Something

public class Foo()
{
        public  Process runProcess() throws IOException
	{
		String execCmd = getTargetAlgorithmExecutionCommand();
		System.out.println(execCmd);
		Process proc = Runtime.getRuntime().exec(execCmd,null, new File(execConfig.getAlgorithmExecutionDirectory()));
	
	
		return proc;
	}

	public void processRunLoop(Scanner procIn)
	{
		while(procIn.hasNext())
		{
			String line = procIn.nextLine();
			processLine(line);
			
		}	
	}
	
	@Override
	public void run() {
			
		Process proc;
		
		
	        proc = runProcess();
	        Scanner procIn = new Scanner(proc.getInputStream());
		
	        processRunLoop(procIn);
         }

}