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
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
// $Id: computeUpAlg.cpp 5988 2009-03-18 18:20:05Z itaymay $
#include "definitions.h"
#include "computeUpAlg.h"
#include "treeIt.h"
#include "seqContainerTreeMap.h"
#include "logFile.h"
#include <iostream>
#include <cassert>
using namespace std;
void computeUpAlg::fillComputeUp(const tree& et,
const sequenceContainer & sc,
const computePijGam& pi,
suffStatGlobalGam& ssc) {
computeUpAlg cupAlg;
ssc.allocatePlace(sc.seqLen(),pi.categories(),et.getNodesNum(),pi.alphabetSize());
for (int pos = 0; pos < sc.seqLen(); ++pos) {
for (int categor = 0; categor < pi.categories(); ++categor) {
cupAlg.fillComputeUp(et,sc,pos,pi[categor],ssc[pos][categor]);
}
}
}
void computeUpAlg::fillComputeUp(const tree& et,
const sequenceContainer& sc,
const int pos,
const computePijHom& pi,
suffStatGlobalHomPos& ssc) {
seqContainerTreeMap sctm(sc,et);
ssc.allocatePlace(et.getNodesNum(),pi.alphabetSize());
treeIterDownTopConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int letter;
if (mynode->isLeaf()) {
for(letter=0; letter<pi.alphabetSize();letter++) {
const int seqID = sctm.seqIdOfNodeI(mynode->id());
doubleRep val = sc.getAlphabet()->relations(sc[seqID][pos],letter);
ssc.set(mynode->id(),letter,val);
}
}
else {
for(letter=0; letter<pi.alphabetSize();letter++) {
doubleRep total_prob=1.0;
for(int i=0; i < mynode->getNumberOfSons();++i){
doubleRep prob=0.0;
for(int letInSon=0; letInSon<pi.alphabetSize();letInSon++) {
prob += ssc.get(mynode->getSon(i)->id(), letInSon)*
pi.getPij(mynode->getSon(i)->id(),letter,letInSon);
}
total_prob*=prob;
}
ssc.set(mynode->id(),letter,total_prob);
}
}
}
}
/*
void computeUpAlg::fillComputeUp(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc) {
seqContainerTreeMap sctm(sc,et);
ssc.allocatePlace(et.getNodesNum(),sp.alphabetSize());
treeIterDownTopConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int letter;
if (mynode->isLeaf()) {// leaf
for(letter=0; letter<sp.alphabetSize();letter++) {
const int seqID = sctm.seqIdOfNodeI(mynode->id());
MDOUBLE val = sc.getAlphabet()->relations(sc[seqID][pos],letter);
ssc.set(mynode->id(),letter,val);
}
}
else {
for(letter=0; letter<sp.alphabetSize();letter++) {
MDOUBLE total_prob=1.0;
for(int i=0; i < mynode->getNumberOfSons();++i){
MDOUBLE prob=0.0;
for(int letInSon=0; letInSon<sp.alphabetSize();letInSon++) {
prob += ssc.get(mynode->getSon(i)->id(),letInSon)*
sp.Pij_t(letter,letInSon,mynode->getSon(i)->dis2father()*sp.getGlobalRate());// taking care of the glubal is new.
}
assert(prob>=0.0);
total_prob*=prob;
}
ssc.set(mynode->id(),letter,total_prob);
}
}
}
}
*/
void computeUpAlg::fillComputeUpSpecificGlobalRate(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc,
const MDOUBLE gRate) {
if (sp.categories() >1) {// because we do not multiply all branch lengths by the rate[categories])
errorMsg::reportError("the function fillComputeUpSpecificGlobalRate should not be used with a gamma model");
}
seqContainerTreeMap sctm(sc,et);
ssc.allocatePlace(et.getNodesNum(),sp.alphabetSize());
treeIterDownTopConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
#ifdef VERBOS
LOG(15,<<endl<<endl<<"doing node: "<<mynode->name()<<endl);
#endif
int letter;
if (mynode->isLeaf()) {
for(letter=0; letter<sp.alphabetSize();letter++) {
const int seqID = sctm.seqIdOfNodeI(mynode->id());
doubleRep val = sc.getAlphabet()->relations(sc[seqID][pos],letter);
ssc.set(mynode->id(),letter,val);
}
}
else {
int letterWithTotalProbEqZero =0;
for(letter=0; letter<sp.alphabetSize();letter++) {
doubleRep total_prob=1.0;
for(int i=0; i < mynode->getNumberOfSons();++i){
doubleRep prob=0.0;
for(int letInSon=0; letInSon<sp.alphabetSize();letInSon++) {
assert(ssc.get(mynode->getSon(i)->id(),letInSon)>=0);
assert(sp.Pij_t(letter,letInSon,mynode->getSon(i)->dis2father()*gRate)>=0);
prob += ssc.get(mynode->getSon(i)->id(),letInSon)*
sp.Pij_t(letter,letInSon,mynode->getSon(i)->dis2father()*gRate);
}
assert(prob>=0.0);
total_prob*=prob;
}
if (total_prob==0.0) ++letterWithTotalProbEqZero;
ssc.set(mynode->id(),letter,total_prob);
} // end of else
if (letterWithTotalProbEqZero == sp.alphabetSize() && (mynode->getNumberOfSons() > 0)) {
LOG(5,<<" total prob =0");
for (int z=0; z <mynode->getNumberOfSons(); ++z) {
LOG(5,<<"son "<<z<<" is "<<mynode->getSon(z)->name()<<endl);
LOG(5,<<"dis2father is "<<mynode->getSon(z)->dis2father()<<endl);
for(int letInSon=0; letInSon<sp.alphabetSize();letInSon++) {
LOG(5,<<"let = "<<letInSon<<endl);
LOG(5,<<"ssc.get(mynode->getSon(z)->id(),letInSon) = "<<convert(ssc.get(mynode->getSon(z)->id(),letInSon))<<endl);
}
}
return;
}
}
}
}
|
