[Bioperl-l] strange error after changing to RC1.5

[Allen Day]

> What are these overloaded methods for?
> Who/What is calling ->ne()?

The SeqFeatureI class has been made, under the hood, to use the 
Bio::AnnotationCollection for storing annotations.  
Bio::AnnotationColleciton holds Bio::AnnotationI objects, not the simple 
strings that were held in older SeqFeatureI implementing classes.  There 
is still a lot of code in bioperl (and bioperl-db I take it) that wants to 
treat the annotations as strings, so we add overloading to allow this to 
happen.  No one is calling the eq() method direcly, it gets triggered when 
someone does like this:

  if ( $obj1->dbxref eq $obj2->dbxref ) { }

It sounds like this might not be what is causing the problem for you, but 
I thought you should be aware as you debug.

-Allen