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

[David Huen]

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?
>