[Biojava-l] DAS questions

[Richard HOLLAND]

If it's any help, you can see what IDs the DAS source is providing by
doing this:

	// construct your DASSequenceDB (dasDB) object as you did before
	Set ids = dasDB.ids();

	// Does the set contain Q12345?
	if (ids.contains("Q12345")) {
		System.out.println("Yes, it does!");
	} else {
		System.out.println("No, it doesn't!");
	}

	// Iterate through the set and print them all out
	for (Iterator i = ids.iterator(); i.hasNext(); ) {
		System.out.println((String)i.next());
	}

Hopefully you will be able to find out whats going on by investigating
the contents of this set.

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 Ola Spjuth
> Sent: Tuesday, November 29, 2005 1:56 AM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] DAS questions
> 
> 
> Hi,
> 
> Experimenting with the DAS client to retrieve proteins from uniprot I
> have a few questions:
> 
> dbURL = new 
> URL("http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/");
> String seqName="Q12345";
> DASSequenceDB dasDB = new DASSequenceDB(dbURL);
> DASSequence dasSeq = (DASSequence) dasDB.getSequence(seqName);
> 
> gives the error:
> 
> org.biojava.bio.seq.db.IllegalIDException: Database does not contain
> Q12345 as a top-level sequence
> 
> but with a browser issuing
> http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/sequence?se
gment=Q12345
yields the result I am looking for.

I assume I am not using DASSequenceDB and DASSequence correctly. I have
not found any JUnit tests so I have no reference code. Could someone
please assist?

On a general basis: Is the DAS client in BioJava mature? Can it handle
all the major DAS-servers for proteins/genes?

Thanks,

   .../Ola



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