Here the Arabic set table of the Unicode, It's more easy to use Regex to filter such complex text.
This is an example for short vowels removing in PHP (I'm not a java programmer)
text.preg_replace("/[\x{064B}-\x{065F}]/u","")
There are more other vowels in Noble Quran you may need to add their ranges.
Just to be more accurate you may need to Normalize the Arabic text.