Program out put:
Starting 4x4 game, words from enable1.txt, min word length 3.
Reading word list from file enable1.txt... Read 172823 words.
Building this game's lexicon... done.
 
Stringpos 0
word to check: doe
wordToCheck.length 3
 Cur Center:  0
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 0
 
 row is: 0
 col is: 0
row: 0 and col: 0
 row is: 0
 col is: 0
Grid[row][col] V
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 1
 
 row is: 0
 col is: 0
row: 0 and col: 1
 row is: 0
 col is: 1
Grid[row][col] I
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 2
 
 row is: 0
 col is: 1
row: 0 and col: 2
 row is: 0
 col is: 2
Grid[row][col] M
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 3
 
 row is: 0
 col is: 2
row: 0 and col: 3
 row is: 0
 col is: 3
Grid[row][col] P
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 4
 
 row is: 0
 col is: 3
row: 1 and col: 0
 row is: 1
 col is: 0
Grid[row][col] E
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 5
 
 row is: 1
 col is: 0
row: 1 and col: 1
 row is: 1
 col is: 1
Grid[row][col] E
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 6
 
 row is: 1
 col is: 1
row: 1 and col: 2
 row is: 1
 col is: 2
Grid[row][col] S
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 7
 
 row is: 1
 col is: 2
row: 1 and col: 3
 row is: 1
 col is: 3
Grid[row][col] H
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 8
 
 row is: 1
 col is: 3
row: 2 and col: 0
 row is: 2
 col is: 0
Grid[row][col] O
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 9
 
 row is: 2
 col is: 0
row: 2 and col: 1
 row is: 2
 col is: 1
Grid[row][col] E
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 10
 
 row is: 2
 col is: 1
row: 2 and col: 2
 row is: 2
 col is: 2
Grid[row][col] M
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 11
 
 row is: 2
 col is: 2
row: 2 and col: 3
 row is: 2
 col is: 3
Grid[row][col] H
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 12
 
 row is: 2
 col is: 3
row: 3 and col: 0
 row is: 3
 col is: 0
Grid[row][col] A
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 0
word to check: doe
Looking for letter : d
wordToCheck.length 3
 Cur Center:  0
 X is : 13
 
 row is: 3
 col is: 0
row: 3 and col: 1
 row is: 3
 col is: 1
Grid[row][col] D
 
SelectedSquare[row][col] == unselected if false: false
 
 row is: 3
 col is: 1
Found & not selected
 Next row: 3
Next col 1
 
Looking for Letter To Check  d
Found letter at 13
Found letter at row: 3 and col: 1
 
 
Selected squre should be true: true
At Spot D
Next Letter is: o
Current Row and Column : 3 1
Found lettertocheck: o
Found it at: 121
next center: 13
List with Locations in order -_-__-_-== 
List with Locations in order: 13
locaTions in order 13
WordToCheck doe
 
 
Stringpos 1
word to check: doe
wordToCheck.length 3
 Cur Center:  13
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 0
 
 row is: 3
 col is: 0
row: 0 and col: 0
 row is: 0
 col is: 0
Grid[row][col] V
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 1
 
 row is: 0
 col is: 0
row: 0 and col: 1
 row is: 0
 col is: 1
Grid[row][col] I
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 2
 
 row is: 0
 col is: 1
row: 0 and col: 2
 row is: 0
 col is: 2
Grid[row][col] M
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 3
 
 row is: 0
 col is: 2
row: 0 and col: 3
 row is: 0
 col is: 3
Grid[row][col] P
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 4
 
 row is: 0
 col is: 3
row: 1 and col: 0
 row is: 1
 col is: 0
Grid[row][col] E
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 5
 
 row is: 1
 col is: 0
row: 1 and col: 1
 row is: 1
 col is: 1
Grid[row][col] E
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 6
 
 row is: 1
 col is: 1
row: 1 and col: 2
 row is: 1
 col is: 2
Grid[row][col] S
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 7
 
 row is: 1
 col is: 2
row: 1 and col: 3
 row is: 1
 col is: 3
Grid[row][col] H
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 1
word to check: doe
Looking for letter : o
wordToCheck.length 3
 Cur Center:  13
 X is : 8
 
 row is: 1
 col is: 3
row: 2 and col: 0
 row is: 2
 col is: 0
Grid[row][col] O
 
SelectedSquare[row][col] == unselected if false: false
 
 row is: 2
 col is: 0
Found & not selected
 Next row: 2
Next col 0
 
Looking for Letter To Check  o
Found letter at 8
Found letter at row: 2 and col: 0
 
 
Selected squre should be true: true
At Spot O
Next Letter is: e
Current Row and Column : 2 0
Found lettertocheck: e
Found it at: 80
next center: 8
List with Locations in order -_-__-_-== 
List with Locations in order: 13
List with Locations in order: 8
locaTions in order 8
WordToCheck doe
 
 
Stringpos 2
word to check: doe
wordToCheck.length 3
 Cur Center:  8
 
NotABaseCase: 
 
Stringpos 2
word to check: doe
Looking for letter : e
wordToCheck.length 3
 Cur Center:  8
 X is : 0
 
 row is: 1
 col is: 3
row: 0 and col: 0
 row is: 0
 col is: 0
Grid[row][col] V
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 2
word to check: doe
Looking for letter : e
wordToCheck.length 3
 Cur Center:  8
 X is : 1
 
 row is: 0
 col is: 0
row: 0 and col: 1
 row is: 0
 col is: 1
Grid[row][col] I
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 2
word to check: doe
Looking for letter : e
wordToCheck.length 3
 Cur Center:  8
 X is : 2
 
 row is: 0
 col is: 1
row: 0 and col: 2
 row is: 0
 col is: 2
Grid[row][col] M
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 2
word to check: doe
Looking for letter : e
wordToCheck.length 3
 Cur Center:  8
 X is : 3
 
 row is: 0
 col is: 2
row: 0 and col: 3
 row is: 0
 col is: 3
Grid[row][col] P
 
SelectedSquare[row][col] == unselected if false: false
 
 
NotABaseCase: 
 
Stringpos 2
word to check: doe
Looking for letter : e
wordToCheck.length 3
 Cur Center:  8
 X is : 4
 
 row is: 0
 col is: 3
row: 1 and col: 0
 row is: 1
 col is: 0
Grid[row][col] E
 
SelectedSquare[row][col] == unselected if false: false
 
 row is: 1
 col is: 0
Found & not selected
 Next row: 1
Next col 0
 
Looking for Letter To Check  e
Found letter at 4
Found letter at row: 1 and col: 0
 
 
Exception in thread "AWT-EventQueue-0" java.lang.StringIndexOutOfBoundsException: String index out of range: 3
	at java.lang.String.charAt(Unknown Source)
	at b0ggleLayout.FindWord(b0ggleLayout.java:107)
	at b0ggleLayout.FindWord(b0ggleLayout.java:126)
	at b0ggleLayout.FindWord(b0ggleLayout.java:126)
	at BogglePlayer.isOnBoard(BogglePlayer.java:26)
	at BoggleGUI.checkAndAddWordHuman(BoggleGUI.java:127)
	at BoggleGUI$WordEntryField$1.actionPerformed(BoggleGUI.java:682)
	at javax.swing.JTextField.fireActionPerformed(Unknown Source)
	at javax.swing.JTextField.postActionEvent(Unknown Source)
	at javax.swing.JTextField$NotifyAction.actionPerformed(Unknown Source)
	at javax.swing.SwingUtilities.notifyAction(Unknown Source)
	at javax.swing.JComponent.processKeyBinding(Unknown Source)
	at javax.swing.JComponent.processKeyBindings(Unknown Source)
	at javax.swing.JComponent.processKeyEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
	at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(Unknown Source)
	at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(Unknown Source)
	at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Source)
	at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
______


import java.util.ArrayList;
import java.util.List;


public class b0ggleLayout {
	
	private String[][] Grid;
	private String[] Board;
	private boolean[][] SelectedSquare;
	List<String> IntRepofStringOnBoard;
	List<Integer> LocationsInOrder = new ArrayList<Integer>();
	
	//sets up the boggle board for use
	//this method works for sure
	
	public String[][] AssignGrid(String[] letterArray){
		Board = letterArray;
		SelectedSquare = new boolean[Board.length][Board.length];
		double sideLengthdbl = Math.sqrt(letterArray.length);
		int sideLengthint = (int)sideLengthdbl;
			Grid = new String[sideLengthint][sideLengthint];
		for (int x = 0; x < letterArray.length; x++){
			int row=x/4;
			int col=x%4;
			Grid[row][col]=letterArray[x];
		} 
		
		return Grid;
	}

	
	public List FindWord(String wordToCheck, int StringPos, int NextCenter, int BoardPosition, int row, int col){
		System.out.println(" ");
		System.out.println("Stringpos " + StringPos);
		System.out.println("word to check: " + wordToCheck);
		System.out.println("wordToCheck.length " + wordToCheck.length());
		System.out.println(" Cur Center:  " + NextCenter);

		
 		for(int x = 0; x < BoardPosition; x++){
 			System.out.println(" "); //finding the first letter linearly
 	
 			if(wordToCheck.length()+1<StringPos ){  //base case when the StringPosition to be checked is beyond the length of the Word To Check. 
 				System.out.println("Base Case!: ");
				
 				for(int y = 0; y < LocationsInOrder.size(); y++){ /* simple loop to see
				       	                                           * if the int representations
				       	                                           * of the string locations are
				       	                                           * being added in the 'correct 
				       	                                           * order
				       	                                           *  */
				
				System.out.println("List with Locations in order: " + LocationsInOrder.get(y));
				}
				System.out.println("locaTions in order "  + LocationsInOrder.get(StringPos));			
				System.out.println("WordToCheck " + wordToCheck);
				System.out.println(" ");
 				
				return LocationsInOrder;
 			} 
 			else{
 				System.out.println("NotABaseCase: ");
 				System.out.println(" ");
 				System.out.println("Stringpos " + StringPos);
 				System.out.println("word to check: " + wordToCheck);
 				System.out.println("Looking for letter : "  +  wordToCheck.charAt(StringPos));
 				System.out.println("wordToCheck.length " + wordToCheck.length());
 				System.out.println(" Cur Center:  " + NextCenter);
 				System.out.println(" X is : " + x);
 				System.out.println(" ");
 				System.out.println(" row is: " + row);
 				System.out.println(" col is: " + col); // I beleive the problem lays somewhere here
 				int oldrow = row;                      // I can't quite think the recursion out correctly here
 				int oldcol = col;
 				String LetterToCheck = wordToCheck.charAt(StringPos)+"";
	 			row = x/Grid.length;
				col = x%Grid.length;
				int CurrentPosition = row * Grid.length+col;
					int nextrow = CurrentPosition/Grid.length; // trying to work some magic
					int nextcol = CurrentPosition%Grid.length;
				System.out.println("row: " + row + " and col: " + col);
				System.out.println(" row is: " + row);
 				System.out.println(" col is: " + col);
 				
				System.out.println("Grid[row][col] " + Grid[row][col]);
				System.out.println(" ");
				System.out.println("SelectedSquare[row][col] == unselected if false: " + SelectedSquare[row][col] );
				System.out.println(" ");
	 			if (LetterToCheck.equalsIgnoreCase(Grid[row][col]) == true && SelectedSquare[row][col] == false ){   //found letter & not previously selected
	 				System.out.println(" row is: " + row);
	 				System.out.println(" col is: " + col);
	 
	 					System.out.println("Found & not selected");
	 					
	 					System.out.println(" Next row: " + nextrow);
	 					System.out.println("Next col " + nextcol); 
	 					System.out.println(" ");
	 					System.out.println("Looking for Letter To Check  " + LetterToCheck);
						System.out.println("Found letter at " + CurrentPosition);
						System.out.println("Found letter at row: " + row + " and col: " + col);
						LocationsInOrder.add(CurrentPosition); // add spot to List of ints to be returned
						System.out.println(" ");
						
						SelectedSquare[row][col]=true; // mark unselectable
						
						System.out.println(" ");
						if (wordToCheck.charAt(StringPos+1)+""!=null){
							String NextLetterToCheck = wordToCheck.charAt(StringPos+1)+""; // get the next letter to check
							NextCenter = FindAround(CurrentPosition, NextLetterToCheck, nextrow, nextcol) ; //next center is the next center to 
						}
						//check around for the next letter
						System.out.println("next center: " + NextCenter);
							if (NextCenter < -50){ // failure case 
								System.out.println("Not Found Around!"); // the next letter is not around this value
								LocationsInOrder.remove(LocationsInOrder.size()-1);
							}
							else{
							System.out.println("List with Locations in order -_-__-_-== ");
							for(int y = 0; y < LocationsInOrder.size(); y++){ // same loop as earlier to check for validity
								System.out.println("List with Locations in order: " + LocationsInOrder.get(y));
							}
							System.out.println("locaTions in order "  + LocationsInOrder.get(StringPos));			
							System.out.println("WordToCheck " + wordToCheck);
							System.out.println(" ");
					
							FindWord(wordToCheck, StringPos+1, NextCenter, BoardPosition, oldrow, oldcol); // recursive search for finding the next value
							}
						}
			}
 		}
		return LocationsInOrder;
	}
	
	public int FindAround(int CenterTile, String NextLetter, int row, int col){
	
		System.out.println("Selected squre should be true: " + SelectedSquare[row][col]);
		System.out.println("At Spot " + Board[CenterTile]);
		System.out.println("Next Letter is: " + NextLetter);

		/*positions to test
		 * 1 row,col-1     left
		 * 2 row-1,col-1   left & up
		 * 3 row-1,col     up
		 * 4 row-1,col+1   up & right
		 * 5 row,col+1     right
		 * 6 row+1,col+1   right & down 
		 * 7 row+1,col     down
		 * 8 row+1,col-1   down & left
		 * 
		 */
		System.out.println("Current Row and Column : " + row + " " + col);
	
			if(row<0 || row > 3 || col <0 || col > 3 ){
				System.out.println("not on board");
				return -101;
			}

			if( ((row >= 0) && (col-1 >=0)) && NextLetter.equalsIgnoreCase(Grid[row][col-1])==true){
				System.out.println("Found lettertocheck: " + NextLetter);
				System.out.println("Found it at: " + row * Grid.length+col);
				return row * Grid.length+col;
			}
			
			if( ((row-1) >=0 && (col-1 >=0)) && NextLetter.equalsIgnoreCase(Grid[row-1][col-1])==true){
				System.out.println("Found lettertocheck: " + NextLetter);
				System.out.println("Found it at: " + row * Grid.length+col);
				return row * Grid.length+col;
			}

			if( ((row-1) >= 0 && (col <= 3)) && NextLetter.equalsIgnoreCase(Grid[row-1][col])==true){
				System.out.println("Found lettertocheck: " + NextLetter);
				System.out.println("Found it at: " + row * Grid.length+col);
				return row * Grid.length+col;
			}
	
			if( ((row-1) >= 0 && (col+1 <=3 )) && NextLetter.equalsIgnoreCase(Grid[row-1][col+1])==true){
				System.out.println("Found lettertocheck: " + NextLetter);
				System.out.println("Found it at: " + row * Grid.length+col);
				return row * Grid.length+col;
			}
	
			if( ((row >= 0) && (col+1 <= 3)) && NextLetter.equalsIgnoreCase(Grid[row][col+1])==true){
				System.out.println("Found lettertocheck: " + NextLetter);
				System.out.println("Found it at: " + row * Grid.length+col);
				return row * Grid.length+col;
			}
	
			if( ((row+1 <=3 ) && (col >=0 )) && NextLetter.equalsIgnoreCase(Grid[row+1][col])==true){
				System.out.println("Found lettertocheck: " + NextLetter);
				System.out.println("Found it at: " + row * Grid.length+col);
				return row * Grid.length+col;
			}
	
			if(  ((row+1 <= 3) && (col-1 >= 0)) && Grid[row+1][col-1]==NextLetter){
				System.out.println("Found lettertocheck: " + NextLetter);
				System.out.println("Found it at: " + row * Grid.length+col);
				return row * Grid.length+col;
			}
		
			if( ((row+1 <= 3) && (col+1 <= 3)) && Grid[row+1][col+1]==NextLetter){
				System.out.println("Found lettertocheck: " + NextLetter);
				System.out.println("Found it at: " + row * Grid.length+col);
				return row * Grid.length+col;
			}
		else 
			System.out.println("LetterToCheck: " + NextLetter);
			System.out.println("LetterToCheck is not found In FindAround");
		
		return -100;

	}
}