Access the parent of a Bio::DB::SeqFeature within a gbrowse config callback function
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Access the parent of a Bio::DB::SeqFeature within a gbrowse config callback function
by Daniel Lang-3
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Hi,
I'm looking for an efficient way (hack) to access the parent of a given feature within a callback function in a gbrowse config. Currently I do it like this: if ($feature->get_tag_values('parent_id')) { my $store= $parent->object_store; if ($store and $store->can_store_parentage) { do { my @p = $parent->get_tag_values('parent_id'); if (@p) { $parent = @{ [ grep {$_ and $_->seq_id eq $feature->seq_id and $_->location->contains($feature->location)} $store->get_features_by_alias($p[0])] }[0]; } else { last; } } until ($parent and ($name = $parent->name)); } } The callback is used in to produce popups within a link attribute (ggbmenu.js). The problems with this approach are a)effciency and b) if a feature on the same region exists with the same ID. So I wonder if there is some "magic" object/variable in the scope of the callback I could use? I originally hoped that this would work with something like $GBROWSE... Additionally, it would be great if someone could point me to code that uses these "meta variables" (e.g. access browser or track or panel objects) to generate content. Thanks in advance, Daniel -- Daniel Lang University of Freiburg, Plant Biotechnology Schaenzlestr. 1, D-79104 Freiburg fax: +49 761 203 6945 phone: +49 761 203 6974 homepage: http://www.plant-biotech.net/ e-mail: daniel.lang@... ################################################# My software never has bugs. It just develops random features. ################################################# ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Access the parent of a Bio::DB::SeqFeature within a gbrowse config callback function
by Lincoln Stein
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The objects are set up without parent pointers in order to avoid circular references, which make memory management a nightmare. It's a bit ugly, but if you set all_callbacks to true, then the callback will be invoked on the parent object as well, and you can simply store it into a global variable for access from the child. The operation is depth first, so the callback will be invoked on the child immediately after the parent.
A better long-term solution would be to add a method such that the parent is available by making a method call on the glyph object. I'll have a look. Lincoln On 6/1/07,
Daniel Lang <daniel.lang@...> wrote: Hi, -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse@... ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Access the parent of a Bio::DB::SeqFeature within a gbrowse config callback function
by Lincoln Stein
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Hi,
This issue has come up again recently and I am posting a fix that is better than the one suggested in the original email thread. Callbacks actually take five arguments, although most people ignore all but the first. The fifth argument is the glyph, and you can get the parent feature from that. Here's the code: bgcolor = sub { my ($feature, $option_name, $part_no, $total_parts, $glyph) = @_; my $parent_feature = $glyph->parent_feature; # do something on the parent feature } You can pass arguments to $glyph->parent_feature() to get the grandparent, great-grandparent, etc. Lincoln On Fri, Jun 1, 2007 at 11:11 AM, Lincoln Stein <lstein@...> wrote: The objects are set up without parent pointers in order to avoid circular references, which make memory management a nightmare. It's a bit ugly, but if you set all_callbacks to true, then the callback will be invoked on the parent object as well, and you can simply store it into a global variable for access from the child. The operation is depth first, so the callback will be invoked on the child immediately after the parent. -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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