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[netcdf-java] Converting Lat, Lon pair into a specific Coordinate System

I have some data which is not in a WGS-84 projection and i need it to be that to match a map that i am viewing that is in the WGS-84 Ellipsoidal projection.
Is there an easy way to read non-WGS84 lat, lon pairs from a netcdf file and convert them on the fly to a WGS-84 lat,lon pair?? 

thanks!

Chad
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