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
|
#include "character.h"
#include "gaps.h"
void character::checkForTriangleInequality(int st1, int st2){
int longestGapStIndex = getLongestGapStIndex();
if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){
_isTriangleInequalityCorrectionNeeded = true;
_stepmatrixTriagleInCorrected = _stepmatrix;
++_stepmatrixTriagleInCorrected[st1][ longestGapStIndex];
++_stepmatrixTriagleInCorrected[longestGapStIndex][st1];
++_stepmatrixTriagleInCorrected[st2][ longestGapStIndex];
++_stepmatrixTriagleInCorrected[longestGapStIndex][st2];
}
};
int character::getLongestGapStIndex(){
int longestGapStIndex;
int longestGapNumOfZeros = 0;
int characterLength = _states[0].size();
for(int st = 0; st<_states.size(); ++st){
int gapNumOfZeros = 0;
for(int ind = 0; ind<characterLength; ++ind){
gapNumOfZeros += _states[st][ind];
}
if(gapNumOfZeros > longestGapNumOfZeros)
longestGapStIndex = st;
}
return longestGapStIndex;
};
//********************************************************************************************
//computeNumOfSteps
// Foreach c in character_1:character_M
// Foreach st_x and st_y in state_0:state_c_ST (There are ST states in character c) (go over all state combinations)
// Do A to E steps for the pair st_x and st_y:
// A) translate into 01 to X set of 5'-3' coordinats of the X gaps within st_x and st_y
// B) ignore 0-0 (cost_c_x_y =- #0-0 colomns)
// C) merge adjacent 0-1 and 1-0 ((cost_c_x_y =- #adjacent 0-1 and 1-0 colomns)
// D) ignore 1-1 (cost_c_x_y =- #1-1 colomns)
//********************************************************************************************
int character::computeNumOfSteps(int st1, int st2){
int numOfSteps =_states[st1].size();
vector<int> state1(_states[st1].size());
state1 = _states[st1];
vector<int> state2(_states[st2].size());
state2 = _states[st2];
vector<int>::iterator iter1 = state1.begin();
vector<int>::iterator iter2 = state2.begin();
vector<int>::iterator iterLastCounted1 = iter1;
vector<int>::iterator iterLastCounted2 = iter2;
LOGnOUT(6,<<" step "<<st1<<" "<<st2<<endl); // DEBUG
int i = 0;
while( iter1!=state1.end() ){ // both same length
if(*iter1 == *iter2
|| (iter1 != state1.begin() && *iter1 == *(iter1-1) && *iter2 == *(iter2-1))
|| (i>0 && *iter1 == *iterLastCounted1 && *iter2 == *iterLastCounted2 && *(iter1-1)==0 )
)
{
LOGnOUT(6,<<i<<" "<<*iter1<<" "<<*iter2<<endl); // DEBUG
//state1.erase(iter1);
//state2.erase(iter2);
--numOfSteps;
}
else{
iterLastCounted1 = iter1;
iterLastCounted2 = iter2;
LOGnOUT(6,<<"Count step "<<i<<" "<<*iter1<<" "<<*iter2<<endl); // DEBUG
}
++iter1;
++iter2;
++i;
}
if(state1.size() != state2.size())
cout<<"error"<<endl;
//numOfSteps = state1.size();
return numOfSteps;
};
|
