[Biojava-dev] Creating SubSequence(s) that are Contained By Location instead of OverlapsLocation

[Matthew Pocock]

Hi Eduardo,

The idea sounds sane. Thomas, would you mind if we added a property on 
SubSequence that switches between the 'clever' fuzzied behavior and this 
pruned behavior?

As a quick fix, you can filter the sequence by a filter on the Location 
  that's a range from 1 to sequence.length(). FilterUtils (or is that 
FilterTools?) has a convenience method to get this filter.

Matthew

eduardo.gonzalezcouto at freesurf.ch wrote:
> Hello,
> 
> As this is my first post to the dev list, I'd like to start by
> congratulating everyone for the great work on the project.
> 
> I'm currently using the SubSequence class to extract features from a parent
> class. This method returns all the translated overlapping features, and
> in
> my case I have to be more restrictive and only keep the features strictly
> contained by the sub-sequence.
> 
> Would it be possible to have more flexibility at the level of the protected
> method entitled createFeatureHolder() returning a FeatureHolder by allowing
> to switch between an OverlapsLocation FeatureFilter and a
> ContainedByLocation FeatureFilter? Overloading the whole
> createFeatureHolder()method is currently, feasible but it is not very
> elegant to copy the whole method just for changing the type of feature
> filter. Alternatively, it is possible to filter the features to only keep
> the Features that are Projected Features, but I don't know if this will
> be
> safe in the future.
> 
> Thank you in advance for your help.
> 
> Best regards,
>  Eduardo
> 
> --
> Eduardo Gonzalez Couto, Ph.D.
> Bioinformatician
> GeneProt Inc. (Geneva Branch)
> Tel. +41 (0)22 719 88 32
> Fax. +41 (0)22 719 88 69
> 
> sunrise premiumsurf - ne vous contentez pas du minimum!
> http://internet.sunrise.ch/fr/internet/int_sps.asp
> 
> 
> 
> 
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> 


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