Otuabaroku: Unfortunately, yes in this case.

lordZOUGA:
but you can do this concurrently... say split the work between five different threads...
I do not know how this is done in java but I suppose this can be done..

import java.io.FileInputStream;
import java.nio.ByteBuffer;
import java.nio.channels.FileChannel;

class Main {
	 public static int x = 4; //increase the value of x as u desire :-) it determines the chunk size
	 public static final int SIZE = 1024 * x;

  public static void main(String[] args) throws Exception {
	    
    FileChannel channel = new FileInputStream( "graph44.txt" ).getChannel();
    ByteBuffer buffer = ByteBuffer.allocate(SIZE);
    channel.read(buffer);
    buffer.flip();
    while (buffer.hasRemaining()){
      //Do Whatever you want
    }
  }
}

Kobojunkie: public static void main(String[] args) throws Exception {


Scanner iFile = new Scanner(new FileReader("graph44.txt";

Graph graph = new Graph();

while(iFile.hasNext())
{

Node<String> a = new Node<String>(iFile.next());
Node<String> b = new Node<String>(iFile.next());
System.out.println(a + " " + b);
int aPosition = graph.indexOf(a);
int bPosition = graph.indexOf(b);

//What you have above is not good logic. You checked if there was a next and obtained Node<String> a, but you did not make sure there an iFile.next() before obtaining Node<String> b. This is a bug that could cause your program to fail

// If a does not exist in the graph yet.
//Try using a less than one instead of an equal to minus 1. The reason I say this is because no where in your code here do you actually set the value of aPosition and bPosition to -1, and in Java, the default value for integers is not really -1.

if(aPosition < 1)
aPosition = graph.addNode(a);
// If b does not exist in the graph yet.
if(bPosition == -1)
bPosition = graph.addNode(b);

Edge edge = new Edge(graph.getNodeAt(aPosition), graph.getNodeAt(bPosition));
graph.addEdge(edge);

}
}


Conclusion
============

It is likely that the program is failing somewhere in your code, but you aren't catching or handling the issue. Please try to unit test your class, and step throu7ggh this bit to find where the potential bugs may exist. Scanner class is not the problem.

Otuabaroku:
How I solved my challenge:
I used BufferedReader and removed the system.out.println(a+ " " + b) statement, since I deliberately included it to check if the data is actually read from the text file. I had three files to test, hence I created multiple thread that accomplished the task concurrently. this obviously required more memory; I added extra memory by doing for example java -XM1024M myclassname. The time it took to test the three test files reduced significantly and I was able to beat the deadline.

Once again thanks a lot Kobojunkie and Prince.