[Biojava-l] http proxy

Dear all: There is a problem in biojava when using biofetch behind a firewall. There is no way to get the httpURLconnection object and set the http proxy. I think there are two solutions: 1. Modify biofetch of the OBDA proctocol, add proxyHost, proxyPort, Login, password to the tag-value pa

Re: [Biojava-l] http proxy

On Thu, Sep 18, 2003 at 04:45:06PM +0800, [EMAIL PROTECTED] wrote: > Dear all: > >There is a problem in biojava when using biofetch behind a firewall. There is no > way > to get the httpURLconnection object and set the http proxy. I think there are two > solutions: > 1. Modify biofetch of th

Re: [Biojava-l] position weight matrix

Schreiber, Mark wrote: Brian, I think we should change WeightMatrix so that N only scores a quater match of A where as R would score a half match. Do others feel this is sensible? - Mark We should be taking the odds score between the weight matrix matching at that pos and the null model - t

[Biojava-l] Biojava GUI and Applets

Hi, I updated Java Plugin, it didn't work. I could notice the following exceptions through Java Console: org.biojava.bio.BioError: Couldn't locate AlphabetManager.xml. This probably means that your biojava.jar file is corrupt or incorrectly built rethrown as org.biojava.bio.BioError: Unable to i

Re: [Biojava-l] Biojava GUI and Applets

Hi, If you remove biojava.jar either from the web server or from the applet tags, do you get exactly the same error? If so, then it looks like the applet's path is not being searched. What is the tag you are using to load the applet? Matthew [EMAIL PROTECTED] wrote: Hi, I updated Java Plugi

RE: [Biojava-l] http proxy

Hi - Unfortunately setting those parameters doesn't work for authenticating firewalls that require usernames and passwords. There needs to be a way to provide a Proxy to biofetch (or at least an input stream). - Mark -Original Message- From: Thomas Down [mailto:[EM

RE: [Biojava-l] Biojava GUI and Applets

Hi - It may also be that you compiled biojava without using Ant. If this is the case you need to place the files in biojava-live/resources into your classpath. - Mark -Original Message- From: Matthew Pocock [mailto:[EMAIL PROTECTED] Sent: Fri 19/09/2003 1:59

Re: Re: [Biojava-l] Biojava GUI and Applets

Hi, Yes, if I remove biojava.jar I get the same error I tried with and Errors remain CLASSPATH is set to C:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;. Also there is a copy of .jar files in C:\Archivos de programa\Java\j2re1.4.1_04\lib\applet, without this copy