bug fixing in read.nexus() + Others....

[ape.git] / src / dist_dna.c

diff --git a/src/dist_dna.c b/src/dist_dna.c
index b8797e955b0647d88ed547e68c22119c9a0112fd..62f8f64c9b5b375a702063f7d11825527a5d6d8b 100644 (file)
--- 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)