code: public static Matrix grayOutCEOrig(Atom[] ca2, int rows, int cols,
  			CECalculator calculator, Matrix origM, int blankWindowSize,
  			double[] gradientPolyCoeff, double gradientExpCoeff) {
  
  		if (origM == null) {
  			origM = new Matrix(calculator.getMatMatrix());
  		}
  
  		// symmetry hack, disable main diagonal
  
  		for (int i = 0; i < rows; i++) {
  			for (int j = 0; j < cols; j++) {
  				int diff = Math.abs(i - j);
  
  				double resetVal = getResetVal(origM.get(i, j), diff,
  						gradientPolyCoeff, gradientExpCoeff);
  
  				if (diff < blankWindowSize) {
  					origM.set(i, j, origM.get(i, j) + resetVal);
  
  				}
  				int diff2 = Math.abs(i - (j - ca2.length / 2)); // other side
  
  				double resetVal2 = getResetVal(origM.get(i, j), diff2,
  						gradientPolyCoeff, gradientExpCoeff);
  
  				if (diff2 < blankWindowSize) {
  					origM.set(i, j, origM.get(i, j) + resetVal2);
  
  				}
  			}
  		}
  		return origM;
  	}
docs: Grays out the main diagonal of a duplicated distance matrix.
  
  @param ca2
  @param rows
  Number of rows
  @param cols
  Number of original columns
  @param calculator
  Used to get the matrix if origM is null
  @param origM
  starting matrix. If null, uses
  {@link CECalculator#getMatMatrix()}
  @param blankWindowSize
  Width of section to gray out
  @param gradientPolyCoeff
  @param gradientExpCoeff
  @return