countlets v1.3, slight optimisation in klets.cpp

Author: bjmt

ChangeLog

@@ -1,3 +1,9 @@
+2019-05-04  Benjamin Jean-Marie Tremblay  <benjmtremblay@gmail.com
+
+* faster char to int conversion in klets.cpp
+* countlets is much faster when providing alphabet (using unordered_map)
+* countlets version bumped to 1.3
+
 2019-05-04  Benjamin Jean-Marie Tremblay  <benjmtremblay@gmail.com>
 
 * Don't bother and try to fill edges of unconnected vertices (shuffle_euler)

README

@@ -45,10 +45,9 @@ This utility counts the total number of k-lets in the input sequence. Be aware
 that the total number of k-lets is n^k, where n is the alphabet length. For use
 cases involving memory constraints, providing the sequence alphabet ahead of
 time will allow countlets to count k-lets while only needing to load k + 1
-letters into memory at a time (at the cost of speed for higher k values). When
-the alphabet is provided, it will typically never take up more than several MBs
-of memory. Optionally, k-lets with counts of zero can be ommitted from the
-output.
+letters into memory at a time. When the alphabet is provided, it will typically
+never take up more than several MBs of memory. Optionally, k-lets with counts of
+zero can be ommitted from the output.
 
 Example usage:
 

src/countlets.cpp

@@ -25,13 +25,13 @@
 #include <string>
 #include <set>
 #include <unistd.h>
-#include <map>
+#include <unordered_map>
 #include "klets.hpp"
 using namespace std;
 
 void usage() {
   printf(
-    "countlets v1.2  Copyright (C) 2019  Benjamin Jean-Marie Tremblay                \n"
+    "countlets v1.3  Copyright (C) 2019  Benjamin Jean-Marie Tremblay                \n"
     "                                                                                \n"
     "Usage:  countlets [options] -i [filename] -o [filename]                         \n"
     "        echo [string] | countlets [options] > [filename]                        \n"
@@ -42,23 +42,23 @@ void usage() {
     "            format.                                                             \n"
     " -a <str>   A string containing all of the alphabet letters present in the      \n"
     "            sequence. This allows the program not to have to load the entire    \n"
-    "            sequence into memory to find all of the unique letters. The downside\n"
-    "            is that runtime increases more with increasing k.                   \n"
+    "            sequence into memory to find all of the unique letters.             \n"
     " -k <int>   K-let size. Defaults to 1.                                          \n"
     " -n         Don't print k-lets with counts of zero.                             \n"
     " -h         Show usage.                                                         \n"
   );
 }
 
-map<string, unsigned int> count_stream(istream &input, vector<string> klets,
+unordered_map<string, unsigned int> count_stream(istream &input, vector<string> klets,
     unsigned int k) {
 
   char l;
 
   string let;
   let.reserve(k + 1);
 
-  map<string, unsigned int> counts;
+  unordered_map<string, unsigned int> counts;
+  counts.reserve(klets.size());
   for (size_t i = 0; i < klets.size(); ++i) {
     counts[klets[i]] = 0;
   }
@@ -199,7 +199,7 @@ int main(int argc, char **argv) {
 
     /* this version only keeps k+1 characters in memory */
 
-    map<string, unsigned int> counts;
+    unordered_map<string, unsigned int> counts;
 
     if (alph.length() < 1) {
       cerr << "Error: could not parse -a option" << endl;
@@ -228,17 +228,15 @@ int main(int argc, char **argv) {
       cerr << "Warning: foreign character(s) encountered" << endl;
     }
 
-    map<string, unsigned int>::iterator it;
-
     if (has_out) {
-      for (it = counts.begin(); it != counts.end(); ++it) {
-        if (it->second > 0 || !nozero)
-          outfile << it->first << "\t" << it->second << endl;
+      for (size_t i = 0; i < klets.size(); ++i) {
+        if (counts[klets[i]] > 0 || !nozero)
+          outfile << klets[i] << "\t" << counts[klets[i]] << "\t" << endl;
       }
     } else {
-      for (it = counts.begin(); it != counts.end(); ++it) {
-        if (it->second > 0 || !nozero)
-          cout << it->first << "\t" << it->second << endl;
+      for (size_t i = 0; i < klets.size(); ++i) {
+        if (counts[klets[i]] > 0 || !nozero)
+          cout << klets[i] << "\t" << counts[klets[i]] << "\t" << endl;
       }
     }
 

src/klets.cpp

@@ -24,8 +24,14 @@
 #include <iomanip>
 #include <cmath>
 #include <algorithm>
+#include <unordered_map>
 using namespace std;
 
+#ifdef ADD_TIMERS
+#include <chrono>
+using Clock = chrono::high_resolution_clock;
+#endif
+
 vector<string> make_klets(vector<char> lets_uniq, unsigned int k) {
 
   size_t alphlen = lets_uniq.size();
@@ -68,25 +74,35 @@ vector<unsigned int> count_klets(vector<char> letters, vector<char> lets_uniq,
    * sequence in memory.
    */
 
+  #ifdef ADD_TIMERS
+  auto t0 = Clock::now();
+  cerr << ">BEGIN count_klets()" << endl;
+  #endif
+
   size_t seqlen = letters.size();
   unsigned int nlets = pow(alphlen, k);
-  vector<unsigned int> intletters;
+  unsigned int l, counter;
   vector<unsigned int> let_counts(nlets, 0);
+  vector<unsigned int> intletters;
   intletters.reserve(seqlen);
+  unordered_map<char, unsigned int> let2int;
+  let2int.reserve(lets_uniq.size());
 
-  for (size_t i = 0; i < seqlen; ++i) {
-
-    for (size_t j = 0; j < alphlen; ++j) {
-      if (letters[i] == lets_uniq[j]) {
-        intletters.push_back(j);
-        break;
-      }
-    }
+  for (size_t i = 0; i < lets_uniq.size(); ++i) {
+    let2int[lets_uniq[i]] = (unsigned int)i;
+  }
 
+  for (size_t i = 0; i < seqlen; ++i) {
+    intletters.push_back(let2int[letters[i]]);
   }
 
-  unsigned int l;
-  unsigned int counter;
+  #ifdef ADD_TIMERS
+  auto t1 = Clock::now();
+  cerr << " lets->ints\t"
+    << chrono::duration_cast<chrono::microseconds>(t1 - t0).count()
+    << " us" << endl;
+  #endif
+
   for (size_t i = 0; i < seqlen - k + 1; ++i) {
 
     l = 0; counter = 0;
@@ -98,6 +114,17 @@ vector<unsigned int> count_klets(vector<char> letters, vector<char> lets_uniq,
 
   }
 
+  #ifdef ADD_TIMERS
+  auto t2 = Clock::now();
+  cerr << " count loop\t"
+    << chrono::duration_cast<chrono::microseconds>(t2 - t1).count()
+    << " us" << endl;
+  cerr << " ---\n fun total\t"
+    << chrono::duration_cast<chrono::microseconds>(t2 - t0).count()
+    << " us" << endl;
+  cerr << ">END count_klets()" << endl;
+  #endif
+
   return let_counts;
 
 }

src/shuffle_euler.cpp

@@ -214,7 +214,7 @@ string shuffle_euler(vector<char> letters, default_random_engine gen, unsigned i
     bool verbose) {
 
   #ifdef ADD_TIMERS
-  cerr << ">shuffler_euler()" << endl;
+  cerr << ">BEGIN shuffler_euler()" << endl;
   auto t0 = Clock::now();
   #endif
 
@@ -341,6 +341,7 @@ string shuffle_euler(vector<char> letters, default_random_engine gen, unsigned i
   cerr << " ---\n fun total\t"
     << chrono::duration_cast<chrono::microseconds>(t16 - t0).count()
     << " us" << endl;
+  cerr << ">END shuffler_euler()" << endl;
   #endif
 
   return out;