[Bioperl-l] [Proposed change] HSP::frame()
cjfields at uiuc.edu
Mon Apr 21 11:07:17 EDT 2008
I have noticed (in relation to bug 2485, http://bugzilla.open-bio.org/show_bug.cgi?id=2485)
that the Bio::Search::HSP::GenericHSP frame() method is implemented
very differently from strand(), start(), end(), and most other HSP
methods. The current behavior is to return an array of two values
(query and hit frame) under list conditions, the query frame if one
value is passed, and the subject frame if no value is passed under
scalar context and both under list context. The latter behavior is
unfortunately leading to the aforementioned bug above. The method is
also implied to be a getter/setter, but the implementation doesn't
allow that; it always sets to the instantiated values (in fact,
In order to fix that and make the interface more consistent I am
changing frame() to behave like strand(), etc., in that the first
argument is 'query/subject/hit/list' (default = 'query' if no arg
specified) and the rest optional values for setting, in query/subject
One issue: I can catch and imitate most of the older behavior with a
few additional checks, the one exception being the old frame() default
return value which is now 'query' (not context-dependent). If needed
we can change the default to 'hit', but I believe method consistency
is probably the better route, and I can always add a warning under old
API circumstances indicating the change.
I am also modifying HSPTableWriter to print frame_hit and frame_query
(previously it was only printing 'frame', which implied the hit
frame). I can see this being an issue with anyone expecting 'frame'
instead of 'frame_hit'; I could hack in a fix for that if needed.
If there aren't any objections or suggestions, I'll commit this in the
next day or two.
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