-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathFluB.java
More file actions
169 lines (125 loc) · 6.06 KB
/
Copy pathFluB.java
File metadata and controls
169 lines (125 loc) · 6.06 KB
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
158
159
160
161
162
163
164
165
166
package teaspoon;
import teaspoon.adaptation.Hemagglutinin;
import teaspoon.adaptation.Methods;
import teaspoon.adaptation.Neuraminidase;
import teaspoon.adaptation.WilliamsonOutputClass;
public class FluB {
/**
* @param args
*/
public static void main(String[] args) {
Methods m = new Methods();
m.SubsetAlignment("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/cleaned_LL1404_B_FullHA_Victoria.fas", "/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/External_Victoria.fas", "/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/Internal_Victoria.fas", new Hemagglutinin().FluB );
m.SubsetAlignment("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/cleaned_LL1404_B_FullHA_Yamagata.fas", "/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/External_Yamagata.fas", "/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/Internal_Yamagata.fas", new Hemagglutinin().FluB );
m.SubsetAlignment("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/pure_Victoria_FluB_NA.fas", "/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/External_Victoria_NA.fas", "/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/Internal_Victoria_NA.fas", new Neuraminidase().FluB );
m.SubsetAlignment("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/pure_Yamagata_FluB_NA.fas", "/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/External_Yamagata_NA.fas", "/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/Internal_Yamagata_NA.fas", new Neuraminidase().FluB );
/* int start=1971;
int end=2014;
String[] files = {"cleaned_LL535_B_HA2_combined.fas",
"cleaned_LL535_B_HA2_Victoria.fas",
"cleaned_LL535_B_HA2_Yamagata.fas",
"cleaned_LL868_B_HA1_combined.fas",
"cleaned_LL868_B_HA1_Victoria.fas",
"cleaned_LL868_B_HA1_Yamagata.fas",
"cleaned_LL1404_B_FullHA_combined.fas",
"cleaned_LL1404_B_FullHA_Victoria.fas",
"cleaned_LL1404_B_FullHA_Yamagata.fas",
"pure_Victoria_FluB_NA.fas",
"pure_Yamagata_FluB_NA.fas"};
int size = end-start;
int[][] store = new int[size][files.length];
for(int x=0;x<files.length;x++){
teaspoon.adaptation.DataSet data = new teaspoon.adaptation.DataSet("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/"+files[x]);
int[][] counter = data.dateCounter(start, end);
for(int i=0;i<counter.length;i++){
store[i][x]=counter[i][1];
}
}
for(int j=0;j<size;j++){
for(int i=0;i<files.length;i++){
System.out.print(store[j][i]+"\t");
}
System.out.println();
}*/
//victoria HA1
String[] DatesVHA1={"1975_1976_1977_1978_1979_1980","1982_1983_1984_1985","1986_1987","1988_1989","1990","1991_1992_1993_1994","1995_1996_1997","1998_1999_2000","2001","2002","2003","2004","2005","2006","2007","2008","2009","2010","2011","2012"};
//victoria HA1
String[] DatesVHA2={"1985_1986","1987_1988_1989_1990","1993_1994_1995_1996_1997","1998_1999_2000_2001","2002","2003","2004","2005","2006","2007","2008","2009","2010","2011_2012"};
//Yamagataha1
String[] DatesYHA1={"1975_1976_1977_1978_1979_1980_1981","1982_1983_1984_1985","1987_1988_1989","1990","1991","1992","1993","1994","1995","1996","1997","1998","1999","2000","2001","2002","2003","2004","2005","2006","2007","2008","2009","2010","2011","2012"};
//Yamagata ha2
String[] DatesYHA2={"1979_1980_1981_1982_1983","1988_1989_1990_1991","1992_1993","1994_1995","1996","1997","1998","1999","2000","2001","2002_2003","2004","2005","2006","2007","2008","2009","2010","2011_2012"};
String[] DatesVHA = {"1985_1986","1987_1988_1989_1990","1993_1994_1995_1996_1997_1998","2001_2002","2003","2004","2005","2006","2007","2008","2009","2010","2011_2012"};
String[] DatesYHA = {"1979_1980_1981_1982_1983","1988_1989_1990_1991","1992_1993","1994_1995","1996","1997","1998","1999","2000","2001","2002_2003","2004","2005","2006","2007","2008","2009","2010","2011_2012"};
String[] DatesVNA = {"2002","2003","2004","2005","2006","2007","2008","2009","2010","2011"};
String[] DatesYNA = {"1988_1989_1990","1991_1992_1993","1994_1995","1996","1997","1998","1999","2000","2001","2002","2003","2004","2005","2006","2007","2008","2009","2010","2011_2012"};
String gene="NA";
if(gene=="HA"){
String choice="V";
int indexHA1=-9;
int indexHA2=-9;
int indexHA=-9;
String[] DatesHA1=DatesVHA1;
String[] DatesHA2=DatesVHA2;
String[] DatesHA=DatesVHA;
String[] files = {
"Internal_Victoria.fas",
"Internal_Yamagata.fas",
"External_Victoria.fas",
"External_Yamagata.fas"};
if(choice=="V"){
indexHA1=2;
indexHA2=0;
DatesHA1=DatesVHA;
DatesHA2=DatesVHA;
}
if(choice=="Y"){
indexHA1=3;
indexHA2=1;
DatesHA1=DatesYHA;
DatesHA2=DatesYHA;
}
FluAnalysis2 F = new FluAnalysis2();
Hemagglutinin H = new Hemagglutinin();
WilliamsonOutputClass woc = F.GenericRunner("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/"+files[indexHA2], DatesHA2, 0.1,2);
double nr = F.CalcNr(woc);
System.out.println(nr);
woc = F.GenericRunner("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/"+files[indexHA1], DatesHA1, nr, 100);
F.print(woc,10,"/Users/Sam/Desktop/VictoriaHA1.txt");
for(int i=0;i<woc.TotalA.size();i++){
System.out.println(woc.dateavg.get(i)+"\t"+woc.TotalA.get(i)+"\t"+woc.Mid_R.get(i)+"\t"+woc.Mid_S.get(i));
}
} else if(gene=="NA"){
String choice="Y";
int indexI=-9;
int indexE=-9;
String[] DatesNA=DatesVNA;
String[] files = {
"Internal_Victoria_NA.fas",
"Internal_Yamagata_NA.fas",
"External_Victoria_NA.fas",
"External_Yamagata_NA.fas"};
if(choice=="V"){
indexE=2;
indexI=0;
DatesNA=DatesVNA;
DatesNA=DatesVNA;
}
if(choice=="Y"){
indexE=3;
indexI=1;
DatesNA=DatesYNA;
DatesNA=DatesYNA;
}
FluAnalysis2 F = new FluAnalysis2();
WilliamsonOutputClass woc = F.GenericRunner("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/"+files[indexI], DatesNA, 0.1,1);
double nr = F.CalcNr(woc);
System.out.println(nr);
woc = F.GenericRunner("/Users/Sam/Desktop/PAPERS/FLUB/B_ready_HA/"+files[indexE], DatesNA, nr, 1);
// F.print(woc,10,"/Users/Sam/Desktop/VictoriaHA1.txt");
for(int i=0;i<woc.TotalA.size();i++){
System.out.println(woc.dateavg.get(i)+"\t"+woc.TotalA.get(i)+"\t"+woc.Mid_R.get(i)+"\t"+woc.Mid_S.get(i));
}
}
}
}