[Biojava-l] GappedSymbol lists and Features

[Matthew Pocock]

Hi Tim,

This is an API bug in GappedSymbolList - it should be exposing the list 
it wraps via a getWrappedSequence type of method. You would then be able 
to cast this to Sequence and play with features.

If you are already playing about with the BioJava source code, would you 
like to expose this property in your private copy and submit the patch 
along with your MSF changes as-and-when?

Matthew

Dudgeon, Tim wrote:
> I've been doing some work on the multiple alignment stuff in biojava. I've
> found that the existing org.biojava.bio.seq.io.MSFAlignmentFormat class
> doesn't really seem to work, and have been re-engineering it to work and be
> more generic. I'll contribute this work when complete.
> 
> My question relates to how alignments should work. Currently
> org.biojava.bio.symbol.Alignment is composed of
> org.biojava.bio.symbol.SymbolList objects, which seems very reasonable. To
> specify an alignment with gaps, you would presumably use a
> org.biojava.bio.symbol.GappedSymbolList, which is a SymbolList that allows
> gaps to be inserted/deleted. This GappedSymbolList seems to wrap another
> SymbolList (without gaps) that contains the underlying sequence (a
> SymbolList could be generated that contained gaps, but as the sequence is
> immutatable you wouldn't be able to add/delete gaps, hence the need for the
> GappedSymbolList).
> 
> Now to my point. I want to be able to use an alignment that contains
> sequences that can have features. I want to be able to add a feature (e.g. a
> prosite motif) to the underlying sequence, but be able access this both
> through the underlying coordinates of the protein and the coordinates within
> the alignment i.e both the GappedSymbolList and the SymbolList it wraps.
> 
> Hence to do this I would need to create the org.biojava.bio.symbol.Alignment
> that contained a GappedSymbolList that wraps a SimpleSequence to which
> Features could be attached. However I see no  way of getting hold of the
> SimpleSequence from the GappedSymbolList that wraps it. Are there any
> solutions here?
> 
> many thanks
> 
> Tim
> 
> 
> 
> --------------------------------------------
> Dr. Tim Dudgeon
> OSI Pharmaceuticals, Watlington Road, Oxford, OX4 6LT, UK
> Tel: +44 (01865) 871 244
> email: tdudgeon@osip.com
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