Nathan S. Haigh
n.haigh at sheffield.ac.uk
Fri Jul 6 08:54:33 EDT 2007
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Nathan S. Haigh wrote:
> I'm taking a look at the tests for Bio::Variation::RNAChange.
> If you create a new oject without arguments:
> my $obj = Bio::Variation::RNAChange->new();
> What do you expect the following to return:
> I thought it would probably be:
> However you get:
> 'inframe, deletion'
> Can anyone in the know explain what behaviour would be expected?
Following on from this, AAChange has the following two methods:
add_Allele() and allele_mut()
It appears that allele_mut is only capable of remembering 1 allele at a
time, whereas add_Allele() is provided to add support for mutliple
alleles - is that correct?
However, add_Allele() also calls allele_mut(), such that mutliple calls
to add_Allele will result in the overwriting of the allele being
remembered by allele_mut(). Things are further complicated by the fact
that label() uses allele_mut() to decide on the label to return.
Shouldn't label know aout multiple alleles set by multiple calls to
It may be my lack of understanding alleles and what these classes are
intending to do, but trying to rewrite the test scripts to improve code
coverage has let me a little confused!
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