>Actually, I am doing all of those things (Graphics2D object,
BufferedImage, etc.). I would like to get the >code that draws vertical
and horizontal labels and such. I have seen the results in Samiul Hasan's
thesis >paper. Ah! I forgot that I can use modern technology as a visual
aid.
>
To: [email protected]
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Help needed tp add "Number of Bits"
vertical and column number
labeling to DistributionLogos
Hello,
I would like to add a "2 Bits" vertical label (w
Hello,
I would like to add a "2 Bits" vertical label (with a bracket) and
column numbering to my DistributionLogos. I have seen both in some
graphics, but haven't been able to find the code in the demos or on the web.
Thanks,
Todd
___
Biojava-l ma
Thanks for all your ideas. It was really useful .
Parveen
Date: Wed, 30 Nov 2005 09:42:51 -0800 (PST)
From: "W. Eric Trull" <[EMAIL PROTECTED]>
Subject: [Biojava-l] help on blast
To: [email protected]
Cc: [EMAIL PROTECTED], [EMAIL PROTECTED]
Message-ID: < [EMAIL PROTECTED]&
I have the same situation where I work, except I have a Swing client instead
of an applet.
I decided to use NCBI's BLAST implementation
(http://www.ncbi.nlm.nih.gov/BLAST/download.shtml) invoked using a command to
org.biojava.utils.ExecRunner. I then wrapped the whole thing in a Web
Service, whic
Hi Parveen,
This might not be as easy as you might like.
The applet runs on the client, so you need the applet to communicate
remotely to the server to send the sequence. Then the easiest way would
be for the server to call blast on the command-line with the sequence
(which is pretty easy), parse
Hi
I'm pretty new to bioinformatics.i have to incorparate balst in my
applet.so that when the client enters the sequence ,it should perform the
blast search against the database we have and return the result.can anyone
guide me in this regard.
--
Regards
Parveen K
YOU MAY SAY I AM A DREAMER, B
t;[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
05/24/2005 02:39 AM
Please respond to Daniela Saccol
To: [email protected]
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Help me, please!!
Hi!
I am starting to work with the Biojava and I
Hi!
I am starting to work with the Biojava and I am finding problems for
which not meeting the answers. If somebody could help me, I would be
immensely been thankful. I have a HMM that have 81 main states, a
beginning state, an end state, 82 delete states and 82 insert states.
The states delete do
Hi all,
I am trying to turn a GenBank file to a Sequence object using
sequenceIterator interface in org.biojava.bio.seq package. However, one line
in the file cannot be parsed. The problem is information after that
unparsable line in the GenBank file are missing from the return Sequence
object. I
Hi,
I am new to Biojava. I just checked out biojava-live
from the cvs.biojava, and compiled the whole packages
and demos successfully. I want to run the BlastParser,
but I got the following errors. Can anybody tell me
how I run this program? Thanks very much!
-Yong
%java -classpath .:../biojava.
Once upon a time, Halfdan Rydbeck wrote:
>
> I have been trying to install BioJava on a Windows 2000 machine for a
> day now but cant get it to work.
> Maybe you could help me out here?
>
> I store my .jar-files (biojava-1.30-jdk14, bytecode-0.92,
> jakarta-regexp, xerces) in C:\biojava.
>
> M
Hello,
I have been trying to install BioJava on a Windows 2000 machine for a
day now but cant get it to work.
Maybe you could help me out here?
I store my .jar-files (biojava-1.30-jdk14, bytecode-0.92,
jakarta-regexp, xerces) in C:\biojava.
My classpath variable is set to the following:
C:\bio
Hello,
I have been trying to install BioJava on a Windows 2000 machine for a
day now but cant get it to work.
Maybe you could help me out here?
I store my .jar-files (biojava-1.30-jdk14, bytecode-0.92,
jakarta-regexp, xerces) in C:\biojava.
My classpath variable is set to the following:
C:\bio
gt; let us know and we can fix them up.
>
> - Mark
>
>
> > -Original Message-
> > From: Hailong Meng [mailto:[EMAIL PROTECTED]
> > Sent: Tuesday, 29 July 2003 4:46 a.m.
> > To: Matthew Pocock
> > Cc: Schreiber, Mark; [EMAIL PROTECTED]
> &g
Message-
> From: Hailong Meng [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, 29 July 2003 4:46 a.m.
> To: Matthew Pocock
> Cc: Schreiber, Mark; [EMAIL PROTECTED]
> Subject: Re: [Biojava-l] Help
>
>
> Hi Mark,
>
> But, how can I input the matrixes from the file to the cl
Hi Mark,
But, how can I input the matrixes from the file to the class
WeightMatrix. Because I did not find any method in class WeightMatrix
which can do that.
Thanks again.
Hailong
--
On Mon, 28 Jul 2003, Matthew Pocock wrote:
> Hi Hailong,
>
> List is nicer than arrays - use something like
Hi Hailong,
List is nicer than arrays - use something like this:
List matricies = new ArrayList();
... loop that loads the next matrix in ...
matricies.add(matrix);
... end of matrix loading loop ...
See java.util.List and java.util.Collection - also, Iterator is your
friend. The sun web site
ailto:[EMAIL PROTECTED]
> Sent: Sat 26/07/2003 8:13 a.m.
> To: [EMAIL PROTECTED]
> Cc:
> Subject: [Biojava-l] Help
>
>
>
> Hello,
>
> I am new to this list. I am planning to write a Java program to do
> some alignments. Ba
a.m.
To: [EMAIL PROTECTED]
Cc:
Subject: [Biojava-l] Help
Hello,
I am new to this list. I am planning to write a Java program to do
some alignments. Basically, the Java program will read two
files. One has a list
Hello,
I am new to this list. I am planning to write a Java program to do
some alignments. Basically, the Java program will read two
files. One has a list of motif matrixes and the other has a list of
sequences. My java program will scan the sequence file to find the
sequence which have the high s
L PROTECTED]>
(BTo: <[EMAIL PROTECTED]>
(BSent: Sunday, December 29, 2002 2:36 PM
(BSubject: [Biojava-l] help
(B
(B
(B> can anyone help me in this..
(B>
(B> may i know how to use "log" in Java.
(B> For example, this is the part that i need to use log algo
can anyone help me in this..
may i know how to use "log" in Java.
For example, this is the part that i need to use log algorithm:
g = (min + log((double)min)) ;
thanks
__
Do you Yahoo!?
Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
Hi,
I am trying to do BLAST from NCBI site directly. Everything is working finebut the problem is while retreiving my program is stopping when ever the status issearching and coming out.
How should I make my application to work and get the complete results withoutstoping in between.
with regar
Hi,
I am presently working on BioJava. I want to retrieve the data from NCBI Site. I have gone though the mailing list and I have tried all of them.
1. I have found blastcl3.exe instead of blastall.exe Which is the best as I am not able to find out blastall.exe 2. I am not able t
Hi -
I have been using the following snippet of code to read files from xembl
that are in AGAVE format. Features seem to be added to the constructed
sequence object ok but annotations seem to go missing.
Do I need to add some sort of listener somewhere? I'm a bit concerned
about using the SeqIOA
rewall doesn't allow ping...
>
> Regards,
>
> Jonathan
>
>
> -Original Message-
> From: Thomas Down [mailto:[EMAIL PROTECTED]]
> Sent: 18 April 2002 10:30
> To: Radford, Jonathan
> Cc: 'David Huen'; '[EMAIL PROTECTED]'
> Subject: Re: [Bio
2 10:30
To: Radford, Jonathan
Cc: 'David Huen'; '[EMAIL PROTECTED]'
Subject: Re: [Biojava-l] HELP (www/cvs.biojava access)
On Thu, Apr 18, 2002 at 10:10:05AM +0100, Radford, Jonathan wrote:
> Has access changed from cvs.biojava.org:2401 to cvs.open-bio.org:2401 ?
>
>
On Thu, Apr 18, 2002 at 10:10:05AM +0100, Radford, Jonathan wrote:
> Has access changed from cvs.biojava.org:2401 to cvs.open-bio.org:2401 ?
>
> I noticed the CVS instructions on the www.biojava.org site indicate you
> login with
>
> cvs -d :pserver:[EMAIL PROTECTED]:/home/repository/biojava log
: David Huen [mailto:[EMAIL PROTECTED]]
Sent: 18 April 2002 10:02
To: Radford, Jonathan
Cc: '[EMAIL PROTECTED]'
Subject: Re: [Biojava-l] HELP (www/cvs.biojava access)
On Thu, 18 Apr 2002, Radford, Jonathan wrote:
> I cannot access cvs.biojava.org anymore, has the password changed or
On Thu, 18 Apr 2002, Radford, Jonathan wrote:
> I cannot access cvs.biojava.org anymore, has the password changed or is CVS
> down ?
>
I've been having a peculiarity with www.biojava.org - I can't get to it
from the university network (Janet) but I can from home. The problem
began recently. Do
I cannot access cvs.biojava.org anymore, has the password changed or is CVS
down ?
Thanks,
Jonathan Radford
AstraZeneca
___
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If Matthew's classpath doesn't work, also try
CLASSPATH=c:\biojava\biojava\biojava-1.21.jar;c:\biojava\bytecode-0.90.jar;c
:\biojava\xerces.jar;.
I'm not sure how windows handles multiple '.'s in a file name, you may have
to rename the jars to biojava.jar and bytecode.jar.
Greg
_
Hi Dr Chen,
You say that you have placed the jar files in a
c:\biojava directory, but your classpath entries don't seem to be respecting
this. Have you tried the classpath:
set
CLASSPATH=CLASSPATH=C:\biojava\biojava.jar;C:\biojava\xerces.jar;C:\biojava\bytecode.jar;.
A good check to mak
On Fri, 22 Mar 2002, YiZhou Chen wrote:
> Dear Biojava friends
>
> I have donwnloaded the three files biojava-1.21jar, bytecode-0.90.jar and
> xerces.ar on my windows2000 machine. I put them in the
> directory c:\biojava. I set up the class path
> CLASSPATH=C:\biojava.jar;C:\xerces.jar;C:\by
Dear Biojava friends
I have donwnloaded the three files biojava-1.21jar, bytecode-0.90.jar and
xerces.ar on my windows2000 machine. I put them in the directory
c:\biojava. I set up the class path
CLASSPATH=C:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;.using control
panel , system, user variables.
Could you send in the run-time error that you see (stack-trace and all)?
Also, if the error happens for one file only, could you send us that file?
Thanks.
M
RAMANA wrote:
> Hello This is ramana from GalaInfotek,
>
> please go through the programme, i am compiling th eprogram successfully
>
mailto:[EMAIL PROTECTED]]
> Sent: Thursday, June 07, 2001 11:21 PM
> To: [EMAIL PROTECTED]
> Subject: [Biojava-l] Help me on Clustering
>
>
> Dear Sir/Madam
>
> I want to use your packages for clustering is it any
> example programme is
> there for this clustering
9175
> -Original Message-
> From: Suryavas .K [mailto:[EMAIL PROTECTED]]
> Sent: Thursday, June 07, 2001 11:22 PM
> To: [EMAIL PROTECTED]
> Subject: [Biojava-l] Help me on Clustering
>
>
> Dear Sir/Madam
>
> I want to use your packages for clustering is it any
Dear Sir/Madam
I want to use your packages for clustering is it any example programme is
there for this clustering using your packages.
___
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
Dear Sir/Madam
I want to use your packages for clustering is it any example programme is
there for this clustering using your packages.
I found some Classes and Interfaces on Sequences Alignment and
SimpleAlignment how to use these classes.
I downloaded completed zip files but i am confus
Our requirement is to read the Chromosome information from GenBank
and populate the biojava objects like SimpleGene, SimpleExon, etc.
I understand we need to use the SeqIOTool class. We are unable to locate
this class
in the jar file we downloaded named "biojava-20010126.jar".
Please help us ou
On Wed, Apr 11, 2001 at 03:27:55PM +0100, Jolyon Holdstock wrote:
> i have downloaded biojava and have a problem compiling the demos. with
> GCContent.java i get a cannot resolve symbol for SeqTools.
> the other classes are seen fine so my classpath should be ok; this is on
> windows but i have h
i have downloaded biojava and have a problem compiling the demos. with
GCContent.java i get a cannot resolve symbol for SeqTools.
the other classes are seen fine so my classpath should be ok; this is on
windows but i have had similar probles on unix.
building the source on unix gave me errors wi
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