[Biojava-l] how to do multi-lined feature display

[Schreiber, Mark]

If you have a nice example I'll be more than happy to post the code to biojava in anger.
 
Thanks
 
Mark
 

	-----Original Message----- 
	From: Patrick McConnell [mailto:MCCon012 at mc.duke.edu] 
	Sent: Fri 28/03/2003 8:18 a.m. 
	To: Keith James 
	Cc: biojava-l at biojava.org 
	Subject: Re: [Biojava-l] how to do multi-lined feature display
	
	



	That helps alot, thanks!  I think the trick that caught me is with the
	FeatureFilter.  I think this would make a great example for BioJava in
	Anger.
	
	I am able to get my features displayed on different "tracks" by specifying
	contrived sources.  I am even able to alter the display color of the
	features based on the annotation (bitscore) by subclassing the
	BasicFeatureRenderer (maybe there's a better way to do this).  This makes
	it look alot more "blast-like".
	
	I am actually doing this to build images to display on a website.  So, I
	need to discover the pixel positions of the rendered features.  By reading
	through the API's, I see no way to do this.  Is this even possible?
	
	Thanks a bunch!
	
	-Patrick
	
	
	
	
	
	Keith James <kdj at sanger.ac.uk> on 03/27/2003 03:05:07 PM
	
	To:    "Patrick McConnell" <MCCon012 at mc.duke.edu>
	cc:    "biojava-l at biojava.org" <biojava-l at biojava.org>
	
	Subject:    Re: [Biojava-l] how to do multi-lined feature display
	
	>>>>> "Patrick" == Patrick McConnell <MCCon012 at mc.duke.edu> writes:
	
	    Patrick> Let me be more specific.  I want to be able to reproduce
	    Patrick> something like EnsEMBL, where I have one sequence and
	    Patrick> multiple tracks of features.
	
	    Patrick> Specifically, I have a sequence and a bunch of blast hits
	    Patrick> from different databases.  I also have some other data,
	    Patrick> such as quality scores for the sequence, that I need to
	    Patrick> build custom renderers for (which will come later).
	
	    Patrick> I think I need to use the MultiLineRenderer in
	    Patrick> conjunction with a SequencePanel, but I cannot figure out
	    Patrick> how to get multiple tracks of annotations.  Do I need to
	    Patrick> add Features to the Sequence in a special manner?
	
	Using a MultiLineRenderer will allow you to have multiple tracks. You
	may then put a different SequenceRenderer in each track.
	
	Take a SequencePanel (easier to implement scrolling -simply place into
	a ScrollPane) or TranslatedSequencepanel (must have scrolling
	implemented manually by hooking a JScrollBar to change the sequence
	position of the area to be viewed, but last benchmarked 7x faster than
	SequencePanel).
	
	Set the Panel's SequenceRenderer to be a MultiLineRenderer. You can
	then add more SequenceRenderers to the multi, each with different
	views of the Sequence and its complement of Features. Make these
	renderers FilteringRenderers (which are SequenceRendererWrappers) to
	get different views per track. Specify a FeatureFilter for each
	FilteringRenderer to determine waht to show in each track. You can
	combine multiple FeatureFilters via the filtering API.
	
	You can also use BeadFeatureRenderer (a SequenceRenderer) to show any
	number of different Feature types, each rendered distinctively, all on
	the same track. It also allows you to have different types of Feature
	at different Y-axis displacements in the same track.
	
	Does this help at all?
	
	Keith
	
	--
	
	- Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
	- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -
	
	
	
	
	
	
	
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