You'll only see blank cells when they have been created, but they have no 
contents.
If a cell has never been created in the first place, the cell iterator will 
just skip over it entirely; and when you specifically ask for it with 
sheet.getRow(y).getCell(x) you'll get a null value back.

If you need to deal with these cases, try iterating numerically instead:
 
        for (int i = 0; i < row.getLastCellNum(); i++) {
                Cell c = row.getCell(i);
                if (c == null) {
                        // ...
                } else {
                        switch (c.getCellType()) {
                                // ...
                        }
                }
        }

Hope that helps!

-- 
Alex Panayotopoulos

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