[Genquire-dev] additional bug fixes - just one left it appears!

[Mark Wilkinson]

Hi developers!

I made some additional updates to several parts of genquire this morning.  In
particular, the Blastmap plugin is now able to map the results onto the
SeqCanvas as it used to before I pulled it out of the main code.  There were
also some very minor errors in the writing of tags to the blue information
screen, and the hand annotation screens.

There is still a problem with the adding/removing of GO annotations.  Dave,
you might want to jump into this since you are more familiar with this bit of
the code:  the $GenericFeature->_wipe_GO call results in a *duplication* of
the GO annotation being attached to the object

These are the offending lines of code:

$self->{GO} = [];
my $list=$self->adaptor->wipe_GO($self);
foreach my $value(@$list) {
     push @{$self->{tagvalues}{GO_annotation}},$value;
}


I believe that $list contains the correct number of elements, but if this
code is called multiple times the push will simply duplicate the existing GO
annotations.  I think this routine should also be clearing the
$self->{tagvalues}{Go_Annotation} list before pushing... or is that too
simplistic?

let me know what you think and I'll fix it.  The actual writing of the
annotation to the database (and wiping from the database) is done correctly,
so it is only the in-memory object that is faulty.  Surprisingly, this error
crashes Genquire on Windows when working in the txtHandAnnotate window, but
Linux doesn't complain..?? Weird???

Anyway, after using Genquire for a few days, those were the only serious
errors I could find.  I'll probably do one more update before packaging it up
once and for all!  I want to get rid of some debugging print statements, and
fix a problem with destroying the SeqCanvas menu widget.

Cheers!

M


--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada