[Bioperl-guts-l] [Bug 2173] Bio::Graphics::Glyph::stackedplot always generates homogenous histogram

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Jan 2 12:36:13 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2173





------- Comment #1 from cjfields at uiuc.edu  2007-01-02 12:36 -------
(In reply to comment #0)
> I am using the Bio::Graphics::Glyph::stackedplot with an older version of
> bioperl which does not have this glyph. The result is always a homogenous
> stacked histogram, i.e. all bars are in the same uniform size. I have traced
> down the bug to the 'clip' method of this class (stackedplot.pm) , which
> assumes $value is a scalar and not an array reference, and thus always returns
> 0 or 1 from the input vector. Thus all bars get the same size, regardless of
> their series values.
> 
> in stackedplot.pm When I replace the line :
>         my $v      = $self->clip($value,$min,$max);
> with:
>         my $v      = $value->[0]; # values must contain a single scalar between
> 0 and 1.
> 
> the bug is fixed.

In general we do not support mixing Bioperl modules from different versions,
simply b/c classes rely on one another to the extent that any changes in one
may have dramatic and unexpected consequences on other related classes.  

As I see it there are two options:

1)  Try installing an updated and complete bioperl version that comes with
Bio::Graphics::Glyph::stackedplot (either the recently released 1.5.2 or CVS),
which may fix the problem.

2)  We can try adding the fix in, but this will rely mostly on Lincoln's or
Scott's input.


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