--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <stdarg.h>
+#include <string.h>
+#include <ctype.h>
+#include "io_lib_header.h"
+#include "util_lib_header.h"
+#include "define_header.h"
+#include "dp_lib_header.h"
+static float dm[]={
+0.178091,
+1.18065, 0.270671, 0.039848, 0.017576, 0.016415, 0.014268, 0.131916, 0.012391, 0.022599, 0.020358, 0.030727, 0.015315, 0.048298, 0.053803, 0.020662, 0.023612, 0.216147, 0.147226, 0.065438, 0.003758, 0.009621,
+0.056591,
+1.35583, 0.021465, 0.0103, 0.011741, 0.010883, 0.385651, 0.016416, 0.076196, 0.035329, 0.013921, 0.093517, 0.022034, 0.028593, 0.013086, 0.023011, 0.018866, 0.029156, 0.018153, 0.0361, 0.07177, 0.419641,
+0.0960191,
+6.66436 ,0.561459, 0.045448, 0.438366, 0.764167, 0.087364, 0.259114, 0.21494, 0.145928, 0.762204, 0.24732, 0.118662, 0.441564, 0.174822, 0.53084, 0.465529, 0.583402, 0.445586, 0.22705, 0.02951, 0.12109,
+0.078123,
+2.08141, 0.070143, 0.01114, 0.019479, 0.094657, 0.013162, 0.048038, 0.077, 0.032939, 0.576639, 0.072293, 0.02824, 0.080372, 0.037661, 0.185037, 0.506783, 0.073732, 0.071587, 0.042532, 0.011254, 0.028723,
+0.0834977,
+2.08101, 0.041103, 0.014794, 0.00561, 0.010216, 0.153602, 0.007797, 0.007175, 0.299635, 0.010849, 0.999446, 0.210189, 0.006127, 0.013021, 0.019798, 0.014509, 0.012049, 0.035799, 0.180085, 0.012744, 0.026466,
+0.0904123,
+2.56819, 0.115607, 0.037381, 0.012414, 0.018179, 0.051778, 0.017255, 0.004911, 0.796882, 0.017074, 0.285858, 0.075811, 0.014548, 0.015092, 0.011382, 0.012696, 0.027535, 0.088333, 0.94434, 0.004373, 0.016741,
+0.114468,
+1.76606, 0.093461, 0.004737, 0.387252, 0.347841, 0.010822, 0.105877, 0.049776, 0.014963, 0.094276, 0.027761, 0.01004, 0.187869, 0.050018, 0.110039, 0.038668, 0.119471, 0.065802, 0.02543, 0.003215, 0.018742,
+0.0682132,
+4.98768, 0.452171, 0.114613, 0.06246, 0.115702, 0.284246, 0.140204, 0.100358, 0.55023, 0.143995, 0.700649, 0.27658, 0.118569, 0.09747, 0.126673, 0.143634, 0.278983, 0.358482, 0.66175, 0.061533, 0.199373,
+0.234585,
+0.0995, 0.005193, 0.004039, 0.006722, 0.006121, 0.003468, 0.016931, 0.003647, 0.002184, 0.005019, 0.00599, 0.001473, 0.004158, 0.009055, 0.00363, 0.006583, 0.003172, 0.00369, 0.002967, 0.002772,0.002686};
+
+double int_logB (int *i, int n)
+ {
+ static double *array;
+ int a;
+
+ if ( array==NULL)array=vcalloc ( 1000, sizeof (double));
+
+ for ( a=0; a< n; a++)
+ array[a]=(double)i[a];
+ return double_logB(array, n);
+ }
+double float_logB (float *i, int n)
+ {
+ static double *array;
+ int a;
+
+ if ( array==NULL)array=vcalloc ( 1000, sizeof (double));
+ for ( a=0; a< n; a++)
+ array[a]=(double)i[a];
+ return double_logB(array, n);
+ }
+
+double double_logB (double *x, int n)
+ {
+ double vx=0;
+ double result=0;
+ int i;
+
+
+ for ( i=0; i<n; i++)vx+=x[i];
+ for ( i=0; i<n; i++)result+=lgamma2(x[i]);
+ return result-lgamma2(vx);
+ }
+double *** make_lup_table ( Mixture *D)
+ {
+ int a, b, c;
+ double ***lup;
+
+ lup=vcalloc ( 9, sizeof (double**));
+ for ( a=0; a<9; a++)
+ {
+ lup[a]=vcalloc ( 20, sizeof (double*));
+ for ( b=0; b< 20; b++)
+ lup[a][b]=vcalloc ( 200, sizeof (double));
+ }
+
+ for ( a=0; a< 9; a++)
+ for ( b=0; b< 20; b++)
+ for ( c=0; c< 100; c++)
+ lup[a][b][c]=lgamma2(D->ALPHA[a][b]+c);
+
+ return lup;
+ }
+
+double double_logB2(int j, double *n,Mixture *D)
+ {
+ double vx=0;
+ double result=0;
+ int i;
+
+ static double ***lup;
+
+
+
+ if ( lup==NULL)lup=make_lup_table (D);
+
+
+
+ for ( i=0; i<D->n_aa; i++)vx+=(double)n[i]+D->ALPHA[j][i];
+ for ( i=0; i<D->n_aa; i++)
+ {
+
+
+ result+=lup[j][i][(int)n[i]];
+ }
+ return result-lgamma2(vx);
+ }
+
+double compute_exponant ( double *n, int j, Mixture *D)
+ {
+
+ if ( j>=9)fprintf ( stderr, "\nPB: j=%d", j);
+
+ return double_logB2(j, n,D)-D->double_logB_alpha[j];
+ }
+
+
+double *compute_matrix_p ( double *n,int Nseq)
+ {
+
+ /*
+ reads in a frquency list of various amino acids:
+
+ sum freq(aa)=1 (gaps are ignored)
+
+ aa[1]=x1
+ aa[2]=x2
+ ....
+
+ Outputs a similar list with frequencies 'Blurred' using a pam250 mt
+ */
+
+
+
+ static int **matrix;
+ double *R;
+ int a, b;
+ double v,min, tot;
+
+
+ if ( !matrix)
+ {
+ matrix=read_matrice ( "pam250mt");
+ }
+
+ R=vcalloc ( 26, sizeof (double));
+
+
+ for ( a=0; a<26; a++)
+ {
+ if (!is_aa(a+'a'))continue;
+ if ( n[a]==0)continue;
+
+ for ( b=0; b< 26; b++)
+ {
+ if (!is_aa(b+'a'))continue;
+ v=n[a]*(matrix[a][b]);
+ if ( v>0)
+ {
+ R[b]+=v+(10*n[a]);
+ }
+ }
+ }
+
+ min=R[0];
+ for ( min=R[0],a=0; a< 26; a++)min=MIN(min,R[a]);
+ for ( tot=0, a=0; a< 26; a++) {R[a]-=min;tot+=R[a];}
+ for ( a=0; a< 26; a++)if ( is_aa(a+'a')){R[a]=R[a]*((float)(100)/(float)tot);}
+ return R;
+ }
+
+
+double *compute_dirichlet_p ( double *n,int Nseq)
+ {
+ /*
+ Given a list of frequenceies measured for the residues, this function returns
+ the p_values associated with each residue in the column
+ */
+
+ int a, b;
+ double X_LIST[100];
+ double sum, log_sum, max;
+ static Mixture *D;
+ static double *R;
+
+
+
+ if (!D)
+ {
+ D=read_dirichlet (NULL);
+
+ D->n_aa=20;
+ R=vcalloc ( D->n_aa, sizeof (double));
+ D->double_logB_alpha=vcalloc (D->N_COMPONENT , sizeof (double));
+
+ D->exponant_list=vcalloc (D->N_COMPONENT , sizeof (double));
+ precompute_log_B ( D->double_logB_alpha,D);
+ D->alpha_tot=vcalloc (D->N_COMPONENT , sizeof (double));
+ for ( a=0; a<D->N_COMPONENT; a++)
+ for ( b=0; b< D->n_aa; b++)
+ D->alpha_tot[a]+=D->ALPHA[a][b];
+ }
+
+
+
+ for ( D->tot_n=0,a=0; a< D->n_aa; a++)D->tot_n+=(double)n[a];
+ max=D->exponant_list[0]=compute_exponant ( n, 0, D);
+ for ( a=1; a<D->N_COMPONENT; a++)
+ {
+ D->exponant_list[a]=compute_exponant ( n, a,D);
+ max= ( max< D->exponant_list[a])?D->exponant_list[a]:max;
+ }
+ for ( a=1; a<D->N_COMPONENT; a++)D->exponant_list[a]=D->exponant_list[a]-max;
+
+
+ for ( sum=0,log_sum=0,a=0; a< D->n_aa; a++)
+ {
+ sum+=X_LIST[a]=compute_X (n, a,D);
+ }
+ log_sum=log(sum);
+
+
+ for (a=0; a<D->n_aa; a++)
+ {
+ R[a]=(log(X_LIST[a])-log_sum);
+ }
+
+
+ /*
+ printf ( "\n[");
+ for ( a=0;a< n_aa; a++)printf ("%d ", n[a]);
+ printf ("] score=%f",(float) result );
+
+ fprintf ( stderr, "\nRESULT=%f", (float)result);
+ exit(0);
+ */
+ return R;
+
+ }
+
+void precompute_log_B ( double *table,Mixture *D)
+ {
+ int a;
+ for ( a=0; a< D->N_COMPONENT; a++)
+ {
+ table[a]=double_logB ( D->ALPHA[a], D->n_aa);
+ }
+ }
+double compute_X (double *n,int i,Mixture *D)
+ {
+ int j;
+ double term1, term2,result;
+ double **alpha;
+ double *q;
+
+
+
+ alpha=D->ALPHA;
+ q=D->DM_Q;
+
+ for (result=0, j=0; j<D->N_COMPONENT; j++)
+ {
+ term1=exp (D->exponant_list[j])*q[j];
+ term2=(alpha[j][i]+(double)n[i])/(D->alpha_tot[j]+D->tot_n);
+ result+=term1*term2;
+ }
+ return result;
+ }
+Mixture * read_dirichlet ( char *name)
+ {
+ FILE *fp;
+ int a,b, c;
+ float f;
+ Mixture *D;
+
+
+ D=vcalloc ( 1, sizeof (Mixture));
+
+
+ D->N_COMPONENT=9;
+ D->ALPHA=vcalloc (9, sizeof (double*));
+ for ( a=0; a< 9; a++)
+ D->ALPHA[a]=vcalloc (20, sizeof (double));
+ D->DM_Q=vcalloc (9, sizeof (double));
+
+ if (name!=NULL)
+ {
+ fp=vfopen ( name, "r");
+ for ( a=0; a< 9; a++)
+ {
+ fscanf(fp, "%f\n", &f);
+ D->DM_Q[a]=(double)f;
+ fscanf(fp, "%f", &f);
+
+ for ( b=0; b<20; b++)
+ {
+ fscanf(fp, "%f", &f);
+ D->ALPHA[a][b]=(double)f;
+ }
+ fscanf(fp, "\n");
+ }
+ for ( a=0; a< 9; a++)
+ {
+ fprintf(stderr, "\n%f\n",(float)D->DM_Q[a] );
+
+ for ( b=0; b<20; b++)
+ {
+ fprintf(stderr, "%f ", (float)D->ALPHA[a][b]);
+ }
+ fprintf(stderr, "\n");
+ }
+ fprintf ( stderr, "\nN_C=%d",D->N_COMPONENT );
+ vfclose ( fp);
+ }
+ else
+ {
+ for (c=0, a=0; a< 9;a++)
+ {
+ D->DM_Q[a]=dm[c++];
+ for (b=0; b<20; b++)
+ D->ALPHA[a][b]=dm[c++];
+ }
+ }
+
+ return D;
+ }
+int dirichlet_code( char aa)
+ {
+
+ char x;
+
+ x=tolower (aa);
+
+ if ( (x<'a') || (x>'z'))
+ crash ( "CODE UNDEFINED");
+ else if ( x<='a')
+ return x-'a';
+ else if ( x<='i')
+ return x-('a'+1);
+ else if ( x<= 'n')
+ return x-('a'+2);
+ else if ( x<='t')
+ return x-('a'+3);
+ else if ( x<='w')
+ return x-('a'+4);
+ else if ( x=='y')
+ return x-('a'+5);
+ else
+ {
+ crash ("ERROR in dirichlet_code");
+ return 0;
+ }
+ return 0;
+
+ }
+
+
+static const double
+two52= 4.50359962737049600000e+15, /* 0x43300000, 0x00000000 */
+half= 5.00000000000000000000e-01, /* 0x3FE00000, 0x00000000 */
+one = 1.00000000000000000000e+00, /* 0x3FF00000, 0x00000000 */
+pi = 3.14159265358979311600e+00, /* 0x400921FB, 0x54442D18 */
+a0 = 7.72156649015328655494e-02, /* 0x3FB3C467, 0xE37DB0C8 */
+a1 = 3.22467033424113591611e-01, /* 0x3FD4A34C, 0xC4A60FAD */
+a2 = 6.73523010531292681824e-02, /* 0x3FB13E00, 0x1A5562A7 */
+a3 = 2.05808084325167332806e-02, /* 0x3F951322, 0xAC92547B */
+a4 = 7.38555086081402883957e-03, /* 0x3F7E404F, 0xB68FEFE8 */
+a5 = 2.89051383673415629091e-03, /* 0x3F67ADD8, 0xCCB7926B */
+a6 = 1.19270763183362067845e-03, /* 0x3F538A94, 0x116F3F5D */
+a7 = 5.10069792153511336608e-04, /* 0x3F40B6C6, 0x89B99C00 */
+a8 = 2.20862790713908385557e-04, /* 0x3F2CF2EC, 0xED10E54D */
+a9 = 1.08011567247583939954e-04, /* 0x3F1C5088, 0x987DFB07 */
+a10 = 2.52144565451257326939e-05, /* 0x3EFA7074, 0x428CFA52 */
+a11 = 4.48640949618915160150e-05, /* 0x3F07858E, 0x90A45837 */
+tc = 1.46163214496836224576e+00, /* 0x3FF762D8, 0x6356BE3F */
+tf = -1.21486290535849611461e-01, /* 0xBFBF19B9, 0xBCC38A42 */
+/* tt = -(tail of tf) */
+tt = -3.63867699703950536541e-18, /* 0xBC50C7CA, 0xA48A971F */
+t0 = 4.83836122723810047042e-01, /* 0x3FDEF72B, 0xC8EE38A2 */
+t1 = -1.47587722994593911752e-01, /* 0xBFC2E427, 0x8DC6C509 */
+t2 = 6.46249402391333854778e-02, /* 0x3FB08B42, 0x94D5419B */
+t3 = -3.27885410759859649565e-02, /* 0xBFA0C9A8, 0xDF35B713 */
+t4 = 1.79706750811820387126e-02, /* 0x3F9266E7, 0x970AF9EC */
+t5 = -1.03142241298341437450e-02, /* 0xBF851F9F, 0xBA91EC6A */
+t6 = 6.10053870246291332635e-03, /* 0x3F78FCE0, 0xE370E344 */
+t7 = -3.68452016781138256760e-03, /* 0xBF6E2EFF, 0xB3E914D7 */
+t8 = 2.25964780900612472250e-03, /* 0x3F6282D3, 0x2E15C915 */
+t9 = -1.40346469989232843813e-03, /* 0xBF56FE8E, 0xBF2D1AF1 */
+t10 = 8.81081882437654011382e-04, /* 0x3F4CDF0C, 0xEF61A8E9 */
+t11 = -5.38595305356740546715e-04, /* 0xBF41A610, 0x9C73E0EC */
+t12 = 3.15632070903625950361e-04, /* 0x3F34AF6D, 0x6C0EBBF7 */
+t13 = -3.12754168375120860518e-04, /* 0xBF347F24, 0xECC38C38 */
+t14 = 3.35529192635519073543e-04, /* 0x3F35FD3E, 0xE8C2D3F4 */
+u0 = -7.72156649015328655494e-02, /* 0xBFB3C467, 0xE37DB0C8 */
+u1 = 6.32827064025093366517e-01, /* 0x3FE4401E, 0x8B005DFF */
+u2 = 1.45492250137234768737e+00, /* 0x3FF7475C, 0xD119BD6F */
+u3 = 9.77717527963372745603e-01, /* 0x3FEF4976, 0x44EA8450 */
+u4 = 2.28963728064692451092e-01, /* 0x3FCD4EAE, 0xF6010924 */
+u5 = 1.33810918536787660377e-02, /* 0x3F8B678B, 0xBF2BAB09 */
+v1 = 2.45597793713041134822e+00, /* 0x4003A5D7, 0xC2BD619C */
+v2 = 2.12848976379893395361e+00, /* 0x40010725, 0xA42B18F5 */
+v3 = 7.69285150456672783825e-01, /* 0x3FE89DFB, 0xE45050AF */
+v4 = 1.04222645593369134254e-01, /* 0x3FBAAE55, 0xD6537C88 */
+v5 = 3.21709242282423911810e-03, /* 0x3F6A5ABB, 0x57D0CF61 */
+s0 = -7.72156649015328655494e-02, /* 0xBFB3C467, 0xE37DB0C8 */
+s1 = 2.14982415960608852501e-01, /* 0x3FCB848B, 0x36E20878 */
+s2 = 3.25778796408930981787e-01, /* 0x3FD4D98F, 0x4F139F59 */
+s3 = 1.46350472652464452805e-01, /* 0x3FC2BB9C, 0xBEE5F2F7 */
+s4 = 2.66422703033638609560e-02, /* 0x3F9B481C, 0x7E939961 */
+s5 = 1.84028451407337715652e-03, /* 0x3F5E26B6, 0x7368F239 */
+s6 = 3.19475326584100867617e-05, /* 0x3F00BFEC, 0xDD17E945 */
+r1 = 1.39200533467621045958e+00, /* 0x3FF645A7, 0x62C4AB74 */
+r2 = 7.21935547567138069525e-01, /* 0x3FE71A18, 0x93D3DCDC */
+r3 = 1.71933865632803078993e-01, /* 0x3FC601ED, 0xCCFBDF27 */
+r4 = 1.86459191715652901344e-02, /* 0x3F9317EA, 0x742ED475 */
+r5 = 7.77942496381893596434e-04, /* 0x3F497DDA, 0xCA41A95B */
+r6 = 7.32668430744625636189e-06, /* 0x3EDEBAF7, 0xA5B38140 */
+w0 = 4.18938533204672725052e-01, /* 0x3FDACFE3, 0x90C97D69 */
+w1 = 8.33333333333329678849e-02, /* 0x3FB55555, 0x5555553B */
+w2 = -2.77777777728775536470e-03, /* 0xBF66C16C, 0x16B02E5C */
+w3 = 7.93650558643019558500e-04, /* 0x3F4A019F, 0x98CF38B6 */
+w4 = -5.95187557450339963135e-04, /* 0xBF4380CB, 0x8C0FE741 */
+w5 = 8.36339918996282139126e-04, /* 0x3F4B67BA, 0x4CDAD5D1 */
+w6 = -1.63092934096575273989e-03; /* 0xBF5AB89D, 0x0B9E43E4 */
+
+static const double zero= 0.00000000000000000000e+00;
+
+static double sin_pi(double x)
+{
+ double y,z;
+ int n,ix;
+
+ ix=(*(long long *)&x)>>32;
+ ix &= 0x7fffffff;
+
+ if(ix<0x3fd00000) return sin(pi*x);
+ y = -x; /* x is assume negative */
+
+ /*
+ * argument reduction, make sure inexact flag not raised if input
+ * is an integer
+ */
+ z = floor(y);
+ if(z!=y) { /* inexact anyway */
+ y *= 0.5;
+ y = 2.0*(y - floor(y)); /* y = |x| mod 2.0 */
+ n = (int) (y*4.0);
+ } else {
+ if(ix>=0x43400000) {
+ y = zero; n = 0; /* y must be even */
+ } else {
+ if(ix<0x43300000) z = y+two52; /* exact */
+ n=(*(long long *)&x);
+ n &= 1;
+ y = n;
+ n<<= 2;
+ }
+ }
+ switch (n) {
+ case 0: y = sin(pi*y); break;
+ case 1:
+ case 2: y = cos(pi*(0.5-y)); break;
+ case 3:
+ case 4: y = sin(pi*(one-y)); break;
+ case 5:
+ case 6: y = -cos(pi*(y-1.5)); break;
+ default: y = sin(pi*(y-2.0)); break;
+ }
+ return -y;
+}
+
+double lgamma2 ( double x)
+{
+ int s;
+ return lgamma_r ( x, &s);
+}
+double lgamma_r(double x, int *signgamp)
+{
+ double t,y,z,nadj=0,p,p1,p2,p3,q,r,w;
+ int i,hx,lx,ix;
+
+ hx=(*(long long *)&x)>>32;
+ lx=(*(long long *)&x);
+
+ /* purge off +-inf, NaN, +-0, and negative arguments */
+ *signgamp = 1;
+ ix = hx&0x7fffffff;
+ if(ix>=0x7ff00000) return x*x;
+ if((ix|lx)==0) return one/fabs(x);
+ if(ix<0x3b900000) { /* |x|<2**-70, return -log(|x|) */
+ if(hx<0) {
+ *signgamp = -1;
+ return -log(-x);
+ } else return -log(x);
+ }
+ if(hx<0) {
+ if(ix>=0x43300000) /* |x|>=2**52, must be -integer */
+ return x/zero;
+ t = sin_pi(x);
+ if(t==zero) return one/fabs(t); /* -integer */
+ nadj = log(pi/fabs(t*x));
+ if(t<zero) *signgamp = -1;
+ x = -x;
+ }
+
+ /* purge off 1 and 2 */
+ if((((ix-0x3ff00000)|lx)==0)||(((ix-0x40000000)|lx)==0)) r = 0;
+ /* for x < 2.0 */
+ else if(ix<0x40000000) {
+ if(ix<=0x3feccccc) { /* lgamma(x) = lgamma(x+1)-log(x) */
+ r = -log(x);
+ if(ix>=0x3FE76944) {y = one-x; i= 0;}
+ else if(ix>=0x3FCDA661) {y= x-(tc-one); i=1;}
+ else {y = x; i=2;}
+ } else {
+ r = zero;
+ if(ix>=0x3FFBB4C3) {y=2.0-x;i=0;} /* [1.7316,2] */
+ else if(ix>=0x3FF3B4C4) {y=x-tc;i=1;} /* [1.23,1.73] */
+ else {y=x-one;i=2;}
+ }
+ switch(i) {
+ case 0:
+ z = y*y;
+ p1 = a0+z*(a2+z*(a4+z*(a6+z*(a8+z*a10))));
+ p2 = z*(a1+z*(a3+z*(a5+z*(a7+z*(a9+z*a11)))));
+ p = y*p1+p2;
+ r += (p-0.5*y); break;
+ case 1:
+ z = y*y;
+ w = z*y;
+ p1 = t0+w*(t3+w*(t6+w*(t9 +w*t12))); /* parallel comp */
+ p2 = t1+w*(t4+w*(t7+w*(t10+w*t13)));
+ p3 = t2+w*(t5+w*(t8+w*(t11+w*t14)));
+ p = z*p1-(tt-w*(p2+y*p3));
+ r += (tf + p); break;
+ case 2:
+ p1 = y*(u0+y*(u1+y*(u2+y*(u3+y*(u4+y*u5)))));
+ p2 = one+y*(v1+y*(v2+y*(v3+y*(v4+y*v5))));
+ r += (-0.5*y + p1/p2);
+ }
+ }
+ else if(ix<0x40200000) { /* x < 8.0 */
+ i = (int)x;
+ t = zero;
+ y = x-(double)i;
+ p = y*(s0+y*(s1+y*(s2+y*(s3+y*(s4+y*(s5+y*s6))))));
+ q = one+y*(r1+y*(r2+y*(r3+y*(r4+y*(r5+y*r6)))));
+ r = half*y+p/q;
+ z = one; /* lgamma(1+s) = log(s) + lgamma(s) */
+ switch(i) {
+ case 7: z *= (y+6.0); /* FALLTHRU */
+ case 6: z *= (y+5.0); /* FALLTHRU */
+ case 5: z *= (y+4.0); /* FALLTHRU */
+ case 4: z *= (y+3.0); /* FALLTHRU */
+ case 3: z *= (y+2.0); /* FALLTHRU */
+ r += log(z); break;
+ }
+ /* 8.0 <= x < 2**58 */
+ } else if (ix < 0x43900000) {
+ t = log(x);
+ z = one/x;
+ y = z*z;
+ w = w0+z*(w1+y*(w2+y*(w3+y*(w4+y*(w5+y*w6)))));
+ r = (x-half)*(t-one)+w;
+ } else
+ /* 2**58 <= x <= inf */
+ r = x*(log(x)-one);
+ if(hx<0) r = nadj - r;
+ return r;
+}
+/******************************COPYRIGHT NOTICE*******************************/
+/*© Centro de Regulacio Genomica */
+/*and */
+/*Cedric Notredame */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*All rights reserved.*/
+/*This file is part of T-COFFEE.*/
+/**/
+/* T-COFFEE is free software; you can redistribute it and/or modify*/
+/* it under the terms of the GNU General Public License as published by*/
+/* the Free Software Foundation; either version 2 of the License, or*/
+/* (at your option) any later version.*/
+/**/
+/* T-COFFEE 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 General Public License for more details.*/
+/**/
+/* You should have received a copy of the GNU General Public License*/
+/* along with Foobar; if not, write to the Free Software*/
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
+/*............................................... |*/
+/* If you need some more information*/
+/* cedric.notredame@europe.com*/
+/*............................................... |*/
+/**/
+/**/
+/* */
+/******************************COPYRIGHT NOTICE*******************************/
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