String index out of range in Java

Question

I am aware there are multiple threads like my assignment below, but I just can't figure it out. I can't exactly figure out the mistake. Help would be appreciated.

I am trying to do this program:

Everything works fine unless I input the same chains or similar (for example ACTG and ACTG or ACTG and ACTGCCCC), when it tells me

string index out of range

This is that part of my code:

int tries=0;
int pos=-1;
int k;

for (int i=0; i<longDNA.length(); i++) {

    tries=0;
    k=i;

    for (int j=0; j<shortDNA.length(); j++) {

        char s=shortDNA.charAt(j);
        char l=longDNA.charAt(k);

        if (canConnect(s,l)) {
            tries+=1;
            k+=1;
        } 
    }

    if (tries==shortDNA.length()-1) {
        pos=i-1;
        break;
    }
}

Answer 1

Let's call the two DNA strings longer and shorter. In order for shorter to attach somewhere on longer, a sequence of bases complementary to shorter must be found somewhere in longer, e.g. if there is ACGT in shorter, then you need to find TGCA somewhere in longer.

So, if you take shorter and flip all of its bases to their complements:

char[] cs = shorter.toCharArray();
for (int i = 0; i < cs.length; ++i) {
  // getComplement changes A->T, C->G, G->C, T->A,
  // and throws an exception in all other cases
  cs[i] = getComplement(cs[i]);
}
String shorterComplement = new String(cs);

For the examples given in your question, the complement of TTGCC is AACGG, and the complement of TGC is ACG.

Then all you have to do is to find shorterComplement within longer. You can do this trivially using indexOf:

return longer.indexOf(shorterComplement);

Of course, if the point of the exercise is to learn how to do string matching, you can look at well-known algorithms for doing the equivalent of indexOf. For instance, Wikipedia has a category for String matching algorithms.