/usr/include/libphylo/computeUpAlg.h is in rate4site 3.0.0-5.
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 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | // $Id: computeUpAlg.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___COMPUTE_UP_ALG
#define ___COMPUTE_UP_ALG
#include "definitions.h"
#include "tree.h"
#include "suffStatComponent.h"
#include "sequenceContainer.h"
#include "computePijComponent.h"
class computeUpAlg {
public:
void fillComputeUp(const tree& et,
const sequenceContainer& sc,
const int pos,
const computePijHom& pi,
suffStatGlobalHomPos& ssc);
void fillComputeUp(const tree& et,
const sequenceContainer & sc,
const computePijGam& pi,
suffStatGlobalGam& ssc);
/*void fillComputeUp(const tree& et, // not to be used at all. problematic in case of a gamma function.
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc);*/
/*void fillComputeUp(const tree& et, // not to be used, accept for debuging (very slow func.)
const sequenceContainer& sc,
const stochasticProcess& sp,
suffStatGlobalGam& ssc);*/
void fillComputeUpSpecificGlobalRate(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc,
const MDOUBLE gRate);
// my attemp to add factors
void fillComputeUpWithFactors(const tree& et,
const sequenceContainer& sc,
const int pos,
const computePijHom& pi,
suffStatGlobalHomPos& ssc,
vector<MDOUBLE>& factors);
void fillComputeUpWithFactors(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc,
vector<MDOUBLE>& factors);
void fillComputeUpSpecificGlobalRateFactors(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc,
const MDOUBLE gRate,
vector<MDOUBLE>& factors);
};
#endif
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