From bugzilla-daemon at portal.open-bio.org  Thu Apr  2 00:22:26 2009
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 2 Apr 2009 00:22:26 -0400
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200904020422.n324MQqk017453@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #14 from gwaldon at geneinfinity.org  2009-04-02 00:22 EST -------
I am closing this. Please reopen if the bug reappears.


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From simpleyrx at 163.com  Thu Apr  2 11:31:03 2009
From: simpleyrx at 163.com (simpleyrx)
Date: Thu, 2 Apr 2009 23:31:03 +0800 (CST)
Subject: [Biojava-dev] How to convert a multiple alignment to a PSSM matrix ?
Message-ID: <11965100.460701238686263309.JavaMail.coremail@bj163app72.163.com>


Hi, friends,
 
  I have a question: How to convert a multiple alignment to a PSSM matrix ?  Is there any code in Biojava implement the function ? Or is there other source code have the function ?
 
Student
 

From markjschreiber at gmail.com  Thu Apr  2 20:07:58 2009
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 3 Apr 2009 08:07:58 +0800
Subject: [Biojava-dev] How to convert a multiple alignment to a PSSM
	matrix ?
In-Reply-To: <93b45ca50904021707h786aeac9sd12f3cd592303981@mail.gmail.com>
References: <11965100.460701238686263309.JavaMail.coremail@bj163app72.163.com>
	<93b45ca50904021707h786aeac9sd12f3cd592303981@mail.gmail.com>
Message-ID: <93b45ca50904021707m1cfd068fv5766e4531bab7991@mail.gmail.com>

There is a class called a WeightMatrix. I think there is an example on the
cookbook.

On 2 Apr 2009, 11:47 PM, "simpleyrx" <simpleyrx at 163.com> wrote:


Hi, friends,

 I have a question: How to convert a multiple alignment to a PSSM matrix ?
 Is there any code in Biojava implement the function ? Or is there other
source code have the function ?

Student


_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev

From bugzilla-daemon at portal.open-bio.org  Sun Apr  5 13:07:48 2009
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 5 Apr 2009 13:07:48 -0400
Subject: [Biojava-dev] [Bug 2434] bio.seq.io.UniProtFormat error?
In-Reply-To: <bug-2434-485@http.bugzilla.open-bio.org/>
Message-ID: <200904051707.n35H7mYs013873@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2434


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from gwaldon at geneinfinity.org  2009-04-05 13:07 EST -------
Fixed UniprotFormat; IPI files are now accepted by the parser.


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From holland at eaglegenomics.com  Mon Apr  6 04:56:44 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 06 Apr 2009 09:56:44 +0100
Subject: [Biojava-dev] Leadership
Message-ID: <49D9C3CC.7010000@eaglegenomics.com>

Hi all.

There were no nominations for the BioJava leadership role by the end of
last week, so I would like to nominate Andreas Prlic to take over the
role as BioJava coordinator/project manager. Andreas has agreed to be
nominated.

If there are no objections lodged on this list by next Monday (13th
April), I'll hand over to Andreas by the end of next week.

thanks,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From heuermh at acm.org  Mon Apr  6 15:43:02 2009
From: heuermh at acm.org (Michael Heuer)
Date: Mon, 6 Apr 2009 15:43:02 -0400 (EDT)
Subject: [Biojava-dev] Leadership
In-Reply-To: <49D9C3CC.7010000@eaglegenomics.com>
Message-ID: <Pine.GSO.4.44.0904061539210.22871-100000@shell3.shore.net>

Richard Holland wrote:

> Hi all.
>
> There were no nominations for the BioJava leadership role by the end of
> last week, so I would like to nominate Andreas Prlic to take over the
> role as BioJava coordinator/project manager. Andreas has agreed to be
> nominated.
>
> If there are no objections lodged on this list by next Monday (13th
> April), I'll hand over to Andreas by the end of next week.

+1

Andreas has my support.

   michael


From jacobsen at ebi.ac.uk  Mon Apr  6 18:19:58 2009
From: jacobsen at ebi.ac.uk (Jules Jacobsen)
Date: Mon, 6 Apr 2009 23:19:58 +0100
Subject: [Biojava-dev] Leadership
In-Reply-To: <Pine.GSO.4.44.0904061539210.22871-100000@shell3.shore.net>
References: <49D9C3CC.7010000@eaglegenomics.com>
	<Pine.GSO.4.44.0904061539210.22871-100000@shell3.shore.net>
Message-ID: <12c279870904061519w655f9a98x604f53415022e79f@mail.gmail.com>

I third that.

On Mon, Apr 6, 2009 at 8:43 PM, Michael Heuer <heuermh at acm.org> wrote:
> Richard Holland wrote:
>
>> Hi all.
>>
>> There were no nominations for the BioJava leadership role by the end of
>> last week, so I would like to nominate Andreas Prlic to take over the
>> role as BioJava coordinator/project manager. Andreas has agreed to be
>> nominated.
>>
>> If there are no objections lodged on this list by next Monday (13th
>> April), I'll hand over to Andreas by the end of next week.
>
> +1
>
> Andreas has my support.
>
> ? michael
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Dr Jules Jacobsen

UniProt-PDB Integration
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK


From andreas at sdsc.edu  Tue Apr  7 01:50:50 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 6 Apr 2009 22:50:50 -0700
Subject: [Biojava-dev] Leadership
In-Reply-To: <49D9C3CC.7010000@eaglegenomics.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
Message-ID: <59a41c430904062250l25a1105dw505ce3edc2651184@mail.gmail.com>

Hi Richard,

Thanks for the nomination. In short I am intending to do the following
things over the next couple of months:

* Release biojava 1.7 - don't forget, code freeze will be on Wed.
April 8th. Please commit your final changes for this release in the
next couple of days, or let me know if you need more time asap.

* Keep maintaining biojava nightly builds at http://www.spice-3d.org/cruise/

* Organize a biojava user meeting around BOSC / ISMB 2009

* After the biojava 1.7 release I want to have a discussion how to
continue with the code base and what to change for the next major
release.

* I will actively seek and invite new contributors and package maintainers.

* My main focus are the further development of the protein structure
related modules. As such I will need YOUR help for maintaining blast,
sequence and any of the other frequently used modules.

Andreas




On Mon, Apr 6, 2009 at 1:56 AM, Richard Holland
<holland at eaglegenomics.com> wrote:
> Hi all.
>
> There were no nominations for the BioJava leadership role by the end of
> last week, so I would like to nominate Andreas Prlic to take over the
> role as BioJava coordinator/project manager. Andreas has agreed to be
> nominated.
>
> If there are no objections lodged on this list by next Monday (13th
> April), I'll hand over to Andreas by the end of next week.
>
> thanks,
> Richard
>
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From holland at eaglegenomics.com  Tue Apr  7 06:09:25 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 07 Apr 2009 11:09:25 +0100
Subject: [Biojava-dev] Leadership
In-Reply-To: <59a41c430904062250l25a1105dw505ce3edc2651184@mail.gmail.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
	<59a41c430904062250l25a1105dw505ce3edc2651184@mail.gmail.com>
Message-ID: <49DB2655.1080500@eaglegenomics.com>

I'd be happy to maintain the parts you request.

Andreas Prlic wrote:
> Hi Richard,
> 
> Thanks for the nomination. In short I am intending to do the following
> things over the next couple of months:
> 
> * Release biojava 1.7 - don't forget, code freeze will be on Wed.
> April 8th. Please commit your final changes for this release in the
> next couple of days, or let me know if you need more time asap.
> 
> * Keep maintaining biojava nightly builds at http://www.spice-3d.org/cruise/
> 
> * Organize a biojava user meeting around BOSC / ISMB 2009
> 
> * After the biojava 1.7 release I want to have a discussion how to
> continue with the code base and what to change for the next major
> release.
> 
> * I will actively seek and invite new contributors and package maintainers.
> 
> * My main focus are the further development of the protein structure
> related modules. As such I will need YOUR help for maintaining blast,
> sequence and any of the other frequently used modules.
> 
> Andreas
> 
> 
> 
> 
> On Mon, Apr 6, 2009 at 1:56 AM, Richard Holland
> <holland at eaglegenomics.com> wrote:
>> Hi all.
>>
>> There were no nominations for the BioJava leadership role by the end of
>> last week, so I would like to nominate Andreas Prlic to take over the
>> role as BioJava coordinator/project manager. Andreas has agreed to be
>> nominated.
>>
>> If there are no objections lodged on this list by next Monday (13th
>> April), I'll hand over to Andreas by the end of next week.
>>
>> thanks,
>> Richard
>>
>> --
>> Richard Holland, BSc MBCS
>> Finance Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>> http://www.eaglegenomics.com/
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From andreas at sdsc.edu  Sat Apr 11 15:05:44 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 11 Apr 2009 12:05:44 -0700
Subject: [Biojava-dev] BOSC abstract
Message-ID: <59a41c430904111205p624821aarf6124d0db2bb7eb9@mail.gmail.com>

Hi,

Submision deadline for the BOSC abstract is on Monday.  The current
version is available at
http://biojava.org/wiki/BOSC2009_Presentation#BioJava_2009:__an_Open-Source_Framework_for_Bioinformatics.
If you are one of the co-authors, can you please make sure I got your
affiliation right? Also if you have any additions or corrections to
the abstract, please feel free to edit. If I missed anybody who should
be co-author, please edit as well...

Andreas

From holland at eaglegenomics.com  Sun Apr 12 06:49:54 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Sun, 12 Apr 2009 11:49:54 +0100
Subject: [Biojava-dev] BOSC abstract
In-Reply-To: <59a41c430904111205p624821aarf6124d0db2bb7eb9@mail.gmail.com>
References: <59a41c430904111205p624821aarf6124d0db2bb7eb9@mail.gmail.com>
Message-ID: <49E1C752.6080702@eaglegenomics.com>

looks good!

Andreas Prlic wrote:
> Hi,
> 
> Submision deadline for the BOSC abstract is on Monday.  The current
> version is available at
> http://biojava.org/wiki/BOSC2009_Presentation#BioJava_2009:__an_Open-Source_Framework_for_Bioinformatics.
> If you are one of the co-authors, can you please make sure I got your
> affiliation right? Also if you have any additions or corrections to
> the abstract, please feel free to edit. If I missed anybody who should
> be co-author, please edit as well...
> 
> Andreas
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From andreas at sdsc.edu  Sun Apr 12 22:47:26 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 12 Apr 2009 19:47:26 -0700
Subject: [Biojava-dev] BioJava 1.7 released
Message-ID: <59a41c430904121947v67c7a7f9v1a236d3ad695760f@mail.gmail.com>

Biojava 1.7 has been released and is available from
http://biojava.org/wiki/BioJava:Download

BioJava is a mature open-source project that provides a framework for
processing of biological data. BioJava contains powerful analysis and
statistical routines, tools for parsing common file formats, and
packages for manipulating sequences and 3D structures. It enables
rapid bioinformatics application development in the Java programming
language.

Besides numerous bug fixes and stability improvements, a lot of
development has been going on in the protein structure modules.
BioJava now provides a framework for parsing mmCif files. The parsing
of PDB header information has been improved and a new tool to read the
Chemical component dictionary is in place.  Biojava 1.7 offers more
functionality and stability over the previous official releases.  We
highly recommend you to upgrade as soon as possible.

Thanks to all contributors for making this release possible.

Happy Biojava-ing,

Andreas

From holland at eaglegenomics.com  Tue Apr 14 04:33:05 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 14 Apr 2009 09:33:05 +0100
Subject: [Biojava-dev]  Leadership
In-Reply-To: <49D9C3CC.7010000@eaglegenomics.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
Message-ID: <49E44A41.2010703@eaglegenomics.com>

Hello again.

Well, nobody objected, and several people supported the idea, so I would
now like to formally hand over control of the BioJava project to Andreas
Prlic with immediate effect.

It's been good fun working with the project over the last 5 years, and
although I'll no longer be in charge, I will still remain on the mailing
lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.

I'll also continue to attend BOSC, including this year in Stockholm, so
I'm looking forward to meeting up with everyone there for a beer or two.

Thanks for the help and support everyone's given, and I'm sure you'll
join me in wishing Andreas the best of luck with the project. He'll be
an excellent leader and with him in charge I believe the project will go
from strength to strength.

cheers,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From holland at eaglegenomics.com  Tue Apr 14 11:07:15 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 14 Apr 2009 16:07:15 +0100
Subject: [Biojava-dev] [Biojava-l]  Leadership
In-Reply-To: <7ceb4beb0904140802g39aa0d0bo7e536fb45523bb78@mail.gmail.com>
References: <49D9C3CC.7010000@eaglegenomics.com>	
	<49E44A41.2010703@eaglegenomics.com>
	<7ceb4beb0904140802g39aa0d0bo7e536fb45523bb78@mail.gmail.com>
Message-ID: <49E4A6A3.6030005@eaglegenomics.com>

The plan was to create separate new BJ3 jars for task-specific code,
exactly as you suggest for phylogenetics. I'd support a biojava-phylo
jar of some kind, and I agree it would probably depend on the BJ3
biojava-core module for sequence handling. The existing BJ code was not
originally going to be refactored into separate jars, unless Andreas has
other plans!

Scooter Willis wrote:
> Andreas
> 
> Congrats on taking on the responsibility of steering BioJava in a
> positive direction.
> 
> I needed the ability to generate phylogenetic trees from aligned
> sequence data and found that the work was started in a google summer
> project but looking at the code it wasn't finished and appeared to focus
> only on loading trees not creating them. I ended up taking the tree
> generation code out of jalview and removing as much jalview dependencies
> as possible and have it as a nice tight collection of classes. My
> assumption without any deep legal review is that because jalview is open
> source that the code can be used and contributed to another open source
> project like BioJava. I will also plan on contributing the code changes
> back to Jalview.
> 
> One of the challenges I ran into with the JalView code is performance
> for building the tree when using 1800+ sequences(takes a very very long
> time) so I am doing some code optimization and finishing up testing on a
> fairly significant performance speedup doing Neighbor_Join with a
> slightly different approach that makes it N2 instead of N3. I have a
> couple things to fix in tree joinging code and then will compare results
> for the quality of the tree compared to the original distance matrix. I
> should know more this week.
> 
> I think I remember a BioJava discussion about trying to seperate parts
> and pieces to that if you try and use a particular feature set of
> BioJava you are not forced into absorbing the entire BioJava collection
> of Jars. In my case I would want a biojava-phylogenetic.jar that has all
> things related to tree creation and/or tree viewing etc. If the common
> data format for handling sequences is RichSequence or Sequence then I
> would expect to have one other Jar requirement of biojava-core.jar. Not
> sure if any work has been done to refactor the BioJava code base into
> multiple jar files in the same way apache does its jars for great java
> code geared to a specific problem domain.
> 
> Let me know what I can do to assist moving forward.
> 
> Thanks
> 
> Scooter Willis
> 
> On Tue, Apr 14, 2009 at 4:33 AM, Richard Holland
> <holland at eaglegenomics.com <mailto:holland at eaglegenomics.com>> wrote:
> 
>     Hello again.
> 
>     Well, nobody objected, and several people supported the idea, so I would
>     now like to formally hand over control of the BioJava project to Andreas
>     Prlic with immediate effect.
> 
>     It's been good fun working with the project over the last 5 years, and
>     although I'll no longer be in charge, I will still remain on the mailing
>     lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.
> 
>     I'll also continue to attend BOSC, including this year in Stockholm, so
>     I'm looking forward to meeting up with everyone there for a beer or two.
> 
>     Thanks for the help and support everyone's given, and I'm sure you'll
>     join me in wishing Andreas the best of luck with the project. He'll be
>     an excellent leader and with him in charge I believe the project will go
>     from strength to strength.
> 
>     cheers,
>     Richard
> 
>     --
>     Richard Holland, BSc MBCS
>     Finance Director, Eagle Genomics Ltd
>     T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>     <mailto:holland at eaglegenomics.com>
>     http://www.eaglegenomics.com/
>     _______________________________________________
>     Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>     <mailto:Biojava-l at lists.open-bio.org>
>     http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From andreas at sdsc.edu  Tue Apr 14 12:45:21 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 14 Apr 2009 09:45:21 -0700
Subject: [Biojava-dev] Leadership
In-Reply-To: <49E44A41.2010703@eaglegenomics.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
	<49E44A41.2010703@eaglegenomics.com>
Message-ID: <59a41c430904140945t30911e33idc8ea095c52e59e3@mail.gmail.com>

Hi Richard,

Again, thanks for your BioJava contributions in the last years and
great to have you still around.

I am looking forward to the next year of BioJava development. Our
google analytics stats reveal that we have an ever growing user base
and it will be a challenge to continue developing BioJava further and
add new and useful features. Of course this is a task that I can't do
alone and I will need the help of everybody who wants to write
documentation, submit bug fixes or wants to become maintainer of one
of the modules.

With BioJava 1.7 being out it is now a good time to start a discussion
at how to improve the code base for the next version.

We also have BOSC coming up in June and it will provide a good
opportunity for people to meet in person.

Hope to see you (Richard, and everybody else!) in Sweden, otherwise we
will keep talking via the lists.

Andreas




On Tue, Apr 14, 2009 at 1:33 AM, Richard Holland
<holland at eaglegenomics.com> wrote:
> Hello again.
>
> Well, nobody objected, and several people supported the idea, so I would
> now like to formally hand over control of the BioJava project to Andreas
> Prlic with immediate effect.
>
> It's been good fun working with the project over the last 5 years, and
> although I'll no longer be in charge, I will still remain on the mailing
> lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.
>
> I'll also continue to attend BOSC, including this year in Stockholm, so
> I'm looking forward to meeting up with everyone there for a beer or two.
>
> Thanks for the help and support everyone's given, and I'm sure you'll
> join me in wishing Andreas the best of luck with the project. He'll be
> an excellent leader and with him in charge I believe the project will go
> from strength to strength.
>
> cheers,
> Richard
>
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>

From gwaldon at geneinfinity.org  Tue Apr 14 13:32:52 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 14 Apr 2009 13:32:52 -0400
Subject: [Biojava-dev] [Biojava-l]  Leadership
Message-ID: <20090414173252.52004.qmail@mxw1102.verio-web.com>

Hi Scooter,

This is not so simple because Jalview is under the GNU General Public License while Biojava is under the Lesser GPL. The simplest way might be to have the authors of the part of Jalview you are interested in to release their code under the LGPL.

Best,
George


> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-
> bounces at lists.open-bio.org] On Behalf Of Scooter Willis
> Sent: Tuesday, April 14, 2009 8:02 AM
> To: Richard Holland
> Cc: biojava-dev; biojava-l at biojava.org
> Subject: Re: [Biojava-l] [Biojava-dev] Leadership
> 

> My assumption without any deep legal
> review is that because jalview is open source that the code can be used
> and
> contributed to another open source project like BioJava. I will also plan
> on
> contributing the code changes back to Jalview.

From andreas at sdsc.edu  Wed Apr 15 01:40:24 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 14 Apr 2009 22:40:24 -0700
Subject: [Biojava-dev] [Biojava-l]  Leadership
In-Reply-To: <7ceb4beb0904140802g39aa0d0bo7e536fb45523bb78@mail.gmail.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
	<49E44A41.2010703@eaglegenomics.com>
	<7ceb4beb0904140802g39aa0d0bo7e536fb45523bb78@mail.gmail.com>
Message-ID: <59a41c430904142240u5a9812eejf11023f69baa27b7@mail.gmail.com>

Hi Scooter,

Thanks for volunteering. I like the idea of modularizing BioJava in
the next version. The details of how to do this still need to be
discussed on the dev mailing list. If you want to be involved into
anything phylo related then this is great and any contribution will be
welcome.

About merging in 3rd party code that is under a different license: For
this you need to get  permission from the original copyright owners or
rewrite the code ....

Andreas


On Tue, Apr 14, 2009 at 8:02 AM, Scooter Willis <willishf at ufl.edu> wrote:
> Andreas
>
> Congrats on taking on the responsibility of steering BioJava in a positive
> direction.
>
> I needed the ability to generate phylogenetic trees from aligned sequence
> data and found that the work was started in a google summer project but
> looking at the code it wasn't finished and appeared to focus only on loading
> trees not creating them. I ended up taking the tree generation code out of
> jalview and removing as much jalview dependencies as possible and have it as
> a nice tight collection of classes. My assumption without any deep legal
> review is that because jalview is open source that the code can be used and
> contributed to another open source project like BioJava. I will also plan on
> contributing the code changes back to Jalview.
>
> One of the challenges I ran into with the JalView code is performance for
> building the tree when using 1800+ sequences(takes a very very long time) so
> I am doing some code optimization and finishing up testing on a fairly
> significant performance speedup doing Neighbor_Join with a slightly
> different approach that makes it N2 instead of N3. I have a couple things to
> fix in tree joinging code and then will compare results for the quality of
> the tree compared to the original distance matrix. I should know more this
> week.
>
> I think I remember a BioJava discussion about trying to seperate parts and
> pieces to that if you try and use a particular feature set of BioJava you
> are not forced into absorbing the entire BioJava collection of Jars. In my
> case I would want a biojava-phylogenetic.jar that has all things related to
> tree creation and/or tree viewing etc. If the common data format for
> handling sequences is RichSequence or Sequence then I would expect to have
> one other Jar requirement of biojava-core.jar. Not sure if any work has been
> done to refactor the BioJava code base into multiple jar files in the same
> way apache does its jars for great java code geared to a specific problem
> domain.
>
> Let me know what I can do to assist moving forward.
>
> Thanks
>
> Scooter Willis
>
> On Tue, Apr 14, 2009 at 4:33 AM, Richard Holland
> <holland at eaglegenomics.com>wrote:
>
>> Hello again.
>>
>> Well, nobody objected, and several people supported the idea, so I would
>> now like to formally hand over control of the BioJava project to Andreas
>> Prlic with immediate effect.
>>
>> It's been good fun working with the project over the last 5 years, and
>> although I'll no longer be in charge, I will still remain on the mailing
>> lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.
>>
>> I'll also continue to attend BOSC, including this year in Stockholm, so
>> I'm looking forward to meeting up with everyone there for a beer or two.
>>
>> Thanks for the help and support everyone's given, and I'm sure you'll
>> join me in wishing Andreas the best of luck with the project. He'll be
>> an excellent leader and with him in charge I believe the project will go
>> from strength to strength.
>>
>> cheers,
>> Richard
>>
>> --
>> Richard Holland, BSc MBCS
>> Finance Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>> http://www.eaglegenomics.com/
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From jolyon.holdstock at ogt.co.uk  Fri Apr 17 06:27:16 2009
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Fri, 17 Apr 2009 11:27:16 +0100
Subject: [Biojava-dev] User interface example for Cookbook
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F026D7EAC@EUCLID.internal.ogtip.com>

Hi,

 

I've been meaning to generate an updated example of code for displaying
a sequence (with some additional functionality) for the cookbook and
finally got off my backside to do it.

 

Code is below; I hope it's of use - feel free to point out errors,
improvements etc...

 

Cheers,

 

Jolyon

 

 

//Code starts
------------------------------------------------------------------------
-------------------

//Java libraries

import java.awt.*;

import java.awt.event.*;

import java.io.*;

import java.util.*;

import javax.swing.*;

//BioJava libraries

import org.biojava.bio.*;

import org.biojava.bio.seq.*;

import org.biojava.bio.gui.sequence.*;

//BioJava extension libraries

import org.biojavax.*;

import org.biojavax.ontology.*;

import org.biojavax.bio.seq.*;

 

public class DisplaySequenceFile extends JFrame implements
SequenceViewerMotionListener {

  private TranslatedSequencePanel tsp = new TranslatedSequencePanel();

  private MultiLineRenderer mlr = new MultiLineRenderer();

  private RulerRenderer rr = new RulerRenderer();

  private SequenceRenderer seqR = new SymbolSequenceRenderer();

  private FeatureBlockSequenceRenderer fbsr;

  private RichSequence richSeq;

  

  private Container con;

  private JPanel controlPanel;

  private JButton mvLeft, mvRight, zoomIn, zoomOut;

  private double sequenceScale = 0.05;

  private int windowWidth = 1200;

  private int windowHeight = 200;

  

  public DisplaySequenceFile(String fileName){

    //Load the sequence file

    try {

      richSeq = RichSequence.IOTools.readEMBLDNA(new BufferedReader(new
FileReader(new File(fileName))), null).nextRichSequence();

    }

    catch (BioException bioe){

      System.err.println("Not an EMBL sequence" + bioe);

    }

    catch(FileNotFoundException fnfe){

       System.err.println("FileNotFoundException: " + fnfe);

    }

    catch (IOException ioe){

      System.err.println("IOException: " + ioe);

    }

    

    //Define the appearance of the rendered Features

    BasicFeatureRenderer bfr = new BasicFeatureRenderer();

    GradientPaint gradient = new GradientPaint(0, 10, Color.RED, 0, 0,
Color.white, true);

    bfr.setFill(gradient);

    bfr.setOutline(Color.RED);

    

    //Form a bridge between Sequence rendering and Feature rendering

    fbsr = new FeatureBlockSequenceRenderer(bfr);

    fbsr.setCollapsing(false);

    

    //Filter for CDS features on the forward strand

    SequenceRenderer fwd_sr = new FilteringRenderer(fbsr, 

            new FeatureFilter.And(new FeatureFilter.ByType("CDS"), 

            new FeatureFilter.StrandFilter(StrandedFeature.POSITIVE)), 

            true);

    //Filter for CDS features on the reverse strand

    SequenceRenderer rev_sr = new FilteringRenderer(fbsr, 

            new FeatureFilter.And(new FeatureFilter.ByType("CDS"), 

            new FeatureFilter.StrandFilter(StrandedFeature.NEGATIVE)), 

            true);

    

    //Add the renderers to the MultiLineRenderer

    mlr.addRenderer(fwd_sr);

    mlr.addRenderer(rr);

    mlr.addRenderer(rev_sr);

    mlr.addRenderer(seqR);

    

    //Set the sequence renderer for the TranslatedSequencePanel

    tsp.setRenderer(mlr);

    //Set the sequence to render

    tsp.setSequence(richSeq);

    //Set the position of the displayed sequence

    tsp.setSymbolTranslation(1);

    //Set the scale as pixels per Symbol.    

    tsp.setScale(sequenceScale);

    

    //Add a sequence viewer motion listener to the
TranslateSequencePanel

    tsp.addSequenceViewerMotionListener(this);

    

    //Generate the control panel

    controlPanel = new JPanel();

    controlPanel.setBackground(Color.lightGray);

    //Move along the sequence towards 5' end 

    mvLeft = new JButton("<<");

    mvLeft.addActionListener(new ActionListener(){

      public void actionPerformed(ActionEvent ae){

        int rightSide = tsp.getRange().getMax();

        int leftSide = tsp.getRange().getMin();

        int newStartPoint = leftSide - (rightSide - leftSide);

        if (newStartPoint < 1){

          newStartPoint = 1;

        }

        tsp.setSymbolTranslation(newStartPoint);  

      }

    });

    //Move along the sequence towards 3' end 

    mvRight = new JButton(">>");

    mvRight.addActionListener(new ActionListener(){

      public void actionPerformed(ActionEvent ae){

        int rightSide = tsp.getRange().getMax();

        int leftSide = tsp.getRange().getMin();

        int screenWidth = rightSide - leftSide;

        if ((rightSide + screenWidth) >= richSeq.length()){

          tsp.setSymbolTranslation(richSeq.length() - screenWidth);

        }

        else {

          tsp.setSymbolTranslation(rightSide); 

        }

      }

    });

    //Increase sequence scale

    zoomIn = new JButton("+");

    zoomIn.addActionListener(new ActionListener(){

      public void actionPerformed(ActionEvent ae){

        sequenceScale = sequenceScale * 2;

        //if sequence scale = 12 the bases are rendered

        //no need to zoom in further so disable the button.

        if (sequenceScale > 12){

          sequenceScale = 12;

          zoomIn.setEnabled(false);

        }

        tsp.setScale(sequenceScale);

      }

    });

    //Reduce sequence scale

    zoomOut = new JButton("-");

    zoomOut.addActionListener(new ActionListener(){

      public void actionPerformed(ActionEvent ae){

        sequenceScale = sequenceScale / 2;

        //if sequence scale is below 12 the enable zoomIn button

        if (sequenceScale < 12){

          zoomIn.setEnabled(true);

        }

        //If the scale allows more than the sequence to be displayed

        //display the whole sequence

        if (sequenceScale <
((double)tsp.getWidth()/(double)richSeq.length())){

          sequenceScale =
(double)tsp.getWidth()/(double)richSeq.length();

          tsp.setSymbolTranslation(1);

        }

        tsp.setScale(sequenceScale);

        //If the new scale coupled with the current SymbolTranslation
means the 

        //displayed can't fill the TranslatedSequencePanel then reset
the SymbolTranlstion

        if(tsp.getRange().getMax() >= richSeq.length()){

          int tmp = (int)((double)tsp.getWidth()/sequenceScale);

          tsp.setSymbolTranslation(richSeq.length() - tmp); 

        }

      }

    });

    controlPanel.add(mvLeft);

    controlPanel.add(mvRight);

    controlPanel.add(zoomIn);

    controlPanel.add(zoomOut);

    

    con = new Container();

    con = getContentPane();

    con.setLayout(new BorderLayout());

    con.add(controlPanel, BorderLayout.NORTH);

    con.add(tsp, BorderLayout.CENTER);

    setLocation(50,50);

    setSize(windowWidth,windowHeight);

    setVisible(true);

    setResizable(false);

  }

  

  /**

   * Detect mouse dragged events

   * @param sve

   */

  public void mouseDragged(SequenceViewerEvent sve) {

  }

  

  /**

   * Detect mouse movement events

   * If the mouse moves over a CDS feature create a tooltiptext stating
the 

   * the name of the gene associated with the CDS feature.

   * @param sve

   */

  public void mouseMoved(SequenceViewerEvent sve) {

    //Manage the tooltip

    ToolTipManager ttm = ToolTipManager.sharedInstance();

    ttm.setDismissDelay(2000);

    //If the mouse have moved over a SimpleFeatureHolder 

    if (sve.getTarget() instanceof SimpleFeatureHolder){

      ComparableTerm gene =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");

      SimpleFeatureHolder sfh = (SimpleFeatureHolder)sve.getTarget();

      FeatureHolder fh = sfh.filter(new FeatureFilter.ByType("CDS"));

      Iterator <RichFeature> i =  fh.features();

      while(i.hasNext()){

        RichFeature rf = i.next();

        RichAnnotation anno = (RichAnnotation) rf.getAnnotation();

        Set annotationNotes = anno.getNoteSet();

        for (Iterator <Note> it = annotationNotes.iterator();
it.hasNext();) {

          Note note = it.next();

          if (note.getTerm().equals(gene)) {

            tsp.setToolTipText("Gene: " + note.getValue());

          }

        }     

      }

    }

    else {

      //Remove the tooltip

      ttm.setDismissDelay(10);

    }

  }

  

  /**

   * Main method

   * @param args

   */

  public static void main(String args []){

    if (args.length == 1){

      new DisplaySequenceFile(args[0]);

    }

    else {

      System.out.println("Usage: java SequenceViewer <Genbank file>");

      System.exit(1);

    }

  }

}

//Code ends
------------------------------------------------------------------------
-------------------

 

 

 

Dr. Jolyon Holdstock                                       
Senior Computational Biologist,

Oxford Gene Technology,                                   
Begbroke Science Park,                                     
Sandy Lane, Yarnton,                                           
Oxford, OX5 1PF, UK.                                             

T: +44 (0)1865 856 852                                     
F: +44 (0)1865 842 116                                     
E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>

W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>


Looking to outsource your microarray studies? Look no further.
Click here to tour our facilities
<http://www.ogt.co.uk/highthroughputservices.html> 

Click here to request a quotation
<http://www.ogt.co.uk/htsquotationrequest.asp> 

 

Scientific pedigree delivering high quality microarray results to you:

*         Service capacity >1000 samples per week

*         Rigorous QC <http://www.ogt.co.uk/hts_qc.html>  from sample to
result

*         Applications <http://www.ogt.co.uk/hts_apps.html>  available
include aCGH, CNV, methylation studies and miRNA



Oxford Gene Technology (Operations) Ltd. Registered in England No:
03845432 Begbroke Science Park Sandy Lane Yarnton Oxford OX5 1PF  

Confidentiality Notice: The contents of this email from Oxford Gene
Technology are confidential and intended solely for the person to whom
it is addressed. It may contain privileged and confidential information.
If you are not the intended recipient you must not read, copy,
distribute, discuss or take any action in reliance on it. If you have
received this email in error please advise the sender so that we can
arrange for proper delivery. Then please delete the message from your
inbox. Thank you.

 

 



From bugzilla-daemon at portal.open-bio.org  Thu Apr  2 04:22:26 2009
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 2 Apr 2009 00:22:26 -0400
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200904020422.n324MQqk017453@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #14 from gwaldon at geneinfinity.org  2009-04-02 00:22 EST -------
I am closing this. Please reopen if the bug reappears.


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From simpleyrx at 163.com  Thu Apr  2 15:31:03 2009
From: simpleyrx at 163.com (simpleyrx)
Date: Thu, 2 Apr 2009 23:31:03 +0800 (CST)
Subject: [Biojava-dev] How to convert a multiple alignment to a PSSM matrix ?
Message-ID: <11965100.460701238686263309.JavaMail.coremail@bj163app72.163.com>


Hi, friends,
 
  I have a question: How to convert a multiple alignment to a PSSM matrix ?  Is there any code in Biojava implement the function ? Or is there other source code have the function ?
 
Student
 


From markjschreiber at gmail.com  Fri Apr  3 00:07:58 2009
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 3 Apr 2009 08:07:58 +0800
Subject: [Biojava-dev] How to convert a multiple alignment to a PSSM
	matrix ?
In-Reply-To: <93b45ca50904021707h786aeac9sd12f3cd592303981@mail.gmail.com>
References: <11965100.460701238686263309.JavaMail.coremail@bj163app72.163.com>
	<93b45ca50904021707h786aeac9sd12f3cd592303981@mail.gmail.com>
Message-ID: <93b45ca50904021707m1cfd068fv5766e4531bab7991@mail.gmail.com>

There is a class called a WeightMatrix. I think there is an example on the
cookbook.

On 2 Apr 2009, 11:47 PM, "simpleyrx" <simpleyrx at 163.com> wrote:


Hi, friends,

 I have a question: How to convert a multiple alignment to a PSSM matrix ?
 Is there any code in Biojava implement the function ? Or is there other
source code have the function ?

Student


_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev


From bugzilla-daemon at portal.open-bio.org  Sun Apr  5 17:07:48 2009
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 5 Apr 2009 13:07:48 -0400
Subject: [Biojava-dev] [Bug 2434] bio.seq.io.UniProtFormat error?
In-Reply-To: <bug-2434-485@http.bugzilla.open-bio.org/>
Message-ID: <200904051707.n35H7mYs013873@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2434


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from gwaldon at geneinfinity.org  2009-04-05 13:07 EST -------
Fixed UniprotFormat; IPI files are now accepted by the parser.


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From holland at eaglegenomics.com  Mon Apr  6 08:56:44 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 06 Apr 2009 09:56:44 +0100
Subject: [Biojava-dev] Leadership
Message-ID: <49D9C3CC.7010000@eaglegenomics.com>

Hi all.

There were no nominations for the BioJava leadership role by the end of
last week, so I would like to nominate Andreas Prlic to take over the
role as BioJava coordinator/project manager. Andreas has agreed to be
nominated.

If there are no objections lodged on this list by next Monday (13th
April), I'll hand over to Andreas by the end of next week.

thanks,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From heuermh at acm.org  Mon Apr  6 19:43:02 2009
From: heuermh at acm.org (Michael Heuer)
Date: Mon, 6 Apr 2009 15:43:02 -0400 (EDT)
Subject: [Biojava-dev] Leadership
In-Reply-To: <49D9C3CC.7010000@eaglegenomics.com>
Message-ID: <Pine.GSO.4.44.0904061539210.22871-100000@shell3.shore.net>

Richard Holland wrote:

> Hi all.
>
> There were no nominations for the BioJava leadership role by the end of
> last week, so I would like to nominate Andreas Prlic to take over the
> role as BioJava coordinator/project manager. Andreas has agreed to be
> nominated.
>
> If there are no objections lodged on this list by next Monday (13th
> April), I'll hand over to Andreas by the end of next week.

+1

Andreas has my support.

   michael



From jacobsen at ebi.ac.uk  Mon Apr  6 22:19:58 2009
From: jacobsen at ebi.ac.uk (Jules Jacobsen)
Date: Mon, 6 Apr 2009 23:19:58 +0100
Subject: [Biojava-dev] Leadership
In-Reply-To: <Pine.GSO.4.44.0904061539210.22871-100000@shell3.shore.net>
References: <49D9C3CC.7010000@eaglegenomics.com>
	<Pine.GSO.4.44.0904061539210.22871-100000@shell3.shore.net>
Message-ID: <12c279870904061519w655f9a98x604f53415022e79f@mail.gmail.com>

I third that.

On Mon, Apr 6, 2009 at 8:43 PM, Michael Heuer <heuermh at acm.org> wrote:
> Richard Holland wrote:
>
>> Hi all.
>>
>> There were no nominations for the BioJava leadership role by the end of
>> last week, so I would like to nominate Andreas Prlic to take over the
>> role as BioJava coordinator/project manager. Andreas has agreed to be
>> nominated.
>>
>> If there are no objections lodged on this list by next Monday (13th
>> April), I'll hand over to Andreas by the end of next week.
>
> +1
>
> Andreas has my support.
>
> ? michael
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Dr Jules Jacobsen

UniProt-PDB Integration
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK



From andreas at sdsc.edu  Tue Apr  7 05:50:50 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 6 Apr 2009 22:50:50 -0700
Subject: [Biojava-dev] Leadership
In-Reply-To: <49D9C3CC.7010000@eaglegenomics.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
Message-ID: <59a41c430904062250l25a1105dw505ce3edc2651184@mail.gmail.com>

Hi Richard,

Thanks for the nomination. In short I am intending to do the following
things over the next couple of months:

* Release biojava 1.7 - don't forget, code freeze will be on Wed.
April 8th. Please commit your final changes for this release in the
next couple of days, or let me know if you need more time asap.

* Keep maintaining biojava nightly builds at http://www.spice-3d.org/cruise/

* Organize a biojava user meeting around BOSC / ISMB 2009

* After the biojava 1.7 release I want to have a discussion how to
continue with the code base and what to change for the next major
release.

* I will actively seek and invite new contributors and package maintainers.

* My main focus are the further development of the protein structure
related modules. As such I will need YOUR help for maintaining blast,
sequence and any of the other frequently used modules.

Andreas




On Mon, Apr 6, 2009 at 1:56 AM, Richard Holland
<holland at eaglegenomics.com> wrote:
> Hi all.
>
> There were no nominations for the BioJava leadership role by the end of
> last week, so I would like to nominate Andreas Prlic to take over the
> role as BioJava coordinator/project manager. Andreas has agreed to be
> nominated.
>
> If there are no objections lodged on this list by next Monday (13th
> April), I'll hand over to Andreas by the end of next week.
>
> thanks,
> Richard
>
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From holland at eaglegenomics.com  Tue Apr  7 10:09:25 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 07 Apr 2009 11:09:25 +0100
Subject: [Biojava-dev] Leadership
In-Reply-To: <59a41c430904062250l25a1105dw505ce3edc2651184@mail.gmail.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
	<59a41c430904062250l25a1105dw505ce3edc2651184@mail.gmail.com>
Message-ID: <49DB2655.1080500@eaglegenomics.com>

I'd be happy to maintain the parts you request.

Andreas Prlic wrote:
> Hi Richard,
> 
> Thanks for the nomination. In short I am intending to do the following
> things over the next couple of months:
> 
> * Release biojava 1.7 - don't forget, code freeze will be on Wed.
> April 8th. Please commit your final changes for this release in the
> next couple of days, or let me know if you need more time asap.
> 
> * Keep maintaining biojava nightly builds at http://www.spice-3d.org/cruise/
> 
> * Organize a biojava user meeting around BOSC / ISMB 2009
> 
> * After the biojava 1.7 release I want to have a discussion how to
> continue with the code base and what to change for the next major
> release.
> 
> * I will actively seek and invite new contributors and package maintainers.
> 
> * My main focus are the further development of the protein structure
> related modules. As such I will need YOUR help for maintaining blast,
> sequence and any of the other frequently used modules.
> 
> Andreas
> 
> 
> 
> 
> On Mon, Apr 6, 2009 at 1:56 AM, Richard Holland
> <holland at eaglegenomics.com> wrote:
>> Hi all.
>>
>> There were no nominations for the BioJava leadership role by the end of
>> last week, so I would like to nominate Andreas Prlic to take over the
>> role as BioJava coordinator/project manager. Andreas has agreed to be
>> nominated.
>>
>> If there are no objections lodged on this list by next Monday (13th
>> April), I'll hand over to Andreas by the end of next week.
>>
>> thanks,
>> Richard
>>
>> --
>> Richard Holland, BSc MBCS
>> Finance Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>> http://www.eaglegenomics.com/
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From andreas at sdsc.edu  Sat Apr 11 19:05:44 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 11 Apr 2009 12:05:44 -0700
Subject: [Biojava-dev] BOSC abstract
Message-ID: <59a41c430904111205p624821aarf6124d0db2bb7eb9@mail.gmail.com>

Hi,

Submision deadline for the BOSC abstract is on Monday.  The current
version is available at
http://biojava.org/wiki/BOSC2009_Presentation#BioJava_2009:__an_Open-Source_Framework_for_Bioinformatics.
If you are one of the co-authors, can you please make sure I got your
affiliation right? Also if you have any additions or corrections to
the abstract, please feel free to edit. If I missed anybody who should
be co-author, please edit as well...

Andreas


From holland at eaglegenomics.com  Sun Apr 12 10:49:54 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Sun, 12 Apr 2009 11:49:54 +0100
Subject: [Biojava-dev] BOSC abstract
In-Reply-To: <59a41c430904111205p624821aarf6124d0db2bb7eb9@mail.gmail.com>
References: <59a41c430904111205p624821aarf6124d0db2bb7eb9@mail.gmail.com>
Message-ID: <49E1C752.6080702@eaglegenomics.com>

looks good!

Andreas Prlic wrote:
> Hi,
> 
> Submision deadline for the BOSC abstract is on Monday.  The current
> version is available at
> http://biojava.org/wiki/BOSC2009_Presentation#BioJava_2009:__an_Open-Source_Framework_for_Bioinformatics.
> If you are one of the co-authors, can you please make sure I got your
> affiliation right? Also if you have any additions or corrections to
> the abstract, please feel free to edit. If I missed anybody who should
> be co-author, please edit as well...
> 
> Andreas
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From andreas at sdsc.edu  Mon Apr 13 02:47:26 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 12 Apr 2009 19:47:26 -0700
Subject: [Biojava-dev] BioJava 1.7 released
Message-ID: <59a41c430904121947v67c7a7f9v1a236d3ad695760f@mail.gmail.com>

Biojava 1.7 has been released and is available from
http://biojava.org/wiki/BioJava:Download

BioJava is a mature open-source project that provides a framework for
processing of biological data. BioJava contains powerful analysis and
statistical routines, tools for parsing common file formats, and
packages for manipulating sequences and 3D structures. It enables
rapid bioinformatics application development in the Java programming
language.

Besides numerous bug fixes and stability improvements, a lot of
development has been going on in the protein structure modules.
BioJava now provides a framework for parsing mmCif files. The parsing
of PDB header information has been improved and a new tool to read the
Chemical component dictionary is in place.  Biojava 1.7 offers more
functionality and stability over the previous official releases.  We
highly recommend you to upgrade as soon as possible.

Thanks to all contributors for making this release possible.

Happy Biojava-ing,

Andreas


From holland at eaglegenomics.com  Tue Apr 14 08:33:05 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 14 Apr 2009 09:33:05 +0100
Subject: [Biojava-dev]  Leadership
In-Reply-To: <49D9C3CC.7010000@eaglegenomics.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
Message-ID: <49E44A41.2010703@eaglegenomics.com>

Hello again.

Well, nobody objected, and several people supported the idea, so I would
now like to formally hand over control of the BioJava project to Andreas
Prlic with immediate effect.

It's been good fun working with the project over the last 5 years, and
although I'll no longer be in charge, I will still remain on the mailing
lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.

I'll also continue to attend BOSC, including this year in Stockholm, so
I'm looking forward to meeting up with everyone there for a beer or two.

Thanks for the help and support everyone's given, and I'm sure you'll
join me in wishing Andreas the best of luck with the project. He'll be
an excellent leader and with him in charge I believe the project will go
from strength to strength.

cheers,
Richard

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From holland at eaglegenomics.com  Tue Apr 14 15:07:15 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 14 Apr 2009 16:07:15 +0100
Subject: [Biojava-dev] [Biojava-l]  Leadership
In-Reply-To: <7ceb4beb0904140802g39aa0d0bo7e536fb45523bb78@mail.gmail.com>
References: <49D9C3CC.7010000@eaglegenomics.com>	
	<49E44A41.2010703@eaglegenomics.com>
	<7ceb4beb0904140802g39aa0d0bo7e536fb45523bb78@mail.gmail.com>
Message-ID: <49E4A6A3.6030005@eaglegenomics.com>

The plan was to create separate new BJ3 jars for task-specific code,
exactly as you suggest for phylogenetics. I'd support a biojava-phylo
jar of some kind, and I agree it would probably depend on the BJ3
biojava-core module for sequence handling. The existing BJ code was not
originally going to be refactored into separate jars, unless Andreas has
other plans!

Scooter Willis wrote:
> Andreas
> 
> Congrats on taking on the responsibility of steering BioJava in a
> positive direction.
> 
> I needed the ability to generate phylogenetic trees from aligned
> sequence data and found that the work was started in a google summer
> project but looking at the code it wasn't finished and appeared to focus
> only on loading trees not creating them. I ended up taking the tree
> generation code out of jalview and removing as much jalview dependencies
> as possible and have it as a nice tight collection of classes. My
> assumption without any deep legal review is that because jalview is open
> source that the code can be used and contributed to another open source
> project like BioJava. I will also plan on contributing the code changes
> back to Jalview.
> 
> One of the challenges I ran into with the JalView code is performance
> for building the tree when using 1800+ sequences(takes a very very long
> time) so I am doing some code optimization and finishing up testing on a
> fairly significant performance speedup doing Neighbor_Join with a
> slightly different approach that makes it N2 instead of N3. I have a
> couple things to fix in tree joinging code and then will compare results
> for the quality of the tree compared to the original distance matrix. I
> should know more this week.
> 
> I think I remember a BioJava discussion about trying to seperate parts
> and pieces to that if you try and use a particular feature set of
> BioJava you are not forced into absorbing the entire BioJava collection
> of Jars. In my case I would want a biojava-phylogenetic.jar that has all
> things related to tree creation and/or tree viewing etc. If the common
> data format for handling sequences is RichSequence or Sequence then I
> would expect to have one other Jar requirement of biojava-core.jar. Not
> sure if any work has been done to refactor the BioJava code base into
> multiple jar files in the same way apache does its jars for great java
> code geared to a specific problem domain.
> 
> Let me know what I can do to assist moving forward.
> 
> Thanks
> 
> Scooter Willis
> 
> On Tue, Apr 14, 2009 at 4:33 AM, Richard Holland
> <holland at eaglegenomics.com <mailto:holland at eaglegenomics.com>> wrote:
> 
>     Hello again.
> 
>     Well, nobody objected, and several people supported the idea, so I would
>     now like to formally hand over control of the BioJava project to Andreas
>     Prlic with immediate effect.
> 
>     It's been good fun working with the project over the last 5 years, and
>     although I'll no longer be in charge, I will still remain on the mailing
>     lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.
> 
>     I'll also continue to attend BOSC, including this year in Stockholm, so
>     I'm looking forward to meeting up with everyone there for a beer or two.
> 
>     Thanks for the help and support everyone's given, and I'm sure you'll
>     join me in wishing Andreas the best of luck with the project. He'll be
>     an excellent leader and with him in charge I believe the project will go
>     from strength to strength.
> 
>     cheers,
>     Richard
> 
>     --
>     Richard Holland, BSc MBCS
>     Finance Director, Eagle Genomics Ltd
>     T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>     <mailto:holland at eaglegenomics.com>
>     http://www.eaglegenomics.com/
>     _______________________________________________
>     Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>     <mailto:Biojava-l at lists.open-bio.org>
>     http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From andreas at sdsc.edu  Tue Apr 14 16:45:21 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 14 Apr 2009 09:45:21 -0700
Subject: [Biojava-dev] Leadership
In-Reply-To: <49E44A41.2010703@eaglegenomics.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
	<49E44A41.2010703@eaglegenomics.com>
Message-ID: <59a41c430904140945t30911e33idc8ea095c52e59e3@mail.gmail.com>

Hi Richard,

Again, thanks for your BioJava contributions in the last years and
great to have you still around.

I am looking forward to the next year of BioJava development. Our
google analytics stats reveal that we have an ever growing user base
and it will be a challenge to continue developing BioJava further and
add new and useful features. Of course this is a task that I can't do
alone and I will need the help of everybody who wants to write
documentation, submit bug fixes or wants to become maintainer of one
of the modules.

With BioJava 1.7 being out it is now a good time to start a discussion
at how to improve the code base for the next version.

We also have BOSC coming up in June and it will provide a good
opportunity for people to meet in person.

Hope to see you (Richard, and everybody else!) in Sweden, otherwise we
will keep talking via the lists.

Andreas




On Tue, Apr 14, 2009 at 1:33 AM, Richard Holland
<holland at eaglegenomics.com> wrote:
> Hello again.
>
> Well, nobody objected, and several people supported the idea, so I would
> now like to formally hand over control of the BioJava project to Andreas
> Prlic with immediate effect.
>
> It's been good fun working with the project over the last 5 years, and
> although I'll no longer be in charge, I will still remain on the mailing
> lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.
>
> I'll also continue to attend BOSC, including this year in Stockholm, so
> I'm looking forward to meeting up with everyone there for a beer or two.
>
> Thanks for the help and support everyone's given, and I'm sure you'll
> join me in wishing Andreas the best of luck with the project. He'll be
> an excellent leader and with him in charge I believe the project will go
> from strength to strength.
>
> cheers,
> Richard
>
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>


From gwaldon at geneinfinity.org  Tue Apr 14 17:32:52 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 14 Apr 2009 13:32:52 -0400
Subject: [Biojava-dev] [Biojava-l]  Leadership
Message-ID: <20090414173252.52004.qmail@mxw1102.verio-web.com>

Hi Scooter,

This is not so simple because Jalview is under the GNU General Public License while Biojava is under the Lesser GPL. The simplest way might be to have the authors of the part of Jalview you are interested in to release their code under the LGPL.

Best,
George


> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-
> bounces at lists.open-bio.org] On Behalf Of Scooter Willis
> Sent: Tuesday, April 14, 2009 8:02 AM
> To: Richard Holland
> Cc: biojava-dev; biojava-l at biojava.org
> Subject: Re: [Biojava-l] [Biojava-dev] Leadership
> 

> My assumption without any deep legal
> review is that because jalview is open source that the code can be used
> and
> contributed to another open source project like BioJava. I will also plan
> on
> contributing the code changes back to Jalview.


From andreas at sdsc.edu  Wed Apr 15 05:40:24 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 14 Apr 2009 22:40:24 -0700
Subject: [Biojava-dev] [Biojava-l]  Leadership
In-Reply-To: <7ceb4beb0904140802g39aa0d0bo7e536fb45523bb78@mail.gmail.com>
References: <49D9C3CC.7010000@eaglegenomics.com>
	<49E44A41.2010703@eaglegenomics.com>
	<7ceb4beb0904140802g39aa0d0bo7e536fb45523bb78@mail.gmail.com>
Message-ID: <59a41c430904142240u5a9812eejf11023f69baa27b7@mail.gmail.com>

Hi Scooter,

Thanks for volunteering. I like the idea of modularizing BioJava in
the next version. The details of how to do this still need to be
discussed on the dev mailing list. If you want to be involved into
anything phylo related then this is great and any contribution will be
welcome.

About merging in 3rd party code that is under a different license: For
this you need to get  permission from the original copyright owners or
rewrite the code ....

Andreas


On Tue, Apr 14, 2009 at 8:02 AM, Scooter Willis <willishf at ufl.edu> wrote:
> Andreas
>
> Congrats on taking on the responsibility of steering BioJava in a positive
> direction.
>
> I needed the ability to generate phylogenetic trees from aligned sequence
> data and found that the work was started in a google summer project but
> looking at the code it wasn't finished and appeared to focus only on loading
> trees not creating them. I ended up taking the tree generation code out of
> jalview and removing as much jalview dependencies as possible and have it as
> a nice tight collection of classes. My assumption without any deep legal
> review is that because jalview is open source that the code can be used and
> contributed to another open source project like BioJava. I will also plan on
> contributing the code changes back to Jalview.
>
> One of the challenges I ran into with the JalView code is performance for
> building the tree when using 1800+ sequences(takes a very very long time) so
> I am doing some code optimization and finishing up testing on a fairly
> significant performance speedup doing Neighbor_Join with a slightly
> different approach that makes it N2 instead of N3. I have a couple things to
> fix in tree joinging code and then will compare results for the quality of
> the tree compared to the original distance matrix. I should know more this
> week.
>
> I think I remember a BioJava discussion about trying to seperate parts and
> pieces to that if you try and use a particular feature set of BioJava you
> are not forced into absorbing the entire BioJava collection of Jars. In my
> case I would want a biojava-phylogenetic.jar that has all things related to
> tree creation and/or tree viewing etc. If the common data format for
> handling sequences is RichSequence or Sequence then I would expect to have
> one other Jar requirement of biojava-core.jar. Not sure if any work has been
> done to refactor the BioJava code base into multiple jar files in the same
> way apache does its jars for great java code geared to a specific problem
> domain.
>
> Let me know what I can do to assist moving forward.
>
> Thanks
>
> Scooter Willis
>
> On Tue, Apr 14, 2009 at 4:33 AM, Richard Holland
> <holland at eaglegenomics.com>wrote:
>
>> Hello again.
>>
>> Well, nobody objected, and several people supported the idea, so I would
>> now like to formally hand over control of the BioJava project to Andreas
>> Prlic with immediate effect.
>>
>> It's been good fun working with the project over the last 5 years, and
>> although I'll no longer be in charge, I will still remain on the mailing
>> lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.
>>
>> I'll also continue to attend BOSC, including this year in Stockholm, so
>> I'm looking forward to meeting up with everyone there for a beer or two.
>>
>> Thanks for the help and support everyone's given, and I'm sure you'll
>> join me in wishing Andreas the best of luck with the project. He'll be
>> an excellent leader and with him in charge I believe the project will go
>> from strength to strength.
>>
>> cheers,
>> Richard
>>
>> --
>> Richard Holland, BSc MBCS
>> Finance Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>> http://www.eaglegenomics.com/
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From jolyon.holdstock at ogt.co.uk  Fri Apr 17 10:27:16 2009
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Fri, 17 Apr 2009 11:27:16 +0100
Subject: [Biojava-dev] User interface example for Cookbook
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F026D7EAC@EUCLID.internal.ogtip.com>

Hi,

 

I've been meaning to generate an updated example of code for displaying
a sequence (with some additional functionality) for the cookbook and
finally got off my backside to do it.

 

Code is below; I hope it's of use - feel free to point out errors,
improvements etc...

 

Cheers,

 

Jolyon

 

 

//Code starts
------------------------------------------------------------------------
-------------------

//Java libraries

import java.awt.*;

import java.awt.event.*;

import java.io.*;

import java.util.*;

import javax.swing.*;

//BioJava libraries

import org.biojava.bio.*;

import org.biojava.bio.seq.*;

import org.biojava.bio.gui.sequence.*;

//BioJava extension libraries

import org.biojavax.*;

import org.biojavax.ontology.*;

import org.biojavax.bio.seq.*;

 

public class DisplaySequenceFile extends JFrame implements
SequenceViewerMotionListener {

  private TranslatedSequencePanel tsp = new TranslatedSequencePanel();

  private MultiLineRenderer mlr = new MultiLineRenderer();

  private RulerRenderer rr = new RulerRenderer();

  private SequenceRenderer seqR = new SymbolSequenceRenderer();

  private FeatureBlockSequenceRenderer fbsr;

  private RichSequence richSeq;

  

  private Container con;

  private JPanel controlPanel;

  private JButton mvLeft, mvRight, zoomIn, zoomOut;

  private double sequenceScale = 0.05;

  private int windowWidth = 1200;

  private int windowHeight = 200;

  

  public DisplaySequenceFile(String fileName){

    //Load the sequence file

    try {

      richSeq = RichSequence.IOTools.readEMBLDNA(new BufferedReader(new
FileReader(new File(fileName))), null).nextRichSequence();

    }

    catch (BioException bioe){

      System.err.println("Not an EMBL sequence" + bioe);

    }

    catch(FileNotFoundException fnfe){

       System.err.println("FileNotFoundException: " + fnfe);

    }

    catch (IOException ioe){

      System.err.println("IOException: " + ioe);

    }

    

    //Define the appearance of the rendered Features

    BasicFeatureRenderer bfr = new BasicFeatureRenderer();

    GradientPaint gradient = new GradientPaint(0, 10, Color.RED, 0, 0,
Color.white, true);

    bfr.setFill(gradient);

    bfr.setOutline(Color.RED);

    

    //Form a bridge between Sequence rendering and Feature rendering

    fbsr = new FeatureBlockSequenceRenderer(bfr);

    fbsr.setCollapsing(false);

    

    //Filter for CDS features on the forward strand

    SequenceRenderer fwd_sr = new FilteringRenderer(fbsr, 

            new FeatureFilter.And(new FeatureFilter.ByType("CDS"), 

            new FeatureFilter.StrandFilter(StrandedFeature.POSITIVE)), 

            true);

    //Filter for CDS features on the reverse strand

    SequenceRenderer rev_sr = new FilteringRenderer(fbsr, 

            new FeatureFilter.And(new FeatureFilter.ByType("CDS"), 

            new FeatureFilter.StrandFilter(StrandedFeature.NEGATIVE)), 

            true);

    

    //Add the renderers to the MultiLineRenderer

    mlr.addRenderer(fwd_sr);

    mlr.addRenderer(rr);

    mlr.addRenderer(rev_sr);

    mlr.addRenderer(seqR);

    

    //Set the sequence renderer for the TranslatedSequencePanel

    tsp.setRenderer(mlr);

    //Set the sequence to render

    tsp.setSequence(richSeq);

    //Set the position of the displayed sequence

    tsp.setSymbolTranslation(1);

    //Set the scale as pixels per Symbol.    

    tsp.setScale(sequenceScale);

    

    //Add a sequence viewer motion listener to the
TranslateSequencePanel

    tsp.addSequenceViewerMotionListener(this);

    

    //Generate the control panel

    controlPanel = new JPanel();

    controlPanel.setBackground(Color.lightGray);

    //Move along the sequence towards 5' end 

    mvLeft = new JButton("<<");

    mvLeft.addActionListener(new ActionListener(){

      public void actionPerformed(ActionEvent ae){

        int rightSide = tsp.getRange().getMax();

        int leftSide = tsp.getRange().getMin();

        int newStartPoint = leftSide - (rightSide - leftSide);

        if (newStartPoint < 1){

          newStartPoint = 1;

        }

        tsp.setSymbolTranslation(newStartPoint);  

      }

    });

    //Move along the sequence towards 3' end 

    mvRight = new JButton(">>");

    mvRight.addActionListener(new ActionListener(){

      public void actionPerformed(ActionEvent ae){

        int rightSide = tsp.getRange().getMax();

        int leftSide = tsp.getRange().getMin();

        int screenWidth = rightSide - leftSide;

        if ((rightSide + screenWidth) >= richSeq.length()){

          tsp.setSymbolTranslation(richSeq.length() - screenWidth);

        }

        else {

          tsp.setSymbolTranslation(rightSide); 

        }

      }

    });

    //Increase sequence scale

    zoomIn = new JButton("+");

    zoomIn.addActionListener(new ActionListener(){

      public void actionPerformed(ActionEvent ae){

        sequenceScale = sequenceScale * 2;

        //if sequence scale = 12 the bases are rendered

        //no need to zoom in further so disable the button.

        if (sequenceScale > 12){

          sequenceScale = 12;

          zoomIn.setEnabled(false);

        }

        tsp.setScale(sequenceScale);

      }

    });

    //Reduce sequence scale

    zoomOut = new JButton("-");

    zoomOut.addActionListener(new ActionListener(){

      public void actionPerformed(ActionEvent ae){

        sequenceScale = sequenceScale / 2;

        //if sequence scale is below 12 the enable zoomIn button

        if (sequenceScale < 12){

          zoomIn.setEnabled(true);

        }

        //If the scale allows more than the sequence to be displayed

        //display the whole sequence

        if (sequenceScale <
((double)tsp.getWidth()/(double)richSeq.length())){

          sequenceScale =
(double)tsp.getWidth()/(double)richSeq.length();

          tsp.setSymbolTranslation(1);

        }

        tsp.setScale(sequenceScale);

        //If the new scale coupled with the current SymbolTranslation
means the 

        //displayed can't fill the TranslatedSequencePanel then reset
the SymbolTranlstion

        if(tsp.getRange().getMax() >= richSeq.length()){

          int tmp = (int)((double)tsp.getWidth()/sequenceScale);

          tsp.setSymbolTranslation(richSeq.length() - tmp); 

        }

      }

    });

    controlPanel.add(mvLeft);

    controlPanel.add(mvRight);

    controlPanel.add(zoomIn);

    controlPanel.add(zoomOut);

    

    con = new Container();

    con = getContentPane();

    con.setLayout(new BorderLayout());

    con.add(controlPanel, BorderLayout.NORTH);

    con.add(tsp, BorderLayout.CENTER);

    setLocation(50,50);

    setSize(windowWidth,windowHeight);

    setVisible(true);

    setResizable(false);

  }

  

  /**

   * Detect mouse dragged events

   * @param sve

   */

  public void mouseDragged(SequenceViewerEvent sve) {

  }

  

  /**

   * Detect mouse movement events

   * If the mouse moves over a CDS feature create a tooltiptext stating
the 

   * the name of the gene associated with the CDS feature.

   * @param sve

   */

  public void mouseMoved(SequenceViewerEvent sve) {

    //Manage the tooltip

    ToolTipManager ttm = ToolTipManager.sharedInstance();

    ttm.setDismissDelay(2000);

    //If the mouse have moved over a SimpleFeatureHolder 

    if (sve.getTarget() instanceof SimpleFeatureHolder){

      ComparableTerm gene =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");

      SimpleFeatureHolder sfh = (SimpleFeatureHolder)sve.getTarget();

      FeatureHolder fh = sfh.filter(new FeatureFilter.ByType("CDS"));

      Iterator <RichFeature> i =  fh.features();

      while(i.hasNext()){

        RichFeature rf = i.next();

        RichAnnotation anno = (RichAnnotation) rf.getAnnotation();

        Set annotationNotes = anno.getNoteSet();

        for (Iterator <Note> it = annotationNotes.iterator();
it.hasNext();) {

          Note note = it.next();

          if (note.getTerm().equals(gene)) {

            tsp.setToolTipText("Gene: " + note.getValue());

          }

        }     

      }

    }

    else {

      //Remove the tooltip

      ttm.setDismissDelay(10);

    }

  }

  

  /**

   * Main method

   * @param args

   */

  public static void main(String args []){

    if (args.length == 1){

      new DisplaySequenceFile(args[0]);

    }

    else {

      System.out.println("Usage: java SequenceViewer <Genbank file>");

      System.exit(1);

    }

  }

}

//Code ends
------------------------------------------------------------------------
-------------------

 

 

 

Dr. Jolyon Holdstock                                       
Senior Computational Biologist,

Oxford Gene Technology,                                   
Begbroke Science Park,                                     
Sandy Lane, Yarnton,                                           
Oxford, OX5 1PF, UK.                                             

T: +44 (0)1865 856 852                                     
F: +44 (0)1865 842 116                                     
E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>

W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>


Looking to outsource your microarray studies? Look no further.
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