[Biojava-l] BioJava <--> BSANE bridges

2002-01-08 Thread Thomas Down
Hi... I've just checked in some code which provides both server and client-side bridges between the BioJava sequence model and BioCorba 0.3 (a.k.a. BSANE). At the moment, the best way to get hold of it is from CVS: check out the `biojava-bsane' module. The CORBA idl files were taken from the Bi

[Biojava-l] Trouble with parsing big Blast result raport

2002-01-08 Thread Petri Pehkonen
Hello, When parsing Blast-result-raport with BlastLikeSAXParser and using TutorialEx1Handler shown in demos in cvs.biojava.org as a contenthandler, I get errormessage like this: --- # # An EXCEPTION_STACK_OVERFLOW exception has been detected in native code outside the VM.

Re: [Biojava-l] Trouble with parsing big Blast result raport

2002-01-08 Thread Simon Brocklehurst
Petri Pehkonen wrote: > Hello, > > When parsing Blast-result-raport with BlastLikeSAXParser and using > TutorialEx1Handler shown in demos in cvs.biojava.org as a contenthandler, > I get errormessage like this: > --- > # > # An EXCEPTION_STACK_OVERFLOW exception has been de

Re: [Biojava-l] Mass Search Results

2002-01-08 Thread Keith James
> "Dr. Jones" == Michael Jones <[EMAIL PROTECTED]> writes: [...] Dr. Jones> The SeqSimilaritySearchResult has the following Dr. Jones> methods. Dr. Jones> List getHits(); The List contains Dr. Jones> SeqSimilaritySearchHit which has methods to return a Dr. Jones> variety

Re: [Biojava-l] Trouble with parsing big Blast result raport

2002-01-08 Thread Petri Pehkonen
Hi, I'm using Java SDK Standard Edition 1.3.1 under Windows 2000. I tried to change the virtual machine to "classic" but it didn't help and I got the same error message. I wonder if anyone has made parsing with result files as big as ours? -Petri Pehkonen- On Tue, 8 Jan 2002, Simon Brocklehur

Re: [Biojava-l] Trouble with parsing big Blast result raport

2002-01-08 Thread Simon Brocklehurst
Petri Pehkonen wrote: > Hi, > > I'm using Java SDK Standard Edition 1.3.1 under Windows 2000. I tried to > change the virtual machine to "classic" but it didn't help and I got the > same error message. I wonder if anyone has made parsing with result files > as big as ours? Hi, I just tried the

Re: [Biojava-l] Trouble with parsing big Blast result raport

2002-01-08 Thread Petri Pehkonen
Hi, It works now! I set the stack size value on hotspot-virtual machine greater, and it goes through. I noticed that the stack of the parser goes very big when parsing. I don't know if it's true but I suspect that the endElement-method of my contenthandler is not executed every time it should. So

Re: [Biojava-l] Re: Bug in assembly behaviour

2002-01-08 Thread Matthew Pocock
Sory if I blundered in and broke stuff by adding the auto-extend code. This shoulds like the behavior I indended (but obviously messed up!) Matthew --- Thomas Down <[EMAIL PROTECTED]> wrote: > On Sat, > How about: > > - newly constructed AssembledSymbolList has length > 0 > > - This alway

Re: [Biojava-l] Mass Search Results

2002-01-08 Thread Michael Jones
It's actually Mr. Jones but I like how evil Dr. Jones sounds. At 12:24 PM 1/8/2002 +, Keith James wrote: > > "Dr. Jones" == Michael Jones <[EMAIL PROTECTED]> writes: > >[...] > > Dr. Jones> The SeqSimilaritySearchResult has the following > Dr. Jones> methods. > > Dr. Jones> L

RE: [Biojava-l] Mass Search Results

2002-01-08 Thread William . Old
> -Original Message- > From: Michael Jones [mailto:[EMAIL PROTECTED]] > Sent: Tuesday, January 08, 2002 8:36 AM > To: Keith James; BioJava List > Subject: Re: [Biojava-l] Mass Search Results > > >> > Create new interface(s) tailored to mass search (or any > other search > > with spe