[Bioperl-l] use of no_* to mean 'number_of', negative booleans

[Chris Fields]

All,

I've noticed a few methods in bioperl with names like 'no_Foo' that  
mean 'number of Foo' (such as SimpleAlign's no_sequences).  The  
problem I foresee are possible ambiguities, particularly with negative  
boolean checks (eg 'no_Foo' could also mean 'this instance contains no  
Foo'), something that BioPerl also has with various settings.

I suggest we alias these as num_* to disambiguate that.  There's no  
easy way to change already in-place flag setting w/o going through a  
deprecation cycle, but we can promote using positive booleans where  
possible (eg 'is_foo' or 'has_foo' instead of 'no_foo').  We can leave  
the older 'no_*' methods as is for the time being and maybe deprecate  
them later.

If no one has objections I'll add these in as needed.

chris