final corrections for ape 3.0-6

[ape.git] / src / dist_dna.c

diff --git a/src/dist_dna.c b/src/dist_dna.c
index 289be088b37878de150195605ce39241be6bb539..67522ff67763705f812ac69ad536886526761e62 100644 (file)
--- a/src/dist_dna.c
+++ b/src/dist_dna.c
@@ -93,14 +93,6 @@ void distDNA_indel(unsigned char *x, int *n, int *s, double *d)
 
 #define X(i, j) i - 1 + *n * (j - 1)
 
-#define DINDEX(i, j) n * (i - 1) - i*(i - 1)/2 + j - i - 1
-
-int give_index(int i, int j, int n)
-{
-       if (i > j) return(DINDEX(j, i));
-       else return(DINDEX(i, j));
-}
-
 void distDNA_indelblock(unsigned char *x, int *n, int *s, double *d)
 {
        int i1, i2, s1, s2, target, N, start_block, end_block;
@@ -1048,52 +1040,6 @@ void distDNA_ParaLin_pairdel(unsigned char *x, int *n, int *s, double *d,
     }
 }
 
-/* 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; */
-
-/*     for (i = 0; i < *n; i++) { */
-/*         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; */
-/*         } */
-/*     } */
-/* } */
-
 /* a hash table is much faster than switch (2012-01-10) */
 void BaseProportion(unsigned char *x, int *n, double *BF)
 {