Updated "new Class" to "Class->new()" per Perl Best Practices.

Hello All -

This is my first Pull request ever on git hub, so please let me know if there's anything else I should do along with this request.

I ran through the Bioperl modules replacing the "new Class" indirect object invocations to "Class->new()". Indirect object invocation can lead to subtle errors. (As per http://www.bioperl.org/wiki/Bioperl_Best_Practices and 'Modern Perl').

Regards,

Benjamin