/usr/include/libphylo/gammaDistribution.h is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | // $Id: gammaDistribution.h 2862 2007-11-27 10:59:03Z itaymay $
#ifndef ___GAMMA_DIST
#define ___GAMMA_DIST
/************************************************************
This distribution can take several forms depending on its free parameter alpha
(beta is assumed to be equal to alpha). For an extensive exlpanation of this distribution
see http://mathworld.wolfram.com/GammaDistribution.html.
please note that the borders of the categories are defined according to calculation of
the gamma integral, according to numerical recipes in gammaUtilities
_globalRate represents the rate for two joint genes.
************************************************************/
#include "definitions.h"
#include "generalGammaDistribution.h"
#include "errorMsg.h"
class gammaDistribution : public generalGammaDistribution {
public:
explicit gammaDistribution() {}
explicit gammaDistribution(MDOUBLE alpha,int in_number_of_categories);
explicit gammaDistribution(const gammaDistribution& other);
virtual ~gammaDistribution() {}
virtual distribution* clone() const { return new gammaDistribution(*this); }
virtual void setAlpha(MDOUBLE newAlpha);
virtual void setGammaParameters(int numOfCategories=1 ,MDOUBLE alpha=1);
virtual void change_number_of_categories(int in_number_of_categories);
// to prevent the user from using alpha!=beta
virtual void setGammaParameters(int numOfCategories ,MDOUBLE alpha, MDOUBLE beta);
virtual void setBeta(MDOUBLE newBeta) {errorMsg::reportError("gammaDistribution::setBeta : can not set beta because alpha=beta");}
};
#endif
|