Bioperl: Feature Table

[Lincoln Stein]

 > I also think that we should link up with people who are doing this 
 > stuff as the main project (not a sideline) - An example would be
 > Lincoln Stein's and Jean Theirry-meig's Jade viewer (? how suitable
 > I don't know - depends on how much of their fmap is in Jade), or Niclas
 > Jareborg's alfresco 
 > 
 > see
 > 
 > http://stein.cshl.org/jade/
 > 
 > http://www.sanger.ac.uk/Users/nic/comp.html

I'd like to help out with viewers and file formats.  I think a goal
should be to keep the core data models as simple and generic as
possible.  It should be possible to extract as much information as
possible from the objects as run time, much as the Java
introspection/reflection techniques work.  For example, the base
sequence "feature" should consist of only a name, a position and an
extent.  Everything else about the feature that the viewer might want
to know about (similarity score, external database URL, alignment), it
should be able to pull out at runtime... or ignore.  

This is what I do with AcePerl (http://stein.cshl.org/AcePerl).  All
the little (and not so little) Ace tags and data fields can be found
at run time and pulled out of the object as needed.  This is not to
say that a strong class hierarchy is not needed: just that viewers
often work best when the GUI is very loosely coupled to the class
hierarchy.

Lincoln

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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