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
|
package driver;
import dna.ChromosomeArray;
import dna.Data;
public class CompareReferenceGenomes {
public static void main(String[] args){
compareGenomes(args[0], args[1]);
}
public static void compareGenomes(String pattern1, String pattern2){
for(byte chrom=1; chrom<=25; chrom++){
System.out.println("Comparing chromosome "+chrom);
String fname1=pattern1.replace("#", ""+chrom);
String fname2=pattern2.replace("#", ""+chrom);
ChromosomeArray cha=ChromosomeArray.read(fname1);
ChromosomeArray chb=ChromosomeArray.read(fname2);
boolean result=compare(cha, chb);
System.out.println("..."+(result ? "identical." : "different."));
}
}
public static boolean compare(ChromosomeArray cha, ChromosomeArray chb){
boolean equal=true;
if(cha.minIndex!=chb.minIndex || cha.maxIndex!=chb.maxIndex){
System.out.println("Index mismatch in chrom "+cha.chromosome+":\n" +
"("+cha.minIndex+" - "+cha.maxIndex+") vs ("+chb.minIndex+" - "+chb.maxIndex+")");
equal=false;
}
int start=Data.max(cha.minIndex, chb.minIndex);
int stop=Data.min(cha.maxIndex, chb.maxIndex);
for(int i=start; i<=stop; i++){
byte a=cha.get(i);
byte b=chb.get(i);
if(a!=b){
System.out.println(((char)cha.chromosome)+"\t"+i+"\t"+((char)a)+" "+((char)b));
equal=false;
}
}
return equal;
}
}
|
