From: Bo Li <bli@cs.wisc.edu>
Date: Fri, 6 Jun 2014 10:41:46 +0000 (-0500)
Subject: Modified the use of uniform_01
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=030b9364ddefc6d4ff17da9d8ae88fc3e4a973a5

Modified the use of uniform_01
---

diff --git a/EM.cpp b/EM.cpp
index 4bda1d8..7016b89 100644
--- a/EM.cpp
+++ b/EM.cpp
@@ -506,7 +506,9 @@ void EM() {
 			READ_INT_TYPE local_N;
 			HIT_INT_TYPE fr, to, len, id;
 			vector<double> arr;
-			uniform01 rg(engine_type(hasSeed ? seed : time(NULL)));
+			engine_type engine(hasSeed ? seed : time(NULL));
+			uniform_01_dist uniform_01;
+			uniform_01_generator rg(engine, uniform_01);
 
 			if (verbose) cout<< "Begin to sample reads from their posteriors."<< endl;
 			for (int i = 0; i < nThreads; i++) {
diff --git a/Gibbs.cpp b/Gibbs.cpp
index 7215c10..d5e0b9c 100644
--- a/Gibbs.cpp
+++ b/Gibbs.cpp
@@ -229,7 +229,7 @@ void* Gibbs(void* arg) {
 	vector<int> z, counts;
 	vector<double> arr;
 
-	uniform01 rg(*params->engine);
+	uniform_01_generator rg(*params->engine, uniform_01_dist());
 
 	// generate initial state
 	sampleTheta(*params->engine, theta);
diff --git a/sampling.h b/sampling.h
index 8f80b72..7e445cf 100644
--- a/sampling.h
+++ b/sampling.h
@@ -10,10 +10,11 @@
 #include "boost/random.hpp"
 
 typedef unsigned int seedType;
-typedef boost::mt19937 engine_type;
-typedef boost::gamma_distribution<> gamma_dist;
-typedef boost::uniform_01<engine_type> uniform01;
-typedef boost::variate_generator<engine_type&, gamma_dist> gamma_generator;
+typedef boost::random::mt19937 engine_type;
+typedef boost::random::uniform_01<> uniform_01_dist;
+typedef boost::random::gamma_distribution<> gamma_dist;
+typedef boost::random::variate_generator<engine_type&, uniform_01_dist> uniform_01_generator;
+typedef boost::random::variate_generator<engine_type&, gamma_dist> gamma_generator;
 
 class engineFactory {
 public:
@@ -46,7 +47,7 @@ engine_type* engineFactory::seedEngine = NULL;
 // interval : [,)
 // random number should be in [0, arr[len - 1])
 // If by chance arr[len - 1] == 0.0, one possibility is to sample uniformly from 0...len-1
-int sample(uniform01& rg, std::vector<double>& arr, int len) {
+int sample(uniform_01_generator& rg, std::vector<double>& arr, int len) {
   int l, r, mid;
   double prb = rg() * arr[len - 1];
 
diff --git a/simul.h b/simul.h
index 07c1c65..b62132a 100644
--- a/simul.h
+++ b/simul.h
@@ -8,8 +8,8 @@
 class simul {
 public:
 
-	simul(unsigned int seed) : rg(boost::mt19937(seed)) {
-	}
+ simul(unsigned int seed) : engine(seed), rg(engine, boost::random::uniform_01<>()) {
+  }
 
 	// interval : [,)
 	// random number should be in [0, arr[len - 1])
@@ -35,7 +35,8 @@ public:
 	double random() { return rg(); };
 
 private:
-	boost::uniform_01<boost::mt19937> rg;
+	boost::random::mt19937 engine;
+	boost::random::variate_generator<boost::random::mt19937&, boost::random::uniform_01<> > rg;
 };
 
 #endif /* SIMUL_H_ */