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
|
/**
* Title: ProAlign<p>
* Description: <p>
* Copyright: Copyright (c) Ari Loytynoja<p>
* License: GNU GENERAL PUBLIC LICENSE<p>
* @see http://www.gnu.org/copyleft/gpl.html
* Company: ULB<p>
* @author Ari Loytynoja
* @version 1.0
*/
package proalign;
class CheckTrailing {
PwAlignment pwa;
CheckTrailing(ProAlign pa) {
ProAlign.log("CheckTrailing");
PwSubstitutionMatrix psm = new PwSubstitutionMatrix();
String pwAlphabet;
int[][] pwSubst;
int gOpen, gExt;
if(ProAlign.isDna){
pwAlphabet = psm.dnaAlphabet;
pwSubst = psm.swdna;
gOpen = -1*pa.pwDnaOpen;
gExt = -1*pa.pwDnaExt;
} else {
pwAlphabet = psm.protAlphabet;
if(pa.pwProtMatrix.equals("pam60")) {
pwSubst = psm.pam60;
} else if(pa.pwProtMatrix.equals("pam160")) {
pwSubst = psm.pam160;
} else if(pa.pwProtMatrix.equals("pam250")) {
pwSubst = psm.pam250;
} else {
pwSubst = psm.pam120;
}
gOpen = -1*pa.pwProtOpen;
gExt = -1*pa.pwProtExt;
}
pwa = new PwAlignment(pwSubst,gOpen,gExt,pwAlphabet,ProAlign.isDna);
}
int[] trailing(String s1, String s2) {
return pwa.trailing(s1,s2);
}
}
|
