[Biojava-l] Sequence Iteration in BioJava(x)

[Richard HOLLAND]

orderNSymbolList splits the sequence into non-overlapping chunks. What
is required here is chunks that are only one base different (further on)
than the previous chunk.

The simplest way would be this:

	SymbolList mySeq; // this is your sequence from somewhere else
	for (int i = 1 ; i <= mySeq.length()-2; i++) {
		SymbolList trimer = mySeq.subSeq(i,i+2); // coords are
inclusive so i to i+2 = 3 bases
		// do something with your trimer here
	}

Note that the index starts at 1 and goes right up to and including
length(), as symbols in a SymbolList are 1-indexed, not 0-indexed.
	
cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of David Huen
> Sent: Friday, December 16, 2005 7:34 AM
> To: m.fortner at sbcglobal.net
> Cc: biojava-list
> Subject: Re: [Biojava-l] Sequence Iteration in BioJava(x)
> 
> 
> On Dec 15 2005, Mark Fortner wrote:
> I think what you want is the SymbolListViews.orderNSymbolList method.
> 
> It will take a SymbolList and turn it into another where it 
> is viewed in 
> another compound alphabet of the required order.
> 
> 
> >I'm looking for the best way to iterate through all
> >nmers within a given sequence.  For example, given a
> >sequence that looks like this:
> >
> >ACTGACTGACTG
> >
> >If I extract all trimers from this I should get:
> >
> >ACT
> >CTG
> >TGA
> >GAC
> >ACT
> >CTG
> >TGA
> >GAC
> >ACT
> >CTG
> >
> >Is there an existing class that will allow me to
> >iterate through a sequence this way, or am I on my
> >own?
> >
> 
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