final commit for ape 3.0-8

[ape.git] / src / dist_dna.c

diff --git a/src/dist_dna.c b/src/dist_dna.c
index ab630a9c0b6fcad71b87e0a410c5e6d597b328c5..c087212dc1b7477435a1fcf6b69630c6811a3466 100644 (file)
--- a/src/dist_dna.c
+++ b/src/dist_dna.c
@@ -1,4 +1,4 @@
-/* dist_dna.c       2012-02-14 */
+/* dist_dna.c       2012-11-28 */
 
 /* Copyright 2005-2012 Emmanuel Paradis
 
@@ -1040,52 +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)
 {
@@ -1189,3 +1143,24 @@ void dist_dna(unsigned char *x, int *n, int *s, int *model, double *d,
     case 17 : distDNA_indelblock(x, n, s, d); break;
     }
 }
+
+void where(unsigned char *x, unsigned char *pat, int *s, int *p,
+          int *ans, int *n)
+{
+       int i, j, k, ln;
+
+       ln = 0; /* local n */
+
+       for (i = 0; i <= *s - *p; i++) {
+               k = i; j = 0;
+               while (1) {
+                       if (x[k] != pat[j]) break;
+                       j++; k++;
+                       if (j == *p) {
+                               ans[ln++] = k - 1;
+                               break;
+                       }
+               }
+       }
+       *n = ln;
+}