[Bioperl-l] Bio::Graphics off by one?

Scott Cain cain at cshl.edu
Wed Feb 22 16:29:21 UTC 2006

Hi Dave,

I took the example code you posted a few days ago and added a few
motifs, one that goes from 1 to 10, and one that goes from 35 to 44 (the
last residue), which results in the attached graphic.

As Lincoln pointed it, the features are drawn from the beginning (1 and
35), and through the last residue (up to but not touching 11 and 45).
So the space between 35 and 36 corresponds to residue 35.  That's the
way it works.


On Wed, 2006-02-22 at 15:13 +0000, Dave Howorth wrote:
> Scott Cain wrote:
> > I don't know if this helps at all, but you could think of that 45 tick
> > mark as the termination, since the space between the 44th and the 45th
> > tick mark corresponds to your 44th residue.
> Yes, that's the way I do think of it and that's the way I expect 
> everybody else to think of it.
> But the numbers need to match the residues in any case. ie. the numbers 
> need to match the spaces not the tick marks, if the spaces match the 
> residues.
> > I suppose it is a matter of correctly training your users :-)
> The important thing is to have a consistent model, then it's easy to 
> explain to users.
> Cheers, Dave
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Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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