harmonize RandomSource with bowtie2

random_source.h

@@ -1,8 +1,13 @@
 #ifndef RANDOM_GEN_H_
 #define RANDOM_GEN_H_
 
+#include <stdint.h>
 #include "assert_helpers.h"
 
+//#define MERSENNE_TWISTER
+
+#ifndef MERSENNE_TWISTER
+
 /**
  * Simple pseudo-random linear congruential generator, a la Numerical
  * Recipes.
@@ -14,14 +19,29 @@ class RandomSource {
 
 	RandomSource() :
 		a(DEFUALT_A), c(DEFUALT_C), inited_(false) { }
+	RandomSource(uint32_t _last) :
+		a(DEFUALT_A), c(DEFUALT_C), last(_last), inited_(true) { }
 	RandomSource(uint32_t _a, uint32_t _c) :
 		a(_a), c(_c), inited_(false) { }
 
 	void init(uint32_t seed = 0) {
 		last = seed;
 		inited_ = true;
+		lastOff = 30;
 	}
 
+	/**
+	 * Get next unsigned 32-bit or 64-bit integer depending on
+	 * type.  Should perhaps use template specialization.
+	 */
+	template <typename T>
+	T nextU() {
+		if(sizeof(T)>4) {
+			return nextU64();
+		}
+		return nextU32();
+	}
+
 	uint32_t nextU32() {
 		assert(inited_);
 		uint32_t ret;
@@ -33,30 +53,37 @@ class RandomSource {
 		return ret;
 	}
 
-    uint64_t nextU64() {
+	uint64_t nextU64() {
 		assert(inited_);
 		uint64_t first = nextU32();
 		first = first << 32;
 		uint64_t second = nextU32();
 		return first | second;
 	}
-
-
+
 	size_t nextSizeT() {
 		if(sizeof(size_t) == 4) {
 			return nextU32();
 		} else {
 			return nextU64();
 		}
 	}
-
-	template <typename T>
-	T nextU() {
-		if(sizeof(T)>4)
-			return nextU64();
-		return nextU32();
+
+	/**
+	 * Return a pseudo-random unsigned 32-bit integer sampled uniformly
+	 * from [lo, hi].
+	 */
+	uint32_t nextU32Range(uint32_t lo, uint32_t hi) {
+		uint32_t ret = lo;
+		if(hi > lo) {
+			ret += (nextU32() % (hi-lo+1));
+		}
+		return ret;
 	}
 
+	/**
+	 * Get next 2-bit unsigned integer.
+	 */
 	uint32_t nextU2() {
 		assert(inited_);
 		if(lastOff > 30) {
@@ -67,12 +94,53 @@ class RandomSource {
 		return ret;
 	}
 
+	/**
+	 * Get next boolean.
+	 */
+	bool nextBool() {
+		assert(inited_);
+		if(lastOff > 31) {
+			nextU32();
+		}
+		uint32_t ret = (last >> lastOff) & 1;
+		lastOff++;
+		return ret;
+	}
+
+	/**
+	 * Return an unsigned int chosen by picking randomly from among
+	 * options weighted by probabilies supplied as the elements of the
+	 * 'weights' array of length 'numWeights'.  The weights should add
+	 * to 1.
+	 */
+	uint32_t nextFromProbs(
+		const float* weights,
+		size_t numWeights)
+	{
+		float f = nextFloat();
+		float tot = 0.0f; // total weight seen so far
+		for(uint32_t i = 0; i < numWeights; i++) {
+			tot += weights[i];
+			if(f < tot) return i;
+		}
+		return (uint32_t)(numWeights-1);
+	}
+
+	float nextFloat() {
+		assert(inited_);
+		return (float)nextU32() / (float)0xffffffff;
+	}
+
 	static uint32_t nextU32(uint32_t last,
 	                        uint32_t a = DEFUALT_A,
 	                        uint32_t c = DEFUALT_C)
 	{
 		return (a * last) + c;
 	}
+
+	uint32_t currentA() const { return a; }
+	uint32_t currentC() const { return c; }
+	uint32_t currentLast() const { return last; }
 
 private:
 	uint32_t a;
@@ -82,4 +150,103 @@ class RandomSource {
 	bool inited_;
 };
 
+#else
+
+class RandomSource { // Mersenne Twister random number generator
+
+public:
+
+	// default constructor: uses default seed only if this is the first instance
+	RandomSource() {
+		reset();
+	}
+
+	// constructor with 32 bit int as seed
+	RandomSource(uint32_t s) {
+		init(s);
+	}
+
+	// constructor with array of size 32 bit ints as seed
+	RandomSource(const uint32_t* array, int size) {
+		init(array, size);
+	}
+
+	void reset() {
+		state_[0] = 0;
+		p_ = 0;
+		inited_ = false;
+	}
+
+	virtual ~RandomSource() { }
+
+	// the two seed functions
+	void init(uint32_t); // seed with 32 bit integer
+	void init(const uint32_t*, int size); // seed with array
+
+	/**
+	 * Return next 1-bit unsigned integer.
+	 */
+	bool nextBool() {
+		return (nextU32() & 1) == 0;
+	}
+
+	/**
+	 * Get next unsigned 32-bit or 64-bit integer depending on
+	 * type.  Should perhaps use template specialization.
+	 */
+	template <typename T>
+	T nextU() {
+		if(sizeof(T)>4) {
+			return nextU64();
+		}
+		return nextU32();
+	}
+
+	/**
+	 * Get next unsigned 32-bit integer.
+	 */
+	inline uint32_t nextU32() {
+		assert(inited_);
+		if(p_ == n) {
+			gen_state(); // new state vector needed
+		}
+		// gen_state() is split off to be non-inline, because it is only called once
+		// in every 624 calls and otherwise irand() would become too big to get inlined
+		uint32_t x = state_[p_++];
+		x ^= (x >> 11);
+		x ^= (x << 7) & 0x9D2C5680UL;
+		x ^= (x << 15) & 0xEFC60000UL;
+		x ^= (x >> 18);
+		return x;
+	}
+
+	/**
+	 * Return next float between 0 and 1.
+	 */
+	float nextFloat() {
+		assert(inited_);
+		return (float)nextU32() / (float)0xffffffff;
+	}
+
+protected: // used by derived classes, otherwise not accessible; use the ()-operator
+
+	static const int n = 624, m = 397; // compile time constants
+
+	// the variables below are static (no duplicates can exist)
+	uint32_t state_[n]; // state vector array
+	int p_; // position in state array
+
+	bool inited_; // true if init function has been called
+
+	// private functions used to generate the pseudo random numbers
+	uint32_t twiddle(uint32_t u, uint32_t v) {
+		return (((u & 0x80000000UL) | (v & 0x7FFFFFFFUL)) >> 1) ^ ((v & 1UL) ? 0x9908B0DFUL : 0x0UL);
+	}
+
+	void gen_state(); // generate new state
+
+};
+
+#endif
+
 #endif /*RANDOM_GEN_H_*/