I want to know if i am on the right track

Question

'm still working on my DNA sequencing project (i am further along thank goodness) but now, i want to check my thought process.
Okay, i have to write a new method public void addEdge(int i, int k)
that creates an edge sequence between vertex j and k.
What these need to do is take the watson-crick compliment of the last half of j concatenated with the watson-crick of the first half of k. So it looks kind of like this:
sequence
ATTATAAACCA
watson-crick edge compliment
TGGTTTATAAT
here is my thought process
1. take the initial sequence array and divide it by 2
2. then go through the first half and change the compliments
3. then do the same with the second half and concantenate them together
so it would look like
for(int i = 0; i < seqArray.length/2; i++){
base = rand.nextInt(4);
if(base==0)
tube+="T";
else if(base==1)
tube+="A";
else if(base==2)
tube+="C";
else if(base==3)
tube+="G";
for(int j = seqArray.length/2; j < seqArray.length; j++){
base = rand.nextInt(4);
if(base==0)
tube+="T";
else if(base==1)
tube+="A";
else if(base==2)
tube+="C";
else if(base==3)
tube+="G";
new Sequence(tube)= seqArray[i] + seqArray[j];What do you think? am i on the right track?
}

Answer 1

Something like the following?
public class WC {
    private static char complement(char base) {
        switch (base) {
            case 'A': return 'T';
            case 'T': return 'A';
            case 'G': return 'C';
            case 'C': return 'G';
            default:
                throw new IllegalArgumentException("unrecognised base "+base);
    private static char[] complement(char[] bases) {
        int size = bases.length;
        char[] complement = new char[size];
        for (int i = 0; i < size; i++) {
            complement[i] = complement(bases);
return complement;
public static void main(String[] args) {
String s = args[0];
String s1 = s.substring(0, s.length()/2);
String s2 = s.substring(s.length()/2);
char[] c1 = s1.toCharArray();
char[] c2 = s2.toCharArray();
s1 = new String(complement(c1));
s2 = new String(complement(c2));
System.out.println(s);
System.out.println(s2+s1);
Cheers, Neil