[Biojava-l] New class RevCompSequence

[Schreiber, Mark]

This looks really nice, one question. Is there a way to find out what a
location on a revComp sequence would be on the 'normal' sequence?

Ie if something is at base 12 on the revcomp sequence what is it on the
'normal sequence'

Mark


> -----Original Message-----
> From: David Waring [mailto:dwaring@u.washington.edu] 
> Sent: Thursday, 7 March 2002 9:29 a.m.
> To: biojava
> Subject: [Biojava-l] New class RevCompSequence
> 
> 
> I just added RevCompSequence to ...bio/seq/impl/. As you 
> might expect it is for reverse complementing a Sequence.
> 
> All features of the underlying sequence are reflected onto 
> the RevCompSequence using a ProjectedFeatureHolder.
> 
> Calling createFeature() on a RevCompSequence creates a 
> feature on the underlying sequence.
> 
> Non-Stranded features will return the reverse compemented 
> view of the sequence when getSymbols() is called that is to 
> say if you get what you expect as if your RevCompSequence.
> 
> All changes in the underlying Sequence are immediatly 
> reflected in the RevCompSequence.
> 
> I have provided a clone() method that will create a new 
> (SimpleSequence) that is no longer tied to the original sequence.
> 
> I think that all sub-features are handled properly, but let 
> me know if you see any potential problems.
> 
> David
> 
> PS. To support this I made small changes to 
> ProjectedFeatureHolder, ProjectedFeature and ProjectedStrandedFeature
> 
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