tools: nChoosek stores some computations to avoid recomputing them again and again.

We have a 500x500 array (half of it is useless…) which takes about 2MB
but avoid lots of computations when computing the e-value.

algo/core/tools.cpp

@@ -218,16 +218,25 @@ string reverse(const string &text) {
   return string(text.rbegin(), text.rend());
 }
 
+double nChoosek_stored[NB_N_CHOOSE_K_STORED][NB_N_CHOOSE_K_STORED] = {};
 double nChoosek(unsigned n, unsigned k)
 {
     if (k > n) return 0;
     if (k * 2 > n) k = n-k;
     if (k == 0) return 1;
 
-    double result = n;
-    for( unsigned i = 2; i <= k; ++i ) {
-        result *= (n-i+1);
-        result /= i;
+    if (n >= NB_N_CHOOSE_K_STORED || nChoosek_stored[n][k] == 0) {
+      double result = 1;
+      unsigned i;
+      for (i = 0; i < k && ((n-i) >= NB_N_CHOOSE_K_STORED || nChoosek_stored[n-i][k-i] == 0); i++ ) {
+        result *= (n - i)*1./(k - i);
+      }
+      if (i < k) {
+        result *= nChoosek_stored[n-i][k-i];
+      }
+      if (n < NB_N_CHOOSE_K_STORED)
+        nChoosek_stored[n][k] = result;
+      return result;
     }
-    return result;
+    return nChoosek_stored[n][k];
 }

algo/core/tools.h

@@ -22,6 +22,8 @@ using namespace std;
 #define SEED_S12 "######-######"
 #define SEED_S13 "#######-######"
 
+#define NB_N_CHOOSE_K_STORED 500
+
 string seed_contiguous(int k);
 
 int seed_weight(const string &seed);
@@ -149,6 +151,7 @@ string reverse(const string &text);
  */
 Sequence create_sequence(string label_full, string label, string sequence, string quality);
 
+extern double nChoosek_stored[NB_N_CHOOSE_K_STORED][NB_N_CHOOSE_K_STORED];
 /**
  * @return the combinatorial of k among n
  * @see http://stackoverflow.com/a/9331125/1192742