X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fdist_dna.c;h=2eb88a6eb7dfa9abb2e2cb3e7c5dca058ffade6f;hb=f3304b6f40610d9b7306a9275d593b5c038ab0a0;hp=b8797e955b0647d88ed547e68c22119c9a0112fd;hpb=f295ab19440298e543db5a270e54f10a84382197;p=ape.git

diff --git a/src/dist_dna.c b/src/dist_dna.c
index b8797e9..2eb88a6 100644
--- a/src/dist_dna.c
+++ b/src/dist_dna.c
@@ -1,6 +1,6 @@
-/* dist_dna.c       2010-09-16 */
+/* dist_dna.c       2011-02-18 */
 
-/* Copyright 2005-2010 Emmanuel Paradis
+/* Copyright 2005-2011 Emmanuel Paradis
 
 /* This file is part of the R-package `ape'. */
 /* See the file ../COPYING for licensing issues. */
@@ -970,23 +970,50 @@ void distDNA_ParaLin_pairdel(unsigned char *x, int *n, int *s, double *d,
     }
 }
 
-void BaseProportion(unsigned char *x, int *n, double *BF, int *freq)
+/* void BaseProportion(unsigned char *x, int *n, double *BF, int *freq) */
+/* { */
+/*     int i, m; */
+
+/*     m = 0; */
+/*     for (i = 0; i < *n; i++) { */
+/*         if (KnownBase(x[i])) { */
+/* 	    m++; */
+/* 	    switch (x[i]) { */
+/* 	    case 136 : BF[0]++; break; */
+/* 	    case 40 : BF[1]++; break; */
+/* 	    case 72 : BF[2]++; break; */
+/* 	    case 24 : BF[3]++; break; */
+/* 	    } */
+/* 	} */
+/*     } */
+/*     if (! *freq) for (i = 0; i < 4; i++) BF[i] /= m; */
+/* } */
+
+void BaseProportion(unsigned char *x, int *n, double *BF)
 {
-    int i, m;
+    int i;
 
-    m = 0;
     for (i = 0; i < *n; i++) {
-        if (KnownBase(x[i])) {
-	    m++;
 	    switch (x[i]) {
 	    case 136 : BF[0]++; break;
 	    case 40 : BF[1]++; break;
 	    case 72 : BF[2]++; break;
 	    case 24 : BF[3]++; break;
+	    case 192 : BF[4]++; break;
+	    case 160 : BF[5]++; break;
+	    case 144 : BF[6]++; break;
+	    case 96 : BF[7]++; break;
+	    case 80 : BF[8]++; break;
+	    case 48 : BF[9]++; break;
+	    case 224 : BF[10]++; break;
+	    case 176 : BF[11]++; break;
+	    case 208 : BF[12]++; break;
+	    case 112 : BF[13]++; break;
+	    case 240 : BF[14]++; break;
+	    case 4 : BF[15]++; break;
+	    case 2 : BF[16]++; break;
 	    }
-	}
     }
-    if (! *freq) for (i = 0; i < 4; i++) BF[i] /= m;
 }
 
 void SegSites(unsigned char *x, int *n, int *s, int *seg)