[Biojava-l] Best way to represent multiple annotation "tracks"

[Schreiber, Mark]

Hi -
 
In biojava Annotations have no location. They are global to the Annotatable object. They can be localized to a region by being applied to a Feature. So to generate a track of "annotations" you would instead create a track of annotated Features.
 
- Mark
 

	-----Original Message----- 
	From: Ihab A.B. Awad [mailto:ihab at stanford.edu] 
	Sent: Tue 9/09/2003 10:53 a.m. 
	To: biojava-l at biojava.org 
	Cc: 
	Subject: [Biojava-l] Best way to represent multiple annotation "tracks"
	
	

	Hi folks,
	
	I'm working on a gene expression data visualization program --
	
	   http://genetics.stanford.edu/~ihab/caryoscope/
	
	I have not used BioJava yet for the data model, but I would like to
	migrate in that direction. It seems that my data model is very
	similar to BioJava's, except for one thing that puzzles me: How would
	you folks represent multiple "tracks" of annotation values? The way I
	have things modeled --
	
	
	http://genetics.stanford.edu/~ihab/caryoscope/doc/api/edu/stanford/genomics/domain/Dataset.html
	
	a Dataset object maps a Feature to a data object (or null). I see you
	folks implement this a bit differently: a Feature implements
	interface Annotatable, whereby it becomes responsible for knowing
	about its own Annotations. Hence my question -- how would you
	represent a "track" of annotations as a single entity?
	
	Thanks a lot for any help you can provide in pointing me in the right
	direction. Peace,
	
	Ihab
	
	--
	Ihab A.B. Awad <ihab at stanford.edu>
	Snr Scientific Programmer, Dept of Genetics
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