I have a java program that seems to work okay when I'm debugging it or running it from the Eclipse IDE. But when I export it into a jar file and run it through a jnlp it hangs at a certain step.

I'm not exactly sure but I think the problem might be a step when I'm converting a file into a text file.

private File INPUT;
	private JTextArea innerTextArea;

	    protected boolean rangeArgsProvided = false;
     Converter(File INPUT, JTextArea innerTextArea) { 
    	 this.INPUT = INPUT;
         this.innerTextArea = innerTextArea;

public File doInBackground() {//replaces doWork
  	File convertedBAM = new File("convertedFile.txt");
	int convertstepcounter=0, convertstepcounter2=0;
I'm not specifying any specific location to get or put the file convertedFile.txt in. Its just a variable that will take the converted information and then pass on in a later step and not be used anymore. Is there a possible problem with this or is the hanging likely due to something else?

PS the jar runs from the Local Settings/Temp Folder in windows. Someone else made it that way.