[Biopython-dev] [GSoC] GSoC python variant update

[Lenna Peterson]

I think my UML diagram may need a legend, or perhaps it should just be abandoned. I've written some skeleton code to try to avoid confusion about the pesky OO terms that have slightly different meanings for every language. 

https://gist.github.com/2649676

Regarding concerns about inheritance: I think the UML diagram implies 3 levels of inheritance. The only inheritance I intended was from abstract interfaces like Parser or Writer, that only contain non-implemented methods. Because I can't guarantee that all future parsers will have common attribute and method names,  the only solution I can see is to write an interface and inherit from that to make wrappers for each parser. Thank you to Eric for this link: (https://en.wikipedia.org/wiki/Fragile_base_class). The page states that the best way to avoid problems is to use an interface. Also thank you to Pjotr for the article about mixins (http://www.cs.utexas.edu/~lin/papers/aop03.pdf). I believe I'm using inheritance in a safe and helpful manner. 

James, 
I hope my clarification and skeleton code answer any questions you have about the implementation. 

Brad, 
I am using if statements to determine which parser to use, but I am still calling wrappers that inherit from an interface. 

Eric,
I looked at the structure of PDBParser. Is the idea that a user might pass in an instance of StructureBuilder that already contained some structure and add to it? Or is there another purpose that isn't jumping out at me? In my skeleton code, I used the example of StructureBuilder, but I'm not sure if there's an advantage to passing the object rather than the object's name. 

And finally, Brad and James, I will do my best to get more conversant with VCF etc. If I'm not a user, I can't be a capable developer. 

Looking forward to any more structural feedback! 

Cheers, 

Lenna