[DAS] Bio::Das::SegmentI methods

[Eric Just]

Hi, its me again

I found another issue ( probably a known issue ).  The Bio::Das::SegmentI 
interface defines

overlapping_features
contained_features
contained_in

methods.  These do not seem to work with the Bio::Das object (using with 
GBrowse).  It seems that the rangetype argument gets passed to 
Bio::Das->features method but this method does not do anything with the 
rangetype argument.  I can assist in coding this functionality if it is not 
already planned or there are other issues.

It also seems that the methods themselves have bugs:

each one has lines:

   my @args = $_[0] !~ /^-/ ? (@_,         -rangetype=>'overlaps')
                            : (-types=>\@_,-rangetype=>'overlaps');


I think it should be

   my @args = $_[0] =~ /^-/ ? (@_,         -rangetype=>'overlaps')
                            : (-types=>\@_,-rangetype=>'overlaps');


so that you are passing in the whole hash if you match /^-/

I don't know if this bug should actually go to bioperl, if so I can post it 
on their bugzilla.

Thanks again,
Eric





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Eric Just
e-just at northwestern.edu
dictyBase Programmer
Center for Genetic Medicine
Northwestern University
http://dictybase.org

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