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intmath.cpp
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intmath.cpp
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#include "muscle.h"
#include <math.h>
PROB ScoreToProb(SCORE Score)
{
if (MINUS_INFINITY >= Score)
return 0.0;
return (PROB) pow(2.0, (double) Score/INTSCALE);
}
//#if 0
//static const double log2e = log2(exp(1.0));
//
//double lnTolog2(double ln)
// {
// return ln*log2e;
// }
//
//double log2(double x)
// {
// if (0 == x)
// return MINUS_INFINITY;
//
// static const double dInvLn2 = 1.0/log(2.0);
//// Multiply by inverse of log(2) just in case multiplication
//// is faster than division.
// return log(x)*dInvLn2;
// }
//#endif
//SCORE ProbToScore(PROB Prob)
// {
// if (0.0 == Prob)
// return MINUS_INFINITY;
//// return (SCORE) floor(INTSCALE*log2(Prob));
// return (SCORE) log2(Prob);
// }
WEIGHT DoubleToWeight(double d)
{
assert(d >= 0);
return (WEIGHT) (INTSCALE*d);
}
double WeightToDouble(WEIGHT w)
{
return (double) w / (double) INTSCALE;
}
SCORE DoubleToScore(double d)
{
return (SCORE)(d*(double) INTSCALE);
}
bool ScoreEq(SCORE s1, SCORE s2)
{
return BTEq(s1, s2);
}
static bool BTEq2(BASETYPE b1, BASETYPE b2)
{
double diff = fabs(b1 - b2);
if (diff < 0.0001)
return true;
double sum = fabs(b1) + fabs(b2);
return diff/sum < 0.005;
}
bool BTEq(double b1, double b2)
{
return BTEq2((BASETYPE) b1, (BASETYPE) b2);
}
//const double dLn2 = log(2.0);
//// pow2(x)=2^x
//double pow2(double x)
// {
// if (MINUS_INFINITY == x)
// return 0;
// return exp(x*dLn2);
// }
//// lp2(x) = log2(1 + 2^-x), x >= 0
//double lp2(double x)
// {
// return log2(1 + pow2(-x));
// }
// SumLog(x, y) = log2(2^x + 2^y)
//SCORE SumLog(SCORE x, SCORE y)
// {
// return (SCORE) log2(pow2(x) + pow2(y));
// }
//
//// SumLog(x, y, z) = log2(2^x + 2^y + 2^z)
//SCORE SumLog(SCORE x, SCORE y, SCORE z)
// {
// return (SCORE) log2(pow2(x) + pow2(y) + pow2(z));
// }
//
//// SumLog(w, x, y, z) = log2(2^w + 2^x + 2^y + 2^z)
//SCORE SumLog(SCORE w, SCORE x, SCORE y, SCORE z)
// {
// return (SCORE) log2(pow2(w) + pow2(x) + pow2(y) + pow2(z));
// }
//SCORE lp2Fast(SCORE x)
// {
// assert(x >= 0);
// const int iTableSize = 1000;
// const double dRange = 20.0;
// const double dScale = dRange/iTableSize;
// static SCORE dValue[iTableSize];
// static bool bInit = false;
// if (!bInit)
// {
// for (int i = 0; i < iTableSize; ++i)
// dValue[i] = (SCORE) lp2(i*dScale);
// bInit = true;
// }
// if (x >= dRange)
// return 0.0;
// int i = (int) (x/dScale);
// assert(i >= 0 && i < iTableSize);
// SCORE dResult = dValue[i];
// assert(BTEq(dResult, lp2(x)));
// return dResult;
// }
//
//// SumLog(x, y) = log2(2^x + 2^y)
//SCORE SumLogFast(SCORE x, SCORE y)
// {
// if (MINUS_INFINITY == x)
// {
// if (MINUS_INFINITY == y)
// return MINUS_INFINITY;
// return y;
// }
// else if (MINUS_INFINITY == y)
// return x;
//
// SCORE dResult;
// if (x > y)
// dResult = x + lp2Fast(x-y);
// else
// dResult = y + lp2Fast(y-x);
// assert(SumLog(x, y) == dResult);
// return dResult;
// }
//
//SCORE SumLogFast(SCORE x, SCORE y, SCORE z)
// {
// SCORE dResult = SumLogFast(x, SumLogFast(y, z));
// assert(SumLog(x, y, z) == dResult);
// return dResult;
// }
//SCORE SumLogFast(SCORE w, SCORE x, SCORE y, SCORE z)
// {
// SCORE dResult = SumLogFast(SumLogFast(w, x), SumLogFast(y, z));
// assert(SumLog(w, x, y, z) == dResult);
// return dResult;
// }
double VecSum(const double v[], unsigned n)
{
double dSum = 0.0;
for (unsigned i = 0; i < n; ++i)
dSum += v[i];
return dSum;
}
void Normalize(PROB p[], unsigned n)
{
unsigned i;
PROB dSum = 0.0;
for (i = 0; i < n; ++i)
dSum += p[i];
if (0.0 == dSum)
Quit("Normalize, sum=0");
for (i = 0; i < n; ++i)
p[i] /= dSum;
}
void NormalizeUnlessZero(PROB p[], unsigned n)
{
unsigned i;
PROB dSum = 0.0;
for (i = 0; i < n; ++i)
dSum += p[i];
if (0.0 == dSum)
return;
for (i = 0; i < n; ++i)
p[i] /= dSum;
}
void Normalize(PROB p[], unsigned n, double dRequiredTotal)
{
unsigned i;
double dSum = 0.0;
for (i = 0; i < n; ++i)
dSum += p[i];
if (0.0 == dSum)
Quit("Normalize, sum=0");
double dFactor = dRequiredTotal / dSum;
for (i = 0; i < n; ++i)
p[i] *= (PROB) dFactor;
}
bool VectorIsZero(const double dValues[], unsigned n)
{
for (unsigned i = 0; i < n; ++i)
if (dValues[i] != 0.0)
return false;
return true;
}
void VectorSet(double dValues[], unsigned n, double d)
{
for (unsigned i = 0; i < n; ++i)
dValues[i] = d;
}
bool VectorIsZero(const float dValues[], unsigned n)
{
for (unsigned i = 0; i < n; ++i)
if (dValues[i] != 0.0)
return false;
return true;
}
void VectorSet(float dValues[], unsigned n, float d)
{
for (unsigned i = 0; i < n; ++i)
dValues[i] = d;
}
double Correl(const double P[], const double Q[], unsigned uCount)
{
double dSumP = 0.0;
double dSumQ = 0.0;
for (unsigned n = 0; n < uCount; ++n)
{
dSumP += P[n];
dSumQ += Q[n];
}
const double dMeanP = dSumP/uCount;
const double dMeanQ = dSumQ/uCount;
double dSum1 = 0.0;
double dSum2 = 0.0;
double dSum3 = 0.0;
for (unsigned n = 0; n < uCount; ++n)
{
const double dDiffP = P[n] - dMeanP;
const double dDiffQ = Q[n] - dMeanQ;
dSum1 += dDiffP*dDiffQ;
dSum2 += dDiffP*dDiffP;
dSum3 += dDiffQ*dDiffQ;
}
if (0 == dSum1)
return 0;
const double dCorrel = dSum1 / sqrt(dSum2*dSum3);
return dCorrel;
}
float Correl(const float P[], const float Q[], unsigned uCount)
{
float dSumP = 0.0;
float dSumQ = 0.0;
for (unsigned n = 0; n < uCount; ++n)
{
dSumP += P[n];
dSumQ += Q[n];
}
const float dMeanP = dSumP/uCount;
const float dMeanQ = dSumQ/uCount;
float dSum1 = 0.0;
float dSum2 = 0.0;
float dSum3 = 0.0;
for (unsigned n = 0; n < uCount; ++n)
{
const float dDiffP = P[n] - dMeanP;
const float dDiffQ = Q[n] - dMeanQ;
dSum1 += dDiffP*dDiffQ;
dSum2 += dDiffP*dDiffP;
dSum3 += dDiffQ*dDiffQ;
}
if (0 == dSum1)
return 0;
const float dCorrel = dSum1 / (float) sqrt(dSum2*dSum3);
return dCorrel;
}
// Simple (but slow) function to compute Pearson ranks
// that allows for ties. Correctness and simplicity
// are priorities over speed here.
void Rank(const float P[], float Ranks[], unsigned uCount)
{
for (unsigned n = 0; n < uCount; ++n)
{
unsigned uNumberGreater = 0;
unsigned uNumberEqual = 0;
unsigned uNumberLess = 0;
double dValue = P[n];
for (unsigned i = 0; i < uCount; ++i)
{
double v = P[i];
if (v == dValue)
++uNumberEqual;
else if (v < dValue)
++uNumberLess;
else
++uNumberGreater;
}
assert(uNumberEqual >= 1);
assert(uNumberEqual + uNumberLess + uNumberGreater == uCount);
Ranks[n] = (float) (1 + uNumberLess + (uNumberEqual - 1)/2.0);
}
}
void Rank(const double P[], double Ranks[], unsigned uCount)
{
for (unsigned n = 0; n < uCount; ++n)
{
unsigned uNumberGreater = 0;
unsigned uNumberEqual = 0;
unsigned uNumberLess = 0;
double dValue = P[n];
for (unsigned i = 0; i < uCount; ++i)
{
double v = P[i];
if (v == dValue)
++uNumberEqual;
else if (v < dValue)
++uNumberLess;
else
++uNumberGreater;
}
assert(uNumberEqual >= 1);
assert(uNumberEqual + uNumberLess + uNumberGreater == uCount);
Ranks[n] = (double) (1 + uNumberLess + (uNumberEqual - 1)/2.0);
}
}
FCOUNT SumCounts(const FCOUNT Counts[])
{
FCOUNT Sum = 0;
for (int i = 0; i < 20; ++i)
Sum += Counts[i];
return Sum;
}