[Biojava-l] Editing a RichSequence

[Richard Holland]

The problem lies in SimpleRichSequenceBuilder:

    public void addSymbols(Alphabet alpha, Symbol[] syms, int start, int
length) throws IllegalAlphabetException {
        if (this.symbols==null) {
            if (threshold<=0) {
                this.symbols = new ChunkedSymbolListFactory(this.factory);
            } else {
                this.symbols = new
ChunkedSymbolListFactory(this.factory,threshold);
            }
        }
        this.symbols.addSymbols(alpha, syms, start, length);
    }

The references to ChunkedSymbolListFactory are causing the problem.
ChunkedSymbolListFactory is supposed to perform the threshold
checking/factory selection. However it is also applying a further layer
of abstraction which forces all symbol lists for sequences over 16k
(1<<14) long to be ChunkedSymbolLists, regardless of the factory
specified - the factory only specifies what the constituent sequences
are within the ChunkedSymbolList. ChunkedSymbolList is immutable so will
not allow edits even if its constituents are mutable. However if your
sequence is less than 16k long, it behaves properly and you will get the
type of sequence you asked for (SimpleSymbolList below the threshold,
whatever you specify above it - SimpleSymbolList also happens to be the
only SymbolList implementation in BioJava that is actually mutable at
present.)

As the older thread describes, ChunkedSymbolList and its Factory are
very embedded into the core of BioJava and are hard to change - it could
break all kinds of things. Therefore the only real solution for now is
to temporarily modify your local copy so that inside ChunkedSymbolList,
you change the CHUNK_SIZE to something much larger than 1<<14.

thanks,
Richard

Ian Yi-Feng Chang wrote:
> Dear All,
> I've a problem while editing a richsequence.
> and got this exception:
> Exception in thread "main" org.biojava.utils.ChangeVetoException:
> AbstractSymbolList is immutable
> 	at org.biojava.bio.symbol.AbstractSymbolList.edit(AbstractSymbolList.java:113)
> 
> 	at org.biojavax.bio.seq.DummyRichSequenceHandler.edit(DummyRichSequenceHandler.java:31)
> 	at org.biojavax.bio.seq.ThinRichSequence.edit(ThinRichSequence.java:163)
> 	at gizmo.tools.GBKCurator.main(GBKCurator.java:176)
> 
> I trace this problem in this mailing list and find a latest thread
> in** *Wed Feb 20 21:33:39 EST 2008*
> 
> However, I still have no idea how to
> 
> Here is the solution (from the JavaDoc)
> 
> 
>  SimpleRichSequenceBuilderFactory public
> SimpleRichSequenceBuilderFactory(SymbolListFactory fact, int threshold)
>  Creates a new instance of SimpleRichSequenceBuilderFactory that uses
> a specified factory for SymbolLists longer than a specified length.
> Before that a SimpleSymbolListFacotry is used.
> 
>  Parameters:
> fact - the factory to use when building the
> SymbolList.threshold - the threshold to exceed before using this factory
> 
> However, could you please help to demonstrate how to use this solution
> to edit a richsequence?
> 
> Thank you so much.
> 
> ian chang
> _______________________________________________
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> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/