[pygr-notify] Issue 57 in pygr: Consider simplifying SeqPath start, stop attribute handling

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Status: New
Owner: cjlee112
Labels: Type-Enhancement Priority-Low Milestone-Release0.8

New issue 57 by cjlee112: Consider simplifying SeqPath start,stop attribute  
handling
http://code.google.com/p/pygr/issues/detail?id=57

The original design of SeqPath included the possibility of "open-ended
sequences", i.e. coordinate systems that could be *expanded* after the
sequence object was first created.  I think VirtualSeq may actually use
this behavior, but I doubt any users are aware either of this capability or
of VirtualSeq for that matter.

This "feature" made the start,stop coordinate handling much more
complicated (it must allow for the possibility that one of the two
coordinates could be None (not yet set by the user), so it must defer
bounds checking until that coordinate is finally set!).

I propose to nuke all this complexity, in favor of the simple rule that
both coordinates must be specified when constructing a SeqPath object.

SeqPath is the base class for all sequence and sequence interval objects,
so any bugs here would affect a lot of applications.  If we make changes
here, we should test them very thoroughly.  The current SeqPath code may be
complicated, but I'm not aware of any signs of bugs...

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