[Biojava-l] Am I misunderstanding?

czaleski czaleski at albany.edu
Wed Jul 26 16:59:48 UTC 2006

I'm worried I may be misunderstanding the intended usage of BioJava. What
made me question this was a simple example...

I followed the tutorial, and examples in the cookbook. I make a Sequence via
the DNATools.createDNASequence(str, str) method. This returns a Sequence
object. Sequence is an Interface, so there must be an implementation I don't
see... however by following the examples, it shouldn't be necessary to worry
about it.
According to the tutorial there are 2 global pieces of annotation that have
their own accessors - name and URN. The name gets set when I called
createDNASequence, but how do I set the URN? There is no method declared on
Sequence, or anything it inherits to be able to set the URN. This seems
So I start to dig through the source code. I find that
createDNASequence(str, str) eventually ends up returning a SimpleSequence
impl object, and sure enough, SimpleSequence implements setURN(str);

So... in my code... if I want to set the URN, I need to create
SimpleSequence objects explicitly instead of referencing them as Sequence
objects. Like this:
SimpleSequence simpSeq = (SimpleSequence)DNATools.createDNASequence(seq,

This seems like an unintentional use of the package, and I only even came to
this possibility by having to search through the source sode.

If this is true and you are you not supposed to use the .impl classes
directly, then how would I perform the simple task of setting the URN?

Am I misunderstanding?

Thanks much.
View this message in context: http://www.nabble.com/Am-I-misunderstanding--tf2004940.html#a5507066
Sent from the BioJava forum at Nabble.com.

More information about the Biojava-l mailing list