Consider simplifying SeqPath start,stop attribute handling

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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...

Original issue reported on code.google.com by cjlee...@gmail.com on 7 Jan 2009 at 4:49

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implemented easily and immediately passed all tests, so I have merged this into 
the
master branch.  Let's see if all the megatests pass.  If so, let's keep this 
for the
0.8 release.

Original comment by cjlee...@gmail.com on 13 Jan 2009 at 3:49

• Changed state: Fixed

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Original comment by mare...@gmail.com on 21 Feb 2009 at 2:07

• Changed state: FixedNeedsReview

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Hi Titus,
could you please verify this simplification of the SeqPath code, and then 
change its
status to Closed?  We are now requiring that each fix be verified by someone 
other
than the developer who made the fix.  I guess you could do this as part of the
planned code review of the sequence / seqdb code.

Thanks!

Chris

Original comment by cjlee...@gmail.com on 5 Mar 2009 at 12:26

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Original comment by mare...@gmail.com on 13 Mar 2009 at 1:01

• Added labels: reviewby-the.good.doctor.is.in

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Looks good. 

This is also a fairly complicated changeset that I can't claim to have tested 
out in
the before state (as one would need to go roll back everything to January)

I will close this since it has been commited.

Original comment by istvan.a...@gmail.com on 14 May 2009 at 2:42

• Changed state: Closed