[Biojava-l] Wrapping SimpleGappedSequence

[Ditlev Egeskov Brodersen]

Hi again,

  I updated CVS and got the new SimpleGappedSymbolList class, but there
seems to be no changes to the SimpleGappedSequence class, which is the one I
need to extend...have I missed something?

  Ditlev

--
 
Ditlev E. Brodersen, Ph.D.
Lektor, Associate Professor
 
Department of Molecular Biology   Office:  +45 89425259
University of Aarhus              Lab:     +45 89425022
Gustav Wieds Vej 10c              Fax:     +45 86123178
DK-8000 Aarhus C                  Email:   deb at mb.au.dk
Denmark                           Lab WWW: www.bioxray.dk/~deb


> -----Original Message-----
> From: Richard Holland [mailto:holland at ebi.ac.uk]
> Sent: 16 November 2007 11:47
> To: Ditlev Egeskov Brodersen
> Cc: biojava-l at biojava.org
> Subject: Re: Wrapping SimpleGappedSequence
> 
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> The easiest way is simply for me to alter the constructor to
> SimpleGappedSequence (and equivalently to SimpleGappedSymbolList) to
> copy all gaps if passed another instance of GappedSymbolList as the
> parameter. I've just done this in CVS so you should be able to update
> your copy and observe the new behaviour.
> 
> cheers,
> Richard
> 
> Ditlev Egeskov Brodersen wrote:
> > Hi again,
> >
> >   thanks for the info - will do the check just to be proper. I have
> another
> > question: In my application, I would like to wrap the retrieved
> > SimpleGappedSequence objects inside another object that extends the
> > functionality with application-specific stuff. Ideally, I would do
> this by
> > extending the SimpleGappedSequence object and create it by passing
> the
> > SimpleGappedSequence from the alignment import to the constructor of
> the
> > parent, like so:
> >
> >   class AlignedSequence extends SimpleGappedSequence {
> >     public AlignedSequence(SimpleGappedSequence aGapped) {
> >       super(aGapped);
> >     }
> >
> >     ..custom stuff..
> >   }
> >
> > However, the problem is that there is only one constructor for the
> > SimpleGappedSequence, one which takes a simple Sequence object. I can
> pass
> > the derived class alright, but all gap information is lost again,
> presumably
> > because the SimpleGappedSequence constructor just takes out the
> seqString()
> > and puts it into its own sequence object.
> >
> > Shouldn't the constructor of the SimpleGappedSequence class recognise
> when a
> > derived (and gapped) sequence object is passed, and process it
> accordingly?
> >
> > As it stands, I am forced to include the SimpleGappedSequence as a
> private
> > member of the AlignedSequence class, which is not near as nice since
> all
> > statement using the class will have to do something like
> >
> >   class AlignedSequence extends SimpleGappedSequence {
> >     private SimpleGappedSequence gapped_sequence;
> >
> >     public AlignedSequence(SimpleGappedSequence aGapped) {
> >       gapped_sequence = aGapped;
> >     }
> >
> >     public SimpleGappedSequence getGappedSequence() {
> >       return(gapped_sequence);
> >   }
> >
> >     ..custom stuff..
> >   }
> >
> >   ...
> >
> >   AlignedSequence aAligned = new AlignedSequence(aGapped);
> >   aAligned.getGappedSequence().seqString();
> >
> > rather than simply:
> >
> >   AlignedSequence aAligned = new AlignedSequence(aGapped);
> >   aAligned.seqString();
> >
> > In other words, is there any solution with the current setup that
> would
> > allow me to extend SimpleGappedSequence and not loose the gap
> information?
> >
> > --  Ditlev
> >
> > --
> >
> > Ditlev E. Brodersen, Ph.D.
> > Lektor, Associate Professor
> >
> > Department of Molecular Biology   Office:  +45 89425259
> > University of Aarhus              Lab:     +45 89425022
> > Gustav Wieds Vej 10c              Fax:     +45 86123178
> > DK-8000 Aarhus C                  Email:   deb at mb.au.dk
> > Denmark                           Lab WWW: www.bioxray.dk/~deb
> >
> >
> >> -----Original Message-----
> >> From: Richard Holland [mailto:holland at ebi.ac.uk]
> >> Sent: 16 November 2007 10:50
> >> To: Ditlev Egeskov Brodersen
> >> Cc: biojava-l at biojava.org
> >> Subject: Re: [Biojava-l] Parsing exising gaps
> >>
> >>>>   The returned gapped sequences are all properly set up with gaps,
> > name etc.
> >>>> But as for other users, I think there may be some problems, since
> the
> >>>> SimpleAlignment object only has a general symbol list iterator,
> the
> > user
> >>>> will have to cast each statement extracting a sequence object, and
> >>>>
> >>>>       SimpleSequence aSimple = (SimpleSequence)aSequences.next();
> >>>>
> >>>> returns an ClassCastException at run time. So old code might not
> run
> > with
> >>>> the update as far as I can see.
> > This is true. However, such code would be unsupported by us as the
> API
> > clearly states that SimpleAlignment returns SymbolList instances, and
> > does not make any guarantees about the exact implementation details
> of
> > the objects it returns. To attempt to cast it to anything other than
> > SymbolList would be a mistake! (Although actually it is now returning
> a
> > guarantee of GappedSymbolList, which is what your code can now take
> > advantage of). To assume it will return SimpleSequence is outside the
> > behaviour defined by the API and therefore should not be relied upon.
> >
> > A more correct behaviour would be to test each item returned:
> >
> > 	SymbolList symlist = aSequences.next();
> > 	if (symlist instanceof SimpleSequence) {
> > 		SimpleSequence seq = (SimpleSequence)symlist;
> > 		// Do simple-sequence stuff
> > 	} else {
> > 		// Do something else!
> > 	}
> >
> > In future, I will modify the API to change the SymbolList guarantee
> to
> > a
> > GappedSymbolList guarantee, but I can't do this right now as this
> > really
> > would break everyone's code!
> >
> > We are currently planning a redesign as you may be aware, so issues
> > like
> > this will hopefully be resolved as part of that process. For a start,
> > if
> > we use Java 5 generics in future as we plan, we can strictly specify
> > what kinds of objects will be returned by things such as the
> alignment
> > API, making it easier for us to enforce API-compliant behaviour in
> > user's code.
> >
> > cheers,
> > Richard
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