[ Pls excuse the poor netiquette for posting a followup to my own message.... ]
So, let's say I have a bunch of ESTs, each of which has been mapped to a location on the genome. To each EST, my data maps a floating point number indicating the expression level.
In this case, each Feature would represent one of the ESTs, right? So what would be the Feature(s) representing the annotation track? Would they be Features owned by the EST Feature (via the inheritance of FeatureHolder by interface Feature)? Or -- ??
Alternatively, would each EST be a SubSequence with Features attached to it, with each Feature representing one of the data "tracks"? If so, then how does one decide when something is a Feature or a SubSequence? I'm not a biologist, so I'm probably way confused here, but it seems to me there is a gray area (ORFs?).
So I guess there are several competing implementations.
1. SEQUENCE BASED, FEATURES REPRESENT DATA TRACKS
"Chromosome 1" : Sequence
"AA504327" : SubSequence
"RAT2N" : Feature
<anon> : Annotation
"Value" => 2.34312
"RAT2_MEAN": Feature
<anon> : Annotation
"Value" => 1.8342
"AA432030" : SubSequence
...2. SEQUENCE BASED, ANNOTATIONS REPRESENT DATA TRACKS
"Chromosome 1" : Sequence
"AA504327" : SubSequence
"Microarray Experiment B2341v" : Feature
<anon> : Annotation
"RAT2N" => 2.34312
"RAT2_MEAN" => 1.8342
"AA432030" : SubSequence
...3. FEATURE BASED, SUB-FEATURES REPRESENT DATA TRACKS
(Very similar to #1, except using Feature instead of SubSequence.)
"Chromosome 1" : Sequence
"AA504327" : Feature
"RAT2N" : Feature
<anon> : Annotation
"Value" => 2.34312
"RAT2_MEAN": Feature
<anon> : Annotation
"Value" => 1.8342
"AA432030" : SubSequence
...4. FEATURE BASED, ANNOTATIONS REPRESENT DATA TRACKS
(Very similar to #2, except using Feature instead of SubSequence.)
"Chromosome 1" : Sequence
"AA504327" : Feature
"Microarray Experiment B2341v" : Feature
<anon> : Annotation
"RAT2N" => 2.34312
"RAT2_MEAN" => 1.8342
"AA432030" : SubSequence
...Thanks a lot again & peace,
Ihab
-- Ihab A.B. Awad <[EMAIL PROTECTED]> Snr Scientific Programmer, Dept of Genetics _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
