Re: [Biojava-l] BLAST from Java

2002-02-20 Thread Thomas Down
Hmmm, are you saying that the command works okay via a batch file, but not if you exec it directly? Very strange... I'm not a Windows user. But one thing which occurs to me: you're handling the output of the process on the same thread as the Process itself. I always use separate threads (I don

Re: [Biojava-l] BLAST from Java

2002-02-20 Thread Simon Brocklehurst
Russell Smithies wrote: > Has anyone had any luck running Blast locally from Java using Runtime.exec() > and command array?? Yes ;-) Running native executables via Runtime.exec() works fine for us - but almost all the Runtime.exec() code we have written is designed to run under Unix. Runtime.e

Re: [Biojava-l] BLAST from Java

2002-02-20 Thread Colin Hardman
Thomas Down wrote > I'm not a Windows user. But one thing which occurs to > me: you're handling the output of the process on the same > thread as the Process itself. I always use separate threads > (I don't know if this is the `official' way of doing things, > but it's a pragmatic approach wh

RE: [Biojava-l] BLAST from Java

2002-02-20 Thread Russell Smithies
Thanx for your help, I've got it working OK now. I downloaded Blast from NCBI and now it works. Test code I'm using now is: ** import java.io.*; public class blasttest{ public static void main(String [] args)throws Exception{ //command strings for BLAST String [] cm

[Biojava-l] Schema and Docs for BioSQL

2002-02-20 Thread Marc Colosimo
Hi, Is there any information about using the BioSQL classes in BioJava, such as the schema for the database or examples in using it? I am interest in using postgre and biojava to store lots of sequence data. Thanks, Marc -- Marc E. Colosimo, Ph.D. Post Doctoral Fellow Brandeis University ___

Subject: Re: [Biojava-l] BLAST from Java

2002-02-20 Thread Tony Obermeit
Thomas Down wrote > I'm not a Windows user. But one thing which occurs to > me: you're handling the output of the process on the same > thread as the Process itself. I always use separate threads > (I don't know if this is the `official' way of doing things, > but it's a pragmatic approach wh

[Biojava-l] Ant-tized das-gui module

2002-02-20 Thread David Huen
I've just made an ant-compilable version of the current das-gui module. Are we agreeable on the classes being in org.biojava.bio.program.das.client? I think for safety I should upload it to a new module called das-client rather than attempting to modify the existing module. If we find that the n

RE: [Biojava-l] Propsed change for fastaFormat

2002-02-20 Thread Schreiber, Mark
Hi - I'm pretty sure the phredFormat should be immune to such a change. Mark Mark Schreiber Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 -Original Message- From: Cox, Greg [mailto:[EMAIL PROTECTED]] Sent: Tuesday, 19 February 2002 1

Re: [Biojava-l] Schema and Docs for BioSQL

2002-02-20 Thread Thomas Down
On Wed, Feb 20, 2002 at 01:52:10PM -0500, Marc Colosimo wrote: > Hi, > > Is there any information about using the BioSQL classes in BioJava, such > as the schema for the database or examples in using it? I am interest in > using postgre and biojava to store lots of sequence data. BioSQL is based

Re: [Biojava-l] Schema and Docs for BioSQL

2002-02-20 Thread Brian Gilman
Hello Thomas, What did you use to generate the postgres ddl?? I haven't found anything that works very well... Thanks! -b --- Brian Gilman <[EMAIL PROTECTED]> Sr. Software Engineer MIT/Whitehea

Re: [Biojava-l] Schema and Docs for BioSQL

2002-02-20 Thread Thomas Down
On Wed, Feb 20, 2002 at 06:16:12PM -0500, Brian Gilman wrote: > Hello Thomas, > > What did you use to generate the postgres ddl?? I haven't found > anything that works very well... The auto-generated version was produced by a Perl script written by Chris. It uses some standard parser modu

Re: [Biojava-l] Schema and Docs for BioSQL

2002-02-20 Thread Brian Gilman
No I meant the DDL conversion...Where can I get that script?? It sounds like something I could absolutely use!! -B --- Brian Gilman <[EMAIL PROTECTED]> Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research One Kendall Square, Bld

Re: [Biojava-l] Schema and Docs for BioSQL

2002-02-20 Thread Thomas Down
On Wed, Feb 20, 2002 at 06:27:13PM -0500, Brian Gilman wrote: > No I meant the DDL conversion...Where can I get that script?? It sounds > like something I could absolutely use!! cvs.open-bio.org:/home/repository/biosql Checkout the biosql-schemas module. Thomas. _

[Biojava-l] a newbie interested in trying biojava

2002-02-20 Thread mandavya
hi all, I am a biologist developing interest in bioinformatics. I have downloaded the following jar files from the biojava site. 1. biojava-1.11 2. biojava-20010702 3. biojava-20010920 4. biojava-20020111 5. bytecode-0.90 6. jakarta-regexp 7. xerces 8. xml I have my jdk1.3/bi

Re: [Biojava-l] a newbie interested in trying biojava

2002-02-20 Thread Thomas Down
On Thu, Feb 21, 2002 at 07:44:59AM +0530, mandavya wrote: > hi all, > I am a biologist developing interest in bioinformatics. > I have downloaded the following jar files from the biojava site. > 1. biojava-1.11 > 2. biojava-20010702 > 3. biojava-20010920 > 4. biojava-20020111 > 5. byte