/usr/include/libphylo/countTableComponent.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 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 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 | // $Id: countTableComponent.h 9595 2011-06-30 18:56:40Z rubi $
#ifndef ___COUNT_TABLE_COMPONENT
#define ___COUNT_TABLE_COMPONENT
#include "definitions.h"
#include <iostream>
#include <cassert>
class countTableComponentHom{
public:
void setCount( const int letter1,
const int letter2,
const MDOUBLE val) {
_countValues[letter1][letter2]=val;
}
int alphabetSize() const {return _countValues.size();}
void zero();
MDOUBLE getCounts( const int letter1,
const int letter2) const {
return _countValues[letter1][letter2];
}
void addToCounts(const int let1,const int let2,const MDOUBLE val) {
_countValues[let1][let2]+=val;
}
int getSize() const {return _countValues.size();}
bool isEmpty (){return (_countValues.empty());};
void countTableComponentAllocatePlace(const int alphabetSize);
void printTable(ostream & out) const;
const Vdouble& operator[] (int i) const {return _countValues[i];}
private:
VVdouble _countValues;//letter1,letter2
};
class countTableComponentGam{
public:
void setCount( const int letter1,
const int letter2,
const int rateCategor,
const MDOUBLE val) {
_countValues[rateCategor].setCount(letter1,letter2,val);
}
int alphabetSize() const {return _countValues.empty()?0:_countValues[0].alphabetSize();}
void zero(){
for (int rateCat=0; rateCat < _countValues.size(); ++rateCat) _countValues[rateCat].zero();
}
MDOUBLE getCounts( const int letter1,
const int letter2,
const int rateCategor) const {
assert(_countValues[rateCategor].getCounts(letter1,letter2)>=0);
return _countValues[rateCategor].getCounts(letter1,letter2);
}
void addToCounts(const int let1,const int let2,
const int rate,const MDOUBLE val) {
_countValues[rate].addToCounts(let1,let2,val);
}
bool isEmpty (){return (_countValues.empty());};
void countTableComponentAllocatePlace(const int alphabetSize,
const int numberOfrateCategories) {
_countValues.resize(numberOfrateCategories);
for (int rateCat=0; rateCat < _countValues.size(); ++rateCat){
_countValues[rateCat].countTableComponentAllocatePlace(alphabetSize);
}
}
void printTable(ostream & out) const {
for (int rateCat=0; rateCat < _countValues.size(); ++rateCat) {
_countValues[rateCat].printTable(out);
}
}
int getSize() const {return _countValues.size();}
countTableComponentHom& operator[] (int i) {return _countValues[i];}
const countTableComponentHom& operator[] (int i) const {return _countValues[i];}
private:
vector<countTableComponentHom> _countValues;//letter1,letter2,rateCategor
};
class countTableComponentGamProportional{
public:
void setCount( const int letter1,
const int letter2,
const int globalRateCategor,
const int localRateCategor,
const MDOUBLE val) {
_countValues[globalRateCategor].setCount(letter1,letter2,localRateCategor,val);
}
int alphabetSize() const {return _countValues.empty()?0:_countValues[0].alphabetSize();}
void zero(){
for (int globalRateCat=0; globalRateCat < _countValues.size(); ++globalRateCat) _countValues[globalRateCat].zero();
}
MDOUBLE getCounts( const int letter1,
const int letter2,
const int globalRateCategor,
const int localRateCategor) const {
assert(_countValues[globalRateCategor].getCounts(letter1,letter2,localRateCategor)>=0);
return _countValues[globalRateCategor].getCounts(letter1,letter2,localRateCategor);
}
void addToCounts(const int let1,const int let2,
const int globalRate,const int localRate,const MDOUBLE val) {
_countValues[globalRate].addToCounts(let1,let2,localRate,val);
}
bool isEmpty (){return (_countValues.empty());}
void countTableComponentAllocatePlace(const int alphabetSize,
const int numberOfGlobalRateCategories,const int numberOfLocalRateCategories) {
_countValues.resize(numberOfGlobalRateCategories);
for(int globalRateCat = 0;globalRateCat < _countValues.size(); ++globalRateCat){
_countValues[globalRateCat].countTableComponentAllocatePlace(alphabetSize,numberOfLocalRateCategories);
}
}
void printTable(ostream & out) const {
for (int globalRateCat=0; globalRateCat < _countValues.size(); ++globalRateCat) {
_countValues[globalRateCat].printTable(out);
}
}
int getSize() const {return _countValues.size();}
countTableComponentGam& operator[] (int i) {return _countValues[i];}
const countTableComponentGam& operator[] (int i) const {return _countValues[i];}
private:
vector<countTableComponentGam> _countValues;//letter1,letter2,globalRateCategor,localRateCategor
};
#endif
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