Hi,
I am investigating the usefulness of BioJava as a backend for sequence
management in Bioclipse (www.bioclipse.net). As a total newbie to
Biojava, I have read the tutorial, BIA examples, glanced at the API,
read my first FASTA-sequence and have come up with a few questions:
1) Is it possible t
Further in my efforts in using the FlexibleAlignment class in conjunction with
the display the alignments I have created some test code, reproduced below.
The sequences are all displaying, but not in the alignment range. Am I
simply missing something simple here, like a symbol renderer that ha
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(se
Hello all,
This question refers to a previous posted question [Biojava-l] removeGap
problem with SimpleGappedSequence back in feb 2004. I was curious if
anyone had a workaround to the problem associated with trying to edit
already gapped sequences using the SimpleGappedSequence class. I am
hittin
>I am investigating the usefulness of BioJava as a backend for sequence
>management in Bioclipse (www.bioclipse.net). As a total newbie to
>Biojava, I have read the tutorial, BIA examples, glanced at the API,
>read my first FASTA-sequence and have come up with a few questions:
>
>1) Is it possible
Hi -
Could you repost some example code of the problem and the version of
biojava. Sorry for the tardy responses, everyone seems to be very busy
this year.
- Mark
"Dan Cardin" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
11/29/2005 07:08 AM
To: biojava-l@biojava.org
Hello Ola,
> 1) Is it possible to search the Biojava-l archives without having to
> manually browse by month?
Not that I know of. Google is a pretty good alternative as it has
indexed all the archive - just add +"biojava-l" to the beginning of your
query.
> 2) Is there a wrapper for SequenceIO.
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.printl
