X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fdist_dna.c;h=2cabb7de56bd3a5a05719623f40a93ff4d44ca9c;hb=2419de65ffb4f7c45eb8c2448bcba3d0df64744f;hp=9057b9be5bfe8190c41d08063496728e910fccb6;hpb=a03a8c554a6fde0dc4313688e3248bfae2e521e4;p=ape.git

diff --git a/src/dist_dna.c b/src/dist_dna.c
index 9057b9b..2cabb7d 100644
--- a/src/dist_dna.c
+++ b/src/dist_dna.c
@@ -1,4 +1,4 @@
-/* dist_dna.c       2010-03-16 */
+/* dist_dna.c       2010-03-29 */
 
 /* Copyright 2005-2010 Emmanuel Paradis
 
@@ -800,67 +800,6 @@ void distDNA_BH87(unsigned char *x, int *n, int *s, double *d,
         for (i2 = i1 + 1; i2 <= *n; i2++) {
 	    for (k = 0; k < 16; k++) Ntab[k] = 0;
 	    for (s1 = i1 - 1, s2 = i2 - 1; s1 < i1 + *n*(*s - 1); s1+= *n, s2 += *n) {
-#define PREPARE_BF_F84\
-    A = (BF[0]*BF[2])/(BF[0] + BF[2]) + (BF[1]*BF[3])/(BF[1] + BF[3]);\
-    B = BF[0]*BF[2] + BF[1]*BF[3];\
-    C = (BF[0] + BF[2])*(BF[1] + BF[3]);
-
-#define COMPUTE_DIST_F84\
-   P = ((double) Ns/L);\
-   Q = ((double) (Nd - Ns)/L);\
-   d[target] = -2*A*log(1 - P/(2*A) - (A - B)*Q/(2*A*C)) + 2*(A - B - C)*log(1 - Q/(2*C));\
-   if (*variance) {\
-       t1 = A*C;\
-       t2 = C*P/2;\
-       t3 = (A - B)*Q/2;\
-       a = t1/(t1 - t2 - t3);\
-       b = A*(A - B)/(t1 - t2 - t3) - (A - B - C)/(C - Q/2);\
-       var[target] = (a*a*P + b*b*Q - pow(a*P + b*Q, 2))/2;\
-   }
-
-void distDNA_F84(unsigned char *x, int *n, int *s, double *d,
-		 double *BF, int *variance, double *var)
-{
-    int i1, i2, Nd, Ns, L, target, s1, s2;
-    double P, Q, A, B, C, a, b, t1, t2, t3;
-
-    PREPARE_BF_F84
-    L = *s;
-
-    target = 0;
-    for (i1 = 1; i1 < *n; i1++) {
-        for (i2 = i1 + 1; i2 <= *n; i2++) {
-	    Nd = Ns = 0;
-	    for (s1 = i1 - 1, s2 = i2 - 1; s1 < i1 + *n*(*s - 1); s1+= *n, s2 += *n) {
-	        COUNT_TS_TV
-	    }
-	    COMPUTE_DIST_F84
-	    target++;
-	}
-    }
-}
-
-void distDNA_F84_pairdel(unsigned char *x, int *n, int *s, double *d,
-			 double *BF, int *variance, double *var)
-{
-    int i1, i2, Nd, Ns, L, target, s1, s2;
-    double P, Q, A, B, C, a, b, t1, t2, t3;
-
-    PREPARE_BF_F84
-
-    target = 0;
-    for (i1 = 1; i1 < *n; i1++) {
-        for (i2 = i1 + 1; i2 <= *n; i2++) {
-	    Nd = Ns = L = 0;
-	    for (s1 = i1 - 1, s2 = i2 - 1; s1 < i1 + *n*(*s - 1); s1+= *n, s2 += *n) {
-		CHECK_PAIRWISE_DELETION
-		COUNT_TS_TV
-	    }
-	    COMPUTE_DIST_F84
-	    target++;
-	}
-    }
-}
 		DO_CONTINGENCY_NUCLEOTIDES
 	    }