[Gmod-help] Re: [Gmod-gbrowse] feature list from annotator plugin not available from SegmentI object?

[Sarah Richardson]

Thank you Dave!


On Dec 4, 2009, at 2:37 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Sarah,
> 
> As you know, I usually send plugin questions from the list to you.  :-)
> 
> I'm hoping that by refreshing this thread, someone else on the list
> will respond.
> 
> Does anyone out there have an suggestions for Sarah?
> 
> Thanks,
> 
> Dave c.
> 
> 
> On Wed, Dec 2, 2009 at 12:51 PM, Sarah Richardson <notadoctor at jhmi.edu> wrote:
>> I hope this is a simple thing that I am overlooking and that someone can easily point me in the right direction.
>> 
>> I have an annotator plugin that overlays several tracks of potential restriction enzyme placements on the view.  Each feature in each track the annotator generates has a custom link that opens up a hidden dumper plugin, which makes edits to the sequence and creates a new source file, configuration file, and database etc based on which placement was chosen.
>> 
>> When I ask the dumper plugin for a list of the features that were in the gbrowse view,
>>        my $self           = shift;
>>        my $segment  = $self->segments->[0];
>>        print ERR  $segment->features();
>> 
>> I only get features that are in the database - that is, nothing generated by the annotator.  As it stands i have to have the dumper repeat the calculations the annotator already performed.
>> 
>> My question is, how do I get the dumper to see the tracks the annotator laid down?
>> 
>> Thank you for your time and assistance!
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> 
> 
> 
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