[Bioperl-l] Changes to Bio::SeqI broke Bio::Graphics

[Lincoln Stein]

We agree violently.  Everything is a feature and sequence is an attribute of 
the feature.  BioPerl has it backward.

Lincoln

On Tuesday 12 November 2002 04:01 pm, Matthew Pocock wrote:
> Lincoln Stein wrote:
> > This allows an
> > entry to be a feature in a larger virtual sequence, such as a genome
> > assembly.  I don't see why we persist in thinking in this flat-file EMBL
> > entry way.
> >
> > Lincoln
>
> In BioJava we have a feature interface ComponentFeature with the two
> important methods getComponentLocation() and getComponentSequence().
> This indicates in an assembled sequence where you are to glue in bits of
> other sequences. The ComponentFeatures location is where it is in the
> assembly and the getComponentLocation is what region of
> getComponentSeqeunce to insert there. This has many advantages over
> making sequences features. Firstly, and most importantly, it allows us
> to project a single sequence (or multiple portions of a single sequence)
> into multiple assemblies (or different places in the same assembly). For
> example, we can take the same clones and project them into multiple
> versions of the human golden path. Translocations can trivialy be
> represented by building one assembled sequence for the normal and
> translocated chromosome, and the same underlying sequences can be used,
> providing a benefit in both memory and integrity of the annotations. It
> has many other benefits from the object modelling view of things,
> allowing us to implement stuff via lazy proxies (portions of an assembly
> don't need to be loaded untill you try to fetch data from them).
>
> I would caution against rolling the location of a sequene in a larger
> assembly ino the sequence itself. At the very least, you are going to
> need to publish a start and stop coordinate within the sequence that
> gets projected. This whole line of modelling in our experience causes
> problems rather than providing solutions.
>
> Matthew
>
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-- 
Lincoln Stein
lstein@cshl.org