 );
+// fprintf( stderr, "s2 = %s\n", s2 );
+// fprintf( stderr, "penal = %d\n", penal );
+
+ valf = 0;
+ p1 = seq1[i]; p2 = seq2[j];
+ pv = 0;
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal;
+// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
+ p1p = p1; p2p = p2;
+ valf += (float)amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
+ while( *p1p )
+ {
+ pv = 0;
+ if( *p1p != '-' && *p2p != '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 != '-' )
+ ;
+ if( *p1 == '-' && *p2 == '-' )
+ ;
+ }
+ if( *p1p == '-' && *p2p == '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal;
+// ;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal;
+// ;
+ if( *p1 != '-' && *p2 != '-' )
+ ;
+ if( *p1 == '-' && *p2 == '-' )
+ ;
+ }
+ if( *p1p != '-' && *p2p == '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal * 2; // ??
+// ;
+ if( *p1 != '-' && *p2 == '-' )
+ ;
+ if( *p1 != '-' && *p2 != '-' )
+ pv = penal;
+// ;
+ if( *p1 == '-' && *p2 == '-' )
+ pv = penal;
+// ;
+ }
+ if( *p1p == '-' && *p2p != '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ ;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal * 2; // ??
+// ;
+ if( *p1 != '-' && *p2 != '-' )
+ pv = penal;
+// ;
+ if( *p1 == '-' && *p2 == '-' )
+ pv = penal;
+// ;
+ }
+// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
+// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
+ valf += amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
+ p1p++; p2p++;
+ }
+// fprintf( stderr, "valf = %d\n", valf );
+ val += deff * ( valf );
+ }
+ fprintf( stderr, "val = %f\n", val );
+ return( val );
+// exit( 1 );
+}
+float naiveQpairscore( int n1, int n2, char **seq1, char **seq2, double *eff1, double *eff2, int penal )
+{
+ int i, j;
+ float val;
+ float valf;
+ int pv;
+ double deff;
+ char *p1, *p2, *p1p, *p2p;
+ return( 0 );
+ val = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ deff = eff1[i] * eff2[j];
+// fprintf( stderr, "feff %d-%d = %f\n", i, j, feff );
+// fprintf( stderr, "i1 = %s\n", seq1[i] );
+// fprintf( stderr, "i2 = %s\n", seq2[j] );
+// fprintf( stderr, "s1 = %s\n", s1 );
+// fprintf( stderr, "s2 = %s\n", s2 );
+// fprintf( stderr, "penal = %d\n", penal );
+
+ valf = 0;
+ p1 = seq1[i]; p2 = seq2[j];
+ pv = 0;
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal;
+// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
+ p1p = p1; p2p = p2;
+ valf += (float)amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
+ while( *p1p )
+ {
+ pv = 0;
+ if( *p1p != '-' && *p2p != '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 != '-' )
+ ;
+ if( *p1 == '-' && *p2 == '-' )
+ ;
+ }
+ if( *p1p == '-' && *p2p == '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+// pv = penal;
+ ;
+ if( *p1 != '-' && *p2 == '-' )
+// pv = penal;
+ ;
+ if( *p1 != '-' && *p2 != '-' )
+ ;
+ if( *p1 == '-' && *p2 == '-' )
+ ;
+ }
+ if( *p1p != '-' && *p2p == '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal * 2; // ??
+// ;
+ if( *p1 != '-' && *p2 == '-' )
+ ;
+ if( *p1 != '-' && *p2 != '-' )
+ pv = penal;
+// ;
+ if( *p1 == '-' && *p2 == '-' )
+// pv = penal;
+ ;
+ }
+ if( *p1p == '-' && *p2p != '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ ;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal * 2; // ??
+// ;
+ if( *p1 != '-' && *p2 != '-' )
+ pv = penal;
+// ;
+ if( *p1 == '-' && *p2 == '-' )
+// pv = penal;
+ ;
+ }
+// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
+// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
+ valf += amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
+ p1p++; p2p++;
+ }
+// fprintf( stderr, "valf = %d\n", valf );
+ val += deff * ( valf );
+ }
+ fprintf( stderr, "val = %f\n", val );
+ return( val );
+// exit( 1 );
+}
+float naiveHpairscore( int n1, int n2, char **seq1, char **seq2, double *eff1, double *eff2, int penal )
+{
+ int i, j;
+ float val;
+ float valf;
+ int pv;
+// float feff = 0.0; // by D.Mathog, a guess
+ double deff;
+ char *p1, *p2, *p1p, *p2p;
+ val = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ deff = eff1[i] * eff2[j];
+// fprintf( stderr, "i1 = %s\n", seq1[i] );
+// fprintf( stderr, "i2 = %s\n", seq2[j] );
+// fprintf( stderr, "s1 = %s\n", s1 );
+// fprintf( stderr, "s2 = %s\n", s2 );
+// fprintf( stderr, "penal = %d\n", penal );
+
+ valf = 0;
+ p1 = seq1[i]; p2 = seq2[j];
+ pv = 0;
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal;
+ if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, (int)(p1-seq1[i]), (int)(p2-seq2[j]) );
+ p1p = p1; p2p = p2;
+ valf += (float)amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
+ while( *p1p )
+ {
+ pv = 0;
+ if( *p1p != '-' && *p2p != '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 == '-' )
+ pv = penal;
+ if( *p1 != '-' && *p2 != '-' )
+ ;
+ if( *p1 == '-' && *p2 == '-' )
+ ;
+ }
+ if( *p1p == '-' && *p2p == '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+// pv = penal;
+ ;
+ if( *p1 != '-' && *p2 == '-' )
+// pv = penal;
+ ;
+ if( *p1 != '-' && *p2 != '-' )
+ ;
+ if( *p1 == '-' && *p2 == '-' )
+ ;
+ }
+ if( *p1p != '-' && *p2p == '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+// pv = penal;
+ ;
+ if( *p1 != '-' && *p2 == '-' )
+ ;
+ if( *p1 != '-' && *p2 != '-' )
+ pv = penal;
+ if( *p1 == '-' && *p2 == '-' )
+// pv = penal;
+ ;
+ }
+ if( *p1p == '-' && *p2p != '-' )
+ {
+ if( *p1 == '-' && *p2 != '-' )
+ ;
+ if( *p1 != '-' && *p2 == '-' )
+// pv = penal;
+ ;
+ if( *p1 != '-' && *p2 != '-' )
+ pv = penal;
+ if( *p1 == '-' && *p2 == '-' )
+// pv = penal;
+ ;
+ }
+// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
+// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
+ valf += amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
+ p1p++; p2p++;
+ }
+// fprintf( stderr, "valf = %d\n", valf );
+ val += deff * ( valf );
+ }
+ fprintf( stderr, "val = %f\n", val );
+ return( val );
+// exit( 1 );
+}
+
+float naivepairscore11( char *seq1, char *seq2, int penal )
+{
+ float vali;
+ int len = strlen( seq1 );
+ char *s1, *s2, *p1, *p2;
+ s1 = calloc( len+1, sizeof( char ) );
+ s2 = calloc( len+1, sizeof( char ) );
+ {
+ vali = 0.0;
+ commongappickpair( s1, s2, seq1, seq2 );
+// fprintf( stderr, "###i1 = %s\n", seq1 );
+// fprintf( stderr, "###i2 = %s\n", seq2 );
+// fprintf( stderr, "###penal = %d\n", penal );
+
+ p1 = s1; p2 = s2;
+ while( *p1 )
+ {
+ if( *p1 == '-' )
+ {
+// fprintf( stderr, "Penal! %c-%c in %d-%d, %f\n", *(p1-1), *(p2-1), i, j, feff );
+ vali += (float)penal;
+// while( *p1 == '-' || *p2 == '-' )
+ while( *p1 == '-' ) // SP
+ {
+ p1++;
+ p2++;
+ }
+ continue;
+ }
+ if( *p2 == '-' )
+ {
+// fprintf( stderr, "Penal! %c-%c in %d-%d, %f\n", *(p1-1), *(p2-1), i, j, feff );
+ vali += (float)penal;
+// while( *p2 == '-' || *p1 == '-' )
+ while( *p2 == '-' ) // SP
+ {
+ p1++;
+ p2++;
+ }
+ continue;
+ }
+// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
+ vali += (float)amino_dis[(int)*p1++][(int)*p2++];
+ }
+ }
+ free( s1 );
+ free( s2 );
+// fprintf( stderr, "###vali = %d\n", vali );
+ return( vali );
+}
+
+float naivepairscore( int n1, int n2, char **seq1, char **seq2, double *eff1, double *eff2, int penal )
+{
+// return( 0.0 );
+ int i, j;
+ float val;
+ int vali;
+ float feff;
+ int len = strlen( seq1[0] );
+ char *s1, *s2, *p1, *p2;
+ s1 = calloc( len+1, sizeof( char ) );
+ s2 = calloc( len+1, sizeof( char ) );
+ val = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ vali = 0;
+ feff = eff1[i] * eff2[j];
+// fprintf( stderr, "feff %d-%d = %f\n", i, j, feff );
+ commongappickpair( s1, s2, seq1[i], seq2[j] );
+// fprintf( stderr, "i1 = %s\n", seq1[i] );
+// fprintf( stderr, "i2 = %s\n", seq2[j] );
+// fprintf( stderr, "s1 = %s\n", s1 );
+// fprintf( stderr, "s2 = %s\n", s2 );
+// fprintf( stderr, "penal = %d\n", penal );
+
+ p1 = s1; p2 = s2;
+ while( *p1 )
+ {
+ if( *p1 == '-' )
+ {
+// fprintf( stderr, "Penal! %c-%c in %d-%d, %f\n", *(p1-1), *(p2-1), i, j, feff );
+ vali += penal;
+// while( *p1 == '-' || *p2 == '-' )
+ while( *p1 == '-' ) // SP
+ {
+ p1++;
+ p2++;
+ }
+ continue;
+ }
+ if( *p2 == '-' )
+ {
+// fprintf( stderr, "Penal! %c-%c in %d-%d, %f\n", *(p1-1), *(p2-1), i, j, feff );
+ vali += penal;
+// while( *p2 == '-' || *p1 == '-' )
+ while( *p2 == '-' ) // SP
+ {
+ p1++;
+ p2++;
+ }
+ continue;
+ }
+// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
+ vali += amino_dis[(int)*p1++][(int)*p2++];
+ }
+// fprintf( stderr, "vali = %d\n", vali );
+ val += feff * vali;
+ }
+ free( s1 );
+ free( s2 );
+ fprintf( stderr, "val = %f\n", val );
+ return( val );
+// exit( 1 );
+}
+
+double plainscore( int nseq, char **s )
+{
+ int i, j, ilim;
+ double v = 0.0;
+
+ ilim = nseq-1;
+ for( i=0; i<ilim; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ v += (double)naivepairscore11( s[i], s[j], penalty );
+ }
+
+ fprintf( stderr, "penalty = %d\n", penalty );
+
+ return( v );
+}
+
--- /dev/null
+#include <stdio.h>
+#include <stddef.h>
+#include <stdlib.h>
+#include <string.h>
+#include "mtxutl.h"
+
+void MtxuntDouble( double **mtx, int n )
+{
+ int i, j;
+ for( i=0; i<n; i++ ) for( j=0; j<n; j++ ) mtx[i][j] = 0.0;
+ for( i=0; i<n; i++ ) mtx[i][i] = 1.0;
+}
+
+void MtxmltDouble( double **mtx1, double **mtx2, int n )
+{
+ int i, j, k;
+ double s, *tmp;
+
+ tmp = (double *)calloc( n, sizeof( double ) );
+ for( i=0; i<n; i++ )
+ {
+ for( k=0; k<n; k++ ) tmp[k] = mtx1[i][k];
+ for( j=0; j<n; j++ )
+ {
+ s = 0.0;
+ for( k=0; k<n; k++ ) s += tmp[k] * mtx2[k][j];
+ mtx1[i][j] = s;
+ }
+ }
+ free( tmp );
+}
+
+char *AllocateCharVec( int l1 )
+{
+ char *cvec;
+
+ cvec = (char *)calloc( l1, sizeof( char ) );
+ if( cvec == NULL )
+ {
+ fprintf( stderr, "Cannot allocate %d character vector.\n", l1 );
+ exit( 1 );
+ }
+ return( cvec );
+}
+
+#if 0
+void ReallocateCharMtx( char **mtx, int l1, int l2 )
+{
+ int i;
+ char *bk = (char *)malloc( l2+1 ); // hontou ha iranai
+ if( bk == NULL )
+ {
+ fprintf( stderr, "Cannot allocate bk in ReallocateCharMtx\n" );
+ exit( 1 );
+ }
+ for( i=0; i<l1; i++ )
+ {
+#if 1
+ strcpy( bk, mtx[i] );
+ mtx[i] = (char *)realloc( mtx[i], (l2+1) * sizeof( char ) );
+ if( mtx[i] == NULL )
+ {
+ fprintf( stderr, "Cannot reallocate %d x %d character matrix.\n", l1, l2 );
+ }
+ if( strcmp( bk, mtx[i] ) ) // hontou ha iranai
+ {
+ fprintf( stderr, "changed!! \n%s\n \nto\n%s\n in realloc..\n", bk, mtx[i] );
+ strcpy( mtx[i], bk );
+ }
+#else
+ strcpy( bk, mtx[i] );
+ free( mtx[i] );
+ mtx[i] = (char *)calloc( (l2+1), sizeof( char ) );
+ strcpy( mtx[i], bk );
+#endif
+ }
+ free( bk ); // hontou ha iranai
+}
+#else
+void ReallocateCharMtx( char **mtx, int l1, int l2 )
+{
+ int i;
+ for( i=0; i<l1; i++ )
+ {
+ mtx[i] = (char *)realloc( mtx[i], (l2+1) * sizeof( char ) );
+ if( mtx[i] == NULL )
+ {
+ fprintf( stderr, "Cannot reallocate %d x %d character matrix.\n", l1, l2 );
+ }
+ }
+}
+#endif
+
+char **AllocateCharMtx( int l1, int l2 )
+{
+ int i;
+ char **cmtx;
+
+ cmtx = (char **)calloc( l1+1, sizeof( char * ) );
+ if( cmtx == NULL )
+ {
+ fprintf( stderr, "Cannot allocate %d x %d character matrix.\n", l1, l2 );
+ exit( 1 );
+ }
+ if( l2 )
+ {
+ for( i=0; i<l1; i++ )
+ {
+ cmtx[i] = AllocateCharVec( l2 );
+ }
+ }
+ cmtx[l1] = NULL;
+ return( cmtx );
+}
+
+void FreeCharMtx( char **mtx )
+{
+/*
+ char **x;
+ x = mtx;
+ while( *x != NULL ) free( *x++ );
+ free( mtx );
+*/
+ int i;
+ for( i=0; mtx[i]; i++ )
+ {
+ free( mtx[i] );
+ }
+ free( mtx );
+}
+
+float *AllocateFloatVec( int l1 )
+{
+ float *vec;
+
+ vec = (float *)calloc( (unsigned int)l1, sizeof( float ) );
+ if( vec == NULL )
+ {
+ fprintf( stderr, "Allocation error ( %d fload vec )\n", l1 );
+ exit( 1 );
+ }
+ return( vec );
+}
+
+void FreeFloatVec( float *vec )
+{
+ free( (char *)vec );
+}
+
+float **AllocateFloatHalfMtx( int ll1 )
+{
+ float **mtx;
+ int i;
+
+ mtx = (float **)calloc( (unsigned int)ll1+1, sizeof( float * ) );
+ if( mtx == NULL )
+ {
+ fprintf( stderr, "Allocation error ( %d fload halfmtx )\n", ll1 );
+ exit( 1 );
+ }
+ for( i=0; i<ll1; i++ )
+ {
+ mtx[i] = (float *)calloc( ll1-i, sizeof( float ) );
+ if( !mtx[i] )
+ {
+ fprintf( stderr, "Allocation error( %d floathalfmtx )\n", ll1 );
+ exit( 1 );
+ }
+ }
+ mtx[ll1] = NULL;
+ return( mtx );
+}
+
+float **AllocateFloatMtx( int ll1, int ll2 )
+{
+ float **mtx;
+ int i;
+
+ mtx = (float **)calloc( (unsigned int)ll1+1, sizeof( float * ) );
+ if( mtx == NULL )
+ {
+ fprintf( stderr, "Allocation error ( %d x %d fload mtx )\n", ll1, ll2 );
+ exit( 1 );
+ }
+ if( ll2 )
+ {
+ for( i=0; i<ll1; i++ )
+ {
+ mtx[i] = (float *)calloc( ll2, sizeof( float ) );
+ if( !mtx[i] )
+ {
+ fprintf( stderr, "Allocation error( %d x %d floatmtx )\n", ll1, ll2 );
+ exit( 1 );
+ }
+ }
+ }
+ mtx[ll1] = NULL;
+ return( mtx );
+}
+
+void FreeFloatHalfMtx( float **mtx, int n )
+{
+ int i;
+
+ for( i=0; i<n; i++ )
+ {
+ if( mtx[i] ) FreeFloatVec( mtx[i] );
+ }
+ free( mtx );
+}
+void FreeFloatMtx( float **mtx )
+{
+ int i;
+
+ for( i=0; mtx[i]; i++ )
+ {
+ FreeFloatVec( mtx[i] );
+ }
+ free( mtx );
+}
+
+int *AllocateIntVec( int ll1 )
+{
+ int *vec;
+
+ vec = (int *)calloc( ll1, sizeof( int ) );
+ if( vec == NULL )
+ {
+ fprintf( stderr, "Allocation error( %d int vec )\n", ll1 );
+ exit( 1 );
+ }
+ return( vec );
+}
+
+void FreeIntVec( int *vec )
+{
+ free( (char *)vec );
+}
+
+float **AllocateFloatTri( int ll1 )
+{
+ float **tri;
+ int i;
+
+ tri = (float **)calloc( (unsigned int)ll1+1, sizeof( float * ) );
+ if( !tri )
+ {
+ fprintf( stderr, "Allocation error ( float tri )\n" );
+ exit( 1 );
+ }
+ for( i=0; i<ll1; i++ )
+ {
+ tri[i] = AllocateFloatVec( i+3 );
+ }
+ tri[ll1] = NULL;
+
+ return( tri );
+}
+
+void FreeFloatTri( float **tri )
+{
+/*
+ float **x;
+ x = tri;
+ while( *tri != NULL ) free( *tri++ );
+ free( x );
+*/
+ int i;
+ for( i=0; tri[i]; i++ )
+ free( tri[i] );
+ free( tri );
+}
+
+int **AllocateIntMtx( int ll1, int ll2 )
+{
+ int i;
+ int **mtx;
+
+ mtx = (int **)calloc( ll1+1, sizeof( int * ) );
+ if( !mtx )
+ {
+ fprintf( stderr, "Allocation error( %d x %d int mtx )\n", ll1, ll2 );
+ exit( 1 );
+ }
+ if( ll2 )
+ {
+ for( i=0; i<ll1; i++ )
+ {
+ mtx[i] = AllocateIntVec( ll2 );
+ }
+ }
+ mtx[ll1] = NULL;
+ return( mtx );
+}
+
+/*
+void FreeIntMtx( int **mtx )
+{
+*
+ int **x;
+ x = mtx;
+ while( !*mtx ) free( *mtx++ );
+ free( x );
+*
+ int i;
+ for( i=0; mtx[i] != NULL; i++ )
+ free( (char *)mtx[i] );
+ free( (char *)mtx );
+}
+*/
+
+char ***AllocateCharCub( int ll1, int ll2, int ll3 )
+{
+ int i;
+ char ***cub;
+
+ cub = (char ***)calloc( ll1+1, sizeof( char ** ) );
+ if( !cub )
+ {
+ fprintf( stderr, "Allocation error( %d x %d x %d char cube\n", ll1, ll2, ll3 );
+ exit( 1 );
+ }
+ if( ll2 )
+ {
+ for( i=0; i<ll1; i++ )
+ {
+ cub[i] = AllocateCharMtx( ll2, ll3 );
+ }
+ }
+ cub[ll1] = NULL;
+ return( cub );
+}
+
+void FreeCharCub( char ***cub )
+{
+ int i;
+
+ for( i=0; cub[i]; i++ )
+ {
+ FreeCharMtx( cub[i] );
+ }
+ free( cub );
+}
+
+void freeintmtx( int **mtx, int ll1, int ll2 )
+{
+ int i;
+
+ for( i=0; i<ll1; i++ )
+ free( (char *)mtx[i] );
+ free( (char *)mtx );
+}
+
+void FreeIntMtx( int **mtx )
+{
+ int i;
+
+ for( i=0; mtx[i]; i++ )
+ free( (char *)mtx[i] );
+ free( (char *)mtx );
+}
+
+char ****AllocateCharHcu( int ll1, int ll2, int ll3, int ll4 )
+{
+ int i;
+ char ****hcu;
+
+ hcu = (char ****)calloc( ll1+1, sizeof( char *** ) );
+ if( hcu == NULL ) exit( 1 );
+ for( i=0; i<ll1; i++ )
+ hcu[i] = AllocateCharCub( ll2, ll3, ll4 );
+ hcu[ll1] = NULL;
+ return( hcu );
+}
+
+void FreeCharHcu( char ****hcu )
+{
+ int i;
+ for( i=0; hcu[i]; i++ )
+ {
+ FreeCharCub( hcu[i] );
+ }
+ free ( (char *)hcu );
+}
+
+double *AllocateDoubleVec( int ll1 )
+{
+ double *vec;
+
+ vec = (double *)calloc( ll1, sizeof( double ) );
+ return( vec );
+}
+
+void FreeDoubleVec( double *vec )
+{
+ free( vec );
+}
+
+int ***AllocateIntCub( int ll1, int ll2, int ll3 )
+{
+ int i;
+ int ***cub;
+
+ cub = (int ***)calloc( ll1+1, sizeof( int ** ) );
+ if( cub == NULL )
+ {
+ fprintf( stderr, "cannot allocate IntCub\n" );
+ exit( 1 );
+ }
+ for( i=0; i<ll1; i++ )
+ cub[i] = AllocateIntMtx( ll2, ll3 );
+ cub[ll1] = NULL;
+
+ return cub;
+}
+
+void FreeIntCub( int ***cub )
+{
+ int i;
+ for( i=0; cub[i]; i++ )
+ {
+ FreeIntMtx( cub[i] );
+ }
+ free( cub );
+}
+
+double **AllocateDoubleMtx( int ll1, int ll2 )
+{
+ int i;
+ double **mtx;
+ mtx = (double **)calloc( ll1+1, sizeof( double * ) );
+ if( !mtx )
+ {
+ fprintf( stderr, "cannot allocate DoubleMtx\n" );
+ exit( 1 );
+ }
+ if( ll2 )
+ {
+ for( i=0; i<ll1; i++ )
+ mtx[i] = AllocateDoubleVec( ll2 );
+ }
+ mtx[ll1] = NULL;
+
+ return mtx;
+}
+
+void FreeDoubleMtx( double **mtx )
+{
+ int i;
+ for( i=0; mtx[i]; i++ )
+ FreeDoubleVec( mtx[i] );
+ free( mtx );
+}
+
+float ***AllocateFloatCub( int ll1, int ll2, int ll3 )
+{
+ int i;
+ float ***cub;
+
+ cub = (float ***)calloc( ll1+1, sizeof( float ** ) );
+ if( !cub )
+ {
+ fprintf( stderr, "cannot allocate float cube.\n" );
+ exit( 1 );
+ }
+ for( i=0; i<ll1; i++ )
+ {
+ cub[i] = AllocateFloatMtx( ll2, ll3 );
+ }
+ cub[ll1] = NULL;
+ return( cub );
+}
+
+void FreeFloatCub( float ***cub )
+{
+ int i;
+
+ for( i=0; cub[i]; i++ )
+ {
+ FreeFloatMtx( cub[i] );
+ }
+ free( cub );
+}
+
+double ***AllocateDoubleCub( int ll1, int ll2, int ll3 )
+{
+ int i;
+ double ***cub;
+
+ cub = (double ***)calloc( ll1+1, sizeof( double ** ) );
+ if( !cub )
+ {
+ fprintf( stderr, "cannot allocate double cube.\n" );
+ exit( 1 );
+ }
+ for( i=0; i<ll1; i++ )
+ {
+ cub[i] = AllocateDoubleMtx( ll2, ll3 );
+ }
+ cub[ll1] = NULL;
+ return( cub );
+}
+
+void FreeDoubleCub( double ***cub )
+{
+ int i;
+
+ for( i=0; cub[i]; i++ )
+ {
+ FreeDoubleMtx( cub[i] );
+ }
+ free( cub );
+}
+
+
+short *AllocateShortVec( int ll1 )
+{
+ short *vec;
+
+ vec = (short *)calloc( ll1, sizeof( short ) );
+ if( vec == NULL )
+ {
+ fprintf( stderr, "Allocation error( %d short vec )\n", ll1 );
+ exit( 1 );
+ }
+ return( vec );
+}
+
+void FreeShortVec( short *vec )
+{
+ free( (char *)vec );
+}
+
+short **AllocateShortMtx( int ll1, int ll2 )
+{
+ int i;
+ short **mtx;
+
+
+ mtx = (short **)calloc( ll1+1, sizeof( short * ) );
+ if( !mtx )
+ {
+ fprintf( stderr, "Allocation error( %d x %d short mtx ) \n", ll1, ll2 );
+ exit( 1 );
+ }
+ for( i=0; i<ll1; i++ )
+ {
+ mtx[i] = AllocateShortVec( ll2 );
+ }
+ mtx[ll1] = NULL;
+ return( mtx );
+}
+
+void FreeShortMtx( short **mtx )
+{
+ int i;
+
+ for( i=0; mtx[i]; i++ )
+ free( (char *)mtx[i] );
+ free( (char *)mtx );
+}
+
--- /dev/null
+void MtxuntDouble( double **, int );
+void MtxmltDouble( double **, double **, int );
+
+char *AllocateCharVec( int );
+void FreeCharVec( char * );
+
+char **AllocateCharMtx( int, int);
+void ReallocateCharMtx( char **, int, int);
+void FreeCharMtx( char ** );
+
+float *AllocateFloatVec( int );
+void FreeFloatVec( float * );
+
+float **AllocateFloatHalfMtx( int );
+float **AllocateFloatMtx( int, int );
+void FreeFloatHalfMtx( float **, int );
+void FreeFloatMtx( float ** );
+
+float **AlocateFloatTri( int );
+void FreeFloatTri( float ** );
+
+int *AllocateIntVec( int );
+void FreeIntVec( int * );
+
+int **AllocateIntMtx( int, int );
+void FreeIntMtx( int ** );
+
+char ***AllocateCharCub( int, int, int );
+void FreeCharCub( char *** );
+
+int ***AllocateIntCub( int, int, int );
+void FreeIntCub( int *** );
+
+double *AllocateDoubleVec( int );
+void FreeDoubleVec( double * );
+
+double **AllocateDoubleMtx( int, int );
+void FreeDoubleMtx( double ** );
+
+double ***AllocateDoubleCub( int, int, int );
+void FreeDoubleCub( double *** );
+
+float ***AllocateFloatCub( int, int, int );
+void FreeFloatCub( float *** );
+
+short *AllocateShortVec( int );
+void FreeShortVec( short * );
+
+short **AllocateShortMtx( int, int );
+void FreeShortMtx( short ** );
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 1
+#define TSUYOSAFACTOR 100
+
+
+static int nhomologs;
+static int seedoffset;
+
+void strip( char *s )
+{
+ char *pt = s;
+ while( *++pt )
+ if( *pt == '\n' ) *pt = 0;
+}
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ seedoffset = 0;
+ nhomologs = 1;
+ inputfile = NULL;
+ fftkeika = 0;
+ pslocal = -1000.0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ divpairscore = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_OP = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ ppenalty_EX = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "seed = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 't':
+ nhomologs = atoi( *++argv );
+ fprintf( stderr, "nhomologs = %d\n", nhomologs );
+ --argc;
+ goto nextoption;
+ case 'o':
+ seedoffset = atoi( *++argv );
+ fprintf( stderr, "seedoffset = %d\n", seedoffset );
+ --argc;
+ goto nextoption;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+int countamino( char *s, int end )
+{
+ int val = 0;
+ while( end-- )
+ if( *s++ != '-' ) val++;
+ return( val );
+}
+
+static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr, int alloclen )
+{
+ int i, j;
+ FILE *hat3p;
+ float pscore = 0.0; // by D.Mathog
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ char *aseq;
+ static char **pseq;
+ LocalHom **localhomtable, *tmpptr;
+ double tsuyosa;
+
+ if( nhomologs < 1 ) nhomologs = 1; // tsuyosa=0.0 wo sakeru
+ tsuyosa = (double)nhomologs * nhomologs * TSUYOSAFACTOR;
+ fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+ }
+ }
+
+ if( effarr1 == NULL )
+ {
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ pseq = AllocateCharMtx( 2, 0 );
+ aseq = AllocateCharVec( nlenmax*9+1 );
+#if 0
+#else
+#endif
+ }
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ fprintf( stderr, "\n" );
+ for( i=0; i<njob-1; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ pseq[0] = seq[i];
+ pseq[1] = seq[j];
+
+ if( strlen( pseq[0] ) != strlen( pseq[1] ) )
+ {
+ fprintf( stderr, "## ERROR ###\n" );
+ fprintf( stderr, "Not aligned, %s - %s\n", name[i], name[j] );
+ fprintf( stderr, "## ERROR ###\n" );
+ exit( 1 );
+ }
+
+
+ fprintf( stderr, "adding %d-%d\r", i, j );
+ putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ if( tmpptr->start1 == -1 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d k\n", i+seedoffset, j+seedoffset, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 );
+ }
+ }
+ }
+ fprintf( stderr, "\n" );
+ fclose( hat3p );
+
+#if DEBUG
+ fprintf( stderr, "calling FreeLocalHomTable\n" );
+#endif
+ FreeLocalHomTable( localhomtable, njob );
+#if DEBUG
+ fprintf( stderr, "done. FreeLocalHomTable\n" );
+#endif
+}
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( treemethod == 'x' )
+ fprintf( fp, "Tree = UPGMA (3).\n" );
+ else if( treemethod == 's' )
+ fprintf( fp, "Tree = UPGMA (2).\n" );
+ else if( treemethod == 'p' )
+ fprintf( fp, "Tree = UPGMA (1).\n" );
+ else
+ fprintf( fp, "Unknown tree.\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int nlen[M];
+ static char name[M][B], **seq;
+ static char **bseq;
+ static double *eff;
+ int i;
+ char c;
+ int alloclen;
+ FILE *infp;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*9+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ alloclen = nlenmax*9;
+
+ eff = AllocateDoubleVec( njob );
+
+#if 0
+ Read( name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illeagal character %c\n", c );
+ exit( 1 );
+ }
+
+// writePre( njob, name, nlen, seq, 0 );
+
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+
+
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+
+ for( i=0; i<njob; i++ ) fprintf( stdout, ">_seed_%s\n%s\n", name[i]+1, bseq[i] );
+
+ pairalign( name, nlen, seq, eff, alloclen );
+
+ fprintf( trap_g, "done.\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+#! /usr/bin/env ruby
+
+#version 2, 2009/01/24
+
+
+if ARGV.length == 1
+ scale = 1.0
+elsif ARGV.length == 2
+ scale = ARGV.shift.to_f
+else
+ STDERR.puts "USAGE: newick2mafft.rb scale input_tree > output"
+ exit
+end
+
+if scale <= 0.0 then
+ STDERR.puts "Inappropriate scale, #{scale.to_s}"
+ exit
+end
+
+STDERR.puts "scale = " + scale.to_s
+
+infp = File.open( ARGV.shift, "r" )
+
+tree = ""
+while line = infp.gets
+ tree += line.strip
+ break if tree =~ /;$/
+end
+infp.close
+
+
+#tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "").gsub(/:\-[0-9\.]+/, ":0.0" )
+tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "")
+
+
+STDERR.puts "Initial tree = " + tree
+
+def resolve( tree )
+
+
+while 1
+# p tree
+ tree.sub!( /\,([0-9]+):(\-?[0-9\.]+)\,([0-9]+):(\-?[0-9\.]+)/, ",XXX" )
+ hit1 = $1
+ hit2 = $2
+ hit3 = $3
+ hit4 = $4
+
+# p hit1
+# p hit2
+# p hit3
+# p hit4
+
+# puts "introduce XXX"
+# p tree
+
+ break unless tree.index(/XXX/)
+
+ poshit = tree.index(/XXX/)
+# puts "poshit=" + poshit.to_s
+
+ i = poshit
+ height = 0
+ while i >= 0
+ break if height == 0 && tree[i..i] == '('
+ if tree[i..i] == ')' then
+ height += 1
+ elsif tree[i..i] == '(' then
+ height -= 1
+ end
+ i -= 1
+ end
+
+ poskakko = i
+# puts "poskakko = " + poskakko.to_s
+ zenhan = tree[0..poskakko]
+ zenhan = "" if poskakko == -1
+# puts "zenhan = " + zenhan
+
+ treelen = tree.length
+ tree = zenhan + "(" + tree[poskakko+1..treelen]
+# puts "add ("
+# p tree
+ tree.sub!( /XXX/, "#{hit1}:#{hit2}):0,#{hit3}:#{hit4}" )
+
+# p tree
+end
+
+
+return tree
+
+end
+
+memi = [-1,-1]
+leni = [-1,-1]
+
+while tree.index( /\(/ )
+
+ tree = resolve( tree )
+
+ tree.sub!( /\(([0-9]+):(\-?[0-9\.]+),([0-9]+):(\-?[0-9\.]+)\)/, "XXX" )
+ memi[0] = $1.to_i
+ leni[0] = $2.to_f * scale
+ memi[1] = $3.to_i
+ leni[1] = $4.to_f * scale
+
+ if leni[0] > 10 || leni[1] > 10 then
+ STDERR.puts ""
+ STDERR.puts "Please check the scale of branch length!"
+ STDERR.puts "The unit of branch lengths must be 'substitution/site'"
+ STDERR.puts "If the unit is 'substition' in your tree, please"
+ STDERR.puts "use the scale argument,"
+ STDERR.puts "% newick2mafft scale in > out"
+ STDERR.puts "where scale = 1/(alignment length)"
+ STDERR.puts ""
+ exit 1
+ end
+
+# STDERR.puts "subtree = " + $&
+
+ if memi[1] < memi[0] then
+ memi.reverse!
+ leni.reverse!
+ end
+
+ tree.sub!( /XXX/, memi[0].to_s )
+
+ STDERR.puts "Tree = " + tree
+
+ printf( "%5d %5d %10.5f %10.5f\n", memi[0], memi[1], leni[0], leni[1] )
+
+end
--- /dev/null
+#include "mltaln.h"
+#define DEBUG 0
+
+
+void topolcpy( int s1[], int s2[], int *mpt1, int *mpt2 )
+{
+ int i;
+
+ *mpt1 = *mpt2;
+ for( i=0; i<*mpt2; i++ )
+ {
+ s1[i] = s2[i];
+ }
+}
+
+void topolcat( int s1[], int s2[], int *mpt1, int *mpt2 )
+{
+ int i;
+
+ for( i=*mpt1; i<*mpt1+*mpt2; i++ )
+ {
+ s1[i] = s2[i-*mpt1];
+ }
+ *mpt1 += *mpt2;
+}
+
+void topolsort( int m, int s[] )
+{
+ int i, j, im;
+ int sm;
+
+ for( j=0; j<m-1; j++ )
+ {
+ sm = s[j]; im = j;
+ for( i=j+1; i<m; i++ )
+ {
+ if( s[i] < sm )
+ {
+ sm = s[i];
+ im = i;
+ }
+ }
+ s[im] = s[j]; s[j] = sm;
+ }
+}
+
+void topolswap( int s1[], int s2[], int *mpt1, int *mpt2 )
+{
+ int i;
+ int im;
+ int b;
+ b = *mpt1; *mpt1 = *mpt2; *mpt2 = b;
+ im = MAX(*mpt1,*mpt2);
+ for( i=0; i<im; i++ )
+ {
+ b = s1[i]; s1[i] = s2[i]; s2[i] = b;
+ /*
+ printf( "s1[%d]=%d\ns2[%d]=%d\n", i, s1[i], i, s2[i] );
+ */
+ }
+}
+
+void reduc( double **mtx, int nseq, int im, int jm )
+{
+ int i;
+ for( i=0; i<nseq; i++ )
+ {
+ if( i==im || i==jm
+ || mtx[MIN(i,im)][MAX(i,im)] == 9999.9
+ || mtx[MIN(i,jm)][MAX(i,jm)] == 9999.9
+ ) continue;
+ mtx[MIN(i,im)][MAX(i,im)]
+ = 0.5 * ( mtx[MIN(i,im)][MAX(i,im)] + mtx[MIN(i,jm)][MAX(i,jm)]
+ - mtx[MIN(im,jm)][MAX(im,jm)] );
+ mtx[MIN(i,jm)][MAX(i,jm)] = 9999.9;
+ }
+ mtx[MIN(im,jm)][MAX(im,jm)] = 9999.9;
+}
+
+
+void nj( int nseq, double **omtx, int ***topol, double **dis )
+{
+ int i, j, l, n, m;
+ int count;
+ double r[M];
+ double t;
+ double s, sm;
+ double totallen = 0.0;
+ int im=0, jm=0;
+ double len1, len2;
+#if 1
+ static char **par = NULL;
+ static double **mtx = NULL;
+ static int **mem = NULL;
+ if( par == NULL )
+ {
+ par = AllocateCharMtx( njob, njob );
+ mtx = AllocateDoubleMtx( njob, njob );
+ mem = AllocateIntMtx( njob, 2 );
+ }
+#else
+ char par[njob][njob];
+ double mtx[njob][njob];
+ int mem[njob][2];
+#endif
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) mtx[i][j] = omtx[i][j];
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) par[i][j] = 0;
+ for( i=0; i<nseq; i++ ) par[i][i] = 1;
+// for( i=0; i<nseq; i++ ) for( j=0; j<2; j++ ) for( l=0; l<nseq+1; l++ ) topol[i][j][l] = -1;
+ for( i=0; i<nseq; i++ ) for( j=0; j<2; j++ ) for( l=0; l<nseq; l++ ) topol[i][j][l] = -1;
+ for( n=nseq, m=0; n>2; n--, m=nseq-n )
+ {
+ t = 0.0;
+ for( i=0; i<nseq-1; i++ ) for( j=0; j<nseq; j++ ) if( mtx[i][j] < 9999.9 )
+ t += mtx[i][j];
+ for( i=0; i<nseq; i++ )
+ {
+ r[i] = 0.0;
+ for( l=0; l<nseq; l++ )
+ if( ( l != i ) && ( mtx[MIN(i,l)][MAX(i,l)] < 9999.9 ) )
+ r[i] += mtx[MIN(i,l)][MAX(i,l)];
+ }
+ sm = 9999.9;
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ ) if( mtx[i][j] < 9999.9)
+ {
+ s = ( ( 2.0 * t - r[i] - r[j] + (n-2.0)*mtx[i][j] ) ) / ( 2.0*(n-2.0) );
+ if ( s < sm )
+ {
+ sm = s;
+ im = i; jm = j;
+ }
+ }
+ len1 = ( (n-2)*mtx[im][jm] + r[im] - r[jm] ) / (2*(n-2));
+ len2 = ( (n-2)*mtx[im][jm] - r[im] + r[jm] ) / (2*(n-2));
+
+#if DEBUG
+ fprintf( stderr, "STEP-%3d %3d: L = %5.5f\n", m+1, im+1, len1 );
+ fprintf( stderr, " %3d: L = %5.5f\n", jm+1, len2 );
+#endif
+
+ totallen += len1;
+ totallen += len2;
+
+ dis[m][0] = len1;
+ dis[m][1] = len2;
+
+ for( l=0, count=0; l<nseq; l++ )
+ if( par[im][l] > 0 )
+ {
+ topol[m][0][count] = l;
+ count++;
+ }
+ mem[m][0] = count;
+ for( l=0, count=0; l<nseq; l++ )
+ if( par[jm][l] > 0 )
+ {
+ topol[m][1][count] = l;
+ count++;
+ }
+ mem[m][1] = count;
+ for( l=0; l<nseq; l++ )
+ par[im][l] += ( par[jm][l] > 0 );
+ if( n > 3 ) reduc( mtx, nseq, im, jm );
+ }
+ for( i=0; i<nseq; i++ )
+ if( i!=im && i!=jm && mtx[MIN(i,im)][MAX(i,im)]<9999.9 )
+ break;
+ len2 = ( mtx[MIN(i,im)][MAX(i,im)] - r[im] + r[i] ) / 2;
+
+/*
+ printf(" %3d: L = %5.5f\n", i+1, len2 );
+*/
+ totallen += len2;
+
+ dis[m][0] = len2;
+ dis[m][1] = 0.0;
+ for( l=0, count=0; l<nseq; l++ )
+ if( par[i][l] > 0 )
+ {
+ topol[m][0][count] = l;
+ count++;
+ }
+ mem[m][0] = count;
+ /*
+ printf( " total length == %f\n", totallen );
+ */
+
+ topolcpy( topol[nseq-2][1], topol[nseq-3][0], mem[nseq-2]+1, mem[nseq-3] );
+ topolcat( topol[nseq-2][1], topol[nseq-3][1], mem[nseq-2]+1, mem[nseq-3]+1 );
+ topolsort( mem[nseq-2][1], topol[nseq-2][1] );
+
+ if( topol[nseq-2][0][0] > topol[nseq-2][1][0] )
+ topolswap( topol[nseq-2][0], topol[nseq-2][1], mem[nseq-2], mem[nseq-2]+1 );
+
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 1
+#define TSUYOSAFACTOR 100
+
+
+static char *pairfile;
+static int nhomologs;
+
+void strip( char *s )
+{
+ char *pt = s;
+ while( *++pt )
+ if( *pt == '\n' ) *pt = 0;
+}
+
+int searchused( char *q, char **keys, int n )
+{
+ int i;
+ for( i=0; i<n; i++ )
+ {
+// fprintf( stderr, "%s ? %s\n", q, names[i] );
+ if( !strcmp( q, keys[i] ) ) return( i );
+ }
+ return( -1 );
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ nhomologs = 2;
+ inputfile = NULL;
+ pairfile = NULL;
+ fftkeika = 0;
+ pslocal = -1000.0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ divpairscore = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_OP = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ ppenalty_EX = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'p':
+ pairfile = *++argv;
+ fprintf( stderr, "pairfile = %s\n", pairfile );
+ --argc;
+ goto nextoption;
+ case 't':
+ nhomologs = atoi( *++argv );
+ fprintf( stderr, "nhomologs = %d\n", nhomologs );
+ --argc;
+ goto nextoption;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+int countamino( char *s, int end )
+{
+ int val = 0;
+ while( end-- )
+ if( *s++ != '-' ) val++;
+ return( val );
+}
+
+static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr, int alloclen )
+{
+ FILE *tmpfp;
+ static char dumm1[B], dumm0[B];
+ int i, j;
+ char *res;
+ FILE *hat3p;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ static char **pseq;
+ LocalHom **localhomtable, *tmpptr;
+ float pscore = 0.0; // by D.Mathog, aguess
+ char *aseq = NULL; // by D.Mathog
+ char **usedseqs = NULL; // by D.Mathog
+ char **usednames = NULL; // by D.Mathog
+ int nused;
+ double tsuyosa;
+
+ tsuyosa = (double)nhomologs * (nhomologs-1) / njob * TSUYOSAFACTOR;
+ fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+ }
+ }
+
+ if( effarr1 == NULL )
+ {
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ pseq = AllocateCharMtx( 2, nlenmax*9+1 );
+ aseq = AllocateCharVec( nlenmax*9+1 );
+ usedseqs = AllocateCharMtx( njob, nlenmax*9+1 );
+ usednames = AllocateCharMtx( njob, B );
+#if 0
+#else
+#endif
+ }
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ fprintf( stderr, "opening %s\n", pairfile );
+ tmpfp = fopen( pairfile, "r" );
+ if( !tmpfp )
+ {
+ fprintf( stderr, "Cannot open %s\n", pairfile );
+ exit( 1 );
+ }
+ searchKUorWA( tmpfp );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ nused = 0;
+ while( 1 )
+ {
+ res = fgets( dumm0, B-1, tmpfp );
+ strip( dumm0 );
+ if( res == NULL )
+ {
+ break;
+ }
+ load1SeqWithoutName_new( tmpfp, pseq[0] );
+ gappick0( aseq, pseq[0] );
+ i = searchused( aseq, usedseqs, nused );
+ if( i == -1 )
+ {
+ strcpy( usednames[nused], dumm0+1 );
+ strcpy( usedseqs[nused], aseq );
+ i = nused;
+ nused++;
+ }
+ fprintf( stderr, "i = %d\n", i );
+
+ res = fgets( dumm1, B-1, tmpfp );
+ strip( dumm1 );
+ if( res == NULL )
+ {
+ fprintf( stderr, "ERROR: The number of sequences in %s must be even.\n", pairfile );
+ exit( 1 );
+ }
+ load1SeqWithoutName_new( tmpfp, pseq[1] );
+ gappick0( aseq, pseq[1] );
+ j = searchused( aseq, usedseqs, nused );
+ if( j == -1 )
+ {
+ strcpy( usednames[nused], dumm1+1 );
+ strcpy( usedseqs[nused], aseq );
+ j = nused;
+ nused++;
+ }
+ fprintf( stderr, "j = %d\n", j );
+
+ if( strlen( pseq[0] ) != strlen( pseq[1] ) )
+ {
+ fprintf( stderr, "Not aligned, %s - %s\n", dumm0, dumm1 );
+ exit( 1 );
+ }
+
+
+ fprintf( stderr, "adding %d-%d\n", i, j );
+ putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
+ }
+ }
+ fclose( tmpfp );
+ fclose( hat3p );
+
+ for( i=0; i<nused; i++ )
+ fprintf( stdout, ">%s\n%s\n", usednames[i], usedseqs[i] );
+
+
+#if 0
+ fprintf( stderr, "##### writing hat3\n" );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ ilim = njob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
+ }
+ }
+ }
+ fclose( hat3p );
+#endif
+#if DEBUG
+ fprintf( stderr, "calling FreeLocalHomTable\n" );
+#endif
+ FreeLocalHomTable( localhomtable, njob );
+#if DEBUG
+ fprintf( stderr, "done. FreeLocalHomTable\n" );
+#endif
+}
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( treemethod == 'x' )
+ fprintf( fp, "Tree = UPGMA (3).\n" );
+ else if( treemethod == 's' )
+ fprintf( fp, "Tree = UPGMA (2).\n" );
+ else if( treemethod == 'p' )
+ fprintf( fp, "Tree = UPGMA (1).\n" );
+ else
+ fprintf( fp, "Unknown tree.\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int nlen[M];
+ static char name[M][B], **seq;
+ static char **bseq;
+ static double *eff;
+ int i;
+ char c;
+ int alloclen;
+ FILE *infp;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ if( !pairfile )
+ {
+ fprintf( stderr, "Usage: %s -p pairfile -i inputfile \n", argv[0] );
+ exit( 1 );
+ }
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*9+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ alloclen = nlenmax*9;
+
+ eff = AllocateDoubleVec( njob );
+
+#if 0
+ Read( name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illeagal character %c\n", c );
+ exit( 1 );
+ }
+
+// writePre( njob, name, nlen, seq, 0 );
+
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+
+
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+
+ pairalign( name, nlen, bseq, eff, alloclen );
+
+ fprintf( trap_g, "done.\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+static int usecache;
+static char *whereispairalign;
+static double scale;
+static int *alreadyoutput;
+static int equivthreshold;
+static int equivwinsize;
+static int equivshortestlen;
+
+static void cutpath( char *s )
+{
+ char *pos;
+ pos = s + strlen( s );
+
+ while( --pos >= s )
+ {
+ if( *pos == '/' ) break;
+ }
+
+ strcpy( s, pos+1 );
+}
+
+static char getchainid( char *s )
+{
+ s += strlen( s ) - 2;
+ if( isspace( s[0] ) && isalnum( s[1] ) )
+ return( s[1] );
+ else
+ return( 'A' );
+}
+
+static void extractfirstword( char *s )
+{
+ while( *s )
+ {
+ if( isspace( *s ) ) break;
+ s++;
+ }
+ *s = 0;
+}
+
+static char *strip( char *s )
+{
+ char *v;
+
+ while( *s )
+ {
+ if( !isspace( *s ) ) break;
+ s++;
+ }
+ v = s;
+
+ s += strlen( v ) - 1;
+ while( s>=v )
+ {
+ if( !isspace( *s ) )
+ {
+ *(s+1) = 0;
+ break;
+ }
+ s--;
+ }
+
+ return( v );
+}
+
+#if 0
+static void makeequivdouble( double *d, char *c )
+{
+ while( *c )
+ {
+ *d++ = (double)( *c++ - '0' );
+ }
+}
+
+static void maskequiv( double *d, int n )
+{
+ int halfwin;
+ int ok;
+ int i, j;
+
+ halfwin = (int)( equivwinsize / 2 );
+
+ for( i=0; i<n; i++ )
+ {
+ ok = 1;
+ for( j = i-halfwin; j<i+halfwin; j++ )
+ {
+ if( j<0 || n=<j ) continue;
+ if( d[j] <= 0.0 )
+ {
+ ok = 0;
+ break;
+ }
+ }
+ if( ok == 0 ) d[i] = 0.0;
+ }
+}
+#else
+static void maskequiv( double *d, int n )
+{
+ int i, len;
+ int count;
+ len = 0;
+ double *dbk, *dori, *dbkori;
+
+ dbk = calloc( n, sizeof( double ) );
+
+ dbkori = dbk;
+ dori = d;
+ count = n;
+ while( count-- )
+ {
+ *dbk++ = *d++;
+ }
+
+ dbk = dbkori;
+ d = dori;
+ len = 0;
+
+
+ for( i=0; i<n; i++ )
+ {
+ if( d[i] > 0.0 )
+ {
+ len += 1;
+ d[i] = 0.0;
+ }
+ else
+ {
+ d[i] = 0.0;
+ if( len >= equivshortestlen )
+ {
+ len++;
+ while( len-- ) d[i-len] = dbk[i-len];
+ }
+ len = 0;
+ }
+ }
+
+ if( len >= equivshortestlen )
+ {
+ len++;
+ while( len-- ) d[n-len] = dbk[n-len];
+ }
+
+ free( dbk );
+}
+#endif
+
+static void makeequivdouble_tmalign( double *d, char *c, int n )
+{
+ double tmpd;
+ double *dbk;
+ int tmpi;
+ char s;
+ dbk = d;
+ while( *c )
+ {
+ if( ( s=*c++ ) == ':' )
+ tmpi = 9;
+ else if( s == '.' )
+ tmpi = 4;
+ else
+ tmpi = 0;
+// tmpd = (double)( tmpi + 1 - equivthreshold ) / ( 10 - equivthreshold ) * 9.0;
+// if( tmpd < 0.0 ) tmpd = 0.0;
+ tmpd = (double)( tmpi );
+// *d++ = (int)tmpd;
+ *d++ = tmpd;
+ }
+
+ d = dbk;
+// maskequiv( d, n );
+}
+
+static void makeequivdouble_threshold( double *d, char *c, int n )
+{
+ double tmpd;
+ double *dbk;
+ int tmpi;
+ dbk = d;
+ while( *c )
+ {
+ tmpi = (int)( *c++ - '0' );
+ tmpd = (double)( tmpi + 1 - equivthreshold ) / ( 10 - equivthreshold ) * 9.0;
+ if( tmpd < 0.0 ) tmpd = 0.0;
+// *d++ = (int)tmpd;
+ *d++ = tmpd;
+ }
+
+ d = dbk;
+ maskequiv( d, n );
+}
+
+static void readtmalign( FILE *fp, char *seq1, char *seq2, double *equiv )
+{
+ static char *line = NULL;
+ static char *equivchar = NULL;
+ int n;
+
+
+ if( equivchar == NULL )
+ {
+ equivchar = calloc( nlenmax * 2 + 1, sizeof( char ) );
+ line = calloc( nlenmax * 2 + 1, sizeof( char ) );
+ }
+ seq1[0] = 0;
+ seq2[0] = 0;
+ equivchar[0] = 0;
+
+
+// system( "vi _tmalignout" );
+ while( 1 )
+ {
+ if( feof( fp ) )
+ {
+ fprintf( stderr, "Error in TMalign\n" );
+ exit( 1 );
+ }
+ fgets( line, 999, fp );
+// fprintf( stdout, "line = :%s:\n", line );
+ if( !strncmp( line+5, "denotes the residue pairs", 20 ) ) break;
+ }
+ fgets( line, nlenmax*2, fp );
+ strcat( seq1, strip( line ) );
+
+ fgets( line, nlenmax*2, fp );
+ strcat( equivchar, strip( line ) );
+
+ fgets( line, nlenmax*2, fp );
+ strcat( seq2, strip( line ) );
+
+#if 0
+ printf( "seq1=%s\n", seq1 );
+ printf( "seq2=%s\n", seq2 );
+ printf( "equi=%s\n", equivchar );
+exit( 1 );
+#endif
+ n = strlen( seq1 );
+ makeequivdouble_tmalign( equiv, equivchar, n );
+
+#if 0
+ fprintf( stdout, "\n" );
+ for( i=0; i<n; i++ )
+ {
+ fprintf( stdout, "%1.0f", equiv[i] );
+ }
+ fprintf( stdout, "\n" );
+ exit( 1 );
+#endif
+}
+static void readrash( FILE *fp, char *seq1, char *seq2, double *equiv )
+{
+ char line[1000];
+ static char *equivchar = NULL;
+ int n;
+
+
+ if( equivchar == NULL )
+ {
+ equivchar = calloc( nlenmax * 2, sizeof( char ) );
+ }
+ seq1[0] = 0;
+ seq2[0] = 0;
+ equivchar[0] = 0;
+
+ while( 1 )
+ {
+ fgets( line, 999, fp );
+// fprintf( stdout, "line = :%s:\n", line );
+ if( !strncmp( line, "Query ", 6 ) ) break;
+ if( feof( fp ) ) break;
+ if( !strncmp( line, "QUERY ", 6 ) )
+ {
+ strcat( seq1, strip( line+5 ) );
+ fgets( line, 999, fp );
+ }
+ if( !strncmp( line, "TEMPL ", 6 ) )
+ {
+ strcat( seq2, strip( line+5 ) );
+ fgets( line, 999, fp );
+ }
+ if( !strncmp( line, "Equiva", 6 ) )
+ {
+ strcat( equivchar, strip( line+11 ) );
+ fgets( line, 999, fp );
+ }
+ }
+#if 0
+ printf( "seq1=:%s:\n", seq1 );
+ printf( "seq2=:%s:\n", seq2 );
+ printf( "equi=:%s:\n", equivchar );
+exit( 1 );
+#endif
+ n = strlen( seq1 );
+ makeequivdouble_threshold( equiv, equivchar, n );
+
+#if 0
+ fprintf( stdout, "\n" );
+ for( i=0; i<n; i++ )
+ {
+ fprintf( stdout, "%1.0f", equiv[i] );
+ }
+ fprintf( stdout, "\n" );
+#endif
+}
+
+static int checkcbeta( FILE *fp )
+{
+ char linec[1000];
+ while( 1 )
+ {
+ fgets( linec, 999, fp );
+ if( feof( fp ) ) break;
+ if( !strncmp( "ATOM ", linec, 5 ) )
+ {
+ if( !strncmp( "CB ", linec+13, 3 ) ) return( 0 );
+ }
+ }
+ return( 1 );
+}
+
+
+static float calltmalign( char **mseq1, char **mseq2, double *equiv, char *fname1, char *chain1, char *fname2, char *chain2, int alloclen )
+{
+ FILE *fp;
+ int res;
+ static char com[10000];
+ float value;
+ char cachedir[10000];
+ char cachefile[10000];
+ int runnow;
+
+
+ if( usecache )
+ {
+ sprintf( cachedir, "%s/.tmalignoutcache", getenv( "HOME" ) );
+ sprintf( com, "mkdir -p %s", cachedir );
+ system( com );
+
+ sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
+
+ runnow = 0;
+ fp = fopen( cachefile, "r" );
+ if( fp == NULL ) runnow = 1;
+ else
+ {
+ fgets( com, 100, fp );
+ if( strncmp( com, "successful", 10 ) ) runnow = 1;
+ fclose( fp );
+ }
+ }
+ else
+ {
+ runnow = 1;
+ }
+
+ if( runnow )
+ {
+#if 0
+ sprintf( com, "ln -s %s %s.pdb 2>_dum", fname1, fname1 );
+ res = system( com );
+ sprintf( com, "ln -s %s %s.pdb 2>_dum", fname2, fname2 );
+ res = system( com );
+#endif
+ sprintf( com, "\"%s/TMalign\" %s.pdb %s.pdb > _tmalignout 2>_dum", whereispairalign, fname1, fname2 );
+ fprintf( stderr, "command = %s\n", com );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in TMalign\n" );
+ exit( 1 );
+ }
+
+ }
+ else
+ {
+ fprintf( stderr, "Cache is not supported!\n" );
+ exit( 1 );
+ }
+
+ fp = fopen( "_tmalignout", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _tmalignout\n" );
+ exit( 1 );
+ }
+
+ readtmalign( fp, *mseq1, *mseq2, equiv );
+
+ fclose( fp );
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+ return( value );
+}
+
+static float callrash( int mem1, int mem2, char **mseq1, char **mseq2, double *equiv, char *fname1, char *chain1, char *fname2, char *chain2, int alloclen )
+{
+ FILE *fp;
+ int res;
+ static char com[10000];
+ float value;
+ char cachedir[10000];
+ char cachefile[10000];
+ int runnow;
+ char pairid[1000];
+
+ sprintf( pairid, "%d-%d", mem1, mem2 );
+// fprintf( stderr, "pairid = %s\n", pairid );
+
+ if( usecache )
+ {
+ sprintf( cachedir, "%s/.rashoutcache", getenv( "HOME" ) );
+ sprintf( com, "mkdir -p %s", cachedir );
+ system( com );
+
+ sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
+
+ runnow = 0;
+ fp = fopen( cachefile, "r" );
+ if( fp == NULL ) runnow = 1;
+ else
+ {
+ fgets( com, 100, fp );
+ if( strncmp( com, "successful", 10 ) ) runnow = 1;
+ fclose( fp );
+ }
+ }
+ else
+ {
+ runnow = 1;
+ }
+
+ if( runnow )
+ {
+#if 0
+ sprintf( com, "ln -s %s %s.pdb 2>_dum", fname1, fname1 );
+ res = system( com );
+ sprintf( com, "ln -s %s %s.pdb 2>_dum", fname2, fname2 );
+ res = system( com );
+#endif
+#if 0 // 091127, pdp nai!
+ sprintf( com, "env PATH=%s PDP_ASH.pl --qf %s.pdb --qc %s --tf %s.pdb --tc %s > _rashout 2>_dum", whereispairalign, fname1, chain1, fname2, chain2 );
+#else
+ sprintf( com, "\"%s/rash\" --qf %s.pdb --qc %s --tf %s.pdb --tc %s --of %s.pdbpair > %s.rashout 2>%s.dum", whereispairalign, fname1, chain1, fname2, chain2, pairid, pairid, pairid );
+#endif
+ fprintf( stderr, "command = %s\n", com );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in structural alignment\n" );
+ exit( 1 );
+ }
+ sprintf( com, "awk '/^REMARK/,/^TER/' %s.pdbpair > %s.%s-x-%s.%s.pdbpair", pairid, fname1, chain1, fname2, chain2 );
+ res = system( com );
+
+ sprintf( com, "awk '/^REMARK/,/^TER/{next} 1' %s.pdbpair > %s.%s-x-%s.%s.pdbpair", pairid, fname2, chain2, fname1, chain1 );
+ res = system( com );
+
+ sprintf( com, "rm %s.pdbpair", pairid );
+ res = system( com );
+
+
+ }
+ else
+ {
+ fprintf( stderr, "Use cache!\n" );
+ sprintf( com, "grep -v successful %s > %s.rashout", cachefile, pairid );
+ system( com );
+ }
+
+ if( usecache && runnow )
+ {
+ sprintf( com, "echo successful > %s", cachefile );
+ system( com );
+ sprintf( com, "cat %s.rashout >> %s", pairid, cachefile );
+ system( com );
+ }
+
+ sprintf( com, "%s.rashout", pairid );
+ fp = fopen( com, "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open %s\n", com );
+ exit( 1 );
+ }
+
+ readrash( fp, *mseq1, *mseq2, equiv );
+
+ fclose( fp );
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+ return( value );
+}
+
+static void preparetmalign( FILE *fp, char ***strfiles, char ***chainids, char ***seqpt, char ***mseq1pt, char ***mseq2pt, double **equivpt, int *alloclenpt )
+{
+ int i, res;
+ char *dumseq;
+ char line[1000];
+ char fname[1000];
+ char command[1000];
+ int linenum, istr, nstr;
+ FILE *checkfp;
+ char *sline;
+ int use[1000];
+ linenum = 0;
+ nstr = 0;
+ while( 1 )
+ {
+ fgets( line, 999, fp );
+ if( feof( fp ) ) break;
+ sline = strip( line );
+ use[linenum] = 1;
+ if( sline[0] == '#' || strlen( sline ) < 2 )
+ {
+ use[linenum] = 0;
+ linenum++;
+ continue;
+ }
+ extractfirstword( sline );
+ checkfp = fopen( sline, "r" );
+ if( checkfp == NULL )
+ {
+ fprintf( stderr, "Cannot open %s.\n", sline );
+ exit( 1 );
+ }
+#if 0
+ fgets( linec, 999, checkfp );
+ if( strncmp( "HEADER ", linec, 7 ) )
+ {
+ fprintf( stderr, "Check the format of %s.\n", sline );
+ exit( 1 );
+ }
+#endif
+ if( checkcbeta( checkfp ) )
+ {
+ fprintf( stderr, "%s has no C-beta atoms.\n", sline );
+ exit( 1 );
+ }
+ else
+ nstr++;
+ fclose( checkfp );
+ linenum++;
+ }
+ njob = nstr;
+ fprintf( stderr, "nstr = %d\n", nstr );
+
+ *strfiles = AllocateCharMtx( nstr, 1000 );
+ *chainids = AllocateCharMtx( nstr, 2 );
+
+ rewind( fp );
+ istr = 0;
+ linenum = 0;
+ while( 1 )
+ {
+ fgets( line, 999, fp );
+ if( feof( fp ) ) break;
+ sline = strip( line );
+ if( use[linenum++] )
+ {
+ (*chainids)[istr][0] = getchainid( sline );
+ (*chainids)[istr][1] = 0;
+ extractfirstword( sline );
+ sprintf( fname, "%s", sline );
+ cutpath( fname );
+ sprintf( command, "cp %s %s.pdb", sline, fname );
+ system( command );
+ sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
+ res = system( command );
+ if( res )
+ {
+ fprintf( stderr, "error: Install clean.pl\n" );
+ exit( 1 );
+ }
+ strcpy( (*strfiles)[istr++], fname );
+ }
+ }
+
+ *seqpt = AllocateCharMtx( njob, nlenmax*2+1 );
+ *mseq1pt = AllocateCharMtx( njob, 0 );
+ *mseq2pt = AllocateCharMtx( njob, 0 );
+ *equivpt = AllocateDoubleVec( nlenmax*2+1 );
+ *alloclenpt = nlenmax*2;
+ dumseq = AllocateCharVec( nlenmax*2+1 );
+ alreadyoutput = AllocateIntVec( njob );
+ for( i=0; i<njob; i++ ) alreadyoutput[i] = 0;
+
+ for( i=0; i<istr; i++ )
+ {
+ fprintf( stderr, "i=%d\n", i );
+ (*seqpt)[i][0] = 0;
+
+ (*mseq1pt)[0] = (*seqpt)[i];
+ (*mseq2pt)[0] = dumseq;
+
+ calltmalign( *mseq1pt, *mseq2pt, *equivpt, (*strfiles)[i], (*chainids)[i], (*strfiles)[i], (*chainids)[i], *alloclenpt );
+ fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, (*strfiles)[i], (*chainids)[i], (*seqpt)[i] );
+ alreadyoutput[i] = 1;
+ }
+}
+
+static void prepareash( FILE *fp, char ***strfiles, char ***chainids, char ***seqpt, char ***mseq1pt, char ***mseq2pt, double **equivpt, int *alloclenpt )
+{
+ int i, res;
+ char *dumseq;
+ char line[1000];
+ char fname[1000];
+ char command[1000];
+ int linenum, istr, nstr;
+ FILE *checkfp;
+ char *sline;
+ int use[1000];
+ linenum = 0;
+ nstr = 0;
+ while( 1 )
+ {
+ fgets( line, 999, fp );
+ if( feof( fp ) ) break;
+ sline = strip( line );
+ use[linenum] = 1;
+ if( sline[0] == '#' || strlen( sline ) < 2 )
+ {
+ use[linenum] = 0;
+ linenum++;
+ continue;
+ }
+ extractfirstword( sline );
+ checkfp = fopen( sline, "r" );
+ if( checkfp == NULL )
+ {
+ fprintf( stderr, "Cannot open %s.\n", sline );
+ exit( 1 );
+ }
+#if 0
+ fgets( linec, 999, checkfp );
+ if( strncmp( "HEADER ", linec, 7 ) )
+ {
+ fprintf( stderr, "Check the format of %s.\n", sline );
+ exit( 1 );
+ }
+#endif
+ if( checkcbeta( checkfp ) )
+ {
+ fprintf( stderr, "%s has no C-beta atoms.\n", sline );
+ exit( 1 );
+ }
+ else
+ nstr++;
+ fclose( checkfp );
+ linenum++;
+ }
+ njob = nstr;
+ fprintf( stderr, "nstr = %d\n", nstr );
+
+ *strfiles = AllocateCharMtx( nstr, 1000 );
+ *chainids = AllocateCharMtx( nstr, 2 );
+
+ rewind( fp );
+ istr = 0;
+ linenum = 0;
+ while( 1 )
+ {
+ fgets( line, 999, fp );
+ if( feof( fp ) ) break;
+ sline = strip( line );
+ if( use[linenum++] )
+ {
+ (*chainids)[istr][0] = getchainid( sline );
+ (*chainids)[istr][1] = 0;
+ extractfirstword( sline );
+ sprintf( fname, "%s", sline );
+ cutpath( fname );
+ sprintf( command, "cp %s %s.pdb", sline, fname );
+ system( command );
+ sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
+ res = system( command );
+ if( res )
+ {
+ fprintf( stderr, "error: Install clean.pl\n" );
+ exit( 1 );
+ }
+ strcpy( (*strfiles)[istr++], fname );
+ }
+ }
+
+ *seqpt = AllocateCharMtx( njob, nlenmax*2+1 );
+ *mseq1pt = AllocateCharMtx( njob, 0 );
+ *mseq2pt = AllocateCharMtx( njob, 0 );
+ *equivpt = AllocateDoubleVec( nlenmax*2+1 );
+ *alloclenpt = nlenmax*2;
+ dumseq = AllocateCharVec( nlenmax*2+1 );
+ alreadyoutput = AllocateIntVec( njob );
+ for( i=0; i<njob; i++ ) alreadyoutput[i] = 0;
+
+ for( i=0; i<istr; i++ )
+ {
+ fprintf( stderr, "i=%d\n", i );
+ (*seqpt)[i][0] = 0;
+
+ (*mseq1pt)[0] = (*seqpt)[i];
+ (*mseq2pt)[0] = dumseq;
+
+ callrash( i, i, *mseq1pt, *mseq2pt, *equivpt, (*strfiles)[i], (*chainids)[i], (*strfiles)[i], (*chainids)[i], *alloclenpt );
+ fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, (*strfiles)[i], (*chainids)[i], (*seqpt)[i] );
+ alreadyoutput[i] = 1;
+ }
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ usecache = 0;
+ scale = 1.0;
+ equivthreshold = 5;
+ equivwinsize = 5;
+ equivshortestlen = 1;
+ inputfile = NULL;
+ fftkeika = 0;
+ pslocal = -1000.0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'R';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ divpairscore = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_OP = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ ppenalty_EX = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ RNAppenalty = NOTSPECIFIED;
+ RNApthr = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'O':
+ ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'E':
+ ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+// fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+// fprintf( stderr, "blosum %d\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "TM %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'd':
+ whereispairalign = *++argv;
+ fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
+ --argc;
+ goto nextoption;
+ case 't':
+ equivthreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ equivwinsize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'l':
+ equivshortestlen = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 's':
+ scale = atof( *++argv );
+ --argc;
+ goto nextoption;
+ case 'c':
+ usecache = 1;
+ break;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+#if 0
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#endif
+ case 'Q':
+ calledByXced = 1;
+ break;
+ case 'x':
+ disp = 1;
+ break;
+#if 0
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'S':
+ alg = 'S';
+ break;
+ case 'L':
+ alg = 'L';
+ break;
+ case 'B':
+ alg = 'B';
+ break;
+ case 'T':
+ alg = 'T';
+ break;
+ case 'H':
+ alg = 'H';
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'R':
+ alg = 'R';
+ break;
+ case 'N':
+ alg = 'N';
+ break;
+ case 'K':
+ alg = 'K';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'V':
+ alg = 'V';
+ break;
+ case 'C':
+ alg = 'C';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'y':
+ divpairscore = 1;
+ break;
+/* Modified 01/08/27, default: user tree */
+ case 'J':
+ tbutree = 0;
+ break;
+/* modification end. */
+#if 0
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'Z':
+ checkC = 1;
+ break;
+#endif
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+int countamino( char *s, int end )
+{
+ int val = 0;
+ while( end-- )
+ if( *s++ != '-' ) val++;
+ return( val );
+}
+
+static void pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *equiv, double *effarr, char **strfiles, char **chainids, int alloclen )
+{
+ int i, j, ilim;
+ int clus1, clus2;
+ int off1, off2;
+ float pscore = 0.0; // by D.Mathog
+ static char *indication1, *indication2;
+ FILE *hat2p, *hat3p;
+ static double **distancemtx;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ char *pt;
+ char *hat2file = "hat2";
+ LocalHom **localhomtable, *tmpptr;
+ static char **pair;
+// int intdum;
+ double bunbo;
+ char **checkseq;
+
+
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+ localhomtable[i][j].nokori = 0;
+ }
+ }
+
+ if( effarr1 == NULL )
+ {
+ distancemtx = AllocateDoubleMtx( njob, njob );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+ checkseq = AllocateCharMtx( njob, alloclen );
+#if 0
+#else
+ pair = AllocateCharMtx( njob, njob );
+#endif
+ }
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
+ for( i=0; i<njob; i++ ) pair[i][i] = 1;
+
+ for( i=0; i<njob; i++ )
+ {
+ strcpy( checkseq[i], seq[i] );
+// fprintf( stderr, "checkseq[%d] = %s\n", i, checkseq[i] );
+ }
+
+
+ ilim = njob - 1;
+ for( i=0; i<ilim; i++ )
+ {
+ fprintf( stderr, "% 5d / %d\r", i, njob );
+
+
+ for( j=i+1; j<njob; j++ )
+ {
+
+
+#if 0
+ if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
+ {
+ distancemtx[i][j] = pscore;
+ continue;
+ }
+#endif
+
+ strcpy( aseq[i], seq[i] );
+ strcpy( aseq[j], seq[j] );
+ clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
+ // fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
+ // fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
+
+#if 0
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ fprintf( stderr, "\n" );
+#endif
+// for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
+
+#if 1
+ {
+ switch( alg )
+ {
+ case( 'T' ):
+ fprintf( stderr, " Calling tmalign %d-%d/%d \r", i+1, j+1, njob );
+ pscore = calltmalign( mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 'R' ):
+ fprintf( stderr, " Calling PDP_ASH.pl %d-%d/%d \r", i+1, j+1, njob );
+ pscore = callrash( i, j, mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen );
+ off1 = off2 = 0;
+ break;
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+#endif
+ distancemtx[i][j] = pscore;
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
+#endif
+
+ putlocalhom_str( mseq1[0], mseq2[0], equiv, scale, localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+#if 1
+
+ if( alreadyoutput[i] == 0 )
+ {
+ alreadyoutput[i] = 1;
+ gappick0( seq[i], mseq1[0] );
+ fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, strfiles[i], chainids[i], seq[i] );
+ strcpy( checkseq[i], seq[i] );
+ }
+ else
+ {
+ gappick0( seq[i], mseq1[0] );
+ fprintf( stderr, "checking seq%d\n", i );
+
+// fprintf( stderr, " seq=%s\n", seq[i] );
+// fprintf( stderr, "checkseq=%s\n", checkseq[i] );
+
+ if( strcmp( checkseq[i], seq[i] ) )
+ {
+ fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" );
+ fprintf( stderr, "i=%d\n", i );
+ fprintf( stderr, " seq=%s\n", seq[i] );
+ fprintf( stderr, "checkseq=%s\n", checkseq[i] );
+ exit( 1 );
+ }
+ }
+ if( alreadyoutput[j] == 0 )
+ {
+ alreadyoutput[j] = 1;
+ gappick0( seq[j], mseq2[0] );
+ fprintf( stdout, ">%d_%s-%s\n%s\n", j+1, strfiles[j], chainids[j], seq[j] );
+ strcpy( checkseq[j], seq[j] );
+ }
+ else
+ {
+ gappick0( seq[j], mseq2[0] );
+ fprintf( stderr, "checking seq%d\n", j );
+ if( strcmp( checkseq[j], seq[j] ) )
+ {
+ fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" );
+ fprintf( stderr, "j=%d\n", j );
+ fprintf( stderr, " seq=%s\n", seq[j] );
+ fprintf( stderr, "checkseq=%s\n", checkseq[j] );
+ exit( 1 );
+ }
+ }
+#endif
+ }
+ }
+ for( i=0; i<njob; i++ )
+ {
+ pscore = 0.0;
+ for( pt=seq[i]; *pt; pt++ )
+ pscore += amino_dis[(int)*pt][(int)*pt];
+ distancemtx[i][i] = pscore;
+
+ }
+
+ ilim = njob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ bunbo = MIN( distancemtx[i][i], distancemtx[j][j] );
+ if( bunbo == 0.0 )
+ distancemtx[i][j] = 2.0;
+ else
+ distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0;
+ }
+ }
+
+ hat2p = fopen( hat2file, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( hat2p, njob, name, distancemtx );
+ fclose( hat2p );
+
+ fprintf( stderr, "##### writing hat3\n" );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ ilim = njob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d k\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 );
+ }
+ }
+ }
+ fclose( hat3p );
+#if DEBUG
+ fprintf( stderr, "calling FreeLocalHomTable\n" );
+#endif
+ FreeLocalHomTable( localhomtable, njob );
+#if DEBUG
+ fprintf( stderr, "done. FreeLocalHomTable\n" );
+#endif
+}
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int nlen[M];
+ static char name[M][B], **seq;
+ static char **mseq1, **mseq2;
+ static char **aseq;
+ static char **bseq;
+ static double *eff;
+ static double *equiv;
+ char **strfiles;
+ char **chainids;
+ int i;
+ FILE *infp;
+ char c;
+ int alloclen;
+
+ arguments( argc, argv );
+
+ if( equivthreshold < 1 || 9 < equivthreshold )
+ {
+ fprintf( stderr, "-t n, n must be 1..9\n" );
+ exit( 1 );
+ }
+
+ if( ( equivwinsize + 1 ) % 2 != 0 )
+ {
+ fprintf( stderr, "equivwinsize = %d\n", equivwinsize );
+ fprintf( stderr, "It must be an odd number.\n" );
+ exit( 1 );
+ }
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ nlenmax = 10000; // tekitou
+
+ if( alg == 'R' )
+ prepareash( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
+ else if( alg == 'T' )
+ preparetmalign( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
+
+ fclose( infp );
+
+ aseq = AllocateCharMtx( njob, nlenmax*2+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*2+1 );
+ eff = AllocateDoubleVec( njob );
+
+ for( i=0; i<njob; i++ )
+ {
+ fprintf( stderr, "str%d = %s-%s\n", i, strfiles[i], chainids[i] );
+ }
+
+ if( njob < 1 )
+ {
+ fprintf( stderr, "No structure found.\n" );
+ exit( 1 );
+ }
+ if( njob < 2 )
+ {
+ fprintf( stderr, "Only %d structure found.\n", njob );
+ exit( 0 );
+ }
+ if( njob > M )
+ {
+ fprintf( stderr, "The number of structures must be < %d\n", M );
+ fprintf( stderr, "Please try sequence-based methods for such large data.\n" );
+ exit( 1 );
+ }
+
+
+
+#if 0
+ readData( infp, name, nlen, seq );
+#endif
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illegal character %c\n", c );
+ exit( 1 );
+ }
+
+// writePre( njob, name, nlen, seq, 0 );
+
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+
+
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+ pairalign( name, nlen, bseq, aseq, mseq1, mseq2, equiv, eff, strfiles, chainids, alloclen );
+
+ fprintf( trap_g, "done.\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+// writePre( njob, name, nlen, aseq, !contin );
+#if 0
+ writeData( stdout, njob, name, nlen, aseq );
+#endif
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+static char *whereispairalign;
+static char *laraparams;
+static char foldalignopt[1000];
+
+static void t2u( char *seq )
+{
+ while( *seq )
+ {
+ if ( *seq == 'A' ) *seq = 'a';
+ else if( *seq == 'a' ) *seq = 'a';
+ else if( *seq == 'T' ) *seq = 'u';
+ else if( *seq == 't' ) *seq = 'u';
+ else if( *seq == 'U' ) *seq = 'u';
+ else if( *seq == 'u' ) *seq = 'u';
+ else if( *seq == 'G' ) *seq = 'g';
+ else if( *seq == 'g' ) *seq = 'g';
+ else if( *seq == 'C' ) *seq = 'c';
+ else if( *seq == 'c' ) *seq = 'c';
+ else *seq = 'n';
+ seq++;
+ }
+}
+
+static float recallpairfoldalign( char **mseq1, char **mseq2, int m1, int m2, int *of1pt, int *of2pt, int alloclen )
+{
+ static FILE *fp = NULL;
+ float value;
+ char *aln1;
+ char *aln2;
+ int of1tmp, of2tmp;
+
+ if( fp == NULL )
+ {
+ fp = fopen( "_foldalignout", "r" );
+ if( fp == NULL )
+ {
+ fprintf( stderr, "Cannot open _foldalignout\n" );
+ exit( 1 );
+ }
+ }
+
+ aln1 = calloc( alloclen, sizeof( char ) );
+ aln2 = calloc( alloclen, sizeof( char ) );
+
+ readpairfoldalign( fp, *mseq1, *mseq2, aln1, aln2, m1, m2, &of1tmp, &of2tmp, alloclen );
+
+ if( strstr( foldalignopt, "-global") )
+ {
+ fprintf( stderr, "Calling G__align11\n" );
+ value = G__align11( mseq1, mseq2, alloclen );
+ *of1pt = 0;
+ *of2pt = 0;
+ }
+ else
+ {
+ fprintf( stderr, "Calling L__align11\n" );
+ value = L__align11( mseq1, mseq2, alloclen, of1pt, of2pt );
+ }
+
+// value = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
+
+ if( aln1[0] == 0 )
+ {
+ fprintf( stderr, "FOLDALIGN returned no alignment between %d and %d. Sequence alignment is used instead.\n", m1+1, m2+1 );
+ }
+ else
+ {
+ strcpy( *mseq1, aln1 );
+ strcpy( *mseq2, aln2 );
+ *of1pt = of1tmp;
+ *of2pt = of2tmp;
+ }
+
+// value = naivepairscore11( *mseq1, *mseq2, penalty ); // v6.511 ha kore wo tsukau, global nomi dakara.
+
+// fclose( fp ); // saigo dake yatta houga yoi.
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+
+ free( aln1 );
+ free( aln2 );
+
+ return( value );
+}
+
+static void callfoldalign( int nseq, char **mseq )
+{
+ FILE *fp;
+ int i;
+ int res;
+ static char com[10000];
+
+ for( i=0; i<nseq; i++ )
+ t2u( mseq[i] );
+
+ fp = fopen( "_foldalignin", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _foldalignin\n" );
+ exit( 1 );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ fprintf( fp, ">%d\n", i+1 );
+ fprintf( fp, "%s\n", mseq[i] );
+ }
+ fclose( fp );
+
+ sprintf( com, "env PATH=%s foldalign210 %s _foldalignin > _foldalignout ", whereispairalign, foldalignopt );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in foldalign\n" );
+ exit( 1 );
+ }
+
+}
+
+static void calllara( int nseq, char **mseq, char *laraarg )
+{
+ FILE *fp;
+ int i;
+ int res;
+ static char com[10000];
+
+ for( i=0; i<nseq; i++ )
+
+ fp = fopen( "_larain", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _larain\n" );
+ exit( 1 );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ fprintf( fp, ">%d\n", i+1 );
+ fprintf( fp, "%s\n", mseq[i] );
+ }
+ fclose( fp );
+
+
+// fprintf( stderr, "calling LaRA\n" );
+ sprintf( com, "env PATH=%s:/bin:/usr/bin mafft_lara -i _larain -w _laraout -o _lara.params %s", whereispairalign, laraarg );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in lara\n" );
+ exit( 1 );
+ }
+}
+
+static float recalllara( char **mseq1, char **mseq2, int alloclen )
+{
+ static FILE *fp = NULL;
+ static char *ungap1;
+ static char *ungap2;
+ static char *ori1;
+ static char *ori2;
+ int res;
+ static char com[10000];
+ float value;
+
+
+ if( fp == NULL )
+ {
+ fp = fopen( "_laraout", "r" );
+ if( fp == NULL )
+ {
+ fprintf( stderr, "Cannot open _laraout\n" );
+ exit( 1 );
+ }
+ ungap1 = AllocateCharVec( alloclen );
+ ungap2 = AllocateCharVec( alloclen );
+ ori1 = AllocateCharVec( alloclen );
+ ori2 = AllocateCharVec( alloclen );
+ }
+
+
+ strcpy( ori1, *mseq1 );
+ strcpy( ori2, *mseq2 );
+
+ fgets( com, 999, fp );
+ myfgets( com, 9999, fp );
+ strcpy( *mseq1, com );
+ myfgets( com, 9999, fp );
+ strcpy( *mseq2, com );
+
+ gappick0( ungap1, *mseq1 );
+ gappick0( ungap2, *mseq2 );
+ t2u( ungap1 );
+ t2u( ungap2 );
+
+ if( strcmp( ungap1, ori1 ) || strcmp( ungap2, ori2 ) )
+ {
+ fprintf( stderr, "SEQUENCE CHANGED!!\n" );
+ fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+ fprintf( stderr, "ungap1 = %s\n", ungap1 );
+ fprintf( stderr, "ori1 = %s\n", ori1 );
+ fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+ fprintf( stderr, "ungap2 = %s\n", ungap2 );
+ fprintf( stderr, "ori2 = %s\n", ori2 );
+ exit( 1 );
+ }
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+// fclose( fp ); // saigo dake yatta houga yoi.
+
+ return( value );
+}
+
+static float callmxscarna( char **mseq1, char **mseq2, int alloclen )
+{
+ FILE *fp;
+ int res;
+ static char com[10000];
+ float value;
+
+
+ t2u( *mseq1 );
+ t2u( *mseq2 );
+ fp = fopen( "_mxscarnain", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _mxscarnain\n" );
+ exit( 1 );
+ }
+ fprintf( fp, ">1\n" );
+ fprintf( fp, "%s\n", *mseq1 );
+ fprintf( fp, ">2\n" );
+ fprintf( fp, "%s\n", *mseq2 );
+ fclose( fp );
+
+ sprintf( com, "env PATH=%s mxscarna _mxscarnain > _mxscarnaout 2>/dev/null", whereispairalign );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in mxscarna\n" );
+ exit( 1 );
+ }
+
+ fp = fopen( "_mxscarnaout", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _mxscarnaout\n" );
+ exit( 1 );
+ }
+
+ fgets( com, 999, fp );
+ load1SeqWithoutName_new( fp, *mseq1 );
+ fgets( com, 999, fp );
+ load1SeqWithoutName_new( fp, *mseq2 );
+
+ fclose( fp );
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+ return( value );
+}
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ foldalignopt[0] = 0;
+ laraparams = NULL;
+ inputfile = NULL;
+ fftkeika = 0;
+ pslocal = -1000.0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ divpairscore = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_OP = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ ppenalty_EX = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ RNAppenalty = NOTSPECIFIED;
+ RNApthr = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'O':
+ ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'E':
+ ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+// fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+// fprintf( stderr, "blosum %d\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "TM %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'l':
+ ppslocal = (int)( atof( *++argv ) * 1000 + 0.5 );
+ pslocal = (int)( 600.0 / 1000.0 * ppslocal + 0.5);
+// fprintf( stderr, "ppslocal = %d\n", ppslocal );
+// fprintf( stderr, "pslocal = %d\n", pslocal );
+ --argc;
+ goto nextoption;
+ case 'd':
+ whereispairalign = *++argv;
+ fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
+ --argc;
+ goto nextoption;
+ case 'p':
+ laraparams = *++argv;
+ fprintf( stderr, "laraparams = %s\n", laraparams );
+ --argc;
+ goto nextoption;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+#if 0
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#endif
+ case 'Q':
+ calledByXced = 1;
+ break;
+ case 'x':
+ disp = 1;
+ break;
+#if 0
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'S':
+ alg = 'S';
+ break;
+ case 'L':
+ alg = 'L';
+ break;
+ case 's':
+ alg = 's';
+ break;
+ case 'B':
+ alg = 'B';
+ break;
+ case 'T':
+ alg = 'T';
+ break;
+ case 'H':
+ alg = 'H';
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'R':
+ alg = 'R';
+ break;
+ case 'N':
+ alg = 'N';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'V':
+ alg = 'V';
+ break;
+ case 'C':
+ alg = 'C';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'y':
+ divpairscore = 1;
+ break;
+/* Modified 01/08/27, default: user tree */
+ case 'J':
+ tbutree = 0;
+ break;
+/* modification end. */
+ case 'o':
+// foldalignopt = *++argv;
+ strcat( foldalignopt, " " );
+ strcat( foldalignopt, *++argv );
+ fprintf( stderr, "foldalignopt = %s\n", foldalignopt );
+ --argc;
+ goto nextoption;
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'Z':
+ checkC = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+int countamino( char *s, int end )
+{
+ int val = 0;
+ while( end-- )
+ if( *s++ != '-' ) val++;
+ return( val );
+}
+
+static void pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *effarr, int alloclen )
+{
+ int i, j, ilim;
+ int clus1, clus2;
+ int off1, off2;
+ float pscore = 0.0; // by D.Mathog
+ static char *indication1, *indication2;
+ FILE *hat2p, *hat3p;
+ static double **distancemtx;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ char *pt;
+ char *hat2file = "hat2";
+ LocalHom **localhomtable, *tmpptr;
+ static char **pair;
+ int intdum;
+ double bunbo;
+
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+ localhomtable[i][j].nokori = 0;
+ }
+ }
+
+ if( effarr1 == NULL )
+ {
+ distancemtx = AllocateDoubleMtx( njob, njob );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+#if 0
+#else
+ pair = AllocateCharMtx( njob, njob );
+#endif
+ }
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
+ for( i=0; i<njob; i++ ) pair[i][i] = 1;
+
+ if( alg == 'H' )
+ {
+ fprintf( stderr, "Calling FOLDALIGN with option '%s'\n", foldalignopt );
+ callfoldalign( njob, seq );
+ fprintf( stderr, "done.\n" );
+ }
+ if( alg == 'B' )
+ {
+ fprintf( stderr, "Calling LARA\n" );
+ calllara( njob, seq, "" );
+ fprintf( stderr, "done.\n" );
+ }
+ if( alg == 'T' )
+ {
+ fprintf( stderr, "Calling SLARA\n" );
+ calllara( njob, seq, "-s" );
+ fprintf( stderr, "done.\n" );
+ }
+
+ ilim = njob - 1;
+ for( i=0; i<ilim; i++ )
+ {
+ fprintf( stderr, "% 5d / %d\r", i, njob );
+ for( j=i+1; j<njob; j++ )
+ {
+
+ if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
+ {
+ distancemtx[i][j] = pscore;
+ continue;
+ }
+
+ strcpy( aseq[i], seq[i] );
+ strcpy( aseq[j], seq[j] );
+ clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
+ // fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
+ // fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
+
+#if 0
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ fprintf( stderr, "\n" );
+#endif
+ // for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
+
+#if 1
+ if( use_fft )
+ {
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
+ off1 = off2 = 0;
+ }
+ else
+#endif
+ {
+ switch( alg )
+ {
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 'A' ):
+ pscore = G__align11( mseq1, mseq2, alloclen, NULL, 0, NULL );
+ off1 = off2 = 0;
+ break;
+#if 0
+ case( 'V' ):
+ pscore = VAalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
+ fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
+ break;
+ case( 'S' ):
+ fprintf( stderr, "aligning %d-%d\n", i, j );
+ pscore = suboptalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
+ fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
+ break;
+#endif
+ case( 'N' ):
+ pscore = genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
+// fprintf( stderr, "pscore = %f\n", pscore );
+ break;
+ case( 'L' ):
+ pscore = L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
+// fprintf( stderr, "pscore (1) = %f\n", pscore );
+// pscore = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
+// fprintf( stderr, "pscore (2) = %f\n\n", pscore );
+ break;
+ case( 'H' ):
+ pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
+ break;
+ case( 'B' ):
+ case( 'T' ):
+ pscore = recalllara( mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+// fprintf( stderr, "lara, pscore = %f\n", pscore );
+ break;
+ case( 's' ):
+ pscore = callmxscarna( mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+// fprintf( stderr, "scarna, pscore = %f\n", pscore );
+ break;
+ case( 'M' ):
+// pscore = MSalign11( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL );
+ pscore = MSalign11( mseq1, mseq2, alloclen );
+// fprintf( stderr, "pscore = %f\n", pscore );
+ break;
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+ distancemtx[i][j] = pscore;
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
+#endif
+// fprintf( stderr, "pslocal = %d\n", pslocal );
+// offset = makelocal( *mseq1, *mseq2, pslocal );
+#if 0
+ fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
+ fprintf( stderr, ">%d\n%s\n>%d\n%s\n>\n", i, mseq1[0], j, mseq2[0] );
+#endif
+
+// putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, countamino( *mseq1, off1 ), countamino( *mseq2, off2 ), pscore, strlen( mseq1[0] ) );
+// fprintf( stderr, "pscore = %f\n", pscore );
+ if( alg == 'H' )
+// if( alg == 'H' || alg == 's' || alg == 'B' ) // next version
+ putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+ else if( alg != 'S' && alg != 'V' )
+ putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+ }
+ }
+ for( i=0; i<njob; i++ )
+ {
+ pscore = 0.0;
+ for( pt=seq[i]; *pt; pt++ )
+ pscore += amino_dis[(int)*pt][(int)*pt];
+ distancemtx[i][i] = pscore;
+
+ }
+
+ ilim = njob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ bunbo = MIN( distancemtx[i][i], distancemtx[j][j] );
+ if( bunbo == 0.0 )
+ distancemtx[i][j] = 2.0;
+ else
+ distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0;
+ }
+ }
+
+ hat2p = fopen( hat2file, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( hat2p, njob, name, distancemtx );
+ fclose( hat2p );
+
+ fprintf( stderr, "##### writing hat3\n" );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ ilim = njob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
+ }
+ }
+ }
+ fclose( hat3p );
+#if DEBUG
+ fprintf( stderr, "calling FreeLocalHomTable\n" );
+#endif
+ FreeLocalHomTable( localhomtable, njob );
+#if DEBUG
+ fprintf( stderr, "done. FreeLocalHomTable\n" );
+#endif
+}
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int nlen[M];
+ static char name[M][B], **seq;
+ static char **mseq1, **mseq2;
+ static char **aseq;
+ static char **bseq;
+ static double *eff;
+ int i;
+ FILE *infp;
+ char c;
+ int alloclen;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+ if( njob > M )
+ {
+ fprintf( stderr, "The number of sequences must be < %d\n", M );
+ fprintf( stderr, "Please try the splittbfast program for such large data.\n" );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*9+1 );
+ aseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ alloclen = nlenmax*9;
+
+ eff = AllocateDoubleVec( njob );
+
+#if 0
+ Read( name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illegal character %c\n", c );
+ exit( 1 );
+ }
+
+// writePre( njob, name, nlen, seq, 0 );
+
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+
+
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+ pairalign( name, nlen, bseq, aseq, mseq1, mseq2, eff, alloclen );
+
+ fprintf( trap_g, "done.\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+// writePre( njob, name, nlen, aseq, !contin );
+#if 0
+ writeData( stdout, njob, name, nlen, aseq );
+#endif
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+#define NODIST -9999
+
+static char *whereispairalign;
+static char *laraparams;
+static char foldalignopt[1000];
+static int stdout_align;
+static int stdout_dist;
+static int store_localhom;
+static int store_dist;
+
+typedef struct _jobtable
+{
+ int i;
+ int j;
+} Jobtable;
+
+#ifdef enablemultithread
+typedef struct _thread_arg
+{
+ int thread_no;
+ int njob;
+ Jobtable *jobpospt;
+ char **name;
+ char **seq;
+ LocalHom **localhomtable;
+ double **distancemtx;
+ double *selfscore;
+ char ***bpp;
+ int alloclen;
+ pthread_mutex_t *mutex_counter;
+ pthread_mutex_t *mutex_stdout;
+} thread_arg_t;
+#endif
+
+static void t2u( char *seq )
+{
+ while( *seq )
+ {
+ if ( *seq == 'A' ) *seq = 'a';
+ else if( *seq == 'a' ) *seq = 'a';
+ else if( *seq == 'T' ) *seq = 'u';
+ else if( *seq == 't' ) *seq = 'u';
+ else if( *seq == 'U' ) *seq = 'u';
+ else if( *seq == 'u' ) *seq = 'u';
+ else if( *seq == 'G' ) *seq = 'g';
+ else if( *seq == 'g' ) *seq = 'g';
+ else if( *seq == 'C' ) *seq = 'c';
+ else if( *seq == 'c' ) *seq = 'c';
+ else *seq = 'n';
+ seq++;
+ }
+}
+
+static float recallpairfoldalign( char **mseq1, char **mseq2, int m1, int m2, int *of1pt, int *of2pt, int alloclen )
+{
+ static FILE *fp = NULL;
+ float value;
+ char *aln1;
+ char *aln2;
+ int of1tmp, of2tmp;
+
+ if( fp == NULL )
+ {
+ fp = fopen( "_foldalignout", "r" );
+ if( fp == NULL )
+ {
+ fprintf( stderr, "Cannot open _foldalignout\n" );
+ exit( 1 );
+ }
+ }
+
+ aln1 = calloc( alloclen, sizeof( char ) );
+ aln2 = calloc( alloclen, sizeof( char ) );
+
+ readpairfoldalign( fp, *mseq1, *mseq2, aln1, aln2, m1, m2, &of1tmp, &of2tmp, alloclen );
+
+ if( strstr( foldalignopt, "-global") )
+ {
+ fprintf( stderr, "Calling G__align11\n" );
+ value = G__align11( mseq1, mseq2, alloclen, outgap, outgap );
+ *of1pt = 0;
+ *of2pt = 0;
+ }
+ else
+ {
+ fprintf( stderr, "Calling L__align11\n" );
+ value = L__align11( mseq1, mseq2, alloclen, of1pt, of2pt );
+ }
+
+// value = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
+
+ if( aln1[0] == 0 )
+ {
+ fprintf( stderr, "FOLDALIGN returned no alignment between %d and %d. Sequence alignment is used instead.\n", m1+1, m2+1 );
+ }
+ else
+ {
+ strcpy( *mseq1, aln1 );
+ strcpy( *mseq2, aln2 );
+ *of1pt = of1tmp;
+ *of2pt = of2tmp;
+ }
+
+// value = naivepairscore11( *mseq1, *mseq2, penalty ); // v6.511 ha kore wo tsukau, global nomi dakara.
+
+// fclose( fp ); // saigo dake yatta houga yoi.
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+
+ free( aln1 );
+ free( aln2 );
+
+ return( value );
+}
+
+static void callfoldalign( int nseq, char **mseq )
+{
+ FILE *fp;
+ int i;
+ int res;
+ static char com[10000];
+
+ for( i=0; i<nseq; i++ )
+ t2u( mseq[i] );
+
+ fp = fopen( "_foldalignin", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _foldalignin\n" );
+ exit( 1 );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ fprintf( fp, ">%d\n", i+1 );
+ fprintf( fp, "%s\n", mseq[i] );
+ }
+ fclose( fp );
+
+ sprintf( com, "env PATH=%s foldalign210 %s _foldalignin > _foldalignout ", whereispairalign, foldalignopt );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in foldalign\n" );
+ exit( 1 );
+ }
+
+}
+
+static void calllara( int nseq, char **mseq, char *laraarg )
+{
+ FILE *fp;
+ int i;
+ int res;
+ static char com[10000];
+
+// for( i=0; i<nseq; i++ )
+
+ fp = fopen( "_larain", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _larain\n" );
+ exit( 1 );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ fprintf( fp, ">%d\n", i+1 );
+ fprintf( fp, "%s\n", mseq[i] );
+ }
+ fclose( fp );
+
+
+// fprintf( stderr, "calling LaRA\n" );
+ sprintf( com, "env PATH=%s:/bin:/usr/bin mafft_lara -i _larain -w _laraout -o _lara.params %s", whereispairalign, laraarg );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in lara\n" );
+ exit( 1 );
+ }
+}
+
+static float recalllara( char **mseq1, char **mseq2, int alloclen )
+{
+ static FILE *fp = NULL;
+ static char *ungap1;
+ static char *ungap2;
+ static char *ori1;
+ static char *ori2;
+// int res;
+ static char com[10000];
+ float value;
+
+
+ if( fp == NULL )
+ {
+ fp = fopen( "_laraout", "r" );
+ if( fp == NULL )
+ {
+ fprintf( stderr, "Cannot open _laraout\n" );
+ exit( 1 );
+ }
+ ungap1 = AllocateCharVec( alloclen );
+ ungap2 = AllocateCharVec( alloclen );
+ ori1 = AllocateCharVec( alloclen );
+ ori2 = AllocateCharVec( alloclen );
+ }
+
+
+ strcpy( ori1, *mseq1 );
+ strcpy( ori2, *mseq2 );
+
+ fgets( com, 999, fp );
+ myfgets( com, 9999, fp );
+ strcpy( *mseq1, com );
+ myfgets( com, 9999, fp );
+ strcpy( *mseq2, com );
+
+ gappick0( ungap1, *mseq1 );
+ gappick0( ungap2, *mseq2 );
+ t2u( ungap1 );
+ t2u( ungap2 );
+ t2u( ori1 );
+ t2u( ori2 );
+
+ if( strcmp( ungap1, ori1 ) || strcmp( ungap2, ori2 ) )
+ {
+ fprintf( stderr, "SEQUENCE CHANGED!!\n" );
+ fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+ fprintf( stderr, "ungap1 = %s\n", ungap1 );
+ fprintf( stderr, "ori1 = %s\n", ori1 );
+ fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+ fprintf( stderr, "ungap2 = %s\n", ungap2 );
+ fprintf( stderr, "ori2 = %s\n", ori2 );
+ exit( 1 );
+ }
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+// fclose( fp ); // saigo dake yatta houga yoi.
+
+ return( value );
+}
+
+
+static float callmxscarna_giving_bpp( char **mseq1, char **mseq2, char **bpp1, char **bpp2, int alloclen, int i, int j )
+{
+ FILE *fp;
+ int res;
+ char *com;
+ float value;
+ char *dirname;
+
+
+ dirname = calloc( 100, sizeof( char ) );
+ com = calloc( 1000, sizeof( char ) );
+ sprintf( dirname, "_%d-%d", i, j );
+ sprintf( com, "rm -rf %s", dirname );
+ system( com );
+ sprintf( com, "mkdir %s", dirname );
+ system( com );
+
+
+ sprintf( com, "%s/_bpporg", dirname );
+ fp = fopen( com, "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot write to %s/_bpporg\n", dirname );
+ exit( 1 );
+ }
+ fprintf( fp, ">a\n" );
+ while( *bpp1 )
+ fprintf( fp, "%s", *bpp1++ );
+
+ fprintf( fp, ">b\n" );
+ while( *bpp2 )
+ fprintf( fp, "%s", *bpp2++ );
+ fclose( fp );
+
+ sprintf( com, "tr -d '\\r' < %s/_bpporg > %s/_bpp", dirname, dirname );
+ system( com ); // for cygwin, wakaran
+
+ t2u( *mseq1 );
+ t2u( *mseq2 );
+
+ sprintf( com, "%s/_mxscarnainorg", dirname );
+ fp = fopen( com, "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open %s/_mxscarnainorg\n", dirname );
+ exit( 1 );
+ }
+ fprintf( fp, ">1\n" );
+// fprintf( fp, "%s\n", *mseq1 );
+ write1seq( fp, *mseq1 );
+ fprintf( fp, ">2\n" );
+// fprintf( fp, "%s\n", *mseq2 );
+ write1seq( fp, *mseq2 );
+ fclose( fp );
+
+ sprintf( com, "tr -d '\\r' < %s/_mxscarnainorg > %s/_mxscarnain", dirname, dirname );
+ system( com ); // for cygwin, wakaran
+
+#if 0
+ sprintf( com, "cd %s; %s/mxscarnamod -readbpp _mxscarnain > _mxscarnaout 2>_dum", dirname, whereispairalign );
+#else
+ sprintf( com, "_mxscarnash%s", dirname );
+ fp = fopen( com, "w" );
+ fprintf( fp, "cd %s\n", dirname );
+ fprintf( fp, "%s/mxscarnamod -readbpp _mxscarnain > _mxscarnaout 2>_dum\n", whereispairalign );
+ fprintf( fp, "exit $tatus\n" );
+ fclose( fp );
+
+ sprintf( com, "tr -d '\\r' < _mxscarnash%s > _mxscarnash%s.unix", dirname, dirname );
+ system( com ); // for cygwin, wakaran
+
+ sprintf( com, "sh _mxscarnash%s.unix 2>_dum%s", dirname, dirname );
+#endif
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in mxscarna\n" );
+ exit( 1 );
+ }
+
+ sprintf( com, "%s/_mxscarnaout", dirname );
+
+ fp = fopen( com, "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open %s/_mxscarnaout\n", dirname );
+ exit( 1 );
+ }
+
+ fgets( com, 999, fp );
+ load1SeqWithoutName_new( fp, *mseq1 );
+ fgets( com, 999, fp );
+ load1SeqWithoutName_new( fp, *mseq2 );
+
+ fclose( fp );
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+#if 0
+ sprintf( com, "rm -rf %s > /dev/null 2>&1", dirname );
+ if( system( com ) )
+ {
+ fprintf( stderr, "retrying to rmdir\n" );
+ usleep( 2000 );
+ system( com );
+ }
+#endif
+
+ free( dirname );
+ free( com );
+
+
+ return( value );
+}
+
+#if 0
+static float callmxscarna_slow( char **mseq1, char **mseq2, int alloclen )
+{
+ FILE *fp;
+ int res;
+ static char com[10000];
+ float value;
+
+
+ t2u( *mseq1 );
+ t2u( *mseq2 );
+ fp = fopen( "_mxscarnain", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _mxscarnain\n" );
+ exit( 1 );
+ }
+ fprintf( fp, ">1\n" );
+ fprintf( fp, "%s\n", *mseq1 );
+ fprintf( fp, ">2\n" );
+ fprintf( fp, "%s\n", *mseq2 );
+ fclose( fp );
+
+ sprintf( com, "env PATH=%s mxscarnamod _mxscarnain > _mxscarnaout 2>_dum", whereispairalign );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in mxscarna\n" );
+ exit( 1 );
+ }
+
+ fp = fopen( "_mxscarnaout", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _mxscarnaout\n" );
+ exit( 1 );
+ }
+
+ fgets( com, 999, fp );
+ load1SeqWithoutName_new( fp, *mseq1 );
+ fgets( com, 999, fp );
+ load1SeqWithoutName_new( fp, *mseq2 );
+
+ fclose( fp );
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+ return( value );
+}
+#endif
+
+static void readhat4( FILE *fp, char ***bpp )
+{
+ char oneline[1000];
+ int bppsize;
+ int onechar;
+// double prob;
+// int posi, posj;
+
+ bppsize = 0;
+// fprintf( stderr, "reading hat4\n" );
+ onechar = getc(fp);
+// fprintf( stderr, "onechar = %c\n", onechar );
+ if( onechar != '>' )
+ {
+ fprintf( stderr, "Format error\n" );
+ exit( 1 );
+ }
+ ungetc( onechar, fp );
+ fgets( oneline, 999, fp );
+ while( 1 )
+ {
+ onechar = getc(fp);
+ ungetc( onechar, fp );
+ if( onechar == '>' || onechar == EOF )
+ {
+// fprintf( stderr, "Next\n" );
+ *bpp = realloc( *bpp, (bppsize+2) * sizeof( char * ) );
+ (*bpp)[bppsize] = NULL;
+ break;
+ }
+ fgets( oneline, 999, fp );
+// fprintf( stderr, "oneline=%s\n", oneline );
+// sscanf( oneline, "%d %d %f", &posi, &posj, &prob );
+// fprintf( stderr, "%d %d -> %f\n", posi, posj, prob );
+ *bpp = realloc( *bpp, (bppsize+2) * sizeof( char * ) );
+ (*bpp)[bppsize] = calloc( 100, sizeof( char ) );
+ strcpy( (*bpp)[bppsize], oneline );
+ bppsize++;
+ }
+}
+
+static void preparebpp( int nseq, char ***bpp )
+{
+ FILE *fp;
+ int i;
+
+ fp = fopen( "hat4", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open hat4\n" );
+ exit( 1 );
+ }
+ for( i=0; i<nseq; i++ )
+ readhat4( fp, bpp+i );
+ fclose( fp );
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ nthread = 1;
+ foldalignopt[0] = 0;
+ laraparams = NULL;
+ inputfile = NULL;
+ fftkeika = 0;
+ pslocal = -1000.0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ divpairscore = 0;
+ stdout_align = 0;
+ stdout_dist = 0;
+ store_dist = 1;
+ store_localhom = 1;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_OP = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ ppenalty_EX = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ RNAppenalty = NOTSPECIFIED;
+ RNApthr = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'O':
+ ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'E':
+ ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+// fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+// fprintf( stderr, "blosum %d\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "TM %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'l':
+ ppslocal = (int)( atof( *++argv ) * 1000 + 0.5 );
+ pslocal = (int)( 600.0 / 1000.0 * ppslocal + 0.5);
+// fprintf( stderr, "ppslocal = %d\n", ppslocal );
+// fprintf( stderr, "pslocal = %d\n", pslocal );
+ --argc;
+ goto nextoption;
+ case 'd':
+ whereispairalign = *++argv;
+ fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
+ --argc;
+ goto nextoption;
+ case 'p':
+ laraparams = *++argv;
+ fprintf( stderr, "laraparams = %s\n", laraparams );
+ --argc;
+ goto nextoption;
+ case 'C':
+ nthread = atoi( *++argv );
+ fprintf( stderr, "nthread = %d\n", nthread );
+ --argc;
+ goto nextoption;
+ case 'c':
+ stdout_dist = 1;
+ break;
+ case 'n':
+ stdout_align = 1;
+ break;
+ case 'x':
+ store_localhom = 0;
+ store_dist = 0;
+ break;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+#if 0
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#endif
+ case 'Q':
+ calledByXced = 1;
+ break;
+#if 0
+ case 'x':
+ disp = 1;
+ break;
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'S':
+ alg = 'S';
+ break;
+ case 't':
+ alg = 't';
+ store_localhom = 0;
+ break;
+ case 'L':
+ alg = 'L';
+ break;
+ case 's':
+ alg = 's';
+ break;
+ case 'B':
+ alg = 'B';
+ break;
+ case 'T':
+ alg = 'T';
+ break;
+ case 'H':
+ alg = 'H';
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'R':
+ alg = 'R';
+ break;
+ case 'N':
+ alg = 'N';
+ break;
+ case 'K':
+ alg = 'K';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'V':
+ alg = 'V';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'y':
+ divpairscore = 1;
+ break;
+/* Modified 01/08/27, default: user tree */
+ case 'J':
+ tbutree = 0;
+ break;
+/* modification end. */
+ case 'o':
+// foldalignopt = *++argv;
+ strcat( foldalignopt, " " );
+ strcat( foldalignopt, *++argv );
+ fprintf( stderr, "foldalignopt = %s\n", foldalignopt );
+ --argc;
+ goto nextoption;
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'Z':
+ checkC = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+}
+
+int countamino( char *s, int end )
+{
+ int val = 0;
+ while( end-- )
+ if( *s++ != '-' ) val++;
+ return( val );
+}
+
+#if enablemultithread
+static void *athread( void *arg )
+{
+ thread_arg_t *targ = (thread_arg_t *)arg;
+ int i, j;
+ int clus1, clus2;
+ int off1, off2;
+ int intdum;
+ double bunbo;
+ float pscore = 0.0; // by D.Mathog
+ double *effarr;
+ double *effarr1;
+ double *effarr2;
+ char **pair;
+ char *indication1, *indication2;
+ char **mseq1, **mseq2;
+ char **aseq;
+
+// thread_arg
+ int thread_no = targ->thread_no;
+ int njob = targ->njob;
+ Jobtable *jobpospt = targ->jobpospt;
+ char **name = targ->name;
+ char **seq = targ->seq;
+ LocalHom **localhomtable = targ->localhomtable;
+ double **distancemtx = targ->distancemtx;
+ double *selfscore = targ->selfscore;
+ char ***bpp = targ->bpp;
+ int alloclen = targ->alloclen;
+
+// fprintf( stderr, "thread %d start!\n", thread_no );
+
+ effarr = AllocateDoubleVec( njob );
+ for( i=0; i<njob; i++ ) effarr[i] = 1.0;
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+ pair = AllocateCharMtx( njob, njob );
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
+ for( i=0; i<njob; i++ ) pair[i][i] = 1;
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ aseq = AllocateCharMtx( njob, alloclen+10 );
+
+ while( 1 )
+ {
+ pthread_mutex_lock( targ->mutex_counter );
+ j = jobpospt->j;
+ i = jobpospt->i;
+ j++;
+ if( j == njob )
+ {
+ i++;
+ j = i + 1;
+ if( i == njob-1 )
+ {
+// fprintf( stderr, "thread %d end!\n", thread_no );
+ pthread_mutex_unlock( targ->mutex_counter );
+
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonIP = NULL;
+ if( commonJP ) FreeIntMtx( commonJP );
+ commonJP = NULL;
+ Falign( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
+ G__align11_noalign( NULL, 0, 0, NULL, NULL, 0 );
+ L__align11( NULL, NULL, 0, NULL, NULL );
+ genL__align11( NULL, NULL, 0, NULL, NULL );
+ free( effarr );
+ free( effarr1 );
+ free( effarr2 );
+ free( indication1 );
+ free( indication2 );
+ FreeCharMtx( pair );
+ free( mseq1 );
+ free( mseq2 );
+ FreeCharMtx( aseq );
+ return( NULL );
+ }
+ }
+ jobpospt->j = j;
+ jobpospt->i = i;
+ pthread_mutex_unlock( targ->mutex_counter );
+
+
+ if( j == i+1 || j % 100 == 0 )
+ {
+ fprintf( stderr, "% 5d / %d (by thread %3d) \r", i, njob, thread_no );
+// fprintf( stderr, "% 5d - %5d / %d (thread %d)\n", i, j, njob, thread_no );
+ }
+
+
+ if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
+ {
+ if( store_dist ) distancemtx[i][j] = 2.0;
+ if( stdout_dist)
+ {
+ pthread_mutex_lock( targ->mutex_stdout );
+ fprintf( stdout, "%d %d d=%.3f\n", i+1, j+1, 2.0 );
+ pthread_mutex_unlock( targ->mutex_stdout );
+ }
+ continue;
+ }
+
+ strcpy( aseq[i], seq[i] );
+ strcpy( aseq[j], seq[j] );
+ clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
+// fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
+// fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
+
+#if 0
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ fprintf( stderr, "\n" );
+#endif
+// for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
+
+ if( use_fft )
+ {
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
+// fprintf( stderr, "pscore (fft) = %f\n", pscore );
+ off1 = off2 = 0;
+ }
+ else
+ {
+ switch( alg )
+ {
+ case( 'L' ):
+ pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
+ L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
+ break;
+ case( 'A' ):
+ pscore = G__align11( mseq1, mseq2, alloclen, outgap, outgap );
+ off1 = off2 = 0;
+ break;
+ case( 'N' ):
+ pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
+ genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
+ break;
+ case( 't' ):
+ pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 's' ):
+ pscore = callmxscarna_giving_bpp( mseq1, mseq2, bpp[i], bpp[j], alloclen, i, j );
+ off1 = off2 = 0;
+ break;
+#if 0
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 'K' ):
+ pscore = genG__align11( mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 'H' ):
+ pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
+ break;
+ case( 'B' ):
+ case( 'T' ):
+ pscore = recalllara( mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 'M' ):
+ pscore = MSalign11( mseq1, mseq2, alloclen );
+ break;
+#endif
+ default:
+ ErrorExit( "\n\nERROR IN SOURCE FILE\n\n" );
+ }
+ }
+
+ if( alg == 't' || ( mseq1[0][0] != 0 && mseq2[0][0] != 0 ) ) // 't' no jouken ha iranai to omou. if( ( mseq1[0][0] != 0 && mseq2[0][0] != 0 ) )
+ {
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
+#endif
+ if( !store_localhom )
+ ;
+ else if( alg == 'H' )
+ putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+ else if( alg != 'S' && alg != 'V' )
+ {
+ putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+ }
+
+ if( (bunbo=MIN( selfscore[i], selfscore[j] )) == 0.0 || bunbo < pscore )
+ pscore = 2.0;
+ else
+ pscore = ( 1.0 - pscore / bunbo ) * 2.0;
+ }
+ else
+ {
+ pscore = 2.0;
+ }
+
+#if 1 // mutex
+ if( stdout_align )
+ {
+ pthread_mutex_lock( targ->mutex_stdout );
+ if( alg != 't' )
+ {
+ fprintf( stdout, "sequence %d - sequence %d, pairwise distance = %10.5f\n", i+1, j+1, pscore );
+ fprintf( stdout, ">%s\n", name[i] );
+ write1seq( stdout, mseq1[0] );
+ fprintf( stdout, ">%s\n", name[j] );
+ write1seq( stdout, mseq2[0] );
+ fprintf( stdout, "\n" );
+ }
+ pthread_mutex_unlock( targ->mutex_stdout );
+ }
+ if( stdout_dist )
+ {
+ pthread_mutex_lock( targ->mutex_stdout );
+ if( j == i+1 ) fprintf( stdout, "%d %d d=%.3f\n", i+1, i+1, 0.0 );
+ fprintf( stdout, "%d %d d=%.3f\n", i+1, j+1, pscore );
+ pthread_mutex_unlock( targ->mutex_stdout );
+ }
+#endif // mutex
+ if( store_dist) distancemtx[i][j] = pscore;
+ }
+}
+#endif
+
+static void pairalign( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *effarr, int alloclen )
+{
+ int i, j, ilim;
+ int clus1, clus2;
+ int off1, off2;
+ float pscore = 0.0; // by D.Mathog
+ static char *indication1, *indication2;
+ FILE *hat2p, *hat3p;
+ double **distancemtx;
+ double *selfscore;
+ double *effarr1;
+ double *effarr2;
+ char *pt;
+ char *hat2file = "hat2";
+ LocalHom **localhomtable = NULL, *tmpptr;
+ static char **pair;
+ int intdum;
+ double bunbo;
+ char ***bpp = NULL; // mxscarna no toki dake
+
+ if( store_localhom )
+ {
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+ localhomtable[i][j].nokori = 0;
+ }
+ }
+ }
+
+ if( store_dist ) distancemtx = AllocateDoubleMtx( njob, njob );
+ else distancemtx = NULL;
+ selfscore = AllocateDoubleVec( njob );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+#if 0
+#else
+ pair = AllocateCharMtx( njob, njob );
+#endif
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
+ for( i=0; i<njob; i++ ) pair[i][i] = 1;
+
+ if( alg == 'H' )
+ {
+ fprintf( stderr, "Calling FOLDALIGN with option '%s'\n", foldalignopt );
+ callfoldalign( njob, seq );
+ fprintf( stderr, "done.\n" );
+ }
+ if( alg == 'B' )
+ {
+ fprintf( stderr, "Running LARA (Bauer et al. http://www.planet-lisa.net/)\n" );
+ calllara( njob, seq, "" );
+ fprintf( stderr, "done.\n" );
+ }
+ if( alg == 'T' )
+ {
+ fprintf( stderr, "Running SLARA (Bauer et al. http://www.planet-lisa.net/)\n" );
+ calllara( njob, seq, "-s" );
+ fprintf( stderr, "done.\n" );
+ }
+ if( alg == 's' )
+ {
+ fprintf( stderr, "Preparing bpp\n" );
+// bpp = AllocateCharCub( njob, nlenmax, 0 );
+ bpp = calloc( njob, sizeof( char ** ) );
+ preparebpp( njob, bpp );
+ fprintf( stderr, "done.\n" );
+ fprintf( stderr, "Running MXSCARNA (Tabei et al. http://www.ncrna.org/software/mxscarna)\n" );
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ pscore = 0.0;
+ for( pt=seq[i]; *pt; pt++ )
+ pscore += amino_dis[(int)*pt][(int)*pt];
+ selfscore[i] = pscore;
+
+ }
+
+#if enablemultithread
+ if( nthread > 0 )
+ {
+ Jobtable jobpos;
+ pthread_t *handle;
+ pthread_mutex_t mutex_counter;
+ pthread_mutex_t mutex_stdout;
+ thread_arg_t *targ;
+
+ jobpos.i = 0;
+ jobpos.j = 0;
+
+ targ = calloc( nthread, sizeof( thread_arg_t ) );
+ handle = calloc( nthread, sizeof( pthread_t ) );
+ pthread_mutex_init( &mutex_counter, NULL );
+ pthread_mutex_init( &mutex_stdout, NULL );
+
+ for( i=0; i<nthread; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].njob = njob;
+ targ[i].jobpospt = &jobpos;
+ targ[i].name = name;
+ targ[i].seq = seq;
+ targ[i].localhomtable = localhomtable;
+ targ[i].distancemtx = distancemtx;
+ targ[i].selfscore = selfscore;
+ targ[i].bpp = bpp;
+ targ[i].alloclen = alloclen;
+ targ[i].mutex_counter = &mutex_counter;
+ targ[i].mutex_stdout = &mutex_stdout;
+
+// athread( (void *)targ );
+ pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
+// pthread_create( handle+i, NULL, bthread, (void *)(targ+i) );
+ }
+
+
+ for( i=0; i<nthread; i++ )
+ {
+ pthread_join( handle[i], NULL );
+ }
+ pthread_mutex_destroy( &mutex_counter );
+ pthread_mutex_destroy( &mutex_stdout );
+ free( handle );
+ free( targ );
+ }
+ else
+#endif
+ {
+ ilim = njob - 1;
+ for( i=0; i<ilim; i++ )
+ {
+ if( stdout_dist) fprintf( stdout, "%d %d d=%.3f\n", i+1, i+1, 0.0 );
+ fprintf( stderr, "% 5d / %d\r", i, njob );
+ fflush( stderr );
+ for( j=i+1; j<njob; j++ )
+ {
+
+ if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
+ {
+ if( store_dist ) distancemtx[i][j] = 2.0;
+ if( stdout_dist) fprintf( stdout, "%d %d d=%.3f\n", i+1, j+1, 2.0 );
+ continue;
+ }
+
+ strcpy( aseq[i], seq[i] );
+ strcpy( aseq[j], seq[j] );
+ clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
+ // fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
+ // fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
+
+#if 0
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ fprintf( stderr, "\n" );
+#endif
+ // for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
+
+ if( use_fft )
+ {
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
+// fprintf( stderr, "pscore (fft) = %f\n", pscore );
+ off1 = off2 = 0;
+ }
+ else
+ {
+ switch( alg )
+ {
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 't' ):
+ pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 'A' ):
+ pscore = G__align11( mseq1, mseq2, alloclen, outgap, outgap );
+ off1 = off2 = 0;
+ break;
+ case( 'N' ):
+ pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
+ genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
+ break;
+ case( 'K' ):
+ pscore = genG__align11( mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 'L' ):
+ pscore = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, alloclen );
+ L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
+ break;
+ case( 'H' ):
+ pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
+ break;
+ case( 'B' ):
+ case( 'T' ):
+ pscore = recalllara( mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 's' ):
+ pscore = callmxscarna_giving_bpp( mseq1, mseq2, bpp[i], bpp[j], alloclen, i, j );
+ off1 = off2 = 0;
+ break;
+ case( 'M' ):
+ pscore = MSalign11( mseq1, mseq2, alloclen );
+ break;
+ default:
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+
+ if( alg == 't' || ( mseq1[0][0] != 0 && mseq2[0][0] != 0 ) ) // 't' no jouken ha iranai to omou. if( ( mseq1[0][0] != 0 && mseq2[0][0] != 0 ) )
+ {
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
+#endif
+ if( !store_localhom )
+ ;
+ else if( alg == 'H' )
+ putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+ else if( alg != 'S' && alg != 'V' )
+ putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+
+
+ if( (bunbo=MIN( selfscore[i], selfscore[j] )) == 0.0 || bunbo < pscore )
+ pscore = 2.0;
+ else
+ pscore = ( 1.0 - pscore / bunbo ) * 2.0;
+ }
+ else
+ {
+ pscore = 2.0;
+ }
+
+ if( stdout_align )
+ {
+ if( alg != 't' )
+ {
+ fprintf( stdout, "sequence %d - sequence %d, pairwise distance = %10.5f\n", i+1, j+1, pscore );
+ fprintf( stdout, ">%s\n", name[i] );
+ write1seq( stdout, mseq1[0] );
+ fprintf( stdout, ">%s\n", name[j] );
+ write1seq( stdout, mseq2[0] );
+ fprintf( stdout, "\n" );
+ }
+ }
+ if( stdout_dist ) fprintf( stdout, "%d %d d=%.3f\n", i+1, j+1, pscore );
+ if( store_dist) distancemtx[i][j] = pscore;
+ }
+ }
+ }
+
+
+ if( store_dist )
+ {
+ hat2p = fopen( hat2file, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open hat2." );
+ WriteHat2_pointer( hat2p, njob, name, distancemtx );
+ fclose( hat2p );
+ }
+
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ if( store_localhom )
+ {
+ fprintf( stderr, "\n\n##### writing hat3\n" );
+ ilim = njob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+// tmptmptmptmptmp
+// if( alg == 'B' || alg == 'T' )
+// fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, 1.0, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
+// else
+ fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d h\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 );
+ }
+ }
+ }
+#if DEBUG
+ fprintf( stderr, "calling FreeLocalHomTable\n" );
+#endif
+ FreeLocalHomTable( localhomtable, njob );
+#if DEBUG
+ fprintf( stderr, "done. FreeLocalHomTable\n" );
+#endif
+ }
+ fclose( hat3p );
+
+ if( alg == 's' )
+ {
+ char **ptpt;
+ for( i=0; i<njob; i++ )
+ {
+ ptpt = bpp[i];
+ while( 1 )
+ {
+ if( *ptpt ) free( *ptpt );
+ else break;
+ ptpt++;
+ }
+ free( bpp[i] );
+ }
+ free( bpp );
+ }
+ free( selfscore );
+ free( effarr1 );
+ free( effarr2 );
+ free( indication1 );
+ free( indication2 );
+ if( store_dist ) FreeDoubleMtx( distancemtx );
+}
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ int nlen[M];
+ char **name, **seq;
+ char **mseq1, **mseq2;
+ char **aseq;
+ char **bseq;
+ double *eff;
+ int i;
+ FILE *infp;
+ char c;
+ int alloclen;
+
+ arguments( argc, argv );
+#ifndef enablemultithread
+ nthread = 0;
+#endif
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+ if( njob > M )
+ {
+ fprintf( stderr, "The number of sequences must be < %d\n", M );
+ fprintf( stderr, "Please try the splittbfast program for such large data.\n" );
+ exit( 1 );
+ }
+
+ alloclen = nlenmax*2;
+ seq = AllocateCharMtx( njob, alloclen+10 );
+ aseq = AllocateCharMtx( njob, alloclen+10 );
+ bseq = AllocateCharMtx( njob, alloclen+10 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ name = AllocateCharMtx( njob, B );
+
+ eff = AllocateDoubleVec( njob );
+
+#if 0
+ Read( name, nlen, seq );
+#else
+ readData_pointer( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illegal character %c\n", c );
+ exit( 1 );
+ }
+
+// writePre( njob, name, nlen, seq, 0 );
+
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+
+
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+ pairalign( name, nlen, bseq, aseq, mseq1, mseq2, eff, alloclen );
+
+ fprintf( trap_g, "done.\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+// writePre( njob, name, nlen, aseq, !contin );
+#if 0
+ writeData( stdout, njob, name, nlen, aseq );
+#endif
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+
+ if( stdout_dist && nthread > 1 )
+ {
+ fprintf( stderr, "\nThe order of distances is not identical to that in the input file, because of the parallel calculation. Reorder them by yourself, using sort -n -k 2 | sort -n -k 1 -s\n" );
+ }
+ if( stdout_align && nthread > 1 )
+ {
+ fprintf( stderr, "\nThe order of pairwise alignments is not identical to that in the input file, because of the parallel calculation. Reorder them by yourself.\n" );
+ }
+ FreeCharMtx( seq );
+ FreeCharMtx( aseq );
+ FreeCharMtx( bseq );
+ FreeCharMtx( name );
+ free( mseq1 );
+ free( mseq2 );
+ free( eff );
+
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 1
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define FASTMATCHCALC 1
+
+
+static int impalloclen = 0;
+static float **impmtx = NULL;
+float part_imp_match_out_scQ( int i1, int j1 )
+{
+// fprintf( stderr, "impalloclen = %d\n", impalloclen );
+// fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] );
+ return( impmtx[i1][j1] );
+#if 0
+ if( i1 == l1 || j1 == l2 ) return( 0.0 );
+ return( impmtx[i1+start1][j1+start2] );
+#endif
+}
+static void part_imp_match_out_vead_gapmapQ( float *imp, int i1, int lgth2, int start2, int *gapmap2 )
+{
+#if FASTMACHCALC
+ float *pt = imp;
+ int *gapmappt = gapmap2;
+ while( lgth2-- )
+ *pt++ += impmtx[i1][start2+*gapmappt++];
+#else
+ int j;
+ for( j=0; j<lgth2; j++ )
+ {
+ imp[j] += impmtx[i1][start2+gapmap2[j]];
+ }
+#endif
+}
+
+static void part_imp_match_out_vead_tate_gapmapQ( float *imp, int j1, int lgth1, int start1, int *gapmap1 )
+{
+#if FASTMACHCALC
+ float *pt = imp;
+ int *gapmappt = gapmap1;
+ while( lgth1-- )
+ *pt++ = impmtx[start1+*gapmappt++][j1];
+#else
+ int i;
+ for( i=0; i<lgth1; i++ )
+ {
+ imp[i] += impmtx[start1+gapmap1[i]][j1];
+ }
+#endif
+}
+
+void part_imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
+{
+ int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ double effij, effijx;
+ char *pt, *pt1, *pt2;
+ LocalHom *tmpptr;
+
+ if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen+100, impalloclen+100 );
+ }
+
+
+#if 0
+ fprintf( stderr, "eff1 in _init_strict = \n" );
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "eff1[] = %f\n", eff1[i] );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "eff2[] = %f\n", eff2[i] );
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ effijx = 1.0 * fastathreshold;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ effij = eff1[i] * eff2[j] * effijx;
+ tmpptr = localhom[i][j];
+ while( tmpptr )
+ {
+// fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
+// fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
+// fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
+// fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start1 ) break;
+ }
+ start1 = (int)( pt - seq1[i] ) - 1;
+
+ if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end1 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end1 = (int)( pt - seq1[i] ) - 1;
+#else
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end1 ) break;
+ }
+ end1 = (int)( pt - seq1[i] ) - 1;
+#endif
+ }
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start2 ) break;
+ }
+ start2 = (int)( pt - seq2[j] ) - 1;
+ if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end2 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end2 = (int)( pt - seq2[j] ) - 1;
+#else
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end2 ) break;
+ }
+ end2 = (int)( pt - seq2[j] ) - 1;
+#endif
+ }
+// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
+// fprintf( stderr, "step 0\n" );
+ if( end1 - start1 != end2 - start2 )
+ {
+// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ }
+
+ k1 = start1; k2 = start2;
+ pt1 = seq1[i] + k1;
+ pt2 = seq2[j] + k2;
+ while( *pt1 && *pt2 )
+ {
+ if( *pt1 != '-' && *pt2 != '-' )
+ {
+// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
+// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
+// impmtx[k1][k2] += tmpptr->importance * effij;
+ impmtx[k1][k2] += tmpptr->fimportance * effij;
+// fprintf( stderr, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen );
+// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; k2++;
+ pt1++; pt2++;
+ }
+ else if( *pt1 != '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k2++; pt2++;
+ }
+ else if( *pt1 == '-' && *pt2 != '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ }
+ else if( *pt1 == '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ k2++; pt2++;
+ }
+ if( k1 > end1 || k2 > end2 ) break;
+ }
+ tmpptr = tmpptr->next;
+ }
+ }
+ }
+#if 0
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d", k1 );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+#endif
+}
+
+
+void part_imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *additionalpair )
+{
+ foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, additionalpair );
+}
+
+
+void part_imp_match_initQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
+{
+ int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ static int impalloclen = 0;
+ char *pt;
+ static char *nocount1 = NULL;
+ static char *nocount2 = NULL;
+
+ if( impalloclen < lgth1 || impalloclen < lgth2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ if( nocount1 ) free( nocount1 );
+ if( nocount2 ) free( nocount2 );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+ nocount1 = AllocateCharVec( impalloclen );
+ nocount2 = AllocateCharVec( impalloclen );
+ impalloclen -= 2;
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<clus1; j++ )
+ if( seq1[j][i] == '-' ) break;
+ if( j != clus1 ) nocount1[i] = 1;
+ else nocount1[i] = 0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ if( seq2[j][i] == '-' ) break;
+ if( j != clus2 ) nocount2[i] = 1;
+ else nocount2[i] = 0;
+ }
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+ fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ for( i=0; i<clus1; i++ )
+ {
+ fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
+ for( j=0; j<clus2; j++ )
+ {
+ fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
+ fprintf( stderr, "end1 = %d\n", localhom[i][j]->end1 );
+ fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->start1 ) break;
+ }
+ start1 = pt - seq1[i] - 1;
+
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->end1 ) break;
+ }
+ end1 = pt - seq1[i] - 1;
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->start2 ) break;
+ }
+ start2 = pt - seq2[j] - 1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->end2 ) break;
+ }
+ end2 = pt - seq2[j] - 1;
+// fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ k1 = start1;
+ k2 = start2;
+ fprintf( stderr, "step 0\n" );
+ while( k1 <= end1 && k2 <= end2 )
+ {
+#if 0
+ if( !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+#else
+ if( !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+#endif
+ }
+
+ dif = ( end1 - start1 ) - ( end2 - start2 );
+ fprintf( stderr, "dif = %d\n", dif );
+ if( dif > 0 )
+ {
+ do
+ {
+ fprintf( stderr, "dif = %d\n", dif );
+ k1 = start1;
+ k2 = start2 - dif;
+ while( k1 <= end1 && k2 <= end2 )
+ {
+ if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+ }
+ }
+ while( dif-- );
+ }
+ else
+ {
+ do
+ {
+ k1 = start1 + dif;
+ k2 = start2;
+ while( k1 <= end1 )
+ {
+ if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+ }
+ }
+ while( dif++ );
+ }
+ }
+ }
+#if 0
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d", k1 );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+#endif
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+ int j, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<26; j++ )
+// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+ scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+#else
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ // simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc,
+ int start1, int end1, int start2, int end2,
+ int *gapmap1, int *gapmap2 )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+// char gap[] = "-";
+ char *gap;
+ float wm;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi+l];
+ k++;
+ }
+ if( iin != lgth1 && jin != lgth2 ) // ??
+ {
+ *impwmpt += part_imp_match_out_scQ( gapmap1[iin]+start1, gapmap2[jin]+start2 );
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+}
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk;
+// char gap[] = "-";
+ char *gap;
+ float wm = 0.0;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+ iin = lgth1; jin = lgth2;
+ lastk = lgth1+lgth2;
+ for( k=0; k<=lastk; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ return( 0.0 );
+}
+
+float partQ__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static float mi, *m;
+ static int **ijp;
+ static int mpi, *mp;
+ static float *w1, *w2;
+ static float *match;
+ static float *initverticalw; /* kufuu sureba iranai */
+ static float *lastverticalw; /* kufuu sureba iranai */
+ static char **mseq1;
+ static char **mseq2;
+ static char **mseq;
+ static float *digf1;
+ static float *digf2;
+ static float *diaf1;
+ static float *diaf2;
+ static float *gapz1;
+ static float *gapz2;
+ static float *gapf1;
+ static float *gapf2;
+ static float *ogcp1g;
+ static float *ogcp2g;
+ static float *fgcp1g;
+ static float *fgcp2g;
+ static float *og_h_dg_n1_p;
+ static float *og_h_dg_n2_p;
+ static float *fg_h_dg_n1_p;
+ static float *fg_h_dg_n2_p;
+ static float *og_t_fg_h_dg_n1_p;
+ static float *og_t_fg_h_dg_n2_p;
+ static float *fg_t_og_h_dg_n1_p;
+ static float *fg_t_og_h_dg_n2_p;
+ static float *gapz_n1;
+ static float *gapz_n2;
+ static float **cpmx1;
+ static float **cpmx2;
+ static int **intwork;
+ static float **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+ float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+ float tmppenal;
+ float *fg_t_og_h_dg_n2_p_pt;
+ float *og_t_fg_h_dg_n2_p_pt;
+ float *og_h_dg_n2_p_pt;
+ float *fg_h_dg_n2_p_pt;
+ float *gapz_n2_pt0;
+ float *gapz_n2_pt1;
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fg_t_og_h_dg_n1_p_va;
+ float og_t_fg_h_dg_n1_p_va;
+ float og_h_dg_n1_p_va;
+ float fg_h_dg_n1_p_va;
+ float gapz_n1_va0;
+ float gapz_n1_va1;
+ float fgcp1va;
+ float ogcp1va;
+
+
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( digf1 );
+ FreeFloatVec( digf2 );
+ FreeFloatVec( diaf1 );
+ FreeFloatVec( diaf2 );
+ FreeFloatVec( gapz1 );
+ FreeFloatVec( gapz2 );
+ FreeFloatVec( gapf1 );
+ FreeFloatVec( gapf2 );
+ FreeFloatVec( ogcp1g );
+ FreeFloatVec( ogcp2g );
+ FreeFloatVec( fgcp1g );
+ FreeFloatVec( fgcp2g );
+ FreeFloatVec( og_h_dg_n1_p );
+ FreeFloatVec( og_h_dg_n2_p );
+ FreeFloatVec( fg_h_dg_n1_p );
+ FreeFloatVec( fg_h_dg_n2_p );
+ FreeFloatVec( og_t_fg_h_dg_n1_p );
+ FreeFloatVec( og_t_fg_h_dg_n2_p );
+ FreeFloatVec( fg_t_og_h_dg_n1_p );
+ FreeFloatVec( fg_t_og_h_dg_n2_p );
+ FreeFloatVec( gapz_n1 );
+ FreeFloatVec( gapz_n2 );
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ digf1 = AllocateFloatVec( ll1+2 );
+ digf2 = AllocateFloatVec( ll2+2 );
+ diaf1 = AllocateFloatVec( ll1+2 );
+ diaf2 = AllocateFloatVec( ll2+2 );
+ gapz1 = AllocateFloatVec( ll1+2 );
+ gapz2 = AllocateFloatVec( ll2+2 );
+ gapf1 = AllocateFloatVec( ll1+2 );
+ gapf2 = AllocateFloatVec( ll2+2 );
+ ogcp1g = AllocateFloatVec( ll1+2 );
+ ogcp2g = AllocateFloatVec( ll2+2 );
+ fgcp1g = AllocateFloatVec( ll1+2 );
+ fgcp2g = AllocateFloatVec( ll2+2 );
+ og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ og_t_fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ og_t_fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ fg_t_og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
+ fg_t_og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
+ gapz_n1 = AllocateFloatVec( ll1+2 );
+ gapz_n2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
+ for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
+ getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
+ getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
+ getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
+ getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
+ getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
+ getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
+ getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
+ getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
+ getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
+ }
+
+#if 1
+ lastj = lgth2+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n2_p[i] = ( 1.0-ogcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ fg_h_dg_n2_p[i] = ( 1.0-fgcp2g[i]-digf2[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n2_p[i] = (1.0-ogcp2g[i]+fgcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n2_p[i] = (1.0-fgcp2g[i]+ogcp2g[i]-digf2[i]) * 0.5 * fpenalty;
+ gapz_n2[i] = (1.0-gapz2[i]);
+ }
+ lastj = lgth1+2;
+ for( i=0; i<lastj; i++ )
+ {
+ og_h_dg_n1_p[i] = ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ fg_h_dg_n1_p[i] = ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
+ og_t_fg_h_dg_n1_p[i] = (1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ fg_t_og_h_dg_n1_p[i] = (1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) * 0.5 * fpenalty;
+ gapz_n1[i] = (1.0-gapz1[i]);
+ }
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ if( localhom )
+ part_imp_match_out_vead_tate_gapmapQ( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );
+
+
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ if( localhom )
+ part_imp_match_out_vead_gapmapQ( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 );
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+ if( outgap == 1 )
+ {
+ g = 0.0;
+
+ g += ogcp1g[0] * og_h_dg_n2_p[0];
+
+ g += ogcp2g[0] * og_h_dg_n1_p[0];
+
+ g += fgcp1g[0] * fg_h_dg_n2_p[0];
+
+ g += fgcp2g[0] * fg_h_dg_n1_p[0];
+
+ initverticalw[0] += g;
+ currentw[0] += g;
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+ tmppenal = gapz_n2[0]*og_t_fg_h_dg_n1_p[0];
+ initverticalw[i] += tmppenal;
+
+ tmppenal = gapz_n2[1]*fg_t_og_h_dg_n1_p[i];
+ initverticalw[i] += tmppenal;
+
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ tmppenal = gapz_n1[0]*og_t_fg_h_dg_n2_p[0];
+ currentw[j] += tmppenal;
+
+ tmppenal = gapz_n1[1]*fg_t_og_h_dg_n2_p[j];
+ currentw[j] += tmppenal;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ m[0] = 0.0; // iranai
+ for( j=1; j<lgth2+1; ++j )
+ {
+ mp[j] = 0;
+ m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
+ }
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+ else
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+ lastj = lgth2+1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+// imp_match_out_vead( currentw, i, lgth2 );
+ part_imp_match_out_vead_gapmapQ( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mpi = 0;
+ mi = previousw[0] + 10000 * fpenalty;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fg_t_og_h_dg_n2_p_pt = fg_t_og_h_dg_n2_p + 1;
+ og_t_fg_h_dg_n2_p_pt = og_t_fg_h_dg_n2_p + 1;
+ og_h_dg_n2_p_pt = og_h_dg_n2_p + 1;
+ fg_h_dg_n2_p_pt = fg_h_dg_n2_p + 1;
+ gapz_n2_pt0 = gapz_n2 + 1;
+ gapz_n2_pt1 = gapz_n2 + 2;
+ fgcp2pt = fgcp2g + 1;
+ ogcp2pt = ogcp2g + 1;
+
+ fg_t_og_h_dg_n1_p_va = fg_t_og_h_dg_n1_p[i];
+ og_t_fg_h_dg_n1_p_va = og_t_fg_h_dg_n1_p[i];
+ og_h_dg_n1_p_va = og_h_dg_n1_p[i];
+ fg_h_dg_n1_p_va = fg_h_dg_n1_p[i];
+ gapz_n1_va0 = gapz_n1[i];
+ gapz_n1_va1 = gapz_n1[i+1];
+ fgcp1va = fgcp1g[i];
+ ogcp1va = ogcp1g[i];
+
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+
+ g = ogcp1va * *og_h_dg_n2_p_pt;
+ wm += g;
+
+ g = *ogcp2pt * og_h_dg_n1_p_va;
+ wm += g;
+
+ g = fgcp1va * *fg_h_dg_n2_p_pt;
+ wm += g;
+
+ g = *fgcp2pt * fg_h_dg_n1_p_va;
+ wm += g;
+
+ *ijppt = 0;
+
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ tmppenal = gapz_n1_va1 * *fg_t_og_h_dg_n2_p_pt;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+tmppenal) > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+
+ tmppenal = gapz_n1_va0 * *og_t_fg_h_dg_n2_p_pt;
+ if( (g=*prept+tmppenal) >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ tmppenal = *gapz_n2_pt1 * fg_t_og_h_dg_n1_p_va;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt+tmppenal) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+
+ tmppenal = *gapz_n2_pt0 * og_t_fg_h_dg_n1_p_va;
+ if( (g=*prept+tmppenal) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ fg_t_og_h_dg_n2_p_pt++;
+ og_t_fg_h_dg_n2_p_pt++;
+ og_h_dg_n2_p_pt++;
+ fg_h_dg_n2_p_pt++;
+ gapz_n2_pt0++;
+ gapz_n2_pt1++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2 );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+
+ return( wm );
+}
+
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 1
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+#define FASTMATCHCALC 1
+
+#if 0
+static void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = 0;
+ for( i=0; i<len; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( !gb * gc ) ogcp[i] += feff;
+ }
+ }
+ }
+}
+
+static void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+ int i, j, gc, gb;
+ float feff;
+
+ for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+ for( j=0; j<clus; j++ )
+ {
+ feff = (float)eff[j];
+ gc = ( seq[j][0] == '-' );
+ for( i=1; i<len+1; i++ )
+ {
+ gb = gc;
+ gc = ( seq[j][i] == '-' );
+ {
+ if( gb * !gc ) fgcp[i-1] += feff;
+ }
+ }
+ }
+}
+#endif
+
+
+
+
+
+static TLS int impalloclen = 0;
+static TLS float **impmtx = NULL;
+float part_imp_match_out_sc( int i1, int j1 )
+{
+// fprintf( stderr, "impalloclen = %d\n", impalloclen );
+// fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] );
+ return( impmtx[i1][j1] );
+#if 0
+ if( i1 == l1 || j1 == l2 ) return( 0.0 );
+ return( impmtx[i1+start1][j1+start2] );
+#endif
+}
+static void part_imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int start2, int *gapmap2 )
+{
+#if FASTMACHCALC
+ float *pt = imp;
+ int *gapmappt = gapmap2;
+ while( lgth2-- )
+ *pt++ += impmtx[i1][start2+*gapmappt++];
+#else
+ int j;
+ for( j=0; j<lgth2; j++ )
+ {
+ imp[j] += impmtx[i1][start2+gapmap2[j]];
+ }
+#endif
+}
+
+static void part_imp_match_out_vead_tate_gapmap( float *imp, int j1, int lgth1, int start1, int *gapmap1 )
+{
+#if FASTMACHCALC
+ float *pt = imp;
+ int *gapmappt = gapmap1;
+ while( lgth1-- )
+ *pt++ = impmtx[start1+*gapmappt++][j1];
+#else
+ int i;
+ for( i=0; i<lgth1; i++ )
+ {
+ imp[i] += impmtx[start1+gapmap1[i]][j1];
+ }
+#endif
+}
+
+void part_imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore )
+{
+ int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ double effij, effijx, effij_kozo;
+ char *pt, *pt1, *pt2;
+ LocalHom *tmpptr;
+
+ if( seq1 == NULL )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ impmtx = NULL;
+ return;
+ }
+
+ if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen+100, impalloclen+100 );
+ }
+
+
+#if 0
+ fprintf( stderr, "eff1 in _init_strict = \n" );
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "eff1[] = %f\n", eff1[i] );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "eff2[] = %f\n", eff2[i] );
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ effijx = 1.0 * fastathreshold;
+ for( i=0; i<clus1; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ {
+ effij = eff1[i] * eff2[j] * effijx;
+ effij_kozo = eff1_kozo[i] * eff2_kozo[j] * effijx;
+ tmpptr = localhom[i][j];
+ while( tmpptr )
+ {
+// fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
+// fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
+// fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
+// fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start1 ) break;
+ }
+ start1 = (int)( pt - seq1[i] ) - 1;
+
+ if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end1 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end1 = (int)( pt - seq1[i] ) - 1;
+#else
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end1 ) break;
+ }
+ end1 = (int)( pt - seq1[i] ) - 1;
+#endif
+ }
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->start2 ) break;
+ }
+ start2 = (int)( pt - seq2[j] ) - 1;
+ if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
+ else
+ {
+#if MACHIGAI
+ while( *pt != 0 )
+ {
+ if( tmpint == tmpptr->end2 ) break;
+ if( *pt++ != '-' ) tmpint++;
+ }
+ end2 = (int)( pt - seq2[j] ) - 1;
+#else
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == tmpptr->end2 ) break;
+ }
+ end2 = (int)( pt - seq2[j] ) - 1;
+#endif
+ }
+// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
+// fprintf( stderr, "step 0\n" );
+ if( end1 - start1 != end2 - start2 )
+ {
+// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ }
+
+ k1 = start1; k2 = start2;
+ pt1 = seq1[i] + k1;
+ pt2 = seq2[j] + k2;
+ while( *pt1 && *pt2 )
+ {
+ if( *pt1 != '-' && *pt2 != '-' )
+ {
+// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
+// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
+// impmtx[k1][k2] += tmpptr->importance * effij;
+// impmtx[k1][k2] += tmpptr->fimportance * effij;
+ if( tmpptr->korh == 'k' )
+ impmtx[k1][k2] += tmpptr->fimportance * effij_kozo;
+ else
+ impmtx[k1][k2] += tmpptr->fimportance * effij;
+// fprintf( stderr, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen );
+// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; k2++;
+ pt1++; pt2++;
+ }
+ else if( *pt1 != '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k2++; pt2++;
+ }
+ else if( *pt1 == '-' && *pt2 != '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ }
+ else if( *pt1 == '-' && *pt2 == '-' )
+ {
+// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+ k1++; pt1++;
+ k2++; pt2++;
+ }
+ if( k1 > end1 || k2 > end2 ) break;
+ }
+ tmpptr = tmpptr->next;
+ }
+ }
+ }
+#if 0
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d", k1 );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+#endif
+}
+
+
+void part_imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *additionalpair )
+{
+ foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, additionalpair );
+}
+
+
+void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
+{
+ int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
+ static TLS int impalloclen = 0;
+ char *pt;
+ static TLS char *nocount1 = NULL;
+ static TLS char *nocount2 = NULL;
+
+ if( impalloclen < lgth1 || impalloclen < lgth2 )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ if( nocount1 ) free( nocount1 );
+ if( nocount2 ) free( nocount2 );
+ impalloclen = MAX( lgth1, lgth2 ) + 2;
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+ nocount1 = AllocateCharVec( impalloclen );
+ nocount2 = AllocateCharVec( impalloclen );
+ impalloclen -= 2;
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<clus1; j++ )
+ if( seq1[j][i] == '-' ) break;
+ if( j != clus1 ) nocount1[i] = 1;
+ else nocount1[i] = 0;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ for( j=0; j<clus2; j++ )
+ if( seq2[j][i] == '-' ) break;
+ if( j != clus2 ) nocount2[i] = 1;
+ else nocount2[i] = 0;
+ }
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+ fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ impmtx[i][j] = 0.0;
+ for( i=0; i<clus1; i++ )
+ {
+ fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
+ for( j=0; j<clus2; j++ )
+ {
+ fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
+ fprintf( stderr, "end1 = %d\n", localhom[i][j]->end1 );
+ fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
+ pt = seq1[i];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->start1 ) break;
+ }
+ start1 = pt - seq1[i] - 1;
+
+ while( *pt != 0 )
+ {
+// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->end1 ) break;
+ }
+ end1 = pt - seq1[i] - 1;
+
+ pt = seq2[j];
+ tmpint = -1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->start2 ) break;
+ }
+ start2 = pt - seq2[j] - 1;
+ while( *pt != 0 )
+ {
+ if( *pt++ != '-' ) tmpint++;
+ if( tmpint == localhom[i][j]->end2 ) break;
+ }
+ end2 = pt - seq2[j] - 1;
+// fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+ k1 = start1;
+ k2 = start2;
+ fprintf( stderr, "step 0\n" );
+ while( k1 <= end1 && k2 <= end2 )
+ {
+#if 0
+ if( !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+#else
+ if( !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+#endif
+ }
+
+ dif = ( end1 - start1 ) - ( end2 - start2 );
+ fprintf( stderr, "dif = %d\n", dif );
+ if( dif > 0 )
+ {
+ do
+ {
+ fprintf( stderr, "dif = %d\n", dif );
+ k1 = start1;
+ k2 = start2 - dif;
+ while( k1 <= end1 && k2 <= end2 )
+ {
+ if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+ }
+ }
+ while( dif-- );
+ }
+ else
+ {
+ do
+ {
+ k1 = start1 + dif;
+ k2 = start2;
+ while( k1 <= end1 )
+ {
+ if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
+ impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
+ k1++; k2++;
+ }
+ }
+ while( dif++ );
+ }
+ }
+ }
+#if 0
+ fprintf( stderr, "impmtx = \n" );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", (double)k2 );
+ fprintf( stderr, "\n" );
+ for( k1=0; k1<lgth1; k1++ )
+ {
+ fprintf( stderr, "%d", k1 );
+ for( k2=0; k2<lgth2; k2++ )
+ fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+#endif
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+ int j, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<26; j++ )
+ scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+#else
+ int j, k, l;
+ float scarr[26];
+ float **cpmxpd = floatwork;
+ int **cpmxpdn = intwork;
+ // simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<26; l++ )
+ {
+ if( cpmx2[l][j] )
+ {
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
+ }
+ }
+ cpmxpdn[count][j] = -1;
+ }
+ }
+ for( l=0; l<26; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<26; k++ )
+ scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[k][j]>-1; k++ )
+ match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+ }
+#endif
+}
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc,
+ int start1, int end1, int start2, int end2,
+ int *gapmap1, int *gapmap2 )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+// char gap[] = "-";
+ char *gap;
+ float wm;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+ iin = lgth1; jin = lgth2;
+ *impwmpt = 0.0;
+ for( k=0; k<=lgth1+lgth2; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi+l];
+ k++;
+ }
+ if( iin != lgth1 && jin != lgth2 ) // ??
+ {
+ *impwmpt += part_imp_match_out_sc( gapmap1[iin]+start1, gapmap2[jin]+start2 );
+// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+}
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp, int icyc, int jcyc )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk;
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ float wm = 0.0;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ if( outgap == 1 )
+ ;
+ else
+ {
+ wm = lastverticalw[0];
+ for( i=0; i<lgth1; i++ )
+ {
+ if( lastverticalw[i] >= wm )
+ {
+ wm = lastverticalw[i];
+ iin = i; jin = lgth2-1;
+ ijp[lgth1][lgth2] = +( lgth1 - i );
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ if( lasthorizontalw[j] >= wm )
+ {
+ wm = lasthorizontalw[j];
+ iin = lgth1-1; jin = j;
+ ijp[lgth1][lgth2] = -( lgth2 - j );
+ }
+ }
+ }
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+ for( i=0; i<icyc; i++ )
+ {
+ mseq1[i] += lgth1+lgth2;
+ *mseq1[i] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ mseq2[j] += lgth1+lgth2;
+ *mseq2[j] = 0;
+ }
+ iin = lgth1; jin = lgth2;
+ lastk = lgth1+lgth2;
+ for( k=0; k<=lastk; k++ )
+ {
+ if( ijp[iin][jin] < 0 )
+ {
+ ifi = iin-1; jfi = jin+ijp[iin][jin];
+ }
+ else if( ijp[iin][jin] > 0 )
+ {
+ ifi = iin-ijp[iin][jin]; jfi = jin-1;
+ }
+ else
+ {
+ ifi = iin-1; jfi = jin-1;
+ }
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ return( 0.0 );
+}
+
+float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *ogcp1;
+ static TLS float *ogcp2;
+ static TLS float *fgcp1;
+ static TLS float *fgcp2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+ float *fgcp2pt;
+ float *ogcp2pt;
+ float fgcp1va;
+ float ogcp1va;
+
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 )
+ {
+// fprintf( stderr, "## Freeing local arrays in A__align\n" );
+ orlgth1 = 0;
+ orlgth2 = 0;
+
+ part_imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
+
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ }
+ else
+ {
+// fprintf( stderr, "## Not allocated\n" );
+ }
+ return( 0.0 );
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 1
+ if( lgth1 == 0 ) fprintf( stderr, "WARNING: lgth1=0 in partA__align\n" );
+ if( lgth2 == 0 ) fprintf( stderr, "WARNING: lgth2=0 in partA__align\n" );
+
+ if( lgth1 == 0 && lgth2 == 0 )
+ return( 0.0 );
+
+ if( lgth1 == 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ {
+ j = lgth2;
+ seq1[i][j] = 0;
+ while( j ) seq1[i][--j] = '-';
+// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+ }
+ return( 0.0 );
+ }
+
+ if( lgth2 == 0 )
+ {
+ for( i=0; i<jcyc; i++ )
+ {
+ j = lgth1;
+ seq2[i][j] = 0;
+ while( j ) seq2[i][--j] = '-';
+// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+ }
+ return( 0.0 );
+ }
+#endif
+
+#if 0
+ fprintf( stderr, "eff in SA+++align\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+ floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+#else
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+#endif
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
+ for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+ cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+ if( sgap1 )
+ {
+ new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+ new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+ new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
+ new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+ st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+ }
+
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+ }
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ if( localhom )
+ part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );
+
+
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ if( localhom )
+ part_imp_match_out_vead_gapmap( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 );
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+ if( outgap == 1 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ }
+ }
+#if OUTGAP0TRY
+ else
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * j / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ initverticalw[i] -= offset * i / 2.0;
+ }
+#endif
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+ lastj = lgth2+1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! i\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+// imp_match_out_vead( currentw, i, lgth2 );
+ part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
+ }
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+
+ mi = previousw[0] + ogcp2[1]; mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ fgcp2pt = fgcp2;
+ ogcp2pt = ogcp2+1;
+ fgcp1va = fgcp1[i-1];
+ ogcp1va = ogcp1[i];
+ for( j=1; j<lastj; j++ )
+ {
+#ifdef xxxenablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! j\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + *fgcp2pt;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + *ogcp2pt;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fgcp1va;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + ogcp1va;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ fgcp2pt++;
+ ogcp2pt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+ }
+
+#if OUTGAP0TRY
+ if( !outgap )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+ for( i=1; i<lgth1+1; i++ )
+ lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
+ }
+#endif
+
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+ fprintf( stderr, "====>" );
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+ */
+ if( localhom )
+ {
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2 );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ /*
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "#####\n" );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+ */
+
+
+ return( wm );
+}
+
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+char *regfile;
+char *eregfile;
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ outnumber = 0;
+ inputfile = NULL;
+ regfile = NULL;
+ eregfile = NULL;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'e':
+ eregfile = *++argv;
+ fprintf( stderr, "eregfile = %s\n", eregfile );
+ --argc;
+ goto nextoption;
+ case 'r':
+ regfile = *++argv;
+ fprintf( stderr, "regfile = %s\n", regfile );
+ --argc;
+ goto nextoption;
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'n' :
+ outnumber = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+void readereg( FILE *regfp, int **regtable, char **revtable, int *outtable, int *noutpt, int *loutpt )
+{
+ char gett[1000];
+ int j;
+ int mem;
+ char cmem;
+ char reg[5][100];
+ char out[100];
+ int startpos, endpos;
+
+ *noutpt = 0;
+ *loutpt = 0;
+ fgets( gett, 999, regfp );
+ sscanf( gett, "%c %s %s %s %s %s", &cmem, reg[0], reg[1], reg[2], reg[3], reg[4] );
+ if( cmem != 'e' )
+ {
+ fprintf( stderr, "Format error\n" );
+ exit( 1 );
+ }
+ for( j=0; j<5; j++ )
+ {
+ sscanf( reg[j], "%d-%d-%c", regtable[0]+(j*2), regtable[0]+(j*2)+1, revtable[0]+j );
+ fprintf( stderr, "%d %d-%d\n", 0, regtable[0][j*2], regtable[0][j*2+1] );
+ startpos = regtable[0][j*2];
+ endpos = regtable[0][j*2+1];
+ if( startpos > endpos )
+ {
+ endpos = regtable[0][j*2];
+ startpos = regtable[0][j*2+1];
+ }
+ if( startpos != -1 && endpos != -1 )
+ *loutpt += endpos - startpos + 1;
+ }
+
+ while( 1 )
+ {
+ fgets( gett, 999, regfp );
+ if( feof( regfp ) ) break;
+ sscanf( gett, "%d o=%s", &mem, out );
+ if( mem >= njob )
+ {
+ fprintf( stderr, "Out of range\n" );
+ exit( 1 );
+ }
+ outtable[mem] = atoi( out );
+ if( outtable[mem] ) *noutpt += 1;
+ }
+}
+
+void readreg( FILE *regfp, int **regtable, char **revtable, int *outtable )
+{
+ char gett[1000];
+ int j;
+ int mem;
+ char reg[5][100];
+ char out[100];
+
+ while( 1 )
+ {
+ fgets( gett, 999, regfp );
+ if( feof( regfp ) ) break;
+ sscanf( gett, "%d %s %s %s %s %s o=%s", &mem, reg[0], reg[1], reg[2], reg[3], reg[4], out );
+ if( mem >= njob )
+ {
+ fprintf( stderr, "Out of range\n" );
+ exit( 1 );
+ }
+ for( j=0; j<5; j++ )
+ {
+ sscanf( reg[j], "%d-%d-%c", regtable[mem]+(j*2), regtable[mem]+(j*2)+1, revtable[mem]+j );
+ fprintf( stderr, "%d %d-%d\n", mem, regtable[mem][j*2], regtable[mem][j*2+1] );
+ }
+ outtable[mem] = atoi( out );
+ }
+}
+
+int main( int argc, char *argv[] )
+{
+ FILE *infp;
+ FILE *regfp;
+ int nlenmin;
+ int **regtable;
+ char **revtable;
+ int *outtable;
+ int i, nout, lout;
+ char **outseq;
+ char **name;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ dorp = NOTSPECIFIED;
+ getnumlen_nogap( infp, &nlenmin );
+
+ if( regfile )
+ {
+ regfp = fopen( regfile, "r" );
+ if( !regfp )
+ {
+ fprintf( stderr, "Cannot open %s\n", regfile );
+ exit( 1 );
+ }
+ regtable = AllocateIntMtx( njob, 5*2 );
+ revtable = AllocateCharMtx( njob, 5 );
+ outtable = AllocateIntVec( njob );
+ readreg( regfp, regtable, revtable, outtable );
+ cutData( infp, regtable, revtable, outtable );
+ }
+ else if( eregfile )
+ {
+ regfp = fopen( eregfile, "r" );
+ if( !regfp )
+ {
+ fprintf( stderr, "Cannot open %s\n", eregfile );
+ exit( 1 );
+ }
+ regtable = AllocateIntMtx( 1, 5*2 );
+ revtable = AllocateCharMtx( 1, 5 );
+ outtable = AllocateIntVec( njob );
+ readereg( regfp, regtable, revtable, outtable, &nout, &lout );
+ fprintf( stderr, "nout = %d, lout = %d\n", nout, lout );
+
+ outseq = AllocateCharMtx( nout, lout+1 );
+ name = AllocateCharMtx( nout, B );
+
+ cutAlignment( infp, regtable, revtable, outtable, name, outseq );
+ fprintf( stderr, "gappick! nout = %d\n", nout );
+ commongappick( nout, outseq );
+ for( i=0; i<nout; i++ )
+ {
+ fprintf( stdout, "%s\n", name[i] );
+ fprintf( stdout, "%s\n", outseq[i] );
+ }
+ }
+ else
+ {
+ catData( infp );
+ }
+
+ fprintf( stderr, "Strategy:\n" );
+ fprintf( stderr, " Not-Aligned\n" );
+
+// fprintf( stdout, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+static int seedoffset;
+
+static void replace_unusual( int n, char **seq, char *usual, char unknown, int (*uporlow)( int ) )
+{
+ int i;
+ char *pt;
+ for( i=0; i<n; i++ )
+ {
+ pt = seq[i];
+ while( *pt )
+ {
+ if( !strchr( usual, *pt ) ) *pt = unknown;
+ else *pt = uporlow( *pt );
+ pt++;
+ }
+ }
+}
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ seedoffset = 0;
+ inputfile = NULL;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'o':
+ seedoffset = atoi( *++argv );
+ fprintf( stderr, "seedoffset = %d\n", seedoffset );
+ --argc;
+ goto nextoption;
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+
+
+int main( int argc, char *argv[] )
+{
+ FILE *infp;
+ int nlenmin;
+ char **name;
+ char **seq;
+ int *nlen;
+ int i;
+ char *usual;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+
+ dorp = NOTSPECIFIED;
+ getnumlen_casepreserve( infp, &nlenmin );
+
+ fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+
+ readData_pointer_casepreserve( infp, name, nlen, seq );
+
+// for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
+
+#if 0
+ FILE *origfp;
+ origfp = fopen( "_original", "w" );
+ if( !origfp )
+ {
+ fprintf( stderr, "Cannot open _original\n" );
+ exit( 1 );
+ }
+ for( i=0; i<njob; i++ )
+ {
+ nlen[i] = strlen( seq[i] );
+ fprintf( origfp, ">%s\n", name[i]+1 );
+ if( seq[i][nlen[i]-1] == '\n' ) seq[i][nlen[i]-1] = 0;
+ fprintf( origfp, "%s\n", seq[i] );
+ }
+ fclose( origfp );
+#endif
+
+ if( dorp == 'p' )
+ {
+ usual = "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv-.";
+ replace_unusual( njob, seq, usual, 'X', toupper );
+ }
+ else
+ {
+ usual = "ATGCUatgcu-";
+ replace_unusual( njob, seq, usual, 'n', tolower );
+ }
+
+
+
+ for( i=0; i<njob; i++ )
+ {
+ fprintf( stdout, ">%d_oripos_%s\n", i+seedoffset, name[i] );
+ fprintf( stdout, "%s\n", seq[i] );
+ }
+
+ free( nlen );
+ FreeCharMtx( seq );
+ FreeCharMtx( name );
+
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+char *alignmentfile;
+
+static void fillorichar( int nseq, int *oripos, char **a, char **s )
+{
+ int i;
+ char *pta, *pts;
+ for( i=0; i<nseq; i++ )
+ {
+ pta = a[i];
+ pts = s[oripos[i]];
+ while( *pta )
+ {
+ if( *pta != '-' ) *pta = *pts++;
+ if( *pta++ == 0 )
+ {
+ fprintf( stderr, "ERROR!!\n" );
+ fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
+ exit( 1 );
+ }
+ }
+ if( *pts != 0 )
+ {
+ fprintf( stderr, "ERROR!!\n" );
+ fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
+ exit( 1 );
+ }
+ }
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ --argc;
+ goto nextoption;
+ case 'a':
+ alignmentfile = *++argv;
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+
+
+int main( int argc, char *argv[] )
+{
+ FILE *infp;
+ FILE *alfp;
+ char **name;
+ char **aname;
+ char **oname;
+ char **seq;
+ char **aseq;
+ int *nlen;
+ int *oripos;
+ char *npt, *npt2;
+ int i, o, prelen;
+ int nlenmin;
+ int njobs, njoba;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ if( alignmentfile )
+ {
+ alfp = fopen( alignmentfile, "r" );
+ if( !alfp )
+ {
+ fprintf( stderr, "Cannot open %s\n", alignmentfile );
+ exit( 1 );
+ }
+ }
+ else
+ {
+ fprintf( stderr, "No alignment is given.\n" );
+ exit( 1 );
+ }
+
+ dorp = NOTSPECIFIED;
+ getnumlen_casepreserve( infp, &nlenmin );
+ njobs = njob;
+// fprintf( stderr, "in infp, %d x %d - %d %c\n", njob, nlenmin, nlenmax, dorp );
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+ oripos = AllocateIntVec( njob );
+ readData_pointer_casepreserve( infp, name, nlen, seq );
+
+ dorp = NOTSPECIFIED;
+ getnumlen( alfp );
+ njoba = njob;
+// fprintf( stderr, "in alfp, %d x %d %c\n", njob, nlenmax, dorp );
+ aseq = AllocateCharMtx( njob, nlenmax+1 );
+ aname = AllocateCharMtx( njob, B+1 );
+ oname = AllocateCharMtx( njob, B+1 );
+ readData_pointer( alfp, aname, nlen, aseq );
+
+ for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
+
+ if( njoba != njobs )
+ {
+ fprintf( stderr, "ERROR!!\n" );
+ fprintf( stderr, "In input file,\n" );
+ fprintf( stderr, "njob = %d\n", njobs );
+ fprintf( stderr, "but in alignment file,\n" );
+ fprintf( stderr, "njob = %d\n", njoba );
+ exit( 1 );
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+#if 0
+ if( strstr( aname[i], "_seed_" ) )
+ {
+ npt2 = aname[i] + 7;
+ strcpy( oname[i], "=_seed_" );
+ }
+ else
+ {
+ npt2 = aname[i] + 1;
+ strcpy( oname[i], "=" );
+ }
+
+ fprintf( stderr, "npt2 = %s\n", npt2 );
+
+ o = oripos[i] = atoi( npt2 );
+ npt = strstr( npt2, "_oripos_" );
+ if( npt == NULL )
+ {
+ fprintf( stderr, "Format error!\n" );
+ exit( 1 );
+ }
+ npt += 8;
+ strcat( oname[i], npt+1 );
+#endif
+ npt = strstr( aname[i], "_oripos_" );
+ if( npt == NULL )
+ {
+ fprintf( stderr, "Format error!\n" );
+ exit( 1 );
+ }
+ npt2 = npt - 2;
+ while( isdigit( *npt2-- ) );
+ npt2 += 2;
+ npt += 8;
+ o = oripos[i] = atoi( npt2 );
+// fprintf( stderr, "npt2 = :%s:\n", npt2 );
+// fprintf( stderr, "npt = :%s:\n", npt );
+// fprintf( stderr, "aname[i] = :%s:\n", aname[i] );
+// fprintf( stderr, "npt2-aname[i] = :%d:\n", npt2-aname[i] );
+
+ prelen = npt2-aname[i];
+ strncpy( oname[i], aname[i], prelen ); oname[i][prelen] = 0;
+ strcat( oname[i], npt+1 );
+
+ if( strncmp( npt, name[o], 10 ) )
+ {
+ fprintf( stderr, "ERROR!!\n" );
+ fprintf( stderr, "In input file,\n" );
+ fprintf( stderr, "name[%d] = %s\n", o, name[o] );
+ fprintf( stderr, "but in alignment file,\n" );
+ fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
+ exit( 1 );
+ }
+#if 0
+ else
+ {
+ fprintf( stderr, "OK!!\n" );
+ fprintf( stderr, "In input file,\n" );
+ fprintf( stderr, "name[%d] = %s\n", o, name[o] );
+ fprintf( stderr, "and in alignment file,\n" );
+ fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
+ fprintf( stderr, "\n" );
+ }
+#endif
+ }
+// fprintf( stderr, "seq[0] = %s\n", seq[0] );
+// fprintf( stderr, "aseq[0] = %s\n", aseq[0] );
+
+ fillorichar( njob, oripos, aseq, seq );
+
+
+ writeData_pointer( stdout, njob, oname, nlen, aseq );
+
+ FreeCharMtx( seq );
+ FreeCharMtx( aseq );
+ FreeCharMtx( name );
+ FreeCharMtx( aname );
+ free( nlen );
+
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define MEMSAVE 1
+
+#define DEBUG 1
+#define USE_PENALTY_EX 1
+#define STOREWM 1
+
+
+
+static float singleribosumscore( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2 )
+{
+ float val;
+ int i, j;
+ int code1, code2;
+
+ val = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ code1 = amino_n[(int)s1[i][p1]];
+ if( code1 > 3 ) code1 = 36;
+ code2 = amino_n[(int)s2[j][p2]];
+ if( code2 > 3 ) code2 = 36;
+
+// fprintf( stderr, "'l'%c-%c: %f\n", s1[i][p1], s2[j][p2], (float)ribosumdis[code1][code2] );
+
+ val += (float)ribosumdis[code1][code2] * eff1[i] * eff2[j];
+ }
+ return( val );
+}
+static float pairedribosumscore53( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2, int c1, int c2 )
+{
+ float val;
+ int i, j;
+ int code1o, code1u, code2o, code2u, code1, code2;
+
+ val = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ code1o = amino_n[(int)s1[i][p1]];
+ code1u = amino_n[(int)s1[i][c1]];
+ if( code1o > 3 ) code1 = code1o = 36;
+ else if( code1u > 3 ) code1 = 36;
+ else code1 = 4 + code1o * 4 + code1u;
+
+ code2o = amino_n[(int)s2[j][p2]];
+ code2u = amino_n[(int)s2[j][c2]];
+ if( code2o > 3 ) code2 = code1o = 36;
+ else if( code2u > 3 ) code2 = 36;
+ else code2 = 4 + code2o * 4 + code2u;
+
+
+// fprintf( stderr, "%c%c-%c%c: %f\n", s1[i][p1], s1[i][c1], s2[j][p2], s2[j][c2], (float)ribosumdis[code1][code2] );
+
+ if( code1 == 36 || code2 == 36 )
+ val += (float)n_dis[code1o][code2o] * eff1[i] * eff2[j];
+ else
+ val += (float)ribosumdis[code1][code2] * eff1[i] * eff2[j];
+ }
+ return( val );
+}
+
+static float pairedribosumscore35( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2, int c1, int c2 )
+{
+ float val;
+ int i, j;
+ int code1o, code1u, code2o, code2u, code1, code2;
+
+ val = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ code1o = amino_n[(int)s1[i][p1]];
+ code1u = amino_n[(int)s1[i][c1]];
+ if( code1o > 3 ) code1 = code1o = 36;
+ else if( code1u > 3 ) code1 = 36;
+ else code1 = 4 + code1u * 4 + code1o;
+
+ code2o = amino_n[(int)s2[j][p2]];
+ code2u = amino_n[(int)s2[j][c2]];
+ if( code2o > 3 ) code2 = code1o = 36;
+ else if( code2u > 3 ) code2 = 36;
+ else code2 = 4 + code2u * 4 + code2o;
+
+
+// fprintf( stderr, "%c%c-%c%c: %f\n", s1[i][p1], s1[i][c1], s2[j][p2], s2[j][c2], (float)ribosumdis[code1][code2] );
+
+ if( code1 == 36 || code2 == 36 )
+ val += (float)n_dis[code1o][code2o] * eff1[i] * eff2[j];
+ else
+ val += (float)ribosumdis[code1][code2] * eff1[i] * eff2[j];
+ }
+ return( val );
+}
+
+
+static void mccaskillextract( char **seq, char **nogap, int nseq, RNApair **pairprob, RNApair ***single, int **sgapmap, double *eff )
+{
+ int lgth;
+ int nogaplgth;
+ int i, j;
+ int left, right, adpos;
+ float prob;
+ static TLS int *pairnum;
+ RNApair *pt, *pt2;
+
+ lgth = strlen( seq[0] );
+ pairnum = calloc( lgth, sizeof( int ) );
+ for( i=0; i<lgth; i++ ) pairnum[i] = 0;
+
+ for( i=0; i<nseq; i++ )
+ {
+ nogaplgth = strlen( nogap[i] );
+ for( j=0; j<nogaplgth; j++ ) for( pt=single[i][j]; pt->bestpos!=-1; pt++ )
+ {
+ left = sgapmap[i][j];
+ right = sgapmap[i][pt->bestpos];
+ prob = pt->bestscore;
+
+
+ for( pt2=pairprob[left]; pt2->bestpos!=-1; pt2++ )
+ if( pt2->bestpos == right ) break;
+
+// fprintf( stderr, "i,j=%d,%d, left=%d, right=%d, pt=%d, pt2->bestpos = %d\n", i, j, left, right, pt-single[i][j], pt2->bestpos );
+ if( pt2->bestpos == -1 )
+ {
+ pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
+ adpos = pairnum[left];
+ pairnum[left]++;
+ pairprob[left][adpos].bestscore = 0.0;
+ pairprob[left][adpos].bestpos = right;
+ pairprob[left][adpos+1].bestscore = -1.0;
+ pairprob[left][adpos+1].bestpos = -1;
+ pt2 = pairprob[left]+adpos;
+ }
+ else
+ adpos = pt2-pairprob[left];
+
+ pt2->bestscore += prob * eff[i];
+
+ if( pt2->bestpos != right )
+ {
+ fprintf( stderr, "okashii!\n" );
+ exit( 1 );
+ }
+// fprintf( stderr, "adding %d-%d, %f\n", left, right, prob );
+// fprintf( stderr, "pairprob[0][0].bestpos=%d\n", pairprob[0][0].bestpos );
+// fprintf( stderr, "pairprob[0][0].bestscore=%f\n", pairprob[0][0].bestscore );
+ }
+ }
+
+// fprintf( stderr, "before taikakuka\n" );
+ for( i=0; i<lgth; i++ ) for( j=0; j<pairnum[i]; j++ )
+ {
+ if( pairprob[i][j].bestpos > -1 )
+ {
+// pairprob[i][j].bestscore /= (float)nseq;
+// fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, pairprob[i][j].bestpos, pairprob[i][j].bestscore, seq[0][i], seq[0][pairprob[i][j].bestpos] );
+ }
+ }
+
+#if 0
+ for( i=0; i<lgth; i++ ) for( j=0; j<pairnum[i]; j++ )
+ {
+ right=pairprob[i][j].bestpos;
+ if( right < i ) continue;
+ fprintf( stderr, "no%d-%d, adding %d -> %d\n", i, j, right, i );
+ pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
+ pairprob[right][pairnum[right]].bestscore = pairprob[i][j].bestscore;
+ pairprob[right][pairnum[right]].bestpos = i;
+ pairnum[right]++;
+ pairprob[right][pairnum[right]].bestscore = -1.0;
+ pairprob[right][pairnum[right]].bestpos = -1;
+ }
+#endif
+
+ free( pairnum );
+
+}
+
+
+void rnaalifoldcall( char **seq, int nseq, RNApair **pairprob )
+{
+ int lgth;
+ int i;
+ static TLS int *order = NULL;
+ static TLS char **name = NULL;
+ char gett[1000];
+ FILE *fp;
+ int left, right, dumm;
+ float prob;
+ static TLS int pid;
+ static TLS char fnamein[100];
+ static TLS char cmd[1000];
+ static TLS int *pairnum;
+
+ lgth = strlen( seq[0] );
+ if( order == NULL )
+ {
+ pid = (int)getpid();
+ sprintf( fnamein, "/tmp/_rnaalifoldin.%d", pid );
+ order = AllocateIntVec( njob );
+ name = AllocateCharMtx( njob, 10 );
+ for( i=0; i<njob; i++ )
+ {
+ order[i] = i;
+ sprintf( name[i], "seq%d", i );
+ }
+ }
+ pairnum = calloc( lgth, sizeof( int ) );
+ for( i=0; i<lgth; i++ ) pairnum[i] = 0;
+
+ fp = fopen( fnamein, "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open /tmp/_rnaalifoldin\n" );
+ exit( 1 );
+ }
+ clustalout_pointer( fp, nseq, lgth, seq, name, NULL, NULL, order, 15 );
+ fclose( fp );
+
+ sprintf( cmd, "RNAalifold -p %s", fnamein );
+ system( cmd );
+
+ fp = fopen( "alifold.out", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open /tmp/_rnaalifoldin\n" );
+ exit( 1 );
+ }
+
+#if 0
+ for( i=0; i<lgth; i++ ) // atode kesu
+ {
+ pairprob[i] = (RNApair *)realloc( pairprob[i], (2) * sizeof( RNApair ) ); // atode kesu
+ pairprob[i][1].bestscore = -1.0;
+ pairprob[i][1].bestpos = -1;
+ }
+#endif
+
+ while( 1 )
+ {
+ fgets( gett, 999, fp );
+ if( gett[0] == '(' ) break;
+ if( gett[0] == '{' ) break;
+ if( gett[0] == '.' ) break;
+ if( gett[0] == ',' ) break;
+ if( gett[0] != ' ' ) continue;
+
+ sscanf( gett, "%d %d %d %f", &left, &right, &dumm, &prob );
+ left--;
+ right--;
+
+
+#if 0
+ if( prob > 50.0 && prob > pairprob[left][0].bestscore )
+ {
+ pairprob[left][0].bestscore = prob;
+ pairprob[left][0].bestpos = right;
+#else
+ if( prob > 0.0 )
+ {
+ pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
+ pairprob[left][pairnum[left]].bestscore = prob / 100.0;
+ pairprob[left][pairnum[left]].bestpos = right;
+ pairnum[left]++;
+ pairprob[left][pairnum[left]].bestscore = -1.0;
+ pairprob[left][pairnum[left]].bestpos = -1;
+ fprintf( stderr, "%d-%d, %f\n", left, right, prob );
+
+ pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
+ pairprob[right][pairnum[right]].bestscore = prob / 100.0;
+ pairprob[right][pairnum[right]].bestpos = left;
+ pairnum[right]++;
+ pairprob[right][pairnum[right]].bestscore = -1.0;
+ pairprob[right][pairnum[right]].bestpos = -1;
+ fprintf( stderr, "%d-%d, %f\n", left, right, prob );
+#endif
+ }
+ }
+ fclose( fp );
+ sprintf( cmd, "rm -f %s", fnamein );
+ system( cmd );
+
+ for( i=0; i<lgth; i++ )
+ {
+ if( (right=pairprob[i][0].bestpos) > -1 )
+ {
+ pairprob[right][0].bestpos = i;
+ pairprob[right][0].bestscore = pairprob[i][0].bestscore;
+ }
+ }
+
+#if 0
+ for( i=0; i<lgth; i++ ) // atode kesu
+ if( pairprob[i][0].bestscore > -1 ) pairprob[i][0].bestscore = 1.0; // atode kesu
+#endif
+
+// fprintf( stderr, "after taikakuka in rnaalifoldcall\n" );
+// for( i=0; i<lgth; i++ )
+// {
+// fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, pairprob[i][0].bestpos, pairprob[i][0].bestscore, seq[0][i], seq[0][pairprob[i][0].bestpos] );
+// }
+
+ free( pairnum );
+}
+
+
+static void utot( int n, int l, char **s )
+{
+ int i, j;
+ for( i=0; i<l; i++ )
+ {
+ for( j=0; j<n; j++ )
+ {
+ if ( s[j][i] == 'a' ) s[j][i] = 'a';
+ else if( s[j][i] == 't' ) s[j][i] = 't';
+ else if( s[j][i] == 'u' ) s[j][i] = 't';
+ else if( s[j][i] == 'g' ) s[j][i] = 'g';
+ else if( s[j][i] == 'c' ) s[j][i] = 'c';
+ else if( s[j][i] == '-' ) s[j][i] = '-';
+ else s[j][i] = 'n';
+ }
+ }
+}
+
+
+void foldrna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *additionalpair )
+{
+ int i, j;
+// int ui, uj;
+// int uiup, ujup;
+ int uido, ujdo;
+ static TLS char **useq1, **useq2;
+ static TLS char **oseq1, **oseq2, **oseq1r, **oseq2r, *odir1, *odir2;
+ static TLS RNApair **pairprob1, **pairprob2;
+ static TLS RNApair *pairpt1, *pairpt2;
+ int lgth1 = strlen( seq1[0] );
+ int lgth2 = strlen( seq2[0] );
+ static TLS float **impmtx2;
+ static TLS float **map;
+// double lenfac;
+ float prob;
+ int **sgapmap1, **sgapmap2;
+ char *nogapdum;
+ float **tbppmtx;
+
+
+// fprintf( stderr, "nseq1=%d, lgth1=%d\n", nseq1, lgth1 );
+ useq1 = AllocateCharMtx( nseq1, lgth1+10 );
+ useq2 = AllocateCharMtx( nseq2, lgth2+10 );
+ oseq1 = AllocateCharMtx( nseq1, lgth1+10 );
+ oseq2 = AllocateCharMtx( nseq2, lgth2+10 );
+ oseq1r = AllocateCharMtx( nseq1, lgth1+10 );
+ oseq2r = AllocateCharMtx( nseq2, lgth2+10 );
+ odir1 = AllocateCharVec( lgth1+10 );
+ odir2 = AllocateCharVec( lgth2+10 );
+ sgapmap1 = AllocateIntMtx( nseq1, lgth1+1 );
+ sgapmap2 = AllocateIntMtx( nseq2, lgth2+1 );
+ nogapdum = AllocateCharVec( MAX( lgth1, lgth2 ) );
+ pairprob1 = (RNApair **)calloc( lgth1, sizeof( RNApair *) );
+ pairprob2 = (RNApair **)calloc( lgth2, sizeof( RNApair *) );
+ map = AllocateFloatMtx( lgth1, lgth2 );
+ impmtx2 = AllocateFloatMtx( lgth1, lgth2 );
+ tbppmtx = AllocateFloatMtx( lgth1, lgth2 );
+
+ for( i=0; i<nseq1; i++ ) strcpy( useq1[i], seq1[i] );
+ for( i=0; i<nseq2; i++ ) strcpy( useq2[i], seq2[i] );
+ for( i=0; i<nseq1; i++ ) strcpy( oseq1[i], seq1[i] );
+ for( i=0; i<nseq2; i++ ) strcpy( oseq2[i], seq2[i] );
+
+ for( i=0; i<nseq1; i++ ) commongappick_record( 1, useq1+i, sgapmap1[i] );
+ for( i=0; i<nseq2; i++ ) commongappick_record( 1, useq2+i, sgapmap2[i] );
+
+ for( i=0; i<lgth1; i++ )
+ {
+ pairprob1[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+ pairprob1[i][0].bestpos = -1;
+ pairprob1[i][0].bestscore = -1;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ pairprob2[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+ pairprob2[i][0].bestpos = -1;
+ pairprob2[i][0].bestscore = -1;
+ }
+
+ utot( nseq1, lgth1, oseq1 );
+ utot( nseq2, lgth2, oseq2 );
+
+// fprintf( stderr, "folding group1\n" );
+// rnalocal( oseq1, useq1, eff1, eff1, nseq1, nseq1, lgth1+10, pair1 );
+
+/* base-pairing probability of group 1 */
+ if( rnaprediction == 'r' )
+ rnaalifoldcall( oseq1, nseq1, pairprob1 );
+ else
+ mccaskillextract( oseq1, useq1, nseq1, pairprob1, grouprna1, sgapmap1, eff1 );
+
+
+// fprintf( stderr, "folding group2\n" );
+// rnalocal( oseq2, useq2, eff2, eff2, nseq2, nseq2, lgth2+10, pair2 );
+
+/* base-pairing probability of group 2 */
+ if( rnaprediction == 'r' )
+ rnaalifoldcall( oseq2, nseq2, pairprob2 );
+ else
+ mccaskillextract( oseq2, useq2, nseq2, pairprob2, grouprna2, sgapmap2, eff2 );
+
+
+
+#if 0
+ makerseq( oseq1, oseq1r, odir1, pairprob1, nseq1, lgth1 );
+ makerseq( oseq2, oseq2r, odir2, pairprob2, nseq2, lgth2 );
+
+ fprintf( stderr, "%s\n", odir2 );
+
+ for( i=0; i<nseq1; i++ )
+ {
+ fprintf( stdout, ">ori\n%s\n", oseq1[0] );
+ fprintf( stdout, ">rev\n%s\n", oseq1r[0] );
+ }
+#endif
+
+/* similarity score */
+ Lalignmm_hmout( oseq1, oseq2, eff1, eff2, nseq1, nseq2, 10000, NULL, NULL, NULL, NULL, map );
+
+ if( 1 )
+ {
+ if( RNAscoremtx == 'n' )
+ {
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ {
+// impmtx2[i][j] = osoiaveragescore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
+ impmtx2[i][j] = 0.0;
+ }
+ }
+ else if( RNAscoremtx == 'r' )
+ {
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ {
+ tbppmtx[i][j] = 1.0;
+ impmtx2[i][j] = 0.0;
+ }
+ for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
+ {
+ for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
+ {
+ uido = pairpt1->bestpos;
+ ujdo = pairpt2->bestpos;
+ prob = pairpt1->bestscore * pairpt2->bestscore;
+ if( uido > -1 && ujdo > -1 )
+ {
+ if( uido > i && j > ujdo )
+ {
+ impmtx2[i][j] += prob * pairedribosumscore53( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j, uido, ujdo ) * consweight_multi;
+ tbppmtx[i][j] -= prob;
+ }
+ else if( i < uido && j < ujdo )
+ {
+ impmtx2[i][j] += prob * pairedribosumscore35( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j, uido, ujdo ) * consweight_multi;
+ tbppmtx[i][j] -= prob;
+ }
+ }
+ }
+ }
+
+
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ impmtx2[i][j] += tbppmtx[i][j] * singleribosumscore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
+ }
+ }
+ }
+
+
+/* four-way consistency */
+
+ for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
+ {
+
+// if( pairprob1[i] == NULL ) continue;
+
+ for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
+ {
+// fprintf( stderr, "i=%d, j=%d, pn1=%d, pn2=%d\n", i, j, pairpt1-pairprob1[i], pairpt2-pairprob2[j] );
+// if( pairprob2[j] == NULL ) continue;
+
+ uido = pairpt1->bestpos;
+ ujdo = pairpt2->bestpos;
+ prob = pairpt1->bestscore * pairpt2->bestscore;
+// prob = 1.0;
+// fprintf( stderr, "i=%d->uido=%d, j=%d->ujdo=%d\n", i, uido, j, ujdo );
+
+// fprintf( stderr, "impmtx2[%d][%d] = %f\n", i, j, impmtx2[i][j] );
+
+// if( i < uido && j > ujdo ) continue;
+// if( i > uido && j < ujdo ) continue;
+
+
+// posdistj = abs( ujdo-j );
+
+// if( uido > -1 && ujdo > -1 )
+ if( uido > -1 && ujdo > -1 && ( ( i > uido && j > ujdo ) || ( i < uido && j < ujdo ) ) )
+ {
+ {
+ impmtx2[i][j] += MAX( 0, map[uido][ujdo] ) * consweight_rna * 600 * prob; // osoi
+ }
+ }
+
+ }
+ }
+ for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+ {
+ impmtx[i][j] += impmtx2[i][j];
+// fprintf( stderr, "fastathreshold=%f, consweight_multi=%f, consweight_rna=%f\n", fastathreshold, consweight_multi, consweight_rna );
+// impmtx[i][j] *= 0.5;
+ }
+
+// impmtx[0][0] += 10000.0;
+// impmtx[lgth1-1][lgth2-1] += 10000.0;
+
+
+
+#if 0
+ fprintf( stdout, "#impmtx2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stdout, "%d %d %f\n", i, j, impmtx2[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+ exit( 1 );
+#endif
+ }
+
+ FreeCharMtx( useq1 );
+ FreeCharMtx( useq2 );
+ FreeCharMtx( oseq1 );
+ FreeCharMtx( oseq2 );
+ FreeCharMtx( oseq1r );
+ FreeCharMtx( oseq2r );
+ free( odir1 );
+ free( odir2 );
+ FreeFloatMtx( impmtx2 );
+ FreeFloatMtx( map );
+ FreeIntMtx( sgapmap1 );
+ FreeIntMtx( sgapmap2 );
+ FreeFloatMtx( tbppmtx );
+
+ for( i=0; i<lgth1; i++ ) free( pairprob1[i] );
+ for( i=0; i<lgth2; i++ ) free( pairprob2[i] );
+ free( pairprob1 );
+ free( pairprob2 );
+}
+
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ inputfile = NULL;
+ fftkeika = 0;
+ pslocal = -1000.0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ divpairscore = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_OP = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ ppenalty_EX = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ RNAppenalty = NOTSPECIFIED;
+ RNApthr = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'o':
+ RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'O':
+ ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'E':
+ ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+// fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+ fprintf( stderr, "blosum %d\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "TM %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'l':
+ ppslocal = (int)( atof( *++argv ) * 1000 + 0.5 );
+ pslocal = (int)( 600.0 / 1000.0 * ppslocal + 0.5);
+// fprintf( stderr, "ppslocal = %d\n", ppslocal );
+// fprintf( stderr, "pslocal = %d\n", pslocal );
+ --argc;
+ goto nextoption;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+#if 0
+ case 'e':
+ fftscore = 0;
+ break;
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+#endif
+ case 'Q':
+ calledByXced = 1;
+ break;
+ case 's':
+ treemethod = 's';
+ break;
+ case 'x':
+ disp = 1;
+ break;
+ case 'p':
+ treemethod = 'p';
+ break;
+#if 0
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'S':
+ alg = 'S';
+ break;
+ case 'L':
+ alg = 'L';
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'R':
+ alg = 'R';
+ break;
+ case 'N':
+ alg = 'N';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'V':
+ alg = 'V';
+ break;
+ case 'C':
+ alg = 'C';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'd':
+ divpairscore = 1;
+ break;
+/* Modified 01/08/27, default: user tree */
+ case 'J':
+ tbutree = 0;
+ break;
+/* modification end. */
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'Z':
+ checkC = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+int countamino( char *s, int end )
+{
+ int val = 0;
+ while( end-- )
+ if( *s++ != '-' ) val++;
+ return( val );
+}
+
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( treemethod == 'x' )
+ fprintf( fp, "Tree = UPGMA (3).\n" );
+ else if( treemethod == 's' )
+ fprintf( fp, "Tree = UPGMA (2).\n" );
+ else if( treemethod == 'p' )
+ fprintf( fp, "Tree = UPGMA (1).\n" );
+ else
+ fprintf( fp, "Unknown tree.\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int *nlen;
+ static char **name, **seq, **useq;
+ static char **mseq1, **mseq2;
+ static char **aseq;
+ static char **bseq;
+ static double *eff;
+ int i;
+ FILE *infp;
+ char c;
+ int alloclen;
+ RNApair **pair1;
+ RNApair **pair2;
+ float **map;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( njob > M )
+ {
+ fprintf( stderr, "The number of sequences must be < %d\n", M );
+ fprintf( stderr, "Please try the splittbfast program for such large data.\n" );
+ exit( 1 );
+ }
+
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+
+ seq = AllocateCharMtx( njob, nlenmax*5+1 );
+ useq = AllocateCharMtx( njob, nlenmax*5+1 );
+ aseq = AllocateCharMtx( njob, nlenmax*5+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*5+1 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ alloclen = nlenmax*5;
+
+ pair1 = calloc( nlenmax*5+1, sizeof( RNApair *) );
+ pair2 = calloc( nlenmax*5+1, sizeof( RNApair *) );
+ map = AllocateFloatMtx( nlenmax+1, nlenmax );
+
+ eff = AllocateDoubleVec( njob );
+
+ readData_pointer( infp, name, nlen, seq );
+ fclose( infp );
+
+ for( i=0; i<njob; i++ ) strcpy( useq[i], seq[i] );
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illeagal character %c\n", c );
+ exit( 1 );
+ }
+
+// writePre( njob, name, nlen, seq, 0 );
+
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+
+// for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+
+ fprintf( stderr, "folding group1\n" );
+// rnalocal( seq, useq, eff, eff, njob, njob, alloclen, pair1 );
+ rnaalifoldcall( seq, njob, pair1 );
+ exit( 1 );
+
+#if 0
+ fprintf( stderr, "folding group1\n" );
+ rnalocal( seq+1, useq+1, eff+1, eff+1, 1, 1, alloclen, pair2 );
+ fprintf( stderr, "aligning 1 and 2, phase 1\n" );
+ Lalignmm_hmout( seq, seq+1, eff, eff+1, 1, 1, alloclen, NULL, NULL, NULL, NULL, map );
+
+
+#if 0
+ lgth1 = strlen( seq[0] );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "\n" );
+ if( pair1[i].pos == -1 ) continue;
+ fprintf( stderr, "i=%d (%c):%d", i, seq[0][i], pair1[i].pos );
+ if( map12[pair1[i].pos].pos == -1 ) continue;
+ fprintf( stderr, "%c -> %c ", seq[0][pair1[i].pos], seq[1][map12[pair1[i].pos].pos] );
+ if( pair2[map12[pair1[i].pos].pos].pos == -1 ) continue;
+ fprintf( stderr, "%d:%d (%c)", map12[pair1[i].pos].pos, pair2[map12[pair1[i].pos].pos].pos, seq[1][pair2[map12[pair1[i].pos].pos].pos] );
+ }
+#endif
+
+
+ exit( 1 );
+
+
+ pairalign( name, nlen, bseq, aseq, mseq1, mseq2, eff, alloclen );
+ fprintf( trap_g, "done.\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+// writePre( njob, name, nlen, aseq, !contin );
+#if 0
+ writeData( stdout, njob, name, nlen, aseq );
+#endif
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+#endif
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ ppenalty = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ scoremtx = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+ fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'D':
+ scoremtx = -1;
+ break;
+ case 'P':
+ scoremtx = 0;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+}
+
+
+int main( int ac, char **av )
+{
+ int nlen[M];
+ static char name[M][B], **seq;
+ double score;
+ extern double score_calc_for_score( int, char ** );
+
+ arguments( ac, av );
+
+ getnumlen( stdin );
+ rewind( stdin );
+
+ seq = AllocateCharMtx( njob, nlenmax );
+
+ readData( stdin, name, nlen, seq );
+
+ if( !isaligned( njob, seq ) ) ErrorExit( "Not aligned." );
+
+ constants( njob, seq );
+
+ score = score_calc_for_score( njob, seq );
+ if( scoremtx == 0 ) score += offset;
+
+ fprintf( stdout, "score = %f\n", score );
+ if ( scoremtx == 0 ) fprintf( stdout, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( stdout, "Dayhoff( machigai ga aru )\n" );
+ else if( scoremtx == 2 ) fprintf( stdout, "M-Y\n" );
+ else if( scoremtx == -1 ) fprintf( stdout, "DNA 1:%d\n", kimuraR );
+
+ fprintf( stdout, "gap penalty = %+6.2f, %+6.2f, %+6.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ exit( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+char *weboutfile = NULL;
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( (c = *++argv[0]) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'w':
+ weboutfile = *++argv;
+ fprintf( stderr, "weboutfile = %s\n", weboutfile );
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+
+int main( int argc, char *argv[] )
+{
+ FILE *infp;
+ FILE *weboutfp;
+ int nlenmin;
+ int isaligned = 0;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ if( weboutfile )
+ {
+ weboutfp = fopen( weboutfile, "w" );
+ if( !weboutfp )
+ {
+ fprintf( stderr, "Cannot open %s\n", weboutfile );
+ exit( 1 );
+ }
+ }
+
+ dorp = NOTSPECIFIED;
+ if( weboutfile )
+ {
+ getnumlen_nogap_outallreg_web( infp, weboutfp, &nlenmin, &isaligned );
+ if( isaligned ) fprintf( stdout, "Aligned\n" );
+ else fprintf( stdout, "Not aligned\n" );
+ }
+ else
+ getnumlen_nogap_outallreg( infp, &nlenmin );
+
+ return( 0 );
+
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 1
+
+double corethr;
+int coreext;
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ fftkeika = 1;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ scoremtx = 0;
+ kobetsubunkatsu = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ corethr = .5;
+ coreext = 0;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+ fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+ fprintf( stderr, "blosum %d\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'l':
+ fastathreshold = atof( *++argv );
+ constraint = 2;
+ fprintf( stderr, "weighti = %f\n", fastathreshold );
+ --argc;
+ goto nextoption;
+ case 'i':
+ corethr = atof( *++argv );
+ fprintf( stderr, "corethr = %f\n", corethr );
+ --argc;
+ goto nextoption;
+ case 'm':
+ fmodel = 1;
+ break;
+ case 'c':
+ coreext = 1;
+ break;
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+ case 'Q':
+ calledByXced = 1;
+ break;
+ case 's':
+ treemethod = 's';
+ break;
+ case 'x':
+ treemethod = 'x';
+ break;
+ case 'p':
+ treemethod = 'p';
+ break;
+ case 'a':
+ alg = 'a';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'S':
+ alg = 'S';
+ break;
+ case 'C':
+ alg = 'C';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'd':
+ disp = 1;
+ break;
+ case 'o':
+ outgap = 0;
+ break;
+/* Modified 01/08/27, default: user tree */
+ case 'J':
+ tbutree = 0;
+ break;
+/* modification end. */
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'Z':
+ checkC = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( treemethod == 'x' )
+ fprintf( fp, "Tree = UPGMA (3).\n" );
+ else if( treemethod == 's' )
+ fprintf( fp, "Tree = UPGMA (2).\n" );
+ else if( treemethod == 'p' )
+ fprintf( fp, "Tree = UPGMA (1).\n" );
+ else
+ fprintf( fp, "Unknown tree.\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int nlen[M];
+ static char **name, **seq;
+ static char **oseq;
+ static double **pscore;
+ static double *eff;
+ static double **node0, **node1;
+ static double *gapc;
+ static double *avgap;
+ double tmpavgap;
+ int i, j, m, goffset;
+ static int ***topol;
+ static double **len;
+ FILE *prep;
+ char c;
+ int corestart, coreend;
+ int alloclen;
+ int winsize;
+ char *pt, *ot;
+ double gapmin;
+
+ arguments( argc, argv );
+
+ getnumlen( stdin );
+ rewind( stdin );
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*9+1 );
+ name = AllocateCharMtx( njob, B+1 );
+ oseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ alloclen = nlenmax*9;
+
+ topol = AllocateIntCub( njob, 2, njob );
+ len = AllocateDoubleMtx( njob, 2 );
+ pscore = AllocateDoubleMtx( njob, njob );
+ eff = AllocateDoubleVec( njob );
+ node0 = AllocateDoubleMtx( njob, njob );
+ node1 = AllocateDoubleMtx( njob, njob );
+ gapc = AllocateDoubleVec( alloclen );
+ avgap = AllocateDoubleVec( alloclen );
+
+#if 0
+ Read( name, nlen, seq );
+#else
+ readData_pointer( stdin, name, nlen, seq );
+#endif
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illeagal character %c\n", c );
+ exit( 1 );
+ }
+
+ writePre( njob, name, nlen, seq, 0 );
+
+ if( tbutree == 0 )
+ {
+ for( i=1; i<njob; i++ )
+ {
+ if( nlen[i] != nlen[0] )
+ {
+ fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
+ exit( 1 );
+ }
+ }
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+ /*
+ pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
+ */
+ pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
+ }
+ }
+ else
+ {
+ fprintf( stderr, "Loading 'hat2' ... " );
+ prep = fopen( "hat2", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat2." );
+ readhat2_pointer( prep, njob, name, pscore );
+ fclose( prep );
+ fprintf( stderr, "done.\n" );
+
+#if 0
+ prep = fopen( "hat2_check", "w" );
+ WriteHat2( prep, njob, name, pscore );
+ fclose( prep );
+#endif
+
+ }
+
+ fprintf( stderr, "Constructing dendrogram ... " );
+ if( treemethod == 'x' )
+ supg( njob, pscore, topol, len );
+ else if( treemethod == 's' )
+ spg( njob, pscore, topol, len );
+ else if( treemethod == 'p' )
+ upg2( njob, pscore, topol, len );
+ else
+ ErrorExit( "Incorrect tree\n" );
+ fprintf( stderr, "done.\n" );
+
+ countnode( njob, topol, node0 );
+ if( tbrweight )
+ {
+ weight = 3;
+#if 0
+ utree = 0; counteff( njob, topol, len, eff ); utree = 1;
+#else
+ counteff_simple( njob, topol, len, eff );
+#endif
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+ }
+
+
+ for( i=0; i<nlenmax; i++ )
+ {
+ gapc[i] = 0.0;
+ for( j=0; j<njob; j++ )
+ {
+ if( seq[j][i] == '-' ) gapc[i] += eff[j];
+ }
+ }
+
+ gapmin = 1.0;
+ winsize = fftWinSize;
+ goffset = winsize/2;
+ tmpavgap = 0.0;
+ corestart = coreend = -1;
+ for( i=0; i<winsize; i++ )
+ {
+ tmpavgap += gapc[i];
+ }
+ for( i=winsize; i<nlenmax; i++ )
+ {
+ m = i - goffset;
+ avgap[m] = tmpavgap / winsize;
+// fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] );
+ if( avgap[m] < corethr )
+ {
+ if( corestart == -1 )
+ corestart = i - winsize;
+// fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend );
+ if( avgap[m] < gapmin )
+ {
+ gapmin = avgap[m];
+ }
+ coreend = i;
+ }
+ tmpavgap -= gapc[i-winsize];
+ tmpavgap += gapc[i];
+ }
+ if( corestart == -1 || coreend == -1 )
+ {
+ corestart = 0;
+ coreend = nlenmax-1;
+ }
+
+ for( i=0; i<njob; i++ )
+ {
+ pt = oseq[i];
+ m = winsize;
+ while( m-- ) *pt++ = '-';
+ for( j=corestart; j<=coreend; j++ )
+ *pt++ = seq[i][j];
+ m = winsize;
+ while( m-- ) *pt++ = '-';
+ *pt = 0;
+
+ ot = oseq[i]+winsize-1;
+ pt = seq[i]+corestart-1;
+ if( coreext ) m = winsize;
+ else m = 0;
+ while( m && --pt > seq[i] )
+ if( *pt != '-' )
+ {
+ *ot-- = *pt;
+ m--;
+ }
+
+ ot = oseq[i]+winsize+coreend-corestart+1;
+ pt = seq[i]+coreend;
+ if( coreext ) m = winsize;
+ else m = 0;
+ while( m && *(++pt) )
+ {
+ if( *pt != '-' )
+ {
+ *ot++ = *pt;
+ m--;
+ }
+ }
+ fprintf( stdout, ">%s\n", name[i] );
+ fprintf( stdout, "%s\n", oseq[i] );
+ }
+
+ exit( 1 );
+
+ SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+#include "mtxutl.h"
+
+#define DEBUG 0
+#define TEST 0
+
+#define END_OF_VEC -1
+
+static int maxl;
+static int tsize;
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ inputfile = NULL;
+ disopt = 0;
+ scoremtx = 1;
+ nblosum = 62;
+ dorp = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'I':
+ disopt = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: -i\n" );
+ exit( 1 );
+ }
+}
+
+void seq_grp_nuc( int *grp, char *seq )
+{
+ int tmp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 4 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\n", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+}
+
+void seq_grp( int *grp, char *seq )
+{
+ int tmp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 6 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\n", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+}
+
+void makecompositiontable_p( short *table, int *pointt )
+{
+ int point;
+
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ table[point]++;
+}
+
+int commonsextet_p( short *table, int *pointt )
+{
+ int value = 0;
+ short tmp;
+ int point;
+ static short *memo = NULL;
+ static int *ct = NULL;
+ static int *cp;
+
+ if( !memo )
+ {
+ memo = (short *)calloc( tsize, sizeof( short ) );
+ if( !memo ) ErrorExit( "Cannot allocate memo\n" );
+ ct = (int *)calloc( MIN( maxl, tsize)+1, sizeof( int ) );
+ if( !ct ) ErrorExit( "Cannot allocate memo\n" );
+ }
+
+ cp = ct;
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ {
+ tmp = memo[point]++;
+ if( tmp < table[point] )
+ value++;
+ if( tmp == 0 ) *cp++ = point;
+// fprintf( stderr, "cp - ct = %d (tsize = %d)\n", cp - ct, tsize );
+ }
+ *cp = END_OF_VEC;
+
+ cp = ct;
+ while( *cp != END_OF_VEC )
+ memo[*cp++] = 0;
+
+ return( value );
+}
+
+void makepointtable_nuc( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ p = n;
+ point = *n++ * 1024;
+ point += *n++ * 256;
+ point += *n++ * 64;
+ point += *n++ * 16;
+ point += *n++ * 4;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 1024;
+ point *= 4;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+void makepointtable( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ p = n;
+ point = *n++ * 7776;
+ point += *n++ * 1296;
+ point += *n++ * 216;
+ point += *n++ * 36;
+ point += *n++ * 6;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 7776;
+ point *= 6;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+int main( int argc, char **argv )
+{
+ int i, j;
+ FILE *fp, *infp;
+ char **seq;
+ int *grpseq;
+ char *tmpseq;
+ int **pointt;
+ static char name[M][B];
+ static int nlen[M];
+ double **mtx;
+ double **mtx2;
+ double score, score0;
+ static short *table1;
+ char b[B];
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+#if 0
+ PreRead( stdin, &njob, &nlenmax );
+#else
+ getnumlen( infp );
+#endif
+ rewind( infp );
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ tmpseq = AllocateCharVec( nlenmax+1 );
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ grpseq = AllocateIntVec( nlenmax+1 );
+ pointt = AllocateIntMtx( njob, nlenmax+1 );
+ mtx = AllocateDoubleMtx( njob, njob );
+ mtx2 = AllocateDoubleMtx( njob, njob );
+ pamN = NOTSPECIFIED;
+
+#if 0
+ FRead( infp, name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+
+ fclose( infp );
+
+ constants( njob, seq );
+
+ if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
+ else tsize = (int)pow( 6, 6 );
+
+ maxl = 0;
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( tmpseq, seq[i] );
+ nlen[i] = strlen( tmpseq );
+ if( nlen[i] < 6 )
+ {
+ fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
+ exit( 1 );
+ }
+ if( nlen[i] > maxl ) maxl = nlen[i];
+ if( dorp == 'd' ) /* nuc */
+ {
+ seq_grp_nuc( grpseq, tmpseq );
+ makepointtable_nuc( pointt[i], grpseq );
+ }
+ else /* amino */
+ {
+ seq_grp( grpseq, tmpseq );
+ makepointtable( pointt[i], grpseq );
+ }
+ }
+ for( i=0; i<njob; i++ )
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "%4d / %4d\r", i+1, njob );
+ }
+ makecompositiontable_p( table1, pointt[i] );
+
+ for( j=i; j<njob; j++ )
+ {
+ score = (double)commonsextet_p( table1, pointt[j] );
+ mtx[i][j] = score;
+ }
+ free( table1 );
+ }
+ for( i=0; i<njob; i++ )
+ {
+ score0 = mtx[i][i];
+ for( j=0; j<njob; j++ )
+ mtx2[i][j] = ( score0 - mtx[MIN(i,j)][MAX(i,j)] ) / score0 * 3.0;
+ }
+ for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+ {
+#if TEST
+ double jscore;
+ jscore = mtx[i][j] / ( MIN( strlen( seq[i] ), strlen( seq[j] ) ) - 2 );
+ fprintf( stdout, "jscore = %f\n", jscore );
+
+ fprintf( stdout, "mtx2[%d][%d] = %f, mtx2[%d][%d] = %f\n", i, j, mtx2[i][j], j, i, mtx2[j][i] );
+#endif
+ mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
+#if TEST
+ fprintf( stdout, "sonokekka mtx2[%d][%d] %f\n", i, j, mtx2[i][j] );
+#endif
+ }
+
+ if( disopt )
+ {
+ for( i=0; i<njob; i++ )
+ {
+ sprintf( b, "=lgth = %04d", nlen[i] );
+ strins( b, name[i] );
+ }
+ }
+
+ fp = fopen( "hat2", "w" );
+ if( !fp ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( fp, njob, name, mtx2 );
+ fclose( fp );
+
+ fprintf( stderr, "\n" );
+ SHOWVERSION;
+ exit( 0 );
+}
--- /dev/null
+#if 0
+#include <sys/types.h>
+#include <sys/ipc.h>
+#include <sys/shm.h>
+
+#endif
+#define IMA_YONDERU 'x' /* iranai */
+#define IMA_KAITERU 0 /* iranai */
+#define KAKIOWATTA 'w'
+#define YOMIOWATTA 'r'
+#define OSHIMAI 'd'
+#define ISRUNNING 0
+#define SEMAPHORE 1
+#define STATUS 2
+
+#define IPC_ALLOC 0100000
--- /dev/null
+#include "mltaln.h"
+
+
+#define TREE 1
+#define PICKSIZE 50 // must be >= 3
+#define WEIGHT 0
+#define TOKYORIPARA 0.70 // 0.70
+#define TOKYORIPARA_A 0.70 // changed
+#define LENFAC 1
+#define HUKINTOTREE 1
+#define DIANA 0
+#define MAX6DIST 10.0
+
+// kouzoutai ni sasareru pointer ha static
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+#define END_OF_VEC -1
+
+static char *fastapath;
+static int doalign;
+static int fromaln;
+static int uselongest;
+static int treeout;
+static int classsize;
+static int picksize;
+static int maxl;
+static int tsize;
+static int reorder;
+static int pid;
+static int maxdepth = 0;
+static double tokyoripara;
+
+static double lenfaca, lenfacb, lenfacc, lenfacd;
+#define PLENFACA 0.01
+#define PLENFACB 10000
+#define PLENFACC 10000
+#define PLENFACD 0.1
+#define DLENFACA 0.01
+#define DLENFACB 2500
+#define DLENFACC 2500
+#define DLENFACD 0.1
+
+static char datafile[1000];
+static char queryfile[1000];
+static char resultfile[1000];
+
+typedef struct _scores
+{
+ double score;
+ int selfscore;
+ int orilen;
+ int *pointt;
+ int numinseq;
+ char *name;
+// char *seq; // reallo
+// char **seqpt;
+ int shimon;
+} Scores;
+
+int intcompare( const int *a, const int *b )
+{
+ return( *a - *b );
+}
+
+int lcompare( const Scores *a, const Scores *b )
+{
+ if( a->orilen < b->orilen ) return 1;
+ else if( a->orilen > b->orilen ) return -1;
+ else return 0;
+}
+
+int dcompare( const Scores *a, const Scores *b )
+{
+ if( a->score > b->score ) return 1;
+ else if( a->score < b->score ) return -1;
+ else
+ {
+ if( a->selfscore < b->selfscore ) return 1;
+ else if( a->selfscore > b->selfscore ) return -1;
+ else
+ {
+ if( a->orilen < b->orilen ) return 1;
+ else if( a->orilen > b->orilen ) return -1;
+ else return 0;
+ }
+ }
+}
+
+#if 0
+static void gappickandx0( char *out, char *in )
+{
+ char c;
+ if( scoremtx == -1 )
+ {
+ while( *in )
+ {
+ if( (c=*in++) == '-' )
+ ;
+ else if( c == 'u' )
+ *out++ = 't';
+ else if( amino_n[c] < 4 && amino_n[c] > -1 )
+ *out++ = c;
+ else
+ *out++ = 'n';
+ }
+ }
+ else
+ {
+ while( *in )
+ {
+ if( (c=*in++) == '-' )
+ ;
+ else if( amino_n[c] < 20 && amino_n[c] > -1 )
+ *out++ = c;
+ else
+ *out++ = 'X';
+ }
+ }
+ *out = 0;
+}
+
+static int getkouho( int *pickkouho, double prob, int nin, Scores *scores, char **seq ) // 0 < prob < 1
+{
+ int nkouho = 0;
+ int i, j;
+ int *iptr = pickkouho;
+ for( i=1; i<nin; i++ )
+ {
+ if( ( nkouho==0 || rnd() < prob ) && ( scores[i].shimon != scores->shimon || strcmp( seq[scores->numinseq], seq[scores[i].numinseq] ) ) )
+ {
+#if 0
+ for( j=0; j<nkouho; j++ )
+ {
+ if( scores[i].shimon == scores[pickkouho[j]].shimon || !strcmp( seq[scores[pickkouho[j]].numinseq], seq[scores[i].numinseq] ) )
+ break;
+ }
+ if( j == nkouho )
+#endif
+ {
+ *iptr++ = i;
+ nkouho++;
+// fprintf( stderr, "ok! nkouho=%d\n", nkouho );
+ }
+ }
+ else
+ {
+ ;
+// fprintf( stderr, "no! %d-%d\n", 0, scores[i].numinseq );
+ }
+ }
+ fprintf( stderr, "\ndone\n\n" );
+ return nkouho;
+}
+
+#endif
+
+static void getfastascoremtx( int **tmpaminodis )
+{
+ FILE *qfp;
+ FILE *dfp;
+ FILE *rfp;
+ int i, j;
+ char aa;
+ int slen;
+ int res;
+ char com[10000];
+ static char *tmpseq;
+ static char *tmpname;
+ double *resvec;
+
+ if( scoremtx == -1 )
+ {
+ tmpaminodis['a']['a'] = 5;
+ tmpaminodis['g']['g'] = 5;
+ tmpaminodis['c']['c'] = 5;
+ tmpaminodis['t']['t'] = 5;
+ tmpaminodis['n']['n'] = -1;
+
+ return;
+ }
+
+
+ tmpseq = calloc( 2000, sizeof( char ) );
+ tmpname = calloc( B, sizeof( char ) );
+ resvec = calloc( 1, sizeof( double ) );
+
+// fprintf( stderr, "xformatting .. " );
+ dfp = fopen( datafile, "w" );
+ if( !dfp ) ErrorExit( "Cannot open datafile." );
+ sprintf( tmpname, ">+===========+%d ", 0 );
+ strcpy( tmpseq, "AAAAAAXXXXXX" );
+ strcat( tmpseq, "CCCCCCXXXXXX" );
+ strcat( tmpseq, "DDDDDDXXXXXX" );
+ strcat( tmpseq, "EEEEEEXXXXXX" );
+ strcat( tmpseq, "FFFFFFXXXXXX" );
+ strcat( tmpseq, "GGGGGGXXXXXX" );
+ strcat( tmpseq, "HHHHHHXXXXXX" );
+ strcat( tmpseq, "IIIIIIXXXXXX" );
+ strcat( tmpseq, "KKKKKKXXXXXX" );
+ strcat( tmpseq, "LLLLLLXXXXXX" );
+ strcat( tmpseq, "MMMMMMXXXXXX" );
+ strcat( tmpseq, "NNNNNNXXXXXX" );
+ strcat( tmpseq, "PPPPPPXXXXXX" );
+ strcat( tmpseq, "QQQQQQXXXXXX" );
+ strcat( tmpseq, "RRRRRRXXXXXX" );
+ strcat( tmpseq, "SSSSSSXXXXXX" );
+ strcat( tmpseq, "TTTTTTXXXXXX" );
+ strcat( tmpseq, "VVVVVVXXXXXX" );
+ strcat( tmpseq, "WWWWWWXXXXXX" );
+ strcat( tmpseq, "YYYYYYXXXXXX" );
+ slen = strlen( tmpseq );
+ writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
+ fclose( dfp );
+ fprintf( stderr, "done.\n" );
+
+ for( i=0; i<20; i++ )
+ {
+ aa = amino[i];
+// fprintf( stderr, "checking %c\n", aa );
+ *tmpseq = 0;
+ sprintf( tmpname, ">+===========+%d ", 0 );
+ for( j=0; j<6; j++ )
+ sprintf( tmpseq+strlen( tmpseq ), "%c", aa );
+ qfp = fopen( queryfile, "w" );
+ if( !qfp ) ErrorExit( "Cannot open queryfile." );
+ writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
+ fclose( qfp );
+
+ if( scoremtx == -1 )
+ sprintf( com, "%s -z3 -m10 -n -Q -H -b%d -E%d -d%d %s %s %d > %s", fastapath, M, M, 0, queryfile, datafile, 6, resultfile );
+ else
+ sprintf( com, "%s -z3 -m10 -p -Q -H -b%d -E%d -d%d %s %s %d > %s", fastapath, M, M, 0, queryfile, datafile, 2, resultfile );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "error in %s", fastapath );
+ exit( 1 );
+ }
+
+ rfp = fopen( resultfile, "r" );
+ if( rfp == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+ res = ReadFasta34m10_scoreonly( rfp, resvec, 1 );
+ fprintf( stderr, "%c: %f\n", 'A'+i, *resvec/6 );
+ fclose( rfp );
+ if( ( (int)*resvec % 6 ) > 0.0 )
+ {
+ fprintf( stderr, "Error in blast, *resvec=%f\n", *resvec );
+ fprintf( stderr, "Error in blast, *resvec/6=%f\n", *resvec/6 );
+ exit( 1 );
+ }
+ tmpaminodis[(int)aa][(int)aa] = (int)( *resvec / 6 );
+// fprintf( stderr, "*resvec=%f, tmpaminodis[aa][aa] = %d\n", *resvec, tmpaminodis[aa][aa] );
+ }
+ tmpaminodis['X']['X'] = -1;
+ free( tmpname );
+ free( tmpseq );
+ free( resvec );
+}
+
+#if 0
+static void getblastscoremtx( int **tmpaminodis )
+{
+ FILE *qfp;
+ FILE *dfp;
+ FILE *rfp;
+ int i, j;
+ char aa;
+ int slen;
+ int res;
+ char com[10000];
+ static char *tmpseq;
+ static char *tmpname;
+ double *resvec;
+
+ if( scoremtx == -1 )
+ {
+ tmpaminodis['a']['a'] = 1;
+ tmpaminodis['g']['g'] = 1;
+ tmpaminodis['c']['c'] = 1;
+ tmpaminodis['t']['t'] = 1;
+
+ return;
+ }
+
+
+ tmpseq = calloc( 2000, sizeof( char ) );
+ tmpname = calloc( B, sizeof( char ) );
+ resvec = calloc( 1, sizeof( double ) );
+
+// fprintf( stderr, "xformatting .. " );
+ dfp = fopen( datafile, "w" );
+ if( !dfp ) ErrorExit( "Cannot open datafile." );
+ sprintf( tmpname, "\0", i ); // BUG!!
+ strcpy( tmpseq, "AAAAAAXXXXXX" );
+ strcat( tmpseq, "CCCCCCXXXXXX" );
+ strcat( tmpseq, "DDDDDDXXXXXX" );
+ strcat( tmpseq, "EEEEEEXXXXXX" );
+ strcat( tmpseq, "FFFFFFXXXXXX" );
+ strcat( tmpseq, "GGGGGGXXXXXX" );
+ strcat( tmpseq, "HHHHHHXXXXXX" );
+ strcat( tmpseq, "IIIIIIXXXXXX" );
+ strcat( tmpseq, "KKKKKKXXXXXX" );
+ strcat( tmpseq, "LLLLLLXXXXXX" );
+ strcat( tmpseq, "MMMMMMXXXXXX" );
+ strcat( tmpseq, "NNNNNNXXXXXX" );
+ strcat( tmpseq, "PPPPPPXXXXXX" );
+ strcat( tmpseq, "QQQQQQXXXXXX" );
+ strcat( tmpseq, "RRRRRRXXXXXX" );
+ strcat( tmpseq, "SSSSSSXXXXXX" );
+ strcat( tmpseq, "TTTTTTXXXXXX" );
+ strcat( tmpseq, "VVVVVVXXXXXX" );
+ strcat( tmpseq, "WWWWWWXXXXXX" );
+ strcat( tmpseq, "YYYYYYXXXXXX" );
+ slen = strlen( tmpseq );
+ writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
+ fclose( dfp );
+ if( scoremtx == -1 )
+ sprintf( com, "formatdb -p f -i %s -o F", datafile );
+ else
+ sprintf( com, "formatdb -i %s -o F", datafile );
+ system( com );
+ fprintf( stderr, "done.\n" );
+
+ for( i=0; i<20; i++ )
+ {
+ aa = amino[i];
+ fprintf( stderr, "checking %c\n", aa );
+ *tmpseq = 0;
+ for( j=0; j<6; j++ )
+ sprintf( tmpseq+strlen( tmpseq ), "%c", aa );
+ qfp = fopen( queryfile, "w" );
+ if( !qfp ) ErrorExit( "Cannot open queryfile." );
+ writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
+ fclose( qfp );
+
+ sprintf( com, "blastall -b %d -G 10 -E 1 -e 1e10 -p blastp -m 7 -i %s -d %s > %s\0", 1, queryfile, datafile, resultfile );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "error in %s", "blastall" );
+ exit( 1 );
+ }
+
+ rfp = fopen( resultfile, "r" );
+ if( rfp == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+ res = ReadBlastm7_scoreonly( rfp, resvec, 1 );
+ fprintf( stdout, "%c: %f\n", 'A'+i, *resvec/6 );
+ fclose( rfp );
+ if( ( (int)*resvec % 6 ) > 0.0 )
+ {
+ fprintf( stderr, "Error in blast, *resvec=%f\n", *resvec );
+ fprintf( stderr, "Error in blast, *resvec/6=%f\n", *resvec/6 );
+ exit( 1 );
+ }
+ tmpaminodis[aa][aa] = (int)( *resvec / 6 );
+ }
+ tmpaminodis['X']['X'] = 0;
+ free( tmpname );
+ free( tmpseq );
+ free( resvec );
+
+}
+#endif
+
+static double *callfasta( char **seq, Scores *scores, int nin, int *picks, int query, int rewritedata )
+{
+ double *val;
+ FILE *qfp;
+ FILE *dfp;
+ FILE *rfp;
+ int i;
+ char com[10000];
+ static char datafile[1000];
+ static char queryfile[1000];
+ static char resultfile[1000];
+ static int pid;
+ static char *tmpseq;
+ static char *tmpname;
+ int slen;
+ int res;
+ static Scores *scoresbk = NULL;
+ static int ninbk = 0;
+
+ if( pid == 0 )
+ {
+ pid = (int)getpid();
+ sprintf( datafile, "/tmp/data-%d", pid );
+ sprintf( queryfile, "/tmp/query-%d", pid );
+ sprintf( resultfile, "/tmp/fasta-%d", pid );
+
+ tmpseq = calloc( nlenmax+1, sizeof( char ) );
+ tmpname = calloc( B+1, sizeof( char ) );
+ }
+
+ val = calloc( nin, sizeof( double ) );
+// fprintf( stderr, "nin=%d, q=%d\n", nin, query );
+
+ if( rewritedata )
+ {
+ scoresbk = scores;
+ ninbk = nin;
+// fprintf( stderr, "\nformatting .. " );
+ dfp = fopen( datafile, "w" );
+ if( !dfp ) ErrorExit( "Cannot open datafile." );
+ if( picks == NULL ) for( i=0; i<nin; i++ )
+ {
+// fprintf( stderr, "i=%d / %d / %d\n", i, nin, njob );
+// fprintf( stderr, "nlenmax = %d\n", nlenmax );
+// fprintf( stderr, "scores[i].orilen = %d\n", scores[i].orilen );
+// fprintf( stderr, "strlen( seq[scores[i].numinseq] = %d\n", strlen( seq[scores[i].numinseq] ) );
+ gappick0( tmpseq, seq[scores[i].numinseq] );
+ sprintf( tmpname, ">+===========+%d ", i );
+ slen = scores[i].orilen;
+ writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
+ }
+ else for( i=0; i<nin; i++ )
+ {
+ gappick0( tmpseq, seq[scores[picks[i]].numinseq] );
+ sprintf( tmpname, ">+===========+%d ", i );
+ slen = scores[picks[i]].orilen;
+ writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
+ }
+ fclose( dfp );
+ }
+
+
+ gappick0( tmpseq, seq[scores[query].numinseq] );
+ sprintf( tmpname, ">+==========+%d ", 0 );
+ slen = scores[query].orilen;
+ qfp = fopen( queryfile, "w" );
+ if( !qfp ) ErrorExit( "Cannot open queryfile." );
+ writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
+ fclose( qfp );
+
+// fprintf( stderr, "calling fasta, nin=%d\n", nin );
+
+ if( scoremtx == -1 )
+ sprintf( com, "%s -z3 -m10 -n -Q -H -b%d -E%d -d%d %s %s %d > %s", fastapath, nin, nin, 0, queryfile, datafile, 6, resultfile );
+ else
+ sprintf( com, "%s -z3 -m10 -p -Q -H -b%d -E%d -d%d %s %s %d > %s", fastapath, nin, nin, 0, queryfile, datafile, 2, resultfile );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "error in %s", fastapath );
+ exit( 1 );
+ }
+// fprintf( stderr, "fasta done\n" );
+
+//exit( 1 );
+
+ rfp = fopen( resultfile, "r" );
+ if( rfp == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+
+// fprintf( stderr, "reading fasta\n" );
+ if( scoremtx == -1 )
+ res = ReadFasta34m10_scoreonly_nuc( rfp, val, nin );
+ else
+ res = ReadFasta34m10_scoreonly( rfp, val, nin );
+// fprintf( stderr, "done. val[0] = %f\n", val[0] );
+
+
+ fclose( rfp );
+
+#if 0
+ for( i=0; i<nin; i++ )
+ fprintf( stderr, "r[%d-%d] = %f\n", 0, i, val[i] );
+ exit( 1 );
+#endif
+
+ return( val );
+}
+#if 0
+static double *callblast( char **seq, Scores *scores, int nin, int query, int rewritedata )
+{
+ double *val;
+ FILE *qfp;
+ FILE *dfp;
+ FILE *rfp;
+ int i, j;
+ char com[10000];
+ static char datafile[1000];
+ static char queryfile[1000];
+ static char resultfile[1000];
+ static int pid;
+ static char *tmpseq;
+ static char *tmpname;
+ char *seqptr;
+ int slen;
+ int res;
+ static Scores *scoresbk = NULL;
+ static int ninbk = 0;
+
+ if( pid == 0 )
+ {
+ pid = (int)getpid();
+ sprintf( datafile, "/tmp/data-%d\0", pid );
+ sprintf( queryfile, "/tmp/query-%d\0", pid );
+ sprintf( resultfile, "/tmp/fasta-%d\0", pid );
+
+ tmpseq = calloc( nlenmax+1, sizeof( char ) );
+ tmpname = calloc( B+1, sizeof( char ) );
+ }
+
+ val = calloc( nin, sizeof( double ) );
+// fprintf( stderr, "nin=%d, q=%d\n", nin, query );
+
+ if( rewritedata )
+ {
+ scoresbk = scores;
+ ninbk = nin;
+ fprintf( stderr, "\nformatting .. " );
+ dfp = fopen( datafile, "w" );
+ if( !dfp ) ErrorExit( "Cannot open datafile." );
+ for( i=0; i<nin; i++ )
+ {
+// fprintf( stderr, "i=%d / %d / %d\n", i, nin, njob );
+// fprintf( stderr, "nlenmax = %d\n", nlenmax );
+// fprintf( stderr, "scores[i].orilen = %d\n", scores[i].orilen );
+// fprintf( stderr, "strlen( seq[scores[i].numinseq] = %d\n", strlen( seq[scores[i].numinseq] ) );
+ gappick0( tmpseq, seq[scores[i].numinseq] );
+ sprintf( tmpname, "+===========+%d \0", i );
+ slen = scores[i].orilen;
+ writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
+ }
+ fclose( dfp );
+
+ if( scoremtx == -1 )
+ sprintf( com, "formatdb -p f -i %s -o F", datafile );
+ else
+ sprintf( com, "formatdb -i %s -o F", datafile );
+ system( com );
+// fprintf( stderr, "done.\n" );
+ }
+
+
+ gappick0( tmpseq, seq[scores[query].numinseq] );
+ sprintf( tmpname, "+==========+%d \0", 0 );
+ slen = scores[query].orilen;
+ qfp = fopen( queryfile, "w" );
+ if( !qfp ) ErrorExit( "Cannot open queryfile." );
+ writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
+ fclose( qfp );
+// fprintf( stderr, "q=%s\n", tmpseq );
+
+ fprintf( stderr, "\ncalling blast .. \n" );
+ if( scoremtx == -1 )
+ sprintf( com, "blastall -b %d -e 1e10 -p blastn -m 7 -i %s -d %s > %s\0", nin, queryfile, datafile, resultfile );
+ else
+ sprintf( com, "blastall -b %d -G 10 -E 1 -e 1e10 -p blastp -m 7 -i %s -d %s > %s\0", nin, queryfile, datafile, resultfile );
+ res = system( com );
+ if( res ) ErrorExit( "error in blast" );
+
+ rfp = fopen( resultfile, "r" );
+ if( rfp == NULL )
+ ErrorExit( "file 'fasta.$$' does not exist\n" );
+ res = ReadBlastm7_scoreonly( rfp, val, nin );
+ fclose( rfp );
+
+#if 0
+ for( i=0; i<nin; i++ )
+ fprintf( stderr, "r[%d-%d] = %f\n", 0, i, val[i] );
+#endif
+
+ return( val );
+}
+#endif
+
+#if 0
+static void selhead( int *ar, int n )
+{
+ int min = *ar;
+ int *minptr = ar;
+ int *ptr = ar;
+ int tmp;
+ n--;
+ ar++;
+ while( n-- )
+ {
+ if( ( tmp = *ptr++ ) < min )
+ {
+ min = tmp;
+ minptr = ptr;
+ }
+ }
+ if( minptr != ar )
+ {
+ tmp = *ar;
+ *ar = min;
+ *minptr = tmp;
+ }
+ return;
+}
+#endif
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ doalign = 0;
+ fromaln = 0;
+ treeout = 0;
+ uselongest = 1;
+ reorder = 1;
+ nevermemsave = 0;
+ inputfile = NULL;
+ fftkeika = 0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0;
+ force_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'X';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = -1530;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = -123;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ TMorJTT = JTT;
+ classsize = NOTSPECIFIED;
+ picksize = NOTSPECIFIED;
+ tokyoripara = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'p':
+ picksize = atoi( *++argv );
+ fprintf( stderr, "picksize = %d\n", picksize );
+ --argc;
+ goto nextoption;
+ case 's':
+ classsize = atoi( *++argv );
+ fprintf( stderr, "groupsize = %d\n", classsize );
+ --argc;
+ goto nextoption;
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+// fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+// fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+ fprintf( stderr, "kimuraR = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+// fprintf( stderr, "blosum %d\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "tm %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'T':
+ tokyoripara = (double)atof( *++argv );
+ --argc;
+ goto nextoption;
+ case 'l':
+ uselongest = 0;
+ break;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'S':
+ doalign = 'f';
+ break;
+ case 'Z':
+ fromaln = 1;
+ break;
+ case 'L':
+ doalign = 1;
+ break;
+ case 'x':
+ reorder = 0;
+ break;
+ case 't':
+ treeout = 1;
+ break;
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+ case 'e':
+ fftscore = 0;
+ break;
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#if 0
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+ case 'Q':
+ calledByXced = 1;
+ break;
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'R':
+ alg = 'R';
+ break;
+ case 'Q':
+ alg = 'Q';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'N':
+ nevermemsave = 1;
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'C':
+ alg = 'C';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'G':
+ use_fft = 1;
+ force_fft = 1;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'd':
+ disp = 1;
+ break;
+ case 'o':
+ outgap = 0;
+ break;
+ case 'J':
+ tbutree = 0;
+ break;
+ case 'X':
+ treemethod = 'X'; // mix
+ break;
+ case 'E':
+ treemethod = 'E'; // upg (average)
+ break;
+ case 'q':
+ treemethod = 'q'; // minimum
+ break;
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+static int maxl;
+static int tsize;
+
+int seq_grp_nuc( int *grp, char *seq )
+{
+ int tmp;
+ int *grpbk = grp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 4 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+ return( grp-grpbk );
+}
+
+int seq_grp( int *grp, char *seq )
+{
+ int tmp;
+ int *grpbk = grp;
+ while( *seq )
+ {
+ tmp = amino_grp[(int)*seq++];
+ if( tmp < 6 )
+ *grp++ = tmp;
+ else
+ fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
+ }
+ *grp = END_OF_VEC;
+ return( grp-grpbk );
+}
+
+void makecompositiontable_p( short *table, int *pointt )
+{
+ int point;
+
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ table[point]++;
+}
+
+int commonsextet_p( short *table, int *pointt )
+{
+ int value = 0;
+ short tmp;
+ int point;
+ static short *memo = NULL;
+ static int *ct = NULL;
+ static int *cp;
+
+ if( !memo )
+ {
+ memo = (short *)calloc( tsize, sizeof( short ) );
+ if( !memo ) ErrorExit( "Cannot allocate memo\n" );
+ ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) );
+ if( !ct ) ErrorExit( "Cannot allocate memo\n" );
+ }
+
+ cp = ct;
+ while( ( point = *pointt++ ) != END_OF_VEC )
+ {
+ tmp = memo[point]++;
+ if( tmp < table[point] )
+ value++;
+ if( tmp == 0 ) *cp++ = point;
+ }
+ *cp = END_OF_VEC;
+
+ cp = ct;
+ while( *cp != END_OF_VEC )
+ memo[*cp++] = 0;
+
+ return( value );
+}
+
+void makepointtable_nuc( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ p = n;
+ point = *n++ * 1024;
+ point += *n++ * 256;
+ point += *n++ * 64;
+ point += *n++ * 16;
+ point += *n++ * 4;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 1024;
+ point *= 4;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+void makepointtable( int *pointt, int *n )
+{
+ int point;
+ register int *p;
+
+ p = n;
+ point = *n++ * 7776;
+ point += *n++ * 1296;
+ point += *n++ * 216;
+ point += *n++ * 36;
+ point += *n++ * 6;
+ point += *n++;
+ *pointt++ = point;
+
+ while( *n != END_OF_VEC )
+ {
+ point -= *p++ * 7776;
+ point *= 6;
+ point += *n++;
+ *pointt++ = point;
+ }
+ *pointt = END_OF_VEC;
+}
+
+#if 1
+static void pairalign( int nseq, int *nlen, char **seq, int *mem1, int *mem2, double *weight, int *alloclen )
+{
+ int l, len1, len2;
+ int clus1, clus2;
+ float pscore, tscore;
+ static int *fftlog;
+ static char *indication1, *indication2;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ static char **mseq1, **mseq2;
+ float dumfl = 0.0;
+ int ffttry;
+ int m1, m2;
+#if 0
+ int i, j;
+#endif
+
+
+ if( effarr1 == NULL )
+ {
+ fftlog = AllocateIntVec( nseq );
+ effarr1 = AllocateDoubleVec( nseq );
+ effarr2 = AllocateDoubleVec( nseq );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+ mseq1 = AllocateCharMtx( nseq, 0 );
+ mseq2 = AllocateCharMtx( nseq, 0 );
+ for( l=0; l<nseq; l++ ) fftlog[l] = 1;
+ }
+
+ tscore = 0.0;
+ m1 = mem1[0];
+ m2 = mem2[0];
+ len1 = strlen( seq[m1] );
+ len2 = strlen( seq[m2] );
+ if( *alloclen < len1 + len2 )
+ {
+ fprintf( stderr, "\nReallocating.." );
+ *alloclen = ( len1 + len2 ) + 1000;
+ ReallocateCharMtx( seq, nseq, *alloclen + 10 );
+ fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
+ }
+
+#if WEIGHT
+ clus1 = fastconjuction_noname( mem1, seq, mseq1, effarr1, weight, indication1 );
+ clus2 = fastconjuction_noname( mem2, seq, mseq2, effarr2, weight, indication2 );
+#else
+ clus1 = fastconjuction_noweight( mem1, seq, mseq1, effarr1, indication1 );
+ clus2 = fastconjuction_noweight( mem2, seq, mseq2, effarr2, indication2 );
+#endif
+
+#if 0
+ for( i=0; i<clus1; i++ )
+ fprintf( stderr, "in p seq[%d] = %s\n", mem1[i], seq[mem1[i]] );
+ for( i=0; i<clus2; i++ )
+ fprintf( stderr, "in p seq[%d] = %s\n", mem2[i], seq[mem2[i]] );
+#endif
+
+#if 0
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+#endif
+
+// fprintf( stdout, "mseq1 = %s\n", mseq1[0] );
+// fprintf( stdout, "mseq2 = %s\n", mseq2[0] );
+
+ if( !nevermemsave && ( alg != 'M' && ( len1 > 10000 || len2 > 10000 ) ) )
+ {
+ fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode\n", len1, len2 );
+ alg = 'M';
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonAlloc1 = 0;
+ commonAlloc2 = 0;
+ }
+
+ if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
+ else ffttry = 0;
+
+ if( force_fft || ( use_fft && ffttry ) )
+ {
+ fprintf( stderr, "\bf" );
+ if( alg == 'M' )
+ {
+ fprintf( stderr, "\bm" );
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
+ }
+ else
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
+ }
+ }
+ else
+ {
+ fprintf( stderr, "\bd" );
+ fftlog[m1] = 0;
+ switch( alg )
+ {
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
+ break;
+ case( 'M' ):
+ fprintf( stderr, "\bm" );
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'Q' ):
+ if( clus1 == 1 && clus2 == 1 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ break;
+ case( 'A' ):
+ if( clus1 == 1 && clus2 == 1 )
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = G__align11( mseq1, mseq2, *alloclen, outgap, outgap );
+ }
+ else
+ {
+// fprintf( stderr, "%d-%d", clus1, clus2 );
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+ break;
+ default:
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f\n", pscore );
+#endif
+ nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
+ return;
+}
+#endif
+
+#if 0
+static void treebase( int nseq, int *nlen, char **aseq, double *eff, int nalign, int ***topol, int *alloclen ) // topol
+{
+ int i, l;
+ int nlim;
+ int clus1, clus2;
+
+ nlim = nalign-1;
+ for( l=0; l<nlim; l++ )
+ {
+ fprintf( stderr, "in treebase, l = %d\n", l );
+ fprintf( stderr, "aseq[0] = %s\n", aseq[0] );
+ fprintf( stderr, "aseq[topol[l][0][0]] = %s\n", aseq[topol[l][0][0]] );
+ pairalign( nseq, nlen, aseq, topol[l][0], topol[l][1], eff, alloclen );
+ free( topol[l][0] );
+ free( topol[l][1] );
+ }
+}
+#endif
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'S' )
+ fprintf( fp, "Apgorithm S\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( treemethod == 'X' )
+ fprintf( fp, "Tree = UPGMA (mix).\n" );
+ else if( treemethod == 'E' )
+ fprintf( fp, "Tree = .UPGMA (average)\n" );
+ else if( treemethod == 'q' )
+ fprintf( fp, "Tree = Minimum linkage.\n" );
+ else
+ fprintf( fp, "Unknown tree.\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+#if 1
+static int splitseq_mq( Scores *scores, int nin, int *nlen, char **seq, char **orialn, char **name, char *inputfile, int uniform, char **tree, int *alloclen, int *order, int *whichgroup, double *weight, int *depthpt, int qinoya )
+{
+ int val;
+ int ii, jj;
+ int *mptr;
+ int treelen = 0; // by Mathog, a guess
+ static int groupid = 0;
+ static int branchid = 0;
+ int i, j;
+ int selfscore0;
+ double **dfromc;
+ double **dfromcp;
+ float **pickmtx;
+ float **yukomtx;
+ static short *table1;
+ Scores **outs, *ptr;
+ int *numin;
+ int *tsukau;
+ int belongto;
+ char **children = NULL; // by Mathog, a guess
+ char *tmptree;
+ static int *orderpos = NULL;
+ int rn;
+ int npick;
+ int nyuko;
+ int *picks;
+ int *yukos;
+ int *s_p_map;
+ int *p_o_map;
+ int *s_y_map;
+ int *y_o_map;
+ int *closeh;
+ int nkouho;
+ int *pickkouho;
+ int *iptr;
+ int *jptr;
+ int aligned;
+ int ***topol;
+ int *treeorder;
+ int picktmp;
+ float **len;
+ double minscore;
+// double *minscoreinpick;
+ float *hanni;
+ double lenfac;
+ double longer;
+ double shorter;
+ static char **mseq1 = NULL;
+ static char **mseq2 = NULL;
+ double *blastresults = NULL; // by Mathog, a guess
+ static int palloclen = 0;
+ float maxdist;
+
+ if( orderpos == NULL )
+ orderpos = order;
+ if( palloclen == 0 )
+ palloclen = *alloclen * 2;
+ if( mseq1 == NULL && doalign == 1 )
+ {
+ mseq1 = AllocateCharMtx( 1, palloclen );
+ mseq2 = AllocateCharMtx( 1, palloclen );
+ }
+
+ if( nin == 0 )
+ {
+#if TREE
+ if( treeout )
+ {
+ *tree = (char *)calloc( 1, sizeof( char ) );
+ **tree = 0;
+ }
+#endif
+ return 1;
+ }
+
+ if( nin < 2 || uniform == -1 ) // kokodato muda deha nai ga
+ {
+ fprintf( stderr, "\nLeaf %d / %d ", ++branchid, njob );
+#if 0
+ outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
+ sprintf( outputfile, "%s-%d", inputfile, branchid );
+ if( uniform > 0 )
+// sprintf( outputfile, "%su%d", outputfile, uniform );
+ sprintf( outputfile + strlen(outputfile), "u%d", uniform );
+ fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
+ outfp = fopen( outputfile, "w" );
+ free( outputfile );
+ if( outfp == NULL )
+ {
+ fprintf( stderr, "Cannot open %s\n", outputfile );
+ exit( 1 );
+ }
+ for( j=0; j<nin; j++ )
+ fprintf( outfp, ">G%d %s\n%s\n", branchid, scores[j].name+1, seq[scores[j].numinseq] );
+ fclose( outfp );
+#endif
+
+
+#if TREE
+ if( treeout )
+ {
+ treelen = 0;
+ tmptree = calloc( 100, sizeof( char ) );
+ for( j=0; j<nin; j++ )
+ {
+ treelen += sprintf( tmptree, "%d", scores[j].numinseq+1 );
+ }
+ free( tmptree );
+
+ *tree = (char *)calloc( treelen + nin + 5, sizeof( char ) );
+ if( nin > 1 ) **tree = '(';
+ else **tree = '\0';
+// **tree = '\0';
+ for( j=0; j<nin-1; j++ )
+ {
+ sprintf( *tree+strlen( *tree ), "%d,", scores[j].numinseq+1 );
+ }
+ sprintf( *tree+strlen( *tree ), "%d", scores[j].numinseq+1 );
+ if( nin > 1 ) strcat( *tree, ")" );
+// fprintf( stdout, "*tree = %s\n", *tree );
+ }
+
+#endif
+ for( j=0; j<nin; j++ )
+ {
+ *orderpos++ = scores[j].numinseq;
+// fprintf( stderr, "*order = %d\n", scores[j].numinseq );
+ }
+
+ return 1;
+ }
+
+
+
+ if( uselongest )
+ {
+ i = nin;
+ ptr = scores;
+ selfscore0 = scores->selfscore;
+ belongto = 0;
+ while( i-- )
+ {
+// fprintf( stderr, "ptr-scores=%d, numinseq = %d, score = %f\n", ptr-scores, ptr->numinseq+1, ptr->score );
+ if( ptr->selfscore > selfscore0 )
+ {
+ selfscore0 = ptr->selfscore;
+ belongto = ptr-scores;
+ }
+ ptr++;
+ }
+#if 1
+ if( belongto != 0 )
+ {
+// fprintf( stderr, "swap %d %s\n<->\n%d %s\n", 0, scores->name, belongto, (scores+belongto)->name );
+ ptr = calloc( 1, sizeof( Scores ) );
+ *ptr = scores[belongto];
+ scores[belongto] = *scores;
+ *scores = *ptr;
+ free( ptr );
+ }
+#endif
+ }
+ else
+ {
+ qsort( scores, nin, sizeof( Scores ), (int (*)())lcompare );
+ belongto = (int)( 0.5 * nin );
+// fprintf( stderr, "lengths = %d, %d, %d\n", scores->orilen, scores[belongto].orilen, scores[nin-1].orilen );
+ if( belongto != 0 )
+ {
+// fprintf( stderr, "swap %d %s\n<->\n%d %s\n", 0, scores->name, belongto, (scores+belongto)->name );
+ ptr = calloc( 1, sizeof( Scores ) );
+ *ptr = scores[belongto];
+ scores[belongto] = *scores;
+ *scores = *ptr;
+ free( ptr );
+ }
+ }
+
+ if( qinoya != scores->numinseq )
+// if( 1 || qinoya != scores->numinseq )
+ {
+// fprintf( stdout, "### scores->numinseq = %d, qinoya=%d, depth=%d\n", scores->numinseq, qinoya, *depthpt );
+
+
+ if( doalign )
+ {
+ if( doalign == 'f' )
+ {
+ blastresults = callfasta( seq, scores, nin, NULL, 0, 1 );
+ if( scores->selfscore != (int)blastresults[0] )
+ {
+ fprintf( stderr, "\n\nWARNING1: selfscore\n" );
+ fprintf( stderr, "scores->numinseq = %d\n", scores->numinseq+1 );
+ fprintf( stderr, "scores->orilen = %d\n", scores->orilen );
+ fprintf( stderr, "scores->selfscore = %d, but blastresults[0] = %f\n", scores->selfscore, blastresults[0] );
+// if( abs( scores->selfscore - (int)blastresults[0] ) > 2 )
+// exit( 1 );
+// scores->selfscore = (int)blastresults[0]; //iinoka?
+
+// exit( 1 );
+ }
+ }
+ else
+ gappick0( mseq1[0], seq[scores->numinseq] );
+ }
+ else
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ makecompositiontable_p( table1, scores[0].pointt );
+ }
+
+ selfscore0 = scores[0].selfscore;
+ for( i=0; i<nin; i++ )
+ {
+ if( scores->orilen > scores[i].orilen )
+ {
+ longer = (double)scores->orilen;
+ shorter = (double)scores[i].orilen;
+ }
+ else
+ {
+ longer = (double)scores[i].orilen; // nai
+ shorter = (double)scores->orilen; //nai
+ }
+
+#if LENFAC
+ lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
+// lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
+// fprintf( stderr, "lenfac = %f l=%d,%d\n", lenfac,scores->orilen, scores[i].orilen );
+#else
+ lenfac = 1.0;
+#endif
+
+ if( doalign )
+ {
+ if( doalign == 'f' )
+ {
+ scores[i].score = ( 1.0 - blastresults[i] / MIN( scores->selfscore, scores[i].selfscore ) ) * 1;
+ if( scores[i].score < 0.0 ) scores[i].score = 0.0;
+ }
+ else
+ {
+ if( fromaln )
+ {
+// scores[i].score = ( 1.0 - (double)G__align11_noalign( amino_disLN, mseq1, mseq2, palloclen ) / MIN( selfscore0, scores[i].selfscore ) ) * 1;
+ scores[i].score = ( 1.0 - (double)naivepairscore11( orialn[scores[i].numinseq], orialn[scores->numinseq], penalty ) / MIN( selfscore0, scores[i].selfscore ) ) * 1;
+ }
+ else
+ {
+ if( *depthpt == 0 ) fprintf( stderr, "\r%d / %d ", i, nin );
+ gappick0( mseq2[0], seq[scores[i].numinseq] );
+// fprintf( stdout, "### before calc scores[%d] = %f (%c)\n", i, scores[i].score, qinoya == scores->numinseq?'o':'x' );
+ scores[i].score = ( 1.0 - (double)G__align11_noalign( amino_disLN, -1200, -60, mseq1, mseq2, palloclen ) / MIN( selfscore0, scores[i].selfscore ) ) * 1;
+// fprintf( stderr, "scores[i] = %f\n", scores[i].score );
+// fprintf( stderr, "m1=%s\n", seq[scores[0].numinseq] );
+// fprintf( stderr, "m2=%s\n", seq[scores[i].numinseq] );
+// fprintf( stdout, "### before calc scores[%d] = %f (%c)\n", i, scores[i].score, qinoya == scores->numinseq?'o':'x' );
+ }
+ }
+ }
+ else
+ {
+ scores[i].score = ( 1.0 - (double)commonsextet_p( table1, scores[i].pointt ) / MIN( selfscore0, scores[i].selfscore ) ) * lenfac;
+ if( scores[i].score > MAX6DIST ) scores[i].score = MAX6DIST;
+ }
+// if( i ) fprintf( stderr, "%d-%d d %4.2f len %d %d\n", 1, i+1, scores[i].score, scores->orilen, scores[i].orilen );
+ }
+ if( doalign == 'f' ) free( blastresults );
+ if( doalign == 0 ) free( table1 );
+//exit( 1 );
+ }
+
+// fprintf( stderr, "sorting .. " );
+ qsort( scores, nin, sizeof( Scores ), (int (*)())dcompare );
+// fprintf( stderr, "done.\n" );
+
+
+ maxdist = scores[nin-1].score;
+ if( fromaln ) // kanzen itch ga misalign sareteiru kamoshirenai.
+ {
+ if( scores[0].shimon == scores[nin-1].shimon && !strcmp( seq[scores[0].numinseq], seq[scores[nin-1].numinseq] ) )
+ {
+ maxdist = 0.0;
+ }
+// fprintf( stderr, "maxdist?? = %f, nin=%d, %d inori\n", scores[nin-1].score, nin, scores[nin-1].numinseq+1 );
+ }
+
+// fprintf( stderr, "maxdist? = %f, nin=%d\n", scores[nin-1].score, nin );
+
+ if( nin == 1 ) fprintf( stderr, "nin=1, scores[0].score = %f\n", scores[0].score );
+
+// kokoni if( nin < 2 || ... )
+
+ picks = AllocateIntVec( nin+1 );
+ s_p_map = AllocateIntVec( nin+1 );
+ s_y_map = AllocateIntVec( nin+1 );
+ pickkouho = AllocateIntVec( nin+1 );
+ closeh = AllocateIntVec( nin+1 );
+
+// nkouho = getkouho( pickkouho, (picksize+100)/nin, nin, scores, seq );
+// nkouho = getkouho( pickkouho, 1.0, nin, scores, seq ); // zenbu
+// fprintf( stderr, "selecting kouhos phase 2\n" );
+// if( nkouho == 0 )
+// {
+// fprintf( stderr, "selecting kouhos, phase 2\n" );
+// nkouho = getkouho( pickkouho, 1.0, nin, scores, seq );
+// }
+// fprintf( stderr, "\ndone\n\n" );
+ for( i=0; i<nin; i++ ) pickkouho[i] = i+1; nkouho = nin-1; // zenbu
+
+
+
+ iptr = picks;
+ *iptr++ = 0;
+ npick = 1;
+ if( nkouho > 0 )
+ {
+// fprintf( stderr, "pickkouho[0] = %d\n", pickkouho[0] );
+// fprintf( stderr, "pickkouho[nin-1] = %d\n", pickkouho[nin-1] );
+ picktmp = pickkouho[nkouho-1];
+// fprintf( stderr, "\nMOST DISTANT kouho=%d, nin=%d, nkouho=%d\n", picktmp, nin, nkouho );
+ nkouho--;
+ if( ( scores[picktmp].shimon == scores[0].shimon ) && ( !strcmp( seq[scores[0].numinseq], seq[scores[picktmp].numinseq] ) ) )
+ {
+// fprintf( stderr, "known, j=%d (%d inori)\n", 0, scores[picks[0]].numinseq );
+// fprintf( stderr, "%s\n%s\n", seq[scores[picktmp].numinseq], seq[scores[picks[0]].numinseq] );
+ ;
+ }
+ else
+ {
+ *iptr++ = picktmp;
+ npick++;
+// fprintf( stderr, "ok, %dth pick = %d (%d inori)\n", npick, picktmp, scores[picktmp].numinseq );
+ }
+ }
+ i = 1;
+ while( npick<picksize && nkouho>0 )
+ {
+ if( i )
+ {
+ i = 0;
+ rn = nkouho * 0.5;
+// fprintf( stderr, "rn = %d\n", rn );
+ }
+ else
+ {
+ rn = rnd() * (nkouho);
+ }
+ picktmp = pickkouho[rn];
+// fprintf( stderr, "rn=%d/%d (%d inori), kouho=%d, nin=%d, nkouho=%d\n", rn, nkouho, scores[pickkouho[rn]].numinseq, pickkouho[rn], nin, nkouho );
+
+// fprintf( stderr, "#kouho before swap\n" );
+// for( i=0; i<nkouho; i++ ) fprintf( stderr, "%d ", pickkouho[i] ); fprintf( stderr, "\n" );
+
+ nkouho--;
+ pickkouho[rn] = pickkouho[nkouho];
+#if 1
+// fprintf( stderr, "#kouho after swap\n" );
+// for( i=0; i<nkouho; i++ ) fprintf( stderr, "%d ", pickkouho[i] ); fprintf( stderr, "\n" );
+ for( j=0; j<npick; j++ )
+ {
+ if( scores[picktmp].shimon == scores[picks[j]].shimon && !strcmp( seq[scores[picks[j]].numinseq], seq[scores[picktmp].numinseq] ) )
+ break;
+ }
+ if( j == npick )
+#endif
+ {
+// fprintf( stderr, "ok, %dth pick = %d (%d inori)\n", npick, picktmp, scores[picktmp].numinseq );
+ npick++;
+ *iptr++ = picktmp;
+ }
+ else
+ {
+// fprintf( stderr, "known, j=%d (%d inori)\n", j, scores[picks[j]].numinseq );
+ }
+ }
+#if 0
+ for( i=0; i<nin; i++ )
+ {
+ fprintf( stderr, "i=%d/%d, scores[%d].score = %f, inori=%d\n", i, nin, i, scores[i].score, scores[i].numinseq );
+ }
+ fprintf( stderr, "range:nin=%d scores[%d].score <= %f\n", nin, npick, scores[nin-1].score);
+ for( i=0; i<npick; i++ )
+ {
+ fprintf( stderr, "i=%d/%d, scores[%d].score = %f, inori=%d\n", i, npick, picks[i], scores[picks[i]].score, scores[picks[i]].numinseq );
+ }
+exit( 1 );
+#endif
+
+// fprintf( stderr, "\nnkouho=%d, defaultq2 = %d (%d inori)\n", nkouho, picks[npick-1], scores[picks[npick-1]].numinseq );
+
+ qsort( picks, npick, sizeof( int ), (int (*)())intcompare );
+
+// fprintf( stderr, "allocating..\n" );
+
+// fprintf( stderr, "allocating outs, npick = %d\n", npick );
+ numin = calloc( npick, sizeof( int ) );
+ tsukau = calloc( npick, sizeof( int ) );
+ outs = calloc( npick, sizeof( Scores * ) );
+ for( i=0; i<npick; i++ ) outs[i] = NULL;
+ topol = AllocateIntCub( npick, 2, 0 );
+ treeorder = AllocateIntVec( npick + 1 );
+ len = AllocateFloatMtx( npick, 2 );
+ pickmtx = AllocateFloatHalfMtx( npick );
+// yukomtx = AllocateFloatHalfMtx( npick );
+// minscoreinpick = AllocateDoubleVec( npick );
+ yukos = AllocateIntVec( npick );
+ p_o_map = AllocateIntVec( npick+1 );
+ y_o_map = AllocateIntVec( npick+1 );
+ hanni = AllocateFloatVec( npick );
+
+ for( i=0; i<nin; i++ ) s_p_map[i] = -1;
+// fprintf( stderr, "npick = %d\n", npick );
+// fprintf( stderr, "picks =" );
+ for( i=0; i<npick; i++ )
+ {
+ s_p_map[picks[i]] = i;
+ p_o_map[i] = scores[picks[i]].numinseq;
+// fprintf( stderr, " %d (%dinori)\n", picks[i], scores[picks[i]].numinseq+1 );
+ }
+// fprintf( stderr, "\n" );
+
+#if 0
+ fprintf( stderr, "p_o_map =" );
+ for( i=0; i<npick; i++ )
+ {
+ fprintf( stderr, " %d", p_o_map[i]+1 );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "picks =" );
+ for( i=0; i<npick; i++ )
+ {
+ fprintf( stderr, " %d", picks[i] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+ for( j=0; j<nin; j++ )
+ {
+ if( s_p_map[j] != -1 )
+ {
+ pickmtx[0][s_p_map[j]] = (float)scores[j].score;
+// fprintf( stderr, "pickmtx[0][%d] = %f\n", s_p_map[j], pickmtx[0][s_p_map[j]] );
+ }
+ }
+
+ for( j=1; j<npick; j++ )
+ {
+ if( doalign )
+ {
+ if( doalign == 'f' )
+ {
+// blastresults = callfasta( seq, scores, npick-j+1, picks+j-1, picks[j], 1 );
+ blastresults = callfasta( seq, scores, npick, picks, picks[j], (j==1) );
+ if( scores[picks[j]].selfscore != (int)blastresults[j] )
+ {
+ fprintf( stderr, "\n\nWARNING2: selfscore j=%d/%d\n", j, npick );
+ fprintf( stderr, "scores[picks[j]].numinseq = %d\n", scores[picks[j]].numinseq+1 );
+ fprintf( stderr, "scores[picks[j]].orilen = %d\n", scores[picks[j]].orilen );
+ fprintf( stderr, "scores[picks[j]].selfscore = %d, but blastresults[j] = %f\n", scores[picks[j]].selfscore, blastresults[j] );
+// if( abs( scores[picks[j]].selfscore - (int)blastresults[j] ) > 2 )
+// exit( 1 );
+// scores->selfscore = (int)blastresults[0]; //iinoka?
+ }
+ }
+ else
+ gappick0( mseq1[0], seq[scores[picks[j]].numinseq] );
+ }
+ else
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ makecompositiontable_p( table1, scores[picks[j]].pointt );
+ }
+
+ selfscore0 = scores[picks[j]].selfscore;
+ pickmtx[j][0] = 0.0;
+ for( i=j+1; i<npick; i++ )
+ {
+ if( scores[picks[j]].orilen > scores[picks[i]].orilen )
+ {
+ longer = (double)scores[picks[j]].orilen;
+ shorter = (double)scores[picks[i]].orilen;
+ }
+ else
+ {
+ longer = (double)scores[picks[i]].orilen;
+ shorter = (double)scores[picks[j]].orilen;
+ }
+
+ #if LENFAC
+ lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
+ // lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
+ // fprintf( stderr, "lenfac = %f l=%d,%d\n", lenfac,scores->orilen, scores[i].orilen );
+ #else
+ lenfac = 1.0;
+ #endif
+
+ if( doalign )
+ {
+ if( doalign == 'f' )
+ {
+ pickmtx[j][i-j] = ( 1.0 - blastresults[i] / MIN( selfscore0, scores[picks[i]].selfscore ) ) * 1;
+ if( pickmtx[j][i-j] < 0.0 ) pickmtx[j][i-j] = 0.0;
+ }
+ else
+ {
+ if( fromaln )
+ {
+ fprintf( stderr, "%d-%d/%d\r", j, i, npick );
+ pickmtx[j][i-j] = ( 1.0 - (double)naivepairscore11( orialn[scores[picks[i]].numinseq], orialn[scores[picks[j]].numinseq], penalty ) / MIN( selfscore0, scores[picks[i]].selfscore ) ) * 1;
+ }
+ else
+ {
+// fprintf( stderr, "\r%d / %d ", i, nin );
+ gappick0( mseq2[0], seq[scores[picks[i]].numinseq] );
+ pickmtx[j][i-j] = ( 1.0 - (double)G__align11_noalign( amino_disLN, -1200, -60, mseq1, mseq2, palloclen ) / MIN( selfscore0, scores[picks[i]].selfscore ) ) * 1;
+ // fprintf( stderr, "scores[picks[i]] = %f\n", scores[picks[i]].score );
+ }
+ }
+ }
+ else
+ {
+ pickmtx[j][i-j] = ( 1.0 - (double)commonsextet_p( table1, scores[picks[i]].pointt ) / MIN( selfscore0, scores[picks[i]].selfscore ) ) * lenfac;
+ if( pickmtx[j][i-j] > MAX6DIST ) pickmtx[j][i-j] = MAX6DIST;
+ }
+
+ }
+ if( doalign == 'f' ) free( blastresults );
+ if( doalign == 0 ) free( table1 );
+ }
+
+ dfromcp = AllocateDoubleMtx( npick, nin );
+ dfromc = AllocateDoubleMtx( npick, 0 );
+
+ for( i=0; i<npick; i++ ) for( j=0; j<nin; j++ )
+ dfromcp[i][j] = -0.5;
+ for( j=0; j<nin; j++ )
+ {
+ dfromcp[0][j] = ( scores[j].score );
+// fprintf( stderr, "j=%d, s_p_map[j]=%d\n", j, s_p_map[j] );
+ }
+
+ for( i=0; i<npick; i++ ) for( j=i; j<npick; j++ )
+ {
+ dfromcp[i][picks[j]] = dfromcp[j][picks[i]] = pickmtx[i][j-i];
+ }
+
+#if 0
+ fprintf( stderr, "pickmtx = \n" );
+ for( i=0; i<npick; i++ )
+ {
+ for( j=i; j<npick; j++ )
+ {
+ fprintf( stderr, "pickmtx[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
+ }
+ }
+ exit( 1 );
+#endif
+
+
+
+// for( i=0; i<npick-1; i++ ) for( j=i; j<npick; j++ )
+// fprintf( stderr, "dist[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
+
+ for( i=0; i<npick; i++ ) tsukau[i] = 1;
+ for( i=0; i<nin; i++ ) closeh[i] = -1;
+ for( i=0; i<npick; i++ )
+ {
+ closeh[picks[i]] = picks[i];
+// fprintf( stderr, "i=%d/%d, picks[i]=%d, %d inori, closeh[%d] = %d \n", i, npick, picks[i], p_o_map[i]+1, picks[i], closeh[picks[i]] );
+ }
+#if 0
+ fprintf( stderr, "closeh = \n" );
+ for( i=0; i<nin; i++ )
+ {
+ fprintf( stderr, "%d ", closeh[i] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+#if DIANA
+ for( i=0; i<npick-1; i++ ) for( j=i; j<npick; j++ )
+ fprintf( stderr, "dist[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
+ fprintf( stderr, "DIANA!!\n" );
+ if( npick > 2 )
+ {
+ float avdist;
+ float avdist1;
+ float avdist2;
+ float maxavdist;
+ int splinter;
+ int count;
+ int dochokoho;
+ splinter = 0;
+ int *docholist;
+ int *docholistbk;
+ maxavdist = 0.0;
+ for( i=0; i<npick; i++ )
+ {
+ avdist = 0.0;
+ for( j=i+1; j<npick; j++ )
+ {
+ avdist += pickmtx[i][j-i];
+ }
+ for( j=0; j<i; j++ )
+ {
+ avdist += pickmtx[j][i-j];
+ }
+ avdist /= (npick-1);
+ fprintf( stderr, "avdist[%d] = %f\n", p_o_map[i] + 1, avdist );
+ if( maxavdist < avdist )
+ {
+ maxavdist = avdist;
+ splinter = i;
+ }
+ }
+ fprintf( stderr, "splinter = %d (%d inori), maxavdist = %f\n", splinter, p_o_map[splinter]+1, maxavdist );
+
+ docholist = AllocateIntVec( npick );
+ docholistbk = AllocateIntVec( npick );
+ for( i=0; i<npick; i++ ) docholist[i] = 0;
+ docholist[splinter] = 1;
+ while( 1 )
+ {
+ for( i=0; i<npick; i++ ) docholistbk[i] = docholist[i];
+ for( dochokoho = 0; dochokoho<npick; dochokoho++ )
+ {
+ fprintf( stderr, "dochokoho=%d\n", dochokoho );
+ if( docholist[dochokoho] ) continue;
+ count = 0;
+ avdist1 = 0.0;
+ i=dochokoho;
+ {
+ for( j=i+1; j<npick; j++ )
+ {
+ if( docholist[j] || j == dochokoho ) continue;
+ avdist1 += pickmtx[i][j-i];
+ count++;
+ }
+ for( j=0; j<i; j++ )
+ {
+ if( docholist[j] || j == dochokoho ) continue;
+ avdist1 += pickmtx[j][i-j];
+ count++;
+ }
+ }
+ if( count < 1 ) avdist1 = 0.0;
+ else avdist1 /= (float)count;
+ fprintf( stderr, "docho %d (%dinori), avdist1 = %f\n", dochokoho, p_o_map[dochokoho] + 1, avdist1 );
+
+ count = 0;
+ avdist2 = 0.0;
+ i=dochokoho;
+ {
+ for( j=i+1; j<npick; j++ )
+ {
+ if( !docholist[j] || j == dochokoho ) continue;
+ avdist2 += pickmtx[i][j-i];
+ count++;
+ }
+ for( j=0; j<i; j++ )
+ {
+ if( !docholist[j] || j == dochokoho ) continue;
+ avdist2 += pickmtx[j][i-j];
+ count++;
+ }
+ }
+ if( count < 1 ) avdist2 = 0.0;
+ else avdist2 /= (float)count;
+ fprintf( stderr, "docho %d (%dinori), avdist2 = %f\n", dochokoho, p_o_map[dochokoho] + 1, avdist2 );
+
+ if( avdist2 < avdist1 )
+ {
+ docholist[dochokoho] = 1;
+ hanni[dochokoho] = avdist2;
+ }
+ else
+ {
+ docholist[dochokoho] = 0;
+ hanni[dochokoho] = avdist1;
+ }
+ fprintf( stderr, "avdist1=%f, avdist2=%f\n", avdist1, avdist2 );
+
+ }
+ for( i=0; i<npick; i++ ) if( docholist[i] != docholistbk[i] ) break;
+ if( i == npick ) break;
+
+ fprintf( stderr, "docholist = \n" );
+ for( i=0; i<npick; i++ ) fprintf( stderr, "%d ", docholist[i] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "docholist = \n" );
+ for( i=0; i<npick; i++ ) fprintf( stderr, "%d ", docholist[i] );
+ fprintf( stderr, "\n" );
+
+ for( i=0; i<npick; i++ ) if( docholist[i] == 0 ) break;
+ yukos[0] = picks[i];
+ for( i=0; i<npick; i++ ) if( docholist[i] == 1 ) break;
+ yukos[1] = picks[splinter];
+
+ for( i=0; i<npick; i++ )
+ {
+ if( docholist[i] == 0 ) closeh[picks[i]] = yukos[0];
+ if( docholist[i] == 1 ) closeh[picks[i]] = yukos[1];
+ }
+// for( i=0; i<npick; i++ ) closeh[picks[i]] = -1; // CHUUI !! iminai
+ nyuko = 2;
+ free( docholist );
+ free( docholistbk );
+ }
+ else if( npick > 1 )
+ {
+ nyuko = 2;
+ yukos[0] = picks[0]; yukos[1] = picks[1];
+ closeh[picks[0]] = yukos[0];
+ closeh[picks[1]] = yukos[1];
+ }
+ else
+ {
+ nyuko = 1;
+ yukos[0] = picks[0];
+ closeh[picks[0]] = yukos[0];
+ }
+#elif HUKINTOTREE
+ if( npick > 2 )
+ {
+#if 0
+ float avdist;
+ float maxavdist;
+ int count;
+ int splinter;
+ maxavdist = 0.0;
+ splinter=0;
+ for( i=0; i<npick; i++ )
+ {
+ avdist = 0.0;
+ for( j=i+1; j<npick; j++ )
+ {
+ avdist += pickmtx[i][j-i];
+ }
+ for( j=0; j<i; j++ )
+ {
+ avdist += pickmtx[j][i-j];
+ }
+ avdist /= (npick-1);
+ fprintf( stderr, "avdist[%d] = %f\n", p_o_map[i] + 1, avdist );
+ if( maxavdist < avdist )
+ {
+ maxavdist = avdist;
+ splinter = i;
+ }
+ }
+ fprintf( stderr, "splinter = %d (%d inori), maxavdist = %f\n", splinter, p_o_map[splinter]+1, maxavdist );
+#endif
+
+
+// fprintf( stderr, "check kaishi =>, npick=%d members = \n", npick );
+// for( i=0; i<npick; i++ ) fprintf( stderr, "%d (%d)", p_o_map[i]+1, picks[i] );
+// fprintf( stderr, "\n" );
+ for( i=0; i<npick-1; i++ )
+ {
+ if( tsukau[i] == 0 ) continue;
+ for( j=i+1; j<npick; j++ )
+ {
+// float kijun = maxdist * 1/(npick-2);
+// float kijun = maxavdist * tokyoripara;
+ float kijun;
+ kijun = maxdist * tokyoripara; // atode kakunin
+// fprintf( stderr, "%d-%d\n", i, j );
+// fprintf( stderr, "maxdist = %f\n", maxdist );
+// if( i==0 && j == 1 ) continue; // machigai!! CHUUI!!
+// if( maxdist == pickmtx[i][j-i] ) continue;
+ if( tsukau[j] == 0 ) continue;
+// fprintf( stderr, "checking %d-%d (%d-%d) %f, kijun=%f\n", p_o_map[i]+1, p_o_map[j]+1, i, j, pickmtx[i][j-i], kijun );
+ if( pickmtx[i][j-i] < kijun )
+ {
+// fprintf( stderr, "dame!! %d => %d, because %f < %f\n", p_o_map[j]+1, p_o_map[i]+1, pickmtx[i][j-i], kijun );
+#if 0
+ if( scores[picks[i]].orilen > scores[picks[j]].orilen )
+ {
+ fprintf( stderr, "%d => %d\n", p_o_map[j]+1, p_o_map[i]+1 );
+ tsukau[j] = 0;
+ }
+ else
+ {
+ fprintf( stderr, "%d => %d\n", p_o_map[i]+1, p_o_map[j]+1 );
+ tsukau[i] = 0;
+ }
+ if( 0 && j == npick-1 ) tsukau[i] = 0;
+ else tsukau[j] = 0;
+ fprintf( stderr, "tsukau[%d] = %d (%d inori)\n", j, tsukau[j], p_o_map[j]+1 );
+#else
+ tsukau[j] = 0;
+ closeh[picks[j]] = closeh[picks[i]];
+// fprintf( stderr, "%d => tsukawanai\n", j );
+#endif
+ }
+ }
+ }
+ }
+ for( ii=0,i=0; i<npick; i++ )
+ {
+ if( tsukau[i] )
+ {
+ dfromc[ii] = dfromcp[i];
+ ii++;
+ }
+ else
+ {
+ free( dfromcp[i] );
+ dfromcp[i] = NULL;
+ }
+ }
+ dfromc[ii] = NULL;
+
+ for( ii=0,i=0; i<npick; i++ )
+ {
+ if( tsukau[i] )
+ {
+ for( jj=ii,j=i; j<npick; j++ )
+ {
+ if( tsukau[j] )
+ {
+ pickmtx[ii][jj-ii] = pickmtx[i][j-i];
+ jj++;
+ }
+ }
+ ii++;
+ }
+ }
+ for( ; ii<npick; ii++ )
+ {
+ free( pickmtx[ii] );
+ pickmtx[ii] = NULL;
+ }
+
+ for( ii=0,i=0; i<npick; i++ )
+ {
+ if( tsukau[i] )
+ {
+ yukos[ii++] = picks[i];
+ }
+ }
+
+
+ nyuko = ii;
+ yukomtx = pickmtx;
+ pickmtx = NULL;
+
+#endif
+#if 0
+ for( i=0; i<npick; i++ ) for( j=i; j<npick; j++ )
+ {
+ if( tsukau[i] == 1 && tsukau[j] == 1 )
+ fprintf( stderr, "dist[%d][%d] = %f (ok)\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
+ else if( tsukau[i] == 0 && tsukau[j] == 0 )
+ fprintf( stderr, "dist[%d][%d] = %f (xx)\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
+ else
+ fprintf( stderr, "%d-%d, okashii\n", p_o_map[i]+1, p_o_map[j]+1 );
+ }
+#endif
+// FreeFloatHalfMtx( pickmtx, npick );
+
+
+ for( i=0; i<nin; i++ ) s_y_map[i] = -1;
+// fprintf( stderr, "npick = %d\n", npick );
+// fprintf( stderr, "yukos =" );
+ for( i=0; i<nyuko; i++ )
+ {
+ s_y_map[yukos[i]] = i;
+ y_o_map[i] = scores[yukos[i]].numinseq;
+// fprintf( stderr, " %d\n", yukos[i] );
+ }
+// fprintf( stderr, "\n" );
+#if 0
+ for( i=0; i<nyuko; i++ )
+ {
+ fprintf( stderr, "y_o_map[%d] = %d\n", i, y_o_map[i]+1 );
+ }
+ for( i=0; i<nyuko; i++ ) for( j=i; j<nyuko; j++ )
+ {
+ fprintf( stderr, "yukodist[%d][%d] = %f (ok)\n", y_o_map[i]+1, y_o_map[j]+1, yukomtx[i][j-i] );
+ }
+#endif
+
+ for( i=0; i<nin; i++ )
+ {
+ if( closeh[i] != -1 )
+ {
+// fprintf( stderr, "closeh[%d,%dinori] = %d,%dinori\n", i, scores[i].numinseq+1, closeh[i], scores[closeh[i]].numinseq+1 );
+ }
+ }
+
+#if 0
+ for( i=0; i<nyuko; i++ )
+ {
+ minscoreinpick[i] = 99.9;
+ for( j=i+1; j<nyuko; j++ )
+ {
+ if( minscoreinpick[i] > yukomtx[i][j-i] )
+ minscoreinpick[i] = yukomtx[i][j-i];
+ }
+ for( j=0; j<i; j++ )
+ {
+ if( minscoreinpick[i] > yukomtx[j][i-j] )
+ minscoreinpick[i] = yukomtx[j][i-j];
+ }
+ fprintf( stderr, "minscoreinpick[%d(%dinori)] = %f\n", i, y_o_map[i]+1, minscoreinpick[i] );
+ }
+#endif
+
+
+#if TREE
+ if( treeout )
+ {
+ children = calloc( nyuko+1, sizeof( char * ) );
+ for( i=0; i<nyuko+1; i++ ) children[i] = NULL;
+ }
+#endif
+// fprintf( stderr, "done..\n" );
+
+// fprintf( stderr, "classifying, nyuko=%d \n", nyuko );
+ if( nyuko == 1 )
+ {
+ if( npick != 1 )
+ {
+ fprintf( stderr, "okashii, nyuko = 1, shikashi npick = %d\n", npick );
+ exit( 1 );
+ }
+// fprintf( stderr, "### itchi suru hazu, nazenara scores[nin-1].score=%f, selfscores=%d,%d\n", scores[nin-1].score, scores[nin-1].selfscore, scores->selfscore );
+// fprintf( stderr, "seq[%d] = scores->seq = \n%s\n", scores->numinseq, seq[scores->numinseq] );
+
+ uniform = -1;
+ for( j=0; j<nin; j++ )
+ {
+ belongto = 0;
+ outs[belongto] = realloc( outs[belongto], sizeof( Scores ) * ( numin[belongto] + 1 ) );
+ outs[belongto][numin[belongto]] = scores[j];
+ numin[belongto]++;
+ }
+ }
+ else
+ {
+
+#if 0
+ fprintf( stderr, "yukos = \n" );
+ for( i=0; i<nyuko; i++ ) fprintf( stderr, "%d ", y_o_map[i] + 1 );
+ fprintf( stderr, "\n" );
+#endif
+ fprintf( stderr, "\n\n%dx%d distance matrix\n", nyuko, nin );
+
+ for( i=1; i<nyuko; i++ )
+ {
+ fprintf( stderr, "%d / %d \r", i, nyuko );
+
+ if( doalign )
+ {
+ if( doalign == 'f' )
+ {
+ blastresults = callfasta( seq, scores, nin, NULL, yukos[i], (i==1) );
+ }
+ else
+ gappick0( mseq1[0], seq[scores[yukos[i]].numinseq] );
+ }
+ else
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ makecompositiontable_p( table1, scores[yukos[i]].pointt );
+ }
+
+ selfscore0 = scores[yukos[i]].selfscore;
+ for( j=0; j<nin; j++ )
+ {
+ if( scores[yukos[i]].orilen > scores[j].orilen )
+ {
+ longer = scores[yukos[i]].orilen;
+ shorter = scores[j].orilen;
+ }
+ else
+ {
+ shorter = scores[yukos[i]].orilen;
+ longer = scores[j].orilen;
+ }
+
+#if LENFAC
+// lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
+ lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
+// lenfac = 1.0 / ( shorter / longer * LENFACD + LENFACB / ( longer + LENFACC ) + LENFACA );
+// fprintf( stderr, "lenfac = %f, l=%d, %d\n", lenfac, scores[yukos[i]].orilen, scores[j].orilen );
+#else
+ lenfac = 1.0;
+#endif
+#if 0 // iihazu -> dame
+ ii = s_y_map[j]; jj=s_y_map[yukos[i]];
+ if( ii != -1 && jj != -1 )
+ {
+ if( dfromc[ii][yukos[jj]] != -0.5 )
+ {
+ dfromc[i][j] = dfromc[ii][yukos[jj]];
+ }
+ else
+ {
+ if( ii > jj )
+ {
+ kk = jj;
+ jj = ii;
+ ii = kk;
+ }
+ dfromc[ii][yukos[jj]] =
+ dfromc[i][j] = yukomtx[ii][jj-ii];
+ }
+ }
+ else
+#else
+ if( dfromc[i][j] == -0.5 )
+#endif
+ {
+ if( doalign )
+ {
+ if( doalign == 'f' )
+ {
+ dfromc[i][j] =
+ ( 1.0 - blastresults[j] / MIN( selfscore0, scores[j].selfscore ) ) * 1;
+ if( dfromc[i][j] < 0.0 ) dfromc[i][j] = 0.0;
+ }
+ else
+ {
+ if( fromaln )
+ {
+ dfromc[i][j] = ( 1.0 - (double)naivepairscore11( orialn[scores[j].numinseq], orialn[scores[yukos[i]].numinseq], penalty ) / MIN( selfscore0, scores[j].selfscore ) ) * 1;
+ }
+ else
+ {
+ gappick0( mseq2[0], seq[scores[j].numinseq] );
+ dfromc[i][j] = ( 1.0 - (double)G__align11_noalign( amino_disLN, -1200, -60, mseq1, mseq2, palloclen ) / MIN( selfscore0, scores[j].selfscore ) ) * 1;
+ }
+ }
+ }
+ else
+ {
+ dfromc[i][j] = ( 1.0 - (double)commonsextet_p( table1, scores[j].pointt ) / MIN( selfscore0, scores[j].selfscore ) ) * lenfac;
+ if( dfromc[i][j] > MAX6DIST ) dfromc[i][j] = MAX6DIST;
+ }
+ }
+// fprintf( stderr, "i,j=%d,%d (%d,%d)/ %d,%d, dfromc[][]=%f \n", i, j, scores[yukos[i]].numinseq+1, scores[j].numinseq+1, nyuko, nin, dfromc[i][j] );
+
+// if( i == 1 )
+// fprintf( stdout, "&&& dfromc[%d][%d] (%d,%d) = %f\n", i, j, p_o_map[i], scores[j].numinseq, dfromc[i][j] );
+ }
+// fprintf( stderr, "i=%d, freeing\n", i );
+ if( !doalign ) free( table1 );
+ if( doalign && doalign == 'f' ) free( blastresults );
+ }
+ fprintf( stderr, " \r" );
+
+
+
+
+ for( i=0; i<nyuko; i++ ) numin[i] = 0;
+// fprintf( stderr, "### itchi shinai hazu, nazenara scores[nin-1].score=%f, selfscores=%d,%d, len=%d,%d, nin=%d\n", scores[nin-1].score, scores[nin-1].selfscore, scores->selfscore, scores->orilen, scores[nin-1].orilen, nin );
+ for( j=0; j<nin; j++ )
+ {
+#if 0
+ belongto = s_y_map[j];
+ {
+ fprintf( stderr, "belongto = %d (%dinori)\n", belongto, y_o_map[belongto]+1 );
+ }
+ if( belongto == -1 && closeh[j] != -1 )
+#endif
+#if 0
+ if( closeh[j] != -1 )
+ {
+ belongto = s_y_map[closeh[j]];
+// if( belongto != -1 )
+// fprintf( stderr, "known, %d(%dinori)->%d(%dinori)\n", j, scores[j].numinseq+1, belongto, y_o_map[belongto]+1 );
+ }
+ else
+// if( belongto == -1 )
+#else
+ belongto = s_y_map[j];
+ if( belongto == -1 )
+#endif
+ {
+ belongto = 0; // default ha horyu
+ minscore = dfromc[0][j];
+ for( i=0; i<nyuko; i++ )
+ {
+// fprintf( stderr, "checking %d/%d,%d/%d (%d-%d inori) minscore=%f, dfromc[0][j]=%f, dfromc[i][j]=%f\n", i, nyuko, j, nin, y_o_map[i], scores[j].numinseq, minscore, dfromc[0][j], dfromc[i][j] );
+ if( scores[j].shimon == scores[yukos[i]].shimon && !strcmp( seq[scores[j].numinseq], seq[y_o_map[i]] ) )
+ {
+// fprintf( stderr, "yuko-%d (%d in ori) to score-%d (%d inori) ha kanzen itch\n", i, y_o_map[i], j, scores[j].numinseq );
+ belongto = i;
+ break;
+ }
+ if( dfromc[i][j] < minscore )
+// if( dfromc[i][j] < minscore && minscore-dfromc[i][j] > ( minscoreinpick[yukos[i]] + minscoreinpick[j] ) * 1.0 )
+// if( rnd() < 0.5 ) // CHUUI !!!!!
+ {
+// fprintf( stderr, "yuko-%d (%d in ori) to score-%d (%d inori) ha tikai, %f>%f\n", i, y_o_map[i]+1, j, scores[j].numinseq+1, minscore, dfromc[i][j] );
+ minscore = dfromc[i][j];
+ belongto = i;
+ }
+ }
+ }
+#if 0
+ if( dfromc[belongto][j] > minscoreinpick[belongto] )
+ {
+ fprintf( stderr, "dame, %f > %f\n", dfromc[belongto][j], minscoreinpick[belongto] );
+ belongto = npick;
+ }
+ else
+ fprintf( stderr, "ok, %f < %f\n", dfromc[belongto][j], minscoreinpick[belongto] );
+#endif
+// fprintf( stderr, "j=%d (%d inori) -> %d (%d inori) d=%f\n", j, scores[j].numinseq+1, belongto, y_o_map[belongto]+1, dfromc[belongto][j] );
+// fprintf( stderr, "numin = %d\n", numin[belongto] );
+ outs[belongto] = realloc( outs[belongto], sizeof( Scores ) * ( numin[belongto] + 1 ) );
+ outs[belongto][numin[belongto]] = scores[j];
+ numin[belongto]++;
+
+ }
+ free( dfromcp );
+ FreeDoubleMtx( dfromc );
+
+// fprintf( stderr, "##### npick = %d\n", npick );
+// fprintf( stderr, "##### nyuko = %d\n", nyuko );
+
+
+ if( nyuko > 2 )
+ {
+ fprintf( stderr, "upgma " );
+// veryfastsupg_float_realloc_nobk_halfmtx( nyuko, yukomtx, topol, len );
+ fixed_musclesupg_float_realloc_nobk_halfmtx( nyuko, yukomtx, topol, len, NULL );
+ fprintf( stderr, "\r \r" );
+ }
+ else
+ {
+ topol[0][0] = (int *)realloc( topol[0][0], 2 * sizeof( int ) );
+ topol[0][1] = (int *)realloc( topol[0][1], 2 * sizeof( int ) );
+ topol[0][0][0] = 0;
+ topol[0][0][1] = -1;
+ topol[0][1][0] = 1;
+ topol[0][1][1] = -1;
+ }
+ FreeFloatHalfMtx( yukomtx, npick );
+
+#if 0
+ ii = nyuko-1;
+ fprintf( stderr, "nyuko = %d, topol[][] = \n", nyuko );
+ for( j=0; j<nyuko-1; j++ )
+ {
+ fprintf( stderr, "STEP%d \n", j );
+ for( i=0; ; i++ )
+ {
+ fprintf( stderr, "%d ", ( topol[j][0][i] )+0 );
+ if( topol[j][0][i] == -1 ) break;
+ }
+ fprintf( stderr, "\n" );
+ for( i=0; ; i++ )
+ {
+ fprintf( stderr, "%d ", ( topol[j][1][i] )+0 );
+ if( topol[j][1][i] == -1 ) break;
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "\n" );
+ }
+ exit( 1 );
+#endif
+ jptr = treeorder;
+ iptr = topol[nyuko-2][0]; while( *iptr != -1 ) *jptr++ = *iptr++;
+ iptr = topol[nyuko-2][1]; while( *iptr != -1 ) *jptr++ = *iptr++;
+ *jptr++ = -1;
+ for( j=0; j<nyuko; j++ )
+ {
+// fprintf( stderr, "treeorder[%d] = %d\n", j, treeorder[j] );
+ if( treeorder[j] == -1 ) break;
+ }
+ }
+
+ aligned = 1;
+ for( i=0; i<nyuko; i++ )
+ {
+ ii = treeorder[i];
+#if 0
+ if( numin[ii] > 1 )
+ {
+ fprintf( stderr, "\ncalling a child, pick%d (%d inori): # of mem=%d\n", i, p_o_map[ii]+1, numin[ii] );
+ for( j=0; j<numin[ii]; j++ )
+ {
+ fprintf( stderr, "%d ", outs[ii][j].numinseq+1 );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+ aligned *= splitseq_mq( outs[ii], numin[ii], nlen, seq, orialn, name, inputfile, uniform, children+ii, alloclen, order, whichgroup, weight, depthpt, scores->numinseq );
+ }
+
+
+ for( i=0; i<nyuko; i++ )
+ {
+ if( !numin[i] )
+ {
+ fprintf( stderr, "i=%d/%d, ERROR!\n", i, nyuko );
+ for( j=0; j<nyuko; j++ )
+ fprintf( stderr, "numin[%d] = %d (rep=%d inori)\n", j, numin[j], y_o_map[j] );
+ exit( 1 );
+ }
+ }
+
+#if TREE
+ if( treeout )
+ {
+ treelen = 0;
+ for( i=0; i<nyuko; i++ )
+ treelen += strlen( children[i] );
+ *tree = calloc( treelen + nin * 3, sizeof ( char ) );
+ }
+#endif
+
+
+ if( nin >= classsize || !aligned )
+ val = 0;
+ else
+ val = 1;
+
+ if( nyuko > 1 )
+ {
+ int *mem1p, *mem2p;
+ int mem1size, mem2size;
+ int v1 = 0, v2 = 0, v3 = 0;
+ int nlim;
+ int l;
+ static int *mem1 = NULL;
+ static int *mem2 = NULL;
+ char **parttree = NULL; // by Mathog
+
+#if TREE
+ if( treeout )
+ {
+ parttree = (char **)calloc( nyuko, sizeof( char * ) );
+ for( i=0; i<nyuko; i++ )
+ {
+// fprintf( stderr, "allocating parttree, size = %d\n", treelen + nin * 5 );
+ parttree[i] = calloc( treelen + nin * 5, sizeof ( char ) );
+ strcpy( parttree[i], children[i] );
+ free( children[i] );
+ }
+ free( children );
+ }
+#endif
+ if( mem1 == NULL )
+ {
+ mem1 = AllocateIntVec( njob+1 );
+ mem2 = AllocateIntVec( njob+1 );
+ }
+
+// veryfastsupg_float_realloc_nobk_halfmtx( nyuko, yukomtx, topol, len );
+
+// counteff_simple_float( nyuko, topol, len, eff );
+
+
+ nlim = nyuko-1;
+ for( l=0; l<nlim; l++ )
+ {
+ mem1p = topol[l][0];
+ mptr = mem1;
+ mem1size = 0;
+ while( *mem1p != -1 )
+ {
+// fprintf( stderr, "*mem1p = %d (%d inori), numin[]=%d\n", *mem1p, p_o_map[*mem1p], numin[*mem1p] );
+ i = numin[*mem1p]; ptr = outs[*(mem1p++)];
+ mem1size += i;
+ while( i-- )
+ {
+ *mptr++ = (ptr++)->numinseq;
+ }
+ }
+ *mptr = -1;
+
+ mem2p = topol[l][1];
+ mptr = mem2;
+ mem2size = 0;
+ while( *mem2p != -1 )
+ {
+// fprintf( stderr, "*mem2p = %d (%d inori), numin[]=%d\n", *mem2p, p_o_map[*mem2p], numin[*mem2p] );
+ i = numin[*mem2p]; ptr = outs[*(mem2p++)];
+ mem2size += i;
+ while( i-- )
+ {
+ *mptr++ = (ptr++)->numinseq;
+ }
+ }
+ *mptr = -1;
+
+ qsort( mem1, mem1size, sizeof( int ), (int (*)())intcompare );
+ qsort( mem2, mem2size, sizeof( int ), (int (*)())intcompare );
+// selhead( mem1, numin[0] );
+// selhead( mem2, numin[1] );
+
+
+#if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "mem1 (nin=%d) = \n", nin );
+ for( i=0; ; i++ )
+ {
+ fprintf( stderr, "%d ", mem1[i]+1 );
+ if( mem1[i] == -1 ) break;
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "mem2 (nin=%d) = \n", nin );
+ for( i=0; ; i++ )
+ {
+ fprintf( stderr, "%d ", mem2[i]+1 );
+ if( mem2[i] == -1 ) break;
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+#if 0
+ fprintf( stderr, "before pairalign, l = %d, nyuko=%d, mem1size=%d, mem2size=%d\n", l, nyuko, mem1size, mem2size );
+ fprintf( stderr, "before alignment\n" );
+ for( j=0; j<mem1size; j++ )
+ fprintf( stderr, "%s\n", seq[mem1[j]] );
+ fprintf( stderr, "----\n" );
+ for( j=0; j<mem2size; j++ )
+ fprintf( stderr, "%s\n", seq[mem2[j]] );
+ fprintf( stderr, "----\n\n" );
+#endif
+
+ if( val )
+ {
+ fprintf( stderr, "\r Alignment %d-%d \r", mem1size, mem2size );
+ if( *mem1 < *mem2 )
+ pairalign( njob, nlen, seq, mem1, mem2, weight, alloclen );
+ else
+ pairalign( njob, nlen, seq, mem2, mem1, weight, alloclen );
+ }
+
+#if TREE
+ if( treeout )
+ {
+ v1 = topol[l][0][0];
+ v2 = topol[l][1][0];
+
+// fprintf( stderr, "nyuko=%d, v1=%d, v2=%d\n", nyuko, v1, v2 );
+ if( v1 > v2 )
+ {
+ v3 = v1;
+ v1 = v2;
+ v2 = v3;
+ }
+// fprintf( stderr, "nyuko=%d, v1=%d, v2=%d after sort\n", nyuko, v1, v2 );
+// fprintf( stderr, "nyuko=%d, v1=%d, v2=%d\n", nyuko, v1, v2 );
+// fprintf( stderr, "v1=%d, v2=%d, parttree[v1]=%s, parttree[v2]=%s\n", v1, v2, parttree[v1], parttree[v2] );
+ sprintf( *tree, "(%s,%s)", parttree[v1], parttree[v2] );
+ strcpy( parttree[v1], *tree );
+// fprintf( stderr, "parttree[%d] = %s\n", v1, parttree[v1] );
+// fprintf( stderr, "*tree = %s\n", *tree );
+ free( parttree[v2] ); parttree[v2] = NULL;
+ }
+#endif
+
+#if 0
+ fprintf( stderr, "after alignment\n" );
+ for( j=0; j<mem1size; j++ )
+ fprintf( stderr, "%s\n", seq[mem1[j]] );
+ fprintf( stderr, "----\n" );
+ for( j=0; j<mem2size; j++ )
+ fprintf( stderr, "%s\n", seq[mem2[j]] );
+ fprintf( stderr, "----\n\n" );
+#endif
+ }
+#if TREE
+ if( treeout )
+ {
+ free( parttree[v1] ); parttree[v1] = NULL;
+// fprintf( stderr, "*tree = %s\n", *tree );
+// FreeCharMtx( parttree );
+ free( parttree ); parttree = NULL;
+ }
+#endif
+
+#if 0
+ fprintf( stderr, "after alignment\n" );
+ for( i=0; i<nyuko; i++ )
+ {
+ for( j=0; j<numin[i]; j++ )
+ fprintf( stderr, "%s\n", seq[outs[i][j].numinseq] );
+ }
+#endif
+
+ if( val )
+ {
+ groupid++;
+ mptr = mem1; while( *mptr != -1 )
+ {
+#if 0
+ fprintf( stdout, "==g1-%d \n", *mptr+1 );
+ fprintf( stdout, "%s \n", seq[*mptr] );
+#endif
+ whichgroup[*mptr] = groupid;
+ weight[*mptr++] *= 0.5;
+ }
+
+ mptr = mem2; while( *mptr != -1 )
+ {
+#if 0
+ fprintf( stdout, "=g2-%d ", *mptr+1 );
+ fprintf( stdout, "%s \n", seq[*mptr] );
+#endif
+ whichgroup[*mptr] = groupid;
+ weight[*mptr++] *= 0.5;
+ }
+
+ if( numin[1] == 0 )
+ {
+ mptr = mem1; while( *mptr != -1 )
+ {
+ whichgroup[*mptr] = groupid;
+ weight[*mptr++] *= (double)2.0/numin[0];
+ }
+ }
+ }
+ {
+ if( *depthpt > maxdepth ) maxdepth = *depthpt;
+ (*depthpt)++;
+ }
+ }
+ else
+ {
+#if TREE
+ if( treeout )
+ {
+ sprintf( *tree, "%s", children[0] );
+ free( children[0] );
+ free( children );
+ }
+#endif
+ }
+ for( i=0; i<npick; i++ ) free( (void *)outs[i] );
+// FreeFloatHalfMtx( pickmtx, npick );
+// FreeFloatHalfMtx( yukomtx, npick );
+ FreeFloatMtx( len );
+ FreeIntCub( topol );
+ FreeIntVec( treeorder );
+ free( outs );
+ free( numin );
+ free( picks );
+ free( yukos );
+ free( s_p_map );
+ free( s_y_map );
+ free( p_o_map );
+ free( y_o_map );
+ free( hanni );
+ free( closeh );
+ free( pickkouho );
+ free( tsukau );
+// free( minscoreinpick );
+ return val;
+}
+#endif
+
+static void alignparaphiles( int nseq, int *nlen, double *weight, char **seq, int nmem, int *members, int *alloclen )
+{
+ int i, ilim;
+ int *mem1 = AllocateIntVec( nmem );
+ int *mem2 = AllocateIntVec( 2 );
+
+ mem2[1] = -1;
+ ilim = nmem-1;
+ for( i=0; i<ilim; i++ )
+ {
+ mem1[i] = members[i];
+ mem1[i+1] = -1;
+ mem2[0] = members[i+1];
+ pairalign( nseq, nlen, seq, mem1, mem2, weight, alloclen );
+ }
+ free( mem1 );
+ free( mem2 );
+}
+
+
+
+
+
+
+
+
+
+
+
+int main( int argc, char *argv[] )
+{
+ static char **name, **seq, **orialn;
+ static int *grpseq;
+ static char *tmpseq;
+ static int **pointt;
+ static int *nlen;
+ int i, st, en;
+ FILE *infp;
+ FILE *treefp;
+ char *treefile = NULL; //by Mathog
+ char c;
+ int alloclen;
+ static int *order;
+ static int *whichgroup;
+ static double *weight;
+ static char tmpname[B+100];
+ int groupnum;
+ int groupid;
+ int pos;
+ int *paramem;
+ int npara;
+ int completed;
+ int orilen;
+ int pscore;
+ char *pt;
+ int **tmpaminodis;
+ static char com[1000];
+ int depth;
+ int aan;
+
+ static Scores *scores;
+ static short *table1;
+ static char **tree;
+
+
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+
+ if( picksize == NOTSPECIFIED || picksize < 2 )
+ picksize = PICKSIZE;
+
+ if( classsize == NOTSPECIFIED || classsize < 0 )
+ {
+ classsize = njob + 1;
+ }
+ else
+ {
+// picksize = MIN( picksize, (int)sqrt( classsize ) + 1);
+ }
+
+ if( tokyoripara == NOTSPECIFIED )
+ {
+ if( doalign ) tokyoripara = TOKYORIPARA_A;
+ else tokyoripara = TOKYORIPARA;
+ }
+ if( picksize > njob )
+ tokyoripara = 0.0;
+
+
+ alloclen = nlenmax * 2;
+ name = AllocateCharMtx( njob, B+1 );
+
+ if( classsize == 1 )
+ seq = AllocateCharMtx( njob, 0 );
+ else
+ seq = AllocateCharMtx( njob, alloclen+1 );
+
+
+ nlen = AllocateIntVec( njob );
+ tmpseq = calloc( nlenmax+1, sizeof( char ) );
+ pointt = AllocateIntMtx( njob, 0 );
+ grpseq = AllocateIntVec( nlenmax + 1 );
+ order = (int *)calloc( njob + 1, sizeof( int ) );
+ whichgroup = (int *)calloc( njob, sizeof( int ) );
+ weight = (double *)calloc( njob, sizeof( double ) );
+
+ fprintf( stderr, "alloclen = %d in main\n", alloclen );
+
+ for( i=0; i<njob; i++ ) whichgroup[i] = 0;
+ for( i=0; i<njob; i++ ) weight[i] = 1.0;
+ for( i=0; i<njob; i++ ) order[i] = -1;
+
+ if( classsize == 1 )
+ readData_varlen( infp, name, nlen, seq );
+ else
+ readData_pointer( infp, name, nlen, seq );
+
+ fclose( infp );
+
+ if( fromaln ) doalign = 1;
+
+ if( fromaln )
+ {
+ orialn = AllocateCharMtx( njob, alloclen+1 );
+ for( i=0; i<njob; i++ )
+ {
+ if( strlen( seq[i] ) != nlenmax )
+ {
+ fprintf( stderr, "Input sequences must be aligned\n" );
+ exit( 1 );
+ }
+ strcpy( orialn[i], seq[i] );
+ }
+ }
+
+ constants( njob, seq );
+
+ if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
+ else tsize = (int)pow( 6, 6 );
+
+ if( dorp == 'd' )
+ {
+ lenfaca = DLENFACA;
+ lenfacb = DLENFACB;
+ lenfacc = DLENFACC;
+ lenfacd = DLENFACD;
+ }
+ else
+ {
+ lenfaca = PLENFACA;
+ lenfacb = PLENFACB;
+ lenfacc = PLENFACC;
+ lenfacd = PLENFACD;
+ }
+
+ maxl = 0;
+ for( i=0; i<njob; i++ )
+ {
+ gappick0( tmpseq, seq[i] );
+ nlen[i] = strlen( tmpseq );
+ strcpy( seq[i], tmpseq );
+ pointt[i] = AllocateIntVec( nlen[i]+1 ); // ??
+
+ if( nlen[i] < 6 )
+ {
+ fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
+ fprintf( stderr, "name = %s\n", name[i] );
+ fprintf( stderr, "seq = %s\n", seq[i] );
+ exit( 1 );
+// continue;
+ }
+ if( nlen[i] > maxl ) maxl = nlen[i];
+ if( dorp == 'd' ) /* nuc */
+ {
+ if( seq_grp_nuc( grpseq, tmpseq ) < 6 )
+ {
+ fprintf( stderr, "Seq %d, too short.\n", i+1 );
+ fprintf( stderr, "name = %s\n", name[i] );
+ fprintf( stderr, "seq = %s\n", seq[i] );
+ exit( 1 );
+// continue;
+ }
+ makepointtable_nuc( pointt[i], grpseq );
+ }
+ else /* amino */
+ {
+ if( seq_grp( grpseq, tmpseq ) < 6 )
+ {
+ fprintf( stderr, "Seq %d, too short.\n", i+1 );
+ fprintf( stderr, "name = %s\n", name[i] );
+ fprintf( stderr, "seq = %s\n", seq[i] );
+ exit( 1 );
+// continue;
+ }
+ makepointtable( pointt[i], grpseq );
+ }
+// fprintf( stdout, ">%s\n", name[i] );
+// fprintf( stdout, "%s\n", seq[i] );
+ }
+// exit( 1 );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illeagal character %c\n", c );
+ exit( 1 );
+ }
+
+ pid = (int)getpid();
+ sprintf( datafile, "/tmp/data-%d", pid );
+ sprintf( queryfile, "/tmp/query-%d", pid );
+ sprintf( resultfile, "/tmp/fasta-%d", pid );
+
+ scores = (Scores *)calloc( njob, sizeof( Scores ) );
+
+// fprintf( stderr, "\nCalculating i-i scores ... \n" );
+ for( i=0; i<njob; i++ )
+ {
+ orilen = strlen( seq[i] );
+ scores[i].numinseq = i; // irimasu
+ scores[i].orilen = orilen;
+ }
+
+ if( doalign == 'f' )
+ {
+ fastapath = getenv( "FASTA_4_MAFFT" );
+ if( !fastapath ) fastapath = "fasta34";
+ fprintf( stderr, "fastapath=%s\n", fastapath );
+ tmpaminodis = AllocateIntMtx( 0x80, 0x80 );
+ getfastascoremtx( tmpaminodis );
+ }
+ else
+ tmpaminodis = NULL;
+
+ for( i=0; i<njob; i++ )
+ {
+ scores[i].pointt = pointt[i];
+ scores[i].shimon = (int)pointt[i][0] + (int)pointt[i][1] + (int)pointt[i][scores[i].orilen-6];
+ scores[i].name = name[i];
+ if( doalign )
+ {
+ fprintf( stderr, "\r %05d/%05d ", i, njob );
+ free( scores[i].pointt );
+ if( doalign == 'f' )
+ {
+#if 0
+#define KIZAMI 100
+ int ipos = (int)( i / KIZAMI ) * KIZAMI;
+ int iposamari = i % KIZAMI;
+
+ fprintf( stderr, "%d / %d\r", i, njob );
+// fprintf( stderr, "ipos = %d\n", ipos );
+// fprintf( stderr, "iposamari = %d\n", iposamari );
+
+// fprintf( stderr, " calling blast, i=%d\n", i );
+// blastresults = callfasta( seq, scores+i, 1, 0, 1 );
+ blastresults = callfasta( seq, scores+ipos, MIN(KIZAMI,njob-ipos), NULL, iposamari, (iposamari==0) );
+// fprintf( stderr, "done., i=%d\n\n", i );
+ scores[i].selfscore = (int)blastresults[iposamari];
+#if 0
+ for( j=0; j<100; j++ )
+ {
+ fprintf( stderr, "res[%d] = %f\n", j, blastresults[j] );
+ }
+#endif
+// fprintf( stderr, "%d->selfscore = %d\n", i, scores[i].selfscore );
+ free( blastresults );
+#else
+ pscore = 0;
+ if( scoremtx == -1 )
+ {
+ st = 1;
+ en = 0;
+ for( pt=seq[i]; *pt; pt++ )
+ {
+ if( *pt == 'u' ) *pt = 't';
+ aan = amino_n[(int)*pt];
+ if( aan<0 || aan >= 4 ) *pt = 'n';
+
+ if( *pt == 'n' )
+ {
+ en++;
+ if( st ) continue;
+ else pscore += tmpaminodis[(int)*pt][(int)*pt];
+ }
+ else
+ {
+ st = 0;
+ en = 0;
+ pscore += tmpaminodis[(int)*pt][(int)*pt];
+ }
+ }
+ scores[i].selfscore = pscore - en * tmpaminodis['n']['n'];
+ }
+ else
+ {
+ st = 1;
+ en = 0;
+ for( pt=seq[i]; *pt; pt++ )
+ {
+ aan = amino_n[(int)*pt];
+ if( aan<0 || aan >= 20 ) *pt = 'X';
+ if( *pt == 'X' )
+ {
+ en++;
+ if( st ) continue;
+ else pscore += tmpaminodis[(int)*pt][(int)*pt];
+ }
+ else
+ {
+ st = 0;
+ en = 0;
+ pscore += tmpaminodis[(int)*pt][(int)*pt];
+ }
+ }
+ scores[i].selfscore = pscore - en * tmpaminodis['X']['X'];
+ }
+#endif
+ }
+ else
+ {
+ pscore = 0;
+ for( pt=seq[i]; *pt; pt++ )
+ {
+ pscore += amino_dis[(int)*pt][(int)*pt];
+ }
+ scores[i].selfscore = pscore;
+ }
+// fprintf( stderr, "selfscore[%d] = %d\n", i+1, scores[i].selfscore );
+ }
+ else
+ {
+ table1 = (short *)calloc( tsize, sizeof( short ) );
+ if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
+ makecompositiontable_p( table1, pointt[i] );
+ scores[i].selfscore = commonsextet_p( table1, pointt[i] );
+ free( table1 );
+ }
+ }
+ if( tmpaminodis ) FreeIntMtx( tmpaminodis );
+
+ depth = 0;
+#if TREE
+ if( treeout )
+ {
+ tree = (char **)calloc( 1, sizeof( char *) );
+ *tree = NULL;
+// splitseq_bin( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight );
+ completed = splitseq_mq( scores, njob, nlen, seq, orialn, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth, -1 );
+ treefile = (char *)calloc( strlen( inputfile ) + 10, sizeof( char ) );
+ if( inputfile )
+ sprintf( treefile, "%s.tree", inputfile );
+ else
+ sprintf( treefile, "splittbfast.tree" );
+ treefp = fopen( treefile, "w" );
+ fprintf( treefp, "%s\n", *tree );
+ fclose( treefp );
+ }
+ else
+ completed = splitseq_mq( scores, njob, nlen, seq, orialn, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth, -1 );
+#else
+ completed = splitseq_mq( scores, njob, nlen, seq, orialn, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth, -1 );
+#endif
+
+ fprintf( stderr, "\nDone.\n\n" );
+
+#if 1
+ groupnum = 0;
+ groupid = -1;
+ paramem = NULL;
+ npara = 0;
+ for( i=0; i<njob; i++ )
+ {
+ pos = order[i];
+ if( whichgroup[pos] != groupid )
+ {
+ groupnum++;
+ groupid = whichgroup[pos];
+ }
+ if( whichgroup[pos] )
+ {
+ if( paramem )
+ {
+ paramem[npara] = -1;
+ if( npara > 1 && classsize > 2 )
+ {
+ qsort( paramem, npara, sizeof( int ), (int (*)(const void *, const void*))intcompare );
+// selhead( paramem, npara );
+ alignparaphiles( njob, nlen, weight, seq, npara, paramem, &alloclen );
+ }
+ free( paramem ); paramem = NULL; npara = 0;
+ }
+ sprintf( tmpname, "Group-%d %s", groupnum, name[pos]+1 );
+ }
+ else
+ {
+ paramem = realloc( paramem, sizeof( int) * ( npara + 2 ) );
+ paramem[npara++] = pos;
+ sprintf( tmpname, "Group-para %s", name[pos]+1 );
+ }
+ tmpname[B-1] = 0;
+ if( classsize > 1 && classsize <= njob )
+ strcpy( name[pos]+1, tmpname );
+ }
+ if( paramem )
+ {
+ paramem[npara] = -1;
+ if( npara > 1 && classsize > 2 )
+ {
+ qsort( paramem, npara, sizeof( int ), (int (*)(const void *, const void*))intcompare );
+// selhead( paramem, npara );
+ alignparaphiles( njob, nlen, weight, seq, npara, paramem, &alloclen );
+ }
+ free( paramem ); paramem = NULL; npara = 0;
+ }
+#else
+ for( i=0; i<njob; i++ )
+ {
+ sprintf( tmpname, "Group-%d %s", whichgroup[i], name[i]+1 );
+ strcpy( name[i]+1, tmpname );
+ }
+#endif
+
+
+// maketanni( name, seq, njob, nlenmax, nlen );
+
+ fclose( trap_g );
+
+#if DEBUG
+ fprintf( stderr, "writing alignment to stdout\n" );
+#endif
+ if( reorder )
+ writeData_reorder_pointer( stdout, njob, name, nlen, seq, order );
+ else
+ writeData_pointer( stdout, njob, name, nlen, seq );
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ if( classsize == 1 )
+ {
+ fprintf( stderr, "\n\n" );
+ fprintf( stderr, "----------------------------------------------------------------------------\n" );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "nseq = %d\n", njob );
+ fprintf( stderr, "groupsize = %d, picksize=%d\n", classsize, picksize );
+ fprintf( stderr, "The input sequences have been sorted so that similar sequences are close.\n" );
+ if( reorder )
+ fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
+#if TREE
+ if( treeout )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
+ }
+// else
+// {
+// fprintf( stderr, "To output guide tree,\n" );
+// fprintf( stderr, "%% %s -t -i %s\n", progName( argv[0] ), "inputfile" );
+// }
+#endif
+ if( !doalign )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
+ fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "----------------------------------------------------------------------------\n" );
+ }
+ else if( groupnum > 1 )
+ {
+ fprintf( stderr, "\n\n" );
+ fprintf( stderr, "----------------------------------------------------------------------------\n" );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "groupsize = %d, picksize=%d\n", classsize, picksize );
+ fprintf( stderr, "The input sequences have been classified into %d groups + some paraphyletic groups\n", groupnum );
+ fprintf( stderr, "Note that the alignment is not completed.\n" );
+ if( reorder )
+ fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
+#if TREE
+ if( treeout )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
+ }
+// else
+// {
+// fprintf( stderr, "To output guide tree,\n" );
+// fprintf( stderr, "%% %s -t -i %s\n", progName( argv[0] ), "inputfile" );
+// }
+#endif
+ if( !doalign )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
+ fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "----------------------------------------------------------------------------\n" );
+ }
+ else
+ {
+ fprintf( stderr, "\n\n" );
+ fprintf( stderr, "----------------------------------------------------------------------------\n" );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "nseq = %d\n", njob );
+ fprintf( stderr, "groupsize = %d, partsize=%d\n", classsize, picksize );
+// fprintf( stderr, "A single alignment containing all the input sequences has been computed.\n" );
+// fprintf( stderr, "If the sequences are highly diverged and you feel there are too many gaps,\n" );
+// fprintf( stderr, "please try \n" );
+// fprintf( stderr, "%% mafft --parttree --groupsize 100 inputfile\n" );
+// fprintf( stderr, "which classifies the sequences into several groups with <~ 100 sequences\n" );
+// fprintf( stderr, "and performs only intra-group alignments.\n" );
+ if( reorder )
+ fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
+#if TREE
+ if( treeout )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
+ }
+// else
+// {
+// fprintf( stderr, "To output guide tree,\n" );
+// fprintf( stderr, "%% %s -t -i %s\n", progName( argv[0] ), "inputfile" );
+// }
+#endif
+ if( !doalign || fromaln )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
+ fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "----------------------------------------------------------------------------\n" );
+ }
+#if TREE
+ if( treeout ) free( treefile );
+#endif
+
+#if 0
+ fprintf( stdout, "weight =\n" );
+ for( i=0; i<njob; i++ )
+ fprintf( stdout, "%d: %f\n", i+1, weight[i] );
+#endif
+
+ if( doalign == 'f' )
+ {
+ strcpy( com, "rm -f" );
+ strcat( com, " " );
+ strcat( com, datafile );
+ strcat( com, "* " );
+ strcat( com, queryfile );
+ strcat( com, " " );
+ strcat( com, resultfile );
+ fprintf( stderr, "%s\n", com );
+ system( com );
+ }
+
+ SHOWVERSION;
+
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define DEBUG2 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+typedef struct _shuryoten
+{
+ int i;
+ int j;
+ float wm;
+ struct _shuryoten *next;
+ struct _shuryoten *prev;
+} Shuryoten;
+
+
+static int localstop;
+
+static int compshuryo( Shuryoten *s1_arg, Shuryoten *s2_arg )
+{
+ Shuryoten *s1 = (Shuryoten *)s1_arg;
+ Shuryoten *s2 = (Shuryoten *)s2_arg;
+ if ( s1->wm > s2->wm ) return( -1 );
+ else if ( s1->wm < s2->wm ) return( 1 );
+ else return( 0 );
+}
+
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ int j;
+
+ for( j=0; j<lgth2; j++ )
+ match[j] = amino_dis[(int)(*s1)[i1]][(int)(*s2)[j]];
+}
+
+static float gentracking( int **used,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijpi, int **ijpj, int *off1pt, int *off2pt, int endi, int endj )
+{
+ int l, iin, jin, lgth1, lgth2, k, limk;
+ int ifi=0, jfi=0;
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ static char *res1 = NULL, *res2 = NULL;
+ char *mspt1, *mspt2;
+ if( res1 == NULL )
+ {
+ res1 = (char *)calloc( N, sizeof( char ) );
+ res2 = (char *)calloc( N, sizeof( char ) );
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ mspt1 = res1 + lgth1+lgth2;
+ *mspt1 = 0;
+ mspt2 = res2 + lgth1+lgth2;
+ *mspt2 = 0;
+ iin = endi; jin = endj;
+
+ limk = lgth1+lgth2;
+ if( used[iin][jin] ) return( -1.0 );
+ for( k=0; k<=limk; k++ )
+ {
+ ifi = ( ijpi[iin][jin] );
+ jfi = ( ijpj[iin][jin] );
+
+ if( used[ifi][jfi] ) return( -1.0 );
+
+ l = iin - ifi;
+ while( --l )
+ {
+ *--mspt1 = seq1[0][ifi+l];
+ *--mspt2 = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mspt1 = *gap;
+ *--mspt2 = seq2[0][jfi+l];
+ k++;
+ }
+
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mspt1 = seq1[0][ifi];
+ *--mspt2 = seq2[0][jfi];
+ if( ijpi[ifi][jfi] == localstop ) break;
+ if( ijpj[ifi][jfi] == localstop ) break;
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
+ if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
+
+// fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
+
+ iin = endi; jin = endj;
+ limk = lgth1+lgth2;
+ for( k=0; k<=limk; k++ )
+ {
+ ifi = ( ijpi[iin][jin] );
+ jfi = ( ijpj[iin][jin] );
+
+ used[ifi][jfi] = 1;
+ if( iin <= 0 || jin <= 0 ) break;
+ if( ijpi[ifi][jfi] == localstop ) break;
+ if( ijpj[ifi][jfi] == localstop ) break;
+
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+
+ strcpy( mseq1[0], mspt1 );
+ strcpy( mseq2[0], mspt2 );
+
+ fprintf( stderr, "mseq1=%s\nmseq2=%s\n", mspt1, mspt2 );
+
+ return( 0.0 );
+}
+
+
+float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+ int k;
+ static int **used;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; // by D.Mathog,
+ float g;
+ float *currentw, *previousw;
+#if 1
+ float *wtmp;
+ int *ijpipt;
+ int *ijpjpt;
+ float *mjpt, *Mjpt, *prept, *curpt;
+ int *mpjpt, *Mpjpt;
+#endif
+ static float mi, *m;
+ static float Mi, *largeM;
+ static int **ijpi;
+ static int **ijpj;
+ static int mpi, *mp;
+ static int Mpi, *Mp;
+ static float *w1, *w2;
+// static float *match;
+ static float *initverticalw; /* kufuu sureba iranai */
+ static float *lastverticalw; /* kufuu sureba iranai */
+ static char **mseq1;
+ static char **mseq2;
+ static float **cpmx1;
+ static float **cpmx2;
+ static int **intwork;
+ static float **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+ float maxwm;
+ float tbk;
+ int tbki, tbkj;
+ int endali, endalj;
+// float localthr = 0.0;
+// float localthr2 = 0.0;
+ float fpenalty = (float)penalty;
+ float fpenalty_OP = (float)penalty_OP;
+ float fpenalty_ex = (float)penalty_ex;
+// float fpenalty_EX = (float)penalty_EX;
+ float foffset = (float)offset;
+ float localthr = -foffset;
+ float localthr2 = -foffset;
+ static Shuryoten *shuryo = NULL;
+ int numshuryo;
+ float minshuryowm = 0.0; // by D.Mathog
+ int minshuryopos = 0; // by D.Mathog
+ float resf;
+
+
+// fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
+
+ fprintf( stderr, "in suboptalign11\n" );
+ if( !shuryo )
+ {
+ shuryo = (Shuryoten *)calloc( 100, sizeof( Shuryoten ) );
+ }
+ for( i=0; i<100; i++ )
+ {
+ shuryo[i].i = -1;
+ shuryo[i].j = -1;
+ shuryo[i].wm = 0.0;
+ }
+ numshuryo = 0;
+
+ if( orlgth1 == 0 )
+ {
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ fprintf( stderr, "in suboptalign11 step 1\n" );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ fprintf( stderr, "in suboptalign11 step 1.3\n" );
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ fprintf( stderr, "in suboptalign11 step 1.4\n" );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+// FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ fprintf( stderr, "in suboptalign11 step 1.5\n" );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+ FreeFloatVec( largeM );
+ FreeIntVec( Mp );
+ fprintf( stderr, "in suboptalign11 step 1.6\n" );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ fprintf( stderr, "in suboptalign11 step 1.7\n" );
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ largeM = AllocateFloatVec( ll2+2 );
+ Mp = AllocateIntVec( ll2+2 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+ mseq1 = AllocateCharMtx( njob, ll1+ll2 );
+ mseq2 = AllocateCharMtx( njob, ll1+ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+ fprintf( stderr, "in suboptalign11 step 1.6\n" );
+
+
+
+ fprintf( stderr, "in suboptalign11 step 2\n" );
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ FreeIntMtx( commonJP );
+ FreeIntMtx( used );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ used = AllocateIntMtx( ll1+10, ll2+10 );
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+ commonJP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijpi = commonIP;
+ ijpj = commonJP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ fprintf( stderr, "in suboptalign11 step 3\n" );
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+
+ lasti = lgth2+1;
+ for( j=1; j<lasti; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+ largeM[j] = currentw[j-1]; Mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+#if 0
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, " " );
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%c ", seq2[0][j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ localstop = lgth1+lgth2+1;
+ maxwm = -999.9;
+ endali = endalj = 0;
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "%c ", seq1[0][0] );
+
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ lasti = lgth1+1;
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if DEBUG2
+ fprintf( stderr, "%c ", seq1[0][i] );
+ fprintf( stderr, "%5.0f ", currentw[0] );
+#endif
+
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+ Mi = previousw[0]; Mpi = 0;
+
+#if 0
+ if( mi < localthr ) mi = localthr2;
+#endif
+
+ ijpipt = ijpi[i] + 1;
+ ijpjpt = ijpj[i] + 1;
+ mjpt = m + 1;
+ Mjpt = largeM + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ Mpjpt = Mp + 1;
+ tbk = -999999.9;
+ tbki = 0;
+ tbkj = 0;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijpipt = i-1;
+ *ijpjpt = j-1;
+
+
+// fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
+// fprintf( stderr, "wm=%f\n", wm );
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijpipt = i - 1;
+ *ijpjpt = mpi;
+ }
+ g = *prept;
+ if( g > mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "m%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijpipt = *mpjpt;
+// *ijpjpt = j - 1;
+ }
+ g = *prept;
+ if( g > *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ *mjpt += fpenalty_ex;
+#endif
+
+
+ g = tbk + fpenalty_OP;
+// g = tbk;
+ if( g > wm )
+ {
+ wm = g;
+ *ijpipt = tbki;
+ *ijpjpt = tbkj;
+// fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
+ }
+ g = Mi;
+ if( g > tbk )
+ {
+ tbk = g;
+ tbki = i-1;
+ tbkj = Mpi;
+ }
+ g = *Mjpt;
+ if( g > tbk )
+ {
+ tbk = g;
+ tbki = *Mpjpt;
+ tbkj = j-1;
+ }
+// tbk += fpenalty_EX;// + foffset;
+
+ g = *prept;
+ if( g > *Mjpt )
+ {
+ *Mjpt = g;
+ *Mpjpt = i-1;
+ }
+// *Mjpt += fpenalty_EX;// + foffset;
+
+ g = *prept;
+ if( g > Mi )
+ {
+ Mi = g;
+ Mpi = j-1;
+ }
+// Mi += fpenalty_EX;// + foffset;
+
+
+// fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
+// fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );
+
+
+ if( maxwm < wm )
+ {
+ maxwm = wm;
+ endali = i;
+ endalj = j;
+ }
+
+#if 1
+ if( numshuryo < 100 )
+ {
+ shuryo[numshuryo].i = i;
+ shuryo[numshuryo].j = j;
+ shuryo[numshuryo].wm = wm;
+
+ if( minshuryowm > wm )
+ {
+ minshuryowm = wm;
+ minshuryopos = numshuryo;
+ }
+ numshuryo++;
+ }
+ else
+ {
+ if( wm > minshuryowm )
+ {
+ shuryo[minshuryopos].i = i;
+ shuryo[minshuryopos].j = j;
+ shuryo[minshuryopos].wm = wm;
+ minshuryowm = wm;
+ for( k=0; k<100; k++ ) // muda
+ {
+ if( shuryo[k].wm < minshuryowm )
+ {
+ minshuryowm = shuryo[k].wm;
+ minshuryopos = k;
+ break;
+ }
+ }
+ }
+ }
+#endif
+#if 1
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ *ijpipt = localstop;
+// *ijpjpt = localstop;
+ wm = localthr2;
+ }
+#endif
+#if 0
+ fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if DEBUG2
+ fprintf( stderr, "%5.0f ", wm );
+// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+
+ *curpt += wm;
+ ijpipt++;
+ ijpjpt++;
+ mjpt++;
+ Mjpt++;
+ prept++;
+ mpjpt++;
+ Mpjpt++;
+ curpt++;
+ }
+#if DEBUG2
+ fprintf( stderr, "\n" );
+#endif
+
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+ for( k=0; k<100; k++ )
+ {
+ fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+ }
+
+
+#if 1
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, "endali = %d\n", endali );
+ fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+ qsort( shuryo, 100, sizeof( Shuryoten ), (int (*)())compshuryo );
+ for( k=0; k<100; k++ )
+ {
+ fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+ }
+
+
+ lasti = lgth1+1;
+ for( i=0; i<lasti; i++ )
+ {
+ ijpi[i][0] = localstop;
+ ijpj[i][0] = localstop;
+ }
+ lastj = lgth2+1;
+ for( j=0; j<lastj; j++ )
+ {
+ ijpi[0][j] = localstop;
+ ijpj[0][j] = localstop;
+ }
+
+ for( i=0; i<lasti; i++ ) for( j=0; j<lastj; j++ ) used[i][j] = 0;
+
+ for( k=0; k<numshuryo; k++ )
+ {
+ if( shuryo[k].wm < shuryo[0].wm * 0.3 ) break;
+ fprintf( stderr, "k=%d, shuryo[k].i,j,wm=%d,%d,%f go\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+ resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shuryo[k].i, shuryo[k].j );
+ if( resf == -1.0 ) continue;
+ putlocalhom3( mseq1[0], mseq2[0], lhmpt, *off1pt, *off2pt, (int)shuryo[k].wm, strlen( mseq1[0] ) );
+#if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+ }
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stderr, "%2d ", used[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ resultlen = strlen( mseq1[0] );
+ if( alloclen < resultlen || resultlen > N )
+ {
+ fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+ ErrorExit( "LENGTH OVER!\n" );
+ }
+
+
+
+
+
+ return( wm );
+}
+
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+static int nadd;
+static int treein;
+static int topin;
+static int treeout;
+static int distout;
+static int noalign;
+
+typedef struct _jobtable
+{
+ int i;
+ int j;
+} Jobtable;
+
+#ifdef enablemultithread
+typedef struct _distancematrixthread_arg
+{
+ int njob;
+ int thread_no;
+ float *selfscore;
+ float **iscore;
+ char **seq;
+ Jobtable *jobpospt;
+ pthread_mutex_t *mutex;
+} distancematrixthread_arg_t;
+
+typedef struct _treebasethread_arg
+{
+ int thread_no;
+ int *nrunpt;
+ int njob;
+ int *nlen;
+ int *jobpospt;
+ int ***topol;
+ Treedep *dep;
+ char **aseq;
+ double *effarr;
+ int *alloclenpt;
+ LocalHom **localhomtable;
+ RNApair ***singlerna;
+ double *effarr_kozo;
+ int *fftlog;
+ pthread_mutex_t *mutex;
+ pthread_cond_t *treecond;
+} treebasethread_arg_t;
+#endif
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ nthread = 1;
+ outnumber = 0;
+ scoreout = 0;
+ treein = 0;
+ topin = 0;
+ rnaprediction = 'm';
+ rnakozo = 0;
+ nevermemsave = 0;
+ inputfile = NULL;
+ addfile = NULL;
+ addprofile = 1;
+ fftkeika = 0;
+ constraint = 0;
+ nblosum = 62;
+ fmodel = 0;
+ calledByXced = 0;
+ devide = 0;
+ use_fft = 0; // chuui
+ force_fft = 0;
+ fftscore = 1;
+ fftRepeatStop = 0;
+ fftNoAnchStop = 0;
+ weight = 3;
+ utree = 1;
+ tbutree = 1;
+ refine = 0;
+ check = 1;
+ cut = 0.0;
+ disp = 0;
+ outgap = 1;
+ alg = 'A';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'X';
+ contin = 0;
+ scoremtx = 1;
+ kobetsubunkatsu = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+ RNAppenalty = NOTSPECIFIED;
+ RNAppenalty_ex = NOTSPECIFIED;
+ RNApthr = NOTSPECIFIED;
+ TMorJTT = JTT;
+ consweight_multi = 1.0;
+ consweight_rna = 0.0;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'I':
+ nadd = atoi( *++argv );
+ fprintf( stderr, "nadd = %d\n", nadd );
+ --argc;
+ goto nextoption;
+ case 'e':
+ RNApthr = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'o':
+ RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+// fprintf( stderr, "ppenalty = %d\n", ppenalty );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+// fprintf( stderr, "poffset = %d\n", poffset );
+ --argc;
+ goto nextoption;
+ case 'k':
+ kimuraR = atoi( *++argv );
+ fprintf( stderr, "kappa = %d\n", kimuraR );
+ --argc;
+ goto nextoption;
+ case 'b':
+ nblosum = atoi( *++argv );
+ scoremtx = 1;
+ fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
+ --argc;
+ goto nextoption;
+ case 'j':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt/kimura %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "tm %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'l':
+ fastathreshold = atof( *++argv );
+ constraint = 2;
+ --argc;
+ goto nextoption;
+ case 'r':
+ consweight_rna = atof( *++argv );
+ rnakozo = 1;
+ --argc;
+ goto nextoption;
+ case 'c':
+ consweight_multi = atof( *++argv );
+ --argc;
+ goto nextoption;
+ case 'C':
+ nthread = atoi( *++argv );
+ fprintf( stderr, "nthread = %d\n", nthread );
+ --argc;
+ goto nextoption;
+ case 'R':
+ rnaprediction = 'r';
+ break;
+ case 's':
+ RNAscoremtx = 'r';
+ break;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'K':
+ addprofile = 0;
+ break;
+ case 'y':
+ distout = 1;
+ break;
+ case 't':
+ treeout = 1;
+ break;
+ case 'T':
+ noalign = 1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+#if 1
+ case 'O':
+ outgap = 0;
+ break;
+#else
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#endif
+ case 'S':
+ scoreout = 1;
+ break;
+#if 0
+ case 'e':
+ fftscore = 0;
+ break;
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+ case 's':
+ treemethod = 's';
+ break;
+#endif
+ case 'X':
+ treemethod = 'X';
+ break;
+ case 'E':
+ treemethod = 'E';
+ break;
+ case 'q':
+ treemethod = 'q';
+ break;
+ case 'n' :
+ outnumber = 1;
+ break;
+#if 0
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'Q':
+ alg = 'Q';
+ break;
+ case 'H':
+ alg = 'H';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'N':
+ nevermemsave = 1;
+ break;
+ case 'B':
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'G':
+ force_fft = 1;
+ use_fft = 1;
+ break;
+ case 'U':
+ treein = 1;
+ break;
+ case 'V':
+ topin = 1;
+ break;
+ case 'u':
+ tbrweight = 0;
+ weight = 0;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'd':
+ disp = 1;
+ break;
+/* Modified 01/08/27, default: user tree */
+ case 'J':
+ tbutree = 0;
+ break;
+/* modification end. */
+ case 'z':
+ fftThreshold = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'w':
+ fftWinSize = atoi( *++argv );
+ --argc;
+ goto nextoption;
+ case 'Z':
+ checkC = 1;
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc == 1 )
+ {
+ cut = atof( (*argv) );
+ argc--;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+ if( tbitr == 1 && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : o, m or u\n" );
+ exit( 1 );
+ }
+ if( alg == 'C' && outgap == 0 )
+ {
+ fprintf( stderr, "conflicting options : C, o\n" );
+ exit( 1 );
+ }
+}
+
+#if 0
+static void *distancematrixthread2( void *arg )
+{
+ distancematrixthread_arg_t *targ = (distancematrixthread_arg_t *)arg;
+ int njob = targ->njob;
+ int thread_no = targ->thread_no;
+ float *selfscore = targ->selfscore;
+ float **iscore = targ->iscore;
+ char **seq = targ->seq;
+ Jobtable *jobpospt = targ->jobpospt;
+
+ float ssi, ssj, bunbo;
+ int i, j;
+
+ while( 1 )
+ {
+ pthread_mutex_lock( targ->mutex );
+ i = jobpospt->i;
+ i++;
+ if( i == njob-1 )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ return( NULL );
+ }
+ jobpospt->i = i;
+ pthread_mutex_unlock( targ->mutex );
+
+ ssi = selfscore[i];
+ if( i % 10 == 0 ) fprintf( stderr, "\r% 5d / %d (thread %4d)", i, njob, thread_no );
+ for( j=i+1; j<njob; j++)
+ {
+ ssj = selfscore[j];
+ bunbo = MIN( ssi, ssj );
+ if( bunbo == 0.0 )
+ iscore[i][j-i] = 1.0;
+ else
+ iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
+ }
+ }
+}
+#endif
+
+#ifdef enablemultithread
+static void *distancematrixthread( void *arg )
+{
+ distancematrixthread_arg_t *targ = (distancematrixthread_arg_t *)arg;
+ int njob = targ->njob;
+ int thread_no = targ->thread_no;
+ float *selfscore = targ->selfscore;
+ float **iscore = targ->iscore;
+ char **seq = targ->seq;
+ Jobtable *jobpospt = targ->jobpospt;
+
+ float ssi, ssj, bunbo;
+ int i, j;
+
+ while( 1 )
+ {
+ pthread_mutex_lock( targ->mutex );
+ j = jobpospt->j;
+ i = jobpospt->i;
+ j++;
+ if( j == njob )
+ {
+ i++;
+ j = i + 1;
+ if( i == njob-1 )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ return( NULL );
+ }
+ }
+ jobpospt->j = j;
+ jobpospt->i = i;
+ pthread_mutex_unlock( targ->mutex );
+
+
+ if( j==i+1 && i % 10 == 0 ) fprintf( stderr, "\r% 5d / %d (thread %4d)", i, njob, thread_no );
+ ssi = selfscore[i];
+ ssj = selfscore[j];
+ bunbo = MIN( ssi, ssj );
+ if( bunbo == 0.0 )
+ iscore[i][j-i] = 1.0;
+ else
+ iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
+ }
+}
+
+static void *treebasethread( void *arg )
+{
+ treebasethread_arg_t *targ = (treebasethread_arg_t *)arg;
+ int *nrunpt = targ->nrunpt;
+ int thread_no = targ->thread_no;
+ int njob = targ->njob;
+ int *nlen = targ->nlen;
+ int *jobpospt = targ->jobpospt;
+ int ***topol = targ->topol;
+ Treedep *dep = targ->dep;
+ char **aseq = targ->aseq;
+ double *effarr = targ->effarr;
+ int *alloclen = targ->alloclenpt;
+ LocalHom **localhomtable = targ->localhomtable;
+ RNApair ***singlerna = targ->singlerna;
+ double *effarr_kozo = targ->effarr_kozo;
+ int *fftlog = targ->fftlog;
+
+ char **mseq1, **mseq2;
+ char **localcopy;
+ int i, j, l;
+ int len1, len2;
+ int clus1, clus2;
+ float pscore;
+ char *indication1, *indication2;
+ double *effarr1 = NULL;
+ double *effarr2 = NULL;
+ double *effarr1_kozo = NULL;
+ double *effarr2_kozo = NULL;
+ LocalHom ***localhomshrink = NULL;
+ int m1, m2;
+ float dumfl = 0.0;
+ int ffttry;
+ RNApair ***grouprna1, ***grouprna2;
+
+
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ localcopy = calloc( njob, sizeof( char * ) );
+
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ }
+ else
+ {
+ grouprna1 = grouprna2 = NULL;
+ }
+
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+#if 0
+#else
+ if( constraint )
+ {
+ localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
+ for( i=0; i<njob; i++)
+ localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ }
+#endif
+ effarr1_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
+ effarr2_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
+ for( i=0; i<njob; i++ ) effarr1_kozo[i] = 0.0;
+ for( i=0; i<njob; i++ ) effarr2_kozo[i] = 0.0;
+
+
+#if 0
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+#if 0 //-> main thread
+ if( constraint )
+ calcimportance( njob, effarr, aseq, localhomtable );
+#endif
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+
+// for( l=0; l<njob-1; l++ )
+ while( 1 )
+ {
+
+ pthread_mutex_lock( targ->mutex );
+ l = *jobpospt;
+ if( l == njob-1 )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonIP = NULL;
+ Falign( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
+ A__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+ free( mseq1 );
+ free( mseq2 );
+ free( localcopy );
+ free( effarr1 );
+ free( effarr2 );
+ free( effarr1_kozo );
+ free( effarr2_kozo );
+ free( indication1 );
+ free( indication2 );
+ if( constraint )
+ {
+ for( i=0; i<njob; i++)
+ free( localhomshrink[i] );
+ free( localhomshrink );
+ }
+ return( NULL );
+ }
+ *jobpospt = l+1;
+
+ if( dep[l].child0 != -1 )
+ {
+ while( dep[dep[l].child0].done == 0 )
+ pthread_cond_wait( targ->treecond, targ->mutex );
+ }
+ if( dep[l].child1 != -1 )
+ {
+ while( dep[dep[l].child1].done == 0 )
+ pthread_cond_wait( targ->treecond, targ->mutex );
+ }
+// while( *nrunpt >= nthread )
+// pthread_cond_wait( targ->treecond, targ->mutex );
+ (*nrunpt)++;
+
+// pthread_mutex_unlock( targ->mutex );
+
+
+ m1 = topol[l][0][0];
+ m2 = topol[l][1][0];
+
+// pthread_mutex_lock( targ->mutex );
+
+ len1 = strlen( aseq[m1] );
+ len2 = strlen( aseq[m2] );
+ if( *alloclen <= len1 + len2 )
+ {
+ fprintf( stderr, "\nReallocating (by thread %d) ..", thread_no );
+ *alloclen = ( len1 + len2 ) + 1000;
+ ReallocateCharMtx( aseq, njob, *alloclen + 10 );
+ fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
+ }
+
+ for( i=0; (j=topol[l][0][i])!=-1; i++ )
+ {
+ localcopy[j] = calloc( *alloclen, sizeof( char ) );
+ strcpy( localcopy[j], aseq[j] );
+ }
+ for( i=0; (j=topol[l][1][i])!=-1; i++ )
+ {
+ localcopy[j] = calloc( *alloclen, sizeof( char ) );
+ strcpy( localcopy[j], aseq[j] );
+ }
+
+ pthread_mutex_unlock( targ->mutex );
+
+ if( effarr_kozo )
+ {
+ clus1 = fastconjuction_noname_kozo( topol[l][0], localcopy, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
+ clus2 = fastconjuction_noname_kozo( topol[l][1], localcopy, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
+ }
+ else
+ {
+ clus1 = fastconjuction_noname( topol[l][0], localcopy, mseq1, effarr1, effarr, indication1 );
+ clus2 = fastconjuction_noname( topol[l][1], localcopy, mseq2, effarr2, effarr, indication2 );
+ }
+
+
+
+#if 1
+ fprintf( stderr, "\rSTEP % 5d /%d (thread %4d) ", l+1, njob-1, thread_no );
+#else
+ fprintf( stderr, "STEP %d /%d (thread %d) \n", l+1, njob-1, thread_no );
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, ", child1 = %d\n", dep[l].child0 );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, ", child2 = %d\n", dep[l].child1 );
+
+ fprintf( stderr, "Group1's lengths = " );
+ for( i=0; i<clus1; i++ ) fprintf( stderr, "%d ", strlen( mseq1[i] ) );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "Group2's lengths = " );
+ for( i=0; i<clus2; i++ ) fprintf( stderr, "%d ", strlen( mseq2[i] ) );
+ fprintf( stderr, "\n" );
+
+#endif
+
+
+
+// for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
+
+ if( constraint )
+ {
+ fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
+// msfastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
+// fprintf( stderr, "localhomshrink =\n" );
+// outlocalhompt( localhomshrink, clus1, clus2 );
+// weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
+// fprintf( stderr, "after weight =\n" );
+// outlocalhompt( localhomshrink, clus1, clus2 );
+ }
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ makegrouprna( grouprna1, singlerna, topol[l][0] );
+ makegrouprna( grouprna2, singlerna, topol[l][1] );
+ }
+
+
+/*
+ fprintf( stderr, "before align all\n" );
+ display( localcopy, njob );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+ if( !nevermemsave && ( constraint != 2 && alg != 'M' && ( len1 > 30000 || len2 > 30000 ) ) )
+ {
+ fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
+ alg = 'M';
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonAlloc1 = 0;
+ commonAlloc2 = 0;
+ }
+
+
+// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
+ if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
+ else ffttry = 0;
+// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
+// fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
+// fprintf( stderr, "f=%d, clus1=%d, fftlog[m1]=%d, clus2=%d, fftlog[m2]=%d\n", ffttry, clus1, fftlog[m1], clus2, fftlog[m2] );
+ if( constraint == 2 )
+ {
+ if( alg == 'M' )
+ {
+ fprintf( stderr, "\n\nMemory saving mode is not supported.\n\n" );
+ exit( 1 );
+ }
+ fprintf( stderr, "c" );
+ if( alg == 'A' )
+ {
+ imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+ else if( alg == 'H' )
+ {
+ imp_match_init_strictH( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ else if( alg == 'Q' )
+ {
+ imp_match_init_strictQ( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
+ pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ else if( alg == 'R' )
+ {
+ imp_match_init_strictR( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ }
+ else if( force_fft || ( use_fft && ffttry ) )
+ {
+ fprintf( stderr, "f" );
+ if( alg == 'M' )
+ {
+ fprintf( stderr, "m" );
+ pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
+ }
+ else
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
+ }
+ else
+ {
+ fprintf( stderr, "d" );
+ fftlog[m1] = 0;
+ switch( alg )
+ {
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
+ break;
+ case( 'M' ):
+ fprintf( stderr, "m" );
+ pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'A' ):
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'Q' ):
+ pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ case( 'R' ):
+ pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ case( 'H' ):
+ pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ default:
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+
+ nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
+
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f\n", pscore );
+#endif
+
+/*
+ fprintf( stderr, "after align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "after align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+// writePre( njob, name, nlen, localcopy, 0 );
+
+ if( disp ) display( localcopy, njob );
+
+ pthread_mutex_lock( targ->mutex );
+ dep[l].done = 1;
+ (*nrunpt)--;
+ pthread_cond_broadcast( targ->treecond );
+
+// pthread_mutex_unlock( targ->mutex );
+// pthread_mutex_lock( targ->mutex );
+
+ for( i=0; (j=topol[l][0][i])!=-1; i++ )
+ strcpy( aseq[j], localcopy[j] );
+ for( i=0; (j=topol[l][1][i])!=-1; i++ )
+ strcpy( aseq[j], localcopy[j] );
+ pthread_mutex_unlock( targ->mutex );
+
+ for( i=0; (j=topol[l][0][i])!=-1; i++ )
+ free( localcopy[j] );
+ for( i=0; (j=topol[l][1][i])!=-1; i++ )
+ free( localcopy[j] );
+ free( topol[l][0] );
+ free( topol[l][1] );
+ free( topol[l] );
+
+ }
+}
+#endif
+
+void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mseq2, int ***topol, double *effarr, int *alloclen, LocalHom **localhomtable, RNApair ***singlerna, double *effarr_kozo )
+{
+ int i, l, m;
+ int len1nocommongap, len2nocommongap;
+ int len1, len2;
+ int clus1, clus2;
+ float pscore, tscore;
+ static char *indication1, *indication2;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ static double *effarr1_kozo = NULL;
+ static double *effarr2_kozo = NULL;
+ static LocalHom ***localhomshrink = NULL;
+ static int *fftlog;
+ int m1, m2;
+ static int *gaplen;
+ static int *gapmap;
+ static int *alreadyaligned;
+ float dumfl = 0.0;
+ int ffttry;
+ RNApair ***grouprna1, ***grouprna2;
+
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ }
+ else
+ {
+ grouprna1 = grouprna2 = NULL;
+ }
+
+ if( effarr1 == NULL )
+ {
+ fftlog = AllocateIntVec( njob );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+ gaplen = AllocateIntVec( *alloclen+10 );
+ gapmap = AllocateIntVec( *alloclen+10 );
+ alreadyaligned = AllocateIntVec( njob );
+#if 0
+#else
+ if( constraint )
+ {
+ localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
+ for( i=0; i<njob; i++)
+ localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ }
+#endif
+ effarr1_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
+ effarr2_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
+ for( i=0; i<njob; i++ ) effarr1_kozo[i] = 0.0;
+ for( i=0; i<njob; i++ ) effarr2_kozo[i] = 0.0;
+ }
+
+ for( i=0; i<njob-nadd; i++ ) alreadyaligned[i] = 1;
+ for( i=njob-nadd; i<njob; i++ ) alreadyaligned[i] = 0;
+
+ for( l=0; l<njob; l++ ) fftlog[l] = 1;
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+
+ if( constraint )
+ calcimportance( njob, effarr, aseq, localhomtable );
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ tscore = 0.0;
+ for( l=0; l<njob-1; l++ )
+ {
+ if( mergeoralign[l] == 'n' )
+ {
+// fprintf( stderr, "SKIP!\n" );
+ free( topol[l][0] );
+ free( topol[l][1] );
+ free( topol[l] );
+ continue;
+ }
+
+ m1 = topol[l][0][0];
+ m2 = topol[l][1][0];
+ len1 = strlen( aseq[m1] );
+ len2 = strlen( aseq[m2] );
+ if( *alloclen < len1 + len2 )
+ {
+ fprintf( stderr, "\nReallocating.." );
+ *alloclen = ( len1 + len2 ) + 1000;
+ ReallocateCharMtx( aseq, njob, *alloclen + 10 );
+ gaplen = realloc( gaplen, ( *alloclen + 10 ) * sizeof( int ) );
+ if( gaplen == NULL )
+ {
+ fprintf( stderr, "Cannot realloc gaplen\n" );
+ exit( 1 );
+ }
+ gapmap = realloc( gapmap, ( *alloclen + 10 ) * sizeof( int ) );
+ if( gapmap == NULL )
+ {
+ fprintf( stderr, "Cannot realloc gapmap\n" );
+ exit( 1 );
+ }
+ fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
+ }
+
+ if( effarr_kozo )
+ {
+ clus1 = fastconjuction_noname_kozo( topol[l][0], aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
+ clus2 = fastconjuction_noname_kozo( topol[l][1], aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
+ }
+ else
+ {
+ clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2 );
+ }
+
+ if( mergeoralign[l] == '1' || mergeoralign[l] == '2' )
+ {
+ newgapstr = "=";
+ }
+ else
+ newgapstr = "-";
+
+
+ len1nocommongap = len1;
+ len2nocommongap = len2;
+ if( mergeoralign[l] == '1' ) // nai
+ {
+ findcommongaps( clus2, mseq2, gapmap );
+ commongappick( clus2, mseq2 );
+ len2nocommongap = strlen( mseq2[0] );
+ }
+ else if( mergeoralign[l] == '2' )
+ {
+ findcommongaps( clus1, mseq1, gapmap );
+ commongappick( clus1, mseq1 );
+ len1nocommongap = strlen( mseq1[0] );
+ }
+
+
+ fprintf( trap_g, "\nSTEP-%d\n", l );
+ fprintf( trap_g, "group1 = %s\n", indication1 );
+ fprintf( trap_g, "group2 = %s\n", indication2 );
+
+#if 1
+ fprintf( stderr, "\rSTEP % 5d /%d ", l+1, njob-1 );
+ fflush( stderr );
+#else
+ fprintf( stdout, "STEP %d /%d\n", l+1, njob-1 );
+ fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+#endif
+
+
+
+// for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
+
+ if( constraint )
+ {
+ fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
+// msfastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
+// fprintf( stderr, "localhomshrink =\n" );
+// outlocalhompt( localhomshrink, clus1, clus2 );
+// weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
+// fprintf( stderr, "after weight =\n" );
+// outlocalhompt( localhomshrink, clus1, clus2 );
+ }
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ makegrouprna( grouprna1, singlerna, topol[l][0] );
+ makegrouprna( grouprna2, singlerna, topol[l][1] );
+ }
+
+
+/*
+ fprintf( stderr, "before align all\n" );
+ display( aseq, njob );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+ if( !nevermemsave && ( constraint != 2 && alg != 'M' && ( len1 > 30000 || len2 > 30000 ) ) )
+ {
+ fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
+ alg = 'M';
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonAlloc1 = 0;
+ commonAlloc2 = 0;
+ }
+
+
+// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
+ if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
+ else ffttry = 0;
+// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
+// fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
+// fprintf( stderr, "f=%d, clus1=%d, fftlog[m1]=%d, clus2=%d, fftlog[m2]=%d\n", ffttry, clus1, fftlog[m1], clus2, fftlog[m2] );
+ if( constraint == 2 )
+ {
+ if( alg == 'M' )
+ {
+ fprintf( stderr, "\n\nMemory saving mode is not supported.\n\n" );
+ exit( 1 );
+ }
+ fprintf( stderr, "c" );
+ if( alg == 'A' )
+ {
+ imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+ else if( alg == 'H' )
+ {
+ imp_match_init_strictH( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ else if( alg == 'Q' )
+ {
+ imp_match_init_strictQ( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
+ pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ else if( alg == 'R' )
+ {
+ imp_match_init_strictR( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
+ }
+ }
+ else if( force_fft || ( use_fft && ffttry ) )
+ {
+ fprintf( stderr, "f" );
+ if( alg == 'M' )
+ {
+ fprintf( stderr, "m" );
+ pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
+ }
+ else
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
+ }
+ else
+ {
+ fprintf( stderr, "d" );
+ fftlog[m1] = 0;
+ switch( alg )
+ {
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
+ break;
+ case( 'M' ):
+ fprintf( stderr, "m" );
+ pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'A' ):
+ pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ break;
+ case( 'Q' ):
+ pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ case( 'R' ):
+ pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ case( 'H' ):
+ pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+ break;
+ default:
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+
+ nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
+
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f\n", pscore );
+#endif
+ tscore += pscore;
+/*
+ fprintf( stderr, "after align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "after align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ if( disp ) display( aseq, njob );
+
+ if( mergeoralign[l] == '1' ) // jissainiha nai. atarashii hairetsu ha saigo dakara.
+ {
+ adjustgapmap( strlen( mseq2[0] )-len2nocommongap+len2, gapmap, mseq2[0] );
+ restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen );
+ findnewgaps( clus2, mseq2, gaplen );
+ insertnewgaps( njob, alreadyaligned, aseq, topol[l][1], topol[l][0], gaplen, gapmap, *alloclen, alg );
+ for( i=0; i<njob; i++ ) eq2dash( aseq[i] );
+ for( i=0; (m=topol[l][0][i])>-1; i++ ) alreadyaligned[m] = 1;
+ }
+ if( mergeoralign[l] == '2' )
+ {
+// fprintf( stderr, ">mseq1[0] = \n%s\n", mseq1[0] );
+// fprintf( stderr, ">mseq2[0] = \n%s\n", mseq2[0] );
+ adjustgapmap( strlen( mseq1[0] )-len1nocommongap+len1, gapmap, mseq1[0] );
+ restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen );
+ findnewgaps( clus1, mseq1, gaplen );
+ insertnewgaps( njob, alreadyaligned, aseq, topol[l][0], topol[l][1], gaplen, gapmap, *alloclen, alg );
+ for( i=0; i<njob; i++ ) eq2dash( aseq[i] );
+ for( i=0; (m=topol[l][1][i])>-1; i++ ) alreadyaligned[m] = 1;
+ }
+
+ free( topol[l][0] );
+ free( topol[l][1] );
+ free( topol[l] );
+ }
+#if SCOREOUT
+ fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
+#endif
+}
+
+static void WriteOptions( FILE *fp )
+{
+
+ if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+ else
+ {
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ }
+ fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ if( use_fft ) fprintf( fp, "FFT on\n" );
+
+ fprintf( fp, "tree-base method\n" );
+ if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+ else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+ if( tbitr || tbweight )
+ {
+ fprintf( fp, "iterate at each step\n" );
+ if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
+ if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
+ if( tbweight ) fprintf( fp, " weighted\n" );
+ fprintf( fp, "\n" );
+ }
+
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+\n" );
+ else if( alg == 'C' )
+ fprintf( fp, "Apgorithm A+/C\n" );
+ else
+ fprintf( fp, "Unknown algorithm\n" );
+
+ if( treemethod == 'X' )
+ fprintf( fp, "Tree = UPGMA (mix).\n" );
+ else if( treemethod == 'E' )
+ fprintf( fp, "Tree = UPGMA (average).\n" );
+ else if( treemethod == 'q' )
+ fprintf( fp, "Tree = Minimum linkage.\n" );
+ else
+ fprintf( fp, "Unknown tree.\n" );
+
+ if( use_fft )
+ {
+ fprintf( fp, "FFT on\n" );
+ if( dorp == 'd' )
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+ else
+ fprintf( fp, "FFT off\n" );
+ fflush( fp );
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int *nlen;
+ static float *selfscore;
+ int nogaplen;
+ static char **name, **seq;
+ static char **mseq1, **mseq2;
+ static char **bseq;
+ static float **iscore, **iscore_kozo;
+ static double *eff, *eff_kozo, *eff_kozo_mapped = NULL;
+ int i, j, ien, ik, jk;
+ static int ***topol, ***topol_kozo;
+ static int *addmem;
+ static Treedep *dep;
+ static float **len, **len_kozo;
+ FILE *prep;
+ FILE *infp;
+ FILE *orderfp;
+ FILE *hat2p;
+ double unweightedspscore;
+ int alignmentlength;
+ char *mergeoralign;
+ int foundthebranch;
+
+ char c;
+ int alloclen;
+ LocalHom **localhomtable = NULL;
+ RNApair ***singlerna;
+ float ssi, ssj, bunbo;
+ static char *kozoarivec;
+ int nkozo;
+
+ arguments( argc, argv );
+#ifndef enablemultithread
+ nthread = 0;
+#endif
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen( infp );
+ rewind( infp );
+
+
+ nkozo = 0;
+
+ if( njob < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax+1 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+ selfscore = AllocateFloatVec( njob );
+
+ topol = AllocateIntCub( njob, 2, 0 );
+ len = AllocateFloatMtx( njob, 2 );
+ iscore = AllocateFloatHalfMtx( njob );
+ eff = AllocateDoubleVec( njob );
+ kozoarivec = AllocateCharVec( njob );
+
+ mergeoralign = AllocateCharVec( njob );
+
+ dep = (Treedep *)calloc( njob, sizeof( Treedep ) );
+ if( nadd ) addmem = AllocateIntVec( nadd+1 );
+
+ if( constraint )
+ {
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].overlapaa = -1.0;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].importance = -1.0;
+ localhomtable[i][j].next = NULL;
+ localhomtable[i][j].korh = 'h';
+ }
+ }
+
+ fprintf( stderr, "Loading 'hat3' ... " );
+ prep = fopen( "hat3", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat3." );
+ readlocalhomtable( prep, njob, localhomtable, kozoarivec );
+ fclose( prep );
+ fprintf( stderr, "\ndone.\n" );
+
+
+ nkozo = 0;
+ for( i=0; i<njob; i++ )
+ {
+// fprintf( stderr, "kozoarivec[%d] = %d\n", i, kozoarivec[i] );
+ if( kozoarivec[i] ) nkozo++;
+ }
+ if( nkozo )
+ {
+ topol_kozo = AllocateIntCub( nkozo, 2, 0 );
+ len_kozo = AllocateFloatMtx( nkozo, 2 );
+ iscore_kozo = AllocateFloatHalfMtx( nkozo );
+ eff_kozo = AllocateDoubleVec( nkozo );
+ eff_kozo_mapped = AllocateDoubleVec( njob );
+ }
+
+
+// outlocalhom( localhomtable, njob );
+
+#if 0
+ fprintf( stderr, "Extending localhom ... " );
+ extendlocalhom2( njob, localhomtable );
+ fprintf( stderr, "done.\n" );
+#endif
+ }
+
+#if 0
+ readData( infp, name, nlen, seq );
+#else
+ readData_pointer( infp, name, nlen, seq );
+ fclose( infp );
+#endif
+
+ constants( njob, seq );
+
+#if 0
+ fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+ initSignalSM();
+
+ initFiles();
+
+ WriteOptions( trap_g );
+
+ c = seqcheck( seq );
+ if( c )
+ {
+ fprintf( stderr, "Illegal character %c\n", c );
+ exit( 1 );
+ }
+
+// writePre( njob, name, nlen, seq, 0 );
+
+ if( treein )
+ {
+#if 0
+ if( nkozo )
+ {
+ fprintf( stderr, "Both structure and user tree have been given. Not yet supported!\n" );
+ exit( 1 );
+ }
+#endif
+ fprintf( stderr, "Loading a tree ... " );
+ loadtree( njob, topol, len, name, nlen, dep );
+ fprintf( stderr, "\ndone.\n\n" );
+ }
+ else
+ {
+ if( tbutree == 0 )
+ {
+ for( i=1; i<njob; i++ )
+ {
+ if( nlen[i] != nlen[0] )
+ {
+ fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
+ exit( 1 );
+ }
+ }
+
+ fprintf( stderr, "Making a distance matrix .. \n" );
+ fflush( stderr );
+ ien = njob-1;
+ for( i=0; i<njob; i++ )
+ {
+ selfscore[i] = naivepairscore11( seq[i], seq[i], penalty );
+ }
+#ifdef enablemultithread
+ if( nthread > 0 )
+ {
+ distancematrixthread_arg_t *targ;
+ Jobtable jobpos;
+ pthread_t *handle;
+ pthread_mutex_t mutex;
+
+ jobpos.i = 0;
+ jobpos.j = 0;
+
+ targ = calloc( nthread, sizeof( distancematrixthread_arg_t ) );
+ handle = calloc( nthread, sizeof( pthread_t ) );
+ pthread_mutex_init( &mutex, NULL );
+
+ for( i=0; i<nthread; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].njob = njob;
+ targ[i].selfscore = selfscore;
+ targ[i].iscore = iscore;
+ targ[i].seq = seq;
+ targ[i].jobpospt = &jobpos;
+ targ[i].mutex = &mutex;
+
+ pthread_create( handle+i, NULL, distancematrixthread, (void *)(targ+i) );
+ }
+
+ for( i=0; i<nthread; i++ )
+ {
+ pthread_join( handle[i], NULL );
+ }
+ pthread_mutex_destroy( &mutex );
+ free( handle );
+ free( targ );
+ }
+ else
+#endif
+ {
+ for( i=0; i<ien; i++ )
+ {
+ if( i % 10 == 0 )
+ {
+ fprintf( stderr, "\r% 5d / %d", i, ien );
+ fflush( stderr );
+ }
+ ssi = selfscore[i];
+ for( j=i+1; j<njob; j++ )
+ {
+ ssj = selfscore[j];
+ bunbo = MIN( ssi, ssj );
+ if( bunbo == 0.0 )
+ iscore[i][j-i] = 1.0;
+ else
+// iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / MIN( selfscore[i], selfscore[j] );
+ iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
+
+#if 0
+ fprintf( stderr, "### ssj = %f\n", ssj );
+ fprintf( stderr, "### selfscore[i] = %f\n", selfscore[i] );
+ fprintf( stderr, "### selfscore[j] = %f\n", selfscore[j] );
+ fprintf( stderr, "### rawscore = %f\n", naivepairscore11( seq[i], seq[j], penalty ) );
+#endif
+ }
+ }
+ }
+ fprintf( stderr, "\ndone.\n\n" );
+ fflush( stderr );
+ }
+ else
+ {
+ fprintf( stderr, "Loading 'hat2' ... " );
+ prep = fopen( "hat2", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat2." );
+ readhat2_floathalf_pointer( prep, njob, name, iscore );
+ fclose( prep );
+ fprintf( stderr, "done.\n" );
+ }
+#if 1
+ if( distout )
+ {
+ hat2p = fopen( "hat2", "w" );
+ WriteFloatHat2_pointer_halfmtx( hat2p, njob, name, iscore );
+ fclose( hat2p );
+ }
+#endif
+ if( nkozo )
+ {
+ ien = njob-1;
+ ik = 0;
+ for( i=0; i<ien; i++ )
+ {
+ jk = ik+1;
+ for( j=i+1; j<njob; j++ )
+ {
+ if( kozoarivec[i] && kozoarivec[j] )
+ {
+ iscore_kozo[ik][jk-ik] = iscore[i][j-i];
+ }
+ if( kozoarivec[j] ) jk++;
+ }
+ if( kozoarivec[i] ) ik++;
+ }
+ }
+
+ fprintf( stderr, "Constructing a UPGMA tree ... " );
+ fflush( stderr );
+ if( topin )
+ {
+ fprintf( stderr, "Loading a topology ... " );
+ loadtop( njob, iscore, topol, len );
+ fprintf( stderr, "\ndone.\n\n" );
+ }
+ else if( treeout )
+ {
+ fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( njob, iscore, topol, len, name, nlen, dep );
+ }
+ else
+ {
+ fixed_musclesupg_float_realloc_nobk_halfmtx( njob, iscore, topol, len, dep );
+ }
+// else
+// ErrorExit( "Incorrect tree\n" );
+
+ if( nkozo )
+ {
+// for( i=0; i<nkozo-1; i++ )
+// for( j=i+1; j<nkozo; j++ )
+// fprintf( stderr, "iscore_kozo[%d][%d] =~ %f\n", i, j, iscore_kozo[i][j-i] );
+ fixed_musclesupg_float_realloc_nobk_halfmtx( nkozo, iscore_kozo, topol_kozo, len_kozo, NULL );
+ }
+ fprintf( stderr, "\ndone.\n\n" );
+ fflush( stderr );
+ }
+
+
+ orderfp = fopen( "order", "w" );
+ if( !orderfp )
+ {
+ fprintf( stderr, "Cannot open 'order'\n" );
+ exit( 1 );
+ }
+ for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
+ {
+ fprintf( orderfp, "%d\n", j );
+ }
+ for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
+ {
+ fprintf( orderfp, "%d\n", j );
+ }
+ fclose( orderfp );
+
+ if( treeout && noalign )
+ {
+ writeData_pointer( prep_g, njob, name, nlen, seq );
+ fprintf( stderr, "\n" );
+ SHOWVERSION;
+ return( 0 );
+ }
+
+// countnode( njob, topol, node0 );
+ if( tbrweight )
+ {
+ weight = 3;
+#if 0
+ utree = 0; counteff( njob, topol, len, eff ); utree = 1;
+#else
+ counteff_simple_float( njob, topol, len, eff );
+
+ if( nkozo )
+ {
+// counteff_simple_float( nkozo, topol_kozo, len_kozo, eff_kozo ); // single weight nanode iranai
+ for( i=0,j=0; i<njob; i++ )
+ {
+ if( kozoarivec[i] )
+ {
+// eff_kozo_mapped[i] = eff_kozo[j]; //
+ eff_kozo_mapped[i] = eff[i]; // single weight
+ j++;
+ }
+ else
+ eff_kozo_mapped[i] = 0.0;
+// fprintf( stderr, "eff_kozo_mapped[%d] = %f\n", i, eff_kozo_mapped[i] );
+// fprintf( stderr, " eff[%d] = %f\n", i, eff[i] );
+ }
+ }
+
+
+#endif
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+ if( nkozo )
+ {
+ for( i=0; i<njob; i++ )
+ {
+ if( kozoarivec[i] )
+ eff_kozo_mapped[i] = 1.0;
+ else
+ eff_kozo_mapped[i] = 0.0;
+ }
+ }
+ }
+
+ FreeFloatHalfMtx( iscore, njob );
+ FreeFloatMtx( len );
+
+ alloclen = nlenmax*2+1; //chuui!
+ bseq = AllocateCharMtx( njob, alloclen );
+
+ if( nadd )
+ {
+ alignmentlength = strlen( seq[0] );
+ for( i=0; i<njob-nadd; i++ )
+ {
+ if( alignmentlength != strlen( seq[i] ) )
+ {
+ fprintf( stderr, "#################################################################################\n" );
+ fprintf( stderr, "# ERROR! #\n" );
+ fprintf( stderr, "# The original%4d sequences must be aligned #\n", njob-nadd );
+ fprintf( stderr, "#################################################################################\n" );
+ exit( 1 );
+ }
+ }
+ if( addprofile )
+ {
+ alignmentlength = strlen( seq[njob-nadd] );
+ for( i=njob-nadd; i<njob; i++ )
+ {
+ if( alignmentlength != strlen( seq[i] ) )
+ {
+ fprintf( stderr, "###############################################################################\n" );
+ fprintf( stderr, "# ERROR! #\n" );
+ fprintf( stderr, "# The%4d additional sequences must be aligned #\n", nadd );
+ fprintf( stderr, "# Otherwise, try the '--add' option, instead of '--addprofile' option. #\n" );
+ fprintf( stderr, "###############################################################################\n" );
+ exit( 1 );
+ }
+ }
+ for( i=0; i<nadd; i++ ) addmem[i] = njob-nadd+i;
+ addmem[nadd] = -1;
+ foundthebranch = 0;
+ for( i=0; i<njob-1; i++ )
+ {
+ if( samemember( topol[i][0], addmem ) ) // jissainiha nai
+ {
+ mergeoralign[i] = '1';
+ foundthebranch = 1;
+ }
+ else if( samemember( topol[i][1], addmem ) )
+ {
+ mergeoralign[i] = '2';
+ foundthebranch = 1;
+ }
+ else
+ {
+ mergeoralign[i] = 'n';
+ }
+ }
+ if( !foundthebranch )
+ {
+ fprintf( stderr, "###############################################################################\n" );
+ fprintf( stderr, "# ERROR! #\n" );
+ fprintf( stderr, "# There is no appropriate position to add the%4d sequences in the guide tree.#\n", nadd );
+ fprintf( stderr, "# Check whether the%4d sequences form a monophyletic cluster. #\n", nadd );
+ fprintf( stderr, "# If not, try the '--add' option, instead of the '--addprofile' option. #\n" );
+ fprintf( stderr, "############################################################################### \n" );
+ exit( 1 );
+ }
+ commongappick( nadd, seq+njob-nadd );
+ for( i=njob-nadd; i<njob; i++ ) strcpy( bseq[i], seq[i] );
+ }
+ else
+ {
+ for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'n';
+ for( j=njob-nadd; j<njob; j++ )
+ {
+ addmem[0] = j;
+ addmem[1] = -1;
+ for( i=0; i<njob-1; i++ )
+ {
+ if( samemember( topol[i][0], addmem ) ) // arieru
+ {
+// fprintf( stderr, "HIT!\n" );
+ if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
+ else mergeoralign[i] = '1';
+ }
+ else if( samemember( topol[i][1], addmem ) )
+ {
+// fprintf( stderr, "HIT!\n" );
+ if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
+ else mergeoralign[i] = '2';
+ }
+ }
+ }
+
+ for( i=0; i<nadd; i++ ) addmem[i] = njob-nadd+i;
+ addmem[nadd] = -1;
+ for( i=0; i<njob-1; i++ )
+ {
+ if( includemember( topol[i][0], addmem ) && includemember( topol[i][1], addmem ) )
+ {
+ mergeoralign[i] = 'w';
+ }
+ else if( includemember( topol[i][0], addmem ) )
+ {
+ mergeoralign[i] = '1';
+ }
+ else if( includemember( topol[i][1], addmem ) )
+ {
+ mergeoralign[i] = '2';
+ }
+ }
+#if 0
+ for( i=0; i<njob-1; i++ )
+ {
+ fprintf( stderr, "mem0 = " );
+ for( j=0; topol[i][0][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][0][j] );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "mem1 = " );
+ for( j=0; topol[i][1][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][1][j] );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "i=%d, mergeoralign[] = %c\n", i, mergeoralign[i] );
+ }
+#endif
+ for( i=njob-nadd; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+ }
+
+ commongappick( njob-nadd, seq );
+ for( i=0; i<njob-nadd; i++ ) strcpy( bseq[i], seq[i] );
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+ for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'a';
+ }
+
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ singlerna = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ prep = fopen( "hat4", "r" );
+ if( prep == NULL ) ErrorExit( "Make hat4 using mccaskill." );
+ fprintf( stderr, "Loading 'hat4' ... " );
+ for( i=0; i<njob; i++ )
+ {
+ nogaplen = strlen( bseq[i] );
+ singlerna[i] = (RNApair **)calloc( nogaplen, sizeof( RNApair * ) );
+ for( j=0; j<nogaplen; j++ )
+ {
+ singlerna[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+ singlerna[i][j][0].bestpos = -1;
+ singlerna[i][j][0].bestscore = -1.0;
+ }
+ readmccaskill( prep, singlerna[i], nogaplen );
+ }
+ fclose( prep );
+ fprintf( stderr, "\ndone.\n" );
+ }
+ else
+ singlerna = NULL;
+
+
+ fprintf( stderr, "Progressive alignment ... \n" );
+
+#ifdef enablemultithread
+ if( nthread > 0 && nadd == 0 )
+ {
+ treebasethread_arg_t *targ;
+ int jobpos;
+ pthread_t *handle;
+ pthread_mutex_t mutex;
+ pthread_cond_t treecond;
+ int *fftlog;
+ int nrun;
+ int nthread_yoyu;
+
+ nthread_yoyu = nthread * 1;
+ nrun = 0;
+ jobpos = 0;
+ targ = calloc( nthread_yoyu, sizeof( treebasethread_arg_t ) );
+ fftlog = AllocateIntVec( njob );
+ handle = calloc( nthread_yoyu, sizeof( pthread_t ) );
+ pthread_mutex_init( &mutex, NULL );
+ pthread_cond_init( &treecond, NULL );
+
+ for( i=0; i<njob; i++ ) dep[i].done = 0;
+ for( i=0; i<njob; i++ ) fftlog[i] = 1;
+
+ if( constraint )
+ calcimportance( njob, eff, bseq, localhomtable );
+
+ for( i=0; i<nthread_yoyu; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].nrunpt = &nrun;
+ targ[i].njob = njob;
+ targ[i].nlen = nlen;
+ targ[i].jobpospt = &jobpos;
+ targ[i].topol = topol;
+ targ[i].dep = dep;
+ targ[i].aseq = bseq;
+ targ[i].effarr = eff;
+ targ[i].alloclenpt = &alloclen;
+ targ[i].localhomtable = localhomtable;
+ targ[i].singlerna = singlerna;
+ targ[i].effarr_kozo = eff_kozo_mapped;
+ targ[i].fftlog = fftlog;
+ targ[i].mutex = &mutex;
+ targ[i].treecond = &treecond;
+
+ pthread_create( handle+i, NULL, treebasethread, (void *)(targ+i) );
+ }
+
+ for( i=0; i<nthread_yoyu; i++ )
+ {
+ pthread_join( handle[i], NULL );
+ }
+ pthread_mutex_destroy( &mutex );
+ pthread_cond_destroy( &treecond );
+ free( handle );
+ free( targ );
+ free( fftlog );
+ }
+ else
+#endif
+ treebase( nlen, bseq, nadd, mergeoralign, mseq1, mseq2, topol, eff, &alloclen, localhomtable, singlerna, eff_kozo_mapped );
+ fprintf( stderr, "\ndone.\n" );
+ if( scoreout )
+ {
+ unweightedspscore = plainscore( njob, bseq );
+ fprintf( stderr, "\nSCORE %s = %.0f, ", "(treebase)", unweightedspscore );
+ fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
+ fprintf( stderr, "\n\n" );
+ }
+
+#if 0
+ if( constraint )
+ {
+ LocalHom *tmppt1, *tmppt2;
+ for( i=0; i<njob; i++)
+ {
+ for( j=0; j<njob; j++)
+ {
+ tmppt1 = localhomtable[i]+j;
+ while( tmppt2 = tmppt1->next )
+ {
+ free( (void *)tmppt1 );
+ tmppt1 = tmppt2;
+ }
+ free( (void *)tmppt1 );
+ }
+ free( (void *)(localhomtable[i]+j) );
+ }
+ free( (void *)localhomtable );
+ }
+#endif
+
+ fprintf( trap_g, "done.\n" );
+ fclose( trap_g );
+ free( mergeoralign );
+
+ writeData_pointer( prep_g, njob, name, nlen, bseq );
+#if 0
+ writeData( stdout, njob, name, nlen, bseq );
+ writePre( njob, name, nlen, bseq, !contin );
+ writeData_pointer( prep_g, njob, name, nlen, aseq );
+#endif
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+
+ if( constraint ) FreeLocalHomTable( localhomtable, njob );
+
+ SHOWVERSION;
+ return( 0 );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+#if 0
+void mdfymtx( char pair[njob][njob], int s1, double **partialmtx, double **mtx )
+#else
+void mdfymtx( char **pair, int s1, double **partialmtx, double **mtx )
+#endif
+{
+ int i, j;
+ int icount, jcount;
+#if DEBUG
+ FILE *fp;
+ static char name[M][B];
+
+ for( i=0; i<M; i++ ) name[i][0] = 0;
+ fprintf( stdout, "s1 = %d\n", s1 );
+ for( i=0; i<njob; i++ )
+ {
+ for( j=0; j<njob; j++ )
+ {
+ printf( "%#2d", pair[i][j] );
+ }
+ printf( "\n" );
+ }
+#endif
+
+ for( i=0, icount=0; i<njob-1; i++ )
+ {
+ if( !pair[s1][i] ) continue;
+ for( j=i+1, jcount=icount+1; j<njob; j++ )
+ {
+ if( !pair[s1][j] ) continue;
+ partialmtx[icount][jcount] = mtx[i][j];
+ jcount++;
+ }
+ icount++;
+ }
+#if DEBUG
+ fp = fopen( "hat2.org", "w" );
+ WriteHat2( fp, njob, name, mtx );
+ fclose( fp );
+ fp = fopen( "hat2.mdf", "w" );
+ WriteHat2( fp, icount, name, partialmtx );
+ fclose( fp );
+#endif
+
+}
+
+
+float score_calc( char **seq, int s ) /* method 3 */
+{
+ int i, j, k, c;
+ int len = strlen( seq[0] );
+ float score;
+ int tmpscore;
+ char *mseq1, *mseq2;
+
+ score = 0.0;
+ for( i=0; i<s-1; i++ )
+ {
+ for( j=i+1; j<s; j++ )
+ {
+ mseq1 = seq[i];
+ mseq2 = seq[j];
+ tmpscore = 0;
+ c = 0;
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ c++;
+ tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
+ if( mseq1[k] == '-' )
+ {
+ tmpscore += penalty;
+ while( mseq1[++k] == '-' )
+ ;
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ if( mseq2[k] == '-' )
+ {
+ tmpscore += penalty;
+ while( mseq2[++k] == '-' )
+ ;
+ k--;
+ if( k > len-2 ) break;
+ continue;
+ }
+ }
+ /*
+ if( mseq1[0] == '-' || mseq2[0] == '-' )
+ {
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ if( !( mseq1[k] != '-' && mseq2[k] != '-' ) )
+ {
+ c--;
+ tmpscore -= penalty;
+ break;
+ }
+ else break;
+ }
+ }
+ if( mseq1[len-1] == '-' || mseq2[len-1] == '-' )
+ {
+ for( k=0; k<len; k++ )
+ {
+ if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
+ if( !( mseq1[k] != '-' && mseq2[k] != '-' ) )
+ {
+ c--;
+ tmpscore -= penalty;
+ break;
+ }
+ else break;
+ }
+ }
+ */
+ score += (double)tmpscore / (double)c;
+ }
+ }
+ score = (float)score / ( ( (double)s * ((double)s-1.0) ) / 2.0 );
+ fprintf( stderr, "score in score_calc = %f\n", score );
+ return( score );
+}
+
+void cpmx_calc( char **seq, float **cpmx, double *eff, int lgth, int clus )
+{
+ int i, j, k;
+ double totaleff = 0.0;
+
+ for( i=0; i<clus; i++ ) totaleff += eff[i];
+ for( i=0; i<26; i++ ) for( j=0; j<lgth; j++ ) cpmx[i][j] = 0.0;
+ for( j=0; j<lgth; j++ ) for( k=0; k<clus; k++ )
+ cpmx[(int)amino_n[(int)seq[k][j]]][j] += (float)eff[k] / totaleff;
+}
+
+
+void cpmx_calc_new_bk( char **seq, float **cpmx, double *eff, int lgth, int clus ) // summ eff must be 1.0
+{
+ int i, j, k;
+ float feff;
+
+ for( i=0; i<26; i++ ) for( j=0; j<lgth; j++ ) cpmx[i][j] = 0.0;
+ for( k=0; k<clus; k++ )
+ {
+ feff = (float)eff[k];
+ for( j=0; j<lgth; j++ )
+ {
+ cpmx[(int)amino_n[(int)seq[k][j]]][j] += feff;
+ }
+ }
+}
+
+void cpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus ) // summ eff must be 1.0
+{
+ int i, j, k;
+ float feff;
+ float *cpmxpt, **cpmxptpt;
+ char *seqpt;
+
+ j = 26;
+ cpmxptpt = cpmx;
+ while( j-- )
+ {
+ cpmxpt = *cpmxptpt++;
+ i = lgth;
+ while( i-- )
+ *cpmxpt++ = 0.0;
+ }
+ for( k=0; k<clus; k++ )
+ {
+ feff = (float)eff[k];
+ seqpt = seq[k];
+// fprintf( stderr, "seqpt = %s, lgth=%d\n", seqpt, lgth );
+ for( j=0; j<lgth; j++ )
+ {
+ cpmx[(int)amino_n[(int)*seqpt++]][j] += feff;
+ }
+ }
+}
+void MScpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus ) // summ eff must be 1.0
+{
+ int i, j, k;
+ float feff;
+ float **cpmxptpt, *cpmxpt;
+ char *seqpt;
+
+ j = lgth;
+ cpmxptpt = cpmx;
+ while( j-- )
+ {
+ cpmxpt = *cpmxptpt++;
+ i = 26;
+ while( i-- )
+ *cpmxpt++ = 0.0;
+ }
+ for( k=0; k<clus; k++ )
+ {
+ feff = (float)eff[k];
+ seqpt = seq[k];
+ cpmxptpt = cpmx;
+ j = lgth;
+ while( j-- )
+ (*cpmxptpt++)[(int)amino_n[(int)*seqpt++]] += feff;
+ }
+#if 0
+ for( j=0; j<lgth; j++ ) for( i=0; i<26; i++ ) cpmx[j][i] = 0.0;
+ for( k=0; k<clus; k++ )
+ {
+ feff = (float)eff[k];
+ for( j=0; j<lgth; j++ )
+ cpmx[j][(int)amino_n[(int)seq[k][j]]] += feff;
+ }
+#endif
+}
+
+void cpmx_ribosum( char **seq, char **seqr, char *dir, float **cpmx, double *eff, int lgth, int clus ) // summ eff must be 1.0
+{
+ int i, j, k;
+ float feff;
+ float **cpmxptpt, *cpmxpt;
+ char *seqpt, *seqrpt, *dirpt;
+ int code, code1, code2;
+
+ j = lgth;
+ cpmxptpt = cpmx;
+ while( j-- )
+ {
+ cpmxpt = *cpmxptpt++;
+ i = 37;
+ while( i-- )
+ *cpmxpt++ = 0.0;
+ }
+ for( k=0; k<clus; k++ )
+ {
+ feff = (float)eff[k];
+ seqpt = seq[k];
+ seqrpt = seqr[k];
+ dirpt = dir;
+ cpmxptpt = cpmx;
+ j = lgth;
+ while( j-- )
+ {
+#if 0
+ code1 = amino_n[(int)*seqpt];
+ if( code1 > 3 ) code = 36;
+ else
+ code = code1;
+#else
+ code1 = amino_n[(int)*seqpt];
+ code2 = amino_n[(int)*seqrpt];
+ if( code1 > 3 )
+ {
+ code = 36;
+ }
+ else if( code2 > 3 )
+ {
+ code = code1;
+ }
+ else if( *dirpt == '5' )
+ {
+ code = 4 + code2 * 4 + code1;
+ }
+ else if( *dirpt == '3' )
+ {
+ code = 20 + code2 * 4 + code1;
+ }
+ else // if( *dirpt == 'o' ) // nai
+ {
+ code = code1;
+ }
+#endif
+
+// fprintf( stderr, "%c -> code=%d toa=%d, tog=%d, toc=%d, tot=%d, ton=%d, efee=%f\n", *seqpt, code%4, ribosumdis[code][4+0], ribosumdis[code][4+1], ribosumdis[code][4+2], ribosumdis[code][20+3], ribosumdis[code][36], feff );
+
+ seqpt++;
+ seqrpt++;
+ dirpt++;
+
+ (*cpmxptpt++)[code] += feff;
+ }
+ }
+}
+
+void mseqcat( char **seq1, char **seq2, double **eff, double *effarr1, double *effarr2, char name1[M][B], char name2[M][B], int clus1, int clus2 )
+{
+ int i, j;
+ for( i=0; i<clus2; i++ )
+ seq1[clus1+i] = seq2[i];
+ for( i=0; i<clus2; i++ ) strcpy( name1[clus1+i], name2[i] );
+
+ for( i=0; i<clus1; i++ ) for( j=0; j<clus1; j++ ) eff[i][j] = effarr1[i]* effarr1[j];
+ for( i=0; i<clus1; i++ ) for( j=clus1; j<clus1+clus2; j++ ) eff[i][j] = effarr1[i]* effarr2[j-clus1];
+ for( i=clus1; i<clus1+clus2; i++ ) for( j=0; j<clus1; j++ ) eff[i][j] = effarr2[i-clus1] * effarr1[j];
+ for( i=clus1; i<clus1+clus2; i++ ) for( j=clus1; j<clus1+clus2; j++ ) eff[i][j] = effarr2[i-clus1] * effarr2[j-clus1];
+}
+
+
+
+#if 0
+int conjuction( char pair[njob][njob], int s, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], char *d )
+#else
+int conjuctionforgaln( int s0, int s1, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d )
+#endif
+{
+ int m, k;
+ char b[B];
+ double total;
+
+#if 0
+ fprintf( stderr, "s0 = %d, s1 = %d\n", s0, s1 );
+#endif
+
+ total = 0.0;
+ d[0] = 0;
+ for( m=s0, k=0; m<s1; m++ )
+ {
+ {
+ sprintf( b, " %d", m+1 );
+#if 1
+ if( strlen( d ) < 100 ) strcat( d, b );
+#else
+ strcat( d, b );
+#endif
+ aseq[k] = seq[m];
+ peff[k] = eff[m];
+ total += peff[k];
+#if 0
+ strcpy( aname[k], name[m] );
+#endif
+ k++;
+ }
+ }
+#if 1
+ for( m=0; m<k; m++ )
+ {
+ peff[m] /= total;
+// fprintf( stderr, "peff[%d] = %f\n", m, peff[m] );
+ }
+#endif
+ return( k );
+}
+
+void makegrouprna( RNApair ***group, RNApair ***all, int *memlist )
+{
+ int k, m;
+ for( k=0; (m=*memlist)!=-1; memlist++, k++ )
+ {
+ group[k] = all[m];
+ }
+}
+
+void makegrouprnait( RNApair ***group, RNApair ***all, char **pair, int s )
+{
+ int k, m;
+ for( m=s, k=0; m<njob; m++ )
+ {
+ if( pair[s][m] != 0 )
+ {
+ group[k++] = all[m];
+ }
+ }
+}
+
+int fastconjuction_noweight( int *memlist, char **seq, char **aseq, double *peff, char *d )
+{
+ int m, k, dln;
+ char b[B];
+ double total;
+
+#if DEBUG
+ fprintf( stderr, "s = %d\n", s );
+#endif
+
+ total = 0.0;
+ d[0] = 0;
+ dln = 0;
+ for( k=0; *memlist!=-1; memlist++, k++ )
+ {
+ m = *memlist;
+ dln += sprintf( b, " %d", m+1 );
+#if 1
+ if( dln < 100 ) strcat( d, b );
+#else
+ strcat( d, b );
+#endif
+ aseq[k] = seq[m];
+ peff[k] = 1.0;
+ total += peff[k];
+ }
+#if 1
+ for( m=0; m<k; m++ )
+ peff[m] /= total;
+#endif
+ return( k );
+}
+
+int fastconjuction_noname_kozo( int *memlist, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d )
+{
+ int m, k, dln;
+ char b[B];
+ double total;
+ double total_kozo;
+
+#if DEBUG
+ fprintf( stderr, "s = %d\n", s );
+#endif
+
+ total = 0.0;
+ total_kozo = 0.0;
+ d[0] = 0;
+ dln = 0;
+ for( k=0; *memlist!=-1; memlist++, k++ )
+ {
+ m = *memlist;
+ dln += sprintf( b, " %d", m+1 );
+#if 1
+ if( dln < 100 ) strcat( d, b );
+#else
+ strcat( d, b );
+#endif
+ aseq[k] = seq[m];
+ peff[k] = eff[m];
+ peff_kozo[k] = eff_kozo[m];
+ total += peff[k];
+ total_kozo += peff_kozo[k];
+ }
+#if 1
+ for( m=0; m<k; m++ )
+ {
+// fprintf( stderr, "peff[%d] = %f\n", m, peff[m] );
+ peff[m] /= total;
+ }
+ if( total_kozo )
+ {
+ for( m=0; m<k; m++ )
+ {
+// fprintf( stderr, "peff[%d] = %f\n", m, peff[m] );
+ peff_kozo[m] /= total_kozo;
+ if( peff_kozo[m] > 0.0 ) peff_kozo[m] += peff[m];
+ }
+ }
+ else //iranai
+ {
+ for( m=0; m<k; m++ )
+ {
+ peff_kozo[m] = 0.0;
+ }
+ }
+#endif
+
+// fprintf( stderr, "\n\ntbfast_total_kozo = %f\n\n", total_kozo );
+ return( k );
+}
+
+
+int fastconjuction_noname( int *memlist, char **seq, char **aseq, double *peff, double *eff, char *d )
+{
+ int m, k, dln;
+ char b[B];
+ double total;
+
+#if DEBUG
+ fprintf( stderr, "s = %d\n", s );
+#endif
+
+ total = 0.0;
+ d[0] = 0;
+ dln = 0;
+ for( k=0; *memlist!=-1; memlist++, k++ )
+ {
+ m = *memlist;
+ dln += sprintf( b, " %d", m+1 );
+#if 1
+ if( dln < 100 ) strcat( d, b );
+#else
+ strcat( d, b );
+#endif
+ aseq[k] = seq[m];
+ peff[k] = eff[m];
+ total += peff[k];
+ }
+#if 1
+ for( m=0; m<k; m++ )
+ {
+// fprintf( stderr, "peff[%d] = %f\n", m, peff[m] );
+ peff[m] /= total;
+ }
+#endif
+ return( k );
+}
+
+int fastconjuction( int *memlist, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], char *d )
+{
+ int m, k, dln;
+ char b[B];
+ double total;
+
+#if DEBUG
+ fprintf( stderr, "s = %d\n", s );
+#endif
+
+ total = 0.0;
+ d[0] = 0;
+ dln = 0;
+ for( k=0; *memlist!=-1; memlist++, k++ )
+ {
+ m = *memlist;
+ dln += sprintf( b, " %d", m+1 );
+#if 1
+ if( dln < 100 ) strcat( d, b );
+#else
+ strcat( d, b );
+#endif
+ aseq[k] = seq[m];
+ peff[k] = eff[m];
+ total += peff[k];
+#if 0
+ strcpy( aname[k], name[m] );
+#endif
+ }
+#if 1
+ for( m=0; m<k; m++ )
+ peff[m] /= total;
+#endif
+ return( k );
+}
+
+
+int conjuctionfortbfast_kozo( double *tmptmptmp, char **pair, int s, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d )
+{
+ int m, k;
+ char b[B];
+ double total;
+ double total_kozo;
+
+#if DEBUG
+ fprintf( stderr, "s = %d\n", s );
+#endif
+
+ total = 0.0;
+// total_kozo = 0.0;
+ total_kozo = *tmptmptmp; // masaka
+ d[0] = 0;
+ for( m=s, k=0; m<njob; m++ )
+ {
+ if( pair[s][m] != 0 )
+ {
+ sprintf( b, " %d", m+1 );
+#if 1
+ if( strlen( d ) < 100 ) strcat( d, b );
+#else
+ strcat( d, b );
+#endif
+ aseq[k] = seq[m];
+ peff[k] = eff[m];
+ peff_kozo[k] = eff_kozo[m];
+ total += peff[k];
+ total_kozo += peff_kozo[k];
+#if 0
+ strcpy( aname[k], name[m] );
+#endif
+ k++;
+ }
+ }
+#if 1
+ for( m=0; m<k; m++ )
+ peff[m] /= total;
+ if( total_kozo > 0.0 )
+ {
+ for( m=0; m<k; m++ )
+ {
+ peff_kozo[m] /= total_kozo;
+ if( peff_kozo[m] > 0.0 ) peff_kozo[m] += peff[m];
+ }
+ }
+ else //iranai
+ {
+ for( m=0; m<k; m++ ) peff_kozo[m] = 0.0;
+ }
+#endif
+// fprintf( stderr, "\n\ndvtditr_total_kozo = %f\n\n", total_kozo );
+ *tmptmptmp = total_kozo;
+ return( k );
+}
+
+int conjuctionfortbfast( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char *d )
+{
+ int m, k;
+ char *b;
+ double total;
+
+ b = calloc( B, sizeof( char ) );
+#if DEBUG
+ fprintf( stderr, "s = %d\n", s );
+#endif
+
+ total = 0.0;
+ d[0] = 0;
+ for( m=s, k=0; m<njob; m++ )
+ {
+ if( pair[s][m] != 0 )
+ {
+ sprintf( b, " %d", m+1 );
+#if 1
+ if( strlen( d ) < 100 ) strcat( d, b );
+#else
+ strcat( d, b );
+#endif
+ aseq[k] = seq[m];
+ peff[k] = eff[m];
+ total += peff[k];
+#if 0
+ strcpy( aname[k], name[m] );
+#endif
+ k++;
+ }
+ }
+#if 1
+ for( m=0; m<k; m++ )
+ peff[m] /= total;
+#endif
+ free( b );
+ return( k );
+}
+int conjuction( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d )
+{
+ int m, k;
+ char b[B];
+ double total;
+
+#if DEBUG
+ fprintf( stderr, "s = %d\n", s );
+#endif
+
+ total = 0.0;
+ d[0] = 0;
+ for( m=s, k=0; m<njob; m++ )
+ {
+ if( pair[s][m] != 0 )
+ {
+ sprintf( b, " %d", m+1 );
+#if 1
+ if( strlen( d ) < 100 ) strcat( d, b );
+#else
+ strcat( d, b );
+#endif
+ aseq[k] = seq[m];
+ peff[k] = eff[m];
+ total += peff[k];
+#if 0
+ strcpy( aname[k], name[m] );
+#endif
+ k++;
+ }
+ }
+#if 0
+ for( m=0; m<k; m++ )
+ peff[m] /= total;
+#endif
+ return( k );
+}
+
+void floatdelete( float **cpmx, int d, int len )
+{
+ int i, j;
+
+ for( i=d; i<len-1; i++ )
+ {
+ for( j=0; j<26; j++ )
+ {
+ cpmx[j][i] = cpmx[j][i+1];
+ }
+ }
+}
+
+void chardelete( char *seq, int d )
+{
+ char b[N];
+
+ strcpy( b, seq+d+1 );
+ strcpy( seq+d, b );
+}
+
+int RootBranchNode( int nseq, int ***topol, int step, int branch )
+{
+ int i, j, s1, s2, value;
+
+ value = 1;
+ for( i=step+1; i<nseq-2; i++ )
+ {
+ for( j=0; (s1=topol[i][0][j])>-1; j++ )
+ if( s1 == topol[step][branch][0] ) value++;
+ for( j=0; (s2=topol[i][1][j])>-1; j++ )
+ if( s2 == topol[step][branch][0] ) value++;
+ }
+ return( value );
+}
+
+void BranchLeafNode( int nseq, int ***topol, int *node, int step, int branch )
+{
+ int i, j, k, s;
+
+ for( i=0; i<nseq; i++ ) node[i] = 0;
+ for( i=0; i<step-1; i++ )
+ for( k=0; k<2; k++ )
+ for( j=0; (s=topol[i][k][j])>-1; j++ )
+ node[s]++;
+ for( k=0; k<branch+1; k++ )
+ for( j=0; (s=topol[step][k][j])>-1; j++ )
+ node[s]++;
+}
+
+void RootLeafNode( int nseq, int ***topol, int *node )
+{
+ int i, j, k, s;
+ for( i=0; i<nseq; i++ ) node[i] = 0;
+ for( i=0; i<nseq-2; i++ )
+ for( k=0; k<2; k++ )
+ for( j=0; (s=topol[i][k][j])>-1; j++ )
+ node[s]++;
+}
+
+void nodeFromABranch( int nseq, int *result, int **pairwisenode, int ***topol, double **len, int step, int num )
+{
+ int i, s, count;
+ int *innergroup;
+ int *outergroup1;
+#if 0
+ int outergroup2[nseq];
+ int table[nseq];
+#else
+ static int *outergroup2 = NULL;
+ static int *table = NULL;
+ if( outergroup2 == NULL )
+ {
+ outergroup2 = AllocateIntVec( nseq );
+ table = AllocateIntVec( nseq );
+ }
+#endif
+ innergroup = topol[step][num];
+ outergroup1 = topol[step][!num];
+ for( i=0; i<nseq; i++ ) table[i] = 1;
+ for( i=0; (s=innergroup[i])>-1; i++ ) table[s] = 0;
+ for( i=0; (s=outergroup1[i])>-1; i++ ) table[s] = 0;
+ for( i=0, count=0; i<nseq; i++ )
+ {
+ if( table[i] )
+ {
+ outergroup2[count] = i;
+ count++;
+ }
+ }
+ outergroup2[count] = -1;
+
+ for( i=0; (s=innergroup[i])>-1; i++ )
+ {
+ result[s] = pairwisenode[s][outergroup1[0]]
+ + pairwisenode[s][outergroup2[0]]
+ - pairwisenode[outergroup1[0]][outergroup2[0]] - 1;
+ result[s] /= 2;
+ }
+ for( i=0; (s=outergroup1[i])>-1; i++ )
+ {
+ result[s] = pairwisenode[s][outergroup2[0]]
+ + pairwisenode[s][innergroup[0]]
+ - pairwisenode[innergroup[0]][outergroup2[0]] + 1;
+ result[s] /= 2;
+ }
+ for( i=0; (s=outergroup2[i])>-1; i++ )
+ {
+ result[s] = pairwisenode[s][outergroup1[0]]
+ + pairwisenode[s][innergroup[0]]
+ - pairwisenode[innergroup[0]][outergroup1[0]] + 1;
+ result[s] /= 2;
+ }
+
+#if 0
+ for( i=0; i<nseq; i++ )
+ fprintf( stderr, "result[%d] = %d\n", i+1, result[i] );
+#endif
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#if 0
+void OneClusterAndTheOther( int locnjob, char pair[njob][njob], int *s1, int *s2, int ***topol, int step, int branch )
+#else
+void OneClusterAndTheOther( int locnjob, char **pair, int *s1, int *s2, int ***topol, int step, int branch )
+#endif
+{
+ int i;
+ int r1;
+
+ *s1 = topol[step][branch][0];
+ for( i=0; (r1=topol[step][branch][i])>-1; i++ )
+ pair[*s1][r1] = 1;
+ for( i=0; i<locnjob; i++ )
+ {
+ if( !pair[*s1][i] )
+ {
+ *s2 = i;
+ break;
+ }
+ }
+ for( i=*s2; i<locnjob; i++ )
+ {
+ if( !pair[*s1][i] )
+ pair[*s2][i] = 1;
+ }
+}
+
+void makeEffMtx( int nseq, double **mtx, double *vec )
+{
+ int i, j;
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+ mtx[i][j] = vec[i] * vec[j];
+}
+
+void node_eff( int nseq, double *eff, int *node )
+{
+ int i;
+ extern double ipower( double, int );
+ for( i=0; i<nseq; i++ )
+ eff[i] = ipower( 0.5, node[i] ) + geta2;
+ /*
+ eff[i] = ipower( 0.5, node[i] ) + 0;
+ */
+#if DEBUG
+ for( i=0; i<nseq; i++ )
+#endif
+}
+
+
+int shrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink )
+{
+ int m1, k1, m2, k2;
+
+ for( m1=s1, k1=0; m1<njob; m1++ )
+ {
+ if( pair[s1][m1] != 0 )
+ {
+ for( m2=s2, k2=0; m2<njob; m2++ )
+ {
+ if( pair[s2][m2] != 0 )
+ {
+ if( localhom[m1][m2].opt == -1 )
+ localhomshrink[k1][k2] = NULL;
+ else
+ localhomshrink[k1][k2] = localhom[m1]+m2;
+ k2++;
+ }
+ }
+ k1++;
+ }
+ }
+ return( 0 );
+}
+int msshrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink )
+{
+ int m1, k1, n1, m2, k2, n2;
+
+ for( m1=s1, k1=0; m1<njob; m1++ )
+ {
+ if( pair[s1][m1] != 0 )
+ {
+ for( m2=s2, k2=0; m2<njob; m2++ )
+ {
+ if( pair[s2][m2] != 0 )
+ {
+ n1 = MIN(m1,m2); n2=MAX(m1,m2);
+ if( localhom[m1][m2].opt == -1 )
+ localhomshrink[k1][k2] = NULL;
+ else
+ localhomshrink[k1][k2] = localhom[n1]+n2;
+ k2++;
+ }
+ }
+ k1++;
+ }
+ }
+ return( 0 );
+}
+
+int fastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink )
+{
+ int k1, k2;
+ int *intpt1, *intpt2;
+
+
+ for( intpt1=mem1, k1=0; *intpt1!=-1; intpt1++, k1++ )
+ {
+ for( intpt2=mem2, k2=0; *intpt2!=-1; intpt2++, k2++ )
+ {
+ if( localhom[*intpt1][*intpt2].opt == -1 )
+ localhomshrink[k1][k2] = NULL;
+ else
+ localhomshrink[k1][k2] = localhom[*intpt1]+*intpt2;
+ }
+ }
+ return( 0 );
+}
+
+int msfastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink )
+{
+ int k1, k2;
+ int *intpt1, *intpt2;
+ int m1, m2;
+
+ for( intpt1=mem1, k1=0; *intpt1!=-1; intpt1++, k1++ )
+ {
+ for( intpt2=mem2, k2=0; *intpt2!=-1; intpt2++, k2++ )
+ {
+ m1 = MIN(*intpt1,*intpt2); m2 = MAX(*intpt1,*intpt2);
+ if( localhom[m1][m2].opt == -1 )
+ localhomshrink[k1][k2] = NULL;
+ else
+ localhomshrink[k1][k2] = localhom[m1]+m2;
+ }
+ }
+ return( 0 );
+}
+
--- /dev/null
+
+/*
+ tree-dependent iteration
+ algorithm A+ when group-to-group, C when group-to-singleSeqence
+ OR
+ algorithm A+
+*/
+
+#include "mltaln.h"
+
+
+#define DEBUG 0
+#define RECORD 0
+
+extern char **seq_g;
+extern char **res_g;
+
+static int nwa;
+
+#ifdef enablemultithread
+typedef struct _threadarg
+{
+ int thread_no;
+ int *jobposintpt;
+ int *ndonept;
+ int *ntrypt;
+ int *collectingpt;
+ int njob;
+ int nbranch;
+ int maxiter;
+ int nkozo;
+ int *subgenerationpt;
+ float *basegainpt;
+ float *gainlist;
+ float *tscorelist;
+ int *generationofinput;
+ char *kozoarivec;
+ char **mastercopy;
+ char ***candidates;
+ int *generationofmastercopypt;
+ int *branchtable;
+ RNApair ***singlerna;
+ LocalHom **localhomtable;
+ int alloclen;
+ Node *stopol;
+ int ***topol;
+// double **len;
+ float **tscorehistory_detail;
+ int *finishpt;
+ pthread_mutex_t *mutex;
+ pthread_cond_t *collection_end;
+ pthread_cond_t *collection_start;
+} threadarg_t;
+#endif
+
+#if 1
+static void shuffle( int *arr, int n )
+{
+ int i;
+ int x;
+ int b;
+
+ for( i=1; i<n; i++ )
+ {
+ x = rand() % (i+1);
+ if( x != i )
+ {
+ b = arr[i];
+ arr[i] = arr[x];
+ arr[x] = b;
+ }
+ }
+}
+#endif
+
+static void Writeoption2( FILE *fp, int cycle, double cut )
+{
+ fprintf( fp, "%dth cycle\n", cycle );
+ fprintf( fp, "marginal score to search : current score * (100-%d) / 100\n", (int)cut );
+}
+
+static void Writeoptions( FILE *fp )
+{
+ fprintf( fp, "Tree-dependent-iteration\n" );
+ if( scoremtx == 1 )
+ fprintf( fp, "Blosum %d\n", nblosum );
+ else if( scoremtx == -1 )
+ fprintf( fp, "DNA\n" );
+ else if( scoremtx == 2 )
+ fprintf( fp, "Miyata-Yasunaga\n" );
+ else
+ fprintf( fp, "JTT %dPAM\n", pamN );
+
+ if( scoremtx == 0 || scoremtx == 1 )
+ fprintf( fp, "Gap Penalty = %+5.3f, %5.2f, %+5.3f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ else
+ fprintf( fp, "Gap Penalty = %+5.3f\n", (double)penalty/1000 );
+
+
+ if( scmtd == 3 )
+ fprintf( fp, "score of rnd or sco\n" );
+ else if( scmtd == 4 )
+ fprintf( fp, "score = sigma( score for a pair of homologous amino acids ) / ( number of amino acids pairs )\n" );
+ else if( scmtd == 5 )
+ fprintf( fp, "score : SP\n" );
+ if( mix )
+ fprintf( fp, "?\n" );
+ else
+ {
+ if( weight == 2 )
+ fprintf( fp, "weighted rationale-1, geta2 = %f\n", geta2 );
+ else if( weight == 3 )
+ fprintf( fp, "weighted like ClustalW," );
+ else if( weight == 4 )
+ fprintf( fp, "weighted rationale-2, geta2 = %f\n", geta2 );
+ else
+ fprintf( fp, "unweighted\n" );
+ }
+ if( weight && utree )
+ fprintf( fp, "using tree defined by the file hat2.\n" );
+ if( weight && !utree )
+ fprintf( fp, "using temporary tree.\n" );
+
+ if( treemethod == 'n' )
+ fprintf( fp, "Tree is calculated with Neighbor-Joining Method.\n" );
+ else if( treemethod == 'q' )
+ fprintf( fp, "Tree is calculated with Minimum linkage.\n" );
+ else if( treemethod == 'X' )
+ fprintf( fp, "Tree is calculated with simplified UPG Method and UPG Method.\n" );
+ else if( treemethod == 'E' )
+ fprintf( fp, "Tree is calculated with UPG Method.\n" );
+ else
+ fprintf( fp, "Tree is calculated with unknown Method.\n" );
+
+ if( alg == 'C' )
+ fprintf( fp, "Algorithm A+ / C\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Algorithm A+ \n" );
+ else if( alg == 'a' )
+ fprintf( fp, "Algorithm A \n" );
+ else
+ fprintf( fp, "Algorithm ? \n" );
+
+ if( use_fft )
+ {
+ if( scoremtx == -1 )
+ {
+ fprintf( fp, "Basis : 4 nucleotides\n" );
+ }
+ else
+ {
+ if( fftscore )
+ fprintf( fp, "Basis : Polarity and Volume\n" );
+ else
+ fprintf( fp, "Basis : 20 amino acids\n" );
+ }
+ fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
+ fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+ }
+}
+
+#ifdef enablemultithread
+
+static void freelocalarrays(
+ float *tscorehistory,
+ RNApair ***grouprna1, RNApair ***grouprna2,
+ RNApair *rnapairboth,
+ char *indication1, char *indication2,
+ double *effarr, double *effarrforlocalhom, double *effarr1, double *effarr2,
+ char **mseq1, char **mseq2,
+ char **localcopy,
+ int *gapmap1, int *gapmap2,
+ double *effarr1_kozo, double *effarr2_kozo, double *effarr_kozo,
+ char **pair,
+ LocalHom *** localhomshrink
+)
+{
+// fprintf( stderr, "Skipping freelocalarrays\n" );
+// return;
+ int i;
+ if( commonIP ) FreeIntMtx( commonIP );
+ commonIP = NULL;
+ Falign( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
+ Falign_localhom( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL,NULL, 0, NULL );
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ free( grouprna1 ); // nakamimo?
+ free( grouprna2 ); // nakamimo?
+ }
+
+ free( tscorehistory );
+ free( indication1 );
+ free( indication2 );
+ free( effarr );
+ free( effarrforlocalhom );
+ free( effarr1 );
+ free( effarr2 );
+ free( mseq1 );
+ free( mseq2 );
+ FreeCharMtx( localcopy );
+ free( gapmap1 );
+ free( gapmap2 );
+
+ free( effarr1_kozo );
+ free( effarr2_kozo );
+ free( effarr_kozo );
+
+ FreeCharMtx( pair );
+
+ if( rnakozo ) free( rnapairboth );
+
+ if( constraint )
+ {
+ for( i=0; i<njob; i++)
+ {
+ free( localhomshrink[i] ); // nakamimo??
+ }
+ free( localhomshrink );
+ }
+}
+
+
+static void *athread( void *arg )
+{
+
+ threadarg_t *targ = (threadarg_t *)arg;
+ int thread_no = targ->thread_no;
+ int njob = targ->njob;
+ int nbranch = targ->nbranch;
+ int maxiter = targ->maxiter;
+ int *ndonept = targ->ndonept;
+ int *ntrypt = targ->ntrypt;
+ int *collectingpt = targ->collectingpt;
+ int *jobposintpt = targ->jobposintpt;
+ int nkozo = targ->nkozo;
+ float *gainlist = targ->gainlist;
+ float *tscorelist = targ->tscorelist;
+ int *generationofinput = targ->generationofinput;
+ int *subgenerationpt = targ->subgenerationpt;
+ float *basegainpt = targ->basegainpt;
+ char *kozoarivec = targ->kozoarivec;
+ char **mastercopy = targ->mastercopy;
+ char ***candidates = targ->candidates;
+ int *generationofmastercopypt = targ->generationofmastercopypt;
+ int *branchtable = targ->branchtable;
+ RNApair ***singlerna = targ->singlerna;
+ LocalHom **localhomtable = targ->localhomtable;
+ int alloclen = targ->alloclen;
+ Node * stopol = targ->stopol;
+ int ***topol = targ->topol;
+// double **len = targ->len;
+ float **tscorehistory_detail = targ->tscorehistory_detail;
+ int *finishpt = targ->finishpt;
+
+ int i, j, k, l, ii;
+ float gain;
+ int iterate;
+ char **pair;
+ int locnjob;
+ int s1, s2;
+ int clus1, clus2;
+ char **localcopy;
+ char **mseq1, **mseq2;
+ double *effarr, *effarr_kozo; // re-calc
+ double *effarr1, *effarr2, *effarr1_kozo, *effarr2_kozo;
+ char *indication1, *indication2;
+ int length;
+ RNApair ***grouprna1, ***grouprna2;
+ RNApair *rnapairboth;
+ LocalHom ***localhomshrink;
+ int *gapmap1, *gapmap2;
+ float tscore, mscore, oimpmatch, impmatch;
+ int identity;
+ double tmpdouble;
+ float naivescore0 = 0, naivescore1;
+ double *effarrforlocalhom;
+ float *tscorehistory;
+ int intdum;
+#if 0
+ int oscillating;
+ int lin, ldf;
+#endif
+ float maxgain;
+ int bestthread;
+ int branchpos;
+ int subgenerationatfirst;
+ double unweightedspscore;
+ int myjob;
+ int converged2 = 0;
+ int chudanres;
+
+
+ locnjob = njob;
+
+ if( utree == 0 )
+ {
+ fprintf( stderr, "Dynamic tree is not supported in the multithread version.\n" );
+ exit( 1 );
+ }
+ if( score_check == 2 )
+ {
+ fprintf( stderr, "Score_check 2 is not supported in the multithread version.\n" );
+ exit( 1 );
+ }
+
+ if( weight == 2 )
+ {
+ fprintf( stderr, "Weight 2 is not supported in the multithread version.\n" );
+ exit( 1 );
+ }
+ if( cooling && cut > 0.0 )
+ {
+ fprintf( stderr, "Cooling is not supported in the multithread version.\n" );
+ exit( 1 );
+ }
+
+ tscorehistory = calloc( maxiter, sizeof( float ) );
+
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ }
+ else
+ {
+ grouprna1 = grouprna2 = NULL;
+ }
+
+ indication1 = AllocateCharVec( njob*3+50 );
+ indication2 = AllocateCharVec( njob*3+50 );
+ effarr = AllocateDoubleVec( locnjob );
+ effarrforlocalhom = AllocateDoubleVec( locnjob );
+ effarr1 = AllocateDoubleVec( locnjob );
+ effarr2 = AllocateDoubleVec( locnjob );
+ mseq1 = AllocateCharMtx( locnjob, 0 );
+ mseq2 = AllocateCharMtx( locnjob, 0 );
+ localcopy = AllocateCharMtx( locnjob, alloclen );
+ gapmap1 = AllocateIntVec( alloclen );
+ gapmap2 = AllocateIntVec( alloclen );
+
+ effarr1_kozo = AllocateDoubleVec( locnjob ); // tsuneni allocate suru.
+ effarr2_kozo = AllocateDoubleVec( locnjob ); // tsuneni allocate suru.
+ effarr_kozo = AllocateDoubleVec( locnjob );
+ for( i=0; i<locnjob; i++ )
+ effarr_kozo[i] = effarr1_kozo[i] = effarr2_kozo[i] = 0.0;
+
+ pair = AllocateCharMtx( locnjob, locnjob );
+
+
+ if( rnakozo ) rnapairboth = (RNApair *)calloc( alloclen, sizeof( RNApair ) );
+
+ if( constraint )
+ {
+ localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
+ for( i=0; i<njob; i++)
+ {
+ localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom * ) );
+ }
+ }
+
+
+ if( thread_no == 0 )
+ {
+ *ntrypt = 0;
+ srand( randomseed );
+ *finishpt = 0;
+ for( iterate=0; iterate<maxiter; iterate++ )
+ {
+ pthread_mutex_lock( targ->mutex );
+
+ if( *collectingpt == 1 )
+ {
+ *collectingpt = 0;
+ *generationofmastercopypt = iterate;
+ *subgenerationpt = 0;
+ *basegainpt = 0.0;
+ *ndonept = 0;
+ *jobposintpt = 0;
+ for( i=0; i<nwa; i++ ) gainlist[i] = 0;
+ for( i=0; i<nwa; i++ ) tscorelist[i] = 0.0;
+ for( i=0; i<nbranch; i++ ) generationofinput[i] = -1;
+ if( parallelizationstrategy != BESTFIRST && randomseed != 0 ) shuffle( branchtable, nbranch );
+ pthread_cond_broadcast( targ->collection_end );
+ pthread_mutex_unlock( targ->mutex );
+ }
+ else
+ {
+ pthread_cond_broadcast( targ->collection_end );
+ pthread_mutex_unlock( targ->mutex );
+ freelocalarrays
+ (
+ tscorehistory,
+ grouprna1, grouprna2,
+ rnapairboth,
+ indication1, indication2,
+ effarr, effarrforlocalhom, effarr1, effarr2,
+ mseq1, mseq2,
+ localcopy,
+ gapmap1, gapmap2,
+ effarr1_kozo, effarr2_kozo, effarr_kozo,
+ pair,
+ localhomshrink
+ );
+// return( NULL );
+ pthread_exit( NULL );
+ }
+
+ pthread_mutex_lock( targ->mutex );
+ while( *ndonept < nbranch )
+ pthread_cond_wait( targ->collection_start, targ->mutex );
+ pthread_mutex_unlock( targ->mutex );
+// fprintf( stderr, "Thread 0 got a signal, *collectionpt = %d\n", *collectingpt );
+
+/*
+ Hoka no thread ga keisan
+*/
+
+ pthread_mutex_lock( targ->mutex );
+ *collectingpt = 1; // chofuku
+
+#if 0
+ for( i=0; i<nbranch; i++ )
+ {
+ if( generationofinput[i] != iterate )
+ {
+ fprintf( stderr, "Error! generationofinput[%d] = %d, but iterate=%d\n", i, generationofinput[i], iterate );
+ exit( 1 );
+
+ }
+ }
+#endif
+
+ maxgain = gainlist[1];
+ bestthread = 1;
+ for( i=2; i<nwa; i++ )
+ {
+ if( gainlist[i] > maxgain )
+ {
+ maxgain = gainlist[i];
+ bestthread = i;
+ }
+ }
+
+ if( maxgain > 0.0 )
+ {
+// fprintf( stderr, "\nGain = %f\n", maxgain );
+// fprintf( stderr, "best gain = %f by thread %d\n", gainlist[bestthread], bestthread );
+// fprintf( stderr, "tscorelist[best] = %f by thread %d\n", tscorelist[bestthread], bestthread );
+ if( parallelizationstrategy == BESTFIRST )
+ {
+ for( i=0; i<locnjob; i++ ) strcpy( mastercopy[i], candidates[bestthread][i] );
+ if( scoreout )
+ {
+ unweightedspscore = plainscore( locnjob, mastercopy );
+ fprintf( stderr, "\nSCORE %d = %.0f, ", iterate * nbranch, unweightedspscore );
+ fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( locnjob * strlen( mastercopy[0] ) ) );
+ if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
+ fprintf( stderr, "\n" );
+ }
+ }
+#if 1
+// fprintf( stderr, "gain(%d, by %d) = %f\n", iterate, bestthread, maxgain );
+ for( i=iterate-1; i>0; i-- )
+ {
+// if( iterate-i < 15 ) fprintf( stderr, "hist[%d] = %f\n", i, tscorehistory[i] );
+ if( tscorehistory[i] == tscorelist[bestthread] )
+ {
+ fprintf( stderr, "\nOscillating? %f == %f\n", tscorehistory[i], tscorelist[bestthread] );
+ *collectingpt = -1;
+ break;
+ }
+ }
+ tscorehistory[iterate] = tscorelist[bestthread];
+#endif
+ }
+ else
+ {
+ fprintf( stderr, "\nConverged.\n" );
+ *collectingpt = -1;
+// pthread_cond_broadcast( targ->collection_end );
+// pthread_mutex_unlock( targ->mutex );
+// freelocalarrays();
+// return( NULL );
+// pthread_exit( NULL );
+ }
+
+#if 1
+ if( *finishpt )
+ {
+ fprintf( stderr, "\nConverged2.\n" );
+ *collectingpt = -1;
+ }
+#endif
+
+ pthread_mutex_unlock( targ->mutex );
+ }
+ pthread_mutex_lock( targ->mutex );
+ fprintf( stderr, "\nReached %d\n", maxiter );
+ *collectingpt = -1;
+ pthread_cond_broadcast( targ->collection_end );
+ pthread_mutex_unlock( targ->mutex );
+ freelocalarrays
+ (
+ tscorehistory,
+ grouprna1, grouprna2,
+ rnapairboth,
+ indication1, indication2,
+ effarr, effarrforlocalhom, effarr1, effarr2,
+ mseq1, mseq2,
+ localcopy,
+ gapmap1, gapmap2,
+ effarr1_kozo, effarr2_kozo, effarr_kozo,
+ pair,
+ localhomshrink
+ );
+ return( NULL );
+ pthread_exit( NULL );
+ }
+ else
+ {
+ while( 1 )
+ {
+#if 0
+ if( iterate % 2 == 0 )
+ {
+ lin = 0; ldf = +1;
+ }
+ else
+ {
+ lin = locnjob - 2; ldf = -1;
+ }
+ for( l=lin; l < locnjob-1 && l >= 0 ; l+=ldf )
+ for( k=0; k<2; k++ )
+#endif
+
+ pthread_mutex_lock( targ->mutex );
+ while( *collectingpt > 0 )
+ pthread_cond_wait( targ->collection_end, targ->mutex );
+ if( *collectingpt == -1 )
+ {
+ pthread_mutex_unlock( targ->mutex );
+ freelocalarrays
+ (
+ tscorehistory,
+ grouprna1, grouprna2,
+ rnapairboth,
+ indication1, indication2,
+ effarr, effarrforlocalhom, effarr1, effarr2,
+ mseq1, mseq2,
+ localcopy,
+ gapmap1, gapmap2,
+ effarr1_kozo, effarr2_kozo, effarr_kozo,
+ pair,
+ localhomshrink
+ );
+ return( NULL );
+ pthread_exit( NULL );
+ }
+// pthread_mutex_unlock( targ->mutex );
+
+
+// pthread_mutex_lock( targ->mutex );
+ if( *jobposintpt == nbranch )
+ {
+ if( *collectingpt != -1 ) *collectingpt = 1; // chofuku
+ pthread_mutex_unlock( targ->mutex );
+ continue;
+ }
+// fprintf( stderr, "JOB jobposintpt=%d\n", *jobposintpt );
+ myjob = branchtable[*jobposintpt];
+ l = myjob / 2;
+ if( l == locnjob-2 ) k = 1;
+ else k = myjob - l * 2;
+// fprintf( stderr, "JOB l=%d, k=%d\n", l, k );
+ branchpos = myjob;
+ (*jobposintpt)++;
+ iterate = *generationofmastercopypt;
+ (*ntrypt)++;
+ pthread_mutex_unlock( targ->mutex );
+
+
+
+// fprintf( stderr, "branchpos = %d (thread %d)\n", branchpos, thread_no );
+
+// fprintf( stderr, "iterate=%d, l=%d, k=%d (thread %d)\n", iterate, l, k, thread_no );
+
+#if 0
+ fprintf( stderr, "STEP %03d-%03d-%d (Thread %d) ", iterate+1, l+1, k, thread_no );
+ fprintf( stderr, "STEP %03d-%03d-%d (thread %d) %s ", iterate+1, l+1, k, thread_no, use_fft?"\n":"\n" );
+#endif
+ for( i=0; i<locnjob; i++ ) for( j=0; j<locnjob; j++ ) pair[i][j] = 0;
+
+ OneClusterAndTheOther( locnjob, pair, &s1, &s2, topol, l, k );
+#if 0
+ fprintf( stderr, "STEP%d-%d\n", l, k );
+ for( i=0; i<locnjob; i++ )
+ {
+ for( j=0; j<locnjob; j++ )
+ {
+ fprintf( stderr, "%#3d", pair[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+ if( !weight )
+ {
+ for( i=0; i<locnjob; i++ ) effarr[i] = 1.0;
+ if( nkozo )
+ {
+ for( i=0; i<locnjob; i++ )
+ {
+ if( kozoarivec[i] )
+ effarr_kozo[i] = 1.0;
+ else
+ effarr_kozo[i] = 0.0;
+ }
+ }
+ }
+ else if( weight == 4 )
+ {
+ weightFromABranch( locnjob, effarr, stopol, topol, l, k );
+ if( nkozo ) // hitomadu single weight.
+ {
+ for( i=0; i<locnjob; i++ )
+ {
+ if( kozoarivec[i] ) effarr_kozo[i] = effarr[i];
+ else effarr_kozo[i] = 0.0;
+ }
+ }
+ }
+ else
+ {
+ fprintf( stderr, "weight error!\n" );
+ exit( 1 );
+ }
+
+ yarinaoshi:
+
+ pthread_mutex_lock( targ->mutex );
+ for( i=0; i<locnjob; i++ ) strcpy( localcopy[i], mastercopy[i] );
+ subgenerationatfirst = *subgenerationpt;
+ pthread_mutex_unlock( targ->mutex );
+ length = strlen( localcopy[0] );
+
+ if( nkozo )
+ {
+ double tmptmptmp;
+ tmptmptmp = 0.0;
+ clus1 = conjuctionfortbfast_kozo( &tmptmptmp, pair, s1, localcopy, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
+ for( i=0; i<clus1; i++ ) effarr1_kozo[i] *= 1.0; // 0.5 ga sairyo ?
+ tmptmptmp = 0.0;
+ clus2 = conjuctionfortbfast_kozo( &tmptmptmp, pair, s2, localcopy, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
+ for( i=0; i<clus2; i++ ) effarr2_kozo[i] *= 1.0; // 0.5 ga sairyo ?
+
+#if 0
+ fprintf( stderr, "\ngroup1 = %s\n", indication1 );
+ for( i=0; i<clus1; i++ ) fprintf( stderr, "effarr1_kozo[%d], effarr1[] = %f, %f\n", i, effarr1_kozo[i], effarr1[i] );
+ fprintf( stderr, "\ngroup2 = %s\n", indication2 );
+ for( i=0; i<clus2; i++ ) fprintf( stderr, "effarr2_kozo[%d], effarr2[] = %f, %f\n", i, effarr2_kozo[i], effarr2[i] );
+#endif
+ }
+ else
+ {
+ clus1 = conjuctionfortbfast( pair, s1, localcopy, mseq1, effarr1, effarr, indication1 );
+ clus2 = conjuctionfortbfast( pair, s2, localcopy, mseq2, effarr2, effarr, indication2 );
+ }
+
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ makegrouprnait( grouprna1, singlerna, pair, s1 );
+ makegrouprnait( grouprna2, singlerna, pair, s2 );
+ }
+
+ if( score_check == 2 )
+ {
+ fprintf( stderr, "Score_check 2 is not supported in the multithread version.\n" );
+ exit( 1 );
+ }
+ else if( score_check )
+ {
+ if( RNAscoremtx == 'r' )
+ intergroup_score_gapnomi( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
+ else
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
+
+ if( constraint )
+ {
+ shrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
+// weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink ); // >>>
+ oimpmatch = 0.0;
+ if( use_fft )
+ {
+ if( alg == 'Q' )
+ {
+ part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) part_imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += part_imp_match_out_scQ( i, i );
+// fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
+ }
+ }
+ else
+ {
+ part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ if( rnakozo ) part_imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += part_imp_match_out_sc( i, i );
+// fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
+ }
+ }
+// fprintf( stderr, "otmpmatch = %f\n", oimpmatch );
+ }
+ else
+ {
+ if( alg == 'Q' )
+ {
+ imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += imp_match_out_scQ( i, i );
+// fprintf( stderr, "#### i=%d, initial impmatch = %f\n", i, oimpmatch );
+ }
+ }
+ else
+ {
+ imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+
+ fprintf( stderr, "not supported\n" );
+ exit( 1 );
+
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += imp_match_out_sc( i, i );
+// fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
+ }
+ }
+// fprintf( stderr, "otmpmatch = %f\n", oimpmatch );
+ }
+// fprintf( stderr, "#### initial impmatch = %f\n", oimpmatch );
+ }
+ else
+ {
+ oimpmatch = 0.0;
+ }
+
+
+// fprintf( stderr, "#### tmpdouble = %f\n", tmpdouble );
+ mscore = (double)oimpmatch + tmpdouble;
+ }
+ else
+ {
+ fprintf( stderr, "score_check = %d\n", score_check );
+ fprintf( stderr, "Not supported\n" );
+ exit( 1 );
+ }
+
+
+// if( rnakozo ) foldalignedrna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, rnapairboth );
+
+// if( !use_fft && !rnakozo )
+ if( !use_fft )
+ {
+ commongappick_record( clus1, mseq1, gapmap1 );
+ commongappick_record( clus2, mseq2, gapmap2 );
+ }
+
+#if 0
+ fprintf( stderr, "##### mscore = %f\n", mscore );
+#endif
+
+#if DEBUG
+ if( !devide )
+ {
+ fprintf( trap_g, "\n%d-%d-%d\n", iterate+1, l+1, k );
+ fprintf( trap_g, "group1 = %s\n", indication1 );
+ fprintf( trap_g, "group2 = %s\n", indication2 );
+ fflush( trap_g );
+ }
+
+#endif
+#if 0
+ printf( "STEP %d-%d-%d\n", iterate, l, k );
+ for( i=0; i<clus2; i++ ) printf( "%f ", effarr2[i] );
+ printf( "\n" );
+#endif
+ if( constraint == 2 )
+ {
+ if( use_fft )
+ {
+// if( alg == 'Q' )
+// part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+// else
+// part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ chudanres = 0;
+ Falign_localhom( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, gapmap1, gapmap2, subgenerationpt, subgenerationatfirst, &chudanres );
+// fprintf( stderr, "##### impmatch = %f\n", impmatch );
+ if( chudanres && parallelizationstrategy == BAATARI2 )
+ {
+// fprintf( stderr, "#### yarinaoshi!!! INS-i\n" );
+ goto yarinaoshi;
+ }
+ }
+ else
+ {
+ if( alg == 'Q' )
+ {
+ float wm;
+// imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap wo tsukuttakara iranai.
+// if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, gapmap1, gapmap2, rnapairboth );
+
+ wm = Q__align_gapmap( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL, gapmap1, gapmap2 );
+ fprintf( stderr, "wm = %f\n", wm );
+#if 0
+ fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
+ naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
+ fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+#if 0 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+// fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
+// rewind( stdout );
+// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+// exit( 1 );
+ }
+#endif
+#endif
+ }
+ else if( alg == 'R' )
+ {
+ float wm;
+ imp_match_init_strictR( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap ha mada
+ wm = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL );
+// fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
+ naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
+// fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: %f->%f UP!\n", clus1, clus2, naivescore0, naivescore1 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+#if 0 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+// fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
+ rewind( stdout );
+ for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ else if( alg == 'H' )
+ {
+ float wm;
+ imp_match_init_strictH( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap ha mada
+ wm = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL );
+ fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
+ naivescore1 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
+ fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+#if 0 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+// fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
+// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+// exit( 1 );
+ }
+#endif
+ }
+ else
+ {
+// imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ A__align_gapmap( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, gapmap1, gapmap2 );
+ fprintf( stderr, "A__align_gapmap\n" );
+// fprintf( stderr, "##### impmatch = %f\n", impmatch );
+ }
+ }
+ }
+ else if( use_fft )
+ {
+ float totalwm;
+ chudanres = 0;
+ totalwm = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, subgenerationpt, subgenerationatfirst, &chudanres );
+ if( chudanres && parallelizationstrategy == BAATARI2 )
+ {
+// fprintf( stderr, "#### yarinaoshi!!! FFT-NS-i\n" );
+ goto yarinaoshi;
+ }
+
+// fprintf( stderr, "totalwm = %f\n", totalwm );
+#if 0
+ if( alg == 'Q' )
+ {
+ fprintf( stderr, "totalwm = %f\n", totalwm );
+ naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+#if 1 // chuui
+ if( totalwm != 0.0 && abs( totalwm - naivescore1 ) > 100 )
+ {
+// fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
+// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+// exit( 1 );
+ }
+#endif
+ }
+#endif
+ if( alg == 'R' )
+ {
+ fprintf( stderr, "totalwm = %f\n", totalwm );
+ naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+#if 1 // chuui
+ if( totalwm != 0.0 && abs( totalwm - naivescore1 ) > 100 )
+ {
+// fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
+// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+// exit( 1 );
+ }
+ }
+#endif
+ }
+ else
+ {
+ if( alg == 'M' )
+ {
+ chudanres = 0;
+ MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, subgenerationpt, subgenerationatfirst, &chudanres, outgap, outgap );
+ if( chudanres && parallelizationstrategy == BAATARI2 )
+ {
+// fprintf( stderr, "#### yarinaoshi!!! NW-NS-i\n" );
+ goto yarinaoshi;
+ }
+ }
+ else if( alg == 'A' )
+ {
+ A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); //outgap==1
+ }
+ else if( alg == 'Q' )
+ {
+ float wm;
+ wm = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
+ fprintf( stderr, "wm = %f\n", wm );
+ fprintf( stderr, "impmatch = %f\n", impmatch );
+ naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN!\n", clus1, clus2 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+#if 1 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+// fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
+// rewind( stderr );
+// rewind( stdout );
+// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+// exit( 1 );
+ }
+#endif
+ }
+ else if( alg == 'R' )
+ {
+ float wm;
+ wm = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
+ naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+#if 1 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+// fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
+// rewind( stderr );
+// rewind( stdout );
+// for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+// for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+// exit( 1 );
+ }
+#endif
+ }
+ else if( alg == 'H' )
+ {
+ float wm;
+ wm = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
+ naivescore1 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ {
+ fprintf( stderr, "%d-%d, ns: DOWN!\n", clus1, clus2 );
+ }
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+
+#if 0 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+ rewind( stdout );
+ for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ else if( alg == 'a' )
+ {
+ Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+ }
+ else ErrorExit( "Sorry!" );
+ }
+// fprintf( stderr, "## impmatch = %f\n", impmatch );
+
+#if 1
+ if( parallelizationstrategy == BAATARI2 && *subgenerationpt != subgenerationatfirst )
+ {
+// fprintf( stderr, "\nYarinaoshi2!! (Thread %d)\n", thread_no );
+ goto yarinaoshi;
+ }
+#endif
+
+ identity = !strcmp( localcopy[s1], mastercopy[s1] );
+ identity *= !strcmp( localcopy[s2], mastercopy[s2] );
+
+
+/* Bug? : idnetitcal but score change when scoreing mtx != JTT */
+
+ length = strlen( mseq1[0] );
+
+ if( identity )
+ {
+ tscore = mscore;
+// if( !devide ) fprintf( trap_g, "tscore = %f identical.\n", tscore );
+// fprintf( stderr, " identical." );
+ fprintf( stderr, "%03d-%04d-%d (thread %4d) identical \r", iterate+1, *ndonept, k, thread_no );
+ }
+ else
+ {
+ if( score_check )
+ {
+ if( constraint == 2 )
+ {
+#if 1
+ if( RNAscoremtx == 'r' )
+ intergroup_score_gapnomi( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+ else
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+#else
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+#endif
+
+ tscore = impmatch + tmpdouble;
+
+// fprintf( stderr, "tmpdouble=%f, impmatch = %f -> %f, tscore = %f\n", tmpdouble, oimpmatch, impmatch, tscore );
+ }
+ else
+ {
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+ tscore = tmpdouble;
+ }
+// fprintf( stderr, "#######ii=%d, iterate=%d score = %f -> %f \n", ii, iterate , mscore, tscore );
+ #if 0
+ for( i=0; i<1; i++ )
+ fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "+++++++\n" );
+ for( i=0; i<1; i++ )
+ fprintf( stderr, "%s\n", mseq2[i] );
+ #endif
+
+ }
+ else
+ {
+ tscore = mscore + 1.0;
+// tscore = 0.0;
+// fprintf( stderr, "in line 705, tscore=%f\n", tscore );
+// for( i=0; i<length; i++ )
+// tscore = tscore + (double)mseq1[0][i];
+// mscore = tscore - 1.0;
+ }
+
+ if( isnan( mscore ) )
+ {
+ fprintf( stderr, "\n\nmscore became NaN\n" );
+ exit( 1 );
+ }
+ if( isnan( tscore ) )
+ {
+ fprintf( stderr, "\n\ntscore became NaN\n" );
+ exit( 1 );
+ }
+
+
+
+// fprintf( stderr, "@@@@@ mscore,tscore = %f,%f\n", mscore, tscore );
+
+#if 1
+ if( parallelizationstrategy == BAATARI1 && *subgenerationpt != subgenerationatfirst )
+ {
+// fprintf( stderr, "\nYarinaoshi1!! (Thread %d)\n", thread_no );
+ goto yarinaoshi;
+ }
+#endif
+ gain = tscore - ( mscore - cut/100.0*mscore );
+ if( gain > 0 )
+ {
+ if( parallelizationstrategy == BESTFIRST )
+ {
+ if( gain > gainlist[thread_no] )
+ {
+ gainlist[thread_no] = gain;
+ for( i=0; i<locnjob; i++ ) strcpy( candidates[thread_no][i], localcopy[i] );
+ tscorelist[thread_no] = tscore;
+// if( iterate == 0 ) fprintf( stderr, "hist %d-%d-%d, gain=%f (Thread %d)\n", iterate, l, k, gain, thread_no );
+ }
+ }
+ else
+ {
+ pthread_mutex_lock( targ->mutex );
+ for( i=0; i<locnjob; i++ ) strcpy( mastercopy[i], localcopy[i] );
+ *subgenerationpt += 1;
+ gainlist[thread_no] = *basegainpt + gain;
+ *basegainpt += gain;
+
+ if( scoreout )
+ {
+ unweightedspscore = plainscore( locnjob, localcopy );
+ fprintf( stderr, "\nSCORE %d = %.0f, ", *ntrypt, unweightedspscore );
+ fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( locnjob * strlen( mastercopy[0] ) ) );
+ if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
+ fprintf( stderr, "\n" );
+ }
+
+ pthread_mutex_unlock( targ->mutex );
+ tscorelist[thread_no] = tscore;
+ }
+#if 0
+ fprintf( stderr, "tscore = %f mscore = %f accepted.\n", tscore, mscore );
+ fprintf( stderr, "\nbetter! gain = %f (thread %d)\r", gain, thread_no );
+#else
+ fprintf( stderr, "%03d-%04d-%d (thread %4d) better \r", iterate+1, *ndonept, k, thread_no );
+#endif
+
+ }
+ else
+ {
+#if 0
+ fprintf( stderr, "tscore = %f mscore = %f rejected.\r", tscore, mscore );
+ fprintf( stderr, "worse! gain = %f", gain );
+#else
+ fprintf( stderr, "%03d-%04d-%d (thread %4d) worse \r", iterate+1, *ndonept, k, thread_no );
+#endif
+ tscore = mscore;
+ }
+ }
+ converged2 = 0;
+ for( ii=iterate-2; ii>=0; ii-=1 )
+ {
+// fprintf( stderr, "Checking tscorehistory %f ?= %f\n", tscore, tscorehistory_detail[ii][branchpos] );
+ if( tscore == tscorehistory_detail[ii][branchpos] )
+ {
+ converged2 = 1;
+ break;
+ }
+ }
+ if( parallelizationstrategy != BESTFIRST && converged2 )
+ {
+// fprintf( stderr, "\nFINISH!\n" );
+ pthread_mutex_lock( targ->mutex );
+ *finishpt = 1;
+ pthread_mutex_unlock( targ->mutex );
+ }
+
+ tscorehistory_detail[iterate][branchpos] = tscore;
+ fprintf( stderr, "\r" );
+
+ pthread_mutex_lock( targ->mutex );
+ (*ndonept)++;
+// fprintf( stderr, "*ndonept = %d, nbranch = %d (thread %d) iterate=%d\n", *ndonept, nbranch, thread_no, iterate );
+ generationofinput[branchpos] = iterate;
+ if( *ndonept == nbranch )
+ {
+ if( *collectingpt != -1 ) *collectingpt = 1; // chofuku
+// fprintf( stderr, "Thread %d sends a signal, *ndonept = %d\n", thread_no, *ndonept );
+ pthread_cond_signal( targ->collection_start );
+ }
+ pthread_mutex_unlock( targ->mutex );
+ } /* while( 1 ) */
+
+ } /* for( iterate ) */
+// return( NULL );
+}
+#endif
+
+
+int TreeDependentIteration( int locnjob, char **name, int nlen[M],
+ char **aseq, char **bseq, int ***topol, double **len,
+ int alloclen, LocalHom **localhomtable,
+ RNApair ***singlerna,
+ int nkozo, char *kozoarivec )
+{
+ int i, j, k, l, iterate, ii, iu, ju;
+ int lin, ldf, length;
+ int clus1, clus2;
+ int s1, s2;
+ static double **imanoten;
+ static Node *stopol;
+ static double *effarrforlocalhom = NULL;
+ static double *effarr = NULL;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ static double *effarr_kozo = NULL;
+ static double *effarr1_kozo = NULL;
+ static double *effarr2_kozo = NULL;
+ static double **mtx = NULL;
+ static int **node = NULL;
+ static int *branchnode = NULL;
+ static double **branchWeight = NULL;
+ static char **mseq1, **mseq2;
+ static float ***history;
+ FILE *trap;
+ double tscore, mscore;
+ int identity;
+ int converged;
+ int oscillating;
+ float naivescore0 = 0.0; // by D.Mathog, a guess
+ float naivescore1;
+#if 0
+ char pair[njob][njob];
+#else
+ static char **pair;
+#endif
+#if DEBUG + RECORD
+ double score_for_check0, score_for_check1;
+ static double **effmtx = NULL;
+ extern double score_calc0();
+#endif
+ static char *indication1, *indication2;
+ static LocalHom ***localhomshrink = NULL;
+ float impmatch = 0.0, oimpmatch = 0.0;
+ static int *gapmap1;
+ static int *gapmap2;
+ double tmpdouble;
+ int intdum;
+ static RNApair *rnapairboth;
+ RNApair ***grouprna1, ***grouprna2;
+ double unweightedspscore;
+
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+ }
+ else
+ {
+ grouprna1 = grouprna2 = NULL;
+ }
+
+ Writeoptions( trap_g );
+ fflush( trap_g );
+
+ if( effarr == NULL ) /* locnjob == njob ni kagiru */
+ {
+ indication1 = AllocateCharVec( njob*3+50 );
+ indication2 = AllocateCharVec( njob*3+50 );
+ effarr = AllocateDoubleVec( locnjob );
+ effarrforlocalhom = AllocateDoubleVec( locnjob );
+ effarr1 = AllocateDoubleVec( locnjob );
+ effarr2 = AllocateDoubleVec( locnjob );
+ mseq1 = AllocateCharMtx( locnjob, 0 );
+ mseq2 = AllocateCharMtx( locnjob, 0 );
+ mtx = AllocateDoubleMtx( locnjob, locnjob );
+ node = AllocateIntMtx( locnjob, locnjob );
+ branchnode = AllocateIntVec( locnjob );
+ branchWeight = AllocateDoubleMtx( locnjob, 2 );
+ history = AllocateFloatCub( niter, locnjob, 2 );
+ stopol = (Node *)calloc( locnjob * 2, sizeof( Node ) );
+ gapmap1 = AllocateIntVec( alloclen );
+ gapmap2 = AllocateIntVec( alloclen );
+ if( score_check == 2 ) imanoten = AllocateDoubleMtx( njob, njob );
+
+ effarr1_kozo = AllocateDoubleVec( locnjob ); // tsuneni allocate suru.
+ effarr2_kozo = AllocateDoubleVec( locnjob ); // tsuneni allocate suru.
+ effarr_kozo = AllocateDoubleVec( locnjob );
+ for( i=0; i<locnjob; i++ )
+ effarr_kozo[i] = effarr1_kozo[i] = effarr2_kozo[i] = 0.0;
+
+#if 0
+#else
+ pair = AllocateCharMtx( locnjob, locnjob );
+ if( rnakozo ) rnapairboth = (RNApair *)calloc( alloclen, sizeof( RNApair ) );
+
+ if( constraint )
+ {
+ localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
+ for( i=0; i<njob; i++)
+ {
+ localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom * ) );
+ }
+ }
+#endif
+ }
+#if DEBUG + RECORD
+ if( !effmtx ) effmtx = AllocateDoubleMtx( locnjob, locnjob );
+ for( i=0; i<locnjob; i++ ) for( j=0; j<locnjob; j++ ) effmtx[i][j] = 1.0;
+#endif
+
+ for( i=0; i<locnjob; i++ ) strcpy( bseq[i], aseq[i] );
+
+ writePre( locnjob, name, nlen, aseq, 0 );
+
+ if( utree )
+ {
+ if( constraint )
+ {
+ counteff_simple( locnjob, topol, len, effarrforlocalhom );
+ calcimportance( locnjob, effarrforlocalhom, aseq, localhomtable );
+ }
+
+ if( weight == 2 )
+ {
+ countnode_int( locnjob, topol, node );
+ if( nkozo )
+ {
+ fprintf( stderr, "Not supported, weight=%d nkozo=%d.\n", weight, nkozo );
+ }
+ }
+ else if( weight == 4 )
+ {
+ treeCnv( stopol, locnjob, topol, len, branchWeight );
+ calcBranchWeight( branchWeight, locnjob, stopol, topol, len );
+ }
+ }
+
+#ifdef enablemultithread
+ if( nthread > 0 )
+ {
+ threadarg_t *targ;
+ pthread_t *handle;
+ pthread_mutex_t mutex;
+ pthread_cond_t collection_end;
+ pthread_cond_t collection_start;
+ int jobposint;
+ int generationofmastercopy;
+ int subgeneration;
+ float basegain;
+ int *generationofinput;
+ float *gainlist;
+ float *tscorelist;
+ int ndone;
+ int ntry;
+ int collecting;
+ int nbranch;
+ int maxiter;
+ char ***candidates;
+ int *branchtable;
+ float **tscorehistory_detail;
+ int finish;
+
+ nwa = nthread + 1;
+ nbranch = (njob-1) * 2 - 1;
+ maxiter = niter;
+
+ targ = calloc( nwa, sizeof( threadarg_t ) );
+ handle = calloc( nwa, sizeof( pthread_t ) );
+ pthread_mutex_init( &mutex, NULL );
+ pthread_cond_init( &collection_end, NULL );
+ pthread_cond_init( &collection_start, NULL );
+
+ gainlist = calloc( nwa, sizeof( float ) );
+ tscorelist = calloc( nwa, sizeof( float ) );
+ branchtable = calloc( nbranch, sizeof( int ) );
+ generationofinput = calloc( nbranch, sizeof( int ) );
+ if( parallelizationstrategy == BESTFIRST )
+ candidates = AllocateCharCub( nwa, locnjob, alloclen );
+ for( i=0; i<nbranch; i++ ) branchtable[i] = i;
+ tscorehistory_detail = AllocateFloatMtx( maxiter, nbranch );
+
+ collecting = 1;
+
+ for( i=0; i<nwa; i++ )
+ {
+ targ[i].thread_no = i;
+ targ[i].njob = njob;
+ targ[i].nbranch = nbranch;
+ targ[i].maxiter = maxiter;
+ targ[i].ndonept = &ndone;
+ targ[i].ntrypt = &ntry;
+ targ[i].collectingpt = &collecting;
+ targ[i].jobposintpt = &jobposint;
+ targ[i].gainlist = gainlist;
+ targ[i].tscorelist = tscorelist;
+ targ[i].nkozo = nkozo;
+ targ[i].kozoarivec = kozoarivec;
+ targ[i].mastercopy = bseq;
+ targ[i].candidates = candidates;
+ targ[i].subgenerationpt = &subgeneration;
+ targ[i].basegainpt = &basegain;
+ targ[i].generationofmastercopypt = &generationofmastercopy;
+ targ[i].generationofinput = generationofinput;
+ targ[i].branchtable = branchtable;
+ targ[i].singlerna = singlerna;
+ targ[i].localhomtable = localhomtable;
+ targ[i].alloclen = alloclen;
+ targ[i].stopol = stopol;
+ targ[i].topol = topol;
+// targ[i].len = len;
+ targ[i].mutex = &mutex;
+ targ[i].collection_end = &collection_end;
+ targ[i].collection_start = &collection_start;
+ targ[i].tscorehistory_detail = tscorehistory_detail;
+ targ[i].finishpt = &finish;
+
+ pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
+ }
+
+ for( i=0; i<nwa; i++ )
+ {
+ pthread_join( handle[i], NULL );
+ }
+
+ pthread_mutex_destroy( &mutex );
+ pthread_cond_destroy( &collection_end );
+ pthread_cond_destroy( &collection_start );
+
+ free( targ );
+ free( handle );
+ free( gainlist );
+ free( tscorelist );
+ free( branchtable );
+ free( generationofinput );
+ if( parallelizationstrategy == BESTFIRST )
+ FreeCharCub( candidates );
+ FreeFloatMtx( tscorehistory_detail );
+ }
+ else
+#endif
+ {
+#if 0
+ int *branchtable;
+ int jobpos;
+ int myjob;
+
+ int nbranch;
+ nbranch = (njob-1) * 2 - 1;
+
+ branchtable = calloc( nbranch, sizeof( int ) );
+ for( i=0; i<nbranch; i++ ) branchtable[i] = i;
+
+ srand( randomseed );
+#endif
+
+ if( parallelizationstrategy == BESTFIRST )
+ {
+ fprintf( stderr, "Not implemented. Try --thread 1 --bestfirst\n" );
+ exit( 1 );
+ }
+ converged = 0;
+ if( cooling ) cut *= 2.0;
+ for( iterate = 0; iterate<niter; iterate++ )
+ {
+ if( cooling ) cut *= 0.5; /* ... */
+
+#if 0
+ if( randomseed != 0 ) shuffle( branchtable, nbranch );
+#endif
+
+ fprintf( trap_g, "\n" );
+ Writeoption2( trap_g, iterate, cut );
+ fprintf( trap_g, "\n" );
+
+
+ if( utree == 0 )
+ {
+ if( nkozo )
+ {
+ fprintf( stderr, "The combination of dynamic tree and kozo is not supported.\n" );
+ exit( 1 );
+ }
+ if( devide )
+ {
+ static char *buff1 = NULL;
+ static char *buff2 = NULL;
+ if( !buff1 )
+ {
+ buff1 = AllocateCharVec( alloclen );
+ buff2 = AllocateCharVec( alloclen );
+ }
+
+ for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ )
+ {
+ buff1[0] = buff2[0] = 0;
+ strcat( buff1, res_g[i] ); strcat( buff2, res_g[j] );
+ strcat( buff1, bseq[i] ); strcat( buff2, bseq[j] );
+ strcat( buff1, seq_g[i] ); strcat( buff2, seq_g[j] );
+
+ mtx[i][j] = (double)substitution_hosei( buff1, buff2 );
+ }
+ }
+ else
+ {
+ for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ )
+ mtx[i][j] = (double)substitution_hosei( bseq[i], bseq[j] );
+ }
+
+ if ( treemethod == 'n' )
+ nj( locnjob, mtx, topol, len );
+ else if( treemethod == 's' )
+ spg( locnjob, mtx, topol, len );
+ else if( treemethod == 'X' )
+ supg( locnjob, mtx, topol, len );
+ else if( treemethod == 'p' )
+ upg2( locnjob, mtx, topol, len );
+ /* veryfastsupg\e$B$O!":#$N$H$3$m;H$($^$;$s!#\e(B*/
+ /* \e$B=gHV$NLdBj$,$"$k$N$G\e(B */
+
+ if( weight == 2 )
+ countnode_int( locnjob, topol, node );
+ else if( weight == 4 )
+ {
+ treeCnv( stopol, locnjob, topol, len, branchWeight );
+ calcBranchWeight( branchWeight, locnjob, stopol, topol, len );
+ }
+ trap = fopen( "hat2", "w" );
+ if( !trap ) ErrorExit( "Cannot open hat2." );
+ WriteHat2_pointer( trap, locnjob, name, mtx );
+ fclose( trap );
+ if( constraint )
+ {
+ counteff_simple( locnjob, topol, len, effarrforlocalhom );
+ calcimportance( locnjob, effarrforlocalhom, aseq, localhomtable );
+ }
+ }
+
+ if( iterate % 2 == 0 )
+ {
+ lin = 0; ldf = +1;
+ }
+ else
+ {
+ lin = locnjob - 2; ldf = -1;
+ }
+
+ if( score_check == 2 )
+ {
+ effarr1[0] = 1.0;
+ effarr2[0] = 1.0;
+ length = strlen( bseq[0] );
+ for( i=0; i<locnjob-1; i++ )
+ for( j=i+1; j<locnjob; j++ )
+ intergroup_score( bseq+i, bseq+j, effarr1, effarr2, 1, 1, length, imanoten[i]+j );
+ }
+
+#if 1
+ for( l=lin; l < locnjob-1 && l >= 0 ; l+=ldf )
+ {
+
+
+ for( k=0; k<2; k++ )
+ {
+ if( l == locnjob-2 ) k = 1;
+#else
+
+ for( jobpos=0; jobpos<nbranch; jobpos++)
+ {
+ {
+ myjob = branchtable[jobpos];
+ l = myjob / 2;
+ if( l == locnjob-2 ) k = 1;
+ else k = myjob - l * 2;
+#endif
+ #if 1
+ fprintf( stderr, "STEP %03d-%03d-%d ", iterate+1, l+1, k );
+ fflush( stderr );
+ #else
+ fprintf( stderr, "STEP %03d-%03d-%d %s", iterate+1, l+1, k, use_fft?"\n":"\n" );
+ #endif
+ for( i=0; i<locnjob; i++ ) for( j=0; j<locnjob; j++ ) pair[i][j] = 0;
+
+ OneClusterAndTheOther( locnjob, pair, &s1, &s2, topol, l, k );
+ #if 0
+ fprintf( stderr, "STEP%d-%d\n", l, k );
+ for( i=0; i<locnjob; i++ )
+ {
+ for( j=0; j<locnjob; j++ )
+ {
+ fprintf( stderr, "%#3d", pair[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ #endif
+ if( !weight )
+ {
+ for( i=0; i<locnjob; i++ ) effarr[i] = 1.0;
+ if( nkozo )
+ {
+ for( i=0; i<locnjob; i++ )
+ {
+ if( kozoarivec[i] )
+ effarr_kozo[i] = 1.0;
+ else
+ effarr_kozo[i] = 0.0;
+ }
+ }
+ }
+ else if( weight == 2 )
+ {
+ nodeFromABranch( locnjob, branchnode, node, topol, len, l, k );
+ node_eff( locnjob, effarr, branchnode );
+ }
+ else if( weight == 4 )
+ {
+ weightFromABranch( locnjob, effarr, stopol, topol, l, k );
+ #if 0
+ if( nkozo )
+ {
+ assignstrweight( locnjob, effarr_kozo, stopol, topol, l, k, kozoarivec, effarr );
+ }
+
+ #else
+ if( nkozo ) // hitomadu single weight.
+ for( i=0; i<locnjob; i++ )
+ {
+ if( kozoarivec[i] ) effarr_kozo[i] = effarr[i];
+ else effarr_kozo[i] = 0.0;
+ }
+ #endif
+ #if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "effarr_kozo = \n" );
+ for( i=0; i<locnjob; i++ ) fprintf( stderr, "%5.3f ", effarr_kozo[i] );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "effarr = \n" );
+ for( i=0; i<locnjob; i++ ) fprintf( stderr, "%5.3f ", effarr[i] );
+ fprintf( stderr, "\n\n" );
+ #endif
+ }
+
+ for( i=0; i<locnjob; i++ ) strcpy( aseq[i], bseq[i] );
+ length = strlen( aseq[0] );
+
+ if( nkozo )
+ {
+ #if 1
+ double tmptmptmp;
+ tmptmptmp = 0.0;
+ clus1 = conjuctionfortbfast_kozo( &tmptmptmp, pair, s1, aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
+ for( i=0; i<clus1; i++ ) effarr1_kozo[i] *= 1.0; // 0.5 ga sairyo ?
+ tmptmptmp = 0.0;
+ clus2 = conjuctionfortbfast_kozo( &tmptmptmp, pair, s2, aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
+ for( i=0; i<clus2; i++ ) effarr2_kozo[i] *= 1.0; // 0.5 ga sairyo ?
+
+ #if 0
+ fprintf( stderr, "\ngroup1 = %s\n", indication1 );
+ for( i=0; i<clus1; i++ ) fprintf( stderr, "effarr1_kozo[%d], effarr1[] = %f, %f\n", i, effarr1_kozo[i], effarr1[i] );
+ fprintf( stderr, "\ngroup2 = %s\n", indication2 );
+ for( i=0; i<clus2; i++ ) fprintf( stderr, "effarr2_kozo[%d], effarr2[] = %f, %f\n", i, effarr2_kozo[i], effarr2[i] );
+ #endif
+
+
+
+
+
+ #else
+ clus1 = conjuctionfortbfast_kozo_BUG( pair, s1, aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
+ clus2 = conjuctionfortbfast_kozo_BUG( pair, s2, aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
+ #endif
+ }
+ else
+ {
+ clus1 = conjuctionfortbfast( pair, s1, aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = conjuctionfortbfast( pair, s2, aseq, mseq2, effarr2, effarr, indication2 );
+ }
+
+
+
+ if( rnakozo && rnaprediction == 'm' )
+ {
+ makegrouprnait( grouprna1, singlerna, pair, s1 );
+ makegrouprnait( grouprna2, singlerna, pair, s2 );
+ }
+
+ if( score_check == 2 )
+ {
+ if( constraint )
+ {
+ // msshrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
+ shrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
+ oimpmatch = 0.0;
+ if( use_fft )
+ {
+ if( alg == 'Q' )
+ {
+ part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) part_imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ for( i=length-1; i>=0; i-- ) oimpmatch += part_imp_match_out_scQ( i, i );
+ }
+ else
+ {
+ part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ if( rnakozo ) part_imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ for( i=length-1; i>=0; i-- ) oimpmatch += part_imp_match_out_sc( i, i );
+ }
+ }
+ else
+ {
+ if( alg == 'Q' )
+ {
+ imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ for( i=length-1; i>=0; i-- ) oimpmatch += imp_match_out_scQ( i, i );
+ }
+ else
+ {
+ imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ fprintf( stderr, "not supported\n" );
+ exit( 1 );
+ }
+ }
+ // fprintf( stderr, "### oimpmatch = %f\n", oimpmatch );
+ }
+ else
+ {
+ oimpmatch = 0.0;
+ }
+ tmpdouble = 0.0;
+ iu=0;
+ for( i=s1; i<locnjob; i++ )
+ {
+ if( !pair[s1][i] ) continue;
+ ju=0;
+ for( j=s2; j<locnjob; j++ )
+ {
+ if( !pair[s2][j] ) continue;
+ // fprintf( stderr, "i = %d, j = %d, effarr1=%f, effarr2=%f\n", i, j, effarr1[iu], effarr2[ju] );
+ tmpdouble += effarr1[iu] * effarr2[ju] * imanoten[MIN(i,j)][MAX(i,j)];
+ ju++;
+ }
+ iu++;
+ }
+ mscore = oimpmatch + tmpdouble;
+ }
+ else if( score_check )
+ {
+ #if 1
+ if( RNAscoremtx == 'r' )
+ intergroup_score_gapnomi( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
+ else
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
+ #else
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble ); // gappick mae denaito dame
+ #endif
+
+ if( constraint )
+ {
+ shrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
+ // weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink ); // >>>
+ oimpmatch = 0.0;
+ if( use_fft )
+ {
+ if( alg == 'Q' )
+ {
+ part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) part_imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += part_imp_match_out_scQ( i, i );
+ // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
+ }
+ }
+ else
+ {
+ part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ if( rnakozo ) part_imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += part_imp_match_out_sc( i, i );
+ // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
+ }
+ }
+ // fprintf( stderr, "otmpmatch = %f\n", oimpmatch );
+ }
+ else
+ {
+ if( alg == 'Q' )
+ {
+ imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += imp_match_out_scQ( i, i );
+ // fprintf( stderr, "#### i=%d, initial impmatch = %f\n", i, oimpmatch );
+ }
+ }
+ else
+ {
+ imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+
+ fprintf( stderr, "not supported\n" );
+ exit( 1 );
+
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += imp_match_out_sc( i, i );
+ // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
+ }
+ }
+ // fprintf( stderr, "otmpmatch = %f\n", oimpmatch );
+ }
+ // fprintf( stderr, "#### initial impmatch = %f\n", oimpmatch );
+ }
+ else
+ {
+ oimpmatch = 0.0;
+ }
+
+
+ // fprintf( stderr, "#### tmpdouble = %f\n", tmpdouble );
+ mscore = (double)oimpmatch + tmpdouble;
+ }
+ else
+ {
+ // fprintf( stderr, "score_check = %d\n", score_check );
+ /* atode kousokuka */
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+ mscore = tmpdouble;
+ /* atode kousokuka */
+
+ if( constraint )
+ {
+ oimpmatch = 0.0;
+ shrinklocalhom( pair, s1, s2, localhomtable, localhomshrink );
+ if( use_fft )
+ {
+ if( alg == 'Q' )
+ {
+ part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) part_imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ }
+ else
+ {
+ part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ if( rnakozo ) part_imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ }
+ }
+ else
+ {
+ if( alg == 'Q' )
+ {
+ imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, gapmap1, gapmap2, NULL );
+ }
+ else
+ {
+ imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ fprintf( stderr, "Not supported\n" );
+ exit( 1 );
+ }
+ }
+ }
+ }
+
+ // oimpmatch = 0.0;
+ if( constraint )
+ {
+ #if 0 // iranai
+ if( alg == 'Q' )
+ {
+ imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += imp_match_out_scQ( i, i );
+ // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
+ }
+ }
+ else
+ {
+ imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ for( i=length-1; i>=0; i-- )
+ {
+ oimpmatch += imp_match_out_sc( i, i );
+ // fprintf( stderr, "#### i=%d, initial impmatch = %f seq1 = %c, seq2 = %c\n", i, oimpmatch, mseq1[0][i], mseq2[0][i] );
+ }
+ }
+ #endif
+ }
+ #if 0
+ if( alg == 'H' )
+ naivescore0 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + oimpmatch;
+ else if( alg == 'Q' )
+ naivescore0 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + oimpmatch;
+ else if( alg == 'R' )
+ naivescore0 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + oimpmatch;
+ #endif
+
+ // if( rnakozo ) foldalignedrna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, rnapairboth );
+
+ // if( !use_fft && !rnakozo )
+ if( !use_fft )
+ {
+ commongappick_record( clus1, mseq1, gapmap1 );
+ commongappick_record( clus2, mseq2, gapmap2 );
+ }
+
+ #if 0
+ fprintf( stderr, "##### mscore = %f\n", mscore );
+ #endif
+
+ #if DEBUG
+ if( !devide )
+ {
+ fprintf( trap_g, "\nSTEP%d-%d-%d\n", iterate+1, l+1, k );
+ fprintf( trap_g, "group1 = %s\n", indication1 );
+ fprintf( trap_g, "group2 = %s\n", indication2 );
+ fflush( trap_g );
+ }
+
+ #endif
+ #if 0
+ printf( "STEP %d-%d-%d\n", iterate, l, k );
+ for( i=0; i<clus2; i++ ) printf( "%f ", effarr2[i] );
+ printf( "\n" );
+ #endif
+ if( constraint == 2 )
+ {
+ if( use_fft )
+ {
+ // if( alg == 'Q' )
+ // part_imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
+ // else
+ // part_imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ Falign_localhom( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, gapmap1, gapmap2, NULL, 0, NULL );
+ // fprintf( stderr, "##### impmatch = %f\n", impmatch );
+ }
+ else
+ {
+ if( alg == 'Q' )
+ {
+ float wm;
+ // imp_match_init_strictQ( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap wo tsukuttakara iranai.
+ // if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, gapmap1, gapmap2, rnapairboth );
+
+ wm = Q__align_gapmap( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL, gapmap1, gapmap2 );
+ fprintf( stderr, "wm = %f\n", wm );
+ #if 0
+ fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
+ naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
+ fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+ #if 0 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+ // fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
+ // rewind( stdout );
+ // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ // exit( 1 );
+ }
+ #endif
+ #endif
+ }
+ else if( alg == 'R' )
+ {
+ float wm;
+ imp_match_init_strictR( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap ha mada
+ wm = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL );
+ // fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
+ naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
+ // fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: %f->%f UP!\n", clus1, clus2, naivescore0, naivescore1 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+ #if 0 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+ // fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
+ rewind( stdout );
+ for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ exit( 1 );
+ }
+ #endif
+ }
+ else if( alg == 'H' )
+ {
+ float wm;
+ imp_match_init_strictH( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 ); // Ichijiteki, gapmap ha mada
+ wm = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, NULL, NULL, NULL, NULL );
+ fprintf( stderr, "##### impmatch = %f->%f\n", oimpmatch, impmatch );
+ naivescore1 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty ) + impmatch;
+ fprintf( stderr, "##### naivscore1 = %f\n", naivescore1 );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+ #if 0 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+ // fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
+ // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ // exit( 1 );
+ }
+ #endif
+ }
+ else
+ {
+ // imp_match_init_strict( NULL, clus1, clus2, length, length, mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
+ A__align_gapmap( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, localhomshrink, &impmatch, gapmap1, gapmap2 );
+ // fprintf( stderr, "##### impmatch = %f\n", impmatch );
+ }
+ }
+ }
+ else if( use_fft )
+ {
+ float totalwm;
+ totalwm = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
+
+ // fprintf( stderr, "totalwm = %f\n", totalwm );
+ #if 0
+ if( alg == 'Q' )
+ {
+ fprintf( stderr, "totalwm = %f\n", totalwm );
+ naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+ #if 1 // chuui
+ if( totalwm != 0.0 && abs( totalwm - naivescore1 ) > 100 )
+ {
+ // fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
+ // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ // exit( 1 );
+ }
+ #endif
+ }
+ #endif
+ if( alg == 'R' )
+ {
+ fprintf( stderr, "totalwm = %f\n", totalwm );
+ naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+ #if 1 // chuui
+ if( totalwm != 0.0 && abs( totalwm - naivescore1 ) > 100 )
+ {
+ // fprintf( stderr, "WARNING, totalwm=%f but naivescore=%f\n", totalwm, naivescore1 );
+ // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ // exit( 1 );
+ }
+ }
+ #endif
+ }
+ else
+ {
+ if( alg == 'M' )
+ {
+ MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+ }
+ else if( alg == 'A' )
+ {
+ A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); // outgap==1
+ }
+ else if( alg == 'Q' )
+ {
+ float wm;
+ wm = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
+ fprintf( stderr, "wm = %f\n", wm );
+ fprintf( stderr, "impmatch = %f\n", impmatch );
+ naivescore1 = naiveQpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN!\n", clus1, clus2 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+ #if 1 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+ // fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
+ // rewind( stderr );
+ // rewind( stdout );
+ // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ // exit( 1 );
+ }
+ #endif
+ }
+ else if( alg == 'R' )
+ {
+ float wm;
+ wm = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
+ naivescore1 = naiveRpairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ fprintf( stderr, "%d-%d, ns: DOWN! %f->%f\n", clus1, clus2, naivescore0, naivescore1 );
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+ #if 1 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+ // fprintf( stderr, "WARNING, wm=%f but naivescore=%f\n", wm, naivescore1 );
+ // rewind( stderr );
+ // rewind( stdout );
+ // for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ // for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ // exit( 1 );
+ }
+ #endif
+ }
+ else if( alg == 'H' )
+ {
+ float wm;
+ wm = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &impmatch, NULL, NULL, NULL, NULL );
+ naivescore1 = naivepairscore( clus1, clus2, mseq1, mseq2, effarr1, effarr2, penalty );
+
+ if( naivescore1 > naivescore0 )
+ fprintf( stderr, "%d-%d, ns: UP!\n", clus1, clus2 );
+ else if( naivescore1 < naivescore0 )
+ {
+ fprintf( stderr, "%d-%d, ns: DOWN!\n", clus1, clus2 );
+ }
+ else
+ fprintf( stderr, "%d-%d, ns: IDENTICAL\n", clus1, clus2 );
+
+ #if 0 // chuui
+ if( abs( wm - naivescore1 ) > 100 )
+ {
+ rewind( stdout );
+ for( i=0; i<clus1; i++ ) printf( ">\n%s\n", mseq1[i] );
+ for( i=0; i<clus2; i++ ) printf( ">\n%s\n", mseq2[i] );
+ exit( 1 );
+ }
+ #endif
+ }
+ else if( alg == 'a' )
+ {
+ Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+ }
+ else ErrorExit( "Sorry!" );
+ }
+ // fprintf( stderr, "## impmatch = %f\n", impmatch );
+
+ if( checkC )
+ {
+ extern double DSPscore();
+ extern double SSPscore();
+ static double cur;
+ static double pre;
+
+ /*
+ pre = SSPscore( locnjob, bseq );
+ cur = SSPscore( locnjob, aseq );
+ */
+ pre = DSPscore( locnjob, bseq );
+ cur = DSPscore( locnjob, aseq );
+
+ fprintf( stderr, "Previous Sscore = %f\n", pre );
+ fprintf( stderr, "Currnet Sscore = %f\n\n", cur );
+ }
+
+ // fprintf( stderr, "## impmatch = %f\n", impmatch );
+ identity = !strcmp( aseq[s1], bseq[s1] );
+ identity *= !strcmp( aseq[s2], bseq[s2] );
+
+
+ /* Bug? : idnetitcal but score change when scoreing mtx != JTT */
+
+ length = strlen( mseq1[0] );
+
+ if( identity )
+ {
+ tscore = mscore;
+ if( !devide ) fprintf( trap_g, "tscore = %f identical.\n", tscore );
+ fprintf( stderr, " identical." );
+ converged++;
+ }
+ else
+ {
+ if( score_check )
+ {
+ if( constraint == 2 )
+ {
+ #if 1
+ if( RNAscoremtx == 'r' )
+ intergroup_score_gapnomi( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+ else
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+ #else
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+ #endif
+
+ tscore = impmatch + tmpdouble;
+
+ // fprintf( stderr, "tmpdouble=%f, impmatch = %f -> %f, tscore = %f\n", tmpdouble, oimpmatch, impmatch, tscore );
+ }
+ else
+ {
+ intergroup_score( mseq1, mseq2, effarr1, effarr2, clus1, clus2, length, &tmpdouble );
+ tscore = tmpdouble;
+ }
+ // fprintf( stderr, "#######ii=%d, iterate=%d score = %f -> %f \n", ii, iterate , mscore, tscore );
+ #if 0
+ for( i=0; i<1; i++ )
+ fprintf( stderr, "%s\n", mseq1[i] );
+ fprintf( stderr, "+++++++\n" );
+ for( i=0; i<1; i++ )
+ fprintf( stderr, "%s\n", mseq2[i] );
+ #endif
+
+ }
+ else
+ {
+ tscore = mscore + 1.0;
+ // tscore = 0.0;
+ // fprintf( stderr, "in line 705, tscore=%f\n", tscore );
+ // for( i=0; i<length; i++ )
+ // tscore = tscore + (double)mseq1[0][i];
+ // mscore = tscore - 1.0;
+ }
+
+ if( isnan( mscore ) )
+ {
+ fprintf( stderr, "\n\nmscore became NaN\n" );
+ exit( 1 );
+ }
+ if( isnan( tscore ) )
+ {
+ fprintf( stderr, "\n\ntscore became NaN\n" );
+ exit( 1 );
+ }
+
+
+
+ // fprintf( stderr, "@@@@@ mscore,tscore = %f,%f\n", mscore, tscore );
+
+ if( tscore > mscore - cut/100.0*mscore )
+ {
+ writePre( locnjob, name, nlen, aseq, 0 );
+ for( i=0; i<locnjob; i++ ) strcpy( bseq[i], aseq[i] );
+ if( score_check == 2 )
+ {
+ effarr1[0] = 1.0;
+ effarr2[0] = 1.0;
+ for( i=0; i<locnjob-1; i++ )
+ for( j=i+1; j<locnjob; j++ )
+ intergroup_score( bseq+i, bseq+j, effarr1, effarr2, 1, 1, length, imanoten[i]+j );
+ }
+
+ #if 0
+ fprintf( stderr, "tscore = %f mscore = %f accepted.\n", tscore, mscore );
+ #endif
+ fprintf( stderr, " accepted." );
+ converged = 0;
+
+ }
+ else
+ {
+ #if 0
+ fprintf( stderr, "tscore = %f mscore = %f rejected.\n", tscore, mscore );
+ #endif
+ fprintf( stderr, " rejected." );
+ tscore = mscore;
+ converged++;
+ }
+ }
+ fprintf( stderr, "\r" );
+
+
+ history[iterate][l][k] = (float)tscore;
+
+ // fprintf( stderr, "tscore = %f\n", tscore );
+
+ if( converged >= locnjob * 2 )
+ {
+ fprintf( trap_g, "Converged.\n\n" );
+ fprintf( stderr, "\nConverged.\n\n" );
+ if( scoreout )
+ {
+ unweightedspscore = plainscore( njob, bseq );
+ fprintf( stderr, "\nSCORE %d = %.0f, ", iterate * ( (njob-1)*2-1 ), unweightedspscore );
+ fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
+ if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
+ fprintf( stderr, "\n\n" );
+ }
+ return( 0 );
+ }
+ if( iterate >= 1 )
+ {
+ /* oscillation check */
+ oscillating = 0;
+ for( ii=iterate-2; ii>=0; ii-=2 )
+ {
+ if( (float)tscore == history[ii][l][k] )
+ {
+ oscillating = 1;
+ break;
+ }
+ }
+ if( ( oscillating && !cooling ) || ( oscillating && cut < 0.001 && cooling ) )
+ {
+ fprintf( trap_g, "Oscillating.\n" );
+ fprintf( stderr, "\nOscillating.\n\n" );
+ if( scoreout )
+ {
+ unweightedspscore = plainscore( njob, bseq );
+ fprintf( stderr, "\nSCORE %d = %.0f, ", iterate * ( (njob-1)*2-1 ), unweightedspscore );
+ fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
+ if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
+ fprintf( stderr, "\n\n" );
+ }
+ #if 1 /* hujuubun */
+ return( -1 );
+ #endif
+ }
+ } /* if( iterate ) */
+ } /* for( k ) */
+ } /* for( l ) */
+ if( scoreout )
+ {
+ unweightedspscore = plainscore( njob, bseq );
+ fprintf( stderr, "\nSCORE %d = %.0f, ", iterate * ( (njob-1)*2-1 ), unweightedspscore );
+ fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
+ if( weight || constraint ) fprintf( stderr, " (differs from the objective score)" );
+ fprintf( stderr, "\n\n" );
+ }
+ } /* for( iterate ) */
+ }
+ return( 2 );
+} /* int Tree... */
--- /dev/null
+#include <stdio.h>
+#include <unistd.h>
+main()
+{
+ fprintf( stdout, "nprocess = %d\n", sysconf( _SC_NPROCESSORS_ONLN ) );
+ fprintf( stdout, "nprocess = %d\n", sysconf( _SC_NPROCESSORS_CONF ) );
+}
--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+#define EF_THREEWAY 1.0
+#define MAXBW 1.0
+#define MINBW 0.01
+
+#define MINLEN 0.001
+
+#if DEBUG
+Node *stopol_g;
+#endif
+
+
+void checkMinusLength( int nseq, double **len )
+{
+ int i, j;
+ for( i=0; i<nseq-1; i++ ) for( j=0; j<2; j++ )
+ if( len[i][j] < MINLEN ) len[i][j] = MINLEN;
+}
+
+void negativeMember2( int *mem, int *query, int locnseq )
+{
+ int *ptr;
+ char *tmp;
+ int i;
+ int n;
+
+ tmp = AllocateCharVec( locnseq );
+
+ for( i=0; i<locnseq; i++ ) tmp[i] = 0;
+ while( (n=*query++) != -1 ) tmp[n] = 1;
+
+ ptr = mem;
+ for( i=0; i<locnseq; i++ )
+ {
+ if( !tmp[i] )
+ {
+ *ptr++ = i;
+ }
+ }
+ *ptr = -1;
+ free( tmp );
+}
+
+int *negativeMember( int *query, int locnseq )
+{
+ int *bk, *value = NULL;
+ char *tmp;
+ int i;
+ int n;
+
+ tmp = AllocateCharVec( locnseq );
+ bk = value = AllocateIntVec( locnseq );
+ if( !value ) ErrorExit( "Cannot allocate value" );
+
+ for( i=0; i<locnseq; i++ ) tmp[i] = 0;
+ while( (n=*query++) != -1 ) tmp[n] = 1;
+
+ for( i=0; i<locnseq; i++ )
+ {
+ if( !tmp[i] )
+ {
+ fprintf( stderr, "%3d ", i );
+ *value++ = i;
+ }
+ }
+ fprintf( stderr, "\n" );
+ *value = -1;
+ free( tmp );
+ return( bk );
+}
+
+int IntExistsInVec( int query, int *vector )
+{
+ while( *vector != -1 )
+ if( query == *vector++ ) return( 1 );
+ return( 0 );
+}
+
+NodeInCub searchParent( int top, int ***topol, int Start, int End )
+{
+ int i, j;
+ NodeInCub value;
+ for( i=Start; i<End; i++ )
+ {
+ for( j=0; j<2; j++ )
+ {
+ if( IntExistsInVec( top, topol[i][j] ) )
+ {
+ value.step = i;
+ value.LorR = j;
+ return( value );
+ }
+ }
+ }
+ fprintf( stderr, "ERROR!!!\n" );
+ ErrorExit( "Error in searchParent" );
+ value.step=0; // by D.Mathog, katoh
+ value.LorR=0; // by D.Mathog, katoh
+ return( value );
+}
+
+void stopolInit( int n, Node *stopol )
+{
+ int i, j;
+ for( i=0; i<n; i++ )
+ {
+ for( j=0; j<3; j++ )
+ {
+ stopol[i].length[j] = 0.0;
+ stopol[i].children[j] = NULL;
+ stopol[i].tmpChildren[j] = -1;
+ stopol[i].top[j] = -1;
+ stopol[i].members[j] = NULL;
+ stopol[i].weightptr[j] = NULL;
+ }
+ }
+#if 0
+ while( --numintvec >= 0 )
+ {
+ free( tmpintvec[numintvec] );
+ }
+ free( tmpintvec );
+ numintvec = 0;
+#endif
+}
+
+void treeCnv( Node *stopol, int locnseq, int ***topol, double **len, double **bw )
+{
+ int i;
+ NodeInCub parent;
+ int *count;
+ int ccount;
+ int rep;
+ int tmpint;
+ static int **tmpintvec = NULL;
+ static int numintvec = 0;
+
+ count = AllocateIntVec( 2 * locnseq ); /* oome */
+ if( !count ) ErrorExit( "Cannot allocate count.\n" );
+
+ checkMinusLength( locnseq, len ); /* uwagaki */
+
+ stopolInit( locnseq * 2, stopol );
+ for( i=0; i<locnseq * 2; i++ ) count[i] = 0;
+
+ for( i=locnseq; i<locnseq*2; i++ )
+ {
+ rep = i - locnseq;
+ parent = searchParent( rep, topol, 0, locnseq-1 );
+#if DEBUG
+ fprintf( stderr, "Parent of node No.%d ( Seq No.%d ) = %d - %d\n", i, i-locnseq, parent.step, parent.LorR );
+#endif
+
+ ccount = count[parent.step];
+ stopol[parent.step].length[ccount] = len[parent.step][parent.LorR];
+ stopol[parent.step].weightptr[ccount] = &(bw[parent.step][parent.LorR]);
+ stopol[parent.step].children[ccount] = &stopol[i];
+ stopol[parent.step].tmpChildren[ccount] = i;
+ stopol[parent.step].members[ccount] = topol[parent.step][parent.LorR];
+ count[parent.step]++;
+
+ ccount = count[i];
+ stopol[i].length[ccount] = len[parent.step][parent.LorR];
+ stopol[i].weightptr[ccount] = &(bw[parent.step][parent.LorR]);
+ stopol[i].children[ccount] = &stopol[parent.step];
+ stopol[i].tmpChildren[ccount] = parent.step;
+ stopol[i].members[ccount] = topol[parent.step][parent.LorR];
+ count[i]++;
+ }
+ for( i=0; i<locnseq-2; i++ )
+ {
+ rep = MIN( topol[i][0][0], topol[i][1][0] );
+ parent = searchParent( rep, topol, i+1, locnseq-1 );
+ ccount = count[parent.step];
+ stopol[parent.step].length[ccount] = len[parent.step][parent.LorR];
+ stopol[parent.step].weightptr[ccount] = &(bw[parent.step][parent.LorR]);
+ stopol[parent.step].children[ccount] = &stopol[i];
+ stopol[parent.step].tmpChildren[ccount] = i;
+ stopol[parent.step].members[ccount] = topol[parent.step][parent.LorR];
+ count[parent.step]++;
+
+ ccount = count[i];
+ stopol[i].length[ccount] = len[parent.step][parent.LorR];
+ stopol[i].weightptr[ccount] = &(bw[parent.step][parent.LorR]);
+ stopol[i].children[ccount] = &stopol[parent.step];
+ stopol[i].tmpChildren[ccount] = parent.step;
+#if 0
+ stopol[i].members[ccount] = negativeMember( topol[parent.step][parent.LorR], locnseq );
+#else
+// fprintf( stderr, "allocating numintvec = %d\n", numintvec );
+ tmpintvec = (int **)realloc( (void *)tmpintvec, (numintvec+1) * sizeof( int * ) );
+ tmpintvec[numintvec] = (int *)calloc( locnseq, sizeof( int ) );
+ negativeMember2( tmpintvec[numintvec], topol[parent.step][parent.LorR], locnseq );
+ stopol[i].members[ccount] = tmpintvec[numintvec];
+ numintvec++;
+#endif
+ count[i]++;
+#if DEBUG
+ fprintf( stderr, "Parent of node No.%d = %d - %d\n", i, parent.step, parent.LorR );
+#endif
+ }
+/*
+ Unrooted tree.
+ locnseq-2 no children no nakade,
+ locnseq-3 wo sashiteinai mono wo sagashite,
+ locnseq-3 no children ni kuwae,
+ locnseq-2 wo sashiteita node no chilren wo
+ locnseq-3 ni kaeru.
+*/
+#if DEBUG
+ fprintf( stderr, "BEFORE MODIFY\n" );
+ for( i=0; i<locnseq*2; i++ )
+ {
+ for( j=0; j<3; j++ )
+ {
+ fprintf( stderr, "stopol[%d].tmpChildren[%d] = %d, children[%d] = %d \n", i, j, stopol[i].tmpChildren[j], j, stopol[i].children[j] - stopol );
+ }
+ }
+#endif
+
+ if ( stopol[locnseq-2].children[0] == &stopol[locnseq-3] ) i = 1;
+ else if( stopol[locnseq-2].children[1] == &stopol[locnseq-3] ) i = 0;
+ else ErrorExit( "?\n" );
+
+ stopol[locnseq-3].length[2] = len[locnseq-2][0] + len[locnseq-2][1];
+ stopol[locnseq-3].weightptr[2] = &bw[locnseq-2][0];
+ stopol[locnseq-3].children[2] = stopol[locnseq-2].children[i];
+ stopol[locnseq-3].tmpChildren[2] = stopol[locnseq-2].tmpChildren[i];
+
+ tmpint = (int)( stopol[locnseq-2].children[i] - stopol );
+
+ stopol[tmpint].children[2] = &stopol[locnseq-3];
+ stopol[tmpint].length[2] = len[locnseq-2][0] + len[locnseq-2][1];
+ stopol[tmpint].weightptr[2] = &bw[locnseq-2][0];
+ stopol[tmpint].tmpChildren[2] = locnseq-3;
+
+
+#if DEBUG
+ for( i=0; i<locnseq*2; i++ )
+ {
+ for( j=0; j<3; j++ )
+ {
+ fprintf( stderr, "stopol[%d].tmpChildren[%d] = %d, children[%d] = %d \n", i, j, stopol[i].tmpChildren[j], j, stopol[i].children[j] - stopol );
+ }
+ }
+
+ for( i=0; i<locnseq*2; i++ )
+ {
+ fprintf( stderr, "-- stopol[%d]\n", i );
+ for( j=0; j<3; j++ )
+ {
+ if( !stopol[i].members[j] )
+ {
+ fprintf( stderr, "LEAF\n" );
+ break;
+ }
+ fprintf( stderr, " group %d are \n", j );
+ for( k=0; (n=stopol[i].members[j][k]) != -1; k++ )
+ {
+ fprintf( stderr, "%#5d", n );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+#if DEBUG
+ stopol_g = stopol;
+#endif
+ free( count );
+}
+
+int isLeaf( Node node )
+{
+ if( node.children[1] ) return( 0 );
+ else return( 1 );
+}
+
+double syntheticLength( Node *ob, Node *oppositeNode )
+{
+ int i, count;
+ int dir_ch[3];
+ int dir_pa = -10; // by katoh
+ double value, tmpvalue0, tmpvalue1;
+ int nanflag = 0;
+
+#if DEBUG
+ fprintf( stderr, "In syntheticLength\n" );
+ fprintf( stderr, "ob - stopol_g = %d\n", ob - stopol_g );
+ fprintf( stderr, "op - stopol_g = %d\n", oppositeNode - stopol_g );
+#endif
+
+ if( isLeaf( *ob ) )
+ {
+#if DEBUG
+ fprintf( stderr, "LEAF\n\n" );
+#endif
+ return( ob->length[0] );
+ }
+
+ for( i=0, count=0; i<3; i++ )
+ {
+#if DEBUG
+ fprintf( stderr, "ob->tmpChildren[%d] = %d\n", i, ob->tmpChildren[i] );
+#endif
+ if( oppositeNode != ob->children[i] ) dir_ch[count++] = i;
+ else dir_pa = i;
+ }
+#if DEBUG
+ fprintf( stderr, "\n" );
+#endif
+ if( count != 2 )
+ {
+#if DEBUG
+ fprintf( stderr, "Node No.%d has no child like No.%d \n", ob-stopol_g, oppositeNode-stopol_g );
+#endif
+ ErrorExit( "Invalid call\n" );
+ }
+
+ tmpvalue0 = syntheticLength( ob->children[dir_ch[0]], ob );
+ tmpvalue1 = syntheticLength( ob->children[dir_ch[1]], ob );
+
+#if DEBUG
+ fprintf( stderr, "tmpvalue0 = %f\n", tmpvalue0 );
+ fprintf( stderr, "tmpvalue1 = %f\n", tmpvalue1 );
+#endif
+ if( tmpvalue0 ) tmpvalue0 = 1.0 / tmpvalue0;
+ else nanflag = 1;
+ if( tmpvalue1 ) tmpvalue1 = 1.0 / tmpvalue1;
+ else nanflag = 1;
+
+ if( nanflag ) value = 0.0;
+ else
+ {
+ value = tmpvalue0 + tmpvalue1;
+ value = 1.0 / value;
+ }
+ value += ob->length[dir_pa];
+#if DEBUG
+ fprintf( stderr, "value = %f\n", value );
+#endif
+
+ return( value );
+}
+
+double calcW( Node *ob, Node *op )
+{
+ int i, count;
+ int dir_ch[3];
+ int dir_pa = -10; // by katoh
+ double a, b, c, f, s;
+ double value;
+
+ if( isLeaf( *ob ) )
+ return( 1.0 );
+
+ for( i=0, count=0; i<3; i++ )
+ {
+ if( op != ob->children[i] ) dir_ch[count++] = i;
+ else dir_pa = i;
+ }
+ if( count != 2 ) ErrorExit( "Invalid call of calcW\n" );
+
+#if DEBUG
+ fprintf( stderr, "In calcW\n" );
+ fprintf( stderr, "ob = %d\n", ob - stopol_g );
+ fprintf( stderr, "op = %d\n", op - stopol_g );
+ fprintf( stderr, "ob->children[c1] = %d\n", ob->children[dir_ch[0]] - stopol_g );
+ fprintf( stderr, "ob->children[c2] = %d\n", ob->children[dir_ch[1]] - stopol_g );
+ fprintf( stderr, "ob->children[pa] = %d\n", ob->children[dir_pa] - stopol_g );
+ fprintf( stderr, "\n" );
+#endif
+
+ a = syntheticLength( ob->children[dir_ch[0]], ob );
+ b = syntheticLength( ob->children[dir_ch[1]], ob );
+ c = syntheticLength( ob->children[dir_pa], ob );
+
+#if DEBUG
+ fprintf( stderr, "a = %f\n", a );
+ fprintf( stderr, "b = %f\n", b );
+ fprintf( stderr, "c = %f\n", c );
+#endif
+
+ if( !c ) return( MAXBW );
+ if ( !a || !b ) return( MINBW ); /* ? */
+
+ f = EF_THREEWAY;
+ s = ( b*c + c*a + a*b );
+
+ value = a*b*(c+a)*(c+b) / ( c*(a+b) * f * s );
+
+ value = sqrt( value );
+
+ return( value );
+}
+
+void calcBranchWeight( double **bw, int locnseq, Node *stopol, int ***topol, double **len )
+{
+ NodeInCub parent;
+ int i;
+ int rep;
+ Node *topNode, *btmNode;
+ double topW, btmW;
+
+ for( i=locnseq; i<locnseq*2; i++ )
+ {
+ rep = i - locnseq;
+ parent = searchParent( rep, topol, 0, locnseq-1 );
+ if( parent.step == locnseq - 2 ) continue;
+
+ topNode = stopol+parent.step; btmNode = stopol+i;
+#if DEBUG
+ fprintf( stderr, "In calcBranchWeight, topNode=%d, btmNode=%d\n", topNode-stopol_g, btmNode-stopol_g );
+#endif
+ topW = calcW( topNode, btmNode );
+ btmW = calcW( btmNode, topNode );
+ bw[parent.step][parent.LorR] = topW * btmW;
+ }
+ for( i=0; i<locnseq-3; i++ )
+ {
+ rep = MIN( topol[i][0][0], topol[i][1][0] );
+ parent = searchParent( rep, topol, i+1, locnseq-1 );
+ if( parent.step == locnseq - 2 ) continue;
+ topNode = stopol+parent.step;
+ btmNode = stopol+i;
+#if DEBUG
+ fprintf( stderr, "In calcBranchWeight, topNode=%d, btmNode=%d\n", topNode-stopol_g, btmNode-stopol_g );
+#endif
+ topW = calcW( topNode, btmNode );
+ btmW = calcW( btmNode, topNode );
+ bw[parent.step][parent.LorR] = topW * btmW;
+ }
+
+ topNode = stopol[locnseq-3].children[2];
+ btmNode = stopol + i;
+ topW = calcW( topNode, btmNode );
+ btmW = calcW( btmNode, topNode );
+ bw[locnseq-2][0] = topW * btmW;
+ bw[locnseq-2][1] = 1.0;
+}
+
+void branchWeightToPairWeight( int locnseq, int ***topol, double **pw, double **bw )
+{
+ int i, j, k, n0, n1;
+#if 0
+ double wFromLeaf[locnseq];
+#else
+ static double *wFromLeaf = NULL;
+ if( wFromLeaf == NULL )
+ wFromLeaf = AllocateDoubleVec( locnseq );
+#endif
+
+#if DEBUG
+ for( i=0; i<locnseq-1; i++ ) for( j=0; j<2; j++ )
+ fprintf( stderr, "pw[%d][%d] = %f\n", i, j, bw[i][j] );
+#endif
+
+ for( i=0; i<locnseq; i++ ) wFromLeaf[i] = 1.0;
+ for( i=0; i<locnseq; i++ ) for( j=0; j<locnseq; j++ )
+ pw[i][j] = 0.0;
+ for( i=0; i<locnseq-1; i++ )
+ {
+ for( j=0; (n0=topol[i][0][j])!=-1; j++ )
+ for( k=0; (n1=topol[i][1][k])!=-1; k++ )
+ pw[MIN( n0, n1 )][MAX( n0, n1 )]
+ = wFromLeaf[n0] * wFromLeaf[n1] * bw[i][0] * bw[i][1];
+ for( j=0; (n0=topol[i][0][j])!=-1; j++ )
+ wFromLeaf[n0] *= bw[i][0];
+ for( j=0; (n1=topol[i][1][j])!=-1; j++ )
+ wFromLeaf[n1] *= bw[i][1];
+ }
+}
+
+void weightFromABranch_rec( double *result, Node *ob, Node *op )
+{
+ int i, n, count;
+ int dir_ch[3], dir_pa;
+
+#if DEBUG
+ fprintf( stderr, "In weightFromABranch_rec, ob = %d\n", ob - stopol_g );
+#endif
+ if( isLeaf( *ob ) ) return;
+ for( i=0, count=0; i<3; i++ )
+ {
+ if( ob->children[i] != op ) dir_ch[count++] = i;
+ else dir_pa = i;
+ }
+ if( count != 2 )
+ {
+#if DEBUG
+ fprintf( stderr, "Node No.%d has no child like No.%d \n", ob-stopol_g, op-stopol_g );
+#endif
+ ErrorExit( "Incorrect call of weightFromABranch_rec" );
+ }
+ for( i=0; (n=ob->members[dir_ch[0]][i])!=-1; i++ )
+ result[n] *= *ob->weightptr[dir_ch[0]];
+ weightFromABranch_rec( result, ob->children[dir_ch[0]], ob );
+
+ for( i=0; (n=ob->members[dir_ch[1]][i])!=-1; i++ )
+ result[n] *= *ob->weightptr[dir_ch[1]];
+ weightFromABranch_rec( result, ob->children[dir_ch[1]], ob );
+}
+
+void weightFromABranch( int nseq, double *result, Node *stopol, int ***topol, int step, int LorR )
+{
+ Node *topNode, *btmNode;
+ int i;
+
+ if( step == nseq - 2 )
+ {
+ topNode = stopol[nseq-2].children[0];
+ btmNode = stopol + nseq-3;
+#if DEBUG
+ fprintf( stderr, "Now step == nseq-3, topNode = %d, btmNode = %d\n", topNode - stopol_g, btmNode-stopol_g );
+#endif
+ }
+
+ else
+ {
+ for( i=0; i<3; i++ )
+ {
+ if( stopol[step].members[i][0] == topol[step][LorR][0] )
+ break;
+ }
+ if( i== 3 ) ErrorExit( "Incorrect call of weightFromABranch." );
+ btmNode = stopol[step].children[i];
+ topNode = stopol+step;
+ }
+
+ for( i=0; i<nseq; i++ ) result[i] = 1.0;
+ weightFromABranch_rec( result, btmNode, topNode );
+ weightFromABranch_rec( result, topNode, btmNode );
+#if 0
+ for( i=0; i<nseq; i++ )
+ fprintf( stdout, "w[%d] = %f\n", i, result[i] );
+#endif
+// fprintf( stderr, "new weight!\n" );
+// for( i=0; i<nseq; i++ )
+// result[i] *= result[i];
+
+
+}
+void assignstrweight_rec( double *strweight, Node *ob, Node *op, char *kozoari, double *seqweight )
+{
+ int i, n, count, lastkozo;
+ int dir_ch[3], dir_pa;
+ double sumweight;
+
+#if DEBUG
+ fprintf( stderr, "In weightFromABranch_rec, ob = %d\n", ob - stopol_g );
+#endif
+ if( isLeaf( *ob ) )
+ {
+// fprintf( stderr, "Leaf!\n" );
+ return;
+ }
+ for( i=0, count=0; i<3; i++ )
+ {
+ if( ob->children[i] != op ) dir_ch[count++] = i;
+ else dir_pa = i;
+ }
+ if( count != 2 )
+ {
+#if DEBUG
+ fprintf( stderr, "Node No.%d has no child like No.%d \n", ob-stopol_g, op-stopol_g );
+#endif
+ ErrorExit( "Incorrect call of weightFromABranch_rec" );
+ }
+
+
+// fprintf( stderr, "\n" );
+ sumweight = 0.0;
+ count = 0;
+ lastkozo = -1;
+ for( i=0; (n=ob->members[dir_ch[0]][i])!=-1; i++ )
+ {
+// fprintf( stderr, "member1! n=%d\n", n );
+ sumweight += seqweight[n];
+ if( kozoari[n] )
+ {
+ count++;
+ lastkozo = n;
+ }
+ }
+ for( i=0; (n=ob->members[dir_ch[1]][i])!=-1; i++ )
+ {
+// fprintf( stderr, "member2! n=%d\n", n );
+ sumweight += seqweight[n];
+ if( kozoari[n] )
+ {
+ count++;
+ lastkozo = n;
+ }
+ }
+
+// fprintf( stderr, "count = %d\n", count );
+
+ if( count == 1 )
+ strweight[lastkozo] = sumweight;
+ else if( count > 1 )
+ {
+ assignstrweight_rec( strweight, ob->children[dir_ch[0]], ob, kozoari, seqweight );
+ assignstrweight_rec( strweight, ob->children[dir_ch[1]], ob, kozoari, seqweight );
+ }
+}
+
+void assignstrweight( int nseq, double *strweight, Node *stopol, int ***topol, int step, int LorR, char *kozoari, double *seqweight )
+{
+ Node *topNode, *btmNode;
+ int i;
+
+ if( step == nseq - 2 )
+ {
+ topNode = stopol[nseq-2].children[0];
+ btmNode = stopol + nseq-3;
+#if DEBUG
+ fprintf( stderr, "Now step == nseq-3, topNode = %d, btmNode = %d\n", topNode - stopol_g, btmNode-stopol_g );
+#endif
+ }
+
+ else
+ {
+ for( i=0; i<3; i++ )
+ {
+ if( stopol[step].members[i][0] == topol[step][LorR][0] )
+ break;
+ }
+ if( i== 3 ) ErrorExit( "Incorrect call of weightFromABranch." );
+ btmNode = stopol[step].children[i];
+ topNode = stopol+step;
+ }
+
+ for( i=0; i<nseq; i++ ) strweight[i] = 0.0;
+ for( i=0; i<nseq; i++ ) if( kozoari[i] ) strweight[i] = seqweight[i];
+// fprintf( stderr, "calling _rec (1)\n" );
+ assignstrweight_rec( strweight, btmNode, topNode, kozoari, seqweight );
+// fprintf( stderr, "calling _rec (2)\n" );
+ assignstrweight_rec( strweight, topNode, btmNode, kozoari, seqweight );
+
+#if 1 // nazeka kokowo tobasuto seido ga sagaru ?????
+ fprintf( stderr, "STEP %d\n", step );
+ for( i=0; topol[step][0][i]>-1; i++ )
+ fprintf( stderr, "%3d ", topol[step][0][i] );
+ fprintf( stderr, "\n" );
+ for( i=0; topol[step][1][i]>-1; i++ )
+ fprintf( stderr, "%3d ", topol[step][1][i] );
+ fprintf( stderr, "\n" );
+ for( i=0; i<nseq; i++ )
+ fprintf( stderr, "seqweight[%d] = %f\n", i, seqweight[i] );
+ for( i=0; i<nseq; i++ )
+ fprintf( stderr, "strweight[%d] = %f\n", i, strweight[i] );
+ fprintf( stderr, "\n" );
+#endif
+}
--- /dev/null
+progs="_PROGS"
+for prog in $progs; do
+ printf $prog" "
+done
+
+make clean
+make CC="gcc-4.0" CFLAGS="-arch ppc64 -m64 -O3 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4"
+for prog in $progs; do
+ mv $prog $prog.ppc64
+done
+
+make clean
+make CC="gcc-4.0" CFLAGS="-arch ppc -m32 -O3 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4"
+for prog in $progs; do
+ mv $prog $prog.ppc32
+done
+
+make clean
+make CC="gcc-4.0" CFLAGS="-arch i386 -fast -m32 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4"
+for prog in $progs; do
+ mv $prog $prog.intel32
+done
+
+make clean
+make CC="gcc-4.0" CFLAGS="-arch x86_64 -fast -m64 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4"
+for prog in $progs; do
+ mv $prog $prog.intel64
+done
+
+set $progs
+for prog in $progs; do
+# lipo -create $prog.icc $prog.ppc32 $prog.ppc64 -output $prog
+ lipo -create $prog.intel64 $prog.intel32 $prog.ppc32 $prog.ppc64 -output $prog
+ cp $prog ../binaries
+done
--- /dev/null
+PREFIX = /usr/local
+LIBDIR = $(PREFIX)/libexec/mafft
+
+#MNO_CYGWIN = -mno-cygwin
+
+INSTALL = install
+
+PROGS = mxscarnamod
+SCARNASRC = mxscarna_src/* mxscarna_src/*/*
+
+all : $(PROGS)
+ cp $(PROGS) ../binaries
+ chmod 755 ../binaries/*
+ @echo done.
+
+univscript: univscript.tmpl Makefile
+ sed "s:_PROGS:$(PROGS):" univscript.tmpl > univscript
+
+
+mxscarnamod: $(SCARNASRC)
+ $(MAKE) CFLAGS1="$(MNO_CYGWIN)" -C mxscarna_src
+ mv mxscarna_src/mxscarna mxscarnamod
+
+
+clean :
+ rm -f *.o *.a *.exe *~ $(PROGS)
+# rm -f ../binaries/* ../scripts/*
+ $(MAKE) clean -C mxscarna_src
+
+install : all
+ mkdir -p $(LIBDIR)
+ chmod 755 $(LIBDIR)
+ chmod 755 $(PROGS)
+ $(INSTALL) $(PROGS) $(LIBDIR)
--- /dev/null
+#include "AlifoldMEA.h"
+
+namespace MXSCARNA{
+
+const int AlifoldMEA::TURN = 3;
+
+void
+AlifoldMEA::
+Run()
+{
+ makeProfileBPPMatrix(alignment);
+ Initialization();
+ DP();
+ TraceBack();
+}
+
+void
+AlifoldMEA::
+makeProfileBPPMatrix(const MultiSequence *Sequences)
+{
+ int length = Sequences->GetSequence(0)->GetLength();
+
+ Trimat<float> *consBppMat = new Trimat<float>(length + 1);
+ fill(consBppMat->begin(), consBppMat->end(), 0);
+
+ for(int i = 1; i <= length; i++)
+ for (int j = i; j <= length; j++)
+ bppMat.ref(i, j) = 0;
+
+
+ int number = Sequences->GetNumSequences();
+ for(int seqNum = 0; seqNum < number; seqNum++) {
+ SafeVector<int> *tmpMap = Sequences->GetSequence(seqNum)->GetMappingNumber();
+ int label = Sequences->GetSequence(seqNum)->GetLabel();
+ BPPMatrix *tmpBppMatrix = BPPMatrices[label];
+
+ for(int i = 1; i <= length ; i++) {
+ int originI = tmpMap->at(i);
+ for(int j = i; j <= length; j++) {
+ int originJ = tmpMap->at(j);
+ if(originI != 0 && originJ != 0) {
+ float tmpProb = tmpBppMatrix->GetProb(originI, originJ);
+ bppMat.ref(i, j) += tmpProb;
+ }
+ }
+ }
+ }
+
+ /* compute the mean of base pairing probability */
+ for(int i = 1; i <= length; i++) {
+ for(int j = i; j <= length; j++) {
+ bppMat.ref(i,j) = bppMat.ref(i,j)/(float)number;
+ }
+ }
+
+ for (int i = 1; i <= length; i++) {
+ float sum = 0;
+ for (int j = i; j <= length; j++) {
+ sum += bppMat.ref(i,j);
+ }
+ Qi[i] = 1 - sum;
+ }
+
+ for (int i = 1; i <= length; i++) {
+ float sum = 0;
+ for (int j = i; j >= 1; j--) {
+ sum += bppMat.ref(j, i);
+ }
+ Qj[i] = 1 - sum;
+ }
+}
+
+void
+AlifoldMEA::
+Initialization()
+{
+ int length = alignment->GetSequence(0)->GetLength();
+
+ for (int i = 1; i <= length; i++) {
+ for (int j = i; j <= length; j++) {
+ M.ref(i,j) = 0;
+ traceI.ref(i,j) = 0;
+ traceJ.ref(i,j) = 0;
+ }
+ }
+
+ for (int i = 1; i <= length; i++) {
+ M.ref(i,i) = Qi[i];
+ traceI.ref(i,i) = 0;
+ traceJ.ref(i,i) = 0;
+ }
+
+ for (int i = 1; i <= length - 1; i++) {
+ M.ref(i, i+1) = Qi[i+1];
+ traceI.ref(i,i + 1) = 0;
+ traceJ.ref(i,i + 1) = 0;
+ }
+
+ for (int i = 0; i <= length; i++) {
+ ssCons[i] = '.';
+ }
+}
+
+void
+AlifoldMEA::
+DP()
+{
+ float g = BasePairConst; // see scarna.hpp
+ int length = alignment->GetSequence(0)->GetLength();
+
+ for (int i = length - 1; i >= 1; i--) {
+ for (int j = i + TURN + 1; j <= length; j++) {
+ float qi = Qi[i];
+ float qj = Qj[j];
+ float p = bppMat.ref(i,j);
+
+
+ float maxScore = qi + M.ref(i+1, j);
+ int tmpI = i+1;
+ int tmpJ = j;
+
+ float tmpScore = qj + M.ref(i, j-1);
+ if (tmpScore > maxScore) {
+ maxScore = tmpScore;
+ tmpI = i;
+ tmpJ = j - 1;
+ }
+
+ tmpScore = g*2*p + M.ref(i+1, j-1);
+ if (tmpScore > maxScore) {
+ maxScore = tmpScore;
+ tmpI = i + 1;
+ tmpJ = j - 1;
+ }
+
+ for (int k = i + 1; k < j - 1; k++) {
+ tmpScore = M.ref(i,k) + M.ref(k+1,j);
+ if (tmpScore > maxScore) {
+ maxScore = tmpScore;
+ tmpI = i;
+ tmpJ = j;
+ }
+ }
+ M.ref(i,j) = maxScore;
+ traceI.ref(i, j) = tmpI;
+ traceJ.ref(i, j) = tmpJ;
+ }
+ }
+}
+
+void
+AlifoldMEA::
+TraceBack()
+{
+
+ int length = alignment->GetSequence(0)->GetLength();
+ SafeVector<int> stackI((length + 1)*(length+1));
+ SafeVector<int> stackJ((length + 1)*(length+1));
+ int pt = 0;
+
+ stackI[pt] = traceI.ref(1, length);
+ stackJ[pt] = traceJ.ref(1, length);
+ ++pt;
+
+ while(pt != 0) {
+ --pt;
+ int tmpI = stackI[pt];
+ int tmpJ = stackJ[pt];
+ int nextI = traceI.ref(tmpI, tmpJ);
+ int nextJ = traceJ.ref(tmpI, tmpJ);
+
+ if (tmpI < tmpJ) {
+ if (tmpI + 1 == nextI && tmpJ == nextJ) {
+ stackI[pt] = nextI;
+ stackJ[pt] = nextJ;
+ ++pt;
+ }
+ else if (tmpI == nextI && tmpJ - 1 == nextJ) {
+ stackI[pt] = nextI;
+ stackJ[pt] = nextJ;
+ ++pt;
+ }
+ else if (tmpI + 1 == nextI && tmpJ - 1== nextJ) {
+ stackI[pt] = nextI;
+ stackJ[pt] = nextJ;
+ ++pt;
+ ssCons[tmpI] = '(';
+ ssCons[tmpJ] = ')';
+ }
+ else if (tmpI == nextI && tmpJ == nextJ) {
+ float maxScore = IMPOSSIBLE;
+ int maxK = 0;
+
+ for (int k = tmpI + 1; k < tmpJ - 1; k++) {
+ float tmpScore = M.ref(tmpI,k) + M.ref(k+1,tmpJ);
+ if (tmpScore > maxScore) {
+ maxScore = tmpScore;
+ maxK = k;
+ }
+ }
+ stackI[pt] = traceI.ref(tmpI, maxK);
+ stackJ[pt] = traceJ.ref(tmpI, maxK);
+ ++pt;
+ stackI[pt] = traceI.ref(maxK+1, tmpJ);
+ stackJ[pt] = traceJ.ref(maxK+1, tmpJ);
+ ++pt;
+ }
+ }
+ }
+}
+}
--- /dev/null
+#ifndef _ALIFOLDMEA_H_
+#define _ALIFOLDMEA_H_
+
+#include <iostream>
+#include <string>
+#include <cassert>
+#include "scarna.hpp"
+#include "nrutil.h"
+#include "Util.hpp"
+#include "Beta.hpp"
+#include "BPPMatrix.hpp"
+#include "MultiSequence.h"
+#include "Sequence.h"
+#include "SafeVector.h"
+
+using namespace std;
+
+namespace MXSCARNA {
+class AlifoldMEA {
+ MultiSequence *alignment;
+ SafeVector<BPPMatrix*> BPPMatrices;
+ float BasePairConst;
+ Trimat<float> M;
+ Trimat<int> traceI;
+ Trimat<int> traceJ;
+ Trimat<float> bppMat;
+ NRVec<float> Qi;
+ NRVec<float> Qj;
+ NRVec<char> ssCons;
+
+ static const int TURN;
+
+ void Initialization();
+ void makeProfileBPPMatrix(const MultiSequence *Sequences);
+ void DP();
+ void TraceBack();
+ public:
+ AlifoldMEA(MultiSequence *inalignment, SafeVector<BPPMatrix*> &inBPPMatrices, float inBasePairConst = 6) :
+ alignment(inalignment), BPPMatrices(inBPPMatrices),
+ BasePairConst(inBasePairConst),
+ M(inalignment->GetSequence(0)->GetLength()+1),
+ traceI(inalignment->GetSequence(0)->GetLength()+1),
+ traceJ(inalignment->GetSequence(0)->GetLength()+1),
+ bppMat(inalignment->GetSequence(0)->GetLength() + 1),
+ Qi(inalignment->GetSequence(0)->GetLength() + 1),
+ Qj(inalignment->GetSequence(0)->GetLength() + 1),
+ ssCons(inalignment->GetSequence(0)->GetLength() + 1){}
+
+ void Run();
+
+ string *getSScons() {
+ string *sscons = new string();
+ sscons->push_back(' ');
+ int length = alignment->GetSequence(0)->GetLength();
+ for (int i = 1; i <= length; i++) {
+ sscons->push_back(ssCons[i]);
+ }
+
+ return sscons;
+ }
+};
+}
+#endif // _ALIFOLDMEA_H_
--- /dev/null
+//////////////////////////////////////////////////////////////
+// BPPMatrix.hpp
+//
+// save the Base Pairing Probability Matrix for each sequences
+//////////////////////////////////////////////////////////////
+
+#ifndef __BBPMatrix_HPP__
+#define __BBPMatrix_HPP__
+
+#include <iostream>
+#include <string>
+#include "SparseMatrix.h"
+#include "McCaskill.hpp"
+#include "nrutil.h"
+
+
+
+using namespace std;
+
+namespace MXSCARNA{
+class BPPMatrix {
+private:
+
+ int seqLength; // sequence length;
+ float cutOff; // the threshold of probability
+
+ BPPMatrix() {}
+public:
+ SparseMatrix bppMat; // base pairing probability matrix 1-origin(1..seqLength)
+ BPPMatrix(int bppmode, const string &seq, int seqLength, float inCutOff = 0.0001) : seqLength (seqLength), cutOff(inCutOff) {
+ if( bppmode == 'r' ) // by katoh
+ readBPPMatrix(seq);
+ else if( bppmode == 'w' )
+ setandwriteBPPMatrix(seq);
+ else
+ setBPPMatrix(seq);
+ }
+ BPPMatrix(int seqLength, float inCutOff, const Trimat<float> & tmpBppMat) : seqLength(seqLength), cutOff(inCutOff) {
+ bppMat.SetSparseMatrix(seqLength, seqLength, tmpBppMat, cutOff);
+ }
+
+
+ void setBPPMatrix(const string &seq) {
+ const char *tmpSeq = seq.c_str();
+ McCaskill mc(seqLength, &tmpSeq[1]);
+ mc.calcPartitionFunction();
+ Trimat<float> tmpBppMat(seqLength + 1);
+
+ for (int i = 0; i < seqLength; i++) {
+ for(int j = i; j < seqLength; j++) {
+ tmpBppMat.ref(i+1, j+1) = mc.getProb(i,j);
+ }
+ }
+ bppMat.SetSparseMatrix(seqLength, seqLength, tmpBppMat, cutOff);
+ }
+
+ void setandwriteBPPMatrix(const string &seq) { // by katoh
+ const char *tmpSeq = seq.c_str();
+ McCaskill mc(seqLength, &tmpSeq[1]);
+ mc.calcPartitionFunction();
+ Trimat<float> tmpBppMat(seqLength + 1);
+ float tmpbp;
+
+ fprintf( stdout, ">\n" );
+ for (int i = 0; i < seqLength; i++) {
+ for(int j = i; j < seqLength; j++) {
+ tmpbp = mc.getProb(i,j);
+ if (tmpbp > 0.0001)
+ fprintf( stdout, "%d %d %50.40f\n", i, j, tmpbp );
+ tmpBppMat.ref(i+1, j+1) = tmpbp;
+ }
+ }
+ bppMat.SetSparseMatrix(seqLength, seqLength, tmpBppMat, cutOff);
+ }
+
+ void readBPPMatrix(const string &seq) { // by katoh
+ const char *tmpSeq = seq.c_str();
+ char oneline[1000];
+ int onechar;
+ float prob;
+ int posi, posj;
+ static FILE *bppfp = NULL;
+
+
+ if( bppfp == NULL )
+ {
+ bppfp = fopen( "_bpp", "r" );
+ if( bppfp == NULL )
+ {
+ fprintf( stderr, "Cannot open _bpp.\n" );
+ exit( 1 );
+ }
+ }
+
+ Trimat<float> tmpBppMat(seqLength + 1);
+ fgets( oneline, 999, bppfp );
+ if( oneline[0] != '>' )
+ {
+ fprintf( stderr, "Format error\n" );
+ exit( 1 );
+ }
+ while( 1 )
+ {
+ onechar = getc( bppfp );
+ ungetc( onechar, bppfp );
+ if( onechar == '>' || onechar == EOF ) break;
+
+ fgets( oneline, 999, bppfp );
+ sscanf( oneline, "%d %d %f", &posi, &posj, &prob );
+// fprintf( stderr, "%d %d -> %f\n", posi, posj, prob );
+ tmpBppMat.ref(posi+1, posj+1) = prob;
+ }
+
+ bppMat.SetSparseMatrix(seqLength, seqLength, tmpBppMat, cutOff);
+ }
+
+ float GetProb(int i, int j) {
+ return bppMat.GetValue(i,j);
+ }
+
+ float GetLength() const {
+ return seqLength;
+ }
+
+ void updateBPPMatrix(const Trimat<float> &inbppMat) {
+ bppMat.SetSparseMatrix(seqLength, seqLength, inbppMat, cutOff);
+ }
+};
+}
+#endif // __BPPMatrix_HPP__
--- /dev/null
+/*
+ *
+ * Beta.hpp
+ *
+ */
+#ifndef BETA_HPP
+#define BETA_HPP
+using namespace std;
+
+struct Beta {
+ static const int NBASE = 4;// A, C, G, U
+ static const int NBASEG = (NBASE + 1); // A, C, G, U, Gap
+ static const int NBASENG = (NBASE + 2); // A, C, G, U, N, Gap
+ static const int NPBASE = (NBASE * NBASE);
+ static const int NPBASEG = (NBASEG * NBASEG);
+ static const int NPBASENG = (NBASENG * NBASENG);
+ static const int NCODE = 7;
+ static const int BASEBIT = 2;
+ static const int BASEMSK = ~(~0 << BASEBIT);
+ enum BaseCode {
+ A_CODE = 0,
+ C_CODE = 1,
+ G_CODE = 2,
+ U_CODE = 3,
+ N_CODE = 4,
+ GAP_CODE = 5,
+ INVALID_CODE = 16
+ };
+ enum PairCode {
+ AA_CODE = 0, AC_CODE = 1, AG_CODE = 2, AU_CODE = 3,
+ CA_CODE = 4, CC_CODE = 5, CG_CODE = 6, CU_CODE = 7,
+ GA_CODE = 8, GC_CODE = 9, GG_CODE = 10, GU_CODE = 11,
+ UA_CODE = 12, UC_CODE = 13, UG_CODE = 14, UU_CODE = 15,
+ INVALID_PAIR_CODE = 16
+ };
+ enum ReducedPairCode {
+ REDUCED_NPBASE = 7,
+ REDUCED_AU_CODE = 0,
+ REDUCED_CG_CODE = 1,
+ REDUCED_GC_CODE = 2,
+ REDUCED_GU_CODE = 3,
+ REDUCED_UA_CODE = 4,
+ REDUCED_UG_CODE = 5,
+ REDUCED_MM_CODE = 6,
+ REDUCED_INVALID_PAIR_CODE = 16
+ };
+
+ static const int N_CANONICAL = 6;
+ static const int canonicalPairs[N_CANONICAL];
+ static const int N_NON_CANONICAL = 10;
+ static const int nonCanonicalPairs[N_NON_CANONICAL];
+ static const int i2nt[NCODE];
+ static const int nt2i[256];
+ static const bool isCanonicalBasePair[NPBASE];
+
+ static bool IsValidCode(const int& c) {return A_CODE <= c && c <= GAP_CODE;}
+ static bool IsBaseCode(const int& c) {return (A_CODE <= c && c <= U_CODE);}
+ static bool IsBasePairCode(const int& c){return (AA_CODE <= c && c <= UU_CODE);}
+ static bool IsReducedBasePairCode(const int& c) {
+ return (REDUCED_AU_CODE <= c && c <= REDUCED_MM_CODE);
+ }
+ static bool IsAmbiguousCode(const int& c) {return c == N_CODE;}
+ static bool IsGapCode(const int& c) {return c == GAP_CODE;}
+ static bool IsValidChar(const unsigned char& c) {
+ return IsValidCode(nt2i[c]);
+ }
+ static bool IsBaseChar(const int& c) {return IsBaseCode(nt2i[c]);}
+ static bool IsAmbiguousChar(const int& c) {return IsAmbiguousCode(nt2i[c]);}
+ static bool IsGapChar(const int& c) {return IsGapCode(nt2i[c]);}
+ static int nt2code(const int& nt) {
+ if (0 <= nt && nt < 256) {
+ return nt2i[nt];
+ } else {
+ return INVALID_CODE;
+ }
+ }
+ static int getPairCode(const int& c, const int& c1) {
+ return (IsBaseCode(c) && IsBaseCode(c1)
+ ? ((c << BASEBIT) | c1)
+ : INVALID_PAIR_CODE);
+ }
+ static bool isValidPairCode(const int& pairCode) {
+ return (0 <= pairCode && pairCode < NPBASE);
+ }
+ static void pair2Bases(const int& pairCode, int& c, int& c1) {
+ //Assert(IsBasePairCode(pairCode));
+ c1 = pairCode & BASEMSK;
+ c = (pairCode >> BASEBIT) & BASEMSK;
+ }
+ static int getReducedPairCode(const int& c, const int& c1) {
+ return reducePairCode(getPairCode(c, c1));
+ }
+ static int reducePairCode(const int& pairCode) {
+ static const int table[NPBASE] = {
+ REDUCED_MM_CODE, REDUCED_MM_CODE, REDUCED_MM_CODE, REDUCED_AU_CODE,
+ REDUCED_MM_CODE, REDUCED_MM_CODE, REDUCED_CG_CODE, REDUCED_MM_CODE,
+ REDUCED_MM_CODE, REDUCED_GC_CODE, REDUCED_MM_CODE, REDUCED_GU_CODE,
+ REDUCED_UA_CODE, REDUCED_MM_CODE, REDUCED_UG_CODE, REDUCED_MM_CODE,
+ };
+ return (IsBasePairCode(pairCode)
+ ? table[pairCode]
+ : REDUCED_INVALID_PAIR_CODE);
+ }
+ static bool isValidReducedPairCode(const int& pairCode) {
+ return (0 <= pairCode && pairCode < REDUCED_NPBASE);
+ }
+ static bool isCanonicalReducedPairCode(const int& pairCode) {
+ return (REDUCED_AU_CODE <= pairCode
+ && pairCode <= REDUCED_UG_CODE);
+ }
+ static int flipReducedPairCode(const int& reducedPairCode) {
+ static const int table[REDUCED_NPBASE + 1] = {
+ REDUCED_UA_CODE,
+ REDUCED_GC_CODE,
+ REDUCED_CG_CODE,
+ REDUCED_UG_CODE,
+ REDUCED_AU_CODE,
+ REDUCED_GU_CODE,
+ REDUCED_MM_CODE,
+ REDUCED_INVALID_PAIR_CODE
+ };
+ return (IsReducedBasePairCode(reducedPairCode)
+ ? table[reducedPairCode] : table[REDUCED_NPBASE]);
+ }
+ static void seq2i(char* s, const char* t, int len) {
+ const char* const s_end = s + len;
+ while (s < s_end) *s++ = nt2i[(unsigned) (*t++)];
+ }
+ static void i2seq(char* s, const char* t, int len) {
+ const char* const s_end = s + len;
+ while (s < s_end) *s++ = i2nt[(unsigned) (*t++)];
+ }
+ static void i2seq(ostream& fo, const char* t, int len) {
+ const char* const t_end = t + len;
+ while (t < t_end) fo << (char) i2nt[(unsigned) (*t++)];
+ }
+ static char* wd2str(unsigned int wdSize, unsigned int wd) {
+ const unsigned int MAX_WD_SIZE = (sizeof(unsigned int) * 8 / BASEBIT);
+ static char buf[MAX_WD_SIZE + 1] = {};
+ //Assert(wdSize <= MAX_WD_SIZE);
+
+ char* s = buf + wdSize;
+ *s = '\0';
+ do {
+ *(--s) = Beta::i2nt[wd & BASEMSK];
+ wd >>= BASEBIT;
+ } while (s > buf);
+ return buf;
+ }
+ static void printWd(ostream& fo, unsigned int wdSize, unsigned int wd) {
+ fo << wd2str(wdSize, wd);
+ }
+ static const char* code2str(const int& code) {
+ static const char table[NBASENG+1][2] = {
+ "A", "C", "G", "U", "N", ".", "?"
+ };
+ return ((A_CODE <= code && code <= GAP_CODE)
+ ? table[code] : table[NBASENG]);
+ }
+ static const char* pairCode2str(const int& pairCode) {
+ static const char table[NPBASE+1][3] = {
+ "AA", "AC", "AG", "AU",
+ "CA", "CC", "CG", "CU",
+ "GA", "GC", "GG", "GU",
+ "UA", "UC", "UG", "UU",
+ "??"
+ };
+ return (IsBasePairCode(pairCode) ? table[pairCode] : table[NPBASE]);
+ }
+ static const char* reducedPairCode2str(const int& reducedPairCode) {
+ static const char table[REDUCED_NPBASE+1][3] = {
+ "AU", "CG", "GC", "GU", "UA", "UG", "MM", "??"
+ };
+ return (IsReducedBasePairCode(reducedPairCode)
+ ? table[reducedPairCode] : table[REDUCED_NPBASE]);
+ }
+ static char nt2Code(const char& c){
+ if (!IsValidChar(c)) { cerr << "character " << c << " is not valid"; }
+
+ return (char) nt2i[(int) c];
+ }
+ static char code2char(const int& c) {
+ static const char table[NBASENG+1] = {
+ 'A', 'C', 'G', 'U', 'N', '.', '?'
+ };
+ return ((A_CODE <= c && c <= GAP_CODE)
+ ? table[(int) c] : table[NBASENG]);
+ }
+ /*
+ static string generateRandomRNA(const int& len) {
+ static const char nt[5] = "ACGU";
+ string rna(len, '\0');
+ for (int i = 0; i < len; i++) {
+ rna[i] = nt[Rand(4)];
+ }
+ return rna;
+ }
+ */
+};
+
+#endif
--- /dev/null
+//////////////////////////////////////////////////////////////
+// GlobalParameters.cpp
+// This file include Global Parameters, command line options, etc.
+//////////////////////////////////////////////////////////////
+
+#include "scarna.hpp"
+
+// These paramenters are defined in scarna.hpp
+
+float RNA_Match_AA = RNAMATCHAA;
+float RNA_Match_AT = RNAMATCHAT;
+float RNA_Match_AG = RNAMATCHAG;
+float RNA_Match_AC = RNAMATCHAC;
+float RNA_Match_TT = RNAMATCHTT;
+float RNA_Match_TG = RNAMATCHTG;
+float RNA_Match_TC = RNAMATCHTC;
+float RNA_Match_GG = RNAMATCHGG;
+float RNA_Match_GC = RNAMATCHGC;
+float RNA_Match_CC = RNAMATCHCC;
+float RNA_Gap_Penalty = GAPPENALTY;
+float RNA_Gap_Extension = GAPEXTENTIONPENALTY;
+
+int numIterativeRefinementReps = REFINEMENTREPS;
+bool PostProcessAlignment = false;
+int scsLength = SCSLENGTH;
+float BaseProbThreshold = BASEPROBTHRESHOLD;
+float BasePairConst = BASEPAIRCONST;
--- /dev/null
+#include "Globaldp.hpp"
+
+namespace MXSCARNA {
+
+double Globaldp::ribosum_matrix[16][16]
+= { { -2.49, -7.04, -8.24, -4.32, -8.84, -14.37, -4.68, -12.64, -6.86, -5.03, -8.39, -5.84, -4.01, -11.32, -6.16, -9.05 },
+ { -7.04, -2.11, -8.89, -2.04, -9.37, -9.08, -5.86, -10.45, -9.73, -3.81, -11.05, -4.72, -5.33, -8.67, -6.93, -7.83 },
+ { -8.24, -8.89, -0.80, -5.13, -10.41, -14.53, -4.57, -10.14, -8.61, -5.77, -5.38, -6.60, -5.43, -8.87, -5.94, -11.07 },
+ { -4.32, -2.04, -5.13, 4.49, -5.56, -6.71, 1.67, -5.17, -5.33, 2.70, -5.61, 0.59, 1.61, -4.81, -0.51, -2.98 },
+ { -8.84, -9.37, -10.41, -5.56, -5.13, -10.45, -3.57, -8.49, -7.98, -5.95, -11.36, -7.93, -2.42, -7.08, -5.63, -8.39 },
+ { -14.37, -9.08, -14.53, -6.71, -10.45, -3.59, -5.71, -5.77, -12.43, -3.70, -12.58, -7.88, -6.88, -7.40, -8.41, -5.41 },
+ { -4.68, -5.86, -4.57, 1.67, -3.57, -5.71, 5.36, -4.96, -6.00, 2.11, -4.66, -0.27, 2.75, -4.91, 1.32, -3.67 },
+ { -12.64, -10.45, -10.14, -5.17, -8.49, -5.77, -4.96, -2.28, -7.71, -5.84, -13.69, -5.61, -4.72, -3.83, -7.36, -5.21 },
+ { -6.86, -9.73, -8.61, -5.33, -7.98, -12.43, -6.00, -7.71, -1.05, -4.88, -8.67, -6.10, -5.85, -6.63, -7.55, -11.54 },
+ { -5.03, -3.81, -5.77, 2.70, -5.95, -3.70, 2.11, -5.84, -4.88, 5.62, -4.13, 1.21, 1.60, -4.49, -0.08, -3.90 },
+ { -8.39, -11.05, -5.38, -5.61, -11.36, -12.58, -4.66, -13.69, -8.67, -4.13, -1.98, -5.77, -5.75, -12.01, -4.27, -10.79 },
+ { -5.84, -4.72, -6.60, 0.59, -7.93, -7.88, -0.27, -5.61, -6.10, 1.21, -5.77, 3.47, -0.57, -5.30, -2.09, -4.45 },
+ { -4.01, -5.33, -5.43, 1.61, -2.42, -6.88, 2.75, -4.72, -5.85, 1.60, -5.75, -0.57, 4.97, -2.98, 1.14, -3.39 },
+ { -11.32, -8.67, -8.87, -4.81, -7.08, -7.40, -4.91, -3.83, -6.63, -4.49, -12.01, -5.30, -2.98, -3.21, -4.76, -5.97 },
+ { -6.16, -6.93, -5.94, -0.51, -5.63, -8.41, 1.32, -7.36, -7.55, -0.08, -4.27, -2.09, 1.14, -4.76, 3.36, -4.28 },
+ { -9.05, -7.83, -11.07, -2.98, -8.39, -5.41, -3.67, -5.21, -11.54, -3.90, -10.79, -4.45, -3.39, -5.97, -4.28, -0.02 }
+};
+
+
+Trimat<float>*
+Globaldp::
+makeProfileBPPMatrix(const MultiSequence *Sequences)
+{
+ int length = Sequences->GetSequence(0)->GetLength();
+ float thr = THR;
+ Trimat<float> *consBppMat = new Trimat<float>(length + 1);
+ fill(consBppMat->begin(), consBppMat->end(), 0);
+
+ int number = Sequences->GetNumSequences();
+ for(int seqNum = 0; seqNum < number; seqNum++) {
+ SafeVector<int> *tmpMap = Sequences->GetSequence(seqNum)->GetMappingNumber();
+ int label = Sequences->GetSequence(seqNum)->GetLabel();
+ BPPMatrix *tmpBppMatrix = BPPMatrices[label];
+
+ for(int i = 1; i <= length ; i++) {
+ int originI = tmpMap->at(i);
+ for(int j = i; j <= length; j++) {
+ int originJ = tmpMap->at(j);
+ if(originI != 0 && originJ != 0) {
+ float tmpProb = tmpBppMatrix->GetProb(originI, originJ);
+
+ if(tmpProb >= thr) {
+ consBppMat->ref(i, j) += tmpProb;
+ }
+ }
+ }
+ }
+ }
+
+ /* compute the mean of base pairing probability */
+ for(int i = 1; i <= length; i++) {
+ for(int j = i; j <= length; j++) {
+ consBppMat->ref(i,j) = consBppMat->ref(i,j)/(float)number;
+ }
+ }
+
+ return consBppMat;
+}
+
+float
+Globaldp::
+incrementalScorePSCPair(const StemCandidate &sc1, const StemCandidate &sc2)
+{
+ int wordLength = WORDLENGTH;
+
+ int pos1, rvpos1;
+ if (sc1.GetDistance() > 0) {
+ pos1 = sc1.GetPosition();
+ rvpos1 = sc1.GetRvposition();
+ }
+ else {
+ pos1 = sc1.GetRvposition();
+ rvpos1 = sc1.GetPosition();
+ }
+
+ int pos2, rvpos2;
+ if (sc2.GetDistance() > 0) {
+ pos2 = sc2.GetPosition();
+ rvpos2 = sc2.GetRvposition();
+ }
+ else {
+ pos2 = sc2.GetRvposition();
+ rvpos2 = sc2.GetPosition();
+ }
+/*
+ cout << "1:" << i << " " << j << " " << sc1.GetDistance() << " " << sc2.GetDistance() << endl;
+ cout << sc1.GetPosition() << " " << sc1.GetRvposition() << " " << sc2.GetPosition() << " " << sc2.GetRvposition() << endl;
+*/
+ float score =
+ posterior[sc1.GetPosition() + wordLength - 1][sc2.GetPosition() + wordLength - 1]
+// * sc1.GetBaseScore(wordLength - 1)
+ * profileBPPMat1->ref(pos1 + wordLength - 1, rvpos1)
+ * posterior[sc1.GetRvposition()][sc2.GetRvposition()]
+// * sc2.GetBaseScore(wordLength - 1);
+ * profileBPPMat2->ref(pos2 + wordLength - 1, rvpos2);
+
+
+/*
+ incrementalWordSimilarity(sc1, sc2, i, j)
+ + incrementalProbabilityScore(sc1, sc2) * multiDeltaScore
+ + incrementalStackingScore(sc1, sc2) * multiDeltaStacking;
+*/
+
+ return score*sc1.GetNumSeq()*sc2.GetNumSeq();
+}
+
+float
+Globaldp::
+incrementalProbabilityScore(const StemCandidate &sc1, const StemCandidate &sc2)
+{
+ int wordLength = WORDLENGTH;
+ return sc1.GetBaseScore(wordLength-1) + sc2.GetBaseScore(wordLength-1);
+}
+
+float
+Globaldp::
+incrementalStackingScore(const StemCandidate &sc1, const StemCandidate &sc2)
+{
+ return - (sc1.GetStacking() + sc2.GetStacking());
+}
+
+float
+Globaldp::
+incrementalWordSimilarity(const StemCandidate &sc1, const StemCandidate &sc2, int i, int j)
+{
+ int numSeq1 = sc1.GetNumSeq();
+ int numSeq2 = sc2.GetNumSeq();
+
+ float score = 0;
+
+ for(int k = 0; k < 16; k++) {
+ for(int l = 0; l < 16; l++) {
+ score += countContConp1[k][i]*countContConp2[l][j]*ribosum_matrix[k][l];
+ }
+ }
+
+ return score/(numSeq1*numSeq2);
+}
+
+float
+Globaldp::
+scorePSCPair(const StemCandidate &sc1, const StemCandidate &sc2)
+{
+
+
+ int wordLength = WORDLENGTH;
+ float score = 0;
+
+ int pos1, rvpos1;
+ if (sc1.GetDistance() > 0) {
+ pos1 = sc1.GetPosition();
+ rvpos1 = sc1.GetRvposition();
+ }
+ else {
+ pos1 = sc1.GetRvposition();
+ rvpos1 = sc1.GetPosition();
+ }
+
+ int pos2, rvpos2;
+ if (sc2.GetDistance() > 0) {
+ pos2 = sc2.GetPosition();
+ rvpos2 = sc2.GetRvposition();
+ }
+ else {
+ pos2 = sc2.GetRvposition();
+ rvpos2 = sc2.GetPosition();
+ }
+
+ for (int k = 0; k < wordLength; k++) {
+ score +=
+ posterior[sc1.GetPosition() + k][sc2.GetPosition() + k]
+ * profileBPPMat1->ref(pos1 + k, rvpos1 + wordLength - 1 - k)
+// * sc1.GetBaseScore(k)
+ * posterior[sc1.GetRvposition() + wordLength - 1 - k][sc2.GetRvposition() + wordLength - 1 - k]
+// * sc2.GetBaseScore(k);
+ * profileBPPMat2->ref(pos2 + k, rvpos2 + wordLength - 1 - k);
+ }
+ // validation code
+ /*
+ if (profileBPPMat1->ref(pos1 , rvpos1 + wordLength - 1) != sc1.GetBaseScore(0)) {
+ cout << "1 " << profileBPPMat1->ref(pos1, rvpos1 + wordLength - 1) << " " << sc1.GetBaseScore(0) << endl;
+ }
+ if (profileBPPMat2->ref(pos2, rvpos2 + wordLength - 1) != sc2.GetBaseScore(0)) {
+ cout << profileBPPMat2->ref(pos2, rvpos2 + wordLength - 1) << " " << sc2.GetBaseScore(0) << endl;
+ }
+ if (profileBPPMat1->ref(pos1 + 1, rvpos1 + wordLength - 1 - 1) != sc1.GetBaseScore(1)) {
+ cout << "1 " << profileBPPMat1->ref(pos1 + 1, rvpos1 + wordLength - 1 - 1) << " " << sc1.GetBaseScore(1) << endl;
+ }
+ if (profileBPPMat2->ref(pos2 + 1, rvpos2 + wordLength - 1 - 1) != sc2.GetBaseScore(1)) {
+ cout << profileBPPMat2->ref(pos2 + 1, rvpos2 + wordLength - 1 - 1) << " " << sc2.GetBaseScore(1) << endl;
+ }*/
+
+// cout << sc1.GetPosition() << " " << sc1.GetRvposition() << " " << sc1.GetDistance() << endl;
+// cout << sc2.GetPosition() << " " << sc2.GetRvposition() << " " << sc2.GetDistance() << endl;
+/*
+ wordSimilarity(sc1, sc2, i, j)
+ + probabilityScore(sc1, sc2) * multiScore
+ + stackingScore(sc1, sc2) * multiStacking
+
+*/
+/*
+ if (sc1.GetDistance() < 0 && sc2.GetDistance() < 0) {
+ cout << "2:" << i << " " << j << " " << sc1.GetDistance() << " " << sc2.GetDistance() << endl;
+ cout << sc1.GetPosition() << " " << sc1.GetRvposition() << " " << sc2.GetPosition() << " " << sc2.GetRvposition() << endl;
+ cout << "2:score" << score << endl;
+
+ }
+*/
+ return score*sc1.GetNumSeq()*sc2.GetNumSeq();
+}
+
+float
+Globaldp::
+wordSimilarity(const StemCandidate &sc1, const StemCandidate &sc2, int i, int j)
+{
+ int wordLength = WORDLENGTH;
+
+ int numSeq1 = sc1.GetNumSeq();
+ int numSeq2 = sc2.GetNumSeq();
+
+ float score = 0;
+
+ for(int k = 0; k < 16; k++) {
+ for(int l = 0; l < 16; l++) {
+ for(int iter = 0; iter < wordLength; iter++) {
+ score += countConp1[iter][k][i]*countConp2[iter][l][j]*ribosum_matrix[k][l];
+ }
+ }
+ }
+
+ return score/(numSeq1*numSeq2);
+}
+
+int
+Globaldp::
+returnBasePairType(char s, char r)
+{
+ if (s == 'A') {
+ if (r == 'A') return 0;
+ else if (r == 'C') return 1;
+ else if (r == 'G') return 2;
+ else if (r == 'U') return 3;
+ }
+ else if (s == 'C') {
+ if (r == 'A') return 4;
+ else if (r == 'C') return 5;
+ else if (r == 'G') return 6;
+ else if (r == 'U') return 7;
+ }
+ else if (s == 'G') {
+ if (r == 'A') return 8;
+ else if (r == 'C') return 9;
+ else if (r == 'G') return 10;
+ else if (r == 'U') return 11;
+ }
+ else if (s == 'U') {
+ if (r == 'A') return 12;
+ else if (r == 'C') return 13;
+ else if (r == 'G') return 14;
+ else if (r == 'U') return 15;
+ }
+
+ return 16;
+}
+
+float
+Globaldp::
+probabilityScore(const StemCandidate &sc1, const StemCandidate &sc2)
+{
+ return sc1.GetScore() + sc2.GetScore();
+}
+
+float
+Globaldp::
+stackingScore(const StemCandidate &sc1, const StemCandidate &sc2)
+{
+ return - (sc1.GetStemStacking() + sc2.GetStemStacking());
+}
+
+float
+Globaldp::
+distancePenalty(const StemCandidate &sc1, const StemCandidate &sc2)
+{
+ return std::sqrt((float)std::abs(sc1.GetDistance() - sc2.GetDistance()));
+}
+
+float
+Globaldp::
+Run()
+{
+ Initialize();
+ DP();
+ float score = traceBack();
+
+ // printMatch();
+ //cout << "score=" << score << endl;
+ return score;
+}
+
+void
+Globaldp::
+Initialize()
+{
+ int nPscs1 = pscs1->size();
+ int nPscs2 = pscs2->size();
+
+
+ for(int i = 0; i < nPscs1; i++) {
+ for(int j = 0; j < nPscs2; j++) {
+ VM[i][j] = 0;
+ VG[i][j] = 0;
+ }
+ }
+
+ VM[0][0] = 0;
+ VG[0][0] = IMPOSSIBLE;
+
+ for (int i = 1; i < nPscs1; i++) {
+ VM[i][0] = IMPOSSIBLE; VG[i][0] = 0;
+ }
+ for (int j = 1; j < nPscs2; j++) {
+ VM[0][j] = IMPOSSIBLE; VG[0][j] = 0;
+ }
+
+ for (int i = 0; i < nPscs1; i++) {
+ for (int j = 0; j < nPscs2; j++) {
+ traceMI[i][j] = 0; traceMJ[i][j] = 0;
+ traceGI[i][j] = 0; traceGJ[i][j] = 0;
+ }
+ }
+
+ int wordLength = WORDLENGTH;
+ int size1 = pscs1->size();
+ int size2 = pscs2->size();
+
+ for(int i = 0; i < wordLength; i++) {
+ for(int j = 0; j < 17; j++) {
+ for(int k = 0; k < (int)pscs1->size(); k++) {
+ countConp1[i][j][k] = 0;
+ }
+ }
+ }
+ for(int i = 0; i < wordLength; i++) {
+ for(int j = 0; j < 17; j++) {
+ for(int k = 0; k < (int)pscs2->size(); k++) {
+ countConp2[i][j][k] = 0;
+ }
+ }
+ }
+ for(int i = 0; i < 17; i++) {
+ for(int j = 0; j < (int)pscs1->size()+1; j++) {
+ countContConp1[i][j] = 0;
+ }
+ }
+ for(int i = 0; i < 17; i++) {
+ for(int j = 0; j < (int)pscs2->size()+1; j++) {
+ countContConp2[i][j] = 0;
+ }
+ }
+
+ for(int iter = 1; iter < size1; iter++) {
+
+ const StemCandidate &sc1 = pscs1->at(iter);
+ int numSeq1 = sc1.GetNumSeq();
+ for (int i = 0; i < wordLength; i++) {
+
+ for(int k = 0; k < numSeq1; k++) {
+// const Sequence *seq = seqs1->GetSequence(k);
+ string substr = sc1.GetSubstr(k);
+ string rvstr = sc1.GetRvstr(k);
+
+ char sChar = substr[i];
+ char rChar = rvstr[wordLength - 1 -i];
+
+ int type = returnBasePairType(sChar, rChar);
+ ++countConp1[i][type][iter];
+ }
+ }
+ for(int k = 0; k < numSeq1; k++) {
+// const Sequence *seq = seqs1->GetSequence(k);
+ string substr = sc1.GetSubstr(k);
+ string rvstr = sc1.GetRvstr(k);
+
+ char sChar = substr[wordLength-1];
+ char rChar = rvstr[0];
+
+ int type = returnBasePairType(sChar, rChar);
+ ++countContConp1[type][iter];
+
+ }
+ }
+ for(int iter = 1; iter < size2; iter++) {
+ const StemCandidate &sc2 = pscs2->at(iter);
+ int numSeq2 = sc2.GetNumSeq();
+ for (int i = 0; i < wordLength; i++) {
+
+ for(int k = 0; k < numSeq2; k++) {
+// const Sequence *seq = seqs2->GetSequence(k);
+ string substr = sc2.GetSubstr(k);
+ string rvstr = sc2.GetRvstr(k);
+
+ char sChar = substr[i];
+ char rChar = rvstr[wordLength - 1 -i];
+
+ int type = returnBasePairType(sChar, rChar);
+ ++countConp2[i][type][iter];
+ }
+ }
+ for(int k = 0; k < numSeq2; k++) {
+// const Sequence *seq = seqs2->GetSequence(k);
+ string substr = sc2.GetSubstr(k);
+ string rvstr = sc2.GetRvstr(k);
+
+ char sChar = substr[wordLength-1];
+ char rChar = rvstr[0];
+
+ int type = returnBasePairType(sChar, rChar);
+ ++countContConp2[type][iter];
+
+ }
+ }
+ profileBPPMat1 = makeProfileBPPMatrix(seqs1);
+ profileBPPMat2 = makeProfileBPPMatrix(seqs2);
+}
+
+void
+Globaldp::
+DP()
+{
+ int nPscs1 = pscs1->size();
+ int nPscs2 = pscs2->size();
+
+ for(int i = 1; i < nPscs1; i++) {
+ const StemCandidate &sc1 = pscs1->at(i);
+
+ for(int j = 1; j < nPscs2; j++) {
+ const StemCandidate &sc2 = pscs2->at(j);
+
+ float max = IMPOSSIBLE;
+ int traceI = 0;
+ int traceJ = 0;
+ int alpha = sc1.GetContPos(), beta = sc2.GetContPos();
+ if( (alpha > 0) && (beta > 0) ) {
+ max = VM[alpha][beta] + incrementalScorePSCPair(sc1, sc2);
+ traceI = alpha;
+ traceJ = beta;
+ }
+
+ float similarity = scorePSCPair(sc1, sc2);
+ int p = sc1.GetBeforePos(), q = sc2.GetBeforePos();
+ float tmpScore = VM[p][q] + similarity;
+// cout << i << " " << j << " " << p << " " << q << " " << tmpScore << " " << VM[p][q] << " " << similarity << " " << endl;
+
+ if(max <= tmpScore) {
+ max = tmpScore;
+ traceI = p;
+ traceJ = q;
+ }
+
+ tmpScore = VG[p][q] + similarity;
+ if(max <= tmpScore) {
+ max = tmpScore;
+ traceI = traceGI[p][q];
+ traceJ = traceGJ[p][q];
+ }
+
+ VM[i][j] = max;
+ traceMI[i][j] = traceI;
+ traceMJ[i][j] = traceJ;
+
+ max = VM[i][j-1];
+ traceI = i;
+ traceJ = j-1;
+
+ tmpScore = VM[i-1][j];
+ if(max <= tmpScore) {
+ max = tmpScore;
+ traceI = i-1;
+ traceJ = j;
+ }
+
+ tmpScore = VG[i-1][j];
+ if(max <= tmpScore) {
+ max = tmpScore;
+ traceI = traceGI[i-1][j];
+ traceJ = traceGJ[i-1][j];
+ }
+
+ tmpScore = VG[i][j-1];
+ if(max <= tmpScore) {
+ max = tmpScore;
+ traceI = traceGI[i][j-1];
+ traceJ = traceGJ[i][j-1];
+ }
+
+ VG[i][j] = max;
+ traceGI[i][j] = traceI;
+ traceGJ[i][j] = traceJ;
+ }
+ }
+}
+
+float
+Globaldp::
+traceBack()
+{
+ int nPscs1 = pscs1->size();
+ int nPscs2 = pscs2->size();
+
+ float max = IMPOSSIBLE;
+ int traceI, traceJ;
+ for (int i = 1; i < nPscs1; i++) {
+ for (int j = 1; j < nPscs2; j++) {
+ if(max < VM[i][j]) {
+ max = VM[i][j];
+ traceI = i;
+ traceJ = j;
+ }
+ }
+ }
+
+ while ( (traceI != 0) && (traceJ != 0) ) {
+ matchPSCS1->push_back(traceI); matchPSCS2->push_back(traceJ);
+ int tmpI = traceMI[traceI][traceJ];
+ int tmpJ = traceMJ[traceI][traceJ];
+ traceI = tmpI; traceJ = tmpJ;
+ }
+
+ if(traceI != 0 && traceJ != 0) {
+ std::cout << "error in trace back of pscs:" << traceI << " " << traceJ << endl;
+ }
+
+ return max;
+}
+
+void
+Globaldp::
+printMatch()
+{
+ int size = matchPSCS1->size();
+ for(int iter = 0; iter < size; iter++) {
+ int i = matchPSCS1->at(iter);
+ int j = matchPSCS2->at(iter);
+
+ const StemCandidate &sc1 = pscs1->at(i);
+ const StemCandidate &sc2 = pscs2->at(j);
+
+ std::cout << iter << "\t" << sc1.GetPosition() << "\t" << sc1.GetRvposition() << "\t" << sc2.GetPosition() << "\t" << sc2.GetRvposition() << endl;
+ }
+
+}
+}
--- /dev/null
+////////////////////////////////////////////////////////////////
+// Globaldp.hpp
+// Global Alignment of two profile computed by SCARNA algorithm
+////////////////////////////////////////////////////////////////
+
+
+#ifndef __GLOBALDP_HPP__
+#define __GLOBALDP_HPP__
+
+#include <string>
+#include <iostream>
+#include "nrutil.h"
+#include "Util.hpp"
+#include "Beta.hpp"
+#include "scarna.hpp"
+#include "StemCandidate.hpp"
+#include "MultiSequence.h"
+#include "Sequence.h"
+#include "BPPMatrix.hpp"
+
+using namespace ProbCons;
+using namespace std;
+namespace MXSCARNA {
+
+typedef std::vector<StemCandidate> stemcandidate;
+class Globaldp {
+private:
+ static double ribosum_matrix[16][16];
+
+ NRMat<float> VM, VG;
+ NRMat<int> traceMI, traceMJ, traceGI, traceGJ;
+
+ const stemcandidate *pscs1, *pscs2;
+ const MultiSequence *seqs1, *seqs2;
+ std::vector<int> *matchPSCS1, *matchPSCS2;
+ SafeVector<BPPMatrix*> &BPPMatrices;
+ NRMat<float> posterior;
+ NRMat3d<int> countConp1, countConp2;
+ NRMat<int> countContConp1, countContConp2;
+ Trimat<float> *profileBPPMat1;
+ Trimat<float> *profileBPPMat2;
+ float multiDeltaScore;
+ float multiDeltaStacking;
+ float multiScore;
+ float multiStacking;
+ float multiPenalty;
+
+ float scorePSCPair(const StemCandidate &sc1, const StemCandidate &sc2);
+ float wordSimilarity(const StemCandidate &sc1, const StemCandidate &sc2, int i, int j);
+ int returnBasePairType(char s, char r);
+ float probabilityScore(const StemCandidate &sc1, const StemCandidate &sc2);
+ float stackingScore(const StemCandidate &sc1, const StemCandidate &sc2);
+ float distancePenalty(const StemCandidate &sc1, const StemCandidate &sc2);
+ float incrementalScorePSCPair(const StemCandidate &sc1, const StemCandidate &sc2);
+ float incrementalProbabilityScore(const StemCandidate &sc1, const StemCandidate &sc2);
+ float incrementalStackingScore(const StemCandidate &sc1, const StemCandidate &sc2);
+ float incrementalWordSimilarity(const StemCandidate &sc1, const StemCandidate &sc2, int i, int j);
+ Trimat<float>* makeProfileBPPMatrix(const MultiSequence *Sequences);
+
+ void Initialize();
+ void DP();
+ float traceBack();
+ void printMatch();
+public:
+
+ Globaldp(const stemcandidate *mypscs1, const stemcandidate *mypscs2,
+ const MultiSequence *myseqs1, const MultiSequence *myseqs2,
+ std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2,
+ VF *myPosterior, SafeVector<BPPMatrix*> &myBPPMatrices,
+ float myMultiDeltaScore = MULTIDELTASCORE, float myMultiDeltaStacking = MULTIDELTASTACKING,
+ float myMultiScore = MULTISCORE, float myMultiStacking = MULTISTACKING,
+ float myMultiPenalty = MULTIPENALTY)
+ : VM(mypscs1->size(), mypscs2->size()),
+ VG(mypscs1->size(), mypscs2->size()),
+ traceMI(mypscs1->size(), mypscs2->size()),
+ traceMJ(mypscs1->size(), mypscs2->size()),
+ traceGI(mypscs1->size(), mypscs2->size()),
+ traceGJ(mypscs1->size(), mypscs2->size()),
+ pscs1(mypscs1), pscs2(mypscs2),
+ seqs1(myseqs1), seqs2(myseqs2),
+ matchPSCS1(matchPSCS1), matchPSCS2(matchPSCS2),
+ BPPMatrices(myBPPMatrices), posterior(myseqs1->GetSequence(0)->GetLength() + 1, myseqs2->GetSequence(0)->GetLength() + 1),
+ countConp1(WORDLENGTH, 17, mypscs1->size()+1), countConp2(WORDLENGTH, 17, mypscs2->size()+1),
+ countContConp1(0, 17, mypscs1->size()+1), countContConp2(0, 17, mypscs2->size()+1),
+ multiDeltaScore(myMultiDeltaScore), multiDeltaStacking(myMultiDeltaStacking),
+ multiScore(myMultiScore), multiStacking(myMultiStacking),
+ multiPenalty(myMultiPenalty) {
+
+ VF::iterator myPosteriorPtr = myPosterior->begin();
+ for (int i = 0; i <= seqs1->GetSequence(0)->GetLength(); i++) {
+ for (int j = 0; j <= seqs2->GetSequence(0)->GetLength(); j++) {
+ posterior[i][j] = (*myPosteriorPtr)/(seqs1->GetSequence(0)->GetLength()*seqs2->GetSequence(0)->GetLength());
+ myPosteriorPtr++;
+ }
+ }
+ }
+
+
+
+ float Run();
+
+ void setMultiDeltaScore(float score) { multiDeltaScore = score; }
+ void setMultiDeltaStacking(float score) { multiDeltaStacking = score; }
+ void setMultiScore(float score) { multiScore = score; }
+ void setMultiStacking(float score) { multiStacking = score; }
+ void setMultiPenalty(float score) { multiPenalty = score; }
+};
+}
+#endif // __GLOBALDP_HPP__
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// Main.cc
+//
+// Main routines for MXSCARNA program.
+/////////////////////////////////////////////////////////////////
+
+#include "scarna.hpp"
+#include "SafeVector.h"
+#include "MultiSequence.h"
+#include "Defaults.h"
+#include "ScoreType.h"
+#include "ProbabilisticModel.h"
+#include "EvolutionaryTree.h"
+#include "SparseMatrix.h"
+#include "BPPMatrix.hpp"
+#include "StemCandidate.hpp"
+#include "Globaldp.hpp"
+#include "nrutil.h"
+#include "AlifoldMEA.h"
+#include <string>
+#include <sstream>
+#include <iomanip>
+#include <iostream>
+#include <list>
+#include <set>
+#include <algorithm>
+#include <cstdio>
+#include <cstdlib>
+#include <cerrno>
+#include <iomanip>
+#include <fstream>
+
+//#include "RfoldWrapper.hpp"
+//static RFOLD::Rfold folder;
+
+using namespace::MXSCARNA;
+
+string parametersInputFilename = "";
+string parametersOutputFilename = "no training";
+string annotationFilename = "";
+string weboutputFileName = "";
+
+ofstream *outputFile;
+
+bool enableTraining = false;
+bool enableVerbose = false;
+bool enableAllPairs = false;
+bool enableAnnotation = false;
+bool enableViterbi = false;
+bool enableClustalWOutput = false;
+bool enableTrainEmissions = false;
+bool enableAlignOrder = false;
+bool enableWebOutput = false;
+bool enableStockholmOutput = false;
+bool enableMXSCARNAOutput = false;
+bool enableMcCaskillMEAMode = false;
+char bppmode = 's'; // by katoh
+int numConsistencyReps = 2;
+int numPreTrainingReps = 0;
+int numIterativeRefinementReps = 100;
+int scsLength = SCSLENGTH;
+float cutoff = 0;
+float gapOpenPenalty = 0;
+float gapContinuePenalty = 0;
+float threshhold = 1.0;
+float BaseProbThreshold = BASEPROBTHRESHOLD;
+float BasePairConst = BASEPAIRCONST;
+int BandWidth = BANDWIDTH;
+
+SafeVector<string> sequenceNames;
+
+VF initDistrib (NumMatrixTypes);
+VF gapOpen (2*NumInsertStates);
+VF gapExtend (2*NumInsertStates);
+VVF emitPairs (256, VF (256, 1e-10));
+VF emitSingle (256, 1e-5);
+
+string alphabet = alphabetDefault;
+
+string *ssCons = NULL;
+
+const int MIN_PRETRAINING_REPS = 0;
+const int MAX_PRETRAINING_REPS = 20;
+const int MIN_CONSISTENCY_REPS = 0;
+const int MAX_CONSISTENCY_REPS = 5;
+const int MIN_ITERATIVE_REFINEMENT_REPS = 0;
+const int MAX_ITERATIVE_REFINEMENT_REPS = 1000;
+
+/////////////////////////////////////////////////////////////////
+// Function prototypes
+/////////////////////////////////////////////////////////////////
+
+void PrintHeading();
+void PrintParameters (const char *message, const VF &initDistrib, const VF &gapOpen,
+ const VF &gapExtend, const VVF &emitPairs, const VF &emitSingle, const char *filename);
+MultiSequence *DoAlign (MultiSequence *sequence, const ProbabilisticModel &model, VF &initDistrib, VF &gapOpen, VF &gapExtend, VVF &emitPairs, VF &emitSingle);
+SafeVector<string> ParseParams (int argc, char **argv);
+void ReadParameters ();
+MultiSequence *ComputeFinalAlignment (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model,
+ SafeVector<BPPMatrix*> &BPPMatrices);
+MultiSequence *AlignAlignments (MultiSequence *align1, MultiSequence *align2,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, SafeVector<BPPMatrix*> &BPPMatrices, float identity);
+SafeVector<SafeVector<SparseMatrix *> > DoRelaxation (MultiSequence *sequences,
+ SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+void Relax (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior);
+void Relax1 (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior);
+void DoBasePairProbabilityRelaxation (MultiSequence *sequences,
+ SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ SafeVector<BPPMatrix*> &BPPMatrices);
+set<int> GetSubtree (const TreeNode *tree);
+void TreeBasedBiPartitioning (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment,
+ const TreeNode *tree, SafeVector<BPPMatrix*> &BPPMatrices);
+void DoIterativeRefinement (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment);
+void WriteAnnotation (MultiSequence *alignment,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+int ComputeScore (const SafeVector<pair<int, int> > &active,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+std::vector<StemCandidate>* seq2scs(MultiSequence *Sequences, SafeVector<BPPMatrix*> &BPPMatrices, int BandWidth);
+void removeConflicts(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2, std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2);
+
+struct prob {
+ int i;
+ int j;
+ float p;
+};
+
+/////////////////////////////////////////////////////////////////
+// main()
+//
+// Calls all initialization routines and runs the MXSCARNA
+// aligner.
+/////////////////////////////////////////////////////////////////
+
+
+int main (int argc, char **argv){
+
+ // print MXSCARNA heading
+ PrintHeading();
+
+ // parse program parameters
+ sequenceNames = ParseParams (argc, argv);
+ ReadParameters();
+ PrintParameters ("Using parameter set:", initDistrib, gapOpen, gapExtend, emitPairs, emitSingle, NULL);
+
+ // now, we'll process all the files given as input. If we are given
+ // several filenames as input, then we'll load all of those sequences
+ // simultaneously, as long as we're not training. On the other hand,
+ // if we are training, then we'll treat each file as a separate
+ // training instance
+
+ if (enableMcCaskillMEAMode) {
+ MultiSequence *sequences = new MultiSequence(); assert (sequences);
+ for (int i = 0; i < (int) sequenceNames.size(); i++){
+ cerr << "Loading sequence file: " << sequenceNames[i] << endl;
+ sequences->LoadMFA (sequenceNames[i], true);
+ }
+
+ const int numSeqs = sequences->GetNumSequences();
+ SafeVector<BPPMatrix*> BPPMatrices;
+
+ // compute the base pairing matrices for each sequences
+ for(int i = 0; i < numSeqs; i++) {
+ Sequence *tmpSeq = sequences->GetSequence(i);
+ string seq = tmpSeq->GetString();
+ int n_seq = tmpSeq->GetLength();
+ BPPMatrix *bppmat = new BPPMatrix(bppmode, seq, n_seq); // modified by katoh
+ BPPMatrices.push_back(bppmat);
+ }
+ if (bppmode=='w') exit( 0 );
+
+ AlifoldMEA alifold(sequences, BPPMatrices, BasePairConst);
+ alifold.Run();
+ ssCons = alifold.getSScons();
+
+ if (enableStockholmOutput) {
+ sequences->WriteSTOCKHOLM (cout, ssCons);
+ }
+ else if (enableMXSCARNAOutput){
+ sequences->WriteMXSCARNA (cout, ssCons);
+ }
+ else {
+ sequences->WriteMFA (cout, ssCons);
+ }
+
+ delete sequences;
+ }
+ // if we are training
+ else if (enableTraining){
+
+ // build new model for aligning
+ ProbabilisticModel model (initDistrib, gapOpen, gapExtend, emitPairs, emitSingle);
+
+ // prepare to average parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] = 0;
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] = 0;
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] = 0;
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] = 0;
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] = 0;
+ }
+
+ // align each file individually
+ for (int i = 0; i < (int) sequenceNames.size(); i++){
+
+ VF thisInitDistrib (NumMatrixTypes);
+ VF thisGapOpen (2*NumInsertStates);
+ VF thisGapExtend (2*NumInsertStates);
+ VVF thisEmitPairs (256, VF (256, 1e-10));
+ VF thisEmitSingle (256, 1e-5);
+
+ // load sequence file
+ MultiSequence *sequences = new MultiSequence(); assert (sequences);
+ cerr << "Loading sequence file: " << sequenceNames[i] << endl;
+ sequences->LoadMFA (sequenceNames[i], true);
+
+ // align sequences
+ DoAlign (sequences, model, thisInitDistrib, thisGapOpen, thisGapExtend, thisEmitPairs, thisEmitSingle);
+
+ // add in contribution of the derived parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] += thisInitDistrib[i];
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] += thisGapOpen[i];
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] += thisGapExtend[i];
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] += thisEmitPairs[i][j];
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] += thisEmitSingle[i];
+ }
+
+ delete sequences;
+ }
+
+ // compute new parameters and print them out
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] /= (int) sequenceNames.size();
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] /= (int) sequenceNames.size();
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] /= (int) sequenceNames.size();
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] /= (int) sequenceNames.size();
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] /= sequenceNames.size();
+ }
+
+ PrintParameters ("Trained parameter set:",
+ initDistrib, gapOpen, gapExtend, emitPairs, emitSingle,
+ parametersOutputFilename.c_str());
+ }
+ // pass
+ // if we are not training, we must simply want to align some sequences
+ else {
+ // load all files together
+ MultiSequence *sequences = new MultiSequence(); assert (sequences);
+ for (int i = 0; i < (int) sequenceNames.size(); i++){
+ cerr << "Loading sequence file: " << sequenceNames[i] << endl;
+
+ sequences->LoadMFA (sequenceNames[i], true);
+ }
+
+ // do all "pre-training" repetitions first
+ // NOT execute
+ for (int ct = 0; ct < numPreTrainingReps; ct++){
+ enableTraining = true;
+
+ // build new model for aligning
+ ProbabilisticModel model (initDistrib, gapOpen, gapExtend,
+ emitPairs, emitSingle);
+
+ // do initial alignments
+ DoAlign (sequences, model, initDistrib, gapOpen, gapExtend, emitPairs, emitSingle);
+
+ // print new parameters
+ PrintParameters ("Recomputed parameter set:", initDistrib, gapOpen, gapExtend, emitPairs, emitSingle, NULL);
+
+ enableTraining = false;
+ }
+
+ // now, we can perform the alignments and write them out
+ if (enableWebOutput) {
+ outputFile = new ofstream(weboutputFileName.c_str());
+ if (!outputFile) {
+ cerr << "cannot open output file." << weboutputFileName << endl;
+ exit(1);
+ }
+ *outputFile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << endl;
+ *outputFile << "<result>" << endl;
+ }
+ MultiSequence *alignment = DoAlign (sequences,
+ ProbabilisticModel (initDistrib, gapOpen, gapExtend, emitPairs, emitSingle),
+ initDistrib, gapOpen, gapExtend, emitPairs, emitSingle);
+
+
+ if (!enableAllPairs){
+ if (enableClustalWOutput) {
+ alignment->WriteALN (cout);
+ }
+ else if (enableWebOutput) {
+ alignment->WriteWEB (*outputFile, ssCons);
+// computeStructureWithAlifold ();
+ }
+ else if (enableStockholmOutput) {
+ alignment->WriteSTOCKHOLM (cout, ssCons);
+ }
+ else if (enableMXSCARNAOutput) {
+ alignment->WriteMXSCARNA (cout, ssCons);
+ }
+ else {
+ alignment->WriteMFA (cout, ssCons);
+ }
+ }
+
+ if (enableWebOutput) {
+ *outputFile << "</result>" << endl;
+ delete outputFile;
+ }
+
+ delete ssCons;
+ delete alignment;
+ delete sequences;
+
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// PrintHeading()
+//
+// Prints heading for PROBCONS program.
+/////////////////////////////////////////////////////////////////
+
+void PrintHeading (){
+ cerr << endl
+ << "Multiplex SCARNA"<< endl
+ << "version " << VERSION << " - align multiple RNA sequences and print to standard output" << endl
+ << "Written by Yasuo Tabei" << endl
+ << endl;
+}
+
+/////////////////////////////////////////////////////////////////
+// PrintParameters()
+//
+// Prints PROBCONS parameters to STDERR. If a filename is
+// specified, then the parameters are also written to the file.
+/////////////////////////////////////////////////////////////////
+
+void PrintParameters (const char *message, const VF &initDistrib, const VF &gapOpen,
+ const VF &gapExtend, const VVF &emitPairs, const VF &emitSingle, const char *filename){
+
+ // print parameters to the screen
+ cerr << message << endl
+ << " initDistrib[] = { ";
+ for (int i = 0; i < NumMatrixTypes; i++) cerr << setprecision (10) << initDistrib[i] << " ";
+ cerr << "}" << endl
+ << " gapOpen[] = { ";
+ for (int i = 0; i < NumInsertStates*2; i++) cerr << setprecision (10) << gapOpen[i] << " ";
+ cerr << "}" << endl
+ << " gapExtend[] = { ";
+ for (int i = 0; i < NumInsertStates*2; i++) cerr << setprecision (10) << gapExtend[i] << " ";
+ cerr << "}" << endl
+ << endl;
+
+ /*
+ for (int i = 0; i < 5; i++){
+ for (int j = 0; j <= i; j++){
+ cerr << emitPairs[(unsigned char) alphabet[i]][(unsigned char) alphabet[j]] << " ";
+ }
+ cerr << endl;
+ }*/
+
+ // if a file name is specified
+ if (filename){
+
+ // attempt to open the file for writing
+ FILE *file = fopen (filename, "w");
+ if (!file){
+ cerr << "ERROR: Unable to write parameter file: " << filename << endl;
+ exit (1);
+ }
+
+ // if successful, then write the parameters to the file
+ for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n");
+ for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n");
+ for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n");
+ fprintf (file, "%s\n", alphabet.c_str());
+ for (int i = 0; i < (int) alphabet.size(); i++){
+ for (int j = 0; j <= i; j++)
+ fprintf (file, "%.10f ", emitPairs[(unsigned char) alphabet[i]][(unsigned char) alphabet[j]]);
+ fprintf (file, "\n");
+ }
+ for (int i = 0; i < (int) alphabet.size(); i++)
+ fprintf (file, "%.10f ", emitSingle[(unsigned char) alphabet[i]]);
+ fprintf (file, "\n");
+ fclose (file);
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// DoAlign()
+//
+// First computes all pairwise posterior probability matrices.
+// Then, computes new parameters if training, or a final
+// alignment, otherwise.
+/////////////////////////////////////////////////////////////////
+MultiSequence *DoAlign (MultiSequence *sequences, const ProbabilisticModel &model, VF &initDistrib, VF &gapOpen, VF &gapExtend, VVF &emitPairs, VF &emitSingle){
+
+
+ assert (sequences);
+
+ const int numSeqs = sequences->GetNumSequences();
+ VVF distances (numSeqs, VF (numSeqs, 0));
+ VVF identities (numSeqs, VF (numSeqs, 0));
+ SafeVector<SafeVector<SparseMatrix *> > sparseMatrices (numSeqs, SafeVector<SparseMatrix *>(numSeqs, NULL));
+
+ SafeVector<BPPMatrix*> BPPMatrices;
+
+ for(int i = 0; i < numSeqs; i++) {
+ Sequence *tmpSeq = sequences->GetSequence(i);
+ string seq = tmpSeq->GetString();
+ int n_seq = tmpSeq->GetLength();
+ BPPMatrix *bppmat = new BPPMatrix(bppmode, seq, n_seq, BASEPROBTHRESHOLD); // modified by katoh
+ BPPMatrices.push_back(bppmat);
+ }
+
+ if (enableTraining){
+ // prepare to average parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] = 0;
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] = 0;
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] = 0;
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] = 0;
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] = 0;
+ }
+ }
+
+ // skip posterior calculations if we just want to do Viterbi alignments
+ if (!enableViterbi){
+
+ // do all pairwise alignments for posterior probability matrices
+ for (int a = 0; a < numSeqs-1; a++){
+ for (int b = a+1; b < numSeqs; b++){
+ Sequence *seq1 = sequences->GetSequence (a);
+ Sequence *seq2 = sequences->GetSequence (b);
+
+ // verbose output
+ if (enableVerbose)
+ cerr << "Computing posterior matrix: (" << a+1 << ") " << seq1->GetHeader() << " vs. "
+ << "(" << b+1 << ") " << seq2->GetHeader() << " -- ";
+
+ // compute forward and backward probabilities
+ VF *forward = model.ComputeForwardMatrix (seq1, seq2); assert (forward);
+ VF *backward = model.ComputeBackwardMatrix (seq1, seq2); assert (backward);
+
+ // if we are training, then we'll simply want to compute the
+ // expected counts for each region within the matrix separately;
+ // otherwise, we'll need to put all of the regions together and
+ // assemble a posterior probability match matrix
+
+ // so, if we're training
+ if (enableTraining){
+
+ // compute new parameters
+ VF thisInitDistrib (NumMatrixTypes);
+ VF thisGapOpen (2*NumInsertStates);
+ VF thisGapExtend (2*NumInsertStates);
+ VVF thisEmitPairs (256, VF (256, 1e-10));
+ VF thisEmitSingle (256, 1e-5);
+
+ model.ComputeNewParameters (seq1, seq2, *forward, *backward, thisInitDistrib, thisGapOpen, thisGapExtend, thisEmitPairs, thisEmitSingle, enableTrainEmissions);
+
+ // add in contribution of the derived parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] += thisInitDistrib[i];
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] += thisGapOpen[i];
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] += thisGapExtend[i];
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] += thisEmitPairs[i][j];
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] += thisEmitSingle[i];
+ }
+
+ // let us know that we're done.
+ if (enableVerbose) cerr << "done." << endl;
+ }
+ // pass
+ else {
+
+ // compute posterior probability matrix
+ VF *posterior = model.ComputePosteriorMatrix (seq1, seq2, *forward, *backward); assert (posterior);
+
+ // compute sparse representations
+ sparseMatrices[a][b] = new SparseMatrix (seq1->GetLength(), seq2->GetLength(), *posterior);
+ sparseMatrices[b][a] = NULL;
+
+ if (!enableAllPairs){
+ // perform the pairwise sequence alignment
+ pair<SafeVector<char> *, float> alignment = model.ComputeAlignment (seq1->GetLength(),
+ seq2->GetLength(),
+ *posterior);
+
+ Sequence *tmpSeq1 = seq1->AddGaps (alignment.first, 'X');
+ Sequence *tmpSeq2 = seq2->AddGaps (alignment.first, 'Y');
+
+ // compute sequence identity for each pair of sequenceses
+ int length = tmpSeq1->GetLength();
+ int matchCount = 0;
+ int misMatchCount = 0;
+ for (int k = 1; k <= length; k++) {
+ int ch1 = tmpSeq1->GetPosition(k);
+ int ch2 = tmpSeq2->GetPosition(k);
+ if (ch1 == ch2 && ch1 != '-' && ch2 != '-') { ++matchCount; }
+ else if (ch1 != ch2 && ch1 != '-' && ch2 != '-') { ++misMatchCount; }
+ }
+
+ identities[a][b] = identities[b][a] = (float)matchCount/(float)(matchCount + misMatchCount);
+
+ // compute "expected accuracy" distance for evolutionary tree computation
+ float distance = alignment.second / min (seq1->GetLength(), seq2->GetLength());
+ distances[a][b] = distances[b][a] = distance;
+
+ if (enableVerbose)
+ cerr << setprecision (10) << distance << endl;
+
+ delete alignment.first;
+ }
+ else {
+ // let us know that we're done.
+ if (enableVerbose) cerr << "done." << endl;
+ }
+
+ delete posterior;
+ }
+
+ delete forward;
+ delete backward;
+ }
+ }
+ }
+
+
+ // now average out parameters derived
+ if (enableTraining){
+ // compute new parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] /= numSeqs * (numSeqs - 1) / 2;
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] /= numSeqs * (numSeqs - 1) / 2;
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] /= numSeqs * (numSeqs - 1) / 2;
+
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] /= numSeqs * (numSeqs - 1) / 2;
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] /= numSeqs * (numSeqs - 1) / 2;
+ }
+ }
+
+ // see if we still want to do some alignments
+ else {
+ // pass
+ if (!enableViterbi){
+
+ // perform the consistency transformation the desired number of times
+ for (int r = 0; r < numConsistencyReps; r++){
+ SafeVector<SafeVector<SparseMatrix *> > newSparseMatrices = DoRelaxation (sequences, sparseMatrices);
+
+ // now replace the old posterior matrices
+ for (int i = 0; i < numSeqs; i++){
+ for (int j = 0; j < numSeqs; j++){
+ delete sparseMatrices[i][j];
+ sparseMatrices[i][j] = newSparseMatrices[i][j];
+ }
+ }
+ }
+ //if (numSeqs > 8) {
+ // for (int r = 0; r < 1; r++)
+ // DoBasePairProbabilityRelaxation(sequences, sparseMatrices, BPPMatrices);
+ //}
+ }
+
+ MultiSequence *finalAlignment = NULL;
+
+ if (enableAllPairs){
+ for (int a = 0; a < numSeqs-1; a++){
+ for (int b = a+1; b < numSeqs; b++){
+ Sequence *seq1 = sequences->GetSequence (a);
+ Sequence *seq2 = sequences->GetSequence (b);
+
+ if (enableVerbose)
+ cerr << "Performing pairwise alignment: (" << a+1 << ") " << seq1->GetHeader() << " vs. "
+ << "(" << b+1 << ") " << seq2->GetHeader() << " -- ";
+
+
+ // perform the pairwise sequence alignment
+ pair<SafeVector<char> *, float> alignment;
+ if (enableViterbi)
+ alignment = model.ComputeViterbiAlignment (seq1, seq2);
+ else {
+
+ // build posterior matrix
+ VF *posterior = sparseMatrices[a][b]->GetPosterior(); assert (posterior);
+ int length = (seq1->GetLength() + 1) * (seq2->GetLength() + 1);
+ for (int i = 0; i < length; i++) (*posterior)[i] -= cutoff;
+
+ alignment = model.ComputeAlignment (seq1->GetLength(), seq2->GetLength(), *posterior);
+ delete posterior;
+ }
+
+
+ // write pairwise alignments
+ string name = seq1->GetHeader() + "-" + seq2->GetHeader() + (enableClustalWOutput ? ".aln" : ".fasta");
+ ofstream outfile (name.c_str());
+
+ MultiSequence *result = new MultiSequence();
+ result->AddSequence (seq1->AddGaps(alignment.first, 'X'));
+ result->AddSequence (seq2->AddGaps(alignment.first, 'Y'));
+ result->WriteMFAseq (outfile); // by katoh
+
+ outfile.close();
+
+ delete alignment.first;
+ }
+ }
+ exit( 0 );
+ }
+
+ // now if we still need to do a final multiple alignment
+ else {
+
+ if (enableVerbose)
+ cerr << endl;
+
+ // compute the evolutionary tree
+ TreeNode *tree = TreeNode::ComputeTree (distances, identities);
+
+ if (enableWebOutput) {
+ *outputFile << "<tree>" << endl;
+ tree->Print (*outputFile, sequences);
+ *outputFile << "</tree>" << endl;
+ }
+ else {
+ tree->Print (cerr, sequences);
+ cerr << endl;
+ }
+ // make the final alignment
+ finalAlignment = ComputeFinalAlignment (tree, sequences, sparseMatrices, model, BPPMatrices);
+
+ // build annotation
+ if (enableAnnotation){
+ WriteAnnotation (finalAlignment, sparseMatrices);
+ }
+
+ delete tree;
+ }
+
+ if (!enableViterbi){
+ // delete sparse matrices
+ for (int a = 0; a < numSeqs-1; a++){
+ for (int b = a+1; b < numSeqs; b++){
+ delete sparseMatrices[a][b];
+ delete sparseMatrices[b][a];
+ }
+ }
+ }
+
+ //AlifoldMEA alifold(finalAlignment, BPPMatrices, BasePairConst);
+ //alifold.Run();
+ //ssCons = alifold.getSScons();
+
+ return finalAlignment;
+
+ }
+
+ return NULL;
+}
+
+/////////////////////////////////////////////////////////////////
+// GetInteger()
+//
+// Attempts to parse an integer from the character string given.
+// Returns true only if no parsing error occurs.
+/////////////////////////////////////////////////////////////////
+
+bool GetInteger (char *data, int *val){
+ char *endPtr;
+ long int retVal;
+
+ assert (val);
+
+ errno = 0;
+ retVal = strtol (data, &endPtr, 0);
+ if (retVal == 0 && (errno != 0 || data == endPtr)) return false;
+ if (errno != 0 && (retVal == LONG_MAX || retVal == LONG_MIN)) return false;
+ if (retVal < (long) INT_MIN || retVal > (long) INT_MAX) return false;
+ *val = (int) retVal;
+ return true;
+}
+
+/////////////////////////////////////////////////////////////////
+// GetFloat()
+//
+// Attempts to parse a float from the character string given.
+// Returns true only if no parsing error occurs.
+/////////////////////////////////////////////////////////////////
+
+bool GetFloat (char *data, float *val){
+ char *endPtr;
+ double retVal;
+
+ assert (val);
+
+ errno = 0;
+ retVal = strtod (data, &endPtr);
+ if (retVal == 0 && (errno != 0 || data == endPtr)) return false;
+ if (errno != 0 && (retVal >= 1000000.0 || retVal <= -1000000.0)) return false;
+ *val = (float) retVal;
+ return true;
+}
+
+/////////////////////////////////////////////////////////////////
+// ParseParams()
+//
+// Parse all command-line options.
+/////////////////////////////////////////////////////////////////
+
+SafeVector<string> ParseParams (int argc, char **argv){
+
+ if (argc < 2){
+
+ cerr << "MXSCARNA comes with ABSOLUTELY NO WARRANTY. This is free software, and" << endl
+ << "you are welcome to redistribute it under certain conditions. See the" << endl
+ << "file COPYING.txt for details." << endl
+ << endl
+ << "Usage:" << endl
+ << " mxscarna [OPTION]... [MFAFILE]..." << endl
+ << endl
+ << "Description:" << endl
+ << " Align sequences in MFAFILE(s) and print result to standard output" << endl
+ << endl
+ << " -clustalw" << endl
+ << " use CLUSTALW output format instead of MFA" << endl
+ << endl
+ << " -stockholm" << endl
+ << " use STOCKHOLM output format instead of MFA" << endl
+ << endl
+ << " -mxscarna" << endl
+ << " use MXSCARNA output format instead of MFA" << endl
+ << endl
+ << " -weboutput /<output_path>/<outputfilename>" << endl
+ << " use web output format" << endl
+ << endl
+ << " -c, --consistency REPS" << endl
+ << " use " << MIN_CONSISTENCY_REPS << " <= REPS <= " << MAX_CONSISTENCY_REPS
+ << " (default: " << numConsistencyReps << ") passes of consistency transformation" << endl
+ << endl
+ << " -ir, --iterative-refinement REPS" << endl
+ << " use " << MIN_ITERATIVE_REFINEMENT_REPS << " <= REPS <= " << MAX_ITERATIVE_REFINEMENT_REPS
+ << " (default: " << numIterativeRefinementReps << ") passes of iterative-refinement" << endl
+ << endl
+ << " -pre, --pre-training REPS" << endl
+ << " use " << MIN_PRETRAINING_REPS << " <= REPS <= " << MAX_PRETRAINING_REPS
+ << " (default: " << numPreTrainingReps << ") rounds of pretraining" << endl
+ << endl
+ << " -pairs" << endl
+ << " generate all-pairs pairwise alignments" << endl
+ << endl
+ << " -viterbi" << endl
+ << " use Viterbi algorithm to generate all pairs (automatically enables -pairs)" << endl
+ << endl
+ << " -v, --verbose" << endl
+ << " report progress while aligning (default: " << (enableVerbose ? "on" : "off") << ")" << endl
+ << endl
+ << " -annot FILENAME" << endl
+ << " write annotation for multiple alignment to FILENAME" << endl
+ << endl
+ << " -t, --train FILENAME" << endl
+ << " compute EM transition probabilities, store in FILENAME (default: "
+ << parametersOutputFilename << ")" << endl
+ << endl
+ << " -e, --emissions" << endl
+ << " also reestimate emission probabilities (default: "
+ << (enableTrainEmissions ? "on" : "off") << ")" << endl
+ << endl
+ << " -p, --paramfile FILENAME" << endl
+ << " read parameters from FILENAME (default: "
+ << parametersInputFilename << ")" << endl
+ << endl
+ << " -a, --alignment-order" << endl
+ << " print sequences in alignment order rather than input order (default: "
+ << (enableAlignOrder ? "on" : "off") << ")" << endl
+ << endl
+ << " -s THRESHOLD" << endl
+ << " the threshold of SCS alignment" << endl
+ << endl
+ << " In default, for less than " << threshhold << ", the SCS aligment is applied. " << endl
+ << " -l SCSLENGTH" << endl
+ << " the length of stem candidates " << SCSLENGTH << endl
+ << endl
+ << " -b BASEPROBTRHESHHOLD" << endl
+ << " the threshold of base pairing probability " << BASEPROBTHRESHOLD << endl
+ << endl
+ << " -m, --mccaskillmea" << endl
+ << " McCaskill MEA MODE: input the clustalw format file and output the secondary structure predicted by McCaskill MEA" << endl
+ << endl
+ << " -g BASEPAIRSCORECONST" << endl
+ << " the control parameter of the prediction of base pairs, default:" << BasePairConst << endl
+ << endl
+ << " -w BANDWIDTH" << endl
+ << " the control parameter of the distance of stem candidates, default:" << BANDWIDTH << endl
+ << endl;
+
+
+ // << " -go, --gap-open VALUE" << endl
+ // << " gap opening penalty of VALUE <= 0 (default: " << gapOpenPenalty << ")" << endl
+ // << endl
+ // << " -ge, --gap-extension VALUE" << endl
+ // << " gap extension penalty of VALUE <= 0 (default: " << gapContinuePenalty << ")" << endl
+ // << endl
+ // << " -co, --cutoff CUTOFF" << endl
+ // << " subtract 0 <= CUTOFF <= 1 (default: " << cutoff << ") from all posterior values before final alignment" << endl
+ // << endl
+
+ exit (1);
+ }
+
+ SafeVector<string> sequenceNames;
+ int tempInt;
+ float tempFloat;
+
+ for (int i = 1; i < argc; i++){
+ if (argv[i][0] == '-'){
+
+ // training
+ if (!strcmp (argv[i], "-t") || !strcmp (argv[i], "--train")){
+ enableTraining = true;
+ if (i < argc - 1)
+ parametersOutputFilename = string (argv[++i]);
+ else {
+ cerr << "ERROR: Filename expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // emission training
+ else if (!strcmp (argv[i], "-e") || !strcmp (argv[i], "--emissions")){
+ enableTrainEmissions = true;
+ }
+
+ // parameter file
+ else if (!strcmp (argv[i], "-p") || !strcmp (argv[i], "--paramfile")){
+ if (i < argc - 1)
+ parametersInputFilename = string (argv[++i]);
+ else {
+ cerr << "ERROR: Filename expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+ else if (! strcmp (argv[i], "-s")) {
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat < 0){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be nagative." << endl;
+ exit (1);
+ }
+ else
+ threshhold = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ else if (! strcmp (argv[i], "-l")) {
+ if (i < argc - 1) {
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt <= 0 || 6 <= tempInt) {
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << "1 and 6" << "." << endl;
+ exit (1);
+ }
+ else
+ scsLength = tempInt;
+ }
+ }
+ }
+ else if (! strcmp (argv[i], "-b")) {
+ if (i < argc - 1) {
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat < 0 && 1 < tempFloat) {
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be nagative." << endl;
+ exit (1);
+ }
+ else
+ BaseProbThreshold = tempFloat;
+ }
+ }
+ }
+ else if (! strcmp (argv[i], "-g")) {
+ if (i < argc - 1) {
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat < 0 && 1 < tempFloat) {
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be nagative." << endl;
+ exit (1);
+ }
+ else
+ BasePairConst = tempFloat;
+ }
+ }
+ }
+
+ // number of consistency transformations
+ else if (!strcmp (argv[i], "-c") || !strcmp (argv[i], "--consistency")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_CONSISTENCY_REPS || tempInt > MAX_CONSISTENCY_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_CONSISTENCY_REPS << " and " << MAX_CONSISTENCY_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numConsistencyReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // number of randomized partitioning iterative refinement passes
+ else if (!strcmp (argv[i], "-ir") || !strcmp (argv[i], "--iterative-refinement")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_ITERATIVE_REFINEMENT_REPS || tempInt > MAX_ITERATIVE_REFINEMENT_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_ITERATIVE_REFINEMENT_REPS << " and " << MAX_ITERATIVE_REFINEMENT_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numIterativeRefinementReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+ // number of EM pre-training rounds
+ else if (!strcmp (argv[i], "-pre") || !strcmp (argv[i], "--pre-training")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_PRETRAINING_REPS || tempInt > MAX_PRETRAINING_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_PRETRAINING_REPS << " and " << MAX_PRETRAINING_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numPreTrainingReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // the distance of stem candidate
+ else if (!strcmp (argv[i], "-w")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ BandWidth = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // gap open penalty
+ else if (!strcmp (argv[i], "-go") || !strcmp (argv[i], "--gap-open")){
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat > 0){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be positive." << endl;
+ exit (1);
+ }
+ else
+ gapOpenPenalty = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // gap extension penalty
+ else if (!strcmp (argv[i], "-ge") || !strcmp (argv[i], "--gap-extension")){
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat > 0){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be positive." << endl;
+ exit (1);
+ }
+ else
+ gapContinuePenalty = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // all-pairs pairwise alignments
+ else if (!strcmp (argv[i], "-pairs")){
+ enableAllPairs = true;
+ }
+
+ // all-pairs pairwise Viterbi alignments
+ else if (!strcmp (argv[i], "-viterbi")){
+ enableAllPairs = true;
+ enableViterbi = true;
+ }
+
+ // read base-pairing probability from the '_bpp' file, by katoh
+ else if (!strcmp (argv[i], "-readbpp")){
+ bppmode = 'r';
+ }
+
+ // write base-pairing probability to stdout, by katoh
+ else if (!strcmp (argv[i], "-writebpp")){
+ bppmode = 'w';
+ }
+
+ // annotation files
+ else if (!strcmp (argv[i], "-annot")){
+ enableAnnotation = true;
+ if (i < argc - 1)
+ annotationFilename = argv[++i];
+ else {
+ cerr << "ERROR: FILENAME expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // clustalw output format
+ else if (!strcmp (argv[i], "-clustalw")){
+ enableClustalWOutput = true;
+ }
+ // mxscarna output format
+ else if (!strcmp (argv[i], "-mxscarna")) {
+ enableMXSCARNAOutput = true;
+ }
+ // stockholm output format
+ else if (!strcmp (argv[i], "-stockholm")) {
+ enableStockholmOutput = true;
+ }
+ // web output format
+ else if (!strcmp (argv[i], "-weboutput")) {
+ if (i < argc - 1) {
+ weboutputFileName = string(argv[++i]);
+ }
+ else {
+ cerr << "ERROR: Invalid following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+
+ enableWebOutput = true;
+ }
+
+ // cutoff
+ else if (!strcmp (argv[i], "-co") || !strcmp (argv[i], "--cutoff")){
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat < 0 || tempFloat > 1){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must be between 0 and 1." << endl;
+ exit (1);
+ }
+ else
+ cutoff = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // verbose reporting
+ else if (!strcmp (argv[i], "-v") || !strcmp (argv[i], "--verbose")){
+ enableVerbose = true;
+ }
+
+ // alignment order
+ else if (!strcmp (argv[i], "-a") || !strcmp (argv[i], "--alignment-order")){
+ enableAlignOrder = true;
+ }
+ // McCaskill MEA MODE
+ else if (!strcmp (argv[i], "-m") || !strcmp (argv[i], "--mccaskillmea")){
+ enableMcCaskillMEAMode = true;
+ }
+ // bad arguments
+ else {
+ cerr << "ERROR: Unrecognized option: " << argv[i] << endl;
+ exit (1);
+ }
+ }
+ else {
+ sequenceNames.push_back (string (argv[i]));
+ }
+ }
+
+ if (enableTrainEmissions && !enableTraining){
+ cerr << "ERROR: Training emissions (-e) requires training (-t)" << endl;
+ exit (1);
+ }
+
+ return sequenceNames;
+}
+
+/////////////////////////////////////////////////////////////////
+// ReadParameters()
+//
+// Read initial distribution, transition, and emission
+// parameters from a file.
+/////////////////////////////////////////////////////////////////
+
+void ReadParameters (){
+
+ ifstream data;
+
+ emitPairs = VVF (256, VF (256, 1e-10));
+ emitSingle = VF (256, 1e-5);
+
+ // read initial state distribution and transition parameters
+ // pass
+ if (parametersInputFilename == string ("")){
+ if (NumInsertStates == 1){
+ for (int i = 0; i < NumMatrixTypes; i++) initDistrib[i] = initDistrib1Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapOpen[i] = gapOpen1Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapExtend[i] = gapExtend1Default[i];
+ }
+ else if (NumInsertStates == 2){
+ for (int i = 0; i < NumMatrixTypes; i++) initDistrib[i] = initDistrib2Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapOpen[i] = gapOpen2Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapExtend[i] = gapExtend2Default[i];
+ }
+ else {
+ cerr << "ERROR: No default initial distribution/parameter settings exist" << endl
+ << " for " << NumInsertStates << " pairs of insert states. Use --paramfile." << endl;
+ exit (1);
+ }
+
+ alphabet = alphabetDefault;
+
+ for (int i = 0; i < (int) alphabet.length(); i++){
+ emitSingle[(unsigned char) tolower(alphabet[i])] = emitSingleDefault[i];
+ emitSingle[(unsigned char) toupper(alphabet[i])] = emitSingleDefault[i];
+ for (int j = 0; j <= i; j++){
+ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) tolower(alphabet[j])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) toupper(alphabet[j])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) tolower(alphabet[j])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) toupper(alphabet[j])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) tolower(alphabet[i])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) toupper(alphabet[i])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) tolower(alphabet[i])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) toupper(alphabet[i])] = emitPairsDefault[i][j];
+ }
+ }
+ }
+ else {
+ data.open (parametersInputFilename.c_str());
+ if (data.fail()){
+ cerr << "ERROR: Unable to read parameter file: " << parametersInputFilename << endl;
+ exit (1);
+ }
+
+ string line[3];
+ for (int i = 0; i < 3; i++){
+ if (!getline (data, line[i])){
+ cerr << "ERROR: Unable to read transition parameters from parameter file: " << parametersInputFilename << endl;
+ exit (1);
+ }
+ }
+ istringstream data2;
+ data2.clear(); data2.str (line[0]); for (int i = 0; i < NumMatrixTypes; i++) data2 >> initDistrib[i];
+ data2.clear(); data2.str (line[1]); for (int i = 0; i < 2*NumInsertStates; i++) data2 >> gapOpen[i];
+ data2.clear(); data2.str (line[2]); for (int i = 0; i < 2*NumInsertStates; i++) data2 >> gapExtend[i];
+
+ if (!getline (data, line[0])){
+ cerr << "ERROR: Unable to read alphabet from scoring matrix file: " << parametersInputFilename << endl;
+ exit (1);
+ }
+
+ // read alphabet as concatenation of all characters on alphabet line
+ alphabet = "";
+ string token;
+ data2.clear(); data2.str (line[0]); while (data2 >> token) alphabet += token;
+
+ for (int i = 0; i < (int) alphabet.size(); i++){
+ for (int j = 0; j <= i; j++){
+ float val;
+ data >> val;
+ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) tolower(alphabet[j])] = val;
+ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) toupper(alphabet[j])] = val;
+ emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) tolower(alphabet[j])] = val;
+ emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) toupper(alphabet[j])] = val;
+ emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) tolower(alphabet[i])] = val;
+ emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) toupper(alphabet[i])] = val;
+ emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) tolower(alphabet[i])] = val;
+ emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) toupper(alphabet[i])] = val;
+ }
+ }
+
+ for (int i = 0; i < (int) alphabet.size(); i++){
+ float val;
+ data >> val;
+ emitSingle[(unsigned char) tolower(alphabet[i])] = val;
+ emitSingle[(unsigned char) toupper(alphabet[i])] = val;
+ }
+ data.close();
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// ProcessTree()
+//
+// Process the tree recursively. Returns the aligned sequences
+// corresponding to a node or leaf of the tree.
+/////////////////////////////////////////////////////////////////
+float ide;
+MultiSequence *ProcessTree (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, SafeVector<BPPMatrix*> &BPPMatrices) {
+ MultiSequence *result;
+
+ // check if this is a node of the alignment tree
+ if (tree->GetSequenceLabel() == -1){
+ MultiSequence *alignLeft = ProcessTree (tree->GetLeftChild(), sequences, sparseMatrices, model, BPPMatrices);
+ MultiSequence *alignRight = ProcessTree (tree->GetRightChild(), sequences, sparseMatrices, model, BPPMatrices);
+
+ assert (alignLeft);
+ assert (alignRight);
+
+ result = AlignAlignments (alignLeft, alignRight, sparseMatrices, model, BPPMatrices, tree->GetIdentity());
+ assert (result);
+
+ delete alignLeft;
+ delete alignRight;
+ }
+
+ // otherwise, this is a leaf of the alignment tree
+ else {
+ result = new MultiSequence(); assert (result);
+ result->AddSequence (sequences->GetSequence(tree->GetSequenceLabel())->Clone());
+ }
+
+ return result;
+}
+
+/////////////////////////////////////////////////////////////////
+// ComputeFinalAlignment()
+//
+// Compute the final alignment by calling ProcessTree(), then
+// performing iterative refinement as needed.
+/////////////////////////////////////////////////////////////////
+
+MultiSequence *ComputeFinalAlignment (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model,
+ SafeVector<BPPMatrix*> &BPPMatrices) {
+
+ MultiSequence *alignment = ProcessTree (tree, sequences, sparseMatrices, model, BPPMatrices);
+
+ if (enableAlignOrder){
+ alignment->SaveOrdering();
+ enableAlignOrder = false;
+ }
+
+ // tree-based refinement
+ // if you use the function, you can degrade the quality of the software.
+ // TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree, BPPMatrices);
+
+ // iterative refinement
+/*
+ for (int i = 0; i < numIterativeRefinementReps; i++)
+ DoIterativeRefinement (sparseMatrices, model, alignment);
+
+ cerr << endl;
+*/
+ // return final alignment
+ return alignment;
+}
+
+/////////////////////////////////////////////////////////////////
+// AlignAlignments()
+//
+// Returns the alignment of two MultiSequence objects.
+/////////////////////////////////////////////////////////////////
+
+MultiSequence *AlignAlignments (MultiSequence *align1, MultiSequence *align2,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model,
+ SafeVector<BPPMatrix*> &BPPMatrices, float identity){
+
+ // print some info about the alignment
+ if (enableVerbose){
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ cerr << ((i==0) ? "[" : ",") << align1->GetSequence(i)->GetLabel();
+ cerr << "] vs. ";
+ for (int i = 0; i < align2->GetNumSequences(); i++)
+ cerr << ((i==0) ? "[" : ",") << align2->GetSequence(i)->GetLabel();
+ cerr << "]: ";
+ }
+
+ VF *posterior = model.BuildPosterior (align1, align2, sparseMatrices, cutoff);
+
+ pair<SafeVector<char> *, float> alignment;
+ // choose the alignment routine depending on the "cosmetic" gap penalties used
+ if (gapOpenPenalty == 0 && gapContinuePenalty == 0) {
+
+ if(identity <= threshhold) {
+ std::vector<StemCandidate> *pscs1, *pscs2;
+ pscs1 = seq2scs(align1, BPPMatrices, BandWidth);
+ pscs2 = seq2scs(align2, BPPMatrices, BandWidth);
+ std::vector<int> *matchPSCS1 = new std::vector<int>;
+ std::vector<int> *matchPSCS2 = new std::vector<int>;
+
+ Globaldp globaldp(pscs1, pscs2, align1, align2, matchPSCS1, matchPSCS2, posterior, BPPMatrices);
+ //float scsScore = globaldp.Run();
+
+ globaldp.Run();
+
+ removeConflicts(pscs1, pscs2, matchPSCS1, matchPSCS2);
+
+ alignment = model.ComputeAlignment2 (align1->GetSequence(0)->GetLength(), align2->GetSequence(0)->GetLength(), *posterior, pscs1, pscs2, matchPSCS1, matchPSCS2);
+ delete matchPSCS1;
+ delete matchPSCS2;
+ } else {
+ alignment = model.ComputeAlignment (align1->GetSequence(0)->GetLength(), align2->GetSequence(0)->GetLength(), *posterior);
+ }
+ }
+ else {
+ alignment = model.ComputeAlignmentWithGapPenalties (align1, align2,
+ *posterior, align1->GetNumSequences(), align2->GetNumSequences(),
+ gapOpenPenalty, gapContinuePenalty);
+ }
+
+ delete posterior;
+
+ if (enableVerbose){
+
+ // compute total length of sequences
+ int totLength = 0;
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ for (int j = 0; j < align2->GetNumSequences(); j++)
+ totLength += min (align1->GetSequence(i)->GetLength(), align2->GetSequence(j)->GetLength());
+
+ // give an "accuracy" measure for the alignment
+ cerr << alignment.second / totLength << endl;
+ }
+
+ // now build final alignment
+ MultiSequence *result = new MultiSequence();
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ result->AddSequence (align1->GetSequence(i)->AddGaps(alignment.first, 'X'));
+ for (int i = 0; i < align2->GetNumSequences(); i++)
+ result->AddSequence (align2->GetSequence(i)->AddGaps(alignment.first, 'Y'));
+ if (!enableAlignOrder)
+ result->SortByLabel();
+
+ // free temporary alignment
+ delete alignment.first;
+
+ return result;
+}
+
+/////////////////////////////////////////////////////////////////
+// DoRelaxation()
+//
+// Performs one round of the consistency transformation. The
+// formula used is:
+// 1
+// P'(x[i]-y[j]) = --- sum sum P(x[i]-z[k]) P(z[k]-y[j])
+// |S| z in S k
+//
+// where S = {x, y, all other sequences...}
+//
+/////////////////////////////////////////////////////////////////
+
+SafeVector<SafeVector<SparseMatrix *> > DoRelaxation (MultiSequence *sequences,
+ SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices){
+ const int numSeqs = sequences->GetNumSequences();
+
+ SafeVector<SafeVector<SparseMatrix *> > newSparseMatrices (numSeqs, SafeVector<SparseMatrix *>(numSeqs, NULL));
+
+ // for every pair of sequences
+ for (int i = 0; i < numSeqs; i++){
+ for (int j = i+1; j < numSeqs; j++){
+ Sequence *seq1 = sequences->GetSequence (i);
+ Sequence *seq2 = sequences->GetSequence (j);
+
+ if (enableVerbose)
+ cerr << "Relaxing (" << i+1 << ") " << seq1->GetHeader() << " vs. "
+ << "(" << j+1 << ") " << seq2->GetHeader() << ": ";
+
+ // get the original posterior matrix
+ VF *posteriorPtr = sparseMatrices[i][j]->GetPosterior(); assert (posteriorPtr);
+ VF &posterior = *posteriorPtr;
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+
+ // contribution from the summation where z = x and z = y
+ for (int k = 0; k < (seq1Length+1) * (seq2Length+1); k++) posterior[k] += posterior[k];
+
+ if (enableVerbose)
+ cerr << sparseMatrices[i][j]->GetNumCells() << " --> ";
+
+ // contribution from all other sequences
+ for (int k = 0; k < numSeqs; k++) if (k != i && k != j){
+ if (k < i)
+ Relax1 (sparseMatrices[k][i], sparseMatrices[k][j], posterior);
+ else if (k > i && k < j)
+ Relax (sparseMatrices[i][k], sparseMatrices[k][j], posterior);
+ else {
+ SparseMatrix *temp = sparseMatrices[j][k]->ComputeTranspose();
+ Relax (sparseMatrices[i][k], temp, posterior);
+ delete temp;
+ }
+ }
+
+ // now renormalization
+ for (int k = 0; k < (seq1Length+1) * (seq2Length+1); k++) posterior[k] /= numSeqs;
+
+ // mask out positions not originally in the posterior matrix
+ SparseMatrix *matXY = sparseMatrices[i][j];
+ for (int y = 0; y <= seq2Length; y++) posterior[y] = 0;
+ for (int x = 1; x <= seq1Length; x++){
+ SafeVector<PIF>::iterator XYptr = matXY->GetRowPtr(x);
+ SafeVector<PIF>::iterator XYend = XYptr + matXY->GetRowSize(x);
+ VF::iterator base = posterior.begin() + x * (seq2Length + 1);
+ int curr = 0;
+ while (XYptr != XYend){
+
+ // zero out all cells until the first filled column
+ while (curr < XYptr->first){
+ base[curr] = 0;
+ curr++;
+ }
+
+ // now, skip over this column
+ curr++;
+ ++XYptr;
+ }
+
+ // zero out cells after last column
+ while (curr <= seq2Length){
+ base[curr] = 0;
+ curr++;
+ }
+ }
+
+ // save the new posterior matrix
+ newSparseMatrices[i][j] = new SparseMatrix (seq1->GetLength(), seq2->GetLength(), posterior);
+ newSparseMatrices[j][i] = NULL;
+
+ if (enableVerbose)
+ cerr << newSparseMatrices[i][j]->GetNumCells() << " -- ";
+
+ delete posteriorPtr;
+
+ if (enableVerbose)
+ cerr << "done." << endl;
+ }
+ }
+
+ return newSparseMatrices;
+}
+
+/////////////////////////////////////////////////////////////////
+// Relax()
+//
+// Computes the consistency transformation for a single sequence
+// z, and adds the transformed matrix to "posterior".
+/////////////////////////////////////////////////////////////////
+
+void Relax (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior){
+
+ assert (matXZ);
+ assert (matZY);
+
+ int lengthX = matXZ->GetSeq1Length();
+ int lengthY = matZY->GetSeq2Length();
+ assert (matXZ->GetSeq2Length() == matZY->GetSeq1Length());
+
+ // for every x[i]
+ for (int i = 1; i <= lengthX; i++){
+ SafeVector<PIF>::iterator XZptr = matXZ->GetRowPtr(i);
+ SafeVector<PIF>::iterator XZend = XZptr + matXZ->GetRowSize(i);
+
+ VF::iterator base = posterior.begin() + i * (lengthY + 1);
+
+ // iterate through all x[i]-z[k]
+ while (XZptr != XZend){
+ SafeVector<PIF>::iterator ZYptr = matZY->GetRowPtr(XZptr->first);
+ SafeVector<PIF>::iterator ZYend = ZYptr + matZY->GetRowSize(XZptr->first);
+ const float XZval = XZptr->second;
+
+ // iterate through all z[k]-y[j]
+ while (ZYptr != ZYend){
+ base[ZYptr->first] += XZval * ZYptr->second;
+ ZYptr++;
+ }
+ XZptr++;
+ }
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// Relax1()
+//
+// Computes the consistency transformation for a single sequence
+// z, and adds the transformed matrix to "posterior".
+/////////////////////////////////////////////////////////////////
+
+void Relax1 (SparseMatrix *matZX, SparseMatrix *matZY, VF &posterior){
+
+ assert (matZX);
+ assert (matZY);
+
+ int lengthZ = matZX->GetSeq1Length();
+ int lengthY = matZY->GetSeq2Length();
+
+ // for every z[k]
+ for (int k = 1; k <= lengthZ; k++){
+ SafeVector<PIF>::iterator ZXptr = matZX->GetRowPtr(k);
+ SafeVector<PIF>::iterator ZXend = ZXptr + matZX->GetRowSize(k);
+
+ // iterate through all z[k]-x[i]
+ while (ZXptr != ZXend){
+ SafeVector<PIF>::iterator ZYptr = matZY->GetRowPtr(k);
+ SafeVector<PIF>::iterator ZYend = ZYptr + matZY->GetRowSize(k);
+ const float ZXval = ZXptr->second;
+ VF::iterator base = posterior.begin() + ZXptr->first * (lengthY + 1);
+
+ // iterate through all z[k]-y[j]
+ while (ZYptr != ZYend){
+ base[ZYptr->first] += ZXval * ZYptr->second;
+ ZYptr++;
+ }
+ ZXptr++;
+ }
+ }
+}
+
+void DoBasePairProbabilityRelaxation (MultiSequence *sequences,
+ SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ SafeVector<BPPMatrix*> &BPPMatrices) {
+ const int numSeqs = sequences->GetNumSequences();
+
+ for (int i = 0; i < numSeqs; i++) {
+ Sequence *seq1 = sequences->GetSequence (i);
+ BPPMatrix *seq1BppMatrix = BPPMatrices[seq1->GetLabel()];
+ Trimat<float> consBppMat(seq1->GetLength() + 1);
+ int seq1Length = seq1->GetLength();
+
+ for (int k = 1; k <= seq1Length; k++) {
+ for (int l = k; l <= seq1Length; l++) {
+ consBppMat.ref(k, l) = seq1BppMatrix->GetProb(k, l);
+ }
+ }
+
+ for (int j = i + 1; j < numSeqs; j++) {
+
+ // VF *posteriorPtr = sparseMatrices[i][j]->GetPosterior()
+ Sequence *seq2 = sequences->GetSequence (j);
+ BPPMatrix *seq2BppMatrix = BPPMatrices[seq2->GetLabel()];
+// int seq2Length = seq2->GetLength();
+ SparseMatrix *matchProb = sparseMatrices[i][j];
+
+// vector<PIF2> &probs1 = seq1BppMatrix->bppMat.data2;
+ for(int k = 1; k <= seq1Length; k++) {
+ for(int m = k, n = k; n <= k + 200 && m >= 1 && n <= seq1Length; m--, n++) {
+
+// for (int k = 0; k < (int)probs1.size(); k++) {
+// float tmpProb1 = probs1[k].prob;
+// int tmp1I = probs1[k].i;
+// int tmp1J = probs1[k].j;
+
+ float sumProb = 0;
+ vector<PIF2> &probs2 = seq2BppMatrix->bppMat.data2;
+ for(int l = 0; l < (int)probs2.size(); l++) {
+ float tmpProb2 = probs2[l].prob;
+ int tmp2I = probs2[l].i;
+ int tmp2J = probs2[l].j;
+ sumProb += matchProb->GetValue(m, tmp2I)*matchProb->GetValue(n, tmp2J)*tmpProb2;
+ }
+
+ consBppMat.ref(m, n) += sumProb;
+ }
+
+ for(int m = k, n = k + 1; n <= k + 200 && m >= 1 && n <= seq1Length; m--, n++) {
+
+// for (int k = 0; k < (int)probs1.size(); k++) {
+// float tmpProb1 = probs1[k].prob;
+// int tmp1I = probs1[k].i;
+// int tmp1J = probs1[k].j;
+
+ float sumProb = 0;
+ vector<PIF2> &probs2 = seq2BppMatrix->bppMat.data2;
+ for(int l = 0; l < (int)probs2.size(); l++) {
+ float tmpProb2 = probs2[l].prob;
+ int tmp2I = probs2[l].i;
+ int tmp2J = probs2[l].j;
+ sumProb += matchProb->GetValue(m, tmp2I)*matchProb->GetValue(n, tmp2J)*tmpProb2;
+ }
+
+ consBppMat.ref(m, n) += sumProb;
+ }
+ }
+ }
+
+/*
+ for(int k = 1; k <= seq1Length; k++) {
+ for(int m = k, n = k; n <= k + 30 && m >= 1 && n <= seq1Length; m--, n++) {
+ float tmpProb = seq1BppMatrix->GetProb(m, n);
+ for(int l = 1; l <= seq2Length; l++) {
+ for(int s = l, t = l; t <= l + 30 && s >= 1 && t <= seq2Length; s--, t++) {
+ tmpProb += matchProb->GetValue(m,s)*matchProb->GetValue(n,t)*seq2BppMatrix->GetProb(s,t);
+ }
+ for(int s = l, t = l + 1; t <= l + 31 && s >= 1 && t <= seq2Length; s--, t++) {
+ tmpProb += matchProb->GetValue(m,s)*matchProb->GetValue(n,t)*seq2BppMatrix->GetProb(s,t);
+ }
+ }
+ consBppMat.ref(m, n) += tmpProb;
+ }
+
+ for(int m = k, n = k + 1; n <= k + 31 && m >= 1 && n <= seq1Length; m--, n++) {
+ float tmpProb = seq1BppMatrix->GetProb(m, n);
+ for(int l = 1; l <= seq2Length; l++) {
+ for(int s = l, t = l; t <= l + 30 && s >= 1 && t <= seq2Length; s--, t++) {
+ tmpProb += matchProb->GetValue(m,s)*matchProb->GetValue(n,t)*seq2BppMatrix->GetProb(s,t);
+ }
+ for(int s = l, t = l + 1; t <= l + 31 && s >= 1 && t <= seq2Length; s--, t++) {
+ tmpProb += matchProb->GetValue(m,s)*matchProb->GetValue(n,t)*seq2BppMatrix->GetProb(s,t);
+ }
+ }
+ consBppMat.ref(m,n) += tmpProb;
+ }
+ }
+ }
+*/
+ for (int m = 1; m <= seq1Length; m++) {
+ for (int n = m + 4; n <= seq1Length; n++) {
+ consBppMat.ref(m,n) = consBppMat.ref(m,n)/(float)numSeqs;
+ }
+ }
+ seq1BppMatrix->updateBPPMatrix(consBppMat);
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// GetSubtree
+//
+// Returns set containing all leaf labels of the current subtree.
+/////////////////////////////////////////////////////////////////
+
+set<int> GetSubtree (const TreeNode *tree){
+ set<int> s;
+
+ if (tree->GetSequenceLabel() == -1){
+ s = GetSubtree (tree->GetLeftChild());
+ set<int> t = GetSubtree (tree->GetRightChild());
+
+ for (set<int>::iterator iter = t.begin(); iter != t.end(); ++iter)
+ s.insert (*iter);
+ }
+ else {
+ s.insert (tree->GetSequenceLabel());
+ }
+
+ return s;
+}
+
+/////////////////////////////////////////////////////////////////
+// TreeBasedBiPartitioning
+//
+// Uses the iterative refinement scheme from MUSCLE.
+/////////////////////////////////////////////////////////////////
+
+void TreeBasedBiPartitioning (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment,
+ const TreeNode *tree, SafeVector<BPPMatrix*> &BPPMatrices){
+ // check if this is a node of the alignment tree
+ if (tree->GetSequenceLabel() == -1){
+ TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree->GetLeftChild(), BPPMatrices);
+ TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree->GetRightChild(), BPPMatrices);
+
+ set<int> leftSubtree = GetSubtree (tree->GetLeftChild());
+ set<int> rightSubtree = GetSubtree (tree->GetRightChild());
+ set<int> leftSubtreeComplement, rightSubtreeComplement;
+
+ // calculate complement of each subtree
+ for (int i = 0; i < alignment->GetNumSequences(); i++){
+ if (leftSubtree.find(i) == leftSubtree.end()) leftSubtreeComplement.insert (i);
+ if (rightSubtree.find(i) == rightSubtree.end()) rightSubtreeComplement.insert (i);
+ }
+
+ // perform realignments for edge to left child
+ if (!leftSubtree.empty() && !leftSubtreeComplement.empty()){
+ MultiSequence *groupOneSeqs = alignment->Project (leftSubtree); assert (groupOneSeqs);
+ MultiSequence *groupTwoSeqs = alignment->Project (leftSubtreeComplement); assert (groupTwoSeqs);
+ delete alignment;
+ alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model, BPPMatrices, tree->GetLeftChild()->GetIdentity());
+ }
+
+ // perform realignments for edge to right child
+ if (!rightSubtree.empty() && !rightSubtreeComplement.empty()){
+ MultiSequence *groupOneSeqs = alignment->Project (rightSubtree); assert (groupOneSeqs);
+ MultiSequence *groupTwoSeqs = alignment->Project (rightSubtreeComplement); assert (groupTwoSeqs);
+ delete alignment;
+ alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model, BPPMatrices, tree->GetRightChild()->GetIdentity());
+ }
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// DoterativeRefinement()
+//
+// Performs a single round of randomized partionining iterative
+// refinement.
+/////////////////////////////////////////////////////////////////
+/*
+void DoIterativeRefinement (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment){
+ set<int> groupOne, groupTwo;
+
+ // create two separate groups
+ for (int i = 0; i < alignment->GetNumSequences(); i++){
+ if (rand() % 2)
+ groupOne.insert (i);
+ else
+ groupTwo.insert (i);
+ }
+
+ if (groupOne.empty() || groupTwo.empty()) return;
+
+ // project into the two groups
+ MultiSequence *groupOneSeqs = alignment->Project (groupOne); assert (groupOneSeqs);
+ MultiSequence *groupTwoSeqs = alignment->Project (groupTwo); assert (groupTwoSeqs);
+ delete alignment;
+
+ // realign
+ alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model);
+
+ delete groupOneSeqs;
+ delete groupTwoSeqs;
+}
+*/
+
+/////////////////////////////////////////////////////////////////
+// WriteAnnotation()
+//
+// Computes annotation for multiple alignment and write values
+// to a file.
+/////////////////////////////////////////////////////////////////
+
+void WriteAnnotation (MultiSequence *alignment,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices){
+ ofstream outfile (annotationFilename.c_str());
+
+ if (outfile.fail()){
+ cerr << "ERROR: Unable to write annotation file." << endl;
+ exit (1);
+ }
+
+ const int alignLength = alignment->GetSequence(0)->GetLength();
+ const int numSeqs = alignment->GetNumSequences();
+
+ SafeVector<int> position (numSeqs, 0);
+ SafeVector<SafeVector<char>::iterator> seqs (numSeqs);
+ for (int i = 0; i < numSeqs; i++) seqs[i] = alignment->GetSequence(i)->GetDataPtr();
+ SafeVector<pair<int,int> > active;
+ active.reserve (numSeqs);
+
+ // for every column
+ for (int i = 1; i <= alignLength; i++){
+
+ // find all aligned residues in this particular column
+ active.clear();
+ for (int j = 0; j < numSeqs; j++){
+ if (seqs[j][i] != '-'){
+ active.push_back (make_pair(j, ++position[j]));
+ }
+ }
+
+ outfile << setw(4) << ComputeScore (active, sparseMatrices) << endl;
+ }
+
+ outfile.close();
+}
+
+/////////////////////////////////////////////////////////////////
+// ComputeScore()
+//
+// Computes the annotation score for a particular column.
+/////////////////////////////////////////////////////////////////
+
+int ComputeScore (const SafeVector<pair<int, int> > &active,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices){
+
+ if (active.size() <= 1) return 0;
+
+ // ALTERNATIVE #1: Compute the average alignment score.
+
+ float val = 0;
+ for (int i = 0; i < (int) active.size(); i++){
+ for (int j = i+1; j < (int) active.size(); j++){
+ val += sparseMatrices[active[i].first][active[j].first]->GetValue(active[i].second, active[j].second);
+ }
+ }
+
+ return (int) (200 * val / ((int) active.size() * ((int) active.size() - 1)));
+
+}
--- /dev/null
+################################################################################
+# Makefile for probcons
+################################################################################
+
+################################################################################
+# 1) Choose C++ compiler.
+################################################################################
+
+CXX = g++
+
+################################################################################
+# 2) Set C++ flags.
+# a) DEBUG mode -- no optimizations, enable SafeVector checking, no inlining
+# b) PROFILE mode -- for gprof
+# c) RELEASE mode
+################################################################################
+BIG_INLINE_LIMIT = 20000
+
+PROBCONS = ./probconsRNA
+VIENNA = ./vienna
+
+# no -Wall option for warning
+CXXFLAGS = -O3 -funroll-loops -finline-limit=$(BIG_INLINE_LIMIT)
+OFLAGS = -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" $(CXXFLAGS) $(CFLAGS1)
+LIBS = -L$(PROBCONS) -L./
+INCL = -I$(PROBCONS) -I$(VIENNA) -I./
+
+################################################################################
+# 3) Dependencies
+################################################################################
+
+TARGETS = mxscarna
+
+OBJS = Main.o McCaskill.o vienna/energy_param.o seq2scs.o Globaldp.o postProcessings.o AlifoldMEA.o
+
+.PHONY : all
+all : $(TARGETS)
+
+mxscarna : $(OBJS)
+ $(CXX) $(LIBS) $(OFLAGS) -lm -o $@ $(OBJS)
+
+rfold:
+ cd $(RFOLD); \
+ make; \
+ cd .. \
+ cd ..
+probcons:
+ cd $(PROBCONS); \
+ make; \
+ cd ..
+
+#probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
+# $(CXX) -lm -o probcons $(OBJS)
+#Main.cc
+
+Main.o : $(PROBCONS)/SafeVector.h $(PROBCONS)/FileBuffer.h $(PROBCONS)/Sequence.h $(PROBCONS)/MultiSequence.h $(PROBCONS)/EvolutionaryTree.h scarna.hpp BPPMatrix.hpp StemCandidate.hpp Globaldp.hpp AlifoldMEA.h Main.cc
+ $(CXX) $(INCL) $(OFLAGS) -c Main.cc -o Main.o
+McCaskill.o: McCaskill.hpp $(VIENNA)/energy_param.hpp Util.hpp Beta.hpp ScoreType.hpp McCaskill.cpp
+ $(CXX) $(INCL) $(OFLAGS) -c McCaskill.cpp -o McCaskill.o
+$(VIENNA)/energy_param.o: $(VIENNA)/energy_param.hpp $(VIENNA)/energy_param.cpp
+ $(CXX) $(INCL) $(OFLAGS) -c $(VIENNA)/energy_param.cpp -o $(VIENNA)/energy_param.o
+seq2scs.o: $(PROBCONS)/SafeVector.h StemCandidate.hpp $(PROBCONS)/Sequence.h $(PROBCONS)/MultiSequence.h BPPMatrix.hpp nrutil.h seq2scs.cpp
+ $(CXX) $(INCL) $(OFLAGS) -c seq2scs.cpp -o seq2scs.o
+Globaldp.o: Globaldp.hpp nrutil.h Util.hpp Beta.hpp scarna.hpp StemCandidate.hpp $(PROBCONS)/MultiSequence.h $(PROBCONS)/Sequence.h BPPMatrix.hpp
+ $(CXX) $(INCL) $(OFLAGS) -c Globaldp.cpp -o Globaldp.o
+GlobalParameters.o: scarna.hpp
+ $(CXX) $(INCL) $(OFLAGS) -c GlobalParameters.cpp -o GlobalParameters.o
+postProcessings.o: StemCandidate.hpp scarna.hpp
+ $(CXX) $(INCL) $(OFLAGS) -c postProcessings.cpp -o postProcessings.o
+AlifoldMEA.o: nrutil.h Util.hpp Beta.hpp BPPMatrix.hpp $(PROBCONS)/MultiSequence.h $(PROBCONS)/Sequence.h $(PROBCONS)/SafeVector.h
+ $(CXX) $(INCL) $(OFLAGS) -c AlifoldMEA.cpp -o AlifoldMEA.o
+
+.PHONY : clean
+clean:
+ rm -f $(TARGETS) *.o *.h~ *.hpp~ *.cpp~ *.cc~ $(VIENNA)/*.o
+ $(MAKE) -C $(PROBCONS) clean
--- /dev/null
+#include <iostream>
+#include "McCaskill.hpp"
+//#include "energy_param3.hpp"
+#include "Util.hpp"
+#include <cstring>
+
+namespace MXSCARNA {
+energy_param McCaskill::energyParam;
+
+float *McCaskill::exphairpin;
+float McCaskill::expninio[5][32];
+float McCaskill::expdangle5[6][4];
+float McCaskill::expdangle3[6][4];
+float McCaskill::expinternalLoop[31];
+float McCaskill::expbulge[31];
+char McCaskill::exptriLoop[2][6];
+float McCaskill::exptriLoopEnergy[2];
+char McCaskill::exptetraLoop[30][7];
+float McCaskill::exptetraLoopEnergy[30];
+float McCaskill::expStack[6][6];
+float McCaskill::expTstackH[6][16];
+float McCaskill::expTstackI[6][16];
+float McCaskill::expint11[6][6][16];
+float McCaskill::expint21[6][6][16][4];
+float McCaskill::expint22[6][6][16][16];
+float McCaskill::expMLclosing;
+float McCaskill::expMLintern[8];
+float McCaskill::expTermAU;
+float McCaskill::expMLbase[31];
+
+const int McCaskill::TURN = 3;
+const float McCaskill::GASCONST = 1.98717;
+const float McCaskill::T = 37 + 273.15;
+const int McCaskill::MAXLOOP = 30;
+const int McCaskill::TETRA_ENTH37 = -400;
+const int McCaskill::NBPAIRS = 7;
+const int McCaskill::SCALE = 10;
+
+
+void
+McCaskill::
+calcPartitionFunction()
+{
+ initParameter();
+ Inside();
+ Outside();
+ convertProbability();
+
+/*
+ for(int i = 0; i < n_seq; i++) {
+ for(int j = i; j < n_seq; j++) {
+ cout << getProb(i, j) << " ";
+ }
+ cout << endl;
+ }
+*/
+}
+
+void
+McCaskill::
+convertProbability()
+{
+ float *pPointer = p.getPointer(0, 0);
+ float *abPointer = ab.getPointer(0,0);
+ for(int i = 0; i < n_seq; i++) {
+ for(int j = i; j < n_seq; j++) {
+ *pPointer += *abPointer++;
+ *pPointer++ = EXP(*pPointer);
+ }
+ }
+}
+
+void
+McCaskill::
+Inside()
+{
+
+ for (int i = n_seq - TURN - 2; i >= 0; i--) {
+ float *abPointer = ab.getPointer(i, i + TURN + 1);
+ float *am1Pointer = am1.getPointer(i, i + TURN + 1);
+ float *amPointer = am.getPointer(i, i + TURN + 1);
+ float *q1Pointer = q1.getPointer(i, i + TURN + 1);
+ float *aPointer = a.getPointer(i, i + TURN + 1);
+ int *typePointer = typeMat.getPointer(i, i+TURN+1);
+ for (int j = i + TURN + 1; j < n_seq; j++) {
+ int tmpType = *typePointer++;
+ *abPointer++ = compQb(i, j, tmpType);
+ am1v.ref(i,j) = *am1Pointer++ = compQm1(i,j, tmpType);
+ amv.ref(i,j) = *amPointer++ = compQm(i,j);
+ q1v.ref(i,j) = *q1Pointer++ = compQ1(i,j, tmpType);
+ *aPointer++ = compQ(i,j);
+ }
+ }
+}
+
+inline float
+McCaskill::
+compQb(int i, int j, int tmpType)
+{
+
+ float tmpAb;
+ int type = tmpType;
+ int u = j - i - 1;
+
+ if(Beta::isCanonicalReducedPairCode(type)) {
+ // hairpin energy
+ assert(u >= 3);
+ tmpAb = expHairpinEnergy(type, u, i + 1, j - 1);
+
+ // base pair, bulge, interior loop energy
+ for(int h = i + 1; h <= MIN(i + MAXLOOP + 1, j - TURN - 2); h++) {
+ int u1 = h-i-1;
+ int max = MAX(h + TURN + 1, j-1-MAXLOOP+u1);
+ float *abPointer = ab.getPointer(h, max - 1);
+ const int *typeMatPointer = typeMat.getPointer(h, max);
+
+ for(int l = max; l < j; l++) {
+ int type2 = *typeMatPointer++;
+ abPointer++;
+ if(!Beta::isCanonicalReducedPairCode(type2)) continue;
+
+ assert(h >= 0 && h < n_seq && l >= 0 && l < n_seq);
+ type2 = Beta::flipReducedPairCode(type2);
+ assert(h-i-1 >= 0); assert(j-l-1 >= 0);
+ float loopE = *abPointer;
+ loopE += expLoopEnergy(u1, j-l-1, tmpType, type2, i+1, j-1, h-1, l+1);
+ tmpAb = LOG_ADD(tmpAb, loopE);
+ }
+ }
+
+ // multi loop
+ float tmpQm = IMPOSSIBLE;
+ float *amPointer = am.getPointer(i + 1, j - TURN - 3);
+ float *am1Pointer = am1v.getPointer(j-TURN-2, j-1);
+ for(int h = j - TURN - 2; h >= i + TURN + 3; h--) {
+ assert(h >= 0 && h < n_seq);
+ float tmpScore = *amPointer--;
+ tmpScore += *am1Pointer--;
+ tmpQm = LOG_ADD(tmpQm, tmpScore);
+ }
+ tmpQm += expMLclosing + expMLintern[type];
+ tmpQm += endStemScore(i, j);
+ tmpAb = LOG_ADD(tmpAb, tmpQm);
+ }
+ else {
+ tmpAb = IMPOSSIBLE;
+ }
+ return tmpAb;
+}
+
+//F = a:ML_closing + b:ML_intern*k + c:ML_BASE*u
+
+inline float
+McCaskill::
+compQm1(int i, int j, int tmpType)
+{
+ float tmpQm1 = IMPOSSIBLE;
+
+ int l = j;
+ if (i + TURN + 1 <= l) {
+ int type = typeMat.ref(i,l);
+ if(Beta::isCanonicalReducedPairCode(type)) {
+ float tmpScore = ab.ref(i,l);
+ tmpScore += beginStemScore(i, l);
+ //tmpScore += expMLbase[1]*(j-l) + expMLintern[type];
+ tmpScore += expMLintern[tmpType];
+ tmpQm1 = LOG_ADD(tmpQm1, tmpScore);
+ }
+ }
+ if(i < j) {
+ tmpQm1 = LOG_ADD(tmpQm1, am1.ref(i,j-1));
+ }
+
+ return tmpQm1;
+}
+
+inline float
+McCaskill::
+compQm(int i, int j)
+{
+ float tmpQm = IMPOSSIBLE;
+ float *amPointer = am.getPointer(i,j-TURN-2);
+ float *am1Pointer = am1v.getPointer(j-TURN-1, j);
+ for(int h = j - TURN - 1; h >= i ; h--) {
+ float tmpScore = 0;
+ float tmpAm1 = *am1Pointer--;
+
+ tmpScore += tmpAm1;
+ tmpQm = LOG_ADD(tmpQm, tmpScore);
+ tmpScore = *amPointer--;
+ tmpScore += tmpAm1;
+ tmpQm = LOG_ADD(tmpQm, tmpScore);
+ }
+
+ return tmpQm;
+}
+
+inline float
+McCaskill::
+compQ1(int i, int j, int tmpType)
+{
+ float tmpQ1 = IMPOSSIBLE;
+
+ if(Beta::isCanonicalReducedPairCode(tmpType)) {
+ float tmpScore = ab.ref(i, j);
+ tmpScore += beginStemScore(i, j);
+ tmpQ1 = LOG_ADD(tmpQ1, tmpScore);
+ }
+ tmpQ1 = LOG_ADD(tmpQ1, q1.ref(i, j - 1));
+
+ return tmpQ1;
+}
+
+inline float
+McCaskill::
+compQ(int i, int j)
+{
+ float tmpQ = 0;
+ tmpQ = LOG_ADD(tmpQ, q1.ref(i,j));
+
+ float *aPointer = a.getPointer(i,j-TURN-2);
+ float *q1Pointer = q1v.getPointer(j-TURN-1, j);
+ for(int h = j - TURN - 1; h >= i + 1; h--) {
+ float tmpScore = *aPointer--;
+ tmpScore += *q1Pointer--;
+ tmpQ = LOG_ADD(tmpQ, tmpScore);
+ }
+
+ return tmpQ;
+}
+
+inline float
+McCaskill::
+beginStemScore(const int i, const int j) const
+{
+ float temp = 0;
+ int type = typeMat.ref(i,j);
+
+ if(0 < i) { temp += expdangle5[type][numSeq[i-1]]; }
+ if(j < n_seq-1) { temp += expdangle3[type][numSeq[j+1]]; }
+ if(type != Beta::REDUCED_CG_CODE && type != Beta::REDUCED_GC_CODE) { temp += expTermAU; }
+ return temp;
+}
+
+inline float
+McCaskill::
+endStemScore(const int i, const int j) const
+{
+ float temp = 0;
+ int type = typeMat.ref(i,j);
+
+ type = Beta::flipReducedPairCode(type);
+
+ if(i < n_seq-1) { temp += expdangle3[type][numSeq[i+1]]; }
+ if(j > 0) { temp += expdangle5[type][numSeq[j-1]]; }
+ if(type != Beta::REDUCED_CG_CODE && type != Beta::REDUCED_GC_CODE) { temp += expTermAU; }
+ return temp;
+}
+
+inline float
+McCaskill::
+compP(int h, int l, int tmpType)
+{
+ float prob = IMPOSSIBLE;
+
+ int type = tmpType;
+ if(Beta::isCanonicalReducedPairCode(type)) {
+
+ /* exterior loop */
+ float tmp_p = 0;
+ tmp_p -= a.ref(0,n_seq-1);
+ if(0 < h) {
+ tmp_p += a.ref(0,h-1);
+ }
+ if(l < n_seq-1) {
+ tmp_p += a.ref(l+1, n_seq-1);
+ }
+ tmp_p += beginStemScore(h, l);
+ prob = LOG_ADD(prob, tmp_p);
+
+ assert(IMPOSSIBLE <= prob && prob <= 0);
+
+ /* internal loop */
+ tmp_p = IMPOSSIBLE;
+ int tt = Beta::flipReducedPairCode(tmpType);
+ int max = MAX(0,h-MAXLOOP-1);
+ for(int i = max; i <= h - 1; i++) {
+ float min = MIN(l+MAXLOOP-h+i+2, n_seq-1);
+ int *typeMatPointer = typeMat.getPointer(i,l+1);
+ float *pPointer = p.getPointer(i,l);
+ for(int j = l + 1; j <= min; j++) {
+ int type2 = *typeMatPointer++;
+ pPointer++;
+ if(!Beta::isCanonicalReducedPairCode(type2)) continue;
+ assert(i >= 0 && i < n_seq && j >= 0 && j < n_seq);
+
+ float tmpScore = *pPointer;
+ tmpScore += expLoopEnergy(h-i-1, j-l-1, type2, tt, i+1, j-1, h-1, l+1);
+ tmp_p = LOG_ADD(tmp_p, tmpScore);
+ }
+ }
+ prob = LOG_ADD(prob, tmp_p);
+ assert(IMPOSSIBLE <= prob && prob <= 0);
+
+ /* multi loop */
+ tmp_p = IMPOSSIBLE;
+ float tmp_begin = beginStemScore(h, l);
+ float *q1Pointer = q1v.getPointer(0, l);
+ float *am1Pointer = am1v.getPointer(0, l);
+ float *amPointer = amv.getPointer(1,h-1);
+ for(int i = 0; i <= h-TURN-1; i++) {
+ float tmpq1 = *q1Pointer++;
+ float tmpam = *amPointer++;
+ float tmpScore = *am1Pointer++;
+
+ tmpScore += tmpam;
+ tmpScore += tmp_begin;
+ tmpScore += expMLclosing + expMLintern[tt];
+ tmp_p = LOG_ADD(tmp_p, tmpScore);
+
+ tmpScore = tmpq1;
+ tmpScore += tmpam;
+ tmpScore += tmp_begin;
+ tmpScore += expMLclosing + expMLintern[tt];
+ tmp_p = LOG_ADD(tmp_p, tmpScore);
+
+ tmpScore = tmpq1;
+ tmpScore += tmp_begin;
+ tmpScore += expMLclosing + expMLintern[tt];
+ tmp_p = LOG_ADD(tmp_p, tmpScore);
+ }
+
+ assert(IMPOSSIBLE <= tmp_p && tmp_p <= 0);
+ prob = LOG_ADD(prob, tmp_p);
+
+ tmp_p = IMPOSSIBLE;
+ for(int i = h-TURN; i <= h-1; i++) {
+ if(i >= 0) {
+ float tmpScore = q1.ref(i,l);
+ tmpScore += tmp_begin;
+ tmpScore += expMLclosing + expMLintern[tt];
+ tmp_p = LOG_ADD(tmp_p, tmpScore);
+ }
+ }
+ assert(IMPOSSIBLE <= tmp_p && tmp_p <= 0);
+ prob = LOG_ADD(prob, tmp_p);
+ }
+ else {
+ prob = IMPOSSIBLE;
+ }
+
+ return prob;
+}
+
+inline float
+McCaskill::
+compPm(int i, int l)
+{
+ float tmpPm = IMPOSSIBLE;
+
+ int *typeMatPointer = typeMat.getPointer(i,n_seq-1);
+ float *pPointer = p.getPointer(i,n_seq);
+ float *amPointer = am.getPointer(l+1,n_seq-1);
+ float *abPointer = ab.getPointer(i, n_seq);
+ for(int j = n_seq - 1; j >= l + TURN + 1; j--) {
+ int type = *typeMatPointer--;
+ pPointer--;
+ amPointer--;
+ abPointer--;
+ if(Beta::isCanonicalReducedPairCode(type)) {
+ float tmp = *pPointer;
+ tmp += *amPointer;
+ tmp += endStemScore(i, j);
+ tmpPm = LOG_ADD(tmpPm, tmp);
+ }
+ }
+ tmpPm += expMLintern[1];
+
+ return tmpPm;
+}
+
+inline float
+McCaskill::
+compPm1(int i, int l)
+{
+ float tmpPm1 = IMPOSSIBLE;
+
+ int j = l + 1;
+ if(j <= n_seq-1) {
+ int type = typeMat.ref(i,j);
+ if(Beta::isCanonicalReducedPairCode(type)) {
+ float tmp = p.ref(i,j);
+ tmp += endStemScore(i, j);
+ tmpPm1 = tmp;
+ }
+ tmpPm1 += expMLintern[1];
+ }
+ if(l+1 <= n_seq - 1) {
+ tmpPm1 = LOG_ADD(tmpPm1, am1.ref(i, l+1));
+ }
+
+ return tmpPm1;
+}
+
+void
+McCaskill::
+Outside()
+{
+ for(int h = 0; h <= n_seq - TURN - 2; h++) {
+ float *pPointer = p.getPointer(h, n_seq-1);
+ float *q1Pointer = q1.getPointer(h, n_seq-1);
+ float *am1Pointer = am1.getPointer(h, n_seq-1);
+ int *typePointer = typeMat.getPointer(h, n_seq-1);
+ for(int l = n_seq-1; l >= h + TURN + 1; l--) {
+ int tmpType = *typePointer--;
+ pv.ref(h,l) = *pPointer-- = compP(h,l,tmpType);
+ q1v.ref(h,l) = *q1Pointer-- = compPm(h,l);
+ am1v.ref(h,l) = *am1Pointer-- = compPm1(h,l);
+
+ assert(p.ref(h,l) <= 0);
+ }
+ }
+}
+
+void
+McCaskill::
+printProbMat()
+{
+ int m = 0;
+ for(int i = 0; i < n_seq; i++) cout << " " << seq[i];
+ cout << endl;
+ for(int i = 0; i < n_seq; i++) {
+ if(m < n_seq) {
+ cout << seq[m];
+ }
+ for(int j = 0; j <= i-1; j++) {
+ if(j != i-1) cout << " ";
+ else cout << " ";
+ }
+ if(i != 0 && i != n_seq-1) {
+ cout << "\\";
+ }
+
+ for(int j = i; j < n_seq; j++) {
+ if(p.ref(i,j) > 0.01) {
+
+ int type = Beta::getReducedPairCode(numSeq[i], numSeq[j]);
+
+ if(!Beta::isCanonicalReducedPairCode(type)) {
+ cout << "\n" << seq[i] << " " << seq[j] << " " << exp(p.ref(i,j)) << endl;
+ }
+
+ if(j != n_seq-1) {
+ cout << "* ";
+ }
+ else {
+ cout << "*";
+ }
+
+ }
+ else {
+
+ if(j != n_seq-1) {
+ cout << " ";
+ }
+ else {
+ cout << " ";
+ }
+
+ }
+
+ }
+ if(m < n_seq) {
+ cout << seq[m++] << endl;
+ }
+ if(i == n_seq - 1) cout << endl;
+ }
+ for(int i = 0; i < n_seq; i++) cout << " " << seq[i];
+ cout << endl;
+}
+
+void
+McCaskill::
+initParameter()
+{
+ float GT;
+ float RT_KCAL_MOL = McCaskill::T*McCaskill::GASCONST;
+ int len = 31;
+
+ for(int i = 0; i < len; i++) {
+ GT = energyParam.getHairpin(i);
+ exphairpin[i] = -GT*10/RT_KCAL_MOL;
+ }
+
+ for (int i = 0; i < len; i++) {
+ GT = energyParam.getBulge(i);
+ expbulge[i] = -GT*10/RT_KCAL_MOL;
+ GT = energyParam.getInternalLoop(i);
+ expinternalLoop[i] = -GT*10/RT_KCAL_MOL;
+ }
+ expinternalLoop[2] = -80*10/RT_KCAL_MOL; /* special case of size 2 interior loops (single mismatch) */
+
+ // float lxc = energy_param3::lxc37;
+ for (int i = 31; i < n_seq; i++) {
+ GT = energyParam.getHairpin(30) + (107.856*LOG((float)i/30));
+ exphairpin[i] = -GT*10/RT_KCAL_MOL;
+ }
+
+ for(int i = 0; i < 5; i++) {
+ GT = energyParam.getNinio(i);
+ for(int j = 0; j <= MAXLOOP; j++) {
+ expninio[i][j] = -MIN(energyParam.getMaxNinio(), j*GT)*10/RT_KCAL_MOL;
+ }
+ }
+
+ for(int i = 0; i < 30; i++) {
+ GT = energyParam.getTetraLoopEnergy(i);
+ exptetraLoopEnergy[i] = -GT*10/RT_KCAL_MOL;
+ }
+
+ /*no parameters for Triloop*/
+ for(int i = 0; i < 2; i++) {
+ GT = 0;
+ exptriLoopEnergy[i] = -GT*10/RT_KCAL_MOL;
+ }
+
+ GT = energyParam.getMLclosing();
+ expMLclosing = -GT*10/RT_KCAL_MOL;
+
+ for(int i = 0; i <= NBPAIRS; i++) {
+ GT = energyParam.getMLintern();
+ expMLintern[i] = -GT*10/RT_KCAL_MOL;
+ }
+
+ expTermAU = -energyParam.getTerminalAU()*10/RT_KCAL_MOL;
+
+ GT = energyParam.getMLBase();
+ for(int i = 0; i < len; i++) {
+ expMLbase[i] = -GT*10*(float)i/RT_KCAL_MOL;
+ }
+
+ /*
+ if danlges = 0 just set their energy to 0,
+ don't let dangle energyies become > 0 (at large temps)
+ but make sure go smoothly to 0
+ */
+ for(int i = 0; i < 6; i++) {
+ for(int j =0; j < 4; j++) {
+ GT = energyParam.getDangle5(i,j);
+ expdangle5[i][j] = -GT*10/RT_KCAL_MOL;
+ GT = energyParam.getDangle3(i,j);
+ expdangle3[i][j] = -GT*10/RT_KCAL_MOL;
+ }
+ }
+
+ /* stacking energies */
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 6; j++) {
+ GT = energyParam.getStack(i,j);
+ expStack[i][j] = -GT*10/RT_KCAL_MOL;
+ }
+ }
+
+ /* mismatch energies */
+ for (int i = 0; i < 6; i++) {
+ for (int j = 0; j < 16; j++) {
+ GT = energyParam.getTstackI(i, j);
+ // cout << i << " " << " " << j << " " << GT << endl;
+ expTstackI[i][j] = -GT*10/RT_KCAL_MOL;
+ GT = energyParam.getTstackH(i, j);
+ expTstackH[i][j] = -GT*10/RT_KCAL_MOL;
+ }
+ }
+
+ /* interior loops of length 2*/
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 6; j++) {
+ for(int k = 0; k < 16; k++) {
+ GT = energyParam.getInt11(i, j, k);
+ expint11[i][j][k] = -GT*10/RT_KCAL_MOL;
+ }
+ }
+ }
+
+ /* interior 2*1 loops */
+ for(int i = 0; i < 6; i++) {
+ for(int j =0; j < 6; j++) {
+ for(int k = 0; k < 16; k++) {
+ for(int l = 0; l < 4; l++) {
+ GT = energyParam.getInt21(i,j,k,l);
+ expint21[i][j][k][l] = -GT*10/RT_KCAL_MOL;
+ }
+ }
+ }
+ }
+
+ /* interior 2*2 loops */
+ for (int i = 0; i < 6; i++) {
+ for(int j = 0; j < 6; j++) {
+ for(int k = 0; k < 16; k++) {
+ for(int l = 0; l < 16; l++) {
+ GT = energyParam.getInt22(i,j,k,l);
+ expint22[i][j][k][l] = -GT*10/RT_KCAL_MOL;
+ }
+ }
+ }
+ }
+}
+
+
+inline float
+McCaskill::
+expHairpinEnergy(const int type, const int l, const int i, const int j)
+{
+ float q;
+ int k;
+
+// assert(l >= 0);
+ q = exphairpin[l];
+
+ if(l == 4) {
+ char temp_seq[7];
+
+ for(int iter = i - 1; iter < i + 5; iter++) {
+ temp_seq[iter - (i-1)] = seq[iter];
+ }
+ temp_seq[6] = '\0';
+
+ for(k = 0; k < 30; k++) {
+ if(strcmp(temp_seq, energyParam.getTetraLoop(k)) == 0) break;
+ }
+ if(k != 30) {
+ q += exptetraLoopEnergy[k];
+ }
+ }
+ if(l == 3) {
+
+ /* no triloop bonus
+ char temp_seq[6];
+
+ for(int iter = i - 1; iter < i + 4; iter++) {
+ temp_seq[iter - (i-1)] = seq[iter];
+ }
+ temp_seq[6] = '\0';
+ for(k = 0; k < 2; k++) {
+ if(strcmp(temp_seq, energyParam.getTriLoop(k)) == 0) break;
+ }
+ if(k != 2) {
+ q *= exptriLoopEnergy[k];
+ }
+ */
+
+ if(type != Beta::REDUCED_CG_CODE && type != Beta::REDUCED_GC_CODE) q += expTermAU;
+ }
+ else {
+ int type2 = Beta::getPairCode(numSeq[i], numSeq[j]);
+ q += expTstackH[type][type2];
+ }
+
+ return q;
+}
+
+
+inline float
+McCaskill::
+expLoopEnergy(int u1, int u2, int type, int type2,
+ int si1, int sj1, int sp1, int sq1)
+{
+ float z = 0;
+
+ if((u1 == 0) && (u2 == 0)) { z = expStack[type][type2]; }
+ else {
+ if((u1 == 0) || (u2 == 0)) {
+ int u;
+ if(u1 == 0) { u = u2; }
+ else { u = u1; }
+ z = expbulge[u];
+ if(u1 + u2 == 1) z += expStack[type][type2];
+ else {
+ if (type != Beta::REDUCED_CG_CODE && type != Beta::REDUCED_GC_CODE) z += expTermAU;
+ if (type2 != Beta::REDUCED_CG_CODE && type2 != Beta::REDUCED_GC_CODE) z += expTermAU;
+ }
+ }
+ else {
+ if(u1 + u2 == 2) {
+ z = expint11[type][type2][Beta::getPairCode(numSeq[si1], numSeq[sj1])];
+ }
+ else if((u1 == 1) && (u2 == 2)) {
+ z = expint21[type][type2][Beta::getPairCode(numSeq[si1], numSeq[sj1])][numSeq[sq1]];
+ }
+ else if((u1 == 2) && (u2 == 1)) {
+ z = expint21[type2][type][Beta::getPairCode(numSeq[sq1], numSeq[sp1])][numSeq[si1]];
+ }
+ else if((u1 == 2) && (u2 == 2)) {
+ z = expint22[type][type2][Beta::getPairCode(numSeq[si1], numSeq[sj1])][Beta::getPairCode(numSeq[sp1], numSeq[sq1])];
+ }
+ else {
+ z = expinternalLoop[u1 + u2] +
+ expTstackI[type][Beta::getPairCode(numSeq[si1], numSeq[sj1])]
+ + expTstackI[type2][Beta::getPairCode(numSeq[sq1], numSeq[sp1])];
+ z += expninio[2][abs(u1-u2)];
+ }
+ }
+ }
+
+ return z;
+}
+
+void
+McCaskill::
+printExpEnergy()
+{
+ cout << "exphairpin:" << endl;
+ for(int i = 0; i < 31; i++) {
+ cout << exphairpin[i] << endl;
+ }
+
+ cout << "expninio[5][32]:" << endl;
+ for(int i = 0; i < 5; i++) {
+ for(int j = 0; j < 32; j++) {
+ cout << expninio[i][j] << " ";
+ }
+ cout << endl;
+ }
+
+ cout << "expdangle5[6][4]:" << endl;
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 4; j++) {
+ cout << expdangle5[i][j] << " ";
+ }
+ cout << endl;
+ }
+
+ cout << "expdangle3[6][4]:" << endl;
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 4; j++) {
+ cout << expdangle3[i][j] << " ";
+ }
+ cout << endl;
+ }
+
+ cout << "expinternalLoop[31]:" << endl;
+ for(int i = 0; i < 31; i++) {
+ cout << i << ":" << expinternalLoop[i] << endl;
+ }
+ cout << "expbulge[31]:" << endl;
+ for(int i = 0; i < 31; i++) {
+ cout << i << ":" << expbulge[i] << endl;
+ }
+
+ cout << "exptriLoopEnergy[2]:" << endl;
+ for(int i = 0; i < 2; i++) {
+ cout << i << ":" << exptriLoopEnergy[i] << endl;
+ }
+
+ cout << "exptetraLoopEnergy[15]" << endl;
+ for(int i = 0; i < 15; i++) {
+ cout << i << ":" << exptetraLoopEnergy[i] << endl;
+ }
+
+ cout << "expStack[6][6]:" << endl;
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 6; j++) {
+ cout << expStack[i][j] << " ";
+ }
+ cout << endl;
+ }
+
+ cout << "expTstackH[6][16]:" << endl;
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 16; j++) {
+ cout << expTstackH[i][j] << " ";
+ }
+ cout << endl;
+ }
+
+ cout << "expTstackI[6][16]:" << endl;
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 16; j++) {
+ cout << expTstackI[i][j] << " ";
+ }
+ cout << endl;
+ }
+
+ cout << "expMLclosing=" << expMLclosing << endl;
+ cout << "expMLintern:" << endl;
+ for(int i = 0; i < 8; i++) {
+ cout << expMLintern[i] << " ";
+ }
+ cout << endl;
+
+ cout << "expMLbase[31]:";
+ for(int i = 0; i < 31; i++) {
+ cout << i << ":" << expMLbase[i] << endl;
+ }
+
+ cout << "expint11[6][6][16]:";
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 6; j++) {
+ for(int k = 0; k < 16; k++) {
+ cout << expint11[i][j][k] << " ";
+ }
+ cout << endl;
+ }
+ cout << endl;
+ }
+
+ cout << "expint21[6][6][16][4]:" << endl;
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 6; j++) {
+ for(int k = 0; k < 16; k++) {
+ for(int l = 0; l < 4; l++) {
+ cout << expint21[i][j][k][l] << " ";
+ }
+ cout << endl;
+ }
+ cout << endl;
+ }
+ cout << endl;
+ }
+
+
+ cout << "expint22[6][6][16][16]:" << endl;
+ for(int i = 0; i < 6; i++) {
+ for(int j = 0; j < 6; j++) {
+ for(int k = 0; k < 16; k++) {
+ for(int l = 0; l < 16; l++) {
+ cout << expint22[i][j][k][l] << " ";
+ }
+ cout << endl;
+ }
+ cout << endl;
+ }
+ cout << endl;
+ }
+
+}
+
+}
--- /dev/null
+
+#ifndef MCCAKILL_H
+#define MCCAKILL_H
+
+//#define NDEBUG
+
+#include <string>
+#include <iostream>
+#include "nrutil.h"
+#include <cassert>
+#include "Util.hpp"
+#include "Beta.hpp"
+
+#include "energy_param.hpp"
+//#include "energy_param3.hpp"
+
+#include "ScoreType.hpp"
+
+
+using namespace std;
+using namespace ProbCons;
+
+namespace MXSCARNA {
+class McCaskill {
+ char *seq;
+ int *numSeq;
+ int n_seq;
+ static energy_param energyParam;
+
+ Trimat<float> a, q1, ab, am, am1, p;
+ TriVertMat<float> q1v, abv, amv, am1v, pv;
+ Trimat<int> typeMat;
+
+ void printExpEnergy();
+ void initParameter();
+ void Inside();
+ void Outside();
+ void convertProbability();
+
+ inline float expHairpinEnergy(const int type, const int l, const int i, const int j);
+ inline float expLoopEnergy(int u1, int u2, int type, int type2,
+ int si1, int sj1, int sp1, int sq1);
+
+ inline float compQb(int i, int j, int tmpType);
+ inline float compQm1(int i, int j, int tmpType);
+ inline float compQm(int i, int j);
+ inline float compQ1(int i, int j, int tmpType);
+ inline float compQ(int i, int j);
+ inline float compP(int h, int l, int tmpType);
+ inline float compPm(int i, int l);
+ inline float compPm1(int i, int l);
+ inline float beginStemScore(const int i, const int j) const;
+ inline float endStemScore(const int i, const int j) const;
+
+ static const float GASCONST;
+ static const float T;
+ static const int MAXLOOP;
+ static const int TETRA_ENTH37;
+ static const int NBPAIRS;
+ static const int SCALE;
+ static const int TURN;
+ static float *exphairpin;
+ static float expninio[5][32];
+ static float expdangle5[6][4];
+ static float expdangle3[6][4];
+ static float expinternalLoop[31];
+ static float expbulge[31];
+ static char exptriLoop[2][6];
+ static float exptriLoopEnergy[2];
+ static char exptetraLoop[30][7];
+ static float exptetraLoopEnergy[30];
+ static float expStack[6][6];
+ static float expTstackH[6][16];
+ static float expTstackI[6][16];
+ static float expint11[6][6][16];
+ static float expint21[6][6][16][4];
+ static float expint22[6][6][16][16];
+ static float expMLclosing;
+ static float expMLintern[8];
+ static float expTermAU;
+ static float expMLbase[31];
+
+ public:
+
+ McCaskill(int n, const char *mySeq) {
+ seq = new char[n + 1];
+ numSeq = new int[n + 1];
+ n_seq = 0;
+
+
+ for(int i = 0; i < n; i++) {
+ if (mySeq[i] == 'a' || mySeq[i] == 'A') { seq[n_seq] = 'A'; numSeq[n_seq] = Beta::A_CODE; n_seq++; }
+ else if(mySeq[i] == 't' || mySeq[i] == 'T' ||
+ mySeq[i] == 'u' || mySeq[i] == 'U') { seq[n_seq] = 'U'; numSeq[n_seq] = Beta::U_CODE; n_seq++; }
+ else if(mySeq[i] == 'g' || mySeq[i] == 'G') { seq[n_seq] = 'G'; numSeq[n_seq] = Beta::G_CODE; n_seq++; }
+ else if(mySeq[i] == 'c' || mySeq[i] == 'C') { seq[n_seq] = 'C'; numSeq[n_seq] = Beta::C_CODE; n_seq++; }
+ else if(mySeq[i] == 'n' || mySeq[i] == 'N') { seq[n_seq] = 'N'; numSeq[n_seq] = Beta::N_CODE; n_seq++; }
+ else if(mySeq[i] == '.' || mySeq[i] == '-') { seq[n_seq] = '-'; numSeq[n_seq] = Beta::GAP_CODE; n_seq++; }
+ else { seq[n_seq] = mySeq[i]; numSeq[n_seq] = Beta::INVALID_CODE; n_seq++; }
+ }
+ seq[n_seq] = '\0';
+ a.Allocator(n_seq);
+ q1.Allocator(n_seq);
+ ab.Allocator(n_seq);
+ am.Allocator(n_seq);
+ am1.Allocator(n_seq);
+ p.Allocator(n_seq);
+ q1v.Allocator(n_seq);
+ abv.Allocator(n_seq);
+ amv.Allocator(n_seq);
+ am1v.Allocator(n_seq);
+ pv.Allocator(n_seq);
+ typeMat.Allocator(n_seq);
+
+ if(n_seq > 31) {
+ exphairpin = new float[n_seq + 1];
+ }
+ else {
+ exphairpin = new float[31];
+ }
+
+ for(int i = 0; i < n_seq; i++) {
+ for(int j = i; j < n_seq; j++) {
+ a.ref(i,j) = q1.ref(i,j) = IMPOSSIBLE;
+ q1v.ref(i,j) = IMPOSSIBLE;
+ }
+ }
+
+ for(int i = 0; i < n_seq; i++) {
+ a.ref(i,i) = 0.0;
+ q1.ref(i,i) = IMPOSSIBLE;
+ q1v.ref(i,i) = IMPOSSIBLE;
+ }
+
+ for(int i = 0; i < n_seq-1; i++) {
+ a.ref(i,i+1) = 0.0;
+ q1.ref(i,i+1) = IMPOSSIBLE;
+ q1v.ref(i,i+1) = IMPOSSIBLE;
+ }
+
+ for(int i = 0; i < n_seq-2; i++) {
+ a.ref(i,i+2) = 0.0;
+ q1.ref(i,i+2) = IMPOSSIBLE;
+ q1v.ref(i,i+2) = IMPOSSIBLE;
+ }
+
+ for(int i = 0; i < n_seq-3; i++) {
+ a.ref(i,i+3) = 0.0;
+ q1.ref(i,i+3) = IMPOSSIBLE;
+ q1v.ref(i,i+3) = IMPOSSIBLE;
+
+ }
+
+ for(int i = 0; i < n_seq; i++) {
+ for(int j = i; j < n_seq; j++) {
+ ab.ref(i,j) = am.ref(i,j) = am1.ref(i,j) = p.ref(i,j) = IMPOSSIBLE;
+ abv.ref(i,j) = amv.ref(i,j) = am1v.ref(i,j) = pv.ref(i,j) = IMPOSSIBLE;
+ }
+ }
+
+ /* the type of base pair */
+ /* C <-> G : type 1 */
+ /* G <-> C : type 2 */
+ /* G <-> U : type 3 */
+ /* U <-> G : type 5 */
+ /* A <-> U : type 0 */
+ /* U <-> A : type 4 */
+ /* ? <-> ? : type 6 */
+ for(int i = 0; i < n_seq; i++) {
+ for(int j = i; j < n_seq; j++) {
+ typeMat.ref(i,j) = Beta::getReducedPairCode(numSeq[i], numSeq[j]);
+ }
+ }
+
+ }
+
+ /*------------------------------------------------------------------------*/
+ /* dangling ends should never be destabilizing, i.e. expdangle>=1 */
+ /* specific heat needs smooth function (2nd derivative) */
+ /* we use a*(sin(x+b)+1)^2, with a=2/(3*sqrt(3)), b=Pi/6-sqrt(3)/2, */
+ /* in the interval b<x<sqrt(3)/2 */
+ float SMOOTH(float X) {
+ return ((X)/SCALE<-1.2283697)?0:(((X)/SCALE>0.8660254)?(X):
+ SCALE*0.38490018*(sin((X)/SCALE-0.34242663)+1)*(sin((X)/SCALE-0.34242663)+1));
+ }
+
+ ~McCaskill() {
+ delete[] seq;
+ delete[] numSeq;
+ delete[] exphairpin;
+ }
+
+ void calcPartitionFunction();
+ void printProbMat();
+
+ inline float getProb(const int i, const int j) const {
+ // 0 origin : 0..(n-1)
+ return p.ref(i, j);
+ }
+};
+}
+#endif // MCCASKILL_H
--- /dev/null
+1.Program name
+ MXSCARNA
+
+2.Author
+ Yasuo Tabei
+
+ Department of Computational Biology,
+ Graduate School of Frontier Science,
+ The University of Tokyo
+ and
+ Computational Biology Research Center (CBRC),
+ National Institute of Advanced Industrial Science and Technology (AIST)
+
+ E-mail: scarna@m.aist.go.jp
+
+3.What is MXSCARNA
+ MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a tool for
+ fast structural multiple alignment of RNA sequences using progressive
+ alignment based on pairwise structural alignment algorithm of SCARNA.
+
+4.License
+ While its original source code is provided as free software, MXSCARNA
+ contains the source codes of ProbCons and Rfold and the energy parameters
+ of Vienna RNA package (version 1.5).
+ The author thanks Dr. Chuong Do, Dr. Hisanori Kiryu and Dr. Ivo Hofacker,
+ the authors of ProbCons, Rfold and Vienna RNA package respectively,
+ and Institute for Theoretical Chemistry of the University of Vienna.
+
+ The source code of Rfold is located in ./src/rfold-0.1, which includes
+ energy parameters of Vienna RNA package in ./src/rfold-0.1/src/vienna.
+ Energy parameters of Vienna RNA package are also included in the source
+ code of MXSCARNA (./src/vienna). Please follow ./src/rfold-0.1/readme.txt
+ file, which describes the license of Rfold, and
+ ./src/rfold-0.1/src/vienna/COPYING file and ./src/vienna/COPYING file,
+ which describe the copyright notice of the Vienna RNA package.
+ The source code of ProbCons is located in ./src/probconsRNA. Please follow
+ ./src/probcons/README.
+
+ The original part of MXSCARNA is provided as free software. It is
+ distributed in the hope that it will be useful but WITHOUT ANY WARRANTY;
+ without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE.
+
+ Permission is granted for research, educational, and commercial use
+ and modification so long as
+ 1) the package and any derived works are not redistributed for any fee,
+ other than media costs,
+ 2) proper credit is given to
+ the authors of MXSCARNA, ProbCons, Rfold and Vienna RNA package,
+ the Univeristy of Tokyo,
+ Computational Biology Research Center (CBRC), AIST
+ and Institute for Theoretical Chemistry of the University of Vienna.
+
+ If you want to include this software in a commercial product, please
+ contact the author.
+
+5.Citation
+ Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
+ "A fast structural multiple alignment method for long RNA sequences,"
+ BMC bioinformatics, to appear.
+
+6.References
+
+ Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005.
+ PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment.
+ Genome Research 15: 330-340.
+
+ Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai
+ Rfold: An exact algorithm for computing local base pairing probabilities
+ Bioinformatics, Advance Access published on December 4, 2007;
+ doi:10.1093/bioinformatics/btm591
+
+ Ivo L. Hofacker
+ Vienna RNA secondary structure server
+ Nucleic Acids Res., Jul 2003; 31: 3429 - 3431.
+
+ Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai
+ SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments
+ Bioinformatics 2006 22(14):1723-1729.
+
+7.Install
+ The program was tested using gcc 3.3.3 on linux machines and gcc 3.4 on
+ cygwin Some gcc specific features are currently used.
+
+ The command to compile this software is as follows:
+
+ make
+ cd program
+
+8.Usage
+
+ ./mxscarna [options] seqfile
+
+ seqfile:
+ sequence file is multi fasta format.
+
+ options:
+ -clustalw
+ use CLUSTALW output format instead of MFA
+
+ -stockholm
+ use STOCKHOLM output format instead of MFA
+
+ -mxscarna
+ use original output format instead of MFA
+
+ -l <SCSLENGTH>
+ the length of stem candidates (default:2)
+
+ -b <BASEPROBTHRESHOLD>
+ the threshold of base-pairing probability (default:0.01)
+
+ -g <BASEPAIRSCORECONT>
+ the control parameter of the prediction of base-pairs, (default:6)
+
+ -rfold
+ use Rfold instead of global McCaskill algorithm to calcurate base
+ paring probality matrices, (default: off)
+
+ -w <BANDWIDTH>
+ the control parameter of the distance of stem candidates, (default:500)
+
+9.Example
+ ./mxscarna -mxscarna ../sample/trna.mfa
+
+10.Version History
+1. 1/16/2008 (Yasuo Tabei)
+-- MXSCARNA ver 2.0 release
+ - Rfold was included.
\ No newline at end of file
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// ScoreType.h
+//
+// Routines for doing math operations in PROBCONS.
+/////////////////////////////////////////////////////////////////
+
+#ifndef SCORETYPE_H
+#define SCORETYPE_H
+
+#include <cmath>
+#include <algorithm>
+#include <cfloat>
+#include <cassert>
+
+typedef float ScoreType;
+
+const float LOG_ZERO = -2e20;
+const float LOG_ONE = 0.0;
+
+/////////////////////////////////////////////////////////////////
+// LOG()
+//
+// Compute the logarithm of x.
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType LOG (ScoreType x){
+ return log (x);
+}
+
+/////////////////////////////////////////////////////////////////
+// EXP()
+//
+// Computes exp(x).
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType EXP (ScoreType x){
+ //return exp(x);
+ if (x > -2){
+ if (x > -0.5){
+ if (x > 0)
+ return exp(x);
+ return (((0.03254409303190190000*x + 0.16280432765779600000)*x + 0.49929760485974900000)*x + 0.99995149601363700000)*x + 0.99999925508501600000;
+ }
+ if (x > -1)
+ return (((0.01973899026052090000*x + 0.13822379685007000000)*x + 0.48056651562365000000)*x + 0.99326940370383500000)*x + 0.99906756856399500000;
+ return (((0.00940528203591384000*x + 0.09414963667859410000)*x + 0.40825793595877300000)*x + 0.93933625499130400000)*x + 0.98369508190545300000;
+ }
+ if (x > -8){
+ if (x > -4)
+ return (((0.00217245711583303000*x + 0.03484829428350620000)*x + 0.22118199801337800000)*x + 0.67049462206469500000)*x + 0.83556950223398500000;
+ return (((0.00012398771025456900*x + 0.00349155785951272000)*x + 0.03727721426017900000)*x + 0.17974997741536900000)*x + 0.33249299994217400000;
+ }
+ if (x > -16)
+ return (((0.00000051741713416603*x + 0.00002721456879608080)*x + 0.00053418601865636800)*x + 0.00464101989351936000)*x + 0.01507447981459420000;
+ return 0;
+}
+
+/*
+/////////////////////////////////////////////////////////////////
+// LOOKUP()
+//
+// Computes log (exp (x) + 1), for 0 <= x <= 7.5.
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType LOOKUP (ScoreType x){
+ //return log (exp(x) + 1);
+ if (x < 2){
+ if (x < 0.5){
+ if (x < 0)
+ return log (exp(x) + 1);
+ return (((-0.00486373205785640000*x - 0.00020245408813934800)*x + 0.12504222666029800000)*x + 0.49999685320563000000)*x + 0.69314723138948900000;
+ }
+ if (x < 1)
+ return (((-0.00278634205460548000*x - 0.00458097251248546000)*x + 0.12865849880472500000)*x + 0.49862228499205200000)*x + 0.69334810088688000000;
+ return (((0.00059633755154209200*x - 0.01918996666063320000)*x + 0.15288232492093800000)*x + 0.48039958825756900000)*x + 0.69857578503189200000;
+ }
+ if (x < 8){
+ if (x < 4)
+ return (((0.00135958539181047000*x - 0.02329807659316430000)*x + 0.15885799609532100000)*x + 0.48167498563270800000)*x + 0.69276185058669200000;
+ return (((0.00011992394456683500*x - 0.00338464503306568000)*x + 0.03622746366545470000)*x + 0.82481250248383700000)*x + 0.32507892994863100000;
+ }
+ if (x < 16)
+ return (((0.00000051726300753785*x - 0.00002720671238876090)*x + 0.00053403733818413500)*x + 0.99536021775747900000)*x + 0.01507065715532010000;
+ return x;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOOKUP_SLOW()
+//
+// Computes log (exp (x) + 1).
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType LOOKUP_SLOW (ScoreType x){
+ return log (exp (x) + 1);
+}
+
+/////////////////////////////////////////////////////////////////
+// MAX()
+//
+// Compute max of three numbers
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType MAX (ScoreType x, ScoreType y, ScoreType z){
+ if (x >= y){
+ if (x >= z)
+ return x;
+ return z;
+ }
+ if (y >= z)
+ return y;
+ return z;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_PLUS_EQUALS()
+//
+// Add two log probabilities and store in the first argument
+/////////////////////////////////////////////////////////////////
+
+inline void LOG_PLUS_EQUALS (ScoreType &x, ScoreType y){
+ if (x < y)
+ x = (x <= LOG_ZERO) ? y : LOOKUP(y-x) + x;
+ else
+ x = (y <= LOG_ZERO) ? x : LOOKUP(x-y) + y;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_PLUS_EQUALS_SLOW()
+//
+// Add two log probabilities and store in the first argument
+/////////////////////////////////////////////////////////////////
+
+inline void LOG_PLUS_EQUALS_SLOW (ScoreType &x, ScoreType y){
+ if (x < y)
+ x = (x <= LOG_ZERO) ? y : LOOKUP_SLOW(y-x) + x;
+ else
+ x = (y <= LOG_ZERO) ? x : LOOKUP_SLOW(x-y) + y;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add two log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType LOG_ADD (ScoreType x, ScoreType y){
+ if (x < y) return (x <= LOG_ZERO) ? y : LOOKUP(y-x) + x;
+ return (y <= LOG_ZERO) ? x : LOOKUP(x-y) + y;
+}
+*/
+
+/*
+/////////////////////////////////////////////////////////////////
+// LOG()
+//
+// Compute the logarithm of x.
+/////////////////////////////////////////////////////////////////
+
+inline float LOG (float x){
+ return log (x);
+}
+
+/////////////////////////////////////////////////////////////////
+// EXP()
+//
+// Computes exp(x), fr -4.6 <= x <= 0.
+/////////////////////////////////////////////////////////////////
+
+inline float EXP (float x){
+ assert (x <= 0.00f);
+ if (x < EXP_UNDERFLOW_THRESHOLD) return 0.0f;
+ return (((0.006349841068584 * x + 0.080775412572352) * x + 0.397982026296272) * x + 0.95279335963787f) * x + 0.995176455837312f;
+ //return (((0.00681169825657f * x + 0.08386267698832f) * x + 0.40413983195844f) * x + 0.95656674979767f) * x + 0.99556744049130f;
+}
+*/
+
+const float EXP_UNDERFLOW_THRESHOLD = -4.6;
+const float LOG_UNDERFLOW_THRESHOLD = 7.5;
+
+/////////////////////////////////////////////////////////////////
+// LOOKUP()
+//
+// Computes log (exp (x) + 1), for 0 <= x <= 7.5.
+/////////////////////////////////////////////////////////////////
+
+inline float LOOKUP (float x){
+ assert (x >= 0.00f);
+ assert (x <= LOG_UNDERFLOW_THRESHOLD);
+ //return ((-0.00653779113685f * x + 0.09537236626558f) * x + 0.55317574459331f) * x + 0.68672959851568f;
+ if (x <= 1.00f) return ((-0.009350833524763f * x + 0.130659527668286f) * x + 0.498799810682272f) * x + 0.693203116424741f;
+ if (x <= 2.50f) return ((-0.014532321752540f * x + 0.139942324101744f) * x + 0.495635523139337f) * x + 0.692140569840976f;
+ if (x <= 4.50f) return ((-0.004605031767994f * x + 0.063427417320019f) * x + 0.695956496475118f) * x + 0.514272634594009f;
+ assert (x <= LOG_UNDERFLOW_THRESHOLD);
+ return ((-0.000458661602210f * x + 0.009695946122598f) * x + 0.930734667215156f) * x + 0.168037164329057f;
+
+ //return (((0.00089738532761f * x - 0.01859488697982f) * x + 0.14415772028626f) * x + 0.49515490689159f) * x + 0.69311928966454f;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOOKUP_SLOW()
+//
+// Computes log (exp (x) + 1).
+/////////////////////////////////////////////////////////////////
+
+inline float LOOKUP_SLOW (float x){
+ return log (exp (x) + 1);
+}
+
+/////////////////////////////////////////////////////////////////
+// MAX()
+//
+// Compute max of three numbers
+/////////////////////////////////////////////////////////////////
+
+inline float MAX (float x, float y, float z){
+ if (x >= y){
+ if (x >= z)
+ return x;
+ return z;
+ }
+ if (y >= z)
+ return y;
+ return z;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_PLUS_EQUALS()
+//
+// Add two log probabilities and store in the first argument
+/////////////////////////////////////////////////////////////////
+
+inline void LOG_PLUS_EQUALS (float &x, float y){
+ if (x < y)
+ x = (x == LOG_ZERO || y - x >= LOG_UNDERFLOW_THRESHOLD) ? y : LOOKUP(y-x) + x;
+ else
+ x = (y == LOG_ZERO || x - y >= LOG_UNDERFLOW_THRESHOLD) ? x : LOOKUP(x-y) + y;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_PLUS_EQUALS_SLOW()
+//
+// Add two log probabilities and store in the first argument
+/////////////////////////////////////////////////////////////////
+
+inline void LOG_PLUS_EQUALS_SLOW (float &x, float y){
+ if (x < y)
+ x = (x == LOG_ZERO) ? y : LOOKUP_SLOW(y-x) + x;
+ else
+ x = (y == LOG_ZERO) ? x : LOOKUP_SLOW(x-y) + y;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add two log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x, float y){
+ if (x < y) return (x == LOG_ZERO || y - x >= LOG_UNDERFLOW_THRESHOLD) ? y : LOOKUP(y-x) + x;
+ return (y == LOG_ZERO || x - y >= LOG_UNDERFLOW_THRESHOLD) ? x : LOOKUP(x-y) + y;
+}
+
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add three log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3){
+ return LOG_ADD (x1, LOG_ADD (x2, x3));
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add four log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3, float x4){
+ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, x4)));
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add five log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5){
+ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, x5))));
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add siz log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5, float x6){
+ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, LOG_ADD (x5, x6)))));
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add seven log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5, float x6, float x7){
+ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, LOG_ADD (x5, LOG_ADD (x6, x7))))));
+}
+
+/////////////////////////////////////////////////////////////////
+// ChooseBestOfThree()
+//
+// Store the largest of three values x1, x2, and x3 in *x. Also
+// if xi is the largest value, then store bi in *b.
+/////////////////////////////////////////////////////////////////
+
+inline void ChooseBestOfThree (float x1, float x2, float x3, char b1, char b2, char b3, float *x, char *b){
+ if (x1 >= x2){
+ if (x1 >= x3){
+ *x = x1;
+ *b = b1;
+ return;
+ }
+ *x = x3;
+ *b = b3;
+ return;
+ }
+ if (x2 >= x3){
+ *x = x2;
+ *b = b2;
+ return;
+ }
+ *x = x3;
+ *b = b3;
+}
+#endif
--- /dev/null
+/////////////////////////////////////////////////////////////
+// StemCandidate.hpp
+// Profile Stem Candidate calcurated by profile base pairing
+// probability matrix
+////////////////////////////////////////////////////////////
+
+#ifndef __STEMCANDIDATE_HPP__
+#define __STEMCANDIDATE_HPP__
+
+#include <string>
+#include <vector>
+
+using namespace std;
+
+namespace MXSCARNA {
+class StemCandidate {
+private:
+ int numSeq; /* the number of sequences in the profile */
+ int length; /* length of profile stem candidate of fixed length */
+ int position; /* 5' start position of SC in profile */
+ int distance;
+ std::vector<std::string> substr; /* profile base string of SC */
+ std::vector<std::string> rvstr; /* profile base string of stem partner of SC */
+ int rvposition; /* 3' end position of stem partner of SC */
+ int rvscnumber; /* SC number of stem partner */
+ int contPos; /* previous stem that corresponds continuous stem and has position -1. */
+ int beforePos; /* most recent stem that doesn't overlap to SC and has position -len. */
+ float score; /* score of the sum of base pairing probability matrix */
+ std::vector<float> baseScore;
+ float stacking; /* the mean of stacking energy */
+ float stemStacking; /* the mean of 1-continuous stacking energy */
+
+public:
+ StemCandidate() : numSeq(0), length(0), position(0), distance(0),
+ rvposition(0), rvscnumber(0), contPos(-1), beforePos(0),
+ score(0), stacking(0), stemStacking(0) {}
+ StemCandidate(int numSeq, int length) : numSeq(numSeq), length(length),
+ substr(numSeq), rvstr(numSeq),
+ contPos(-1) { }
+
+ void SetNumSeq(int num) { numSeq = num; }
+ void SetLength(int len) { length = len; }
+ void SetNumSubstr(int num) {
+ substr.resize(num);
+ for(int i = 0; i < num; i++) {
+ string &tmpStr = substr[i];
+ tmpStr = "";
+ substr[i] = tmpStr;
+ }
+ }
+ void SetNumRvstr(int num) {
+ rvstr.resize(num);
+
+ for(int i = 0; i < num; i++) {
+ string &tmpStr = rvstr[i];
+ tmpStr = "";
+ rvstr[i] = tmpStr;
+ }
+ }
+ void SetPosition(int pos) { position = pos; }
+
+ void AddSubstr(int num, char word) {
+ std::string &tmpStr = substr[num];
+ tmpStr += word;
+ substr[num] = tmpStr;
+ }
+
+ void AddRvstr(int num, char word) {
+ std::string &tmpStr = rvstr[num];
+ tmpStr += word;
+ rvstr[num] = tmpStr;
+ }
+
+ void AddBaseScore(float score) {
+ baseScore.push_back(score);
+ }
+
+ void SetRvposition(int pos) { rvposition = pos; }
+ void SetRvscnumber(int num) { rvscnumber = num; }
+ void SetContPos(int pos) { contPos = pos; }
+ void SetBeforePos(int pos) { beforePos = pos; }
+ void SetDistance(int d) { distance = d; }
+ void SetScore(float s) { score = s; }
+ void AddScore(float s) { score += s; }
+ void SetStacking(float s) { stacking = s; }
+ void AddStacking(float s) { stacking += s; }
+ void SetStemStacking(float s) { stemStacking = s; }
+ int GetNumSeq() const { return numSeq; }
+ int GetLength() const { return length; }
+ int GetPosition() const { return position; }
+
+ string GetSubstr(int num) const {
+ const std::string &tmpStr = substr[num];
+ return tmpStr;
+ }
+ string GetRvstr(int num) const {
+ const std::string &tmpStr = rvstr[num];
+ return tmpStr;
+ }
+ float GetBaseScore(int i) const {
+ return baseScore[i];
+ }
+ int GetRvposition() const {
+ return rvposition;
+ }
+ int GetRvscnumber() const {
+ return rvscnumber;
+ }
+ int GetContPos() const {
+ return contPos;
+ }
+ int GetBeforePos() const {
+ return beforePos;
+ }
+ int GetDistance() const {
+ return distance;
+ }
+ float GetScore() const {
+ return score;
+ }
+ float GetStacking() const {
+ return stacking;
+ }
+ float GetStemStacking() const {
+ return stemStacking;
+ }
+};
+}
+#endif // __STEMCANDIDATE_HPP__
--- /dev/null
+#ifndef UTIL_H
+#define UTIL_H
+
+#include <algorithm>
+#include <cassert>
+#include <cstdio>
+#include <cstdlib>
+#include <cstdarg>
+#include <cstring>
+#include <cmath>
+#include <cctype>
+#include <climits>
+#include <cfloat>
+#include <ctime>
+#include <fstream>
+#include <functional>
+#include <iomanip>
+#include <iostream>
+#include <iterator>
+#include <list>
+#include <map>
+#include <numeric>
+#include <string>
+#include <sstream>
+#include <stack>
+#include <vector>
+#include <fcntl.h>
+#include <unistd.h>
+//#include <pthread.h> // mingw de error, by katoh
+#include <signal.h>
+
+namespace ProbCons {
+
+const double IMPOSSIBLE = -FLT_MAX + 1000;
+const double IMPOSSIBLEDBL = -DBL_MAX + 10000;
+
+namespace MXSCARNA {
+template <typename T>
+inline bool
+IsPossible(const T& v) {
+ return (v > (IMPOSSIBLE + 1.0e-5));
+}
+
+template <typename T>
+inline T
+logSum(const T& a, const T& b)
+{
+ if (a >= b) {
+ return a + log(1.0 + exp(b - a));
+ } else {
+ return b + log(1.0 + exp(a - b));
+ }
+}
+
+template <typename T>
+inline T
+logSub(const T&a, const T& b)
+{
+ if(a > b) {
+ return log(exp(a) - exp(b));
+ }
+ else {
+ return log(exp(a) - exp(b));
+ }
+}
+
+template <typename T>
+inline T
+logSum(const T& a, const T& b, const T& c)
+{
+ if (a >= b) {
+ if( a >= c ) {
+ return a + log(1.0 + (exp(b - a) + exp(c - a)));
+ }
+ else {
+ if( b >= c) {
+ return b + log(exp(a - b) + 1.0 + exp(c - b));
+ }
+ }
+ }
+ return c + log(exp(a - c) + exp(b - c) + 1.0);
+}
+
+}
+
+template <typename T>
+inline T
+logSumExp(const T& x, const T& y)
+{
+ if(x == y) return x + 0.69314718055;
+ double vmin = std::min(x, y);
+ double vmax = std::max(x, y);
+
+ if (vmax > vmin + 50) {
+ return vmax;
+ }
+ else {
+ return vmax + std::log (std::exp (vmin - vmax) + 1.0);
+ }
+}
+}
+#endif /* UTIL_H */
--- /dev/null
+/* config.h. Generated by configure. */
+/* config.h.in. Generated from configure.in by autoheader. */
+
+/* Define to 1 if you have the `erand48' function. */
+#define HAVE_ERAND48 1
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#define HAVE_INTTYPES_H 1
+
+/* Define to 1 if you have the <malloc.h> header file. */
+#define HAVE_MALLOC_H 1
+
+/* Define to 1 if you have the <memory.h> header file. */
+#define HAVE_MEMORY_H 1
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#define HAVE_STDINT_H 1
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#define HAVE_STDLIB_H 1
+
+/* Define to 1 if you have the `strchr' function. */
+#define HAVE_STRCHR 1
+
+/* Define to 1 if you have the `strdup' function. */
+#define HAVE_STRDUP 1
+
+/* Define to 1 if you have the <strings.h> header file. */
+#define HAVE_STRINGS_H 1
+
+/* Define to 1 if you have the <string.h> header file. */
+#define HAVE_STRING_H 1
+
+/* Define to 1 if you have the `strstr' function. */
+#define HAVE_STRSTR 1
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#define HAVE_SYS_STAT_H 1
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#define HAVE_SYS_TYPES_H 1
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#define HAVE_UNISTD_H 1
+
+/* Name of package */
+#define PACKAGE "ViennaRNA"
+
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"
+
+/* Define to the full name of this package. */
+#define PACKAGE_NAME "ViennaRNA"
+
+/* Define to the full name and version of this package. */
+#define PACKAGE_STRING "ViennaRNA 1.6.1"
+
+/* Define to the one symbol short name of this package. */
+#define PACKAGE_TARNAME "ViennaRNA"
+
+/* Define to the version of this package. */
+#define PACKAGE_VERSION "1.6.1"
+
+/* Define to 1 if you have the ANSI C header files. */
+#define STDC_HEADERS 1
+
+/* only for gcc */
+#define UNUSED __attribute__ ((unused))
+
+/* Version number of package */
+#define VERSION "1.6.1"
+
+/* Define if using the dmalloc debugging malloc package */
+/* #undef WITH_DMALLOC */
+
+/* Define to empty if `const' does not conform to ANSI C. */
+/* #undef const */
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+ calls it, or to nothing if 'inline' is not supported under any name. */
+#ifndef __cplusplus
+/* #undef inline */
+#endif
+
+/* Define to `unsigned' if <sys/types.h> does not define. */
+/* #undef size_t */
--- /dev/null
+/*
+ McCaskill's Algorithm -- The algorithm calculates a base paring probability matrix from the input of one sequence.
+
+ $Id: nrutil.h,v 1.0 2005/10/20 14:22 $;
+
+ Copyright (C) 2005 Yasuo Tabei <tabei@cb.k.u-tokyo.ac.jp>
+
+ This is free software with ABSOLUTELY NO WARRANTY.
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+#ifndef _NR_UTIL_H_
+#define _NR_UTIL_H_
+#include <string>
+#include <cmath>
+#include <complex>
+#include <iostream>
+#include <cstdlib> // by katoh
+
+using namespace std;
+
+typedef double DP;
+
+template<class T>
+inline const T SQR(const T a) {return a*a;}
+
+template<class T>
+inline const T MAX(const T &a, const T &b)
+{return b > a ? (b) : (a);}
+
+inline float MAX(const double &a, const float &b)
+{return b > a ? (b) : float(a);}
+
+inline float MAX(const float &a, const double &b)
+{return b > a ? float(b) : (a);}
+
+template<class T>
+inline const T MIN(const T &a, const T &b)
+{return b < a ? (b) : (a);}
+
+inline float MIN(const double &a, const float &b)
+{return b < a ? (b) : float(a);}
+
+inline float MIN(const float &a, const double &b)
+{return b < a ? float(b) : (a);}
+
+template<class T>
+inline const T SIGN(const T &a, const T &b)
+{return b >= 0 ? (a >= 0 ? a : -a) : (a >= 0 ? -a : a);}
+
+inline float SIGN(const float &a, const double &b)
+{return b >= 0 ? (a >= 0 ? a : -a) : (a >= 0 ? -a : a);}
+
+inline float SIGN(const double &a, const float &b)
+{return b >= 0 ? (a >= 0 ? a : -a) : (a >= 0 ? -a : a);}
+
+template<class T>
+inline void SWAP(T &a, T &b)
+{T dum=a; a=b; b=dum;}
+namespace NR {
+ inline void nrerror(const string error_text)
+// Numerical Recipes standard error handler
+ {
+ cerr << "Numerical Recipes run-time error..." << endl;
+ cerr << error_text << endl;
+ cerr << "...now exiting to system..." << endl;
+ exit(1);
+ }
+}
+
+template <class T>
+class NRVec {
+ private:
+ int nn; // size of array. upper index is nn-1
+ T *v;
+ public:
+ NRVec();
+ explicit NRVec(int n); // Zero-based array
+ NRVec(const T &a, int n); //initialize to constant value
+ NRVec(const T *a, int n); // Initialize to array
+ NRVec(const NRVec &rhs); // Copy constructor
+ NRVec & operator=(const NRVec &rhs); //assignment
+ NRVec & operator=(const T &a); //assign a to every element
+ inline T & operator[](const int i); //i¡Çth element
+ inline const T & operator[](const int i) const;
+ void Allocator(int i);
+ inline int size() const;
+ ~NRVec();
+};
+
+template <class T>
+NRVec<T>::NRVec() : nn(0), v(0) {}
+
+template <class T>
+NRVec<T>::NRVec(int n) : nn(n), v(new T[n]) {}
+
+template <class T>
+NRVec<T>::NRVec(const T& a, int n) : nn(n), v(new T[n])
+{
+ for(int i=0; i<n; i++)
+ v[i] = a;
+}
+
+template <class T>
+NRVec<T>::NRVec(const T *a, int n) : nn(n), v(new T[n])
+{
+for(int i=0; i<n; i++)
+ v[i] = *a++;
+}
+
+template <class T>
+void NRVec<T>::Allocator(int n = 0)
+{
+ v = new T[n];
+}
+
+template <class T>
+NRVec<T>::NRVec(const NRVec<T> &rhs) : nn(rhs.nn), v(new T[nn])
+{
+ for(int i=0; i<nn; i++)
+ v[i] = rhs[i];
+}
+
+template <class T>
+NRVec<T> & NRVec<T>::operator=(const NRVec<T> &rhs)
+// postcondition: normal assignment via copying has been performed;
+// if vector and rhs were different sizes, vector
+// has been resized to match the size of rhs
+{
+ if (this != &rhs)
+{
+ if (nn != rhs.nn) {
+ if (v != 0) delete [] (v);
+ nn=rhs.nn;
+ v= new T[nn];
+ }
+ for (int i=0; i<nn; i++)
+ v[i]=rhs[i];
+}
+ return *this;
+}
+
+template <class T>
+NRVec<T> & NRVec<T>::operator=(const T &a) //assign a to every element
+{
+ for (int i=0; i<nn; i++)
+ v[i]=a;
+ return *this;
+}
+
+template <class T>
+inline T & NRVec<T>::operator[](const int i) //subscripting
+{
+ return v[i];
+}
+
+template <class T>
+inline const T & NRVec<T>::operator[](const int i) const //subscripting
+{
+ return v[i];
+}
+
+template <class T>
+inline int NRVec<T>::size() const
+{
+ return nn;
+}
+
+template <class T>
+NRVec<T>::~NRVec()
+{
+ if (v != 0)
+ delete[] (v);
+}
+
+template <class T>
+class NRMat {
+ private:
+ int nn;
+ int mm;
+ T **v;
+ public:
+ NRMat();
+ NRMat(int n, int m); // Zero-based array
+ NRMat(const T &a, int n, int m); //Initialize to constant
+ NRMat(const T *a, int n, int m); // Initialize to array
+ NRMat(const NRMat &rhs); // Copy constructor
+ void Allocator(int n, int m);
+ void Allocator(const T &a, int n, int m);
+ void Allocator(const T *a, int n, int m);
+ NRMat & operator=(const NRMat &rhs); //assignment
+ NRMat & operator=(const T &a); //assign a to every element
+ inline T* operator[](const int i); //subscripting: pointer to row i
+ inline const T* operator[](const int i) const;
+ inline T & ref(const int i, const int j);
+ inline const T ref(const int i, const int j) const;
+ inline int nrows() const;
+ inline int ncols() const;
+ ~NRMat();
+};
+
+template <class T>
+NRMat<T>::NRMat() : nn(0), mm(0), v(0) {}
+
+template <class T>
+NRMat<T>::NRMat(int n, int m) : nn(n), mm(m), v(new T*[n])
+{
+ v[0] = new T[m*n];
+ for (int i=1; i< n; i++)
+ v[i] = v[i-1] + m;
+}
+
+template <class T>
+NRMat<T>::NRMat(const T &a, int n, int m) : nn(n), mm(m), v(new T*[n])
+{
+ int i,j;
+ v[0] = new T[m*n];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + m;
+ for (i=0; i< n; i++)
+ for (j=0; j<m; j++)
+ v[i][j] = a;
+}
+
+template <class T>
+NRMat<T>::NRMat(const T *a, int n, int m) : nn(n), mm(m), v(new T*[n])
+{
+ int i,j;
+ v[0] = new T[m*n];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + m;
+ for (i=0; i< n; i++)
+ for (j=0; j<m; j++)
+ v[i][j] = *a++;
+}
+
+template <class T>
+void NRMat<T>::Allocator(int n, int m)
+{
+ if( v != 0 ) {
+ delete[] (v[0]); delete (v);
+ }
+
+ nn = n; mm = m; v = new T*[n];
+
+ v[0] = new T[m*n];
+ for (int i=1; i< n; i++)
+ v[i] = v[i-1] + m;
+}
+
+template <class T>
+void NRMat<T>::Allocator(const T &a, int n, int m)
+{
+ if( v != 0 ) {
+ delete[] (v[0]); delete (v);
+ }
+
+ int i,j;
+
+ nn = n; mm = m; v = new T*[n];
+
+ v[0] = new T[m*n];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + m;
+ for (i=0; i< n; i++)
+ for (j=0; j<m; j++)
+ v[i][j] = a;
+}
+
+template <class T>
+void NRMat<T>::Allocator(const T *a, int n, int m)
+{
+ if( v != 0 ) {
+ delete[] (v[0]); delete (v);
+ }
+
+ int i,j;
+
+ nn = n; mm = m; v = new T*[n];
+
+ v[0] = new T[m*n];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + m;
+ for (i=0; i< n; i++)
+ for (j=0; j<m; j++)
+ v[i][j] = *a++;
+}
+
+template <class T>
+NRMat<T>::NRMat(const NRMat &rhs) : nn(rhs.nn), mm(rhs.mm), v(new T*[nn])
+{
+ int i,j;
+ v[0] = new T[mm*nn];
+ for (i=1; i< nn; i++)
+ v[i] = v[i-1] + mm;
+ for (i=0; i< nn; i++)
+ for (j=0; j<mm; j++)
+ v[i][j] = rhs[i][j];
+}
+template <class T>
+NRMat<T> & NRMat<T>::operator=(const NRMat<T> &rhs)
+// postcondition: normal assignment via copying has been performed;
+// if matrix and rhs were different sizes, matrix
+// has been resized to match the size of rhs
+{
+ if (this != &rhs) {
+ int i,j;
+ if (nn != rhs.nn || mm != rhs.mm) {
+ if (v != 0) {
+ delete[] (v[0]);
+ delete[] (v);
+ }
+ nn=rhs.nn;
+ mm=rhs.mm;
+ v = new T*[nn];
+ v[0] = new T[mm*nn];
+ }
+ for (i=1; i< nn; i++)
+ v[i] = v[i-1] + mm;
+ for (i=0; i< nn; i++)
+ for (j=0; j<mm; j++)
+ v[i][j] = rhs[i][j];
+ }
+ return *this;
+}
+
+template <class T>
+NRMat<T> & NRMat<T>::operator=(const T &a) //assign a to every element
+{
+ for (int i=0; i< nn; i++)
+ for (int j=0; j<mm; j++)
+ v[i][j] = a;
+ return *this;
+}
+
+template <class T>
+inline T* NRMat<T>::operator[](const int i) //subscripting: pointer to row i
+{
+ return v[i];
+}
+
+template <class T>
+inline const T* NRMat<T>::operator[](const int i) const
+{
+ return v[i];
+}
+
+template <class T>
+inline T & NRMat<T>::ref(const int i, const int j)
+{
+ return v[i][j];
+}
+
+template <class T>
+inline const T NRMat<T>::ref(const int i, const int j) const
+{
+ return v[i][j];
+}
+
+template <class T>
+inline int NRMat<T>::nrows() const
+{
+ return nn;
+}
+
+template <class T>
+inline int NRMat<T>::ncols() const
+{
+ return mm;
+}
+
+template <class T>
+NRMat<T>::~NRMat()
+{
+ if (v != 0) {
+ delete[] (v[0]);
+ delete[] (v);
+ }
+}
+
+template <class T>
+class NRMat3d {
+ private:
+ int nn;
+ int mm;
+ int kk;
+ T ***v;
+ public:
+ NRMat3d();
+ NRMat3d(int n, int m, int k);
+ inline void Allocator(int n, int m, int k);
+ inline T** operator[](const int i); //subscripting: pointer to row i
+ inline const T* const * operator[](const int i) const;
+ inline int dim1() const;
+ inline int dim2() const;
+ inline int dim3() const;
+ ~NRMat3d();
+};
+
+template <class T>
+NRMat3d<T>::NRMat3d(): nn(0), mm(0), kk(0), v(0) {}
+template <class T>
+NRMat3d<T>::NRMat3d(int n, int m, int k) : nn(n), mm(m), kk(k), v(new T**[n])
+{
+ int i,j;
+ v[0] = new T*[n*m];
+ v[0][0] = new T[n*m*k];
+ for(j=1; j<m; j++)
+ v[0][j] = v[0][j-1] + k;
+ for(i=1; i<n; i++) {
+ v[i] = v[i-1] + m;
+ v[i][0] = v[i-1][0] + m*k;
+ for(j=1; j<m; j++)
+ v[i][j] = v[i][j-1] + k;
+ }
+}
+
+template <class T>
+inline void NRMat3d<T>::Allocator(int n, int m, int k)
+{
+ int i,j;
+ v[0] = new T*[n*m];
+ v[0][0] = new T[n*m*k];
+ for(j=1; j<m; j++)
+ v[0][j] = v[0][j-1] + k;
+ for(i=1; i<n; i++) {
+ v[i] = v[i-1] + m;
+ v[i][0] = v[i-1][0] + m*k;
+ for(j=1; j<m; j++)
+ v[i][j] = v[i][j-1] + k;
+ }
+}
+
+template <class T>
+inline T** NRMat3d<T>::operator[](const int i) //subscripting: pointer to row i
+{
+ return v[i];
+}
+
+template <class T>
+inline const T* const * NRMat3d<T>::operator[](const int i) const
+{
+ return v[i];
+}
+
+template <class T>
+inline int NRMat3d<T>::dim1() const
+{
+ return nn;
+}
+
+template <class T>
+inline int NRMat3d<T>::dim2() const
+{
+ return mm;
+}
+
+template <class T>
+inline int NRMat3d<T>::dim3() const
+{
+ return kk;
+}
+
+template <class T>
+NRMat3d<T>::~NRMat3d()
+{
+ if (v != 0) {
+ delete[] (v[0][0]);
+ delete[] (v[0]);
+ delete[] (v);
+ }
+}
+
+//The next 3 classes are used in artihmetic coding, Huffman coding, and
+//wavelet transforms respectively. This is as good a place as any to put them!
+class arithcode {
+ private:
+ NRVec<unsigned long> *ilob_p,*iupb_p,*ncumfq_p;
+ public:
+ NRVec<unsigned long> &ilob,&iupb,&ncumfq;
+ unsigned long jdif,nc,minint,nch,ncum,nrad;
+ arithcode(unsigned long n1, unsigned long n2, unsigned long n3)
+ : ilob_p(new NRVec<unsigned long>(n1)),
+ iupb_p(new NRVec<unsigned long>(n2)),
+ ncumfq_p(new NRVec<unsigned long>(n3)),
+ ilob(*ilob_p),iupb(*iupb_p),ncumfq(*ncumfq_p) {}
+ ~arithcode() {
+ if (ilob_p != 0) delete ilob_p;
+ if (iupb_p != 0) delete iupb_p;
+ if (ncumfq_p != 0) delete ncumfq_p;
+ }
+};
+
+class huffcode {
+ private:
+ NRVec<unsigned long> *icod_p,*ncod_p,*left_p,*right_p;
+ public:
+ NRVec<unsigned long> &icod,&ncod,&left,&right;
+ int nch,nodemax;
+ huffcode(unsigned long n1, unsigned long n2, unsigned long n3,
+ unsigned long n4) :
+ icod_p(new NRVec<unsigned long>(n1)),
+ ncod_p(new NRVec<unsigned long>(n2)),
+ left_p(new NRVec<unsigned long>(n3)),
+ right_p(new NRVec<unsigned long>(n4)),
+ icod(*icod_p),ncod(*ncod_p),left(*left_p),right(*right_p) {}
+ ~huffcode() {
+ if (icod_p != 0) delete icod_p;
+ if (ncod_p != 0) delete ncod_p;
+ if (left_p != 0) delete left_p;
+ if (right_p != 0) delete right_p;
+ }
+};
+
+class wavefilt {
+ private:
+ NRVec<DP> *cc_p,*cr_p;
+ public:
+ int ncof,ioff,joff;
+ NRVec<DP> &cc,&cr;
+ wavefilt() : cc(*cc_p),cr(*cr_p) {}
+ wavefilt(const DP *a, const int n) : //initialize to array
+ cc_p(new NRVec<DP>(n)),cr_p(new NRVec<DP>(n)),
+ ncof(n),ioff(-(n >> 1)),joff(-(n >> 1)),cc(*cc_p),cr(*cr_p) {
+ int i;
+ for (i=0; i<n; i++)
+ cc[i] = *a++;
+ DP sig = -1.0;
+ for (i=0; i<n; i++) {
+ cr[n-1-i]=sig*cc[i];
+ sig = -sig;
+ }
+ }
+ ~wavefilt() {
+ if (cc_p != 0) delete cc_p;
+ if (cr_p != 0) delete cr_p;
+ }
+};
+
+
+/* Triangle Matrix Class
+ ---------------------------------------------------------
+ |v[0][0]|v[0][1]| | | |v[0][n-1]|
+ |-------|-------|------|------------|---------|---------|
+ |v[1][1]|v[1][2]| | |v[1][n-2]| |
+ |-------|-------|------|------------|---------|---------|
+ | | | | | | |
+ |-------|-------|------|------------|---------|---------|
+ | | |
+ | | |
+ | | |
+ |-------|-----------------------------------------------|
+ | | |
+ |-------|-----------------------------------------------|
+ |v[n-2][0]|v[n-2][1]| |
+ |-------|-----------------------------------------------|
+ |v[n-1][0]| |
+ |-------------------------------------------------------|
+ */
+template <class T>
+class Trimat {
+ private:
+ int nn;
+ T **v;
+ inline T* operator[](const int i); //subscripting: pointer to row i
+ inline const T* operator[](const int i) const;
+ public:
+ Trimat();
+ Trimat(int n); // Zero-based array
+ Trimat(const T &a, int n); //Initialize to constant
+ Trimat(const T *a, int n); // Initialize to array
+ Trimat(const Trimat &rhs); // Copy constructor
+ void Allocator(int n);
+ void Allocator(const T &a, int n);
+ void Allocator(const T *a, int n);
+ Trimat & operator=(const Trimat &rhs); //assignment
+ Trimat & operator=(const T &a); //assign a to every element
+ inline T & ref(const int i, const int j);
+ inline T * getPointer(const int i, const int j);
+ inline T * begin() const;
+ inline T * end() const;
+ inline const T ref(const int i, const int j) const;
+ inline int nrows() const;
+ ~Trimat();
+};
+
+template <class T>
+Trimat<T>::Trimat() : nn(0), v(0) {}
+
+template <class T>
+Trimat<T>::Trimat(int n) : nn(n), v(new T*[n])
+{
+ v[0] = new T[n*(n+1)/2];
+ for (int i=1; i< n; i++)
+ v[i] = v[i-1] + (n-i+1);
+
+ for (int i=0; i< n; i++)
+ for (int j=0; j<(n-i); j++)
+ v[i][j] = 0;
+}
+template <class T>
+Trimat<T>::Trimat(const T &a, int n) : nn(n), v(new T*[n])
+{
+ int i,j;
+ v[0] = new T[n*(n+1)/2];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + (n-i+1);
+ for (i=0; i< n; i++)
+ for (j=0; j<(n-i); j++)
+ v[i][j] = a;
+}
+
+template <class T>
+Trimat<T>::Trimat(const T *a, int n) : nn(n), v(new T*[n])
+{
+ int i,j;
+ v[0] = new T[n*(n+1)/2];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + (n-i+1);
+ for (i=0; i< n; i++)
+ for (j=0; j<(n-i); j++)
+ v[i][j] = *a++;
+}
+
+
+template <class T>
+void Trimat<T>::Allocator(int n)
+{
+ nn = n; v = new T*[n];
+
+ v[0] = new T[n*(n+1)/2];
+ for (int i=1; i< n; i++)
+ v[i] = v[i-1] + (n-i+1);
+}
+
+template <class T>
+void Trimat<T>::Allocator(const T &a, int n)
+{
+ nn = n; v = new T*[n];
+
+ int i,j;
+ v[0] = new T[n*(n+1)/2];
+ for (i=1; i < n; i++)
+ v[i] = v[i-1] + (n-i+1);
+ for (i=0; i < n; i++)
+ for (j=0; j < (n-i); j++)
+ v[i][j] = a;
+}
+
+template <class T>
+void Trimat<T>::Allocator(const T *a, int n)
+{
+ nn = n; v = new T*[n];
+ int i,j;
+ v[0] = new T[n*(n+1)/2];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + (n-i+1);
+ for (i=0; i< n; i++)
+ for (j=0; j<(n-i); j++)
+ v[i][j] = *a++;
+}
+
+
+template <class T>
+Trimat<T>::Trimat(const Trimat &rhs) : nn(rhs.nn), v(new T*[nn])
+{
+ int i,j;
+ v[0] = new T[nn*(nn+1)/2];
+ for (i=1; i< nn; i++)
+ v[i] = v[i-1] + (nn-i+1);
+ for (i=0; i< nn; i++)
+ for (j=0; j<(nn-i); j++)
+ v[i][j] = rhs[i][j];
+}
+template <class T>
+Trimat<T> & Trimat<T>::operator=(const Trimat<T> &rhs)
+// postcondition: normal assignment via copying has been performed;
+// if matrix and rhs were different sizes, matrix
+// has been resized to match the size of rhs
+{
+ if (this != &rhs) {
+ int i,j;
+ if (nn != rhs.nn) {
+ if (v != 0) {
+ delete[] (v[0]);
+ delete[] (v);
+ }
+ nn=rhs.nn;
+ v = new T*[nn];
+ v[0] = new T[nn*(nn+1)/2];
+ }
+ for (i=1; i< nn; i++)
+ v[i] = v[i-1] + (nn-i+1);
+ for (i=0; i< nn; i++)
+ for (j=0; j<(nn-i); j++)
+ v[i][j] = rhs[i][j];
+ }
+ return *this;
+}
+
+template <class T>
+Trimat<T> & Trimat<T>::operator=(const T &a) //assign a to every element
+{
+ for (int i=0; i< nn; i++)
+ for (int j=0; j<nn-i; j++)
+ v[i][j] = a;
+ return *this;
+}
+
+template <class T>
+inline T & Trimat<T>::ref(const int i, const int j)
+{
+ return v[i][j-i];
+}
+
+template <class T>
+inline const T Trimat<T>::ref(const int i, const int j) const
+{
+ return v[i][j-i];
+}
+
+template <class T>
+inline T * Trimat<T>::getPointer(const int i, const int j)
+{
+ return &v[i][j-i];
+}
+
+template <class T>
+inline T * Trimat<T>::begin() const
+{
+ return &v[0][0];
+}
+
+template <class T>
+inline T * Trimat<T>::end() const
+{
+ return (&v[nn-1][0] + 1);
+}
+
+template <class T>
+inline int Trimat<T>::nrows() const
+{
+ return nn;
+}
+
+template <class T>
+Trimat<T>::~Trimat()
+{
+ if (v != 0) {
+ delete[] (v[0]);
+ delete[] (v);
+ }
+}
+
+
+/* Triangle Vertical Matrix Class
+ ---------------------------------------------------------
+ |v[0][0]|v[1][0]| | | |v[n-1][0]|
+ |-------|-------|------|------------|---------|---------|
+ |v[0][1]|v[1][1]| | |v[n-2][1]| |
+ |-------|-------|------|------------|---------|---------|
+ | | | | | | |
+ |-------|-------|------|------------|---------|---------|
+ | | |
+ | | |
+ | | |
+ |-------|-----------------------------------------------|
+ | | |
+ |-------|-----------------------------------------------|
+ |v[0][n-2]|v[n-2][n-2]| |
+ |-------|-----------------------------------------------|
+ |v[0][n-1]| |
+ |-------------------------------------------------------|
+ */
+template <class T>
+class TriVertMat {
+ private:
+ int nn;
+ T **v;
+ inline T* operator[](const int i); //subscripting: pointer to row i
+ inline const T* operator[](const int i) const;
+ public:
+ TriVertMat();
+ TriVertMat(int n); // Zero-based array
+ TriVertMat(const T &a, int n); //Initialize to constant
+ TriVertMat(const T *a, int n); // Initialize to array
+ TriVertMat(const TriVertMat &rhs); // Copy constructor
+ void Allocator(int n);
+ void Allocator(const T &a, int n);
+ void Allocator(const T *a, int n);
+ TriVertMat & operator=(const TriVertMat &rhs); //assignment
+ TriVertMat & operator=(const T &a); //assign a to every element
+ inline T & ref(const int i, const int j);
+ inline T * getPointer(const int i, const int j);
+ inline const T ref(const int i, const int j) const;
+ inline int nrows() const;
+ ~TriVertMat();
+};
+
+template <class T>
+TriVertMat<T>::TriVertMat() : nn(0), v(0) {}
+
+template <class T>
+TriVertMat<T>::TriVertMat(int n) : nn(n), v(new T*[n])
+{
+ v[0] = new T[n*(n+1)/2];
+ for (int i=1; i< n; i++)
+ v[i] = v[i-1] + i;
+}
+
+template <class T>
+TriVertMat<T>::TriVertMat(const T &a, int n) : nn(n), v(new T*[n])
+{
+ int i,j;
+ v[0] = new T[n*(n+1)/2];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + i;
+ for (i=0; i< n; i++)
+ for (j=0; j<(n-i); j++)
+ v[i][j] = a;
+}
+
+template <class T>
+TriVertMat<T>::TriVertMat(const T *a, int n) : nn(n), v(new T*[n])
+{
+ int i,j;
+ v[0] = new T[n*(n+1)/2];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + i;
+ for (i=0; i< n; i++)
+ for (j=0; j<(n-i); j++)
+ v[i][j] = *a++;
+}
+
+
+template <class T>
+void TriVertMat<T>::Allocator(int n)
+{
+ nn = n; v = new T*[n];
+
+ v[0] = new T[n*(n+1)/2];
+ for (int i=1; i< n; i++)
+ v[i] = v[i-1] + i;
+}
+
+template <class T>
+void TriVertMat<T>::Allocator(const T &a, int n)
+{
+ nn = n; v = new T*[n];
+
+ int i,j;
+ v[0] = new T[n*(n+1)/2];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + i;
+ for (i=0; i< n; i++)
+ for (j=0; j<(n-i); j++)
+ v[i][j] = a;
+}
+
+template <class T>
+void TriVertMat<T>::Allocator(const T *a, int n)
+{
+ nn = n; v = new T*[n];
+ int i,j;
+ v[0] = new T[n*(n+1)/2];
+ for (i=1; i< n; i++)
+ v[i] = v[i-1] + i;
+ for (i=0; i< n; i++)
+ for (j=0; j<(n-i); j++)
+ v[i][j] = *a++;
+}
+
+
+template <class T>
+TriVertMat<T>::TriVertMat(const TriVertMat &rhs) : nn(rhs.nn), v(new T*[nn])
+{
+ int i,j;
+ v[0] = new T[nn*(nn+1)/2];
+ for (i=1; i< nn; i++)
+ v[i] = v[i-1] + i;
+ for (i=0; i< nn; i++)
+ for (j=0; j<(nn-i); j++)
+ v[i][j] = rhs[i][j];
+}
+template <class T>
+TriVertMat<T> & TriVertMat<T>::operator=(const TriVertMat<T> &rhs)
+// postcondition: normal assignment via copying has been performed;
+// if matrix and rhs were different sizes, matrix
+// has been resized to match the size of rhs
+{
+ if (this != &rhs) {
+ int i,j;
+ if (nn != rhs.nn) {
+ if (v != 0) {
+ delete[] (v[0]);
+ delete[] (v);
+ }
+ nn=rhs.nn;
+ v = new T*[nn];
+ v[0] = new T[nn*(nn+1)/2];
+ }
+ for (i=1; i< nn; i++)
+ v[i] = v[i-1] + i;
+ for (i=0; i< nn; i++)
+ for (j=0; j<(nn-i); j++)
+ v[i][j] = rhs[i][j];
+ }
+ return *this;
+}
+
+template <class T>
+TriVertMat<T> & TriVertMat<T>::operator=(const T &a) //assign a to every element
+{
+ for (int i=0; i< nn; i++)
+ for (int j=0; j<nn-i; j++)
+ v[i][j] = a;
+ return *this;
+}
+
+template <class T>
+inline T & TriVertMat<T>::ref(const int i, const int j)
+{
+ return v[j][i];
+}
+
+template <class T>
+inline const T TriVertMat<T>::ref(const int i, const int j) const
+{
+ return v[j][i];
+}
+
+template <class T>
+inline T * TriVertMat<T>::getPointer(const int i, const int j)
+{
+ return &v[j][i];
+}
+
+template <class T>
+inline int TriVertMat<T>::nrows() const
+{
+ return nn;
+}
+
+template <class T>
+TriVertMat<T>::~TriVertMat()
+{
+ if (v != 0) {
+ delete[] (v[0]);
+ delete[] (v);
+ }
+}
+
+
+//Overloaded complex operations to handle mixed float and double
+//This takes care of e.g. 1.0/z, z complex<float>
+inline const complex<float> operator+(const double &a,
+ const complex<float> &b) { return float(a)+b; }
+inline const complex<float> operator+(const complex<float> &a,
+ const double &b) { return a+float(b); }
+inline const complex<float> operator-(const double &a,
+ const complex<float> &b) { return float(a)-b; }
+inline const complex<float> operator-(const complex<float> &a,
+ const double &b) { return a-float(b); }
+inline const complex<float> operator*(const double &a,
+ const complex<float> &b) { return float(a)*b; }
+inline const complex<float> operator*(const complex<float> &a,
+ const double &b) { return a*float(b); }
+inline const complex<float> operator/(const double &a,
+ const complex<float> &b) { return float(a)/b; }
+inline const complex<float> operator/(const complex<float> &a,
+ const double &b) { return a/float(b); }
+//some compilers choke on pow(float,double) in single precision. also atan2
+inline float pow (float x, double y) {return pow(double(x),y);}
+inline float pow (double x, float y) {return pow(x,double(y));}
+inline float atan2 (float x, double y) {return atan2(double(x),y);}
+inline float atan2 (double x, float y) {return atan2(x,double(y));}
+
+#endif /* _NR_UTIL_H_ */
--- /dev/null
+0.8969780803 0.0000000001 0.0000000001 0.0515111387 0.0515111387
+0.0006874357 0.0006874357 0.0502248816 0.0502248816
+0.1025763303 0.1025763303 0.2891978920 0.2891978920
+ACGTN
+0.1907979101
+0.0187792275 0.2023714036
+0.0437292010 0.0242512580 0.2525959611
+0.0171148051 0.0289713815 0.0146772768 0.1689696163
+0.0000359111 0.0000737346 0.0000853324 0.0000768761 0.0000296087
+0.1390289217 0.2925130725 0.1882306933 0.2944687903 0.0016553127
--- /dev/null
+//////////////////////////////////////////////////////////////////////////////////////
+// postProcessings.cpp
+//
+// several post process functions after aligning two profile stem candidate sequences
+//////////////////////////////////////////////////////////////////////////////////////
+
+#include <iostream>
+#include "scarna.hpp"
+#include "StemCandidate.hpp"
+#include <vector>
+#include <string>
+
+using namespace::MXSCARNA;
+
+void printStructure(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2, std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2);
+
+void removeConflicts(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2, std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2)
+{
+ int size = matchPSCS1->size();
+
+ std::vector<int> found(size, 0);
+ for(int k = size - 1; k >= 0; k--) {
+ int i = matchPSCS1->at(k);
+ int i_rv = pscs1->at(i).GetRvscnumber();
+ int j = matchPSCS2->at(k);
+ int j_rv = pscs2->at(j).GetRvscnumber();
+
+ found[k] = 0;
+
+ for(int m = size - 1; m >= 0; m--) {
+ if ( (matchPSCS1->at(m) == i_rv) && (matchPSCS2->at(m) == j_rv) ) {
+ found[k] = 1;
+ break;
+ }
+ }
+ }
+
+ int pt = 0;
+ for(int k = 0; k < size; k++) {
+ matchPSCS1->at(pt) = matchPSCS1->at(k);
+ matchPSCS2->at(pt) = matchPSCS2->at(k);
+ if(found[k] == 1) ++pt;
+ }
+
+ matchPSCS1->resize(pt);
+ matchPSCS2->resize(pt);
+
+ //printStructure (pscs1, pscs2, matchPSCS1, matchPSCS2);
+}
+
+void printStructure(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2, std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2)
+{
+ int size = matchPSCS1->size();
+ int len = WORDLENGTH;
+ std::vector<char> structure1(100, '.');
+ std::vector<char> structure2(100, '.');
+ for(int k = 0; k < size; k++) {
+ int i = matchPSCS1->at(k);
+ int pos1 = pscs1->at(i).GetPosition();
+ int j = matchPSCS2->at(k);
+ int pos2 = pscs2->at(j).GetPosition();
+ for(int l = 0; l < len; l++) {
+ if(pscs1->at(i).GetDistance() > 0) {
+ structure1[pos1 + l] = '(';
+ }
+ else {
+ structure1[pos1 + l] = ')';
+ }
+
+ if(pscs2->at(j).GetDistance() > 0) {
+ structure2[pos2 + l] = '(';
+ }
+ else {
+ structure2[pos2 + l] = ')';
+ }
+ }
+ /*
+ std::cout << i << "\t" << pscs1->at(i).GetLength() << "\t" << pscs1->at(i).GetPosition() << "\t" << pscs1->at(i).GetRvposition() << "\t" << pscs1->at(i).GetDistance() << "\t" << pscs1->at(i).GetContPos() << "\t" << pscs1->at(i).GetBeforePos() << "\t" << pscs1->at(i).GetRvscnumber() << endl;
+ */
+ }
+ size = structure1.size();
+ for(int k = 0; k < size; k++) {
+ std::cout << structure1[k];
+ }
+ std::cout << endl;
+ for(int k = 0; k < size; k++) {
+ std::cout << structure2[k];
+ }
+ std::cout << endl;
+}
+
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// CompareToRef.cc
+//
+// Program for scoring alignments according to the SUM-OF-PAIRS
+// or COLUMN score.
+/////////////////////////////////////////////////////////////////
+
+#include "SafeVector.h"
+#include "MultiSequence.h"
+#include <string>
+#include <sstream>
+#include <iomanip>
+#include <iostream>
+#include <list>
+#include <set>
+#include <limits>
+#include <cstdio>
+#include <cstdlib>
+#include <cerrno>
+#include <iomanip>
+
+const char CORE_BLOCK = 'h';
+typedef pair<int,int> PII;
+bool useCoreBlocks = false;
+bool useColScore = false;
+bool useCaps = false;
+bool useBaliAnnot = false;
+bool makeAnnot = false;
+
+/////////////////////////////////////////////////////////////////
+// Function prototypes
+/////////////////////////////////////////////////////////////////
+
+set<PII> ComputePairs (MultiSequence *align, bool isRef);
+set<VI> ComputeColumns (MultiSequence *align, bool isRef);
+string GetName (string s);
+set<int> coreCols;
+
+set<VI> refCols, testCols;
+set<PII> refPairs, testPairs;
+VI annotation;
+
+/////////////////////////////////////////////////////////////////
+// main()
+//
+// Main program.
+/////////////////////////////////////////////////////////////////
+
+int main (int argc, char **argv){
+
+ // check arguments
+ if (argc < 3){
+ cerr << "Usage: score TEST_ALIGNMENT REFERENCE_ALIGNMENT [BALIBASE_ANNOT_FILE] [-col] [-core] [-caps] [-annot FILENAME]" << endl;
+ exit (1);
+ }
+
+ // try opening file
+ FileBuffer infile (argv[1]);
+
+ MultiSequence *testAlign;
+ if (infile.fail()){
+ cerr << "ERROR: Could not open file '" << argv[1] << "' for reading." << endl;
+ testAlign = NULL;
+ }
+ else {
+ testAlign = new MultiSequence(); assert (testAlign);
+ testAlign->LoadMFA (infile);
+ }
+ infile.close();
+
+ MultiSequence *refAlign = new MultiSequence (string (argv[2])); assert (refAlign);
+
+ string outFilename = "";
+
+ for (int i = 3; i < argc; i++){
+ if (strcmp (argv[i], "-core") == 0)
+ useCoreBlocks = true;
+ else if (strcmp (argv[i], "-col") == 0)
+ useColScore = true;
+ else if (strcmp (argv[i], "-caps") == 0)
+ useCaps = true;
+ else if (strcmp (argv[i], "-annot") == 0){
+ makeAnnot = true;
+ outFilename = string (argv[++i]);
+ }
+ else { // annotation file
+ useBaliAnnot = true;
+
+ ifstream annotFile (argv[i]);
+ if (annotFile.fail()){
+ cerr << "ERROR: Could not read BAliBASE annotation file." << endl;
+ exit (1);
+ }
+
+ SafeVector<int> *indices = refAlign->GetSequence(0)->GetMapping();
+
+ char buffer[10000];
+ while (annotFile.getline (buffer, 10000)){
+ istringstream ss;
+ ss.str (string (buffer));
+
+ string s;
+
+ if ((ss >> s) && s == string ("BPOS")){
+ while (ss >> s){
+ int begin=-1, end=-1;
+ if (sscanf (s.c_str(), "%d=%d", &begin, &end) == 2){
+ for (int i = (*indices)[begin]; i <= (*indices)[end]; i++)
+ coreCols.insert (i);
+ }
+ }
+ }
+ }
+
+ delete indices;
+
+ annotFile.close();
+ }
+ }
+
+ if (useColScore) makeAnnot = false;
+
+ if (testAlign){
+ for (int i = 0; i < testAlign->GetNumSequences(); i++){
+ bool found = false;
+
+ for (int j = 0; !found && j < refAlign->GetNumSequences(); j++){
+ if (testAlign->GetSequence(i)->GetHeader() == refAlign->GetSequence(j)->GetHeader())
+ found = true;
+ }
+
+ if (!found){
+ testAlign->RemoveSequence (i);
+ i--;
+ }
+ }
+
+ for (int i = 0; i < refAlign->GetNumSequences(); i++){
+ bool found = false;
+
+ for (int j = 0; !found && j < testAlign->GetNumSequences(); j++){
+ if (refAlign->GetSequence(i)->GetHeader() == testAlign->GetSequence(j)->GetHeader())
+ found = true;
+ }
+
+ if (!found){
+ refAlign->RemoveSequence (i);
+ i--;
+ }
+ }
+
+ testAlign->SortByHeader();
+ refAlign->SortByHeader();
+ }
+
+ int TP = 0;
+ int TPFN = 0;
+ int TPFP = 0;
+ double FD, FM;
+ if (useColScore){
+ refCols = ComputeColumns (refAlign, true);
+ if (testAlign) testCols = ComputeColumns (testAlign, false);
+ set<VI> colIntersect;
+ insert_iterator<set<VI> > colIntersectIter (colIntersect, colIntersect.begin());
+ set_intersection (testCols.begin(), testCols.end(), refCols.begin(), refCols.end(), colIntersectIter);
+ TP = (int) colIntersect.size();
+ TPFN = (int) refCols.size();
+ if (testAlign) TPFP = (int) testCols.size();
+ }
+ else {
+ refPairs = ComputePairs (refAlign, true);
+ if (testAlign) testPairs = ComputePairs (testAlign, false);
+ set<PII> pairIntersect;
+
+ insert_iterator<set<PII> > pairIntersectIter (pairIntersect, pairIntersect.begin());
+ set_intersection (testPairs.begin(), testPairs.end(), refPairs.begin(), refPairs.end(), pairIntersectIter);
+ TP = (int) pairIntersect.size();
+ TPFN = (int) refPairs.size();
+ if (testAlign) TPFP = (int) testPairs.size();
+ }
+
+ FD = (double) TP / TPFN;
+ FM = (double) TP / TPFP;
+
+ cout << GetName(string (argv[2])) << " " << TP << " " << TPFN << " " << TPFP << " " << FD << " " << FM << endl;
+
+ if (makeAnnot){
+ ofstream outfile (outFilename.c_str());
+ for (int i = 0; i < (int) annotation.size(); i++){
+ outfile << annotation[i] << endl;
+ }
+ outfile.close();
+ }
+
+ if (testAlign) delete testAlign;
+ delete refAlign;
+}
+
+int GetOffset (Sequence *testSeq, Sequence *refSeq){
+ string test = testSeq->GetString();
+ string ref = refSeq->GetString();
+
+ for (int i = 0; i < (int) test.length(); i++) test[i] = toupper(test[i]);
+ for (int i = 0; i < (int) ref.length(); i++) ref[i] = toupper(ref[i]);
+
+ size_t offset = test.find (ref, 0);
+ if (offset == string::npos){
+ cerr << "ERROR: Reference string not found in original sequence!" << endl;
+ cerr << " test = " << test << endl;
+ cerr << " ref = " << ref << endl;
+ exit (1);
+ }
+
+ cerr << "Offset found: " << offset << endl;
+
+ return (int) offset;
+}
+
+string GetName (string s){
+
+ size_t index1 = s.rfind ('/');
+ size_t index2 = s.rfind ('.');
+
+ if (index1 == string::npos) index1 = 0; else index1++;
+ if (index2 == string::npos) index2 = s.length();
+
+ if (index2 < index1) index2 = s.length();
+
+ return s.substr (index1, index2 - index1);
+}
+
+bool isCore (char ch, int col){
+ if (ch == '-') return false;
+ if (useBaliAnnot){
+ return coreCols.find (col) != coreCols.end();
+ }
+ if (useCaps){
+ return ch >= 'A' && ch <= 'Z';
+ }
+ return ch == CORE_BLOCK;
+}
+
+/////////////////////////////////////////////////////////////////
+// ComputePairs
+//
+// Returns the set of all matching pairs.
+/////////////////////////////////////////////////////////////////
+
+set<PII> ComputePairs (MultiSequence *align, bool isRef){
+ int N = align->GetNumSequences();
+ int L = align->GetSequence(0)->GetLength();
+
+ // retrieve all sequence data pointers
+ SafeVector<SafeVector<char>::iterator> seqs (N);
+ for (int i = 0; i < N; i++){
+ seqs[i] = align->GetSequence(i)->GetDataPtr();
+ assert (align->GetSequence(i)->GetLength() == L);
+ }
+
+ set<PII> ret;
+ VI ctr(N);
+
+ // compute pairs
+ for (int i = 1; i <= L; i++){
+
+ // ctr keeps track of the current position in each sequence
+ for (int j = 0; j < N; j++){
+ ctr[j] += (seqs[j][i] != '-');
+ }
+
+ int good = 0;
+ int ct = 0;
+
+ // check for all matching pairs
+ for (int j = 0; j < N - 1; j++){
+ for (int k = j + 1; k < N; k++){
+
+ // skip if one of the sequences is gapped
+ if (seqs[j][i] == '-' || seqs[k][i] == '-') continue;
+
+ // check for core blocks in the reference sequence
+ if (isRef && useCoreBlocks)
+ if (!isCore (seqs[j][i], i) || !isCore (seqs[k][i], i)) continue;
+
+ // if all ok, then add pair to list of pairs
+ pair<int,int> p (10000 * j + ctr[j], 10000 * k + ctr[k]);
+
+ // if we're making an annotation, compute annotation statistics
+ if (makeAnnot && !isRef){
+ ct++;
+ if (refPairs.find (p) != refPairs.end()) good++;
+ }
+ ret.insert (p);
+ }
+ }
+
+ // build annotation
+ if (makeAnnot && !isRef){
+ annotation.push_back ((ct == 0) ? 0 : 100 * good / ct);
+ }
+
+ }
+
+ return ret;
+}
+
+/////////////////////////////////////////////////////////////////
+// ComputeColumns
+//
+// Returns the set of all columns.
+/////////////////////////////////////////////////////////////////
+
+set<VI> ComputeColumns (MultiSequence *align, bool isRef){
+ int N = align->GetNumSequences();
+ int L = align->GetSequence(0)->GetLength();
+
+ // retrieve all sequence data pointers
+ SafeVector<SafeVector<char>::iterator> seqs (N);
+ for (int i = 0; i < N; i++){
+ seqs[i] = align->GetSequence(i)->GetDataPtr();
+ }
+
+ set<VI> ret;
+ VI ctr(N);
+
+ // compute pairs
+ for (int i = 1; i <= L; i++){
+
+ // ctr keeps track of the current position in each sequence
+ for (int j = 0; j < N; j++){
+ ctr[j] += (seqs[j][i] != '-');
+ }
+
+ // add column, pick only positions that are matched
+ SafeVector<int> column (N);
+ bool useThisColumn = !useCoreBlocks;
+
+ for (int j = 0; j < N; j++){
+ if (isCore (seqs[j][i], i)) useThisColumn = true;
+ column[j] = (seqs[j][i] == '-') ? -1 : ctr[j];
+ }
+
+ if (useThisColumn || !isRef)
+ ret.insert (column);
+ }
+
+ return ret;
+}
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// Defaults.h
+//
+// Default constants for use in PROBCONS. The emission
+// probabilities were computed using the program used to build
+// the BLOSUM62 matrix from the BLOCKS 5.0 dataset. Transition
+// parameters were obtained via unsupervised EM training on the
+// BALIBASE 2.0 benchmark alignment database.
+/////////////////////////////////////////////////////////////////
+
+#ifndef DEFAULTS_H
+#define DEFAULTS_H
+
+#include <string>
+
+using namespace std;
+/* Default */
+namespace MXSCARNA {
+/*
+float initDistrib1Default[] = { 0.9588437676f, 0.0205782652f, 0.0205782652f };
+float gapOpen1Default[] = { 0.0190259293f, 0.0190259293f };
+float gapExtend1Default[] = { 0.3269913495f, 0.3269913495f };
+*/
+
+/* EMtrainingALL.txt*/
+float initDistrib1Default[] = { 0.9234497547, 0.0385021642, 0.0385021642 };
+float gapOpen1Default[] = { 0.0266662259, 0.0266662259 };
+float gapExtend1Default[] = { 0.3849118352, 0.3849118352 };
+
+
+float initDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f };
+float gapOpen2Default[] = { 0.0082473317f, 0.0082473317f, 0.0107844425f, 0.0107844425f };
+float gapExtend2Default[] = { 0.3210460842f, 0.3210460842f, 0.3298229277f, 0.3298229277f };
+
+string alphabetDefault = "ACGUTN";
+
+//float emitSingleDefault[6] = {
+// 0.2174750715, 0.2573366761, 0.3005372882, 0.2233072966, 0.2233072966, 0.0004049665
+//};
+
+/* Default */
+/*
+float emitSingleDefault[6] = {
+ 0.2270790040f, 0.2422080040f, 0.2839320004f, 0.2464679927f, 0.2464679927f, 0.0003124650f
+};
+*/
+
+/* EMtrainingALL.txt */
+float emitSingleDefault[6] = {
+ 0.2017124593, 0.2590311766, 0.2929603755, 0.2453189045, 0.2453189045, 0.0000873194 };
+
+/* ACGUTN */
+/* Default */
+/*
+float emitPairsDefault[6][6] = {
+ { 0.1487240046f, 0.0184142999f, 0.0361397006f, 0.0238473993f, 0.0238473993f, 0.0000375308f },
+ { 0.0184142999f, 0.1583919972f, 0.0275536999f, 0.0389291011f, 0.0389291011f, 0.0000815823f },
+ { 0.0361397006f, 0.0275536999f, 0.1979320049f, 0.0244289003f, 0.0244289003f, 0.0000824765f },
+ { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+ { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+ { 0.0000375308f, 0.0000815823f, 0.0000824765f, 0.0000743985f, 0.0000743985f, 0.0000263252f }
+};
+*/
+/* EMtrainingALL.txt */
+float emitPairsDefault[6][6] = {
+ { 0.1659344733, 0.0298952684, 0.0543937907, 0.0344539173, 0.0344539173, 0.0000032761 },
+ { 0.0298952684, 0.1817403436, 0.0415624641, 0.0589077808, 0.0589077808, 0.0000117011 },
+ { 0.0543937907, 0.0415624641, 0.2342105955, 0.0410407558, 0.0410407558, 0.0000072893 },
+ { 0.0344539173, 0.0589077808, 0.0410407558, 0.1578272283, 0.1578272283, 0.0000067871 },
+ { 0.0344539173, 0.0589077808, 0.0410407558, 0.1578272283, 0.1578272283, 0.0000067871 },
+ { 0.0344539173, 0.0589077808, 0.0410407558, 0.1578272283, 0.1578272283, 0.0000067871 },
+// { 0.0000032761, 0.0000117011, 0.0000072893, 0.0000067871, 0.0000067871, 0.0000000166 }
+};
+
+ /*
+float emitPairsDefault[6][6] = {
+ {0.1731323451, 0.0378843173, 0.0656677559, 0.0450690985, 0.0450690985, 0.0000215275},
+ {0.0378843173, 0.1611578614, 0.0492933467, 0.0651549697, 0.0651549697, 0.0000362353},
+ {0.0656677559, 0.0492933467, 0.1937607974, 0.0464556068, 0.0464556068, 0.0000293904},
+ {0.0450690985, 0.0651549697, 0.0464556068, 0.1622997671, 0.1622997671, 0.0000352637},
+ {0.0450690985, 0.0651549697, 0.0464556068, 0.1622997671, 0.1622997671, 0.0000352637},
+ {0.0000215275, 0.0000362353, 0.0000293904, 0.0000352637, 0.0000352637, 0.0000000000}
+};
+ */
+}
+#endif
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// Defaults.h
+//
+// Default constants for use in PROBCONS. The emission
+// probabilities were computed using the program used to build
+// the BLOSUM62 matrix from the BLOCKS 5.0 dataset. Transition
+// parameters were obtained via unsupervised EM training on the
+// BALIBASE 2.0 benchmark alignment database.
+/////////////////////////////////////////////////////////////////
+
+#ifndef DEFAULTS_H
+#define DEFAULTS_H
+
+#include <string>
+
+using namespace std;
+
+float initDistrib1Default[] = { 0.9588437676f, 0.0205782652f, 0.0205782652f };
+float gapOpen1Default[] = { 0.0190259293f, 0.0190259293f };
+float gapExtend1Default[] = { 0.3269913495f, 0.3269913495f };
+
+float initDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f };
+float gapOpen2Default[] = { 0.0082473317f, 0.0082473317f, 0.0107844425f, 0.0107844425f };
+float gapExtend2Default[] = { 0.3210460842f, 0.3210460842f, 0.3298229277f, 0.3298229277f };
+
+string alphabetDefault = "ACGUTN";
+
+//float emitSingleDefault[6] = {
+// 0.2174750715, 0.2573366761, 0.3005372882, 0.2233072966, 0.2233072966, 0.0004049665
+//};
+
+float emitSingleDefault[6] = {
+ 0.2270790040f, 0.2422080040f, 0.2839320004f, 0.2464679927f, 0.2464679927f, 0.0003124650f
+};
+
+/* ACGUTN */
+
+float emitPairsDefault[6][6] = {
+ { 0.1487240046f, 0.0184142999f, 0.0361397006f, 0.0238473993f, 0.0238473993f, 0.0000375308f },
+ { 0.0184142999f, 0.1583919972f, 0.0275536999f, 0.0389291011f, 0.0389291011f, 0.0000815823f },
+ { 0.0361397006f, 0.0275536999f, 0.1979320049f, 0.0244289003f, 0.0244289003f, 0.0000824765f },
+ { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+ { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+ { 0.0000375308f, 0.0000815823f, 0.0000824765f, 0.0000743985f, 0.0000743985f, 0.0000263252f }
+};
+
+ /*
+float emitPairsDefault[6][6] = {
+ {0.1731323451, 0.0378843173, 0.0656677559, 0.0450690985, 0.0450690985, 0.0000215275},
+ {0.0378843173, 0.1611578614, 0.0492933467, 0.0651549697, 0.0651549697, 0.0000362353},
+ {0.0656677559, 0.0492933467, 0.1937607974, 0.0464556068, 0.0464556068, 0.0000293904},
+ {0.0450690985, 0.0651549697, 0.0464556068, 0.1622997671, 0.1622997671, 0.0000352637},
+ {0.0450690985, 0.0651549697, 0.0464556068, 0.1622997671, 0.1622997671, 0.0000352637},
+ {0.0000215275, 0.0000362353, 0.0000293904, 0.0000352637, 0.0000352637, 0.0000000000}
+};
+ */
+#endif
--- /dev/null
+0.9234497547 0.0385021642 0.0385021642
+0.0266662259 0.0266662259
+0.3849118352 0.3849118352
+ACGUTN
+0.1659344733
+0.0298952684 0.1817403436
+0.0543937907 0.0415624641 0.2342105955
+0.0344539173 0.0589077808 0.0410407558 0.1578272283
+0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
+0.0000032761 0.0000117011 0.0000072893 0.0000067871 0.0000000000 0.0000000166
+0.2017124593 0.2590311766 0.2929603755 0.2453189045 0.0000000000 0.0000873194
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// EvolutionaryTree.hpp
+//
+// Utilities for reading/writing multiple sequence data.
+/////////////////////////////////////////////////////////////////
+
+#ifndef __EVOLUTIONARYTREE_HPP__
+#define __EVOLUTIONARYTREE_HPP__
+
+#include <string>
+#include <list>
+#include <stdio.h>
+#include "SafeVector.h"
+#include "MultiSequence.h"
+#include "Sequence.h"
+#include "Util.hpp"
+
+using namespace std;
+
+
+/////////////////////////////////////////////////////////////////
+// TreeNode
+//
+// The fundamental unit for representing an alignment tree. The
+// guide tree is represented as a binary tree.
+/////////////////////////////////////////////////////////////////
+namespace MXSCARNA {
+class TreeNode {
+ int sequenceLabel; // sequence label
+ float sequenceIdentity; // sequence identity
+ TreeNode *left, *right, *parent; // pointers to left, right children
+ float leftLength, rightLength; // the length of left and right edge
+ /////////////////////////////////////////////////////////////////
+ // TreeNode::PrintNode()
+ //
+ // Internal routine used to print out the sequence comments
+ // associated with the evolutionary tree, using a hierarchical
+ // parenthesized format.
+ /////////////////////////////////////////////////////////////////
+
+ void PrintNode (ostream &outfile, const MultiSequence *sequences) const {
+
+ // if this is a leaf node, print out the associated sequence comment
+ if (sequenceLabel >= 0)
+ //outfile << sequences->GetSequence (sequenceLabel)->GetHeader();
+ outfile << sequences->GetSequence (sequenceLabel)->GetLabel();
+
+ // otherwise, it must have two children; print out their subtrees recursively
+ else {
+ assert (left);
+ assert (right);
+
+ outfile << "(";
+ left->PrintNode (outfile, sequences);
+ outfile << ",";
+ right->PrintNode (outfile, sequences);
+ outfile << ")";
+ }
+ }
+
+ public:
+
+ /////////////////////////////////////////////////////////////////
+ // TreeNode::TreeNode()
+ //
+ // Constructor for a tree node. Note that sequenceLabel = -1
+ // implies that the current node is not a leaf in the tree.
+ /////////////////////////////////////////////////////////////////
+
+ TreeNode (int sequenceLabel) : sequenceLabel (sequenceLabel),
+ left (NULL), right (NULL), parent (NULL) {
+ assert (sequenceLabel >= -1);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // TreeNode::~TreeNode()
+ //
+ // Destructor for a tree node. Recursively deletes all children.
+ /////////////////////////////////////////////////////////////////
+
+ ~TreeNode (){
+ if (left){ delete left; left = NULL; }
+ if (right){ delete right; right = NULL; }
+ parent = NULL;
+ }
+
+
+ // getters
+ int GetSequenceLabel () const { return sequenceLabel; }
+ TreeNode *GetLeftChild () const { return left; }
+ TreeNode *GetRightChild () const { return right; }
+ TreeNode *GetParent () const { return parent; }
+ float GetIdentity () const { return sequenceIdentity; }
+ float GetLeftLength () const { return leftLength; }
+ float GetRightLength () const { return rightLength; }
+ // setters
+ void SetSequenceLabel (int sequenceLabel){ this->sequenceLabel = sequenceLabel; assert (sequenceLabel >= -1); }
+ void SetLeftChild (TreeNode *left){ this->left = left; }
+ void SetRightChild (TreeNode *right){ this->right = right; }
+ void SetParent (TreeNode *parent){ this->parent = parent; }
+ void SetIdentity (float identity) { this->sequenceIdentity = identity; }
+ void SetLeftLength (float identity) { this->leftLength = identity; }
+ void SetRightLength (float identity) {this->rightLength = identity; }
+ /////////////////////////////////////////////////////////////////
+ // TreeNode::ComputeTree()
+ //
+ // Routine used to compute an evolutionary tree based on the
+ // given distance matrix. We assume the distance matrix has the
+ // form, distMatrix[i][j] = expected accuracy of aligning i with j.
+ /////////////////////////////////////////////////////////////////
+
+ static TreeNode *ComputeTree (const VVF &distMatrix, const VVF &identityMatrix){
+
+ int numSeqs = distMatrix.size(); // number of sequences in distance matrix
+ VVF distances (numSeqs, VF (numSeqs)); // a copy of the distance matrix
+ SafeVector<TreeNode *> nodes (numSeqs, NULL); // list of nodes for each sequence
+ SafeVector<int> valid (numSeqs, 1); // valid[i] tells whether or not the ith
+ // nodes in the distances and nodes array
+ // are valid
+ VVF identities (numSeqs, VF (numSeqs));
+ SafeVector<int> countCluster (numSeqs, 1);
+
+ // initialization: make a copy of the distance matrix
+ for (int i = 0; i < numSeqs; i++) {
+ for (int j = 0; j < numSeqs; j++) {
+ distances[i][j] = distMatrix[i][j];
+ identities[i][j] = identityMatrix[i][j];
+ }
+ }
+
+ // initialization: create all the leaf nodes
+ for (int i = 0; i < numSeqs; i++){
+ nodes[i] = new TreeNode (i);
+ assert (nodes[i]);
+ }
+
+ // repeat until only a single node left
+ for (int numNodesLeft = numSeqs; numNodesLeft > 1; numNodesLeft--){
+ float bestProb = -1;
+ pair<int,int> bestPair;
+
+ // find the closest pair
+ for (int i = 0; i < numSeqs; i++) if (valid[i]){
+ for (int j = i+1; j < numSeqs; j++) if (valid[j]){
+ if (distances[i][j] > bestProb){
+ bestProb = distances[i][j];
+ bestPair = make_pair(i, j);
+ }
+ }
+ }
+
+ // merge the closest pair
+ TreeNode *newParent = new TreeNode (-1);
+ newParent->SetLeftChild (nodes[bestPair.first]);
+ newParent->SetRightChild (nodes[bestPair.second]);
+ nodes[bestPair.first]->SetParent (newParent);
+ nodes[bestPair.second]->SetParent (newParent);
+ nodes[bestPair.first] = newParent;
+ nodes[bestPair.second] = NULL;
+ newParent->SetIdentity(identities[bestPair.first][bestPair.second]);
+
+
+ // now update the distance matrix
+ for (int i = 0; i < numSeqs; i++) if (valid[i]){
+ distances[bestPair.first][i] = distances[i][bestPair.first]
+ = (distances[i][bestPair.first]*countCluster[bestPair.first]
+ + distances[i][bestPair.second]*countCluster[bestPair.second])
+ / (countCluster[bestPair.first] + countCluster[bestPair.second]);
+// distances[bestPair.first][i] = distances[i][bestPair.first]
+// = (distances[i][bestPair.first] + distances[i][bestPair.second]) * bestProb / 2;
+ identities[bestPair.first][i] = identities[i][bestPair.first]
+ = (identities[i][bestPair.first]*countCluster[bestPair.first]
+ + identities[i][bestPair.second]*countCluster[bestPair.second])
+ / (countCluster[bestPair.first] + countCluster[bestPair.second]);
+ }
+
+ // finally, mark the second node entry as no longer valid
+ countCluster[bestPair.first] += countCluster[bestPair.second];
+ valid[bestPair.second] = 0;
+ }
+
+ assert (nodes[0]);
+ return nodes[0];
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // TreeNode::Print()
+ //
+ // Print out the subtree associated with this node in a
+ // parenthesized representation.
+ /////////////////////////////////////////////////////////////////
+
+ void Print (ostream &outfile, const MultiSequence *sequences) const {
+// outfile << "Alignment tree: ";
+ PrintNode (outfile, sequences);
+ outfile << endl;
+ }
+};
+}
+#endif //__EVOLUTIONARYTREE_HPP__
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// FileBuffer.h
+//
+// Buffered file reading.
+/////////////////////////////////////////////////////////////////
+
+
+#ifndef FILEBUFFER_H
+#define FILEBUFFER_H
+
+#include <string>
+#include <fstream>
+#include <iostream>
+
+using namespace std;
+
+const int BufferSize = 1000;
+
+/////////////////////////////////////////////////////////////////
+// FileBuffer
+//
+// Class for buffering file reading.
+/////////////////////////////////////////////////////////////////
+namespace MXSCARNA {
+class FileBuffer {
+ ifstream file;
+ char buffer[BufferSize];
+ int currPos;
+ int size;
+ bool isEOF;
+ bool isValid;
+ bool canUnget;
+
+ public:
+
+ // Some common routines
+
+ FileBuffer (const char *filename) : file (filename), currPos (0), size (0), isEOF (false), isValid (!file.fail()), canUnget (false){}
+ ~FileBuffer (){ close(); }
+ bool fail () const { return !isValid; }
+ bool eof () const { return (!isValid || isEOF); }
+ void close(){ file.close(); isValid = false; }
+
+ /////////////////////////////////////////////////////////////////
+ // FileBuffer::Get()
+ //
+ // Retrieve a character from the file buffer. Returns true if
+ // and only if a character is read.
+ /////////////////////////////////////////////////////////////////
+
+ bool Get (char &ch){
+
+ // check to make sure that there's more stuff in the file
+ if (!isValid || isEOF) return false;
+
+ // if the buffer is empty, it's time to reload it
+ if (currPos == size){
+ file.read (buffer, BufferSize);
+ size = file.gcount();
+ isEOF = (size == 0);
+ currPos = 0;
+ if (isEOF) return false;
+ }
+
+ // store the read character
+ ch = buffer[currPos++];
+ canUnget = true;
+ return true;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // FileBuffer::UnGet()
+ //
+ // Unretrieve the most recently read character from the file
+ // buffer. Note that this allows only a one-level undo.
+ /////////////////////////////////////////////////////////////////
+
+ void UnGet (){
+ assert (canUnget);
+ assert (isValid);
+ assert (currPos > 0);
+ currPos--;
+ assert (currPos < size);
+ isEOF = false;
+ canUnget = false;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // FileBuffer::GetLine()
+ //
+ // Retrieve characters of text until a newline character is
+ // encountered. Terminates properly on end-of-file condition.
+ /////////////////////////////////////////////////////////////////
+
+ void GetLine (string &s){
+ char ch;
+ s = "";
+ while (Get (ch) && ch != '\n')
+ s += ch;
+ }
+
+};
+}
+#endif
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// Main.cc
+/////////////////////////////////////////////////////////////////
+
+#include "SafeVector.h"
+#include "MultiSequence.h"
+#include "Defaults.h"
+#include "ScoreType.h"
+#include "ProbabilisticModel.h"
+#include "EvolutionaryTree.h"
+#include "SparseMatrix.h"
+#include <string>
+#include <iomanip>
+#include <iostream>
+#include <list>
+#include <set>
+#include <algorithm>
+#include <cstdio>
+#include <cstdlib>
+#include <cerrno>
+#include <iomanip>
+
+string matrixFilename = "";
+string parametersInputFilename = "";
+string parametersOutputFilename = "no training";
+
+bool enableTraining = false;
+bool enableVerbose = false;
+int numConsistencyReps = 2;
+int numPreTrainingReps = 0;
+int numIterativeRefinementReps = 100;
+
+float gapOpenPenalty = 0;
+float gapContinuePenalty = 0;
+VF initDistrib (NumMatrixTypes);
+VF gapOpen (2*NumInsertStates);
+VF gapExtend (2*NumInsertStates);
+SafeVector<char> alphabet;
+VVF emitPairs;
+VF emitSingle;
+
+const int MIN_PRETRAINING_REPS = 0;
+const int MAX_PRETRAINING_REPS = 20;
+const int MIN_CONSISTENCY_REPS = 0;
+const int MAX_CONSISTENCY_REPS = 5;
+const int MIN_ITERATIVE_REFINEMENT_REPS = 0;
+const int MAX_ITERATIVE_REFINEMENT_REPS = 1000;
+
+/////////////////////////////////////////////////////////////////
+// Function prototypes
+/////////////////////////////////////////////////////////////////
+
+void PrintHeading();
+void PrintParameters (const char *message, const VF &initDistrib, const VF &gapOpen,
+ const VF &gapExtend, const char *filename);
+MultiSequence *DoAlign (MultiSequence *sequence, const ProbabilisticModel &model);
+SafeVector<string> ParseParams (int argc, char **argv);
+void ReadParameters ();
+MultiSequence *ComputeFinalAlignment (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model);
+MultiSequence *AlignAlignments (MultiSequence *align1, MultiSequence *align2,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model);
+void DoRelaxation (MultiSequence *sequences, SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+void Relax (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior);
+void DoIterativeRefinement (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment);
+//float ScoreAlignment (MultiSequence *alignment, MultiSequence *sequences, SparseMatrix **sparseMatrices, const int numSeqs);
+
+/////////////////////////////////////////////////////////////////
+// main()
+//
+// Calls all initialization routines and runs the PROBCONS
+// aligner.
+/////////////////////////////////////////////////////////////////
+
+int main (int argc, char **argv){
+
+ if (argc != 3){
+ cerr << "Usage: FixRef inputfile reffile" << endl;
+ exit (1);
+ }
+
+ string inputFilename = string (argv[1]);
+ string refFilename = string (argv[2]);
+
+ ReadParameters();
+
+ // build new model for aligning
+ ProbabilisticModel model (initDistrib, gapOpen, gapExtend,
+ alphabet, emitPairs, emitSingle);
+
+ MultiSequence *inputSeq = new MultiSequence(); inputSeq->LoadMFA (inputFilename);
+ MultiSequence *refSeq = new MultiSequence(); refSeq->LoadMFA (refFilename);
+
+ SafeVector<char> *ali = new SafeVector<char>;
+
+ if (refSeq->GetNumSequences() != 2){
+ cerr << "ERROR: Expected two sequences in reference alignment." << endl;
+ exit (1);
+ }
+ set<int> s; s.insert (0);
+ MultiSequence *ref1 = refSeq->Project (s);
+ s.clear(); s.insert (1);
+ MultiSequence *ref2 = refSeq->Project (s);
+
+ for (int i = 0; i < inputSeq->GetNumSequences(); i++){
+ if (inputSeq->GetSequence(i)->GetHeader() == ref1->GetSequence(0)->GetHeader()){
+ ref1->AddSequence (inputSeq->GetSequence(i)->Clone());
+ }
+ if (inputSeq->GetSequence(i)->GetHeader() == ref2->GetSequence(0)->GetHeader())
+ ref2->AddSequence (inputSeq->GetSequence(i)->Clone());
+ }
+ if (ref1->GetNumSequences() != 2){
+ cerr << "ERROR: Expected two sequences in reference1 alignment." << endl;
+ exit (1);
+ }
+ if (ref2->GetNumSequences() != 2){
+ cerr << "ERROR: Expected two sequences in reference2 alignment." << endl;
+ exit (1);
+ }
+
+ ref1->GetSequence(0)->SetLabel(0);
+ ref2->GetSequence(0)->SetLabel(0);
+ ref1->GetSequence(1)->SetLabel(1);
+ ref2->GetSequence(1)->SetLabel(1);
+
+ // cerr << "Aligning..." << endl;
+
+ // now, we can perform the alignments and write them out
+ MultiSequence *alignment1 = DoAlign (ref1,
+ ProbabilisticModel (initDistrib, gapOpen, gapExtend,
+ alphabet, emitPairs, emitSingle));
+
+ //cerr << "Aligning second..." << endl;
+ MultiSequence *alignment2 = DoAlign (ref2,
+ ProbabilisticModel (initDistrib, gapOpen, gapExtend,
+ alphabet, emitPairs, emitSingle));
+
+ SafeVector<char>::iterator iter1 = alignment1->GetSequence(0)->GetDataPtr();
+ SafeVector<char>::iterator iter2 = alignment1->GetSequence(1)->GetDataPtr();
+ for (int i = 1; i <= alignment1->GetSequence(0)->GetLength(); i++){
+ if (islower(iter1[i])) iter2[i] = tolower(iter2[i]);
+ if (isupper(iter1[i])) iter2[i] = toupper(iter2[i]);
+ }
+ iter1 = alignment2->GetSequence(0)->GetDataPtr();
+ iter2 = alignment2->GetSequence(1)->GetDataPtr();
+ for (int i = 1; i <= alignment2->GetSequence(0)->GetLength(); i++){
+ if (islower(iter1[i])) iter2[i] = tolower(iter2[i]);
+ if (isupper(iter1[i])) iter2[i] = toupper(iter2[i]);
+ }
+ //alignment1->WriteMFA (cout);
+ //alignment2->WriteMFA (cout);
+
+ int a1 = 0, a = 0;
+ int b1 = 0, b = 0;
+
+ for (int i = 1; i <= refSeq->GetSequence(0)->GetLength(); i++){
+
+ // catch up in filler sequences
+ if (refSeq->GetSequence(0)->GetPosition(i) != '-'){
+ while (true){
+ a++;
+ if (alignment1->GetSequence(0)->GetPosition(a) != '-') break;
+ ali->push_back ('X');
+ }
+ }
+ if (refSeq->GetSequence(1)->GetPosition(i) != '-'){
+ while (true){
+ b++;
+ if (alignment2->GetSequence(0)->GetPosition(b) != '-') break;
+ ali->push_back ('Y');
+ }
+ }
+
+ if (refSeq->GetSequence(0)->GetPosition(i) != '-' &&
+ refSeq->GetSequence(1)->GetPosition(i) != '-'){
+ //cerr << "M: " << refSeq->GetSequence(0)->GetPosition(i) << refSeq->GetSequence(1)->GetPosition(i) << endl;
+ ali->push_back ('B');
+ }
+ else if (refSeq->GetSequence(0)->GetPosition(i) != '-'){
+ //cerr << "X" << endl;
+ ali->push_back ('X');
+ }
+ else if (refSeq->GetSequence(1)->GetPosition(i) != '-'){
+ //cerr << "Y" << endl;
+ ali->push_back ('Y');
+ }
+ }
+
+ while (a < alignment1->GetSequence(0)->GetLength()){
+ a++;
+ ali->push_back ('X');
+ if (alignment1->GetSequence(0)->GetPosition(a) != '-') a1++;
+ }
+ while (b < alignment2->GetSequence(0)->GetLength()){
+ b++;
+ ali->push_back ('Y');
+ if (alignment2->GetSequence(0)->GetPosition(b) != '-') b1++;
+ }
+
+ Sequence *seq1 = alignment1->GetSequence(1)->AddGaps (ali, 'X');
+ Sequence *seq2 = alignment2->GetSequence(1)->AddGaps (ali, 'Y');
+ seq1->WriteMFA (cout, 60);
+ seq2->WriteMFA (cout, 60);
+
+ delete seq1;
+ delete seq2;
+
+ delete ali;
+ delete alignment1;
+ delete alignment2;
+ delete inputSeq;
+ delete refSeq;
+}
+
+/////////////////////////////////////////////////////////////////
+// PrintHeading()
+//
+// Prints heading for PROBCONS program.
+/////////////////////////////////////////////////////////////////
+
+void PrintHeading (){
+ cerr << endl
+ << "PROBCONS version 1.02 - align multiple protein sequences and print to standard output" << endl
+ << "Copyright (C) 2004 Chuong Ba Do" << endl
+ << endl;
+}
+
+/////////////////////////////////////////////////////////////////
+// PrintParameters()
+//
+// Prints PROBCONS parameters to STDERR. If a filename is
+// specified, then the parameters are also written to the file.
+/////////////////////////////////////////////////////////////////
+
+void PrintParameters (const char *message, const VF &initDistrib, const VF &gapOpen,
+ const VF &gapExtend, const char *filename){
+
+ // print parameters to the screen
+ cerr << message << endl
+ << " initDistrib[] = { ";
+ for (int i = 0; i < NumMatrixTypes; i++) cerr << setprecision (10) << initDistrib[i] << " ";
+ cerr << "}" << endl
+ << " gapOpen[] = { ";
+ for (int i = 0; i < NumInsertStates*2; i++) cerr << setprecision (10) << gapOpen[i] << " ";
+ cerr << "}" << endl
+ << " gapExtend[] = { ";
+ for (int i = 0; i < NumInsertStates*2; i++) cerr << setprecision (10) << gapExtend[i] << " ";
+ cerr << "}" << endl
+ << endl;
+
+ // if a file name is specified
+ if (filename){
+
+ // attempt to open the file for writing
+ FILE *file = fopen (filename, "w");
+ if (!file){
+ cerr << "ERROR: Unable to write parameter file: " << filename << endl;
+ exit (1);
+ }
+
+ // if successful, then write the parameters to the file
+ for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n");
+ for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n");
+ for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n");
+ fclose (file);
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// DoAlign()
+//
+// First computes all pairwise posterior probability matrices.
+// Then, computes new parameters if training, or a final
+// alignment, otherwise.
+/////////////////////////////////////////////////////////////////
+
+MultiSequence *DoAlign (MultiSequence *sequences, const ProbabilisticModel &model){
+
+ assert (sequences);
+
+ const int numSeqs = sequences->GetNumSequences();
+ VVF distances (numSeqs, VF (numSeqs, 0));
+ SafeVector<SafeVector<SparseMatrix *> > sparseMatrices (numSeqs, SafeVector<SparseMatrix *>(numSeqs, NULL));
+
+ // do all pairwise alignments
+ for (int a = 0; a < numSeqs-1; a++){
+ for (int b = a+1; b < numSeqs; b++){
+ Sequence *seq1 = sequences->GetSequence (a);
+ Sequence *seq2 = sequences->GetSequence (b);
+
+ // verbose output
+ if (enableVerbose)
+ cerr << "(" << a+1 << ") " << seq1->GetHeader() << " vs. "
+ << "(" << b+1 << ") " << seq2->GetHeader() << ": ";
+
+ // compute forward and backward probabilities
+ VF *forward = model.ComputeForwardMatrix (seq1, seq2); assert (forward);
+ VF *backward = model.ComputeBackwardMatrix (seq1, seq2); assert (backward);
+
+ // if we are training, then we'll simply want to compute the
+ // expected counts for each region within the matrix separately;
+ // otherwise, we'll need to put all of the regions together and
+ // assemble a posterior probability match matrix
+
+ // compute posterior probability matrix
+ VF *posterior = model.ComputePosteriorMatrix (seq1, seq2, *forward, *backward); assert (posterior);
+
+ // compute "expected accuracy" distance for evolutionary tree computation
+ pair<SafeVector<char> *, float> alignment = model.ComputeAlignment (seq1->GetLength(),
+ seq2->GetLength(),
+ *posterior);
+
+ float distance = alignment.second / min (seq1->GetLength(), seq2->GetLength());
+
+ if (enableVerbose)
+ cerr << setprecision (10) << distance << endl;
+
+ // save posterior probability matrices in sparse format
+ distances[a][b] = distances[b][a] = distance;
+ sparseMatrices[a][b] = new SparseMatrix (seq1->GetLength(), seq2->GetLength(), *posterior);
+ sparseMatrices[b][a] = sparseMatrices[a][b]->ComputeTranspose();
+
+ delete alignment.first;
+ delete posterior;
+
+ delete forward;
+ delete backward;
+ }
+ }
+
+ if (!enableTraining){
+ if (enableVerbose)
+ cerr << endl;
+
+ // now, perform the consistency transformation the desired number of times
+ for (int i = 0; i < numConsistencyReps; i++)
+ DoRelaxation (sequences, sparseMatrices);
+
+ // compute the evolutionary tree
+ TreeNode *tree = TreeNode::ComputeTree (distances);
+
+ //tree->Print (cerr, sequences);
+ //cerr << endl;
+
+ // make the final alignment
+ MultiSequence *alignment = ComputeFinalAlignment (tree, sequences, sparseMatrices, model);
+ delete tree;
+
+ return alignment;
+ }
+
+ return NULL;
+}
+
+/////////////////////////////////////////////////////////////////
+// GetInteger()
+//
+// Attempts to parse an integer from the character string given.
+// Returns true only if no parsing error occurs.
+/////////////////////////////////////////////////////////////////
+
+bool GetInteger (char *data, int *val){
+ char *endPtr;
+ long int retVal;
+
+ assert (val);
+
+ errno = 0;
+ retVal = strtol (data, &endPtr, 0);
+ if (retVal == 0 && (errno != 0 || data == endPtr)) return false;
+ if (errno != 0 && (retVal == LONG_MAX || retVal == LONG_MIN)) return false;
+ if (retVal < (long) INT_MIN || retVal > (long) INT_MAX) return false;
+ *val = (int) retVal;
+ return true;
+}
+
+/////////////////////////////////////////////////////////////////
+// GetFloat()
+//
+// Attempts to parse a float from the character string given.
+// Returns true only if no parsing error occurs.
+/////////////////////////////////////////////////////////////////
+
+bool GetFloat (char *data, float *val){
+ char *endPtr;
+ double retVal;
+
+ assert (val);
+
+ errno = 0;
+ retVal = strtod (data, &endPtr);
+ if (retVal == 0 && (errno != 0 || data == endPtr)) return false;
+ if (errno != 0 && (retVal >= 1000000.0 || retVal <= -1000000.0)) return false;
+ *val = (float) retVal;
+ return true;
+}
+
+/////////////////////////////////////////////////////////////////
+// ParseParams()
+//
+// Parse all command-line options.
+/////////////////////////////////////////////////////////////////
+
+SafeVector<string> ParseParams (int argc, char **argv){
+
+ if (argc < 2){
+
+ cerr << "PROBCONS comes with ABSOLUTELY NO WARRANTY. This is free software, and" << endl
+ << "you are welcome to redistribute it under certain conditions. See the" << endl
+ << "file COPYING.txt for details." << endl
+ << endl
+ << "Usage:" << endl
+ << " probcons [OPTION]... [MFAFILE]..." << endl
+ << endl
+ << "Description:" << endl
+ << " Align sequences in MFAFILE(s) and print result to standard output" << endl
+ << endl
+ << " -t, --train FILENAME" << endl
+ << " compute EM transition probabilities, store in FILENAME (default: "
+ << parametersOutputFilename << ")" << endl
+ << endl
+ << " -m, --matrixfile FILENAME" << endl
+ << " read transition parameters from FILENAME (default: "
+ << matrixFilename << ")" << endl
+ << endl
+ << " -p, --paramfile FILENAME" << endl
+ << " read scoring matrix probabilities from FILENAME (default: "
+ << parametersInputFilename << ")" << endl
+ << endl
+ << " -c, --consistency REPS" << endl
+ << " use " << MIN_CONSISTENCY_REPS << " <= REPS <= " << MAX_CONSISTENCY_REPS
+ << " (default: " << numConsistencyReps << ") passes of consistency transformation" << endl
+ << endl
+ << " -ir, --iterative-refinement REPS" << endl
+ << " use " << MIN_ITERATIVE_REFINEMENT_REPS << " <= REPS <= " << MAX_ITERATIVE_REFINEMENT_REPS
+ << " (default: " << numIterativeRefinementReps << ") passes of iterative-refinement" << endl
+ << endl
+ << " -pre, --pre-training REPS" << endl
+ << " use " << MIN_PRETRAINING_REPS << " <= REPS <= " << MAX_PRETRAINING_REPS
+ << " (default: " << numPreTrainingReps << ") rounds of pretraining" << endl
+ << endl
+ << " -go, --gap-open VALUE" << endl
+ << " gap opening penalty of VALUE <= 0 (default: " << gapOpenPenalty << ")" << endl
+ << endl
+ << " -ge, --gap-extension VALUE" << endl
+ << " gap extension penalty of VALUE <= 0 (default: " << gapContinuePenalty << ")" << endl
+ << endl
+ << " -v, --verbose" << endl
+ << " report progress while aligning (default: " << (enableVerbose ? "on" : "off") << ")" << endl
+ << endl;
+
+ exit (1);
+ }
+
+ SafeVector<string> sequenceNames;
+ int tempInt;
+ float tempFloat;
+
+ for (int i = 1; i < argc; i++){
+ if (argv[i][0] == '-'){
+
+ // training
+ if (!strcmp (argv[i], "-t") || !strcmp (argv[i], "--train")){
+ enableTraining = true;
+ if (i < argc - 1)
+ parametersOutputFilename = string (argv[++i]);
+ else {
+ cerr << "ERROR: Filename expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // scoring matrix file
+ else if (!strcmp (argv[i], "-m") || !strcmp (argv[i], "--matrixfile")){
+ if (i < argc - 1)
+ matrixFilename = string (argv[++i]);
+ else {
+ cerr << "ERROR: Filename expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // transition/initial distribution parameter file
+ else if (!strcmp (argv[i], "-p") || !strcmp (argv[i], "--paramfile")){
+ if (i < argc - 1)
+ parametersInputFilename = string (argv[++i]);
+ else {
+ cerr << "ERROR: Filename expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // number of consistency transformations
+ else if (!strcmp (argv[i], "-c") || !strcmp (argv[i], "--consistency")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_CONSISTENCY_REPS || tempInt > MAX_CONSISTENCY_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_CONSISTENCY_REPS << " and " << MAX_CONSISTENCY_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numConsistencyReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // number of randomized partitioning iterative refinement passes
+ else if (!strcmp (argv[i], "-ir") || !strcmp (argv[i], "--iterative-refinement")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_ITERATIVE_REFINEMENT_REPS || tempInt > MAX_ITERATIVE_REFINEMENT_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_ITERATIVE_REFINEMENT_REPS << " and " << MAX_ITERATIVE_REFINEMENT_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numIterativeRefinementReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // number of EM pre-training rounds
+ else if (!strcmp (argv[i], "-pre") || !strcmp (argv[i], "--pre-training")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_PRETRAINING_REPS || tempInt > MAX_PRETRAINING_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_PRETRAINING_REPS << " and " << MAX_PRETRAINING_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numPreTrainingReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // gap open penalty
+ else if (!strcmp (argv[i], "-go") || !strcmp (argv[i], "--gap-open")){
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat > 0){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be positive." << endl;
+ exit (1);
+ }
+ else
+ gapOpenPenalty = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // gap extension penalty
+ else if (!strcmp (argv[i], "-ge") || !strcmp (argv[i], "--gap-extension")){
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat > 0){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be positive." << endl;
+ exit (1);
+ }
+ else
+ gapContinuePenalty = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // verbose reporting
+ else if (!strcmp (argv[i], "-v") || !strcmp (argv[i], "--verbose")){
+ enableVerbose = true;
+ }
+
+ // bad arguments
+ else {
+ cerr << "ERROR: Unrecognized option: " << argv[i] << endl;
+ exit (1);
+ }
+ }
+ else {
+ sequenceNames.push_back (string (argv[i]));
+ }
+ }
+
+ return sequenceNames;
+}
+
+/////////////////////////////////////////////////////////////////
+// ReadParameters()
+//
+// Read initial distribution, transition, and emission
+// parameters from a file.
+/////////////////////////////////////////////////////////////////
+
+void ReadParameters (){
+
+ ifstream data;
+
+ // read initial state distribution and transition parameters
+ if (parametersInputFilename == string ("")){
+ if (NumInsertStates == 1){
+ for (int i = 0; i < NumMatrixTypes; i++) initDistrib[i] = initDistrib1Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapOpen[i] = gapOpen1Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapExtend[i] = gapExtend1Default[i];
+ }
+ else if (NumInsertStates == 2){
+ for (int i = 0; i < NumMatrixTypes; i++) initDistrib[i] = initDistrib2Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapOpen[i] = gapOpen2Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapExtend[i] = gapExtend2Default[i];
+ }
+ else {
+ cerr << "ERROR: No default initial distribution/parameter settings exist" << endl
+ << " for " << NumInsertStates << " pairs of insert states. Use --paramfile." << endl;
+ exit (1);
+ }
+ }
+ else {
+ data.open (parametersInputFilename.c_str());
+ if (data.fail()){
+ cerr << "ERROR: Unable to read parameter file: " << parametersInputFilename << endl;
+ exit (1);
+ }
+ for (int i = 0; i < NumMatrixTypes; i++) data >> initDistrib[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) data >> gapOpen[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) data >> gapExtend[i];
+ data.close();
+ }
+
+ // read emission parameters
+ int alphabetSize = 20;
+
+ // allocate memory
+ alphabet = SafeVector<char>(alphabetSize);
+ emitPairs = VVF (alphabetSize, VF (alphabetSize, 0));
+ emitSingle = VF (alphabetSize);
+
+ if (matrixFilename == string ("")){
+ for (int i = 0; i < alphabetSize; i++) alphabet[i] = alphabetDefault[i];
+ for (int i = 0; i < alphabetSize; i++){
+ emitSingle[i] = emitSingleDefault[i];
+ for (int j = 0; j <= i; j++){
+ emitPairs[i][j] = emitPairs[j][i] = (i == j);
+ }
+ }
+ }
+ else {
+ data.open (matrixFilename.c_str());
+ if (data.fail()){
+ cerr << "ERROR: Unable to read scoring matrix file: " << matrixFilename << endl;
+ exit (1);
+ }
+
+ for (int i = 0; i < alphabetSize; i++) data >> alphabet[i];
+ for (int i = 0; i < alphabetSize; i++){
+ for (int j = 0; j <= i; j++){
+ data >> emitPairs[i][j];
+ emitPairs[j][i] = emitPairs[i][j];
+ }
+ }
+ for (int i = 0; i < alphabetSize; i++){
+ char ch;
+ data >> ch;
+ assert (ch == alphabet[i]);
+ }
+ for (int i = 0; i < alphabetSize; i++) data >> emitSingle[i];
+ data.close();
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// ProcessTree()
+//
+// Process the tree recursively. Returns the aligned sequences
+// corresponding to a node or leaf of the tree.
+/////////////////////////////////////////////////////////////////
+
+MultiSequence *ProcessTree (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model){
+ MultiSequence *result;
+
+ // check if this is a node of the alignment tree
+ if (tree->GetSequenceLabel() == -1){
+ MultiSequence *alignLeft = ProcessTree (tree->GetLeftChild(), sequences, sparseMatrices, model);
+ MultiSequence *alignRight = ProcessTree (tree->GetRightChild(), sequences, sparseMatrices, model);
+
+ assert (alignLeft);
+ assert (alignRight);
+
+ result = AlignAlignments (alignLeft, alignRight, sparseMatrices, model);
+ assert (result);
+
+ delete alignLeft;
+ delete alignRight;
+ }
+
+ // otherwise, this is a leaf of the alignment tree
+ else {
+ result = new MultiSequence(); assert (result);
+ result->AddSequence (sequences->GetSequence(tree->GetSequenceLabel())->Clone());
+ }
+
+ return result;
+}
+
+/////////////////////////////////////////////////////////////////
+// ComputeFinalAlignment()
+//
+// Compute the final alignment by calling ProcessTree(), then
+// performing iterative refinement as needed.
+/////////////////////////////////////////////////////////////////
+
+MultiSequence *ComputeFinalAlignment (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model){
+
+ MultiSequence *alignment = ProcessTree (tree, sequences, sparseMatrices, model);
+
+ // iterative refinement
+ for (int i = 0; i < numIterativeRefinementReps; i++)
+ DoIterativeRefinement (sparseMatrices, model, alignment);
+
+ cerr << endl;
+
+ // return final alignment
+ return alignment;
+}
+
+/////////////////////////////////////////////////////////////////
+// AlignAlignments()
+//
+// Returns the alignment of two MultiSequence objects.
+/////////////////////////////////////////////////////////////////
+
+MultiSequence *AlignAlignments (MultiSequence *align1, MultiSequence *align2,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model){
+
+ // print some info about the alignment
+ if (enableVerbose){
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ cerr << ((i==0) ? "[" : ",") << align1->GetSequence(i)->GetLabel();
+ cerr << "] vs. ";
+ for (int i = 0; i < align2->GetNumSequences(); i++)
+ cerr << ((i==0) ? "[" : ",") << align2->GetSequence(i)->GetLabel();
+ cerr << "]: ";
+ }
+
+ VF *posterior = model.BuildPosterior (align1, align2, sparseMatrices);
+ pair<SafeVector<char> *, float> alignment;
+
+ // choose the alignment routine depending on the "cosmetic" gap penalties used
+ if (gapOpenPenalty == 0 && gapContinuePenalty == 0)
+ alignment = model.ComputeAlignment (align1->GetSequence(0)->GetLength(), align2->GetSequence(0)->GetLength(), *posterior);
+ else
+ alignment = model.ComputeAlignmentWithGapPenalties (align1, align2,
+ *posterior, align1->GetNumSequences(), align2->GetNumSequences(),
+ gapOpenPenalty, gapContinuePenalty);
+
+ delete posterior;
+
+ if (enableVerbose){
+
+ // compute total length of sequences
+ int totLength = 0;
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ for (int j = 0; j < align2->GetNumSequences(); j++)
+ totLength += min (align1->GetSequence(i)->GetLength(), align2->GetSequence(j)->GetLength());
+
+ // give an "accuracy" measure for the alignment
+ cerr << alignment.second / totLength << endl;
+ }
+
+ // now build final alignment
+ MultiSequence *result = new MultiSequence();
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ result->AddSequence (align1->GetSequence(i)->AddGaps(alignment.first, 'X'));
+ for (int i = 0; i < align2->GetNumSequences(); i++)
+ result->AddSequence (align2->GetSequence(i)->AddGaps(alignment.first, 'Y'));
+ result->SortByLabel();
+
+ // free temporary alignment
+ delete alignment.first;
+
+ return result;
+}
+
+/////////////////////////////////////////////////////////////////
+// DoRelaxation()
+//
+// Performs one round of the consistency transformation. The
+// formula used is:
+// 1
+// P'(x[i]-y[j]) = --- sum sum P(x[i]-z[k]) P(z[k]-y[j])
+// |S| z in S k
+//
+// where S = {x, y, all other sequences...}
+//
+/////////////////////////////////////////////////////////////////
+
+void DoRelaxation (MultiSequence *sequences, SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices){
+ const int numSeqs = sequences->GetNumSequences();
+
+ SafeVector<SafeVector<SparseMatrix *> > newSparseMatrices (numSeqs, SafeVector<SparseMatrix *>(numSeqs, NULL));
+
+ // for every pair of sequences
+ for (int i = 0; i < numSeqs; i++){
+ for (int j = i+1; j < numSeqs; j++){
+ Sequence *seq1 = sequences->GetSequence (i);
+ Sequence *seq2 = sequences->GetSequence (j);
+
+ if (enableVerbose)
+ cerr << "Relaxing (" << i+1 << ") " << seq1->GetHeader() << " vs. "
+ << "(" << j+1 << ") " << seq2->GetHeader() << ": ";
+
+ // get the original posterior matrix
+ VF *posteriorPtr = sparseMatrices[i][j]->GetPosterior(); assert (posteriorPtr);
+ VF &posterior = *posteriorPtr;
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+
+ // contribution from the summation where z = x and z = y
+ for (int k = 0; k < (seq1Length+1) * (seq2Length+1); k++) posterior[k] += posterior[k];
+
+ if (enableVerbose)
+ cerr << sparseMatrices[i][j]->GetNumCells() << " --> ";
+
+ // contribution from all other sequences
+ for (int k = 0; k < numSeqs; k++) if (k != i && k != j){
+ Relax (sparseMatrices[i][k], sparseMatrices[k][j], posterior);
+ }
+
+ // now renormalization
+ for (int k = 0; k < (seq1Length+1) * (seq2Length+1); k++) posterior[k] /= numSeqs;
+
+ // save the new posterior matrix
+ newSparseMatrices[i][j] = new SparseMatrix (seq1->GetLength(), seq2->GetLength(), posterior);
+ newSparseMatrices[j][i] = newSparseMatrices[i][j]->ComputeTranspose();
+
+ if (enableVerbose)
+ cerr << newSparseMatrices[i][j]->GetNumCells() << " -- ";
+
+ delete posteriorPtr;
+
+ if (enableVerbose)
+ cerr << "done." << endl;
+ }
+ }
+
+ // now replace the old posterior matrices
+ for (int i = 0; i < numSeqs; i++){
+ for (int j = 0; j < numSeqs; j++){
+ delete sparseMatrices[i][j];
+ sparseMatrices[i][j] = newSparseMatrices[i][j];
+ }
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// DoRelaxation()
+//
+// Computes the consistency transformation for a single sequence
+// z, and adds the transformed matrix to "posterior".
+/////////////////////////////////////////////////////////////////
+
+void Relax (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior){
+
+ assert (matXZ);
+ assert (matZY);
+
+ int lengthX = matXZ->GetSeq1Length();
+ int lengthY = matZY->GetSeq2Length();
+ assert (matXZ->GetSeq2Length() == matZY->GetSeq1Length());
+
+ // for every x[i]
+ for (int i = 1; i <= lengthX; i++){
+ SafeVector<PIF>::iterator XZptr = matXZ->GetRowPtr(i);
+ SafeVector<PIF>::iterator XZend = XZptr + matXZ->GetRowSize(i);
+
+ VF::iterator base = posterior.begin() + i * (lengthY + 1);
+
+ // iterate through all x[i]-z[k]
+ while (XZptr != XZend){
+ SafeVector<PIF>::iterator ZYptr = matZY->GetRowPtr(XZptr->first);
+ SafeVector<PIF>::iterator ZYend = ZYptr + matZY->GetRowSize(XZptr->first);
+ const float XZval = XZptr->second;
+
+ // iterate through all z[k]-y[j]
+ while (ZYptr != ZYend){
+ base[ZYptr->first] += XZval * ZYptr->second;;
+ ZYptr++;
+ }
+ XZptr++;
+ }
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// DoIterativeRefinement()
+//
+// Performs a single round of randomized partionining iterative
+// refinement.
+/////////////////////////////////////////////////////////////////
+
+void DoIterativeRefinement (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment){
+ set<int> groupOne, groupTwo;
+
+ // create two separate groups
+ for (int i = 0; i < alignment->GetNumSequences(); i++){
+ if (random() % 2)
+ groupOne.insert (i);
+ else
+ groupTwo.insert (i);
+ }
+
+ if (groupOne.empty() || groupTwo.empty()) return;
+
+ // project into the two groups
+ MultiSequence *groupOneSeqs = alignment->Project (groupOne); assert (groupOneSeqs);
+ MultiSequence *groupTwoSeqs = alignment->Project (groupTwo); assert (groupTwoSeqs);
+ delete alignment;
+
+ // realign
+ alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model);
+}
+
+/*
+float ScoreAlignment (MultiSequence *alignment, MultiSequence *sequences, SparseMatrix **sparseMatrices, const int numSeqs){
+ int totLength = 0;
+ float score = 0;
+
+ for (int a = 0; a < alignment->GetNumSequences(); a++){
+ for (int b = a+1; b < alignment->GetNumSequences(); b++){
+ Sequence *seq1 = alignment->GetSequence(a);
+ Sequence *seq2 = alignment->GetSequence(b);
+
+ const int seq1Length = sequences->GetSequence(seq1->GetLabel())->GetLength();
+ const int seq2Length = sequences->GetSequence(seq2->GetLabel())->GetLength();
+
+ totLength += min (seq1Length, seq2Length);
+
+ int pos1 = 0, pos2 = 0;
+ for (int i = 1; i <= seq1->GetLength(); i++){
+ char ch1 = seq1->GetPosition(i);
+ char ch2 = seq2->GetPosition(i);
+
+ if (ch1 != '-') pos1++;
+ if (ch2 != '-') pos2++;
+ if (ch1 != '-' && ch2 != '-'){
+ score += sparseMatrices[a * numSeqs + b]->GetValue (pos1, pos2);
+ }
+ }
+ }
+ }
+
+ return score / totLength;
+}
+*/
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// Main.cc
+//
+// Main routines for MXSCARNA program.
+/////////////////////////////////////////////////////////////////
+
+#include "scarna.hpp"
+#include "SafeVector.h"
+#include "MultiSequence.h"
+#include "Defaults.h"
+#include "ScoreType.h"
+#include "ProbabilisticModel.h"
+#include "EvolutionaryTree.h"
+#include "SparseMatrix.h"
+#include "BPPMatrix.hpp"
+#include "StemCandidate.hpp"
+#include "Globaldp.hpp"
+#include "nrutil.h"
+#include "AlifoldMEA.h"
+#include <string>
+#include <sstream>
+#include <iomanip>
+#include <iostream>
+#include <list>
+#include <set>
+#include <algorithm>
+#include <cstdio>
+#include <cstdlib>
+#include <cerrno>
+#include <iomanip>
+#include <fstream>
+
+#include "RfoldWrapper.hpp"
+//static RFOLD::Rfold folder;
+
+using namespace::MXSCARNA;
+using namespace::RFOLD;
+
+string parametersInputFilename = "";
+string parametersOutputFilename = "no training";
+string annotationFilename = "";
+string weboutputFileName = "";
+
+ofstream *outputFile;
+
+bool enableTraining = false;
+bool enableVerbose = false;
+bool enableAllPairs = false;
+bool enableAnnotation = false;
+bool enableViterbi = false;
+bool enableClustalWOutput = false;
+bool enableTrainEmissions = false;
+bool enableAlignOrder = false;
+bool enableWebOutput = false;
+bool enableStockholmOutput = false;
+bool enableMXSCARNAOutput = false;
+bool enableMcCaskillMEAMode = false;
+int numConsistencyReps = 2;
+int numPreTrainingReps = 0;
+int numIterativeRefinementReps = 100;
+int scsLength = SCSLENGTH;
+float cutoff = 0;
+float gapOpenPenalty = 0;
+float gapContinuePenalty = 0;
+float threshhold = 1.0;
+float BaseProbThreshold = BASEPROBTHRESHOLD;
+float BasePairConst = BASEPAIRCONST;
+int BandWidth = BANDWIDTH;
+bool useRfold = USERFOLD;
+SafeVector<string> sequenceNames;
+
+VF initDistrib (NumMatrixTypes);
+VF gapOpen (2*NumInsertStates);
+VF gapExtend (2*NumInsertStates);
+VVF emitPairs (256, VF (256, 1e-10));
+VF emitSingle (256, 1e-5);
+
+string alphabet = alphabetDefault;
+
+string *ssCons = NULL;
+
+const int MIN_PRETRAINING_REPS = 0;
+const int MAX_PRETRAINING_REPS = 20;
+const int MIN_CONSISTENCY_REPS = 0;
+const int MAX_CONSISTENCY_REPS = 5;
+const int MIN_ITERATIVE_REFINEMENT_REPS = 0;
+const int MAX_ITERATIVE_REFINEMENT_REPS = 1000;
+
+/////////////////////////////////////////////////////////////////
+// Function prototypes
+/////////////////////////////////////////////////////////////////
+
+void PrintHeading();
+void PrintParameters (const char *message, const VF &initDistrib, const VF &gapOpen,
+ const VF &gapExtend, const VVF &emitPairs, const VF &emitSingle, const char *filename);
+MultiSequence *DoAlign (MultiSequence *sequence, const ProbabilisticModel &model, VF &initDistrib, VF &gapOpen, VF &gapExtend, VVF &emitPairs, VF &emitSingle);
+SafeVector<string> ParseParams (int argc, char **argv);
+void ReadParameters ();
+MultiSequence *ComputeFinalAlignment (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model,
+ SafeVector<BPPMatrix*> &BPPMatrices);
+MultiSequence *AlignAlignments (MultiSequence *align1, MultiSequence *align2,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, SafeVector<BPPMatrix*> &BPPMatrices, float identity);
+SafeVector<SafeVector<SparseMatrix *> > DoRelaxation (MultiSequence *sequences,
+ SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+void Relax (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior);
+void Relax1 (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior);
+void DoBasePairProbabilityRelaxation (MultiSequence *sequences,
+ SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ SafeVector<BPPMatrix*> &BPPMatrices);
+set<int> GetSubtree (const TreeNode *tree);
+void TreeBasedBiPartitioning (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment,
+ const TreeNode *tree, SafeVector<BPPMatrix*> &BPPMatrices);
+void DoIterativeRefinement (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment);
+void WriteAnnotation (MultiSequence *alignment,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+int ComputeScore (const SafeVector<pair<int, int> > &active,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices);
+std::vector<StemCandidate>* seq2scs(MultiSequence *Sequences, SafeVector<BPPMatrix*> &BPPMatrices, int BandWidth);
+void removeConflicts(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2, std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2);
+
+struct prob {
+ int i;
+ int j;
+ float p;
+};
+
+/////////////////////////////////////////////////////////////////
+// main()
+//
+// Calls all initialization routines and runs the MXSCARNA
+// aligner.
+/////////////////////////////////////////////////////////////////
+
+
+int main (int argc, char **argv){
+
+ // print MXSCARNA heading
+ PrintHeading();
+
+ // parse program parameters
+ sequenceNames = ParseParams (argc, argv);
+ ReadParameters();
+ PrintParameters ("Using parameter set:", initDistrib, gapOpen, gapExtend, emitPairs, emitSingle, NULL);
+
+ // now, we'll process all the files given as input. If we are given
+ // several filenames as input, then we'll load all of those sequences
+ // simultaneously, as long as we're not training. On the other hand,
+ // if we are training, then we'll treat each file as a separate
+ // training instance
+
+ if (enableMcCaskillMEAMode) {
+ MultiSequence *sequences = new MultiSequence(); assert (sequences);
+ for (int i = 0; i < (int) sequenceNames.size(); i++){
+ cerr << "Loading sequence file: " << sequenceNames[i] << endl;
+ sequences->LoadMFA (sequenceNames[i], true);
+ }
+
+ const int numSeqs = sequences->GetNumSequences();
+ SafeVector<BPPMatrix*> BPPMatrices;
+
+ // compute the base pairing matrices for each sequences
+ for(int i = 0; i < numSeqs; i++) {
+ Sequence *tmpSeq = sequences->GetSequence(i);
+ string seq = tmpSeq->GetString();
+ int n_seq = tmpSeq->GetLength();
+ BPPMatrix *bppmat = new BPPMatrix(seq, n_seq);
+ BPPMatrices.push_back(bppmat);
+ }
+ AlifoldMEA alifold(sequences, BPPMatrices, BasePairConst);
+ alifold.Run();
+ ssCons = alifold.getSScons();
+
+ if (enableStockholmOutput) {
+ sequences->WriteSTOCKHOLM (cout, ssCons);
+ }
+ else if (enableMXSCARNAOutput){
+ sequences->WriteMXSCARNA (cout, ssCons);
+ }
+ else {
+ sequences->WriteMFA (cout, ssCons);
+ }
+
+ delete sequences;
+ }
+ // if we are training
+ else if (enableTraining){
+
+ // build new model for aligning
+ ProbabilisticModel model (initDistrib, gapOpen, gapExtend, emitPairs, emitSingle);
+
+ // prepare to average parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] = 0;
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] = 0;
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] = 0;
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] = 0;
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] = 0;
+ }
+
+ // align each file individually
+ for (int i = 0; i < (int) sequenceNames.size(); i++){
+
+ VF thisInitDistrib (NumMatrixTypes);
+ VF thisGapOpen (2*NumInsertStates);
+ VF thisGapExtend (2*NumInsertStates);
+ VVF thisEmitPairs (256, VF (256, 1e-10));
+ VF thisEmitSingle (256, 1e-5);
+
+ // load sequence file
+ MultiSequence *sequences = new MultiSequence(); assert (sequences);
+ cerr << "Loading sequence file: " << sequenceNames[i] << endl;
+ sequences->LoadMFA (sequenceNames[i], true);
+
+ // align sequences
+ DoAlign (sequences, model, thisInitDistrib, thisGapOpen, thisGapExtend, thisEmitPairs, thisEmitSingle);
+
+ // add in contribution of the derived parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] += thisInitDistrib[i];
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] += thisGapOpen[i];
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] += thisGapExtend[i];
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] += thisEmitPairs[i][j];
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] += thisEmitSingle[i];
+ }
+
+ delete sequences;
+ }
+
+ // compute new parameters and print them out
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] /= (int) sequenceNames.size();
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] /= (int) sequenceNames.size();
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] /= (int) sequenceNames.size();
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] /= (int) sequenceNames.size();
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] /= sequenceNames.size();
+ }
+
+ PrintParameters ("Trained parameter set:",
+ initDistrib, gapOpen, gapExtend, emitPairs, emitSingle,
+ parametersOutputFilename.c_str());
+ }
+ // pass
+ // if we are not training, we must simply want to align some sequences
+ else {
+ // load all files together
+ MultiSequence *sequences = new MultiSequence(); assert (sequences);
+ for (int i = 0; i < (int) sequenceNames.size(); i++){
+ cerr << "Loading sequence file: " << sequenceNames[i] << endl;
+
+ sequences->LoadMFA (sequenceNames[i], true);
+ }
+
+ // do all "pre-training" repetitions first
+ // NOT execute
+ for (int ct = 0; ct < numPreTrainingReps; ct++){
+ enableTraining = true;
+
+ // build new model for aligning
+ ProbabilisticModel model (initDistrib, gapOpen, gapExtend,
+ emitPairs, emitSingle);
+
+ // do initial alignments
+ DoAlign (sequences, model, initDistrib, gapOpen, gapExtend, emitPairs, emitSingle);
+
+ // print new parameters
+ PrintParameters ("Recomputed parameter set:", initDistrib, gapOpen, gapExtend, emitPairs, emitSingle, NULL);
+
+ enableTraining = false;
+ }
+
+ // now, we can perform the alignments and write them out
+ if (enableWebOutput) {
+ outputFile = new ofstream(weboutputFileName.c_str());
+ if (!outputFile) {
+ cerr << "cannot open output file." << weboutputFileName << endl;
+ exit(1);
+ }
+ *outputFile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << endl;
+ *outputFile << "<result>" << endl;
+ }
+ MultiSequence *alignment = DoAlign (sequences,
+ ProbabilisticModel (initDistrib, gapOpen, gapExtend, emitPairs, emitSingle),
+ initDistrib, gapOpen, gapExtend, emitPairs, emitSingle);
+
+
+ if (!enableAllPairs){
+ if (enableClustalWOutput) {
+ alignment->WriteALN (cout);
+ }
+ else if (enableWebOutput) {
+ alignment->WriteWEB (*outputFile, ssCons);
+// computeStructureWithAlifold ();
+ }
+ else if (enableStockholmOutput) {
+ alignment->WriteSTOCKHOLM (cout, ssCons);
+ }
+ else if (enableMXSCARNAOutput) {
+ alignment->WriteMXSCARNA (cout, ssCons);
+ }
+ else {
+ alignment->WriteMFA (cout, ssCons);
+ }
+ }
+
+ if (enableWebOutput) {
+ *outputFile << "</result>" << endl;
+ delete outputFile;
+ }
+
+ delete ssCons;
+ delete alignment;
+ delete sequences;
+
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// PrintHeading()
+//
+// Prints heading for PROBCONS program.
+/////////////////////////////////////////////////////////////////
+
+void PrintHeading (){
+ cerr << endl
+ << "Multiplex SCARNA"<< endl
+ << "version " << VERSION << " - align multiple RNA sequences and print to standard output" << endl
+ << "Written by Yasuo Tabei" << endl
+ << endl;
+}
+
+/////////////////////////////////////////////////////////////////
+// PrintParameters()
+//
+// Prints PROBCONS parameters to STDERR. If a filename is
+// specified, then the parameters are also written to the file.
+/////////////////////////////////////////////////////////////////
+
+void PrintParameters (const char *message, const VF &initDistrib, const VF &gapOpen,
+ const VF &gapExtend, const VVF &emitPairs, const VF &emitSingle, const char *filename){
+
+ // print parameters to the screen
+ cerr << message << endl
+ << " initDistrib[] = { ";
+ for (int i = 0; i < NumMatrixTypes; i++) cerr << setprecision (10) << initDistrib[i] << " ";
+ cerr << "}" << endl
+ << " gapOpen[] = { ";
+ for (int i = 0; i < NumInsertStates*2; i++) cerr << setprecision (10) << gapOpen[i] << " ";
+ cerr << "}" << endl
+ << " gapExtend[] = { ";
+ for (int i = 0; i < NumInsertStates*2; i++) cerr << setprecision (10) << gapExtend[i] << " ";
+ cerr << "}" << endl
+ << endl;
+
+ /*
+ for (int i = 0; i < 5; i++){
+ for (int j = 0; j <= i; j++){
+ cerr << emitPairs[(unsigned char) alphabet[i]][(unsigned char) alphabet[j]] << " ";
+ }
+ cerr << endl;
+ }*/
+
+ // if a file name is specified
+ if (filename){
+
+ // attempt to open the file for writing
+ FILE *file = fopen (filename, "w");
+ if (!file){
+ cerr << "ERROR: Unable to write parameter file: " << filename << endl;
+ exit (1);
+ }
+
+ // if successful, then write the parameters to the file
+ for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n");
+ for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n");
+ for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n");
+ fprintf (file, "%s\n", alphabet.c_str());
+ for (int i = 0; i < (int) alphabet.size(); i++){
+ for (int j = 0; j <= i; j++)
+ fprintf (file, "%.10f ", emitPairs[(unsigned char) alphabet[i]][(unsigned char) alphabet[j]]);
+ fprintf (file, "\n");
+ }
+ for (int i = 0; i < (int) alphabet.size(); i++)
+ fprintf (file, "%.10f ", emitSingle[(unsigned char) alphabet[i]]);
+ fprintf (file, "\n");
+ fclose (file);
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// DoAlign()
+//
+// First computes all pairwise posterior probability matrices.
+// Then, computes new parameters if training, or a final
+// alignment, otherwise.
+/////////////////////////////////////////////////////////////////
+MultiSequence *DoAlign (MultiSequence *sequences, const ProbabilisticModel &model, VF &initDistrib, VF &gapOpen, VF &gapExtend, VVF &emitPairs, VF &emitSingle){
+
+ assert (sequences);
+
+ const int numSeqs = sequences->GetNumSequences();
+ VVF distances (numSeqs, VF (numSeqs, 0));
+ VVF identities (numSeqs, VF (numSeqs, 0));
+ SafeVector<SafeVector<SparseMatrix *> > sparseMatrices (numSeqs, SafeVector<SparseMatrix *>(numSeqs, NULL));
+
+ SafeVector<BPPMatrix*> BPPMatrices;
+
+ RfoldWrapper rfoldWrapper;
+ if (useRfold) {
+ BPPMatrices
+ = rfoldWrapper.getProb(sequenceNames, sequences, BASEPROBTHRESHOLD, BandWidth);
+ }
+ else {
+ for(int i = 0; i < numSeqs; i++) {
+ Sequence *tmpSeq = sequences->GetSequence(i);
+ string seq = tmpSeq->GetString();
+ int n_seq = tmpSeq->GetLength();
+ BPPMatrix *bppmat = new BPPMatrix(seq, n_seq, BASEPROBTHRESHOLD);
+ BPPMatrices.push_back(bppmat);
+ }
+ }
+
+ if (enableTraining){
+ // prepare to average parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] = 0;
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] = 0;
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] = 0;
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] = 0;
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] = 0;
+ }
+ }
+
+ // skip posterior calculations if we just want to do Viterbi alignments
+ if (!enableViterbi){
+
+ // do all pairwise alignments for posterior probability matrices
+ for (int a = 0; a < numSeqs-1; a++){
+ for (int b = a+1; b < numSeqs; b++){
+ Sequence *seq1 = sequences->GetSequence (a);
+ Sequence *seq2 = sequences->GetSequence (b);
+
+ // verbose output
+ if (enableVerbose)
+ cerr << "Computing posterior matrix: (" << a+1 << ") " << seq1->GetHeader() << " vs. "
+ << "(" << b+1 << ") " << seq2->GetHeader() << " -- ";
+
+ // compute forward and backward probabilities
+ VF *forward = model.ComputeForwardMatrix (seq1, seq2); assert (forward);
+ VF *backward = model.ComputeBackwardMatrix (seq1, seq2); assert (backward);
+
+ // if we are training, then we'll simply want to compute the
+ // expected counts for each region within the matrix separately;
+ // otherwise, we'll need to put all of the regions together and
+ // assemble a posterior probability match matrix
+
+ // so, if we're training
+ if (enableTraining){
+
+ // compute new parameters
+ VF thisInitDistrib (NumMatrixTypes);
+ VF thisGapOpen (2*NumInsertStates);
+ VF thisGapExtend (2*NumInsertStates);
+ VVF thisEmitPairs (256, VF (256, 1e-10));
+ VF thisEmitSingle (256, 1e-5);
+
+ model.ComputeNewParameters (seq1, seq2, *forward, *backward, thisInitDistrib, thisGapOpen, thisGapExtend, thisEmitPairs, thisEmitSingle, enableTrainEmissions);
+
+ // add in contribution of the derived parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] += thisInitDistrib[i];
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] += thisGapOpen[i];
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] += thisGapExtend[i];
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] += thisEmitPairs[i][j];
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] += thisEmitSingle[i];
+ }
+
+ // let us know that we're done.
+ if (enableVerbose) cerr << "done." << endl;
+ }
+ // pass
+ else {
+
+ // compute posterior probability matrix
+ VF *posterior = model.ComputePosteriorMatrix (seq1, seq2, *forward, *backward); assert (posterior);
+
+ // compute sparse representations
+ sparseMatrices[a][b] = new SparseMatrix (seq1->GetLength(), seq2->GetLength(), *posterior);
+ sparseMatrices[b][a] = NULL;
+
+ if (!enableAllPairs){
+ // perform the pairwise sequence alignment
+ pair<SafeVector<char> *, float> alignment = model.ComputeAlignment (seq1->GetLength(),
+ seq2->GetLength(),
+ *posterior);
+
+ Sequence *tmpSeq1 = seq1->AddGaps (alignment.first, 'X');
+ Sequence *tmpSeq2 = seq2->AddGaps (alignment.first, 'Y');
+
+ // compute sequence identity for each pair of sequenceses
+ int length = tmpSeq1->GetLength();
+ int matchCount = 0;
+ int misMatchCount = 0;
+ for (int k = 1; k <= length; k++) {
+ int ch1 = tmpSeq1->GetPosition(k);
+ int ch2 = tmpSeq2->GetPosition(k);
+ if (ch1 == ch2 && ch1 != '-' && ch2 != '-') { ++matchCount; }
+ else if (ch1 != ch2 && ch1 != '-' && ch2 != '-') { ++misMatchCount; }
+ }
+
+ identities[a][b] = identities[b][a] = (float)matchCount/(float)(matchCount + misMatchCount);
+
+ // compute "expected accuracy" distance for evolutionary tree computation
+ float distance = alignment.second / min (seq1->GetLength(), seq2->GetLength());
+ distances[a][b] = distances[b][a] = distance;
+
+ if (enableVerbose)
+ cerr << setprecision (10) << distance << endl;
+
+ delete alignment.first;
+ }
+ else {
+ // let us know that we're done.
+ if (enableVerbose) cerr << "done." << endl;
+ }
+
+ delete posterior;
+ }
+
+ delete forward;
+ delete backward;
+ }
+ }
+ }
+
+ // now average out parameters derived
+ if (enableTraining){
+ // compute new parameters
+ for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] /= numSeqs * (numSeqs - 1) / 2;
+ for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] /= numSeqs * (numSeqs - 1) / 2;
+ for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] /= numSeqs * (numSeqs - 1) / 2;
+
+ if (enableTrainEmissions){
+ for (int i = 0; i < (int) emitPairs.size(); i++)
+ for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] /= numSeqs * (numSeqs - 1) / 2;
+ for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] /= numSeqs * (numSeqs - 1) / 2;
+ }
+ }
+
+ // see if we still want to do some alignments
+ else {
+ // pass
+ if (!enableViterbi){
+
+ // perform the consistency transformation the desired number of times
+ for (int r = 0; r < numConsistencyReps; r++){
+ SafeVector<SafeVector<SparseMatrix *> > newSparseMatrices = DoRelaxation (sequences, sparseMatrices);
+
+ // now replace the old posterior matrices
+ for (int i = 0; i < numSeqs; i++){
+ for (int j = 0; j < numSeqs; j++){
+ delete sparseMatrices[i][j];
+ sparseMatrices[i][j] = newSparseMatrices[i][j];
+ }
+ }
+ }
+ if (numSeqs > 8) {
+ for (int r = 0; r < 1; r++)
+ DoBasePairProbabilityRelaxation(sequences, sparseMatrices, BPPMatrices);
+ }
+ }
+
+ MultiSequence *finalAlignment = NULL;
+
+ if (enableAllPairs){
+ for (int a = 0; a < numSeqs-1; a++){
+ for (int b = a+1; b < numSeqs; b++){
+ Sequence *seq1 = sequences->GetSequence (a);
+ Sequence *seq2 = sequences->GetSequence (b);
+
+ if (enableVerbose)
+ cerr << "Performing pairwise alignment: (" << a+1 << ") " << seq1->GetHeader() << " vs. "
+ << "(" << b+1 << ") " << seq2->GetHeader() << " -- ";
+
+
+ // perform the pairwise sequence alignment
+ pair<SafeVector<char> *, float> alignment;
+ if (enableViterbi)
+ alignment = model.ComputeViterbiAlignment (seq1, seq2);
+ else {
+
+ // build posterior matrix
+ VF *posterior = sparseMatrices[a][b]->GetPosterior(); assert (posterior);
+ int length = (seq1->GetLength() + 1) * (seq2->GetLength() + 1);
+ for (int i = 0; i < length; i++) (*posterior)[i] -= cutoff;
+
+ alignment = model.ComputeAlignment (seq1->GetLength(), seq2->GetLength(), *posterior);
+ delete posterior;
+ }
+
+ // write pairwise alignments
+ string name = seq1->GetHeader() + "-" + seq2->GetHeader() + (enableClustalWOutput ? ".aln" : ".fasta");
+ ofstream outfile (name.c_str());
+
+ MultiSequence *result = new MultiSequence();
+ result->AddSequence (seq1->AddGaps(alignment.first, 'X'));
+ result->AddSequence (seq2->AddGaps(alignment.first, 'Y'));
+ if (enableClustalWOutput)
+ result->WriteALN (outfile);
+ else
+ result->WriteMFA (outfile);
+
+ outfile.close();
+
+ delete alignment.first;
+ }
+ }
+ }
+
+ // now if we still need to do a final multiple alignment
+ else {
+
+ if (enableVerbose)
+ cerr << endl;
+
+ // compute the evolutionary tree
+ TreeNode *tree = TreeNode::ComputeTree (distances, identities);
+
+ if (enableWebOutput) {
+ *outputFile << "<tree>" << endl;
+ tree->Print (*outputFile, sequences);
+ *outputFile << "</tree>" << endl;
+ }
+ else {
+ tree->Print (cerr, sequences);
+ cerr << endl;
+ }
+ // make the final alignment
+ finalAlignment = ComputeFinalAlignment (tree, sequences, sparseMatrices, model, BPPMatrices);
+
+ // build annotation
+ if (enableAnnotation){
+ WriteAnnotation (finalAlignment, sparseMatrices);
+ }
+
+ delete tree;
+ }
+
+ if (!enableViterbi){
+ // delete sparse matrices
+ for (int a = 0; a < numSeqs-1; a++){
+ for (int b = a+1; b < numSeqs; b++){
+ delete sparseMatrices[a][b];
+ delete sparseMatrices[b][a];
+ }
+ }
+ }
+
+ AlifoldMEA alifold(finalAlignment, BPPMatrices, BasePairConst);
+ alifold.Run();
+ ssCons = alifold.getSScons();
+
+ return finalAlignment;
+
+ }
+
+ return NULL;
+}
+
+/////////////////////////////////////////////////////////////////
+// GetInteger()
+//
+// Attempts to parse an integer from the character string given.
+// Returns true only if no parsing error occurs.
+/////////////////////////////////////////////////////////////////
+
+bool GetInteger (char *data, int *val){
+ char *endPtr;
+ long int retVal;
+
+ assert (val);
+
+ errno = 0;
+ retVal = strtol (data, &endPtr, 0);
+ if (retVal == 0 && (errno != 0 || data == endPtr)) return false;
+ if (errno != 0 && (retVal == LONG_MAX || retVal == LONG_MIN)) return false;
+ if (retVal < (long) INT_MIN || retVal > (long) INT_MAX) return false;
+ *val = (int) retVal;
+ return true;
+}
+
+/////////////////////////////////////////////////////////////////
+// GetFloat()
+//
+// Attempts to parse a float from the character string given.
+// Returns true only if no parsing error occurs.
+/////////////////////////////////////////////////////////////////
+
+bool GetFloat (char *data, float *val){
+ char *endPtr;
+ double retVal;
+
+ assert (val);
+
+ errno = 0;
+ retVal = strtod (data, &endPtr);
+ if (retVal == 0 && (errno != 0 || data == endPtr)) return false;
+ if (errno != 0 && (retVal >= 1000000.0 || retVal <= -1000000.0)) return false;
+ *val = (float) retVal;
+ return true;
+}
+
+/////////////////////////////////////////////////////////////////
+// ParseParams()
+//
+// Parse all command-line options.
+/////////////////////////////////////////////////////////////////
+
+SafeVector<string> ParseParams (int argc, char **argv){
+
+ if (argc < 2){
+
+ cerr << "MXSCARNA comes with ABSOLUTELY NO WARRANTY. This is free software, and" << endl
+ << "you are welcome to redistribute it under certain conditions. See the" << endl
+ << "file COPYING.txt for details." << endl
+ << endl
+ << "Usage:" << endl
+ << " mxscarna [OPTION]... [MFAFILE]..." << endl
+ << endl
+ << "Description:" << endl
+ << " Align sequences in MFAFILE(s) and print result to standard output" << endl
+ << endl
+ << " -clustalw" << endl
+ << " use CLUSTALW output format instead of MFA" << endl
+ << endl
+ << " -stockholm" << endl
+ << " use STOCKHOLM output format instead of MFA" << endl
+ << endl
+ << " -mxscarna" << endl
+ << " use MXSCARNA output format instead of MFA" << endl
+ << endl
+ << " -weboutput /<output_path>/<outputfilename>" << endl
+ << " use web output format" << endl
+ << endl
+ << " -c, --consistency REPS" << endl
+ << " use " << MIN_CONSISTENCY_REPS << " <= REPS <= " << MAX_CONSISTENCY_REPS
+ << " (default: " << numConsistencyReps << ") passes of consistency transformation" << endl
+ << endl
+ << " -ir, --iterative-refinement REPS" << endl
+ << " use " << MIN_ITERATIVE_REFINEMENT_REPS << " <= REPS <= " << MAX_ITERATIVE_REFINEMENT_REPS
+ << " (default: " << numIterativeRefinementReps << ") passes of iterative-refinement" << endl
+ << endl
+ << " -pre, --pre-training REPS" << endl
+ << " use " << MIN_PRETRAINING_REPS << " <= REPS <= " << MAX_PRETRAINING_REPS
+ << " (default: " << numPreTrainingReps << ") rounds of pretraining" << endl
+ << endl
+ << " -pairs" << endl
+ << " generate all-pairs pairwise alignments" << endl
+ << endl
+ << " -viterbi" << endl
+ << " use Viterbi algorithm to generate all pairs (automatically enables -pairs)" << endl
+ << endl
+ << " -v, --verbose" << endl
+ << " report progress while aligning (default: " << (enableVerbose ? "on" : "off") << ")" << endl
+ << endl
+ << " -annot FILENAME" << endl
+ << " write annotation for multiple alignment to FILENAME" << endl
+ << endl
+ << " -t, --train FILENAME" << endl
+ << " compute EM transition probabilities, store in FILENAME (default: "
+ << parametersOutputFilename << ")" << endl
+ << endl
+ << " -e, --emissions" << endl
+ << " also reestimate emission probabilities (default: "
+ << (enableTrainEmissions ? "on" : "off") << ")" << endl
+ << endl
+ << " -p, --paramfile FILENAME" << endl
+ << " read parameters from FILENAME (default: "
+ << parametersInputFilename << ")" << endl
+ << endl
+ << " -a, --alignment-order" << endl
+ << " print sequences in alignment order rather than input order (default: "
+ << (enableAlignOrder ? "on" : "off") << ")" << endl
+ << endl
+ << " -s THRESHOLD" << endl
+ << " the threshold of SCS alignment" << endl
+ << endl
+ << " In default, for less than " << threshhold << ", the SCS aligment is applied. " << endl
+ << " -l SCSLENGTH" << endl
+ << " the length of stem candidates " << SCSLENGTH << endl
+ << endl
+ << " -b BASEPROBTRHESHHOLD" << endl
+ << " the threshold of base pairing probability " << BASEPROBTHRESHOLD << endl
+ << endl
+ << " -m, --mccaskillmea" << endl
+ << " McCaskill MEA MODE: input the clustalw format file and output the secondary structure predicted by McCaskill MEA" << endl
+ << endl
+ << " -g BASEPAIRSCORECONST" << endl
+ << " the control parameter of the prediction of base pairs, default:" << BasePairConst << endl
+ << endl
+ << " -w BANDWIDTH" << endl
+ << " the control parameter of the distance of stem candidates, default:" << BANDWIDTH << endl
+ << " -rfold" << endl
+ << " use Rfold instead of global McCaskill algorithm to calcurate base paring probality matrices, default: (" << (useRfold? "on" : "off") << ")" << endl
+ << endl;
+
+
+ // << " -go, --gap-open VALUE" << endl
+ // << " gap opening penalty of VALUE <= 0 (default: " << gapOpenPenalty << ")" << endl
+ // << endl
+ // << " -ge, --gap-extension VALUE" << endl
+ // << " gap extension penalty of VALUE <= 0 (default: " << gapContinuePenalty << ")" << endl
+ // << endl
+ // << " -co, --cutoff CUTOFF" << endl
+ // << " subtract 0 <= CUTOFF <= 1 (default: " << cutoff << ") from all posterior values before final alignment" << endl
+ // << endl
+
+ exit (1);
+ }
+
+ SafeVector<string> sequenceNames;
+ int tempInt;
+ float tempFloat;
+
+ for (int i = 1; i < argc; i++){
+ if (argv[i][0] == '-'){
+
+ // training
+ if (!strcmp (argv[i], "-t") || !strcmp (argv[i], "--train")){
+ enableTraining = true;
+ if (i < argc - 1)
+ parametersOutputFilename = string (argv[++i]);
+ else {
+ cerr << "ERROR: Filename expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // emission training
+ else if (!strcmp (argv[i], "-e") || !strcmp (argv[i], "--emissions")){
+ enableTrainEmissions = true;
+ }
+
+ // parameter file
+ else if (!strcmp (argv[i], "-p") || !strcmp (argv[i], "--paramfile")){
+ if (i < argc - 1)
+ parametersInputFilename = string (argv[++i]);
+ else {
+ cerr << "ERROR: Filename expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+ else if (! strcmp (argv[i], "-s")) {
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat < 0){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be nagative." << endl;
+ exit (1);
+ }
+ else
+ threshhold = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ else if (! strcmp (argv[i], "-l")) {
+ if (i < argc - 1) {
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt <= 0 || 6 <= tempInt) {
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << "1 and 6" << "." << endl;
+ exit (1);
+ }
+ else
+ scsLength = tempInt;
+ }
+ }
+ }
+ else if (! strcmp (argv[i], "-b")) {
+ if (i < argc - 1) {
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat < 0 && 1 < tempFloat) {
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be nagative." << endl;
+ exit (1);
+ }
+ else
+ BaseProbThreshold = tempFloat;
+ }
+ }
+ }
+ else if (! strcmp (argv[i], "-g")) {
+ if (i < argc - 1) {
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat < 0 && 1 < tempFloat) {
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be nagative." << endl;
+ exit (1);
+ }
+ else
+ BasePairConst = tempFloat;
+ }
+ }
+ }
+
+ // number of consistency transformations
+ else if (!strcmp (argv[i], "-c") || !strcmp (argv[i], "--consistency")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_CONSISTENCY_REPS || tempInt > MAX_CONSISTENCY_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_CONSISTENCY_REPS << " and " << MAX_CONSISTENCY_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numConsistencyReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // number of randomized partitioning iterative refinement passes
+ else if (!strcmp (argv[i], "-ir") || !strcmp (argv[i], "--iterative-refinement")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_ITERATIVE_REFINEMENT_REPS || tempInt > MAX_ITERATIVE_REFINEMENT_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_ITERATIVE_REFINEMENT_REPS << " and " << MAX_ITERATIVE_REFINEMENT_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numIterativeRefinementReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+ else if (!strcmp (argv[i], "-rfold")){
+ useRfold = true;
+ }
+ // number of EM pre-training rounds
+ else if (!strcmp (argv[i], "-pre") || !strcmp (argv[i], "--pre-training")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempInt < MIN_PRETRAINING_REPS || tempInt > MAX_PRETRAINING_REPS){
+ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between "
+ << MIN_PRETRAINING_REPS << " and " << MAX_PRETRAINING_REPS << "." << endl;
+ exit (1);
+ }
+ else
+ numPreTrainingReps = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // the distance of stem candidate
+ else if (!strcmp (argv[i], "-w")){
+ if (i < argc - 1){
+ if (!GetInteger (argv[++i], &tempInt)){
+ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ BandWidth = tempInt;
+ }
+ }
+ else {
+ cerr << "ERROR: Integer expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // gap open penalty
+ else if (!strcmp (argv[i], "-go") || !strcmp (argv[i], "--gap-open")){
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat > 0){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be positive." << endl;
+ exit (1);
+ }
+ else
+ gapOpenPenalty = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // gap extension penalty
+ else if (!strcmp (argv[i], "-ge") || !strcmp (argv[i], "--gap-extension")){
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat > 0){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be positive." << endl;
+ exit (1);
+ }
+ else
+ gapContinuePenalty = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // all-pairs pairwise alignments
+ else if (!strcmp (argv[i], "-pairs")){
+ enableAllPairs = true;
+ }
+
+ // all-pairs pairwise Viterbi alignments
+ else if (!strcmp (argv[i], "-viterbi")){
+ enableAllPairs = true;
+ enableViterbi = true;
+ }
+
+ // annotation files
+ else if (!strcmp (argv[i], "-annot")){
+ enableAnnotation = true;
+ if (i < argc - 1)
+ annotationFilename = argv[++i];
+ else {
+ cerr << "ERROR: FILENAME expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // clustalw output format
+ else if (!strcmp (argv[i], "-clustalw")){
+ enableClustalWOutput = true;
+ }
+ // mxscarna output format
+ else if (!strcmp (argv[i], "-mxscarna")) {
+ enableMXSCARNAOutput = true;
+ }
+ // stockholm output format
+ else if (!strcmp (argv[i], "-stockholm")) {
+ enableStockholmOutput = true;
+ }
+ // web output format
+ else if (!strcmp (argv[i], "-weboutput")) {
+ if (i < argc - 1) {
+ weboutputFileName = string(argv[++i]);
+ }
+ else {
+ cerr << "ERROR: Invalid following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+
+ enableWebOutput = true;
+ }
+
+ // cutoff
+ else if (!strcmp (argv[i], "-co") || !strcmp (argv[i], "--cutoff")){
+ if (i < argc - 1){
+ if (!GetFloat (argv[++i], &tempFloat)){
+ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl;
+ exit (1);
+ }
+ else {
+ if (tempFloat < 0 || tempFloat > 1){
+ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must be between 0 and 1." << endl;
+ exit (1);
+ }
+ else
+ cutoff = tempFloat;
+ }
+ }
+ else {
+ cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ // verbose reporting
+ else if (!strcmp (argv[i], "-v") || !strcmp (argv[i], "--verbose")){
+ enableVerbose = true;
+ }
+
+ // alignment order
+ else if (!strcmp (argv[i], "-a") || !strcmp (argv[i], "--alignment-order")){
+ enableAlignOrder = true;
+ }
+ // McCaskill MEA MODE
+ else if (!strcmp (argv[i], "-m") || !strcmp (argv[i], "--mccaskillmea")){
+ enableMcCaskillMEAMode = true;
+ }
+ // bad arguments
+ else {
+ cerr << "ERROR: Unrecognized option: " << argv[i] << endl;
+ exit (1);
+ }
+ }
+ else {
+ sequenceNames.push_back (string (argv[i]));
+ }
+ }
+
+ if (enableTrainEmissions && !enableTraining){
+ cerr << "ERROR: Training emissions (-e) requires training (-t)" << endl;
+ exit (1);
+ }
+
+ return sequenceNames;
+}
+
+/////////////////////////////////////////////////////////////////
+// ReadParameters()
+//
+// Read initial distribution, transition, and emission
+// parameters from a file.
+/////////////////////////////////////////////////////////////////
+
+void ReadParameters (){
+
+ ifstream data;
+
+ emitPairs = VVF (256, VF (256, 1e-10));
+ emitSingle = VF (256, 1e-5);
+
+ // read initial state distribution and transition parameters
+ // pass
+ if (parametersInputFilename == string ("")){
+ if (NumInsertStates == 1){
+ for (int i = 0; i < NumMatrixTypes; i++) initDistrib[i] = initDistrib1Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapOpen[i] = gapOpen1Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapExtend[i] = gapExtend1Default[i];
+ }
+ else if (NumInsertStates == 2){
+ for (int i = 0; i < NumMatrixTypes; i++) initDistrib[i] = initDistrib2Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapOpen[i] = gapOpen2Default[i];
+ for (int i = 0; i < 2*NumInsertStates; i++) gapExtend[i] = gapExtend2Default[i];
+ }
+ else {
+ cerr << "ERROR: No default initial distribution/parameter settings exist" << endl
+ << " for " << NumInsertStates << " pairs of insert states. Use --paramfile." << endl;
+ exit (1);
+ }
+
+ alphabet = alphabetDefault;
+
+ for (int i = 0; i < (int) alphabet.length(); i++){
+ emitSingle[(unsigned char) tolower(alphabet[i])] = emitSingleDefault[i];
+ emitSingle[(unsigned char) toupper(alphabet[i])] = emitSingleDefault[i];
+ for (int j = 0; j <= i; j++){
+ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) tolower(alphabet[j])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) toupper(alphabet[j])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) tolower(alphabet[j])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) toupper(alphabet[j])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) tolower(alphabet[i])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) toupper(alphabet[i])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) tolower(alphabet[i])] = emitPairsDefault[i][j];
+ emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) toupper(alphabet[i])] = emitPairsDefault[i][j];
+ }
+ }
+ }
+ else {
+ data.open (parametersInputFilename.c_str());
+ if (data.fail()){
+ cerr << "ERROR: Unable to read parameter file: " << parametersInputFilename << endl;
+ exit (1);
+ }
+
+ string line[3];
+ for (int i = 0; i < 3; i++){
+ if (!getline (data, line[i])){
+ cerr << "ERROR: Unable to read transition parameters from parameter file: " << parametersInputFilename << endl;
+ exit (1);
+ }
+ }
+ istringstream data2;
+ data2.clear(); data2.str (line[0]); for (int i = 0; i < NumMatrixTypes; i++) data2 >> initDistrib[i];
+ data2.clear(); data2.str (line[1]); for (int i = 0; i < 2*NumInsertStates; i++) data2 >> gapOpen[i];
+ data2.clear(); data2.str (line[2]); for (int i = 0; i < 2*NumInsertStates; i++) data2 >> gapExtend[i];
+
+ if (!getline (data, line[0])){
+ cerr << "ERROR: Unable to read alphabet from scoring matrix file: " << parametersInputFilename << endl;
+ exit (1);
+ }
+
+ // read alphabet as concatenation of all characters on alphabet line
+ alphabet = "";
+ string token;
+ data2.clear(); data2.str (line[0]); while (data2 >> token) alphabet += token;
+
+ for (int i = 0; i < (int) alphabet.size(); i++){
+ for (int j = 0; j <= i; j++){
+ float val;
+ data >> val;
+ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) tolower(alphabet[j])] = val;
+ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) toupper(alphabet[j])] = val;
+ emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) tolower(alphabet[j])] = val;
+ emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) toupper(alphabet[j])] = val;
+ emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) tolower(alphabet[i])] = val;
+ emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) toupper(alphabet[i])] = val;
+ emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) tolower(alphabet[i])] = val;
+ emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) toupper(alphabet[i])] = val;
+ }
+ }
+
+ for (int i = 0; i < (int) alphabet.size(); i++){
+ float val;
+ data >> val;
+ emitSingle[(unsigned char) tolower(alphabet[i])] = val;
+ emitSingle[(unsigned char) toupper(alphabet[i])] = val;
+ }
+ data.close();
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// ProcessTree()
+//
+// Process the tree recursively. Returns the aligned sequences
+// corresponding to a node or leaf of the tree.
+/////////////////////////////////////////////////////////////////
+float ide;
+MultiSequence *ProcessTree (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, SafeVector<BPPMatrix*> &BPPMatrices) {
+ MultiSequence *result;
+
+ // check if this is a node of the alignment tree
+ if (tree->GetSequenceLabel() == -1){
+ MultiSequence *alignLeft = ProcessTree (tree->GetLeftChild(), sequences, sparseMatrices, model, BPPMatrices);
+ MultiSequence *alignRight = ProcessTree (tree->GetRightChild(), sequences, sparseMatrices, model, BPPMatrices);
+
+ assert (alignLeft);
+ assert (alignRight);
+
+ result = AlignAlignments (alignLeft, alignRight, sparseMatrices, model, BPPMatrices, tree->GetIdentity());
+ assert (result);
+
+ delete alignLeft;
+ delete alignRight;
+ }
+
+ // otherwise, this is a leaf of the alignment tree
+ else {
+ result = new MultiSequence(); assert (result);
+ result->AddSequence (sequences->GetSequence(tree->GetSequenceLabel())->Clone());
+ }
+
+ return result;
+}
+
+/////////////////////////////////////////////////////////////////
+// ComputeFinalAlignment()
+//
+// Compute the final alignment by calling ProcessTree(), then
+// performing iterative refinement as needed.
+/////////////////////////////////////////////////////////////////
+
+MultiSequence *ComputeFinalAlignment (const TreeNode *tree, MultiSequence *sequences,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model,
+ SafeVector<BPPMatrix*> &BPPMatrices) {
+
+ MultiSequence *alignment = ProcessTree (tree, sequences, sparseMatrices, model, BPPMatrices);
+
+ if (enableAlignOrder){
+ alignment->SaveOrdering();
+ enableAlignOrder = false;
+ }
+
+ // tree-based refinement
+ // if you use the function, you can degrade the quality of the software.
+ // TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree, BPPMatrices);
+
+ // iterative refinement
+/*
+ for (int i = 0; i < numIterativeRefinementReps; i++)
+ DoIterativeRefinement (sparseMatrices, model, alignment);
+
+ cerr << endl;
+*/
+ // return final alignment
+ return alignment;
+}
+
+/////////////////////////////////////////////////////////////////
+// AlignAlignments()
+//
+// Returns the alignment of two MultiSequence objects.
+/////////////////////////////////////////////////////////////////
+
+MultiSequence *AlignAlignments (MultiSequence *align1, MultiSequence *align2,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model,
+ SafeVector<BPPMatrix*> &BPPMatrices, float identity){
+
+ // print some info about the alignment
+ if (enableVerbose){
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ cerr << ((i==0) ? "[" : ",") << align1->GetSequence(i)->GetLabel();
+ cerr << "] vs. ";
+ for (int i = 0; i < align2->GetNumSequences(); i++)
+ cerr << ((i==0) ? "[" : ",") << align2->GetSequence(i)->GetLabel();
+ cerr << "]: ";
+ }
+
+ VF *posterior = model.BuildPosterior (align1, align2, sparseMatrices, cutoff);
+
+ pair<SafeVector<char> *, float> alignment;
+ // choose the alignment routine depending on the "cosmetic" gap penalties used
+ if (gapOpenPenalty == 0 && gapContinuePenalty == 0) {
+
+ if(identity < threshhold) {
+ std::vector<StemCandidate> *pscs1, *pscs2;
+ pscs1 = seq2scs(align1, BPPMatrices, BandWidth);
+ pscs2 = seq2scs(align2, BPPMatrices, BandWidth);
+ std::vector<int> *matchPSCS1 = new std::vector<int>;
+ std::vector<int> *matchPSCS2 = new std::vector<int>;
+
+ Globaldp globaldp(pscs1, pscs2, align1, align2, matchPSCS1, matchPSCS2, posterior, BPPMatrices);
+ //float scsScore = globaldp.Run();
+
+ globaldp.Run();
+
+ removeConflicts(pscs1, pscs2, matchPSCS1, matchPSCS2);
+
+ alignment = model.ComputeAlignment2 (align1->GetSequence(0)->GetLength(), align2->GetSequence(0)->GetLength(), *posterior, pscs1, pscs2, matchPSCS1, matchPSCS2);
+
+ } else {
+ alignment = model.ComputeAlignment (align1->GetSequence(0)->GetLength(), align2->GetSequence(0)->GetLength(), *posterior);
+ }
+ }
+ else {
+ alignment = model.ComputeAlignmentWithGapPenalties (align1, align2,
+ *posterior, align1->GetNumSequences(), align2->GetNumSequences(),
+ gapOpenPenalty, gapContinuePenalty);
+ }
+
+ delete posterior;
+
+ if (enableVerbose){
+
+ // compute total length of sequences
+ int totLength = 0;
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ for (int j = 0; j < align2->GetNumSequences(); j++)
+ totLength += min (align1->GetSequence(i)->GetLength(), align2->GetSequence(j)->GetLength());
+
+ // give an "accuracy" measure for the alignment
+ cerr << alignment.second / totLength << endl;
+ }
+
+ // now build final alignment
+ MultiSequence *result = new MultiSequence();
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ result->AddSequence (align1->GetSequence(i)->AddGaps(alignment.first, 'X'));
+ for (int i = 0; i < align2->GetNumSequences(); i++)
+ result->AddSequence (align2->GetSequence(i)->AddGaps(alignment.first, 'Y'));
+ if (!enableAlignOrder)
+ result->SortByLabel();
+
+ // free temporary alignment
+ delete alignment.first;
+
+ return result;
+}
+
+/////////////////////////////////////////////////////////////////
+// DoRelaxation()
+//
+// Performs one round of the consistency transformation. The
+// formula used is:
+// 1
+// P'(x[i]-y[j]) = --- sum sum P(x[i]-z[k]) P(z[k]-y[j])
+// |S| z in S k
+//
+// where S = {x, y, all other sequences...}
+//
+/////////////////////////////////////////////////////////////////
+
+SafeVector<SafeVector<SparseMatrix *> > DoRelaxation (MultiSequence *sequences,
+ SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices){
+ const int numSeqs = sequences->GetNumSequences();
+
+ SafeVector<SafeVector<SparseMatrix *> > newSparseMatrices (numSeqs, SafeVector<SparseMatrix *>(numSeqs, NULL));
+
+ // for every pair of sequences
+ for (int i = 0; i < numSeqs; i++){
+ for (int j = i+1; j < numSeqs; j++){
+ Sequence *seq1 = sequences->GetSequence (i);
+ Sequence *seq2 = sequences->GetSequence (j);
+
+ if (enableVerbose)
+ cerr << "Relaxing (" << i+1 << ") " << seq1->GetHeader() << " vs. "
+ << "(" << j+1 << ") " << seq2->GetHeader() << ": ";
+
+ // get the original posterior matrix
+ VF *posteriorPtr = sparseMatrices[i][j]->GetPosterior(); assert (posteriorPtr);
+ VF &posterior = *posteriorPtr;
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+
+ // contribution from the summation where z = x and z = y
+ for (int k = 0; k < (seq1Length+1) * (seq2Length+1); k++) posterior[k] += posterior[k];
+
+ if (enableVerbose)
+ cerr << sparseMatrices[i][j]->GetNumCells() << " --> ";
+
+ // contribution from all other sequences
+ for (int k = 0; k < numSeqs; k++) if (k != i && k != j){
+ if (k < i)
+ Relax1 (sparseMatrices[k][i], sparseMatrices[k][j], posterior);
+ else if (k > i && k < j)
+ Relax (sparseMatrices[i][k], sparseMatrices[k][j], posterior);
+ else {
+ SparseMatrix *temp = sparseMatrices[j][k]->ComputeTranspose();
+ Relax (sparseMatrices[i][k], temp, posterior);
+ delete temp;
+ }
+ }
+
+ // now renormalization
+ for (int k = 0; k < (seq1Length+1) * (seq2Length+1); k++) posterior[k] /= numSeqs;
+
+ // mask out positions not originally in the posterior matrix
+ SparseMatrix *matXY = sparseMatrices[i][j];
+ for (int y = 0; y <= seq2Length; y++) posterior[y] = 0;
+ for (int x = 1; x <= seq1Length; x++){
+ SafeVector<PIF>::iterator XYptr = matXY->GetRowPtr(x);
+ SafeVector<PIF>::iterator XYend = XYptr + matXY->GetRowSize(x);
+ VF::iterator base = posterior.begin() + x * (seq2Length + 1);
+ int curr = 0;
+ while (XYptr != XYend){
+
+ // zero out all cells until the first filled column
+ while (curr < XYptr->first){
+ base[curr] = 0;
+ curr++;
+ }
+
+ // now, skip over this column
+ curr++;
+ ++XYptr;
+ }
+
+ // zero out cells after last column
+ while (curr <= seq2Length){
+ base[curr] = 0;
+ curr++;
+ }
+ }
+
+ // save the new posterior matrix
+ newSparseMatrices[i][j] = new SparseMatrix (seq1->GetLength(), seq2->GetLength(), posterior);
+ newSparseMatrices[j][i] = NULL;
+
+ if (enableVerbose)
+ cerr << newSparseMatrices[i][j]->GetNumCells() << " -- ";
+
+ delete posteriorPtr;
+
+ if (enableVerbose)
+ cerr << "done." << endl;
+ }
+ }
+
+ return newSparseMatrices;
+}
+
+/////////////////////////////////////////////////////////////////
+// Relax()
+//
+// Computes the consistency transformation for a single sequence
+// z, and adds the transformed matrix to "posterior".
+/////////////////////////////////////////////////////////////////
+
+void Relax (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior){
+
+ assert (matXZ);
+ assert (matZY);
+
+ int lengthX = matXZ->GetSeq1Length();
+ int lengthY = matZY->GetSeq2Length();
+ assert (matXZ->GetSeq2Length() == matZY->GetSeq1Length());
+
+ // for every x[i]
+ for (int i = 1; i <= lengthX; i++){
+ SafeVector<PIF>::iterator XZptr = matXZ->GetRowPtr(i);
+ SafeVector<PIF>::iterator XZend = XZptr + matXZ->GetRowSize(i);
+
+ VF::iterator base = posterior.begin() + i * (lengthY + 1);
+
+ // iterate through all x[i]-z[k]
+ while (XZptr != XZend){
+ SafeVector<PIF>::iterator ZYptr = matZY->GetRowPtr(XZptr->first);
+ SafeVector<PIF>::iterator ZYend = ZYptr + matZY->GetRowSize(XZptr->first);
+ const float XZval = XZptr->second;
+
+ // iterate through all z[k]-y[j]
+ while (ZYptr != ZYend){
+ base[ZYptr->first] += XZval * ZYptr->second;
+ ZYptr++;
+ }
+ XZptr++;
+ }
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// Relax1()
+//
+// Computes the consistency transformation for a single sequence
+// z, and adds the transformed matrix to "posterior".
+/////////////////////////////////////////////////////////////////
+
+void Relax1 (SparseMatrix *matZX, SparseMatrix *matZY, VF &posterior){
+
+ assert (matZX);
+ assert (matZY);
+
+ int lengthZ = matZX->GetSeq1Length();
+ int lengthY = matZY->GetSeq2Length();
+
+ // for every z[k]
+ for (int k = 1; k <= lengthZ; k++){
+ SafeVector<PIF>::iterator ZXptr = matZX->GetRowPtr(k);
+ SafeVector<PIF>::iterator ZXend = ZXptr + matZX->GetRowSize(k);
+
+ // iterate through all z[k]-x[i]
+ while (ZXptr != ZXend){
+ SafeVector<PIF>::iterator ZYptr = matZY->GetRowPtr(k);
+ SafeVector<PIF>::iterator ZYend = ZYptr + matZY->GetRowSize(k);
+ const float ZXval = ZXptr->second;
+ VF::iterator base = posterior.begin() + ZXptr->first * (lengthY + 1);
+
+ // iterate through all z[k]-y[j]
+ while (ZYptr != ZYend){
+ base[ZYptr->first] += ZXval * ZYptr->second;
+ ZYptr++;
+ }
+ ZXptr++;
+ }
+ }
+}
+
+void DoBasePairProbabilityRelaxation (MultiSequence *sequences,
+ SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ SafeVector<BPPMatrix*> &BPPMatrices) {
+ const int numSeqs = sequences->GetNumSequences();
+
+ for (int i = 0; i < numSeqs; i++) {
+ Sequence *seq1 = sequences->GetSequence (i);
+ BPPMatrix *seq1BppMatrix = BPPMatrices[seq1->GetLabel()];
+ Trimat<float> consBppMat(seq1->GetLength() + 1);
+ int seq1Length = seq1->GetLength();
+
+ for (int k = 1; k <= seq1Length; k++) {
+ for (int l = k; l <= seq1Length; l++) {
+ consBppMat.ref(k, l) = seq1BppMatrix->GetProb(k, l);
+ }
+ }
+
+ for (int j = i + 1; j < numSeqs; j++) {
+
+ // VF *posteriorPtr = sparseMatrices[i][j]->GetPosterior()
+ Sequence *seq2 = sequences->GetSequence (j);
+ BPPMatrix *seq2BppMatrix = BPPMatrices[seq2->GetLabel()];
+// int seq2Length = seq2->GetLength();
+ SparseMatrix *matchProb = sparseMatrices[i][j];
+
+// vector<PIF2> &probs1 = seq1BppMatrix->bppMat.data2;
+ for(int k = 1; k <= seq1Length; k++) {
+ for(int m = k, n = k; n <= k + 200 && m >= 1 && n <= seq1Length; m--, n++) {
+
+// for (int k = 0; k < (int)probs1.size(); k++) {
+// float tmpProb1 = probs1[k].prob;
+// int tmp1I = probs1[k].i;
+// int tmp1J = probs1[k].j;
+
+ float sumProb = 0;
+ vector<PIF2> &probs2 = seq2BppMatrix->bppMat.data2;
+ for(int l = 0; l < (int)probs2.size(); l++) {
+ float tmpProb2 = probs2[l].prob;
+ int tmp2I = probs2[l].i;
+ int tmp2J = probs2[l].j;
+ sumProb += matchProb->GetValue(m, tmp2I)*matchProb->GetValue(n, tmp2J)*tmpProb2;
+ }
+
+ consBppMat.ref(m, n) += sumProb;
+ }
+
+ for(int m = k, n = k + 1; n <= k + 200 && m >= 1 && n <= seq1Length; m--, n++) {
+
+// for (int k = 0; k < (int)probs1.size(); k++) {
+// float tmpProb1 = probs1[k].prob;
+// int tmp1I = probs1[k].i;
+// int tmp1J = probs1[k].j;
+
+ float sumProb = 0;
+ vector<PIF2> &probs2 = seq2BppMatrix->bppMat.data2;
+ for(int l = 0; l < (int)probs2.size(); l++) {
+ float tmpProb2 = probs2[l].prob;
+ int tmp2I = probs2[l].i;
+ int tmp2J = probs2[l].j;
+ sumProb += matchProb->GetValue(m, tmp2I)*matchProb->GetValue(n, tmp2J)*tmpProb2;
+ }
+
+ consBppMat.ref(m, n) += sumProb;
+ }
+ }
+ }
+
+/*
+ for(int k = 1; k <= seq1Length; k++) {
+ for(int m = k, n = k; n <= k + 30 && m >= 1 && n <= seq1Length; m--, n++) {
+ float tmpProb = seq1BppMatrix->GetProb(m, n);
+ for(int l = 1; l <= seq2Length; l++) {
+ for(int s = l, t = l; t <= l + 30 && s >= 1 && t <= seq2Length; s--, t++) {
+ tmpProb += matchProb->GetValue(m,s)*matchProb->GetValue(n,t)*seq2BppMatrix->GetProb(s,t);
+ }
+ for(int s = l, t = l + 1; t <= l + 31 && s >= 1 && t <= seq2Length; s--, t++) {
+ tmpProb += matchProb->GetValue(m,s)*matchProb->GetValue(n,t)*seq2BppMatrix->GetProb(s,t);
+ }
+ }
+ consBppMat.ref(m, n) += tmpProb;
+ }
+
+ for(int m = k, n = k + 1; n <= k + 31 && m >= 1 && n <= seq1Length; m--, n++) {
+ float tmpProb = seq1BppMatrix->GetProb(m, n);
+ for(int l = 1; l <= seq2Length; l++) {
+ for(int s = l, t = l; t <= l + 30 && s >= 1 && t <= seq2Length; s--, t++) {
+ tmpProb += matchProb->GetValue(m,s)*matchProb->GetValue(n,t)*seq2BppMatrix->GetProb(s,t);
+ }
+ for(int s = l, t = l + 1; t <= l + 31 && s >= 1 && t <= seq2Length; s--, t++) {
+ tmpProb += matchProb->GetValue(m,s)*matchProb->GetValue(n,t)*seq2BppMatrix->GetProb(s,t);
+ }
+ }
+ consBppMat.ref(m,n) += tmpProb;
+ }
+ }
+ }
+*/
+ for (int m = 1; m <= seq1Length; m++) {
+ for (int n = m + 4; n <= seq1Length; n++) {
+ consBppMat.ref(m,n) = consBppMat.ref(m,n)/(float)numSeqs;
+ }
+ }
+ seq1BppMatrix->updateBPPMatrix(consBppMat);
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// GetSubtree
+//
+// Returns set containing all leaf labels of the current subtree.
+/////////////////////////////////////////////////////////////////
+
+set<int> GetSubtree (const TreeNode *tree){
+ set<int> s;
+
+ if (tree->GetSequenceLabel() == -1){
+ s = GetSubtree (tree->GetLeftChild());
+ set<int> t = GetSubtree (tree->GetRightChild());
+
+ for (set<int>::iterator iter = t.begin(); iter != t.end(); ++iter)
+ s.insert (*iter);
+ }
+ else {
+ s.insert (tree->GetSequenceLabel());
+ }
+
+ return s;
+}
+
+/////////////////////////////////////////////////////////////////
+// TreeBasedBiPartitioning
+//
+// Uses the iterative refinement scheme from MUSCLE.
+/////////////////////////////////////////////////////////////////
+
+void TreeBasedBiPartitioning (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment,
+ const TreeNode *tree, SafeVector<BPPMatrix*> &BPPMatrices){
+ // check if this is a node of the alignment tree
+ if (tree->GetSequenceLabel() == -1){
+ TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree->GetLeftChild(), BPPMatrices);
+ TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree->GetRightChild(), BPPMatrices);
+
+ set<int> leftSubtree = GetSubtree (tree->GetLeftChild());
+ set<int> rightSubtree = GetSubtree (tree->GetRightChild());
+ set<int> leftSubtreeComplement, rightSubtreeComplement;
+
+ // calculate complement of each subtree
+ for (int i = 0; i < alignment->GetNumSequences(); i++){
+ if (leftSubtree.find(i) == leftSubtree.end()) leftSubtreeComplement.insert (i);
+ if (rightSubtree.find(i) == rightSubtree.end()) rightSubtreeComplement.insert (i);
+ }
+
+ // perform realignments for edge to left child
+ if (!leftSubtree.empty() && !leftSubtreeComplement.empty()){
+ MultiSequence *groupOneSeqs = alignment->Project (leftSubtree); assert (groupOneSeqs);
+ MultiSequence *groupTwoSeqs = alignment->Project (leftSubtreeComplement); assert (groupTwoSeqs);
+ delete alignment;
+ alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model, BPPMatrices, tree->GetLeftChild()->GetIdentity());
+ }
+
+ // perform realignments for edge to right child
+ if (!rightSubtree.empty() && !rightSubtreeComplement.empty()){
+ MultiSequence *groupOneSeqs = alignment->Project (rightSubtree); assert (groupOneSeqs);
+ MultiSequence *groupTwoSeqs = alignment->Project (rightSubtreeComplement); assert (groupTwoSeqs);
+ delete alignment;
+ alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model, BPPMatrices, tree->GetRightChild()->GetIdentity());
+ }
+ }
+}
+
+/////////////////////////////////////////////////////////////////
+// DoterativeRefinement()
+//
+// Performs a single round of randomized partionining iterative
+// refinement.
+/////////////////////////////////////////////////////////////////
+/*
+void DoIterativeRefinement (const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ const ProbabilisticModel &model, MultiSequence* &alignment){
+ set<int> groupOne, groupTwo;
+
+ // create two separate groups
+ for (int i = 0; i < alignment->GetNumSequences(); i++){
+ if (rand() % 2)
+ groupOne.insert (i);
+ else
+ groupTwo.insert (i);
+ }
+
+ if (groupOne.empty() || groupTwo.empty()) return;
+
+ // project into the two groups
+ MultiSequence *groupOneSeqs = alignment->Project (groupOne); assert (groupOneSeqs);
+ MultiSequence *groupTwoSeqs = alignment->Project (groupTwo); assert (groupTwoSeqs);
+ delete alignment;
+
+ // realign
+ alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model);
+
+ delete groupOneSeqs;
+ delete groupTwoSeqs;
+}
+*/
+
+/////////////////////////////////////////////////////////////////
+// WriteAnnotation()
+//
+// Computes annotation for multiple alignment and write values
+// to a file.
+/////////////////////////////////////////////////////////////////
+
+void WriteAnnotation (MultiSequence *alignment,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices){
+ ofstream outfile (annotationFilename.c_str());
+
+ if (outfile.fail()){
+ cerr << "ERROR: Unable to write annotation file." << endl;
+ exit (1);
+ }
+
+ const int alignLength = alignment->GetSequence(0)->GetLength();
+ const int numSeqs = alignment->GetNumSequences();
+
+ SafeVector<int> position (numSeqs, 0);
+ SafeVector<SafeVector<char>::iterator> seqs (numSeqs);
+ for (int i = 0; i < numSeqs; i++) seqs[i] = alignment->GetSequence(i)->GetDataPtr();
+ SafeVector<pair<int,int> > active;
+ active.reserve (numSeqs);
+
+ // for every column
+ for (int i = 1; i <= alignLength; i++){
+
+ // find all aligned residues in this particular column
+ active.clear();
+ for (int j = 0; j < numSeqs; j++){
+ if (seqs[j][i] != '-'){
+ active.push_back (make_pair(j, ++position[j]));
+ }
+ }
+
+ outfile << setw(4) << ComputeScore (active, sparseMatrices) << endl;
+ }
+
+ outfile.close();
+}
+
+/////////////////////////////////////////////////////////////////
+// ComputeScore()
+//
+// Computes the annotation score for a particular column.
+/////////////////////////////////////////////////////////////////
+
+int ComputeScore (const SafeVector<pair<int, int> > &active,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices){
+
+ if (active.size() <= 1) return 0;
+
+ // ALTERNATIVE #1: Compute the average alignment score.
+
+ float val = 0;
+ for (int i = 0; i < (int) active.size(); i++){
+ for (int j = i+1; j < (int) active.size(); j++){
+ val += sparseMatrices[active[i].first][active[j].first]->GetValue(active[i].second, active[j].second);
+ }
+ }
+
+ return (int) (200 * val / ((int) active.size() * ((int) active.size() - 1)));
+
+}
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// MakeGnuPlot.cc
+/////////////////////////////////////////////////////////////////
+
+#include <iostream>
+#include <fstream>
+
+using namespace std;
+
+int main (int argc, char **argv){
+
+ if (argc == 1 || argc > 3){
+ cerr << "Usage: makegnuplot annotscores [refscores]" << endl;
+ exit (1);
+ }
+
+ ifstream data (argv[1]);
+
+ if (data.fail()){
+ cerr << "ERROR: Could not open file " << argv[1] << endl;
+ exit (1);
+ }
+
+ int x, ct = 0;
+ while (data >> x) ct++;
+ data.close();
+
+ ofstream out ("temporary_gnuplot_script");
+
+ if (out.fail()){
+ cerr << "ERROR: Could not create temporary file." << endl;
+ exit (1);
+ }
+
+ out << "set title \"Column Reliability Scores\"" << endl
+ << "set xlabel \"Alignment Position\"" << endl
+ << "set ylabel \"Column Reliability\"" << endl
+ << "set xr [1:" << ct << "]" << endl
+ << "set term postscript enhanced color" << endl
+ << "set output \"reliability.ps\"" << endl;
+
+ if (argc == 3){
+ out << "set style fill solid 0.5 noborder" << endl
+ << "plot \"" << argv[2] << "\" title \"actual\" with boxes lt 2, \\" << endl
+ << " \"" << argv[1] << "\" title \"predicted\" with histeps lt 1 lw 3" << endl;
+ }
+ else
+ out << "plot \"" << argv[1] << "\" title \"predicted\" with histeps lt 1 lw 3" << endl;
+
+ out.close();
+
+ if (system ("gnuplot temporary_gnuplot_script") == -1){
+ cerr << "ERROR: Could not run Gnuplot correctly." << endl;
+ exit (1);
+ }
+
+ //system ("rm temporary_gnuplot_script");
+}
--- /dev/null
+################################################################################
+# Makefile for probcons
+################################################################################
+
+################################################################################
+# 1) Choose C++ compiler.
+################################################################################
+
+CXX = g++
+
+################################################################################
+# 2) Set C++ flags.
+# a) DEBUG mode -- no optimizations, enable SafeVector checking, no inlining
+# b) PROFILE mode -- for gprof
+# c) RELEASE mode
+################################################################################
+
+OTHERFLAGS = -DNumInsertStates=1 -DVERSION="1.10"
+
+# debug mode
+#CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
+
+# profile mode
+#CXXFLAGS = -pg -W -Wall -pedantic $(OTHERFLAGS)
+
+# release mode
+#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
+CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+
+################################################################################
+# 3) Dependencies
+################################################################################
+
+TARGETS = probcons
+#compare project makegnuplot
+
+.PHONY : all
+all : $(TARGETS)
+
+#probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
+probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h
+ $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc
+
+compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+ $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
+
+fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+ $(CXX) $(CXXFLAGS) -o fixref FixRef.cc
+
+project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+ $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
+
+makegnuplot : MakeGnuPlot.cc
+ $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
+
+.PHONY : clean
+clean:
+ rm -f $(TARGETS)
--- /dev/null
+////////////////////////////////////////////////////////////////
+// MultiSequence.h
+//
+// Utilities for reading/writing multiple sequence data.
+/////////////////////////////////////////////////////////////////
+
+#ifndef MULTISEQUENCE_H
+#define MULTISEQUENCE_H
+
+#include <cctype>
+#include <string>
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <algorithm>
+#include <set>
+#include "SafeVector.h"
+#include "Sequence.h"
+#include "FileBuffer.h"
+
+/////////////////////////////////////////////////////////////////
+// MultiSequence
+//
+// Class for multiple sequence alignment input/output.
+/////////////////////////////////////////////////////////////////
+
+namespace MXSCARNA {
+class MultiSequence {
+
+ SafeVector<Sequence *> *sequences;
+
+ public:
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::MultiSequence()
+ //
+ // Default constructor.
+ /////////////////////////////////////////////////////////////////
+
+ MultiSequence () : sequences (NULL) {}
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::MultiSequence()
+ //
+ // Constructor. Load MFA from a FileBuffer object.
+ /////////////////////////////////////////////////////////////////
+
+ MultiSequence (FileBuffer &infile) : sequences (NULL) {
+ LoadMFA (infile);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::MultiSequence()
+ //
+ // Constructor. Load MFA from a filename.
+ /////////////////////////////////////////////////////////////////
+
+ MultiSequence (const string &filename) : sequences (NULL){
+ LoadMFA (filename);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::~MultiSequence()
+ //
+ // Destructor. Gets rid of sequence objects contained in the
+ // multiple alignment.
+ /////////////////////////////////////////////////////////////////
+
+ ~MultiSequence(){
+
+ // if sequences allocated
+ if (sequences){
+
+ // free all sequences
+ for (SafeVector<Sequence *>::iterator iter = sequences->begin(); iter != sequences->end(); ++iter){
+ assert (*iter);
+ delete *iter;
+ *iter = NULL;
+ }
+
+ // free sequence vector
+ delete sequences;
+ sequences = NULL;
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::LoadMFA()
+ //
+ // Load MFA from a filename.
+ /////////////////////////////////////////////////////////////////
+
+ void LoadMFA (const string &filename, bool stripGaps = false){
+
+ // try opening file
+ FileBuffer infile (filename.c_str());
+
+ if (infile.fail()){
+ cerr << "ERROR: Could not open file '" << filename << "' for reading." << endl;
+ exit (1);
+ }
+
+ // if successful, then load using other LoadMFA() routine
+ LoadMFA (infile, stripGaps);
+
+ infile.close();
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::LoadMFA()
+ //
+ // Load MSF from a FileBuffer object.
+ /////////////////////////////////////////////////////////////////
+
+ void ParseMSF (FileBuffer &infile, string header, bool stripGaps = false){
+
+ SafeVector<SafeVector<char> *> seqData;
+ SafeVector<string> seqNames;
+ SafeVector<int> seqLengths;
+
+ istringstream in;
+ bool valid = true;
+ bool missingHeader = false;
+ bool clustalW = false;
+
+ // read until data starts
+ while (!infile.eof() && header.find ("..", 0) == string::npos){
+ if (header.find ("CLUSTAL", 0) == 0 || header.find ("PROBCONS", 0) == 0){
+ clustalW = true;
+ break;
+ }
+ infile.GetLine (header);
+ if (header.find ("//", 0) != string::npos){
+ missingHeader = true;
+ break;
+ }
+ }
+
+ // read until end-of-file
+ while (valid){
+ infile.GetLine (header);
+ if (infile.eof()) break;
+
+ string word;
+ in.clear();
+ in.str(header);
+
+ // check if there's anything on this line
+ if (in >> word){
+
+ // clustalw name parsing
+ if (clustalW){
+ if (!isspace(header[0]) && find (seqNames.begin(), seqNames.end(), word) == seqNames.end()){
+ seqNames.push_back (word);
+ seqData.push_back (new SafeVector<char>());
+ seqLengths.push_back (0);
+ seqData[(int) seqData.size() - 1]->push_back ('@');
+ }
+ }
+
+ // look for new sequence label
+ if (word == string ("Name:")){
+ if (in >> word){
+ seqNames.push_back (word);
+ seqData.push_back (new SafeVector<char>());
+ seqLengths.push_back (0);
+ seqData[(int) seqData.size() - 1]->push_back ('@');
+ }
+ else
+ valid = false;
+ }
+
+ // check if this is sequence data
+ else if (find (seqNames.begin(), seqNames.end(), word) != seqNames.end()){
+ int index = find (seqNames.begin(), seqNames.end(), word) - seqNames.begin();
+
+ // read all remaining characters on the line
+ char ch;
+ while (in >> ch){
+ if (isspace (ch)) continue;
+// if (ch >= 'a' && ch <= 'z') ch = ch - 'a' + 'A';
+ if (ch == '.') ch = '-';
+ if (stripGaps && ch == '-') continue;
+/*
+ if (!((ch >= 'A' && ch <= 'Z') || ch == '*' || ch == '-')){
+ cerr << "ERROR: Unknown character encountered: " << ch << endl;
+ exit (1);
+ }
+*/
+ if (!((ch >= 'A' && ch <= 'Z') || (ch >= 'a' && ch <= 'z') || ch == '*' || ch == '-')){
+ cerr << "ERROR: Unknown character encountered: " << ch << endl;
+ exit (1);
+ }
+
+ // everything's ok so far, so just store this character.
+ seqData[index]->push_back (ch);
+ seqLengths[index]++;
+ }
+ }
+ else if (missingHeader){
+ seqNames.push_back (word);
+ seqData.push_back (new SafeVector<char>());
+ seqLengths.push_back (0);
+ seqData[(int) seqData.size() - 1]->push_back ('@');
+
+ int index = (int) seqNames.size() - 1;
+
+ // read all remaining characters on the line
+ char ch;
+ while (in >> ch){
+ if (isspace (ch)) continue;
+// if (ch >= 'a' && ch <= 'z') ch = ch - 'a' + 'A';
+ if (ch == '.') ch = '-';
+ if (stripGaps && ch == '-') continue;
+
+ if (!((ch >= 'A' && ch <= 'Z') || ch == '*' || ch == '-')){
+ cerr << "ERROR: Unknown character encountered: " << ch << endl;
+ exit (1);
+ }
+/*
+ if (!((ch >= 'A' && ch <= 'Z') || (ch >= 'a' && ch <= 'z') || ch == '*' || ch == '-')){
+ cerr << "ERROR: Unknown character encountered: " << ch << endl;
+ exit (1);
+ }
+*/
+ // everything's ok so far, so just store this character.
+ seqData[index]->push_back (ch);
+ seqLengths[index]++;
+ }
+ }
+ }
+ }
+
+ // check for errorsq
+ if (seqNames.size() == 0){
+ cerr << "ERROR: No sequences read!" << endl;
+ exit (1);
+ }
+
+ assert (!sequences);
+ sequences = new SafeVector<Sequence *>;
+ for (int i = 0; i < (int) seqNames.size(); i++){
+ if (seqLengths[i] == 0){
+ cerr << "ERROR: Sequence of zero length!" << endl;
+ exit (1);
+ }
+ Sequence *seq = new Sequence (seqData[i], seqNames[i], seqLengths[i], i, i);
+ sequences->push_back (seq);
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::LoadMFA()
+ //
+ // Load MFA from a FileBuffer object.
+ /////////////////////////////////////////////////////////////////
+
+ void LoadMFA (FileBuffer &infile, bool stripGaps = false){
+
+ // check to make sure that file reading is ok
+ if (infile.fail()){
+ cerr << "ERROR: Error reading file." << endl;
+ exit (1);
+ }
+
+ // read all sequences
+ while (true){
+
+ // get the sequence label as being the current # of sequences
+ // NOTE: sequence labels here are zero-based
+ int index = (!sequences) ? 0 : sequences->size();
+
+ // read the sequence
+ Sequence *seq = new Sequence (infile, stripGaps);
+ if (seq->Fail()){
+
+ // check if alternative file format (i.e. not MFA)
+ if (index == 0){
+ string header = seq->GetHeader();
+ if (header.length() > 0 && header[0] != '>'){
+ // try MSF format
+ ParseMSF (infile, header);
+ break;
+ }
+ }
+
+ delete seq;
+ break;
+ }
+ seq->SetLabel (index);
+
+ // add the sequence to the list of current sequences
+ if (!sequences) sequences = new SafeVector<Sequence *>;
+ sequences->push_back (seq);
+ }
+
+ // make sure at least one sequence was read
+ if (!sequences){
+ cerr << "ERROR: No sequences read." << endl;
+ exit (1);
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::AddSequence()
+ //
+ // Add another sequence to an existing sequence list
+ /////////////////////////////////////////////////////////////////
+
+ void AddSequence (Sequence *sequence){
+ assert (sequence);
+ assert (!sequence->Fail());
+
+ // add sequence
+ if (!sequences) sequences = new SafeVector<Sequence *>;
+ sequences->push_back (sequence);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::RemoveSequence()
+ //
+ // Remove a sequence from the MultiSequence
+ /////////////////////////////////////////////////////////////////
+
+ void RemoveSequence (int index){
+ assert (sequences);
+
+ assert (index >= 0 && index < (int) sequences->size());
+ delete (*sequences)[index];
+
+ sequences->erase (sequences->begin() + index);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::WriteMFA()
+ //
+ // Write MFA to the outfile. Allows the user to specify the
+ // number of columns for the output. Also, useIndices determines
+ // whether or not the actual sequence comments will be printed
+ // out or whether the artificially assigned sequence labels will
+ // be used instead.
+ /////////////////////////////////////////////////////////////////
+
+ void WriteMFA (ostream &outfile, string *ssCons = NULL, int numColumns = 60, bool useIndices = false){
+ if (!sequences) return;
+
+ // loop through all sequences and write them out
+ for (SafeVector<Sequence *>::iterator iter = sequences->begin(); iter != sequences->end(); ++iter){
+ (*iter)->WriteMFA (outfile, numColumns, useIndices);
+ }
+
+ int count = 0;
+ if (ssCons != NULL) {
+ outfile << ">#=GC SS_cons" << endl;
+ int length = ssCons->length();
+ for (int i = 1; i < length; i++ ) {
+ outfile << ssCons->at(i);
+ ++count;
+
+ if (numColumns <= count) {
+ outfile << endl;
+ count = 0;
+ }
+
+ }
+ }
+ outfile << endl;
+ }
+
+ void WriteMFAseq (ostream &outfile, int numColumns = 60, bool useIndices = false){
+ if (!sequences) return;
+
+ // loop through all sequences and write them out
+ for (SafeVector<Sequence *>::iterator iter = sequences->begin(); iter != sequences->end(); ++iter){
+ (*iter)->WriteMFA (outfile, numColumns, useIndices);
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::GetAnnotationChar()
+ //
+ // Return CLUSTALW annotation for column.
+ /////////////////////////////////////////////////////////////////
+
+ char GetAnnotationChar (SafeVector<char> &column){
+ SafeVector<int> counts (256, 0);
+ int allChars = (int) column.size();
+
+ for (int i = 0; i < allChars; i++){
+ counts[(unsigned char) toupper(column[i])]++;
+ }
+
+ allChars -= counts[(unsigned char) '-'];
+ if (allChars == 1) return ' ';
+
+ for (int i = 0; i < 256; i++) if ((char) i != '-' && counts[i] == allChars) return '*';
+
+ if (counts[(unsigned char) 'S'] +
+ counts[(unsigned char) 'T'] +
+ counts[(unsigned char) 'A'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'N'] +
+ counts[(unsigned char) 'E'] +
+ counts[(unsigned char) 'Q'] +
+ counts[(unsigned char) 'K'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'N'] +
+ counts[(unsigned char) 'H'] +
+ counts[(unsigned char) 'Q'] +
+ counts[(unsigned char) 'K'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'N'] +
+ counts[(unsigned char) 'D'] +
+ counts[(unsigned char) 'E'] +
+ counts[(unsigned char) 'Q'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'Q'] +
+ counts[(unsigned char) 'H'] +
+ counts[(unsigned char) 'R'] +
+ counts[(unsigned char) 'K'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'M'] +
+ counts[(unsigned char) 'I'] +
+ counts[(unsigned char) 'L'] +
+ counts[(unsigned char) 'V'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'M'] +
+ counts[(unsigned char) 'I'] +
+ counts[(unsigned char) 'L'] +
+ counts[(unsigned char) 'F'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'H'] +
+ counts[(unsigned char) 'Y'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'F'] +
+ counts[(unsigned char) 'Y'] +
+ counts[(unsigned char) 'W'] == allChars)
+ return ':';
+
+ if (counts[(unsigned char) 'C'] +
+ counts[(unsigned char) 'S'] +
+ counts[(unsigned char) 'A'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'A'] +
+ counts[(unsigned char) 'T'] +
+ counts[(unsigned char) 'V'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'S'] +
+ counts[(unsigned char) 'A'] +
+ counts[(unsigned char) 'G'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'S'] +
+ counts[(unsigned char) 'T'] +
+ counts[(unsigned char) 'N'] +
+ counts[(unsigned char) 'K'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'S'] +
+ counts[(unsigned char) 'T'] +
+ counts[(unsigned char) 'P'] +
+ counts[(unsigned char) 'A'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'S'] +
+ counts[(unsigned char) 'G'] +
+ counts[(unsigned char) 'N'] +
+ counts[(unsigned char) 'D'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'S'] +
+ counts[(unsigned char) 'N'] +
+ counts[(unsigned char) 'D'] +
+ counts[(unsigned char) 'E'] +
+ counts[(unsigned char) 'Q'] +
+ counts[(unsigned char) 'K'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'N'] +
+ counts[(unsigned char) 'D'] +
+ counts[(unsigned char) 'E'] +
+ counts[(unsigned char) 'Q'] +
+ counts[(unsigned char) 'H'] +
+ counts[(unsigned char) 'K'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'N'] +
+ counts[(unsigned char) 'E'] +
+ counts[(unsigned char) 'H'] +
+ counts[(unsigned char) 'Q'] +
+ counts[(unsigned char) 'R'] +
+ counts[(unsigned char) 'K'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'F'] +
+ counts[(unsigned char) 'V'] +
+ counts[(unsigned char) 'L'] +
+ counts[(unsigned char) 'I'] +
+ counts[(unsigned char) 'M'] == allChars)
+ return '.';
+
+ if (counts[(unsigned char) 'H'] +
+ counts[(unsigned char) 'F'] +
+ counts[(unsigned char) 'Y'] == allChars)
+ return '.';
+
+ return ' ';
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::WriteALN()
+ //
+ // Write ALN to the outfile. Allows the user to specify the
+ // number of columns for the output.
+ /////////////////////////////////////////////////////////////////
+
+ void WriteALN (ostream &outfile, int numColumns = 60){
+ if (!sequences) return;
+
+// outfile << "Multplex SCARNA version " << VERSION << " multiple sequence alignment" << endl;
+// outfile << "PROBCONS version " << VERSION << " multiple sequence alignment" << endl;
+ outfile << "CLUSTAL W(1.83) multiple sequence alignment" << endl;
+// outfile << "//" << endl;
+
+ int longestComment = 0;
+ SafeVector<SafeVector<char>::iterator> ptrs (GetNumSequences());
+ SafeVector<int> lengths (GetNumSequences());
+ for (int i = 0; i < GetNumSequences(); i++){
+ ptrs[i] = GetSequence (i)->GetDataPtr();
+ lengths[i] = GetSequence (i)->GetLength();
+ longestComment = max (longestComment, (int) GetSequence(i)->GetName().length());
+ }
+ longestComment += 4;
+
+ int writtenChars = 0;
+ bool allDone = false;
+
+ while (!allDone){
+ outfile << endl;
+ allDone = true;
+
+ // loop through all sequences and write them out
+ for (int i = 0; i < GetNumSequences(); i++){
+
+ if (writtenChars < lengths[i]){
+ outfile << GetSequence(i)->GetName();
+ for (int j = 0; j < longestComment - (int) GetSequence(i)->GetName().length(); j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++){
+ if (writtenChars + j < lengths[i])
+ outfile << ptrs[i][writtenChars + j + 1];
+ else
+ break;
+ }
+
+ outfile << endl;
+
+ if (writtenChars + numColumns < lengths[i]) allDone = false;
+ }
+ }
+
+ // write annotation line
+ for (int j = 0; j < longestComment; j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++){
+ SafeVector<char> column;
+
+ for (int i = 0; i < GetNumSequences(); i++)
+ if (writtenChars + j < lengths[i])
+ column.push_back (ptrs[i][writtenChars + j + 1]);
+
+ if (column.size() > 0)
+ outfile << GetAnnotationChar (column);
+ }
+
+ outfile << endl;
+ writtenChars += numColumns;
+ }
+ outfile << endl;
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // MultiSequence::WriteWEB();
+ //
+ // Write ALN to the outfile. Allows the user to specify the
+ // number of columns for the output.
+ ///////////////////////////////////////////////////////////////
+ void WriteWEB (ostream &outfile, string *ssCons = NULL, int numColumns = 60, bool useIndices = false){
+ if (!sequences) return;
+
+ // loop through all sequences and write them out
+ for (SafeVector<Sequence *>::iterator iter = sequences->begin(); iter != sequences->end(); ++iter){
+ (*iter)->WriteWEB (outfile, numColumns, useIndices);
+ }
+
+ // write conservation
+ outfile << "<conservation>" << endl;
+ int longestComment = 0;
+ SafeVector<SafeVector<char>::iterator> ptrs (GetNumSequences());
+ SafeVector<int> lengths (GetNumSequences());
+ for (int i = 0; i < GetNumSequences(); i++){
+ ptrs[i] = GetSequence (i)->GetDataPtr();
+ lengths[i] = GetSequence (i)->GetLength();
+ longestComment = max (longestComment, (int) GetSequence(i)->GetName().length());
+ }
+ longestComment += 4;
+
+ int writtenChars = 0;
+ bool allDone = false;
+
+ while (!allDone){
+// outfile << endl;
+ allDone = true;
+
+ // loop through all sequences and write them out
+ for (int i = 0; i < GetNumSequences(); i++){
+
+ if (writtenChars < lengths[i]){
+// outfile << GetSequence(i)->GetName();
+ for (int j = 0; j < longestComment - (int) GetSequence(i)->GetName().length(); j++)
+// outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++){
+ if (writtenChars + j < lengths[i]);
+// outfile << ptrs[i][writtenChars + j + 1];
+ else
+ break;
+ }
+
+// outfile << endl;
+
+ if (writtenChars + numColumns < lengths[i]) allDone = false;
+ }
+ }
+
+ // write annotation line
+// for (int j = 0; j < longestComment; j++)
+// outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++){
+ SafeVector<char> column;
+
+ for (int i = 0; i < GetNumSequences(); i++)
+ if (writtenChars + j < lengths[i])
+ column.push_back (ptrs[i][writtenChars + j + 1]);
+
+ if (column.size() > 0)
+ outfile << GetAnnotationChar (column);
+ }
+
+// outfile << endl;
+ writtenChars += numColumns;
+ }
+ outfile << endl;
+ outfile << "</conservation>" << endl;
+
+ // write structure information
+ if (ssCons != NULL) {
+ outfile << "<structure>" << endl;
+ int length = ssCons->length();
+ for (int i = 1; i < length; i++ ) {
+ outfile << ssCons->at(i);
+ }
+ outfile << endl;
+ outfile << "</structure>" << endl;
+
+ // add coordinate information 06/09/14
+ outfile << "<coordinate>" << endl;
+
+ int segmentPos = 1;
+ for (int i = 1; i < length; i++) {
+ int count = 0;
+
+ if ( ssCons->at(i) == '(' ) {
+ ++count;
+
+ int j = i;
+ while (count != 0) {
+ char ch = ssCons->at(++j);
+ if (ch == '(')
+ ++count;
+ else if (ch == ')')
+ --count;
+ }
+
+ outfile << "<segment position=\"" << segmentPos++ << "\" starts=\""
+ << i << "\"" << " ends=\"" << j << "\"/>" << endl;
+
+ }
+ }
+ }
+ outfile << "</coordinate>" << endl;
+
+ outfile << "<mxscarna>" << endl;
+ WriteMXSCARNA (outfile, ssCons);
+ outfile << "</mxscarna>" << endl;
+
+ outfile << "<aln>" << endl;
+ WriteALN (outfile);
+ outfile << "</aln>" << endl;
+
+ outfile << "<mfa>" << endl;
+ WriteMFA (outfile, ssCons);
+ outfile << "</mfa>" << endl;
+
+ outfile << "<stockholm>" << endl;
+ WriteWebSTOCKHOLM (outfile, ssCons);
+ outfile << "</stockholm>" << endl;
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // MultiSequence::WriteSTOCKHOLM();
+ //
+ // Write STOCKHOLM to the outfile. Allows the user to specify the
+ // number of columns for the output.
+ ///////////////////////////////////////////////////////////////
+ void WriteSTOCKHOLM (ostream &outfile, string *ssCons = NULL, int numColumns = 60) {
+ if (!sequences) return;
+
+ outfile << "# STOCKHOLM 1.0" << endl;
+
+ int longestComment = 0;
+ SafeVector<SafeVector<char>::iterator> ptrs (GetNumSequences());
+ SafeVector<int> lengths (GetNumSequences());
+ for (int i = 0; i < GetNumSequences(); i++){
+ ptrs[i] = GetSequence (i)->GetDataPtr();
+ lengths[i] = GetSequence (i)->GetLength();
+ longestComment = max (longestComment, (int) GetSequence(i)->GetName().length());
+ }
+ longestComment += 4;
+
+ int writtenChars = 0;
+ bool allDone = false;
+
+ while (!allDone){
+ outfile << endl;
+ allDone = true;
+
+ // loop through all sequences and write them out
+ for (int i = 0; i < GetNumSequences(); i++){
+
+ if (writtenChars < lengths[i]){
+ outfile << GetSequence(i)->GetName();
+ for (int j = 0; j < longestComment - (int) GetSequence(i)->GetName().length(); j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++){
+ if (writtenChars + j < lengths[i])
+ if (ptrs[i][writtenChars + j + 1] != '-')
+ outfile << ptrs[i][writtenChars + j + 1];
+ else
+ outfile << ".";
+ else
+ break;
+ }
+
+ outfile << endl;
+
+ if (writtenChars + numColumns < lengths[i]) allDone = false;
+ }
+ }
+
+ // write ssCons
+
+ if (ssCons != NULL) {
+ outfile << "#=GC SS_cons";
+ int lengthSScons = 12;
+ for (int j = 0; j < longestComment - lengthSScons; j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++) {
+ if (ssCons->at(writtenChars + j + 1) == '(')
+ outfile << "<";
+ else if (ssCons->at(writtenChars + j + 1) == ')')
+ outfile << ">";
+ else
+ outfile << ".";
+ if ((unsigned int)writtenChars + j + 1 >= ssCons->length() - 1)
+ break;
+ }
+ outfile << endl;
+ }
+
+ writtenChars += numColumns;
+ }
+ outfile << "//";
+ outfile << endl;
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // MultiSequence::WriteSTOCKHOLM();
+ //
+ // Write STOCKHOLM to the outfile. Allows the user to specify the
+ // number of columns for the output.
+ ///////////////////////////////////////////////////////////////
+ void WriteWebSTOCKHOLM (ostream &outfile, string *ssCons = NULL, int numColumns = 60) {
+ if (!sequences) return;
+
+ outfile << "# STOCKHOLM 1.0" << endl;
+
+ int longestComment = 0;
+ SafeVector<SafeVector<char>::iterator> ptrs (GetNumSequences());
+ SafeVector<int> lengths (GetNumSequences());
+ for (int i = 0; i < GetNumSequences(); i++){
+ ptrs[i] = GetSequence (i)->GetDataPtr();
+ lengths[i] = GetSequence (i)->GetLength();
+ longestComment = max (longestComment, (int) GetSequence(i)->GetName().length());
+ }
+ longestComment += 4;
+
+ int writtenChars = 0;
+ bool allDone = false;
+
+ while (!allDone){
+ outfile << endl;
+ allDone = true;
+
+ // loop through all sequences and write them out
+ for (int i = 0; i < GetNumSequences(); i++){
+
+ if (writtenChars < lengths[i]){
+ outfile << GetSequence(i)->GetName();
+ for (int j = 0; j < longestComment - (int) GetSequence(i)->GetName().length(); j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++){
+ if (writtenChars + j < lengths[i])
+ if (ptrs[i][writtenChars + j + 1] != '-')
+ outfile << ptrs[i][writtenChars + j + 1];
+ else
+ outfile << ".";
+ else
+ break;
+ }
+
+ outfile << endl;
+
+ if (writtenChars + numColumns < lengths[i]) allDone = false;
+ }
+ }
+
+ // write ssCons
+
+ if (ssCons != NULL) {
+ outfile << "#=GC SS_cons";
+ int lengthSScons = 12;
+ for (int j = 0; j < longestComment - lengthSScons; j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++) {
+ outfile << ssCons->at(writtenChars + j + 1);
+
+ if ((unsigned int)writtenChars + j + 1 >= ssCons->length() - 1)
+ break;
+ }
+ outfile << endl;
+ }
+
+ writtenChars += numColumns;
+ }
+ outfile << "//";
+ outfile << endl;
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // MultiSequence::WriteMXSCARNA();
+ //
+ // Write MXSCARNA to the outfile. Allows the user to specify the
+ // number of columns for the output.
+ ///////////////////////////////////////////////////////////////
+ void WriteMXSCARNA (ostream &outfile, string *ssCons = NULL, int numColumns = 60){
+ if (!sequences) return;
+
+ outfile << "Multplex SCARNA version " << VERSION << " multiple sequence alignment" << endl;
+
+ int longestComment = 0;
+ SafeVector<SafeVector<char>::iterator> ptrs (GetNumSequences());
+ SafeVector<int> lengths (GetNumSequences());
+ for (int i = 0; i < GetNumSequences(); i++){
+ ptrs[i] = GetSequence (i)->GetDataPtr();
+ lengths[i] = GetSequence (i)->GetLength();
+ longestComment = max (longestComment, (int) GetSequence(i)->GetName().length());
+ }
+ longestComment += 4;
+
+ int writtenChars = 0;
+ bool allDone = false;
+
+ while (!allDone){
+ outfile << endl;
+ allDone = true;
+
+ // loop through all sequences and write them out
+ for (int i = 0; i < GetNumSequences(); i++){
+
+ if (writtenChars < lengths[i]){
+ outfile << GetSequence(i)->GetName();
+ for (int j = 0; j < longestComment - (int) GetSequence(i)->GetName().length(); j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++){
+ if (writtenChars + j < lengths[i])
+ outfile << ptrs[i][writtenChars + j + 1];
+ else
+ break;
+ }
+
+ outfile << endl;
+
+ if (writtenChars + numColumns < lengths[i]) allDone = false;
+ }
+ }
+
+ // write ssCons
+ if (ssCons != NULL) {
+ outfile << "ss_cons";
+ int lengthSScons = 7;
+ for (int j = 0; j < longestComment - lengthSScons; j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++) {
+ outfile << ssCons->at(writtenChars + j + 1);
+ if ((unsigned int)writtenChars + j + 1 >= ssCons->length() - 1)
+ break;
+ }
+ outfile << endl;
+ }
+
+ // write annotation line
+ for (int j = 0; j < longestComment; j++)
+ outfile << ' ';
+
+ for (int j = 0; j < numColumns; j++){
+ SafeVector<char> column;
+
+ for (int i = 0; i < GetNumSequences(); i++)
+ if (writtenChars + j < lengths[i])
+ column.push_back (ptrs[i][writtenChars + j + 1]);
+
+ if (column.size() > 0)
+ outfile << GetAnnotationChar (column);
+ }
+
+ outfile << endl;
+ writtenChars += numColumns;
+ }
+ outfile << endl;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::GetSequence()
+ //
+ // Retrieve a sequence from the MultiSequence object.
+ /////////////////////////////////////////////////////////////////
+
+ Sequence* GetSequence (int i){
+ assert (sequences);
+ assert (0 <= i && i < (int) sequences->size());
+
+ return (*sequences)[i];
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::GetSequence()
+ //
+ // Retrieve a sequence from the MultiSequence object
+ // (const version).
+ /////////////////////////////////////////////////////////////////
+
+ const Sequence* GetSequence (int i) const {
+ assert (sequences);
+ assert (0 <= i && i < (int) sequences->size());
+
+ return (*sequences)[i];
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::GetNumSequences()
+ //
+ // Returns the number of sequences in the MultiSequence.
+ /////////////////////////////////////////////////////////////////
+
+ int GetNumSequences () const {
+ if (!sequences) return 0;
+ return (int) sequences->size();
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::SortByHeader()
+ //
+ // Organizes the sequences according to their sequence headers
+ // in ascending order.
+ /////////////////////////////////////////////////////////////////
+
+ void SortByHeader () {
+ assert (sequences);
+
+ // a quick and easy O(n^2) sort
+ for (int i = 0; i < (int) sequences->size()-1; i++){
+ for (int j = i+1; j < (int) sequences->size(); j++){
+ if ((*sequences)[i]->GetHeader() > (*sequences)[j]->GetHeader())
+ swap ((*sequences)[i], (*sequences)[j]);
+ }
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::SortByLabel()
+ //
+ // Organizes the sequences according to their sequence labels
+ // in ascending order.
+ /////////////////////////////////////////////////////////////////
+
+ void SortByLabel () {
+ assert (sequences);
+
+ // a quick and easy O(n^2) sort
+ for (int i = 0; i < (int) sequences->size()-1; i++){
+ for (int j = i+1; j < (int) sequences->size(); j++){
+ if ((*sequences)[i]->GetSortLabel() > (*sequences)[j]->GetSortLabel())
+ swap ((*sequences)[i], (*sequences)[j]);
+ }
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::SaveOrdering()
+ //
+ // Relabels sequences so as to preserve the current ordering.
+ /////////////////////////////////////////////////////////////////
+
+ void SaveOrdering () {
+ assert (sequences);
+
+ for (int i = 0; i < (int) sequences->size(); i++)
+ (*sequences)[i]->SetSortLabel (i);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // MultiSequence::Project()
+ //
+ // Given a set of indices, extract all sequences from the current
+ // MultiSequence object whose index is included in the set.
+ // Then, project the multiple alignments down to the desired
+ // subset, and return the projection as a new MultiSequence
+ // object.
+ /////////////////////////////////////////////////////////////////
+
+ MultiSequence *Project (const set<int> &indices){
+ SafeVector<SafeVector<char>::iterator> oldPtrs (indices.size());
+ SafeVector<SafeVector<char> *> newPtrs (indices.size());
+
+ assert (indices.size() != 0);
+
+ // grab old data
+ int i = 0;
+ for (set<int>::const_iterator iter = indices.begin(); iter != indices.end(); ++iter){
+ oldPtrs[i++] = GetSequence (*iter)->GetDataPtr();
+ }
+
+ // compute new length
+ int oldLength = GetSequence (*indices.begin())->GetLength();
+ int newLength = 0;
+ for (i = 1; i <= oldLength; i++){
+
+ // check to see if there is a gap in every sequence of the set
+ bool found = false;
+ for (int j = 0; !found && j < (int) indices.size(); j++)
+ found = (oldPtrs[j][i] != '-');
+
+ // if not, then this column counts towards the sequence length
+ if (found) newLength++;
+ }
+
+ // build new alignments
+ for (i = 0; i < (int) indices.size(); i++){
+ newPtrs[i] = new SafeVector<char>(); assert (newPtrs[i]);
+ newPtrs[i]->push_back ('@');
+ }
+
+ // add all needed columns
+ for (i = 1; i <= oldLength; i++){
+
+ // make sure column is not gapped in all sequences in the set
+ bool found = false;
+ for (int j = 0; !found && j < (int) indices.size(); j++)
+ found = (oldPtrs[j][i] != '-');
+
+ // if not, then add it
+ if (found){
+ for (int j = 0; j < (int) indices.size(); j++)
+ newPtrs[j]->push_back (oldPtrs[j][i]);
+ }
+ }
+
+ // wrap sequences in MultiSequence object
+ MultiSequence *ret = new MultiSequence();
+ i = 0;
+ for (set<int>::const_iterator iter = indices.begin(); iter != indices.end(); ++iter){
+ ret->AddSequence (new Sequence (newPtrs[i++], GetSequence (*iter)->GetHeader(), newLength,
+ GetSequence (*iter)->GetSortLabel(), GetSequence (*iter)->GetLabel()));
+ }
+
+ return ret;
+ }
+};
+}
+#endif
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// ProbabilisticModel.h
+//
+// Routines for (1) posterior probability computations
+// (2) chained anchoring
+// (3) maximum weight trace alignment
+/////////////////////////////////////////////////////////////////
+
+#ifndef PROBABILISTICMODEL_H
+#define PROBABILISTICMODEL_H
+
+#include <list>
+#include <cmath>
+#include <cstdio>
+#include "SafeVector.h"
+#include "ScoreType.h"
+#include "SparseMatrix.h"
+#include "MultiSequence.h"
+#include "StemCandidate.hpp"
+#include "scarna.hpp"
+#include "nrutil.h"
+#include <vector>
+
+using namespace std;
+
+const int NumMatchStates = 1; // note that in this version the number
+ // of match states is fixed at 1...will
+ // change in future versions
+const int NumMatrixTypes = NumMatchStates + NumInsertStates * 2;
+
+/////////////////////////////////////////////////////////////////
+// ProbabilisticModel
+//
+// Class for storing the parameters of a probabilistic model and
+// performing different computations based on those parameters.
+// In particular, this class handles the computation of
+// posterior probabilities that may be used in alignment.
+/////////////////////////////////////////////////////////////////
+namespace MXSCARNA {
+class ProbabilisticModel {
+
+ float initialDistribution[NumMatrixTypes]; // holds the initial probabilities for each state
+ float transProb[NumMatrixTypes][NumMatrixTypes]; // holds all state-to-state transition probabilities
+ float matchProb[256][256]; // emission probabilities for match states
+ float insProb[256][NumMatrixTypes]; // emission probabilities for insert states
+ NRMat<float> WM;
+
+ public:
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ProbabilisticModel()
+ //
+ // Constructor. Builds a new probabilistic model using the
+ // given parameters.
+ /////////////////////////////////////////////////////////////////
+
+ ProbabilisticModel (const VF &initDistribMat, const VF &gapOpen, const VF &gapExtend,
+ const VVF &emitPairs, const VF &emitSingle){
+
+ // build transition matrix
+ VVF transMat (NumMatrixTypes, VF (NumMatrixTypes, 0.0f));
+ transMat[0][0] = 1;
+ for (int i = 0; i < NumInsertStates; i++){
+ transMat[0][2*i+1] = gapOpen[2*i];
+ transMat[0][2*i+2] = gapOpen[2*i+1];
+ transMat[0][0] -= (gapOpen[2*i] + gapOpen[2*i+1]);
+ assert (transMat[0][0] > 0);
+ transMat[2*i+1][2*i+1] = gapExtend[2*i];
+ transMat[2*i+2][2*i+2] = gapExtend[2*i+1];
+ transMat[2*i+1][2*i+2] = 0;
+ transMat[2*i+2][2*i+1] = 0;
+ transMat[2*i+1][0] = 1 - gapExtend[2*i];
+ transMat[2*i+2][0] = 1 - gapExtend[2*i+1];
+ }
+
+ // create initial and transition probability matrices
+ for (int i = 0; i < NumMatrixTypes; i++){
+ initialDistribution[i] = LOG (initDistribMat[i]);
+ for (int j = 0; j < NumMatrixTypes; j++)
+ transProb[i][j] = LOG (transMat[i][j]);
+ }
+
+ // create insertion and match probability matrices
+ for (int i = 0; i < 256; i++){
+ for (int j = 0; j < NumMatrixTypes; j++)
+ insProb[i][j] = LOG (emitSingle[i]);
+ for (int j = 0; j < 256; j++)
+ matchProb[i][j] = LOG (emitPairs[i][j]);
+ }
+ }
+
+ NRMat<float> weightMatchScore(std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2,
+ std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2, NRMat<float> WM) {
+ int len = WORDLENGTH;
+ int size = matchPSCS1->size();
+ float weight = 1000;
+
+ for(int iter = 0; iter < size; iter++) {
+ int i = matchPSCS1->at(iter);
+ int j = matchPSCS2->at(iter);
+
+ const StemCandidate &sc1 = pscs1->at(i);
+ const StemCandidate &sc2 = pscs2->at(j);
+
+ for(int k = 0; k < len; k++) {
+ WM[sc1.GetPosition() + k][sc2.GetPosition() + k] += weight;
+// sumWeight += weight;
+ }
+ }
+ return WM;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeForwardMatrix()
+ //
+ // Computes a set of forward probability matrices for aligning
+ // seq1 and seq2.
+ //
+ // For efficiency reasons, a single-dimensional floating-point
+ // array is used here, with the following indexing scheme:
+ //
+ // forward[i + NumMatrixTypes * (j * (seq2Length+1) + k)]
+ // refers to the probability of aligning through j characters
+ // of the first sequence, k characters of the second sequence,
+ // and ending in state i.
+ /////////////////////////////////////////////////////////////////
+
+ VF *ComputeForwardMatrix (Sequence *seq1, Sequence *seq2) const {
+
+ assert (seq1);
+ assert (seq2);
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+
+ // retrieve the points to the beginning of each sequence
+ SafeVector<char>::iterator iter1 = seq1->GetDataPtr();
+ SafeVector<char>::iterator iter2 = seq2->GetDataPtr();
+
+ // create matrix
+ VF *forwardPtr = new VF (NumMatrixTypes * (seq1Length+1) * (seq2Length+1), LOG_ZERO);
+ assert (forwardPtr);
+ VF &forward = *forwardPtr;
+
+ // initialization condition
+ forward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)] =
+ initialDistribution[0] + matchProb[(unsigned char) iter1[1]][(unsigned char) iter2[1]];
+
+ for (int k = 0; k < NumInsertStates; k++){
+ forward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)] =
+ initialDistribution[2*k+1] + insProb[(unsigned char) iter1[1]][k];
+ forward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)] =
+ initialDistribution[2*k+2] + insProb[(unsigned char) iter2[1]][k];
+ }
+
+ // remember offset for each index combination
+ int ij = 0;
+ int i1j = -seq2Length - 1;
+ int ij1 = -1;
+ int i1j1 = -seq2Length - 2;
+
+ ij *= NumMatrixTypes;
+ i1j *= NumMatrixTypes;
+ ij1 *= NumMatrixTypes;
+ i1j1 *= NumMatrixTypes;
+
+ // compute forward scores
+ for (int i = 0; i <= seq1Length; i++){
+ unsigned char c1 = (i == 0) ? '~' : (unsigned char) iter1[i];
+ for (int j = 0; j <= seq2Length; j++){
+ unsigned char c2 = (j == 0) ? '~' : (unsigned char) iter2[j];
+
+ if (i > 1 || j > 1){
+ if (i > 0 && j > 0){
+ forward[0 + ij] = forward[0 + i1j1] + transProb[0][0];
+ for (int k = 1; k < NumMatrixTypes; k++)
+ LOG_PLUS_EQUALS (forward[0 + ij], forward[k + i1j1] + transProb[k][0]);
+ forward[0 + ij] += matchProb[c1][c2];
+ }
+ if (i > 0){
+ for (int k = 0; k < NumInsertStates; k++)
+ forward[2*k+1 + ij] = insProb[c1][k] +
+ LOG_ADD (forward[0 + i1j] + transProb[0][2*k+1],
+ forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1]);
+ }
+ if (j > 0){
+ for (int k = 0; k < NumInsertStates; k++)
+ forward[2*k+2 + ij] = insProb[c2][k] +
+ LOG_ADD (forward[0 + ij1] + transProb[0][2*k+2],
+ forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2]);
+ }
+ }
+
+ ij += NumMatrixTypes;
+ i1j += NumMatrixTypes;
+ ij1 += NumMatrixTypes;
+ i1j1 += NumMatrixTypes;
+ }
+ }
+
+ return forwardPtr;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeBackwardMatrix()
+ //
+ // Computes a set of backward probability matrices for aligning
+ // seq1 and seq2.
+ //
+ // For efficiency reasons, a single-dimensional floating-point
+ // array is used here, with the following indexing scheme:
+ //
+ // backward[i + NumMatrixTypes * (j * (seq2Length+1) + k)]
+ // refers to the probability of starting in state i and
+ // aligning from character j+1 to the end of the first
+ // sequence and from character k+1 to the end of the second
+ // sequence.
+ /////////////////////////////////////////////////////////////////
+
+ VF *ComputeBackwardMatrix (Sequence *seq1, Sequence *seq2) const {
+
+ assert (seq1);
+ assert (seq2);
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+ SafeVector<char>::iterator iter1 = seq1->GetDataPtr();
+ SafeVector<char>::iterator iter2 = seq2->GetDataPtr();
+
+ // create matrix
+ VF *backwardPtr = new VF (NumMatrixTypes * (seq1Length+1) * (seq2Length+1), LOG_ZERO);
+ assert (backwardPtr);
+ VF &backward = *backwardPtr;
+
+ // initialization condition
+ for (int k = 0; k < NumMatrixTypes; k++)
+ backward[NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1) + k] = initialDistribution[k];
+
+ // remember offset for each index combination
+ int ij = (seq1Length+1) * (seq2Length+1) - 1;
+ int i1j = ij + seq2Length + 1;
+ int ij1 = ij + 1;
+ int i1j1 = ij + seq2Length + 2;
+
+ ij *= NumMatrixTypes;
+ i1j *= NumMatrixTypes;
+ ij1 *= NumMatrixTypes;
+ i1j1 *= NumMatrixTypes;
+
+ // compute backward scores
+ for (int i = seq1Length; i >= 0; i--){
+ unsigned char c1 = (i == seq1Length) ? '~' : (unsigned char) iter1[i+1];
+ for (int j = seq2Length; j >= 0; j--){
+ unsigned char c2 = (j == seq2Length) ? '~' : (unsigned char) iter2[j+1];
+
+ if (i < seq1Length && j < seq2Length){
+ const float ProbXY = backward[0 + i1j1] + matchProb[c1][c2];
+ for (int k = 0; k < NumMatrixTypes; k++)
+ LOG_PLUS_EQUALS (backward[k + ij], ProbXY + transProb[k][0]);
+ }
+ if (i < seq1Length){
+ for (int k = 0; k < NumInsertStates; k++){
+ LOG_PLUS_EQUALS (backward[0 + ij], backward[2*k+1 + i1j] + insProb[c1][k] + transProb[0][2*k+1]);
+ LOG_PLUS_EQUALS (backward[2*k+1 + ij], backward[2*k+1 + i1j] + insProb[c1][k] + transProb[2*k+1][2*k+1]);
+ }
+ }
+ if (j < seq2Length){
+ for (int k = 0; k < NumInsertStates; k++){
+ LOG_PLUS_EQUALS (backward[0 + ij], backward[2*k+2 + ij1] + insProb[c2][k] + transProb[0][2*k+2]);
+ LOG_PLUS_EQUALS (backward[2*k+2 + ij], backward[2*k+2 + ij1] + insProb[c2][k] + transProb[2*k+2][2*k+2]);
+ }
+ }
+
+ ij -= NumMatrixTypes;
+ i1j -= NumMatrixTypes;
+ ij1 -= NumMatrixTypes;
+ i1j1 -= NumMatrixTypes;
+ }
+ }
+
+ return backwardPtr;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeTotalProbability()
+ //
+ // Computes the total probability of an alignment given
+ // the forward and backward matrices.
+ /////////////////////////////////////////////////////////////////
+
+ float ComputeTotalProbability (int seq1Length, int seq2Length,
+ const VF &forward, const VF &backward) const {
+
+ // compute total probability
+ float totalForwardProb = LOG_ZERO;
+ float totalBackwardProb = LOG_ZERO;
+ for (int k = 0; k < NumMatrixTypes; k++){
+ LOG_PLUS_EQUALS (totalForwardProb,
+ forward[k + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] +
+ backward[k + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]);
+ }
+
+ totalBackwardProb =
+ forward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)] +
+ backward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)];
+
+ for (int k = 0; k < NumInsertStates; k++){
+ LOG_PLUS_EQUALS (totalBackwardProb,
+ forward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)] +
+ backward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)]);
+ LOG_PLUS_EQUALS (totalBackwardProb,
+ forward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)] +
+ backward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)]);
+ }
+
+ // cerr << totalForwardProb << " " << totalBackwardProb << endl;
+
+ return (totalForwardProb + totalBackwardProb) / 2;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputePosteriorMatrix()
+ //
+ // Computes the posterior probability matrix based on
+ // the forward and backward matrices.
+ /////////////////////////////////////////////////////////////////
+
+ VF *ComputePosteriorMatrix (Sequence *seq1, Sequence *seq2,
+ const VF &forward, const VF &backward) const {
+
+ assert (seq1);
+ assert (seq2);
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+
+ float totalProb = ComputeTotalProbability (seq1Length, seq2Length,
+ forward, backward);
+
+ // compute posterior matrices
+ VF *posteriorPtr = new VF((seq1Length+1) * (seq2Length+1)); assert (posteriorPtr);
+ VF &posterior = *posteriorPtr;
+
+ int ij = 0;
+ VF::iterator ptr = posterior.begin();
+
+ for (int i = 0; i <= seq1Length; i++){
+ for (int j = 0; j <= seq2Length; j++){
+ *(ptr++) = EXP (min (LOG_ONE, forward[ij] + backward[ij] - totalProb));
+ ij += NumMatrixTypes;
+ }
+ }
+
+ posterior[0] = 0;
+
+ return posteriorPtr;
+ }
+
+ /*
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeExpectedCounts()
+ //
+ // Computes the expected counts for the various transitions.
+ /////////////////////////////////////////////////////////////////
+
+ VVF *ComputeExpectedCounts () const {
+
+ assert (seq1);
+ assert (seq2);
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+ SafeVector<char>::iterator iter1 = seq1->GetDataPtr();
+ SafeVector<char>::iterator iter2 = seq2->GetDataPtr();
+
+ // compute total probability
+ float totalProb = ComputeTotalProbability (seq1Length, seq2Length,
+ forward, backward);
+
+ // initialize expected counts
+ VVF *countsPtr = new VVF(NumMatrixTypes + 1, VF(NumMatrixTypes, LOG_ZERO)); assert (countsPtr);
+ VVF &counts = *countsPtr;
+
+ // remember offset for each index combination
+ int ij = 0;
+ int i1j = -seq2Length - 1;
+ int ij1 = -1;
+ int i1j1 = -seq2Length - 2;
+
+ ij *= NumMatrixTypes;
+ i1j *= NumMatrixTypes;
+ ij1 *= NumMatrixTypes;
+ i1j1 *= NumMatrixTypes;
+
+ // compute expected counts
+ for (int i = 0; i <= seq1Length; i++){
+ unsigned char c1 = (i == 0) ? '~' : (unsigned char) iter1[i];
+ for (int j = 0; j <= seq2Length; j++){
+ unsigned char c2 = (j == 0) ? '~' : (unsigned char) iter2[j];
+
+ if (i > 0 && j > 0){
+ for (int k = 0; k < NumMatrixTypes; k++)
+ LOG_PLUS_EQUALS (counts[k][0],
+ forward[k + i1j1] + transProb[k][0] +
+ matchProb[c1][c2] + backward[0 + ij]);
+ }
+ if (i > 0){
+ for (int k = 0; k < NumInsertStates; k++){
+ LOG_PLUS_EQUALS (counts[0][2*k+1],
+ forward[0 + i1j] + transProb[0][2*k+1] +
+ insProb[c1][k] + backward[2*k+1 + ij]);
+ LOG_PLUS_EQUALS (counts[2*k+1][2*k+1],
+ forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1] +
+ insProb[c1][k] + backward[2*k+1 + ij]);
+ }
+ }
+ if (j > 0){
+ for (int k = 0; k < NumInsertStates; k++){
+ LOG_PLUS_EQUALS (counts[0][2*k+2],
+ forward[0 + ij1] + transProb[0][2*k+2] +
+ insProb[c2][k] + backward[2*k+2 + ij]);
+ LOG_PLUS_EQUALS (counts[2*k+2][2*k+2],
+ forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2] +
+ insProb[c2][k] + backward[2*k+2 + ij]);
+ }
+ }
+
+ ij += NumMatrixTypes;
+ i1j += NumMatrixTypes;
+ ij1 += NumMatrixTypes;
+ i1j1 += NumMatrixTypes;
+ }
+ }
+
+ // scale all expected counts appropriately
+ for (int i = 0; i < NumMatrixTypes; i++)
+ for (int j = 0; j < NumMatrixTypes; j++)
+ counts[i][j] -= totalProb;
+
+ }
+ */
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeNewParameters()
+ //
+ // Computes a new parameter set based on the expected counts
+ // given.
+ /////////////////////////////////////////////////////////////////
+
+ void ComputeNewParameters (Sequence *seq1, Sequence *seq2,
+ const VF &forward, const VF &backward,
+ VF &initDistribMat, VF &gapOpen,
+ VF &gapExtend, VVF &emitPairs, VF &emitSingle, bool enableTrainEmissions) const {
+
+ assert (seq1);
+ assert (seq2);
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+ SafeVector<char>::iterator iter1 = seq1->GetDataPtr();
+ SafeVector<char>::iterator iter2 = seq2->GetDataPtr();
+
+ // compute total probability
+ float totalProb = ComputeTotalProbability (seq1Length, seq2Length,
+ forward, backward);
+
+ // initialize expected counts
+ VVF transCounts (NumMatrixTypes, VF (NumMatrixTypes, LOG_ZERO));
+ VF initCounts (NumMatrixTypes, LOG_ZERO);
+ VVF pairCounts (256, VF (256, LOG_ZERO));
+ VF singleCounts (256, LOG_ZERO);
+
+ // remember offset for each index combination
+ int ij = 0;
+ int i1j = -seq2Length - 1;
+ int ij1 = -1;
+ int i1j1 = -seq2Length - 2;
+
+ ij *= NumMatrixTypes;
+ i1j *= NumMatrixTypes;
+ ij1 *= NumMatrixTypes;
+ i1j1 *= NumMatrixTypes;
+
+ // compute initial distribution posteriors
+ initCounts[0] = LOG_ADD (forward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)] +
+ backward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)],
+ forward[0 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] +
+ backward[0 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]);
+ for (int k = 0; k < NumInsertStates; k++){
+ initCounts[2*k+1] = LOG_ADD (forward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)] +
+ backward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)],
+ forward[2*k+1 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] +
+ backward[2*k+1 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]);
+ initCounts[2*k+2] = LOG_ADD (forward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)] +
+ backward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)],
+ forward[2*k+2 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] +
+ backward[2*k+2 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]);
+ }
+
+ // compute expected counts
+ for (int i = 0; i <= seq1Length; i++){
+ unsigned char c1 = (i == 0) ? '~' : (unsigned char) toupper(iter1[i]);
+ for (int j = 0; j <= seq2Length; j++){
+ unsigned char c2 = (j == 0) ? '~' : (unsigned char) toupper(iter2[j]);
+
+ if (i > 0 && j > 0){
+ if (enableTrainEmissions && i == 1 && j == 1){
+ LOG_PLUS_EQUALS (pairCounts[c1][c2],
+ initialDistribution[0] + matchProb[c1][c2] + backward[0 + ij]);
+ LOG_PLUS_EQUALS (pairCounts[c2][c1],
+ initialDistribution[0] + matchProb[c2][c1] + backward[0 + ij]);
+ }
+
+ for (int k = 0; k < NumMatrixTypes; k++){
+ LOG_PLUS_EQUALS (transCounts[k][0],
+ forward[k + i1j1] + transProb[k][0] +
+ matchProb[c1][c2] + backward[0 + ij]);
+ if (enableTrainEmissions && i != 1 || j != 1){
+ LOG_PLUS_EQUALS (pairCounts[c1][c2],
+ forward[k + i1j1] + transProb[k][0] +
+ matchProb[c1][c2] + backward[0 + ij]);
+ LOG_PLUS_EQUALS (pairCounts[c2][c1],
+ forward[k + i1j1] + transProb[k][0] +
+ matchProb[c2][c1] + backward[0 + ij]);
+ }
+ }
+ }
+ if (i > 0){
+ for (int k = 0; k < NumInsertStates; k++){
+ LOG_PLUS_EQUALS (transCounts[0][2*k+1],
+ forward[0 + i1j] + transProb[0][2*k+1] +
+ insProb[c1][k] + backward[2*k+1 + ij]);
+ LOG_PLUS_EQUALS (transCounts[2*k+1][2*k+1],
+ forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1] +
+ insProb[c1][k] + backward[2*k+1 + ij]);
+ if (enableTrainEmissions){
+ if (i == 1 && j == 0){
+ LOG_PLUS_EQUALS (singleCounts[c1],
+ initialDistribution[2*k+1] + insProb[c1][k] + backward[2*k+1 + ij]);
+ }
+ else {
+ LOG_PLUS_EQUALS (singleCounts[c1],
+ forward[0 + i1j] + transProb[0][2*k+1] +
+ insProb[c1][k] + backward[2*k+1 + ij]);
+ LOG_PLUS_EQUALS (singleCounts[c1],
+ forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1] +
+ insProb[c1][k] + backward[2*k+1 + ij]);
+ }
+ }
+ }
+ }
+ if (j > 0){
+ for (int k = 0; k < NumInsertStates; k++){
+ LOG_PLUS_EQUALS (transCounts[0][2*k+2],
+ forward[0 + ij1] + transProb[0][2*k+2] +
+ insProb[c2][k] + backward[2*k+2 + ij]);
+ LOG_PLUS_EQUALS (transCounts[2*k+2][2*k+2],
+ forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2] +
+ insProb[c2][k] + backward[2*k+2 + ij]);
+ if (enableTrainEmissions){
+ if (i == 0 && j == 1){
+ LOG_PLUS_EQUALS (singleCounts[c2],
+ initialDistribution[2*k+2] + insProb[c2][k] + backward[2*k+2 + ij]);
+ }
+ else {
+ LOG_PLUS_EQUALS (singleCounts[c2],
+ forward[0 + ij1] + transProb[0][2*k+2] +
+ insProb[c2][k] + backward[2*k+2 + ij]);
+ LOG_PLUS_EQUALS (singleCounts[c2],
+ forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2] +
+ insProb[c2][k] + backward[2*k+2 + ij]);
+ }
+ }
+ }
+ }
+
+ ij += NumMatrixTypes;
+ i1j += NumMatrixTypes;
+ ij1 += NumMatrixTypes;
+ i1j1 += NumMatrixTypes;
+ }
+ }
+
+ // scale all expected counts appropriately
+ for (int i = 0; i < NumMatrixTypes; i++){
+ initCounts[i] -= totalProb;
+ for (int j = 0; j < NumMatrixTypes; j++)
+ transCounts[i][j] -= totalProb;
+ }
+ if (enableTrainEmissions){
+ for (int i = 0; i < 256; i++){
+ for (int j = 0; j < 256; j++)
+ pairCounts[i][j] -= totalProb;
+ singleCounts[i] -= totalProb;
+ }
+ }
+
+ // compute new initial distribution
+ float totalInitDistribCounts = 0;
+ for (int i = 0; i < NumMatrixTypes; i++)
+ totalInitDistribCounts += exp (initCounts[i]); // should be 2
+ initDistribMat[0] = min (1.0f, max (0.0f, (float) exp (initCounts[0]) / totalInitDistribCounts));
+ for (int k = 0; k < NumInsertStates; k++){
+ float val = (exp (initCounts[2*k+1]) + exp (initCounts[2*k+2])) / 2;
+ initDistribMat[2*k+1] = initDistribMat[2*k+2] = min (1.0f, max (0.0f, val / totalInitDistribCounts));
+ }
+
+ // compute total counts for match state
+ float inMatchStateCounts = 0;
+ for (int i = 0; i < NumMatrixTypes; i++)
+ inMatchStateCounts += exp (transCounts[0][i]);
+ for (int i = 0; i < NumInsertStates; i++){
+
+ // compute total counts for gap state
+ float inGapStateCounts =
+ exp (transCounts[2*i+1][0]) +
+ exp (transCounts[2*i+1][2*i+1]) +
+ exp (transCounts[2*i+2][0]) +
+ exp (transCounts[2*i+2][2*i+2]);
+
+ gapOpen[2*i] = gapOpen[2*i+1] =
+ (exp (transCounts[0][2*i+1]) +
+ exp (transCounts[0][2*i+2])) /
+ (2 * inMatchStateCounts);
+
+ gapExtend[2*i] = gapExtend[2*i+1] =
+ (exp (transCounts[2*i+1][2*i+1]) +
+ exp (transCounts[2*i+2][2*i+2])) /
+ inGapStateCounts;
+ }
+
+ if (enableTrainEmissions){
+ float totalPairCounts = 0;
+ float totalSingleCounts = 0;
+ for (int i = 0; i < 256; i++){
+ for (int j = 0; j <= i; j++)
+ totalPairCounts += exp (pairCounts[j][i]);
+ totalSingleCounts += exp (singleCounts[i]);
+ }
+
+ for (int i = 0; i < 256; i++) if (!islower ((char) i)){
+ int li = (int)((unsigned char) tolower ((char) i));
+ for (int j = 0; j <= i; j++) if (!islower ((char) j)){
+ int lj = (int)((unsigned char) tolower ((char) j));
+ emitPairs[i][j] = emitPairs[i][lj] = emitPairs[li][j] = emitPairs[li][lj] =
+ emitPairs[j][i] = emitPairs[j][li] = emitPairs[lj][i] = emitPairs[lj][li] = exp(pairCounts[j][i]) / totalPairCounts;
+ }
+ emitSingle[i] = emitSingle[li] = exp(singleCounts[i]) / totalSingleCounts;
+ }
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeAlignment()
+ //
+ // Computes an alignment based on the given posterior matrix.
+ // This is done by finding the maximum summing path (or
+ // maximum weight trace) through the posterior matrix. The
+ // final alignment is returned as a pair consisting of:
+ // (1) a string (e.g., XXXBBXXXBBBBBBYYYYBBB) where X's and
+ // denote insertions in one of the two sequences and
+ // B's denote that both sequences are present (i.e.
+ // matches).
+ // (2) a float indicating the sum achieved
+ /////////////////////////////////////////////////////////////////
+
+ pair<SafeVector<char> *, float> ComputeAlignment (int seq1Length, int seq2Length, const VF &posterior) const {
+
+ float *twoRows = new float[(seq2Length+1)*2]; assert (twoRows);
+ float *oldRow = twoRows;
+ float *newRow = twoRows + seq2Length + 1;
+
+ char *tracebackMatrix = new char[(seq1Length+1)*(seq2Length+1)]; assert (tracebackMatrix);
+ char *tracebackPtr = tracebackMatrix;
+
+ VF::const_iterator posteriorPtr = posterior.begin() + seq2Length + 1;
+
+ // initialization
+ for (int i = 0; i <= seq2Length; i++){
+ oldRow[i] = 0;
+ *(tracebackPtr++) = 'L';
+ }
+
+ // fill in matrix
+ for (int i = 1; i <= seq1Length; i++){
+
+ // initialize left column
+ newRow[0] = 0;
+ posteriorPtr++;
+ *(tracebackPtr++) = 'U';
+
+ // fill in rest of row
+ for (int j = 1; j <= seq2Length; j++){
+ ChooseBestOfThree (*(posteriorPtr++) + oldRow[j-1], newRow[j-1], oldRow[j],
+ 'D', 'L', 'U', &newRow[j], tracebackPtr++); // Match, insert, delete
+ }
+
+ // swap rows
+ float *temp = oldRow;
+ oldRow = newRow;
+ newRow = temp;
+ }
+
+ // store best score
+ float total = oldRow[seq2Length];
+ delete [] twoRows;
+
+ // compute traceback
+ SafeVector<char> *alignment = new SafeVector<char>; assert (alignment);
+ int r = seq1Length, c = seq2Length;
+ while (r != 0 || c != 0){
+ char ch = tracebackMatrix[r*(seq2Length+1) + c];
+ switch (ch){
+ case 'L': c--; alignment->push_back ('Y'); break;
+ case 'U': r--; alignment->push_back ('X'); break;
+ case 'D': c--; r--; alignment->push_back ('B'); break;
+ default: assert (false);
+ }
+ }
+
+ delete [] tracebackMatrix;
+
+ reverse (alignment->begin(), alignment->end());
+
+ return make_pair(alignment, total);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeAlignment2()
+ //
+ // Computes an alignment based on the given posterior matrix.
+ // This is done by finding the maximum summing path (or
+ // maximum weight trace) through the posterior matrix. The
+ // final alignment is returned as a pair consisting of:
+ // (1) a string (e.g., XXXBBXXXBBBBBBYYYYBBB) where X's and
+ // denote insertions in one of the two sequences and
+ // B's denote that both sequences are present (i.e.
+ // matches).
+ // (2) a float indicating the sum achieved
+ /////////////////////////////////////////////////////////////////
+
+ pair<SafeVector<char> *, float> ComputeAlignment2 (int seq1Length, int seq2Length,
+ const VF &posterior, std::vector<StemCandidate> *pscs1, std::vector<StemCandidate> *pscs2,
+ std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2) const {
+ NRMat<float> WM(seq1Length + 1, seq2Length + 1);
+ for (int i = 0; i <= seq1Length; i++) {
+ for (int j = 0; j <= seq2Length; j++) {
+ WM[i][j] = 0;
+ }
+ }
+
+ int len = WORDLENGTH;
+ int size = matchPSCS1->size();
+ float weight = 1000;
+
+ for(int iter = 0; iter < size; iter++) {
+ int i = matchPSCS1->at(iter);
+ int j = matchPSCS2->at(iter);
+
+ const StemCandidate &sc1 = pscs1->at(i);
+ const StemCandidate &sc2 = pscs2->at(j);
+ for(int k = 0; k < len; k++) {
+ WM[sc1.GetPosition() + k][sc2.GetPosition() + k] += weight;
+ }
+ }
+ float *twoRows = new float[(seq2Length+1)*2]; assert (twoRows);
+ float *oldRow = twoRows;
+ float *newRow = twoRows + seq2Length + 1;
+
+ char *tracebackMatrix = new char[(seq1Length+1)*(seq2Length+1)]; assert (tracebackMatrix);
+ char *tracebackPtr = tracebackMatrix;
+
+ VF::const_iterator posteriorPtr = posterior.begin() + seq2Length + 1;
+
+ // initialization
+ for (int i = 0; i <= seq2Length; i++){
+ oldRow[i] = 0;
+ *(tracebackPtr++) = 'L';
+ }
+
+ // fill in matrix
+ for (int i = 1; i <= seq1Length; i++){
+
+ // initialize left column
+ newRow[0] = 0;
+ posteriorPtr++;
+ *(tracebackPtr++) = 'U';
+
+ // fill in rest of row
+ for (int j = 1; j <= seq2Length; j++){
+ ChooseBestOfThree (*(posteriorPtr++) + oldRow[j-1] + WM[i][j], newRow[j-1], oldRow[j],
+ 'D', 'L', 'U', &newRow[j], tracebackPtr++);
+ }
+
+ // swap rows
+ float *temp = oldRow;
+ oldRow = newRow;
+ newRow = temp;
+ }
+
+ // store best score
+ float total = oldRow[seq2Length];
+ delete [] twoRows;
+
+ // compute traceback
+ SafeVector<char> *alignment = new SafeVector<char>; assert (alignment);
+ int r = seq1Length, c = seq2Length;
+ while (r != 0 || c != 0){
+ char ch = tracebackMatrix[r*(seq2Length+1) + c];
+ switch (ch){
+ case 'L': c--; alignment->push_back ('Y'); break;
+ case 'U': r--; alignment->push_back ('X'); break;
+ case 'D': c--; r--; alignment->push_back ('B'); break;
+ default: assert (false);
+ }
+ }
+
+ delete [] tracebackMatrix;
+
+ reverse (alignment->begin(), alignment->end());
+
+ return make_pair(alignment, total);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeAlignmentWithGapPenalties()
+ //
+ // Similar to ComputeAlignment() except with gap penalties.
+ /////////////////////////////////////////////////////////////////
+
+ pair<SafeVector<char> *, float> ComputeAlignmentWithGapPenalties (MultiSequence *align1,
+ MultiSequence *align2,
+ const VF &posterior, int numSeqs1,
+ int numSeqs2,
+ float gapOpenPenalty,
+ float gapContinuePenalty) const {
+ int seq1Length = align1->GetSequence(0)->GetLength();
+ int seq2Length = align2->GetSequence(0)->GetLength();
+ SafeVector<SafeVector<char>::iterator > dataPtrs1 (align1->GetNumSequences());
+ SafeVector<SafeVector<char>::iterator > dataPtrs2 (align2->GetNumSequences());
+
+ // grab character data
+ for (int i = 0; i < align1->GetNumSequences(); i++)
+ dataPtrs1[i] = align1->GetSequence(i)->GetDataPtr();
+ for (int i = 0; i < align2->GetNumSequences(); i++)
+ dataPtrs2[i] = align2->GetSequence(i)->GetDataPtr();
+
+ // the number of active sequences at any given column is defined to be the
+ // number of non-gap characters in that column; the number of gap opens at
+ // any given column is defined to be the number of gap characters in that
+ // column where the previous character in the respective sequence was not
+ // a gap
+ SafeVector<int> numActive1 (seq1Length+1), numGapOpens1 (seq1Length+1);
+ SafeVector<int> numActive2 (seq2Length+1), numGapOpens2 (seq2Length+1);
+
+ // compute number of active sequences and gap opens for each group
+ for (int i = 0; i < align1->GetNumSequences(); i++){
+ SafeVector<char>::iterator dataPtr = align1->GetSequence(i)->GetDataPtr();
+ numActive1[0] = numGapOpens1[0] = 0;
+ for (int j = 1; j <= seq1Length; j++){
+ if (dataPtr[j] != '-'){
+ numActive1[j]++;
+ numGapOpens1[j] += (j != 1 && dataPtr[j-1] != '-');
+ }
+ }
+ }
+ for (int i = 0; i < align2->GetNumSequences(); i++){
+ SafeVector<char>::iterator dataPtr = align2->GetSequence(i)->GetDataPtr();
+ numActive2[0] = numGapOpens2[0] = 0;
+ for (int j = 1; j <= seq2Length; j++){
+ if (dataPtr[j] != '-'){
+ numActive2[j]++;
+ numGapOpens2[j] += (j != 1 && dataPtr[j-1] != '-');
+ }
+ }
+ }
+
+ VVF openingPenalty1 (numSeqs1+1, VF (numSeqs2+1));
+ VF continuingPenalty1 (numSeqs1+1);
+ VVF openingPenalty2 (numSeqs1+1, VF (numSeqs2+1));
+ VF continuingPenalty2 (numSeqs2+1);
+
+ // precompute penalties
+ for (int i = 0; i <= numSeqs1; i++)
+ for (int j = 0; j <= numSeqs2; j++)
+ openingPenalty1[i][j] = i * (gapOpenPenalty * j + gapContinuePenalty * (numSeqs2 - j));
+ for (int i = 0; i <= numSeqs1; i++)
+ continuingPenalty1[i] = i * gapContinuePenalty * numSeqs2;
+ for (int i = 0; i <= numSeqs2; i++)
+ for (int j = 0; j <= numSeqs1; j++)
+ openingPenalty2[i][j] = i * (gapOpenPenalty * j + gapContinuePenalty * (numSeqs1 - j));
+ for (int i = 0; i <= numSeqs2; i++)
+ continuingPenalty2[i] = i * gapContinuePenalty * numSeqs1;
+
+ float *twoRows = new float[6*(seq2Length+1)]; assert (twoRows);
+ float *oldRowMatch = twoRows;
+ float *newRowMatch = twoRows + (seq2Length+1);
+ float *oldRowInsertX = twoRows + 2*(seq2Length+1);
+ float *newRowInsertX = twoRows + 3*(seq2Length+1);
+ float *oldRowInsertY = twoRows + 4*(seq2Length+1);
+ float *newRowInsertY = twoRows + 5*(seq2Length+1);
+
+ char *tracebackMatrix = new char[3*(seq1Length+1)*(seq2Length+1)]; assert (tracebackMatrix);
+ char *tracebackPtr = tracebackMatrix;
+
+ VF::const_iterator posteriorPtr = posterior.begin() + seq2Length + 1;
+
+ // initialization
+ for (int i = 0; i <= seq2Length; i++){
+ oldRowMatch[i] = oldRowInsertX[i] = (i == 0) ? 0 : LOG_ZERO;
+ oldRowInsertY[i] = (i == 0) ? 0 : oldRowInsertY[i-1] + continuingPenalty2[numActive2[i]];
+ *(tracebackPtr) = *(tracebackPtr+1) = *(tracebackPtr+2) = 'Y';
+ tracebackPtr += 3;
+ }
+
+ // fill in matrix
+ for (int i = 1; i <= seq1Length; i++){
+
+ // initialize left column
+ newRowMatch[0] = newRowInsertY[0] = LOG_ZERO;
+ newRowInsertX[0] = oldRowInsertX[0] + continuingPenalty1[numActive1[i]];
+ posteriorPtr++;
+ *(tracebackPtr) = *(tracebackPtr+1) = *(tracebackPtr+2) = 'X';
+ tracebackPtr += 3;
+
+ // fill in rest of row
+ for (int j = 1; j <= seq2Length; j++){
+
+ // going to MATCH state
+ ChooseBestOfThree (oldRowMatch[j-1],
+ oldRowInsertX[j-1],
+ oldRowInsertY[j-1],
+ 'M', 'X', 'Y', &newRowMatch[j], tracebackPtr++);
+ newRowMatch[j] += *(posteriorPtr++);
+
+ // going to INSERT X state
+ ChooseBestOfThree (oldRowMatch[j] + openingPenalty1[numActive1[i]][numGapOpens2[j]],
+ oldRowInsertX[j] + continuingPenalty1[numActive1[i]],
+ oldRowInsertY[j] + openingPenalty1[numActive1[i]][numGapOpens2[j]],
+ 'M', 'X', 'Y', &newRowInsertX[j], tracebackPtr++);
+
+ // going to INSERT Y state
+ ChooseBestOfThree (newRowMatch[j-1] + openingPenalty2[numActive2[j]][numGapOpens1[i]],
+ newRowInsertX[j-1] + openingPenalty2[numActive2[j]][numGapOpens1[i]],
+ newRowInsertY[j-1] + continuingPenalty2[numActive2[j]],
+ 'M', 'X', 'Y', &newRowInsertY[j], tracebackPtr++);
+ }
+
+ // swap rows
+ float *temp;
+ temp = oldRowMatch; oldRowMatch = newRowMatch; newRowMatch = temp;
+ temp = oldRowInsertX; oldRowInsertX = newRowInsertX; newRowInsertX = temp;
+ temp = oldRowInsertY; oldRowInsertY = newRowInsertY; newRowInsertY = temp;
+ }
+
+ // store best score
+ float total;
+ char matrix;
+ ChooseBestOfThree (oldRowMatch[seq2Length], oldRowInsertX[seq2Length], oldRowInsertY[seq2Length],
+ 'M', 'X', 'Y', &total, &matrix);
+
+ delete [] twoRows;
+
+ // compute traceback
+ SafeVector<char> *alignment = new SafeVector<char>; assert (alignment);
+ int r = seq1Length, c = seq2Length;
+ while (r != 0 || c != 0){
+
+ int offset = (matrix == 'M') ? 0 : (matrix == 'X') ? 1 : 2;
+ char ch = tracebackMatrix[(r*(seq2Length+1) + c) * 3 + offset];
+ switch (matrix){
+ case 'Y': c--; alignment->push_back ('Y'); break;
+ case 'X': r--; alignment->push_back ('X'); break;
+ case 'M': c--; r--; alignment->push_back ('B'); break;
+ default: assert (false);
+ }
+ matrix = ch;
+ }
+
+ delete [] tracebackMatrix;
+
+ reverse (alignment->begin(), alignment->end());
+
+ return make_pair(alignment, 1.0f);
+ }
+
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::ComputeViterbiAlignment()
+ //
+ // Computes the highest probability pairwise alignment using the
+ // probabilistic model. The final alignment is returned as a
+ // pair consisting of:
+ // (1) a string (e.g., XXXBBXXXBBBBBBYYYYBBB) where X's and
+ // denote insertions in one of the two sequences and
+ // B's denote that both sequences are present (i.e.
+ // matches).
+ // (2) a float containing the log probability of the best
+ // alignment (not used)
+ /////////////////////////////////////////////////////////////////
+
+ pair<SafeVector<char> *, float> ComputeViterbiAlignment (Sequence *seq1, Sequence *seq2) const {
+
+ assert (seq1);
+ assert (seq2);
+
+ const int seq1Length = seq1->GetLength();
+ const int seq2Length = seq2->GetLength();
+
+ // retrieve the points to the beginning of each sequence
+ SafeVector<char>::iterator iter1 = seq1->GetDataPtr();
+ SafeVector<char>::iterator iter2 = seq2->GetDataPtr();
+
+ // create viterbi matrix
+ VF *viterbiPtr = new VF (NumMatrixTypes * (seq1Length+1) * (seq2Length+1), LOG_ZERO);
+ assert (viterbiPtr);
+ VF &viterbi = *viterbiPtr;
+
+ // create traceback matrix
+ VI *tracebackPtr = new VI (NumMatrixTypes * (seq1Length+1) * (seq2Length+1), -1);
+ assert (tracebackPtr);
+ VI &traceback = *tracebackPtr;
+
+ // initialization condition
+ for (int k = 0; k < NumMatrixTypes; k++)
+ viterbi[k] = initialDistribution[k];
+
+ // remember offset for each index combination
+ int ij = 0;
+ int i1j = -seq2Length - 1;
+ int ij1 = -1;
+ int i1j1 = -seq2Length - 2;
+
+ ij *= NumMatrixTypes;
+ i1j *= NumMatrixTypes;
+ ij1 *= NumMatrixTypes;
+ i1j1 *= NumMatrixTypes;
+
+ // compute viterbi scores
+ for (int i = 0; i <= seq1Length; i++){
+ unsigned char c1 = (i == 0) ? '~' : (unsigned char) iter1[i];
+ for (int j = 0; j <= seq2Length; j++){
+ unsigned char c2 = (j == 0) ? '~' : (unsigned char) iter2[j];
+
+ if (i > 0 && j > 0){
+ for (int k = 0; k < NumMatrixTypes; k++){
+ float newVal = viterbi[k + i1j1] + transProb[k][0] + matchProb[c1][c2];
+ if (viterbi[0 + ij] < newVal){
+ viterbi[0 + ij] = newVal;
+ traceback[0 + ij] = k;
+ }
+ }
+ }
+ if (i > 0){
+ for (int k = 0; k < NumInsertStates; k++){
+ float valFromMatch = insProb[c1][k] + viterbi[0 + i1j] + transProb[0][2*k+1];
+ float valFromIns = insProb[c1][k] + viterbi[2*k+1 + i1j] + transProb[2*k+1][2*k+1];
+ if (valFromMatch >= valFromIns){
+ viterbi[2*k+1 + ij] = valFromMatch;
+ traceback[2*k+1 + ij] = 0;
+ }
+ else {
+ viterbi[2*k+1 + ij] = valFromIns;
+ traceback[2*k+1 + ij] = 2*k+1;
+ }
+ }
+ }
+ if (j > 0){
+ for (int k = 0; k < NumInsertStates; k++){
+ float valFromMatch = insProb[c2][k] + viterbi[0 + ij1] + transProb[0][2*k+2];
+ float valFromIns = insProb[c2][k] + viterbi[2*k+2 + ij1] + transProb[2*k+2][2*k+2];
+ if (valFromMatch >= valFromIns){
+ viterbi[2*k+2 + ij] = valFromMatch;
+ traceback[2*k+2 + ij] = 0;
+ }
+ else {
+ viterbi[2*k+2 + ij] = valFromIns;
+ traceback[2*k+2 + ij] = 2*k+2;
+ }
+ }
+ }
+
+ ij += NumMatrixTypes;
+ i1j += NumMatrixTypes;
+ ij1 += NumMatrixTypes;
+ i1j1 += NumMatrixTypes;
+ }
+ }
+
+ // figure out best terminating cell
+ float bestProb = LOG_ZERO;
+ int state = -1;
+ for (int k = 0; k < NumMatrixTypes; k++){
+ float thisProb = viterbi[k + NumMatrixTypes * ((seq1Length+1)*(seq2Length+1) - 1)] + initialDistribution[k];
+ if (bestProb < thisProb){
+ bestProb = thisProb;
+ state = k;
+ }
+ }
+ assert (state != -1);
+
+ delete viterbiPtr;
+
+ // compute traceback
+ SafeVector<char> *alignment = new SafeVector<char>; assert (alignment);
+ int r = seq1Length, c = seq2Length;
+ while (r != 0 || c != 0){
+ int newState = traceback[state + NumMatrixTypes * (r * (seq2Length+1) + c)];
+
+ if (state == 0){ c--; r--; alignment->push_back ('B'); }
+ else if (state % 2 == 1){ r--; alignment->push_back ('X'); }
+ else { c--; alignment->push_back ('Y'); }
+
+ state = newState;
+ }
+
+ delete tracebackPtr;
+
+ reverse (alignment->begin(), alignment->end());
+
+ return make_pair(alignment, bestProb);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // ProbabilisticModel::BuildPosterior()
+ //
+ // Builds a posterior probability matrix needed to align a pair
+ // of alignments. Mathematically, the returned matrix M is
+ // defined as follows:
+ // M[i,j] = sum sum f(s,t,i,j)
+ // s in align1 t in align2
+ // where
+ // [ P(s[i'] <--> t[j'])
+ // [ if s[i'] is a letter in the ith column of align1 and
+ // [ t[j'] it a letter in the jth column of align2
+ // f(s,t,i,j) = [
+ // [ 0 otherwise
+ //
+ /////////////////////////////////////////////////////////////////
+
+ VF *BuildPosterior (MultiSequence *align1, MultiSequence *align2,
+ const SafeVector<SafeVector<SparseMatrix *> > &sparseMatrices,
+ float cutoff = 0.0f) const {
+ const int seq1Length = align1->GetSequence(0)->GetLength();
+ const int seq2Length = align2->GetSequence(0)->GetLength();
+
+ VF *posteriorPtr = new VF((seq1Length+1) * (seq2Length+1), 0); assert (posteriorPtr);
+ VF &posterior = *posteriorPtr;
+ VF::iterator postPtr = posterior.begin();
+
+ // for each s in align1
+ for (int i = 0; i < align1->GetNumSequences(); i++){
+ int first = align1->GetSequence(i)->GetLabel();
+ SafeVector<int> *mapping1 = align1->GetSequence(i)->GetMapping();
+
+ // for each t in align2
+ for (int j = 0; j < align2->GetNumSequences(); j++){
+ int second = align2->GetSequence(j)->GetLabel();
+ SafeVector<int> *mapping2 = align2->GetSequence(j)->GetMapping();
+ if (first < second){
+
+ // get the associated sparse matrix
+ SparseMatrix *matrix = sparseMatrices[first][second];
+
+ for (int ii = 1; ii <= matrix->GetSeq1Length(); ii++){
+ SafeVector<PIF>::iterator row = matrix->GetRowPtr(ii);
+ int base = (*mapping1)[ii] * (seq2Length+1);
+ int rowSize = matrix->GetRowSize(ii);
+ // add in all relevant values
+ for (int jj = 0; jj < rowSize; jj++)
+ posterior[base + (*mapping2)[row[jj].first]] += row[jj].second;
+
+ // subtract cutoff
+ for (int jj = 0; jj < matrix->GetSeq2Length(); jj++) {
+ posterior[base + (*mapping2)[jj]] -= cutoff;
+ }
+
+ }
+
+ } else {
+ // get the associated sparse matrix
+ SparseMatrix *matrix = sparseMatrices[second][first];
+
+ for (int jj = 1; jj <= matrix->GetSeq1Length(); jj++){
+ SafeVector<PIF>::iterator row = matrix->GetRowPtr(jj);
+ int base = (*mapping2)[jj];
+ int rowSize = matrix->GetRowSize(jj);
+
+ // add in all relevant values
+ for (int ii = 0; ii < rowSize; ii++)
+ posterior[base + (*mapping1)[row[ii].first] * (seq2Length + 1)] += row[ii].second;
+
+ // subtract cutoff
+ for (int ii = 0; ii < matrix->GetSeq2Length(); ii++)
+ posterior[base + (*mapping1)[ii] * (seq2Length + 1)] -= cutoff;
+ }
+
+ }
+
+
+ delete mapping2;
+ }
+
+ delete mapping1;
+ }
+
+ return posteriorPtr;
+ }
+};
+}
+#endif
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// ProjectPairwise
+//
+// Program for projecting multiple alignments to all pairwise
+// alignments.
+/////////////////////////////////////////////////////////////////
+
+#include "SafeVector.h"
+#include "MultiSequence.h"
+#include <string>
+#include <sstream>
+#include <iomanip>
+#include <iostream>
+#include <list>
+#include <set>
+#include <limits>
+#include <cstdio>
+#include <cstdlib>
+#include <cerrno>
+#include <iomanip>
+
+bool compressGaps = true;
+
+/////////////////////////////////////////////////////////////////
+// main()
+//
+// Main program.
+/////////////////////////////////////////////////////////////////
+
+int main (int argc, char **argv){
+
+ // check arguments
+ if (argc < 2){
+ cerr << "Usage: project ALIGNMENT [-nocompressgaps]" << endl;
+ exit (1);
+ }
+
+ for (int i = 2; i < argc; i++){
+ if (strcmp (argv[i], "-nocompressgaps") == 0)
+ compressGaps = false;
+ else {
+ cerr << "Unrecognized option: " << argv[i] << endl;
+ exit (1);
+ }
+ }
+
+ MultiSequence *align = new MultiSequence (string (argv[1])); assert (align);
+
+ int N = align->GetNumSequences();
+ for (int i = 0; i < N; i++){
+ for (int j = i+1; j < N; j++){
+ string name = align->GetSequence(i)->GetHeader() + "-" + align->GetSequence(j)->GetHeader() + ".fasta";
+ ofstream outfile (name.c_str());
+
+ if (compressGaps){
+ set<int> s;
+ s.insert (i); s.insert (j);
+ MultiSequence *proj = align->Project (s);
+ proj->WriteMFA (outfile);
+ delete proj;
+ }
+ else {
+ align->GetSequence(i)->WriteMFA (outfile, 60);
+ align->GetSequence(j)->WriteMFA (outfile, 60);
+ }
+ outfile.close();
+ }
+ }
+
+ delete align;
+}
--- /dev/null
+
+ PROBCONS
+ ~~~~~~~~
+
+ Probabilistic consistency-based multiple sequence alignment
+
+-----------------------------------------------------------------
+
+PROBCONS is a novel tool for generating multiple alignments
+of protein sequences. Using a combination of probabilistic
+modeling and consistency-based alignment techniques, PROBCONS
+has achieved the highest accuracy of all alignment methods to
+date.
+
+PROBCONS was developed by Chuong B. Do in collaboration with
+Michael Brudno in the research group of Serafim Batzoglou,
+Department of Computer Science, Stanford University.
+
+For more information on the algorithms, please see
+
+ Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS:
+ Probabilistic Consistency-based Multiple Alignment of
+ Amino Acid Sequences. 12th International Conference on
+ Intelligent Systems for Molecular Biology. In press.
+
+and
+
+ Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS:
+ Probabilistic Consistency-based Multiple Alignment of
+ Amino Acid Sequences. The 19th National Conference on
+ Artificial Intelligence (AAAI-04). In press.
+
+-----------------------------------------------------------------
+
+PROBCONS has been made freely available as PUBLIC DOMAIN
+software and hence is not subject to copyright in the United
+States. This system and/or any portion of the source code
+may be used, modified, or redistributed without restrictions.
+PROBCONS is distributed WITHOUT WARRANTY, express or implied.
+The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
+loss due to reliance on the program.
+
+-----------------------------------------------------------------
+
+Version History
+
+1.0, 3/23/2004 (Chuong Do)
+ -- initial release
+
+1.01, 3/25/2004 (Chuong Do)
+ -- fixed error in training procedure
+ -- retrained default parameters for 1 and 2 pairs of insert
+ states
+
+1.02, 4/17/2004 (Chuong Do)
+ -- replaced LOG_ADD and EXP routines
+ -- added support for reading MSF format files
+ -- added two extra utilities for scoring PROBCONS alignments
+ (for benchmarking purposes)
+ -- added the "compare" program for scoring alignments
+ according to a reference alignment with respect to
+ sum-of-pairs and column scores
+ -- added the "fixref" program for adjusting PREFAB
+ alignments to contain all letters of the input
+ sequences; basically the main program for PROBCONS
+ "hacked" to get the job done
+
+1.03, 5/3/2004 (Chuong Do)
+ -- added option to do all-pairs pairwise alignments instead
+ of constructing a full multiple alignment
+ -- added support for reading DIALIGN style files
+ -- enabled support for using BAliBASE annotations for scoring
+ BAliBASE alignments
+ -- several minor bug fixes thanks to Bob Edgar
+ -- added "project" program to project multiple alignment to
+ pairwise alignments
+
+1.04, 5/9/2004 (Chuong Do)
+ -- switched over to default of one-insert state pair
+ -- retrained default parameters
+ -- added annotation scores
+ -- small changes to model topology to make end gaps symmetrical
+ -- added makegnuplot utility to plot annotation scores
+
+1.05, 5/26/2004 (Chuong Do)
+ -- added cutoff filtering for posterior scores
+ -- made small corrections to recurrences for computing alignments
+ -- added CLUSTALW output support
+
+1.06, 7/13/2004 (Chuong Do)
+ -- ProbCons is now PUBLIC DOMAIN software.
+
+1.07, 8/30/2004 (Chuong Do)
+ -- Fixed CLUSTALW output for sequence names (thanks to John Calley
+ for pointing this out)
+
+1.08, 8/31/2004 (Chuong Do)
+ -- Added option for alignment order output (-a).
+
+1.09, 9/1/2004 (Chuong Do)
+ -- PROBCONS now allows input files with existing gaps -- these are
+ automatically stripped before alignment.
+
+1.10, 3/16/2005 (Chuong Do)
+ -- Reduced memory consumption by
+ -- not storing posterior matrix transposes
+ -- restricting consistency-derived posterior matrices to original posterior matrix
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// SafeVector.h
+//
+// STL vector with array bounds checking. To enable bounds
+// checking, #define ENABLE_CHECKS.
+/////////////////////////////////////////////////////////////////
+
+#ifndef SAFEVECTOR_H
+#define SAFEVECTOR_H
+
+#include <cassert>
+#include <vector>
+
+/////////////////////////////////////////////////////////////////
+// SafeVector
+//
+// Class derived from the STL std::vector for bounds checking.
+/////////////////////////////////////////////////////////////////
+namespace MXSCARNA {
+template<class TYPE>
+class SafeVector : public std::vector<TYPE>{
+ public:
+
+ // miscellaneous constructors
+ SafeVector() : std::vector<TYPE>() {}
+ SafeVector (size_t size) : std::vector<TYPE>(size) {}
+ SafeVector (size_t size, const TYPE &value) : std::vector<TYPE>(size, value) {}
+ SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
+
+#ifdef ENABLE_CHECKS
+
+ // [] array bounds checking
+ TYPE &operator[](int index){
+ assert (index >= 0 && index < (int) size());
+ return std::vector<TYPE>::operator[] ((size_t) index);
+ }
+
+ // [] const array bounds checking
+ const TYPE &operator[] (int index) const {
+ assert (index >= 0 && index < (int) size());
+ return std::vector<TYPE>::operator[] ((size_t) index) ;
+ }
+
+#endif
+
+};
+
+// some commonly used vector types
+typedef SafeVector<int> VI;
+typedef SafeVector<VI> VVI;
+typedef SafeVector<VVI> VVVI;
+typedef SafeVector<float> VF;
+typedef SafeVector<VF> VVF;
+typedef SafeVector<VVF> VVVF;
+}
+#endif
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// ScoreType.h
+//
+// Routines for doing math operations in PROBCONS.
+/////////////////////////////////////////////////////////////////
+
+#ifndef SCORETYPE_H
+#define SCORETYPE_H
+
+#include <cmath>
+#include <algorithm>
+#include <cfloat>
+
+typedef float ScoreType;
+
+const float LOG_ZERO = -2e20;
+const float LOG_ONE = 0.0;
+
+/////////////////////////////////////////////////////////////////
+// LOG()
+//
+// Compute the logarithm of x.
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType LOG (ScoreType x){
+ return log (x);
+}
+
+/////////////////////////////////////////////////////////////////
+// EXP()
+//
+// Computes exp(x).
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType EXP (ScoreType x){
+ //return exp(x);
+ if (x > -2){
+ if (x > -0.5){
+ if (x > 0)
+ return exp(x);
+ return (((0.03254409303190190000*x + 0.16280432765779600000)*x + 0.49929760485974900000)*x + 0.99995149601363700000)*x + 0.99999925508501600000;
+ }
+ if (x > -1)
+ return (((0.01973899026052090000*x + 0.13822379685007000000)*x + 0.48056651562365000000)*x + 0.99326940370383500000)*x + 0.99906756856399500000;
+ return (((0.00940528203591384000*x + 0.09414963667859410000)*x + 0.40825793595877300000)*x + 0.93933625499130400000)*x + 0.98369508190545300000;
+ }
+ if (x > -8){
+ if (x > -4)
+ return (((0.00217245711583303000*x + 0.03484829428350620000)*x + 0.22118199801337800000)*x + 0.67049462206469500000)*x + 0.83556950223398500000;
+ return (((0.00012398771025456900*x + 0.00349155785951272000)*x + 0.03727721426017900000)*x + 0.17974997741536900000)*x + 0.33249299994217400000;
+ }
+ if (x > -16)
+ return (((0.00000051741713416603*x + 0.00002721456879608080)*x + 0.00053418601865636800)*x + 0.00464101989351936000)*x + 0.01507447981459420000;
+ return 0;
+}
+
+/*
+/////////////////////////////////////////////////////////////////
+// LOOKUP()
+//
+// Computes log (exp (x) + 1), for 0 <= x <= 7.5.
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType LOOKUP (ScoreType x){
+ //return log (exp(x) + 1);
+ if (x < 2){
+ if (x < 0.5){
+ if (x < 0)
+ return log (exp(x) + 1);
+ return (((-0.00486373205785640000*x - 0.00020245408813934800)*x + 0.12504222666029800000)*x + 0.49999685320563000000)*x + 0.69314723138948900000;
+ }
+ if (x < 1)
+ return (((-0.00278634205460548000*x - 0.00458097251248546000)*x + 0.12865849880472500000)*x + 0.49862228499205200000)*x + 0.69334810088688000000;
+ return (((0.00059633755154209200*x - 0.01918996666063320000)*x + 0.15288232492093800000)*x + 0.48039958825756900000)*x + 0.69857578503189200000;
+ }
+ if (x < 8){
+ if (x < 4)
+ return (((0.00135958539181047000*x - 0.02329807659316430000)*x + 0.15885799609532100000)*x + 0.48167498563270800000)*x + 0.69276185058669200000;
+ return (((0.00011992394456683500*x - 0.00338464503306568000)*x + 0.03622746366545470000)*x + 0.82481250248383700000)*x + 0.32507892994863100000;
+ }
+ if (x < 16)
+ return (((0.00000051726300753785*x - 0.00002720671238876090)*x + 0.00053403733818413500)*x + 0.99536021775747900000)*x + 0.01507065715532010000;
+ return x;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOOKUP_SLOW()
+//
+// Computes log (exp (x) + 1).
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType LOOKUP_SLOW (ScoreType x){
+ return log (exp (x) + 1);
+}
+
+/////////////////////////////////////////////////////////////////
+// MAX()
+//
+// Compute max of three numbers
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType MAX (ScoreType x, ScoreType y, ScoreType z){
+ if (x >= y){
+ if (x >= z)
+ return x;
+ return z;
+ }
+ if (y >= z)
+ return y;
+ return z;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_PLUS_EQUALS()
+//
+// Add two log probabilities and store in the first argument
+/////////////////////////////////////////////////////////////////
+
+inline void LOG_PLUS_EQUALS (ScoreType &x, ScoreType y){
+ if (x < y)
+ x = (x <= LOG_ZERO) ? y : LOOKUP(y-x) + x;
+ else
+ x = (y <= LOG_ZERO) ? x : LOOKUP(x-y) + y;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_PLUS_EQUALS_SLOW()
+//
+// Add two log probabilities and store in the first argument
+/////////////////////////////////////////////////////////////////
+
+inline void LOG_PLUS_EQUALS_SLOW (ScoreType &x, ScoreType y){
+ if (x < y)
+ x = (x <= LOG_ZERO) ? y : LOOKUP_SLOW(y-x) + x;
+ else
+ x = (y <= LOG_ZERO) ? x : LOOKUP_SLOW(x-y) + y;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add two log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline ScoreType LOG_ADD (ScoreType x, ScoreType y){
+ if (x < y) return (x <= LOG_ZERO) ? y : LOOKUP(y-x) + x;
+ return (y <= LOG_ZERO) ? x : LOOKUP(x-y) + y;
+}
+*/
+
+/*
+/////////////////////////////////////////////////////////////////
+// LOG()
+//
+// Compute the logarithm of x.
+/////////////////////////////////////////////////////////////////
+
+inline float LOG (float x){
+ return log (x);
+}
+
+/////////////////////////////////////////////////////////////////
+// EXP()
+//
+// Computes exp(x), fr -4.6 <= x <= 0.
+/////////////////////////////////////////////////////////////////
+
+inline float EXP (float x){
+ assert (x <= 0.00f);
+ if (x < EXP_UNDERFLOW_THRESHOLD) return 0.0f;
+ return (((0.006349841068584 * x + 0.080775412572352) * x + 0.397982026296272) * x + 0.95279335963787f) * x + 0.995176455837312f;
+ //return (((0.00681169825657f * x + 0.08386267698832f) * x + 0.40413983195844f) * x + 0.95656674979767f) * x + 0.99556744049130f;
+}
+*/
+
+const float EXP_UNDERFLOW_THRESHOLD = -4.6;
+const float LOG_UNDERFLOW_THRESHOLD = 7.5;
+
+/////////////////////////////////////////////////////////////////
+// LOOKUP()
+//
+// Computes log (exp (x) + 1), for 0 <= x <= 7.5.
+/////////////////////////////////////////////////////////////////
+
+inline float LOOKUP (float x){
+ assert (x >= 0.00f);
+ assert (x <= LOG_UNDERFLOW_THRESHOLD);
+ //return ((-0.00653779113685f * x + 0.09537236626558f) * x + 0.55317574459331f) * x + 0.68672959851568f;
+ if (x <= 1.00f) return ((-0.009350833524763f * x + 0.130659527668286f) * x + 0.498799810682272f) * x + 0.693203116424741f;
+ if (x <= 2.50f) return ((-0.014532321752540f * x + 0.139942324101744f) * x + 0.495635523139337f) * x + 0.692140569840976f;
+ if (x <= 4.50f) return ((-0.004605031767994f * x + 0.063427417320019f) * x + 0.695956496475118f) * x + 0.514272634594009f;
+ assert (x <= LOG_UNDERFLOW_THRESHOLD);
+ return ((-0.000458661602210f * x + 0.009695946122598f) * x + 0.930734667215156f) * x + 0.168037164329057f;
+
+ //return (((0.00089738532761f * x - 0.01859488697982f) * x + 0.14415772028626f) * x + 0.49515490689159f) * x + 0.69311928966454f;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOOKUP_SLOW()
+//
+// Computes log (exp (x) + 1).
+/////////////////////////////////////////////////////////////////
+
+inline float LOOKUP_SLOW (float x){
+ return log (exp (x) + 1);
+}
+
+/////////////////////////////////////////////////////////////////
+// MAX()
+//
+// Compute max of three numbers
+/////////////////////////////////////////////////////////////////
+
+inline float MAX (float x, float y, float z){
+ if (x >= y){
+ if (x >= z)
+ return x;
+ return z;
+ }
+ if (y >= z)
+ return y;
+ return z;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_PLUS_EQUALS()
+//
+// Add two log probabilities and store in the first argument
+/////////////////////////////////////////////////////////////////
+
+inline void LOG_PLUS_EQUALS (float &x, float y){
+ if (x < y)
+ x = (x == LOG_ZERO || y - x >= LOG_UNDERFLOW_THRESHOLD) ? y : LOOKUP(y-x) + x;
+ else
+ x = (y == LOG_ZERO || x - y >= LOG_UNDERFLOW_THRESHOLD) ? x : LOOKUP(x-y) + y;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_PLUS_EQUALS_SLOW()
+//
+// Add two log probabilities and store in the first argument
+/////////////////////////////////////////////////////////////////
+
+inline void LOG_PLUS_EQUALS_SLOW (float &x, float y){
+ if (x < y)
+ x = (x == LOG_ZERO) ? y : LOOKUP_SLOW(y-x) + x;
+ else
+ x = (y == LOG_ZERO) ? x : LOOKUP_SLOW(x-y) + y;
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add two log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x, float y){
+ if (x < y) return (x == LOG_ZERO || y - x >= LOG_UNDERFLOW_THRESHOLD) ? y : LOOKUP(y-x) + x;
+ return (y == LOG_ZERO || x - y >= LOG_UNDERFLOW_THRESHOLD) ? x : LOOKUP(x-y) + y;
+}
+
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add three log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3){
+ return LOG_ADD (x1, LOG_ADD (x2, x3));
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add four log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3, float x4){
+ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, x4)));
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add five log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5){
+ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, x5))));
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add siz log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5, float x6){
+ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, LOG_ADD (x5, x6)))));
+}
+
+/////////////////////////////////////////////////////////////////
+// LOG_ADD()
+//
+// Add seven log probabilities
+/////////////////////////////////////////////////////////////////
+
+inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5, float x6, float x7){
+ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, LOG_ADD (x5, LOG_ADD (x6, x7))))));
+}
+
+/////////////////////////////////////////////////////////////////
+// ChooseBestOfThree()
+//
+// Store the largest of three values x1, x2, and x3 in *x. Also
+// if xi is the largest value, then store bi in *b.
+/////////////////////////////////////////////////////////////////
+
+inline void ChooseBestOfThree (float x1, float x2, float x3, char b1, char b2, char b3, float *x, char *b){
+ if (x1 >= x2){
+ if (x1 >= x3){
+ *x = x1;
+ *b = b1;
+ return;
+ }
+ *x = x3;
+ *b = b3;
+ return;
+ }
+ if (x2 >= x3){
+ *x = x2;
+ *b = b2;
+ return;
+ }
+ *x = x3;
+ *b = b3;
+}
+
+#endif
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// Sequence.h
+//
+// Class for reading/manipulating single sequence character data.
+/////////////////////////////////////////////////////////////////
+
+#ifndef __SEQUENCE_H__
+#define __SEQUENCE_H__
+
+#include <string>
+#include <fstream>
+#include <iostream>
+#include <cctype>
+#include <cstdlib>
+#include "SafeVector.h"
+#include "FileBuffer.h"
+
+/////////////////////////////////////////////////////////////////
+// Sequence
+//
+// Class for storing sequence information.
+/////////////////////////////////////////////////////////////////
+namespace MXSCARNA {
+class Sequence {
+
+ bool isValid; // a boolean indicating whether the sequence data is valid or not
+ string header; // string containing the comment line of the FASTA file
+ SafeVector<char> *data; // pointer to character data
+ int length; // length of the sequence
+ int sequenceLabel; // integer sequence label, typically to indicate the ordering of sequences
+ // in a Multi-FASTA file
+ int inputLabel; // position of sequence in original input
+ float weight;
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::Sequence()
+ //
+ // Default constructor. Does nothing.
+ /////////////////////////////////////////////////////////////////
+
+ Sequence () : isValid (false), header (""), data (NULL), length (0), sequenceLabel (0), inputLabel (0) {}
+
+ public:
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::Sequence()
+ //
+ // Constructor. Reads the sequence from a FileBuffer.
+ /////////////////////////////////////////////////////////////////
+
+ Sequence (FileBuffer &infile, bool stripGaps = false) : isValid (false), header ("~"), data (NULL), length(0), sequenceLabel (0), inputLabel (0) {
+
+ // read until the first non-blank line
+ while (!infile.eof()){
+ infile.GetLine (header);
+ if (header.length() != 0) break;
+ }
+
+ // check to make sure that it is a correct header line
+ if (header[0] == '>'){
+
+ // if so, remove the leading ">"
+ header = header.substr (1);
+
+ // remove any leading or trailing white space in the header comment
+ while (header.length() > 0 && isspace (header[0])) header = header.substr (1);
+ while (header.length() > 0 && isspace (header[header.length() - 1])) header = header.substr(0, header.length() - 1);
+
+ // get ready to read the data[] array; note that data[0] is always '@'
+ char ch;
+ data = new SafeVector<char>; assert (data);
+ data->push_back ('@');
+
+ // get a character from the file
+ while (infile.Get(ch)){
+
+ // if we've reached a new comment line, put the character back and stop
+ if (ch == '>'){ infile.UnGet(); break; }
+
+ // skip whitespace
+ if (isspace (ch)) continue;
+
+ // substitute gap character
+ if (ch == '.') ch = '-';
+ if (stripGaps && ch == '-') continue;
+
+ // check for known characters
+ if (!((ch >= 'A' && ch <= 'Z') || (ch >= 'a' && ch <= 'z') || ch == '*' || ch == '-')){
+ cerr << "ERROR: Unknown character encountered: " << ch << endl;
+ exit (1);
+ }
+
+ // everything's ok so far, so just store this character.
+ data->push_back(ch);
+ ++length;
+ }
+
+ // sequence must contain data in order to be valid
+ isValid = length > 0;
+ if (!isValid){
+ delete data;
+ data = NULL;
+ }
+ }
+ }
+
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::Sequence()
+ //
+ // Constructor. Builds a sequence from existing data. Note
+ // that the data must use one-based indexing where data[0] should
+ // be set to '@'.
+ /////////////////////////////////////////////////////////////////
+
+ Sequence (SafeVector<char> *data, string header, int length, int sequenceLabel, int inputLabel) :
+ isValid (data != NULL), header(header), data(data), length (length), sequenceLabel (sequenceLabel), inputLabel (inputLabel) {
+ assert (data);
+ assert ((*data)[0] == '@');
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::Sequence()
+ //
+ // Destructor. Release allocated memory.
+ /////////////////////////////////////////////////////////////////
+
+ ~Sequence (){
+ if (data){
+ assert (isValid);
+ delete data;
+ data = NULL;
+ isValid = false;
+ }
+ }
+
+ void SetWeight(float myWeight) {
+ weight = myWeight;
+ }
+ float GetWeight() const {
+ return weight;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetHeader()
+ //
+ // Return the string comment associated with this sequence.
+ /////////////////////////////////////////////////////////////////
+
+ string GetHeader () const {
+ return header;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetName()
+ //
+ // Return the first word of the string comment associated with this sequence.
+ /////////////////////////////////////////////////////////////////
+
+ string GetName () const {
+ char name[1024];
+ sscanf (header.c_str(), "%s", name);
+ return string(name);
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetDataPtr()
+ //
+ // Return the iterator to data associated with this sequence.
+ /////////////////////////////////////////////////////////////////
+
+ SafeVector<char>::iterator GetDataPtr(){
+ assert (isValid);
+ assert (data);
+ return data->begin();
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetPosition()
+ //
+ // Return the character at position i. Recall that the character
+ // data is stored with one-based indexing.
+ /////////////////////////////////////////////////////////////////
+
+ char GetPosition (int i) const {
+ assert (isValid);
+ assert (data);
+ assert (i >= 0 && i <= length);
+ return (*data)[i];
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::SetLabel()
+ //
+ // Sets the sequence label to i.
+ /////////////////////////////////////////////////////////////////
+
+ void SetLabel (int i){
+ assert (isValid);
+ sequenceLabel = i;
+ inputLabel = i;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::SetSortLabel()
+ //
+ // Sets the sequence sorting label to i.
+ /////////////////////////////////////////////////////////////////
+
+ void SetSortLabel (int i){
+ assert (isValid);
+ sequenceLabel = i;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetLabel()
+ //
+ // Retrieves the input label.
+ /////////////////////////////////////////////////////////////////
+
+ int GetLabel () const {
+ assert (isValid);
+ return inputLabel;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetSortLabel()
+ //
+ // Retrieves the sorting label.
+ /////////////////////////////////////////////////////////////////
+
+ int GetSortLabel () const {
+ assert (isValid);
+ return sequenceLabel;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::Fail()
+ //
+ // Checks to see if the sequence successfully loaded.
+ /////////////////////////////////////////////////////////////////
+
+ bool Fail () const {
+ return !isValid;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::Length()
+ //
+ // Returns the length of the sequence.
+ /////////////////////////////////////////////////////////////////
+
+ int GetLength () const {
+ assert (isValid);
+ assert (data);
+ return length;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::WriteMFA()
+ //
+ // Writes the sequence to outfile in MFA format. Uses numColumns
+ // columns per line. If useIndex is set to false, then the
+ // header is printed as normal, but if useIndex is true, then
+ // ">S###" is printed where ### represents the sequence label.
+ /////////////////////////////////////////////////////////////////
+
+ void WriteMFA (ostream &outfile, int numColumns, bool useIndex = false) const {
+ assert (isValid);
+ assert (data);
+ assert (!outfile.fail());
+
+ // print out heading
+ if (useIndex)
+ outfile << ">S" << GetLabel() << endl;
+ else
+ outfile << ">" << header << endl;
+
+ // print out character data
+ int ct = 1;
+ for (; ct <= length; ct++){
+ outfile << (*data)[ct];
+ if (ct % numColumns == 0) outfile << endl;
+ }
+ if ((ct-1) % numColumns != 0) outfile << endl;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::WriteWEB()
+ //
+ // output for web interfase based on Sequence::WriteMFA()
+ /////////////////////////////////////////////////////////////////
+
+ void WriteWEB (ostream &outfile, int numColumns, bool useIndex = false) const {
+ assert (isValid);
+ assert (data);
+ assert (!outfile.fail());
+
+ outfile << "<php ref=\"" << GetLabel() << "\">" << endl;
+ outfile << "<name>" << endl;
+ // print out heading
+ if (useIndex)
+ outfile << "S" << GetLabel() << endl;
+ else
+ outfile << "" << header << endl;
+
+ outfile << "</name>" << endl;
+
+ // print out character data
+ outfile << "<sequence>" << endl;
+ int ct = 1;
+ for (; ct <= length; ct++){
+ outfile << (*data)[ct];
+ if (ct % numColumns == 0) outfile << endl;
+ }
+ if ((ct-1) % numColumns != 0) outfile << endl;
+
+ outfile << "</sequence>" << endl;
+ outfile << "</php>" << endl;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::Clone()
+ //
+ // Returns a new deep copy of the seqeuence.
+ /////////////////////////////////////////////////////////////////
+
+ Sequence *Clone () const {
+ Sequence *ret = new Sequence();
+ assert (ret);
+
+ ret->isValid = isValid;
+ ret->header = header;
+ ret->data = new SafeVector<char>; assert (ret->data);
+ *(ret->data) = *data;
+ ret->length = length;
+ ret->sequenceLabel = sequenceLabel;
+ ret->inputLabel = inputLabel;
+ ret->weight = weight;
+
+ return ret;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetRange()
+ //
+ // Returns a new sequence object consisting of a range of
+ // characters from the current seuquence.
+ /////////////////////////////////////////////////////////////////
+
+ Sequence *GetRange (int start, int end) const {
+ Sequence *ret = new Sequence();
+ assert (ret);
+
+ assert (start >= 1 && start <= length);
+ assert (end >= 1 && end <= length);
+ assert (start <= end);
+
+ ret->isValid = isValid;
+ ret->header = header;
+ ret->data = new SafeVector<char>; assert (ret->data);
+ ret->data->push_back ('@');
+ for (int i = start; i <= end; i++)
+ ret->data->push_back ((*data)[i]);
+ ret->length = end - start + 1;
+ ret->sequenceLabel = sequenceLabel;
+ ret->inputLabel = inputLabel;
+
+ return ret;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::AddGaps()
+ //
+ // Given an SafeVector<char> containing the skeleton for an
+ // alignment and the identity of the current character, this
+ // routine will create a new sequence with all necesssary gaps added.
+ // For instance,
+ // alignment = "XXXBBYYYBBYYXX"
+ // id = 'X'
+ // will perform the transformation
+ // "ATGCAGTCA" --> "ATGCC---GT--CA"
+ // (XXXBBYYYBBYYXX)
+ /////////////////////////////////////////////////////////////////
+
+ Sequence *AddGaps (SafeVector<char> *alignment, char id){
+ Sequence *ret = new Sequence();
+ assert (ret);
+
+ ret->isValid = isValid;
+ ret->header = header;
+ ret->data = new SafeVector<char>; assert (ret->data);
+ ret->length = (int) alignment->size();
+ ret->sequenceLabel = sequenceLabel;
+ ret->inputLabel = inputLabel;
+ ret->data->push_back ('@');
+
+ SafeVector<char>::iterator dataIter = data->begin() + 1;
+ for (SafeVector<char>::iterator iter = alignment->begin(); iter != alignment->end(); ++iter){
+ if (*iter == 'B' || *iter == id){
+ ret->data->push_back (*dataIter);
+ ++dataIter;
+ }
+ else
+ ret->data->push_back ('-');
+ }
+
+ return ret;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::AddGaps()
+ //
+ // Given an SafeVector<char> containing the skeleton for an
+ // alignment and the identity of the current character, this
+ // routine will create a new sequence with all necesssary gaps added.
+ // For instance,
+ // alignment = "XXXBBYYYBBYYXX"
+ // id = 'X'
+ // will perform the transformation
+ // "ATGCAGTCA" --> "ATGCC---GT--CA"
+ // (XXXBBYYYBBYYXX)
+ /////////////////////////////////////////////////////////////////
+ Sequence *AddGapsReverse (SafeVector<char> *alignment, char id){
+ Sequence *ret = new Sequence();
+ assert (ret);
+
+ ret->isValid = isValid;
+ ret->header = header;
+ ret->data = new SafeVector<char>; assert (ret->data);
+ ret->length = (int) alignment->size();
+ ret->sequenceLabel = sequenceLabel;
+ ret->inputLabel = inputLabel;
+ ret->data->push_back ('@');
+
+ SafeVector<char>::iterator dataIter = data->begin() + 1;
+ for (SafeVector<char>::reverse_iterator iter = alignment->rbegin(); iter != alignment->rend(); ++iter){
+ if (*iter == 'B' || *iter == id){
+ ret->data->push_back (*dataIter);
+ ++dataIter;
+ }
+ else
+ ret->data->push_back ('-');
+ }
+
+ return ret;
+ }
+
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetString()
+ //
+ // Returns the sequence as a string with gaps removed.
+ /////////////////////////////////////////////////////////////////
+
+ string GetString (){
+ string s = " ";
+ for (int i = 1; i <= length; i++){
+ if ((*data)[i] != '-') s += (*data)[i];
+ }
+ return s;
+ }
+
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetMapping()
+ //
+ // Returns a SafeVector<int> containing the indices of every
+ // character in the sequence. For instance, if the data is
+ // "ATGCC---GT--CA", the method returns {1,2,3,4,5,9,10,13,14}.
+ /////////////////////////////////////////////////////////////////
+
+ SafeVector<int> *GetMapping () const {
+ SafeVector<int> *ret = new SafeVector<int>(1, 0);
+ for (int i = 1; i <= length; i++){
+ if ((*data)[i] != '-') ret->push_back (i);
+ }
+ return ret;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::GetMappingNumber()
+ //
+ // Returns a SafeVector<int> containing the indices of every
+ // character in the sequence. For instance, if the data is
+ // "ATGCC---GT--CA", the method returns {1,2,3,4,5,0,0,0,6,7,0,0,8,9}.
+ /////////////////////////////////////////////////////////////////
+ SafeVector<int> *GetMappingNumber () const {
+ SafeVector<int> *ret = new SafeVector<int>(1, 0);
+ int count = 0;
+ for(int i = 1; i <= length; i++) {
+ if((*data)[i] != '-') ret->push_back(++count);
+ else ret->push_back(0);
+ }
+ return ret;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // Sequence::Highlight()
+ //
+ // Changes all positions with score >= cutoff to upper case and
+ // all positions with score < cutoff to lower case.
+ /////////////////////////////////////////////////////////////////
+
+ void Highlight (const SafeVector<float> &scores, const float cutoff){
+ for (int i = 1; i <= length; i++){
+ if (scores[i-1] >= cutoff)
+ (*data)[i] = toupper ((*data)[i]);
+ else
+ (*data)[i] = tolower ((*data)[i]);
+ }
+ }
+};
+}
+#endif // __SQUENCE_HPP__
--- /dev/null
+/////////////////////////////////////////////////////////////////
+// SparseMatrix.h
+//
+// Sparse matrix computations
+/////////////////////////////////////////////////////////////////
+
+#ifndef SPARSEMATRIX_H
+#define SPARSEMATRIX_H
+
+#include <iostream>
+#include "SafeVector.h"
+#include "nrutil.h"
+
+using namespace std;
+
+const float POSTERIOR_CUTOFF = 0.01; // minimum posterior probability
+ // value that is maintained in the
+ // sparse matrix representation
+
+typedef pair<int,float> PIF; // Sparse matrix entry type
+ // first --> column
+ // second --> value
+
+namespace MXSCARNA {
+struct PIF2 { // Sparse matrix entry type
+ int i;
+ int j;
+ float prob;
+};
+}
+
+/////////////////////////////////////////////////////////////////
+// SparseMatrix
+//
+// Class for sparse matrix computations
+/////////////////////////////////////////////////////////////////
+namespace MXSCARNA {
+class SparseMatrix {
+
+ int seq1Length, seq2Length; // dimensions of matrix
+ VI rowSize; // rowSize[i] = # of cells in row i
+ SafeVector<PIF> data; // data values
+ SafeVector<SafeVector<PIF>::iterator> rowPtrs; // pointers to the beginning of each row
+
+ public:
+ SafeVector<PIF2> data2;
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::SparseMatrix()
+ //
+ // Private constructor.1
+ /////////////////////////////////////////////////////////////////
+ SparseMatrix() { }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::SparseMatrix()
+ //
+ // Constructor. Builds a sparse matrix from a posterior matrix.
+ // Note that the expected format for the posterior matrix is as
+ // a (seq1Length+1) x (seq2Length+1) matrix where the 0th row
+ // and 0th column are ignored (they should contain all zeroes).
+ /////////////////////////////////////////////////////////////////
+
+ SparseMatrix (int seq1Length, int seq2Length, const VF &posterior) :
+ seq1Length (seq1Length), seq2Length (seq2Length) {
+
+ int numCells = 0;
+
+ assert (seq1Length > 0);
+ assert (seq2Length > 0);
+
+ // calculate memory required; count the number of cells in the
+ // posterior matrix above the threshold
+ VF::const_iterator postPtr = posterior.begin();
+ for (int i = 0; i <= seq1Length; i++){
+ for (int j = 0; j <= seq2Length; j++){
+ if (*(postPtr++) >= POSTERIOR_CUTOFF){
+ assert (i != 0 && j != 0);
+ numCells++;
+ }
+ }
+ }
+
+ // allocate memory
+ data.resize(numCells);
+ rowSize.resize (seq1Length + 1); rowSize[0] = -1;
+ rowPtrs.resize (seq1Length + 1); rowPtrs[0] = data.end();
+
+ // build sparse matrix
+ postPtr = posterior.begin() + seq2Length + 1; // note that we're skipping the first row here
+ SafeVector<PIF>::iterator dataPtr = data.begin();
+ for (int i = 1; i <= seq1Length; i++){
+ postPtr++; // and skipping the first column of each row
+ rowPtrs[i] = dataPtr;
+ for (int j = 1; j <= seq2Length; j++){
+ if (*postPtr >= POSTERIOR_CUTOFF){
+ dataPtr->first = j;
+ dataPtr->second = *postPtr;
+ dataPtr++;
+ }
+ postPtr++;
+ }
+ rowSize[i] = dataPtr - rowPtrs[i];
+ }
+ }
+
+ //////////////////////////////////////////////////////////////////////////
+ // SparseMatrix::SetSparseMatrix()
+ //
+ // Constructor.
+ //////////////////////////////////////////////////////////////////////////
+ void SetSparseMatrix(int inseq1Length, int inseq2Length, const Trimat<float> &bppMat, float cutoff = 0.01) {
+ seq1Length = inseq1Length;
+ seq2Length = inseq2Length;
+
+ int numCells = 0;
+
+ assert (seq1Length > 0);
+ assert (seq2Length > 0);
+
+ data.clear();
+ rowSize.clear();
+ rowPtrs.clear();
+ for (int i = 1; i <= seq1Length; i++) {
+ for (int j = i; j <= seq2Length; j++) {
+ if (bppMat.ref(i, j) >= cutoff ) {
+ numCells++;
+ }
+ }
+ }
+
+ // allocate memory
+ data.resize(numCells);
+ for (int i = 0; i < numCells; i++) {
+ data[i].first = 0;
+ data[i].second = 0;
+ }
+ rowSize.resize (seq1Length + 1); rowSize[0] = -1;
+ rowPtrs.resize (seq1Length + 1); rowPtrs[0] = data.end();
+
+ SafeVector<PIF>::iterator dataPtr = data.begin();
+ for (int i = 1; i <= seq1Length; i++) {
+ rowPtrs[i] = dataPtr;
+ for (int j = i; j <= seq2Length; j++) {
+ if ( bppMat.ref(i, j) >= cutoff ) {
+ dataPtr->first = j;
+ dataPtr->second = bppMat.ref(i, j);
+ dataPtr++;
+ }
+ }
+ rowSize[i] = dataPtr - rowPtrs[i];
+ }
+
+ float tmp;
+ for(int k = 1; k <= seq1Length; k++) {
+ for(int m = k, n = k; n <= k + 300 && m >= 1 && n <= seq2Length; m--, n++) {
+ if ((tmp = GetValue(m, n)) > 0) {
+ PIF2 p;
+ p.i = m;
+ p.j = n;
+ p.prob = tmp;
+ data2.push_back(p);
+ }
+ }
+
+ for(int m = k, n = k + 1; n <= k + 300 && m >= 1 && n <= seq2Length; m--, n++) {
+ if ((tmp = GetValue(m, n)) > 0) {
+ PIF2 p;
+ p.i = m;
+ p.j = n;
+ p.prob = tmp;
+ data2.push_back(p);
+ }
+ }
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::GetRowPtr()
+ //
+ // Returns the pointer to a particular row in the sparse matrix.
+ /////////////////////////////////////////////////////////////////
+
+ SafeVector<PIF>::iterator GetRowPtr (int row) const {
+ assert (row >= 1 && row <= seq1Length);
+ return rowPtrs[row];
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::GetValue()
+ //
+ // Returns value at a particular row, column.
+ /////////////////////////////////////////////////////////////////
+
+ float GetValue (int row, int col){
+ assert (row >= 1 && row <= seq1Length);
+ assert (col >= 1 && col <= seq2Length);
+ for (int i = 0; i < rowSize[row]; i++){
+ if (rowPtrs[row][i].first == col) return rowPtrs[row][i].second;
+ }
+ return 0;
+ }
+
+ void SetValue(int row, int col, float value) {
+ assert (row >= 1 && row <= seq1Length);
+ assert (col >= 1 && col <= seq2Length);
+ for (int i = 0; i < rowSize[row]; i++){
+ if (rowPtrs[row][i].first == col) rowPtrs[row][i].second = value;
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::GetRowSize()
+ //
+ // Returns the number of entries in a particular row.
+ /////////////////////////////////////////////////////////////////
+
+ int GetRowSize (int row) const {
+ assert (row >= 1 && row <= seq1Length);
+ return rowSize[row];
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::GetSeq1Length()
+ //
+ // Returns the first dimension of the matrix.
+ /////////////////////////////////////////////////////////////////
+
+ int GetSeq1Length () const {
+ return seq1Length;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::GetSeq2Length()
+ //
+ // Returns the second dimension of the matrix.
+ /////////////////////////////////////////////////////////////////
+
+ int GetSeq2Length () const {
+ return seq2Length;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::GetRowPtr
+ //
+ // Returns the pointer to a particular row in the sparse matrix.
+ /////////////////////////////////////////////////////////////////
+
+ int GetNumCells () const {
+ return data.size();
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::Print()
+ //
+ // Prints out a sparse matrix.
+ /////////////////////////////////////////////////////////////////
+
+ void Print (ostream &outfile) const {
+ outfile << "Sparse Matrix:" << endl;
+ for (int i = 1; i <= seq1Length; i++){
+ outfile << " " << i << ":";
+ for (int j = 0; j < rowSize[i]; j++){
+ outfile << " (" << rowPtrs[i][j].first << "," << rowPtrs[i][j].second << ")";
+ }
+ outfile << endl;
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::ComputeTranspose()
+ //
+ // Returns a new sparse matrix containing the transpose of the
+ // current matrix.
+ /////////////////////////////////////////////////////////////////
+
+ SparseMatrix *ComputeTranspose () const {
+
+ // create a new sparse matrix
+ SparseMatrix *ret = new SparseMatrix();
+ int numCells = data.size();
+
+ ret->seq1Length = seq2Length;
+ ret->seq2Length = seq1Length;
+
+ // allocate memory
+ ret->data.resize (numCells);
+ ret->rowSize.resize (seq2Length + 1); ret->rowSize[0] = -1;
+ ret->rowPtrs.resize (seq2Length + 1); ret->rowPtrs[0] = ret->data.end();
+
+ // compute row sizes
+ for (int i = 1; i <= seq2Length; i++) ret->rowSize[i] = 0;
+ for (int i = 0; i < numCells; i++)
+ ret->rowSize[data[i].first]++;
+
+ // compute row ptrs
+ for (int i = 1; i <= seq2Length; i++){
+ ret->rowPtrs[i] = (i == 1) ? ret->data.begin() : ret->rowPtrs[i-1] + ret->rowSize[i-1];
+ }
+
+ // now fill in data
+ SafeVector<SafeVector<PIF>::iterator> currPtrs = ret->rowPtrs;
+
+ for (int i = 1; i <= seq1Length; i++){
+ SafeVector<PIF>::iterator row = rowPtrs[i];
+ for (int j = 0; j < rowSize[i]; j++){
+ currPtrs[row[j].first]->first = i;
+ currPtrs[row[j].first]->second = row[j].second;
+ currPtrs[row[j].first]++;
+ }
+ }
+
+ return ret;
+ }
+
+ /////////////////////////////////////////////////////////////////
+ // SparseMatrix::GetPosterior()
+ //
+ // Return the posterior representation of the sparse matrix.
+ /////////////////////////////////////////////////////////////////
+
+ VF *GetPosterior () const {
+
+ // create a new posterior matrix
+ VF *posteriorPtr = new VF((seq1Length+1) * (seq2Length+1)); assert (posteriorPtr);
+ VF &posterior = *posteriorPtr;
+
+ // build the posterior matrix
+ for (int i = 0; i < (seq1Length+1) * (seq2Length+1); i++) posterior[i] = 0;
+ for (int i = 1; i <= seq1Length; i++){
+ VF::iterator postPtr = posterior.begin() + i * (seq2Length+1);
+ for (int j = 0; j < rowSize[i]; j++){
+ postPtr[rowPtrs[i][j].first] = rowPtrs[i][j].second;
+ }
+ }
+
+ return posteriorPtr;
+ }
+
+};
+}
+#endif
--- /dev/null
+0.96 0.02 0.02
+0.01 0.01
+0.4 0.4
+ACGUTN
+0.148724
+0.0184143 0.158392
+0.0361397 0.0275537 0.197932
+0.0238474 0.0389291 0.0244289 0.155748
+0.0238474 0.0389291 0.0244289 0.155748 0.155748
+3.75308e-05 8.15823e-05 8.24765e-05 7.43985e-05 7.43985e-05 2.63252e-05
+0.227079 0.242208 0.283932 0.246468 0.246468 0.000312465
--- /dev/null
+./probcons -p mlparams0 -t params1 ../bralibase/*
+./probcons -p params1 -t params2 ../bralibase/*
+./probcons -p params2 -t params3 ../bralibase/*
+./probcons -p params3 -t params4 ../bralibase/*
+./probcons -p params4 -t params5 ../bralibase/*
+./probcons -p params5 -t params6 ../bralibase/*
+./probcons -p params6 -t params7 ../bralibase/*
+./probcons -p params7 -t params8 ../bralibase/*
+./probcons -p params8 -t params9 ../bralibase/*
+./probcons -p params9 -t params10 ../bralibase/*
+./probcons -p params10 -t params11 ../bralibase/*
+./probcons -p params11 -t params12 ../bralibase/*
+./probcons -p params12 -t params13 ../bralibase/*
+./probcons -p params13 -t params14 ../bralibase/*
+./probcons -p params14 -t params15 ../bralibase/*
+./probcons -p params15 -t params16 ../bralibase/*
+./probcons -p params16 -t params17 ../bralibase/*
+./probcons -p params17 -t params18 ../bralibase/*
+./probcons -p params18 -t params19 ../bralibase/*
+./probcons -p params19 -t params20 ../bralibase/*
+./probcons -p params20 -t params21 ../bralibase/*
+./probcons -p params21 -t params22 ../bralibase/*
+./probcons -p params22 -t params23 ../bralibase/*
+./probcons -p params23 -t params24 ../bralibase/*
+./probcons -p params24 -t params25 ../bralibase/*
+./probcons -p params25 -t params26 ../bralibase/*
+./probcons -p params26 -t params27 ../bralibase/*
+./probcons -p params27 -t params28 ../bralibase/*
+./probcons -p params28 -t params29 ../bralibase/*
+./probcons -p params29 -t params30 ../bralibase/*
--- /dev/null
+
+#ifndef __SCARNA_HPP__
+#define __SCARNA_HPP__
+
+#include <iostream>
+using namespace std;
+
+#define WORDLENGTH 2 /* default word length in stem candidates (SCs) */
+
+#define THR 0.01
+
+// the parameter trained by maximazing the sps of tRNA
+//#define MULTISCORE 9.870619 //multiple score with the constant.
+//#define MULTIRIBOSUM 0.452626 //multiple ribosum_score with the constant
+//#define MULTIPENALTY 24.263776 //multiple penalty with the constatnt
+//#define MULTISTACKING 45.208927 //multiple stacking energy with the constatnt
+
+/*
+#define MULTIRIBOSUM 1
+#define MULTIPENALTY 3.1
+#define MULTISCORE 3.7
+#define MULTISTACKING 0.1
+#define MULTIDELTASCORE 9.4
+#define MULTIDELTASTACKING 8.6
+*/
+/*
+#define MULTIRIBOSUM 1
+#define MULTIPENALTY 1.1162
+#define MULTISCORE 0.53299
+#define MULTISTACKING 4.25669
+#define MULTIDELTASCORE 1.17805
+#define MULTIDELTASTACKING 4.2016
+*/
+// new CRF DATA 550 sigma 1
+
+#define MULTIRIBOSUM 1
+#define MULTIPENALTY 1.82294
+#define MULTISCORE 0.250631
+#define MULTISTACKING 2.35517
+#define MULTIDELTASCORE 1.1781
+#define MULTIDELTASTACKING 2.45417
+
+/*
+#define MULTIRIBOSUM 1
+#define MULTIPENALTY 0.478054
+#define MULTISCORE 1.36322
+#define MULTISTACKING 4.96635
+#define MULTIDELTASCORE 1.14239
+#define MULTIDELTASTACKING 7.32992
+*/
+// CRF DATA 900 sigma 1
+/*
+#define MULTIRIBOSUM 1
+#define MULTIPENALTY 2.28364
+#define MULTISCORE 0.00945681
+#define MULTISTACKING 2.25357
+#define MULTIDELTASCORE 1.02201
+#define MULTIDELTASTACKING 2.21293
+*/
+
+/*
+#define RNAMATCHAA 506159
+#define RNAMATCHAT 359916
+#define RNAMATCHAG 451319
+#define RNAMATCHAC 390720
+#define RNAMATCHTT 398658
+#define RNAMATCHTG 377069
+#define RNAMATCHTC 378456
+#define RNAMATCHGG 554695
+#define RNAMATCHGC 419950
+#define RNAMATCHCC 479030
+#define GAPPENALTY 190947
+#define GAPEXTENTIONPENALTY -118817
+*/
+// RIBOSUM
+#define RNAMATCHAA 2.22
+#define RNAMATCHAT -1.39
+#define RNAMATCHAG -1.46
+#define RNAMATCHAC -1.86
+#define RNAMATCHTT 1.65
+#define RNAMATCHTG -1.74
+#define RNAMATCHTC -1.05
+#define RNAMATCHGG 1.03
+#define RNAMATCHGC -2.48
+#define RNAMATCHCC 1.16
+//#define GAPPENALTY 9.42 // 3default linear gap penalry in RNA sequence alignment
+//#define GAPPENALTY 9.18743
+//#define GAPPENALTY 5.00
+//#define GAPEXTENTIONPENALTY 7.15
+//#define GAPEXTENTIONPENALTY 9.62003
+
+#define GAPPENALTY 5
+#define GAPEXTENTIONPENALTY 2.5
+//#define GAPPENALTY 8.08875
+//#define GAPEXTENTIONPENALTY 3.89655
+
+#define REFINEMENTREPS 0
+#define SCSLENGTH 2
+#define BASEPROBTHRESHOLD 0.01
+#define BASEPAIRCONST 6
+#define BANDWIDTH 500
+#define USERFOLD false
+
+extern float RNA_Match_AA;
+extern float RNA_Match_AT;
+extern float RNA_Match_AG;
+extern float RNA_Match_AC;
+extern float RNA_Match_TT;
+extern float RNA_Match_TG;
+extern float RNA_Match_TC;
+extern float RNA_Match_GG;
+extern float RNA_Match_GC;
+extern float RNA_Match_CC;
+extern float RNA_Gap_Penalty;
+extern float RNA_Gap_Extension;
+
+extern int numIterativeRefinementReps;
+extern bool PostProcessAlignment;
+extern int scsLength;
+extern float BaseProbThreshold;
+extern float BasePairConst;
+
+#endif /*__SCARNA_HPP__*/
+
--- /dev/null
+///////////////////////////////////////////////////////////////
+// seq2scs.cpp
+//
+// make SCS(Stem Candidate Sequence) from the profile
+//////////////////////////////////////////////////////////////
+
+#include "scarna.hpp"
+#include "SafeVector.h"
+#include "StemCandidate.hpp"
+#include "Sequence.h"
+#include "MultiSequence.h"
+#include "BPPMatrix.hpp"
+#include "nrutil.h"
+#include <vector>
+#include <algorithm>
+#include <stdio.h>
+#include <cstring>
+#include <stdio.h>
+#include <math.h>
+
+using namespace std;
+using namespace::MXSCARNA;
+
+// for alipfold
+/*
+#include "utils.h"
+#include "fold_vars.h"
+#include "fold.h"
+#include "part_func.h"
+#include "inverse.h"
+#include "RNAstruct.h"
+#include "treedist.h"
+#include "stringdist.h"
+#include "profiledist.h"
+#include "alifold.h"
+#include "aln_util.h"
+#include "dist_vars.h"
+*/
+double Stacking_Energy[36] ={
+ -0.9,-2.1,-1.7,-0.5,-0.9,-1.0,
+ -1.8,-2.9,-2.0,-1.2,-1.7,-1.9,
+ -2.3,-3.4,-2.9,-1.4,-2.1,-2.1,
+ -1.1,-2.1,-1.9,-0.4,-1.0,1.5,
+ -1.1,-2.3,-1.8,-0.8,-0.9,-1.1,
+ -0.8,-1.4,-1.2,-0.2,-0.5,-0.4 };
+
+static Trimat<float>* makeProfileBPPMatrix(MultiSequence *Sequences, SafeVector<BPPMatrix*> &BPPMatrices);
+static int countSCS(MultiSequence *Sequences, Trimat<float>* consBppMat, int BandWidth);
+static std::vector<StemCandidate>* makeProfileScs(std::vector<StemCandidate> *pscs, MultiSequence *Sequences, Trimat<float>* consBppMat, int BandWidth);
+static void printScs(std::vector<StemCandidate> *pscs);
+static std::vector<StemCandidate>* doubleScs(std::vector<StemCandidate> *pscs);
+static std::vector<StemCandidate>* findRelations(std::vector<StemCandidate> *pscs);
+static std::vector<StemCandidate>* findCorresponding(std::vector<StemCandidate>* pscs);
+static std::vector<StemCandidate>* calculateStackingEnergy(std::vector<StemCandidate>* pscs);
+
+//float alipf_fold(char **sequences, char *structure, pair_info **pi);
+
+struct SortCmp {
+ bool operator()(const StemCandidate &sc1, const StemCandidate &sc2) const {
+ if (sc1.GetPosition() > sc2.GetPosition()) return false;
+ else if (sc1.GetPosition() < sc2.GetPosition()) return true;
+ else if (sc1.GetDistance() > sc2.GetDistance()) return false;
+ else return true;
+ }
+};
+
+
+vector<StemCandidate>*
+seq2scs(MultiSequence *Sequences, SafeVector<BPPMatrix*> &BPPMatrices, int BandWidth)
+{
+
+ Trimat<float> *consBppMat = makeProfileBPPMatrix(Sequences, BPPMatrices);
+
+ int numberScs = countSCS(Sequences, consBppMat, BandWidth);
+
+ std::vector<StemCandidate> *pscs = new std::vector<StemCandidate>(); // Profile Stem Candidate Sequence
+// cout << "numberScs=" << numberScs << endl;
+ pscs->resize(numberScs+1);
+
+ pscs = makeProfileScs(pscs, Sequences, consBppMat, BandWidth);
+
+ pscs = doubleScs(pscs);
+
+ std::vector<StemCandidate>::iterator startIter = pscs->begin();
+ std::vector<StemCandidate>::iterator endIter = pscs->end();
+ ++startIter;
+ std::sort(startIter, endIter, SortCmp());
+
+// printScs(pscs);
+ pscs = findRelations(pscs);
+
+ pscs = findCorresponding(pscs);
+
+ pscs = calculateStackingEnergy(pscs);
+
+// findStemRelation()
+
+// exit(1);
+ delete consBppMat;
+
+ return pscs;
+}
+
+static Trimat<float>*
+makeProfileBPPMatrix(MultiSequence *Sequences, SafeVector<BPPMatrix*> &BPPMatrices)
+{
+ int length = Sequences->GetSequence(0)->GetLength();
+// float thr = BaseProbThreshold;
+ Trimat<float> *consBppMat = new Trimat<float>(length + 1);
+ fill(consBppMat->begin(), consBppMat->end(), 0);
+
+// gabage
+// for(int i = 0; i <= length; i++)
+// for(int j = i; j <= length; j++)
+// cout << "i=" << i << " j=" << j << " " << consBppMat->ref(i,j) << endl;
+// consBppMat->ref(i,j) = 0;
+
+
+ int number = Sequences->GetNumSequences();
+// if( number == 1) {
+ for(int seqNum = 0; seqNum < number; seqNum++) {
+ SafeVector<int> *tmpMap = Sequences->GetSequence(seqNum)->GetMappingNumber();
+ int label = Sequences->GetSequence(seqNum)->GetLabel();
+ BPPMatrix *tmpBppMatrix = BPPMatrices[label];
+
+ for(int i = 1; i <= length ; i++) {
+ int originI = tmpMap->at(i);
+ for(int j = i + 3; j <= length; j++) {
+ int originJ = tmpMap->at(j);
+ if(originI != 0 && originJ != 0) {
+ float tmpProb = tmpBppMatrix->GetProb(originI, originJ);
+
+// if(tmpProb >= thr) {
+ consBppMat->ref(i, j) += tmpProb;
+// cout << i << " " << j << " " << consBppMat->ref(i,j) << endl;
+// }
+ }
+ }
+ }
+ }
+
+ /* compute the mean of base pairing probability */
+ for(int i = 1; i <= length; i++) {
+ for(int j = i + 3; j <= length; j++) {
+ consBppMat->ref(i,j) = consBppMat->ref(i,j)/(float)number;
+ //consBppMat->ref(i,j) = std::sqrt[number](consBppMat->ref(i,j));
+ // cout << i << " " << j << " " << consBppMat->ref(i,j) << endl;
+ }
+ }
+
+
+/*
+ else {
+ char **Seqs;
+ Seqs = (char **) malloc(sizeof(char*) * number);
+
+ for(int i = 0; i < number; i++) {
+ Seqs[i] = (char *) malloc(sizeof(char) * (length + 1));
+ for(int j = 1; j <= length; j++) {
+ Seqs[i][j-1] = Sequences->GetSequence(i)->GetPosition(j);
+ }
+ Seqs[i][length] = '\0';
+ }
+
+
+ char *structure = NULL;
+ pair_info *pi;
+
+ alipf_fold(Seqs, structure, &pi, number);
+
+ for(int iter = 0; iter < length; iter++) {
+ if(pi[iter].i == 0) break;
+ consBppMat->ref(pi[iter].i, pi[iter].j) = pi[iter].p;
+ }
+
+ for(int i = 0; i < number; i++) {
+ free (Seqs[i]);
+ }
+ free (Seqs);
+
+// free_alifold_arrays(void);
+ }
+*/
+
+ return consBppMat;
+}
+
+static int
+countSCS(MultiSequence *Sequences, Trimat<float> *consBppMat, int BandWidth)
+{
+
+ int length = Sequences->GetSequence(0)->GetLength();
+ int Word_Length = scsLength;
+
+ int i, j, k, s;
+ int count;
+ int sum;
+
+ sum = 0;
+ for(k = 1; k <= length; k++) {
+ count = 0;
+
+ for(i = k, j = k; i >= 1 && j <= (k + BandWidth - 1) && j <= length; i--, j++) {
+ if(consBppMat->ref(i, j) >= BaseProbThreshold) {
+ count++;
+ }
+ else if(count >= Word_Length) {
+ for(s = 0; s <= count - Word_Length; s++)
+ sum++;
+
+ count = 0;
+ }
+ else {
+ count = 0;
+ }
+ if(consBppMat->ref(i, j) >= BaseProbThreshold && count >= Word_Length && (i == 1 || j == length || j == (k + BandWidth - 1))) {
+ for(s = 0; s <= count - Word_Length; s++)
+ sum++;
+
+ count = 0;
+ }
+ }
+
+ count = 0;
+ for(i = k, j = k + 1; i >= 1 && j <= (k + BandWidth - 1) && j <= length; i--, j++) {
+ if(consBppMat->ref(i, j) >= BaseProbThreshold) {
+ count++;
+ }
+ else if(count >= Word_Length) {
+ for(s = 0; s <= count - Word_Length; s++) sum++;
+
+ count = 0;
+ }
+ else {
+ count = 0;
+ }
+
+ if(consBppMat->ref(i, j) >= BaseProbThreshold && count >= Word_Length && (i == 1 || j == length || j == (k + BandWidth - 1))) {
+ for(s = 0; s <= count - Word_Length; s++) sum++;
+
+ count = 0;
+ }
+ }
+ }
+
+ return 2 * sum;
+}
+
+static std::vector<StemCandidate>*
+makeProfileScs(std::vector<StemCandidate> *pscs, MultiSequence *Sequences, Trimat<float>* consBppMat, int BandWidth)
+{
+
+ int length = Sequences->GetSequence(0)->GetLength();
+ int Word_Length = scsLength;
+ float Thr = BaseProbThreshold;
+ int i, j, k, s, t, m, n, l;
+ int count;
+ int sum;
+
+ sum = 0;
+ for(k = 1; k <= length; k++) {
+ count = 0;
+ for(i = k, j = k; i >= 1 && j <= (k + BandWidth - 1) && j <= length; i--, j++) {
+ if(consBppMat->ref(i,j) >= Thr) {
+ count++;
+ }
+ else if(count >= Word_Length) {
+ for(s = 0; s <= count- Word_Length; s++) {
+ sum++;
+ pscs->at(sum).SetLength(Word_Length);
+ pscs->at(sum).SetPosition(i+1+s);
+ pscs->at(sum).SetRvposition(j-count+(count-Word_Length-s));
+ pscs->at(sum).SetDistance((j-count+count-Word_Length-s) - (i+1+s+Word_Length));
+ pscs->at(sum).SetNumSeq(Sequences->GetNumSequences());
+ pscs->at(sum).SetNumSubstr(Sequences->GetNumSequences());
+ pscs->at(sum).SetNumRvstr(Sequences->GetNumSequences());
+ for(m = i + 1 + s, n = j - count + (count-Word_Length-s), l = j - 1 - s, t = 0; n < j-s; m++, n++, l--, t++) {
+ for(int num = 0; num < Sequences->GetNumSequences(); num++) {
+ Sequence *seq = Sequences->GetSequence(num);
+// cout << num << "; " << m << ":" << seq->GetPosition(m) << " " << n << ":" << seq->GetPosition(n) << endl;
+ pscs->at(sum).AddSubstr(num, seq->GetPosition(m));
+ pscs->at(sum).AddRvstr(num, seq->GetPosition(n));
+ }
+ // assert(pr[iindx[m]-l] > Thr);
+// cout << "prob=" << consBppMat->ref(m,l) << endl;
+ pscs->at(sum).AddScore(consBppMat->ref(m,l));
+ pscs->at(sum).AddBaseScore(consBppMat->ref(m, l));
+ }
+ for(int num = 0; num < Sequences->GetNumSequences(); num++) {
+ pscs->at(sum).AddSubstr(num, '\0');
+ pscs->at(sum).AddRvstr(num, '\0');
+ }
+ }
+ count = 0;
+ }
+ else {
+ count = 0;
+ }
+ if(consBppMat->ref(i,j) >= Thr && count >= Word_Length && (i == 1 || j == length || j == (k + BandWidth - 1))) {
+ for(s = 0; s <= count- Word_Length; s++) {
+ sum++;
+ pscs->at(sum).SetLength(Word_Length);
+ pscs->at(sum).SetPosition(i+s);
+ pscs->at(sum).SetRvposition(j-count+1+(count-Word_Length-s));
+ pscs->at(sum).SetDistance((j-count+1+count-Word_Length-s) - (i+s+Word_Length));
+ pscs->at(sum).SetNumSeq(Sequences->GetNumSequences());
+ pscs->at(sum).SetNumSubstr(Sequences->GetNumSequences());
+ pscs->at(sum).SetNumRvstr(Sequences->GetNumSequences());
+ for(m = i + s, n = j - count + 1 + (count-Word_Length-s), l = j - s, t = 0; n <= j-s; m++, n++, l--, t++) {
+ for(int num = 0; num < Sequences->GetNumSequences(); num++) {
+ Sequence *seq = Sequences->GetSequence(num);
+ pscs->at(sum).AddSubstr(num, seq->GetPosition(m));
+ pscs->at(sum).AddRvstr(num, seq->GetPosition(n));
+ }
+
+ pscs->at(sum).AddScore(consBppMat->ref(m,l));
+ pscs->at(sum).AddBaseScore(consBppMat->ref(m, l));
+ }
+ for(int num = 0; num < Sequences->GetNumSequences(); num++) {
+ pscs->at(sum).AddSubstr(num, '\0');
+ pscs->at(sum).AddRvstr(num, '\0');
+ }
+ }
+ count = 0;
+ }
+ }
+ count = 0;
+ for(i = k, j = k + 1; i >= 1 && j <= (k + BandWidth - 1) && j <= length; i--, j++) {
+ if(consBppMat->ref(i,j) >= Thr) {
+ count++;
+ }
+ else if(count >= Word_Length) {
+ for(s = 0; s <= count- Word_Length; s++) {
+ sum++;
+ pscs->at(sum).SetLength(Word_Length);
+ pscs->at(sum).SetPosition(i+1+s);
+ pscs->at(sum).SetRvposition( j-count+(count-Word_Length-s));
+ pscs->at(sum).SetDistance((j-count+count-Word_Length-s) - (i+1+s+Word_Length));
+ pscs->at(sum).SetNumSeq(Sequences->GetNumSequences());
+ pscs->at(sum).SetNumSubstr(Sequences->GetNumSequences());
+ pscs->at(sum).SetNumRvstr(Sequences->GetNumSequences());
+ for(m = i + 1 + s, n = j - count + (count-Word_Length-s), l = j - 1 - s, t = 0; n < j-s; m++, n++, l--, t++) {
+ for(int num = 0; num < Sequences->GetNumSequences(); num++) {
+ Sequence *seq = Sequences->GetSequence(num);
+ pscs->at(sum).AddSubstr(num, seq->GetPosition(m));
+ pscs->at(sum).AddRvstr(num, seq->GetPosition(n));
+ }
+
+ pscs->at(sum).AddScore(consBppMat->ref(m,l));
+ pscs->at(sum).AddBaseScore(consBppMat->ref(m, l));
+ }
+ for(int num = 0; num < Sequences->GetNumSequences(); num++) {
+ pscs->at(sum).AddSubstr(num, '\0');
+ pscs->at(sum).AddRvstr(num, '\0');
+ }
+ }
+ count = 0;
+ }
+ else {
+ count = 0;
+ }
+ if(consBppMat->ref(i,j) >= Thr && count >= Word_Length && (i == 1 || j == length || j == (k + BandWidth - 1))) {
+ for(s = 0; s <= count - Word_Length; s++) {
+ sum++;
+ pscs->at(sum).SetLength(Word_Length);
+ pscs->at(sum).SetPosition(i+s);
+ pscs->at(sum).SetRvposition(j-count+1+(count-Word_Length-s));
+ pscs->at(sum).SetDistance((j-count+1+count-Word_Length-s) - (i+s+Word_Length));
+// pscs->at(sum).SetDistance((j-count+count-Word_Length-s) - (i+1+s+Word_Length));
+ pscs->at(sum).SetNumSeq(Sequences->GetNumSequences());
+ pscs->at(sum).SetNumSubstr(Sequences->GetNumSequences());
+ pscs->at(sum).SetNumRvstr(Sequences->GetNumSequences());
+ for(m = i + s, n = j - count + 1 + (count-Word_Length-s), l = j - s, t=0; n <= j-s; m++, n++, l--, t++) {
+ for(int num = 0; num < Sequences->GetNumSequences(); num++) {
+ Sequence *seq = Sequences->GetSequence(num);
+ pscs->at(sum).AddSubstr(num, seq->GetPosition(m));
+ pscs->at(sum).AddRvstr(num, seq->GetPosition(n));
+ }
+
+ pscs->at(sum).AddScore(consBppMat->ref(m,l));
+ pscs->at(sum).AddBaseScore(consBppMat->ref(m, l));
+ }
+ for(int num = 0; num < Sequences->GetNumSequences(); num++) {
+ pscs->at(sum).AddSubstr(num, '\0');
+ pscs->at(sum).AddRvstr(num, '\0');
+ }
+ }
+ count = 0;
+ }
+ }
+ }
+
+ return pscs;
+}
+
+static std::vector<StemCandidate>*
+doubleScs(std::vector<StemCandidate> *pscs)
+{
+ int num = pscs->size()/2;
+
+ for(int i = 1; i <= num; i++) {
+ int latter = num + i;
+ //cout << i << " " << latter << endl;
+ StemCandidate &tmpScs = pscs->at(i);
+ pscs->at(latter).SetLength(tmpScs.GetLength());
+ pscs->at(latter).SetPosition(tmpScs.GetRvposition());
+ pscs->at(latter).SetRvposition(tmpScs.GetPosition());
+ pscs->at(latter).SetDistance(-tmpScs.GetDistance());
+ pscs->at(latter).SetNumSeq(tmpScs.GetNumSeq());
+ pscs->at(latter).SetNumSubstr(tmpScs.GetNumSeq());
+ pscs->at(latter).SetNumRvstr(tmpScs.GetNumSeq());
+
+ pscs->at(latter).SetScore(tmpScs.GetScore());
+ for(int num = 0; num < tmpScs.GetNumSeq(); num++) {
+ string tmpSubstr = tmpScs.GetSubstr(num);
+ string tmpRvstr = tmpScs.GetRvstr(num);
+
+ for(int k = 0; k < tmpScs.GetLength(); k++) {
+ pscs->at(latter).AddSubstr(num, tmpSubstr[k]);
+ pscs->at(latter).AddRvstr(num, tmpRvstr[k]);
+ }
+ }
+ for(int k = 0; k < tmpScs.GetLength(); k++) {
+ pscs->at(latter).AddBaseScore(tmpScs.GetBaseScore(k));
+ }
+ }
+ return pscs;
+}
+
+
+static void
+printScs(std::vector<StemCandidate> *pscs)
+{
+ int num = pscs->size();
+// std::cout << "size = " << num << endl;
+ for(int i = 1; i < num; i++) {
+ StemCandidate &sc = pscs->at(i);
+
+ std::cout << i << "\t" << sc.GetLength() << "\t" << sc.GetPosition() << "\t" <<
+ sc.GetRvposition() << "\t" << sc.GetDistance() << "\t" << sc.GetNumSeq() <<
+ "\t" << sc.GetScore() << "\t" << sc.GetContPos() << "\t" << sc.GetBeforePos() <<
+ "\t" << sc.GetRvscnumber() << "\t" << sc.GetStacking() << "\t" << sc.GetStemStacking() <<
+ "\t" << sc.GetBaseScore(0) << "\t" << sc.GetBaseScore(1) << endl;
+ cout << "substr:" << endl;
+ for(int k = 0; k < sc.GetNumSeq(); k++) {
+ cout << k << "\t" << sc.GetSubstr(k) << "\t" << sc.GetRvstr(k) << "\t" << endl;
+ }
+
+ }
+
+}
+
+static std::vector<StemCandidate>*
+findRelations(std::vector<StemCandidate> *pscs)
+{
+ int num = pscs->size();
+
+ for(int i = 1; i < num; i++) {
+ int pt = i-1;
+ StemCandidate &sc = pscs->at(i);
+ sc.SetContPos(-1);
+ while(sc.GetPosition() == pscs->at(pt).GetPosition()) { pt--; }
+
+ while((sc.GetPosition() == pscs->at(pt).GetPosition() + 1) && (pt > 0)) {
+ if(sc.GetRvposition() == pscs->at(pt).GetRvposition() - 1) {
+ sc.SetContPos(pt);
+ break;
+ }
+ --pt;
+ }
+ while((sc.GetPosition() < pscs->at(pt).GetPosition() + pscs->at(pt).GetLength())&&(pt > 0)) { pt--; }
+ sc.SetBeforePos(pt);
+ }
+
+ return pscs;
+}
+
+static std::vector<StemCandidate>*
+findCorresponding(std::vector<StemCandidate>* pscs)
+{
+ int num = pscs->size();
+
+ for(int i = 1; i < num; i++) { pscs->at(i).SetRvscnumber(0); }
+
+ for(int i = 1; i < num; i++) {
+ if(pscs->at(i).GetDistance() > 0) {
+ for(int j = i + 1; j < num; j++) {
+ if ( (pscs->at(j).GetPosition() == pscs->at(i).GetRvposition())
+ && (pscs->at(i).GetPosition() == pscs->at(j).GetRvposition()) ) {
+ pscs->at(i).SetRvscnumber(j);
+ pscs->at(j).SetRvscnumber(i);
+ break;
+ }
+ }
+ }
+ if(pscs->at(i).GetRvscnumber() == 0) {
+ std::cerr << "error in findCorresponding" << " i=" << i << endl;
+// exit(1);
+ }
+ }
+
+ return pscs;
+}
+
+static std::vector<StemCandidate>*
+calculateStackingEnergy(std::vector<StemCandidate>* pscs)
+{
+ int num = pscs->size();
+ int wordLength = scsLength;
+
+ for(int i = 1; i < num; i++) {
+ StemCandidate &scI = pscs->at(i);
+ int j = pscs->at(i).GetContPos();
+
+ if(j > 0) {
+
+ StemCandidate &scJ = pscs->at(j);
+ float stacking = 0;
+ int profNum = scJ.GetNumSeq();
+ for(int k = 0; k < profNum; k++) {
+ string substr = scJ.GetSubstr(k);
+ string rvstr = scJ.GetRvstr(k);
+ int index = 0;
+ switch(substr[wordLength - 1]) {
+ case 'A': if( rvstr[0]=='U' ) {index += 0;}
+ else{ index = -1000; }
+ break;
+ case 'C': if( rvstr[0]=='G' ) {index += 6;}
+ else{ index = -1000; }
+ break;
+ case 'G': if( rvstr[0]=='C'){index += 12;}
+ else if(rvstr[0]=='U'){index += 18;}
+ else{ index = -1000; }
+ break;
+ case 'U': if( rvstr[0]=='A'){index += 24;}
+ else if(rvstr[0]=='G'){index += 30;}
+ else{ index = - 1000; }
+ break;
+ }
+ substr = scI.GetSubstr(k);
+ rvstr = scI.GetRvstr(k);
+ switch(substr[wordLength - 1]){
+ case 'A': if( rvstr[0]=='U'){index += 0;}
+ else{ index = -1000; }
+ break;
+ case 'C': if( rvstr[0]=='G'){index += 1;}
+ else{ index = -1000; }
+ break;
+ case 'G': if( rvstr[0]=='C'){index += 2;}
+ else if(rvstr[0]=='U'){index += 3;}
+ else{ index = -1000; }
+ break;
+ case 'U': if( rvstr[0]=='A'){index += 4;}
+ else if(rvstr[0]=='G'){index += 5;}
+ else{ index = -1000; }
+ break;
+ }
+ if(index > 0) {
+ stacking += Stacking_Energy[index];
+ }
+ }
+ scI.SetStacking(stacking/(float)profNum);
+ }
+ else {
+ scI.SetStacking(1000);
+ }
+ }
+
+ for(int i = 1; i < num; i++) {
+ StemCandidate &sc = pscs->at(i);
+ float stemStacking = 0;
+ int profNum = sc.GetNumSeq();
+ for(int k = 0; k < profNum; k++) {
+ string substr = sc.GetSubstr(k);
+ string rvstr = sc.GetRvstr(k);
+ for(int j = 0; j < wordLength-1; j++) {
+ int index = 0;
+
+ switch(substr[j]) {
+ case 'A': if( rvstr[wordLength-1-j]=='U'){index += 0;}
+ else{ index = -1000; }
+ break;
+ case 'C': if( rvstr[wordLength-1-j]=='G'){index += 6;}
+ else{ index = -1000; }
+ break;
+ case 'G': if( rvstr[wordLength-1-j]=='C'){index += 12;}
+ else if(rvstr[wordLength-1-j]=='U'){index += 18;}
+ else{ index = -1000; }
+ break;
+ case 'U': if( rvstr[wordLength-1-j]=='A'){index += 24;}
+ else if(rvstr[wordLength-1-j]=='G'){index += 30;}
+ else{ index = -1000; }
+ break;
+ }
+ switch(substr[j+1]){
+ case 'A': if( rvstr[wordLength-1-(j+1)]=='U'){index += 0;}
+ else{ index = -1000; }
+ break;
+ case 'C': if( rvstr[wordLength-1-(j+1)]=='G'){index += 1;}
+ else{ index = -1000; }
+ break;
+ case 'G': if( rvstr[wordLength-1-(j+1)]=='C'){index += 2;}
+ else if(rvstr[wordLength-1-(j+1)]=='U'){index += 3;}
+ else{ index = -1000; }
+ break;
+ case 'U': if( rvstr[wordLength-1-(j+1)]=='A'){index += 4;}
+ else if(rvstr[wordLength-1-(j+1)]=='G'){index += 5;}
+ else{ index = -1000; }
+ break;
+ }
+ if(index > 0) {
+ stemStacking += Stacking_Energy[index];
+ }
+ }
+ sc.SetStemStacking(stemStacking/(float)profNum);
+ }
+ }
+ return pscs;
+}
+
--- /dev/null
+ Disclaimer and Copyright
+
+The programs, library and source code of the Vienna RNA Package are free
+software. They are distributed in the hope that they will be useful
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+Permission is granted for research, educational, and commercial use
+and modification so long as 1) the package and any derived works are not
+redistributed for any fee, other than media costs, 2) proper credit is
+given to the authors and the Institute for Theoretical Chemistry of the
+University of Vienna.
+
+If you want to include this software in a commercial product, please contact
+the authors.
\ No newline at end of file
--- /dev/null
+/*
+
+ energy constants, formerly defined in
+ energy_par.h
+
+ customized for use with RNAedit by
+ S.Kopp, IMB-Jena, Germany, Mar 1996
+
+*/
+
+#ifndef _ENERGY_CONST_H
+#define _ENERGY_CONST_H 1
+
+#define GASCONST 1.98717 /* in [cal/K] */
+#define K0 273.15
+#define INF 1000000
+#define FORBIDDEN 9999
+#define BONUS 10000
+#define NBPAIRS 7
+#define TURN 3
+#define MAXLOOP 30
+
+#endif
--- /dev/null
+/*
+ prototypes for energy_par.c
+*/
+
+#include "energy_const.h"
+namespace MXSCARNA {
+extern double lxc37; /* parameter for logarithmic loop
+ energy extrapolation */
+
+extern int stack37[NBPAIRS+1][NBPAIRS+1];
+extern int enthalpies[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */
+extern int entropies[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */
+
+extern int hairpin37[31];
+extern int bulge37[31];
+extern int internal_loop37[31];
+extern int internal2_energy;
+extern int old_mismatch_37[NBPAIRS+1][5][5];
+extern int mismatchI37[NBPAIRS+1][5][5]; /* interior loop mismatches */
+extern int mismatchH37[NBPAIRS+1][5][5]; /* same for hairpins */
+extern int mismatchM37[NBPAIRS+1][5][5]; /* same for multiloops */
+extern int mism_H[NBPAIRS+1][5][5]; /* mismatch enthalpies */
+
+extern int dangle5_37[NBPAIRS+1][5]; /* 5' dangle exterior of pair */
+extern int dangle3_37[NBPAIRS+1][5]; /* 3' dangle */
+extern int dangle3_H[NBPAIRS+1][5]; /* corresponding enthalpies */
+extern int dangle5_H[NBPAIRS+1][5];
+
+extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
+extern int int11_H[NBPAIRS+1][NBPAIRS+1][5][5];
+
+extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
+extern int int21_H[NBPAIRS+1][NBPAIRS+1][5][5][5];
+
+extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
+extern int int22_H[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
+
+/* constants for linearly destabilizing contributions for multi-loops
+ F = ML_closing + ML_intern*(k-1) + ML_BASE*u */
+extern int ML_BASE37;
+extern int ML_closing37;
+extern int ML_intern37;
+
+/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
+/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
+extern int MAX_NINIO; /* maximum correction */
+extern int F_ninio37[5];
+
+/* penalty for helices terminated by AU (actually not GC) */
+extern int TerminalAU;
+/* penalty for forming bi-molecular duplex */
+extern int DuplexInit;
+/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
+extern char Tetraloops[]; /* string containing the special tetraloops */
+extern int TETRA_ENERGY37[]; /* Bonus energy for special tetraloops */
+extern int TETRA_ENTH37;
+extern char Triloops[]; /* string containing the special triloops */
+extern int Triloop_E37[]; /* Bonus energy for special Triloops */
+
+extern double Tmeasure; /* temperature of param measurements */
+}
--- /dev/null
+#include "energy_param.hpp"
+
+
+
+namespace MXSCARNA {
+const int energy_param::INF = 10000;
+const int energy_param::NST = 0;
+const int energy_param::DEF = -50;
+const double energy_param::lxc37 = 107.856;
+const int
+energy_param::
+stack37[8][8] =
+/* CG GC GU UG AU UA */
+{ { INF, INF, INF, INF, INF, INF, INF, INF},
+ { INF, -240, -330, -210, -140, -210, -210, NST}, // CG
+ { INF, -330, -340, -250, -150, -220, -240, NST}, // GC
+ { INF, -210, -250, 130, -50, -140, -130, NST}, // GU
+ { INF, -140, -150, -50, 30, -60, -100, NST}, // UG
+ { INF, -210, -220, -140, -60, -110, -90, NST}, // AU
+ { INF, -210, -240, -130, -100, -90, -130, NST}, // UA
+ { INF, NST, NST, NST, NST, NST, NST, NST}};
+
+/* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */
+/* different from mfold-2.3, which uses values from mfold-2.2 */
+const int
+energy_param::
+enthalpies[8][8] =
+/* CG GC GU UG AU UA */
+{ { INF, INF, INF, INF, INF, INF, INF, INF},
+ { INF, -1060, -1340, -1210, -560, -1050, -1040, NST},
+ { INF, -1340, -1490, -1260, -830, -1140, -1240, NST},
+ { INF, -1210, -1260, -1460, -1350, -880, -1280, NST},
+ { INF, -560, -830, -1350, -930, -320, -700, NST},
+ { INF, -1050, -1140, -880, -320, -940, -680, NST},
+ { INF, -1040, -1240, -1280, -700, -680, -770, NST},
+ { INF, NST, NST, NST, NST, NST, NST, NST}};
+
+/* old values are here just for comparison */
+const int energy_param::oldhairpin37[31] = { /* from ViennaRNA 1.3 */
+ INF, INF, INF, 410, 490, 440, 470, 500, 510, 520, 531,
+ 542, 551, 560, 568, 575, 582, 589, 595, 601, 606,
+ 611, 616, 621, 626, 630, 634, 638, 642, 646, 650};
+
+const int energy_param::hairpin37[31] = {
+ INF, INF, INF, 570, 560, 560, 540, 590, 560, 640, 650,
+ 660, 670, 678, 686, 694, 701, 707, 713, 719, 725,
+ 730, 735, 740, 744, 749, 753, 757, 761, 765, 769};
+
+const int energy_param::oldbulge37[31] = {
+ INF, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555,
+ 565, 574, 583, 591, 598, 605, 612, 618, 624, 630,
+ 635, 640, 645, 649, 654, 658, 662, 666, 670, 673};
+
+const int energy_param::bulge37[31] = {
+ INF, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490,
+ 500, 510, 519, 527, 534, 541, 548, 554, 560, 565,
+ 571, 576, 580, 585, 589, 594, 598, 602, 605, 609};
+
+const int energy_param::oldinternal_loop37[31] = {
+ INF, INF, 410, 510, 490, 530, 570, 587, 601, 614, 625,
+ 635, 645, 653, 661, 669, 676, 682, 688, 694, 700,
+ 705, 710, 715, 720, 724, 728, 732, 736, 740, 744};
+
+const int energy_param::internal_loop37[31] = {
+ INF, INF, 410, 510, 170, 180, 200, 220, 230, 240, 250,
+ 260, 270, 278, 286, 294, 301, 307, 313, 319, 325,
+ 330, 335, 340, 345, 349, 353, 357, 361, 365, 369};
+
+/* terminal mismatches */
+/* mismatch free energies for interior loops at 37C */
+const int energy_param::mismatchI37[8][5][5] =
+{ /* @@ */
+ {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+ { /* CG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 0, 0, -110, 0}, /* A@ AA AC AG AU */
+ { 0, 0, 0, 0, 0}, /* C@ CA CC CG CU */
+ { 0, -110, 0, 0, 0}, /* G@ GA GC GG GU */
+ { 0, 0, 0, 0, -70}},/* U@ UA UC UG UU */
+ { /* GC */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 0, 0, -110, 0}, /* A@ AA AC AG AU */
+ { 0, 0, 0, 0, 0}, /* C@ CA CC CG CU */
+ { 0, -110, 0, 0, 0}, /* G@ GA GC GG GU */
+ { 0, 0, 0, 0, -70}},/* U@ UA UC UG UU */
+ { /* GU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
+ { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
+ { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
+ { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
+ { /* UG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
+ { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
+ { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
+ { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
+ { /* AU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
+ { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
+ { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
+ { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
+ { /* UA */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 70, 70, -40, 70}, /* A@ AA AC AG AU */
+ { 0, 70, 70, 70, 70}, /* C@ CA CC CG CU */
+ { 0, -40, 70, 70, 70}, /* G@ GA GC GG GU */
+ { 0, 70, 70, 70, 0}},/* U@ UA UC UG UU */
+ { /* @@ */
+ { 90, 90, 90, 90, 90},{ 90, 90, 90, 90,-20},{ 90, 90, 90, 90, 90},
+ { 90,-20, 90, 90, 90},{ 90, 90, 90, 90, 20}}
+};
+
+/* mismatch free energies for hairpins at 37C */
+const int energy_param::mismatchH37[8][5][5] =
+{ /* @@ */
+ {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+ { /* CG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { -90, -150, -150, -140, -180}, /* A@ AA AC AG AU */
+ { -90, -100, -90, -290, -80}, /* C@ CA CC CG CU */
+ { -90, -220, -200, -160, -110}, /* G@ GA GC GG GU */
+ { -90, -170, -140, -180, -200}},/* U@ UA UC UG UU */
+ { /* GC */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { -70, -110, -150, -130, -210}, /* A@ AA AC AG AU */
+ { -70, -110, -70, -240, -50}, /* C@ CA CC CG CU */
+ { -70, -240, -290, -140, -120}, /* G@ GA GC GG GU */
+ { -70, -190, -100, -220, -150}},/* U@ UA UC UG UU */
+ { /* GU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, 20, -50, -30, -30}, /* A@ AA AC AG AU */
+ { 0, -10, -20, -150, -20}, /* C@ CA CC CG CU */
+ { 0, -90, -110, -30, 0}, /* G@ GA GC GG GU */
+ { 0, -30, -30, -40, -110}},/* U@ UA UC UG UU */
+ { /* UG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, -50, -30, -60, -50}, /* A@ AA AC AG AU */
+ { 0, -20, -10, -170, 0}, /* C@ CA CC CG CU */
+ { 0, -80, -120, -30, -70}, /* G@ GA GC GG GU */
+ { 0, -60, -10, -60, -80}},/* U@ UA UC UG UU */
+ { /* AU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, -30, -50, -30, -30}, /* A@ AA AC AG AU */
+ { 0, -10, -20, -150, -20}, /* C@ CA CC CG CU */
+ { 0, -110, -120, -20, 20}, /* G@ GA GC GG GU */
+ { 0, -30, -30, -60, -110}},/* U@ UA UC UG UU */
+ { /* UA */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { 0, -50, -30, -60, -50}, /* A@ AA AC AG AU */
+ { 0, -20, -10, -120, -0}, /* C@ CA CC CG CU */
+ { 0, -140, -120, -70, -20}, /* G@ GA GC GG GU */
+ { 0, -30, -10, -50, -80}},/* U@ UA UC UG UU */
+ { /* @@ */
+ { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0},
+ { 0, 0, 0, 0, 0},{ 0, 0, 0, 0, 0}}
+};
+
+/* mismatch energies in multiloops */
+
+/* these are probably junk */
+/* mismatch enthalpies for temperature scaling */
+const int energy_param::mism_H[8][5][5] =
+{ /* no pair */
+ {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},
+ { /* CG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF,-1030, -950,-1030,-1030}, /* A@ AA AC AG AU */
+ { DEF, -520, -450, -520, -670}, /* C@ CA CC CG CU */
+ { DEF, -940, -940, -940, -940}, /* G@ GA GC GG GU */
+ { DEF, -810, -740, -810, -860}},/* U@ UA UC UG UU */
+ { /* GC */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -520, -880, -560, -880}, /* A@ AA AC AG AU */
+ { DEF, -720, -310, -310, -390}, /* C@ CA CC CG CU */
+ { DEF, -710, -740, -620, -740}, /* G@ GA GC GG GU */
+ { DEF, -500, -500, -500, -570}},/* U@ UA UC UG UU */
+ { /* GU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -430, -600, -600, -600}, /* A@ AA AC AG AU */
+ { DEF, -260, -240, -240, -240}, /* C@ CA CC CG CU */
+ { DEF, -340, -690, -690, -690}, /* G@ GA GC GG GU */
+ { DEF, -330, -330, -330, -330}},/* U@ UA UC UG UU */
+ { /* UG */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -720, -790, -960, -810}, /* A@ AA AC AG AU */
+ { DEF, -480, -480, -360, -480}, /* C@ CA CC CG CU */
+ { DEF, -660, -810, -920, -810}, /* G@ GA GC GG GU */
+ { DEF, -550, -440, -550, -360}},/* U@ UA UC UG UU */
+ { /* AU */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -430, -600, -600, -600}, /* A@ AA AC AG AU */
+ { DEF, -260, -240, -240, -240}, /* C@ CA CC CG CU */
+ { DEF, -340, -690, -690, -690}, /* G@ GA GC GG GU */
+ { DEF, -330, -330, -330, -330}},/* U@ UA UC UG UU */
+ { /* UA */
+ { 0, 0, 0, 0, 0}, /* @@ @A @C @G @U */
+ { DEF, -400, -630, -890, -590}, /* A@ AA AC AG AU */
+ { DEF, -430, -510, -200, -180}, /* C@ CA CC CG CU */
+ { DEF, -380, -680, -890, -680}, /* G@ GA GC GG GU */
+ { DEF, -280, -140, -280, -140}},/* U@ UA UC UG UU */
+ { /* nonstandard pair */
+ {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},
+ {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}}
+};
+
+/* 5' dangling ends (unpaird base stacks on first paired base) */
+const int energy_param::dangle5_37[8][5]=
+{/* @ A C G U */
+ { INF, INF, INF, INF, INF}, /* no pair */
+ { INF, -50, -30, -20, -10}, /* CG (stacks on C) */
+ { INF, -20, -30, -0, -0}, /* GC (stacks on G) */
+ { INF, -30, -30, -40, -20}, /* GU */
+ { INF, -30, -10, -20, -20}, /* UG */
+ { INF, -30, -30, -40, -20}, /* AU */
+ { INF, -30, -10, -20, -20}, /* UA */
+ { 0, 0, 0, 0, 0} /* @ */
+};
+
+/* 3' dangling ends (unpaired base stacks on second paired base */
+const int energy_param::dangle3_37[8][5]=
+{/* @ A C G U */
+ { INF, INF, INF, INF, INF}, /* no pair */
+ { INF, -110, -40, -130, -60}, /* CG (stacks on G) */
+ { INF, -170, -80, -170, -120}, /* GC */
+ { INF, -70, -10, -70, -10}, /* GU */
+ { INF, -80, -50, -80, -60}, /* UG */
+ { INF, -70, -10, -70, -10}, /* AU */
+ { INF, -80, -50, -80, -60}, /* UA */
+ { 0, 0, 0, 0, 0} /* @ */
+};
+
+/* enthalpies for temperature scaling */
+const int energy_param::dangle3_H[8][5] =
+{/* @ A C G U */
+ { INF, INF, INF, INF, INF}, /* no pair */
+ { 0, -740, -280, -640, -360},
+ { 0, -900, -410, -860, -750},
+ { 0, -740, -240, -720, -490},
+ { 0, -490, -90, -550, -230},
+ { 0, -570, -70, -580, -220},
+ { 0, -490, -90, -550, -230},
+ { 0, 0, 0, 0, 0}
+};
+
+const int energy_param::dangle5_H[8][5] =
+{/* @ A C G U */
+ { INF, INF, INF, INF, INF}, /* no pair */
+ { 0, -240, 330, 80, -140},
+ { 0, -160, 70, -460, -40},
+ { 0, 160, 220, 70, 310},
+ { 0, -150, 510, 10, 100},
+ { 0, 160, 220, 70, 310},
+ { 0, -50, 690, -60, -60},
+ { 0, 0, 0, 0, 0}
+};
+
+
+/* constants for linearly destabilizing contributions for multi-loops
+ F = ML_closing + ML_intern*k + ML_BASE*u */
+/* old versions erroneously used ML_intern*(k-1) */
+
+const int energy_param::ML_BASE37 = 0;
+const int energy_param::ML_closing37 = 340;
+const int energy_param::ML_intern37 = 40;
+
+
+/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
+/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
+const int energy_param::MAX_NINIO = 300; /* maximum correction */
+const int energy_param::F_ninio37[5] = { 0, 40, 50, 20, 10 }; /* only F[2] used */
+
+/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
+
+const char energy_param::Tetraloops[1400] = /* place for up to 200 tetra loops */
+ "GGGGAC "
+ "GGUGAC "
+ "CGAAAG "
+ "GGAGAC "
+ "CGCAAG "
+ "GGAAAC "
+ "CGGAAG "
+ "CUUCGG "
+ "CGUGAG "
+ "CGAAGG "
+ "CUACGG "
+ "GGCAAC "
+ "CGCGAG "
+ "UGAGAG "
+ "CGAGAG "
+ "AGAAAU "
+ "CGUAAG "
+ "CUAACG "
+ "UGAAAG "
+ "GGAAGC "
+ "GGGAAC "
+ "UGAAAA "
+ "AGCAAU "
+ "AGUAAU "
+ "CGGGAG "
+ "AGUGAU "
+ "GGCGAC "
+ "GGGAGC "
+ "GUGAAC "
+ "UGGAAA "
+;
+
+const char energy_param::Tetrastrings[30][7] = {
+ "GGGGAC",
+ "GGUGAC",
+ "CGAAAG",
+ "GGAGAC",
+ "CGCAAG",
+ "GGAAAC",
+ "CGGAAG",
+ "CUUCGG",
+ "CGUGAG",
+ "CGAAGG",
+ "CUACGG",
+ "GGCAAC",
+ "CGCGAG",
+ "UGAGAG",
+ "CGAGAG",
+ "AGAAAU",
+ "CGUAAG",
+ "CUAACG",
+ "UGAAAG",
+ "GGAAGC",
+ "GGGAAC",
+ "UGAAAA",
+ "AGCAAU",
+ "AGUAAU",
+ "CGGGAG",
+ "AGUGAU",
+ "GGCGAC",
+ "GGGAGC",
+ "GUGAAC",
+ "UGGAAA"
+};
+
+const int energy_param::TETRA_ENERGY37[200] = {
+ -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250,
+ -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150,
+ -150, -150, -150, -150, -150, -150};
+
+const int energy_param::TETRA_ENTH37 = -400;
+
+
+/* penalty for AU (or GU) terminating helix) */
+/* mismatches already contain these */
+const int energy_param::TerminalAU = 50;
+
+/* penalty for forming a bi-molecular duplex */
+const int energy_param::DuplexInit = 410;
+
+//#include "intloops.h"
+
+
+const int energy_param::int11_37[8][8][5][5] =
+{ /* noPair */ {{{0}}},
+ { /* noPair */ {{0}},
+/* CG..CG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 40, 40, 40},
+{ 110, 40, 40, 40, 40},
+{ 110, 40, 40, -140, 40},
+{ 110, 40, 40, 40, 40}
+},
+/* CG..GC */
+{{ 110, 110, 110, 110, 110},
+{ 110, 40, -40, 40, 40},
+{ 110, 30, 50, 40, 50},
+{ 110, -10, 40, -170, 40},
+{ 110, 40, 0, 40, -30}
+},
+/* CG..GU */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* CG..UG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* CG..AU */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* CG..UA */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* CG..?? */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110}
+}
+},
+{ /* noPair */ {{0}},
+/* GC..CG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 40, 30, -10, 40},
+{ 110, -40, 50, 40, 0},
+{ 110, 40, 40, -170, 40},
+{ 110, 40, 50, 40, -30}
+},
+/* GC..GC */
+{{ 110, 110, 110, 110, 110},
+{ 110, 80, 40, 40, 40},
+{ 110, 40, 40, 40, 40},
+{ 110, 40, 40, -210, 40},
+{ 110, 40, 40, 40, -70}
+},
+/* GC..GU */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* GC..UG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* GC..AU */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 100}
+},
+/* GC..UA */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* GC..?? */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110}
+}
+},
+{ /* noPair */ {{0}},
+/* GU..CG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* GU..GC */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* GU..GU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* GU..UG */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* GU..AU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* GU..UA */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* GU..?? */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+}
+},
+{ /* noPair */ {{0}},
+/* UG..CG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* UG..GC */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* UG..GU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* UG..UG */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* UG..AU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* UG..UA */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* UG..?? */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+}
+},
+{ /* noPair */ {{0}},
+/* AU..CG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* AU..GC */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 100}
+},
+/* AU..GU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* AU..UG */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* AU..AU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 120}
+},
+/* AU..UA */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 150}
+},
+/* AU..?? */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+}
+},
+{ /* noPair */ {{0}},
+/* UA..CG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* UA..GC */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, -100, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* UA..GU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* UA..UG */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* UA..AU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 150}
+},
+/* UA..UA */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, -40, 170},
+{ 170, 170, 170, 170, 180}
+},
+/* UA..?? */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+}
+},
+{ /* noPair */ {{0}},
+/* ??..CG */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* ??..GC */
+{{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110},
+{ 110, 110, 110, 110, 110}
+},
+/* ??..GU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* ??..UG */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* ??..AU */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* ??..UA */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+},
+/* ??..?? */
+{{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170},
+{ 170, 170, 170, 170, 170}
+}
+}
+};
+
+const int energy_param::int11_H[8][8][5][5] =
+ /* GC..GC */
+{ /* noPair */ {{{0}}},
+{ /* noPair */ {{0}},
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GC..CG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GC..GU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GC..UG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GC..AU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GC..UA */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GC.. @ */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}}},
+ /* CG..GC */
+{ /* noPair */ {{0}},
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* CG..CG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* CG..GU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* CG..UG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* CG..AU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* CG..UA */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* CG.. @ */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}}},
+ /* GU..GC */
+{ /* noPair */ {{0}},
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GU..CG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GU..GU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GU..UG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GU..AU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GU..UA */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* GU.. @ */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}}},
+ /* UG..GC */
+{ /* noPair */ {{0}},
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UG..CG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UG..GU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UG..UG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UG..AU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UG..UA */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UG.. @ */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}}},
+ /* AU..GC */
+{ /* noPair */ {{0}},
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* AU..CG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* AU..GU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* AU..UG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* AU..AU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* AU..UA */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* AU.. @ */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}}},
+ /* UA..GC */
+{ /* noPair */ {{0}},
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UA..CG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UA..GU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UA..UG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UA..AU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UA..UA */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* UA.. @ */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}}},
+ /* @..GC */
+{ /* noPair */ {{0}},
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* @..CG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* @..GU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* @..UG */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* @..AU */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* @..UA */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}},
+ /* @.. @ */
+{ { 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0},
+{ 0, 0, 0, 0, 0}}}};
+
+const int energy_param::int21_37[8][8][5][5][5] =
+{ /* noPair */ {{{{0}}}},
+{ /* noPair */ {{{0}}},
+{
+/* CG.@..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.A..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 240, 220, 160, 400},{ 550, 210, 170, 160, 400},{ 550, 100, 60, 40, 400},{ 550, 400, 400, 400, 400}},
+/* CG.C..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 400, 220},{ 550, 220, 250, 400, 220},{ 550, 400, 400, 400, 400},{ 550, 250, 190, 400, 220}},
+/* CG.G..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 170, 400, 80, 400},{ 550, 400, 400, 400, 400},{ 550, 80, 400, 220, 400},{ 550, 400, 400, 400, 400}},
+/* CG.U..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 400, 400, 400, 400},{ 550, 400, 220, 400, 130},{ 550, 400, 400, 400, 400},{ 550, 400, 170, 400, 120}}
+},
+{
+/* CG.@..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.A..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 110, 400},{ 550, 210, 170, 160, 400},{ 550, 80, 60, 40, 400},{ 550, 400, 400, 400, 400}},
+/* CG.C..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 400, 220},{ 550, 220, 250, 400, 220},{ 550, 400, 400, 400, 400},{ 550, 250, 190, 400, 220}},
+/* CG.G..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 170, 400, 80, 400},{ 550, 400, 400, 400, 400},{ 550, 80, 400, 220, 400},{ 550, 400, 400, 400, 400}},
+/* CG.U..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 400, 400, 400, 400},{ 550, 400, 220, 400, 150},{ 550, 400, 400, 400, 400},{ 550, 400, 170, 400, 120}}
+},
+{
+/* CG.@..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.A..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* CG.C..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* CG.G..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* CG.U..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* CG.@..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.A..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* CG.C..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* CG.G..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* CG.U..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* CG.@..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.A..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* CG.C..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* CG.G..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* CG.U..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* CG.@..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.A..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* CG.C..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* CG.G..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* CG.U..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* CG.@..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.A..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.C..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.G..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* CG.U..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* GC.@..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.A..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 220, 210, 400},{ 550, 210, 170, 160, 400},{ 550, 120, 60, 40, 400},{ 550, 400, 400, 400, 400}},
+/* GC.C..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 400, 220},{ 550, 220, 250, 400, 220},{ 550, 400, 400, 400, 400},{ 550, 250, 190, 400, 220}},
+/* GC.G..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 170, 400, 80, 400},{ 550, 400, 400, 400, 400},{ 550, 80, 400, 220, 400},{ 550, 400, 400, 400, 400}},
+/* GC.U..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 400, 400, 400, 400},{ 550, 400, 220, 400, 120},{ 550, 400, 400, 400, 400},{ 550, 400, 170, 400, 120}}
+},
+{
+/* GC.@..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.A..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 240, 220, 160, 400},{ 550, 210, 170, 160, 400},{ 550, 100, 60, 40, 400},{ 550, 400, 400, 400, 400}},
+/* GC.C..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 400, 220},{ 550, 220, 250, 400, 220},{ 550, 400, 400, 400, 400},{ 550, 250, 190, 400, 220}},
+/* GC.G..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 170, 400, 80, 400},{ 550, 400, 400, 400, 400},{ 550, 80, 400, 220, 400},{ 550, 400, 400, 400, 400}},
+/* GC.U..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 400, 400, 400, 400},{ 550, 400, 220, 400, 130},{ 550, 400, 400, 400, 400},{ 550, 400, 170, 400, 120}}
+},
+{
+/* GC.@..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.A..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* GC.C..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* GC.G..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* GC.U..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* GC.@..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.A..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* GC.C..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* GC.G..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* GC.U..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* GC.@..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.A..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* GC.C..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* GC.G..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* GC.U..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* GC.@..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.A..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* GC.C..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* GC.G..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* GC.U..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* GC.@..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.A..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.C..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.G..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GC.U..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* GU.@..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.A..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* GU.C..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* GU.G..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* GU.U..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* GU.@..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.A..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* GU.C..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* GU.G..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* GU.U..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* GU.@..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.A..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* GU.C..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* GU.G..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* GU.U..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* GU.@..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.A..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* GU.C..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* GU.G..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* GU.U..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* GU.@..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.A..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* GU.C..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* GU.G..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* GU.U..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* GU.@..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.A..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* GU.C..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* GU.G..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* GU.U..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* GU.@..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.A..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.C..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.G..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* GU.U..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* UG.@..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.A..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* UG.C..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* UG.G..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* UG.U..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* UG.@..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.A..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* UG.C..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* UG.G..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* UG.U..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* UG.@..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.A..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* UG.C..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* UG.G..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* UG.U..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* UG.@..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.A..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* UG.C..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* UG.G..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* UG.U..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* UG.@..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.A..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* UG.C..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* UG.G..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* UG.U..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* UG.@..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.A..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* UG.C..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* UG.G..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* UG.U..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* UG.@..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.A..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.C..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.G..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UG.U..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* AU.@..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.A..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* AU.C..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* AU.G..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* AU.U..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* AU.@..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.A..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* AU.C..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* AU.G..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* AU.U..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* AU.@..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.A..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* AU.C..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* AU.G..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* AU.U..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* AU.@..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.A..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* AU.C..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* AU.G..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* AU.U..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* AU.@..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.A..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* AU.C..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* AU.G..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* AU.U..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* AU.@..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.A..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* AU.C..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* AU.G..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* AU.U..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* AU.@..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.A..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.C..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.G..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* AU.U..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* UA.@..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.A..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* UA.C..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* UA.G..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* UA.U..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* UA.@..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.A..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},
+/* UA.C..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},
+/* UA.G..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},
+/* UA.U..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}
+},
+{
+/* UA.@..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.A..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* UA.C..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* UA.G..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* UA.U..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* UA.@..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.A..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* UA.C..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* UA.G..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* UA.U..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* UA.@..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.A..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* UA.C..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* UA.G..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* UA.U..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* UA.@..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.A..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},
+/* UA.C..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},
+/* UA.G..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},
+/* UA.U..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}
+},
+{
+/* UA.@..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.A..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.C..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.G..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* UA.U..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* ??.@..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.A..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.C..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.G..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.U..GC */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+},
+{
+/* ??.@..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.A..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.C..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.G..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.U..CG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+},
+{
+/* ??.@..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.A..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.C..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.G..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.U..UG */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+},
+{
+/* ??.@..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.A..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.C..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.G..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.U..GU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+},
+{
+/* ??.@..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.A..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.C..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.G..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.U..UA */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+},
+{
+/* ??.@..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.A..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.C..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.G..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.U..AU */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+},
+{
+/* ??.@..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.A..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.C..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.G..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},
+/* ??.U..?? */
+{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}
+}
+}
+};
+
+const int energy_param::int21_H[8][8][5][5][5] =
+{ /* noPair */ {{{{0}}}},
+{ /* noPair */ {{{0}}},
+{
+/* CG.@..CG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* CG.A..CG */
+{{ -50,-1029, -949,-1029,-1029},{-1079,-2058,-1978,-2058,-2058},{ -569,-1548,-1468,-1548,-1548},{ -989,-1968,-1888,-1968,-1968},{ -859,-1838,-1758,-1838,-1838}},
+/* CG.C..CG */
+{{ -50, -519, -449, -519, -669},{ -999,-1468,-1398,-1468,-1618},{ -499, -968, -898, -968,-1118},{ -989,-1458,-1388,-1458,-1608},{ -789,-1258,-1188,-1258,-1408}},
+/* CG.G..CG */
+{{ -50, -939, -939, -939, -939},{-1079,-1968,-1968,-1968,-1968},{ -569,-1458,-1458,-1458,-1458},{ -989,-1878,-1878,-1878,-1878},{ -859,-1748,-1748,-1748,-1748}},
+/* CG.U..CG */
+{{ -50, -809, -739, -809, -859},{-1079,-1838,-1768,-1838,-1888},{ -719,-1478,-1408,-1478,-1528},{ -989,-1748,-1678,-1748,-1798},{ -909,-1668,-1598,-1668,-1718}}
+},
+{
+/* CG.@..GC */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* CG.A..GC */
+{{ -50,-1029, -949,-1029,-1029},{ -569,-1548,-1468,-1548,-1548},{ -769,-1748,-1668,-1748,-1748},{ -759,-1738,-1658,-1738,-1738},{ -549,-1528,-1448,-1528,-1528}},
+/* CG.C..GC */
+{{ -50, -519, -449, -519, -669},{ -929,-1398,-1328,-1398,-1548},{ -359, -828, -758, -828, -978},{ -789,-1258,-1188,-1258,-1408},{ -549,-1018, -948,-1018,-1168}},
+/* CG.G..GC */
+{{ -50, -939, -939, -939, -939},{ -609,-1498,-1498,-1498,-1498},{ -359,-1248,-1248,-1248,-1248},{ -669,-1558,-1558,-1558,-1558},{ -549,-1438,-1438,-1438,-1438}},
+/* CG.U..GC */
+{{ -50, -809, -739, -809, -859},{ -929,-1688,-1618,-1688,-1738},{ -439,-1198,-1128,-1198,-1248},{ -789,-1548,-1478,-1548,-1598},{ -619,-1378,-1308,-1378,-1428}}
+},
+{
+/* CG.@..GU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* CG.A..GU */
+{{ -50,-1029, -949,-1029,-1029},{ -479,-1458,-1378,-1458,-1458},{ -309,-1288,-1208,-1288,-1288},{ -389,-1368,-1288,-1368,-1368},{ -379,-1358,-1278,-1358,-1358}},
+/* CG.C..GU */
+{{ -50, -519, -449, -519, -669},{ -649,-1118,-1048,-1118,-1268},{ -289, -758, -688, -758, -908},{ -739,-1208,-1138,-1208,-1358},{ -379, -848, -778, -848, -998}},
+/* CG.G..GU */
+{{ -50, -939, -939, -939, -939},{ -649,-1538,-1538,-1538,-1538},{ -289,-1178,-1178,-1178,-1178},{ -739,-1628,-1628,-1628,-1628},{ -379,-1268,-1268,-1268,-1268}},
+/* CG.U..GU */
+{{ -50, -809, -739, -809, -859},{ -649,-1408,-1338,-1408,-1458},{ -289,-1048, -978,-1048,-1098},{ -739,-1498,-1428,-1498,-1548},{ -379,-1138,-1068,-1138,-1188}}
+},
+{
+/* CG.@..UG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* CG.A..UG */
+{{ -50,-1029, -949,-1029,-1029},{ -769,-1748,-1668,-1748,-1748},{ -529,-1508,-1428,-1508,-1508},{ -709,-1688,-1608,-1688,-1688},{ -599,-1578,-1498,-1578,-1578}},
+/* CG.C..UG */
+{{ -50, -519, -449, -519, -669},{ -839,-1308,-1238,-1308,-1458},{ -529, -998, -928, -998,-1148},{ -859,-1328,-1258,-1328,-1478},{ -489, -958, -888, -958,-1108}},
+/* CG.G..UG */
+{{ -50, -939, -939, -939, -939},{-1009,-1898,-1898,-1898,-1898},{ -409,-1298,-1298,-1298,-1298},{ -969,-1858,-1858,-1858,-1858},{ -599,-1488,-1488,-1488,-1488}},
+/* CG.U..UG */
+{{ -50, -809, -739, -809, -859},{ -859,-1618,-1548,-1618,-1668},{ -529,-1288,-1218,-1288,-1338},{ -859,-1618,-1548,-1618,-1668},{ -409,-1168,-1098,-1168,-1218}}
+},
+{
+/* CG.@..AU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* CG.A..AU */
+{{ -50,-1029, -949,-1029,-1029},{ -479,-1458,-1378,-1458,-1458},{ -309,-1288,-1208,-1288,-1288},{ -389,-1368,-1288,-1368,-1368},{ -379,-1358,-1278,-1358,-1358}},
+/* CG.C..AU */
+{{ -50, -519, -449, -519, -669},{ -649,-1118,-1048,-1118,-1268},{ -289, -758, -688, -758, -908},{ -739,-1208,-1138,-1208,-1358},{ -379, -848, -778, -848, -998}},
+/* CG.G..AU */
+{{ -50, -939, -939, -939, -939},{ -649,-1538,-1538,-1538,-1538},{ -289,-1178,-1178,-1178,-1178},{ -739,-1628,-1628,-1628,-1628},{ -379,-1268,-1268,-1268,-1268}},
+/* CG.U..AU */
+{{ -50, -809, -739, -809, -859},{ -649,-1408,-1338,-1408,-1458},{ -289,-1048, -978,-1048,-1098},{ -739,-1498,-1428,-1498,-1548},{ -379,-1138,-1068,-1138,-1188}}
+},
+{
+/* CG.@..UA */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* CG.A..UA */
+{{ -50,-1029, -949,-1029,-1029},{ -449,-1428,-1348,-1428,-1428},{ -479,-1458,-1378,-1458,-1458},{ -429,-1408,-1328,-1408,-1408},{ -329,-1308,-1228,-1308,-1308}},
+/* CG.C..UA */
+{{ -50, -519, -449, -519, -669},{ -679,-1148,-1078,-1148,-1298},{ -559,-1028, -958,-1028,-1178},{ -729,-1198,-1128,-1198,-1348},{ -189, -658, -588, -658, -808}},
+/* CG.G..UA */
+{{ -50, -939, -939, -939, -939},{ -939,-1828,-1828,-1828,-1828},{ -249,-1138,-1138,-1138,-1138},{ -939,-1828,-1828,-1828,-1828},{ -329,-1218,-1218,-1218,-1218}},
+/* CG.U..UA */
+{{ -50, -809, -739, -809, -859},{ -639,-1398,-1328,-1398,-1448},{ -229, -988, -918, -988,-1038},{ -729,-1488,-1418,-1488,-1538},{ -190, -949, -879, -949, -999}}
+},
+{
+/* CG.@.. @ */
+{{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* CG.A.. @ */
+{{ -100,-1079, -999,-1079,-1079},{ -100,-1079, -999,-1079,-1079},{ -100,-1079, -999,-1079,-1079},{ -100,-1079, -999,-1079,-1079},{ -100,-1079, -999,-1079,-1079}},
+/* CG.C.. @ */
+{{ -100, -569, -499, -569, -719},{ -100, -569, -499, -569, -719},{ -100, -569, -499, -569, -719},{ -100, -569, -499, -569, -719},{ -100, -569, -499, -569, -719}},
+/* CG.G.. @ */
+{{ -100, -989, -989, -989, -989},{ -100, -989, -989, -989, -989},{ -100, -989, -989, -989, -989},{ -100, -989, -989, -989, -989},{ -100, -989, -989, -989, -989}},
+/* CG.U.. @ */
+{{ -100, -859, -789, -859, -909},{ -100, -859, -789, -859, -909},{ -100, -859, -789, -859, -909},{ -100, -859, -789, -859, -909},{ -100, -859, -789, -859, -909}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* GC.@..CG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GC.A..CG */
+{{ -50, -519, -879, -559, -879},{-1079,-1548,-1908,-1588,-1908},{ -569,-1038,-1398,-1078,-1398},{ -989,-1458,-1818,-1498,-1818},{ -859,-1328,-1688,-1368,-1688}},
+/* GC.C..CG */
+{{ -50, -719, -309, -309, -389},{ -999,-1668,-1258,-1258,-1338},{ -499,-1168, -758, -758, -838},{ -989,-1658,-1248,-1248,-1328},{ -789,-1458,-1048,-1048,-1128}},
+/* GC.G..CG */
+{{ -50, -709, -739, -619, -739},{-1079,-1738,-1768,-1648,-1768},{ -569,-1228,-1258,-1138,-1258},{ -989,-1648,-1678,-1558,-1678},{ -859,-1518,-1548,-1428,-1548}},
+/* GC.U..CG */
+{{ -50, -499, -499, -499, -569},{-1079,-1528,-1528,-1528,-1598},{ -719,-1168,-1168,-1168,-1238},{ -989,-1438,-1438,-1438,-1508},{ -909,-1358,-1358,-1358,-1428}}
+},
+{
+/* GC.@..GC */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GC.A..GC */
+{{ -50, -519, -879, -559, -879},{ -569,-1038,-1398,-1078,-1398},{ -769,-1238,-1598,-1278,-1598},{ -759,-1228,-1588,-1268,-1588},{ -549,-1018,-1378,-1058,-1378}},
+/* GC.C..GC */
+{{ -50, -719, -309, -309, -389},{ -929,-1598,-1188,-1188,-1268},{ -359,-1028, -618, -618, -698},{ -789,-1458,-1048,-1048,-1128},{ -549,-1218, -808, -808, -888}},
+/* GC.G..GC */
+{{ -50, -709, -739, -619, -739},{ -609,-1268,-1298,-1178,-1298},{ -359,-1018,-1048, -928,-1048},{ -669,-1328,-1358,-1238,-1358},{ -549,-1208,-1238,-1118,-1238}},
+/* GC.U..GC */
+{{ -50, -499, -499, -499, -569},{ -929,-1378,-1378,-1378,-1448},{ -439, -888, -888, -888, -958},{ -789,-1238,-1238,-1238,-1308},{ -619,-1068,-1068,-1068,-1138}}
+},
+{
+/* GC.@..GU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GC.A..GU */
+{{ -50, -519, -879, -559, -879},{ -479, -948,-1308, -988,-1308},{ -309, -778,-1138, -818,-1138},{ -389, -858,-1218, -898,-1218},{ -379, -848,-1208, -888,-1208}},
+/* GC.C..GU */
+{{ -50, -719, -309, -309, -389},{ -649,-1318, -908, -908, -988},{ -289, -958, -548, -548, -628},{ -739,-1408, -998, -998,-1078},{ -379,-1048, -638, -638, -718}},
+/* GC.G..GU */
+{{ -50, -709, -739, -619, -739},{ -649,-1308,-1338,-1218,-1338},{ -289, -948, -978, -858, -978},{ -739,-1398,-1428,-1308,-1428},{ -379,-1038,-1068, -948,-1068}},
+/* GC.U..GU */
+{{ -50, -499, -499, -499, -569},{ -649,-1098,-1098,-1098,-1168},{ -289, -738, -738, -738, -808},{ -739,-1188,-1188,-1188,-1258},{ -379, -828, -828, -828, -898}}
+},
+{
+/* GC.@..UG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GC.A..UG */
+{{ -50, -519, -879, -559, -879},{ -769,-1238,-1598,-1278,-1598},{ -529, -998,-1358,-1038,-1358},{ -709,-1178,-1538,-1218,-1538},{ -599,-1068,-1428,-1108,-1428}},
+/* GC.C..UG */
+{{ -50, -719, -309, -309, -389},{ -839,-1508,-1098,-1098,-1178},{ -529,-1198, -788, -788, -868},{ -859,-1528,-1118,-1118,-1198},{ -489,-1158, -748, -748, -828}},
+/* GC.G..UG */
+{{ -50, -709, -739, -619, -739},{-1009,-1668,-1698,-1578,-1698},{ -409,-1068,-1098, -978,-1098},{ -969,-1628,-1658,-1538,-1658},{ -599,-1258,-1288,-1168,-1288}},
+/* GC.U..UG */
+{{ -50, -499, -499, -499, -569},{ -859,-1308,-1308,-1308,-1378},{ -529, -978, -978, -978,-1048},{ -859,-1308,-1308,-1308,-1378},{ -409, -858, -858, -858, -928}}
+},
+{
+/* GC.@..AU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GC.A..AU */
+{{ -50, -519, -879, -559, -879},{ -479, -948,-1308, -988,-1308},{ -309, -778,-1138, -818,-1138},{ -389, -858,-1218, -898,-1218},{ -379, -848,-1208, -888,-1208}},
+/* GC.C..AU */
+{{ -50, -719, -309, -309, -389},{ -649,-1318, -908, -908, -988},{ -289, -958, -548, -548, -628},{ -739,-1408, -998, -998,-1078},{ -379,-1048, -638, -638, -718}},
+/* GC.G..AU */
+{{ -50, -709, -739, -619, -739},{ -649,-1308,-1338,-1218,-1338},{ -289, -948, -978, -858, -978},{ -739,-1398,-1428,-1308,-1428},{ -379,-1038,-1068, -948,-1068}},
+/* GC.U..AU */
+{{ -50, -499, -499, -499, -569},{ -649,-1098,-1098,-1098,-1168},{ -289, -738, -738, -738, -808},{ -739,-1188,-1188,-1188,-1258},{ -379, -828, -828, -828, -898}}
+},
+{
+/* GC.@..UA */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GC.A..UA */
+{{ -50, -519, -879, -559, -879},{ -449, -918,-1278, -958,-1278},{ -479, -948,-1308, -988,-1308},{ -429, -898,-1258, -938,-1258},{ -329, -798,-1158, -838,-1158}},
+/* GC.C..UA */
+{{ -50, -719, -309, -309, -389},{ -679,-1348, -938, -938,-1018},{ -559,-1228, -818, -818, -898},{ -729,-1398, -988, -988,-1068},{ -189, -858, -448, -448, -528}},
+/* GC.G..UA */
+{{ -50, -709, -739, -619, -739},{ -939,-1598,-1628,-1508,-1628},{ -249, -908, -938, -818, -938},{ -939,-1598,-1628,-1508,-1628},{ -329, -988,-1018, -898,-1018}},
+/* GC.U..UA */
+{{ -50, -499, -499, -499, -569},{ -639,-1088,-1088,-1088,-1158},{ -229, -678, -678, -678, -748},{ -729,-1178,-1178,-1178,-1248},{ -190, -639, -639, -639, -709}}
+},
+{
+/* GC.@.. @ */
+{{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GC.A.. @ */
+{{ -100, -569, -929, -609, -929},{ -100, -569, -929, -609, -929},{ -100, -569, -929, -609, -929},{ -100, -569, -929, -609, -929},{ -100, -569, -929, -609, -929}},
+/* GC.C.. @ */
+{{ -100, -769, -359, -359, -439},{ -100, -769, -359, -359, -439},{ -100, -769, -359, -359, -439},{ -100, -769, -359, -359, -439},{ -100, -769, -359, -359, -439}},
+/* GC.G.. @ */
+{{ -100, -759, -789, -669, -789},{ -100, -759, -789, -669, -789},{ -100, -759, -789, -669, -789},{ -100, -759, -789, -669, -789},{ -100, -759, -789, -669, -789}},
+/* GC.U.. @ */
+{{ -100, -549, -549, -549, -619},{ -100, -549, -549, -549, -619},{ -100, -549, -549, -549, -619},{ -100, -549, -549, -549, -619},{ -100, -549, -549, -549, -619}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* GU.@..CG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GU.A..CG */
+{{ -50, -429, -599, -599, -599},{-1079,-1458,-1628,-1628,-1628},{ -569, -948,-1118,-1118,-1118},{ -989,-1368,-1538,-1538,-1538},{ -859,-1238,-1408,-1408,-1408}},
+/* GU.C..CG */
+{{ -50, -259, -239, -239, -239},{ -999,-1208,-1188,-1188,-1188},{ -499, -708, -688, -688, -688},{ -989,-1198,-1178,-1178,-1178},{ -789, -998, -978, -978, -978}},
+/* GU.G..CG */
+{{ -50, -339, -689, -689, -689},{-1079,-1368,-1718,-1718,-1718},{ -569, -858,-1208,-1208,-1208},{ -989,-1278,-1628,-1628,-1628},{ -859,-1148,-1498,-1498,-1498}},
+/* GU.U..CG */
+{{ -50, -329, -329, -329, -329},{-1079,-1358,-1358,-1358,-1358},{ -719, -998, -998, -998, -998},{ -989,-1268,-1268,-1268,-1268},{ -909,-1188,-1188,-1188,-1188}}
+},
+{
+/* GU.@..GC */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GU.A..GC */
+{{ -50, -429, -599, -599, -599},{ -569, -948,-1118,-1118,-1118},{ -769,-1148,-1318,-1318,-1318},{ -759,-1138,-1308,-1308,-1308},{ -549, -928,-1098,-1098,-1098}},
+/* GU.C..GC */
+{{ -50, -259, -239, -239, -239},{ -929,-1138,-1118,-1118,-1118},{ -359, -568, -548, -548, -548},{ -789, -998, -978, -978, -978},{ -549, -758, -738, -738, -738}},
+/* GU.G..GC */
+{{ -50, -339, -689, -689, -689},{ -609, -898,-1248,-1248,-1248},{ -359, -648, -998, -998, -998},{ -669, -958,-1308,-1308,-1308},{ -549, -838,-1188,-1188,-1188}},
+/* GU.U..GC */
+{{ -50, -329, -329, -329, -329},{ -929,-1208,-1208,-1208,-1208},{ -439, -718, -718, -718, -718},{ -789,-1068,-1068,-1068,-1068},{ -619, -898, -898, -898, -898}}
+},
+{
+/* GU.@..GU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GU.A..GU */
+{{ -50, -429, -599, -599, -599},{ -479, -858,-1028,-1028,-1028},{ -309, -688, -858, -858, -858},{ -389, -768, -938, -938, -938},{ -379, -758, -928, -928, -928}},
+/* GU.C..GU */
+{{ -50, -259, -239, -239, -239},{ -649, -858, -838, -838, -838},{ -289, -498, -478, -478, -478},{ -739, -948, -928, -928, -928},{ -379, -588, -568, -568, -568}},
+/* GU.G..GU */
+{{ -50, -339, -689, -689, -689},{ -649, -938,-1288,-1288,-1288},{ -289, -578, -928, -928, -928},{ -739,-1028,-1378,-1378,-1378},{ -379, -668,-1018,-1018,-1018}},
+/* GU.U..GU */
+{{ -50, -329, -329, -329, -329},{ -649, -928, -928, -928, -928},{ -289, -568, -568, -568, -568},{ -739,-1018,-1018,-1018,-1018},{ -379, -658, -658, -658, -658}}
+},
+{
+/* GU.@..UG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GU.A..UG */
+{{ -50, -429, -599, -599, -599},{ -769,-1148,-1318,-1318,-1318},{ -529, -908,-1078,-1078,-1078},{ -709,-1088,-1258,-1258,-1258},{ -599, -978,-1148,-1148,-1148}},
+/* GU.C..UG */
+{{ -50, -259, -239, -239, -239},{ -839,-1048,-1028,-1028,-1028},{ -529, -738, -718, -718, -718},{ -859,-1068,-1048,-1048,-1048},{ -489, -698, -678, -678, -678}},
+/* GU.G..UG */
+{{ -50, -339, -689, -689, -689},{-1009,-1298,-1648,-1648,-1648},{ -409, -698,-1048,-1048,-1048},{ -969,-1258,-1608,-1608,-1608},{ -599, -888,-1238,-1238,-1238}},
+/* GU.U..UG */
+{{ -50, -329, -329, -329, -329},{ -859,-1138,-1138,-1138,-1138},{ -529, -808, -808, -808, -808},{ -859,-1138,-1138,-1138,-1138},{ -409, -688, -688, -688, -688}}
+},
+{
+/* GU.@..AU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GU.A..AU */
+{{ -50, -429, -599, -599, -599},{ -479, -858,-1028,-1028,-1028},{ -309, -688, -858, -858, -858},{ -389, -768, -938, -938, -938},{ -379, -758, -928, -928, -928}},
+/* GU.C..AU */
+{{ -50, -259, -239, -239, -239},{ -649, -858, -838, -838, -838},{ -289, -498, -478, -478, -478},{ -739, -948, -928, -928, -928},{ -379, -588, -568, -568, -568}},
+/* GU.G..AU */
+{{ -50, -339, -689, -689, -689},{ -649, -938,-1288,-1288,-1288},{ -289, -578, -928, -928, -928},{ -739,-1028,-1378,-1378,-1378},{ -379, -668,-1018,-1018,-1018}},
+/* GU.U..AU */
+{{ -50, -329, -329, -329, -329},{ -649, -928, -928, -928, -928},{ -289, -568, -568, -568, -568},{ -739,-1018,-1018,-1018,-1018},{ -379, -658, -658, -658, -658}}
+},
+{
+/* GU.@..UA */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GU.A..UA */
+{{ -50, -429, -599, -599, -599},{ -449, -828, -998, -998, -998},{ -479, -858,-1028,-1028,-1028},{ -429, -808, -978, -978, -978},{ -329, -708, -878, -878, -878}},
+/* GU.C..UA */
+{{ -50, -259, -239, -239, -239},{ -679, -888, -868, -868, -868},{ -559, -768, -748, -748, -748},{ -729, -938, -918, -918, -918},{ -189, -398, -378, -378, -378}},
+/* GU.G..UA */
+{{ -50, -339, -689, -689, -689},{ -939,-1228,-1578,-1578,-1578},{ -249, -538, -888, -888, -888},{ -939,-1228,-1578,-1578,-1578},{ -329, -618, -968, -968, -968}},
+/* GU.U..UA */
+{{ -50, -329, -329, -329, -329},{ -639, -918, -918, -918, -918},{ -229, -508, -508, -508, -508},{ -729,-1008,-1008,-1008,-1008},{ -190, -469, -469, -469, -469}}
+},
+{
+/* GU.@.. @ */
+{{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* GU.A.. @ */
+{{ -100, -479, -649, -649, -649},{ -100, -479, -649, -649, -649},{ -100, -479, -649, -649, -649},{ -100, -479, -649, -649, -649},{ -100, -479, -649, -649, -649}},
+/* GU.C.. @ */
+{{ -100, -309, -289, -289, -289},{ -100, -309, -289, -289, -289},{ -100, -309, -289, -289, -289},{ -100, -309, -289, -289, -289},{ -100, -309, -289, -289, -289}},
+/* GU.G.. @ */
+{{ -100, -389, -739, -739, -739},{ -100, -389, -739, -739, -739},{ -100, -389, -739, -739, -739},{ -100, -389, -739, -739, -739},{ -100, -389, -739, -739, -739}},
+/* GU.U.. @ */
+{{ -100, -379, -379, -379, -379},{ -100, -379, -379, -379, -379},{ -100, -379, -379, -379, -379},{ -100, -379, -379, -379, -379},{ -100, -379, -379, -379, -379}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* UG.@..CG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UG.A..CG */
+{{ -50, -719, -789, -959, -809},{-1079,-1748,-1818,-1988,-1838},{ -569,-1238,-1308,-1478,-1328},{ -989,-1658,-1728,-1898,-1748},{ -859,-1528,-1598,-1768,-1618}},
+/* UG.C..CG */
+{{ -50, -479, -479, -359, -479},{ -999,-1428,-1428,-1308,-1428},{ -499, -928, -928, -808, -928},{ -989,-1418,-1418,-1298,-1418},{ -789,-1218,-1218,-1098,-1218}},
+/* UG.G..CG */
+{{ -50, -659, -809, -919, -809},{-1079,-1688,-1838,-1948,-1838},{ -569,-1178,-1328,-1438,-1328},{ -989,-1598,-1748,-1858,-1748},{ -859,-1468,-1618,-1728,-1618}},
+/* UG.U..CG */
+{{ -50, -549, -439, -549, -359},{-1079,-1578,-1468,-1578,-1388},{ -719,-1218,-1108,-1218,-1028},{ -989,-1488,-1378,-1488,-1298},{ -909,-1408,-1298,-1408,-1218}}
+},
+{
+/* UG.@..GC */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UG.A..GC */
+{{ -50, -719, -789, -959, -809},{ -569,-1238,-1308,-1478,-1328},{ -769,-1438,-1508,-1678,-1528},{ -759,-1428,-1498,-1668,-1518},{ -549,-1218,-1288,-1458,-1308}},
+/* UG.C..GC */
+{{ -50, -479, -479, -359, -479},{ -929,-1358,-1358,-1238,-1358},{ -359, -788, -788, -668, -788},{ -789,-1218,-1218,-1098,-1218},{ -549, -978, -978, -858, -978}},
+/* UG.G..GC */
+{{ -50, -659, -809, -919, -809},{ -609,-1218,-1368,-1478,-1368},{ -359, -968,-1118,-1228,-1118},{ -669,-1278,-1428,-1538,-1428},{ -549,-1158,-1308,-1418,-1308}},
+/* UG.U..GC */
+{{ -50, -549, -439, -549, -359},{ -929,-1428,-1318,-1428,-1238},{ -439, -938, -828, -938, -748},{ -789,-1288,-1178,-1288,-1098},{ -619,-1118,-1008,-1118, -928}}
+},
+{
+/* UG.@..GU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UG.A..GU */
+{{ -50, -719, -789, -959, -809},{ -479,-1148,-1218,-1388,-1238},{ -309, -978,-1048,-1218,-1068},{ -389,-1058,-1128,-1298,-1148},{ -379,-1048,-1118,-1288,-1138}},
+/* UG.C..GU */
+{{ -50, -479, -479, -359, -479},{ -649,-1078,-1078, -958,-1078},{ -289, -718, -718, -598, -718},{ -739,-1168,-1168,-1048,-1168},{ -379, -808, -808, -688, -808}},
+/* UG.G..GU */
+{{ -50, -659, -809, -919, -809},{ -649,-1258,-1408,-1518,-1408},{ -289, -898,-1048,-1158,-1048},{ -739,-1348,-1498,-1608,-1498},{ -379, -988,-1138,-1248,-1138}},
+/* UG.U..GU */
+{{ -50, -549, -439, -549, -359},{ -649,-1148,-1038,-1148, -958},{ -289, -788, -678, -788, -598},{ -739,-1238,-1128,-1238,-1048},{ -379, -878, -768, -878, -688}}
+},
+{
+/* UG.@..UG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UG.A..UG */
+{{ -50, -719, -789, -959, -809},{ -769,-1438,-1508,-1678,-1528},{ -529,-1198,-1268,-1438,-1288},{ -709,-1378,-1448,-1618,-1468},{ -599,-1268,-1338,-1508,-1358}},
+/* UG.C..UG */
+{{ -50, -479, -479, -359, -479},{ -839,-1268,-1268,-1148,-1268},{ -529, -958, -958, -838, -958},{ -859,-1288,-1288,-1168,-1288},{ -489, -918, -918, -798, -918}},
+/* UG.G..UG */
+{{ -50, -659, -809, -919, -809},{-1009,-1618,-1768,-1878,-1768},{ -409,-1018,-1168,-1278,-1168},{ -969,-1578,-1728,-1838,-1728},{ -599,-1208,-1358,-1468,-1358}},
+/* UG.U..UG */
+{{ -50, -549, -439, -549, -359},{ -859,-1358,-1248,-1358,-1168},{ -529,-1028, -918,-1028, -838},{ -859,-1358,-1248,-1358,-1168},{ -409, -908, -798, -908, -718}}
+},
+{
+/* UG.@..AU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UG.A..AU */
+{{ -50, -719, -789, -959, -809},{ -479,-1148,-1218,-1388,-1238},{ -309, -978,-1048,-1218,-1068},{ -389,-1058,-1128,-1298,-1148},{ -379,-1048,-1118,-1288,-1138}},
+/* UG.C..AU */
+{{ -50, -479, -479, -359, -479},{ -649,-1078,-1078, -958,-1078},{ -289, -718, -718, -598, -718},{ -739,-1168,-1168,-1048,-1168},{ -379, -808, -808, -688, -808}},
+/* UG.G..AU */
+{{ -50, -659, -809, -919, -809},{ -649,-1258,-1408,-1518,-1408},{ -289, -898,-1048,-1158,-1048},{ -739,-1348,-1498,-1608,-1498},{ -379, -988,-1138,-1248,-1138}},
+/* UG.U..AU */
+{{ -50, -549, -439, -549, -359},{ -649,-1148,-1038,-1148, -958},{ -289, -788, -678, -788, -598},{ -739,-1238,-1128,-1238,-1048},{ -379, -878, -768, -878, -688}}
+},
+{
+/* UG.@..UA */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UG.A..UA */
+{{ -50, -719, -789, -959, -809},{ -449,-1118,-1188,-1358,-1208},{ -479,-1148,-1218,-1388,-1238},{ -429,-1098,-1168,-1338,-1188},{ -329, -998,-1068,-1238,-1088}},
+/* UG.C..UA */
+{{ -50, -479, -479, -359, -479},{ -679,-1108,-1108, -988,-1108},{ -559, -988, -988, -868, -988},{ -729,-1158,-1158,-1038,-1158},{ -189, -618, -618, -498, -618}},
+/* UG.G..UA */
+{{ -50, -659, -809, -919, -809},{ -939,-1548,-1698,-1808,-1698},{ -249, -858,-1008,-1118,-1008},{ -939,-1548,-1698,-1808,-1698},{ -329, -938,-1088,-1198,-1088}},
+/* UG.U..UA */
+{{ -50, -549, -439, -549, -359},{ -639,-1138,-1028,-1138, -948},{ -229, -728, -618, -728, -538},{ -729,-1228,-1118,-1228,-1038},{ -190, -689, -579, -689, -499}}
+},
+{
+/* UG.@.. @ */
+{{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UG.A.. @ */
+{{ -100, -769, -839,-1009, -859},{ -100, -769, -839,-1009, -859},{ -100, -769, -839,-1009, -859},{ -100, -769, -839,-1009, -859},{ -100, -769, -839,-1009, -859}},
+/* UG.C.. @ */
+{{ -100, -529, -529, -409, -529},{ -100, -529, -529, -409, -529},{ -100, -529, -529, -409, -529},{ -100, -529, -529, -409, -529},{ -100, -529, -529, -409, -529}},
+/* UG.G.. @ */
+{{ -100, -709, -859, -969, -859},{ -100, -709, -859, -969, -859},{ -100, -709, -859, -969, -859},{ -100, -709, -859, -969, -859},{ -100, -709, -859, -969, -859}},
+/* UG.U.. @ */
+{{ -100, -599, -489, -599, -409},{ -100, -599, -489, -599, -409},{ -100, -599, -489, -599, -409},{ -100, -599, -489, -599, -409},{ -100, -599, -489, -599, -409}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* AU.@..CG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* AU.A..CG */
+{{ -50, -429, -599, -599, -599},{-1079,-1458,-1628,-1628,-1628},{ -569, -948,-1118,-1118,-1118},{ -989,-1368,-1538,-1538,-1538},{ -859,-1238,-1408,-1408,-1408}},
+/* AU.C..CG */
+{{ -50, -259, -239, -239, -239},{ -999,-1208,-1188,-1188,-1188},{ -499, -708, -688, -688, -688},{ -989,-1198,-1178,-1178,-1178},{ -789, -998, -978, -978, -978}},
+/* AU.G..CG */
+{{ -50, -339, -689, -689, -689},{-1079,-1368,-1718,-1718,-1718},{ -569, -858,-1208,-1208,-1208},{ -989,-1278,-1628,-1628,-1628},{ -859,-1148,-1498,-1498,-1498}},
+/* AU.U..CG */
+{{ -50, -329, -329, -329, -329},{-1079,-1358,-1358,-1358,-1358},{ -719, -998, -998, -998, -998},{ -989,-1268,-1268,-1268,-1268},{ -909,-1188,-1188,-1188,-1188}}
+},
+{
+/* AU.@..GC */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* AU.A..GC */
+{{ -50, -429, -599, -599, -599},{ -569, -948,-1118,-1118,-1118},{ -769,-1148,-1318,-1318,-1318},{ -759,-1138,-1308,-1308,-1308},{ -549, -928,-1098,-1098,-1098}},
+/* AU.C..GC */
+{{ -50, -259, -239, -239, -239},{ -929,-1138,-1118,-1118,-1118},{ -359, -568, -548, -548, -548},{ -789, -998, -978, -978, -978},{ -549, -758, -738, -738, -738}},
+/* AU.G..GC */
+{{ -50, -339, -689, -689, -689},{ -609, -898,-1248,-1248,-1248},{ -359, -648, -998, -998, -998},{ -669, -958,-1308,-1308,-1308},{ -549, -838,-1188,-1188,-1188}},
+/* AU.U..GC */
+{{ -50, -329, -329, -329, -329},{ -929,-1208,-1208,-1208,-1208},{ -439, -718, -718, -718, -718},{ -789,-1068,-1068,-1068,-1068},{ -619, -898, -898, -898, -898}}
+},
+{
+/* AU.@..GU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* AU.A..GU */
+{{ -50, -429, -599, -599, -599},{ -479, -858,-1028,-1028,-1028},{ -309, -688, -858, -858, -858},{ -389, -768, -938, -938, -938},{ -379, -758, -928, -928, -928}},
+/* AU.C..GU */
+{{ -50, -259, -239, -239, -239},{ -649, -858, -838, -838, -838},{ -289, -498, -478, -478, -478},{ -739, -948, -928, -928, -928},{ -379, -588, -568, -568, -568}},
+/* AU.G..GU */
+{{ -50, -339, -689, -689, -689},{ -649, -938,-1288,-1288,-1288},{ -289, -578, -928, -928, -928},{ -739,-1028,-1378,-1378,-1378},{ -379, -668,-1018,-1018,-1018}},
+/* AU.U..GU */
+{{ -50, -329, -329, -329, -329},{ -649, -928, -928, -928, -928},{ -289, -568, -568, -568, -568},{ -739,-1018,-1018,-1018,-1018},{ -379, -658, -658, -658, -658}}
+},
+{
+/* AU.@..UG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* AU.A..UG */
+{{ -50, -429, -599, -599, -599},{ -769,-1148,-1318,-1318,-1318},{ -529, -908,-1078,-1078,-1078},{ -709,-1088,-1258,-1258,-1258},{ -599, -978,-1148,-1148,-1148}},
+/* AU.C..UG */
+{{ -50, -259, -239, -239, -239},{ -839,-1048,-1028,-1028,-1028},{ -529, -738, -718, -718, -718},{ -859,-1068,-1048,-1048,-1048},{ -489, -698, -678, -678, -678}},
+/* AU.G..UG */
+{{ -50, -339, -689, -689, -689},{-1009,-1298,-1648,-1648,-1648},{ -409, -698,-1048,-1048,-1048},{ -969,-1258,-1608,-1608,-1608},{ -599, -888,-1238,-1238,-1238}},
+/* AU.U..UG */
+{{ -50, -329, -329, -329, -329},{ -859,-1138,-1138,-1138,-1138},{ -529, -808, -808, -808, -808},{ -859,-1138,-1138,-1138,-1138},{ -409, -688, -688, -688, -688}}
+},
+{
+/* AU.@..AU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* AU.A..AU */
+{{ -50, -429, -599, -599, -599},{ -479, -858,-1028,-1028,-1028},{ -309, -688, -858, -858, -858},{ -389, -768, -938, -938, -938},{ -379, -758, -928, -928, -928}},
+/* AU.C..AU */
+{{ -50, -259, -239, -239, -239},{ -649, -858, -838, -838, -838},{ -289, -498, -478, -478, -478},{ -739, -948, -928, -928, -928},{ -379, -588, -568, -568, -568}},
+/* AU.G..AU */
+{{ -50, -339, -689, -689, -689},{ -649, -938,-1288,-1288,-1288},{ -289, -578, -928, -928, -928},{ -739,-1028,-1378,-1378,-1378},{ -379, -668,-1018,-1018,-1018}},
+/* AU.U..AU */
+{{ -50, -329, -329, -329, -329},{ -649, -928, -928, -928, -928},{ -289, -568, -568, -568, -568},{ -739,-1018,-1018,-1018,-1018},{ -379, -658, -658, -658, -658}}
+},
+{
+/* AU.@..UA */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* AU.A..UA */
+{{ -50, -429, -599, -599, -599},{ -449, -828, -998, -998, -998},{ -479, -858,-1028,-1028,-1028},{ -429, -808, -978, -978, -978},{ -329, -708, -878, -878, -878}},
+/* AU.C..UA */
+{{ -50, -259, -239, -239, -239},{ -679, -888, -868, -868, -868},{ -559, -768, -748, -748, -748},{ -729, -938, -918, -918, -918},{ -189, -398, -378, -378, -378}},
+/* AU.G..UA */
+{{ -50, -339, -689, -689, -689},{ -939,-1228,-1578,-1578,-1578},{ -249, -538, -888, -888, -888},{ -939,-1228,-1578,-1578,-1578},{ -329, -618, -968, -968, -968}},
+/* AU.U..UA */
+{{ -50, -329, -329, -329, -329},{ -639, -918, -918, -918, -918},{ -229, -508, -508, -508, -508},{ -729,-1008,-1008,-1008,-1008},{ -190, -469, -469, -469, -469}}
+},
+{
+/* AU.@.. @ */
+{{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* AU.A.. @ */
+{{ -100, -479, -649, -649, -649},{ -100, -479, -649, -649, -649},{ -100, -479, -649, -649, -649},{ -100, -479, -649, -649, -649},{ -100, -479, -649, -649, -649}},
+/* AU.C.. @ */
+{{ -100, -309, -289, -289, -289},{ -100, -309, -289, -289, -289},{ -100, -309, -289, -289, -289},{ -100, -309, -289, -289, -289},{ -100, -309, -289, -289, -289}},
+/* AU.G.. @ */
+{{ -100, -389, -739, -739, -739},{ -100, -389, -739, -739, -739},{ -100, -389, -739, -739, -739},{ -100, -389, -739, -739, -739},{ -100, -389, -739, -739, -739}},
+/* AU.U.. @ */
+{{ -100, -379, -379, -379, -379},{ -100, -379, -379, -379, -379},{ -100, -379, -379, -379, -379},{ -100, -379, -379, -379, -379},{ -100, -379, -379, -379, -379}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* UA.@..CG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UA.A..CG */
+{{ -50, -399, -629, -889, -589},{-1079,-1428,-1658,-1918,-1618},{ -569, -918,-1148,-1408,-1108},{ -989,-1338,-1568,-1828,-1528},{ -859,-1208,-1438,-1698,-1398}},
+/* UA.C..CG */
+{{ -50, -429, -509, -199, -179},{ -999,-1378,-1458,-1148,-1128},{ -499, -878, -958, -648, -628},{ -989,-1368,-1448,-1138,-1118},{ -789,-1168,-1248, -938, -918}},
+/* UA.G..CG */
+{{ -50, -379, -679, -889, -679},{-1079,-1408,-1708,-1918,-1708},{ -569, -898,-1198,-1408,-1198},{ -989,-1318,-1618,-1828,-1618},{ -859,-1188,-1488,-1698,-1488}},
+/* UA.U..CG */
+{{ -50, -279, -139, -279, -140},{-1079,-1308,-1168,-1308,-1169},{ -719, -948, -808, -948, -809},{ -989,-1218,-1078,-1218,-1079},{ -909,-1138, -998,-1138, -999}}
+},
+{
+/* UA.@..GC */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UA.A..GC */
+{{ -50, -399, -629, -889, -589},{ -569, -918,-1148,-1408,-1108},{ -769,-1118,-1348,-1608,-1308},{ -759,-1108,-1338,-1598,-1298},{ -549, -898,-1128,-1388,-1088}},
+/* UA.C..GC */
+{{ -50, -429, -509, -199, -179},{ -929,-1308,-1388,-1078,-1058},{ -359, -738, -818, -508, -488},{ -789,-1168,-1248, -938, -918},{ -549, -928,-1008, -698, -678}},
+/* UA.G..GC */
+{{ -50, -379, -679, -889, -679},{ -609, -938,-1238,-1448,-1238},{ -359, -688, -988,-1198, -988},{ -669, -998,-1298,-1508,-1298},{ -549, -878,-1178,-1388,-1178}},
+/* UA.U..GC */
+{{ -50, -279, -139, -279, -140},{ -929,-1158,-1018,-1158,-1019},{ -439, -668, -528, -668, -529},{ -789,-1018, -878,-1018, -879},{ -619, -848, -708, -848, -709}}
+},
+{
+/* UA.@..GU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UA.A..GU */
+{{ -50, -399, -629, -889, -589},{ -479, -828,-1058,-1318,-1018},{ -309, -658, -888,-1148, -848},{ -389, -738, -968,-1228, -928},{ -379, -728, -958,-1218, -918}},
+/* UA.C..GU */
+{{ -50, -429, -509, -199, -179},{ -649,-1028,-1108, -798, -778},{ -289, -668, -748, -438, -418},{ -739,-1118,-1198, -888, -868},{ -379, -758, -838, -528, -508}},
+/* UA.G..GU */
+{{ -50, -379, -679, -889, -679},{ -649, -978,-1278,-1488,-1278},{ -289, -618, -918,-1128, -918},{ -739,-1068,-1368,-1578,-1368},{ -379, -708,-1008,-1218,-1008}},
+/* UA.U..GU */
+{{ -50, -279, -139, -279, -140},{ -649, -878, -738, -878, -739},{ -289, -518, -378, -518, -379},{ -739, -968, -828, -968, -829},{ -379, -608, -468, -608, -469}}
+},
+{
+/* UA.@..UG */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UA.A..UG */
+{{ -50, -399, -629, -889, -589},{ -769,-1118,-1348,-1608,-1308},{ -529, -878,-1108,-1368,-1068},{ -709,-1058,-1288,-1548,-1248},{ -599, -948,-1178,-1438,-1138}},
+/* UA.C..UG */
+{{ -50, -429, -509, -199, -179},{ -839,-1218,-1298, -988, -968},{ -529, -908, -988, -678, -658},{ -859,-1238,-1318,-1008, -988},{ -489, -868, -948, -638, -618}},
+/* UA.G..UG */
+{{ -50, -379, -679, -889, -679},{-1009,-1338,-1638,-1848,-1638},{ -409, -738,-1038,-1248,-1038},{ -969,-1298,-1598,-1808,-1598},{ -599, -928,-1228,-1438,-1228}},
+/* UA.U..UG */
+{{ -50, -279, -139, -279, -140},{ -859,-1088, -948,-1088, -949},{ -529, -758, -618, -758, -619},{ -859,-1088, -948,-1088, -949},{ -409, -638, -498, -638, -499}}
+},
+{
+/* UA.@..AU */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UA.A..AU */
+{{ -50, -399, -629, -889, -589},{ -479, -828,-1058,-1318,-1018},{ -309, -658, -888,-1148, -848},{ -389, -738, -968,-1228, -928},{ -379, -728, -958,-1218, -918}},
+/* UA.C..AU */
+{{ -50, -429, -509, -199, -179},{ -649,-1028,-1108, -798, -778},{ -289, -668, -748, -438, -418},{ -739,-1118,-1198, -888, -868},{ -379, -758, -838, -528, -508}},
+/* UA.G..AU */
+{{ -50, -379, -679, -889, -679},{ -649, -978,-1278,-1488,-1278},{ -289, -618, -918,-1128, -918},{ -739,-1068,-1368,-1578,-1368},{ -379, -708,-1008,-1218,-1008}},
+/* UA.U..AU */
+{{ -50, -279, -139, -279, -140},{ -649, -878, -738, -878, -739},{ -289, -518, -378, -518, -379},{ -739, -968, -828, -968, -829},{ -379, -608, -468, -608, -469}}
+},
+{
+/* UA.@..UA */
+{{ 0, 0, 0, 0, 0},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UA.A..UA */
+{{ -50, -399, -629, -889, -589},{ -449, -798,-1028,-1288, -988},{ -479, -828,-1058,-1318,-1018},{ -429, -778,-1008,-1268, -968},{ -329, -678, -908,-1168, -868}},
+/* UA.C..UA */
+{{ -50, -429, -509, -199, -179},{ -679,-1058,-1138, -828, -808},{ -559, -938,-1018, -708, -688},{ -729,-1108,-1188, -878, -858},{ -189, -568, -648, -338, -318}},
+/* UA.G..UA */
+{{ -50, -379, -679, -889, -679},{ -939,-1268,-1568,-1778,-1568},{ -249, -578, -878,-1088, -878},{ -939,-1268,-1568,-1778,-1568},{ -329, -658, -958,-1168, -958}},
+/* UA.U..UA */
+{{ -50, -279, -139, -279, -140},{ -639, -868, -728, -868, -729},{ -229, -458, -318, -458, -319},{ -729, -958, -818, -958, -819},{ -190, -419, -279, -419, -280}}
+},
+{
+/* UA.@.. @ */
+{{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50},{ -50, -50, -50, -50, -50}},
+/* UA.A.. @ */
+{{ -100, -449, -679, -939, -639},{ -100, -449, -679, -939, -639},{ -100, -449, -679, -939, -639},{ -100, -449, -679, -939, -639},{ -100, -449, -679, -939, -639}},
+/* UA.C.. @ */
+{{ -100, -479, -559, -249, -229},{ -100, -479, -559, -249, -229},{ -100, -479, -559, -249, -229},{ -100, -479, -559, -249, -229},{ -100, -479, -559, -249, -229}},
+/* UA.G.. @ */
+{{ -100, -429, -729, -939, -729},{ -100, -429, -729, -939, -729},{ -100, -429, -729, -939, -729},{ -100, -429, -729, -939, -729},{ -100, -429, -729, -939, -729}},
+/* UA.U.. @ */
+{{ -100, -329, -189, -329, -190},{ -100, -329, -189, -329, -190},{ -100, -329, -189, -329, -190},{ -100, -329, -189, -329, -190},{ -100, -329, -189, -329, -190}}
+}
+},
+{ /* noPair */ {{{0}}},
+{
+/* @.@..CG */
+{{ -50, -50, -50, -50, -50},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.A..CG */
+{{ -50, -50, -50, -50, -50},{-1079,-1079,-1079,-1079,-1079},{ -569, -569, -569, -569, -569},{ -989, -989, -989, -989, -989},{ -859, -859, -859, -859, -859}},
+/* @.C..CG */
+{{ -50, -50, -50, -50, -50},{ -999, -999, -999, -999, -999},{ -499, -499, -499, -499, -499},{ -989, -989, -989, -989, -989},{ -789, -789, -789, -789, -789}},
+/* @.G..CG */
+{{ -50, -50, -50, -50, -50},{-1079,-1079,-1079,-1079,-1079},{ -569, -569, -569, -569, -569},{ -989, -989, -989, -989, -989},{ -859, -859, -859, -859, -859}},
+/* @.U..CG */
+{{ -50, -50, -50, -50, -50},{-1079,-1079,-1079,-1079,-1079},{ -719, -719, -719, -719, -719},{ -989, -989, -989, -989, -989},{ -909, -909, -909, -909, -909}}
+},
+{
+/* @.@..GC */
+{{ -50, -50, -50, -50, -50},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.A..GC */
+{{ -50, -50, -50, -50, -50},{ -569, -569, -569, -569, -569},{ -769, -769, -769, -769, -769},{ -759, -759, -759, -759, -759},{ -549, -549, -549, -549, -549}},
+/* @.C..GC */
+{{ -50, -50, -50, -50, -50},{ -929, -929, -929, -929, -929},{ -359, -359, -359, -359, -359},{ -789, -789, -789, -789, -789},{ -549, -549, -549, -549, -549}},
+/* @.G..GC */
+{{ -50, -50, -50, -50, -50},{ -609, -609, -609, -609, -609},{ -359, -359, -359, -359, -359},{ -669, -669, -669, -669, -669},{ -549, -549, -549, -549, -549}},
+/* @.U..GC */
+{{ -50, -50, -50, -50, -50},{ -929, -929, -929, -929, -929},{ -439, -439, -439, -439, -439},{ -789, -789, -789, -789, -789},{ -619, -619, -619, -619, -619}}
+},
+{
+/* @.@..GU */
+{{ -50, -50, -50, -50, -50},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.A..GU */
+{{ -50, -50, -50, -50, -50},{ -479, -479, -479, -479, -479},{ -309, -309, -309, -309, -309},{ -389, -389, -389, -389, -389},{ -379, -379, -379, -379, -379}},
+/* @.C..GU */
+{{ -50, -50, -50, -50, -50},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}},
+/* @.G..GU */
+{{ -50, -50, -50, -50, -50},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}},
+/* @.U..GU */
+{{ -50, -50, -50, -50, -50},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}}
+},
+{
+/* @.@..UG */
+{{ -50, -50, -50, -50, -50},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.A..UG */
+{{ -50, -50, -50, -50, -50},{ -769, -769, -769, -769, -769},{ -529, -529, -529, -529, -529},{ -709, -709, -709, -709, -709},{ -599, -599, -599, -599, -599}},
+/* @.C..UG */
+{{ -50, -50, -50, -50, -50},{ -839, -839, -839, -839, -839},{ -529, -529, -529, -529, -529},{ -859, -859, -859, -859, -859},{ -489, -489, -489, -489, -489}},
+/* @.G..UG */
+{{ -50, -50, -50, -50, -50},{-1009,-1009,-1009,-1009,-1009},{ -409, -409, -409, -409, -409},{ -969, -969, -969, -969, -969},{ -599, -599, -599, -599, -599}},
+/* @.U..UG */
+{{ -50, -50, -50, -50, -50},{ -859, -859, -859, -859, -859},{ -529, -529, -529, -529, -529},{ -859, -859, -859, -859, -859},{ -409, -409, -409, -409, -409}}
+},
+{
+/* @.@..AU */
+{{ -50, -50, -50, -50, -50},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.A..AU */
+{{ -50, -50, -50, -50, -50},{ -479, -479, -479, -479, -479},{ -309, -309, -309, -309, -309},{ -389, -389, -389, -389, -389},{ -379, -379, -379, -379, -379}},
+/* @.C..AU */
+{{ -50, -50, -50, -50, -50},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}},
+/* @.G..AU */
+{{ -50, -50, -50, -50, -50},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}},
+/* @.U..AU */
+{{ -50, -50, -50, -50, -50},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}}
+},
+{
+/* @.@..UA */
+{{ -50, -50, -50, -50, -50},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.A..UA */
+{{ -50, -50, -50, -50, -50},{ -449, -449, -449, -449, -449},{ -479, -479, -479, -479, -479},{ -429, -429, -429, -429, -429},{ -329, -329, -329, -329, -329}},
+/* @.C..UA */
+{{ -50, -50, -50, -50, -50},{ -679, -679, -679, -679, -679},{ -559, -559, -559, -559, -559},{ -729, -729, -729, -729, -729},{ -189, -189, -189, -189, -189}},
+/* @.G..UA */
+{{ -50, -50, -50, -50, -50},{ -939, -939, -939, -939, -939},{ -249, -249, -249, -249, -249},{ -939, -939, -939, -939, -939},{ -329, -329, -329, -329, -329}},
+/* @.U..UA */
+{{ -50, -50, -50, -50, -50},{ -639, -639, -639, -639, -639},{ -229, -229, -229, -229, -229},{ -729, -729, -729, -729, -729},{ -190, -190, -190, -190, -190}}
+},
+{
+/* @.@.. @ */
+{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.A.. @ */
+{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.C.. @ */
+{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.G.. @ */
+{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},
+/* @.U.. @ */
+{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}}
+}
+}
+};
+
+const int energy_param::int22_37[8][8][5][5][5][5] = {
+/* noPair */ {{{{{0}}}}},
+{ /* noPair */ {{{{0}}}},
+/* CG....CG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 160, 30, 200},{ 340, 120, 150, 20, 200},{ 340, 30, 60, -70, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 60, 200},{ 340, 210, 180, 150, 200},{ 340, 200, 200, 200, 200},{ 340, 190, 170, 130, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 30, 60, -70, 200},{ 340, 200, 200, 200, 200},{ 340, 100, 140, 0, 200},{ 340, -40, -110, -60, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 190, 170, 130, 200},{ 340, 110, 40, 90, 200},{ 340, 140, 80, 130, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 120, 210, 200, 190},{ 340, 110, 140, 200, 120},{ 340, 20, 150, 200, 130},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 180, 200, 170},{ 340, 140, 170, 200, 150},{ 340, 200, 200, 200, 200},{ 340, 120, 150, 200, 140}},
+{{ 340, 340, 340, 340, 340},{ 340, 20, 150, 200, 130},{ 340, 200, 200, 200, 200},{ 340, 90, 180, 200, 170},{ 340, -150, -20, 200, -40}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 120, 150, 200, 140},{ 340, 0, 130, 200, 110},{ 340, 30, 60, 200, 50}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 30, 200, 100, 110},{ 340, 20, 200, 90, 0},{ 340, -70, 200, 0, 90},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 60, 200, 140, 40},{ 340, 150, 200, 180, 130},{ 340, 200, 200, 200, 200},{ 340, 130, 200, 170, 110}},
+{{ 340, 340, 340, 340, 340},{ 340, -70, 200, 0, 90},{ 340, 200, 200, 200, 200},{ 340, 0, 200, 80, 90},{ 340, -60, 200, -70, -260}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 130, 200, 170, 110},{ 340, 90, 200, 90, -110},{ 340, 130, 200, 120, 110}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 190, -40, 140},{ 340, 200, 120, -150, 30},{ 340, 200, 130, -60, 130},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 170, -110, 80},{ 340, 200, 150, -20, 60},{ 340, 200, 200, 200, 200},{ 340, 200, 140, -40, 50}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 130, -60, 130},{ 340, 200, 200, 200, 200},{ 340, 200, 170, -70, 120},{ 340, 200, -40, -420, -50}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 140, -40, 50},{ 340, 200, 110, -260, 110},{ 340, 200, 50, -50, -40}}
+}
+},
+/* CG....GC */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 60, 0, 200},{ 340, 110, 150, -70, 200},{ 340, -30, 10, -160, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 110, -100, 200},{ 340, 170, 150, -60, 200},{ 340, 200, 200, 200, 200},{ 340, 70, 50, 20, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 40, 50, -70, 200},{ 340, 200, 200, 200, 200},{ 340, 100, 140, 0, 200},{ 340, 10, -70, -80, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 150, 120, 200},{ 340, -50, -60, -60, 200},{ 340, 150, 0, 90, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 200},{ 340, 100, 130, 200, 120},{ 340, -70, 70, 200, 40},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 190, 200, 110},{ 340, 100, 130, 200, 120},{ 340, 200, 200, 200, 200},{ 340, 0, 30, 200, 170}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 70, 200, 100},{ 340, 200, 200, 200, 200},{ 340, 90, 180, 200, 170},{ 340, -190, -30, 200, -70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 110, 140, 200, 120},{ 340, -150, -20, 200, -30},{ 340, -20, -10, 200, 20}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, -20, 200, 110, 90},{ 340, -40, 200, 90, 0},{ 340, -170, 200, -90, 30},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 200, 80, -10},{ 340, 110, 200, 150, 100},{ 340, 200, 200, 200, 200},{ 340, 20, 200, 50, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, -50, 200, -20, 60},{ 340, 200, 200, 200, 200},{ 340, 0, 200, 80, 90},{ 340, -90, 200, -100, -300}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 120, 200, 150, 100},{ 340, -130, 200, -60, -240},{ 340, 90, 200, 110, 60}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, -10, 140},{ 340, 200, 120, -160, 30},{ 340, 200, 40, -160, 50},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 110, -160, 30},{ 340, 200, 120, -60, 30},{ 340, 200, 200, 200, 200},{ 340, 200, 20, -160, 10}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 50, -60, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 170, -70, 120},{ 340, 200, -70, -440, -100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 120, -50, 30},{ 340, 200, -10, -410, 10},{ 340, 200, 40, -100, 60}}
+}
+},
+/* CG....GU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 180, 210, 80, 200},{ 340, 80, 110, -20, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 220, 90, 200},{ 340, 230, 210, 170, 200},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 110, -20, 200},{ 340, 200, 200, 200, 200},{ 340, 130, 170, 30, 200},{ 340, 60, 0, 40, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200},{ 340, 160, 90, 140, 200},{ 340, 190, 130, 180, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 280, 200, 270},{ 340, 170, 200, 200, 180},{ 340, 70, 200, 200, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 180, 210, 200, 190},{ 340, 160, 190, 200, 180},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 200, 200, 180},{ 340, 200, 200, 200, 200},{ 340, 120, 210, 200, 200},{ 340, -50, 80, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180},{ 340, 50, 180, 200, 160},{ 340, 80, 110, 200, 100}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 180},{ 340, 80, 200, 150, 60},{ 340, -20, 200, 50, 140},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 200, 160, 70},{ 340, 170, 200, 210, 150},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150}},
+{{ 340, 340, 340, 340, 340},{ 340, -20, 200, 50, 140},{ 340, 200, 200, 200, 200},{ 340, 30, 200, 110, 110},{ 340, 40, 200, 40, -160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150},{ 340, 140, 200, 130, -60},{ 340, 180, 200, 170, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 30, 220},{ 340, 200, 180, -90, 90},{ 340, 200, 180, -10, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 190, -80, 100},{ 340, 200, 180, 0, 90},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 0, 90}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 180, -10, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 200, -40, 150},{ 340, 200, 70, -310, 60}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 0, 90},{ 340, 200, 160, -210, 160},{ 340, 200, 100, 0, 10}}
+}
+},
+/* CG....UG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 160, 190, 60, 200},{ 340, 100, 130, 0, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 260, 240, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 260, 240, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 130, 0, 200},{ 340, 200, 200, 200, 200},{ 340, 140, 170, 40, 200},{ 340, 20, -40, 0, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200},{ 340, 150, 80, 130, 200},{ 340, 220, 150, 200, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 280, 200, 270},{ 340, 150, 180, 200, 160},{ 340, 90, 220, 200, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 220, 200, 210},{ 340, 190, 220, 200, 210},{ 340, 200, 200, 200, 200},{ 340, 190, 220, 200, 210}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 220, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 130, 220, 200, 200},{ 340, -90, 40, 200, 30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180},{ 340, 40, 170, 200, 150},{ 340, 110, 140, 200, 120}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 180},{ 340, 60, 200, 130, 40},{ 340, 0, 200, 70, 160},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 80},{ 340, 200, 200, 240, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 240, 180}},
+{{ 340, 340, 340, 340, 340},{ 340, 0, 200, 70, 160},{ 340, 200, 200, 200, 200},{ 340, 40, 200, 110, 120},{ 340, 0, 200, 0, -200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150},{ 340, 130, 200, 120, -70},{ 340, 200, 200, 190, 180}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 30, 220},{ 340, 200, 160, -110, 70},{ 340, 200, 200, 10, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 210, -70, 120},{ 340, 200, 210, 30, 120},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 30, 120}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 10, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 200, -30, 150},{ 340, 200, 30, -350, 20}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 0, 90},{ 340, 200, 150, -220, 150},{ 340, 200, 120, 30, 30}}
+}
+},
+/* CG....AU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 180, 210, 80, 200},{ 340, 80, 110, -20, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 220, 90, 200},{ 340, 230, 210, 170, 200},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 110, -20, 200},{ 340, 200, 200, 200, 200},{ 340, 130, 170, 30, 200},{ 340, 60, 0, 40, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200},{ 340, 160, 90, 140, 200},{ 340, 190, 130, 180, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 280, 200, 270},{ 340, 170, 200, 200, 180},{ 340, 70, 200, 200, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 180, 210, 200, 190},{ 340, 160, 190, 200, 180},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 200, 200, 180},{ 340, 200, 200, 200, 200},{ 340, 120, 210, 200, 200},{ 340, -50, 80, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180},{ 340, 50, 180, 200, 160},{ 340, 80, 110, 200, 100}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 180},{ 340, 80, 200, 150, 60},{ 340, -20, 200, 50, 140},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 200, 160, 70},{ 340, 170, 200, 210, 150},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150}},
+{{ 340, 340, 340, 340, 340},{ 340, -20, 200, 50, 140},{ 340, 200, 200, 200, 200},{ 340, 30, 200, 110, 110},{ 340, 40, 200, 40, -160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150},{ 340, 140, 200, 130, -60},{ 340, 180, 200, 170, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 30, 220},{ 340, 200, 180, -90, 90},{ 340, 200, 180, -10, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 190, -80, 100},{ 340, 200, 180, 0, 90},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 0, 90}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 180, -10, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 200, -40, 150},{ 340, 200, 70, -310, 60}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 0, 90},{ 340, 200, 160, -210, 160},{ 340, 200, 100, 0, 10}}
+}
+},
+/* CG....UA */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 160, 190, 60, 200},{ 340, 100, 130, 0, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 260, 240, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 260, 240, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 130, 0, 200},{ 340, 200, 200, 200, 200},{ 340, 140, 170, 40, 200},{ 340, 20, -40, 0, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200},{ 340, 150, 80, 130, 200},{ 340, 220, 150, 200, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 280, 200, 270},{ 340, 150, 180, 200, 160},{ 340, 90, 220, 200, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 220, 200, 210},{ 340, 190, 220, 200, 210},{ 340, 200, 200, 200, 200},{ 340, 190, 220, 200, 210}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 220, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 130, 220, 200, 200},{ 340, -90, 40, 200, 30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180},{ 340, 40, 170, 200, 150},{ 340, 110, 140, 200, 120}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 180},{ 340, 60, 200, 130, 40},{ 340, 0, 200, 70, 160},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 80},{ 340, 200, 200, 240, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 240, 180}},
+{{ 340, 340, 340, 340, 340},{ 340, 0, 200, 70, 160},{ 340, 200, 200, 200, 200},{ 340, 40, 200, 110, 120},{ 340, 0, 200, 0, -200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150},{ 340, 130, 200, 120, -70},{ 340, 200, 200, 190, 180}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 30, 220},{ 340, 200, 160, -110, 70},{ 340, 200, 200, 10, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 210, -70, 120},{ 340, 200, 210, 30, 120},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 30, 120}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 10, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 200, -30, 150},{ 340, 200, 30, -350, 20}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 0, 90},{ 340, 200, 150, -220, 150},{ 340, 200, 120, 30, 30}}
+}
+},
+/* CG....?? */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+}
+},
+{ /* noPair */ {{{{0}}}},
+/* GC....CG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 110, 40, 200},{ 340, 130, 100, 70, 200},{ 340, -20, 70, -50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 60, 110, 50, 200},{ 340, 220, 190, 70, 200},{ 340, 200, 200, 200, 200},{ 340, 200, 110, 50, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 0, -100, -70, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 80, -20, 200},{ 340, -10, -160, -60, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 110, 100, 200},{ 340, 90, -10, 60, 200},{ 340, 140, 30, 140, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 170, 200, 180},{ 340, 100, 100, 200, 110},{ 340, -40, 110, 200, 120},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 150, 200, 150},{ 340, 130, 130, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 120, 120, 200, 120}},
+{{ 340, 340, 340, 340, 340},{ 340, -70, -60, 200, 120},{ 340, 200, 200, 200, 200},{ 340, 90, 150, 200, 150},{ 340, -160, -60, 200, -50}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 120, 120, 200, 120},{ 340, 0, 100, 200, 100},{ 340, 30, 30, 200, 30}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, -30, 200, 100, -50},{ 340, -70, 200, 90, -150},{ 340, -170, 200, 0, -130},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 10, 200, 140, -60},{ 340, 70, 200, 180, -20},{ 340, 200, 200, 200, 200},{ 340, 40, 200, 170, -10}},
+{{ 340, 340, 340, 340, 340},{ 340, -160, 200, 0, -60},{ 340, 200, 200, 200, 200},{ 340, -90, 200, 80, -60},{ 340, -160, 200, -70, -410}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 40, 200, 170, -30},{ 340, 30, 200, 90, -240},{ 340, 50, 200, 120, 10}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 70, 10, 150},{ 340, 200, 0, -190, -20},{ 340, 200, 20, -90, 90},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 50, -70, 0},{ 340, 200, 30, -30, -10},{ 340, 200, 200, 200, 200},{ 340, 200, 20, -70, 40}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 20, -80, 90},{ 340, 200, 200, 200, 200},{ 340, 200, 50, -100, 110},{ 340, 200, -160, -440, -100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 170, -70, 20},{ 340, 200, 0, -300, 60},{ 340, 200, 10, -100, 60}}
+}
+},
+/* GC....GC */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 120, 10, 200},{ 340, 120, 90, -10, 200},{ 340, -50, -80, -190, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 120, 90, -20, 200},{ 340, 180, 90, 90, 200},{ 340, 200, 200, 200, 200},{ 340, 80, 0, -10, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 10, -20, -130, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 80, -20, 200},{ 340, -70, -200, -130, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 190, 100, 90, 200},{ 340, -30, -160, -90, 200},{ 340, 150, 20, 90, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 120, 180, 200, 190},{ 340, 100, 100, 200, 100},{ 340, -80, 20, 200, 30},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 90, 200, 100},{ 340, 100, 100, 200, 100},{ 340, 200, 200, 200, 200},{ 340, 0, 0, 200, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, -10, 90, 200, 90},{ 340, 200, 200, 200, 200},{ 340, 90, 150, 200, 150},{ 340, -190, -90, 200, -90}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 100, 100, 200, 110},{ 340, -150, -50, 200, -50},{ 340, 20, 20, 200, 30}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, -50, 200, 110, -30},{ 340, -80, 200, 90, -150},{ 340, -260, 200, -90, -150},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, -80, 200, 80, -160},{ 340, 20, 200, 150, -50},{ 340, 200, 200, 200, 200},{ 340, -80, 200, 50, -150}},
+{{ 340, 340, 340, 340, 340},{ 340, -190, 200, -20, -90},{ 340, 200, 200, 200, 200},{ 340, -90, 200, 80, -60},{ 340, -190, 200, -100, -450}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 30, 200, 150, -50},{ 340, -150, 200, -60, -410},{ 340, 30, 200, 110, -50}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 80, -70, 150},{ 340, 200, 0, -190, 20},{ 340, 200, -80, -190, 30},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 0, -200, 20},{ 340, 200, 0, -90, 20},{ 340, 200, 200, 200, 200},{ 340, 200, -100, -190, -70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, -10, -130, 90},{ 340, 200, 200, 200, 200},{ 340, 200, 50, -100, 110},{ 340, 200, -190, -490, -90}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 0, -90, 30},{ 340, 200, -150, -450, -50},{ 340, 200, -70, -90, -50}}
+}
+},
+/* GC....GU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 180, 70, 200},{ 340, 190, 160, 50, 200},{ 340, 90, 60, -50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 170, 60, 200},{ 340, 240, 150, 140, 200},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 60, -50, 200},{ 340, 200, 200, 200, 200},{ 340, 140, 110, 0, 200},{ 340, 70, -60, 10, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200},{ 340, 170, 40, 110, 200},{ 340, 200, 70, 150, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 250, 200, 250},{ 340, 160, 160, 200, 170},{ 340, 60, 160, 200, 170},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 170, 200, 180},{ 340, 160, 160, 200, 160},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160}},
+{{ 340, 340, 340, 340, 340},{ 340, 60, 160, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 120, 180, 200, 180},{ 340, -50, 50, 200, 50}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160},{ 340, 40, 140, 200, 150},{ 340, 80, 80, 200, 80}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 10, 200, 180, 40},{ 340, -10, 200, 150, -90},{ 340, -110, 200, 50, -10},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 0, 200, 160, -80},{ 340, 80, 200, 210, 10},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 210, 10}},
+{{ 340, 340, 340, 340, 340},{ 340, -110, 200, 50, -10},{ 340, 200, 200, 200, 200},{ 340, -60, 200, 110, -30},{ 340, -50, 200, 40, -310}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 210, 10},{ 340, 50, 200, 130, -210},{ 340, 80, 200, 170, 10}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 150, 0, 210},{ 340, 200, 60, -130, 90},{ 340, 200, 70, -50, 170},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 70, -120, 100},{ 340, 200, 60, -30, 80},{ 340, 200, 200, 200, 200},{ 340, 200, 60, -30, 80}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 70, -50, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 80, -70, 140},{ 340, 200, -50, -350, 50}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 60, -30, 80},{ 340, 200, 50, -250, 150},{ 340, 200, -20, -30, 0}}
+}
+},
+/* GC....UG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 180, 70, 200},{ 340, 170, 140, 30, 200},{ 340, 110, 80, -30, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 180, 70, 200},{ 340, 270, 180, 170, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 180, 170, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 80, -30, 200},{ 340, 200, 200, 200, 200},{ 340, 150, 120, 10, 200},{ 340, 30, -100, -30, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200},{ 340, 160, 30, 100, 200},{ 340, 230, 100, 170, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 250, 200, 250},{ 340, 140, 140, 200, 150},{ 340, 80, 180, 200, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 190, 200, 190},{ 340, 190, 190, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 190, 190, 200, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 180, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 120, 180, 200, 190},{ 340, -90, 10, 200, 10}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160},{ 340, 30, 130, 200, 140},{ 340, 100, 100, 200, 110}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 10, 200, 180, 40},{ 340, -30, 200, 130, -110},{ 340, -90, 200, 70, 10},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 10, 200, 180, -60},{ 340, 110, 200, 240, 40},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 240, 40}},
+{{ 340, 340, 340, 340, 340},{ 340, -90, 200, 70, 10},{ 340, 200, 200, 200, 200},{ 340, -50, 200, 110, -30},{ 340, -90, 200, 0, -350}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 210, 10},{ 340, 40, 200, 120, -220},{ 340, 110, 200, 190, 30}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 150, 0, 210},{ 340, 200, 40, -150, 70},{ 340, 200, 90, -30, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 90, -100, 110},{ 340, 200, 90, 0, 110},{ 340, 200, 200, 200, 200},{ 340, 200, 90, 0, 110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 90, -30, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 80, -70, 150},{ 340, 200, -90, -390, 10}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 60, -30, 80},{ 340, 200, 40, -260, 140},{ 340, 200, 0, -10, 30}}
+}
+},
+/* GC....AU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 180, 70, 200},{ 340, 190, 160, 50, 200},{ 340, 90, 60, -50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 170, 60, 200},{ 340, 240, 150, 140, 200},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 60, -50, 200},{ 340, 200, 200, 200, 200},{ 340, 140, 110, 0, 200},{ 340, 70, -60, 10, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200},{ 340, 170, 40, 110, 200},{ 340, 200, 70, 150, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 250, 200, 250},{ 340, 160, 160, 200, 170},{ 340, 60, 160, 200, 170},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 170, 200, 180},{ 340, 160, 160, 200, 160},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160}},
+{{ 340, 340, 340, 340, 340},{ 340, 60, 160, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 120, 180, 200, 180},{ 340, -50, 50, 200, 50}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160},{ 340, 40, 140, 200, 150},{ 340, 80, 80, 200, 80}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 10, 200, 180, 40},{ 340, -10, 200, 150, -90},{ 340, -110, 200, 50, -10},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 0, 200, 160, -80},{ 340, 80, 200, 210, 10},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 210, 10}},
+{{ 340, 340, 340, 340, 340},{ 340, -110, 200, 50, -10},{ 340, 200, 200, 200, 200},{ 340, -60, 200, 110, -30},{ 340, -50, 200, 40, -310}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 210, 10},{ 340, 50, 200, 130, -210},{ 340, 80, 200, 170, 10}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 150, 0, 210},{ 340, 200, 60, -130, 90},{ 340, 200, 70, -50, 170},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 70, -120, 100},{ 340, 200, 60, -30, 80},{ 340, 200, 200, 200, 200},{ 340, 200, 60, -30, 80}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 70, -50, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 80, -70, 140},{ 340, 200, -50, -350, 50}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 60, -30, 80},{ 340, 200, 50, -250, 150},{ 340, 200, -20, -30, 0}}
+}
+},
+/* GC....UA */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 180, 70, 200},{ 340, 170, 140, 30, 200},{ 340, 110, 80, -30, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 180, 70, 200},{ 340, 270, 180, 170, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 180, 170, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 80, -30, 200},{ 340, 200, 200, 200, 200},{ 340, 150, 120, 10, 200},{ 340, 30, -100, -30, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200},{ 340, 160, 30, 100, 200},{ 340, 230, 100, 170, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 250, 200, 250},{ 340, 140, 140, 200, 150},{ 340, 80, 180, 200, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 190, 200, 190},{ 340, 190, 190, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 190, 190, 200, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 180, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 120, 180, 200, 190},{ 340, -90, 10, 200, 10}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160},{ 340, 30, 130, 200, 140},{ 340, 100, 100, 200, 110}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 10, 200, 180, 40},{ 340, -30, 200, 130, -110},{ 340, -90, 200, 70, 10},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 10, 200, 180, -60},{ 340, 110, 200, 240, 40},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 240, 40}},
+{{ 340, 340, 340, 340, 340},{ 340, -90, 200, 70, 10},{ 340, 200, 200, 200, 200},{ 340, -50, 200, 110, -30},{ 340, -90, 200, 0, -350}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 210, 10},{ 340, 40, 200, 120, -220},{ 340, 110, 200, 190, 30}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 150, 0, 210},{ 340, 200, 40, -150, 70},{ 340, 200, 90, -30, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 90, -100, 110},{ 340, 200, 90, 0, 110},{ 340, 200, 200, 200, 200},{ 340, 200, 90, 0, 110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 90, -30, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 80, -70, 150},{ 340, 200, -90, -390, 10}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 60, -30, 80},{ 340, 200, 40, -260, 140},{ 340, 200, 0, -10, 30}}
+}
+},
+/* GC....?? */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+}
+},
+{ /* noPair */ {{{{0}}}},
+/* GU....CG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 190, 80, 200},{ 340, 190, 180, 70, 200},{ 340, 100, 90, -20, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 240, 220, 110, 200},{ 340, 280, 210, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 190, 180, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 90, -20, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 160, 50, 200},{ 340, 30, -80, -10, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 270, 190, 180, 200},{ 340, 180, 70, 140, 200},{ 340, 220, 100, 180, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 180, 230, 200, 230},{ 340, 170, 160, 200, 160},{ 340, 80, 170, 200, 170},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 210, 200, 210},{ 340, 200, 190, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 200, 180}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 170, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 150, 210, 200, 210},{ 340, -90, 0, 200, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 200, 180},{ 340, 60, 150, 200, 150},{ 340, 90, 90, 200, 90}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 200, 130, 160},{ 340, 70, 200, 120, 50},{ 340, -20, 200, 30, 140},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 200, 170, 90},{ 340, 200, 200, 210, 180},{ 340, 200, 200, 200, 200},{ 340, 180, 200, 200, 160}},
+{{ 340, 340, 340, 340, 340},{ 340, -20, 200, 30, 140},{ 340, 200, 200, 200, 200},{ 340, 50, 200, 110, 130},{ 340, -10, 200, -40, -210}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 200, 200, 160},{ 340, 140, 200, 110, -60},{ 340, 180, 200, 150, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 230, 60, 190},{ 340, 200, 160, -50, 80},{ 340, 200, 170, 40, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 210, 0, 130},{ 340, 200, 190, 80, 110},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 70, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 170, 40, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 40, 170},{ 340, 200, 0, -310, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 70, 100},{ 340, 200, 150, -160, 160},{ 340, 200, 90, 60, 10}}
+}
+},
+/* GU....GC */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 200, 90, 200},{ 340, 190, 170, 60, 200},{ 340, 10, 0, -110, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 180, 170, 60, 200},{ 340, 250, 170, 160, 200},{ 340, 200, 200, 200, 200},{ 340, 150, 70, 70, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 60, -50, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 160, 50, 200},{ 340, 0, -120, -50, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 250, 180, 170, 200},{ 340, 40, -80, -10, 200},{ 340, 210, 100, 170, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 240, 200, 240},{ 340, 160, 160, 200, 160},{ 340, -10, 80, 200, 80},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 150, 200, 150},{ 340, 160, 160, 200, 160},{ 340, 200, 200, 200, 200},{ 340, 60, 60, 200, 60}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 140, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 150, 210, 200, 210},{ 340, -130, -30, 200, -30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 160, 200, 160},{ 340, -90, 10, 200, 10},{ 340, 90, 80, 200, 80}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 200, 140, 170},{ 340, 60, 200, 120, 40},{ 340, -110, 200, -60, 50},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 60, 200, 110, 40},{ 340, 160, 200, 180, 140},{ 340, 200, 200, 200, 200},{ 340, 70, 200, 80, 50}},
+{{ 340, 340, 340, 340, 340},{ 340, -50, 200, 0, 110},{ 340, 200, 200, 200, 200},{ 340, 50, 200, 110, 130},{ 340, -50, 200, -70, -250}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 180, 150},{ 340, -10, 200, -30, -210},{ 340, 170, 200, 140, 150}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 70, 200},{ 340, 200, 160, -50, 80},{ 340, 200, 80, -50, 80},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 150, -60, 70},{ 340, 200, 160, 50, 80},{ 340, 200, 200, 200, 200},{ 340, 200, 60, -50, -20}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 140, 10, 150},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 40, 170},{ 340, 200, -30, -350, -30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 160, 50, 80},{ 340, 200, 10, -310, 10},{ 340, 200, 80, 50, 0}}
+}
+},
+/* GU....GU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 250, 240, 130, 200},{ 340, 150, 140, 30, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 260, 250, 140, 200},{ 340, 310, 230, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 140, 30, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 190, 80, 200},{ 340, 130, 20, 90, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 230, 120, 190, 200},{ 340, 270, 150, 220, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 230, 220, 200, 220},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 240, 230, 200, 230},{ 340, 220, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 180, 240, 200, 240},{ 340, 10, 100, 200, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 110, 200, 200, 200},{ 340, 140, 140, 200, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 130, 200, 180, 110},{ 340, 30, 200, 80, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 140, 200, 190, 120},{ 340, 220, 200, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 30, 200, 80, 190},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 140, 160},{ 340, 90, 200, 70, -110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 190, 200, 160, -10},{ 340, 220, 200, 200, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 220, 10, 140},{ 340, 200, 220, 90, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 230, 20, 150},{ 340, 200, 220, 100, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 220, 90, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 70, 200},{ 340, 200, 100, -210, 110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 200, -110, 200},{ 340, 200, 140, 110, 60}}
+}
+},
+/* GU....UG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 230, 220, 110, 200},{ 340, 170, 160, 50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 340, 260, 250, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 260, 250, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 160, 50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 200, 90, 200},{ 340, 100, -20, 50, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 220, 110, 180, 200},{ 340, 290, 180, 250, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 210, 200, 200, 200},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 250, 200, 250},{ 340, 250, 250, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 250, 250, 200, 250}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 190, 240, 200, 240},{ 340, -30, 70, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 100, 190, 200, 190},{ 340, 170, 160, 200, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 110, 200, 160, 90},{ 340, 50, 200, 100, 210},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 130},{ 340, 250, 200, 270, 230},{ 340, 200, 200, 200, 200},{ 340, 250, 200, 270, 230}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 200, 100, 210},{ 340, 200, 200, 200, 200},{ 340, 90, 200, 140, 170},{ 340, 50, 200, 30, -150}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 180, 200, 150, -20},{ 340, 250, 200, 220, 230}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 200, -10, 120},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 250, 30, 170},{ 340, 200, 250, 130, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 130, 170}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 70, 200},{ 340, 200, 70, -250, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 190, -120, 190},{ 340, 200, 160, 130, 80}}
+}
+},
+/* GU....AU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 250, 240, 130, 200},{ 340, 150, 140, 30, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 260, 250, 140, 200},{ 340, 310, 230, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 140, 30, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 190, 80, 200},{ 340, 130, 20, 90, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 230, 120, 190, 200},{ 340, 270, 150, 220, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 230, 220, 200, 220},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 240, 230, 200, 230},{ 340, 220, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 180, 240, 200, 240},{ 340, 10, 100, 200, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 110, 200, 200, 200},{ 340, 140, 140, 200, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 130, 200, 180, 110},{ 340, 30, 200, 80, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 140, 200, 190, 120},{ 340, 220, 200, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 30, 200, 80, 190},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 140, 160},{ 340, 90, 200, 70, -110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 190, 200, 160, -10},{ 340, 220, 200, 200, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 220, 10, 140},{ 340, 200, 220, 90, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 230, 20, 150},{ 340, 200, 220, 100, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 220, 90, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 70, 200},{ 340, 200, 100, -210, 110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 200, -110, 200},{ 340, 200, 140, 110, 60}}
+}
+},
+/* GU....UA */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 230, 220, 110, 200},{ 340, 170, 160, 50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 340, 260, 250, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 260, 250, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 160, 50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 200, 90, 200},{ 340, 100, -20, 50, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 220, 110, 180, 200},{ 340, 290, 180, 250, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 210, 200, 200, 200},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 250, 200, 250},{ 340, 250, 250, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 250, 250, 200, 250}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 190, 240, 200, 240},{ 340, -30, 70, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 100, 190, 200, 190},{ 340, 170, 160, 200, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 110, 200, 160, 90},{ 340, 50, 200, 100, 210},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 130},{ 340, 250, 200, 270, 230},{ 340, 200, 200, 200, 200},{ 340, 250, 200, 270, 230}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 200, 100, 210},{ 340, 200, 200, 200, 200},{ 340, 90, 200, 140, 170},{ 340, 50, 200, 30, -150}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 180, 200, 150, -20},{ 340, 250, 200, 220, 230}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 200, -10, 120},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 250, 30, 170},{ 340, 200, 250, 130, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 130, 170}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 70, 200},{ 340, 200, 70, -250, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 190, -120, 190},{ 340, 200, 160, 130, 80}}
+}
+},
+/* GU....?? */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+}
+},
+{ /* noPair */ {{{{0}}}},
+/* UG....CG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 100, 200},{ 340, 190, 190, 90, 200},{ 340, 100, 100, 0, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 240, 240, 130, 200},{ 340, 280, 220, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 210, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 100, 0, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 70, 200},{ 340, 30, -70, 10, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 270, 210, 200, 200},{ 340, 180, 80, 160, 200},{ 340, 220, 120, 190, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 260, 200, 230},{ 340, 150, 190, 200, 160},{ 340, 60, 200, 200, 170},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 240, 200, 210},{ 340, 180, 220, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 160, 210, 200, 180}},
+{{ 340, 340, 340, 340, 340},{ 340, 60, 200, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 130, 240, 200, 210},{ 340, -110, 30, 200, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 210, 200, 180},{ 340, 40, 180, 200, 150},{ 340, 70, 120, 200, 90}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 140, 150},{ 340, 90, 200, 130, 40},{ 340, 0, 200, 40, 130},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 200, 170, 80},{ 340, 220, 200, 220, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 200, 150}},
+{{ 340, 340, 340, 340, 340},{ 340, 0, 200, 40, 130},{ 340, 200, 200, 200, 200},{ 340, 70, 200, 110, 120},{ 340, 10, 200, -30, -220}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 200, 150},{ 340, 160, 200, 120, -70},{ 340, 190, 200, 150, 150}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 260, 20, 220},{ 340, 200, 190, -90, 110},{ 340, 200, 200, 0, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, -40, 150},{ 340, 200, 220, 40, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 30, 120}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 0, 200},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 0, 190},{ 340, 200, 30, -350, 30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 30, 120},{ 340, 200, 180, -200, 180},{ 340, 200, 120, 20, 30}}
+}
+},
+/* UG....GC */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 210, 110, 200},{ 340, 190, 190, 80, 200},{ 340, 10, 10, -90, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 180, 180, 80, 200},{ 340, 250, 190, 180, 200},{ 340, 200, 200, 200, 200},{ 340, 150, 90, 90, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 70, -30, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 70, 200},{ 340, 0, -100, -30, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 250, 190, 190, 200},{ 340, 40, -60, 10, 200},{ 340, 210, 110, 190, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 270, 200, 240},{ 340, 140, 190, 200, 160},{ 340, -30, 110, 200, 80},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 140, 180, 200, 150},{ 340, 140, 190, 200, 160},{ 340, 200, 200, 200, 200},{ 340, 40, 90, 200, 60}},
+{{ 340, 340, 340, 340, 340},{ 340, 30, 170, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 130, 240, 200, 210},{ 340, -150, 0, 200, -30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 150, 190, 200, 160},{ 340, -110, 40, 200, 10},{ 340, 70, 110, 200, 80}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 200, 150, 160},{ 340, 80, 200, 120, 30},{ 340, -90, 200, -50, 40},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 200, 120, 30},{ 340, 180, 200, 180, 130},{ 340, 200, 200, 200, 200},{ 340, 90, 200, 80, 40}},
+{{ 340, 340, 340, 340, 340},{ 340, -30, 200, 10, 100},{ 340, 200, 200, 200, 200},{ 340, 70, 200, 110, 120},{ 340, -30, 200, -70, -260}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 190, 200, 190, 140},{ 340, 10, 200, -30, -220},{ 340, 190, 200, 150, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 30, 230},{ 340, 200, 190, -90, 100},{ 340, 200, 110, -90, 110},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 180, -100, 100},{ 340, 200, 190, 10, 100},{ 340, 200, 200, 200, 200},{ 340, 200, 90, -90, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 170, -30, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 0, 190},{ 340, 200, 0, -390, -10}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 190, 10, 110},{ 340, 200, 40, -350, 30},{ 340, 200, 110, 10, 30}}
+}
+},
+/* UG....GU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 250, 250, 150, 200},{ 340, 150, 150, 50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 260, 260, 160, 200},{ 340, 310, 250, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 150, 50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 100, 200},{ 340, 130, 30, 110, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 230, 130, 210, 200},{ 340, 270, 170, 240, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 210, 250, 200, 220},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 220, 260, 200, 230},{ 340, 200, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 160, 270, 200, 240},{ 340, -10, 130, 200, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340, 90, 230, 200, 200},{ 340, 120, 170, 200, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 150, 200, 190, 100},{ 340, 50, 200, 90, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 200, 110},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 200, 90, 180},{ 340, 200, 200, 200, 200},{ 340, 100, 200, 140, 150},{ 340, 110, 200, 70, -120}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 210, 200, 170, -20},{ 340, 240, 200, 200, 190}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 250, -30, 170},{ 340, 200, 250, 50, 250},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 260, -20, 180},{ 340, 200, 250, 70, 160},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 250, 50, 250},{ 340, 200, 200, 200, 200},{ 340, 200, 270, 30, 220},{ 340, 200, 130, -250, 130}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160},{ 340, 200, 230, -150, 230},{ 340, 200, 170, 70, 80}}
+}
+},
+/* UG....UG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 230, 230, 130, 200},{ 340, 170, 170, 70, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 340, 280, 270, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 280, 270, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 170, 70, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 110, 200},{ 340, 100, 0, 70, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 220, 120, 200, 200},{ 340, 290, 190, 270, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 190, 230, 200, 200},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 280, 200, 250},{ 340, 230, 280, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 230, 280, 200, 250}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 170, 270, 200, 240},{ 340, -50, 100, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340, 80, 220, 200, 190},{ 340, 150, 190, 200, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 130, 200, 170, 80},{ 340, 70, 200, 110, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 120},{ 340, 270, 200, 270, 220},{ 340, 200, 200, 200, 200},{ 340, 270, 200, 270, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 200, 110, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 150, 160},{ 340, 70, 200, 30, -160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 160, -30},{ 340, 270, 200, 230, 220}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 230, -50, 150},{ 340, 200, 270, 70, 270},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 280, 0, 190},{ 340, 200, 280, 100, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 280, 100, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 70, 270},{ 340, 200, 200, 200, 200},{ 340, 200, 270, 30, 230},{ 340, 200, 100, -290, 90}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160},{ 340, 200, 220, -160, 220},{ 340, 200, 190, 90, 110}}
+}
+},
+/* UG....AU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 250, 250, 150, 200},{ 340, 150, 150, 50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 260, 260, 160, 200},{ 340, 310, 250, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 150, 50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 100, 200},{ 340, 130, 30, 110, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 230, 130, 210, 200},{ 340, 270, 170, 240, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 210, 250, 200, 220},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 220, 260, 200, 230},{ 340, 200, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 160, 270, 200, 240},{ 340, -10, 130, 200, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340, 90, 230, 200, 200},{ 340, 120, 170, 200, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 150, 200, 190, 100},{ 340, 50, 200, 90, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 200, 110},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 200, 90, 180},{ 340, 200, 200, 200, 200},{ 340, 100, 200, 140, 150},{ 340, 110, 200, 70, -120}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 210, 200, 170, -20},{ 340, 240, 200, 200, 190}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 250, -30, 170},{ 340, 200, 250, 50, 250},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 260, -20, 180},{ 340, 200, 250, 70, 160},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 250, 50, 250},{ 340, 200, 200, 200, 200},{ 340, 200, 270, 30, 220},{ 340, 200, 130, -250, 130}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160},{ 340, 200, 230, -150, 230},{ 340, 200, 170, 70, 80}}
+}
+},
+/* UG....UA */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 230, 230, 130, 200},{ 340, 170, 170, 70, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 340, 280, 270, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 280, 270, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 170, 70, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 110, 200},{ 340, 100, 0, 70, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 220, 120, 200, 200},{ 340, 290, 190, 270, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 190, 230, 200, 200},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 280, 200, 250},{ 340, 230, 280, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 230, 280, 200, 250}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 170, 270, 200, 240},{ 340, -50, 100, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340, 80, 220, 200, 190},{ 340, 150, 190, 200, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 130, 200, 170, 80},{ 340, 70, 200, 110, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 120},{ 340, 270, 200, 270, 220},{ 340, 200, 200, 200, 200},{ 340, 270, 200, 270, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 200, 110, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 150, 160},{ 340, 70, 200, 30, -160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 160, -30},{ 340, 270, 200, 230, 220}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 230, -50, 150},{ 340, 200, 270, 70, 270},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 280, 0, 190},{ 340, 200, 280, 100, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 280, 100, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 70, 270},{ 340, 200, 200, 200, 200},{ 340, 200, 270, 30, 230},{ 340, 200, 100, -290, 90}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160},{ 340, 200, 220, -160, 220},{ 340, 200, 190, 90, 110}}
+}
+},
+/* UG....?? */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+}
+},
+{ /* noPair */ {{{{0}}}},
+/* AU....CG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 190, 80, 200},{ 340, 190, 180, 70, 200},{ 340, 100, 90, -20, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 240, 220, 110, 200},{ 340, 280, 210, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 190, 180, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 90, -20, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 160, 50, 200},{ 340, 30, -80, -10, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 270, 190, 180, 200},{ 340, 180, 70, 140, 200},{ 340, 220, 100, 180, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 180, 230, 200, 230},{ 340, 170, 160, 200, 160},{ 340, 80, 170, 200, 170},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 210, 200, 210},{ 340, 200, 190, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 200, 180}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 170, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 150, 210, 200, 210},{ 340, -90, 0, 200, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 200, 180},{ 340, 60, 150, 200, 150},{ 340, 90, 90, 200, 90}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 200, 130, 160},{ 340, 70, 200, 120, 50},{ 340, -20, 200, 30, 140},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 200, 170, 90},{ 340, 200, 200, 210, 180},{ 340, 200, 200, 200, 200},{ 340, 180, 200, 200, 160}},
+{{ 340, 340, 340, 340, 340},{ 340, -20, 200, 30, 140},{ 340, 200, 200, 200, 200},{ 340, 50, 200, 110, 130},{ 340, -10, 200, -40, -210}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 200, 200, 160},{ 340, 140, 200, 110, -60},{ 340, 180, 200, 150, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 230, 60, 190},{ 340, 200, 160, -50, 80},{ 340, 200, 170, 40, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 210, 0, 130},{ 340, 200, 190, 80, 110},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 70, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 170, 40, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 40, 170},{ 340, 200, 0, -310, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180, 70, 100},{ 340, 200, 150, -160, 160},{ 340, 200, 90, 60, 10}}
+}
+},
+/* AU....GC */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 200, 90, 200},{ 340, 190, 170, 60, 200},{ 340, 10, 0, -110, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 180, 170, 60, 200},{ 340, 250, 170, 160, 200},{ 340, 200, 200, 200, 200},{ 340, 150, 70, 70, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 60, -50, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 160, 50, 200},{ 340, 0, -120, -50, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 250, 180, 170, 200},{ 340, 40, -80, -10, 200},{ 340, 210, 100, 170, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 240, 200, 240},{ 340, 160, 160, 200, 160},{ 340, -10, 80, 200, 80},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 150, 200, 150},{ 340, 160, 160, 200, 160},{ 340, 200, 200, 200, 200},{ 340, 60, 60, 200, 60}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 140, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 150, 210, 200, 210},{ 340, -130, -30, 200, -30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 160, 200, 160},{ 340, -90, 10, 200, 10},{ 340, 90, 80, 200, 80}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 90, 200, 140, 170},{ 340, 60, 200, 120, 40},{ 340, -110, 200, -60, 50},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 60, 200, 110, 40},{ 340, 160, 200, 180, 140},{ 340, 200, 200, 200, 200},{ 340, 70, 200, 80, 50}},
+{{ 340, 340, 340, 340, 340},{ 340, -50, 200, 0, 110},{ 340, 200, 200, 200, 200},{ 340, 50, 200, 110, 130},{ 340, -50, 200, -70, -250}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 180, 150},{ 340, -10, 200, -30, -210},{ 340, 170, 200, 140, 150}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 70, 200},{ 340, 200, 160, -50, 80},{ 340, 200, 80, -50, 80},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 150, -60, 70},{ 340, 200, 160, 50, 80},{ 340, 200, 200, 200, 200},{ 340, 200, 60, -50, -20}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 140, 10, 150},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 40, 170},{ 340, 200, -30, -350, -30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 160, 50, 80},{ 340, 200, 10, -310, 10},{ 340, 200, 80, 50, 0}}
+}
+},
+/* AU....GU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 250, 240, 130, 200},{ 340, 150, 140, 30, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 260, 250, 140, 200},{ 340, 310, 230, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 140, 30, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 190, 80, 200},{ 340, 130, 20, 90, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 230, 120, 190, 200},{ 340, 270, 150, 220, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 230, 220, 200, 220},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 240, 230, 200, 230},{ 340, 220, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 180, 240, 200, 240},{ 340, 10, 100, 200, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 110, 200, 200, 200},{ 340, 140, 140, 200, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 130, 200, 180, 110},{ 340, 30, 200, 80, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 140, 200, 190, 120},{ 340, 220, 200, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 30, 200, 80, 190},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 140, 160},{ 340, 90, 200, 70, -110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 190, 200, 160, -10},{ 340, 220, 200, 200, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 220, 10, 140},{ 340, 200, 220, 90, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 230, 20, 150},{ 340, 200, 220, 100, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 220, 90, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 70, 200},{ 340, 200, 100, -210, 110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 200, -110, 200},{ 340, 200, 140, 110, 60}}
+}
+},
+/* AU....UG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 230, 220, 110, 200},{ 340, 170, 160, 50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 340, 260, 250, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 260, 250, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 160, 50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 200, 90, 200},{ 340, 100, -20, 50, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 220, 110, 180, 200},{ 340, 290, 180, 250, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 210, 200, 200, 200},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 250, 200, 250},{ 340, 250, 250, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 250, 250, 200, 250}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 190, 240, 200, 240},{ 340, -30, 70, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 100, 190, 200, 190},{ 340, 170, 160, 200, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 110, 200, 160, 90},{ 340, 50, 200, 100, 210},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 130},{ 340, 250, 200, 270, 230},{ 340, 200, 200, 200, 200},{ 340, 250, 200, 270, 230}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 200, 100, 210},{ 340, 200, 200, 200, 200},{ 340, 90, 200, 140, 170},{ 340, 50, 200, 30, -150}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 180, 200, 150, -20},{ 340, 250, 200, 220, 230}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 200, -10, 120},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 250, 30, 170},{ 340, 200, 250, 130, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 130, 170}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 70, 200},{ 340, 200, 70, -250, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 190, -120, 190},{ 340, 200, 160, 130, 80}}
+}
+},
+/* AU....AU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 250, 240, 130, 200},{ 340, 150, 140, 30, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 260, 250, 140, 200},{ 340, 310, 230, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 140, 30, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 190, 80, 200},{ 340, 130, 20, 90, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 230, 120, 190, 200},{ 340, 270, 150, 220, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 230, 220, 200, 220},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 240, 230, 200, 230},{ 340, 220, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 180, 240, 200, 240},{ 340, 10, 100, 200, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 110, 200, 200, 200},{ 340, 140, 140, 200, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 130, 200, 180, 110},{ 340, 30, 200, 80, 190},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 140, 200, 190, 120},{ 340, 220, 200, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 30, 200, 80, 190},{ 340, 200, 200, 200, 200},{ 340, 80, 200, 140, 160},{ 340, 90, 200, 70, -110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 190, 200, 160, -10},{ 340, 220, 200, 200, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 220, 10, 140},{ 340, 200, 220, 90, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 230, 20, 150},{ 340, 200, 220, 100, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 220, 90, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 70, 200},{ 340, 200, 100, -210, 110}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 200, -110, 200},{ 340, 200, 140, 110, 60}}
+}
+},
+/* AU....UA */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 230, 220, 110, 200},{ 340, 170, 160, 50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 340, 260, 250, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 260, 250, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 160, 50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 200, 90, 200},{ 340, 100, -20, 50, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 220, 110, 180, 200},{ 340, 290, 180, 250, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 210, 200, 200, 200},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 250, 250, 200, 250},{ 340, 250, 250, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 250, 250, 200, 250}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 190, 240, 200, 240},{ 340, -30, 70, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 100, 190, 200, 190},{ 340, 170, 160, 200, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 110, 200, 160, 90},{ 340, 50, 200, 100, 210},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 130},{ 340, 250, 200, 270, 230},{ 340, 200, 200, 200, 200},{ 340, 250, 200, 270, 230}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 200, 100, 210},{ 340, 200, 200, 200, 200},{ 340, 90, 200, 140, 170},{ 340, 50, 200, 30, -150}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 180, 200, 150, -20},{ 340, 250, 200, 220, 230}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 200, -10, 120},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 250, 30, 170},{ 340, 200, 250, 130, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 130, 170}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 70, 200},{ 340, 200, 70, -250, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 190, -120, 190},{ 340, 200, 160, 130, 80}}
+}
+},
+/* AU....?? */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+}
+},
+{ /* noPair */ {{{{0}}}},
+/* UA....CG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 100, 200},{ 340, 190, 190, 90, 200},{ 340, 100, 100, 0, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 240, 240, 130, 200},{ 340, 280, 220, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 210, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 100, 0, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 70, 200},{ 340, 30, -70, 10, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 270, 210, 200, 200},{ 340, 180, 80, 160, 200},{ 340, 220, 120, 190, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 260, 200, 230},{ 340, 150, 190, 200, 160},{ 340, 60, 200, 200, 170},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 190, 240, 200, 210},{ 340, 180, 220, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 160, 210, 200, 180}},
+{{ 340, 340, 340, 340, 340},{ 340, 60, 200, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 130, 240, 200, 210},{ 340, -110, 30, 200, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 210, 200, 180},{ 340, 40, 180, 200, 150},{ 340, 70, 120, 200, 90}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 140, 150},{ 340, 90, 200, 130, 40},{ 340, 0, 200, 40, 130},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 200, 170, 80},{ 340, 220, 200, 220, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 200, 150}},
+{{ 340, 340, 340, 340, 340},{ 340, 0, 200, 40, 130},{ 340, 200, 200, 200, 200},{ 340, 70, 200, 110, 120},{ 340, 10, 200, -30, -220}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 200, 150},{ 340, 160, 200, 120, -70},{ 340, 190, 200, 150, 150}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 260, 20, 220},{ 340, 200, 190, -90, 110},{ 340, 200, 200, 0, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 240, -40, 150},{ 340, 200, 220, 40, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 30, 120}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 0, 200},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 0, 190},{ 340, 200, 30, -350, 30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 210, 30, 120},{ 340, 200, 180, -200, 180},{ 340, 200, 120, 20, 30}}
+}
+},
+/* UA....GC */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 210, 210, 110, 200},{ 340, 190, 190, 80, 200},{ 340, 10, 10, -90, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 180, 180, 80, 200},{ 340, 250, 190, 180, 200},{ 340, 200, 200, 200, 200},{ 340, 150, 90, 90, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 70, -30, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 70, 200},{ 340, 0, -100, -30, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 250, 190, 190, 200},{ 340, 40, -60, 10, 200},{ 340, 210, 110, 190, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 270, 200, 240},{ 340, 140, 190, 200, 160},{ 340, -30, 110, 200, 80},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 140, 180, 200, 150},{ 340, 140, 190, 200, 160},{ 340, 200, 200, 200, 200},{ 340, 40, 90, 200, 60}},
+{{ 340, 340, 340, 340, 340},{ 340, 30, 170, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 130, 240, 200, 210},{ 340, -150, 0, 200, -30}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 150, 190, 200, 160},{ 340, -110, 40, 200, 10},{ 340, 70, 110, 200, 80}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 200, 150, 160},{ 340, 80, 200, 120, 30},{ 340, -90, 200, -50, 40},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 80, 200, 120, 30},{ 340, 180, 200, 180, 130},{ 340, 200, 200, 200, 200},{ 340, 90, 200, 80, 40}},
+{{ 340, 340, 340, 340, 340},{ 340, -30, 200, 10, 100},{ 340, 200, 200, 200, 200},{ 340, 70, 200, 110, 120},{ 340, -30, 200, -70, -260}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 190, 200, 190, 140},{ 340, 10, 200, -30, -220},{ 340, 190, 200, 150, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 30, 230},{ 340, 200, 190, -90, 100},{ 340, 200, 110, -90, 110},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 180, -100, 100},{ 340, 200, 190, 10, 100},{ 340, 200, 200, 200, 200},{ 340, 200, 90, -90, 0}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 170, -30, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 240, 0, 190},{ 340, 200, 0, -390, -10}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 190, 10, 110},{ 340, 200, 40, -350, 30},{ 340, 200, 110, 10, 30}}
+}
+},
+/* UA....GU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 250, 250, 150, 200},{ 340, 150, 150, 50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 260, 260, 160, 200},{ 340, 310, 250, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 150, 50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 100, 200},{ 340, 130, 30, 110, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 230, 130, 210, 200},{ 340, 270, 170, 240, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 210, 250, 200, 220},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 220, 260, 200, 230},{ 340, 200, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 160, 270, 200, 240},{ 340, -10, 130, 200, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340, 90, 230, 200, 200},{ 340, 120, 170, 200, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 150, 200, 190, 100},{ 340, 50, 200, 90, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 200, 110},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 200, 90, 180},{ 340, 200, 200, 200, 200},{ 340, 100, 200, 140, 150},{ 340, 110, 200, 70, -120}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 210, 200, 170, -20},{ 340, 240, 200, 200, 190}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 250, -30, 170},{ 340, 200, 250, 50, 250},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 260, -20, 180},{ 340, 200, 250, 70, 160},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 250, 50, 250},{ 340, 200, 200, 200, 200},{ 340, 200, 270, 30, 220},{ 340, 200, 130, -250, 130}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160},{ 340, 200, 230, -150, 230},{ 340, 200, 170, 70, 80}}
+}
+},
+/* UA....UG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 230, 230, 130, 200},{ 340, 170, 170, 70, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 340, 280, 270, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 280, 270, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 170, 70, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 110, 200},{ 340, 100, 0, 70, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 220, 120, 200, 200},{ 340, 290, 190, 270, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 190, 230, 200, 200},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 280, 200, 250},{ 340, 230, 280, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 230, 280, 200, 250}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 170, 270, 200, 240},{ 340, -50, 100, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340, 80, 220, 200, 190},{ 340, 150, 190, 200, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 130, 200, 170, 80},{ 340, 70, 200, 110, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 120},{ 340, 270, 200, 270, 220},{ 340, 200, 200, 200, 200},{ 340, 270, 200, 270, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 200, 110, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 150, 160},{ 340, 70, 200, 30, -160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 160, -30},{ 340, 270, 200, 230, 220}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 230, -50, 150},{ 340, 200, 270, 70, 270},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 280, 0, 190},{ 340, 200, 280, 100, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 280, 100, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 70, 270},{ 340, 200, 200, 200, 200},{ 340, 200, 270, 30, 230},{ 340, 200, 100, -290, 90}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160},{ 340, 200, 220, -160, 220},{ 340, 200, 190, 90, 110}}
+}
+},
+/* UA....AU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 250, 250, 150, 200},{ 340, 150, 150, 50, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 260, 260, 160, 200},{ 340, 310, 250, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 150, 150, 50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 100, 200},{ 340, 130, 30, 110, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 230, 130, 210, 200},{ 340, 270, 170, 240, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 210, 250, 200, 220},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 220, 260, 200, 230},{ 340, 200, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 160, 270, 200, 240},{ 340, -10, 130, 200, 100}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340, 90, 230, 200, 200},{ 340, 120, 170, 200, 140}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 150, 200, 190, 100},{ 340, 50, 200, 90, 180},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 200, 110},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 50, 200, 90, 180},{ 340, 200, 200, 200, 200},{ 340, 100, 200, 140, 150},{ 340, 110, 200, 70, -120}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 210, 200, 170, -20},{ 340, 240, 200, 200, 190}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 250, -30, 170},{ 340, 200, 250, 50, 250},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 260, -20, 180},{ 340, 200, 250, 70, 160},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 250, 50, 250},{ 340, 200, 200, 200, 200},{ 340, 200, 270, 30, 220},{ 340, 200, 130, -250, 130}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160},{ 340, 200, 230, -150, 230},{ 340, 200, 170, 70, 80}}
+}
+},
+/* UA....UA */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 230, 230, 130, 200},{ 340, 170, 170, 70, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 340, 280, 270, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 280, 270, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 170, 70, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 110, 200},{ 340, 100, 0, 70, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 220, 120, 200, 200},{ 340, 290, 190, 270, 200}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 190, 230, 200, 200},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 230, 280, 200, 250},{ 340, 230, 280, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 230, 280, 200, 250}},
+{{ 340, 340, 340, 340, 340},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 170, 270, 200, 240},{ 340, -50, 100, 200, 70}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340, 80, 220, 200, 190},{ 340, 150, 190, 200, 160}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 130, 200, 170, 80},{ 340, 70, 200, 110, 200},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 120},{ 340, 270, 200, 270, 220},{ 340, 200, 200, 200, 200},{ 340, 270, 200, 270, 220}},
+{{ 340, 340, 340, 340, 340},{ 340, 70, 200, 110, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 150, 160},{ 340, 70, 200, 30, -160}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 160, -30},{ 340, 270, 200, 230, 220}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 230, -50, 150},{ 340, 200, 270, 70, 270},{ 340, 200, 200, 200, 200}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 280, 0, 190},{ 340, 200, 280, 100, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 280, 100, 190}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 270, 70, 270},{ 340, 200, 200, 200, 200},{ 340, 200, 270, 30, 230},{ 340, 200, 100, -290, 90}},
+{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 70, 160},{ 340, 200, 220, -160, 220},{ 340, 200, 190, 90, 110}}
+}
+},
+/* UA....?? */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+}
+},
+{ /* noPair */ {{{{0}}}},
+/* ??....CG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+},
+/* ??....GC */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+},
+/* ??....GU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+},
+/* ??....UG */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+},
+/* ??....AU */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+},
+/* ??....UA */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+},
+/* ??....?? */
+{{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+},
+{
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},
+{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}
+}
+}
+}
+};
+
+const int energy_param::int22_H[8][8][5][5][5][5] =
+{ /* noPair */ {{{{{0}}}}},
+{ /* noPair */ {{{{0}}}},
+/* CG.@@..CG */
+{ { { { 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@A..CG */
+{ { 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* CG.@C..CG */
+{ { 0, 0, 0, 0, 0},
+{ -949, -949, -949, -949, -949},
+{ -449, -449, -449, -449, -449},
+{ -939, -939, -939, -939, -939},
+{ -739, -739, -739, -739, -739}},
+/* CG.@G..CG */
+{ { 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* CG.@U..CG */
+{ { 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -669, -669, -669, -669, -669},
+{ -939, -939, -939, -939, -939},
+{ -859, -859, -859, -859, -859}}},
+/* CG.A@..CG */
+{{{ -50,-1029, -949,-1029,-1029},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AA..CG */
+{{ -50,-1029, -949,-1029,-1029},
+{-1079,-2058,-1978,-2058,-2058},
+{ -569,-1548,-1468,-1548,-1548},
+{ -989,-1968,-1888,-1968,-1968},
+{ -859,-1838,-1758,-1838,-1838}},
+/* CG.AC..CG */
+{{ -50,-1029, -949,-1029,-1029},
+{ -999,-1978,-1898,-1978,-1978},
+{ -499,-1478,-1398,-1478,-1478},
+{ -989,-1968,-1888,-1968,-1968},
+{ -789,-1768,-1688,-1768,-1768}},
+/* CG.AG..CG */
+{{ -50,-1029, -949,-1029,-1029},
+{-1079,-2058,-1978,-2058,-2058},
+{ -569,-1548,-1468,-1548,-1548},
+{ -989,-1968,-1888,-1968,-1968},
+{ -859,-1838,-1758,-1838,-1838}},
+/* CG.AU..CG */
+{{ -50,-1029, -949,-1029,-1029},
+{-1079,-2058,-1978,-2058,-2058},
+{ -719,-1698,-1618,-1698,-1698},
+{ -989,-1968,-1888,-1968,-1968},
+{ -909,-1888,-1808,-1888,-1888}}},
+/* CG.C@..CG */
+{{{ -50, -519, -449, -519, -669},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CA..CG */
+{{ -50, -519, -449, -519, -669},
+{-1079,-1548,-1478,-1548,-1698},
+{ -569,-1038, -968,-1038,-1188},
+{ -989,-1458,-1388,-1458,-1608},
+{ -859,-1328,-1258,-1328,-1478}},
+/* CG.CC..CG */
+{{ -50, -519, -449, -519, -669},
+{ -999,-1468,-1398,-1468,-1618},
+{ -499, -968, -898, -968,-1118},
+{ -989,-1458,-1388,-1458,-1608},
+{ -789,-1258,-1188,-1258,-1408}},
+/* CG.CG..CG */
+{{ -50, -519, -449, -519, -669},
+{-1079,-1548,-1478,-1548,-1698},
+{ -569,-1038, -968,-1038,-1188},
+{ -989,-1458,-1388,-1458,-1608},
+{ -859,-1328,-1258,-1328,-1478}},
+/* CG.CU..CG */
+{{ -50, -519, -449, -519, -669},
+{-1079,-1548,-1478,-1548,-1698},
+{ -719,-1188,-1118,-1188,-1338},
+{ -989,-1458,-1388,-1458,-1608},
+{ -909,-1378,-1308,-1378,-1528}}},
+/* CG.G@..CG */
+{{{ -50, -939, -939, -939, -939},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GA..CG */
+{{ -50, -939, -939, -939, -939},
+{-1079,-1968,-1968,-1968,-1968},
+{ -569,-1458,-1458,-1458,-1458},
+{ -989,-1878,-1878,-1878,-1878},
+{ -859,-1748,-1748,-1748,-1748}},
+/* CG.GC..CG */
+{{ -50, -939, -939, -939, -939},
+{ -999,-1888,-1888,-1888,-1888},
+{ -499,-1388,-1388,-1388,-1388},
+{ -989,-1878,-1878,-1878,-1878},
+{ -789,-1678,-1678,-1678,-1678}},
+/* CG.GG..CG */
+{{ -50, -939, -939, -939, -939},
+{-1079,-1968,-1968,-1968,-1968},
+{ -569,-1458,-1458,-1458,-1458},
+{ -989,-1878,-1878,-1878,-1878},
+{ -859,-1748,-1748,-1748,-1748}},
+/* CG.GU..CG */
+{{ -50, -939, -939, -939, -939},
+{-1079,-1968,-1968,-1968,-1968},
+{ -719,-1608,-1608,-1608,-1608},
+{ -989,-1878,-1878,-1878,-1878},
+{ -909,-1798,-1798,-1798,-1798}}},
+/* CG.U@..CG */
+{{{ -50, -809, -739, -809, -859},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UA..CG */
+{{ -50, -809, -739, -809, -859},
+{-1079,-1838,-1768,-1838,-1888},
+{ -569,-1328,-1258,-1328,-1378},
+{ -989,-1748,-1678,-1748,-1798},
+{ -859,-1618,-1548,-1618,-1668}},
+/* CG.UC..CG */
+{{ -50, -809, -739, -809, -859},
+{ -999,-1758,-1688,-1758,-1808},
+{ -499,-1258,-1188,-1258,-1308},
+{ -989,-1748,-1678,-1748,-1798},
+{ -789,-1548,-1478,-1548,-1598}},
+/* CG.UG..CG */
+{{ -50, -809, -739, -809, -859},
+{-1079,-1838,-1768,-1838,-1888},
+{ -569,-1328,-1258,-1328,-1378},
+{ -989,-1748,-1678,-1748,-1798},
+{ -859,-1618,-1548,-1618,-1668}},
+/* CG.UU..CG */
+{{ -50, -809, -739, -809, -859},
+{-1079,-1838,-1768,-1838,-1888},
+{ -719,-1478,-1408,-1478,-1528},
+{ -989,-1748,-1678,-1748,-1798},
+{ -909,-1668,-1598,-1668,-1718}}}},
+/* CG.@@..GC */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@A..GC */
+{{ 0, 0, 0, 0, 0},
+{ -519, -519, -519, -519, -519},
+{ -719, -719, -719, -719, -719},
+{ -709, -709, -709, -709, -709},
+{ -499, -499, -499, -499, -499}},
+/* CG.@C..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -309, -309, -309, -309, -309},
+{ -739, -739, -739, -739, -739},
+{ -499, -499, -499, -499, -499}},
+/* CG.@G..GC */
+{{ 0, 0, 0, 0, 0},
+{ -559, -559, -559, -559, -559},
+{ -309, -309, -309, -309, -309},
+{ -619, -619, -619, -619, -619},
+{ -499, -499, -499, -499, -499}},
+/* CG.@U..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -389, -389, -389, -389, -389},
+{ -739, -739, -739, -739, -739},
+{ -569, -569, -569, -569, -569}}},
+/* CG.A@..GC */
+{{{ -50,-1029, -949,-1029,-1029},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AA..GC */
+{{ -50,-1029, -949,-1029,-1029},
+{ -569,-1548,-1468,-1548,-1548},
+{ -769,-1748,-1668,-1748,-1748},
+{ -759,-1738,-1658,-1738,-1738},
+{ -549,-1528,-1448,-1528,-1528}},
+/* CG.AC..GC */
+{{ -50,-1029, -949,-1029,-1029},
+{ -929,-1908,-1828,-1908,-1908},
+{ -359,-1338,-1258,-1338,-1338},
+{ -789,-1768,-1688,-1768,-1768},
+{ -549,-1528,-1448,-1528,-1528}},
+/* CG.AG..GC */
+{{ -50,-1029, -949,-1029,-1029},
+{ -609,-1588,-1508,-1588,-1588},
+{ -359,-1338,-1258,-1338,-1338},
+{ -669,-1648,-1568,-1648,-1648},
+{ -549,-1528,-1448,-1528,-1528}},
+/* CG.AU..GC */
+{{ -50,-1029, -949,-1029,-1029},
+{ -929,-1908,-1828,-1908,-1908},
+{ -439,-1418,-1338,-1418,-1418},
+{ -789,-1768,-1688,-1768,-1768},
+{ -619,-1598,-1518,-1598,-1598}}},
+/* CG.C@..GC */
+{{{ -50, -519, -449, -519, -669},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CA..GC */
+{{ -50, -519, -449, -519, -669},
+{ -569,-1038, -968,-1038,-1188},
+{ -769,-1238,-1168,-1238,-1388},
+{ -759,-1228,-1158,-1228,-1378},
+{ -549,-1018, -948,-1018,-1168}},
+/* CG.CC..GC */
+{{ -50, -519, -449, -519, -669},
+{ -929,-1398,-1328,-1398,-1548},
+{ -359, -828, -758, -828, -978},
+{ -789,-1258,-1188,-1258,-1408},
+{ -549,-1018, -948,-1018,-1168}},
+/* CG.CG..GC */
+{{ -50, -519, -449, -519, -669},
+{ -609,-1078,-1008,-1078,-1228},
+{ -359, -828, -758, -828, -978},
+{ -669,-1138,-1068,-1138,-1288},
+{ -549,-1018, -948,-1018,-1168}},
+/* CG.CU..GC */
+{{ -50, -519, -449, -519, -669},
+{ -929,-1398,-1328,-1398,-1548},
+{ -439, -908, -838, -908,-1058},
+{ -789,-1258,-1188,-1258,-1408},
+{ -619,-1088,-1018,-1088,-1238}}},
+/* CG.G@..GC */
+{{{ -50, -939, -939, -939, -939},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GA..GC */
+{{ -50, -939, -939, -939, -939},
+{ -569,-1458,-1458,-1458,-1458},
+{ -769,-1658,-1658,-1658,-1658},
+{ -759,-1648,-1648,-1648,-1648},
+{ -549,-1438,-1438,-1438,-1438}},
+/* CG.GC..GC */
+{{ -50, -939, -939, -939, -939},
+{ -929,-1818,-1818,-1818,-1818},
+{ -359,-1248,-1248,-1248,-1248},
+{ -789,-1678,-1678,-1678,-1678},
+{ -549,-1438,-1438,-1438,-1438}},
+/* CG.GG..GC */
+{{ -50, -939, -939, -939, -939},
+{ -609,-1498,-1498,-1498,-1498},
+{ -359,-1248,-1248,-1248,-1248},
+{ -669,-1558,-1558,-1558,-1558},
+{ -549,-1438,-1438,-1438,-1438}},
+/* CG.GU..GC */
+{{ -50, -939, -939, -939, -939},
+{ -929,-1818,-1818,-1818,-1818},
+{ -439,-1328,-1328,-1328,-1328},
+{ -789,-1678,-1678,-1678,-3080},
+{ -619,-1508,-1508,-1508,-1508}}},
+/* CG.U@..GC */
+{{{ -50, -809, -739, -809, -859},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UA..GC */
+{{ -50, -809, -739, -809, -859},
+{ -569,-1328,-1258,-1328,-1378},
+{ -769,-1528,-1458,-1528,-1578},
+{ -759,-1518,-1448,-1518,-1568},
+{ -549,-1308,-1238,-1308,-1358}},
+/* CG.UC..GC */
+{{ -50, -809, -739, -809, -859},
+{ -929,-1688,-1618,-1688,-1738},
+{ -359,-1118,-1048,-1118,-1168},
+{ -789,-1548,-1478,-1548,-1598},
+{ -549,-1308,-1238,-1308,-1358}},
+/* CG.UG..GC */
+{{ -50, -809, -739, -809, -859},
+{ -609,-1368,-1298,-1368,-1418},
+{ -359,-1118,-1048,-1118,-1168},
+{ -669,-1428,-1358,-1428,-1478},
+{ -549,-1308,-1238,-1308,-1358}},
+/* CG.UU..GC */
+{{ -50, -809, -739, -809, -859},
+{ -929,-1688,-1618,-1688,-1738},
+{ -439,-1198,-1128,-1198,-1248},
+{ -789,-1548,-1478,-1548,-1598},
+{ -619,-1378,-1308,-1378,-1428}}}},
+/* CG.@@..GU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@A..GU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* CG.@C..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* CG.@G..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* CG.@U..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* CG.A@..GU */
+{{{ -50,-1029, -949,-1029,-1029},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AA..GU */
+{{ -50,-1029, -949,-1029,-1029},
+{ -479,-1458,-1378,-1458,-1458},
+{ -309,-1288,-1208,-1288,-1288},
+{ -389,-1368,-1288,-1368,-1368},
+{ -379,-1358,-1278,-1358,-1358}},
+/* CG.AC..GU */
+{{ -50,-1029, -949,-1029,-1029},
+{ -649,-1628,-1548,-1628,-1628},
+{ -289,-1268,-1188,-1268,-1268},
+{ -739,-1718,-1638,-1718,-1718},
+{ -379,-1358,-1278,-1358,-1358}},
+/* CG.AG..GU */
+{{ -50,-1029, -949,-1029,-1029},
+{ -649,-1628,-1548,-1628,-1628},
+{ -289,-1268,-1188,-1268,-1268},
+{ -739,-1718,-1638,-1718,-1718},
+{ -379,-1358,-1278,-1358,-1358}},
+/* CG.AU..GU */
+{{ -50,-1029, -949,-1029,-1029},
+{ -649,-1628,-1548,-1628,-1628},
+{ -289,-1268,-1188,-1268,-1268},
+{ -739,-1718,-1638,-1718,-1718},
+{ -379,-1358,-1278,-1358,-1358}}},
+/* CG.C@..GU */
+{{{ -50, -519, -449, -519, -669},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CA..GU */
+{{ -50, -519, -449, -519, -669},
+{ -479, -948, -878, -948,-1098},
+{ -309, -778, -708, -778, -928},
+{ -389, -858, -788, -858,-1008},
+{ -379, -848, -778, -848, -998}},
+/* CG.CC..GU */
+{{ -50, -519, -449, -519, -669},
+{ -649,-1118,-1048,-1118,-1268},
+{ -289, -758, -688, -758, -908},
+{ -739,-1208,-1138,-1208,-1358},
+{ -379, -848, -778, -848, -998}},
+/* CG.CG..GU */
+{{ -50, -519, -449, -519, -669},
+{ -649,-1118,-1048,-1118,-1268},
+{ -289, -758, -688, -758, -908},
+{ -739,-1208,-1138,-1208,-1358},
+{ -379, -848, -778, -848, -998}},
+/* CG.CU..GU */
+{{ -50, -519, -449, -519, -669},
+{ -649,-1118,-1048,-1118,-1268},
+{ -289, -758, -688, -758, -908},
+{ -739,-1208,-1138,-1208,-1358},
+{ -379, -848, -778, -848, -998}}},
+/* CG.G@..GU */
+{{{ -50, -939, -939, -939, -939},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GA..GU */
+{{ -50, -939, -939, -939, -939},
+{ -479,-1368,-1368,-1368,-1368},
+{ -309,-1198,-1198,-1198,-1198},
+{ -389,-1278,-1278,-1278,-1278},
+{ -379,-1268,-1268,-1268,-1268}},
+/* CG.GC..GU */
+{{ -50, -939, -939, -939, -939},
+{ -649,-1538,-1538,-1538,-1538},
+{ -289,-1178,-1178,-1178,-1178},
+{ -739,-1628,-1628,-1628,-1628},
+{ -379,-1268,-1268,-1268,-1268}},
+/* CG.GG..GU */
+{{ -50, -939, -939, -939, -939},
+{ -649,-1538,-1538,-1538,-1538},
+{ -289,-1178,-1178,-1178,-1178},
+{ -739,-1628,-1628,-1628,-1628},
+{ -379,-1268,-1268,-1268,-1268}},
+/* CG.GU..GU */
+{{ -50, -939, -939, -939, -939},
+{ -649,-1538,-1538,-1538,-1538},
+{ -289,-1178,-1178,-1178,-1178},
+{ -739,-1628,-1628,-1628,-1628},
+{ -379,-1268,-1268,-1268,-1268}}},
+/* CG.U@..GU */
+{{{ -50, -809, -739, -809, -859},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UA..GU */
+{{ -50, -809, -739, -809, -859},
+{ -479,-1238,-1168,-1238,-1288},
+{ -309,-1068, -998,-1068,-1118},
+{ -389,-1148,-1078,-1148,-1198},
+{ -379,-1138,-1068,-1138,-1188}},
+/* CG.UC..GU */
+{{ -50, -809, -739, -809, -859},
+{ -649,-1408,-1338,-1408,-1458},
+{ -289,-1048, -978,-1048,-1098},
+{ -739,-1498,-1428,-1498,-1548},
+{ -379,-1138,-1068,-1138,-1188}},
+/* CG.UG..GU */
+{{ -50, -809, -739, -809, -859},
+{ -649,-1408,-1338,-1408,-1458},
+{ -289,-1048, -978,-1048,-1098},
+{ -739,-1498,-1428,-1498,-1548},
+{ -379,-1138,-1068,-1138,-1188}},
+/* CG.UU..GU */
+{{ -50, -809, -739, -809, -859},
+{ -649,-1408,-1338,-1408,-1458},
+{ -289,-1048, -978,-1048,-1098},
+{ -739,-1498,-1428,-1498,-1548},
+{ -379,-1138,-1068,-1138,-1188}}}},
+/* CG.@@..UG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@A..UG */
+{{ 0, 0, 0, 0, 0},
+{ -719, -719, -719, -719, -719},
+{ -479, -479, -479, -479, -479},
+{ -659, -659, -659, -659, -659},
+{ -549, -549, -549, -549, -549}},
+/* CG.@C..UG */
+{{ 0, 0, 0, 0, 0},
+{ -789, -789, -789, -789, -789},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -439, -439, -439, -439, -439}},
+/* CG.@G..UG */
+{{ 0, 0, 0, 0, 0},
+{ -959, -959, -959, -959, -959},
+{ -359, -359, -359, -359, -359},
+{ -919, -919, -919, -919, -919},
+{ -549, -549, -549, -549, -549}},
+/* CG.@U..UG */
+{{ 0, 0, 0, 0, 0},
+{ -809, -809, -809, -809, -809},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -359, -359, -359, -359, -359}}},
+/* CG.A@..UG */
+{{{ -50,-1029, -949,-1029,-1029},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AA..UG */
+{{ -50,-1029, -949,-1029,-1029},
+{ -769,-1748,-1668,-1748,-1748},
+{ -529,-1508,-1428,-1508,-1508},
+{ -709,-1688,-1608,-1688,-1688},
+{ -599,-1578,-1498,-1578,-1578}},
+/* CG.AC..UG */
+{{ -50,-1029, -949,-1029,-1029},
+{ -839,-1818,-1738,-1818,-1818},
+{ -529,-1508,-1428,-1508,-1508},
+{ -859,-1838,-1758,-1838,-1838},
+{ -489,-1468,-1388,-1468,-1468}},
+/* CG.AG..UG */
+{{ -50,-1029, -949,-1029,-1029},
+{-1009,-1988,-1908,-1988,-1988},
+{ -409,-1388,-1308,-1388,-1388},
+{ -969,-1948,-1868,-1948,-1948},
+{ -599,-1578,-1498,-1578,-1578}},
+/* CG.AU..UG */
+{{ -50,-1029, -949,-1029,-1029},
+{ -859,-1838,-1758,-1838,-1838},
+{ -529,-1508,-1428,-1508,-1508},
+{ -859,-1838,-1758,-1838,-1838},
+{ -409,-1388,-1308,-1388,-1388}}},
+/* CG.C@..UG */
+{{{ -50, -519, -449, -519, -669},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CA..UG */
+{{ -50, -519, -449, -519, -669},
+{ -769,-1238,-1168,-1238,-1388},
+{ -529, -998, -928, -998,-1148},
+{ -709,-1178,-1108,-1178,-1328},
+{ -599,-1068, -998,-1068,-1218}},
+/* CG.CC..UG */
+{{ -50, -519, -449, -519, -669},
+{ -839,-1308,-1238,-1308,-1458},
+{ -529, -998, -928, -998,-1148},
+{ -859,-1328,-1258,-1328,-1478},
+{ -489, -958, -888, -958,-1108}},
+/* CG.CG..UG */
+{{ -50, -519, -449, -519, -669},
+{-1009,-1478,-1408,-1478,-1628},
+{ -409, -878, -808, -878,-1028},
+{ -969,-1438,-1368,-1438,-1588},
+{ -599,-1068, -998,-1068,-1218}},
+/* CG.CU..UG */
+{{ -50, -519, -449, -519, -669},
+{ -859,-1328,-1258,-1328,-1478},
+{ -529, -998, -928, -998,-1148},
+{ -859,-1328,-1258,-1328,-1478},
+{ -409, -878, -808, -878,-1028}}},
+/* CG.G@..UG */
+{{{ -50, -939, -939, -939, -939},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GA..UG */
+{{ -50, -939, -939, -939, -939},
+{ -769,-1658,-1658,-1658,-1658},
+{ -529,-1418,-1418,-1418,-1418},
+{ -709,-1598,-1598,-1598,-1598},
+{ -599,-1488,-1488,-1488,-1488}},
+/* CG.GC..UG */
+{{ -50, -939, -939, -939, -939},
+{ -839,-1728,-1728,-1728,-1728},
+{ -529,-1418,-1418,-1418,-1418},
+{ -859,-1748,-1748,-1748,-1748},
+{ -489,-1378,-1378,-1378,-1378}},
+/* CG.GG..UG */
+{{ -50, -939, -939, -939, -939},
+{-1009,-1898,-1898,-1898,-1898},
+{ -409,-1298,-1298,-1298,-1298},
+{ -969,-1858,-1858,-1858,-1858},
+{ -599,-1488,-1488,-1488,-1488}},
+/* CG.GU..UG */
+{{ -50, -939, -939, -939, -939},
+{ -859,-1748,-1748,-1748,-1748},
+{ -529,-1418,-1418,-1418,-1418},
+{ -859,-1748,-1748,-1748,-1748},
+{ -409,-1298,-1298,-1298,-1298}}},
+/* CG.U@..UG */
+{{{ -50, -809, -739, -809, -859},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UA..UG */
+{{ -50, -809, -739, -809, -859},
+{ -769,-1528,-1458,-1528,-1578},
+{ -529,-1288,-1218,-1288,-1338},
+{ -709,-1468,-1398,-1468,-1518},
+{ -599,-1358,-1288,-1358,-1408}},
+/* CG.UC..UG */
+{{ -50, -809, -739, -809, -859},
+{ -839,-1598,-1528,-1598,-1648},
+{ -529,-1288,-1218,-1288,-1338},
+{ -859,-1618,-1548,-1618,-1668},
+{ -489,-1248,-1178,-1248,-1298}},
+/* CG.UG..UG */
+{{ -50, -809, -739, -809, -859},
+{-1009,-1768,-1698,-1768,-1818},
+{ -409,-1168,-1098,-1168,-1218},
+{ -969,-1728,-1658,-1728,-1778},
+{ -599,-1358,-1288,-1358,-1408}},
+/* CG.UU..UG */
+{{ -50, -809, -739, -809, -859},
+{ -859,-1618,-1548,-1618,-1668},
+{ -529,-1288,-1218,-1288,-1338},
+{ -859,-1618,-1548,-1618,-1668},
+{ -409,-1168,-1098,-1168,-1218}}}},
+/* CG.@@..AU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@A..AU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* CG.@C..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* CG.@G..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* CG.@U..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* CG.A@..AU */
+{{{ -50,-1029, -949,-1029,-1029},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AA..AU */
+{{ -50,-1029, -949,-1029,-1029},
+{ -479,-1458,-1378,-1458,-1458},
+{ -309,-1288,-1208,-1288,-1288},
+{ -389,-1368,-1288,-1368,-1368},
+{ -379,-1358,-1278,-1358,-1358}},
+/* CG.AC..AU */
+{{ -50,-1029, -949,-1029,-1029},
+{ -649,-1628,-1548,-1628,-1628},
+{ -289,-1268,-1188,-1268,-1268},
+{ -739,-1718,-1638,-1718,-1718},
+{ -379,-1358,-1278,-1358,-1358}},
+/* CG.AG..AU */
+{{ -50,-1029, -949,-1029,-1029},
+{ -649,-1628,-1548,-1628,-1628},
+{ -289,-1268,-1188,-1268,-1268},
+{ -739,-1718,-1638,-1718,-1718},
+{ -379,-1358,-1278,-1358,-1358}},
+/* CG.AU..AU */
+{{ -50,-1029, -949,-1029,-1029},
+{ -649,-1628,-1548,-1628,-1628},
+{ -289,-1268,-1188,-1268,-1268},
+{ -739,-1718,-1638,-1718,-1718},
+{ -379,-1358,-1278,-1358,-1358}}},
+/* CG.C@..AU */
+{{{ -50, -519, -449, -519, -669},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CA..AU */
+{{ -50, -519, -449, -519, -669},
+{ -479, -948, -878, -948,-1098},
+{ -309, -778, -708, -778, -928},
+{ -389, -858, -788, -858,-1008},
+{ -379, -848, -778, -848, -998}},
+/* CG.CC..AU */
+{{ -50, -519, -449, -519, -669},
+{ -649,-1118,-1048,-1118,-1268},
+{ -289, -758, -688, -758, -908},
+{ -739,-1208,-1138,-1208,-1358},
+{ -379, -848, -778, -848, -998}},
+/* CG.CG..AU */
+{{ -50, -519, -449, -519, -669},
+{ -649,-1118,-1048,-1118,-1268},
+{ -289, -758, -688, -758, -908},
+{ -739,-1208,-1138,-1208,-1358},
+{ -379, -848, -778, -848, -998}},
+/* CG.CU..AU */
+{{ -50, -519, -449, -519, -669},
+{ -649,-1118,-1048,-1118,-1268},
+{ -289, -758, -688, -758, -908},
+{ -739,-1208,-1138,-1208,-1358},
+{ -379, -848, -778, -848, -998}}},
+/* CG.G@..AU */
+{{{ -50, -939, -939, -939, -939},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GA..AU */
+{{ -50, -939, -939, -939, -939},
+{ -479,-1368,-1368,-1368,-1368},
+{ -309,-1198,-1198,-1198,-1198},
+{ -389,-1278,-1278,-1278,-1278},
+{ -379,-1268,-1268,-1268,-1268}},
+/* CG.GC..AU */
+{{ -50, -939, -939, -939, -939},
+{ -649,-1538,-1538,-1538,-1538},
+{ -289,-1178,-1178,-1178,-1178},
+{ -739,-1628,-1628,-1628,-1628},
+{ -379,-1268,-1268,-1268,-1268}},
+/* CG.GG..AU */
+{{ -50, -939, -939, -939, -939},
+{ -649,-1538,-1538,-1538,-1538},
+{ -289,-1178,-1178,-1178,-1178},
+{ -739,-1628,-1628,-1628,-1628},
+{ -379,-1268,-1268,-1268,-1268}},
+/* CG.GU..AU */
+{{ -50, -939, -939, -939, -939},
+{ -649,-1538,-1538,-1538,-1538},
+{ -289,-1178,-1178,-1178,-1178},
+{ -739,-1628,-1628,-1628,-1628},
+{ -379,-1268,-1268,-1268,-1268}}},
+/* CG.U@..AU */
+{{{ -50, -809, -739, -809, -859},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UA..AU */
+{{ -50, -809, -739, -809, -859},
+{ -479,-1238,-1168,-1238,-1288},
+{ -309,-1068, -998,-1068,-1118},
+{ -389,-1148,-1078,-1148,-1198},
+{ -379,-1138,-1068,-1138,-1188}},
+/* CG.UC..AU */
+{{ -50, -809, -739, -809, -859},
+{ -649,-1408,-1338,-1408,-1458},
+{ -289,-1048, -978,-1048,-1098},
+{ -739,-1498,-1428,-1498,-1548},
+{ -379,-1138,-1068,-1138,-1188}},
+/* CG.UG..AU */
+{{ -50, -809, -739, -809, -859},
+{ -649,-1408,-1338,-1408,-1458},
+{ -289,-1048, -978,-1048,-1098},
+{ -739,-1498,-1428,-1498,-1548},
+{ -379,-1138,-1068,-1138,-1188}},
+/* CG.UU..AU */
+{{ -50, -809, -739, -809, -859},
+{ -649,-1408,-1338,-1408,-1458},
+{ -289,-1048, -978,-1048,-1098},
+{ -739,-1498,-1428,-1498,-1548},
+{ -379,-1138,-1068,-1138,-1188}}}},
+/* CG.@@..UA */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@A..UA */
+{{ 0, 0, 0, 0, 0},
+{ -399, -399, -399, -399, -399},
+{ -429, -429, -429, -429, -429},
+{ -379, -379, -379, -379, -379},
+{ -279, -279, -279, -279, -279}},
+/* CG.@C..UA */
+{{ 0, 0, 0, 0, 0},
+{ -629, -629, -629, -629, -629},
+{ -509, -509, -509, -509, -509},
+{ -679, -679, -679, -679, -679},
+{ -139, -139, -139, -139, -139}},
+/* CG.@G..UA */
+{{ 0, 0, 0, 0, 0},
+{ -889, -889, -889, -889, -889},
+{ -199, -199, -199, -199, -199},
+{ -889, -889, -889, -889, -889},
+{ -279, -279, -279, -279, -279}},
+/* CG.@U..UA */
+{{ 0, 0, 0, 0, 0},
+{ -589, -589, -589, -589, -589},
+{ -179, -179, -179, -179, -179},
+{ -679, -679, -679, -679, -679},
+{ -140, -140, -140, -140, -140}}},
+/* CG.A@..UA */
+{{{ -50,-1029, -949,-1029,-1029},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AA..UA */
+{{ -50,-1029, -949,-1029,-1029},
+{ -449,-1428,-1348,-1428,-1428},
+{ -479,-1458,-1378,-1458,-1458},
+{ -429,-1408,-1328,-1408,-1408},
+{ -329,-1308,-1228,-1308,-1308}},
+/* CG.AC..UA */
+{{ -50,-1029, -949,-1029,-1029},
+{ -679,-1658,-1578,-1658,-1658},
+{ -559,-1538,-1458,-1538,-1538},
+{ -729,-1708,-1628,-1708,-1708},
+{ -189,-1168,-1088,-1168,-1168}},
+/* CG.AG..UA */
+{{ -50,-1029, -949,-1029,-1029},
+{ -939,-1918,-1838,-1918,-1918},
+{ -249,-1228,-1148,-1228,-1228},
+{ -939,-1918,-1838,-1918,-1918},
+{ -329,-1308,-1228,-1308,-1308}},
+/* CG.AU..UA */
+{{ -50,-1029, -949,-1029,-1029},
+{ -639,-1618,-1538,-1618,-1618},
+{ -229,-1208,-1128,-1208,-1208},
+{ -729,-1708,-1628,-1708,-1708},
+{ -190,-1169,-1089,-1169,-1169}}},
+/* CG.C@..UA */
+{{{ -50, -519, -449, -519, -669},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CA..UA */
+{{ -50, -519, -449, -519, -669},
+{ -449, -918, -848, -918,-1068},
+{ -479, -948, -878, -948,-1098},
+{ -429, -898, -828, -898,-1048},
+{ -329, -798, -728, -798, -948}},
+/* CG.CC..UA */
+{{ -50, -519, -449, -519, -669},
+{ -679,-1148,-1078,-1148,-1298},
+{ -559,-1028, -958,-1028,-1178},
+{ -729,-1198,-1128,-1198,-1348},
+{ -189, -658, -588, -658, -808}},
+/* CG.CG..UA */
+{{ -50, -519, -449, -519, -669},
+{ -939,-1408,-1338,-1408,-1558},
+{ -249, -718, -648, -718, -868},
+{ -939,-1408,-1338,-1408,-1558},
+{ -329, -798, -728, -798, -948}},
+/* CG.CU..UA */
+{{ -50, -519, -449, -519, -669},
+{ -639,-1108,-1038,-1108,-1258},
+{ -229, -698, -628, -698, -848},
+{ -729,-1198,-1128,-1198,-1348},
+{ -190, -659, -589, -659, -809}}},
+/* CG.G@..UA */
+{{{ -50, -939, -939, -939, -939},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GA..UA */
+{{ -50, -939, -939, -939, -939},
+{ -449,-1338,-1338,-1338,-1338},
+{ -479,-1368,-1368,-1368,-1368},
+{ -429,-1318,-1318,-1318,-1318},
+{ -329,-1218,-1218,-1218,-1218}},
+/* CG.GC..UA */
+{{ -50, -939, -939, -939, -939},
+{ -679,-1568,-1568,-1568,-1568},
+{ -559,-1448,-1448,-1448,-1448},
+{ -729,-1618,-1618,-1618,-1618},
+{ -189,-1078,-1078,-1078,-1078}},
+/* CG.GG..UA */
+{{ -50, -939, -939, -939, -939},
+{ -939,-1828,-1828,-1828,-1828},
+{ -249,-1138,-1138,-1138,-1138},
+{ -939,-1828,-1828,-1828,-1828},
+{ -329,-1218,-1218,-1218,-1218}},
+/* CG.GU..UA */
+{{ -50, -939, -939, -939, -939},
+{ -639,-1528,-1528,-1528,-1528},
+{ -229,-1118,-1118,-1118,-1118},
+{ -729,-1618,-1618,-1618,-1618},
+{ -190,-1079,-1079,-1079,-1079}}},
+/* CG.U@..UA */
+{{{ -50, -809, -739, -809, -859},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UA..UA */
+{{ -50, -809, -739, -809, -859},
+{ -449,-1208,-1138,-1208,-1258},
+{ -479,-1238,-1168,-1238,-1288},
+{ -429,-1188,-1118,-1188,-1238},
+{ -329,-1088,-1018,-1088,-1138}},
+/* CG.UC..UA */
+{{ -50, -809, -739, -809, -859},
+{ -679,-1438,-1368,-1438,-1488},
+{ -559,-1318,-1248,-1318,-1368},
+{ -729,-1488,-1418,-1488,-1538},
+{ -189, -948, -878, -948, -998}},
+/* CG.UG..UA */
+{{ -50, -809, -739, -809, -859},
+{ -939,-1698,-1628,-1698,-1748},
+{ -249,-1008, -938,-1008,-1058},
+{ -939,-1698,-1628,-1698,-1748},
+{ -329,-1088,-1018,-1088,-1138}},
+/* CG.UU..UA */
+{{ -50, -809, -739, -809, -859},
+{ -639,-1398,-1328,-1398,-1448},
+{ -229, -988, -918, -988,-1038},
+{ -729,-1488,-1418,-1488,-1538},
+{ -190, -949, -879, -949, -999}}}},
+/* CG.@@.. @ */
+{{{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@A.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@C.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@G.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* CG.@U.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}}},
+/* CG.A@.. @ */
+{{{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AA.. @ */
+{{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AC.. @ */
+{{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AG.. @ */
+{{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}},
+/* CG.AU.. @ */
+{{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079},
+{ -100,-1079, -999,-1079,-1079}}},
+/* CG.C@.. @ */
+{{{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CA.. @ */
+{{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CC.. @ */
+{{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CG.. @ */
+{{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}},
+/* CG.CU.. @ */
+{{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719},
+{ -100, -569, -499, -569, -719}}},
+/* CG.G@.. @ */
+{{{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GA.. @ */
+{{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GC.. @ */
+{{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GG.. @ */
+{{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}},
+/* CG.GU.. @ */
+{{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989},
+{ -100, -989, -989, -989, -989}}},
+/* CG.U@.. @ */
+{{{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UA.. @ */
+{{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UC.. @ */
+{{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UG.. @ */
+{{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}},
+/* CG.UU.. @ */
+{{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909},
+{ -100, -859, -789, -859, -909}}}}},
+{ /* noPair */ {{{{0}}}},
+/* GC.@@..CG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@A..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* GC.@C..CG */
+{{ 0, 0, 0, 0, 0},
+{ -949, -949, -949, -949, -949},
+{ -449, -449, -449, -449, -449},
+{ -939, -939, -939, -939, -939},
+{ -739, -739, -739, -739, -739}},
+/* GC.@G..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* GC.@U..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -669, -669, -669, -669, -669},
+{ -939, -939, -939, -939, -939},
+{ -859, -859, -859, -859, -859}}},
+/* GC.A@..CG */
+{{{ -50, -519, -879, -559, -879},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AA..CG */
+{{ -50, -519, -879, -559, -879},
+{-1079,-1548,-1908,-1588,-1908},
+{ -569,-1038,-1398,-1078,-1398},
+{ -989,-1458,-1818,-1498,-1818},
+{ -859,-1328,-1688,-1368,-1688}},
+/* GC.AC..CG */
+{{ -50, -519, -879, -559, -879},
+{ -999,-1468,-1828,-1508,-1828},
+{ -499, -968,-1328,-1008,-1328},
+{ -989,-1458,-1818,-1498,-1818},
+{ -789,-1258,-1618,-1298,-1618}},
+/* GC.AG..CG */
+{{ -50, -519, -879, -559, -879},
+{-1079,-1548,-1908,-1588,-1908},
+{ -569,-1038,-1398,-1078,-1398},
+{ -989,-1458,-1818,-1498,-1818},
+{ -859,-1328,-1688,-1368,-1688}},
+/* GC.AU..CG */
+{{ -50, -519, -879, -559, -879},
+{-1079,-1548,-1908,-1588,-1908},
+{ -719,-1188,-1548,-1228,-1548},
+{ -989,-1458,-1818,-1498,-1818},
+{ -909,-1378,-1738,-1418,-1738}}},
+/* GC.C@..CG */
+{{{ -50, -719, -309, -309, -389},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CA..CG */
+{{ -50, -719, -309, -309, -389},
+{-1079,-1748,-1338,-1338,-1418},
+{ -569,-1238, -828, -828, -908},
+{ -989,-1658,-1248,-1248,-1328},
+{ -859,-1528,-1118,-1118,-1198}},
+/* GC.CC..CG */
+{{ -50, -719, -309, -309, -389},
+{ -999,-1668,-1258,-1258,-1338},
+{ -499,-1168, -758, -758, -838},
+{ -989,-1658,-1248,-1248,-1328},
+{ -789,-1458,-1048,-1048,-1128}},
+/* GC.CG..CG */
+{{ -50, -719, -309, -309, -389},
+{-1079,-1748,-1338,-1338,-1418},
+{ -569,-1238, -828, -828, -908},
+{ -989,-1658,-1248,-1248,-1328},
+{ -859,-1528,-1118,-1118,-1198}},
+/* GC.CU..CG */
+{{ -50, -719, -309, -309, -389},
+{-1079,-1748,-1338,-1338,-1418},
+{ -719,-1388, -978, -978,-1058},
+{ -989,-1658,-1248,-1248,-1328},
+{ -909,-1578,-1168,-1168,-1248}}},
+/* GC.G@..CG */
+{{{ -50, -709, -739, -619, -739},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GA..CG */
+{{ -50, -709, -739, -619, -739},
+{-1079,-1738,-1768,-1648,-1768},
+{ -569,-1228,-1258,-1138,-1258},
+{ -989,-1648,-1678,-1558,-1678},
+{ -859,-1518,-1548,-1428,-1548}},
+/* GC.GC..CG */
+{{ -50, -709, -739, -619, -739},
+{ -999,-1658,-1688,-1568,-1688},
+{ -499,-1158,-1188,-1068,-1188},
+{ -989,-1648,-1678,-1558,-1678},
+{ -789,-1448,-1478,-1358,-1478}},
+/* GC.GG..CG */
+{{ -50, -709, -739, -619, -739},
+{-1079,-1738,-1768,-1648,-1768},
+{ -569,-1228,-1258,-1138,-1258},
+{ -989,-1648,-1678,-1558,-1678},
+{ -859,-1518,-1548,-1428,-1548}},
+/* GC.GU..CG */
+{{ -50, -709, -739, -619, -739},
+{-1079,-1738,-1768,-1648,-1768},
+{ -719,-1378,-1408,-1288,-1408},
+{ -989,-1648,-1678,-1558,-3080},
+{ -909,-1568,-1598,-1478,-1598}}},
+/* GC.U@..CG */
+{{{ -50, -499, -499, -499, -569},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UA..CG */
+{{ -50, -499, -499, -499, -569},
+{-1079,-1528,-1528,-1528,-1598},
+{ -569,-1018,-1018,-1018,-1088},
+{ -989,-1438,-1438,-1438,-1508},
+{ -859,-1308,-1308,-1308,-1378}},
+/* GC.UC..CG */
+{{ -50, -499, -499, -499, -569},
+{ -999,-1448,-1448,-1448,-1518},
+{ -499, -948, -948, -948,-1018},
+{ -989,-1438,-1438,-1438,-1508},
+{ -789,-1238,-1238,-1238,-1308}},
+/* GC.UG..CG */
+{{ -50, -499, -499, -499, -569},
+{-1079,-1528,-1528,-1528,-1598},
+{ -569,-1018,-1018,-1018,-1088},
+{ -989,-1438,-1438,-1438,-1508},
+{ -859,-1308,-1308,-1308,-1378}},
+/* GC.UU..CG */
+{{ -50, -499, -499, -499, -569},
+{-1079,-1528,-1528,-1528,-1598},
+{ -719,-1168,-1168,-1168,-1238},
+{ -989,-1438,-1438,-1438,-1508},
+{ -909,-1358,-1358,-1358,-1428}}}},
+/* GC.@@..GC */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@A..GC */
+{{ 0, 0, 0, 0, 0},
+{ -519, -519, -519, -519, -519},
+{ -719, -719, -719, -719, -719},
+{ -709, -709, -709, -709, -709},
+{ -499, -499, -499, -499, -499}},
+/* GC.@C..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -309, -309, -309, -309, -309},
+{ -739, -739, -739, -739, -739},
+{ -499, -499, -499, -499, -499}},
+/* GC.@G..GC */
+{{ 0, 0, 0, 0, 0},
+{ -559, -559, -559, -559, -559},
+{ -309, -309, -309, -309, -309},
+{ -619, -619, -619, -619, -619},
+{ -499, -499, -499, -499, -499}},
+/* GC.@U..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -389, -389, -389, -389, -389},
+{ -739, -739, -739, -739, -739},
+{ -569, -569, -569, -569, -569}}},
+/* GC.A@..GC */
+{{{ -50, -519, -879, -559, -879},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AA..GC */
+{{ -50, -519, -879, -559, -879},
+{ -569,-1038,-1398,-1078,-1398},
+{ -769,-1238,-1598,-1278,-1598},
+{ -759,-1228,-1588,-1268,-1588},
+{ -549,-1018,-1378,-1058,-1378}},
+/* GC.AC..GC */
+{{ -50, -519, -879, -559, -879},
+{ -929,-1398,-1758,-1438,-1758},
+{ -359, -828,-1188, -868,-1188},
+{ -789,-1258,-1618,-1298,-1618},
+{ -549,-1018,-1378,-1058,-1378}},
+/* GC.AG..GC */
+{{ -50, -519, -879, -559, -879},
+{ -609,-1078,-1438,-1118,-1438},
+{ -359, -828,-1188, -868,-1188},
+{ -669,-1138,-1498,-1178,-1498},
+{ -549,-1018,-1378,-1058,-1378}},
+/* GC.AU..GC */
+{{ -50, -519, -879, -559, -879},
+{ -929,-1398,-1758,-1438,-1758},
+{ -439, -908,-1268, -948,-1268},
+{ -789,-1258,-1618,-1298,-1618},
+{ -619,-1088,-1448,-1128,-1448}}},
+/* GC.C@..GC */
+{{{ -50, -719, -309, -309, -389},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CA..GC */
+{{ -50, -719, -309, -309, -389},
+{ -569,-1238, -828, -828, -908},
+{ -769,-1438,-1028,-1028,-1108},
+{ -759,-1428,-1018,-1018,-1098},
+{ -549,-1218, -808, -808, -888}},
+/* GC.CC..GC */
+{{ -50, -719, -309, -309, -389},
+{ -929,-1598,-1188,-1188,-1268},
+{ -359,-1028, -618, -618, -698},
+{ -789,-1458,-1048,-1048,-1128},
+{ -549,-1218, -808, -808, -888}},
+/* GC.CG..GC */
+{{ -50, -719, -309, -309, -389},
+{ -609,-1278, -868, -868, -948},
+{ -359,-1028, -618, -618, -698},
+{ -669,-1338, -928, -928,-1008},
+{ -549,-1218, -808, -808, -888}},
+/* GC.CU..GC */
+{{ -50, -719, -309, -309, -389},
+{ -929,-1598,-1188,-1188,-1268},
+{ -439,-1108, -698, -698, -778},
+{ -789,-1458,-1048,-1048,-1128},
+{ -619,-1288, -878, -878, -958}}},
+/* GC.G@..GC */
+{{{ -50, -709, -739, -619, -739},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GA..GC */
+{{ -50, -709, -739, -619, -739},
+{ -569,-1228,-1258,-1138,-1258},
+{ -769,-1428,-1458,-1338,-1458},
+{ -759,-1418,-1448,-1328,-1448},
+{ -549,-1208,-1238,-1118,-1238}},
+/* GC.GC..GC */
+{{ -50, -709, -739, -619, -739},
+{ -929,-1588,-1618,-1498,-1618},
+{ -359,-1018,-1048, -928,-1048},
+{ -789,-1448,-1478,-1358,-1478},
+{ -549,-1208,-1238,-1118,-1238}},
+/* GC.GG..GC */
+{{ -50, -709, -739, -619, -739},
+{ -609,-1268,-1298,-1178,-1298},
+{ -359,-1018,-1048, -928,-1048},
+{ -669,-1328,-1358,-1238,-1358},
+{ -549,-1208,-1238,-1118,-1238}},
+/* GC.GU..GC */
+{{ -50, -709, -739, -619, -739},
+{ -929,-1588,-1618,-1498,-1618},
+{ -439,-1098,-1128,-1008,-1128},
+{ -789,-1448,-1478,-1358,-3080},
+{ -619,-1278,-1308,-1188,-1308}}},
+/* GC.U@..GC */
+{{{ -50, -499, -499, -499, -569},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UA..GC */
+{{ -50, -499, -499, -499, -569},
+{ -569,-1018,-1018,-1018,-1088},
+{ -769,-1218,-1218,-1218,-1288},
+{ -759,-1208,-1208,-1208,-1278},
+{ -549, -998, -998, -998,-1068}},
+/* GC.UC..GC */
+{{ -50, -499, -499, -499, -569},
+{ -929,-1378,-1378,-1378,-1448},
+{ -359, -808, -808, -808, -878},
+{ -789,-1238,-1238,-1238,-1308},
+{ -549, -998, -998, -998,-1068}},
+/* GC.UG..GC */
+{{ -50, -499, -499, -499, -569},
+{ -609,-1058,-1058,-1058,-1128},
+{ -359, -808, -808, -808, -878},
+{ -669,-1118,-1118,-1118,-1188},
+{ -549, -998, -998, -998,-1068}},
+/* GC.UU..GC */
+{{ -50, -499, -499, -499, -569},
+{ -929,-1378,-1378,-1378,-1448},
+{ -439, -888, -888, -888, -958},
+{ -789,-1238,-1238,-1238,-1308},
+{ -619,-1068,-1068,-1068,-1138}}}},
+/* GC.@@..GU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@A..GU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* GC.@C..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* GC.@G..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* GC.@U..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* GC.A@..GU */
+{{{ -50, -519, -879, -559, -879},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AA..GU */
+{{ -50, -519, -879, -559, -879},
+{ -479, -948,-1308, -988,-1308},
+{ -309, -778,-1138, -818,-1138},
+{ -389, -858,-1218, -898,-1218},
+{ -379, -848,-1208, -888,-1208}},
+/* GC.AC..GU */
+{{ -50, -519, -879, -559, -879},
+{ -649,-1118,-1478,-1158,-1478},
+{ -289, -758,-1118, -798,-1118},
+{ -739,-1208,-1568,-1248,-1568},
+{ -379, -848,-1208, -888,-1208}},
+/* GC.AG..GU */
+{{ -50, -519, -879, -559, -879},
+{ -649,-1118,-1478,-1158,-1478},
+{ -289, -758,-1118, -798,-1118},
+{ -739,-1208,-1568,-1248,-1568},
+{ -379, -848,-1208, -888,-1208}},
+/* GC.AU..GU */
+{{ -50, -519, -879, -559, -879},
+{ -649,-1118,-1478,-1158,-1478},
+{ -289, -758,-1118, -798,-1118},
+{ -739,-1208,-1568,-1248,-1568},
+{ -379, -848,-1208, -888,-1208}}},
+/* GC.C@..GU */
+{{{ -50, -719, -309, -309, -389},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CA..GU */
+{{ -50, -719, -309, -309, -389},
+{ -479,-1148, -738, -738, -818},
+{ -309, -978, -568, -568, -648},
+{ -389,-1058, -648, -648, -728},
+{ -379,-1048, -638, -638, -718}},
+/* GC.CC..GU */
+{{ -50, -719, -309, -309, -389},
+{ -649,-1318, -908, -908, -988},
+{ -289, -958, -548, -548, -628},
+{ -739,-1408, -998, -998,-1078},
+{ -379,-1048, -638, -638, -718}},
+/* GC.CG..GU */
+{{ -50, -719, -309, -309, -389},
+{ -649,-1318, -908, -908, -988},
+{ -289, -958, -548, -548, -628},
+{ -739,-1408, -998, -998,-1078},
+{ -379,-1048, -638, -638, -718}},
+/* GC.CU..GU */
+{{ -50, -719, -309, -309, -389},
+{ -649,-1318, -908, -908, -988},
+{ -289, -958, -548, -548, -628},
+{ -739,-1408, -998, -998,-1078},
+{ -379,-1048, -638, -638, -718}}},
+/* GC.G@..GU */
+{{{ -50, -709, -739, -619, -739},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GA..GU */
+{{ -50, -709, -739, -619, -739},
+{ -479,-1138,-1168,-1048,-1168},
+{ -309, -968, -998, -878, -998},
+{ -389,-1048,-1078, -958,-1078},
+{ -379,-1038,-1068, -948,-1068}},
+/* GC.GC..GU */
+{{ -50, -709, -739, -619, -739},
+{ -649,-1308,-1338,-1218,-1338},
+{ -289, -948, -978, -858, -978},
+{ -739,-1398,-1428,-1308,-1428},
+{ -379,-1038,-1068, -948,-1068}},
+/* GC.GG..GU */
+{{ -50, -709, -739, -619, -739},
+{ -649,-1308,-1338,-1218,-1338},
+{ -289, -948, -978, -858, -978},
+{ -739,-1398,-1428,-1308,-1428},
+{ -379,-1038,-1068, -948,-1068}},
+/* GC.GU..GU */
+{{ -50, -709, -739, -619, -739},
+{ -649,-1308,-1338,-1218,-1338},
+{ -289, -948, -978, -858, -978},
+{ -739,-1398,-1428,-1308,-1428},
+{ -379,-1038,-1068, -948,-1068}}},
+/* GC.U@..GU */
+{{{ -50, -499, -499, -499, -569},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UA..GU */
+{{ -50, -499, -499, -499, -569},
+{ -479, -928, -928, -928, -998},
+{ -309, -758, -758, -758, -828},
+{ -389, -838, -838, -838, -908},
+{ -379, -828, -828, -828, -898}},
+/* GC.UC..GU */
+{{ -50, -499, -499, -499, -569},
+{ -649,-1098,-1098,-1098,-1168},
+{ -289, -738, -738, -738, -808},
+{ -739,-1188,-1188,-1188,-1258},
+{ -379, -828, -828, -828, -898}},
+/* GC.UG..GU */
+{{ -50, -499, -499, -499, -569},
+{ -649,-1098,-1098,-1098,-1168},
+{ -289, -738, -738, -738, -808},
+{ -739,-1188,-1188,-1188,-1258},
+{ -379, -828, -828, -828, -898}},
+/* GC.UU..GU */
+{{ -50, -499, -499, -499, -569},
+{ -649,-1098,-1098,-1098,-1168},
+{ -289, -738, -738, -738, -808},
+{ -739,-1188,-1188,-1188,-1258},
+{ -379, -828, -828, -828, -898}}}},
+/* GC.@@..UG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@A..UG */
+{{ 0, 0, 0, 0, 0},
+{ -719, -719, -719, -719, -719},
+{ -479, -479, -479, -479, -479},
+{ -659, -659, -659, -659, -659},
+{ -549, -549, -549, -549, -549}},
+/* GC.@C..UG */
+{{ 0, 0, 0, 0, 0},
+{ -789, -789, -789, -789, -789},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -439, -439, -439, -439, -439}},
+/* GC.@G..UG */
+{{ 0, 0, 0, 0, 0},
+{ -959, -959, -959, -959, -959},
+{ -359, -359, -359, -359, -359},
+{ -919, -919, -919, -919, -919},
+{ -549, -549, -549, -549, -549}},
+/* GC.@U..UG */
+{{ 0, 0, 0, 0, 0},
+{ -809, -809, -809, -809, -809},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -359, -359, -359, -359, -359}}},
+/* GC.A@..UG */
+{{{ -50, -519, -879, -559, -879},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AA..UG */
+{{ -50, -519, -879, -559, -879},
+{ -769,-1238,-1598,-1278,-1598},
+{ -529, -998,-1358,-1038,-1358},
+{ -709,-1178,-1538,-1218,-1538},
+{ -599,-1068,-1428,-1108,-1428}},
+/* GC.AC..UG */
+{{ -50, -519, -879, -559, -879},
+{ -839,-1308,-1668,-1348,-1668},
+{ -529, -998,-1358,-1038,-1358},
+{ -859,-1328,-1688,-1368,-1688},
+{ -489, -958,-1318, -998,-1318}},
+/* GC.AG..UG */
+{{ -50, -519, -879, -559, -879},
+{-1009,-1478,-1838,-1518,-1838},
+{ -409, -878,-1238, -918,-1238},
+{ -969,-1438,-1798,-1478,-1798},
+{ -599,-1068,-1428,-1108,-1428}},
+/* GC.AU..UG */
+{{ -50, -519, -879, -559, -879},
+{ -859,-1328,-1688,-1368,-1688},
+{ -529, -998,-1358,-1038,-1358},
+{ -859,-1328,-1688,-1368,-1688},
+{ -409, -878,-1238, -918,-1238}}},
+/* GC.C@..UG */
+{{{ -50, -719, -309, -309, -389},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CA..UG */
+{{ -50, -719, -309, -309, -389},
+{ -769,-1438,-1028,-1028,-1108},
+{ -529,-1198, -788, -788, -868},
+{ -709,-1378, -968, -968,-1048},
+{ -599,-1268, -858, -858, -938}},
+/* GC.CC..UG */
+{{ -50, -719, -309, -309, -389},
+{ -839,-1508,-1098,-1098,-1178},
+{ -529,-1198, -788, -788, -868},
+{ -859,-1528,-1118,-1118,-1198},
+{ -489,-1158, -748, -748, -828}},
+/* GC.CG..UG */
+{{ -50, -719, -309, -309, -389},
+{-1009,-1678,-1268,-1268,-1348},
+{ -409,-1078, -668, -668, -748},
+{ -969,-1638,-1228,-1228,-1308},
+{ -599,-1268, -858, -858, -938}},
+/* GC.CU..UG */
+{{ -50, -719, -309, -309, -389},
+{ -859,-1528,-1118,-1118,-1198},
+{ -529,-1198, -788, -788, -868},
+{ -859,-1528,-1118,-1118,-1198},
+{ -409,-1078, -668, -668, -748}}},
+/* GC.G@..UG */
+{{{ -50, -709, -739, -619, -739},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GA..UG */
+{{ -50, -709, -739, -619, -739},
+{ -769,-1428,-1458,-1338,-1458},
+{ -529,-1188,-1218,-1098,-1218},
+{ -709,-1368,-1398,-1278,-1398},
+{ -599,-1258,-1288,-1168,-1288}},
+/* GC.GC..UG */
+{{ -50, -709, -739, -619, -739},
+{ -839,-1498,-1528,-1408,-1528},
+{ -529,-1188,-1218,-1098,-1218},
+{ -859,-1518,-1548,-1428,-1548},
+{ -489,-1148,-1178,-1058,-1178}},
+/* GC.GG..UG */
+{{ -50, -709, -739, -619, -739},
+{-1009,-1668,-1698,-1578,-1698},
+{ -409,-1068,-1098, -978,-1098},
+{ -969,-1628,-1658,-1538,-1658},
+{ -599,-1258,-1288,-1168,-1288}},
+/* GC.GU..UG */
+{{ -50, -709, -739, -619, -739},
+{ -859,-1518,-1548,-1428,-1548},
+{ -529,-1188,-1218,-1098,-1218},
+{ -859,-1518,-1548,-1428,-1548},
+{ -409,-1068,-1098, -978,-1098}}},
+/* GC.U@..UG */
+{{{ -50, -499, -499, -499, -569},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UA..UG */
+{{ -50, -499, -499, -499, -569},
+{ -769,-1218,-1218,-1218,-1288},
+{ -529, -978, -978, -978,-1048},
+{ -709,-1158,-1158,-1158,-1228},
+{ -599,-1048,-1048,-1048,-1118}},
+/* GC.UC..UG */
+{{ -50, -499, -499, -499, -569},
+{ -839,-1288,-1288,-1288,-1358},
+{ -529, -978, -978, -978,-1048},
+{ -859,-1308,-1308,-1308,-1378},
+{ -489, -938, -938, -938,-1008}},
+/* GC.UG..UG */
+{{ -50, -499, -499, -499, -569},
+{-1009,-1458,-1458,-1458,-1528},
+{ -409, -858, -858, -858, -928},
+{ -969,-1418,-1418,-1418,-1488},
+{ -599,-1048,-1048,-1048,-1118}},
+/* GC.UU..UG */
+{{ -50, -499, -499, -499, -569},
+{ -859,-1308,-1308,-1308,-1378},
+{ -529, -978, -978, -978,-1048},
+{ -859,-1308,-1308,-1308,-1378},
+{ -409, -858, -858, -858, -928}}}},
+/* GC.@@..AU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@A..AU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* GC.@C..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* GC.@G..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* GC.@U..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* GC.A@..AU */
+{{{ -50, -519, -879, -559, -879},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AA..AU */
+{{ -50, -519, -879, -559, -879},
+{ -479, -948,-1308, -988,-1308},
+{ -309, -778,-1138, -818,-1138},
+{ -389, -858,-1218, -898,-1218},
+{ -379, -848,-1208, -888,-1208}},
+/* GC.AC..AU */
+{{ -50, -519, -879, -559, -879},
+{ -649,-1118,-1478,-1158,-1478},
+{ -289, -758,-1118, -798,-1118},
+{ -739,-1208,-1568,-1248,-1568},
+{ -379, -848,-1208, -888,-1208}},
+/* GC.AG..AU */
+{{ -50, -519, -879, -559, -879},
+{ -649,-1118,-1478,-1158,-1478},
+{ -289, -758,-1118, -798,-1118},
+{ -739,-1208,-1568,-1248,-1568},
+{ -379, -848,-1208, -888,-1208}},
+/* GC.AU..AU */
+{{ -50, -519, -879, -559, -879},
+{ -649,-1118,-1478,-1158,-1478},
+{ -289, -758,-1118, -798,-1118},
+{ -739,-1208,-1568,-1248,-1568},
+{ -379, -848,-1208, -888,-1208}}},
+/* GC.C@..AU */
+{{{ -50, -719, -309, -309, -389},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CA..AU */
+{{ -50, -719, -309, -309, -389},
+{ -479,-1148, -738, -738, -818},
+{ -309, -978, -568, -568, -648},
+{ -389,-1058, -648, -648, -728},
+{ -379,-1048, -638, -638, -718}},
+/* GC.CC..AU */
+{{ -50, -719, -309, -309, -389},
+{ -649,-1318, -908, -908, -988},
+{ -289, -958, -548, -548, -628},
+{ -739,-1408, -998, -998,-1078},
+{ -379,-1048, -638, -638, -718}},
+/* GC.CG..AU */
+{{ -50, -719, -309, -309, -389},
+{ -649,-1318, -908, -908, -988},
+{ -289, -958, -548, -548, -628},
+{ -739,-1408, -998, -998,-1078},
+{ -379,-1048, -638, -638, -718}},
+/* GC.CU..AU */
+{{ -50, -719, -309, -309, -389},
+{ -649,-1318, -908, -908, -988},
+{ -289, -958, -548, -548, -628},
+{ -739,-1408, -998, -998,-1078},
+{ -379,-1048, -638, -638, -718}}},
+/* GC.G@..AU */
+{{{ -50, -709, -739, -619, -739},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GA..AU */
+{{ -50, -709, -739, -619, -739},
+{ -479,-1138,-1168,-1048,-1168},
+{ -309, -968, -998, -878, -998},
+{ -389,-1048,-1078, -958,-1078},
+{ -379,-1038,-1068, -948,-1068}},
+/* GC.GC..AU */
+{{ -50, -709, -739, -619, -739},
+{ -649,-1308,-1338,-1218,-1338},
+{ -289, -948, -978, -858, -978},
+{ -739,-1398,-1428,-1308,-1428},
+{ -379,-1038,-1068, -948,-1068}},
+/* GC.GG..AU */
+{{ -50, -709, -739, -619, -739},
+{ -649,-1308,-1338,-1218,-1338},
+{ -289, -948, -978, -858, -978},
+{ -739,-1398,-1428,-1308,-1428},
+{ -379,-1038,-1068, -948,-1068}},
+/* GC.GU..AU */
+{{ -50, -709, -739, -619, -739},
+{ -649,-1308,-1338,-1218,-1338},
+{ -289, -948, -978, -858, -978},
+{ -739,-1398,-1428,-1308,-1428},
+{ -379,-1038,-1068, -948,-1068}}},
+/* GC.U@..AU */
+{{{ -50, -499, -499, -499, -569},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UA..AU */
+{{ -50, -499, -499, -499, -569},
+{ -479, -928, -928, -928, -998},
+{ -309, -758, -758, -758, -828},
+{ -389, -838, -838, -838, -908},
+{ -379, -828, -828, -828, -898}},
+/* GC.UC..AU */
+{{ -50, -499, -499, -499, -569},
+{ -649,-1098,-1098,-1098,-1168},
+{ -289, -738, -738, -738, -808},
+{ -739,-1188,-1188,-1188,-1258},
+{ -379, -828, -828, -828, -898}},
+/* GC.UG..AU */
+{{ -50, -499, -499, -499, -569},
+{ -649,-1098,-1098,-1098,-1168},
+{ -289, -738, -738, -738, -808},
+{ -739,-1188,-1188,-1188,-1258},
+{ -379, -828, -828, -828, -898}},
+/* GC.UU..AU */
+{{ -50, -499, -499, -499, -569},
+{ -649,-1098,-1098,-1098,-1168},
+{ -289, -738, -738, -738, -808},
+{ -739,-1188,-1188,-1188,-1258},
+{ -379, -828, -828, -828, -898}}}},
+/* GC.@@..UA */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@A..UA */
+{{ 0, 0, 0, 0, 0},
+{ -399, -399, -399, -399, -399},
+{ -429, -429, -429, -429, -429},
+{ -379, -379, -379, -379, -379},
+{ -279, -279, -279, -279, -279}},
+/* GC.@C..UA */
+{{ 0, 0, 0, 0, 0},
+{ -629, -629, -629, -629, -629},
+{ -509, -509, -509, -509, -509},
+{ -679, -679, -679, -679, -679},
+{ -139, -139, -139, -139, -139}},
+/* GC.@G..UA */
+{{ 0, 0, 0, 0, 0},
+{ -889, -889, -889, -889, -889},
+{ -199, -199, -199, -199, -199},
+{ -889, -889, -889, -889, -889},
+{ -279, -279, -279, -279, -279}},
+/* GC.@U..UA */
+{{ 0, 0, 0, 0, 0},
+{ -589, -589, -589, -589, -589},
+{ -179, -179, -179, -179, -179},
+{ -679, -679, -679, -679, -679},
+{ -140, -140, -140, -140, -140}}},
+/* GC.A@..UA */
+{{{ -50, -519, -879, -559, -879},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AA..UA */
+{{ -50, -519, -879, -559, -879},
+{ -449, -918,-1278, -958,-1278},
+{ -479, -948,-1308, -988,-1308},
+{ -429, -898,-1258, -938,-1258},
+{ -329, -798,-1158, -838,-1158}},
+/* GC.AC..UA */
+{{ -50, -519, -879, -559, -879},
+{ -679,-1148,-1508,-1188,-1508},
+{ -559,-1028,-1388,-1068,-1388},
+{ -729,-1198,-1558,-1238,-1558},
+{ -189, -658,-1018, -698,-1018}},
+/* GC.AG..UA */
+{{ -50, -519, -879, -559, -879},
+{ -939,-1408,-1768,-1448,-1768},
+{ -249, -718,-1078, -758,-1078},
+{ -939,-1408,-1768,-1448,-1768},
+{ -329, -798,-1158, -838,-1158}},
+/* GC.AU..UA */
+{{ -50, -519, -879, -559, -879},
+{ -639,-1108,-1468,-1148,-1468},
+{ -229, -698,-1058, -738,-1058},
+{ -729,-1198,-1558,-1238,-1558},
+{ -190, -659,-1019, -699,-1019}}},
+/* GC.C@..UA */
+{{{ -50, -719, -309, -309, -389},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CA..UA */
+{{ -50, -719, -309, -309, -389},
+{ -449,-1118, -708, -708, -788},
+{ -479,-1148, -738, -738, -818},
+{ -429,-1098, -688, -688, -768},
+{ -329, -998, -588, -588, -668}},
+/* GC.CC..UA */
+{{ -50, -719, -309, -309, -389},
+{ -679,-1348, -938, -938,-1018},
+{ -559,-1228, -818, -818, -898},
+{ -729,-1398, -988, -988,-1068},
+{ -189, -858, -448, -448, -528}},
+/* GC.CG..UA */
+{{ -50, -719, -309, -309, -389},
+{ -939,-1608,-1198,-1198,-1278},
+{ -249, -918, -508, -508, -588},
+{ -939,-1608,-1198,-1198,-1278},
+{ -329, -998, -588, -588, -668}},
+/* GC.CU..UA */
+{{ -50, -719, -309, -309, -389},
+{ -639,-1308, -898, -898, -978},
+{ -229, -898, -488, -488, -568},
+{ -729,-1398, -988, -988,-1068},
+{ -190, -859, -449, -449, -529}}},
+/* GC.G@..UA */
+{{{ -50, -709, -739, -619, -739},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GA..UA */
+{{ -50, -709, -739, -619, -739},
+{ -449,-1108,-1138,-1018,-1138},
+{ -479,-1138,-1168,-1048,-1168},
+{ -429,-1088,-1118, -998,-1118},
+{ -329, -988,-1018, -898,-1018}},
+/* GC.GC..UA */
+{{ -50, -709, -739, -619, -739},
+{ -679,-1338,-1368,-1248,-1368},
+{ -559,-1218,-1248,-1128,-1248},
+{ -729,-1388,-1418,-1298,-1418},
+{ -189, -848, -878, -758, -878}},
+/* GC.GG..UA */
+{{ -50, -709, -739, -619, -739},
+{ -939,-1598,-1628,-1508,-1628},
+{ -249, -908, -938, -818, -938},
+{ -939,-1598,-1628,-1508,-1628},
+{ -329, -988,-1018, -898,-1018}},
+/* GC.GU..UA */
+{{ -50, -709, -739, -619, -739},
+{ -639,-1298,-1328,-1208,-1328},
+{ -229, -888, -918, -798, -918},
+{ -729,-1388,-1418,-1298,-1418},
+{ -190, -849, -879, -759, -879}}},
+/* GC.U@..UA */
+{{{ -50, -499, -499, -499, -569},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UA..UA */
+{{ -50, -499, -499, -499, -569},
+{ -449, -898, -898, -898, -968},
+{ -479, -928, -928, -928, -998},
+{ -429, -878, -878, -878, -948},
+{ -329, -778, -778, -778, -848}},
+/* GC.UC..UA */
+{{ -50, -499, -499, -499, -569},
+{ -679,-1128,-1128,-1128,-1198},
+{ -559,-1008,-1008,-1008,-1078},
+{ -729,-1178,-1178,-1178,-1248},
+{ -189, -638, -638, -638, -708}},
+/* GC.UG..UA */
+{{ -50, -499, -499, -499, -569},
+{ -939,-1388,-1388,-1388,-1458},
+{ -249, -698, -698, -698, -768},
+{ -939,-1388,-1388,-1388,-1458},
+{ -329, -778, -778, -778, -848}},
+/* GC.UU..UA */
+{{ -50, -499, -499, -499, -569},
+{ -639,-1088,-1088,-1088,-1158},
+{ -229, -678, -678, -678, -748},
+{ -729,-1178,-1178,-1178,-1248},
+{ -190, -639, -639, -639, -709}}}},
+/* GC.@@.. @ */
+{{{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@A.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@C.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@G.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GC.@U.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}}},
+/* GC.A@.. @ */
+{{{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AA.. @ */
+{{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AC.. @ */
+{{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AG.. @ */
+{{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}},
+/* GC.AU.. @ */
+{{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929},
+{ -100, -569, -929, -609, -929}}},
+/* GC.C@.. @ */
+{{{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CA.. @ */
+{{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CC.. @ */
+{{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CG.. @ */
+{{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}},
+/* GC.CU.. @ */
+{{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439},
+{ -100, -769, -359, -359, -439}}},
+/* GC.G@.. @ */
+{{{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GA.. @ */
+{{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GC.. @ */
+{{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GG.. @ */
+{{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}},
+/* GC.GU.. @ */
+{{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789},
+{ -100, -759, -789, -669, -789}}},
+/* GC.U@.. @ */
+{{{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UA.. @ */
+{{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UC.. @ */
+{{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UG.. @ */
+{{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}},
+/* GC.UU.. @ */
+{{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619},
+{ -100, -549, -549, -549, -619}}}}},
+{ /* noPair */ {{{{0}}}},
+/* GU.@@..CG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@A..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* GU.@C..CG */
+{{ 0, 0, 0, 0, 0},
+{ -949, -949, -949, -949, -949},
+{ -449, -449, -449, -449, -449},
+{ -939, -939, -939, -939, -939},
+{ -739, -739, -739, -739, -739}},
+/* GU.@G..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* GU.@U..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -669, -669, -669, -669, -669},
+{ -939, -939, -939, -939, -939},
+{ -859, -859, -859, -859, -859}}},
+/* GU.A@..CG */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AA..CG */
+{{ -50, -429, -599, -599, -599},
+{-1079,-1458,-1628,-1628,-1628},
+{ -569, -948,-1118,-1118,-1118},
+{ -989,-1368,-1538,-1538,-1538},
+{ -859,-1238,-1408,-1408,-1408}},
+/* GU.AC..CG */
+{{ -50, -429, -599, -599, -599},
+{ -999,-1378,-1548,-1548,-1548},
+{ -499, -878,-1048,-1048,-1048},
+{ -989,-1368,-1538,-1538,-1538},
+{ -789,-1168,-1338,-1338,-1338}},
+/* GU.AG..CG */
+{{ -50, -429, -599, -599, -599},
+{-1079,-1458,-1628,-1628,-1628},
+{ -569, -948,-1118,-1118,-1118},
+{ -989,-1368,-1538,-1538,-1538},
+{ -859,-1238,-1408,-1408,-1408}},
+/* GU.AU..CG */
+{{ -50, -429, -599, -599, -599},
+{-1079,-1458,-1628,-1628,-1628},
+{ -719,-1098,-1268,-1268,-1268},
+{ -989,-1368,-1538,-1538,-1538},
+{ -909,-1288,-1458,-1458,-1458}}},
+/* GU.C@..CG */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CA..CG */
+{{ -50, -259, -239, -239, -239},
+{-1079,-1288,-1268,-1268,-1268},
+{ -569, -778, -758, -758, -758},
+{ -989,-1198,-1178,-1178,-1178},
+{ -859,-1068,-1048,-1048,-1048}},
+/* GU.CC..CG */
+{{ -50, -259, -239, -239, -239},
+{ -999,-1208,-1188,-1188,-1188},
+{ -499, -708, -688, -688, -688},
+{ -989,-1198,-1178,-1178,-1178},
+{ -789, -998, -978, -978, -978}},
+/* GU.CG..CG */
+{{ -50, -259, -239, -239, -239},
+{-1079,-1288,-1268,-1268,-1268},
+{ -569, -778, -758, -758, -758},
+{ -989,-1198,-1178,-1178,-1178},
+{ -859,-1068,-1048,-1048,-1048}},
+/* GU.CU..CG */
+{{ -50, -259, -239, -239, -239},
+{-1079,-1288,-1268,-1268,-1268},
+{ -719, -928, -908, -908, -908},
+{ -989,-1198,-1178,-1178,-1178},
+{ -909,-1118,-1098,-1098,-1098}}},
+/* GU.G@..CG */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GA..CG */
+{{ -50, -339, -689, -689, -689},
+{-1079,-1368,-1718,-1718,-1718},
+{ -569, -858,-1208,-1208,-1208},
+{ -989,-1278,-1628,-1628,-1628},
+{ -859,-1148,-1498,-1498,-1498}},
+/* GU.GC..CG */
+{{ -50, -339, -689, -689, -689},
+{ -999,-1288,-1638,-1638,-1638},
+{ -499, -788,-1138,-1138,-1138},
+{ -989,-1278,-1628,-1628,-1628},
+{ -789,-1078,-1428,-1428,-1428}},
+/* GU.GG..CG */
+{{ -50, -339, -689, -689, -689},
+{-1079,-1368,-1718,-1718,-1718},
+{ -569, -858,-1208,-1208,-1208},
+{ -989,-1278,-1628,-1628,-1628},
+{ -859,-1148,-1498,-1498,-1498}},
+/* GU.GU..CG */
+{{ -50, -339, -689, -689, -689},
+{-1079,-1368,-1718,-1718,-1718},
+{ -719,-1008,-1358,-1358,-1358},
+{ -989,-1278,-1628,-1628,-1628},
+{ -909,-1198,-1548,-1548,-1548}}},
+/* GU.U@..CG */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UA..CG */
+{{ -50, -329, -329, -329, -329},
+{-1079,-1358,-1358,-1358,-1358},
+{ -569, -848, -848, -848, -848},
+{ -989,-1268,-1268,-1268,-1268},
+{ -859,-1138,-1138,-1138,-1138}},
+/* GU.UC..CG */
+{{ -50, -329, -329, -329, -329},
+{ -999,-1278,-1278,-1278,-1278},
+{ -499, -778, -778, -778, -778},
+{ -989,-1268,-1268,-1268,-1268},
+{ -789,-1068,-1068,-1068,-1068}},
+/* GU.UG..CG */
+{{ -50, -329, -329, -329, -329},
+{-1079,-1358,-1358,-1358,-1358},
+{ -569, -848, -848, -848, -848},
+{ -989,-1268,-1268,-1268,-1268},
+{ -859,-1138,-1138,-1138,-1138}},
+/* GU.UU..CG */
+{{ -50, -329, -329, -329, -329},
+{-1079,-1358,-1358,-1358,-1358},
+{ -719, -998, -998, -998, -998},
+{ -989,-1268,-1268,-1268,-1268},
+{ -909,-1188,-1188,-1188,-1188}}}},
+/* GU.@@..GC */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@A..GC */
+{{ 0, 0, 0, 0, 0},
+{ -519, -519, -519, -519, -519},
+{ -719, -719, -719, -719, -719},
+{ -709, -709, -709, -709, -709},
+{ -499, -499, -499, -499, -499}},
+/* GU.@C..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -309, -309, -309, -309, -309},
+{ -739, -739, -739, -739, -739},
+{ -499, -499, -499, -499, -499}},
+/* GU.@G..GC */
+{{ 0, 0, 0, 0, 0},
+{ -559, -559, -559, -559, -559},
+{ -309, -309, -309, -309, -309},
+{ -619, -619, -619, -619, -619},
+{ -499, -499, -499, -499, -499}},
+/* GU.@U..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -389, -389, -389, -389, -389},
+{ -739, -739, -739, -739, -739},
+{ -569, -569, -569, -569, -569}}},
+/* GU.A@..GC */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AA..GC */
+{{ -50, -429, -599, -599, -599},
+{ -569, -948,-1118,-1118,-1118},
+{ -769,-1148,-1318,-1318,-1318},
+{ -759,-1138,-1308,-1308,-1308},
+{ -549, -928,-1098,-1098,-1098}},
+/* GU.AC..GC */
+{{ -50, -429, -599, -599, -599},
+{ -929,-1308,-1478,-1478,-1478},
+{ -359, -738, -908, -908, -908},
+{ -789,-1168,-1338,-1338,-1338},
+{ -549, -928,-1098,-1098,-1098}},
+/* GU.AG..GC */
+{{ -50, -429, -599, -599, -599},
+{ -609, -988,-1158,-1158,-1158},
+{ -359, -738, -908, -908, -908},
+{ -669,-1048,-1218,-1218,-1218},
+{ -549, -928,-1098,-1098,-1098}},
+/* GU.AU..GC */
+{{ -50, -429, -599, -599, -599},
+{ -929,-1308,-1478,-1478,-1478},
+{ -439, -818, -988, -988, -988},
+{ -789,-1168,-1338,-1338,-1338},
+{ -619, -998,-1168,-1168,-1168}}},
+/* GU.C@..GC */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CA..GC */
+{{ -50, -259, -239, -239, -239},
+{ -569, -778, -758, -758, -758},
+{ -769, -978, -958, -958, -958},
+{ -759, -968, -948, -948, -948},
+{ -549, -758, -738, -738, -738}},
+/* GU.CC..GC */
+{{ -50, -259, -239, -239, -239},
+{ -929,-1138,-1118,-1118,-1118},
+{ -359, -568, -548, -548, -548},
+{ -789, -998, -978, -978, -978},
+{ -549, -758, -738, -738, -738}},
+/* GU.CG..GC */
+{{ -50, -259, -239, -239, -239},
+{ -609, -818, -798, -798, -798},
+{ -359, -568, -548, -548, -548},
+{ -669, -878, -858, -858, -858},
+{ -549, -758, -738, -738, -738}},
+/* GU.CU..GC */
+{{ -50, -259, -239, -239, -239},
+{ -929,-1138,-1118,-1118,-1118},
+{ -439, -648, -628, -628, -628},
+{ -789, -998, -978, -978, -978},
+{ -619, -828, -808, -808, -808}}},
+/* GU.G@..GC */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GA..GC */
+{{ -50, -339, -689, -689, -689},
+{ -569, -858,-1208,-1208,-1208},
+{ -769,-1058,-1408,-1408,-1408},
+{ -759,-1048,-1398,-1398,-1398},
+{ -549, -838,-1188,-1188,-1188}},
+/* GU.GC..GC */
+{{ -50, -339, -689, -689, -689},
+{ -929,-1218,-1568,-1568,-1568},
+{ -359, -648, -998, -998, -998},
+{ -789,-1078,-1428,-1428,-1428},
+{ -549, -838,-1188,-1188,-1188}},
+/* GU.GG..GC */
+{{ -50, -339, -689, -689, -689},
+{ -609, -898,-1248,-1248,-1248},
+{ -359, -648, -998, -998, -998},
+{ -669, -958,-1308,-1308,-1308},
+{ -549, -838,-1188,-1188,-1188}},
+/* GU.GU..GC */
+{{ -50, -339, -689, -689, -689},
+{ -929,-1218,-1568,-1568,-1568},
+{ -439, -728,-1078,-1078,-1078},
+{ -789,-1078,-1428,-1428,-1428},
+{ -619, -908,-1258,-1258,-1258}}},
+/* GU.U@..GC */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UA..GC */
+{{ -50, -329, -329, -329, -329},
+{ -569, -848, -848, -848, -848},
+{ -769,-1048,-1048,-1048,-1048},
+{ -759,-1038,-1038,-1038,-1038},
+{ -549, -828, -828, -828, -828}},
+/* GU.UC..GC */
+{{ -50, -329, -329, -329, -329},
+{ -929,-1208,-1208,-1208,-1208},
+{ -359, -638, -638, -638, -638},
+{ -789,-1068,-1068,-1068,-1068},
+{ -549, -828, -828, -828, -828}},
+/* GU.UG..GC */
+{{ -50, -329, -329, -329, -329},
+{ -609, -888, -888, -888, -888},
+{ -359, -638, -638, -638, -638},
+{ -669, -948, -948, -948, -948},
+{ -549, -828, -828, -828, -828}},
+/* GU.UU..GC */
+{{ -50, -329, -329, -329, -329},
+{ -929,-1208,-1208,-1208,-1208},
+{ -439, -718, -718, -718, -718},
+{ -789,-1068,-1068,-1068,-1068},
+{ -619, -898, -898, -898, -898}}}},
+/* GU.@@..GU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@A..GU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* GU.@C..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* GU.@G..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* GU.@U..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* GU.A@..GU */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AA..GU */
+{{ -50, -429, -599, -599, -599},
+{ -479, -858,-1028,-1028,-1028},
+{ -309, -688, -858, -858, -858},
+{ -389, -768, -938, -938, -938},
+{ -379, -758, -928, -928, -928}},
+/* GU.AC..GU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}},
+/* GU.AG..GU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}},
+/* GU.AU..GU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}}},
+/* GU.C@..GU */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CA..GU */
+{{ -50, -259, -239, -239, -239},
+{ -479, -688, -668, -668, -668},
+{ -309, -518, -498, -498, -498},
+{ -389, -598, -578, -578, -578},
+{ -379, -588, -568, -568, -568}},
+/* GU.CC..GU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}},
+/* GU.CG..GU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}},
+/* GU.CU..GU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}}},
+/* GU.G@..GU */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GA..GU */
+{{ -50, -339, -689, -689, -689},
+{ -479, -768,-1118,-1118,-1118},
+{ -309, -598, -948, -948, -948},
+{ -389, -678,-1028,-1028,-1028},
+{ -379, -668,-1018,-1018,-1018}},
+/* GU.GC..GU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}},
+/* GU.GG..GU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}},
+/* GU.GU..GU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}}},
+/* GU.U@..GU */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UA..GU */
+{{ -50, -329, -329, -329, -329},
+{ -479, -758, -758, -758, -758},
+{ -309, -588, -588, -588, -588},
+{ -389, -668, -668, -668, -668},
+{ -379, -658, -658, -658, -658}},
+/* GU.UC..GU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}},
+/* GU.UG..GU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}},
+/* GU.UU..GU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}}}},
+/* GU.@@..UG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@A..UG */
+{{ 0, 0, 0, 0, 0},
+{ -719, -719, -719, -719, -719},
+{ -479, -479, -479, -479, -479},
+{ -659, -659, -659, -659, -659},
+{ -549, -549, -549, -549, -549}},
+/* GU.@C..UG */
+{{ 0, 0, 0, 0, 0},
+{ -789, -789, -789, -789, -789},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -439, -439, -439, -439, -439}},
+/* GU.@G..UG */
+{{ 0, 0, 0, 0, 0},
+{ -959, -959, -959, -959, -959},
+{ -359, -359, -359, -359, -359},
+{ -919, -919, -919, -919, -919},
+{ -549, -549, -549, -549, -549}},
+/* GU.@U..UG */
+{{ 0, 0, 0, 0, 0},
+{ -809, -809, -809, -809, -809},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -359, -359, -359, -359, -359}}},
+/* GU.A@..UG */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AA..UG */
+{{ -50, -429, -599, -599, -599},
+{ -769,-1148,-1318,-1318,-1318},
+{ -529, -908,-1078,-1078,-1078},
+{ -709,-1088,-1258,-1258,-1258},
+{ -599, -978,-1148,-1148,-1148}},
+/* GU.AC..UG */
+{{ -50, -429, -599, -599, -599},
+{ -839,-1218,-1388,-1388,-1388},
+{ -529, -908,-1078,-1078,-1078},
+{ -859,-1238,-1408,-1408,-1408},
+{ -489, -868,-1038,-1038,-1038}},
+/* GU.AG..UG */
+{{ -50, -429, -599, -599, -599},
+{-1009,-1388,-1558,-1558,-1558},
+{ -409, -788, -958, -958, -958},
+{ -969,-1348,-1518,-1518,-1518},
+{ -599, -978,-1148,-1148,-1148}},
+/* GU.AU..UG */
+{{ -50, -429, -599, -599, -599},
+{ -859,-1238,-1408,-1408,-1408},
+{ -529, -908,-1078,-1078,-1078},
+{ -859,-1238,-1408,-1408,-1408},
+{ -409, -788, -958, -958, -958}}},
+/* GU.C@..UG */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CA..UG */
+{{ -50, -259, -239, -239, -239},
+{ -769, -978, -958, -958, -958},
+{ -529, -738, -718, -718, -718},
+{ -709, -918, -898, -898, -898},
+{ -599, -808, -788, -788, -788}},
+/* GU.CC..UG */
+{{ -50, -259, -239, -239, -239},
+{ -839,-1048,-1028,-1028,-1028},
+{ -529, -738, -718, -718, -718},
+{ -859,-1068,-1048,-1048,-1048},
+{ -489, -698, -678, -678, -678}},
+/* GU.CG..UG */
+{{ -50, -259, -239, -239, -239},
+{-1009,-1218,-1198,-1198,-1198},
+{ -409, -618, -598, -598, -598},
+{ -969,-1178,-1158,-1158,-1158},
+{ -599, -808, -788, -788, -788}},
+/* GU.CU..UG */
+{{ -50, -259, -239, -239, -239},
+{ -859,-1068,-1048,-1048,-1048},
+{ -529, -738, -718, -718, -718},
+{ -859,-1068,-1048,-1048,-1048},
+{ -409, -618, -598, -598, -598}}},
+/* GU.G@..UG */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GA..UG */
+{{ -50, -339, -689, -689, -689},
+{ -769,-1058,-1408,-1408,-1408},
+{ -529, -818,-1168,-1168,-1168},
+{ -709, -998,-1348,-1348,-1348},
+{ -599, -888,-1238,-1238,-1238}},
+/* GU.GC..UG */
+{{ -50, -339, -689, -689, -689},
+{ -839,-1128,-1478,-1478,-1478},
+{ -529, -818,-1168,-1168,-1168},
+{ -859,-1148,-1498,-1498,-1498},
+{ -489, -778,-1128,-1128,-1128}},
+/* GU.GG..UG */
+{{ -50, -339, -689, -689, -689},
+{-1009,-1298,-1648,-1648,-1648},
+{ -409, -698,-1048,-1048,-1048},
+{ -969,-1258,-1608,-1608,-1608},
+{ -599, -888,-1238,-1238,-1238}},
+/* GU.GU..UG */
+{{ -50, -339, -689, -689, -689},
+{ -859,-1148,-1498,-1498,-1498},
+{ -529, -818,-1168,-1168,-1168},
+{ -859,-1148,-1498,-1498,-1498},
+{ -409, -698,-1048,-1048,-1048}}},
+/* GU.U@..UG */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UA..UG */
+{{ -50, -329, -329, -329, -329},
+{ -769,-1048,-1048,-1048,-1048},
+{ -529, -808, -808, -808, -808},
+{ -709, -988, -988, -988, -988},
+{ -599, -878, -878, -878, -878}},
+/* GU.UC..UG */
+{{ -50, -329, -329, -329, -329},
+{ -839,-1118,-1118,-1118,-1118},
+{ -529, -808, -808, -808, -808},
+{ -859,-1138,-1138,-1138,-1138},
+{ -489, -768, -768, -768, -768}},
+/* GU.UG..UG */
+{{ -50, -329, -329, -329, -329},
+{-1009,-1288,-1288,-1288,-1288},
+{ -409, -688, -688, -688, -688},
+{ -969,-1248,-1248,-1248,-1248},
+{ -599, -878, -878, -878, -878}},
+/* GU.UU..UG */
+{{ -50, -329, -329, -329, -329},
+{ -859,-1138,-1138,-1138,-1138},
+{ -529, -808, -808, -808, -808},
+{ -859,-1138,-1138,-1138,-1138},
+{ -409, -688, -688, -688, -688}}}},
+/* GU.@@..AU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@A..AU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* GU.@C..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* GU.@G..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* GU.@U..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* GU.A@..AU */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AA..AU */
+{{ -50, -429, -599, -599, -599},
+{ -479, -858,-1028,-1028,-1028},
+{ -309, -688, -858, -858, -858},
+{ -389, -768, -938, -938, -938},
+{ -379, -758, -928, -928, -928}},
+/* GU.AC..AU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}},
+/* GU.AG..AU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}},
+/* GU.AU..AU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}}},
+/* GU.C@..AU */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CA..AU */
+{{ -50, -259, -239, -239, -239},
+{ -479, -688, -668, -668, -668},
+{ -309, -518, -498, -498, -498},
+{ -389, -598, -578, -578, -578},
+{ -379, -588, -568, -568, -568}},
+/* GU.CC..AU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}},
+/* GU.CG..AU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}},
+/* GU.CU..AU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}}},
+/* GU.G@..AU */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GA..AU */
+{{ -50, -339, -689, -689, -689},
+{ -479, -768,-1118,-1118,-1118},
+{ -309, -598, -948, -948, -948},
+{ -389, -678,-1028,-1028,-1028},
+{ -379, -668,-1018,-1018,-1018}},
+/* GU.GC..AU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}},
+/* GU.GG..AU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}},
+/* GU.GU..AU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}}},
+/* GU.U@..AU */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UA..AU */
+{{ -50, -329, -329, -329, -329},
+{ -479, -758, -758, -758, -758},
+{ -309, -588, -588, -588, -588},
+{ -389, -668, -668, -668, -668},
+{ -379, -658, -658, -658, -658}},
+/* GU.UC..AU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}},
+/* GU.UG..AU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}},
+/* GU.UU..AU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}}}},
+/* GU.@@..UA */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@A..UA */
+{{ 0, 0, 0, 0, 0},
+{ -399, -399, -399, -399, -399},
+{ -429, -429, -429, -429, -429},
+{ -379, -379, -379, -379, -379},
+{ -279, -279, -279, -279, -279}},
+/* GU.@C..UA */
+{{ 0, 0, 0, 0, 0},
+{ -629, -629, -629, -629, -629},
+{ -509, -509, -509, -509, -509},
+{ -679, -679, -679, -679, -679},
+{ -139, -139, -139, -139, -139}},
+/* GU.@G..UA */
+{{ 0, 0, 0, 0, 0},
+{ -889, -889, -889, -889, -889},
+{ -199, -199, -199, -199, -199},
+{ -889, -889, -889, -889, -889},
+{ -279, -279, -279, -279, -279}},
+/* GU.@U..UA */
+{{ 0, 0, 0, 0, 0},
+{ -589, -589, -589, -589, -589},
+{ -179, -179, -179, -179, -179},
+{ -679, -679, -679, -679, -679},
+{ -140, -140, -140, -140, -140}}},
+/* GU.A@..UA */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AA..UA */
+{{ -50, -429, -599, -599, -599},
+{ -449, -828, -998, -998, -998},
+{ -479, -858,-1028,-1028,-1028},
+{ -429, -808, -978, -978, -978},
+{ -329, -708, -878, -878, -878}},
+/* GU.AC..UA */
+{{ -50, -429, -599, -599, -599},
+{ -679,-1058,-1228,-1228,-1228},
+{ -559, -938,-1108,-1108,-1108},
+{ -729,-1108,-1278,-1278,-1278},
+{ -189, -568, -738, -738, -738}},
+/* GU.AG..UA */
+{{ -50, -429, -599, -599, -599},
+{ -939,-1318,-1488,-1488,-1488},
+{ -249, -628, -798, -798, -798},
+{ -939,-1318,-1488,-1488,-1488},
+{ -329, -708, -878, -878, -878}},
+/* GU.AU..UA */
+{{ -50, -429, -599, -599, -599},
+{ -639,-1018,-1188,-1188,-1188},
+{ -229, -608, -778, -778, -778},
+{ -729,-1108,-1278,-1278,-1278},
+{ -190, -569, -739, -739, -739}}},
+/* GU.C@..UA */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CA..UA */
+{{ -50, -259, -239, -239, -239},
+{ -449, -658, -638, -638, -638},
+{ -479, -688, -668, -668, -668},
+{ -429, -638, -618, -618, -618},
+{ -329, -538, -518, -518, -518}},
+/* GU.CC..UA */
+{{ -50, -259, -239, -239, -239},
+{ -679, -888, -868, -868, -868},
+{ -559, -768, -748, -748, -748},
+{ -729, -938, -918, -918, -918},
+{ -189, -398, -378, -378, -378}},
+/* GU.CG..UA */
+{{ -50, -259, -239, -239, -239},
+{ -939,-1148,-1128,-1128,-1128},
+{ -249, -458, -438, -438, -438},
+{ -939,-1148,-1128,-1128,-1128},
+{ -329, -538, -518, -518, -518}},
+/* GU.CU..UA */
+{{ -50, -259, -239, -239, -239},
+{ -639, -848, -828, -828, -828},
+{ -229, -438, -418, -418, -418},
+{ -729, -938, -918, -918, -918},
+{ -190, -399, -379, -379, -379}}},
+/* GU.G@..UA */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GA..UA */
+{{ -50, -339, -689, -689, -689},
+{ -449, -738,-1088,-1088,-1088},
+{ -479, -768,-1118,-1118,-1118},
+{ -429, -718,-1068,-1068,-1068},
+{ -329, -618, -968, -968, -968}},
+/* GU.GC..UA */
+{{ -50, -339, -689, -689, -689},
+{ -679, -968,-1318,-1318,-1318},
+{ -559, -848,-1198,-1198,-1198},
+{ -729,-1018,-1368,-1368,-1368},
+{ -189, -478, -828, -828, -828}},
+/* GU.GG..UA */
+{{ -50, -339, -689, -689, -689},
+{ -939,-1228,-1578,-1578,-1578},
+{ -249, -538, -888, -888, -888},
+{ -939,-1228,-1578,-1578,-1578},
+{ -329, -618, -968, -968, -968}},
+/* GU.GU..UA */
+{{ -50, -339, -689, -689, -689},
+{ -639, -928,-1278,-1278,-1278},
+{ -229, -518, -868, -868, -868},
+{ -729,-1018,-1368,-1368,-1368},
+{ -190, -479, -829, -829, -829}}},
+/* GU.U@..UA */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UA..UA */
+{{ -50, -329, -329, -329, -329},
+{ -449, -728, -728, -728, -728},
+{ -479, -758, -758, -758, -758},
+{ -429, -708, -708, -708, -708},
+{ -329, -608, -608, -608, -608}},
+/* GU.UC..UA */
+{{ -50, -329, -329, -329, -329},
+{ -679, -958, -958, -958, -958},
+{ -559, -838, -838, -838, -838},
+{ -729,-1008,-1008,-1008,-1008},
+{ -189, -468, -468, -468, -468}},
+/* GU.UG..UA */
+{{ -50, -329, -329, -329, -329},
+{ -939,-1218,-1218,-1218,-1218},
+{ -249, -528, -528, -528, -528},
+{ -939,-1218,-1218,-1218,-1218},
+{ -329, -608, -608, -608, -608}},
+/* GU.UU..UA */
+{{ -50, -329, -329, -329, -329},
+{ -639, -918, -918, -918, -918},
+{ -229, -508, -508, -508, -508},
+{ -729,-1008,-1008,-1008,-1008},
+{ -190, -469, -469, -469, -469}}}},
+/* GU.@@.. @ */
+{{{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@A.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@C.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@G.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* GU.@U.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}}},
+/* GU.A@.. @ */
+{{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AA.. @ */
+{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AC.. @ */
+{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AG.. @ */
+{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* GU.AU.. @ */
+{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}}},
+/* GU.C@.. @ */
+{{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CA.. @ */
+{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CC.. @ */
+{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CG.. @ */
+{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* GU.CU.. @ */
+{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}}},
+/* GU.G@.. @ */
+{{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GA.. @ */
+{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GC.. @ */
+{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GG.. @ */
+{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* GU.GU.. @ */
+{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}}},
+/* GU.U@.. @ */
+{{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UA.. @ */
+{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UC.. @ */
+{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UG.. @ */
+{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* GU.UU.. @ */
+{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}}}}},
+{ /* noPair */ {{{{0}}}},
+/* UG.@@..CG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@A..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* UG.@C..CG */
+{{ 0, 0, 0, 0, 0},
+{ -949, -949, -949, -949, -949},
+{ -449, -449, -449, -449, -449},
+{ -939, -939, -939, -939, -939},
+{ -739, -739, -739, -739, -739}},
+/* UG.@G..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* UG.@U..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -669, -669, -669, -669, -669},
+{ -939, -939, -939, -939, -939},
+{ -859, -859, -859, -859, -859}}},
+/* UG.A@..CG */
+{{{ -50, -719, -789, -959, -809},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AA..CG */
+{{ -50, -719, -789, -959, -809},
+{-1079,-1748,-1818,-1988,-1838},
+{ -569,-1238,-1308,-1478,-1328},
+{ -989,-1658,-1728,-1898,-1748},
+{ -859,-1528,-1598,-1768,-1618}},
+/* UG.AC..CG */
+{{ -50, -719, -789, -959, -809},
+{ -999,-1668,-1738,-1908,-1758},
+{ -499,-1168,-1238,-1408,-1258},
+{ -989,-1658,-1728,-1898,-1748},
+{ -789,-1458,-1528,-1698,-1548}},
+/* UG.AG..CG */
+{{ -50, -719, -789, -959, -809},
+{-1079,-1748,-1818,-1988,-1838},
+{ -569,-1238,-1308,-1478,-1328},
+{ -989,-1658,-1728,-1898,-1748},
+{ -859,-1528,-1598,-1768,-1618}},
+/* UG.AU..CG */
+{{ -50, -719, -789, -959, -809},
+{-1079,-1748,-1818,-1988,-1838},
+{ -719,-1388,-1458,-1628,-1478},
+{ -989,-1658,-1728,-1898,-1748},
+{ -909,-1578,-1648,-1818,-1668}}},
+/* UG.C@..CG */
+{{{ -50, -479, -479, -359, -479},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CA..CG */
+{{ -50, -479, -479, -359, -479},
+{-1079,-1508,-1508,-1388,-1508},
+{ -569, -998, -998, -878, -998},
+{ -989,-1418,-1418,-1298,-1418},
+{ -859,-1288,-1288,-1168,-1288}},
+/* UG.CC..CG */
+{{ -50, -479, -479, -359, -479},
+{ -999,-1428,-1428,-1308,-1428},
+{ -499, -928, -928, -808, -928},
+{ -989,-1418,-1418,-1298,-1418},
+{ -789,-1218,-1218,-1098,-1218}},
+/* UG.CG..CG */
+{{ -50, -479, -479, -359, -479},
+{-1079,-1508,-1508,-1388,-1508},
+{ -569, -998, -998, -878, -998},
+{ -989,-1418,-1418,-1298,-1418},
+{ -859,-1288,-1288,-1168,-1288}},
+/* UG.CU..CG */
+{{ -50, -479, -479, -359, -479},
+{-1079,-1508,-1508,-1388,-1508},
+{ -719,-1148,-1148,-1028,-1148},
+{ -989,-1418,-1418,-1298,-1418},
+{ -909,-1338,-1338,-1218,-1338}}},
+/* UG.G@..CG */
+{{{ -50, -659, -809, -919, -809},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GA..CG */
+{{ -50, -659, -809, -919, -809},
+{-1079,-1688,-1838,-1948,-1838},
+{ -569,-1178,-1328,-1438,-1328},
+{ -989,-1598,-1748,-1858,-1748},
+{ -859,-1468,-1618,-1728,-1618}},
+/* UG.GC..CG */
+{{ -50, -659, -809, -919, -809},
+{ -999,-1608,-1758,-1868,-1758},
+{ -499,-1108,-1258,-1368,-1258},
+{ -989,-1598,-1748,-1858,-1748},
+{ -789,-1398,-1548,-1658,-1548}},
+/* UG.GG..CG */
+{{ -50, -659, -809, -919, -809},
+{-1079,-1688,-1838,-1948,-1838},
+{ -569,-1178,-1328,-1438,-1328},
+{ -989,-1598,-1748,-1858,-1748},
+{ -859,-1468,-1618,-1728,-1618}},
+/* UG.GU..CG */
+{{ -50, -659, -809, -919, -809},
+{-1079,-1688,-1838,-1948,-1838},
+{ -719,-1328,-1478,-1588,-1478},
+{ -989,-1598,-1748,-1858,-1748},
+{ -909,-1518,-1668,-1778,-1668}}},
+/* UG.U@..CG */
+{{{ -50, -549, -439, -549, -359},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UA..CG */
+{{ -50, -549, -439, -549, -359},
+{-1079,-1578,-1468,-1578,-1388},
+{ -569,-1068, -958,-1068, -878},
+{ -989,-1488,-1378,-1488,-1298},
+{ -859,-1358,-1248,-1358,-1168}},
+/* UG.UC..CG */
+{{ -50, -549, -439, -549, -359},
+{ -999,-1498,-1388,-1498,-1308},
+{ -499, -998, -888, -998, -808},
+{ -989,-1488,-1378,-1488,-1298},
+{ -789,-1288,-1178,-1288,-1098}},
+/* UG.UG..CG */
+{{ -50, -549, -439, -549, -359},
+{-1079,-1578,-1468,-1578,-1388},
+{ -569,-1068, -958,-1068, -878},
+{ -989,-1488,-1378,-1488,-1298},
+{ -859,-1358,-1248,-1358,-1168}},
+/* UG.UU..CG */
+{{ -50, -549, -439, -549, -359},
+{-1079,-1578,-1468,-1578,-1388},
+{ -719,-1218,-1108,-1218,-1028},
+{ -989,-1488,-1378,-1488,-1298},
+{ -909,-1408,-1298,-1408,-1218}}}},
+/* UG.@@..GC */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@A..GC */
+{{ 0, 0, 0, 0, 0},
+{ -519, -519, -519, -519, -519},
+{ -719, -719, -719, -719, -719},
+{ -709, -709, -709, -709, -709},
+{ -499, -499, -499, -499, -499}},
+/* UG.@C..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -309, -309, -309, -309, -309},
+{ -739, -739, -739, -739, -739},
+{ -499, -499, -499, -499, -499}},
+/* UG.@G..GC */
+{{ 0, 0, 0, 0, 0},
+{ -559, -559, -559, -559, -559},
+{ -309, -309, -309, -309, -309},
+{ -619, -619, -619, -619, -619},
+{ -499, -499, -499, -499, -499}},
+/* UG.@U..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -389, -389, -389, -389, -389},
+{ -739, -739, -739, -739, -739},
+{ -569, -569, -569, -569, -569}}},
+/* UG.A@..GC */
+{{{ -50, -719, -789, -959, -809},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AA..GC */
+{{ -50, -719, -789, -959, -809},
+{ -569,-1238,-1308,-1478,-1328},
+{ -769,-1438,-1508,-1678,-1528},
+{ -759,-1428,-1498,-1668,-1518},
+{ -549,-1218,-1288,-1458,-1308}},
+/* UG.AC..GC */
+{{ -50, -719, -789, -959, -809},
+{ -929,-1598,-1668,-1838,-1688},
+{ -359,-1028,-1098,-1268,-1118},
+{ -789,-1458,-1528,-1698,-1548},
+{ -549,-1218,-1288,-1458,-1308}},
+/* UG.AG..GC */
+{{ -50, -719, -789, -959, -809},
+{ -609,-1278,-1348,-1518,-1368},
+{ -359,-1028,-1098,-1268,-1118},
+{ -669,-1338,-1408,-1578,-1428},
+{ -549,-1218,-1288,-1458,-1308}},
+/* UG.AU..GC */
+{{ -50, -719, -789, -959, -809},
+{ -929,-1598,-1668,-1838,-1688},
+{ -439,-1108,-1178,-1348,-1198},
+{ -789,-1458,-1528,-1698,-1548},
+{ -619,-1288,-1358,-1528,-1378}}},
+/* UG.C@..GC */
+{{{ -50, -479, -479, -359, -479},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CA..GC */
+{{ -50, -479, -479, -359, -479},
+{ -569, -998, -998, -878, -998},
+{ -769,-1198,-1198,-1078,-1198},
+{ -759,-1188,-1188,-1068,-1188},
+{ -549, -978, -978, -858, -978}},
+/* UG.CC..GC */
+{{ -50, -479, -479, -359, -479},
+{ -929,-1358,-1358,-1238,-1358},
+{ -359, -788, -788, -668, -788},
+{ -789,-1218,-1218,-1098,-1218},
+{ -549, -978, -978, -858, -978}},
+/* UG.CG..GC */
+{{ -50, -479, -479, -359, -479},
+{ -609,-1038,-1038, -918,-1038},
+{ -359, -788, -788, -668, -788},
+{ -669,-1098,-1098, -978,-1098},
+{ -549, -978, -978, -858, -978}},
+/* UG.CU..GC */
+{{ -50, -479, -479, -359, -479},
+{ -929,-1358,-1358,-1238,-1358},
+{ -439, -868, -868, -748, -868},
+{ -789,-1218,-1218,-1098,-1218},
+{ -619,-1048,-1048, -928,-1048}}},
+/* UG.G@..GC */
+{{{ -50, -659, -809, -919, -809},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GA..GC */
+{{ -50, -659, -809, -919, -809},
+{ -569,-1178,-1328,-1438,-1328},
+{ -769,-1378,-1528,-1638,-1528},
+{ -759,-1368,-1518,-1628,-1518},
+{ -549,-1158,-1308,-1418,-1308}},
+/* UG.GC..GC */
+{{ -50, -659, -809, -919, -809},
+{ -929,-1538,-1688,-1798,-1688},
+{ -359, -968,-1118,-1228,-1118},
+{ -789,-1398,-1548,-1658,-1548},
+{ -549,-1158,-1308,-1418,-1308}},
+/* UG.GG..GC */
+{{ -50, -659, -809, -919, -809},
+{ -609,-1218,-1368,-1478,-1368},
+{ -359, -968,-1118,-1228,-1118},
+{ -669,-1278,-1428,-1538,-1428},
+{ -549,-1158,-1308,-1418,-1308}},
+/* UG.GU..GC */
+{{ -50, -659, -809, -919, -809},
+{ -929,-1538,-1688,-1798,-1688},
+{ -439,-1048,-1198,-1308,-1198},
+{ -789,-1398,-1548,-1658,-1548},
+{ -619,-1228,-1378,-1488,-1378}}},
+/* UG.U@..GC */
+{{{ -50, -549, -439, -549, -359},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UA..GC */
+{{ -50, -549, -439, -549, -359},
+{ -569,-1068, -958,-1068, -878},
+{ -769,-1268,-1158,-1268,-1078},
+{ -759,-1258,-1148,-1258,-1068},
+{ -549,-1048, -938,-1048, -858}},
+/* UG.UC..GC */
+{{ -50, -549, -439, -549, -359},
+{ -929,-1428,-1318,-1428,-1238},
+{ -359, -858, -748, -858, -668},
+{ -789,-1288,-1178,-1288,-1098},
+{ -549,-1048, -938,-1048, -858}},
+/* UG.UG..GC */
+{{ -50, -549, -439, -549, -359},
+{ -609,-1108, -998,-1108, -918},
+{ -359, -858, -748, -858, -668},
+{ -669,-1168,-1058,-1168, -978},
+{ -549,-1048, -938,-1048, -858}},
+/* UG.UU..GC */
+{{ -50, -549, -439, -549, -359},
+{ -929,-1428,-1318,-1428,-1238},
+{ -439, -938, -828, -938, -748},
+{ -789,-1288,-1178,-1288,-1098},
+{ -619,-1118,-1008,-1118, -928}}}},
+/* UG.@@..GU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@A..GU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* UG.@C..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* UG.@G..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* UG.@U..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* UG.A@..GU */
+{{{ -50, -719, -789, -959, -809},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AA..GU */
+{{ -50, -719, -789, -959, -809},
+{ -479,-1148,-1218,-1388,-1238},
+{ -309, -978,-1048,-1218,-1068},
+{ -389,-1058,-1128,-1298,-1148},
+{ -379,-1048,-1118,-1288,-1138}},
+/* UG.AC..GU */
+{{ -50, -719, -789, -959, -809},
+{ -649,-1318,-1388,-1558,-1408},
+{ -289, -958,-1028,-1198,-1048},
+{ -739,-1408,-1478,-1648,-1498},
+{ -379,-1048,-1118,-1288,-1138}},
+/* UG.AG..GU */
+{{ -50, -719, -789, -959, -809},
+{ -649,-1318,-1388,-1558,-1408},
+{ -289, -958,-1028,-1198,-1048},
+{ -739,-1408,-1478,-1648,-1498},
+{ -379,-1048,-1118,-1288,-1138}},
+/* UG.AU..GU */
+{{ -50, -719, -789, -959, -809},
+{ -649,-1318,-1388,-1558,-1408},
+{ -289, -958,-1028,-1198,-1048},
+{ -739,-1408,-1478,-1648,-1498},
+{ -379,-1048,-1118,-1288,-1138}}},
+/* UG.C@..GU */
+{{{ -50, -479, -479, -359, -479},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CA..GU */
+{{ -50, -479, -479, -359, -479},
+{ -479, -908, -908, -788, -908},
+{ -309, -738, -738, -618, -738},
+{ -389, -818, -818, -698, -818},
+{ -379, -808, -808, -688, -808}},
+/* UG.CC..GU */
+{{ -50, -479, -479, -359, -479},
+{ -649,-1078,-1078, -958,-1078},
+{ -289, -718, -718, -598, -718},
+{ -739,-1168,-1168,-1048,-1168},
+{ -379, -808, -808, -688, -808}},
+/* UG.CG..GU */
+{{ -50, -479, -479, -359, -479},
+{ -649,-1078,-1078, -958,-1078},
+{ -289, -718, -718, -598, -718},
+{ -739,-1168,-1168,-1048,-1168},
+{ -379, -808, -808, -688, -808}},
+/* UG.CU..GU */
+{{ -50, -479, -479, -359, -479},
+{ -649,-1078,-1078, -958,-1078},
+{ -289, -718, -718, -598, -718},
+{ -739,-1168,-1168,-1048,-1168},
+{ -379, -808, -808, -688, -808}}},
+/* UG.G@..GU */
+{{{ -50, -659, -809, -919, -809},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GA..GU */
+{{ -50, -659, -809, -919, -809},
+{ -479,-1088,-1238,-1348,-1238},
+{ -309, -918,-1068,-1178,-1068},
+{ -389, -998,-1148,-1258,-1148},
+{ -379, -988,-1138,-1248,-1138}},
+/* UG.GC..GU */
+{{ -50, -659, -809, -919, -809},
+{ -649,-1258,-1408,-1518,-1408},
+{ -289, -898,-1048,-1158,-1048},
+{ -739,-1348,-1498,-1608,-1498},
+{ -379, -988,-1138,-1248,-1138}},
+/* UG.GG..GU */
+{{ -50, -659, -809, -919, -809},
+{ -649,-1258,-1408,-1518,-1408},
+{ -289, -898,-1048,-1158,-1048},
+{ -739,-1348,-1498,-1608,-1498},
+{ -379, -988,-1138,-1248,-1138}},
+/* UG.GU..GU */
+{{ -50, -659, -809, -919, -809},
+{ -649,-1258,-1408,-1518,-1408},
+{ -289, -898,-1048,-1158,-1048},
+{ -739,-1348,-1498,-1608,-1498},
+{ -379, -988,-1138,-1248,-1138}}},
+/* UG.U@..GU */
+{{{ -50, -549, -439, -549, -359},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UA..GU */
+{{ -50, -549, -439, -549, -359},
+{ -479, -978, -868, -978, -788},
+{ -309, -808, -698, -808, -618},
+{ -389, -888, -778, -888, -698},
+{ -379, -878, -768, -878, -688}},
+/* UG.UC..GU */
+{{ -50, -549, -439, -549, -359},
+{ -649,-1148,-1038,-1148, -958},
+{ -289, -788, -678, -788, -598},
+{ -739,-1238,-1128,-1238,-1048},
+{ -379, -878, -768, -878, -688}},
+/* UG.UG..GU */
+{{ -50, -549, -439, -549, -359},
+{ -649,-1148,-1038,-1148, -958},
+{ -289, -788, -678, -788, -598},
+{ -739,-1238,-1128,-1238,-1048},
+{ -379, -878, -768, -878, -688}},
+/* UG.UU..GU */
+{{ -50, -549, -439, -549, -359},
+{ -649,-1148,-1038,-1148, -958},
+{ -289, -788, -678, -788, -598},
+{ -739,-1238,-1128,-1238,-1048},
+{ -379, -878, -768, -878, -688}}}},
+/* UG.@@..UG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@A..UG */
+{{ 0, 0, 0, 0, 0},
+{ -719, -719, -719, -719, -719},
+{ -479, -479, -479, -479, -479},
+{ -659, -659, -659, -659, -659},
+{ -549, -549, -549, -549, -549}},
+/* UG.@C..UG */
+{{ 0, 0, 0, 0, 0},
+{ -789, -789, -789, -789, -789},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -439, -439, -439, -439, -439}},
+/* UG.@G..UG */
+{{ 0, 0, 0, 0, 0},
+{ -959, -959, -959, -959, -959},
+{ -359, -359, -359, -359, -359},
+{ -919, -919, -919, -919, -919},
+{ -549, -549, -549, -549, -549}},
+/* UG.@U..UG */
+{{ 0, 0, 0, 0, 0},
+{ -809, -809, -809, -809, -809},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -359, -359, -359, -359, -359}}},
+/* UG.A@..UG */
+{{{ -50, -719, -789, -959, -809},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AA..UG */
+{{ -50, -719, -789, -959, -809},
+{ -769,-1438,-1508,-1678,-1528},
+{ -529,-1198,-1268,-1438,-1288},
+{ -709,-1378,-1448,-1618,-1468},
+{ -599,-1268,-1338,-1508,-1358}},
+/* UG.AC..UG */
+{{ -50, -719, -789, -959, -809},
+{ -839,-1508,-1578,-1748,-1598},
+{ -529,-1198,-1268,-1438,-1288},
+{ -859,-1528,-1598,-1768,-1618},
+{ -489,-1158,-1228,-1398,-1248}},
+/* UG.AG..UG */
+{{ -50, -719, -789, -959, -809},
+{-1009,-1678,-1748,-1918,-1768},
+{ -409,-1078,-1148,-1318,-1168},
+{ -969,-1638,-1708,-1878,-1728},
+{ -599,-1268,-1338,-1508,-1358}},
+/* UG.AU..UG */
+{{ -50, -719, -789, -959, -809},
+{ -859,-1528,-1598,-1768,-1618},
+{ -529,-1198,-1268,-1438,-1288},
+{ -859,-1528,-1598,-1768,-1618},
+{ -409,-1078,-1148,-1318,-1168}}},
+/* UG.C@..UG */
+{{{ -50, -479, -479, -359, -479},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CA..UG */
+{{ -50, -479, -479, -359, -479},
+{ -769,-1198,-1198,-1078,-1198},
+{ -529, -958, -958, -838, -958},
+{ -709,-1138,-1138,-1018,-1138},
+{ -599,-1028,-1028, -908,-1028}},
+/* UG.CC..UG */
+{{ -50, -479, -479, -359, -479},
+{ -839,-1268,-1268,-1148,-1268},
+{ -529, -958, -958, -838, -958},
+{ -859,-1288,-1288,-1168,-1288},
+{ -489, -918, -918, -798, -918}},
+/* UG.CG..UG */
+{{ -50, -479, -479, -359, -479},
+{-1009,-1438,-1438,-1318,-1438},
+{ -409, -838, -838, -718, -838},
+{ -969,-1398,-1398,-1278,-1398},
+{ -599,-1028,-1028, -908,-1028}},
+/* UG.CU..UG */
+{{ -50, -479, -479, -359, -479},
+{ -859,-1288,-1288,-1168,-1288},
+{ -529, -958, -958, -838, -958},
+{ -859,-1288,-1288,-1168,-1288},
+{ -409, -838, -838, -718, -838}}},
+/* UG.G@..UG */
+{{{ -50, -659, -809, -919, -809},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GA..UG */
+{{ -50, -659, -809, -919, -809},
+{ -769,-1378,-1528,-1638,-1528},
+{ -529,-1138,-1288,-1398,-1288},
+{ -709,-1318,-1468,-1578,-1468},
+{ -599,-1208,-1358,-1468,-1358}},
+/* UG.GC..UG */
+{{ -50, -659, -809, -919, -809},
+{ -839,-1448,-1598,-1708,-1598},
+{ -529,-1138,-1288,-1398,-1288},
+{ -859,-1468,-1618,-1728,-1618},
+{ -489,-1098,-1248,-1358,-1248}},
+/* UG.GG..UG */
+{{ -50, -659, -809, -919, -809},
+{-1009,-1618,-1768,-1878,-1768},
+{ -409,-1018,-1168,-1278,-1168},
+{ -969,-1578,-1728,-1838,-1728},
+{ -599,-1208,-1358,-1468,-1358}},
+/* UG.GU..UG */
+{{ -50, -659, -809, -919, -809},
+{ -859,-1468,-1618,-1728,-1618},
+{ -529,-1138,-1288,-1398,-1288},
+{ -859,-1468,-1618,-1728,-1618},
+{ -409,-1018,-1168,-1278,-1168}}},
+/* UG.U@..UG */
+{{{ -50, -549, -439, -549, -359},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UA..UG */
+{{ -50, -549, -439, -549, -359},
+{ -769,-1268,-1158,-1268,-1078},
+{ -529,-1028, -918,-1028, -838},
+{ -709,-1208,-1098,-1208,-1018},
+{ -599,-1098, -988,-1098, -908}},
+/* UG.UC..UG */
+{{ -50, -549, -439, -549, -359},
+{ -839,-1338,-1228,-1338,-1148},
+{ -529,-1028, -918,-1028, -838},
+{ -859,-1358,-1248,-1358,-1168},
+{ -489, -988, -878, -988, -798}},
+/* UG.UG..UG */
+{{ -50, -549, -439, -549, -359},
+{-1009,-1508,-1398,-1508,-1318},
+{ -409, -908, -798, -908, -718},
+{ -969,-1468,-1358,-1468,-1278},
+{ -599,-1098, -988,-1098, -908}},
+/* UG.UU..UG */
+{{ -50, -549, -439, -549, -359},
+{ -859,-1358,-1248,-1358,-1168},
+{ -529,-1028, -918,-1028, -838},
+{ -859,-1358,-1248,-1358,-1168},
+{ -409, -908, -798, -908, -718}}}},
+/* UG.@@..AU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@A..AU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* UG.@C..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* UG.@G..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* UG.@U..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* UG.A@..AU */
+{{{ -50, -719, -789, -959, -809},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AA..AU */
+{{ -50, -719, -789, -959, -809},
+{ -479,-1148,-1218,-1388,-1238},
+{ -309, -978,-1048,-1218,-1068},
+{ -389,-1058,-1128,-1298,-1148},
+{ -379,-1048,-1118,-1288,-1138}},
+/* UG.AC..AU */
+{{ -50, -719, -789, -959, -809},
+{ -649,-1318,-1388,-1558,-1408},
+{ -289, -958,-1028,-1198,-1048},
+{ -739,-1408,-1478,-1648,-1498},
+{ -379,-1048,-1118,-1288,-1138}},
+/* UG.AG..AU */
+{{ -50, -719, -789, -959, -809},
+{ -649,-1318,-1388,-1558,-1408},
+{ -289, -958,-1028,-1198,-1048},
+{ -739,-1408,-1478,-1648,-1498},
+{ -379,-1048,-1118,-1288,-1138}},
+/* UG.AU..AU */
+{{ -50, -719, -789, -959, -809},
+{ -649,-1318,-1388,-1558,-1408},
+{ -289, -958,-1028,-1198,-1048},
+{ -739,-1408,-1478,-1648,-1498},
+{ -379,-1048,-1118,-1288,-1138}}},
+/* UG.C@..AU */
+{{{ -50, -479, -479, -359, -479},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CA..AU */
+{{ -50, -479, -479, -359, -479},
+{ -479, -908, -908, -788, -908},
+{ -309, -738, -738, -618, -738},
+{ -389, -818, -818, -698, -818},
+{ -379, -808, -808, -688, -808}},
+/* UG.CC..AU */
+{{ -50, -479, -479, -359, -479},
+{ -649,-1078,-1078, -958,-1078},
+{ -289, -718, -718, -598, -718},
+{ -739,-1168,-1168,-1048,-1168},
+{ -379, -808, -808, -688, -808}},
+/* UG.CG..AU */
+{{ -50, -479, -479, -359, -479},
+{ -649,-1078,-1078, -958,-1078},
+{ -289, -718, -718, -598, -718},
+{ -739,-1168,-1168,-1048,-1168},
+{ -379, -808, -808, -688, -808}},
+/* UG.CU..AU */
+{{ -50, -479, -479, -359, -479},
+{ -649,-1078,-1078, -958,-1078},
+{ -289, -718, -718, -598, -718},
+{ -739,-1168,-1168,-1048,-1168},
+{ -379, -808, -808, -688, -808}}},
+/* UG.G@..AU */
+{{{ -50, -659, -809, -919, -809},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GA..AU */
+{{ -50, -659, -809, -919, -809},
+{ -479,-1088,-1238,-1348,-1238},
+{ -309, -918,-1068,-1178,-1068},
+{ -389, -998,-1148,-1258,-1148},
+{ -379, -988,-1138,-1248,-1138}},
+/* UG.GC..AU */
+{{ -50, -659, -809, -919, -809},
+{ -649,-1258,-1408,-1518,-1408},
+{ -289, -898,-1048,-1158,-1048},
+{ -739,-1348,-1498,-1608,-1498},
+{ -379, -988,-1138,-1248,-1138}},
+/* UG.GG..AU */
+{{ -50, -659, -809, -919, -809},
+{ -649,-1258,-1408,-1518,-1408},
+{ -289, -898,-1048,-1158,-1048},
+{ -739,-1348,-1498,-1608,-1498},
+{ -379, -988,-1138,-1248,-1138}},
+/* UG.GU..AU */
+{{ -50, -659, -809, -919, -809},
+{ -649,-1258,-1408,-1518,-1408},
+{ -289, -898,-1048,-1158,-1048},
+{ -739,-1348,-1498,-1608,-1498},
+{ -379, -988,-1138,-1248,-1138}}},
+/* UG.U@..AU */
+{{{ -50, -549, -439, -549, -359},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UA..AU */
+{{ -50, -549, -439, -549, -359},
+{ -479, -978, -868, -978, -788},
+{ -309, -808, -698, -808, -618},
+{ -389, -888, -778, -888, -698},
+{ -379, -878, -768, -878, -688}},
+/* UG.UC..AU */
+{{ -50, -549, -439, -549, -359},
+{ -649,-1148,-1038,-1148, -958},
+{ -289, -788, -678, -788, -598},
+{ -739,-1238,-1128,-1238,-1048},
+{ -379, -878, -768, -878, -688}},
+/* UG.UG..AU */
+{{ -50, -549, -439, -549, -359},
+{ -649,-1148,-1038,-1148, -958},
+{ -289, -788, -678, -788, -598},
+{ -739,-1238,-1128,-1238,-1048},
+{ -379, -878, -768, -878, -688}},
+/* UG.UU..AU */
+{{ -50, -549, -439, -549, -359},
+{ -649,-1148,-1038,-1148, -958},
+{ -289, -788, -678, -788, -598},
+{ -739,-1238,-1128,-1238,-1048},
+{ -379, -878, -768, -878, -688}}}},
+/* UG.@@..UA */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@A..UA */
+{{ 0, 0, 0, 0, 0},
+{ -399, -399, -399, -399, -399},
+{ -429, -429, -429, -429, -429},
+{ -379, -379, -379, -379, -379},
+{ -279, -279, -279, -279, -279}},
+/* UG.@C..UA */
+{{ 0, 0, 0, 0, 0},
+{ -629, -629, -629, -629, -629},
+{ -509, -509, -509, -509, -509},
+{ -679, -679, -679, -679, -679},
+{ -139, -139, -139, -139, -139}},
+/* UG.@G..UA */
+{{ 0, 0, 0, 0, 0},
+{ -889, -889, -889, -889, -889},
+{ -199, -199, -199, -199, -199},
+{ -889, -889, -889, -889, -889},
+{ -279, -279, -279, -279, -279}},
+/* UG.@U..UA */
+{{ 0, 0, 0, 0, 0},
+{ -589, -589, -589, -589, -589},
+{ -179, -179, -179, -179, -179},
+{ -679, -679, -679, -679, -679},
+{ -140, -140, -140, -140, -140}}},
+/* UG.A@..UA */
+{{{ -50, -719, -789, -959, -809},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AA..UA */
+{{ -50, -719, -789, -959, -809},
+{ -449,-1118,-1188,-1358,-1208},
+{ -479,-1148,-1218,-1388,-1238},
+{ -429,-1098,-1168,-1338,-1188},
+{ -329, -998,-1068,-1238,-1088}},
+/* UG.AC..UA */
+{{ -50, -719, -789, -959, -809},
+{ -679,-1348,-1418,-1588,-1438},
+{ -559,-1228,-1298,-1468,-1318},
+{ -729,-1398,-1468,-1638,-1488},
+{ -189, -858, -928,-1098, -948}},
+/* UG.AG..UA */
+{{ -50, -719, -789, -959, -809},
+{ -939,-1608,-1678,-1848,-1698},
+{ -249, -918, -988,-1158,-1008},
+{ -939,-1608,-1678,-1848,-1698},
+{ -329, -998,-1068,-1238,-1088}},
+/* UG.AU..UA */
+{{ -50, -719, -789, -959, -809},
+{ -639,-1308,-1378,-1548,-1398},
+{ -229, -898, -968,-1138, -988},
+{ -729,-1398,-1468,-1638,-1488},
+{ -190, -859, -929,-1099, -949}}},
+/* UG.C@..UA */
+{{{ -50, -479, -479, -359, -479},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CA..UA */
+{{ -50, -479, -479, -359, -479},
+{ -449, -878, -878, -758, -878},
+{ -479, -908, -908, -788, -908},
+{ -429, -858, -858, -738, -858},
+{ -329, -758, -758, -638, -758}},
+/* UG.CC..UA */
+{{ -50, -479, -479, -359, -479},
+{ -679,-1108,-1108, -988,-1108},
+{ -559, -988, -988, -868, -988},
+{ -729,-1158,-1158,-1038,-1158},
+{ -189, -618, -618, -498, -618}},
+/* UG.CG..UA */
+{{ -50, -479, -479, -359, -479},
+{ -939,-1368,-1368,-1248,-1368},
+{ -249, -678, -678, -558, -678},
+{ -939,-1368,-1368,-1248,-1368},
+{ -329, -758, -758, -638, -758}},
+/* UG.CU..UA */
+{{ -50, -479, -479, -359, -479},
+{ -639,-1068,-1068, -948,-1068},
+{ -229, -658, -658, -538, -658},
+{ -729,-1158,-1158,-1038,-1158},
+{ -190, -619, -619, -499, -619}}},
+/* UG.G@..UA */
+{{{ -50, -659, -809, -919, -809},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GA..UA */
+{{ -50, -659, -809, -919, -809},
+{ -449,-1058,-1208,-1318,-1208},
+{ -479,-1088,-1238,-1348,-1238},
+{ -429,-1038,-1188,-1298,-1188},
+{ -329, -938,-1088,-1198,-1088}},
+/* UG.GC..UA */
+{{ -50, -659, -809, -919, -809},
+{ -679,-1288,-1438,-1548,-1438},
+{ -559,-1168,-1318,-1428,-1318},
+{ -729,-1338,-1488,-1598,-1488},
+{ -189, -798, -948,-1058, -948}},
+/* UG.GG..UA */
+{{ -50, -659, -809, -919, -809},
+{ -939,-1548,-1698,-1808,-1698},
+{ -249, -858,-1008,-1118,-1008},
+{ -939,-1548,-1698,-1808,-1698},
+{ -329, -938,-1088,-1198,-1088}},
+/* UG.GU..UA */
+{{ -50, -659, -809, -919, -809},
+{ -639,-1248,-1398,-1508,-1398},
+{ -229, -838, -988,-1098, -988},
+{ -729,-1338,-1488,-1598,-1488},
+{ -190, -799, -949,-1059, -949}}},
+/* UG.U@..UA */
+{{{ -50, -549, -439, -549, -359},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UA..UA */
+{{ -50, -549, -439, -549, -359},
+{ -449, -948, -838, -948, -758},
+{ -479, -978, -868, -978, -788},
+{ -429, -928, -818, -928, -738},
+{ -329, -828, -718, -828, -638}},
+/* UG.UC..UA */
+{{ -50, -549, -439, -549, -359},
+{ -679,-1178,-1068,-1178, -988},
+{ -559,-1058, -948,-1058, -868},
+{ -729,-1228,-1118,-1228,-1038},
+{ -189, -688, -578, -688, -498}},
+/* UG.UG..UA */
+{{ -50, -549, -439, -549, -359},
+{ -939,-1438,-1328,-1438,-1248},
+{ -249, -748, -638, -748, -558},
+{ -939,-1438,-1328,-1438,-1248},
+{ -329, -828, -718, -828, -638}},
+/* UG.UU..UA */
+{{ -50, -549, -439, -549, -359},
+{ -639,-1138,-1028,-1138, -948},
+{ -229, -728, -618, -728, -538},
+{ -729,-1228,-1118,-1228,-1038},
+{ -190, -689, -579, -689, -499}}}},
+/* UG.@@.. @ */
+{{{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@A.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@C.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@G.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UG.@U.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}}},
+/* UG.A@.. @ */
+{{{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AA.. @ */
+{{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AC.. @ */
+{{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AG.. @ */
+{{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}},
+/* UG.AU.. @ */
+{{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859},
+{ -100, -769, -839,-1009, -859}}},
+/* UG.C@.. @ */
+{{{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CA.. @ */
+{{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CC.. @ */
+{{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CG.. @ */
+{{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}},
+/* UG.CU.. @ */
+{{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529},
+{ -100, -529, -529, -409, -529}}},
+/* UG.G@.. @ */
+{{{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GA.. @ */
+{{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GC.. @ */
+{{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GG.. @ */
+{{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}},
+/* UG.GU.. @ */
+{{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859},
+{ -100, -709, -859, -969, -859}}},
+/* UG.U@.. @ */
+{{{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UA.. @ */
+{{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UC.. @ */
+{{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UG.. @ */
+{{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}},
+/* UG.UU.. @ */
+{{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409},
+{ -100, -599, -489, -599, -409}}}}},
+{ /* noPair */ {{{{0}}}},
+/* AU.@@..CG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@A..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* AU.@C..CG */
+{{ 0, 0, 0, 0, 0},
+{ -949, -949, -949, -949, -949},
+{ -449, -449, -449, -449, -449},
+{ -939, -939, -939, -939, -939},
+{ -739, -739, -739, -739, -739}},
+/* AU.@G..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* AU.@U..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -669, -669, -669, -669, -669},
+{ -939, -939, -939, -939, -939},
+{ -859, -859, -859, -859, -859}}},
+/* AU.A@..CG */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AA..CG */
+{{ -50, -429, -599, -599, -599},
+{-1079,-1458,-1628,-1628,-1628},
+{ -569, -948,-1118,-1118,-1118},
+{ -989,-1368,-1538,-1538,-1538},
+{ -859,-1238,-1408,-1408,-1408}},
+/* AU.AC..CG */
+{{ -50, -429, -599, -599, -599},
+{ -999,-1378,-1548,-1548,-1548},
+{ -499, -878,-1048,-1048,-1048},
+{ -989,-1368,-1538,-1538,-1538},
+{ -789,-1168,-1338,-1338,-1338}},
+/* AU.AG..CG */
+{{ -50, -429, -599, -599, -599},
+{-1079,-1458,-1628,-1628,-1628},
+{ -569, -948,-1118,-1118,-1118},
+{ -989,-1368,-1538,-1538,-1538},
+{ -859,-1238,-1408,-1408,-1408}},
+/* AU.AU..CG */
+{{ -50, -429, -599, -599, -599},
+{-1079,-1458,-1628,-1628,-1628},
+{ -719,-1098,-1268,-1268,-1268},
+{ -989,-1368,-1538,-1538,-1538},
+{ -909,-1288,-1458,-1458,-1458}}},
+/* AU.C@..CG */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CA..CG */
+{{ -50, -259, -239, -239, -239},
+{-1079,-1288,-1268,-1268,-1268},
+{ -569, -778, -758, -758, -758},
+{ -989,-1198,-1178,-1178,-1178},
+{ -859,-1068,-1048,-1048,-1048}},
+/* AU.CC..CG */
+{{ -50, -259, -239, -239, -239},
+{ -999,-1208,-1188,-1188,-1188},
+{ -499, -708, -688, -688, -688},
+{ -989,-1198,-1178,-1178,-1178},
+{ -789, -998, -978, -978, -978}},
+/* AU.CG..CG */
+{{ -50, -259, -239, -239, -239},
+{-1079,-1288,-1268,-1268,-1268},
+{ -569, -778, -758, -758, -758},
+{ -989,-1198,-1178,-1178,-1178},
+{ -859,-1068,-1048,-1048,-1048}},
+/* AU.CU..CG */
+{{ -50, -259, -239, -239, -239},
+{-1079,-1288,-1268,-1268,-1268},
+{ -719, -928, -908, -908, -908},
+{ -989,-1198,-1178,-1178,-1178},
+{ -909,-1118,-1098,-1098,-1098}}},
+/* AU.G@..CG */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GA..CG */
+{{ -50, -339, -689, -689, -689},
+{-1079,-1368,-1718,-1718,-1718},
+{ -569, -858,-1208,-1208,-1208},
+{ -989,-1278,-1628,-1628,-1628},
+{ -859,-1148,-1498,-1498,-1498}},
+/* AU.GC..CG */
+{{ -50, -339, -689, -689, -689},
+{ -999,-1288,-1638,-1638,-1638},
+{ -499, -788,-1138,-1138,-1138},
+{ -989,-1278,-1628,-1628,-1628},
+{ -789,-1078,-1428,-1428,-1428}},
+/* AU.GG..CG */
+{{ -50, -339, -689, -689, -689},
+{-1079,-1368,-1718,-1718,-1718},
+{ -569, -858,-1208,-1208,-1208},
+{ -989,-1278,-1628,-1628,-1628},
+{ -859,-1148,-1498,-1498,-1498}},
+/* AU.GU..CG */
+{{ -50, -339, -689, -689, -689},
+{-1079,-1368,-1718,-1718,-1718},
+{ -719,-1008,-1358,-1358,-1358},
+{ -989,-1278,-1628,-1628,-1628},
+{ -909,-1198,-1548,-1548,-1548}}},
+/* AU.U@..CG */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UA..CG */
+{{ -50, -329, -329, -329, -329},
+{-1079,-1358,-1358,-1358,-1358},
+{ -569, -848, -848, -848, -848},
+{ -989,-1268,-1268,-1268,-1268},
+{ -859,-1138,-1138,-1138,-1138}},
+/* AU.UC..CG */
+{{ -50, -329, -329, -329, -329},
+{ -999,-1278,-1278,-1278,-1278},
+{ -499, -778, -778, -778, -778},
+{ -989,-1268,-1268,-1268,-1268},
+{ -789,-1068,-1068,-1068,-1068}},
+/* AU.UG..CG */
+{{ -50, -329, -329, -329, -329},
+{-1079,-1358,-1358,-1358,-1358},
+{ -569, -848, -848, -848, -848},
+{ -989,-1268,-1268,-1268,-1268},
+{ -859,-1138,-1138,-1138,-1138}},
+/* AU.UU..CG */
+{{ -50, -329, -329, -329, -329},
+{-1079,-1358,-1358,-1358,-1358},
+{ -719, -998, -998, -998, -998},
+{ -989,-1268,-1268,-1268,-1268},
+{ -909,-1188,-1188,-1188,-1188}}}},
+/* AU.@@..GC */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@A..GC */
+{{ 0, 0, 0, 0, 0},
+{ -519, -519, -519, -519, -519},
+{ -719, -719, -719, -719, -719},
+{ -709, -709, -709, -709, -709},
+{ -499, -499, -499, -499, -499}},
+/* AU.@C..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -309, -309, -309, -309, -309},
+{ -739, -739, -739, -739, -739},
+{ -499, -499, -499, -499, -499}},
+/* AU.@G..GC */
+{{ 0, 0, 0, 0, 0},
+{ -559, -559, -559, -559, -559},
+{ -309, -309, -309, -309, -309},
+{ -619, -619, -619, -619, -619},
+{ -499, -499, -499, -499, -499}},
+/* AU.@U..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -389, -389, -389, -389, -389},
+{ -739, -739, -739, -739, -739},
+{ -569, -569, -569, -569, -569}}},
+/* AU.A@..GC */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AA..GC */
+{{ -50, -429, -599, -599, -599},
+{ -569, -948,-1118,-1118,-1118},
+{ -769,-1148,-1318,-1318,-1318},
+{ -759,-1138,-1308,-1308,-1308},
+{ -549, -928,-1098,-1098,-1098}},
+/* AU.AC..GC */
+{{ -50, -429, -599, -599, -599},
+{ -929,-1308,-1478,-1478,-1478},
+{ -359, -738, -908, -908, -908},
+{ -789,-1168,-1338,-1338,-1338},
+{ -549, -928,-1098,-1098,-1098}},
+/* AU.AG..GC */
+{{ -50, -429, -599, -599, -599},
+{ -609, -988,-1158,-1158,-1158},
+{ -359, -738, -908, -908, -908},
+{ -669,-1048,-1218,-1218,-1218},
+{ -549, -928,-1098,-1098,-1098}},
+/* AU.AU..GC */
+{{ -50, -429, -599, -599, -599},
+{ -929,-1308,-1478,-1478,-1478},
+{ -439, -818, -988, -988, -988},
+{ -789,-1168,-1338,-1338,-1338},
+{ -619, -998,-1168,-1168,-1168}}},
+/* AU.C@..GC */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CA..GC */
+{{ -50, -259, -239, -239, -239},
+{ -569, -778, -758, -758, -758},
+{ -769, -978, -958, -958, -958},
+{ -759, -968, -948, -948, -948},
+{ -549, -758, -738, -738, -738}},
+/* AU.CC..GC */
+{{ -50, -259, -239, -239, -239},
+{ -929,-1138,-1118,-1118,-1118},
+{ -359, -568, -548, -548, -548},
+{ -789, -998, -978, -978, -978},
+{ -549, -758, -738, -738, -738}},
+/* AU.CG..GC */
+{{ -50, -259, -239, -239, -239},
+{ -609, -818, -798, -798, -798},
+{ -359, -568, -548, -548, -548},
+{ -669, -878, -858, -858, -858},
+{ -549, -758, -738, -738, -738}},
+/* AU.CU..GC */
+{{ -50, -259, -239, -239, -239},
+{ -929,-1138,-1118,-1118,-1118},
+{ -439, -648, -628, -628, -628},
+{ -789, -998, -978, -978, -978},
+{ -619, -828, -808, -808, -808}}},
+/* AU.G@..GC */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GA..GC */
+{{ -50, -339, -689, -689, -689},
+{ -569, -858,-1208,-1208,-1208},
+{ -769,-1058,-1408,-1408,-1408},
+{ -759,-1048,-1398,-1398,-1398},
+{ -549, -838,-1188,-1188,-1188}},
+/* AU.GC..GC */
+{{ -50, -339, -689, -689, -689},
+{ -929,-1218,-1568,-1568,-1568},
+{ -359, -648, -998, -998, -998},
+{ -789,-1078,-1428,-1428,-1428},
+{ -549, -838,-1188,-1188,-1188}},
+/* AU.GG..GC */
+{{ -50, -339, -689, -689, -689},
+{ -609, -898,-1248,-1248,-1248},
+{ -359, -648, -998, -998, -998},
+{ -669, -958,-1308,-1308,-1308},
+{ -549, -838,-1188,-1188,-1188}},
+/* AU.GU..GC */
+{{ -50, -339, -689, -689, -689},
+{ -929,-1218,-1568,-1568,-1568},
+{ -439, -728,-1078,-1078,-1078},
+{ -789,-1078,-1428,-1428,-1428},
+{ -619, -908,-1258,-1258,-1258}}},
+/* AU.U@..GC */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UA..GC */
+{{ -50, -329, -329, -329, -329},
+{ -569, -848, -848, -848, -848},
+{ -769,-1048,-1048,-1048,-1048},
+{ -759,-1038,-1038,-1038,-1038},
+{ -549, -828, -828, -828, -828}},
+/* AU.UC..GC */
+{{ -50, -329, -329, -329, -329},
+{ -929,-1208,-1208,-1208,-1208},
+{ -359, -638, -638, -638, -638},
+{ -789,-1068,-1068,-1068,-1068},
+{ -549, -828, -828, -828, -828}},
+/* AU.UG..GC */
+{{ -50, -329, -329, -329, -329},
+{ -609, -888, -888, -888, -888},
+{ -359, -638, -638, -638, -638},
+{ -669, -948, -948, -948, -948},
+{ -549, -828, -828, -828, -828}},
+/* AU.UU..GC */
+{{ -50, -329, -329, -329, -329},
+{ -929,-1208,-1208,-1208,-1208},
+{ -439, -718, -718, -718, -718},
+{ -789,-1068,-1068,-1068,-1068},
+{ -619, -898, -898, -898, -898}}}},
+/* AU.@@..GU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@A..GU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* AU.@C..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* AU.@G..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* AU.@U..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* AU.A@..GU */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AA..GU */
+{{ -50, -429, -599, -599, -599},
+{ -479, -858,-1028,-1028,-1028},
+{ -309, -688, -858, -858, -858},
+{ -389, -768, -938, -938, -938},
+{ -379, -758, -928, -928, -928}},
+/* AU.AC..GU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}},
+/* AU.AG..GU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}},
+/* AU.AU..GU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}}},
+/* AU.C@..GU */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CA..GU */
+{{ -50, -259, -239, -239, -239},
+{ -479, -688, -668, -668, -668},
+{ -309, -518, -498, -498, -498},
+{ -389, -598, -578, -578, -578},
+{ -379, -588, -568, -568, -568}},
+/* AU.CC..GU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}},
+/* AU.CG..GU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}},
+/* AU.CU..GU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}}},
+/* AU.G@..GU */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GA..GU */
+{{ -50, -339, -689, -689, -689},
+{ -479, -768,-1118,-1118,-1118},
+{ -309, -598, -948, -948, -948},
+{ -389, -678,-1028,-1028,-1028},
+{ -379, -668,-1018,-1018,-1018}},
+/* AU.GC..GU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}},
+/* AU.GG..GU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}},
+/* AU.GU..GU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}}},
+/* AU.U@..GU */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UA..GU */
+{{ -50, -329, -329, -329, -329},
+{ -479, -758, -758, -758, -758},
+{ -309, -588, -588, -588, -588},
+{ -389, -668, -668, -668, -668},
+{ -379, -658, -658, -658, -658}},
+/* AU.UC..GU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}},
+/* AU.UG..GU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}},
+/* AU.UU..GU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}}}},
+/* AU.@@..UG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@A..UG */
+{{ 0, 0, 0, 0, 0},
+{ -719, -719, -719, -719, -719},
+{ -479, -479, -479, -479, -479},
+{ -659, -659, -659, -659, -659},
+{ -549, -549, -549, -549, -549}},
+/* AU.@C..UG */
+{{ 0, 0, 0, 0, 0},
+{ -789, -789, -789, -789, -789},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -439, -439, -439, -439, -439}},
+/* AU.@G..UG */
+{{ 0, 0, 0, 0, 0},
+{ -959, -959, -959, -959, -959},
+{ -359, -359, -359, -359, -359},
+{ -919, -919, -919, -919, -919},
+{ -549, -549, -549, -549, -549}},
+/* AU.@U..UG */
+{{ 0, 0, 0, 0, 0},
+{ -809, -809, -809, -809, -809},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -359, -359, -359, -359, -359}}},
+/* AU.A@..UG */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AA..UG */
+{{ -50, -429, -599, -599, -599},
+{ -769,-1148,-1318,-1318,-1318},
+{ -529, -908,-1078,-1078,-1078},
+{ -709,-1088,-1258,-1258,-1258},
+{ -599, -978,-1148,-1148,-1148}},
+/* AU.AC..UG */
+{{ -50, -429, -599, -599, -599},
+{ -839,-1218,-1388,-1388,-1388},
+{ -529, -908,-1078,-1078,-1078},
+{ -859,-1238,-1408,-1408,-1408},
+{ -489, -868,-1038,-1038,-1038}},
+/* AU.AG..UG */
+{{ -50, -429, -599, -599, -599},
+{-1009,-1388,-1558,-1558,-1558},
+{ -409, -788, -958, -958, -958},
+{ -969,-1348,-1518,-1518,-1518},
+{ -599, -978,-1148,-1148,-1148}},
+/* AU.AU..UG */
+{{ -50, -429, -599, -599, -599},
+{ -859,-1238,-1408,-1408,-1408},
+{ -529, -908,-1078,-1078,-1078},
+{ -859,-1238,-1408,-1408,-1408},
+{ -409, -788, -958, -958, -958}}},
+/* AU.C@..UG */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CA..UG */
+{{ -50, -259, -239, -239, -239},
+{ -769, -978, -958, -958, -958},
+{ -529, -738, -718, -718, -718},
+{ -709, -918, -898, -898, -898},
+{ -599, -808, -788, -788, -788}},
+/* AU.CC..UG */
+{{ -50, -259, -239, -239, -239},
+{ -839,-1048,-1028,-1028,-1028},
+{ -529, -738, -718, -718, -718},
+{ -859,-1068,-1048,-1048,-1048},
+{ -489, -698, -678, -678, -678}},
+/* AU.CG..UG */
+{{ -50, -259, -239, -239, -239},
+{-1009,-1218,-1198,-1198,-1198},
+{ -409, -618, -598, -598, -598},
+{ -969,-1178,-1158,-1158,-1158},
+{ -599, -808, -788, -788, -788}},
+/* AU.CU..UG */
+{{ -50, -259, -239, -239, -239},
+{ -859,-1068,-1048,-1048,-1048},
+{ -529, -738, -718, -718, -718},
+{ -859,-1068,-1048,-1048,-1048},
+{ -409, -618, -598, -598, -598}}},
+/* AU.G@..UG */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GA..UG */
+{{ -50, -339, -689, -689, -689},
+{ -769,-1058,-1408,-1408,-1408},
+{ -529, -818,-1168,-1168,-1168},
+{ -709, -998,-1348,-1348,-1348},
+{ -599, -888,-1238,-1238,-1238}},
+/* AU.GC..UG */
+{{ -50, -339, -689, -689, -689},
+{ -839,-1128,-1478,-1478,-1478},
+{ -529, -818,-1168,-1168,-1168},
+{ -859,-1148,-1498,-1498,-1498},
+{ -489, -778,-1128,-1128,-1128}},
+/* AU.GG..UG */
+{{ -50, -339, -689, -689, -689},
+{-1009,-1298,-1648,-1648,-1648},
+{ -409, -698,-1048,-1048,-1048},
+{ -969,-1258,-1608,-1608,-1608},
+{ -599, -888,-1238,-1238,-1238}},
+/* AU.GU..UG */
+{{ -50, -339, -689, -689, -689},
+{ -859,-1148,-1498,-1498,-1498},
+{ -529, -818,-1168,-1168,-1168},
+{ -859,-1148,-1498,-1498,-1498},
+{ -409, -698,-1048,-1048,-1048}}},
+/* AU.U@..UG */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UA..UG */
+{{ -50, -329, -329, -329, -329},
+{ -769,-1048,-1048,-1048,-1048},
+{ -529, -808, -808, -808, -808},
+{ -709, -988, -988, -988, -988},
+{ -599, -878, -878, -878, -878}},
+/* AU.UC..UG */
+{{ -50, -329, -329, -329, -329},
+{ -839,-1118,-1118,-1118,-1118},
+{ -529, -808, -808, -808, -808},
+{ -859,-1138,-1138,-1138,-1138},
+{ -489, -768, -768, -768, -768}},
+/* AU.UG..UG */
+{{ -50, -329, -329, -329, -329},
+{-1009,-1288,-1288,-1288,-1288},
+{ -409, -688, -688, -688, -688},
+{ -969,-1248,-1248,-1248,-1248},
+{ -599, -878, -878, -878, -878}},
+/* AU.UU..UG */
+{{ -50, -329, -329, -329, -329},
+{ -859,-1138,-1138,-1138,-1138},
+{ -529, -808, -808, -808, -808},
+{ -859,-1138,-1138,-1138,-1138},
+{ -409, -688, -688, -688, -688}}}},
+/* AU.@@..AU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@A..AU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* AU.@C..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* AU.@G..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* AU.@U..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* AU.A@..AU */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AA..AU */
+{{ -50, -429, -599, -599, -599},
+{ -479, -858,-1028,-1028,-1028},
+{ -309, -688, -858, -858, -858},
+{ -389, -768, -938, -938, -938},
+{ -379, -758, -928, -928, -928}},
+/* AU.AC..AU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}},
+/* AU.AG..AU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}},
+/* AU.AU..AU */
+{{ -50, -429, -599, -599, -599},
+{ -649,-1028,-1198,-1198,-1198},
+{ -289, -668, -838, -838, -838},
+{ -739,-1118,-1288,-1288,-1288},
+{ -379, -758, -928, -928, -928}}},
+/* AU.C@..AU */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CA..AU */
+{{ -50, -259, -239, -239, -239},
+{ -479, -688, -668, -668, -668},
+{ -309, -518, -498, -498, -498},
+{ -389, -598, -578, -578, -578},
+{ -379, -588, -568, -568, -568}},
+/* AU.CC..AU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}},
+/* AU.CG..AU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}},
+/* AU.CU..AU */
+{{ -50, -259, -239, -239, -239},
+{ -649, -858, -838, -838, -838},
+{ -289, -498, -478, -478, -478},
+{ -739, -948, -928, -928, -928},
+{ -379, -588, -568, -568, -568}}},
+/* AU.G@..AU */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GA..AU */
+{{ -50, -339, -689, -689, -689},
+{ -479, -768,-1118,-1118,-1118},
+{ -309, -598, -948, -948, -948},
+{ -389, -678,-1028,-1028,-1028},
+{ -379, -668,-1018,-1018,-1018}},
+/* AU.GC..AU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}},
+/* AU.GG..AU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}},
+/* AU.GU..AU */
+{{ -50, -339, -689, -689, -689},
+{ -649, -938,-1288,-1288,-1288},
+{ -289, -578, -928, -928, -928},
+{ -739,-1028,-1378,-1378,-1378},
+{ -379, -668,-1018,-1018,-1018}}},
+/* AU.U@..AU */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UA..AU */
+{{ -50, -329, -329, -329, -329},
+{ -479, -758, -758, -758, -758},
+{ -309, -588, -588, -588, -588},
+{ -389, -668, -668, -668, -668},
+{ -379, -658, -658, -658, -658}},
+/* AU.UC..AU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}},
+/* AU.UG..AU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}},
+/* AU.UU..AU */
+{{ -50, -329, -329, -329, -329},
+{ -649, -928, -928, -928, -928},
+{ -289, -568, -568, -568, -568},
+{ -739,-1018,-1018,-1018,-1018},
+{ -379, -658, -658, -658, -658}}}},
+/* AU.@@..UA */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@A..UA */
+{{ 0, 0, 0, 0, 0},
+{ -399, -399, -399, -399, -399},
+{ -429, -429, -429, -429, -429},
+{ -379, -379, -379, -379, -379},
+{ -279, -279, -279, -279, -279}},
+/* AU.@C..UA */
+{{ 0, 0, 0, 0, 0},
+{ -629, -629, -629, -629, -629},
+{ -509, -509, -509, -509, -509},
+{ -679, -679, -679, -679, -679},
+{ -139, -139, -139, -139, -139}},
+/* AU.@G..UA */
+{{ 0, 0, 0, 0, 0},
+{ -889, -889, -889, -889, -889},
+{ -199, -199, -199, -199, -199},
+{ -889, -889, -889, -889, -889},
+{ -279, -279, -279, -279, -279}},
+/* AU.@U..UA */
+{{ 0, 0, 0, 0, 0},
+{ -589, -589, -589, -589, -589},
+{ -179, -179, -179, -179, -179},
+{ -679, -679, -679, -679, -679},
+{ -140, -140, -140, -140, -140}}},
+/* AU.A@..UA */
+{{{ -50, -429, -599, -599, -599},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AA..UA */
+{{ -50, -429, -599, -599, -599},
+{ -449, -828, -998, -998, -998},
+{ -479, -858,-1028,-1028,-1028},
+{ -429, -808, -978, -978, -978},
+{ -329, -708, -878, -878, -878}},
+/* AU.AC..UA */
+{{ -50, -429, -599, -599, -599},
+{ -679,-1058,-1228,-1228,-1228},
+{ -559, -938,-1108,-1108,-1108},
+{ -729,-1108,-1278,-1278,-1278},
+{ -189, -568, -738, -738, -738}},
+/* AU.AG..UA */
+{{ -50, -429, -599, -599, -599},
+{ -939,-1318,-1488,-1488,-1488},
+{ -249, -628, -798, -798, -798},
+{ -939,-1318,-1488,-1488,-1488},
+{ -329, -708, -878, -878, -878}},
+/* AU.AU..UA */
+{{ -50, -429, -599, -599, -599},
+{ -639,-1018,-1188,-1188,-1188},
+{ -229, -608, -778, -778, -778},
+{ -729,-1108,-1278,-1278,-1278},
+{ -190, -569, -739, -739, -739}}},
+/* AU.C@..UA */
+{{{ -50, -259, -239, -239, -239},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CA..UA */
+{{ -50, -259, -239, -239, -239},
+{ -449, -658, -638, -638, -638},
+{ -479, -688, -668, -668, -668},
+{ -429, -638, -618, -618, -618},
+{ -329, -538, -518, -518, -518}},
+/* AU.CC..UA */
+{{ -50, -259, -239, -239, -239},
+{ -679, -888, -868, -868, -868},
+{ -559, -768, -748, -748, -748},
+{ -729, -938, -918, -918, -918},
+{ -189, -398, -378, -378, -378}},
+/* AU.CG..UA */
+{{ -50, -259, -239, -239, -239},
+{ -939,-1148,-1128,-1128,-1128},
+{ -249, -458, -438, -438, -438},
+{ -939,-1148,-1128,-1128,-1128},
+{ -329, -538, -518, -518, -518}},
+/* AU.CU..UA */
+{{ -50, -259, -239, -239, -239},
+{ -639, -848, -828, -828, -828},
+{ -229, -438, -418, -418, -418},
+{ -729, -938, -918, -918, -918},
+{ -190, -399, -379, -379, -379}}},
+/* AU.G@..UA */
+{{{ -50, -339, -689, -689, -689},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GA..UA */
+{{ -50, -339, -689, -689, -689},
+{ -449, -738,-1088,-1088,-1088},
+{ -479, -768,-1118,-1118,-1118},
+{ -429, -718,-1068,-1068,-1068},
+{ -329, -618, -968, -968, -968}},
+/* AU.GC..UA */
+{{ -50, -339, -689, -689, -689},
+{ -679, -968,-1318,-1318,-1318},
+{ -559, -848,-1198,-1198,-1198},
+{ -729,-1018,-1368,-1368,-1368},
+{ -189, -478, -828, -828, -828}},
+/* AU.GG..UA */
+{{ -50, -339, -689, -689, -689},
+{ -939,-1228,-1578,-1578,-1578},
+{ -249, -538, -888, -888, -888},
+{ -939,-1228,-1578,-1578,-1578},
+{ -329, -618, -968, -968, -968}},
+/* AU.GU..UA */
+{{ -50, -339, -689, -689, -689},
+{ -639, -928,-1278,-1278,-1278},
+{ -229, -518, -868, -868, -868},
+{ -729,-1018,-1368,-1368,-1368},
+{ -190, -479, -829, -829, -829}}},
+/* AU.U@..UA */
+{{{ -50, -329, -329, -329, -329},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UA..UA */
+{{ -50, -329, -329, -329, -329},
+{ -449, -728, -728, -728, -728},
+{ -479, -758, -758, -758, -758},
+{ -429, -708, -708, -708, -708},
+{ -329, -608, -608, -608, -608}},
+/* AU.UC..UA */
+{{ -50, -329, -329, -329, -329},
+{ -679, -958, -958, -958, -958},
+{ -559, -838, -838, -838, -838},
+{ -729,-1008,-1008,-1008,-1008},
+{ -189, -468, -468, -468, -468}},
+/* AU.UG..UA */
+{{ -50, -329, -329, -329, -329},
+{ -939,-1218,-1218,-1218,-1218},
+{ -249, -528, -528, -528, -528},
+{ -939,-1218,-1218,-1218,-1218},
+{ -329, -608, -608, -608, -608}},
+/* AU.UU..UA */
+{{ -50, -329, -329, -329, -329},
+{ -639, -918, -918, -918, -918},
+{ -229, -508, -508, -508, -508},
+{ -729,-1008,-1008,-1008,-1008},
+{ -190, -469, -469, -469, -469}}}},
+/* AU.@@.. @ */
+{{{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@A.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@C.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@G.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* AU.@U.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}}},
+/* AU.A@.. @ */
+{{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AA.. @ */
+{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AC.. @ */
+{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AG.. @ */
+{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}},
+/* AU.AU.. @ */
+{{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649},
+{ -100, -479, -649, -649, -649}}},
+/* AU.C@.. @ */
+{{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CA.. @ */
+{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CC.. @ */
+{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CG.. @ */
+{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}},
+/* AU.CU.. @ */
+{{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289},
+{ -100, -309, -289, -289, -289}}},
+/* AU.G@.. @ */
+{{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GA.. @ */
+{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GC.. @ */
+{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GG.. @ */
+{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}},
+/* AU.GU.. @ */
+{{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739},
+{ -100, -389, -739, -739, -739}}},
+/* AU.U@.. @ */
+{{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UA.. @ */
+{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UC.. @ */
+{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UG.. @ */
+{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}},
+/* AU.UU.. @ */
+{{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379},
+{ -100, -379, -379, -379, -379}}}}},
+{ /* noPair */ {{{{0}}}},
+/* UA.@@..CG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@A..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* UA.@C..CG */
+{{ 0, 0, 0, 0, 0},
+{ -949, -949, -949, -949, -949},
+{ -449, -449, -449, -449, -449},
+{ -939, -939, -939, -939, -939},
+{ -739, -739, -739, -739, -739}},
+/* UA.@G..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -519, -519, -519, -519, -519},
+{ -939, -939, -939, -939, -939},
+{ -809, -809, -809, -809, -809}},
+/* UA.@U..CG */
+{{ 0, 0, 0, 0, 0},
+{-1029,-1029,-1029,-1029,-1029},
+{ -669, -669, -669, -669, -669},
+{ -939, -939, -939, -939, -939},
+{ -859, -859, -859, -859, -859}}},
+/* UA.A@..CG */
+{{{ -50, -399, -629, -889, -589},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AA..CG */
+{{ -50, -399, -629, -889, -589},
+{-1079,-1428,-1658,-1918,-1618},
+{ -569, -918,-1148,-1408,-1108},
+{ -989,-1338,-1568,-1828,-1528},
+{ -859,-1208,-1438,-1698,-1398}},
+/* UA.AC..CG */
+{{ -50, -399, -629, -889, -589},
+{ -999,-1348,-1578,-1838,-1538},
+{ -499, -848,-1078,-1338,-1038},
+{ -989,-1338,-1568,-1828,-1528},
+{ -789,-1138,-1368,-1628,-1328}},
+/* UA.AG..CG */
+{{ -50, -399, -629, -889, -589},
+{-1079,-1428,-1658,-1918,-1618},
+{ -569, -918,-1148,-1408,-1108},
+{ -989,-1338,-1568,-1828,-1528},
+{ -859,-1208,-1438,-1698,-1398}},
+/* UA.AU..CG */
+{{ -50, -399, -629, -889, -589},
+{-1079,-1428,-1658,-1918,-1618},
+{ -719,-1068,-1298,-1558,-1258},
+{ -989,-1338,-1568,-1828,-1528},
+{ -909,-1258,-1488,-1748,-1448}}},
+/* UA.C@..CG */
+{{{ -50, -429, -509, -199, -179},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CA..CG */
+{{ -50, -429, -509, -199, -179},
+{-1079,-1458,-1538,-1228,-1208},
+{ -569, -948,-1028, -718, -698},
+{ -989,-1368,-1448,-1138,-1118},
+{ -859,-1238,-1318,-1008, -988}},
+/* UA.CC..CG */
+{{ -50, -429, -509, -199, -179},
+{ -999,-1378,-1458,-1148,-1128},
+{ -499, -878, -958, -648, -628},
+{ -989,-1368,-1448,-1138,-1118},
+{ -789,-1168,-1248, -938, -918}},
+/* UA.CG..CG */
+{{ -50, -429, -509, -199, -179},
+{-1079,-1458,-1538,-1228,-1208},
+{ -569, -948,-1028, -718, -698},
+{ -989,-1368,-1448,-1138,-1118},
+{ -859,-1238,-1318,-1008, -988}},
+/* UA.CU..CG */
+{{ -50, -429, -509, -199, -179},
+{-1079,-1458,-1538,-1228,-1208},
+{ -719,-1098,-1178, -868, -848},
+{ -989,-1368,-1448,-1138,-1118},
+{ -909,-1288,-1368,-1058,-1038}}},
+/* UA.G@..CG */
+{{{ -50, -379, -679, -889, -679},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GA..CG */
+{{ -50, -379, -679, -889, -679},
+{-1079,-1408,-1708,-1918,-1708},
+{ -569, -898,-1198,-1408,-1198},
+{ -989,-1318,-1618,-1828,-1618},
+{ -859,-1188,-1488,-1698,-1488}},
+/* UA.GC..CG */
+{{ -50, -379, -679, -889, -679},
+{ -999,-1328,-1628,-1838,-1628},
+{ -499, -828,-1128,-1338,-1128},
+{ -989,-1318,-1618,-1828,-1618},
+{ -789,-1118,-1418,-1628,-1418}},
+/* UA.GG..CG */
+{{ -50, -379, -679, -889, -679},
+{-1079,-1408,-1708,-1918,-1708},
+{ -569, -898,-1198,-1408,-1198},
+{ -989,-1318,-1618,-1828,-1618},
+{ -859,-1188,-1488,-1698,-1488}},
+/* UA.GU..CG */
+{{ -50, -379, -679, -889, -679},
+{-1079,-1408,-1708,-1918,-1708},
+{ -719,-1048,-1348,-1558,-1348},
+{ -989,-1318,-1618,-1828,-1618},
+{ -909,-1238,-1538,-1748,-1538}}},
+/* UA.U@..CG */
+{{{ -50, -279, -139, -279, -140},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UA..CG */
+{{ -50, -279, -139, -279, -140},
+{-1079,-1308,-1168,-1308,-1169},
+{ -569, -798, -658, -798, -659},
+{ -989,-1218,-1078,-1218,-1079},
+{ -859,-1088, -948,-1088, -949}},
+/* UA.UC..CG */
+{{ -50, -279, -139, -279, -140},
+{ -999,-1228,-1088,-1228,-1089},
+{ -499, -728, -588, -728, -589},
+{ -989,-1218,-1078,-1218,-1079},
+{ -789,-1018, -878,-1018, -879}},
+/* UA.UG..CG */
+{{ -50, -279, -139, -279, -140},
+{-1079,-1308,-1168,-1308,-1169},
+{ -569, -798, -658, -798, -659},
+{ -989,-1218,-1078,-1218,-1079},
+{ -859,-1088, -948,-1088, -949}},
+/* UA.UU..CG */
+{{ -50, -279, -139, -279, -140},
+{-1079,-1308,-1168,-1308,-1169},
+{ -719, -948, -808, -948, -809},
+{ -989,-1218,-1078,-1218,-1079},
+{ -909,-1138, -998,-1138, -999}}}},
+/* UA.@@..GC */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@A..GC */
+{{ 0, 0, 0, 0, 0},
+{ -519, -519, -519, -519, -519},
+{ -719, -719, -719, -719, -719},
+{ -709, -709, -709, -709, -709},
+{ -499, -499, -499, -499, -499}},
+/* UA.@C..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -309, -309, -309, -309, -309},
+{ -739, -739, -739, -739, -739},
+{ -499, -499, -499, -499, -499}},
+/* UA.@G..GC */
+{{ 0, 0, 0, 0, 0},
+{ -559, -559, -559, -559, -559},
+{ -309, -309, -309, -309, -309},
+{ -619, -619, -619, -619, -619},
+{ -499, -499, -499, -499, -499}},
+/* UA.@U..GC */
+{{ 0, 0, 0, 0, 0},
+{ -879, -879, -879, -879, -879},
+{ -389, -389, -389, -389, -389},
+{ -739, -739, -739, -739, -739},
+{ -569, -569, -569, -569, -569}}},
+/* UA.A@..GC */
+{{{ -50, -399, -629, -889, -589},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AA..GC */
+{{ -50, -399, -629, -889, -589},
+{ -569, -918,-1148,-1408,-1108},
+{ -769,-1118,-1348,-1608,-1308},
+{ -759,-1108,-1338,-1598,-1298},
+{ -549, -898,-1128,-1388,-1088}},
+/* UA.AC..GC */
+{{ -50, -399, -629, -889, -589},
+{ -929,-1278,-1508,-1768,-1468},
+{ -359, -708, -938,-1198, -898},
+{ -789,-1138,-1368,-1628,-1328},
+{ -549, -898,-1128,-1388,-1088}},
+/* UA.AG..GC */
+{{ -50, -399, -629, -889, -589},
+{ -609, -958,-1188,-1448,-1148},
+{ -359, -708, -938,-1198, -898},
+{ -669,-1018,-1248,-1508,-1208},
+{ -549, -898,-1128,-1388,-1088}},
+/* UA.AU..GC */
+{{ -50, -399, -629, -889, -589},
+{ -929,-1278,-1508,-1768,-1468},
+{ -439, -788,-1018,-1278, -978},
+{ -789,-1138,-1368,-1628,-1328},
+{ -619, -968,-1198,-1458,-1158}}},
+/* UA.C@..GC */
+{{{ -50, -429, -509, -199, -179},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CA..GC */
+{{ -50, -429, -509, -199, -179},
+{ -569, -948,-1028, -718, -698},
+{ -769,-1148,-1228, -918, -898},
+{ -759,-1138,-1218, -908, -888},
+{ -549, -928,-1008, -698, -678}},
+/* UA.CC..GC */
+{{ -50, -429, -509, -199, -179},
+{ -929,-1308,-1388,-1078,-1058},
+{ -359, -738, -818, -508, -488},
+{ -789,-1168,-1248, -938, -918},
+{ -549, -928,-1008, -698, -678}},
+/* UA.CG..GC */
+{{ -50, -429, -509, -199, -179},
+{ -609, -988,-1068, -758, -738},
+{ -359, -738, -818, -508, -488},
+{ -669,-1048,-1128, -818, -798},
+{ -549, -928,-1008, -698, -678}},
+/* UA.CU..GC */
+{{ -50, -429, -509, -199, -179},
+{ -929,-1308,-1388,-1078,-1058},
+{ -439, -818, -898, -588, -568},
+{ -789,-1168,-1248, -938, -918},
+{ -619, -998,-1078, -768, -748}}},
+/* UA.G@..GC */
+{{{ -50, -379, -679, -889, -679},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GA..GC */
+{{ -50, -379, -679, -889, -679},
+{ -569, -898,-1198,-1408,-1198},
+{ -769,-1098,-1398,-1608,-1398},
+{ -759,-1088,-1388,-1598,-1388},
+{ -549, -878,-1178,-1388,-1178}},
+/* UA.GC..GC */
+{{ -50, -379, -679, -889, -679},
+{ -929,-1258,-1558,-1768,-1558},
+{ -359, -688, -988,-1198, -988},
+{ -789,-1118,-1418,-1628,-1418},
+{ -549, -878,-1178,-1388,-1178}},
+/* UA.GG..GC */
+{{ -50, -379, -679, -889, -679},
+{ -609, -938,-1238,-1448,-1238},
+{ -359, -688, -988,-1198, -988},
+{ -669, -998,-1298,-1508,-1298},
+{ -549, -878,-1178,-1388,-1178}},
+/* UA.GU..GC */
+{{ -50, -379, -679, -889, -679},
+{ -929,-1258,-1558,-1768,-1558},
+{ -439, -768,-1068,-1278,-1068},
+{ -789,-1118,-1418,-1628,-1418},
+{ -619, -948,-1248,-1458,-1248}}},
+/* UA.U@..GC */
+{{{ -50, -279, -139, -279, -140},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UA..GC */
+{{ -50, -279, -139, -279, -140},
+{ -569, -798, -658, -798, -659},
+{ -769, -998, -858, -998, -859},
+{ -759, -988, -848, -988, -849},
+{ -549, -778, -638, -778, -639}},
+/* UA.UC..GC */
+{{ -50, -279, -139, -279, -140},
+{ -929,-1158,-1018,-1158,-1019},
+{ -359, -588, -448, -588, -449},
+{ -789,-1018, -878,-1018, -879},
+{ -549, -778, -638, -778, -639}},
+/* UA.UG..GC */
+{{ -50, -279, -139, -279, -140},
+{ -609, -838, -698, -838, -699},
+{ -359, -588, -448, -588, -449},
+{ -669, -898, -758, -898, -759},
+{ -549, -778, -638, -778, -639}},
+/* UA.UU..GC */
+{{ -50, -279, -139, -279, -140},
+{ -929,-1158,-1018,-1158,-1019},
+{ -439, -668, -528, -668, -529},
+{ -789,-1018, -878,-1018, -879},
+{ -619, -848, -708, -848, -709}}}},
+/* UA.@@..GU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@A..GU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* UA.@C..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* UA.@G..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* UA.@U..GU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* UA.A@..GU */
+{{{ -50, -399, -629, -889, -589},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AA..GU */
+{{ -50, -399, -629, -889, -589},
+{ -479, -828,-1058,-1318,-1018},
+{ -309, -658, -888,-1148, -848},
+{ -389, -738, -968,-1228, -928},
+{ -379, -728, -958,-1218, -918}},
+/* UA.AC..GU */
+{{ -50, -399, -629, -889, -589},
+{ -649, -998,-1228,-1488,-1188},
+{ -289, -638, -868,-1128, -828},
+{ -739,-1088,-1318,-1578,-1278},
+{ -379, -728, -958,-1218, -918}},
+/* UA.AG..GU */
+{{ -50, -399, -629, -889, -589},
+{ -649, -998,-1228,-1488,-1188},
+{ -289, -638, -868,-1128, -828},
+{ -739,-1088,-1318,-1578,-1278},
+{ -379, -728, -958,-1218, -918}},
+/* UA.AU..GU */
+{{ -50, -399, -629, -889, -589},
+{ -649, -998,-1228,-1488,-1188},
+{ -289, -638, -868,-1128, -828},
+{ -739,-1088,-1318,-1578,-1278},
+{ -379, -728, -958,-1218, -918}}},
+/* UA.C@..GU */
+{{{ -50, -429, -509, -199, -179},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CA..GU */
+{{ -50, -429, -509, -199, -179},
+{ -479, -858, -938, -628, -608},
+{ -309, -688, -768, -458, -438},
+{ -389, -768, -848, -538, -518},
+{ -379, -758, -838, -528, -508}},
+/* UA.CC..GU */
+{{ -50, -429, -509, -199, -179},
+{ -649,-1028,-1108, -798, -778},
+{ -289, -668, -748, -438, -418},
+{ -739,-1118,-1198, -888, -868},
+{ -379, -758, -838, -528, -508}},
+/* UA.CG..GU */
+{{ -50, -429, -509, -199, -179},
+{ -649,-1028,-1108, -798, -778},
+{ -289, -668, -748, -438, -418},
+{ -739,-1118,-1198, -888, -868},
+{ -379, -758, -838, -528, -508}},
+/* UA.CU..GU */
+{{ -50, -429, -509, -199, -179},
+{ -649,-1028,-1108, -798, -778},
+{ -289, -668, -748, -438, -418},
+{ -739,-1118,-1198, -888, -868},
+{ -379, -758, -838, -528, -508}}},
+/* UA.G@..GU */
+{{{ -50, -379, -679, -889, -679},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GA..GU */
+{{ -50, -379, -679, -889, -679},
+{ -479, -808,-1108,-1318,-1108},
+{ -309, -638, -938,-1148, -938},
+{ -389, -718,-1018,-1228,-1018},
+{ -379, -708,-1008,-1218,-1008}},
+/* UA.GC..GU */
+{{ -50, -379, -679, -889, -679},
+{ -649, -978,-1278,-1488,-1278},
+{ -289, -618, -918,-1128, -918},
+{ -739,-1068,-1368,-1578,-1368},
+{ -379, -708,-1008,-1218,-1008}},
+/* UA.GG..GU */
+{{ -50, -379, -679, -889, -679},
+{ -649, -978,-1278,-1488,-1278},
+{ -289, -618, -918,-1128, -918},
+{ -739,-1068,-1368,-1578,-1368},
+{ -379, -708,-1008,-1218,-1008}},
+/* UA.GU..GU */
+{{ -50, -379, -679, -889, -679},
+{ -649, -978,-1278,-1488,-1278},
+{ -289, -618, -918,-1128, -918},
+{ -739,-1068,-1368,-1578,-1368},
+{ -379, -708,-1008,-1218,-1008}}},
+/* UA.U@..GU */
+{{{ -50, -279, -139, -279, -140},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UA..GU */
+{{ -50, -279, -139, -279, -140},
+{ -479, -708, -568, -708, -569},
+{ -309, -538, -398, -538, -399},
+{ -389, -618, -478, -618, -479},
+{ -379, -608, -468, -608, -469}},
+/* UA.UC..GU */
+{{ -50, -279, -139, -279, -140},
+{ -649, -878, -738, -878, -739},
+{ -289, -518, -378, -518, -379},
+{ -739, -968, -828, -968, -829},
+{ -379, -608, -468, -608, -469}},
+/* UA.UG..GU */
+{{ -50, -279, -139, -279, -140},
+{ -649, -878, -738, -878, -739},
+{ -289, -518, -378, -518, -379},
+{ -739, -968, -828, -968, -829},
+{ -379, -608, -468, -608, -469}},
+/* UA.UU..GU */
+{{ -50, -279, -139, -279, -140},
+{ -649, -878, -738, -878, -739},
+{ -289, -518, -378, -518, -379},
+{ -739, -968, -828, -968, -829},
+{ -379, -608, -468, -608, -469}}}},
+/* UA.@@..UG */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@A..UG */
+{{ 0, 0, 0, 0, 0},
+{ -719, -719, -719, -719, -719},
+{ -479, -479, -479, -479, -479},
+{ -659, -659, -659, -659, -659},
+{ -549, -549, -549, -549, -549}},
+/* UA.@C..UG */
+{{ 0, 0, 0, 0, 0},
+{ -789, -789, -789, -789, -789},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -439, -439, -439, -439, -439}},
+/* UA.@G..UG */
+{{ 0, 0, 0, 0, 0},
+{ -959, -959, -959, -959, -959},
+{ -359, -359, -359, -359, -359},
+{ -919, -919, -919, -919, -919},
+{ -549, -549, -549, -549, -549}},
+/* UA.@U..UG */
+{{ 0, 0, 0, 0, 0},
+{ -809, -809, -809, -809, -809},
+{ -479, -479, -479, -479, -479},
+{ -809, -809, -809, -809, -809},
+{ -359, -359, -359, -359, -359}}},
+/* UA.A@..UG */
+{{{ -50, -399, -629, -889, -589},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AA..UG */
+{{ -50, -399, -629, -889, -589},
+{ -769,-1118,-1348,-1608,-1308},
+{ -529, -878,-1108,-1368,-1068},
+{ -709,-1058,-1288,-1548,-1248},
+{ -599, -948,-1178,-1438,-1138}},
+/* UA.AC..UG */
+{{ -50, -399, -629, -889, -589},
+{ -839,-1188,-1418,-1678,-1378},
+{ -529, -878,-1108,-1368,-1068},
+{ -859,-1208,-1438,-1698,-1398},
+{ -489, -838,-1068,-1328,-1028}},
+/* UA.AG..UG */
+{{ -50, -399, -629, -889, -589},
+{-1009,-1358,-1588,-1848,-1548},
+{ -409, -758, -988,-1248, -948},
+{ -969,-1318,-1548,-1808,-1508},
+{ -599, -948,-1178,-1438,-1138}},
+/* UA.AU..UG */
+{{ -50, -399, -629, -889, -589},
+{ -859,-1208,-1438,-1698,-1398},
+{ -529, -878,-1108,-1368,-1068},
+{ -859,-1208,-1438,-1698,-1398},
+{ -409, -758, -988,-1248, -948}}},
+/* UA.C@..UG */
+{{{ -50, -429, -509, -199, -179},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CA..UG */
+{{ -50, -429, -509, -199, -179},
+{ -769,-1148,-1228, -918, -898},
+{ -529, -908, -988, -678, -658},
+{ -709,-1088,-1168, -858, -838},
+{ -599, -978,-1058, -748, -728}},
+/* UA.CC..UG */
+{{ -50, -429, -509, -199, -179},
+{ -839,-1218,-1298, -988, -968},
+{ -529, -908, -988, -678, -658},
+{ -859,-1238,-1318,-1008, -988},
+{ -489, -868, -948, -638, -618}},
+/* UA.CG..UG */
+{{ -50, -429, -509, -199, -179},
+{-1009,-1388,-1468,-1158,-1138},
+{ -409, -788, -868, -558, -538},
+{ -969,-1348,-1428,-1118,-1098},
+{ -599, -978,-1058, -748, -728}},
+/* UA.CU..UG */
+{{ -50, -429, -509, -199, -179},
+{ -859,-1238,-1318,-1008, -988},
+{ -529, -908, -988, -678, -658},
+{ -859,-1238,-1318,-1008, -988},
+{ -409, -788, -868, -558, -538}}},
+/* UA.G@..UG */
+{{{ -50, -379, -679, -889, -679},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GA..UG */
+{{ -50, -379, -679, -889, -679},
+{ -769,-1098,-1398,-1608,-1398},
+{ -529, -858,-1158,-1368,-1158},
+{ -709,-1038,-1338,-1548,-1338},
+{ -599, -928,-1228,-1438,-1228}},
+/* UA.GC..UG */
+{{ -50, -379, -679, -889, -679},
+{ -839,-1168,-1468,-1678,-1468},
+{ -529, -858,-1158,-1368,-1158},
+{ -859,-1188,-1488,-1698,-1488},
+{ -489, -818,-1118,-1328,-1118}},
+/* UA.GG..UG */
+{{ -50, -379, -679, -889, -679},
+{-1009,-1338,-1638,-1848,-1638},
+{ -409, -738,-1038,-1248,-1038},
+{ -969,-1298,-1598,-1808,-1598},
+{ -599, -928,-1228,-1438,-1228}},
+/* UA.GU..UG */
+{{ -50, -379, -679, -889, -679},
+{ -859,-1188,-1488,-1698,-1488},
+{ -529, -858,-1158,-1368,-1158},
+{ -859,-1188,-1488,-1698,-1488},
+{ -409, -738,-1038,-1248,-1038}}},
+/* UA.U@..UG */
+{{{ -50, -279, -139, -279, -140},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UA..UG */
+{{ -50, -279, -139, -279, -140},
+{ -769, -998, -858, -998, -859},
+{ -529, -758, -618, -758, -619},
+{ -709, -938, -798, -938, -799},
+{ -599, -828, -688, -828, -689}},
+/* UA.UC..UG */
+{{ -50, -279, -139, -279, -140},
+{ -839,-1068, -928,-1068, -929},
+{ -529, -758, -618, -758, -619},
+{ -859,-1088, -948,-1088, -949},
+{ -489, -718, -578, -718, -579}},
+/* UA.UG..UG */
+{{ -50, -279, -139, -279, -140},
+{-1009,-1238,-1098,-1238,-1099},
+{ -409, -638, -498, -638, -499},
+{ -969,-1198,-1058,-1198,-1059},
+{ -599, -828, -688, -828, -689}},
+/* UA.UU..UG */
+{{ -50, -279, -139, -279, -140},
+{ -859,-1088, -948,-1088, -949},
+{ -529, -758, -618, -758, -619},
+{ -859,-1088, -948,-1088, -949},
+{ -409, -638, -498, -638, -499}}}},
+/* UA.@@..AU */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@A..AU */
+{{ 0, 0, 0, 0, 0},
+{ -429, -429, -429, -429, -429},
+{ -259, -259, -259, -259, -259},
+{ -339, -339, -339, -339, -339},
+{ -329, -329, -329, -329, -329}},
+/* UA.@C..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* UA.@G..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}},
+/* UA.@U..AU */
+{{ 0, 0, 0, 0, 0},
+{ -599, -599, -599, -599, -599},
+{ -239, -239, -239, -239, -239},
+{ -689, -689, -689, -689, -689},
+{ -329, -329, -329, -329, -329}}},
+/* UA.A@..AU */
+{{{ -50, -399, -629, -889, -589},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AA..AU */
+{{ -50, -399, -629, -889, -589},
+{ -479, -828,-1058,-1318,-1018},
+{ -309, -658, -888,-1148, -848},
+{ -389, -738, -968,-1228, -928},
+{ -379, -728, -958,-1218, -918}},
+/* UA.AC..AU */
+{{ -50, -399, -629, -889, -589},
+{ -649, -998,-1228,-1488,-1188},
+{ -289, -638, -868,-1128, -828},
+{ -739,-1088,-1318,-1578,-1278},
+{ -379, -728, -958,-1218, -918}},
+/* UA.AG..AU */
+{{ -50, -399, -629, -889, -589},
+{ -649, -998,-1228,-1488,-1188},
+{ -289, -638, -868,-1128, -828},
+{ -739,-1088,-1318,-1578,-1278},
+{ -379, -728, -958,-1218, -918}},
+/* UA.AU..AU */
+{{ -50, -399, -629, -889, -589},
+{ -649, -998,-1228,-1488,-1188},
+{ -289, -638, -868,-1128, -828},
+{ -739,-1088,-1318,-1578,-1278},
+{ -379, -728, -958,-1218, -918}}},
+/* UA.C@..AU */
+{{{ -50, -429, -509, -199, -179},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CA..AU */
+{{ -50, -429, -509, -199, -179},
+{ -479, -858, -938, -628, -608},
+{ -309, -688, -768, -458, -438},
+{ -389, -768, -848, -538, -518},
+{ -379, -758, -838, -528, -508}},
+/* UA.CC..AU */
+{{ -50, -429, -509, -199, -179},
+{ -649,-1028,-1108, -798, -778},
+{ -289, -668, -748, -438, -418},
+{ -739,-1118,-1198, -888, -868},
+{ -379, -758, -838, -528, -508}},
+/* UA.CG..AU */
+{{ -50, -429, -509, -199, -179},
+{ -649,-1028,-1108, -798, -778},
+{ -289, -668, -748, -438, -418},
+{ -739,-1118,-1198, -888, -868},
+{ -379, -758, -838, -528, -508}},
+/* UA.CU..AU */
+{{ -50, -429, -509, -199, -179},
+{ -649,-1028,-1108, -798, -778},
+{ -289, -668, -748, -438, -418},
+{ -739,-1118,-1198, -888, -868},
+{ -379, -758, -838, -528, -508}}},
+/* UA.G@..AU */
+{{{ -50, -379, -679, -889, -679},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GA..AU */
+{{ -50, -379, -679, -889, -679},
+{ -479, -808,-1108,-1318,-1108},
+{ -309, -638, -938,-1148, -938},
+{ -389, -718,-1018,-1228,-1018},
+{ -379, -708,-1008,-1218,-1008}},
+/* UA.GC..AU */
+{{ -50, -379, -679, -889, -679},
+{ -649, -978,-1278,-1488,-1278},
+{ -289, -618, -918,-1128, -918},
+{ -739,-1068,-1368,-1578,-1368},
+{ -379, -708,-1008,-1218,-1008}},
+/* UA.GG..AU */
+{{ -50, -379, -679, -889, -679},
+{ -649, -978,-1278,-1488,-1278},
+{ -289, -618, -918,-1128, -918},
+{ -739,-1068,-1368,-1578,-1368},
+{ -379, -708,-1008,-1218,-1008}},
+/* UA.GU..AU */
+{{ -50, -379, -679, -889, -679},
+{ -649, -978,-1278,-1488,-1278},
+{ -289, -618, -918,-1128, -918},
+{ -739,-1068,-1368,-1578,-1368},
+{ -379, -708,-1008,-1218,-1008}}},
+/* UA.U@..AU */
+{{{ -50, -279, -139, -279, -140},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UA..AU */
+{{ -50, -279, -139, -279, -140},
+{ -479, -708, -568, -708, -569},
+{ -309, -538, -398, -538, -399},
+{ -389, -618, -478, -618, -479},
+{ -379, -608, -468, -608, -469}},
+/* UA.UC..AU */
+{{ -50, -279, -139, -279, -140},
+{ -649, -878, -738, -878, -739},
+{ -289, -518, -378, -518, -379},
+{ -739, -968, -828, -968, -829},
+{ -379, -608, -468, -608, -469}},
+/* UA.UG..AU */
+{{ -50, -279, -139, -279, -140},
+{ -649, -878, -738, -878, -739},
+{ -289, -518, -378, -518, -379},
+{ -739, -968, -828, -968, -829},
+{ -379, -608, -468, -608, -469}},
+/* UA.UU..AU */
+{{ -50, -279, -139, -279, -140},
+{ -649, -878, -738, -878, -739},
+{ -289, -518, -378, -518, -379},
+{ -739, -968, -828, -968, -829},
+{ -379, -608, -468, -608, -469}}}},
+/* UA.@@..UA */
+{{{{ 0, 0, 0, 0, 0},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@A..UA */
+{{ 0, 0, 0, 0, 0},
+{ -399, -399, -399, -399, -399},
+{ -429, -429, -429, -429, -429},
+{ -379, -379, -379, -379, -379},
+{ -279, -279, -279, -279, -279}},
+/* UA.@C..UA */
+{{ 0, 0, 0, 0, 0},
+{ -629, -629, -629, -629, -629},
+{ -509, -509, -509, -509, -509},
+{ -679, -679, -679, -679, -679},
+{ -139, -139, -139, -139, -139}},
+/* UA.@G..UA */
+{{ 0, 0, 0, 0, 0},
+{ -889, -889, -889, -889, -889},
+{ -199, -199, -199, -199, -199},
+{ -889, -889, -889, -889, -889},
+{ -279, -279, -279, -279, -279}},
+/* UA.@U..UA */
+{{ 0, 0, 0, 0, 0},
+{ -589, -589, -589, -589, -589},
+{ -179, -179, -179, -179, -179},
+{ -679, -679, -679, -679, -679},
+{ -140, -140, -140, -140, -140}}},
+/* UA.A@..UA */
+{{{ -50, -399, -629, -889, -589},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AA..UA */
+{{ -50, -399, -629, -889, -589},
+{ -449, -798,-1028,-1288, -988},
+{ -479, -828,-1058,-1318,-1018},
+{ -429, -778,-1008,-1268, -968},
+{ -329, -678, -908,-1168, -868}},
+/* UA.AC..UA */
+{{ -50, -399, -629, -889, -589},
+{ -679,-1028,-1258,-1518,-1218},
+{ -559, -908,-1138,-1398,-1098},
+{ -729,-1078,-1308,-1568,-1268},
+{ -189, -538, -768,-1028, -728}},
+/* UA.AG..UA */
+{{ -50, -399, -629, -889, -589},
+{ -939,-1288,-1518,-1778,-1478},
+{ -249, -598, -828,-1088, -788},
+{ -939,-1288,-1518,-1778,-1478},
+{ -329, -678, -908,-1168, -868}},
+/* UA.AU..UA */
+{{ -50, -399, -629, -889, -589},
+{ -639, -988,-1218,-1478,-1178},
+{ -229, -578, -808,-1068, -768},
+{ -729,-1078,-1308,-1568,-1268},
+{ -190, -539, -769,-1029, -729}}},
+/* UA.C@..UA */
+{{{ -50, -429, -509, -199, -179},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CA..UA */
+{{ -50, -429, -509, -199, -179},
+{ -449, -828, -908, -598, -578},
+{ -479, -858, -938, -628, -608},
+{ -429, -808, -888, -578, -558},
+{ -329, -708, -788, -478, -458}},
+/* UA.CC..UA */
+{{ -50, -429, -509, -199, -179},
+{ -679,-1058,-1138, -828, -808},
+{ -559, -938,-1018, -708, -688},
+{ -729,-1108,-1188, -878, -858},
+{ -189, -568, -648, -338, -318}},
+/* UA.CG..UA */
+{{ -50, -429, -509, -199, -179},
+{ -939,-1318,-1398,-1088,-1068},
+{ -249, -628, -708, -398, -378},
+{ -939,-1318,-1398,-1088,-1068},
+{ -329, -708, -788, -478, -458}},
+/* UA.CU..UA */
+{{ -50, -429, -509, -199, -179},
+{ -639,-1018,-1098, -788, -768},
+{ -229, -608, -688, -378, -358},
+{ -729,-1108,-1188, -878, -858},
+{ -190, -569, -649, -339, -319}}},
+/* UA.G@..UA */
+{{{ -50, -379, -679, -889, -679},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GA..UA */
+{{ -50, -379, -679, -889, -679},
+{ -449, -778,-1078,-1288,-1078},
+{ -479, -808,-1108,-1318,-1108},
+{ -429, -758,-1058,-1268,-1058},
+{ -329, -658, -958,-1168, -958}},
+/* UA.GC..UA */
+{{ -50, -379, -679, -889, -679},
+{ -679,-1008,-1308,-1518,-1308},
+{ -559, -888,-1188,-1398,-1188},
+{ -729,-1058,-1358,-1568,-1358},
+{ -189, -518, -818,-1028, -818}},
+/* UA.GG..UA */
+{{ -50, -379, -679, -889, -679},
+{ -939,-1268,-1568,-1778,-1568},
+{ -249, -578, -878,-1088, -878},
+{ -939,-1268,-1568,-1778,-1568},
+{ -329, -658, -958,-1168, -958}},
+/* UA.GU..UA */
+{{ -50, -379, -679, -889, -679},
+{ -639, -968,-1268,-1478,-1268},
+{ -229, -558, -858,-1068, -858},
+{ -729,-1058,-1358,-1568,-1358},
+{ -190, -519, -819,-1029, -819}}},
+/* UA.U@..UA */
+{{{ -50, -279, -139, -279, -140},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UA..UA */
+{{ -50, -279, -139, -279, -140},
+{ -449, -678, -538, -678, -539},
+{ -479, -708, -568, -708, -569},
+{ -429, -658, -518, -658, -519},
+{ -329, -558, -418, -558, -419}},
+/* UA.UC..UA */
+{{ -50, -279, -139, -279, -140},
+{ -679, -908, -768, -908, -769},
+{ -559, -788, -648, -788, -649},
+{ -729, -958, -818, -958, -819},
+{ -189, -418, -278, -418, -279}},
+/* UA.UG..UA */
+{{ -50, -279, -139, -279, -140},
+{ -939,-1168,-1028,-1168,-1029},
+{ -249, -478, -338, -478, -339},
+{ -939,-1168,-1028,-1168,-1029},
+{ -329, -558, -418, -558, -419}},
+/* UA.UU..UA */
+{{ -50, -279, -139, -279, -140},
+{ -639, -868, -728, -868, -729},
+{ -229, -458, -318, -458, -319},
+{ -729, -958, -818, -958, -819},
+{ -190, -419, -279, -419, -280}}}},
+/* UA.@@.. @ */
+{{{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@A.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@C.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@G.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}},
+/* UA.@U.. @ */
+{{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50},
+{ -50, -50, -50, -50, -50}}},
+/* UA.A@.. @ */
+{{{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AA.. @ */
+{{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AC.. @ */
+{{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AG.. @ */
+{{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}},
+/* UA.AU.. @ */
+{{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639},
+{ -100, -449, -679, -939, -639}}},
+/* UA.C@.. @ */
+{{{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CA.. @ */
+{{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CC.. @ */
+{{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CG.. @ */
+{{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}},
+/* UA.CU.. @ */
+{{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229},
+{ -100, -479, -559, -249, -229}}},
+/* UA.G@.. @ */
+{{{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GA.. @ */
+{{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GC.. @ */
+{{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GG.. @ */
+{{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}},
+/* UA.GU.. @ */
+{{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729},
+{ -100, -429, -729, -939, -729}}},
+/* UA.U@.. @ */
+{{{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UA.. @ */
+{{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UC.. @ */
+{{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UG.. @ */
+{{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}},
+/* UA.UU.. @ */
+{{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190},
+{ -100, -329, -189, -329, -190}}}}},
+{ /* noPair */ {{{{0}}}},
+/* @.@@..CG */
+{{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@A..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.@C..CG */
+{{ -50, -50, -50, -50, -50},
+{ -999, -999, -999, -999, -999},
+{ -499, -499, -499, -499, -499},
+{ -989, -989, -989, -989, -989},
+{ -789, -789, -789, -789, -789}},
+/* @.@G..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.@U..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -719, -719, -719, -719, -719},
+{ -989, -989, -989, -989, -989},
+{ -909, -909, -909, -909, -909}}},
+/* @.A@..CG */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AA..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.AC..CG */
+{{ -50, -50, -50, -50, -50},
+{ -999, -999, -999, -999, -999},
+{ -499, -499, -499, -499, -499},
+{ -989, -989, -989, -989, -989},
+{ -789, -789, -789, -789, -789}},
+/* @.AG..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.AU..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -719, -719, -719, -719, -719},
+{ -989, -989, -989, -989, -989},
+{ -909, -909, -909, -909, -909}}},
+/* @.C@..CG */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CA..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.CC..CG */
+{{ -50, -50, -50, -50, -50},
+{ -999, -999, -999, -999, -999},
+{ -499, -499, -499, -499, -499},
+{ -989, -989, -989, -989, -989},
+{ -789, -789, -789, -789, -789}},
+/* @.CG..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.CU..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -719, -719, -719, -719, -719},
+{ -989, -989, -989, -989, -989},
+{ -909, -909, -909, -909, -909}}},
+/* @.G@..CG */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GA..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.GC..CG */
+{{ -50, -50, -50, -50, -50},
+{ -999, -999, -999, -999, -999},
+{ -499, -499, -499, -499, -499},
+{ -989, -989, -989, -989, -989},
+{ -789, -789, -789, -789, -789}},
+/* @.GG..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.GU..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -719, -719, -719, -719, -719},
+{ -989, -989, -989, -989, -989},
+{ -909, -909, -909, -909, -909}}},
+/* @.U@..CG */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UA..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.UC..CG */
+{{ -50, -50, -50, -50, -50},
+{ -999, -999, -999, -999, -999},
+{ -499, -499, -499, -499, -499},
+{ -989, -989, -989, -989, -989},
+{ -789, -789, -789, -789, -789}},
+/* @.UG..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -569, -569, -569, -569, -569},
+{ -989, -989, -989, -989, -989},
+{ -859, -859, -859, -859, -859}},
+/* @.UU..CG */
+{{ -50, -50, -50, -50, -50},
+{-1079,-1079,-1079,-1079,-1079},
+{ -719, -719, -719, -719, -719},
+{ -989, -989, -989, -989, -989},
+{ -909, -909, -909, -909, -909}}}},
+/* @.@@..GC */
+{{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@A..GC */
+{{ -50, -50, -50, -50, -50},
+{ -569, -569, -569, -569, -569},
+{ -769, -769, -769, -769, -769},
+{ -759, -759, -759, -759, -759},
+{ -549, -549, -549, -549, -549}},
+/* @.@C..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -359, -359, -359, -359, -359},
+{ -789, -789, -789, -789, -789},
+{ -549, -549, -549, -549, -549}},
+/* @.@G..GC */
+{{ -50, -50, -50, -50, -50},
+{ -609, -609, -609, -609, -609},
+{ -359, -359, -359, -359, -359},
+{ -669, -669, -669, -669, -669},
+{ -549, -549, -549, -549, -549}},
+/* @.@U..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -439, -439, -439, -439, -439},
+{ -789, -789, -789, -789, -789},
+{ -619, -619, -619, -619, -619}}},
+/* @.A@..GC */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AA..GC */
+{{ -50, -50, -50, -50, -50},
+{ -569, -569, -569, -569, -569},
+{ -769, -769, -769, -769, -769},
+{ -759, -759, -759, -759, -759},
+{ -549, -549, -549, -549, -549}},
+/* @.AC..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -359, -359, -359, -359, -359},
+{ -789, -789, -789, -789, -789},
+{ -549, -549, -549, -549, -549}},
+/* @.AG..GC */
+{{ -50, -50, -50, -50, -50},
+{ -609, -609, -609, -609, -609},
+{ -359, -359, -359, -359, -359},
+{ -669, -669, -669, -669, -669},
+{ -549, -549, -549, -549, -549}},
+/* @.AU..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -439, -439, -439, -439, -439},
+{ -789, -789, -789, -789, -789},
+{ -619, -619, -619, -619, -619}}},
+/* @.C@..GC */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CA..GC */
+{{ -50, -50, -50, -50, -50},
+{ -569, -569, -569, -569, -569},
+{ -769, -769, -769, -769, -769},
+{ -759, -759, -759, -759, -759},
+{ -549, -549, -549, -549, -549}},
+/* @.CC..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -359, -359, -359, -359, -359},
+{ -789, -789, -789, -789, -789},
+{ -549, -549, -549, -549, -549}},
+/* @.CG..GC */
+{{ -50, -50, -50, -50, -50},
+{ -609, -609, -609, -609, -609},
+{ -359, -359, -359, -359, -359},
+{ -669, -669, -669, -669, -669},
+{ -549, -549, -549, -549, -549}},
+/* @.CU..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -439, -439, -439, -439, -439},
+{ -789, -789, -789, -789, -789},
+{ -619, -619, -619, -619, -619}}},
+/* @.G@..GC */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GA..GC */
+{{ -50, -50, -50, -50, -50},
+{ -569, -569, -569, -569, -569},
+{ -769, -769, -769, -769, -769},
+{ -759, -759, -759, -759, -759},
+{ -549, -549, -549, -549, -549}},
+/* @.GC..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -359, -359, -359, -359, -359},
+{ -789, -789, -789, -789, -789},
+{ -549, -549, -549, -549, -549}},
+/* @.GG..GC */
+{{ -50, -50, -50, -50, -50},
+{ -609, -609, -609, -609, -609},
+{ -359, -359, -359, -359, -359},
+{ -669, -669, -669, -669, -669},
+{ -549, -549, -549, -549, -549}},
+/* @.GU..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -439, -439, -439, -439, -439},
+{ -789, -789, -789, -789, -789},
+{ -619, -619, -619, -619, -619}}},
+/* @.U@..GC */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UA..GC */
+{{ -50, -50, -50, -50, -50},
+{ -569, -569, -569, -569, -569},
+{ -769, -769, -769, -769, -769},
+{ -759, -759, -759, -759, -759},
+{ -549, -549, -549, -549, -549}},
+/* @.UC..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -359, -359, -359, -359, -359},
+{ -789, -789, -789, -789, -789},
+{ -549, -549, -549, -549, -549}},
+/* @.UG..GC */
+{{ -50, -50, -50, -50, -50},
+{ -609, -609, -609, -609, -609},
+{ -359, -359, -359, -359, -359},
+{ -669, -669, -669, -669, -669},
+{ -549, -549, -549, -549, -549}},
+/* @.UU..GC */
+{{ -50, -50, -50, -50, -50},
+{ -929, -929, -929, -929, -929},
+{ -439, -439, -439, -439, -439},
+{ -789, -789, -789, -789, -789},
+{ -619, -619, -619, -619, -619}}}},
+/* @.@@..GU */
+{{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@A..GU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.@C..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.@G..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.@U..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}},
+/* @.A@..GU */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AA..GU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.AC..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.AG..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.AU..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}},
+/* @.C@..GU */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CA..GU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.CC..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.CG..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.CU..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}},
+/* @.G@..GU */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GA..GU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.GC..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.GG..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.GU..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}},
+/* @.U@..GU */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UA..GU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.UC..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.UG..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.UU..GU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}}},
+/* @.@@..UG */
+{{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@A..UG */
+{{ -50, -50, -50, -50, -50},
+{ -769, -769, -769, -769, -769},
+{ -529, -529, -529, -529, -529},
+{ -709, -709, -709, -709, -709},
+{ -599, -599, -599, -599, -599}},
+/* @.@C..UG */
+{{ -50, -50, -50, -50, -50},
+{ -839, -839, -839, -839, -839},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -489, -489, -489, -489, -489}},
+/* @.@G..UG */
+{{ -50, -50, -50, -50, -50},
+{-1009,-1009,-1009,-1009,-1009},
+{ -409, -409, -409, -409, -409},
+{ -969, -969, -969, -969, -969},
+{ -599, -599, -599, -599, -599}},
+/* @.@U..UG */
+{{ -50, -50, -50, -50, -50},
+{ -859, -859, -859, -859, -859},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -409, -409, -409, -409, -409}}},
+/* @.A@..UG */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AA..UG */
+{{ -50, -50, -50, -50, -50},
+{ -769, -769, -769, -769, -769},
+{ -529, -529, -529, -529, -529},
+{ -709, -709, -709, -709, -709},
+{ -599, -599, -599, -599, -599}},
+/* @.AC..UG */
+{{ -50, -50, -50, -50, -50},
+{ -839, -839, -839, -839, -839},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -489, -489, -489, -489, -489}},
+/* @.AG..UG */
+{{ -50, -50, -50, -50, -50},
+{-1009,-1009,-1009,-1009,-1009},
+{ -409, -409, -409, -409, -409},
+{ -969, -969, -969, -969, -969},
+{ -599, -599, -599, -599, -599}},
+/* @.AU..UG */
+{{ -50, -50, -50, -50, -50},
+{ -859, -859, -859, -859, -859},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -409, -409, -409, -409, -409}}},
+/* @.C@..UG */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CA..UG */
+{{ -50, -50, -50, -50, -50},
+{ -769, -769, -769, -769, -769},
+{ -529, -529, -529, -529, -529},
+{ -709, -709, -709, -709, -709},
+{ -599, -599, -599, -599, -599}},
+/* @.CC..UG */
+{{ -50, -50, -50, -50, -50},
+{ -839, -839, -839, -839, -839},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -489, -489, -489, -489, -489}},
+/* @.CG..UG */
+{{ -50, -50, -50, -50, -50},
+{-1009,-1009,-1009,-1009,-1009},
+{ -409, -409, -409, -409, -409},
+{ -969, -969, -969, -969, -969},
+{ -599, -599, -599, -599, -599}},
+/* @.CU..UG */
+{{ -50, -50, -50, -50, -50},
+{ -859, -859, -859, -859, -859},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -409, -409, -409, -409, -409}}},
+/* @.G@..UG */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GA..UG */
+{{ -50, -50, -50, -50, -50},
+{ -769, -769, -769, -769, -769},
+{ -529, -529, -529, -529, -529},
+{ -709, -709, -709, -709, -709},
+{ -599, -599, -599, -599, -599}},
+/* @.GC..UG */
+{{ -50, -50, -50, -50, -50},
+{ -839, -839, -839, -839, -839},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -489, -489, -489, -489, -489}},
+/* @.GG..UG */
+{{ -50, -50, -50, -50, -50},
+{-1009,-1009,-1009,-1009,-1009},
+{ -409, -409, -409, -409, -409},
+{ -969, -969, -969, -969, -969},
+{ -599, -599, -599, -599, -599}},
+/* @.GU..UG */
+{{ -50, -50, -50, -50, -50},
+{ -859, -859, -859, -859, -859},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -409, -409, -409, -409, -409}}},
+/* @.U@..UG */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UA..UG */
+{{ -50, -50, -50, -50, -50},
+{ -769, -769, -769, -769, -769},
+{ -529, -529, -529, -529, -529},
+{ -709, -709, -709, -709, -709},
+{ -599, -599, -599, -599, -599}},
+/* @.UC..UG */
+{{ -50, -50, -50, -50, -50},
+{ -839, -839, -839, -839, -839},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -489, -489, -489, -489, -489}},
+/* @.UG..UG */
+{{ -50, -50, -50, -50, -50},
+{-1009,-1009,-1009,-1009,-1009},
+{ -409, -409, -409, -409, -409},
+{ -969, -969, -969, -969, -969},
+{ -599, -599, -599, -599, -599}},
+/* @.UU..UG */
+{{ -50, -50, -50, -50, -50},
+{ -859, -859, -859, -859, -859},
+{ -529, -529, -529, -529, -529},
+{ -859, -859, -859, -859, -859},
+{ -409, -409, -409, -409, -409}}}},
+/* @.@@..AU */
+{{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@A..AU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.@C..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.@G..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.@U..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}},
+/* @.A@..AU */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AA..AU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.AC..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.AG..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.AU..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}},
+/* @.C@..AU */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CA..AU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.CC..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.CG..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.CU..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}},
+/* @.G@..AU */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GA..AU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.GC..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.GG..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.GU..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}},
+/* @.U@..AU */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UA..AU */
+{{ -50, -50, -50, -50, -50},
+{ -479, -479, -479, -479, -479},
+{ -309, -309, -309, -309, -309},
+{ -389, -389, -389, -389, -389},
+{ -379, -379, -379, -379, -379}},
+/* @.UC..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.UG..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}},
+/* @.UU..AU */
+{{ -50, -50, -50, -50, -50},
+{ -649, -649, -649, -649, -649},
+{ -289, -289, -289, -289, -289},
+{ -739, -739, -739, -739, -739},
+{ -379, -379, -379, -379, -379}}}},
+/* @.@@..UA */
+{{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@A..UA */
+{{ -50, -50, -50, -50, -50},
+{ -449, -449, -449, -449, -449},
+{ -479, -479, -479, -479, -479},
+{ -429, -429, -429, -429, -429},
+{ -329, -329, -329, -329, -329}},
+/* @.@C..UA */
+{{ -50, -50, -50, -50, -50},
+{ -679, -679, -679, -679, -679},
+{ -559, -559, -559, -559, -559},
+{ -729, -729, -729, -729, -729},
+{ -189, -189, -189, -189, -189}},
+/* @.@G..UA */
+{{ -50, -50, -50, -50, -50},
+{ -939, -939, -939, -939, -939},
+{ -249, -249, -249, -249, -249},
+{ -939, -939, -939, -939, -939},
+{ -329, -329, -329, -329, -329}},
+/* @.@U..UA */
+{{ -50, -50, -50, -50, -50},
+{ -639, -639, -639, -639, -639},
+{ -229, -229, -229, -229, -229},
+{ -729, -729, -729, -729, -729},
+{ -190, -190, -190, -190, -190}}},
+/* @.A@..UA */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AA..UA */
+{{ -50, -50, -50, -50, -50},
+{ -449, -449, -449, -449, -449},
+{ -479, -479, -479, -479, -479},
+{ -429, -429, -429, -429, -429},
+{ -329, -329, -329, -329, -329}},
+/* @.AC..UA */
+{{ -50, -50, -50, -50, -50},
+{ -679, -679, -679, -679, -679},
+{ -559, -559, -559, -559, -559},
+{ -729, -729, -729, -729, -729},
+{ -189, -189, -189, -189, -189}},
+/* @.AG..UA */
+{{ -50, -50, -50, -50, -50},
+{ -939, -939, -939, -939, -939},
+{ -249, -249, -249, -249, -249},
+{ -939, -939, -939, -939, -939},
+{ -329, -329, -329, -329, -329}},
+/* @.AU..UA */
+{{ -50, -50, -50, -50, -50},
+{ -639, -639, -639, -639, -639},
+{ -229, -229, -229, -229, -229},
+{ -729, -729, -729, -729, -729},
+{ -190, -190, -190, -190, -190}}},
+/* @.C@..UA */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CA..UA */
+{{ -50, -50, -50, -50, -50},
+{ -449, -449, -449, -449, -449},
+{ -479, -479, -479, -479, -479},
+{ -429, -429, -429, -429, -429},
+{ -329, -329, -329, -329, -329}},
+/* @.CC..UA */
+{{ -50, -50, -50, -50, -50},
+{ -679, -679, -679, -679, -679},
+{ -559, -559, -559, -559, -559},
+{ -729, -729, -729, -729, -729},
+{ -189, -189, -189, -189, -189}},
+/* @.CG..UA */
+{{ -50, -50, -50, -50, -50},
+{ -939, -939, -939, -939, -939},
+{ -249, -249, -249, -249, -249},
+{ -939, -939, -939, -939, -939},
+{ -329, -329, -329, -329, -329}},
+/* @.CU..UA */
+{{ -50, -50, -50, -50, -50},
+{ -639, -639, -639, -639, -639},
+{ -229, -229, -229, -229, -229},
+{ -729, -729, -729, -729, -729},
+{ -190, -190, -190, -190, -190}}},
+/* @.G@..UA */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GA..UA */
+{{ -50, -50, -50, -50, -50},
+{ -449, -449, -449, -449, -449},
+{ -479, -479, -479, -479, -479},
+{ -429, -429, -429, -429, -429},
+{ -329, -329, -329, -329, -329}},
+/* @.GC..UA */
+{{ -50, -50, -50, -50, -50},
+{ -679, -679, -679, -679, -679},
+{ -559, -559, -559, -559, -559},
+{ -729, -729, -729, -729, -729},
+{ -189, -189, -189, -189, -189}},
+/* @.GG..UA */
+{{ -50, -50, -50, -50, -50},
+{ -939, -939, -939, -939, -939},
+{ -249, -249, -249, -249, -249},
+{ -939, -939, -939, -939, -939},
+{ -329, -329, -329, -329, -329}},
+/* @.GU..UA */
+{{ -50, -50, -50, -50, -50},
+{ -639, -639, -639, -639, -639},
+{ -229, -229, -229, -229, -229},
+{ -729, -729, -729, -729, -729},
+{ -190, -190, -190, -190, -190}}},
+/* @.U@..UA */
+{{{ -50, -50, -50, -50, -50},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UA..UA */
+{{ -50, -50, -50, -50, -50},
+{ -449, -449, -449, -449, -449},
+{ -479, -479, -479, -479, -479},
+{ -429, -429, -429, -429, -429},
+{ -329, -329, -329, -329, -329}},
+/* @.UC..UA */
+{{ -50, -50, -50, -50, -50},
+{ -679, -679, -679, -679, -679},
+{ -559, -559, -559, -559, -559},
+{ -729, -729, -729, -729, -729},
+{ -189, -189, -189, -189, -189}},
+/* @.UG..UA */
+{{ -50, -50, -50, -50, -50},
+{ -939, -939, -939, -939, -939},
+{ -249, -249, -249, -249, -249},
+{ -939, -939, -939, -939, -939},
+{ -329, -329, -329, -329, -329}},
+/* @.UU..UA */
+{{ -50, -50, -50, -50, -50},
+{ -639, -639, -639, -639, -639},
+{ -229, -229, -229, -229, -229},
+{ -729, -729, -729, -729, -729},
+{ -190, -190, -190, -190, -190}}}},
+/* @.@@.. @ */
+{{{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@A.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@C.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@G.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.@U.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}}},
+/* @.A@.. @ */
+{{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AA.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AC.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AG.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.AU.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}}},
+/* @.C@.. @ */
+{{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CA.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CC.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CG.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.CU.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}}},
+/* @.G@.. @ */
+{{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GA.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GC.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GG.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.GU.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}}},
+/* @.U@.. @ */
+{{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UA.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UC.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UG.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}},
+/* @.UU.. @ */
+{{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100},
+{ -100, -100, -100, -100, -100}}}}}};
+
+int
+energy_param::
+getMaxNinio()
+{ return MAX_NINIO; }
+
+int
+energy_param::
+getNinio(int i)
+{ return F_ninio37[i]; }
+
+int
+energy_param::getDangle5(int i, int j)
+{ return dangle5_37[convertPairType(i)][convertBaseType(j)]; }
+
+int
+energy_param::
+getDangle3(int i, int j)
+{ return dangle3_37[convertPairType(i)][convertBaseType(j)]; }
+
+int
+energy_param::
+getHairpin(int i)
+{ return hairpin37[i]; }
+
+int
+energy_param::
+getInternalLoop(int i)
+{ return internal_loop37[i]; }
+
+int
+energy_param::getBulge(int i)
+{ return bulge37[i]; }
+
+const char
+*energy_param::
+getTetraLoop(int i)
+{ return Tetrastrings[i]; }
+
+int
+energy_param::
+getTetraLoopEnergy(int i)
+{ return TETRA_ENERGY37[i]; }
+
+int
+energy_param::
+getStack(int i, int j)
+{ return stack37[convertPairType(i)][convertPairType(j)]; }
+
+int
+energy_param::
+getTstackH(int i, int j)
+{ return mismatchH37[convertPairType(i)][convertLeftType(j)][convertRightType(j)]; }
+
+int
+energy_param::
+getTstackI(int i, int j)
+{ return mismatchI37[convertPairType(i)][convertLeftType(j)][convertRightType(j)]; }
+
+int
+energy_param::
+getInt11(int i, int j, int k)
+{ return int11_37[convertPairType(i)][convertPairType(j)][convertLeftType(k)][convertRightType(k)]; }
+
+int
+energy_param::
+getInt21(int i, int j, int k, int l)
+{ return int21_37[convertPairType(i)][convertPairType(j)][convertLeftType(k)][convertBaseType(l)][convertRightType(k)]; }
+
+int
+energy_param::
+getInt22(int i, int j, int k, int l)
+{ return int22_37[convertPairType(i)][convertPairType(j)][convertLeftType(k)][convertLeftType(l)][convertRightType(l)][convertRightType(k)]; }
+
+int
+energy_param::
+getMLintern()
+{ return ML_intern37; }
+
+int
+energy_param::
+getMLBase()
+{ return ML_BASE37; }
+
+int
+energy_param::
+getMLclosing()
+{ return ML_closing37; }
+
+int
+energy_param::
+getTerminalAU()
+{ return TerminalAU; }
+
+/*
+ 1 C<->G 1
+ 2 G<->C 2
+ 3 G<->U 3
+ 5 U<->G 4
+ 0 A<->U 5
+ 4 U<->A 6
+ 6 0
+ */
+int
+energy_param::
+convertPairType(int type)
+{
+ if (type == 0) return 5;
+ else if(type == 1) return 1;
+ else if(type == 2) return 2;
+ else if(type == 3) return 3;
+ else if(type == 4) return 6;
+ else if(type == 5) return 4;
+ else if(type == 6) return 0;
+ else { cerr << "error convertPairType" << endl; exit(1); }
+}
+
+/*
+ 0 A 1
+ 1 C 2
+ 2 G 3
+ 3 U 4
+ */
+int
+energy_param::
+convertBaseType(int type)
+{
+ if (type == 0) return 1;
+ else if(type == 1) return 2;
+ else if(type == 2) return 3;
+ else if(type == 3) return 4;
+ else { cerr << "error convertBaseType" << endl; exit(1); }
+}
+
+/*
+ A<->A 0
+ A<->C 1
+ A<->G 2
+ A<->U 3
+ C<->A 4
+ C<->C 5
+ C<->G 6
+ C<->U 7
+ G<->A 8
+ G<->C 9
+ G<->G 10
+ G<->U 11
+ U<->A 12
+ U<->C 13
+ U<->G 14
+ U<->U 15
+ */
+int
+energy_param::
+convertLeftType(int type)
+{
+ if (0 <= type && type <= 3 ) { return 1; }
+ else if(4 <= type && type <= 7 ) { return 2; }
+ else if(8 <= type && type <= 11) { return 3; }
+ else if(12<= type && type <= 15) { return 4; }
+ else { cerr << "convertLeftType" << endl; exit(1); }
+}
+
+int
+energy_param::
+convertRightType(int type)
+{
+ if (type % 4 == 0) { return 1; }
+ else if(type % 4 == 1) { return 2; }
+ else if(type % 4 == 2) { return 3; }
+ else if(type % 4 == 3) { return 4; }
+ else { cerr << "convertRightType" << endl; exit(1); }
+}
+}
--- /dev/null
+/*
+ Current free energy parameters are summarized in:
+
+ D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner
+ "Expanded sequence dependence of thermodynamic parameters improves
+ prediction of RNA secondary structure"
+ JMB, 288, pp 911-940, 1999
+
+ Enthalpies taken from:
+
+ A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker
+ "Coaxial stckaing of helices enhances binding of oligoribonucleotides.."
+ PNAS, 91, pp 9218-9222, 1994
+
+ D.H. Turner, N. Sugimoto, and S.M. Freier.
+ "RNA Structure Prediction",
+ Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988.
+
+ John A.Jaeger, Douglas H.Turner, and Michael Zuker.
+ "Improved predictions of secondary structures for RNA",
+ PNAS, 86, 7706-7710, October 1989.
+
+ L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner
+ "Nearest-Neughbor Parameters for GU Mismatches...."
+ Biochemistry 1991, 30 11124-11132
+
+ A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner
+ "Thermodynamic Study of Internal Loops in Oligoribonucleotides..."
+ Biochemistry 1991, 30, 6428--6435
+
+
+*/
+
+#ifndef ENERGY_PARAM_H
+#define ENERGY_PARAM_H
+
+#include <iostream>
+#include <cstdlib> // by katoh
+
+using namespace std;
+namespace MXSCARNA {
+class energy_param {
+
+ static const int INF;
+ static const int NST;
+ static const int DEF;
+
+ static const double lxc37; /* parameter for logarithmic loop
+ energy extrapolation */
+ static const int stack37[8][8];
+ static const int enthalpies[8][8];
+ static const int oldhairpin37[31];
+ static const int hairpin37[31];
+ static const int oldbulge37[31];
+ static const int bulge37[31];
+ static const int oldinternal_loop37[31];
+ static const int internal_loop37[31];
+ static const int mismatchI37[8][5][5];
+ static const int mismatchH37[8][5][5];
+ static const int mism_H[8][5][5];
+ static const int dangle5_37[8][5];
+ static const int dangle3_37[8][5];
+ static const int dangle3_H[8][5];
+ static const int dangle5_H[8][5];
+ static const int ML_BASE37;
+ static const int ML_closing37;
+ static const int ML_intern37;
+ static const int MAX_NINIO;
+ static const int F_ninio37[5];
+ static const char Tetraloops[1400];
+ static const char Tetrastrings[30][7];
+ static const int TETRA_ENERGY37[200];
+ static const int TETRA_ENTH37;
+ static const int TerminalAU;
+ static const int DuplexInit;
+
+ static const int int11_37[8][8][5][5];
+ static const int int11_H[8][8][5][5];
+ static const int int21_37[8][8][5][5][5];
+ static const int int21_H[8][8][5][5][5];
+ static const int int22_37[8][8][5][5][5][5];
+ static const int int22_H[8][8][5][5][5][5];
+
+ int convertPairType(int type);
+ int convertBaseType(int type);
+ int convertLeftType(int type);
+ int convertRightType(int type);
+
+ public:
+ int getMaxNinio();
+ int getNinio(int i);
+ int getDangle5(int i, int j);
+ int getDangle3(int i, int j);
+ int getHairpin(int i);
+ int getInternalLoop(int i);
+ int getBulge(int i);
+ const char *getTetraLoop(int i);
+ int getTetraLoopEnergy(int i);
+ int getStack(int i, int j);
+ int getTstackH(int i, int j);
+ int getTstackI(int i, int j);
+ int getInt11(int i, int j, int k);
+ int getInt21(int i, int j, int k, int l);
+ int getInt22(int i, int j, int k, int l);
+ int getMLintern();
+ int getMLBase();
+ int getMLclosing();
+ int getTerminalAU();
+};
+}
+#endif
--- /dev/null
+#include "energy_const.h"
+typedef struct {
+ int id;
+ int stack[NBPAIRS+1][NBPAIRS+1];
+ int hairpin[31];
+ int bulge[MAXLOOP+1];
+ int internal_loop[MAXLOOP+1];
+ int mismatchI[NBPAIRS+1][5][5];
+ int mismatchH[NBPAIRS+1][5][5];
+ int mismatchM[NBPAIRS+1][5][5];
+ int dangle5[NBPAIRS+1][5];
+ int dangle3[NBPAIRS+1][5];
+ int int11[NBPAIRS+1][NBPAIRS+1][5][5];
+ int int21[NBPAIRS+1][NBPAIRS+1][5][5][5];
+ int int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
+ int F_ninio[5];
+ double lxc;
+ int MLbase;
+ int MLintern[NBPAIRS+1];
+ int MLclosing;
+ int TerminalAU;
+ int DuplexInit;
+ int TETRA_ENERGY[200];
+ char Tetraloops[1401];
+ int Triloop_E[40];
+ char Triloops[241];
+ double temperature;
+} paramT;
+
+extern paramT *scale_parameters(void);
+extern paramT *copy_parameters(void);
+extern paramT *set_parameters(paramT *dest);
--- /dev/null
+progs="_PROGS"
+for prog in $progs; do
+ printf $prog" "
+done
+
+
+make clean
+make CC="gcc-4.0" CFLAGS="-arch ppc64 -m64 -O3 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4" CXX="g++-4.0" CXXFLAGS="-arch ppc64 -m64 -O3 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4"
+for prog in $progs; do
+ mv $prog $prog.ppc64
+done
+
+make clean
+make CC="gcc-4.0" CFLAGS="-arch ppc -m32 -O3 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4" CXX="g++-4.0" CXXFLAGS="-arch ppc -m32 -O3 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4"
+for prog in $progs; do
+ mv $prog $prog.ppc32
+done
+
+make clean
+make CC="gcc-4.0" CFLAGS="-arch x86_64 -fast -m64 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4" CXX="g++-4.0" CXXFLAGS="-arch x86_64 -fast -m64 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4"
+for prog in $progs; do
+ mv $prog $prog.intel64
+done
+
+make clean
+make CC="gcc-4.0" CFLAGS="-arch i386 -fast -m32 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4" CXX="g++-4.0" CXXFLAGS="-arch i386 -fast -m32 -mmacosx-version-min=10.4 -isysroot/Developer/SDKs/MacOSX10.4u.sdk -DMACOSX_DEPLOYMENT_TARGET=10.4"
+for prog in $progs; do
+ mv $prog $prog.intel32
+done
+
+set $progs
+for prog in $progs; do
+# lipo -create $prog.icc $prog.ppc32 $prog.ppc64 -output $prog
+ lipo -create $prog.intel64 $prog.intel32 $prog.ppc32 $prog.ppc64 -output $prog
+ cp $prog ../binaries
+done
--- /dev/null
+============================================================
+
+If you have the './extensions' directory, please also see
+license.extensions file.
+
+============================================================
+
+The codes in the './core' directory is distributed with
+the BSD license.
+
+MAFFT: multiple sequence alignment program
+Copyright (c) 2009 Kazutaka Katoh
+
+Redistribution and use in source and binary forms,
+with or without modification, are permitted provided
+that the following conditions are met:
+
+Redistributions of source code must retain the
+above copyright notice, this list of conditions
+and the following disclaimer. Redistributions in
+binary form must reproduce the above copyright
+notice, this list of conditions and the following
+disclaimer in the documentation and/or other
+materials provided with the distribution.
+
+The name of the author may not be used to endorse
+or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
+OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
+AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+OF SUCH DAMAGE.
+---------------------------------------------------------------------------------
+
+
+
--- /dev/null
+The 'extension' directory contains codes from
+
+(1) the Vienna RNA package
+(2) MXSCARNA
+(3) ProbConsRNA
+
+These packages are distributed under different licenses:
+
+-------------------------------------------------------------------------------
+(1) The Vienna RNA package
+
+See ./extensions/mxscarna_src/vienna/COPYING and http://www.tbi.univie.ac.at/~ivo/RNA/
+
+ Disclaimer and Copyright
+
+The programs, library and source code of the Vienna RNA Package are free
+software. They are distributed in the hope that they will be useful
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+Permission is granted for research, educational, and commercial use
+and modification so long as 1) the package and any derived works are not
+redistributed for any fee, other than media costs, 2) proper credit is
+given to the authors and the Institute for Theoretical Chemistry of the
+University of Vienna.
+
+If you want to include this software in a commercial product, please contact
+the authors.
+
+Reference:
+ Ivo L Hofacker and Martin Fekete and Peter F Stadler
+ Secondary structure prediction for aligned RNA sequences.
+ J Mol Biol. 2002 vol. 319 (18) pp.3724-32
+
+-------------------------------------------------------------------------------
+(2) MXSCARNA
+
+See ./extensions/mxscarna_src/README and http://www.ncrna.org/software/mxscarna/
+
+* Author
+ Yasuo Tabei
+
+ Department of Computational Biology,
+ Graduate School of Frontier Science,
+ The University of Tokyo
+ and
+ Computational Biology Research Center (CBRC),
+ National Institute of Advanced Industrial Science and Technology (AIST)
+
+ E-mail: scarna AT m.aist.go.jp
+
+* What is MXSCARNA
+ MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a tool for
+ fast structural multiple alignment of RNA sequences using progressive
+ alignment based on pairwise structural alignment algorithm of SCARNA.
+
+* License
+ While its original source code is provided as free software, MXSCARNA
+ contains the source codes of ProbCons and Rfold and the energy parameters
+ of Vienna RNA package (version 1.5).
+ The author thanks Dr. Chuong Do, Dr. Hisanori Kiryu and Dr. Ivo Hofacker,
+ the authors of ProbCons, Rfold and Vienna RNA package respectively,
+ and Institute for Theoretical Chemistry of the University of Vienna.
+
+ The source code of Rfold is located in ./extensions/mxscarna_src/rfold-0.1, which includes
+ energy parameters of Vienna RNA package in ./extensions/mxscarna_src/rfold-0.1/src/vienna.
+ Energy parameters of Vienna RNA package are also included in the source
+ code of MXSCARNA (./extensions/mxscarna_src/vienna). Please follow ./extensions/mxscarna_src/rfold-0.1/readme.txt
+ file, which describes the license of Rfold, and
+ ./extensions/mxscarna_src/rfold-0.1/src/vienna/COPYING file and ./extensions/mxscarna_src/vienna/COPYING file,
+ which describe the copyright notice of the Vienna RNA package.
+ The source code of ProbCons is located in ./extensions/mxscarna_src/probconsRNA. Please follow
+ ./extensions/mxscarna_src/probcons/README.
+
+ The original part of MXSCARNA is provided as free software. It is
+ distributed in the hope that it will be useful but WITHOUT ANY WARRANTY;
+ without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE.
+
+ Permission is granted for research, educational, and commercial use
+ and modification so long as
+ 1) the package and any derived works are not redistributed for any fee,
+ other than media costs,
+ 2) proper credit is given to
+ the authors of MXSCARNA, ProbCons, Rfold and Vienna RNA package,
+ the Univeristy of Tokyo,
+ Computational Biology Research Center (CBRC), AIST
+ and Institute for Theoretical Chemistry of the University of Vienna.
+
+ If you want to include this software in a commercial product, please
+ contact the author.
+
+* Citation
+ Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
+ A fast structural multiple alignment method for long RNA sequences.
+ BMC bioinformatics 9:33 (2008)
+
+---------------------------------------------------------------------------------
+(3) ProbCons
+
+See ./extensions/mxscarna_src/probconsRNA/README and http://probcons.stanford.edu/
+
+* Author
+ Chuong Do
+
+* License
+PROBCONS has been made freely available as PUBLIC DOMAIN
+software and hence is not subject to copyright in the United
+States. This system and/or any portion of the source code
+may be used, modified, or redistributed without restrictions.
+PROBCONS is distributed WITHOUT WARRANTY, express or implied.
+The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
+loss due to reliance on the program.
+
+* Citation
+Do CB, Mahabhashyam MS, Brudno M, Batzoglou S.
+ProbCons: Probabilistic consistency-based multiple sequence alignment.
+Genome Res. 2005 15:330-40.
+
+-------------------------------------------------------------------------------
--- /dev/null
+-----------------------------------------------------------------------
+ MAFFT: a multiple sequence alignment program
+ version 6.857beta, 2011/05/30
+
+ http://mafft.cbrc.jp/alignment/software/
+ kazutaka.katoh@aist.go.jp
+-----------------------------------------------------------------------
+
+1. COMPILE
+ % cd core
+ % make clean
+ % make
+ % cd ..
+
+ To enable multithreading (linux only),
+ % cd core
+ Uncomment line 8 of Makefile,
+ ENABLE_MULTITHREAD = -Denablemultithread
+ % make clean
+ % make
+ % cd ..
+
+ If you have the './extensions' directory, which is for RNA alignments,
+ % cd extensions
+ % make clean
+ % make
+ % cd ..
+
+
+2. INSTALL (select 2a or 2b [])
+2a. Install as root
+ # cd core
+ # make install
+ # cd ..
+
+ If you have the './extensions' directory,
+ # cd extensions
+ # make install
+ # cd ..
+
+ By this procedure (2a), programs are installed into
+ /usr/local/bin/. Some binaries, which are not directly
+ used by a user, are installed into /usr/local/libexec/mafft/.
+
+ If the MAFFT_BINARIES environment variable is set to /somewhare/else/,
+ the binaries in the /somewhere/else/ directory are used, instead
+ of those in /usr/local/libexec/mafft/.
+
+2b. Install without being root
+ % cd core/
+ Edit the first line of Makefile
+ From:
+ PREFIX = ${PKGDIR}/usr/local
+ To:
+ PREFIX = /home/your_home/somewhere
+
+ Edit the third line of Makefile
+ From:
+ BINDIR = $(PREFIX)/bin
+ To:
+ BINDIR = /home/your_home/bin
+ (or elsewhere in your command-search path)
+ % make clean
+ % make
+ % make install
+
+ If you have the './extensions' directory,
+ % cd ../extensions/
+ Edit the first line of Makefile
+ From:
+ PREFIX = ${PKGDIR}/usr/local
+ To:
+ PREFIX = /home/your_home/somewhere
+ % make clean
+ % make
+ % make install
+
+ The MAFFT_BINARIES environment variable *must not be* set.
+
+ If the MAFFT_BINARIES environment variable is set to /somewhare/else/,
+ it overrides the setting of PREFIX (/home/your_home/somewhere/ in the
+ above example) in Makefile.
+
+3. CHECK
+ % cd test
+ % rehash # if necessary
+ % mafft sample > test.fftns2 # FFT-NS-2
+ % mafft --maxiterate 100 sample > test.fftnsi # FFT-NS-i
+ % mafft --globalpair sample > test.gins1 # G-INS-1
+ % mafft --globalpair --maxiterate 100 sample > test.ginsi # G-INS-i
+ % mafft --localpair sample > test.lins1 # L-INS-1
+ % mafft --localpair --maxiterate 100 sample > test.linsi # L-INS-i
+ % diff test.fftns2 sample.fftns2
+ % diff test.fftnsi sample.fftnsi
+ % diff test.gins1 sample.gins1
+ % diff test.ginsi sample.ginsi
+ % diff test.lins1 sample.lins1
+
+ If you have the './extensions' directory,
+ % mafft-qinsi samplerna > test.qinsi # Q-INS-i
+ % mafft-xinsi samplerna > test.xinsi # X-INS-i
+ % diff test.qinsi samplerna.qinsi
+ % diff test.xinsi samplerna.xinsi
+
+ If you use the multithread version, the results of iterative refinement
+ methods (*-*-i) are not always identical. Try this test with the single-
+ thread mode (--thread 0).
+
+
+4. INPUT FORMAT
+ fasta format.
+
+ The type of input sequences (nucleotide or amino acid) is
+ automatically recognized based on the frequency of A, T, G, C, U and N.
+
+
+5. USAGE
+ % /usr/local/bin/mafft input > output
+
+See also http://mafft.cbrc.jp/alignment/software/
+
+
+6. UNINSTALL
+ # rm -r /usr/local/libexec/mafft
+ # rm /usr/local/bin/mafft
+ # rm /usr/local/bin/fftns
+ # rm /usr/local/bin/fftnsi
+ # rm /usr/local/bin/nwns
+ # rm /usr/local/bin/nwnsi
+ # rm /usr/local/bin/linsi
+ # rm /usr/local/bin/ginsi
+ # rm /usr/local/bin/mafft-*
+ # rm /usr/local/share/man/man1/mafft*
+
+
+7. LICENSE
+ See the './license' file.
+
+ If you have the extensions, see also the './license.extensions' file,
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF
+VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG
+GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP
+EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES
+ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL
+YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
+VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
+GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
+EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
+ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI
+YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL
+VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG
+GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP
+EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES
+ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL
+YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV
+VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP
+EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL
+YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI
+CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP
+EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL
+YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI
+LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL
+ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS
+RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA
+QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK
+ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL
+RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV
+TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL
+QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT
+QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP
+IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN
+> 8=opsin, greensensitive human (fragment) S07060
+DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP
+FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS
+YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
+PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+> 10== Z68193 1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFH
+PLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDDDDTTRGSVFTYTNTNNTRGPFEGPNYHIAPRWVYNLVSFFMI
+IVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVASTISVFNQIFGYFIL
+GHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNIKFDSKLAIIGIVFSWVWAW
+GWSAPPIFGWSRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQ
+VWMAIRAVAAQQKESESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAANPGYAFHP
+LAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLFGKKVDDGSEASTTSRTEVSSVSNS
+SVAPA
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MAAWEAAFAARRRHEEEDTTRDSVFTYTNSNNTRGPFEGPNYHIAPRWVYNLTSVWMIFV
+VAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGH
+PMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAW
+TAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVW
+LAIRAVAAQQKESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLA
+AALPAYFAKSATIYNPIIYVFMNRQFRNCILQLFGKKVDDGSEVSTSRTEVSSVSNSSVS
+PA
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+MSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYK
+KLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLW
+SLAILALERYVVVCKPLGDFQFQRRHAVSGCAFTWGWALLWSAPPLLGWSSYVPEGLRTS
+CGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAER
+EVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVF
+MNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPEARLSAETRLLGWNVPPEELRHIPEHWLTYPEPPESMNYL
+LGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVKTPIFIYNSFH
+QGYALGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEGKMTHGKAIAMIIFIY
+MYATPWVVACYTETWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYY
+YSQIVGHVFSHEKALRDQAKKMNVESLRSNVDKNKETAEIRIAKAAITICFLFFCSWTPY
+GVMSLIGAFGDKTLLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLALNE
+KAPESSAVASTSTTQEPQQTTAA
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVLGNVSSVLRPDARLSAESRLLGWNVPPDELRHIPEHWLIYPEPPESMNYLL
+GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIKTPIFIYNSFHQ
+GYALGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEGKMTHGKAIAMIIFIYL
+YATPWVVACYTESWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYYY
+SQIVGHVFSHEKALRDQAKKMNVDSLRSNVDKSKEAAEIRIAKAAITICFLFFASWTPYG
+VMSLIGAFGDKTLLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAISEK
+APESRAAISTSTTQEQQQTTAA
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+MEPLCNASEPPLRPEARSSGNGDLQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGVF
+YIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFNSFHRGFAIY
+LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYCT
+PWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFFFSFVCPTLMILYYYSQI
+VGHVFSHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMS
+LIGAFGDKSLLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGVNEKSGE
+ISSAQSTTTQEQQQTTAA
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MDALCNASEPPLRPEARMSSGSDELQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGV
+FYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFIYNSFHRGF
+ALGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYC
+TPWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFLFSFVVPTLMILYYYSQ
+IVGHVFNHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVM
+SLIGAFGDKSLLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGVNEKSG
+EASSAQSTTTQEQTQQTSAA
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI
+YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV
+WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV
+IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI
+SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET
+KSNDDSQSNSTVAQDKA
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+MANVTGPQMAFYGSGAATFGYPEGMTVADFVPDRVKHMVLDHWYNYPPVNPMWHYLLGVV
+YLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNFPPFCYNCFSGGR
+WMFSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGPKLTQGKATFMCGLAWV
+ISVGWSLPPFFGWGSYTLEGILDSCSYDYFTRDMNTITYNICIFIFDFFLPASVIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVTNLRSNEAETQRAEIRIAKTALVNVSLWFICWTPYAAI
+TIQGLLGNAEGITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCVHEKDP
+NDVEENQSSNTQTQEKS
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKMYVPEGNLTSC
+GIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSL
+RSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLFKFEGLTPLNTIWGACFAKS
+AACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDAQSQATASEAESKA
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSSIW
+CLAPAFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAA
+VSAHEKAMREQAKKMNVKSLRSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGL
+FKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDA
+QSQATASEAESKA
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MDSFAAVATQLGPQFAAPSNGSVVDKVTPDMAHLISPYWDQFPAMDPIWAKILTAYMIII
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSTIW
+CCLAPVFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIA
+AVSAHEKAMREQAKKMNVKSLRSSEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMG
+LFKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSE
+AQSQATTSEAESKA
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKIL
+GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFI
+WMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYS
+YWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYL
+VICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTD
+EPKPDAPASDTETTSEADSKA
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFEAQTGGNRSVLDNVLPDMAPLVNPHWSRFAPMDPTMSKIL
+GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIAFI
+WMMAVFWTIMPLIGWSSYVPEGNLTACSIDYMTRQWNPRSYLITYSLFVYYTPLFMICYS
+YWFIIATVAAHEKAMRDQAKKMNVKSLRSSEDCDKSAENKLAKVALTTISLWFMAWTPYL
+IICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVCGTTD
+EPKPDAPPSDTETTSEAESKD
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG
+MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL
+GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL
+GWTIAPMFGWNRYVPEGNMTACGTDYFNRGLLSASYLVCYGIWVYFVPLFLIIYSYWFII
+QAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVINFS
+GIFNLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSSDAV
+STTSGTTTVTDNEKSNA
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+MANQLSYSSLGWPYQPNASVVDTMPKEMLYMIHEHWYAFPPMNPLWYSILGVAMIILGII
+CVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFMMPTMTSNCFAETWILGPFMC
+EVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAAPLTHKKATLLLLFVWIWSGGWTIL
+PFFGWSRYVPEGNLTSCTVDYLTKDWSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAE
+HEKQLREQAKKMNVASLRANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVFS
+SGTRLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLACGSGESGSDVKSE
+ASATTTMEEKPKIPEA
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+MVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLF
+SKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFG
+FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVP
+EGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAK
+RLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAEL
+PVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASER
+GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPP
+QGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+MGRDLRDNETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFT
+KTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGF
+MSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLE
+GVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR
+LNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLP
+VMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGESS
+DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGY
+PPPPQGAPPQGAPPAAPPQGVDNQAYQA
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSEVTASPAPTW
+DAPPDNASGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLI
+VSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAMDVMCCTASIMTLCVISIDR
+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT
+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE
+ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC
+IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK
+LAERPERPEFVLQNADYCRKKGHDS
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT
+RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN
+SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RQ
+> 33=p A35181 serotonin receptor class 1A - rat
+MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT
+SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN
+SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RR
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR
+AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV
+YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM
+IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI
+LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI
+SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR
+ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT
+VFSPEFRHAFQRLLCGRRVRRRRAPQ
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+M-----------------------------------------------------------
+-----------------------------------NGTE--GDNFYVPF-----------
+---------------------------------------------SNKTGLARSPYEYPQ
+Y-YLAEPW------------K--------------------------------YSALAAY
+MFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTS-MN-
+GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGNTHAIMGV
+AFTWIMALAC-AAPPLVG-WSRYIP-------EGM----QCSCGPDYYTLNPNFNNESYV
+VYMFVVHFLVPFVIIFFCYGRLLCTV----KE----------------------------
+------------------------------------------------------------
+----------------------------------------------AAAAQQE-------
+------------------------------SASTQKAEKEVTRMVVLMVIGFLVCWVPYA
+SVAFYIFT-HQG-S--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLC-C-
+--GKNP-------------------LGDDE--SGASTSKT-E--VSSVS-TSPV------
+------------------------------------------------------------
+-------------------SP-A---
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+M-----------------------------------------------------------
+-----------------------------------NGTE--GPNFYVPF-----------
+---------------------------------------------SNITGVVRSPFEQPQ
+Y-YLAEPW------------Q--------------------------------FSMLAAY
+MFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTS-LH-
+GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGENHAIMGV
+AFTWVMALAC-AAPPLVG-WSRYIP-------EGM----QCSCGIDYYTLKPEVNNESFV
+IYMFVVHFTIPMIVIFFCYGQLVFTV----KE----------------------------
+------------------------------------------------------------
+----------------------------------------------AAAQQQE-------
+------------------------------SATTQKAEKEVTRMVIIMVIFFLICWLPYA
+SVAMYIFT-HQG-S--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLC-C-
+--GKNP-------------------LGDDE--ASATASKT-E--------TSQV------
+------------------------------------------------------------
+-------------------AP-A---
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+M-----------------------------------------------------------
+-----------------------------------NGTE--GINFYVPM-----------
+---------------------------------------------SNKTGVVRSPFEYPQ
+Y-YLAEPW------------K--------------------------------YRLVCCY
+IFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTA-WN-
+GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSATHAMMGI
+AFTWVMAFSC-AAPPLFG-WSRYMP-------EGM----QCSCGPDYYTHNPDYHNESYV
+LYMFVIHFIIPVVVIFFSYGRLICKV----RE----------------------------
+------------------------------------------------------------
+----------------------------------------------AAAQQQE-------
+------------------------------SATTQKAEKEVTRMVILMVLGFMLAWTPYA
+VVAFWIFT-NKG-A--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTIC-C-
+--GKNP-------------------FGDEDVSSTVSQSKT-E--VSSVS-SSQV------
+------------------------------------------------------------
+-------------------SP-A---
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+M-----------------------------------------------------------
+-----------------------------------NGTE--GKNFYVPM-----------
+---------------------------------------------SNRTGLVRSPFEYPQ
+Y-YLAEPW------------Q--------------------------------FKILALY
+LFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTA-IN-
+GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSSHAFAGI
+AFTWVMALAC-AAPPLFG-WSRYIP-------EGM----QCSCGPDYYTLNPDYNNESYV
+IYMFVCHFILPVAVIFFTYGRLVCTV----KA----------------------------
+------------------------------------------------------------
+----------------------------------------------AAAQQQD-------
+------------------------------SASTQKAEREVTKMVILMVFGFLIAWTPYA
+TVAAWIFF-NKG-A--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIF-C-
+--GKNP-------------------LGDDE-SSTVSTSKT-E--VSS------V------
+------------------------------------------------------------
+-------------------SP-A---
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+M-----------------------------------------------------------
+-----------------------------------NGTE--GNNFYVPL-----------
+---------------------------------------------SNRTGLVRSPFEYPQ
+Y-YLAEPW------------Q--------------------------------FKLLAVY
+MFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTA-IN-
+GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSTHASAGI
+AFTWVMAMAC-AAPPLVG-WSRYIP-------EGI----QCSCGPDYYTLNPEYNNESYV
+LYMFICHFILPVTIIFFTYGRLVCTV----KA----------------------------
+------------------------------------------------------------
+----------------------------------------------AAAQQQD-------
+------------------------------SASTQKAEREVTKMVILMVLGFLVAWTPYA
+TVAAWIFF-NKG-A--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLF-C-
+--GKNP-------------------LGDEE-SSTVSTSKT-E--VSS------V------
+------------------------------------------------------------
+-------------------SP-A---
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+M-----------------------------------------------------------
+-----------------------------------KQVPEFHEDFYIPIPL---------
+-------------------------------------------DINNLS--AYSPFLVPQ
+D-HLGNQG------------I--------------------------------FMAMSVF
+MFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSF-FN-
+RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FTFKTPHAIAGC
+ILPWISALAA-SLPPLFG-WSRYIP-------EGL----QCSCGPDWYTTNNKYNNESYV
+MFLFCFCFAVPFGTIVFCYGQLLITL----KL----------------------------
+------------------------------------------------------------
+----------------------------------------------AAKAQAD-------
+------------------------------SASTQKAEREVTKMVVVMVLGFLVCWAPYA
+SFSLWIVS-HRG-E--EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMV-C-
+--GKN--------------------IEEDE--ASTSSQVT-Q--VSS------V------
+------------------------------------------------------------
+-------------------APEK---
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+M-----------------------------------------------------------
+-----------------------------------RKMS--EEEFYL---F---------
+---------------------------------------------KNISSV--GPWDGPQ
+Y-HIAPVW------------A--------------------------------FYLQAAF
+MGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPVFVAS-CN-
+GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FRFSSKHALTVV
+LATWTIGIGV-SIPPFFG-WSRFIP-------EGL----QCSCGPDWYTVGTKYRSESYT
+WFLFIFCFIVPLSLICFSYTQLLRAL----KA----------------------------
+------------------------------------------------------------
+----------------------------------------------VAAQQQE-------
+------------------------------SATTQKAEREVSRMVVVMVGSFCVCYVPYA
+AFAMYMVN-NRN-H--GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMV-C-
+--GKA--------------------MTDES--DTCSSQKT-E--VSTVS-STQV------
+------------------------------------------------------------
+-------------------GP-N---
+> 8=opsin, greensensitive human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------DLAETVIA-STISIVNQ-VS-
+GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLAIVGI
+AFSWIWAAVW-TAPPIFG-WSRYWP-------HGL----KTSCGPDVFSGSSYPGVQSYM
+IVLMVTCCITPLSIIVLCYLQVWLAI----RA----------------------------
+------------------------------------------------------------
+----------------------------------------------VAKQQKE-------
+------------------------------SESTQKAEKEVTRMVVVMVLAFC-------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+M--------------AQQWSLQRLAGRHPQDSYE--------------------------
+-----------------------------------DSTQ--SSIFTYTN-----------
+---------------------------------------------SNST---RGPFEGPN
+Y-HIAPRW------------V--------------------------------YHLTSVW
+MIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQ-VY-
+GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VRFDAKLAIVGI
+AFSWIWAAVW-TAPPIFG-WSRYWP-------HGL----KTSCGPDVFSGSSYPGVQSYM
+IVLMVTCCITPLSIIVLCYLQVWLAI----RA----------------------------
+------------------------------------------------------------
+----------------------------------------------VAKQQKE-------
+------------------------------SESTQKAEKEVTRMVVVMVLAFCFCWGPYA
+FFACFAAA-NPG-Y--PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCIL-QLF---
+--GKK--------------------VDDGS--ELSSASKT-E--VSSV---SSV------
+------------------------------------------------------------
+-------------------SP-A---
+> 10== Z68193 1 human Red Opsin <>[]
+M--------------AQQWSLQRLAGRHPQDSYE--------------------------
+-----------------------------------DSTQ--SSIFTYTN-----------
+---------------------------------------------SNST---RGPFEGPN
+Y-HIAPRW------------V--------------------------------YHLTSVW
+MIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQ-VS-
+GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLAIVGI
+AFSWIWSAVW-TAPPIFG-WSRYWP-------HGL----KTSCGPDVFSGSSYPGVQSYM
+IVLMVTCCIIPLAIIMLCYLQVWLAI----RA----------------------------
+------------------------------------------------------------
+----------------------------------------------VAKQQKE-------
+------------------------------SESTQKAEKEVTRMVVVMIFAYCVCWGPYT
+FFACFAAA-NPG-Y--AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCIL-QLF---
+--GKK--------------------VDDGS--ELSSASKT-E--VSSV---SSV------
+------------------------------------------------------------
+-------------------SP-A---
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+M--------------TEAWNVAVFAARRSRDD-D--------------------------
+-----------------------------------DTTR--GSVFTYTN-----------
+---------------------------------------------TNNT---RGPFEGPN
+Y-HIAPRW------------V--------------------------------YNLVSFF
+MIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQ-IF-
+GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IKFDSKLAIIGI
+VFSWVWAWGW-SAPPIFG-WSRYWP-------HGL----KTSCGPDVFSGSVELGCQSFM
+LTLMITCCFLPLFIIIVCYLQVWMAI----RA----------------------------
+------------------------------------------------------------
+----------------------------------------------VAAQQKE-------
+------------------------------SESTQKAEREVSRMVVVMIVAFCICWGPYA
+SFVSFAAA-NPG-Y--AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIM-QLF---
+--GKK--------------------VDDGS--EASTTSRT-E--VSSVS-NSSV------
+------------------------------------------------------------
+-------------------AP-A---
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+M--------------AA-WEAAFAARRRHEE--E--------------------------
+-----------------------------------DTTR--DSVFTYTN-----------
+---------------------------------------------SNNT---RGPFEGPN
+Y-HIAPRW------------V--------------------------------YNLTSVW
+MIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQ-IS-
+GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IKFDGKLAVAGI
+LFSWLWSCAW-TAPPIFG-WSRYWP-------HGL----KTSCGPDVFSGSSDPGVQSYM
+VVLMVTCCFFPLAIIILCYLQVWLAI----RA----------------------------
+------------------------------------------------------------
+----------------------------------------------VAAQQKE-------
+------------------------------SESTQKAEKEVSRMVVVMIVAYCFCWGPYT
+FFACFAAA-NPG-Y--AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIL-QLF---
+--GKK--------------------VDDGS--EVST-SRT-E--VSSVS-NSSV------
+------------------------------------------------------------
+-------------------SP-A---
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+M--------------S-----------------S--------------------------
+-----------------------------------NSSQ--AP-----------------
+---------------------------------------------PNGT---PGPFDGPQ
+WPYQAPQS------------T--------------------------------YVGVAVL
+MGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNN-IN-
+GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQFQRRHAVSGC
+AFTWGWALLW-SAPPLLG-WSSYVP-------EGL----RTSCGPNWYTGGSNN--NSYI
+LSLFVTCFVLPLSLILFSYTNLLLTL----RA----------------------------
+------------------------------------------------------------
+----------------------------------------------AAAQQKE-------
+------------------------------ADTTQRAEREVTRMVIVMVMAFLLCWLPYS
+TFALVVAT-HKG-I--IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLL-EMLCCG
+YQPQR--------------------TGKAS--PGTPGPHA-D--VTAAGLRNKV------
+------------------------------------------------------------
+-------------------MP-AHPV
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+M--------------------------------ES-G-----------------------
+-----------------------------------NVSS-----------SLFGNVSTAL
+RPEA------------------RLSA---ETRLLGWNVPPEELR----------------
+--HIPEHW------------LT---------YPEPPESM--------------NYLLGTL
+YIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIFIYNS-FH-
+QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTHGKAIAMI
+IFIYMYATPW-VVACYTETWGRFVP-------EGY----LTSCTFDYLT--DNFDTRLFV
+ACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------LRDQAKK--MNVES
+L------------------------RS-NVDKNKETAEIRIAKAAITICFLFFCSWTPYG
+VMSLIGAF-GDK-T--LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQ-------
+--KRCP----WLALNE---KAPE--SSAVA--STSTTQEP-Q------------------
+-------QT---------------------------------------------------
+-------------------TA-A---
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+M--------------------------------EY-H-----------------------
+-----------------------------------NVSS-----------VL-GNVSSVL
+RPDA------------------RLSA---ESRLLGWNVPPDELR----------------
+--HIPEHW------------LI---------YPEPPESM--------------NYLLGTL
+YIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIFIYNS-FH-
+QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTHGKAIAMI
+IFIYLYATPW-VVACYTESWGRFVP-------EGY----LTSCTFDYLT--DNFDTRLFV
+ACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------LRDQAKK--MNVDS
+L------------------------RS-NVDKSKEAAEIRIAKAAITICFLFFASWTPYG
+VMSLIGAF-GDK-T--LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQ-------
+--KRCP----WLAISE---KAPE--SRAAI--STSTTQEQ-Q------------------
+-------QT---------------------------------------------------
+-------------------TA-A---
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+M--------------------------------EPLC-----------------------
+-----------------------------------NASE-----------PP-------L
+RPEA------------------R-SSGNGDLQFLGWNVPPDQIQ----------------
+--YIPEHW------------LT---------QLEPPASM--------------HYMLGVF
+YIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF--NS-FH-
+RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVIMN
+IIIWLYCTPW-VVLPLTQFWDRFVP-------EGY----LTSCSFDYLS--DNFDTRLFV
+GTIFFFSFVCPTLMILYYYSQIVGHVFSHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------LREQAKK--MNVES
+L------------------------RS-NVDKSKETAEIRIAKAAITICFLFFVSWTPYG
+VMSLIGAF-GDK-S--LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQ-------
+--KRCP----WLGVNE---KSGE--ISSAQ--ST-TTQEQ-Q------------------
+-------QT---------------------------------------------------
+-------------------TA-A---
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+M--------------------------------DALC-----------------------
+-----------------------------------NASE-----------PP-------L
+RPEA------------------RMSSGSDELQFLGWNVPPDQIQ----------------
+--YIPEHW------------LT---------QLEPPASM--------------HYMLGVF
+YIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIFIYNS-FH-
+RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVIMN
+IIIWLYCTPW-VVLPLTQFWDRFVP-------EGY----LTSCSFDYLS--DNFDTRLFV
+GTIFLFSFVVPTLMILYYYSQIVGHVFNHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------LREQAKK--MNVES
+L------------------------RS-NVDKSKETAEIRIAKAAITICFLFFVSWTPYG
+VMSLIGAF-GDK-S--LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQ-------
+--KRCP----WLGVNE---KSGE--ASSAQ--ST-TTQEQTQ------------------
+-------QT---------------------------------------------------
+-------------------SA-A---
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+M--------------------------------------------TNATGPQMAYYGAAS
+MDFGYPE----------------------------GVSI-----------VD--------
+------------------------------------FVRPEIKP----------------
+--YVHQHW------------YN---------YPPVNPMW--------------HYLLGVI
+YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNC-FSG
+GVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PKLTTGKAVVFA
+LISWVIAIGC-ALPPFFG-WGNYIL-------EGI----LDSCSYDYLT--QDFNTFSYN
+IFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAA----------------------------
+------------------------------------------------------------
+----------------------------------------------MRAQAKK--MNVST
+L------------------------RS-N-EADAQRAEIRIAKTALVNVSLWFICWTPYA
+LISLKGVM-GDT-S--GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAIT-------
+--QHLP----WFCVHE---TETKS-NDDSQ--SNSTVAQ---------------------
+------------------------------------------------------------
+-------------------DK-A---
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+M--------------------------------------------ANVTGPQMAFYGSGA
+ATFGYPE----------------------------GMTV-----------AD--------
+------------------------------------FVPDRVKH----------------
+--MVLDHW------------YN---------YPPVNPMW--------------HYLLGVV
+YLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNC-FSG
+GRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PKLTQGKATFMC
+GLAWVISVGW-SLPPFFG-WGSYTL-------EGI----LDSCSYDYFT--RDMNTITYN
+ICIFIFDFFLPASVIVFSYVFIVKAIFAHEAA----------------------------
+------------------------------------------------------------
+----------------------------------------------MRAQAKK--MNVTN
+L------------------------RS-N-EAETQRAEIRIAKTALVNVSLWFICWTPYA
+AITIQGLL-GNA-E--GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAIT-------
+--QHLP----WFCVHE---KDPND-VEENQ--SSNTQTQ---------------------
+------------------------------------------------------------
+-------------------EK-S---
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+M--------------------------------E------SFAVAAAQLGPHFAPLS---
+-----------------------------------NGSV-----------VD--------
+------------------------------------KVTPDMAH----------------
+--LISPYW------------NQ---------FPAMDPIW--------------AKILTAY
+MIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINL-YF-
+ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKM
+----------------------YVP-------EGN----LTSCGIDYLE--RDWNPRSYL
+IFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------MREQAKK--MNVKS
+L------------------------RS-S-EDAEKSAEGKLAKVALVTITLWFMAWTPYL
+VINCMGLF--KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALK-------
+--EKCP----CCVFGK---VDDGK-SSDAQ--SQATASEA-E------------------
+------------------------------------------------------------
+-------------------SK-A---
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+M--------------------------------E------SFAVAAAQLGPHFAPLS---
+-----------------------------------NGSV-----------VD--------
+------------------------------------KVTPDMAH----------------
+--LISPYW------------NQ---------FPAMDPIW--------------AKILTAY
+MIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINL-YF-
+ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKI
+AYIWFMSSIW-CLAPAFG-WSRYVP-------EGN----LTSCGIDYLE--RDWNPRSYL
+IFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------MREQAKK--MNVKS
+L------------------------RS-S-EDAEKSAEGKLAKVALVTITLWFMAWTPYL
+VINCMGLF--KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALK-------
+--EKCP----CCVFGK---VDDGK-SSDAQ--SQATASEA-E------------------
+------------------------------------------------------------
+-------------------SK-A---
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+M--------------------------------D------SFAAVATQLGPQFAAPS---
+-----------------------------------NGSV-----------VD--------
+------------------------------------KVTPDMAH----------------
+--LISPYW------------DQ---------FPAMDPIW--------------AKILTAY
+MIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINL-YF-
+ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALGKI
+AYIWFMSTIWCCLAPVFG-WSRYVP-------EGN----LTSCGIDYLE--RDWNPRSYL
+IFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------MREQAKK--MNVKS
+L------------------------RS-S-EDADKSAEGKLAKVALVTISLWFMAWTPYL
+VINCMGLF--KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALK-------
+--EKCP----CCVFGK---VDDGK-SSEAQ--SQATTSEA-E------------------
+------------------------------------------------------------
+-------------------SK-A---
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+M--------------------------------ER-SHLPETPFDLAHSGPRFQAQSSG-
+-----------------------------------NGSV-----------LD--------
+------------------------------------NVLPDMAH----------------
+--LVNPYW------------SR---------FAPMDPMM--------------SKILGLF
+TLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINF-YY-
+ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIMKI
+LFIWMMAVFW-TVMPLIG-WSAYVP-------EGN----LTACSIDYMT--RMWNPRSYL
+ITYSLFVYYTPLFLICYSYWFIIAAVAAHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------MREQAKK--MNVKS
+L------------------------RS-S-EDCDKSAEGKLAKVALTTISLWFMAWTPYL
+VICYFGLF--KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLK-------
+--EKCP----MCVFGN---TDEPKPDAPAS--DTETTSEA-D------------------
+------------------------------------------------------------
+-------------------SK-A---
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+M--------------------------------ER-SLLPEPPLAMALLGPRFEAQTGG-
+-----------------------------------NRSV-----------LD--------
+------------------------------------NVLPDMAP----------------
+--LVNPHW------------SR---------FAPMDPTM--------------SKILGLF
+TLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINF-YY-
+ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIMKI
+AFIWMMAVFW-TIMPLIG-WSSYVP-------EGN----LTACSIDYMT--RQWNPRSYL
+ITYSLFVYYTPLFMICYSYWFIIATVAAHEKA----------------------------
+------------------------------------------------------------
+----------------------------------------------MRDQAKK--MNVKS
+L------------------------RS-S-EDCDKSAENKLAKVALTTISLWFMAWTPYL
+IICYFGLF--KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLK-------
+--EKCP----MCVCGT---TDEPKPDAPPS--DTETTSEA-E------------------
+------------------------------------------------------------
+-------------------SK-D---
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+M--------------------------------------------IAVSGPSYEAFSYG-
+---GQAR--------------------------FNNQTV-----------VD--------
+------------------------------------KVPPDMLH----------------
+--LIDANW------------YQ---------YPPLNPMW--------------HGILGFV
+IGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINC-YY-
+ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KPLSINGALIRI
+IAIWLFSLGW-TIAPMFG-WNRYVP-------EGN----MTACGTDYFN--RGLLSASYL
+VCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKN----------------------------
+------------------------------------------------------------
+----------------------------------------------MREQAKK--MNVAS
+L------------------------RS-S-ENQNTSAECKLAKVALMTISLWFMAWTPYL
+VINFSGIF--NL-V--KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALF-------
+--AKFP----SLAC-A---AEPSS-DAVST--TSGTTTVT-D------------------
+------------------------------------------------------------
+---------------NEK-SN-A---
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+M----------------------------------------------ANQLSYSSLGWP-
+---YQP-----------------------------NASV-----------VD--------
+------------------------------------TMPKEMLY----------------
+--MIHEHW------------YA---------FPPMNPLW--------------YSILGVA
+MIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNC-FA-
+ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-APLTHKKATLLL
+LFVWIWSGGW-TILPFFG-WSRYVP-------EGN----LTSCTVDYLT--KDWSSASYV
+VIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQ----------------------------
+------------------------------------------------------------
+----------------------------------------------LREQAKK--MNVAS
+L------------------------RANA-DQQKQSAECRLAKVAMMTVGLWFMAWTPYL
+IISWAGVF--SSGT--RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALY-------
+--QRFP----SLACGS---GESGS-DVKSE--ASATTTME-E------------------
+------------------------------------------------------------
+---------------KPKIPE-A---
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+M-----------------------------------------------------------
+---VESTTLV------------------NQTWWY-NPTV-----------D---------
+------------------------------------------------------------
+---IHPHW------------AK---------FDPIPDAV--------------YYSVGIF
+IGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISA-FM-
+KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMI
+IFVWMWSIVW-SVGPVFN-WGAYVP-------EGI----LTSCSFDYLS--TDPSTRSFI
+LCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKE----------------------------
+------------------------------------------------------------
+----------------------------------------------MAAMAKR--LNAKE
+L------------------------RK---AQAGASAEMKLAKISMVIITQFMLSWSPYA
+IIALLAQF-GPA-E--WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQ-------
+--TTFPWLLTCCQFDE---KECED-ANDAE--EEVVASER---GGESRD-AAQMKEMMAM
+MQKMQAQQAAYQPPPPPQGY--PPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAP
+PQVEAPQGAPPQGVDNQA-YQ-A---
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+M-----------------------------------------------------------
+---GRDLR-D------------------NETWWY-NPSI-----------V---------
+------------------------------------------------------------
+---VHPHW------------RE---------FDQVPDAV--------------YYSLGIF
+IGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISC-FL-
+KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMI
+IFVWLWSVLW-AIGPIFG-WGAYTL-------EGV----LCNCSFDYIS--RDSTTRSNI
+LCMFILGFFGPILIIFFCYFNIVMSVSNHEKE----------------------------
+------------------------------------------------------------
+----------------------------------------------MAAMAKR--LNAKE
+L------------------------RK---AQAGANAEMRLAKISIVIVSQFLLSWSPYA
+VVALLAQF-GPL-E--WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAIS-------
+--QTFPWVLTCCQFDD---KETED-DKDAE--TEIPAGES-SDAAPSAD-AAQMKEMMAM
+MQKMQQQQAAY----PPQGYAPPPQGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAP
+PQ-GAPPAAPPQGVDNQA-YQ-A---
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLY-----------------------------------------------
+-----------------GHLRSFL--LPEVGR---GLPD--------------------L
+SPDGGADPVAGSWAPHLLS---EVTA----------------------------------
+--SPAPTW-----------------------DAPPDNAS--GCGEQINYGRVEKVVIGSI
+LTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIG-
+GKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMI
+LSVWLLSASI-TLPPLFG-WAQNVN--DDK---------VCLISQDF----------GYT
+IYSTAVAFYIPMSVMLFMYYQIYKAAR---------------------------------
+-----------------KSAAKHKFPGFPRVEPDSVI----------------------A
+LNGIVK----------------------LQKEVEECAN--------LSRLLKH-------
+-------------------------ER-K-NISIFKREQKAATTLGIIVGAFTVCWLPFF
+LLSTARPFICGT-SCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYR-SLL---
+----------QCQYRN-INRKLSA-AGMHE--ALKLAERP-E--------RPEF-----V
+LQNADY--------CRKKGHD---------------------------------------
+----------------------S---
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+M-----------------------------------------------------------
+------------------------------------------------------------
+--------------PHLLSGFLEVTA----------------------------------
+--SPAPTW-----------------------DAPPDNVS--GCGEQINYGRVEKVVIGSI
+LTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIG-
+GKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMI
+LSVWLLSASI-TLPPLFG-WAQNVN--DDK---------VCLISQDF----------GYT
+IYSTAVAFYIPMSVMLFMYYQIYKAAR---------------------------------
+-----------------KSAAKHKFPGFPRVQPESVI----------------------S
+LNGVVK----------------------LQKEVEECAN--------LSRLLKH-------
+-------------------------ER-K-NISIFKREQKAATTLGIIVGAFTVCWLPFF
+LLSTARPFICGT-SCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSR-SLL---
+----------QCQYRN-INRKLSA-AGMHE--ALKLAERP-E--------RSEF-----V
+LQNSDH--------CGKKGHD---------------------------------------
+----------------------T---
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+M-----------------------------------------------------------
+------------------------------------------------------------
+--------------PHLLSGFLEVTA----------------------------------
+--SPAPTW-----------------------DAPPDNVS--GCGEQINYGRVEKVVIGSI
+LTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIG-
+GKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMI
+LSVWLLSASI-TLPPLFG-WAQNVN--DDK---------VCLISQDF----------GYT
+IYSTAVAFYIPMSVMLFMYYQIYKAAR---------------------------------
+-----------------KSAAKHKFPGFPRVQPESVI----------------------S
+LNGVVK----------------------LQKEVEECAN--------LSRLLKH-------
+-------------------------ER-K-NISIFKREQKAATTLGIIVGAFTVCWLPFF
+LLSTARPFICGT-SCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYR-SLL---
+----------QCQYRN-INRKLSA-AGMHE--ALKLAERP-E--------RSEF-----V
+LQNSDH--------CGKKGHD---------------------------------------
+----------------------T---
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+M-DVLSPGQ---------------------------------------------------
+-----------------GNNTTSPPAPFETGG---NTTG--------------------I
+-------------------------S----------------------------------
+--DVTVSY---------------------------------------------QVITSLL
+LGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQ-VL-
+NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALI
+SLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---------ACTISKDH----------GYT
+IYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK----------------------------
+-----------TVKKVEKTGADTRHGASPAPQPKKSVNGESGSRNWRLGVESKAGGAL-C
+ANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAP-----ASFERK-------
+----NERNA----------------EA-K-RKMALARERKTVKTLGIIMGTFILCWLPFF
+IVALVLPF-CES-SC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFK-KII---
+----------KCKFCR--------------------------------------------
+------------------------------------------------------------
+----------------------Q---
+> 33=p A35181 serotonin receptor class 1A - rat
+M-DVFSFGQ---------------------------------------------------
+-----------------GNNTTASQEPFGTGG---NVTS--------------------I
+-------------------------S----------------------------------
+--DVTFSY---------------------------------------------QVITSLL
+LGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQ-VL-
+NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALI
+SLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---------ACTISKDH----------GYT
+IYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK----------------------------
+-----------TVRKVEKKGAGTSLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTP-C
+TNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESGSNSYAP-----ACLERK-------
+----NERNA----------------EA-K-RKMALARERKTVKTLGIIMGTFILCWLPFF
+IVALVLPF-CES-SC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFK-KII---
+----------KCKFCR--------------------------------------------
+------------------------------------------------------------
+----------------------R---
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+M-ANFTFGDLALD-----------------------------------------------
+-------------VARMGGLASTPSGLRSTGL---TTPG--------------------L
+SPTG------------------LVTS----------------------------------
+--DFNDSYGLTGQFINGSHSSRSRDNASAN-DTSATNMTDDRYWSLTVYSHEHLVLTSVI
+LGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSE-IS-
+KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMI
+MVVWIVALFI-SIPPLFG-WRDPNN--DPD------KTGTCIISQDK----------GYT
+IFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVV
+SDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKK----------------NRAKKLPEN
+ANGVNSNSSSSERLKQIQIE-----------TAEAFANGCAEEAS-IAMLERQ-CNNGKK
+ISSNDTPYS----------------RT-R-EKLELKRERKAARTLAIITGAFLICWLPFF
+IIALIGPF-VDP-E--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQ-KIL---
+----------FGKYRR--------------------------------------------
+------------------GH----------------------------------------
+----------------------R---
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+M-ANFTFGDLALD-----------------------------------------------
+-------------VARMGGLASTPSGLRSTGL---TTPG--------------------L
+SPTG------------------LVTS----------------------------------
+--DFNDSYGLTGQFINGSHSSRSRDNASAN-DTSATNMTDDRYWSLTVYSHEHLVLTSVI
+LGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSE-IS-
+KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMI
+MVVWIVALFI-SIPPLFG-WRDPNN--DPD------KTGTCIISQDK----------GYT
+IFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVV
+SDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKK----------------NRAKKLPEN
+ANGVNSNSSSSERLKQIQIE-----------TAEAFANGCAEEAS-IAMLERQ-CNNGKK
+ISSNDTPYS----------------RT-R-EKLELKRERKAARTLAIITGAFLICWLPFF
+IIALIGPF-VDP-E--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQ-KIL---
+----------FGKYRR--------------------------------------------
+------------------GH----------------------------------------
+----------------------R---
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+M-EGAE-GQEELDWEA--------------------------------------------
+---------LYLRLP-----------LQNCSW---NSTG--------------------W
+EPNW------------------NVTV----------------------------------
+--VPNTTW----------------WQASAPFDTPAALVR--------------AAAKAVV
+LGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYE-VV-
+QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRVGMMI
+ACVWTVSFFV-CIAQLLG-WK------DPDWNQRVSEDLRCVVSQDV----------GYQ
+IFATASSFYVPVLIILILYWRIYQTARKRIRR----------------------------
+-----------------RRGATARGGVGPPPVP---------------------------
+AGGALVAGGGSGGIAAAVVAVIGRP---LPTISETTTTGFTNVSSNNTSPEKQSCANGLE
+A---DPPTTGYGAVAAAYYPSLVRRKP-K-EAADSKRERKAAKTLAIITGAFVACWLPFF
+VLAILVPT-CDC-E---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQ-RLL---
+----------CGRRVRRR------------------------------------------
+-----------------RAP----------------------------------------
+----------------------Q---
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+------------------------------------------------------------
+---------MNGTE--GDNFYVP----FSNKTGLARSPYEYPQY-YLAEPWK--------
+-YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVT
+MYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGN
+THAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESY
+VVYMFVVHFLVPFVIIFFCYGRLLCTV---------------------------------
+------------------------------------------------------------
+------------------------------KEAAAAQQ----------ESASTQKA----
+-------------------------EKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGS
+D---FGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCCGKN------PLGDDE
+--SGASTSKTEVSSVS-TSPVSPA------------------------------------
+---------------------------------------------------
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+------------------------------------------------------------
+---------MNGTE--GPNFYVP----FSNITGVVRSPFEQPQY-YLAEPWQ--------
+-FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTT
+LYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGE
+NHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESF
+VIYMFVVHFTIPMIVIFFCYGQLVFTV---------------------------------
+------------------------------------------------------------
+------------------------------KEAAAQQQ----------ESATTQKA----
+-------------------------EKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGS
+N---FGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCCGKN------PLGDDE
+--ASATASKTE------TSQVAPA------------------------------------
+---------------------------------------------------
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+------------------------------------------------------------
+---------MNGTE--GINFYVP----MSNKTGVVRSPFEYPQY-YLAEPWK--------
+-YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVT
+FYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSA
+THAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESY
+VLYMFVIHFIIPVVVIFFSYGRLICKV---------------------------------
+------------------------------------------------------------
+------------------------------REAAAQQQ----------ESATTQKA----
+-------------------------EKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGA
+D---FTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICCGKN------PFGDED
+VSSTVSQSKTEVSSVS-SSQVSPA------------------------------------
+---------------------------------------------------
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+------------------------------------------------------------
+---------MNGTE--GKNFYVP----MSNRTGLVRSPFEYPQY-YLAEPWQ--------
+-FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVT
+FYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSS
+SHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNNESY
+VIYMFVCHFILPVAVIFFTYGRLVCTV---------------------------------
+------------------------------------------------------------
+------------------------------KAAAAQQQ----------DSASTQKA----
+-------------------------EREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGA
+D---FSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFCGKN------PLGDDE
+-SSTVSTSKTEVSS------VSPA------------------------------------
+---------------------------------------------------
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+------------------------------------------------------------
+---------MNGTE--GNNFYVP----LSNRTGLVRSPFEYPQY-YLAEPWQ--------
+-FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVT
+FYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSS
+THASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNNESY
+VLYMFICHFILPVTIIFFTYGRLVCTV---------------------------------
+------------------------------------------------------------
+------------------------------KAAAAQQQ----------DSASTQKA----
+-------------------------EREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGA
+A---FSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFCGKN------PLGDEE
+-SSTVSTSKTEVSS------VSPA------------------------------------
+---------------------------------------------------
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+------------------------------------------------------------
+---------MKQVPEFHEDFYIPIPLDINNLS--AYSPFLVPQD-HLGNQGI--------
+-FMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLS
+FYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FTFKT
+PHAIAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNNESY
+VMFLFCFCFAVPFGTIVFCYGQLLITL---------------------------------
+------------------------------------------------------------
+------------------------------KLAAKAQA----------DSASTQKA----
+-------------------------EREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGE
+E---FDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVCGKN-------IEEDE
+--ASTSSQVTQVSS------VAPEK-----------------------------------
+---------------------------------------------------
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+------------------------------------------------------------
+---------MRKMS--EEEFYL-----FKNISSV--GPWDGPQY-HIAPVWA--------
+-FYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPV
+FVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FRFSS
+KHALTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRSESY
+TWFLFIFCFIVPLSLICFSYTQLLRAL---------------------------------
+------------------------------------------------------------
+------------------------------KAVAAQQQ----------ESATTQKA----
+-------------------------EREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNH
+G---LDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVCGKA-------MTDES
+--DTCSSQKTEVSTVS-STQVGPN------------------------------------
+---------------------------------------------------
+> 8=opsin, greensensitive human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------------DLAETVIA-STIS
+IVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDA
+KLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSY
+MIVLMVTCCITPLSIIVLCYLQVWLAI---------------------------------
+------------------------------------------------------------
+------------------------------RAVAKQQK----------ESESTQKA----
+-------------------------EKEVTRMVVVMVLAFC-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+----------------------------------------------------------MA
+QQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNS-TRGPFEGPNY-HIAPRWV--------
+-YHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STIS
+VVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VRFDA
+KLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSY
+MIVLMVTCCITPLSIIVLCYLQVWLAI---------------------------------
+------------------------------------------------------------
+------------------------------RAVAKQQK----------ESESTQKA----
+-------------------------EKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGY
+P---FHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLF-----------GKKVDD
+GSELSSASKTEVSSV---SSVSPA------------------------------------
+---------------------------------------------------
+> 10== Z68193 1 human Red Opsin <>[]
+----------------------------------------------------------MA
+QQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNS-TRGPFEGPNY-HIAPRWV--------
+-YHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STIS
+IVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDA
+KLAIVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSY
+MIVLMVTCCIIPLAIIMLCYLQVWLAI---------------------------------
+------------------------------------------------------------
+------------------------------RAVAKQQK----------ESESTQKA----
+-------------------------EKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGY
+A---FHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLF-----------GKKVDD
+GSELSSASKTEVSSV---SSVSPA------------------------------------
+---------------------------------------------------
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+----------------------------------------------------------MT
+EAWNVAVFAARRSRDD-DDTTRGSVFTYTNTNN-TRGPFEGPNY-HIAPRWV--------
+-YNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STIS
+VFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IKFDS
+KLAIIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGCQSF
+MLTLMITCCFLPLFIIIVCYLQVWMAI---------------------------------
+------------------------------------------------------------
+------------------------------RAVAAQQK----------ESESTQKA----
+-------------------------EREVSRMVVVMIVAFCICWGPYASFVSFAAANPGY
+A---FHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLF-----------GKKVDD
+GSEASTTSRTEVSSVS-NSSVAPA------------------------------------
+---------------------------------------------------
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+-----------------------------------------------------------M
+AAWEAAFAARRRHEE--EDTTRDSVFTYTNSNN-TRGPFEGPNY-HIAPRWV--------
+-YNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STIS
+VINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IKFDG
+KLAVAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGVQSY
+MVVLMVTCCFFPLAIIILCYLQVWLAI---------------------------------
+------------------------------------------------------------
+------------------------------RAVAAQQK----------ESESTQKA----
+-------------------------EKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGY
+A---FHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCILQLF-----------GKKVDD
+GSEVST-SRTEVSSVS-NSSVSPA------------------------------------
+---------------------------------------------------
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+------------------------------------------------------------
+---------------------MSSNSSQAPPNG-TPGPFDGPQWPYQAPQST--------
+-YVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVS
+LSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQFQR
+RHAVSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--NSY
+ILSLFVTCFVLPLSLILFSYTNLLLTL---------------------------------
+------------------------------------------------------------
+------------------------------RAAAAQQK----------EADTTQRA----
+-------------------------EREVTRMVIVMVMAFLLCWLPYSTFALVVATHKGI
+I---IQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLLEMLCCGYQ------PQRTGK
+ASPGTPGPHADVTAAGLRNKVMPAHPV---------------------------------
+---------------------------------------------------
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+------------------------------------------------------MESGNV
+SSSLFGNVSTALRPEARLSA---E-----TRLLGWNVPPEELR--HIPEHWLTYPEPPES
+MNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIF
+IYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTH
+GKAIAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDTRLF
+VACIFFFSFVCPTTMITYYYSQIVGHVFSH------------------------------
+------------------------------------------------------------
+-----------------------------EKALRDQAKKMNVESLRSNVDKNKETA----
+-------------------------EIRIAKAAITICFLFFCSWTPYGVMSLIGAFGDKT
+L---LTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL---------NEK
+APESSAVASTSTTQEPQQTTAA--------------------------------------
+---------------------------------------------------
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+------------------------------------------------------MEYHNV
+SSVL-GNVSSVLRPDARLSA---E-----SRLLGWNVPPDELR--HIPEHWLIYPEPPES
+MNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIF
+IYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTH
+GKAIAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDTRLF
+VACIFFFSFVCPTTMITYYYSQIVGHVFSH------------------------------
+------------------------------------------------------------
+-----------------------------EKALRDQAKKMNVDSLRSNVDKSKEAA----
+-------------------------EIRIAKAAITICFLFFASWTPYGVMSLIGAFGDKT
+L---LTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI---------SEK
+APESRAAISTSTTQEQQQTTAA--------------------------------------
+---------------------------------------------------
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+------------------------------------------------------ME----
+--PLCNASEPPLRPEAR-SSGNGD-----LQFLGWNVPPDQIQ--YIPEHWLTQLEPPAS
+MHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF
+--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTF
+TKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLF
+VGTIFFFSFVCPTLMILYYYSQIVGHVFSH------------------------------
+------------------------------------------------------------
+-----------------------------EKALREQAKKMNVESLRSNVDKSKETA----
+-------------------------EIRIAKAAITICFLFFVSWTPYGVMSLIGAFGDKS
+L---LTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV---------NEK
+SGEISSAQSTTTQEQ-QQTTAA--------------------------------------
+---------------------------------------------------
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+------------------------------------------------------MD----
+--ALCNASEPPLRPEARMSSGSDE-----LQFLGWNVPPDQIQ--YIPEHWLTQLEPPAS
+MHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF
+IYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTF
+TKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLF
+VGTIFLFSFVVPTLMILYYYSQIVGHVFNH------------------------------
+------------------------------------------------------------
+-----------------------------EKALREQAKKMNVESLRSNVDKSKETA----
+-------------------------EIRIAKAAITICFLFFVSWTPYGVMSLIGAFGDKS
+L---LTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV---------NEK
+SGEASSAQSTTTQEQTQQTSAA--------------------------------------
+---------------------------------------------------
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+------------------------------------------------------------
+---MTNATGPQMAYYGAASMDFGYPE---GVSIVDFVRPEIKP--YVHQHWYNYPPVNPM
+WHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFF
+TYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PKLTT
+GKAVVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNTFSY
+NIFIFVFDYFLPAAIIVFSYVFIVKAIFAH------------------------------
+------------------------------------------------------------
+-----------------------------EAAMRAQAKKMNVSTLRS-NEADAQRA----
+-------------------------EIRIAKTALVNVSLWFICWTPYALISLKGVMGDTS
+G---ITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HETETK
+SNDDSQSNSTVAQDKA--------------------------------------------
+---------------------------------------------------
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+------------------------------------------------------------
+---MANVTGPQMAFYGSGAATFGYPE---GMTVADFVPDRVKH--MVLDHWYNYPPVNPM
+WHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPF
+CYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PKLTQ
+GKATFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNTITY
+NICIFIFDFFLPASVIVFSYVFIVKAIFAH------------------------------
+------------------------------------------------------------
+-----------------------------EAAMRAQAKKMNVTNLRS-NEAETQRA----
+-------------------------EIRIAKTALVNVSLWFICWTPYAAITIQGLLGNAE
+G---ITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HEKDPN
+DVEENQSSNTQTQEKS--------------------------------------------
+---------------------------------------------------
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+---------------------------------------------------------MES
+FAVAAAQLGPHFA-----PLS--------NGSVVDKVTPDMAH--LISPYWNQFPAMDPI
+WAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMM
+GINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTI
+PLALGKM---------------------------YVPEGNLTSCGIDYLE--RDWNPRSY
+LIFYSIFVYYIPLFLICYSYWFIIAAVSAH------------------------------
+------------------------------------------------------------
+-----------------------------EKAMREQAKKMNVKSLRS-SEDAEKSA----
+-------------------------EGKLAKVALVTITLWFMAWTPYLVINCMGLFKF-E
+G---LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKVDDG
+K-SSDAQSQATASEAESKA-----------------------------------------
+---------------------------------------------------
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+---------------------------------------------------------MES
+FAVAAAQLGPHFA-----PLS--------NGSVVDKVTPDMAH--LISPYWNQFPAMDPI
+WAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMM
+GINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTI
+PLALGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSY
+LIFYSIFVYYIPLFLICYSYWFIIAAVSAH------------------------------
+------------------------------------------------------------
+-----------------------------EKAMREQAKKMNVKSLRS-SEDAEKSA----
+-------------------------EGKLAKVALVTITLWFMAWTPYLVINCMGLFKF-E
+G---LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKVDDG
+K-SSDAQSQATASEAESKA-----------------------------------------
+---------------------------------------------------
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+---------------------------------------------------------MDS
+FAAVATQLGPQFA-----APS--------NGSVVDKVTPDMAH--LISPYWDQFPAMDPI
+WAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMM
+GINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTI
+PLALGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSY
+LIFYSIFVYYIPLFLICYSYWFIIAAVSAH------------------------------
+------------------------------------------------------------
+-----------------------------EKAMREQAKKMNVKSLRS-SEDADKSA----
+-------------------------EGKLAKVALVTISLWFMAWTPYLVINCMGLFKF-E
+G---LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKVDDG
+K-SSEAQSQATTSEAESKA-----------------------------------------
+---------------------------------------------------
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+----------------------------------------------------MERSHLPE
+TPFDLAHSGPRFQ-----AQSSG------NGSVLDNVLPDMAH--LVNPYWSRFAPMDPM
+MSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVM
+IINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTI
+KTSIMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNPRSY
+LITYSLFVYYTPLFLICYSYWFIIAAVAAH------------------------------
+------------------------------------------------------------
+-----------------------------EKAMREQAKKMNVKSLRS-SEDCDKSA----
+-------------------------EGKLAKVALTTISLWFMAWTPYLVICYFGLFKI-D
+G---LTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GNTDEP
+KPDAPASDTETTSEADSKA-----------------------------------------
+---------------------------------------------------
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+----------------------------------------------------MERSLLPE
+PPLAMALLGPRFE-----AQTGG------NRSVLDNVLPDMAP--LVNPHWSRFAPMDPT
+MSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVM
+IINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTI
+KTSIMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNPRSY
+LITYSLFVYYTPLFMICYSYWFIIATVAAH------------------------------
+------------------------------------------------------------
+-----------------------------EKAMRDQAKKMNVKSLRS-SEDCDKSA----
+-------------------------ENKLAKVALTTISLWFMAWTPYLIICYFGLFKI-D
+G---LTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GTTDEP
+KPDAPPSDTETTSEAESKD-----------------------------------------
+---------------------------------------------------
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+------------------------------------------------------------
+---MIAVSGPSYE-----AFSYGGQARFNNQTVVDKVPPDMLH--LIDANWYQYPPLNPM
+WHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPM
+VINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KPLSI
+NGALIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLSASY
+LVCYGIWVYFVPLFLIIYSYWFIIQAVAAH------------------------------
+------------------------------------------------------------
+-----------------------------EKNMREQAKKMNVASLRS-SENQNTSA----
+-------------------------ECKLAKVALMTISLWFMAWTPYLVINFSGIFNL-V
+K---ISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------AAEPS
+SDAVSTTSGTTTVTDNEKSNA---------------------------------------
+---------------------------------------------------
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+------------------------------------------------------------
+-----MANQLSYS-----SLGWPYQP---NASVVDTMPKEMLY--MIHEHWYAFPPMNPL
+WYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTM
+TSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-APLTH
+KKATLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSSASY
+VVIYGLAVYFLPLITMIYCYFFIVHAVAEH------------------------------
+------------------------------------------------------------
+-----------------------------EKQLREQAKKMNVASLRANADQQKQSA----
+-------------------------ECRLAKVAMMTVGLWFMAWTPYLIISWAGVFSSGT
+R---LTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GSGESG
+SDVKSEASATTTMEEKPKIPEA--------------------------------------
+---------------------------------------------------
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+------------------------------------------------------------
+----------MVESTTLVNQTWWY-----NPTVD------------IHPHWAKFDPIPDA
+VYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLK
+TISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSH
+RRAFLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPSTRSF
+ILCMYFCGFMLPIIIIAFCYFNIVMSVSNH------------------------------
+------------------------------------------------------------
+-----------------------------EKEMAAMAKRLNAKELR--KAQAGASA----
+-------------------------EMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAE
+W---VTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDA
+NDAEEEVVASER--GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPPQ
+GAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+------------------------------------------------------------
+-----------MGRDLRDNETWWY-----NPSIV------------VHPHWREFDQVPDA
+VYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLM
+TISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSH
+RRAFIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTTRSN
+ILCMFILGFFGPILIIFFCYFNIVMSVSNH------------------------------
+------------------------------------------------------------
+-----------------------------EKEMAAMAKRLNAKELR--KAQAGANA----
+-------------------------EMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLE
+W---VTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDD
+KDAETEIPAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPPQ
+GY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+---------MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLS-
+--EVTASPAPTW------------DAPPDNASGCGEQIN-----------------YGRV
+EKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFV
+SVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNG
+KCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GY
+TIYSTAVAFYIPMSVMLFMYYQIYKAAR--------------------------------
+------------------KSAAKHKFPGFPRVEPDSVIAL--------------------
+-----------------------------NGIVKLQKEVEECANLSRLL-----------
+-------------KHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGT
+SCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMH
+EALKLAERPERPEFVLQNADYCRKKGHDS-------------------------------
+---------------------------------------------------
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+-----------------------------------------------------MPHLLSG
+FLEVTASPAPTW------------DAPPDNVSGCGEQIN-----------------YGRV
+EKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFV
+SVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNG
+KCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GY
+TIYSTAVAFYIPMSVMLFMYYQIYKAAR--------------------------------
+------------------KSAAKHKFPGFPRVQPESVISL--------------------
+-----------------------------NGVVKLQKEVEECANLSRLL-----------
+-------------KHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGT
+SCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYRNINRKLSAAGMH
+EALKLAERPERSEFVLQNSDHCGKKGHDT-------------------------------
+---------------------------------------------------
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+-----------------------------------------------------MPHLLSG
+FLEVTASPAPTW------------DAPPDNVSGCGEQIN-----------------YGRV
+EKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFV
+SVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNG
+KCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GY
+TIYSTAVAFYIPMSVMLFMYYQIYKAAR--------------------------------
+------------------KSAAKHKFPGFPRVQPESVISL--------------------
+-----------------------------NGVVKLQKEVEECANLSRLL-----------
+-------------KHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGT
+SCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMH
+EALKLAERPERSEFVLQNSDHCGKKGHDT-------------------------------
+---------------------------------------------------
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+----------MDVLSPGQ-------GN----------------------NTTSPPAPFET
+GGNTTGISDVTV-----------------------------------------------S
+YQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMA
+ALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTP
+RRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH----------GY
+TIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK---------------------------
+------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR----
+-----NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG--PT
+PCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CES
+SCH-MPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRQ----------
+------------------------------------------------------------
+---------------------------------------------------
+> 33=p A35181 serotonin receptor class 1A - rat
+----------MDVFSFGQ-------GN----------------------NTTASQEPFGT
+GGNVTSISDVTF-----------------------------------------------S
+YQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMA
+ALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTP
+RRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH----------GY
+TIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK---------------------------
+------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG----
+-----DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG--SN
+SYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CES
+SCH-MPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRR----------
+------------------------------------------------------------
+---------------------------------------------------
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLR----------------------STGLTTPGLSP
+TGLVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATN-----MTDDRYWSLTVYSHE
+HLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLS
+VVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSA
+RRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GY
+TIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSV
+VSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS-----
+-----SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS----
+---------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-VDP
+E-G-IPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYRRGHR--------
+------------------------------------------------------------
+---------------------------------------------------
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLR----------------------STGLTTPGLSP
+TGLVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATN-----MTDDRYWSLTVYSHE
+HLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLS
+VVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSA
+RRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GY
+TIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSV
+VSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS-----
+-----SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS----
+---------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-VDP
+E-G-IPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYRRGHR--------
+------------------------------------------------------------
+---------------------------------------------------
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+-MEGAEGQEELDWEAL--YLRLP--LQ----------------------NCSWNSTGWEP
+NWNVTVVPNTTW---------WQASAPFDTPAALVRAAAK--------------------
+-----AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLG
+AVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTA
+KRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV----------GY
+QIFATASSFYVPVLIILILYWRIYQTARKRIR----------------------------
+-----------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGIAAA
+VVAVIGRPLPTISETTTTGFTNVSS----NNTS---PEKQSCANGLEADPPTTGYGAVAA
+AYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-CDC
+E---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRVRRRRAPQ-----
+------------------------------------------------------------
+---------------------------------------------------
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+------------------------------------------------------------
+---------MNGTE--GDNFYVP----FSNKTGLARSPYEYPQYYLAEPWK---------
+YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTM
+YTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGNT
+HAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESYV
+VYMFVVHFLVPFVIIFFCYGRLLCTV----------------------------------
+------------------------------------------------------------
+-------------------KEAAAAQQ-----------------------------ESAS
+TQKA----------EKEVTRMVVLMVIGFLVCWVPYASVAFYIFT---HQGSD-FGATFM
+TLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCCGKN------PLGDDE--SGASTSKT
+EVSSVS-TSPVSPA----------------------------------------------
+-----------------------------------------
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+------------------------------------------------------------
+---------MNGTE--GPNFYVP----FSNITGVVRSPFEQPQYYLAEPWQ---------
+FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTL
+YTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGEN
+HAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESFV
+IYMFVVHFTIPMIVIFFCYGQLVFTV----------------------------------
+------------------------------------------------------------
+-------------------KEAAAQQQ-----------------------------ESAT
+TQKA----------EKEVTRMVIIMVIFFLICWLPYASVAMYIFT---HQGSN-FGPIFM
+TLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCCGKN------PLGDDE--ASATASKT
+ETSQ------VAPA----------------------------------------------
+-----------------------------------------
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+------------------------------------------------------------
+---------MNGTE--GINFYVP----MSNKTGVVRSPFEYPQYYLAEPWK---------
+YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTF
+YTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSAT
+HAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESYV
+LYMFVIHFIIPVVVIFFSYGRLICKV----------------------------------
+------------------------------------------------------------
+-------------------REAAAQQQ-----------------------------ESAT
+TQKA----------EKEVTRMVILMVLGFMLAWTPYAVVAFWIFT---NKGAD-FTATLM
+AVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICCGKN------PFGDEDVSSTVSQSKT
+EVSSVS-SSQVSPA----------------------------------------------
+-----------------------------------------
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+------------------------------------------------------------
+---------MNGTE--GKNFYVP----MSNRTGLVRSPFEYPQYYLAEPWQ---------
+FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTF
+YTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSS
+HAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNNESYV
+IYMFVCHFILPVAVIFFTYGRLVCTV----------------------------------
+------------------------------------------------------------
+-------------------KAAAAQQQ-----------------------------DSAS
+TQKA----------EREVTKMVILMVFGFLIAWTPYATVAAWIFF---NKGAD-FSAKFM
+AIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFCGKN------PLGDDE-SSTVSTSKT
+EVSS------VSPA----------------------------------------------
+-----------------------------------------
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+------------------------------------------------------------
+---------MNGTE--GNNFYVP----LSNRTGLVRSPFEYPQYYLAEPWQ---------
+FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTF
+YTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSST
+HASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNNESYV
+LYMFICHFILPVTIIFFTYGRLVCTV----------------------------------
+------------------------------------------------------------
+-------------------KAAAAQQQ-----------------------------DSAS
+TQKA----------EREVTKMVILMVLGFLVAWTPYATVAAWIFF---NKGAA-FSAQFM
+AIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFCGKN------PLGDEE-SSTVSTSKT
+EVSS------VSPA----------------------------------------------
+-----------------------------------------
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+------------------------------------------------------------
+---------MKQVPEFHEDFYIPIPLDINNLS--AYSPFLVPQDHLGNQGI---------
+FMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSF
+YSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FTFKTP
+HAIAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNNESYV
+MFLFCFCFAVPFGTIVFCYGQLLITL----------------------------------
+------------------------------------------------------------
+-------------------KLAAKAQA-----------------------------DSAS
+TQKA----------EREVTKMVVVMVLGFLVCWAPYASFSLWIVS---HRGEE-FDLRMA
+TIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVCGKN-------IEEDE--ASTSSQVT
+QVSS------VAPEK---------------------------------------------
+-----------------------------------------
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+------------------------------------------------------------
+---------MRKMS--EEEFYL-----FKNISSV--GPWDGPQYHIAPVWA---------
+FYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPVF
+VASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FRFSSK
+HALTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRSESYT
+WFLFIFCFIVPLSLICFSYTQLLRAL----------------------------------
+------------------------------------------------------------
+-------------------KAVAAQQQ-----------------------------ESAT
+TQKA----------EREVSRMVVVMVGSFCVCYVPYAAFAMYMVN---NRNHG-LDLRLV
+TIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVCGKA-------MTDES--DTCSSQKT
+EVSTVS-STQVGPN----------------------------------------------
+-----------------------------------------
+> 8=opsin, greensensitive human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------DLAETVIA-STISI
+VNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAK
+LAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYM
+IVLMVTCCITPLSIIVLCYLQVWLAI----------------------------------
+------------------------------------------------------------
+-------------------RAVAKQQK-----------------------------ESES
+TQKA----------EKEVTRMVVVMVLAFC------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+----------------------------------------------------------MA
+QQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNS-TRGPFEGPNYHIAPRWV---------
+YHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISV
+VNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VRFDAK
+LAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYM
+IVLMVTCCITPLSIIVLCYLQVWLAI----------------------------------
+------------------------------------------------------------
+-------------------RAVAKQQK-----------------------------ESES
+TQKA----------EKEVTRMVVVMVLAFCFCWGPYAFFACFAAA---NPGYP-FHPLMA
+ALPAFFAKSATIYNPVIYVFMNRQFRNCILQLF-----------GKKVDDGSELSSASKT
+EVSSV---SSVSPA----------------------------------------------
+-----------------------------------------
+> 10== Z68193 1 human Red Opsin <>[]
+----------------------------------------------------------MA
+QQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNS-TRGPFEGPNYHIAPRWV---------
+YHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISI
+VNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAK
+LAIVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYM
+IVLMVTCCIIPLAIIMLCYLQVWLAI----------------------------------
+------------------------------------------------------------
+-------------------RAVAKQQK-----------------------------ESES
+TQKA----------EKEVTRMVVVMIFAYCVCWGPYTFFACFAAA---NPGYA-FHPLMA
+ALPAYFAKSATIYNPVIYVFMNRQFRNCILQLF-----------GKKVDDGSELSSASKT
+EVSSV---SSVSPA----------------------------------------------
+-----------------------------------------
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+----------------------------------------------------------MT
+EAWNVAVFAARRSRD-DDDTTRGSVFTYTNTNN-TRGPFEGPNYHIAPRWV---------
+YNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISV
+FNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IKFDSK
+LAIIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGCQSFM
+LTLMITCCFLPLFIIIVCYLQVWMAI----------------------------------
+------------------------------------------------------------
+-------------------RAVAAQQK-----------------------------ESES
+TQKA----------EREVSRMVVVMIVAFCICWGPYASFVSFAAA---NPGYA-FHPLAA
+ALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLF-----------GKKVDDGSEASTTSRT
+EVSSVS-NSSVAPA----------------------------------------------
+-----------------------------------------
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+-----------------------------------------------------------M
+AAWEAAFAARRRHE--EEDTTRDSVFTYTNSNN-TRGPFEGPNYHIAPRWV---------
+YNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISV
+INQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IKFDGK
+LAVAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGVQSYM
+VVLMVTCCFFPLAIIILCYLQVWLAI----------------------------------
+------------------------------------------------------------
+-------------------RAVAAQQK-----------------------------ESES
+TQKA----------EKEVSRMVVVMIVAYCFCWGPYTFFACFAAA---NPGYA-FHPLAA
+ALPAYFAKSATIYNPIIYVFMNRQFRNCILQLF-----------GKKVDDGSEVST-SRT
+EVSSVS-NSSVSPA----------------------------------------------
+-----------------------------------------
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+------------------------------------------------------------
+----------------------------MSSNSSQAPPNGTPGPFDGPQWP--YQAPQST
+YVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSL
+SNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQFQRR
+HAVSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGS--NNNSYI
+LSLFVTCFVLPLSLILFSYTNLLLTL----------------------------------
+------------------------------------------------------------
+-------------------RAAAAQQK-----------------------------EADT
+TQRA----------EREVTRMVIVMVMAFLLCWLPYSTFALVVAT---HKGII-IQPVLA
+SLPSYFSKTATVYNPIIYVFMNKQFQSCLLEMLCCGYQ------PQRTGKASPGTPGPHA
+DVTAAGLRNKVMPAHPV-------------------------------------------
+-----------------------------------------
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+------------------------------------------------------MESGNV
+SSSLFGNVSTALRPEARLSAE--------TRLLGWNVPPEELR-HIPEHWLTYPEPPESM
+NYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIFI
+YNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTHG
+KAIAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFV
+ACIFFFSFVCPTTMITYYYSQIVGHVFSH-------------------------------
+------------------------------------------------------------
+------------------EKALRDQAKKMNVESLRS-------------------NVDKN
+KETA----------EIRIAKAAITICFLFFCSWTPYGVMSLIGAF---GDKTL-LTPGAT
+MIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL---------NEKAPESSAVAST
+STTQEPQQTTAA------------------------------------------------
+-----------------------------------------
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+------------------------------------------------------MEYHNV
+S-SVLGNVSSVLRPDARLSAE--------SRLLGWNVPPDELR-HIPEHWLIYPEPPESM
+NYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIFI
+YNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTHG
+KAIAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFV
+ACIFFFSFVCPTTMITYYYSQIVGHVFSH-------------------------------
+------------------------------------------------------------
+------------------EKALRDQAKKMNVDSLRS-------------------NVDKS
+KEAA----------EIRIAKAAITICFLFFASWTPYGVMSLIGAF---GDKTL-LTPGAT
+MIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI---------SEKAPESRAAIST
+STTQEQQQTTAA------------------------------------------------
+-----------------------------------------
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+------------------------------------------------------ME----
+--PLCNASEPPLRPEARSSGNGD------LQFLGWNVPPDQIQ-YIPEHWLTQLEPPASM
+HYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF-
+-NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFT
+KAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFV
+GTIFFFSFVCPTLMILYYYSQIVGHVFSH-------------------------------
+------------------------------------------------------------
+------------------EKALREQAKKMNVESLRS-------------------NVDKS
+KETA----------EIRIAKAAITICFLFFVSWTPYGVMSLIGAF---GDKSL-LTQGAT
+MIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV---------NEKSGEISSAQST
+TTQEQ-QQTTAA------------------------------------------------
+-----------------------------------------
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+------------------------------------------------------MD----
+--ALCNASEPPLRPEARMSSGSDE-----LQFLGWNVPPDQIQ-YIPEHWLTQLEPPASM
+HYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIFI
+YNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFT
+KAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFV
+GTIFLFSFVVPTLMILYYYSQIVGHVFNH-------------------------------
+------------------------------------------------------------
+------------------EKALREQAKKMNVESLRS-------------------NVDKS
+KETA----------EIRIAKAAITICFLFFVSWTPYGVMSLIGAF---GDKSL-LTPGAT
+MIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV---------NEKSGEASSAQST
+TTQEQTQQTSAA------------------------------------------------
+-----------------------------------------
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+------------------------------------------------------------
+---MTNATGPQMAYYGAASMDFGYPE---GVSIVDFVRPEIKP-YVHQHWYNYPPVNPMW
+HYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFT
+YNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PKLTTG
+KAVVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNTFSYN
+IFIFVFDYFLPAAIIVFSYVFIVKAIFAH-------------------------------
+------------------------------------------------------------
+------------------EAAMRAQAKKMNVSTLRS--------------------NEAD
+AQRA----------EIRIAKTALVNVSLWFICWTPYALISLKGVM---GDTSG-ITPLVS
+TLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HETETKSNDDSQSNST
+VAQDKA------------------------------------------------------
+-----------------------------------------
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+------------------------------------------------------------
+---MANVTGPQMAFYGSGAATFGYPE---GMTVADFVPDRVKH-MVLDHWYNYPPVNPMW
+HYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFC
+YNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PKLTQG
+KATFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNTITYN
+ICIFIFDFFLPASVIVFSYVFIVKAIFAH-------------------------------
+------------------------------------------------------------
+------------------EAAMRAQAKKMNVTNLRS--------------------NEAE
+TQRA----------EIRIAKTALVNVSLWFICWTPYAAITIQGLL---GNAEG-ITPLLT
+TLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HEKDPNDVEENQSSNT
+QTQEKS------------------------------------------------------
+-----------------------------------------
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+---------------------------------------------------------MES
+FAVAAAQLGPHFA-----PLS--------NGSVVDKVTPDMAH-LISPYWNQFPAMDPIW
+AKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMG
+INLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIP
+LALGKM---------------------------YVPEGNLTSCGIDYLE--RDWNPRSYL
+IFYSIFVYYIPLFLICYSYWFIIAAVSAH-------------------------------
+------------------------------------------------------------
+------------------EKAMREQAKKMNVKSLRS--------------------SEDA
+EKSA----------EGKLAKVALVTITLWFMAWTPYLVINCMGLF---KF-EG-LTPLNT
+IWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKVDDGK-SSDAQSQA
+TASEAESKA---------------------------------------------------
+-----------------------------------------
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+---------------------------------------------------------MES
+FAVAAAQLGPHFA-----PLS--------NGSVVDKVTPDMAH-LISPYWNQFPAMDPIW
+AKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMG
+INLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIP
+LALGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYL
+IFYSIFVYYIPLFLICYSYWFIIAAVSAH-------------------------------
+------------------------------------------------------------
+------------------EKAMREQAKKMNVKSLRS--------------------SEDA
+EKSA----------EGKLAKVALVTITLWFMAWTPYLVINCMGLF---KF-EG-LTPLNT
+IWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKVDDGK-SSDAQSQA
+TASEAESKA---------------------------------------------------
+-----------------------------------------
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+---------------------------------------------------------MDS
+FAAVATQLGPQFA-----APS--------NGSVVDKVTPDMAH-LISPYWDQFPAMDPIW
+AKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMG
+INLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIP
+LALGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYL
+IFYSIFVYYIPLFLICYSYWFIIAAVSAH-------------------------------
+------------------------------------------------------------
+------------------EKAMREQAKKMNVKSLRS--------------------SEDA
+DKSA----------EGKLAKVALVTISLWFMAWTPYLVINCMGLF---KF-EG-LTPLNT
+IWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKVDDGK-SSEAQSQA
+TTSEAESKA---------------------------------------------------
+-----------------------------------------
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+----------------------------------------------------MERSHLPE
+TPFDLAHSGPRFQ-----AQSSG------NGSVLDNVLPDMAH-LVNPYWSRFAPMDPMM
+SKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMI
+INFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIK
+TSIMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNPRSYL
+ITYSLFVYYTPLFLICYSYWFIIAAVAAH-------------------------------
+------------------------------------------------------------
+------------------EKAMREQAKKMNVKSLRS--------------------SEDC
+DKSA----------EGKLAKVALTTISLWFMAWTPYLVICYFGLF---KI-DG-LTPLTT
+IWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GNTDEPKPDAPASDTE
+TTSEADSKA---------------------------------------------------
+-----------------------------------------
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+----------------------------------------------------MERSLLPE
+PPLAMALLGPRFE-----AQTGG------NRSVLDNVLPDMAP-LVNPHWSRFAPMDPTM
+SKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMI
+INFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIK
+TSIMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNPRSYL
+ITYSLFVYYTPLFMICYSYWFIIATVAAH-------------------------------
+------------------------------------------------------------
+------------------EKAMRDQAKKMNVKSLRS--------------------SEDC
+DKSA----------ENKLAKVALTTISLWFMAWTPYLIICYFGLF---KI-DG-LTPLTT
+IWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GTTDEPKPDAPPSDTE
+TTSEAESKD---------------------------------------------------
+-----------------------------------------
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+------------------------------------------------------------
+---MIAVSGPSYE-----AFSYGGQARFNNQTVVDKVPPDMLH-LIDANWYQYPPLNPMW
+HGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMV
+INCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KPLSIN
+GALIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLSASYL
+VCYGIWVYFVPLFLIIYSYWFIIQAVAAH-------------------------------
+------------------------------------------------------------
+------------------EKNMREQAKKMNVASLRS--------------------SENQ
+NTSA----------ECKLAKVALMTISLWFMAWTPYLVINFSGIF---NL-VK-ISPLFT
+IWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------AAEPSSDAVSTTSGT
+TTVTDNEKSNA-------------------------------------------------
+-----------------------------------------
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+------------------------------------------------------------
+-----MANQLSYS-----SLGWPYQP---NASVVDTMPKEMLY-MIHEHWYAFPPMNPLW
+YSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMT
+SNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-APLTHK
+KATLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSSASYV
+VIYGLAVYFLPLITMIYCYFFIVHAVAEH-------------------------------
+------------------------------------------------------------
+------------------EKQLREQAKKMNVASLRA-------------------NADQQ
+KQSA----------ECRLAKVAMMTVGLWFMAWTPYLIISWAGVF---SSGTR-LTPLAT
+IWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GSGESGSDVKSEASAT
+TTMEEKPKIPEA------------------------------------------------
+-----------------------------------------
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+------------------------------------------------------------
+----------MVESTTLVNQTWWY-----NPTVD-----------IHPHWAKFDPIPDAV
+YYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKT
+ISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHR
+RAFLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPSTRSFI
+LCMYFCGFMLPIIIIAFCYFNIVMSVSNH-------------------------------
+------------------------------------------------------------
+------------------EKEMAAMAKRLNAKELR---------------------KAQA
+GASA----------EMKLAKISMVIITQFMLSWSPYAIIALLAQF---GPAEW-VTPYAA
+ELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVAS
+ER--GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPPQGAYPPPQGYP
+PQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+------------------------------------------------------------
+-----------MGRDLRDNETWWY-----NPSIV-----------VHPHWREFDQVPDAV
+YYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMT
+ISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHR
+RAFIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTTRSNI
+LCMFILGFFGPILIIFFCYFNIVMSVSNH-------------------------------
+------------------------------------------------------------
+------------------EKEMAAMAKRLNAKELR---------------------KAQA
+GANA----------EMRLAKISIVIVSQFLLSWSPYAVVALLAQF---GPLEW-VTPYAA
+QLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAG
+ESSDAAPSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPPQGY--PPQGYP
+PQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+---------MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLS-
+--EVTASPAPTWDAPPDNASGCGEQINYGRVE----------------------------
+KVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVS
+VTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGK
+CMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYT
+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIAL-----------
+------------------------------------------------------------
+------------------NGIVKLQKEVEECANLSR-------------------LLKHE
+RKNI-----SIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC-IPLWVE
+RTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALKLAERPE
+RPEFVLQNADYCRKKGHDS-----------------------------------------
+-----------------------------------------
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+-----------------------------------------------------MPHLLSG
+FLEVTASPAPTWDAPPDNVSGCGEQINYGRVE----------------------------
+KVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVS
+VTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGK
+CMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYT
+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVQPESVISL-----------
+------------------------------------------------------------
+------------------NGVVKLQKEVEECANLSR-------------------LLKHE
+RKNI-----SIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC-IPLWVE
+RTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYRNINRKLSAAGMHEALKLAERPE
+RSEFVLQNSDHCGKKGHDT-----------------------------------------
+-----------------------------------------
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+-----------------------------------------------------MPHLLSG
+FLEVTASPAPTWDAPPDNVSGCGEQINYGRVE----------------------------
+KVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVS
+VTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGK
+CMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYT
+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVQPESVISL-----------
+------------------------------------------------------------
+------------------NGVVKLQKEVEECANLSR-------------------LLKHE
+RKNI-----SIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC-IPLWVE
+RTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALKLAERPE
+RSEFVLQNSDHCGKKGHDT-----------------------------------------
+-----------------------------------------
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPGQGN---------------------------------------NTTSPPAPFET
+GGNTTGISDVTVSY----------------------------------------------
+QVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAA
+LYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPR
+RAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDACTISKDH----------GYT
+IYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK----------------------------
+-----------TVKKVEKTGADTRHGASPAPQPKKS----------VNGESGSRNWRLGV
+ESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCA--PASFERKN
+ERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF---CESSCHMPTLLG
+AIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRQ--------------------
+------------------------------------------------------------
+-----------------------------------------
+> 33=p A35181 serotonin receptor class 1A - rat
+MDVFSFGQGN---------------------------------------NTTASQEPFGT
+GGNVTSISDVTFSY----------------------------------------------
+QVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAA
+LYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPR
+RAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDACTISKDH----------GYT
+IYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK----------------------------
+-----------TVRKVEKKGAGTSLGTSSAPPPKKS----------LNGQPGSGDWRRCA
+ENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESGSNSYA--PACLERKN
+ERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF---CESSCHMPALLG
+AIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRR--------------------
+------------------------------------------------------------
+-----------------------------------------
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLR----------------------STGLTTPGLSP
+TGLVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATN----MTDDRYWSLTVYSHEH
+LVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSV
+VSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSAR
+RILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYT
+IFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVV
+SDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQ
+IQIETAEAFANGCA----EEASIAMLERQ-CNNGKK-------------------ISSND
+TPYSRTREKLELKRERKAARTLAIITGAFLICWLPFFIIALIGPF---VDPEG-IPPFAR
+SFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYRRGHR------------------
+------------------------------------------------------------
+-----------------------------------------
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLR----------------------STGLTTPGLSP
+TGLVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATN----MTDDRYWSLTVYSHEH
+LVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSV
+VSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSAR
+RILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYT
+IFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVV
+SDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQ
+IQIETAEAFANGCA----EEASIAMLERQ-CNNGKK-------------------ISSND
+TPYSRTREKLELKRERKAARTLAIITGAFLICWLPFFIIALIGPF---VDPEG-IPPFAR
+SFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYRRGHR------------------
+------------------------------------------------------------
+-----------------------------------------
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+---------------------------MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEP
+NWNVTVVPNTTWWQ--------------------ASAPFDTPAALVR-------------
+AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGA
+VYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAK
+RVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV----------GYQ
+IFATASSFYVPVLIILILYWRIYQTARKRIRR----------------------------
+-----------------RRGATARGGVGPPPVPAGGALVA------GGGSGGIAAAVVAV
+IGRPLPTISETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKP
+KEAA------DSKRERKAAKTLAIITGAFVACWLPFFVLAILVPT---CDCE--VSPVLT
+SLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRVRRRRAPQ---------------
+------------------------------------------------------------
+-----------------------------------------
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+--------------------MNGTE--GDNFYVPFSNKTG--LARSP-------------
+-------------------------------YEYPQY-YLAEPW----------------
+------KYSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLF
+G-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN
+F-RFGNTHAIMGVAFTWIMALAC-AAPPLVG-WS-----RYIPEGMQCSCGPDYYTLNPN
+FNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQESA----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT--HQGSD-FGATFMTLPAF
+FAKSSALYNPVIYILMNKQFRNCMITTL-----CCGKNPLGDDE-SG-ASTSKTEVSSVS
+T-----------------------------------------------------------
+-----------------------------------SPV-------SP-A
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+--------------------MNGTE--GPNFYVPFSNITG--VVRSP-------------
+-------------------------------FEQPQY-YLAEPW----------------
+------QFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFG
+G-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN
+F-RFGENHAIMGVAFTWVMALAC-AAPPLVG-WS-----RYIPEGMQCSCGIDYYTLKPE
+VNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESA----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----TTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFT--HQGSN-FGPIFMTLPAF
+FAKTASIYNPIIYIMMNKQFRNCMLTSL-----CCGKNPLGDDE-AS-ATASKTE-----
+T-----------------------------------------------------------
+-----------------------------------SQV-------AP-A
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+--------------------MNGTE--GINFYVPMSNKTG--VVRSP-------------
+-------------------------------FEYPQY-YLAEPW----------------
+------KYRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACF
+G-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN
+F-RFSATHAMMGIAFTWVMAFSC-AAPPLFG-WS-----RYMPEGMQCSCGPDYYTHNPD
+YHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQESA----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----TTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT--NKGAD-FTATLMAVPAF
+FSKSSSLYNPIIYVLMNKQFRNCMITTI-----CCGKNPFGDEDVSSTVSQSKTEVSSVS
+S-----------------------------------------------------------
+-----------------------------------SQV-------SP-A
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+--------------------MNGTE--GKNFYVPMSNRTG--LVRSP-------------
+-------------------------------FEYPQY-YLAEPW----------------
+------QFKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCF
+G-FTVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS
+F-KFSSSHAFAGIAFTWVMALAC-AAPPLFG-WS-----RYIPEGMQCSCGPDYYTLNPD
+YNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDSA----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFF--NKGAD-FSAKFMAIPAF
+FSKSSALYNPVIYVLLNKQFRNCMLTTI-----FCGKNPLGDDE-SSTVSTSKTEVSS--
+------------------------------------------------------------
+-------------------------------------V-------SP-A
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+--------------------MNGTE--GNNFYVPLSNRTG--LVRSP-------------
+-------------------------------FEYPQY-YLAEPW----------------
+------QFKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCF
+G-FTVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS
+F-KFSSTHASAGIAFTWVMAMAC-AAPPLVG-WS-----RYIPEGIQCSCGPDYYTLNPE
+YNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDSA----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFF--NKGAA-FSAQFMAIPAF
+FSKTSALYNPVIYVLLNKQFRSCMLTTL-----FCGKNPLGDEE-SSTVSTSKTEVSS--
+------------------------------------------------------------
+-------------------------------------V-------SP-A
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+--------------------MKQVPEFHEDFYIPIPLDINNLSAYSP-------------
+-------------------------------FLVPQD-HLGNQG----------------
+------IFMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIF
+G-SPLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN
+F-TFKTPHAIAGCILPWISALAA-SLPPLFG-WS-----RYIPEGLQCSCGPDWYTTNNK
+YNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKAQADSA----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVS--HRGEE-FDLRMATIPSC
+LSKASTVYNPVIYVLMNKQFRSCMM-KM-----VCGKN-IEEDE-AS-TSSQVTQVSS--
+------------------------------------------------------------
+-------------------------------------V-------APEK
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+--------------------MRKMS--EEEFYL-FKNISS----VGP-------------
+-------------------------------WDGPQY-HIAPVW----------------
+------AFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIF
+S-VFPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN
+F-RFSSKHALTVVLATWTIGIGV-SIPPFFG-WS-----RFIPEGLQCSCGPDWYTVGTK
+YRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESA----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----TTQKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN--NRNHG-LDLRLVTIPSF
+FSKSACIYNPIIYCFMNKQFQACIM-KM-----VCGKA-MTDES-DT-CSSQKTEVSTVS
+S-----------------------------------------------------------
+-----------------------------------TQV-------GP-N
+> 8=opsin, greensensitive human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------------------DLAETVI
+A-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN
+V-RFDAKLAIVGIAFSWIWAAVW-TAPPIFG-WS-----RYWPHGLKTSCGPDVFSGSSY
+PGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEKEVTRMVVVMVLAFC----------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------------------------
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+MAQQWS-LQRLAGRHPQDSYEDSTQ--SSIFTYTNSNST-----RGP-------------
+-------------------------------FEGPNY-HIAPRW----------------
+------VYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVI
+A-STISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN
+V-RFDAKLAIVGIAFSWIWAAVW-TAPPIFG-WS-----RYWPHGLKTSCGPDVFSGSSY
+PGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA--NPGYP-FHPLMAALPAF
+FAKSATIYNPVIYVFMNRQFRNCILQLF-------GKKVDDGSE-LS--SASKTEVSSV-
+------------------------------------------------------------
+-----------------------------------SSV-------SP-A
+> 10== Z68193 1 human Red Opsin <>[]
+MAQQWS-LQRLAGRHPQDSYEDSTQ--SSIFTYTNSNST-----RGP-------------
+-------------------------------FEGPNY-HIAPRW----------------
+------VYHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVI
+A-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN
+V-RFDAKLAIVGIAFSWIWSAVW-TAPPIFG-WS-----RYWPHGLKTSCGPDVFSGSSY
+PGVQSYMIVLMVTCCIIPLAIIMLCYLQVWLAIRAVAKQQKESE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA--NPGYA-FHPLMAALPAY
+FAKSATIYNPVIYVFMNRQFRNCILQLF-------GKKVDDGSE-LS--SASKTEVSSV-
+------------------------------------------------------------
+-----------------------------------SSV-------SP-A
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDD--DDTTR--GSVFTYTNTNNT-----RGP-------------
+-------------------------------FEGPNY-HIAPRW----------------
+------VYNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLV
+A-STISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN
+I-KFDSKLAIIGIVFSWVWAWGW-SAPPIFG-WS-----RYWPHGLKTSCGPDVFSGSVE
+LGCQSFMLTLMITCCFLPLFIIIVCYLQVWMAIRAVAAQQKESE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAA--NPGYA-FHPLAAALPAY
+FAKSATIYNPVIYVFMNRQFRNCIMQLF-------GKKVDDGSE-AS--TTSRTEVSSVS
+N-----------------------------------------------------------
+-----------------------------------SSV-------AP-A
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MA-AWE-AAFAARRRHEE--EDTTR--DSVFTYTNSNNT-----RGP-------------
+-------------------------------FEGPNY-HIAPRW----------------
+------VYNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVI
+A-STISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN
+I-KFDGKLAVAGILFSWLWSCAW-TAPPIFG-WS-----RYWPHGLKTSCGPDVFSGSSD
+PGVQSYMVVLMVTCCFFPLAIIILCYLQVWLAIRAVAAQQKESE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----STQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA--NPGYA-FHPLAAALPAY
+FAKSATIYNPIIYVFMNRQFRNCILQLF-------GKKVDDGSE-VS--T-SRTEVSSVS
+N-----------------------------------------------------------
+-----------------------------------SSV-------SP-A
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+------------------------M--SSNSSQAPPNGT-----PGP-------------
+-------------------------------FDGPQWPYQAPQS----------------
+------TYVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLC
+G-SSVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD
+F-QFQRRHAVSGCAFTWGWALLW-SAPPLLG-WS-----SYVPEGLRTSCGPNWYTGGSN
+--NNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEAD----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----TTQRAEREVTRMVIVMVMAFLLCWLPYSTFALVVAT--HKGII-IQPVLASLPSY
+FSKTATVYNPIIYVFMNKQFQSCLLEML-----CCGYQPQRTGK-AS--PGTPGPHADVT
+A-----------------------------------------------------------
+-----------------------------------AGLRNKVMPAHP-V
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPE----ARLSA---E---TRLLGWNVPP-------------
+-------------------------------EELR---HIPEHWLTYPE-----------
+--PPESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK
+--TPIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG
+--KMTHGKAIAMIIFIYMYATPW-VVACYTETWG-----RFVPEGYLTSCTFDYLTDN--
+FDTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKMNVESLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+SNVDKNKETAEIRIAKAAITICFLFFCSWTPYGVMSLIGAF--GDKTL-LTPGATMIPAC
+ACKMVACIDPFVYAISHPRYRMELQKRCPWL--ALNEKAPESSA----VASTST---TQE
+P-----------------------------------------------------------
+-----------------------------------QQT-------TA-A
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVL-GNVSSVLRPD----ARLSA---E---SRLLGWNVPP-------------
+-------------------------------DELR---HIPEHWLIYPE-----------
+--PPESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK
+--TPIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG
+--KMTHGKAIAMIIFIYLYATPW-VVACYTESWG-----RFVPEGYLTSCTFDYLTDN--
+FDTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKMNVDSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+SNVDKSKEAAEIRIAKAAITICFLFFASWTPYGVMSLIGAF--GDKTL-LTPGATMIPAC
+TCKMVACIDPFVYAISHPRYRMELQKRCPWL--AISEKAPESRA----AISTST---TQE
+Q-----------------------------------------------------------
+-----------------------------------QQT-------TA-A
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+ME------PLCNASEPPLRPE----AR-SSGNGD---LQFLGWNVPP-------------
+-------------------------------DQIQ---YIPEHWLTQLE-----------
+--PPASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK
+--APIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR
+--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFWD-----RFVPEGYLTSCSFDYLSDN--
+FDTRLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKKMNVESLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+SNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMSLIGAF--GDKSL-LTQGATMIPAC
+TCKLVACIDPFVYAISHPRYRLELQKRCPWL--GVNEKSGEISS----AQSTTT---QEQ
+------------------------------------------------------------
+-----------------------------------QQT-------TA-A
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MD------ALCNASEPPLRPE----ARMSSGSDE---LQFLGWNVPP-------------
+-------------------------------DQIQ---YIPEHWLTQLE-----------
+--PPASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK
+--APIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR
+--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFWD-----RFVPEGYLTSCSFDYLSDN--
+FDTRLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKKMNVESLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+SNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMSLIGAF--GDKSL-LTPGATMIPAC
+TCKLVACIEPFVYAISHPRYRMELQKRCPWL--GVNEKSGEASS----AQSTTT---QEQ
+T-----------------------------------------------------------
+-----------------------------------QQT-------SA-A
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+MT-----------NATGPQMAYYGAASMDFGYPE---GVSIVDFVRP-------------
+-------------------------------EIKP---YVHQHWYNYPP-----------
+--VNPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTT
+N-VPFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG
+P-KLTTGKAVVFALISWVIAIGC-ALPPFFG-WG-----NYILEGILDSCSYDYLTQD--
+FNTFSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKKMNVSTLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-NEADAQRAEIRIAKTALVNVSLWFICWTPYALISLKGVM--GDTSG-ITPLVSTLPAL
+LAKSCSCYNPFVYAISHPKYRLAITQHLPWF--CVHETETKSND----DSQSNS---TVA
+Q-----------------------------------------------------------
+---------------------------------------------DK-A
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+MA-----------NVTGPQMAFYGSGAATFGYPE---GMTVADFVPD-------------
+-------------------------------RVKH---MVLDHWYNYPP-----------
+--VNPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTT
+N-FPPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG
+P-KLTQGKATFMCGLAWVISVGW-SLPPFFG-WG-----SYTLEGILDSCSYDYFTRD--
+MNTITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKKMNVTNLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-NEAETQRAEIRIAKTALVNVSLWFICWTPYAAITIQGLL--GNAEG-ITPLLTTLPAL
+LAKSCSCYNPFVYAISHPKFRLAITQHLPWF--CVHEKDPNDVE----ENQSSN---TQT
+Q-----------------------------------------------------------
+---------------------------------------------EK-S
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+ME-----SFAVAAAQLGPHFA-----PLS--------NGSVVDKVTP-------------
+-------------------------------DMAH---LISPYWNQFPA-----------
+--MDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMIT
+N-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG
+R-PMTIPLALGKM---------------------------YVPEGNLTSCGIDYLERD--
+WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGAC
+FAKSAACYNPIVYGISHPKYRLALKEKCPCC--VFGKVDDGKSS----DAQSQA-TASEA
+E-----------------------------------------------------------
+---------------------------------------------SK-A
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+ME-----SFAVAAAQLGPHFA-----PLS--------NGSVVDKVTP-------------
+-------------------------------DMAH---LISPYWNQFPA-----------
+--MDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMIT
+N-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG
+R-PMTIPLALGKIAYIWFMSSIW-CLAPAFG-WS-----RYVPEGNLTSCGIDYLERD--
+WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGAC
+FAKSAACYNPIVYGISHPKYRLALKEKCPCC--VFGKVDDGKSS----DAQSQA-TASEA
+E-----------------------------------------------------------
+---------------------------------------------SK-A
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MD-----SFAAVATQLGPQFA-----APS--------NGSVVDKVTP-------------
+-------------------------------DMAH---LISPYWDQFPA-----------
+--MDPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMIT
+N-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG
+R-PMTIPLALGKIAYIWFMSTIWCCLAPVFG-WS-----RYVPEGNLTSCGIDYLERD--
+WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGAC
+FAKSAACYNPIVYGISHPKYRLALKEKCPCC--VFGKVDDGKSS----EAQSQA-TTSEA
+E-----------------------------------------------------------
+---------------------------------------------SK-A
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQ-----AQSSG------NGSVLDNVLP-------------
+-------------------------------DMAH---LVNPYWSRFAP-----------
+--MDPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMAS
+Q-SPVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING
+T-PMTIKTSIMKILFIWMMAVFW-TVMPLIG-WS-----AYVPEGNLTACSIDYMTRM--
+WNPRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDCDKSAEGKLAKVALTTISLWFMAWTPYLVICYFGLF--KI-DG-LTPLTTIWGAT
+FAKTSAVYNPIVYGISHPKYRIVLKEKCPMC--VFGNTDEPKPD----APASDTETTSEA
+D-----------------------------------------------------------
+---------------------------------------------SK-A
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFE-----AQTGG------NRSVLDNVLP-------------
+-------------------------------DMAP---LVNPHWSRFAP-----------
+--MDPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMAS
+Q-SPVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING
+T-PMTIKTSIMKIAFIWMMAVFW-TIMPLIG-WS-----SYVPEGNLTACSIDYMTRQ--
+WNPRSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDCDKSAENKLAKVALTTISLWFMAWTPYLIICYFGLF--KI-DG-LTPLTTIWGAT
+FAKTSAVYNPIVYGISHPNDRLVLKEKCPMC--VCGTTDEPKPD----APPSDTETTSEA
+E-----------------------------------------------------------
+---------------------------------------------SK-D
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+MI-----------AVSGPSYE-----AFSYGGQARFNNQTVVDKVPP-------------
+-------------------------------DMLH---LIDANWYQYPP-----------
+--LNPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFC
+M-SPPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG
+K-PLSINGALIRIIAIWLFSLGW-TIAPMFG-WN-----RYVPEGNMTACGTDYFNRG--
+LLSASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKKMNVASLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SENQNTSAECKLAKVALMTISLWFMAWTPYLVINFSGIF--NL-VK-ISPLFTIWGSL
+FAKANAVYNPIVYGISHPKYRAALFAKFPSL--AC-AAEPSSDA----VSTTSG-TTTVT
+D-----------------------------------------------------------
+----------------------------------NEK--------SN-A
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+M-------------ANQLSYS-----SLGWPYQP---NASVVDTMPK-------------
+-------------------------------EMLY---MIHEHWYAFPP-----------
+--MNPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAF
+M-MPTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA
+A-PLTHKKATLLLLFVWIWSGGW-TILPFFG-WS-----RYVPEGNLTSCTVDYLTKD--
+WSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKKMNVASLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+ANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVF--SSGTR-LTPLATIWGSV
+FAKANSCYNPIVYGISHPRYKAALYQRFPSL--ACGSGESGSDV----KSEASA-TTTME
+E-----------------------------------------------------------
+----------------------------------KPKI-------PE-A
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+MV-------------ESTTLV-----NQTWWY-----NPTV-------------------
+--------------------------------------DIHPHWAKFDP-----------
+--IPDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAI
+NGFPLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAA
+SKKMSHRRAFLMIIFVWMWSIVW-SVGPVFN-WG-----AYVPEGILTSCSFDYLSTD--
+PSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKRLNAKELR-------
+------------------------------------------------------------
+------------------------------------------------------------
+K-AQ-AGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQF--GPAEW-VTPYAAELPVL
+FAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECED----ANDAEEEVVASE
+R--GGESRDAAQMKEMMAMMQKMQAQQAAYQP---PPPPQGYPPQGYPPQGAYPPPQGYP
+PQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQA-------YQ-A
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+MG-------------RDLR-D-----NETWWY-----NPSI-------------------
+--------------------------------------VVHPHWREFDQ-----------
+--VPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLV
+NGFPLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAA
+SKKMSHRRAFIMIIFVWLWSVLW-AIGPIFG-WG-----AYTLEGVLCNCSFDYISRD--
+STTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKELR-------
+------------------------------------------------------------
+------------------------------------------------------------
+K-AQ-AGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQF--GPLEW-VTPYAAQLPVM
+FAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETED----DKDAETEIPAGE
+SSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGY--PPQGYP
+PQGYPP---PPQGAPPQGAPP------AAPPQGVDNQA-------YQ-A
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDG-----------------GADPVAGS
+WAPHLLS------------------------EVTAS---PAPTW---DAPPDNASGCGEQ
+INYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVA
+V-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTY
+PVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKVCLISQDF------
+----GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------------PGFP
+RVEPDSVIALNG------------------------------------------------
+----IVKLQKE------------------VEECAN------------------LSRLLKH
+ERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTFLW
+LGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALKLAERPERPEFV
+L-----------------------------------------------------------
+-----------------------------------QNADYCRKKGHD-S
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+------------------------------------------------------------
+-MPHLLSGFL---------------------EVTAS---PAPTW---DAPPDNVSGCGEQ
+INYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVA
+V-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTY
+PVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKVCLISQDF------
+----GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------------PGFP
+RVQPESVISLNG------------------------------------------------
+----VVKLQKE------------------VEECAN------------------LSRLLKH
+ERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLW
+LGYANSLINPFIYAFFNRDLRPTSRSLLQCQYRNINRKLSAAGMHEALKLAERPERSEFV
+L-----------------------------------------------------------
+-----------------------------------QNSDHCGKKGHD-T
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+------------------------------------------------------------
+-MPHLLSGFL---------------------EVTAS---PAPTW---DAPPDNVSGCGEQ
+INYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVA
+V-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTY
+PVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKVCLISQDF------
+----GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------------PGFP
+RVQPESVISLNG------------------------------------------------
+----VVKLQKE------------------VEECAN------------------LSRLLKH
+ERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLW
+LGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALKLAERPERSEFV
+L-----------------------------------------------------------
+-----------------------------------QNSDHCGKKGHD-T
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPG-----------------------------------------------------
+--------------------QGNNT------TSPPAPFETGGNTTGISD-----------
+--VTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVL
+V-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDY
+VNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH------
+----GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQ
+PKK-----SVNG--ESGSRNWRLGVESKAGGALCANGAVRQGDDGAAL--EVIEVHRVGN
+SKEHLPLPSEAGPTPCAPAS------------------FERKNERNA-------------
+EAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CESSCH-MPTLLGAIINW
+LGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKF----------------------------
+------------------------------------------------------------
+-------------------------------------------CR---Q
+> 33=p A35181 serotonin receptor class 1A - rat
+MDVFSFG-----------------------------------------------------
+--------------------QGNNT------TASQEPFGTGGNVTSISD-----------
+--VTFSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVL
+V-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDY
+VNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH------
+----GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGTSLGTSSAPP
+PKK-----SLNG--QPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATL--EVIEVHRVGN
+SKEHLPLPSESGSNSYAPAC------------------LERKNERNA-------------
+EAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CESSCH-MPALLGAIINW
+LGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKF----------------------------
+------------------------------------------------------------
+-------------------------------------------CR---R
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRD-----------NASANDT------SATNM---TDDRYWSLTV-----------
+--YSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVL
+V-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDY
+IRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDPNN--DPDKTGTCIISQDK------
+----GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASP
+KTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSS
+SSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYS-------------
+RTREKLELKRERKAARTLAIITGAFLICWLPFFIIALIGPF-VDPE-G-IPPFARSFVLW
+LGYFNSLLNPIIYTIFSPEFRSAFQKILFGKY----------------------------
+------------------------------------------------------------
+-------------------------------------------RRGH-R
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRD-----------NASANDT------SATNM---TDDRYWSLTV-----------
+--YSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVL
+V-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDY
+IRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDPNN--DPDKTGTCIISQDK------
+----GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASP
+KTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSS
+SSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYS-------------
+RTREKLELKRERKAARTLAIITGAFLICWLPFFIIALIGPF-VDPE-G-IPPFARSFVLW
+LGYFNSLLNPIIYTIFSPEFRSAFQKILFGKY----------------------------
+------------------------------------------------------------
+-------------------------------------------RRGH-R
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+M--------------------------------------------------------EGA
+EGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVV---PNTTWWQASAPFDTP------
+--AALVRAAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACL
+V-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDY
+IHASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV------
+----GYQIFATASSFYVPVLIILILYWRIYQTARKRIRR------RRGATARGGVGPPPV
+PAG---------------------------------GALVAGGGSGGIAAAVVAV-----
+IGRPLPTISETTTTGFTNVSSNNTSPE--KQSCANGLEADPPTTGYGAVAAAYYPSLVRR
+KPKEAADSKRERKAAKTLAIITGAFVACWLPFFVLAILVPT-CD--CE-VSPVLTSLSLW
+LGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRR----------------------------
+------------------------------------------------------------
+----------------------------------------VRRRRAP-Q
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+M-------------------NGTE--GDNFYVPFSNKTGLA--RSPYEYPQY-YL-----
+------------------------------------------------------------
+--AEPWKYSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLF
+G-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN
+F-RFGNTHAIMGVAFTWIMALAC-AAPPLV-GWS-----RYIPEGMQCSCGPDYYTLNPN
+FNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQ-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT--HQGSD-FGATFMTLPAF
+FAKSSALYNPVIYILMNKQFRNCMITTL-----CCGKNPLGDDE--SGASTSKTEVSSVS
+T-----------------------------------------------------------
+-----------------------------------SPVSPA
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+M-------------------NGTE--GPNFYVPFSNITGVV--RSPFEQPQY-YL-----
+------------------------------------------------------------
+--AEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFG
+G-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN
+F-RFGENHAIMGVAFTWVMALAC-AAPPLV-GWS-----RYIPEGMQCSCGIDYYTLKPE
+VNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQ-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFT--HQGSN-FGPIFMTLPAF
+FAKTASIYNPIIYIMMNKQFRNCMLTSL-----CCGKNPLGDDE--ASATASKTET----
+------------------------------------------------------------
+-----------------------------------SQVAPA
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+M-------------------NGTE--GINFYVPMSNKTGVV--RSPFEYPQY-YL-----
+------------------------------------------------------------
+--AEPWKYRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACF
+G-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN
+F-RFSATHAMMGIAFTWVMAFSC-AAPPLF-GWS-----RYMPEGMQCSCGPDYYTHNPD
+YHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQ-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT--NKGAD-FTATLMAVPAF
+FSKSSSLYNPIIYVLMNKQFRNCMITTI-----CCGKNPFGDEDVSSTVSQSKTEVSSVS
+S-----------------------------------------------------------
+-----------------------------------SQVSPA
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+M-------------------NGTE--GKNFYVPMSNRTGLV--RSPFEYPQY-YL-----
+------------------------------------------------------------
+--AEPWQFKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCF
+G-FTVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS
+F-KFSSSHAFAGIAFTWVMALAC-AAPPLF-GWS-----RYIPEGMQCSCGPDYYTLNPD
+YNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQ-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--DSASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFF--NKGAD-FSAKFMAIPAF
+FSKSSALYNPVIYVLLNKQFRNCMLTTI-----FCGKNPLGDDE-SSTVSTSKTEVSS--
+------------------------------------------------------------
+-------------------------------------VSPA
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+M-------------------NGTE--GNNFYVPLSNRTGLV--RSPFEYPQY-YL-----
+------------------------------------------------------------
+--AEPWQFKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCF
+G-FTVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS
+F-KFSSTHASAGIAFTWVMAMAC-AAPPLV-GWS-----RYIPEGIQCSCGPDYYTLNPE
+YNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQ-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--DSASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFF--NKGAA-FSAQFMAIPAF
+FSKTSALYNPVIYVLLNKQFRSCMLTTL-----FCGKNPLGDEE-SSTVSTSKTEVSS--
+------------------------------------------------------------
+-------------------------------------VSPA
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+M-------------------KQVPEFHEDFYIPIPLDINNLSAYSPFLVPQD-HL-----
+------------------------------------------------------------
+--GNQGIFMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIF
+G-SPLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN
+F-TFKTPHAIAGCILPWISALAA-SLPPLF-GWS-----RYIPEGLQCSCGPDWYTTNNK
+YNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKAQA-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--DSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVS--HRGEE-FDLRMATIPSC
+LSKASTVYNPVIYVLMNKQFRSCMMKMV------CGKNIEEDEA---STSSQVTQVSSVA
+P-----------------------------------------------------------
+---------------------------------------EK
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+M-------------------RKMS--EEEFYLFKNISS-----VGPWDGPQY-HI-----
+------------------------------------------------------------
+--APVWAFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIF
+S-VFPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN
+F-RFSSKHALTVVLATWTIGIGV-SIPPFF-GWS-----RFIPEGLQCSCGPDWYTVGTK
+YRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQ-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESATTQKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN--NRNHG-LDLRLVTIPSF
+FSKSACIYNPIIYCFMNKQFQACIMKMV------CGKAMTDESD---TCSSQKTEVSTVS
+S-----------------------------------------------------------
+-----------------------------------TQVGPN
+> 8=opsin, greensensitive human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------------------DLAETVI
+A-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN
+V-RFDAKLAIVGIAFSWIWAAVW-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSY
+PGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQK-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESESTQKAEKEVTRMVVVMVLAFC----------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDSYEDSTQ--SSIFTYTNSNST-----RGPFEGPNY-HI-----
+------------------------------------------------------------
+--APRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVI
+A-STISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN
+V-RFDAKLAIVGIAFSWIWAAVW-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSY
+PGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQK-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA--NPGYP-FHPLMAALPAF
+FAKSATIYNPVIYVFMNRQFRNCILQLF-------GKKVDDGSE-LS--SASKTEVSSV-
+------------------------------------------------------------
+-----------------------------------SSVSPA
+> 10== Z68193 1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDSYEDSTQ--SSIFTYTNSNST-----RGPFEGPNY-HI-----
+------------------------------------------------------------
+--APRWVYHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVI
+A-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN
+V-RFDAKLAIVGIAFSWIWSAVW-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSY
+PGVQSYMIVLMVTCCIIPLAIIMLCYLQVWLAIRAVAKQQK-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA--NPGYA-FHPLMAALPAY
+FAKSATIYNPVIYVFMNRQFRNCILQLF-------GKKVDDGSE-LS--SASKTEVSSV-
+------------------------------------------------------------
+-----------------------------------SSVSPA
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDD-DDTTR--GSVFTYTNTNNT-----RGPFEGPNY-HI-----
+------------------------------------------------------------
+--APRWVYNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLV
+A-STISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN
+I-KFDSKLAIIGIVFSWVWAWGW-SAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSVE
+LGCQSFMLTLMITCCFLPLFIIIVCYLQVWMAIRAVAAQQK-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAA--NPGYA-FHPLAAALPAY
+FAKSATIYNPVIYVFMNRQFRNCIMQLF-------GKKVDDGSE-AS--TTSRTEVSSVS
+N-----------------------------------------------------------
+-----------------------------------SSVAPA
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MA-AWE-AAFAARRRHEE-EDTTR--DSVFTYTNSNNT-----RGPFEGPNY-HI-----
+------------------------------------------------------------
+--APRWVYNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVI
+A-STISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN
+I-KFDGKLAVAGILFSWLWSCAW-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSD
+PGVQSYMVVLMVTCCFFPLAIIILCYLQVWLAIRAVAAQQK-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--ESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA--NPGYA-FHPLAAALPAY
+FAKSATIYNPIIYVFMNRQFRNCILQLF-------GKKVDDGSE-VS---TSRTEVSSVS
+N-----------------------------------------------------------
+-----------------------------------SSVSPA
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+M-------------------------SSNSSQAPPNGT-----PGPFDGPQWPYQ-----
+------------------------------------------------------------
+--APQSTYVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLC
+G-SSVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD
+F-QFQRRHAVSGCAFTWGWALLW-SAPPLL-GWS-----SYVPEGLRTSCGPNWYTGGS-
+-NNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQK-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--EADTTQRAEREVTRMVIVMVMAFLLCWLPYSTFALVVAT--HKGII-IQPVLASLPSY
+FSKTATVYNPIIYVFMNKQFQSCLLEML-----CCGYQPQRTGKASPGTPGPHADVTAAG
+L-----------------------------------------------------------
+-------------------------------RNKVMPAHPV
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPEARLSAE----------TRLLGWNVPPEELR---H-----
+---------------------------------------IPEHWLTYPE-----------
+--PPESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK
+--TPIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG
+--KMTHGKAIAMIIFIYMYATPW-VVACYTETWG-----RFVPEGYLTSCTFDYLTDNF-
+-DTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKMNVESLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+SNVDKNKETAEIRIAKAAITICFLFFCSWTPYGVMSLIGAF--GDKTL-LTPGATMIPAC
+ACKMVACIDPFVYAISHPRYRMELQKRCPWL--ALNEKAPE-------SSAVASTSTTQE
+P-----------------------------------------------------------
+-----------------------------------QQTTAA
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVL-GNVSSVLRPDARLSAE----------SRLLGWNVPPDELR---H-----
+---------------------------------------IPEHWLIYPE-----------
+--PPESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK
+--TPIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG
+--KMTHGKAIAMIIFIYLYATPW-VVACYTESWG-----RFVPEGYLTSCTFDYLTDNF-
+-DTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKMNVDSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+SNVDKSKEAAEIRIAKAAITICFLFFASWTPYGVMSLIGAF--GDKTL-LTPGATMIPAC
+TCKMVACIDPFVYAISHPRYRMELQKRCPWL--AISEKAPE-------SRAAISTSTTQE
+Q-----------------------------------------------------------
+-----------------------------------QQTTAA
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+ME------PLCNASEPPLRPEAR-SSGNGD-------LQFLGWNVPPDQIQ---Y-----
+---------------------------------------IPEHWLTQLE-----------
+--PPASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK
+--APIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR
+--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFWD-----RFVPEGYLTSCSFDYLSDNF-
+-DTRLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKKMNVESLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+SNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMSLIGAF--GDKSL-LTQGATMIPAC
+TCKLVACIDPFVYAISHPRYRLELQKRCPWL--GVNEKSGE-------ISSAQSTTTQEQ
+------------------------------------------------------------
+-----------------------------------QQTTAA
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MD------ALCNASEPPLRPEARMSSGSDE-------LQFLGWNVPPDQIQ---Y-----
+---------------------------------------IPEHWLTQLE-----------
+--PPASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK
+--APIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR
+--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFWD-----RFVPEGYLTSCSFDYLSDNF-
+-DTRLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKKMNVESLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+SNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMSLIGAF--GDKSL-LTPGATMIPAC
+TCKLVACIEPFVYAISHPRYRMELQKRCPWL--GVNEKSGE-------ASSAQSTTTQEQ
+T-----------------------------------------------------------
+-----------------------------------QQTSAA
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+MT-----------NATGPQMAYYGAASMDFGYPE---GVSIVDFVRPEIKP---Y-----
+---------------------------------------VHQHWYNYPP-----------
+--VNPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTT
+N-VPFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG
+P-KLTTGKAVVFALISWVIAIGC-ALPPFF-GWG-----NYILEGILDSCSYDYLTQDF-
+-NTFSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKKMNVSTLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-NEADAQRAEIRIAKTALVNVSLWFICWTPYALISLKGVM--GDTSG-ITPLVSTLPAL
+LAKSCSCYNPFVYAISHPKYRLAITQHLPWF--CVHETETK-------SNDDSQSNSTVA
+Q-----------------------------------------------------------
+--------------------------------------DKA
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+MA-----------NVTGPQMAFYGSGAATFGYPE---GMTVADFVPDRVKH---M-----
+---------------------------------------VLDHWYNYPP-----------
+--VNPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTT
+N-FPPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG
+P-KLTQGKATFMCGLAWVISVGW-SLPPFF-GWG-----SYTLEGILDSCSYDYFTRDM-
+-NTITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKKMNVTNLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-NEAETQRAEIRIAKTALVNVSLWFICWTPYAAITIQGLL--GNAEG-ITPLLTTLPAL
+LAKSCSCYNPFVYAISHPKFRLAITQHLPWF--CVHEKDPN-------DVEENQSSNTQT
+Q-----------------------------------------------------------
+--------------------------------------EKS
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+ME-----SFAVAAAQLGPHFA-----PLS--------NGSVVDKVTPDMAH---L-----
+---------------------------------------ISPYWNQFPA-----------
+--MDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMIT
+N-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG
+R-PMTIPLALGKM---------------------------YVPEGNLTSCGIDYLERDW-
+-NPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGAC
+FAKSAACYNPIVYGISHPKYRLALKEKCPCC--VFGKVDDGKSS----DAQSQA-TASEA
+E-----------------------------------------------------------
+--------------------------------------SKA
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+ME-----SFAVAAAQLGPHFA-----PLS--------NGSVVDKVTPDMAH---L-----
+---------------------------------------ISPYWNQFPA-----------
+--MDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMIT
+N-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG
+R-PMTIPLALGKIAYIWFMSSIW-CLAPAF-GWS-----RYVPEGNLTSCGIDYLERDW-
+-NPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGAC
+FAKSAACYNPIVYGISHPKYRLALKEKCPCC--VFGKVDDGKSS----DAQSQA-TASEA
+E-----------------------------------------------------------
+--------------------------------------SKA
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MD-----SFAAVATQLGPQFA-----APS--------NGSVVDKVTPDMAH---L-----
+---------------------------------------ISPYWDQFPA-----------
+--MDPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMIT
+N-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG
+R-PMTIPLALGKIAYIWFMSTIWCCLAPVF-GWS-----RYVPEGNLTSCGIDYLERDW-
+-NPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGAC
+FAKSAACYNPIVYGISHPKYRLALKEKCPCC--VFGKVDDGKSS----EAQSQA-TTSEA
+E-----------------------------------------------------------
+--------------------------------------SKA
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQ-----AQSSG------NGSVLDNVLPDMAH---L-----
+---------------------------------------VNPYWSRFAP-----------
+--MDPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMAS
+Q-SPVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING
+T-PMTIKTSIMKILFIWMMAVFW-TVMPLI-GWS-----AYVPEGNLTACSIDYMTRMW-
+-NPRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDCDKSAEGKLAKVALTTISLWFMAWTPYLVICYFGLF--KI-DG-LTPLTTIWGAT
+FAKTSAVYNPIVYGISHPKYRIVLKEKCPMC--VFGNTDEPKPD----APASDTETTSEA
+D-----------------------------------------------------------
+--------------------------------------SKA
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFE-----AQTGG------NRSVLDNVLPDMAP---L-----
+---------------------------------------VNPHWSRFAP-----------
+--MDPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMAS
+Q-SPVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING
+T-PMTIKTSIMKIAFIWMMAVFW-TIMPLI-GWS-----SYVPEGNLTACSIDYMTRQW-
+-NPRSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKKMNVKSLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SEDCDKSAENKLAKVALTTISLWFMAWTPYLIICYFGLF--KI-DG-LTPLTTIWGAT
+FAKTSAVYNPIVYGISHPNDRLVLKEKCPMC--VCGTTDEPKPD----APPSDTETTSEA
+E-----------------------------------------------------------
+--------------------------------------SKD
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+MI-----------AVSGPSYE-----AFSYGGQARFNNQTVVDKVPPDMLH---L-----
+---------------------------------------IDANWYQYPP-----------
+--LNPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFC
+M-SPPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG
+K-PLSINGALIRIIAIWLFSLGW-TIAPMF-GWN-----RYVPEGNMTACGTDYFNRGL-
+-LSASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKKMNVASLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+S-SENQNTSAECKLAKVALMTISLWFMAWTPYLVINFSGIF--NL-VK-ISPLFTIWGSL
+FAKANAVYNPIVYGISHPKYRAALFAKFPSL--ACAA--EPSSD----AVSTTSGTTTVT
+D-----------------------------------------------------------
+-----------------------------------NEKSNA
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+MA------------------NQLSYSSLGWPYQP---NASVVDTMPKEMLY---M-----
+---------------------------------------IHEHWYAFPP-----------
+--MNPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAF
+M-MPTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA
+A-PLTHKKATLLLLFVWIWSGGW-TILPFF-GWS-----RYVPEGNLTSCTVDYLTKDW-
+-SSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKKMNVASLR-------
+------------------------------------------------------------
+------------------------------------------------------------
+ANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVF--SSGTR-LTPLATIWGSV
+FAKANSCYNPIVYGISHPRYKAALYQRFPSL--ACGSGESGSDV----KSEASATTTMEE
+K-----------------------------------------------------------
+-----------------------------------PKIPEA
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+MV------------------ESTTLVNQTWWYNPTVD-----------------------
+---------------------------------------IHPHWAKFDP-----------
+--IPDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAI
+NGFPLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAA
+SKKMSHRRAFLMIIFVWMWSIVW-SVGPVF-NWG-----AYVPEGILTSCSFDYLSTDP-
+-STRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKRLNAKELR-------
+------------------------------------------------------------
+------------------------------------------------------------
+--KAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQF--GPAEW-VTPYAAELPVL
+FAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECED----ANDAEEEVVASE
+R--GGESRDAAQMKEMMAMMQKMQAQQAAYQP---PPPPQGYPPQGYPPQGAYPPPQGYP
+PQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+MG------------------RDLR-DNETWWYNPSIV-----------------------
+---------------------------------------VHPHWREFDQ-----------
+--VPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLV
+NGFPLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAA
+SKKMSHRRAFIMIIFVWLWSVLW-AIGPIF-GWG-----AYTLEGVLCNCSFDYISRDS-
+-TTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKELR-------
+------------------------------------------------------------
+------------------------------------------------------------
+--KAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQF--GPLEW-VTPYAAQLPVM
+FAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETED----DKDAETEIPAGE
+SSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGY--PPQGYP
+PQGYPP---PPQGAPPQGAPP------AAPPQGVDNQAYQA
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMD-----------------VNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGS
+WAPHLLS------------------------EVTAS---PAPTW---DAPPDNASGCGEQ
+INYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVA
+V-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTY
+PVRQNGKCMAKMILSVWLLSASI-TLPPLF-GWA-----QNVNDDKVCLISQDF------
+----GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------------PGFP
+RVEPDSVIALNG------------------------------------------------
+----IVKLQKE------------------VEECAN------------------LSRLLKH
+ERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTFLW
+LGYANSLINPFIYAFFNRDLRTTYRSLL-----QCQYRNINRKLSAAGMHEALKLAERPE
+RPEFV-------------------------------------------------------
+---------------------------LQNADYCRKKGHDS
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+M-----------------------------------------------------------
+--PHLLS---------------------GFLEVTAS---PAPTW---DAPPDNVSGCGEQ
+INYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVA
+V-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTY
+PVRQNGKCMAKMILSVWLLSASI-TLPPLF-GWA-----QNVNDDKVCLISQDF------
+----GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------------PGFP
+RVQPESVISLNG------------------------------------------------
+----VVKLQKE------------------VEECAN------------------LSRLLKH
+ERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLW
+LGYANSLINPFIYAFFNRDLRPTSRSLL-----QCQYRNINRKLSAAGMHEALKLAERPE
+RSEFV-------------------------------------------------------
+---------------------------LQNSDHCGKKGHDT
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+M-----------------------------------------------------------
+--PHLLS---------------------GFLEVTAS---PAPTW---DAPPDNVSGCGEQ
+INYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVA
+V-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTY
+PVRQNGKCMAKMILSVWLLSASI-TLPPLF-GWA-----QNVNDDKVCLISQDF------
+----GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------------PGFP
+RVQPESVISLNG------------------------------------------------
+----VVKLQKE------------------VEECAN------------------LSRLLKH
+ERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLW
+LGYANSLINPFIYAFFNRDLRTTYRSLL-----QCQYRNINRKLSAAGMHEALKLAERPE
+RSEFV-------------------------------------------------------
+---------------------------LQNSDHCGKKGHDT
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+M-----------------------------------------------------------
+--------------------DVLSPGQGNNTTSPPAPFETGGNTTGISD-----------
+--VTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVL
+V-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDY
+VNKRTPRRAAALISLTWLIGFLI-SIPPML-GWRTP---EDRSDPDACTISKDH------
+----GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQ
+PKK---------SVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN
+SKEHLPLPSEAGPTPCAPASFERKNERNA-------------------------------
+EAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CESSCH-MPTLLGAIINW
+LGYSNSLLNPVIYAYFNKDFQNAFKKII-----KCKF-----------------------
+------------------------------------------------------------
+--------------------------------------CRQ
+> 33=p A35181 serotonin receptor class 1A - rat
+M-----------------------------------------------------------
+--------------------DVFSFGQGNNTTASQEPFGTGGNVTSISD-----------
+--VTFSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVL
+V-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDY
+VNKRTPRRAAALISLTWLIGFLI-SIPPML-GWRTP---EDRSDPDACTISKDH------
+----GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGTSLGTSSAPP
+PKK---------SLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN
+SKEHLPLPSESGSNSYAPACLERKNERNA-------------------------------
+EAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CESSCH-MPALLGAIINW
+LGYSNSLLNPVIYAYFNKDFQNAFKKII-----KCKF-----------------------
+------------------------------------------------------------
+--------------------------------------CRR
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRD-----------------NASANDTSATNM---TDDRYWSLTV-----------
+--YSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVL
+V-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDY
+IRRRSARRILLMIMVVWIVALFI-SIPPLF-GWRDP--NNDPDKTGTCIISQDK------
+----GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASP
+KTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSS
+SSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYS-------------
+RTREKLELKRERKAARTLAIITGAFLICWLPFFIIALIGPF--VDPEG-IPPFARSFVLW
+LGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKY-----------------------
+------------------------------------------------------------
+------------------------------------RRGHR
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRD-----------------NASANDTSATNM---TDDRYWSLTV-----------
+--YSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVL
+V-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDY
+IRRRSARRILLMIMVVWIVALFI-SIPPLF-GWRDP--NNDPDKTGTCIISQDK------
+----GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASP
+KTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSS
+SSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYS-------------
+RTREKLELKRERKAARTLAIITGAFLICWLPFFIIALIGPF--VDPEG-IPPFARSFVLW
+LGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKY-----------------------
+------------------------------------------------------------
+------------------------------------RRGHR
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+M--------------------------------------------------------EGA
+EGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVV---PNTTWWQASAPFDTP------
+--AALVRAAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACL
+V-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDY
+IHASTAKRVGMMIACVWTVSFFV-CIAQLL-GWKDPDWNQRVSEDLRCVVSQDV------
+----GYQIFATASSFYVPVLIILILYWRIYQTARKRIRRRRGATARGGV--------GPP
+PVPAGGALVAGGGSGG------------------------------------IAAAVVAV
+IGRPLPTISETTTTGFTNVSSNNTSPE--KQSCANGLEADPPTTGYGAVAAAYYPSLVRR
+KPKEAADSKRERKAAKTLAIITGAFVACWLPFFVLAILVPT---CDCE-VSPVLTSLSLW
+LGYFNSTLNPVIYTVFSPEFRHAFQRLL-----CGRR-----------------------
+------------------------------------------------------------
+---------------------------------VRRRRAPQ
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+MN--------------------GTE--GDNFYVPFSNKTG--LARSP-------------
+--------------------YEYPQY-YLAEPW---------KYSA-----LAAYMFFLI
+LVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSMN-GYFV--
+FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGNF-RFGNTHAIMGVAFTWIM
+ALAC-AAPPLV-GWS-----RYIPEGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPF
+VIIFFCYGRLLCTVKEAAAAQQESA-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEKEVTRMVV
+LMVIGFLVCWVPYASVAFYIFT--HQGSD-FGATFMTLPAFFAKSSALYNPVIYILMNKQ
+FRNCMITTL-----CCGKNPLGDDE-SG-ASTSKTEVS----------------------
+------------------------------------------------------------
+----------------SVS-TSPVSPA---
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+MN--------------------GTE--GPNFYVPFSNITG--VVRSP-------------
+--------------------FEQPQY-YLAEPW---------QFSM-----LAAYMFLLI
+VLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSLH-GYFV--
+FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSNF-RFGENHAIMGVAFTWVM
+ALAC-AAPPLV-GWS-----RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPM
+IVIFFCYGQLVFTVKEAAAQQQESA-----------------------------------
+------------------------------------------------------------
+----------------------------------------------TTQKAEKEVTRMVI
+IMVIFFLICWLPYASVAMYIFT--HQGSN-FGPIFMTLPAFFAKTASIYNPIIYIMMNKQ
+FRNCMLTSL-----CCGKNPLGDDE-AS-ATASKTETS----------------------
+------------------------------------------------------------
+----------------QVA-PA--------
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+MN--------------------GTE--GINFYVPMSNKTG--VVRSP-------------
+--------------------FEYPQY-YLAEPW---------KYRL-----VCCYIFFLI
+STGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAWN-GYFV--
+FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGNF-RFSATHAMMGIAFTWVM
+AFSC-AAPPLF-GWS-----RYMPEGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPV
+VVIFFSYGRLICKVREAAAQQQESA-----------------------------------
+------------------------------------------------------------
+----------------------------------------------TTQKAEKEVTRMVI
+LMVLGFMLAWTPYAVVAFWIFT--NKGAD-FTATLMAVPAFFSKSSSLYNPIIYVLMNKQ
+FRNCMITTI-----CCGKNPFGDEDVSSTVSQSKTEVS----------------------
+------------------------------------------------------------
+----------------SVS-SSQVSPA---
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+MN--------------------GTE--GKNFYVPMSNRTG--LVRSP-------------
+--------------------FEYPQY-YLAEPW---------QFKI-----LALYLFFLM
+SMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAIN-GYFV--
+LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGSF-KFSSSHAFAGIAFTWVM
+ALAC-AAPPLF-GWS-----RYIPEGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPV
+AVIFFTYGRLVCTVKAAAAQQQDSA-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEREVTKMVI
+LMVFGFLIAWTPYATVAAWIFF--NKGAD-FSAKFMAIPAFFSKSSALYNPVIYVLLNKQ
+FRNCMLTTI-----FCGKNPLGDDE-SSTVSTSKTEVS----------------------
+------------------------------------------------------------
+----------------SVS-PA--------
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+MN--------------------GTE--GNNFYVPLSNRTG--LVRSP-------------
+--------------------FEYPQY-YLAEPW---------QFKL-----LAVYMFFLI
+CLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAIN-GYFA--
+LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGSF-KFSSTHASAGIAFTWVM
+AMAC-AAPPLV-GWS-----RYIPEGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPV
+TIIFFTYGRLVCTVKAAAAQQQDSA-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEREVTKMVI
+LMVLGFLVAWTPYATVAAWIFF--NKGAA-FSAQFMAIPAFFSKTSALYNPVIYVLLNKQ
+FRSCMLTTL-----FCGKNPLGDEE-SSTVSTSKTEVS----------------------
+------------------------------------------------------------
+----------------SVS-PA--------
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+MK--------------------QVPEFHEDFYIPIPLDINNLSAYSP-------------
+--------------------FLVPQD-HLGNQG---------IFMA-----MSVFMFFIF
+IGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSFFN-RYFI--
+FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGNF-TFKTPHAIAGCILPWIS
+ALAA-SLPPLF-GWS-----RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPF
+GTIVFCYGQLLITLKLAAKAQADSA-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEREVTKMVV
+VMVLGFLVCWAPYASFSLWIVS--HRGEE-FDLRMATIPSCLSKASTVYNPVIYVLMNKQ
+FRSCMM-KM-----VCGKN-IEEDE-AS-TSSQVTQVS----------------------
+------------------------------------------------------------
+----------------SVA-PEK-------
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+MR--------------------KMS--EEEFYL-----FKNISSVGP-------------
+--------------------WDGPQY-HIAPVW---------AFYL-----QAAFMGTVF
+LIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPVFVASCN-GYFV--
+FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGNF-RFSSKHALTVVLATWTI
+GIGV-SIPPFF-GWS-----RFIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPL
+SLICFSYTQLLRALKAVAAQQQESA-----------------------------------
+------------------------------------------------------------
+----------------------------------------------TTQKAEREVSRMVV
+VMVGSFCVCYVPYAAFAMYMVN--NRNHG-LDLRLVTIPSFFSKSACIYNPIIYCFMNKQ
+FQACIM-KM-----VCGKA-MTDES-DT-CSSQKTEVS----------------------
+------------------------------------------------------------
+----------------TVS-STQVGPN---
+> 8=opsin, greensensitive human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------DLAETVIA-STISIVNQVS-GYFV--
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNV-RFDAKLAIVGIAFSWIW
+AAVW-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPL
+SIIVLCYLQVWLAIRAVAKQQKESE-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEKEVTRMVV
+VMVLAFC-----------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+MAQQWS-LQRLAGRHPQDSYEDSTQ--SSIFTY-----TNSNSTRGP-------------
+--------------------FEGPNY-HIAPRW---------VYHL-----TSVWMIFVV
+IASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQVY-GYFV--
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNV-RFDAKLAIVGIAFSWIW
+AAVW-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPL
+SIIVLCYLQVWLAIRAVAKQQKESE-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEKEVTRMVV
+VMVLAFCFCWGPYAFFACFAAA--NPGYP-FHPLMAALPAFFAKSATIYNPVIYVFMNRQ
+FRNCILQLF----------GKKVDDGSELSSASKTEVS----------------------
+------------------------------------------------------------
+----------------SV---SSVSPA---
+> 10== Z68193 1 human Red Opsin <>[]
+MAQQWS-LQRLAGRHPQDSYEDSTQ--SSIFTY-----TNSNSTRGP-------------
+--------------------FEGPNY-HIAPRW---------VYHL-----TSVWMIFVV
+TASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQVS-GYFV--
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNV-RFDAKLAIVGIAFSWIW
+SAVW-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPL
+AIIMLCYLQVWLAIRAVAKQQKESE-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEKEVTRMVV
+VMIFAYCVCWGPYTFFACFAAA--NPGYA-FHPLMAALPAYFAKSATIYNPVIYVFMNRQ
+FRNCILQLF----------GKKVDDGSELSSASKTEVS----------------------
+------------------------------------------------------------
+----------------SV---SSVSPA---
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDD--DDTTR--GSVFTY-----TNTNNTRGP-------------
+--------------------FEGPNY-HIAPRW---------VYNL-----VSFFMIIVV
+IASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQIF-GYFI--
+LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNI-KFDSKLAIIGIVFSWVW
+AWGW-SAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPL
+FIIIVCYLQVWMAIRAVAAQQKESE-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEREVSRMVV
+VMIVAFCICWGPYASFVSFAAA--NPGYA-FHPLAAALPAYFAKSATIYNPVIYVFMNRQ
+FRNCIMQLF----------GKKVDDGSEASTTSRTEVS----------------------
+------------------------------------------------------------
+----------------SVS-NSSVAPA---
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MA-AWE-AAFAARRRHEE--EDTTR--DSVFTY-----TNSNNTRGP-------------
+--------------------FEGPNY-HIAPRW---------VYNL-----TSVWMIFVV
+AASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQIS-GYFI--
+LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNI-KFDGKLAVAGILFSWLW
+SCAW-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPL
+AIIILCYLQVWLAIRAVAAQQKESE-----------------------------------
+------------------------------------------------------------
+----------------------------------------------STQKAEKEVSRMVV
+VMIVAYCFCWGPYTFFACFAAA--NPGYA-FHPLAAALPAYFAKSATIYNPIIYVFMNRQ
+FRNCILQLF----------GKKVDDGSEVST-SRTEVS----------------------
+------------------------------------------------------------
+----------------SVS-NSSVSPA---
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+MS--------------------------SNSSQ-----APPNGTPGP-------------
+--------------------FDGPQWPYQAPQS---------TYVG-----VAVLMGTVV
+ACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNNIN-GFFV--
+FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGDF-QFQRRHAVSGCAFTWGW
+ALLW-SAPPLL-GWS-----SYVPEGLRTSCGPNWYTGGSN--NNSYILSLFVTCFVLPL
+SLILFSYTNLLLTLRAAAAQQKEAD-----------------------------------
+------------------------------------------------------------
+----------------------------------------------TTQRAEREVTRMVI
+VMVMAFLLCWLPYSTFALVVAT--HKGII-IQPVLASLPSYFSKTATVYNPIIYVFMNKQ
+FQSCLLEML-----CCGYQPQRTGKASPGTPGPHADVT----------------------
+------------------------------------------------------------
+----------------AAGLRNKVMPAHPV
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPE----ARLSA---E---TRLLGWNVPP-------------
+--------------------EELR---HIPEHWLTYPEPPESMNYL-----LGTLYIFFT
+LMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIFIYNSFH-QGYA--
+LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTHGKAIAMIIFIYMY
+ATPW-VVACYTETWG-----RFVPEGYLTSCTFDYLTDN--FDTRLFVACIFFFSFVCPT
+TMITYYYSQIVGHVFSHEKALRDQAKKMNVESLR--------------------------
+------------------------------------------------------------
+-----------------------------------------SNVDKNKETAEIRIAKAAI
+TICFLFFCSWTPYGVMSLIGAF--GDKTL-LTPGATMIPACACKMVACIDPFVYAISHPR
+YRMELQKRCPWL--ALNEKAPESSAVASTST-TQEPQQT---------------------
+------------------------------------------------------------
+----------------TAA-----------
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVL-GNVSSVLRPD----ARLSA---E---SRLLGWNVPP-------------
+--------------------DELR---HIPEHWLIYPEPPESMNYL-----LGTLYIFFT
+VISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIFIYNSFH-QGYA--
+LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTHGKAIAMIIFIYLY
+ATPW-VVACYTESWG-----RFVPEGYLTSCTFDYLTDN--FDTRLFVACIFFFSFVCPT
+TMITYYYSQIVGHVFSHEKALRDQAKKMNVDSLR--------------------------
+------------------------------------------------------------
+-----------------------------------------SNVDKSKEAAEIRIAKAAI
+TICFLFFASWTPYGVMSLIGAF--GDKTL-LTPGATMIPACTCKMVACIDPFVYAISHPR
+YRMELQKRCPWL--AISEKAPESRAAISTST-TQEQQQT---------------------
+------------------------------------------------------------
+----------------TAA-----------
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+ME------PLCNASEPPLRPE----AR-SSGNGD---LQFLGWNVPP-------------
+--------------------DQIQ---YIPEHWLTQLEPPASMHYM-----LGVFYIFLF
+CASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF--NSFH-RGFAIY
+LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVIMNIIIWLY
+CTPW-VVLPLTQFWD-----RFVPEGYLTSCSFDYLSDN--FDTRLFVGTIFFFSFVCPT
+LMILYYYSQIVGHVFSHEKALREQAKKMNVESLR--------------------------
+------------------------------------------------------------
+-----------------------------------------SNVDKSKETAEIRIAKAAI
+TICFLFFVSWTPYGVMSLIGAF--GDKSL-LTQGATMIPACTCKLVACIDPFVYAISHPR
+YRLELQKRCPWL--GVNEKSGEISSAQSTTT-QEQQQTT---------------------
+------------------------------------------------------------
+----------------AA------------
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MD------ALCNASEPPLRPE----ARMSSGSDE---LQFLGWNVPP-------------
+--------------------DQIQ---YIPEHWLTQLEPPASMHYM-----LGVFYIFLF
+FASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIFIYNSFH-RGFA--
+LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVIMNIIIWLY
+CTPW-VVLPLTQFWD-----RFVPEGYLTSCSFDYLSDN--FDTRLFVGTIFLFSFVVPT
+LMILYYYSQIVGHVFNHEKALREQAKKMNVESLR--------------------------
+------------------------------------------------------------
+-----------------------------------------SNVDKSKETAEIRIAKAAI
+TICFLFFVSWTPYGVMSLIGAF--GDKSL-LTPGATMIPACTCKLVACIEPFVYAISHPR
+YRMELQKRCPWL--GVNEKSGEASSAQSTTT-QEQTQQT---------------------
+------------------------------------------------------------
+----------------SAA-----------
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+M-----------TNATGPQMAYYGAASMDFGYPE---GVSIVDFVRP-------------
+--------------------EIKP---YVHQHWYNYPPVNPMWHYL-----LGVIYLFLG
+TVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNCFSGGVWM--
+FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGP-KLTTGKAVVFALISWVI
+AIGC-ALPPFF-GWG-----NYILEGILDSCSYDYLTQD--FNTFSYNIFIFVFDYFLPA
+AIIVFSYVFIVKAIFAHEAAMRAQAKKMNVSTLR--------------------------
+------------------------------------------------------------
+-----------------------------------------S-NEADAQRAEIRIAKTAL
+VNVSLWFICWTPYALISLKGVM--GDTSG-ITPLVSTLPALLAKSCSCYNPFVYAISHPK
+YRLAITQHLPWF--CVHETETKSNDDSQSNS-TVAQDK----------------------
+------------------------------------------------------------
+------------------A-----------
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+M-----------ANVTGPQMAFYGSGAATFGYPE---GMTVADFVPD-------------
+--------------------RVKH---MVLDHWYNYPPVNPMWHYL-----LGVVYLFLG
+VISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNCFSGGRWM--
+FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGP-KLTQGKATFMCGLAWVI
+SVGW-SLPPFF-GWG-----SYTLEGILDSCSYDYFTRD--MNTITYNICIFIFDFFLPA
+SVIVFSYVFIVKAIFAHEAAMRAQAKKMNVTNLR--------------------------
+------------------------------------------------------------
+-----------------------------------------S-NEAETQRAEIRIAKTAL
+VNVSLWFICWTPYAAITIQGLL--GNAEG-ITPLLTTLPALLAKSCSCYNPFVYAISHPK
+FRLAITQHLPWF--CVHEKDPNDVEENQSSN-TQTQEK----------------------
+------------------------------------------------------------
+------------------S-----------
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+ME-----SFAVAAAQLGPHFA-----PLS--------NGSVVDKVTP-------------
+--------------------DMAH---LISPYWNQFPAMDPIWAKI-----LTAYMIMIG
+MISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYF-ETWV--
+LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGR-PMTIPLALGKM------
+---------------------YVPEGNLTSCGIDYLERD--WNPRSYLIFYSIFVYYIPL
+FLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR--------------------------
+------------------------------------------------------------
+-----------------------------------------S-SEDAEKSAEGKLAKVAL
+VTITLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGACFAKSAACYNPIVYGISHPK
+YRLALKEKCPCC--VFGKVDDGKSSDAQSQA-TASEAE----------------------
+------------------------------------------------------------
+----------------SKA-----------
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+ME-----SFAVAAAQLGPHFA-----PLS--------NGSVVDKVTP-------------
+--------------------DMAH---LISPYWNQFPAMDPIWAKI-----LTAYMIMIG
+MISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYF-ETWV--
+LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGR-PMTIPLALGKIAYIWFM
+SSIW-CLAPAF-GWS-----RYVPEGNLTSCGIDYLERD--WNPRSYLIFYSIFVYYIPL
+FLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR--------------------------
+------------------------------------------------------------
+-----------------------------------------S-SEDAEKSAEGKLAKVAL
+VTITLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGACFAKSAACYNPIVYGISHPK
+YRLALKEKCPCC--VFGKVDDGKSSDAQSQA-TASEAE----------------------
+------------------------------------------------------------
+----------------SKA-----------
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MD-----SFAAVATQLGPQFA-----APS--------NGSVVDKVTP-------------
+--------------------DMAH---LISPYWDQFPAMDPIWAKI-----LTAYMIIIG
+MISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYF-ETWV--
+LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGR-PMTIPLALGKIAYIWFM
+STIWCCLAPVF-GWS-----RYVPEGNLTSCGIDYLERD--WNPRSYLIFYSIFVYYIPL
+FLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLR--------------------------
+------------------------------------------------------------
+-----------------------------------------S-SEDADKSAEGKLAKVAL
+VTISLWFMAWTPYLVINCMGLF--KF-EG-LTPLNTIWGACFAKSAACYNPIVYGISHPK
+YRLALKEKCPCC--VFGKVDDGKSSEAQSQA-TTSEAE----------------------
+------------------------------------------------------------
+----------------SKA-----------
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQ-----AQSSG------NGSVLDNVLP-------------
+--------------------DMAH---LVNPYWSRFAPMDPMMSKI-----LGLFTLAIM
+IISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYY-ETWV--
+LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGT-PMTIKTSIMKILFIWMM
+AVFW-TVMPLI-GWS-----AYVPEGNLTACSIDYMTRM--WNPRSYLITYSLFVYYTPL
+FLICYSYWFIIAAVAAHEKAMREQAKKMNVKSLR--------------------------
+------------------------------------------------------------
+-----------------------------------------S-SEDCDKSAEGKLAKVAL
+TTISLWFMAWTPYLVICYFGLF--KI-DG-LTPLTTIWGATFAKTSAVYNPIVYGISHPK
+YRIVLKEKCPMC--VFGNTDEPKPDAPASDTETTSEAD----------------------
+------------------------------------------------------------
+----------------SKA-----------
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFE-----AQTGG------NRSVLDNVLP-------------
+--------------------DMAP---LVNPHWSRFAPMDPTMSKI-----LGLFTLVIL
+IISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYY-ETWV--
+LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGT-PMTIKTSIMKIAFIWMM
+AVFW-TIMPLI-GWS-----SYVPEGNLTACSIDYMTRQ--WNPRSYLITYSLFVYYTPL
+FMICYSYWFIIATVAAHEKAMRDQAKKMNVKSLR--------------------------
+------------------------------------------------------------
+-----------------------------------------S-SEDCDKSAENKLAKVAL
+TTISLWFMAWTPYLIICYFGLF--KI-DG-LTPLTTIWGATFAKTSAVYNPIVYGISHPN
+DRLVLKEKCPMC--VCGTTDEPKPDAPPSDTETTSEAE----------------------
+------------------------------------------------------------
+----------------SKD-----------
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+M-----------IAVSGPSYE-----AFSYGGQARFNNQTVVDKVPP-------------
+--------------------DMLH---LIDANWYQYPPLNPMWHGI-----LGFVIGMLG
+FVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINCYY-ETWV--
+LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGK-PLSINGALIRIIAIWLF
+SLGW-TIAPMF-GWN-----RYVPEGNMTACGTDYFNRG--LLSASYLVCYGIWVYFVPL
+FLIIYSYWFIIQAVAAHEKNMREQAKKMNVASLR--------------------------
+------------------------------------------------------------
+-----------------------------------------S-SENQNTSAECKLAKVAL
+MTISLWFMAWTPYLVINFSGIF--NL-VK-ISPLFTIWGSLFAKANAVYNPIVYGISHPK
+YRAALFAKFPSL--AC-AAEPSSDAVSTTSG-TTTVTDN---------------------
+------------------------------------------------------------
+-------------EK-SNA-----------
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+M-------------ANQLSYS-----SLGWPYQP---NASVVDTMPK-------------
+--------------------EMLY---MIHEHWYAFPPMNPLWYSI-----LGVAMIILG
+IICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNCFA-ETWI--
+LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAA-PLTHKKATLLLLFVWIW
+SGGW-TILPFF-GWS-----RYVPEGNLTSCTVDYLTKD--WSSASYVVIYGLAVYFLPL
+ITMIYCYFFIVHAVAEHEKQLREQAKKMNVASLR--------------------------
+------------------------------------------------------------
+-----------------------------------------ANADQQKQSAECRLAKVAM
+MTVGLWFMAWTPYLIISWAGVF--SSGTR-LTPLATIWGSVFAKANSCYNPIVYGISHPR
+YKAALYQRFPSL--ACGSGESGSDVKSEASA-TTTMEEK---------------------
+------------------------------------------------------------
+-------------PKIPEA-----------
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+M-------------VESTTLV-----NQTWWY-----NPTV-------------------
+---------------------------DIHPHWAKFDPIPDAVYYS-----VGIFIGVVG
+IIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFM-KKWI--
+FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMW
+SIVW-SVGPVF-NWG-----AYVPEGILTSCSFDYLSTD--PSTRSFILCMYFCGFMLPI
+IIIAFCYFNIVMSVSNHEKEMAAMAKRLNAKELR--------------------------
+------------------------------------------------------------
+-----------------------------------------K-AQ-AGASAEMKLAKISM
+VIITQFMLSWSPYAIIALLAQF--GPAEW-VTPYAAELPVLFAKASAIHNPIVYSVSHPK
+FREAIQTTFPWLLTCCQFDEKECEDANDAEE-EVVASER--GGESRDAAQMKEMMAMMQK
+MQAQQAAYQP---PPPPQGYPPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQ
+VEAPQGAPPQGVDNQAYQA-----------
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+M-------------GRDLR-D-----NETWWY-----NPSI-------------------
+---------------------------VVHPHWREFDQVPDAVYYS-----LGIFIGICG
+IIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFL-KKWI--
+FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLW
+SVLW-AIGPIF-GWG-----AYTLEGVLCNCSFDYISRD--STTRSNILCMFILGFFGPI
+LIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKELR--------------------------
+------------------------------------------------------------
+-----------------------------------------K-AQ-AGANAEMRLAKISI
+VIVSQFLLSWSPYAVVALLAQF--GPLEW-VTPYAAQLPVMFAKASAIHNPMIYSVSHPK
+FREAISQTFPWVLTCCQFDDKETEDDKDAET-EIPAGESSDAAPSADAAQMKEMMAMMQK
+MQQQQAAYPPQGYAPPPQGYPPQGYPPQGY--PPQGYPPQGYPP---PPQGAPPQGAPP-
+-----AAPPQGVDNQAYQA-----------
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDG----GADPVAGSWAPHLLS---EVT
+ASPAPTWDAPPDNA------SGCGE----------QINYGRVEKVV-----IGSILTLIT
+LLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGGKWI--
+FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLL
+SASI-TLPPLF-GWA-----QNVNDDKVCLISQDF----------GYTIYSTAVAFYIPM
+SVMLFMYYQIYKAARKSAAKHKF--------------PGFPRVEPDSVIALNG-------
+---------------------------------------------IVKLQKE--------
+----------VEECAN------------------LSRLLKHERKNISIFKREQKAATTLG
+IIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRD
+LRTTYRSLL-----QCQYRNINRKLSAAGMHEALKLAERPERPEFVLQNADYCRKKGHDS
+------------------------------------------------------------
+------------------------------
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+M------------------------------------------------PHLLSGFLEVT
+ASPAPTWDAPPDNV------SGCGE----------QINYGRVEKVV-----IGSILTLIT
+LLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGGKWI--
+FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLL
+SASI-TLPPLF-GWA-----QNVNDDKVCLISQDF----------GYTIYSTAVAFYIPM
+SVMLFMYYQIYKAARKSAAKHKF--------------PGFPRVQPESVISLNG-------
+---------------------------------------------VVKLQKE--------
+----------VEECAN------------------LSRLLKHERKNISIFKREQKAATTLG
+IIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRD
+LRPTSRSLL-----QCQYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+------------------------------------------------------------
+------------------------------
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+M------------------------------------------------PHLLSGFLEVT
+ASPAPTWDAPPDNV------SGCGE----------QINYGRVEKVV-----IGSILTLIT
+LLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGGKWI--
+FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLL
+SASI-TLPPLF-GWA-----QNVNDDKVCLISQDF----------GYTIYSTAVAFYIPM
+SVMLFMYYQIYKAARKSAAKHKF--------------PGFPRVQPESVISLNG-------
+---------------------------------------------VVKLQKE--------
+----------VEECAN------------------LSRLLKHERKNISIFKREQKAATTLG
+IIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRD
+LRTTYRSLL-----QCQYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+------------------------------------------------------------
+------------------------------
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPG-----------------------------------------------------
+---------QGNNT------TSPPAPFETGGNTTGISDVTVSYQVI-----TSLLLGTLI
+FCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVL-NKWT--
+LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLI
+GFLI-SIPPML-GWRTPEDRSDPD---ACTISKDH----------GYTIYSTFGAFYIPL
+LLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQPKK-----SVNG--ESGSR
+NWRLGVESKAGGALCANGAVRQGDDGAAL--EVIEVHRVGNSKEHLPLPSEAGPTPCAPA
+S------------------FERKNERNA-------------EAKRKMALARERKTVKTLG
+IIMGTFILCWLPFFIVALVLPF-CESSCH-MPTLLGAIINWLGYSNSLLNPVIYAYFNKD
+FQNAFKKII-----KCKFCR--Q-------------------------------------
+------------------------------------------------------------
+------------------------------
+> 33=p A35181 serotonin receptor class 1A - rat
+MDVFSFG-----------------------------------------------------
+---------QGNNT------TASQEPFGTGGNVTSISDVTFSYQVI-----TSLLLGTLI
+FCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVL-NKWT--
+LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLI
+GFLI-SIPPML-GWRTPEDRSDPD---ACTISKDH----------GYTIYSTFGAFYIPL
+LLMLVLYGRIFRAARFRIRKTVRKVEKKGAGTSLGTSSAPPPKK-----SLNG--QPGSG
+DWRRCAENRAVGTPCTNGAVRQGDDEATL--EVIEVHRVGNSKEHLPLPSESGSNSYAPA
+C------------------LERKNERNA-------------EAKRKMALARERKTVKTLG
+IIMGTFILCWLPFFIVALVLPF-CESSCH-MPALLGAIINWLGYSNSLLNPVIYAYFNKD
+FQNAFKKII-----KCKFCR--R-------------------------------------
+------------------------------------------------------------
+------------------------------
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDT------SATNM---TDDRYWSLTVYSHEHLVL-----TSVILGLFV
+LCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEIS-KVWF--
+LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMVVWIV
+ALFI-SIPPLF-GWRDPNN--DPDKTGTCIISQDK----------GYTIFSTVGAFYLPM
+LVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVVSDCNGCNSPDST
+TEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQIQIETAEAFANG
+CAEEASIAMLERQCNNGKKISSNDTPYS-------------RTREKLELKRERKAARTLA
+IITGAFLICWLPFFIIALIGPF-VDPE-G-IPPFARSFVLWLGYFNSLLNPIIYTIFSPE
+FRSAFQKIL-----FGKYRRGHR-------------------------------------
+------------------------------------------------------------
+------------------------------
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDT------SATNM---TDDRYWSLTVYSHEHLVL-----TSVILGLFV
+LCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEIS-KVWF--
+LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMVVWIV
+ALFI-SIPPLF-GWRDPNN--DPDKTGTCIISQDK----------GYTIFSTVGAFYLPM
+LVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVVSDCNGCNSPDST
+TEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQIQIETAEAFANG
+CAEEASIAMLERQCNNGKKISSNDTPYS-------------RTREKLELKRERKAARTLA
+IITGAFLICWLPFFIIALIGPF-VDPE-G-IPPFARSFVLWLGYFNSLLNPIIYTIFSPE
+FRSAFQKIL-----FGKYRRGHR-------------------------------------
+------------------------------------------------------------
+------------------------------
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+MEG-AEGQEELDWEAL--------------------------------------------
+YLRLPLQNCSWNSTGWEPNWNVTVV---PNTTWWQASAPFDTPAALVRAAAKAVVLGLLI
+LATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEVV-QRWT--
+LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRVGMMIACVWTV
+SFFV-CIAQLL-GWKDPDWNQRVSEDLRCVVSQDV----------GYQIFATASSFYVPV
+LIILILYWRIYQTARKRIRR------RRGATARGGVGPPPVPAG----------------
+-----------------GALVAGGGSGGIAAAVVAV-----IGRPLPTISETTTTGFTNV
+SSNNTSPE--KQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKRERKAAKTLA
+IITGAFVACWLPFFVLAILVPT-CD--CE-VSPVLTSLSLWLGYFNSTLNPVIYTVFSPE
+FRHAFQRLL-----CGRRVRRRRA----------------------------------PQ
+------------------------------------------------------------
+------------------------------
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+MN----------------------GTEGDNFYVPFSNKTGLA--RSPYEYPQY-------
+------------------YLAEPW-------------------KYSALAAYMFFLILVGF
+PVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSMN-GYFV--FGPT
+MCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGNF-RFGNTHAIMGVAFTWIMALAC
+-AAPPLV-GWS-----RYIPEGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIF
+FCYGRLLCTVKEAAAAQQESA---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEKEVTRMVVLMVI
+GFLVCWVPYASVAFYIFT--HQGSD-FGATFMTLPAFFAKSSALYNPVIYILMNKQFRNC
+MITTL-----CCGKNPLGDDESG--AS-TSKTEVS-------------------------
+------------------------------------------------------------
+-SVS-TSPVSPA---
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+MN----------------------GTEGPNFYVPFSNITGVV--RSPFEQPQY-------
+------------------YLAEPW-------------------QFSMLAAYMFLLIVLGF
+PINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSLH-GYFV--FGPT
+GCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSNF-RFGENHAIMGVAFTWVMALAC
+-AAPPLV-GWS-----RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF
+FCYGQLVFTVKEAAAQQQESA---------------------------------------
+------------------------------------------------------------
+------------------------------------------TTQKAEKEVTRMVIIMVI
+FFLICWLPYASVAMYIFT--HQGSN-FGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNC
+MLTSL-----CCGKNPLGDDEAS--AT-ASKTETS-------------------------
+------------------------------------------------------------
+-QVA-PA--------
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+MN----------------------GTEGINFYVPMSNKTGVV--RSPFEYPQY-------
+------------------YLAEPW-------------------KYRLVCCYIFFLISTGL
+PINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAWN-GYFV--FGPV
+GCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGNF-RFSATHAMMGIAFTWVMAFSC
+-AAPPLF-GWS-----RYMPEGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIF
+FSYGRLICKVREAAAQQQESA---------------------------------------
+------------------------------------------------------------
+------------------------------------------TTQKAEKEVTRMVILMVL
+GFMLAWTPYAVVAFWIFT--NKGAD-FTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNC
+MITTI-----CCGKNPFGDEDVSSTVS-QSKTEVS-------------------------
+------------------------------------------------------------
+-SVS-SSQVSPA---
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+MN----------------------GTEGKNFYVPMSNRTGLV--RSPFEYPQY-------
+------------------YLAEPW-------------------QFKILALYLFFLMSMGL
+PINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAIN-GYFV--LGPT
+GCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGSF-KFSSSHAFAGIAFTWVMALAC
+-AAPPLF-GWS-----RYIPEGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIF
+FTYGRLVCTVKAAAAQQQDSA---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEREVTKMVILMVF
+GFLIAWTPYATVAAWIFF--NKGAD-FSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNC
+MLTTI-----FCGKNPLGDDESS-TVS-TSKTEVS-------------------------
+------------------------------------------------------------
+-SVS-PA--------
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+MN----------------------GTEGNNFYVPLSNRTGLV--RSPFEYPQY-------
+------------------YLAEPW-------------------QFKLLAVYMFFLICLGL
+PINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAIN-GYFA--LGPT
+GCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGSF-KFSSTHASAGIAFTWVMAMAC
+-AAPPLV-GWS-----RYIPEGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIF
+FTYGRLVCTVKAAAAQQQDSA---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEREVTKMVILMVL
+GFLVAWTPYATVAAWIFF--NKGAA-FSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSC
+MLTTL-----FCGKNPLGDEESS-TVS-TSKTEVS-------------------------
+------------------------------------------------------------
+-SVS-PA--------
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+MK--------------------QVPEFHEDFYIPIPLDINNLSAYSPFLVPQD-------
+------------------HLGNQG-------------------IFMAMSVFMFFIFIGGA
+SINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSFFN-RYFI--FGAT
+ACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGNF-TFKTPHAIAGCILPWISALAA
+-SLPPLF-GWS-----RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIV
+FCYGQLLITLKLAAKAQADSA---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEREVTKMVVVMVL
+GFLVCWAPYASFSLWIVS--HRGEE-FDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSC
+MMKMV------CGKN-IEEDEAS--TS-SQVTQVS-------------------------
+------------------------------------------------------------
+-SVA-PEK-------
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+MR----------------------KMSEEEFYL-----FKNISSVGPWDGPQY-------
+------------------HIAPVW-------------------AFYLQAAFMGTVFLIGF
+PLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPVFVASCN-GYFV--FGRH
+VCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGNF-RFSSKHALTVVLATWTIGIGV
+-SIPPFF-GWS-----RFIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLIC
+FSYTQLLRALKAVAAQQQESA---------------------------------------
+------------------------------------------------------------
+------------------------------------------TTQKAEREVSRMVVVMVG
+SFCVCYVPYAAFAMYMVN--NRNHG-LDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQAC
+IMKMV------CGKA---MTDESDTCS-SQKTEVS-------------------------
+------------------------------------------------------------
+-TVS-STQVGPN---
+> 8=opsin, greensensitive human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------DLAETVIA-STISIVNQVS-GYFV--LGHP
+MCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNV-RFDAKLAIVGIAFSWIWAAVW
+-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIV
+LCYLQVWLAIRAVAKQQKESE---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEKEVTRMVVVMVL
+AFC---------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDS-YEDSTQ--SSIFTY-----TNSNSTRGPFEGPNY-------
+------------------HIAPRW-------------------VYHLTSVWMIFVVIASV
+FTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQVY-GYFV--LGHP
+MCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNV-RFDAKLAIVGIAFSWIWAAVW
+-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIV
+LCYLQVWLAIRAVAKQQKESE---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEKEVTRMVVVMVL
+AFCFCWGPYAFFACFAAA--NPGYP-FHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNC
+ILQLF----------GKKVDDGSELSS-ASKTEVS-------------------------
+------------------------------------------------------------
+-SVS---SVSPA---
+> 10== Z68193 1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDS-YEDSTQ--SSIFTY-----TNSNSTRGPFEGPNY-------
+------------------HIAPRW-------------------VYHLTSVWMIFVVTASV
+FTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQVS-GYFV--LGHP
+MCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNV-RFDAKLAIVGIAFSWIWSAVW
+-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIM
+LCYLQVWLAIRAVAKQQKESE---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEKEVTRMVVVMIF
+AYCVCWGPYTFFACFAAA--NPGYA-FHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNC
+ILQLF----------GKKVDDGSELSS-ASKTEVS-------------------------
+------------------------------------------------------------
+-SVS---SVSPA---
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDD--DDTTR--GSVFTY-----TNTNNTRGPFEGPNY-------
+------------------HIAPRW-------------------VYNLVSFFMIIVVIASC
+FTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQIF-GYFI--LGHP
+LCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNI-KFDSKLAIIGIVFSWVWAWGW
+-SAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIII
+VCYLQVWMAIRAVAAQQKESE---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEREVSRMVVVMIV
+AFCICWGPYASFVSFAAA--NPGYA-FHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNC
+IMQLF----------GKKVDDGSEAST-TSRTEVS-------------------------
+------------------------------------------------------------
+-SVS-NSSVAPA---
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MA-AWE-AAFAARRRHEE--EDTTR--DSVFTY-----TNSNNTRGPFEGPNY-------
+------------------HIAPRW-------------------VYNLTSVWMIFVVAASV
+FTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQIS-GYFI--LGHP
+MCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNI-KFDGKLAVAGILFSWLWSCAW
+-TAPPIF-GWS-----RYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIII
+LCYLQVWLAIRAVAAQQKESE---------------------------------------
+------------------------------------------------------------
+------------------------------------------STQKAEKEVSRMVVVMIV
+AYCFCWGPYTFFACFAAA--NPGYA-FHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNC
+ILQLF----------GKKVDDGSEVST--SRTEVS-------------------------
+------------------------------------------------------------
+-SVS-NSSVSPA---
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+MS-------------------------------SNSSQAPPNGTPGPFDGPQWP------
+------------------YQAPQS-------------------TYVGVAVLMGTVVACAS
+VVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNNIN-GFFV--FGRR
+MCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGDF-QFQRRHAVSGCAFTWGWALLW
+-SAPPLL-GWS-----SYVPEGLRTSCGPNWYTGGS--NNNSYILSLFVTCFVLPLSLIL
+FSYTNLLLTLRAAAAQQKEAD---------------------------------------
+------------------------------------------------------------
+------------------------------------------TTQRAEREVTRMVIVMVM
+AFLLCWLPYSTFALVVAT--HKGII-IQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSC
+LLEML-----CCGYQPQRTGKASPGTP-GPHADVT-------------------------
+------------------------------------------------------------
+-AAGLRNKVMPAHPV
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPEARLSAE----------TRLLGWNVPPEELR---------
+------------------HIPEHWLTYP----------EPPESMNYLLGTLYIFFTLMSM
+LGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIFIYNSFH-QGYA--LGHL
+GCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTHGKAIAMIIFIYMYATPW
+-VVACYTETWG-----RFVPEGYLTSCTFDYLTDN--FDTRLFVACIFFFSFVCPTTMIT
+YYYSQIVGHVFSHEKALRDQAKKMNVESLR------------------------------
+------------------------------------------------------------
+-------------------------------------SNVDKNKETAEIRIAKAAITICF
+LFFCSWTPYGVMSLIGAF--GDKTL-LTPGATMIPACACKMVACIDPFVYAISHPRYRME
+LQKRCPWL--ALNEKAPESSAVASTST-TQEPQQT-------------------------
+------------------------------------------------------------
+-TAA-----------
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVL-GNVSSVLRPDARLSAE----------SRLLGWNVPPDELR---------
+------------------HIPEHWLIYP----------EPPESMNYLLGTLYIFFTVISM
+IGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIFIYNSFH-QGYA--LGHL
+GCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTHGKAIAMIIFIYLYATPW
+-VVACYTESWG-----RFVPEGYLTSCTFDYLTDN--FDTRLFVACIFFFSFVCPTTMIT
+YYYSQIVGHVFSHEKALRDQAKKMNVDSLR------------------------------
+------------------------------------------------------------
+-------------------------------------SNVDKSKEAAEIRIAKAAITICF
+LFFASWTPYGVMSLIGAF--GDKTL-LTPGATMIPACTCKMVACIDPFVYAISHPRYRME
+LQKRCPWL--AISEKAPESRAAISTST-TQEQQQT-------------------------
+------------------------------------------------------------
+-TAA-----------
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+ME------PLCNASEPPLRPEAR-SSGNGD-------LQFLGWNVPPDQIQ---------
+------------------YIPEHWLTQL----------EPPASMHYMLGVFYIFLFCAST
+VGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF--NSFH-RGFAIYLGNT
+WCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVIMNIIIWLYCTPW
+-VVLPLTQFWD-----RFVPEGYLTSCSFDYLSDN--FDTRLFVGTIFFFSFVCPTLMIL
+YYYSQIVGHVFSHEKALREQAKKMNVESLR------------------------------
+------------------------------------------------------------
+-------------------------------------SNVDKSKETAEIRIAKAAITICF
+LFFVSWTPYGVMSLIGAF--GDKSL-LTQGATMIPACTCKLVACIDPFVYAISHPRYRLE
+LQKRCPWL--GVNEKSGEISSAQSTTT-QEQQQTT-------------------------
+------------------------------------------------------------
+-AA------------
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MD------ALCNASEPPLRPEARMSSGSDE-------LQFLGWNVPPDQIQ---------
+------------------YIPEHWLTQL----------EPPASMHYMLGVFYIFLFFAST
+LGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIFIYNSFH-RGFA--LGNT
+WCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVIMNIIIWLYCTPW
+-VVLPLTQFWD-----RFVPEGYLTSCSFDYLSDN--FDTRLFVGTIFLFSFVVPTLMIL
+YYYSQIVGHVFNHEKALREQAKKMNVESLR------------------------------
+------------------------------------------------------------
+-------------------------------------SNVDKSKETAEIRIAKAAITICF
+LFFVSWTPYGVMSLIGAF--GDKSL-LTPGATMIPACTCKLVACIEPFVYAISHPRYRME
+LQKRCPWL--GVNEKSGEASSAQSTTT-QEQTQQT-------------------------
+------------------------------------------------------------
+-SAA-----------
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+M-----------TNATGPQMAYYGAASMDFGYPE---GVSIVDFVRPEIKP---------
+------------------YVHQHWYNYP----------PVNPMWHYLLGVIYLFLGTVSI
+FGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNCFSGGVWM--FSPQ
+YCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGP-KLTTGKAVVFALISWVIAIGC
+-ALPPFF-GWG-----NYILEGILDSCSYDYLTQD--FNTFSYNIFIFVFDYFLPAAIIV
+FSYVFIVKAIFAHEAAMRAQAKKMNVSTLR------------------------------
+------------------------------------------------------------
+-------------------------------------S-NEADAQRAEIRIAKTALVNVS
+LWFICWTPYALISLKGVM--GDTSG-ITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLA
+ITQHLPWF--CVHETETKSNDDSQSNS-TVAQDKA-------------------------
+------------------------------------------------------------
+---------------
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+M-----------ANVTGPQMAFYGSGAATFGYPE---GMTVADFVPDRVKH---------
+------------------MVLDHWYNYP----------PVNPMWHYLLGVVYLFLGVISI
+AGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNCFSGGRWM--FSGT
+YCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGP-KLTQGKATFMCGLAWVISVGW
+-SLPPFF-GWG-----SYTLEGILDSCSYDYFTRD--MNTITYNICIFIFDFFLPASVIV
+FSYVFIVKAIFAHEAAMRAQAKKMNVTNLR------------------------------
+------------------------------------------------------------
+-------------------------------------S-NEAETQRAEIRIAKTALVNVS
+LWFICWTPYAAITIQGLL--GNAEG-ITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLA
+ITQHLPWF--CVHEKDPNDVEENQSSN-TQTQEKS-------------------------
+------------------------------------------------------------
+---------------
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+ME-----SFAVAAAQLGPHFAPLS-------------NGSVVDKVTPDMAH---------
+------------------LISPYWNQFP----------AMDPIWAKILTAYMIMIGMISW
+CGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYF-ETWV--LGPM
+MCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGR-PMTIPLALGKM----------
+-----------------YVPEGNLTSCGIDYLERD--WNPRSYLIFYSIFVYYIPLFLIC
+YSYWFIIAAVSAHEKAMREQAKKMNVKSLR------------------------------
+------------------------------------------------------------
+-------------------------------------S-SEDAEKSAEGKLAKVALVTIT
+LWFMAWTPYLVINCMGLF---KFEG-LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLA
+LKEKCPCC--VFGKVDDGKSSDAQSQA-TASEAESKA-----------------------
+------------------------------------------------------------
+---------------
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+ME-----SFAVAAAQLGPHFAPLS-------------NGSVVDKVTPDMAH---------
+------------------LISPYWNQFP----------AMDPIWAKILTAYMIMIGMISW
+CGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYF-ETWV--LGPM
+MCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGR-PMTIPLALGKIAYIWFMSSIW
+-CLAPAF-GWS-----RYVPEGNLTSCGIDYLERD--WNPRSYLIFYSIFVYYIPLFLIC
+YSYWFIIAAVSAHEKAMREQAKKMNVKSLR------------------------------
+------------------------------------------------------------
+-------------------------------------S-SEDAEKSAEGKLAKVALVTIT
+LWFMAWTPYLVINCMGLF---KFEG-LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLA
+LKEKCPCC--VFGKVDDGKSSDAQSQA-TASEAESKA-----------------------
+------------------------------------------------------------
+---------------
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MD-----SFAAVATQLGPQFAAPS-------------NGSVVDKVTPDMAH---------
+------------------LISPYWDQFP----------AMDPIWAKILTAYMIIIGMISW
+CGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLYF-ETWV--LGPM
+MCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGR-PMTIPLALGKIAYIWFMSTIW
+CCLAPVF-GWS-----RYVPEGNLTSCGIDYLERD--WNPRSYLIFYSIFVYYIPLFLIC
+YSYWFIIAAVSAHEKAMREQAKKMNVKSLR------------------------------
+------------------------------------------------------------
+-------------------------------------S-SEDADKSAEGKLAKVALVTIS
+LWFMAWTPYLVINCMGLF---KFEG-LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLA
+LKEKCPCC--VFGKVDDGKSSEAQSQA-TTSEAESKA-----------------------
+------------------------------------------------------------
+---------------
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQAQSSG-----------NGSVLDNVLPDMAH---------
+------------------LVNPYWSRFA----------PMDPMMSKILGLFTLAIMIISC
+CGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYY-ETWV--LGPL
+WCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGT-PMTIKTSIMKILFIWMMAVFW
+-TVMPLI-GWS-----AYVPEGNLTACSIDYMTRM--WNPRSYLITYSLFVYYTPLFLIC
+YSYWFIIAAVAAHEKAMREQAKKMNVKSLR------------------------------
+------------------------------------------------------------
+-------------------------------------S-SEDCDKSAEGKLAKVALTTIS
+LWFMAWTPYLVICYFGLF---KIDG-LTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIV
+LKEKCPMC--VFGNTDEPKPDAPASDTETTSEADSKA-----------------------
+------------------------------------------------------------
+---------------
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFEAQTGG-----------NRSVLDNVLPDMAP---------
+------------------LVNPHWSRFA----------PMDPTMSKILGLFTLVILIISC
+CGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFYY-ETWV--LGPL
+WCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGT-PMTIKTSIMKIAFIWMMAVFW
+-TIMPLI-GWS-----SYVPEGNLTACSIDYMTRQ--WNPRSYLITYSLFVYYTPLFMIC
+YSYWFIIATVAAHEKAMRDQAKKMNVKSLR------------------------------
+------------------------------------------------------------
+-------------------------------------S-SEDCDKSAENKLAKVALTTIS
+LWFMAWTPYLIICYFGLF---KIDG-LTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLV
+LKEKCPMC--VCGTTDEPKPDAPPSDTETTSEAESKD-----------------------
+------------------------------------------------------------
+---------------
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+M-----------IAVSGPSYEAFSYGGQARFN-----NQTVVDKVPPDMLH---------
+------------------LIDANWYQYP----------PLNPMWHGILGFVIGMLGFVSA
+MGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINCYY-ETWV--LGPL
+FCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGK-PLSINGALIRIIAIWLFSLGW
+-TIAPMF-GWN-----RYVPEGNMTACGTDYFNRG--LLSASYLVCYGIWVYFVPLFLII
+YSYWFIIQAVAAHEKNMREQAKKMNVASLR------------------------------
+------------------------------------------------------------
+-------------------------------------S-SENQNTSAECKLAKVALMTIS
+LWFMAWTPYLVINFSGIF---NLVK-ISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAA
+LFAKFPSL--ACAA-EPSSDAVSTTSG-TTTVTDNEKSNA--------------------
+------------------------------------------------------------
+---------------
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+M------ANQLSYSSLGWPYQP---------------NASVVDTMPKEMLY---------
+------------------MIHEHWYAFP----------PMNPLWYSILGVAMIILGIICV
+LGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNCFA-ETWI--LGPF
+MCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAA-PLTHKKATLLLLFVWIWSGGW
+-TILPFF-GWS-----RYVPEGNLTSCTVDYLTKD--WSSASYVVIYGLAVYFLPLITMI
+YCYFFIVHAVAEHEKQLREQAKKMNVASLR------------------------------
+------------------------------------------------------------
+-------------------------------------ANADQQKQSAECRLAKVAMMTVG
+LWFMAWTPYLIISWAGVF--SSGTR-LTPLATIWGSVFAKANSCYNPIVYGISHPRYKAA
+LYQRFPSL--ACGSGESGSDVKSEASA-TTTMEEKPKIPEA-------------------
+------------------------------------------------------------
+---------------
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+M-------------------------------VESTTLVNQTWWYNPTV-----------
+------------------DIHPHWAKFD----------PIPDAVYYSVGIFIGVVGIIGI
+LGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFM-KKWI--FGKV
+ACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVW
+-SVGPVF-NWG-----AYVPEGILTSCSFDYLSTD--PSTRSFILCMYFCGFMLPIIIIA
+FCYFNIVMSVSNHEKEMAAMAKRLNAKELR------------------------------
+------------------------------------------------------------
+---------------------------------------KAQAGASAEMKLAKISMVIIT
+QFMLSWSPYAIIALLAQF--GPAEW-VTPYAAELPVLFAKASAIHNPIVYSVSHPKFREA
+IQTTFPWLLTCCQFDEKECEDANDAEE-EVVASER--GGESRDAAQMKEMMAMMQKMQAQ
+QAAYQP---PPPPQGYPPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAP
+QGAPPQGVDNQAYQA
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+M--------------------------------GRDLRDNETWWYNPSI-----------
+------------------VVHPHWREFD----------QVPDAVYYSLGIFIGICGIIGC
+GGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFL-KKWI--FGFA
+ACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLW
+-AIGPIF-GWG-----AYTLEGVLCNCSFDYISRD--STTRSNILCMFILGFFGPILIIF
+FCYFNIVMSVSNHEKEMAAMAKRLNAKELR------------------------------
+------------------------------------------------------------
+---------------------------------------KAQAGANAEMRLAKISIVIVS
+QFLLSWSPYAVVALLAQF--GPLEW-VTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREA
+ISQTFPWVLTCCQFDDKETEDDKDAET-EIPAGESSDAAPSADAAQMKEMMAMMQKMQQQ
+QAAYPPQGYAPPPQGYPPQGYPPQGY--PPQGYPPQGYPP---PPQGAPPQGAPP-----
+-AAPPQGVDNQAYQA
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLS---EVTA---
+------------------SPAPTWDAPPDNASGCGEQINYGRVEKVVIGSILTLITLLTI
+AGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGGKWI--FGHF
+FCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASI
+-TLPPLF-GWA-----QNVNDDKVCLISQDF----------GYTIYSTAVAFYIPMSVML
+FMYYQIYKAARKSAAKHKFP--------------GFPRVEPDSVIALNGIVKLQKEVEE-
+------------------------------------------------------------
+---------------------------CANLSRLLKHERKNISIFKREQKAATTLGIIVG
+AFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTT
+YRSLL-----QCQYRNINRKLSAAGMH-EALKLAERPERPEFVLQNADYCRKKGHDS---
+------------------------------------------------------------
+---------------
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+M--------------------------------------------PHLLSGFLEVTA---
+------------------SPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTI
+AGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGGKWI--FGHF
+FCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASI
+-TLPPLF-GWA-----QNVNDDKVCLISQDF----------GYTIYSTAVAFYIPMSVML
+FMYYQIYKAARKSAAKHKFP--------------GFPRVQPESVISLNGVVKLQKEVEE-
+------------------------------------------------------------
+---------------------------CANLSRLLKHERKNISIFKREQKAATTLGIIVG
+AFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPT
+SRSLL-----QCQYRNINRKLSAAGMH-EALKLAERPERSEFVLQNSDHCGKKGHDT---
+------------------------------------------------------------
+---------------
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+M--------------------------------------------PHLLSGFLEVTA---
+------------------SPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTI
+AGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDLIGGKWI--FGHF
+FCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASI
+-TLPPLF-GWA-----QNVNDDKVCLISQDF----------GYTIYSTAVAFYIPMSVML
+FMYYQIYKAARKSAAKHKFP--------------GFPRVQPESVISLNGVVKLQKEVEE-
+------------------------------------------------------------
+---------------------------CANLSRLLKHERKNISIFKREQKAATTLGIIVG
+AFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTT
+YRSLL-----QCQYRNINRKLSAAGMH-EALKLAERPERSEFVLQNSDHCGKKGHDT---
+------------------------------------------------------------
+---------------
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPGQGNNTTSPPAPF-----------------------------------------
+------------------ETGGNTTGIS----------DVTVSYQVITSLLLGTLIFCAV
+LGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVL-NKWT--LGQV
+TCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLI
+-SIPPML-GWRTP---EDRSDPDACTISKDH----------GYTIYSTFGAFYIPLLLML
+VLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQPKKS---------VNGESGSRNW
+RLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAPASFER
+KNERNA-------------------------------EAKRKMALARERKTVKTLGIIMG
+TFILCWLPFFIVALVLPF-CESSCH-MPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNA
+FKKII-----KCKFCRQ-------------------------------------------
+------------------------------------------------------------
+---------------
+> 33=p A35181 serotonin receptor class 1A - rat
+MDVFSFGQGNNTTASQEPF-----------------------------------------
+------------------GTGGNVTSIS----------DVTFSYQVITSLLLGTLIFCAV
+LGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQVL-NKWT--LGQV
+TCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLI
+-SIPPML-GWRTP---EDRSDPDACTISKDH----------GYTIYSTFGAFYIPLLLML
+VLYGRIFRAARFRIRKTVRKVEKKGAGTSLGTSSAPPPKKS---------LNGQPGSGDW
+RRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESGSNSYAPACLER
+KNERNA-------------------------------EAKRKMALARERKTVKTLGIIMG
+TFILCWLPFFIVALVLPF-CESSCH-MPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNA
+FKKII-----KCKFCRR-------------------------------------------
+------------------------------------------------------------
+---------------
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLT----------VYSHEHLVLTSVILGLFVLCCI
+IGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEIS-KVWF--LHSE
+VCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMVVWIVALFI
+-SIPPLF-GWRDP--NNDPDKTGTCIISQDK----------GYTIFSTVGAFYLPMLVMM
+IIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVVSDCNGCNSPDSTTEKK
+KRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQIQIETAEAFANGCAEE
+ASIAMLERQCNNGKKISSNDTPYS-------------RTREKLELKRERKAARTLAIITG
+AFLICWLPFFIIALIGPF--VDPEG-IPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSA
+FQKIL-----FGKYRRGHR-----------------------------------------
+------------------------------------------------------------
+---------------
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLT----------VYSHEHLVLTSVILGLFVLCCI
+IGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEIS-KVWF--LHSE
+VCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILLMIMVVWIVALFI
+-SIPPLF-GWRDP--NNDPDKTGTCIISQDK----------GYTIFSTVGAFYLPMLVMM
+IIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVVSDCNGCNSPDSTTEKK
+KRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSSSERLKQIQIETAEAFANGCAEE
+ASIAMLERQCNNGKKISSNDTPYS-------------RTREKLELKRERKAARTLAIITG
+AFLICWLPFFIIALIGPF--VDPEG-IPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSA
+FQKIL-----FGKYRRGHR-----------------------------------------
+------------------------------------------------------------
+---------------
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTV---------------------
+------------------VPNTTWWQASAPF-----DTPAALVRAAAKAVVLGLLILATV
+VGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEVV-QRWT--LGPE
+LCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRVGMMIACVWTVSFFV
+-CIAQLL-GWKDPDWNQRVSEDLRCVVSQDV----------GYQIFATASSFYVPVLIIL
+ILYWRIYQTARKRIRRRRGATARGGV--------GPPPVPAGGALVAGGGSGG-------
+-----------------------------IAAAVVAVIGRPLPTISETTTTGFTNVSSNN
+TSPE--KQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKRERKAAKTLAIITG
+AFVACWLPFFVLAILVPT---CDCE-VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHA
+FQRLL-----CGRRVRRRRAPQ--------------------------------------
+------------------------------------------------------------
+---------------
--- /dev/null
+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+M-----------------------------------------------------------
+------------------------------NGTE--GDNFYV----PF------------
+--------------------------SNKTGLARSPYEYPQY-YLA-----EPWK-----
+----YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-F
+TVTMYTS-MN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-F
+RFGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFN
+NESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KEAAAAQQE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SASTQKAEKEVTRMV
+VLMVIGFLVCWVPYASVAFYIFT-HQG-S--DFGATFMTLPAFFAKSSALYNPVIYILMN
+KQFRNCMITTLC-C---GKNP------------------------------LGDDE--SG
+ASTSKT-E--VSSVS-TSPV----------------------------------------
+---------------------------------------------SP-A---
+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+M-----------------------------------------------------------
+------------------------------NGTE--GPNFYV----PF------------
+--------------------------SNITGVVRSPFEQPQY-YLA-----EPWQ-----
+----FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-F
+TTTLYTS-LH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-F
+RFGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVN
+NESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KEAAAQQQE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SATTQKAEKEVTRMV
+IIMVIFFLICWLPYASVAMYIFT-HQG-S--NFGPIFMTLPAFFAKTASIYNPIIYIMMN
+KQFRNCMLTSLC-C---GKNP------------------------------LGDDE--AS
+ATASKT-E--------TSQV----------------------------------------
+---------------------------------------------AP-A---
+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+M-----------------------------------------------------------
+------------------------------NGTE--GINFYV----PM------------
+--------------------------SNKTGVVRSPFEYPQY-YLA-----EPWK-----
+----YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-F
+TVTFYTA-WN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-F
+RFSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYH
+NESYVLYMFVIHFIIPVVVIFFSYGRLICKV----REAAAQQQE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SATTQKAEKEVTRMV
+ILMVLGFMLAWTPYAVVAFWIFT-NKG-A--DFTATLMAVPAFFSKSSSLYNPIIYVLMN
+KQFRNCMITTIC-C---GKNP------------------------------FGDEDVSST
+VSQSKT-E--VSSVS-SSQV----------------------------------------
+---------------------------------------------SP-A---
+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+M-----------------------------------------------------------
+------------------------------NGTE--GKNFYV----PM------------
+--------------------------SNRTGLVRSPFEYPQY-YLA-----EPWQ-----
+----FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-F
+TVTFYTA-IN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-F
+KFSSSHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYN
+NESYVIYMFVCHFILPVAVIFFTYGRLVCTV----KAAAAQQQD----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SASTQKAEREVTKMV
+ILMVFGFLIAWTPYATVAAWIFF-NKG-A--DFSAKFMAIPAFFSKSSALYNPVIYVLLN
+KQFRNCMLTTIF-C---GKNP------------------------------LGDDE-SST
+VSTSKT-E--VSS------V----------------------------------------
+---------------------------------------------SP-A---
+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+M-----------------------------------------------------------
+------------------------------NGTE--GNNFYV----PL------------
+--------------------------SNRTGLVRSPFEYPQY-YLA-----EPWQ-----
+----FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-F
+TVTFYTA-IN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-F
+KFSSTHASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYN
+NESYVLYMFICHFILPVTIIFFTYGRLVCTV----KAAAAQQQD----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SASTQKAEREVTKMV
+ILMVLGFLVAWTPYATVAAWIFF-NKG-A--AFSAQFMAIPAFFSKTSALYNPVIYVLLN
+KQFRSCMLTTLF-C---GKNP------------------------------LGDEE-SST
+VSTSKT-E--VSS------V----------------------------------------
+---------------------------------------------SP-A---
+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+M-----------------------------------------------------------
+------------------------------KQVPEFHEDFYI----PIPL----------
+------------------------DINNLS--AYSPFLVPQD-HLG-----NQGI-----
+----FMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-S
+PLSFYSF-FN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-F
+TFKTPHAIAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYN
+NESYVMFLFCFCFAVPFGTIVFCYGQLLITL----KLAAKAQAD----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SASTQKAEREVTKMV
+VVMVLGFLVCWAPYASFSLWIVS-HRG-E--EFDLRMATIPSCLSKASTVYNPVIYVLMN
+KQFRSCMM-KMV-C---GKN-------------------------------IEEDE--AS
+TSSQVT-Q--VSS------V----------------------------------------
+---------------------------------------------APEK---
+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]
+M-----------------------------------------------------------
+------------------------------RKMS--EEEFYL-------F----------
+--------------------------KNISSV--GPWDGPQY-HIA-----PVWA-----
+----FYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-V
+FPVFVAS-CN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-F
+RFSSKHALTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYR
+SESYTWFLFIFCFIVPLSLICFSYTQLLRAL----KAVAAQQQE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SATTQKAEREVSRMV
+VVMVGSFCVCYVPYAAFAMYMVN-NRN-H--GLDLRLVTIPSFFSKSACIYNPIIYCFMN
+KQFQACIM-KMV-C---GKA-------------------------------MTDES--DT
+CSSQKT-E--VSTVS-STQV----------------------------------------
+---------------------------------------------GP-N---
+> 8=opsin, greensensitive human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------------------------DLAETVIA-S
+TISIVNQ-VS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-V
+RFDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPG
+VQSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RAVAKQQKE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SESTQKAEKEVTRMV
+VVMVLAFC----------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------
+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]
+M-------------AQQWSLQRLA--GRHPQDSYE-------------------------
+------------------------------DSTQ--SSIFTY----TN------------
+--------------------------SNST---RGPFEGPNY-HIA-----PRWV-----
+----YHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
+TISVVNQ-VY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-V
+RFDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPG
+VQSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RAVAKQQKE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SESTQKAEKEVTRMV
+VVMVLAFCFCWGPYAFFACFAAA-NPG-Y--PFHPLMAALPAFFAKSATIYNPVIYVFMN
+RQFRNCIL-QLF-----GKK-------------------------------VDDGS--EL
+SSASKT-E--VSSV---SSV----------------------------------------
+---------------------------------------------SP-A---
+> 10== Z68193 1 human Red Opsin <>[]
+M-------------AQQWSLQRLA--GRHPQDSYE-------------------------
+------------------------------DSTQ--SSIFTY----TN------------
+--------------------------SNST---RGPFEGPNY-HIA-----PRWV-----
+----YHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
+TISIVNQ-VS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-V
+RFDAKLAIVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPG
+VQSYMIVLMVTCCIIPLAIIMLCYLQVWLAI----RAVAKQQKE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SESTQKAEKEVTRMV
+VVMIFAYCVCWGPYTFFACFAAA-NPG-Y--AFHPLMAALPAYFAKSATIYNPVIYVFMN
+RQFRNCIL-QLF-----GKK-------------------------------VDDGS--EL
+SSASKT-E--VSSV---SSV----------------------------------------
+---------------------------------------------SP-A---
+> 11== M92036 1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+M-------------TEAWNVAVFA--ARRSRDD-D-------------------------
+------------------------------DTTR--GSVFTY----TN------------
+--------------------------TNNT---RGPFEGPNY-HIA-----PRWV-----
+----YNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-S
+TISVFNQ-IF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-I
+KFDSKLAIIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELG
+CQSFMLTLMITCCFLPLFIIIVCYLQVWMAI----RAVAAQQKE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SESTQKAEREVSRMV
+VVMIVAFCICWGPYASFVSFAAA-NPG-Y--AFHPLAAALPAYFAKSATIYNPVIYVFMN
+RQFRNCIM-QLF-----GKK-------------------------------VDDGS--EA
+STTSRT-E--VSSVS-NSSV----------------------------------------
+---------------------------------------------AP-A---
+> 12== M62903 1 chicken visual pigment <>[BBRC173,1212-1217'90]
+M-------------AA-WEAAFAA--RRRHEE--E-------------------------
+------------------------------DTTR--DSVFTY----TN------------
+--------------------------SNNT---RGPFEGPNY-HIA-----PRWV-----
+----YNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-S
+TISVINQ-IS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-I
+KFDGKLAVAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPG
+VQSYMVVLMVTCCFFPLAIIILCYLQVWLAI----RAVAAQQKE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------SESTQKAEKEVSRMV
+VVMIVAYCFCWGPYTFFACFAAA-NPG-Y--AFHPLAAALPAYFAKSATIYNPIIYVFMN
+RQFRNCIL-QLF-----GKK-------------------------------VDDGS--EV
+ST-SRT-E--VSSVS-NSSV----------------------------------------
+---------------------------------------------SP-A---
+> 13== S75720 1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+M-------------S-------------------S-------------------------
+------------------------------NSSQ--AP----------------------
+--------------------------PNGT---PGPFDGPQWPYQA-----PQST-----
+----YVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-S
+SVSLSNN-IN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-F
+QFQRRHAVSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN-
+-NSYILSLFVTCFVLPLSLILFSYTNLLLTL----RAAAAQQKE----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------ADTTQRAEREVTRMV
+IVMVMAFLLCWLPYSTFALVVAT-HKG-I--IIQPVLASLPSYFSKTATVYNPIIYVFMN
+KQFQSCLL-EMLCCGYQPQR-------------------------------TGKAS--PG
+TPGPHA-D--VTAAGLRNKV----------------------------------------
+---------------------------------------------MP-AHPV
+> 14== M17718 1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+M---------------------------------ES-G----------------------
+------------------------------NVSS---------------SLFGNVSTALR
+PEARLSA---ETRLLGWNVPPEELR------------------HIP-----EHWLTYPEP
+PESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--T
+PIFIYNS-FH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--
+KMTHGKAIAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFD
+TRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVESL---------------------RS-NVDKNKETAEIRIAKAA
+ITICFLFFCSWTPYGVMSLIGAF-GDK-T--LLTPGATMIPACACKMVACIDPFVYAISH
+PRYRMELQ---------KRCP------------------WLALNEKAPE--SSAVA--ST
+STTQEP-Q-------------------------QT-------------------------
+---------------------------------------------TA-A---
+> 15== X65879 1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+M---------------------------------EY-H----------------------
+------------------------------NVSS---------------VL-GNVSSVLR
+PDARLSA---ESRLLGWNVPPDELR------------------HIP-----EHWLIYPEP
+PESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--T
+PIFIYNS-FH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--
+KMTHGKAIAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFD
+TRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVDSL---------------------RS-NVDKSKEAAEIRIAKAA
+ITICFLFFASWTPYGVMSLIGAF-GDK-T--LLTPGATMIPACTCKMVACIDPFVYAISH
+PRYRMELQ---------KRCP------------------WLAISEKAPE--SRAAI--ST
+STTQEQ-Q-------------------------QT-------------------------
+---------------------------------------------TA-A---
+> 16== M17730 1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+M---------------------------------EPLC----------------------
+------------------------------NASE---------------PP-------LR
+PEAR-SSGNGDLQFLGWNVPPDQIQ------------------YIP-----EHWLTQLEP
+PASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
+PIF--NS-FH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--
+NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFD
+TRLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVESL---------------------RS-NVDKSKETAEIRIAKAA
+ITICFLFFVSWTPYGVMSLIGAF-GDK-S--LLTQGATMIPACTCKLVACIDPFVYAISH
+PRYRLELQ---------KRCP------------------WLGVNEKSGE--ISSAQ--ST
+-TTQEQ-Q-------------------------QT-------------------------
+---------------------------------------------TA-A---
+> 17== X65880 1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+M---------------------------------DALC----------------------
+------------------------------NASE---------------PP-------LR
+PEARMSSGSDELQFLGWNVPPDQIQ------------------YIP-----EHWLTQLEP
+PASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
+PIFIYNS-FH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--
+NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFD
+TRLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVESL---------------------RS-NVDKSKETAEIRIAKAA
+ITICFLFFVSWTPYGVMSLIGAF-GDK-S--LLTPGATMIPACTCKLVACIEPFVYAISH
+PRYRMELQ---------KRCP------------------WLGVNEKSGE--ASSAQ--ST
+-TTQEQTQ-------------------------QT-------------------------
+---------------------------------------------SA-A---
+> 18== D50584 1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+M---------------------------------------------TNATGPQMAYYG--
+---AASMDFGYPE-----------------GVSI---------------VD---------
+-----------------FVRPEIKP------------------YVH-----QHWYNYPPV
+NPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-V
+PFFTYNC-FSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-P
+KLTTGKAVVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFN
+TFSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVSTL---------------------RS-N-EADAQRAEIRIAKTA
+LVNVSLWFICWTPYALISLKGVM-GDT-S--GITPLVSTLPALLAKSCSCYNPFVYAISH
+PKYRLAIT---------QHLP------------------WFCVHETETKS-NDDSQ--SN
+STVAQ-------------------------------------------------------
+---------------------------------------------DK-A---
+> 19== D50583 1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+M---------------------------------------------ANVTGPQMAFYG--
+---SGAATFGYPE-----------------GMTV---------------AD---------
+-----------------FVPDRVKH------------------MVL-----DHWYNYPPV
+NPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-F
+PPFCYNC-FSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-P
+KLTQGKATFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMN
+TITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVTNL---------------------RS-N-EAETQRAEIRIAKTA
+LVNVSLWFICWTPYAAITIQGLL-GNA-E--GITPLLTTLPALLAKSCSCYNPFVYAISH
+PKFRLAIT---------QHLP------------------WFCVHEKDPND-VEENQ--SS
+NTQTQ-------------------------------------------------------
+---------------------------------------------EK-S---
+> 20== K02320 1 D.melanogaster opsin <>[Cell40,851-858'85]
+M---------------------------------E------SFAVAAAQLGPHFAPLS--
+------------------------------NGSV---------------VD---------
+-----------------KVTPDMAH------------------LIS-----PYWNQFPAM
+DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINL-YF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-R
+PMTIPLALGKM---------------------------YVPEGNLTSCGIDYLE--RDWN
+PRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVKSL---------------------RS-S-EDAEKSAEGKLAKVA
+LVTITLWFMAWTPYLVINCMGLF--KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISH
+PKYRLALK---------EKCP------------------CCVFGKVDDGK-SSDAQ--SQ
+ATASEA-E----------------------------------------------------
+---------------------------------------------SK-A---
+> 21== K02315 1 D.melanogaster ninaE <>[Cell40,839-850'85]
+M---------------------------------E------SFAVAAAQLGPHFAPLS--
+------------------------------NGSV---------------VD---------
+-----------------KVTPDMAH------------------LIS-----PYWNQFPAM
+DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINL-YF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-R
+PMTIPLALGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWN
+PRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVKSL---------------------RS-S-EDAEKSAEGKLAKVA
+LVTITLWFMAWTPYLVINCMGLF--KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISH
+PKYRLALK---------EKCP------------------CCVFGKVDDGK-SSDAQ--SQ
+ATASEA-E----------------------------------------------------
+---------------------------------------------SK-A---
+> 22== X65877 1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+M---------------------------------D------SFAAVATQLGPQFAAPS--
+------------------------------NGSV---------------VD---------
+-----------------KVTPDMAH------------------LIS-----PYWDQFPAM
+DPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINL-YF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-R
+PMTIPLALGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWN
+PRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVKSL---------------------RS-S-EDADKSAEGKLAKVA
+LVTISLWFMAWTPYLVINCMGLF--KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISH
+PKYRLALK---------EKCP------------------CCVFGKVDDGK-SSEAQ--SQ
+ATTSEA-E----------------------------------------------------
+---------------------------------------------SK-A---
+> 23== M12896 1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+M---------------------------------ER-SHLPETPFDLAHSGPRFQAQS--
+---SG-------------------------NGSV---------------LD---------
+-----------------NVLPDMAH------------------LVN-----PYWSRFAPM
+DPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
+PVMIINF-YY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-T
+PMTIKTSIMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWN
+PRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVKSL---------------------RS-S-EDCDKSAEGKLAKVA
+LTTISLWFMAWTPYLVICYFGLF--KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISH
+PKYRIVLK---------EKCP------------------MCVFGNTDEPKPDAPAS--DT
+ETTSEA-D----------------------------------------------------
+---------------------------------------------SK-A---
+> 24== X65878 1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+M---------------------------------ER-SLLPEPPLAMALLGPRFEAQT--
+---GG-------------------------NRSV---------------LD---------
+-----------------NVLPDMAP------------------LVN-----PHWSRFAPM
+DPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
+PVMIINF-YY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-T
+PMTIKTSIMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWN
+PRSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVKSL---------------------RS-S-EDCDKSAENKLAKVA
+LTTISLWFMAWTPYLIICYFGLF--KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISH
+PNDRLVLK---------EKCP------------------MCVCGTTDEPKPDAPPS--DT
+ETTSEA-E----------------------------------------------------
+---------------------------------------------SK-D---
+> 25== U26026 1 Apis mellifera long-wavelength rhodopsin <>[]
+M---------------------------------------------IAVSGPSYEAFS--
+---YG----GQAR---------------FNNQTV---------------VD---------
+-----------------KVPPDMLH------------------LID-----ANWYQYPPL
+NPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-S
+PPMVINC-YY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-K
+PLSINGALIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLL
+SASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVASL---------------------RS-S-ENQNTSAECKLAKVA
+LMTISLWFMAWTPYLVINFSGIF--NL-V--KISPLFTIWGSLFAKANAVYNPIVYGISH
+PKYRAALF---------AKFP------------------SLAC-AAEPSS-DAVST--TS
+GTTTVT-D----------------------------------------------------
+-----------------------------------------NEK-SN-A---
+> 26== L03781 1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+M-----------------------------------------------ANQLSYSSLG--
+---WP----YQP------------------NASV---------------VD---------
+-----------------TMPKEMLY------------------MIH-----EHWYAFPPM
+NPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-M
+PTMTSNC-FA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-A
+PLTHKKATLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWS
+SASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKK----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------MNVASL---------------------RANA-DQQKQSAECRLAKVA
+MMTVGLWFMAWTPYLIISWAGVF--SSGT--RLTPLATIWGSVFAKANSCYNPIVYGISH
+PRYKAALY---------QRFP------------------SLACGSGESGS-DVKSE--AS
+ATTTME-E----------------------------------------------------
+-----------------------------------------KPKIPE-A---
+> 27== X07797 1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+M-----------------------------------------------------------
+---------VESTTLVNQTW-------WY-NPTV---------------D----------
+--------------------------------------------IH-----PHWAKFDPI
+PDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGF
+PLKTISA-FM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASK
+KMSHRRAFLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPS
+TRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKR----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------LNAKEL---------------------RK---AQAGASAEMKLAKIS
+MVIITQFMLSWSPYAIIALLAQF-GPA-E--WVTPYAAELPVLFAKASAIHNPIVYSVSH
+PKFREAIQ---------TTFPWL--------------LTCCQFDEKECED-ANDAE--EE
+VVASER---GGESRD-AAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPPQGAYP
+PPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQA-YQ-A---
+> 28== X70498 1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+M-----------------------------------------------------------
+---------GRDLR-DNETW-------WY-NPSI---------------V----------
+--------------------------------------------VH-----PHWREFDQV
+PDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGF
+PLMTISC-FL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASK
+KMSHRRAFIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDST
+TRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------LNAKEL---------------------RK---AQAGANAEMRLAKIS
+IVIVSQFLLSWSPYAVVALLAQF-GPL-E--WVTPYAAQLPVMFAKASAIHNPMIYSVSH
+PKFREAIS---------QTFPWV--------------LTCCQFDDKETED-DKDAE--TE
+IPAGES-SDAAPSAD-AAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPPQGY--
+PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQA-YQ-A---
+> 29== L21195 1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDL----YGHLRSFL--LPE-----------------VGRGLPDLSPDGGA
+DPVAG-------------SWAPHLLS----EVTA--SPAPTW------------------
+-----------------DAPPDNAS-GCGE-------------QIN-------------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIG-GKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPV
+RQNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF--------
+--GYTIYSTAVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF-------------
+----PGF---------------------------------PRVEPDS-------------
+--------VIALNGIVKLQKEV--------------------------------------
+--------EE--CANLSRLLKH------------------ER-K-NISIFKREQKAATTL
+GIIVGAFTVCWLPFFLLSTARPFICGT-SCSCIPLWVERTFLWLGYANSLINPFIYAFFN
+RDLRTTYR-SLL----------QC---QYRNINRKLSA-------------AGMHE--AL
+KLAERP-E--------RPEF-----VL------QN-------------------------
+------ADYCRKKGHD--------------------------------S---
+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+M-----------------------------------------------------------
+---------------------PHLLSGFL-EVTA--SPAPTW------------------
+-----------------DAPPDNVS-GCGE-------------QIN-------------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIG-GKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPV
+RQNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF--------
+--GYTIYSTAVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF-------------
+----PGF---------------------------------PRVQPES-------------
+--------VISLNGVVKLQKEV--------------------------------------
+--------EE--CANLSRLLKH------------------ER-K-NISIFKREQKAATTL
+GIIVGAFTVCWLPFFLLSTARPFICGT-SCSCIPLWVERTCLWLGYANSLINPFIYAFFN
+RDLRPTSR-SLL----------QC---QYRNINRKLSA-------------AGMHE--AL
+KLAERP-E--------RSEF-----VL------QN-------------------------
+------SDHCGKKGHD--------------------------------T---
+> 31=p A47425 serotonin receptor 5HT-7 - rat
+M-----------------------------------------------------------
+---------------------PHLLSGFL-EVTA--SPAPTW------------------
+-----------------DAPPDNVS-GCGE-------------QIN-------------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIG-GKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPV
+RQNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF--------
+--GYTIYSTAVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF-------------
+----PGF---------------------------------PRVQPES-------------
+--------VISLNGVVKLQKEV--------------------------------------
+--------EE--CANLSRLLKH------------------ER-K-NISIFKREQKAATTL
+GIIVGAFTVCWLPFFLLSTARPFICGT-SCSCIPLWVERTCLWLGYANSLINPFIYAFFN
+RDLRTTYR-SLL----------QC---QYRNINRKLSA-------------AGMHE--AL
+KLAERP-E--------RSEF-----VL------QN-------------------------
+------SDHCGKKGHD--------------------------------T---
+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+M-DVLSPGQ-----------------GNN-----------------TTSPPAPFETGG--
+------------------------------NTTG--ISDVTV------------------
+------------------------------------------------------------
+--SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
+PMAALYQ-VL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVN
+KRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDACTISKDH--------
+--GYTIYSTFGAFYIPLLLMLVLYGRIF-------RAARFRIRK----------------
+-----------------------TVKKVEKTGADTRHGASPAPQPKKSVNGESGSRNWRL
+GVESKAGGALCANGAVRQGDDG----AALEVIEVHRVGNSKEHLPLPSEAGPTPCAPASF
+ERKN----ERN--------------------A--------EA-K-RKMALARERKTVKTL
+GIIMGTFILCWLPFFIVALVLPF-CES-SC-HMPTLLGAIINWLGYSNSLLNPVIYAYFN
+KDFQNAFK-KII---------------KCKFCRQ--------------------------
+------------------------------------------------------------
+----------------------------------------------------
+> 33=p A35181 serotonin receptor class 1A - rat
+M-DVFSFGQ-----------------GNN-----------------TTASQEPFGTGG--
+------------------------------NVTS--ISDVTF------------------
+------------------------------------------------------------
+--SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
+PMAALYQ-VL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVN
+KRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDACTISKDH--------
+--GYTIYSTFGAFYIPLLLMLVLYGRIF-------RAARFRIRK----------------
+-----------------------TVRKVEKKGAGTSLGTSSAPPPKKSLNGQPGSGDWRR
+CAENRAVGTPCTNGAVRQGDDE----ATLEVIEVHRVGNSKEHLPLPSESGSNSYAPACL
+ERKN----ERN--------------------A--------EA-K-RKMALARERKTVKTL
+GIIMGTFILCWLPFFIVALVLPF-CES-SC-HMPALLGAIINWLGYSNSLLNPVIYAYFN
+KDFQNAFK-KII---------------KCKFCRR--------------------------
+------------------------------------------------------------
+----------------------------------------------------
+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+M-ANFTFGDLALDVARMGGLASTPSGLRS-----------------TGLTTPGLSPTG--
+------------------------------LVTS--DFNDSYGLTGQF-IN-GSHS----
+-----------------SRSRDNAS-ANDT-------------SATNMTDDRYWS-LTVY
+SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
+PLSVVSE-IS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIR
+RRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK--------
+--GYTIFSTVGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETT
+LVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKK-------------
+---NRAKKLPENANGVNSNSSS------------------SERLKQIQIETAEAFANGCA
+EEASIAMLERQ-CNNGKKISSNDTPYS-------------RT-R-EKLELKRERKAARTL
+AIITGAFLICWLPFFIIALIGPF-VDP-E--GIPPFARSFVLWLGYFNSLLNPIIYTIFS
+PEFRSAFQ-KIL----------FG---KYRRGHR--------------------------
+------------------------------------------------------------
+----------------------------------------------------
+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+M-ANFTFGDLALDVARMGGLASTPSGLRS-----------------TGLTTPGLSPTG--
+------------------------------LVTS--DFNDSYGLTGQF-IN-GSHS----
+-----------------SRSRDNAS-ANDT-------------SATNMTDDRYWS-LTVY
+SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
+PLSVVSE-IS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIR
+RRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK--------
+--GYTIFSTVGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETT
+LVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKK-------------
+---NRAKKLPENANGVNSNSSS------------------SERLKQIQIETAEAFANGCA
+EEASIAMLERQ-CNNGKKISSNDTPYS-------------RT-R-EKLELKRERKAARTL
+AIITGAFLICWLPFFIIALIGPF-VDP-E--GIPPFARSFVLWLGYFNSLLNPIIYTIFS
+PEFRSAFQ-KIL----------FG---KYRRGHR--------------------------
+------------------------------------------------------------
+----------------------------------------------------
+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+M-EGAE-GQEELDWEAL--YLRLP--LQN-----------------CSWNSTGWEPNW--
+------------------------------NVTV--VPNTTW-----------WQA----
+-----------------SAPFDTPA-ALVR-------------AAAK-------------
+--------AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-M
+PLGAVYE-VV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIH
+ASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV--------
+--GYQIFATASSFYVPVLIILILYWRIY-------QTARKRIR-----------------
+----------------------------RRRGATARGGVGPPP-----------------
+--------VPAGGALVAGGGSGGIAAAVVAVI--------GRPLPTISETTTTGFTNVSS
+NNTS---PEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKP-K-EAADSKRERKAAKTL
+AIITGAFVACWLPFFVLAILVPT-CDC-E---VSPVLTSLSLWLGYFNSTLNPVIYTVFS
+PEFRHAFQ-RLL----------CGRRVRRRRAPQ--------------------------
+------------------------------------------------------------
+----------------------------------------------------
--- /dev/null
+>AJ006331.1_1230
+ccauggcguuaguau
+gagugucgugcagccuccaggccccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaaucgcuggggugaccggguccuuucuuggaacaacccgc
+ucaauacccagaaauuugggcgugcccccgcgagaucacuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcgagu
+
+>Z84287.1_1250
+uucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggaucaacccgc
+ucgaugccuggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcucgagagu
+
+>AF064490.1_2296
+ugagu
+gucgaacagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccgggaugaccggguccuuucuuggauaaacccgc
+ucaaugcccggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcgagugccccgggaggucucguag
+accgugcaacaugagcacgaauccuaaaccucaaagaaaaaccaaaagaaacaccaaccg
+>Z84230.1_1250
+uucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggauaagcccgc
+ucaaugccuggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcucgagagu
+
+>AB049100.1_1360
+auagaucacuccccugugaggaacuacugucuucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggaucaacccgc
+ucaaugccuggagauuugggcgugcccccgcgagaccgcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcgagugccccgggaggucucguag
+accgugcaccaugagcacgaauccuaaaccucaaagaaaaaccaaacguaacaccaaccg
+
--- /dev/null
+>AJ006331.1_1230
+---------------------------------------------------ccauggcgu
+uaguaugagugucgugcagccuccaggccccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaaucgcuggggugaccggguccuuucuuggaacaacccgc
+ucaauacccagaaauuugggcgugcccccgcgagaucacuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcgagu-------------------
+------------------------------------------------------------
+>Z84287.1_1250
+-------------------------------uucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggaucaacccgc
+ucgaugccuggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcucgagagu-------------------
+------------------------------------------------------------
+>AF064490.1_2296
+------------------------------------------------------------
+-----ugagugucgaacagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccgggaugaccggguccuuucuuggauaaacccgc
+ucaaugcccggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcgagugccccgggaggucucguag
+accgugcaacaugagcacgaauccuaaaccucaaagaaaaaccaaaagaaacaccaaccg
+>Z84230.1_1250
+-------------------------------uucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggauaagcccgc
+ucaaugccuggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcucgagagu-------------------
+------------------------------------------------------------
+>AB049100.1_1360
+auagaucacuccccugugaggaacuacugucuucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggaucaacccgc
+ucaaugccuggagauuugggcgugcccccgcgagaccgcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcgagugccccgggaggucucguag
+accgugcaccaugagcacgaauccuaaaccucaaagaaaaaccaaacguaacaccaaccg
--- /dev/null
+>AJ006331.1_1230
+c---------------------------------------------------cauggcgu
+uaguaugagugucgugcagccuccaggccccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaaucgcuggggugaccggguccuuucuuggaacaacccgc
+ucaauacccagaaauuugggcgugcccccgcgagaucacuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcga---------------------
+----------------------------------------------------------gu
+>Z84287.1_1250
+u-------------------------------ucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggaucaacccgc
+ucgaugccuggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcucgaga---------------------
+----------------------------------------------------------gu
+>AF064490.1_2296
+u-----------------------------------------------------------
+------gagugucgaacagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccgggaugaccggguccuuucuuggauaaacccgc
+ucaaugcccggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcgagugccccgggaggucucguag
+accgugcaacaugagcacgaauccuaaaccucaaagaaaaaccaaaagaaacaccaaccg
+>Z84230.1_1250
+u-------------------------------ucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggauaagcccgc
+ucaaugccuggagauuugggcgugcccccgcgagacugcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcucgaga---------------------
+----------------------------------------------------------gu
+>AB049100.1_1360
+auagaucacuccccugugaggaacuacugucuucacgcagaaagcgucuagccauggcgu
+uaguaugagugucgugcagccuccaggacccccccucccgggagagccauaguggucugc
+ggaaccggugaguacaccggaauugccaggacgaccggguccuuucuuggaucaacccgc
+ucaaugccuggagauuugggcgugcccccgcgagaccgcuagccgaguaguguugggucg
+cgaaaggccuugugguacugccugauagggugcuugcgagugccccgggaggucucguag
+accgugcaccaugagcacgaauccuaaaccucaaagaaaaaccaaacguaacaccaaccg
git://source.jalview.org / jabaws.git / commitdiff