/usr/include/libphylo/computeCounts.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 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 | // $Id: computeCounts.h 9903 2011-10-11 20:16:28Z rubi $
// version 1.00
// last modified 3 Nov 2002
#ifndef ___COMPUTE_COUNTS
#define ___COMPUTE_COUNTS
#include "definitions.h"
#include "countTableComponent.h"
#include "sequenceContainer.h"
#include "computePijComponent.h"
#include "suffStatComponent.h"
// things included for the function "fillCountTableComponentGam"
#include "sequenceContainer.h"
class computeCounts {
public:
explicit computeCounts() {};
void computeCountsNodeFatherNodeSonHomPos(const sequenceContainer& sc,
const computePijHom& pi,
const stochasticProcess& sp,
const suffStatGlobalHomPos& cup,
const suffStatGlobalHomPos& cdown,
const MDOUBLE weight,
const doubleRep posProb,
const tree::nodeP nodeSon,
countTableComponentHom& _ctc,
const MDOUBLE rateCategorProb = 1.0); //CODE_RED
//Proportional rate implementation - old
void computeCountsNodeFatherNodeSonHomPosProportionalEB(const sequenceContainer& sc,
const computePijHom& pi,
const stochasticProcess& sp,
const suffStatGlobalHomPos& cup,
const suffStatGlobalHomPos& cdown,
const MDOUBLE weight,
const doubleRep posProb,
const tree::nodeP nodeSon,
countTableComponentHom& _ctc,
const MDOUBLE globalLocalRateCategorProb = 1.0); //CODE_RED
//Proportional rate implementation - new
void computeCountsNodeFatherNodeSonHomPosProportionalEB(const sequenceContainer& sc,
const computePijHom& pi,
const stochasticProcess& sp,
const suffStatGlobalHomPos& cup,
const suffStatGlobalHomPos& cdown,
const MDOUBLE weight,
const VdoubleRep posProbVec,
const tree::nodeP nodeSon,
countTableComponentHom& _ctc);
void computeCountsNodeFatherNodeSonHomPos(const sequenceContainer& sc,
const computePijHom& pi,
const stochasticProcess& sp,
const suffStatGlobalHomPos& cup,
const suffStatGlobalHomPos& cdown,
const MDOUBLE weight,
const doubleRep posProb,
const tree::nodeP nodeSon,
countTableComponentHom& _ctc,
const MDOUBLE rateCategorProb,
const int letterInRoot);
void fillCountTableComponentGam(countTableComponentGam& ctcGam,
const stochasticProcess& sp,
const sequenceContainer& sc,
const computePijGam& pij0,
const suffStatGlobalGam& cup,
const suffStatGlobalGam& cdown,
const Vdouble * weights,
tree::nodeP nodeSon,
const VdoubleRep& posProbVec);
void fillCountTableComponentGamSpecRateCategor(const int rateCategor,
countTableComponentHom& ctcHom,
const stochasticProcess& sp,
const sequenceContainer& sc,
const computePijHom& pi,
const suffStatGlobalGam& cup,
const suffStatGlobalGam& cdown,
const Vdouble * weights,
const VdoubleRep& posProbVec, //prob of the position with gamma
tree::nodeP nodeSon);
};
#endif
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