Rubik Cube - Aligning Middle Side Color With Bottom Middle Side Color

I am trying to align the core/middle side color of a cube, index 4, with the bottom middle color of the same side, index 7. (Each side has values 0-8 where 0 - is the top left corner, 1 is the top mid corner, 2 is the top right corner, 3 is the middle left corner, etc).

In addition to lining up those two colors, I am also making sure that the neighbor color of index 7(the color that it is attached), in this case the bottom color, matches with the top core/middle color. I will attach some pictures and a print out to show what I am talking about...

However, in my code when I am trying to align all of these up together, it does not go into the while loop. Each of the loops essentially is trying to get a match of same color with index 4 and 7, as well as making sure that index 7's neighbor color (the bottom color, in this case) matches with the top color.

Here is what I have tried:

private void alignSideColor(){//make the bottom colors neighbor match with a middle side value and rotate it to the top, for the top cross

if(cube.bottom.square[1].charAt(0) == topColor){
while(cube.front.square[7].charAt(0) != frontColor && cube.bottom.square[1].charAt(0) != topColor){
rotateBottomClockwise(1);
System.out.println("Trying to align side color...");

[Code] .....

The print out of the ELSE IF is:
alignment is: W-G and tops: R-R
NOW ITS ALIGNED
even though the sides, index 4 and 7, are NOT aligned with each other

I have also tried the same thing but with out the 2nd condition in each while loop, and although is DOES enter the while loop, it does not perform correctly -- index 4 and 7 WILL have matches colors, but it does not check to see if index 7's neighbor matches with the top color.

Here is how it prints out
** ** ** G7 B6 Y1 ** ** **//this portion is the back of the cube
** ** ** R6 W5 O4 ** ** **
** ** ** R3 W2 O1 ** ** **
B3 G4 Y9 W9 O8 Y7 W3 B4 G9//this portion is the left, top, and right of the cube
B2 G5 R8 W4 R5 Y6 O2 B5 G8
O7 W8 R9 B7 B8 B9 R1 R4 R7
** ** ** O3 O6 O9 ** ** **//this portion is the front of the cube
** ** ** Y2 Y5 Y8 ** ** **
** ** ** B1 G6 W7 ** ** **
** ** ** Y3 Y4 G1 ** ** **//this portion is the bottom the cube
** ** ** R2 O5 G2 ** ** **
** ** ** W1 W6 G3 ** ** **

Here is the cube showing the top, left and front side

Here is the left and bottom side. As you can see index 4, G5 -- yes that is a 5 lol -- does not have the same color as index 7, W8.

I need to rotate the bottom until W8 is aligned with a middle white value. An examples of a neighbor is: W8-R2