import java.awt.*;
import java.awt.event.*;
import java.awt.geom.*;
import javax.swing.*;
import java.io.*;
import java.util.Scanner;

	private void saveFile(File file) //throws IOException
	{

		FileWriter fw = null;	
			
		try
		{
			fw = new FileWriter(file);
		}
		
		catch (IOException e)
		{
			System.out.println("Usage : java FileIOdemo <filename> " );
			System.exit(0);
		}
		
		BufferedWriter bw = new BufferedWriter(fw);
		PrintWriter outFile = new PrintWriter(bw);

		for (int i = 0 ; i < eng.returnRowCount() ; i++)
		{
			for (int j = 0 ; j < eng.returnColumnCount(i) ; j++)
				outFile.print(booleanToString(eng.getCell(i, j)) + " ") ;
			outFile.println();
		}
		
		outFile.close();
	}
	
	private void openFile(File file) //throws IOException
	{
		
		try
		{
			scan = new Scanner(file);
		}
		catch (IOException e)
		{
			System.exit(0);
		}
		
		String s1;
		
		s1 = scan.nextLine();
		String tmp[] = s1.split(" ");
		
		for (int i=0; i < eng.returnRowCount(); i++)
		{
			s1 = scan.nextLine();
			tmp[] = s1.split(" ");
			
			for (int j=0; j < eng.returnColumnCount(0); j++)
			{
				eng.setCell(i, j, stringToBoolean(tmp[j]));
				System.out.println (i + " " + j);
			}
		}
	}
	
	public static final boolean stringToBoolean(String str) 
	{
	        if (str.equals("0")) {
	            return false;
	        }
	        //if it's non false, it's true by definition
	        else 
	        	return true;
	}
	
	public static final int booleanToString(boolean bool)
	{
		if (bool)
		{
			int a = 1;
			return a;
		}
		else 
		{
			int a = 0;
			return a;
		}
		
	}

}

Upon running this code to output, I get a 100x100 grid (0-99 x 0-99), which is correct.

However, when trying to take that back in as input, it processes up through row #98, column 99, and then throws this exception:
98 99 <--- this being the output generated by nested for loops to show which cell the loop is handling.
Exception in thread "AWT-EventQueue-0" java.util.NoSuchElementException: No line found
        at java.util.Scanner.nextLine(Scanner.java:1471)
        at GridPanel.openFile(GridPanel.java:252)
        at GridPanel.access$700(GridPanel.java:8)
        at GridPanel$ComboListener.actionPerformed(GridPanel.java:196)
        at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1197)
        at javax.swing.JComboBox.setSelectedItem(JComboBox.java:561)
        at javax.swing.JComboBox.setSelectedIndex(JComboBox.java:597)
        at javax.swing.plaf.basic.BasicComboPopup$Handler.mouseReleased(BasicComboPopup.java:808)
        at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:232)
        at java.awt.Component.processMouseEvent(Component.java:5554)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
        at apple.laf.AquaComboBoxUI$AquaComboPopup$1.processMouseEvent(AquaComboBoxUI.java:443)
        at java.awt.Component.processEvent(Component.java:5319)
        at java.awt.Container.processEvent(Container.java:2010)
        at java.awt.Component.dispatchEventImpl(Component.java:4021)
        at java.awt.Container.dispatchEventImpl(Container.java:2068)
        at java.awt.Component.dispatchEvent(Component.java:3869)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
        at java.awt.Container.dispatchEventImpl(Container.java:2054)
        at java.awt.Window.dispatchEventImpl(Window.java:1774)
        at java.awt.Component.dispatchEvent(Component.java:3869)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
        at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)