[Bioperl-l] Re: Bio::FeatureHolderI interface confusion

Paul Edlefsen pedlefsen at systemsbiology.org
Wed Jun 18 13:26:30 EDT 2003

I've been keeping silent on this (didja notice?), but as Ewan predicted, I have views here.

The idea of protocols -- per-method contracts -- intrigues me; Perl offers the can() facility, which could be used here.  I personally have not experienced any necessity for this, but I'm willing to believe that y'all have.

Perl, as we are painfully aware, does not enforce contracts.  In my experience as a Java developer and a bioperl developer I have come to appreciate the necessity of enforcing contracts; my interpretation of the complexity of bioperl -- the near impossibility of treating it as a component model -- is that a failure to enforce interface contracts is the principal stumbling point.

It has been mentioned in this thread that complex interfaces are devised and then ignored.  I suspect that the concept of enforcing these interfaces is terrifying at first blush: does that mean that I have to actually implement all of this crap?  There's a couple of points to consider before dismissing enforcement, though: 1) if we used interfaces correctly then they would not be impossible to implement; 2) interface contracts may allow null-responses (eg. if a SeqFeatureI isa FeatureHolderI it does not *necessarily* contain subfeatures, but you can ask it how many subfeatures it has (it has 0); although FeatureHolderI presently asserts the often-un-supportable contract that FeatureHolderI implementers always accept the addition and removal of subfeatures, this is not a failure in Object Oriented Programming, it is a failure in our FeatureHolderI contract design).

I have personally consolodated the FeatureHolderI variants, so I'm pretty familiar with this particular area of the bioperl library.  I found that this contract is duplicated (eg. GFFI, DasI, FeatureHolderI, SeqFeature::CollectionI), unused (eg. CollectionI), and ignored (eg. gbrowse accesses all feature providers as if they are GFF.pm).  On what we affectionately refer to as the 'freaky dev branch', branch-1-2-collection, I have unified these things into one interface, called Bio::SeqFeature::CollectionI (which inherits, for backwards compatability, from FeatureHolderI).  SeqFeatureI is capable of holding subfeatures, so on this branch Bio::SeqFeatureI isa Bio::SeqFeature::CollectionI.  I have also made a version of gbrowse that uses this interface, as well as a data provision interface called Bio::DB::FeatureProviderI, that fetches feature collections from a backing store.

I agree that the interfaces presented to novices should be few and simple and straightforward.  I do not think, though, that the interfaces presented to programmers need be otherwise.  I am not the best designer of interfaces, and those that I have designed might not be the best solution, but if we as a community can commit to the concept that an interface is an inviolable contract and that use of interfaces is prerequisite to component-oriented development, then the failures in an interface will lead not to its violation, ignorance, or duplication, but to its correction.

I can see that the culture of bioinformatics software development is presently disinclined towards self-enforcement of software design contracts.  We will not abandon bioperl, though; the only direction forward (IMO) is through some sort of refactoring.  If we cannot rely on contributors to enforce interface contracts, could we perhaps enforce them through some software solution (in Java or C++ this is the compiler's job)?  Like runnable synopses, could we not test *on checkin*, or at least in the test suite, that interface contracts are enforced?

If anyone is interested, to this end I have created a very small number of initial interface tests, in the ti directory, on the freaky dev branch.  The ultimate idea is that the ISA hierarchy will be climbed and anything claiming to support an interface will have to pass the test corresponding to that interface.  This is, after all, what ISA means: it is safe to think of me as a BLAH.  Why not test this?

Okay, thanks for reading my rant.


|    o-o     Paul T. Edlefsen
|    o---o   Computational Biologist
|  o----o    mailto:paul at systemsbiology.org
| O----O     Institute for Systems Biology
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