Re: [Biojava-l] Remove features from a sequence

> "Mark" == Schreiber, Mark <[EMAIL PROTECTED]> writes: Mark> Hi - As this is the second time this has come up, Keith, can Mark> I put your solution on Biojava in Anger? [...] Hi, Sure, feel free to do anything you like with it. Perhaps a link could be added to the Iterator page at

[Biojava-l] Dox on biojava.org

Is it just me or are the .html files for the stable 1.30 version in docs section all 0KB in length? Vasa ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] Dox on biojava.org

Once upon a time, Vasa Curcin wrote: > Is it just me or are the .html files for the stable 1.30 version in docs > section all 0KB in length? I'm very sorry -- a lot of the files do seem to be truncated. The only explanation I can think of is that the machine where I built the release ran out of d

Re: [Biojava-l] Remove features from a sequence

Once upon a time, Keith James wrote: > > It may also be worth noting that you /can/ do this: > > while (seqI.hasNext()) > { > Sequence seq = seqI.nextSequence(); > > for (Iterator i = seq.features(); i.hasNext();) > { > i.next(); > i.remove(); > } > } > > which i

[Biojava-l] XML Blast parse

Has anyone got some sample code showing parsing blast XML results? i.e. blast with the -m7 output. thanx Russell ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] how to use BlastXMLParser

On Monday 23 Jun 2003 7:07 am, [EMAIL PROTECTED] wrote: > Greetings, > > I wonder how to use BlastXMLParser? I don't know where I can set my XML > filename and how to get parser result. Where can I get a sample file > using BlastXMLParser? > OK, I will write an example for this parser. I noticed t

Re: [Biojava-l] how to use BlastXMLParser

Thanx :-) I just noticed there is a BlastXMLParser but haven't looked at it yet. I also noticed most of the docs have zero length .html files so browsing the documentation is a little difficult :-) Russell - Original Message - From: "David Huen" <[EMAIL PROTECTED]> To: <[EMAIL PROTEC

[Biojava-l] ontology

I feel I'm stupid but I can't find the ontology stuff you guys wrote at the hackathon. Can you give me a hint? I thought there's got to be a Term class or interface or something? -hilmar -- - Hilmar Lapp

[Biojava-l] Problems running SearchProfile demo

Hi, I can't get the SearchProfile demo to work and I have tried various input files. Is there a sample file available that will work so I can test if something else is wrong? Thanks, Henry Romijn Quoting [EMAIL PROTECTED]: > Hi, > > I have tried to run the SearchProfile demo with something

[Biojava-l] SAX parser

It it just me or is Blast's XML screwed? I've spent a whole day shagging about but couldn't a SAX parser to identify anything but each elements localName :-( The Attributes always seem to be empty. What have I missed? Russell --- import java.io.*; import

[Biojava-l] Re: ontology

Once upon a time, Hilmar Lapp wrote: > I feel I'm stupid but I can't find the ontology stuff you guys wrote at > the hackathon. Can you give me a hint? I thought there's got to be a > Term class or interface or something? In CVS HEAD BioJava (not the 1.3x series), look in the org.biojava.bio.ont