From zagato.gekko at gmail.com  Thu Mar  1 21:27:12 2007
From: zagato.gekko at gmail.com (Zagato)
Date: Thu, 1 Mar 2007 21:27:12 -0500
Subject: [Biojava-l] (pre-Singapore) BioSQL ???
Message-ID: <98028b00703011827j67e6772fm66903d5175ff1845@mail.gmail.com>

Hello everyone... i'm experimenting with connection to a BioSQL database on
postgres, i'm follow this guide:
http://www.biojava.org/wiki/BioJava:CookBook:BioSQL:Manage, and change the
parameter to connect to postrges, but i get an error and i don't know why (i
download the scripts for postgres from:
http://www.biojava.org/download/biosql/), my error is:

org.biojava.bio.BioException: This database appears to be an old
(pre-Singapore) BioSQL. If you need to access it, try an older BioJava
snapshot (1.3pre1 or earlier)
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(
BioSQLSequenceDB.java:227)
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(
BioSQLSequenceDB.java:195)
        at Connect.main(Connect.java:40)

I cannot using the CVS version of BioJava and can't use an older because a
bug. Someone can give me some guide.... Thanks !!!

Alan Acosta

-- 
Farewell.
ruby << __EOF__
  puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
__EOF__

From mark.schreiber at novartis.com  Thu Mar  1 21:48:31 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 2 Mar 2007 10:48:31 +0800
Subject: [Biojava-l] (pre-Singapore) BioSQL ???
Message-ID: <OFE4065DF5.D95034D7-ON48257292.000F0D4C-48257292.000F6DAE@ah.novartis.com>

Hi -

I think those scripts are particularly old. You could try getting the 
appropriate ones from 
http://code.open-bio.org/cgi/viewcvs.cgi/biosql-schema/sql/?cvsroot=biosql

You should also know that we are no longer supporting the biojava 1.4 
bindings to biosql. As of biojava 1.5 we are using Hibernate to do a much 
better job of the ORM. You also get much better control over transactions. 
I strongly recommend you download biojava1.5-pre2 from 
http://biojava.org/wiki/BioJava:Download.

For instructions on using Hibernate with Biojava take a look at 
http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate.

Best regards,

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





Zagato <zagato.gekko at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
03/02/2007 10:27 AM

 
        To:     Biojava-l at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] (pre-Singapore) BioSQL ???


Hello everyone... i'm experimenting with connection to a BioSQL database 
on
postgres, i'm follow this guide:
http://www.biojava.org/wiki/BioJava:CookBook:BioSQL:Manage, and change the
parameter to connect to postrges, but i get an error and i don't know why 
(i
download the scripts for postgres from:
http://www.biojava.org/download/biosql/), my error is:

org.biojava.bio.BioException: This database appears to be an old
(pre-Singapore) BioSQL. If you need to access it, try an older BioJava
snapshot (1.3pre1 or earlier)
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(
BioSQLSequenceDB.java:227)
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(
BioSQLSequenceDB.java:195)
        at Connect.main(Connect.java:40)

I cannot using the CVS version of BioJava and can't use an older because a
bug. Someone can give me some guide.... Thanks !!!

Alan Acosta

-- 
Farewell.
ruby << __EOF__
  puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
__EOF__
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From zagato.gekko at gmail.com  Fri Mar  2 09:09:54 2007
From: zagato.gekko at gmail.com (Zagato)
Date: Fri, 2 Mar 2007 09:09:54 -0500
Subject: [Biojava-l] (pre-Singapore) BioSQL ???
In-Reply-To: <OFE4065DF5.D95034D7-ON48257292.000F0D4C-48257292.000F6DAE@ah.novartis.com>
References: <OFE4065DF5.D95034D7-ON48257292.000F0D4C-48257292.000F6DAE@ah.novartis.com>
Message-ID: <98028b00703020609vb00c5cdgcb38462b7cc1a4a5@mail.gmail.com>

Thanks for the answer, i will check the hibernate alternative :D

Alan

On 3/1/07, mark.schreiber at novartis.com <mark.schreiber at novartis.com> wrote:
>
> Hi -
>
> I think those scripts are particularly old. You could try getting the
> appropriate ones from
> http://code.open-bio.org/cgi/viewcvs.cgi/biosql-schema/sql/?cvsroot=biosql
>
> You should also know that we are no longer supporting the biojava 1.4
> bindings to biosql. As of biojava 1.5 we are using Hibernate to do a much
> better job of the ORM. You also get much better control over transactions.
> I strongly recommend you download biojava1.5-pre2 from
> http://biojava.org/wiki/BioJava:Download.
>
> For instructions on using Hibernate with Biojava take a look at
> http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate.
>
> Best regards,
>
> - Mark
>
> Mark Schreiber
> Research Investigator (Bioinformatics)
>
> Novartis Institute for Tropical Diseases (NITD)
> 10 Biopolis Road
> #05-01 Chromos
> Singapore 138670
> www.nitd.novartis.com
> www.dengueinfo.org
>
> phone +65 6722 2973
> fax  +65 6722 2910
>
>
>
>
>
> Zagato <zagato.gekko at gmail.com>
> Sent by: biojava-l-bounces at lists.open-bio.org
> 03/02/2007 10:27 AM
>
>
>         To:     Biojava-l at lists.open-bio.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] (pre-Singapore) BioSQL ???
>
>
> Hello everyone... i'm experimenting with connection to a BioSQL database
> on
> postgres, i'm follow this guide:
> http://www.biojava.org/wiki/BioJava:CookBook:BioSQL:Manage, and change the
> parameter to connect to postrges, but i get an error and i don't know why
> (i
> download the scripts for postgres from:
> http://www.biojava.org/download/biosql/), my error is:
>
> org.biojava.bio.BioException: This database appears to be an old
> (pre-Singapore) BioSQL. If you need to access it, try an older BioJava
> snapshot (1.3pre1 or earlier)
>         at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(
> BioSQLSequenceDB.java:227)
>         at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(
> BioSQLSequenceDB.java:195)
>         at Connect.main(Connect.java:40)
>
> I cannot using the CVS version of BioJava and can't use an older because a
> bug. Someone can give me some guide.... Thanks !!!
>
> Alan Acosta
>
> --
> Farewell.
> ruby << __EOF__
>   puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
> __EOF__
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>


-- 
Farewell.
ruby << __EOF__
  puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
__EOF__

From alexamies at gmail.com  Fri Mar  2 22:03:44 2007
From: alexamies at gmail.com (Alex Amies)
Date: Fri, 2 Mar 2007 19:03:44 -0800
Subject: [Biojava-l] [BioJava] New Article Approaches to Web Development for
	Bioinformatics
Message-ID: <1ad8057e0703021903y535f3a14xcf5df2eb39ef2f87@mail.gmail.com>

I have written an article titled Approaches to Web Development for
Bioinformatics at

http://medicalcomputing.net/tools_dna1.php

There is a section on BioJava at

http://medicalcomputing.net/tools_dna14.php

Hopefully, someone will get something out of it.  Please let me know
if you have any comments or find mistakes.

Alex

From markjschreiber at gmail.com  Sat Mar  3 00:39:05 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sat, 3 Mar 2007 13:39:05 +0800
Subject: [Biojava-l] [BioJava] New Article Approaches to Web Development
	for Bioinformatics
In-Reply-To: <1ad8057e0703021903y535f3a14xcf5df2eb39ef2f87@mail.gmail.com>
References: <1ad8057e0703021903y535f3a14xcf5df2eb39ef2f87@mail.gmail.com>
Message-ID: <93b45ca50703022139i7d281ff0jd9b95a3e57ccfb96@mail.gmail.com>

Hi Alex -

This is a nice introduction. Please feel free to put a link in the
biojava wiki (www.biojava.org)  probably somewhere in the cookbook
section would be good.

- Mark

On 3/3/07, Alex Amies <alexamies at gmail.com> wrote:
> I have written an article titled Approaches to Web Development for
> Bioinformatics at
>
> http://medicalcomputing.net/tools_dna1.php
>
> There is a section on BioJava at
>
> http://medicalcomputing.net/tools_dna14.php
>
> Hopefully, someone will get something out of it.  Please let me know
> if you have any comments or find mistakes.
>
> Alex
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From arareko at campus.iztacala.unam.mx  Sat Mar  3 17:32:46 2007
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Sat, 03 Mar 2007 16:32:46 -0600
Subject: [Biojava-l] [Bioperl-l] New Article on Approaches to Web
 Development for Bioinformatics
In-Reply-To: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com>
References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com>
Message-ID: <45E9F78E.8040406@campus.iztacala.unam.mx>

Hi Alex,

I think you've put a very nice & concise introductory article. I'd like 
to comment a little on some sections I've read:

* Introduction

 > "Given that you have an idea for analyzing or presenting data in a
 > particular was, a complete bioinformatics web application depends of
 > these basic pieces, which is what this article is all about:
 >
 >    1. A source of data...
 >    2. An application programming language...
 >    3. A web application platform...
 >    4. Optionally, a data store...
 >    5. Optionally, you would reuse software tools..."

Even though you do a small mention about Web Services at the very end of 
the article (under Application Integration -> Programmatic Integration), 
I believe that Web Services can be another optional (or even basic) 
piece of a web application. In fact, many web applications consist only 
of Web Services without HTML user interfaces.

* Application Development Languages

 > "There are many different programming platforms and tools available to
 > solve bioinformatics problems.  It can be bewildering at first, but it
 > makes more sense to build on top of some of these tools rather than
 > build from scratch.  Some the problems with using these tools for a
 > bioinformatics portal are
 >
 >    1. Many tools are written...
 >    2. Some tools have particular prerequisites...
 >    3. Many may not be in a form...
 >    4. The context that gives meaning...
 >
 > Standardization on a particular platform can help manageability but
 > for most organizations a compromise between standardization and
 > adoption of several different platforms will allow many people to
 > develop software in platforms that they are already comfortable with
 > and allow the reuse of a large amount of freely available software..."

I would add to the problems list the fact that building web (or other 
kind of) applications on top of a platform whose codebase is evolving 
constantly, can make them very difficult to maintain. The case of 
EnsEMBL comes to my mind here: they opted to stick with BioPerl 1.2.3 as 
a core library and haven't moved onto a higher version of it because the 
EnsEMBL code is so vast, that a simple upgrade of BioPerl would break a 
lot of their code. AFAIK, it's because of this and the slowness at some 
parts of BioPerl that EnsEMBL is gradually saying goodbye to BioPerl.

Also, I think that depending on the amount of available code you plan to 
import into your application, sometimes having a whole platform at the 
very bottom can add unnecessary extra weight to your application. More 
weight could be equal to less speed, this is critical in web development.

* Application Integration -> Navigation

 > "The basic way that users will navigate into and around your
 > application should be using HTTP GET and POST requests with specific
 > URL's. Users bookmark these URL's and other applications will link to
 > them. Most applications developers did not realize it at first, but
 > these URL's are, in fact, an interface into your application that you
 > must maintain in a consistent way as you change and evolve your
 > software. Otherwise, they will find dead links..."

Just as I clicked the bookmark button for your article :) The same 
principle could apply to its filenames. A URL of the form: 
http://medicalcomputing.net/tools_dna17.php is less indicative of the 
real content of the article and can mislead potential readers. 
Optimising the URL's will make them better to be indexed by search 
engines, something like: 
http://medicalcomputing.net/web-development-bioinformatics17.php would 
do the trick.

To conclude my comments, I was surprised to see a section about BioPHP 
and not about other more-known toolkits like BioPython or BioRuby. What 
about their role in web development? Python is also a common language 
for web programming and with all the recent *hot* stuff like Ruby On 
Rails, it's very likely that both Bio* toolkits are more than ready for 
deploying web applications. I'm Cc'ing this to their respective mailing 
lists to see if someone wants to give you some feedback about them in 
order to complement your article. Other than that, I really liked your 
work :)

Cheers,
Mauricio.

Alex Amies wrote:
> I have written an article on Approaches to Web Development for
> Bioinformatics at
> 
> http://medicalcomputing.net/tools_dna1.php
> 
> There is a fairly large section on BioPerl at
> 
> http://medicalcomputing.net/tools_dna13.php
> 
> I hope that someone gets something useful out of it.  I also looking for
> feedback on it and, in particular, please let me know about any mistakes in
> it.
> 
> The intent of the article is to give an overview of various approaches to
> developing web based tools for bioinformatics. It describes the alternatives
> at each layer of the system, including the data layer and sources of data,
> the application programming layer, the web layer, and bioinformatics tools
> and software libraries.
> 
> Alex
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM




From alexamies at gmail.com  Sat Mar  3 22:09:51 2007
From: alexamies at gmail.com (Alex Amies)
Date: Sat, 3 Mar 2007 19:09:51 -0800
Subject: [Biojava-l] [Bioperl-l] New Article on Approaches to Web
	Development for Bioinformatics
In-Reply-To: <45E9F78E.8040406@campus.iztacala.unam.mx>
References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com>
	<45E9F78E.8040406@campus.iztacala.unam.mx>
Message-ID: <1ad8057e0703031909v4880f5f1t3c4159b75c36bcca@mail.gmail.com>

Mauricio,

Thanks for your comments.

You are right that I could have said a lot more about web services.  I
plan on doing that but I haven't got there yet.  Actually, with all
the hype about web services I have been surprised to find the
programming model so complicated.

As you mention, I certainly could have thought out my own URL's better.

I have been surprised not to find more PHP activity in bioinformatics.
 To me, besides being a lightweight and pleasant language to program
in it is incredibly economical for hosting Internet applications and
there is a huge open source community around PHP in general.  The same
can be said of Perl.  It is because of my own ignorance and lack of
time that I have not investigated Python and Ruby.  I may do in the
future and write about them.

Alex

On 3/3/07, Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx> wrote:
> Hi Alex,
>
> I think you've put a very nice & concise introductory article. I'd like
> to comment a little on some sections I've read:
>
> * Introduction
>
>  > "Given that you have an idea for analyzing or presenting data in a
>  > particular was, a complete bioinformatics web application depends of
>  > these basic pieces, which is what this article is all about:
>  >
>  >    1. A source of data...
>  >    2. An application programming language...
>  >    3. A web application platform...
>  >    4. Optionally, a data store...
>  >    5. Optionally, you would reuse software tools..."
>
> Even though you do a small mention about Web Services at the very end of
> the article (under Application Integration -> Programmatic Integration),
> I believe that Web Services can be another optional (or even basic)
> piece of a web application. In fact, many web applications consist only
> of Web Services without HTML user interfaces.
>
> * Application Development Languages
>
>  > "There are many different programming platforms and tools available to
>  > solve bioinformatics problems.  It can be bewildering at first, but it
>  > makes more sense to build on top of some of these tools rather than
>  > build from scratch.  Some the problems with using these tools for a
>  > bioinformatics portal are
>  >
>  >    1. Many tools are written...
>  >    2. Some tools have particular prerequisites...
>  >    3. Many may not be in a form...
>  >    4. The context that gives meaning...
>  >
>  > Standardization on a particular platform can help manageability but
>  > for most organizations a compromise between standardization and
>  > adoption of several different platforms will allow many people to
>  > develop software in platforms that they are already comfortable with
>  > and allow the reuse of a large amount of freely available software..."
>
> I would add to the problems list the fact that building web (or other
> kind of) applications on top of a platform whose codebase is evolving
> constantly, can make them very difficult to maintain. The case of
> EnsEMBL comes to my mind here: they opted to stick with BioPerl 1.2.3 as
> a core library and haven't moved onto a higher version of it because the
> EnsEMBL code is so vast, that a simple upgrade of BioPerl would break a
> lot of their code. AFAIK, it's because of this and the slowness at some
> parts of BioPerl that EnsEMBL is gradually saying goodbye to BioPerl.
>
> Also, I think that depending on the amount of available code you plan to
> import into your application, sometimes having a whole platform at the
> very bottom can add unnecessary extra weight to your application. More
> weight could be equal to less speed, this is critical in web development.
>
> * Application Integration -> Navigation
>
>  > "The basic way that users will navigate into and around your
>  > application should be using HTTP GET and POST requests with specific
>  > URL's. Users bookmark these URL's and other applications will link to
>  > them. Most applications developers did not realize it at first, but
>  > these URL's are, in fact, an interface into your application that you
>  > must maintain in a consistent way as you change and evolve your
>  > software. Otherwise, they will find dead links..."
>
> Just as I clicked the bookmark button for your article :) The same
> principle could apply to its filenames. A URL of the form:
> http://medicalcomputing.net/tools_dna17.php is less indicative of the
> real content of the article and can mislead potential readers.
> Optimising the URL's will make them better to be indexed by search
> engines, something like:
> http://medicalcomputing.net/web-development-bioinformatics17.php would
> do the trick.
>
> To conclude my comments, I was surprised to see a section about BioPHP
> and not about other more-known toolkits like BioPython or BioRuby. What
> about their role in web development? Python is also a common language
> for web programming and with all the recent *hot* stuff like Ruby On
> Rails, it's very likely that both Bio* toolkits are more than ready for
> deploying web applications. I'm Cc'ing this to their respective mailing
> lists to see if someone wants to give you some feedback about them in
> order to complement your article. Other than that, I really liked your
> work :)
>
> Cheers,
> Mauricio.
>
> Alex Amies wrote:
> > I have written an article on Approaches to Web Development for
> > Bioinformatics at
> >
> > http://medicalcomputing.net/tools_dna1.php
> >
> > There is a fairly large section on BioPerl at
> >
> > http://medicalcomputing.net/tools_dna13.php
> >
> > I hope that someone gets something useful out of it.  I also looking for
> > feedback on it and, in particular, please let me know about any mistakes in
> > it.
> >
> > The intent of the article is to give an overview of various approaches to
> > developing web based tools for bioinformatics. It describes the alternatives
> > at each layer of the system, including the data layer and sources of data,
> > the application programming layer, the web layer, and bioinformatics tools
> > and software libraries.
> >
> > Alex
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
> --
> MAURICIO HERRERA CUADRA
> arareko at campus.iztacala.unam.mx
> Laboratorio de Gen?tica
> Unidad de Morfofisiolog?a y Funci?n
> Facultad de Estudios Superiores Iztacala, UNAM
>
>
>
>


From christoph.gille at charite.de  Mon Mar  5 16:51:34 2007
From: christoph.gille at charite.de (Dr. Christoph Gille)
Date: Mon, 5 Mar 2007 22:51:34 +0100 (CET)
Subject: [Biojava-l] Biojava plugin
Message-ID: <55580.141.42.56.114.1173131494.squirrel@webmail.charite.de>

If you have developed an application based on Biojava which operates
on nucleotide or amino acid sequences, or even on protein
3D-structures, you can make a plugin for STRAP with relatively little
effort.

Plugins can be downloaded and run in STRAP with only a few mouse
clicks.  Therefore your plugin may be well accepted by the growing
number of STRAP users.

STRAP still lacks tools for restriction site analysis, proteolytic
site prediction, promotor and transcription factor binding site
analyses and gene prediction.

It would be nice if you could extend the functionality of STRAP
with your application.

Christoph



From dankoc at gmail.com  Sun Mar 11 16:22:48 2007
From: dankoc at gmail.com (Charles Danko)
Date: Sun, 11 Mar 2007 16:22:48 -0400
Subject: [Biojava-l] Ambiguity consensus string search
Message-ID: <8adccabf0703111322ya303927o194eabcd9c5978c@mail.gmail.com>

Hi,

I'm trying to search a Sequence or SymbolList object for a consensus
sequence that contains IUPac ambiguity codes.

Without ambiguity codes, I could write a function that breaks the sequence
into "windows" the size of the consensus, and checks each window for a
match.  Am I missing a simple function that does this for me?

Next, adding ambiguity codes ... do I have to define my own alphabet for the
DNA IUPac codes, or are these already included in the distribution
somewhere?

I have found the weight matrix class, and realize that I could create one of
these objects and calculate a threshold that will work in the same manner as
a consensus, but this seems like a bit of a hack for some functionality I am
most likely overlooking.

Thanks very much!

Charles

From heuermh at acm.org  Sun Mar 11 17:58:04 2007
From: heuermh at acm.org (Michael Heuer)
Date: Sun, 11 Mar 2007 16:58:04 -0500 (EST)
Subject: [Biojava-l] Ambiguity consensus string search
In-Reply-To: <8adccabf0703111322ya303927o194eabcd9c5978c@mail.gmail.com>
Message-ID: <Pine.GSO.4.44.0703111655220.6445-100000@shell3.shore.net>

Hello Charles,

You may find the org.biojava.utils.regex package useful in this regard:

> http://www.biojava.org/docs/api15b/index.html

   michael


Charles Danko wrote:

> Hi,
>
> I'm trying to search a Sequence or SymbolList object for a consensus
> sequence that contains IUPac ambiguity codes.
>
> Without ambiguity codes, I could write a function that breaks the sequence
> into "windows" the size of the consensus, and checks each window for a
> match.  Am I missing a simple function that does this for me?
>
> Next, adding ambiguity codes ... do I have to define my own alphabet for the
> DNA IUPac codes, or are these already included in the distribution
> somewhere?
>
> I have found the weight matrix class, and realize that I could create one of
> these objects and calculate a threshold that will work in the same manner as
> a consensus, but this seems like a bit of a hack for some functionality I am
> most likely overlooking.
>
> Thanks very much!
>
> Charles


From dankoc at gmail.com  Wed Mar 14 12:15:11 2007
From: dankoc at gmail.com (Charles Danko)
Date: Wed, 14 Mar 2007 12:15:11 -0400
Subject: [Biojava-l] Having problems using biojava regex.
Message-ID: <8adccabf0703140915s7e955c4et6fd86a12d2f21d8b@mail.gmail.com>

Hi,

I'm having problems using the biojava regex classes.

According to my understanding, the code posted below is the simplest
possible example of this class.

However, my output is:
TAG
false
0
TAG

The TAG, TAG part of the output is for pattern.patternAsString() and
occurence.pattern().patternAsString().  As I understand it, both of these
are correct, leading me to believe that both the Pattern and Matcher objects
are being created correctly.  However, occurences.find() = false and
occurences.groupCount() = 0 ... meaning it's not finding any matches!?

Where am I going wrong?

Many thanks!
Charles

import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
import org.biojava.utils.regex.*;
import java.util.*;
import java.io.*;

public class Ambiguity2 {
  public static void main(String[] args) {
    try {
        FiniteAlphabet IUPAC = DNATools.getDNA();

        // Create pattern using pattern factory.
        Pattern pattern;
        PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC);
        try{
            pattern = FACTORY.compile("TAG");
        } catch(Exception e) {e.printStackTrace(); return;}
        System.out.println(pattern.patternAsString());

        // Variables needed...
        Matcher occurences;

        // Promoter & Element
        Element WorkingElement = new Element("ElementName");
        SymbolList WorkingPromoter = DNATools.createDNA
("TAGAGATAGACGATAGC");

        // Obtain iterator of patterns.
        try {
            occurences = pattern.matcher( WorkingPromoter );
        } catch(Exception e) {e.printStackTrace(); return;}
        System.out.println(occurences.find());
        System.out.println(occurences.groupCount());
        System.out.println(occurences.pattern().patternAsString());
        // Foreach match
        while( occurences.find() ) {
                // Create Occurence object using information from patterns.
            System.out.println("Match: " +"\t"+ WorkingPromoter +"\n"+
occurences.start() +"\t"+ occurences.group().seqString());
        }
    }

    catch (Exception ex) {
      ex.printStackTrace();
    }
  }
}

From markjschreiber at gmail.com  Wed Mar 14 21:37:06 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 15 Mar 2007 09:37:06 +0800
Subject: [Biojava-l] Having problems using biojava regex.
In-Reply-To: <8adccabf0703140915s7e955c4et6fd86a12d2f21d8b@mail.gmail.com>
References: <8adccabf0703140915s7e955c4et6fd86a12d2f21d8b@mail.gmail.com>
Message-ID: <93b45ca50703141837g15a8de9fr5bc01341d8cd57c8@mail.gmail.com>

Hi -

>From memory everything should be lower case. BioJava always represents DNA
as lowercase and protein as upper case as per convention.

Try that.

- Mark


On 3/15/07, Charles Danko <dankoc at gmail.com> wrote:
>
> Hi,
>
> I'm having problems using the biojava regex classes.
>
> According to my understanding, the code posted below is the simplest
> possible example of this class.
>
> However, my output is:
> TAG
> false
> 0
> TAG
>
> The TAG, TAG part of the output is for pattern.patternAsString() and
> occurence.pattern().patternAsString().  As I understand it, both of these
> are correct, leading me to believe that both the Pattern and Matcher
> objects
> are being created correctly.  However, occurences.find() = false and
> occurences.groupCount() = 0 ... meaning it's not finding any matches!?
>
> Where am I going wrong?
>
> Many thanks!
> Charles
>
> import org.biojava.bio.*;
> import org.biojava.bio.seq.*;
> import org.biojava.bio.symbol.*;
> import org.biojava.utils.regex.*;
> import java.util.*;
> import java.io.*;
>
> public class Ambiguity2 {
> public static void main(String[] args) {
>    try {
>        FiniteAlphabet IUPAC = DNATools.getDNA();
>
>        // Create pattern using pattern factory.
>        Pattern pattern;
>        PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC);
>        try{
>            pattern = FACTORY.compile("TAG");
>        } catch(Exception e) {e.printStackTrace(); return;}
>        System.out.println(pattern.patternAsString());
>
>        // Variables needed...
>        Matcher occurences;
>
>        // Promoter & Element
>        Element WorkingElement = new Element("ElementName");
>        SymbolList WorkingPromoter = DNATools.createDNA
> ("TAGAGATAGACGATAGC");
>
>        // Obtain iterator of patterns.
>        try {
>            occurences = pattern.matcher( WorkingPromoter );
>        } catch(Exception e) {e.printStackTrace(); return;}
>        System.out.println(occurences.find());
>        System.out.println(occurences.groupCount());
>        System.out.println(occurences.pattern().patternAsString());
>        // Foreach match
>        while( occurences.find() ) {
>                // Create Occurence object using information from patterns.
>            System.out.println("Match: " +"\t"+ WorkingPromoter +"\n"+
> occurences.start() +"\t"+ occurences.group().seqString());
>        }
>    }
>
>    catch (Exception ex) {
>      ex.printStackTrace();
>    }
> }
> }
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From dankoc at gmail.com  Wed Mar 14 22:20:54 2007
From: dankoc at gmail.com (Charles Danko)
Date: Wed, 14 Mar 2007 22:20:54 -0400
Subject: [Biojava-l] Having problems using biojava regex.
In-Reply-To: <93b45ca50703141837g15a8de9fr5bc01341d8cd57c8@mail.gmail.com>
References: <8adccabf0703140915s7e955c4et6fd86a12d2f21d8b@mail.gmail.com>
	<93b45ca50703141837g15a8de9fr5bc01341d8cd57c8@mail.gmail.com>
Message-ID: <8adccabf0703141920w1246c3b0u39e288941c20cb17@mail.gmail.com>

Thank worked!  I had no idea it would matter!

Thanks very much for the response!

Charles

On 3/14/07, Mark Schreiber <markjschreiber at gmail.com> wrote:
>
> Hi -
>
> From memory everything should be lower case. BioJava always represents DNA
> as lowercase and protein as upper case as per convention.
>
> Try that.
>
> - Mark
>
>
> On 3/15/07, Charles Danko <dankoc at gmail.com> wrote:
>
> > Hi,
> >
> > I'm having problems using the biojava regex classes.
> >
> > According to my understanding, the code posted below is the simplest
> > possible example of this class.
> >
> > However, my output is:
> > TAG
> > false
> > 0
> > TAG
> >
> > The TAG, TAG part of the output is for pattern.patternAsString() and
> > occurence.pattern().patternAsString().  As I understand it, both of
> > these
> > are correct, leading me to believe that both the Pattern and Matcher
> > objects
> > are being created correctly.  However, occurences.find() = false and
> > occurences.groupCount() = 0 ... meaning it's not finding any matches!?
> >
> > Where am I going wrong?
> >
> > Many thanks!
> > Charles
> >
> > import org.biojava.bio.*;
> > import org.biojava.bio.seq.*;
> > import org.biojava.bio.symbol.*;
> > import org.biojava.utils.regex.*;
> > import java.util.* ;
> > import java.io.*;
> >
> > public class Ambiguity2 {
> > public static void main(String[] args) {
> >    try {
> >        FiniteAlphabet IUPAC = DNATools.getDNA();
> >
> >        // Create pattern using pattern factory.
> >        Pattern pattern;
> >        PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC);
> >        try{
> >            pattern = FACTORY.compile("TAG");
> >        } catch(Exception e) {e.printStackTrace(); return;}
> >        System.out.println(pattern.patternAsString());
> >
> >        // Variables needed...
> >        Matcher occurences;
> >
> >        // Promoter & Element
> >        Element WorkingElement = new Element("ElementName");
> >        SymbolList WorkingPromoter = DNATools.createDNA
> > ("TAGAGATAGACGATAGC");
> >
> >        // Obtain iterator of patterns.
> >        try {
> >            occurences = pattern.matcher( WorkingPromoter );
> >        } catch(Exception e) {e.printStackTrace(); return;}
> >        System.out.println(occurences.find());
> >        System.out.println(occurences.groupCount());
> >        System.out.println(occurences.pattern().patternAsString());
> >        // Foreach match
> >        while( occurences.find() ) {
> >                // Create Occurence object using information from
> > patterns.
> >            System.out.println("Match: " +"\t"+ WorkingPromoter +"\n"+
> > occurences.start() +"\t"+ occurences.group().seqString());
> >        }
> >    }
> >
> >    catch (Exception ex) {
> >      ex.printStackTrace();
> >    }
> > }
> > }
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>

From mark.schreiber at novartis.com  Wed Mar 14 22:27:14 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 15 Mar 2007 10:27:14 +0800
Subject: [Biojava-l] Having problems using biojava regex.
Message-ID: <OF44671D3F.80370BA4-ON4825729F.000D3226-4825729F.000D7B0D@ah.novartis.com>

It's not so much that biojava is case sensitive as it is that regexes are. 
You could probably set your regex to be case insensitive to avoid this 
kind of problem. 

As a cool trick though, it is possible to soft-mask sequences in BioJava 
such that lower case and upper case have different meaning. Typically 
lower case is being masked due to repeats or similar. You could then make 
a regex that finds only matches in the unmasked regions or alternatively 
the masked regions.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Charles Danko" <dankoc at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
03/15/2007 10:20 AM

 
        To:     "Mark Schreiber" <markjschreiber at gmail.com>
        cc:     biojava-l at lists.open-bio.org, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] Having problems using biojava regex.


Thank worked!  I had no idea it would matter!

Thanks very much for the response!

Charles

On 3/14/07, Mark Schreiber <markjschreiber at gmail.com> wrote:
>
> Hi -
>
> From memory everything should be lower case. BioJava always represents 
DNA
> as lowercase and protein as upper case as per convention.
>
> Try that.
>
> - Mark
>
>
> On 3/15/07, Charles Danko <dankoc at gmail.com> wrote:
>
> > Hi,
> >
> > I'm having problems using the biojava regex classes.
> >
> > According to my understanding, the code posted below is the simplest
> > possible example of this class.
> >
> > However, my output is:
> > TAG
> > false
> > 0
> > TAG
> >
> > The TAG, TAG part of the output is for pattern.patternAsString() and
> > occurence.pattern().patternAsString().  As I understand it, both of
> > these
> > are correct, leading me to believe that both the Pattern and Matcher
> > objects
> > are being created correctly.  However, occurences.find() = false and
> > occurences.groupCount() = 0 ... meaning it's not finding any matches!?
> >
> > Where am I going wrong?
> >
> > Many thanks!
> > Charles
> >
> > import org.biojava.bio.*;
> > import org.biojava.bio.seq.*;
> > import org.biojava.bio.symbol.*;
> > import org.biojava.utils.regex.*;
> > import java.util.* ;
> > import java.io.*;
> >
> > public class Ambiguity2 {
> > public static void main(String[] args) {
> >    try {
> >        FiniteAlphabet IUPAC = DNATools.getDNA();
> >
> >        // Create pattern using pattern factory.
> >        Pattern pattern;
> >        PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC);
> >        try{
> >            pattern = FACTORY.compile("TAG");
> >        } catch(Exception e) {e.printStackTrace(); return;}
> >        System.out.println(pattern.patternAsString());
> >
> >        // Variables needed...
> >        Matcher occurences;
> >
> >        // Promoter & Element
> >        Element WorkingElement = new Element("ElementName");
> >        SymbolList WorkingPromoter = DNATools.createDNA
> > ("TAGAGATAGACGATAGC");
> >
> >        // Obtain iterator of patterns.
> >        try {
> >            occurences = pattern.matcher( WorkingPromoter );
> >        } catch(Exception e) {e.printStackTrace(); return;}
> >        System.out.println(occurences.find());
> >        System.out.println(occurences.groupCount());
> >        System.out.println(occurences.pattern().patternAsString());
> >        // Foreach match
> >        while( occurences.find() ) {
> >                // Create Occurence object using information from
> > patterns.
> >            System.out.println("Match: " +"\t"+ WorkingPromoter +"\n"+
> > occurences.start() +"\t"+ occurences.group().seqString());
> >        }
> >    }
> >
> >    catch (Exception ex) {
> >      ex.printStackTrace();
> >    }
> > }
> > }
> > _______________________________________________
> > 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 Sofia.Burvall at hgen.slu.se  Fri Mar 16 12:31:23 2007
From: Sofia.Burvall at hgen.slu.se (Sofia Burvall)
Date: Fri, 16 Mar 2007 17:31:23 +0100
Subject: [Biojava-l] Uniprot files
Message-ID: <D0232C4A-5FDB-46A2-B213-80CBDB82C946@hgen.slu.se>

Hi!

I have just started to get to know biojava. I have written a small  
program that reads a file with the help of the biojavax method

  	RichSequence.IOTools.readFile(filen,ns );

and then tries to write the file as UniProt using

	RichSequence.IOTools.writeUniProt(System.out, seqit, ns);

This works nicely when I read a fasta file. But when I try to read a  
Uniprot file I get this error message:

org.biojava.bio.BioException: Could not read sequence
	at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence 
(RichStreamReader.java:113)
	at org.biojavax.bio.seq.io.RichStreamReader.nextSequence 
(RichStreamReader.java:92)
	at org.biojavax.bio.seq.io.RichStreamWriter.writeStream 
(RichStreamWriter.java:66)
	at org.biojavax.bio.seq.RichSequence$IOTools.writeUniProt 
(RichSequence.java:1426)
	at bc_biojava.GeneralReader.main(GeneralReader.java:81)
Caused by: org.biojava.bio.seq.io.ParseException: Bad date line  
found: 01-JAN-1990 (Rel. 13, Created)
	at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence 
(UniProtFormat.java:349)
	at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence 
(RichStreamReader.java:110)
	... 4 more


  When I try other uniprot files i get the same error. It complains  
about "Bad date line..".
What can be the reason for this? Is it the wrong file format?


Cheers
/Sofia

***
Here is the UniProt flat file:
***
ID   FOSB_MOUSE     STANDARD;      PRT;   338 AA.
AC   P13346;
DT   01-JAN-1990 (Rel. 13, Created)
DT   01-JAN-1990 (Rel. 13, Last sequence update)
DT   15-JUN-2002 (Rel. 41, Last annotation update)
DE   Protein fosB.
GN   FOSB.
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
OX   NCBI_Taxid=10090;
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=89251612; PubMed=2498083;
RA   Zerial M., Toschi L., Ryseck R.-P., Schuermann M., Mueller R.,
RA   Bravo R.;
RT   "The product of a novel growth factor activated gene, fos B,  
interacts
RT   with JUN proteins enhancing their DNA binding activity.";
RL   EMBO J. 8:805-813(1989).
RN   [2]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=92158623; PubMed=1741260;
RA   Lazo P.S., Dorfman K., Noguchi T., Mattei M.-G., Bravo R.;
RT   "Structure and mapping of the fosB gene. FosB downregulates the
RT   activity of the fosB promoter.";
RL   Nucleic Acids Res. 20:343-350(1992).
CC   -!- FUNCTION: FOSB INTERACTS WITH JUN PROTEINS ENHANCING THEIR DNA
CC       BINDING ACTIVITY.
CC   -!- SUBUNIT: HETERODIMER (BY SIMILARITY).
CC   -!- SUBCELLULAR LOCATION: NUCLEAR.
CC   -!- INDUCTION: BY GROWTH FACTORS.
CC   -!- SIMILARITY: BELONGS TO THE BZIP FAMILY. FOS SUBFAMILY.
CC    
------------------------------------------------------------------------ 
--
CC   This Swiss-Prot entry is copyright. It is produced through a  
collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL  
outstation -
CC   the European Bioinformatics Institute.  There are no   
restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is   
in  no  way
CC   modified and this statement is not removed.  Usage  by  and for  
commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/ 
announce/
CC   or send an email to license at isb-sib.ch).
CC    
------------------------------------------------------------------------ 
--
DR   EMBL; X14897; CAA33026.1; -.
DR   EMBL; AF093624; AAD13196.1; -.
DR   PIR; S04108; TVMSFB.
DR   PIR; S35477; S35477.
DR   HSSP; P01100; 1FOS.
DR   TRANSFAC; T00291; -.
DR   MGD; MGI:95575; Fosb.
DR   InterPro; IPR000837; Leuzip_Fos.
DR   InterPro; IPR004827; TF_bZIP.
DR   Pfam; PF00170; bZIP; 1.
DR   PRINTS; PR00042; LEUZIPPRFOS.
DR   SMART; SM00338; BRLZ; 1.
DR   PROSITE; PS00036; BZIP_BASIC; 1.
KW   Nuclear protein; DNA-binding.
FT   DNA_BIND    161    179       BASIC MOTIF.
FT   DOMAIN      183    211       LEUCINE-ZIPPER.
SQ   SEQUENCE   338 AA;  35976 MW;  E9D031A4BEAE48EC CRC64;
      MFQAFPGDYD SGSRCSSSPS AESQYLSSVD SFGSPPTAAA SQECAGLGEM PGSFVPTVTA
      ITTSQDLQWL VQPTLISSMA QSQGQPLASQ PPAVDPYDMP GTSYSTPGLS AYSTGGASGS
      GGPSTSTTTS GPVSARPARA RPRRPREETL TPEEEEKRRV RRERNKLAAA KCRNRRRELT
      DRLQAETDQL EEEKAELESE IAELQKEKER LEFVLVAHKP GCKIPYEEGP GPGPLAEVRD
      LPGSTSAKED GFGWLLPPPP PPPLPFQSSR DAPPNLTASL FTHSEVQVLG DPFPVVSPSY
      TSSFVLTCPE VSAFAGAQRT SGSEQPSDPL NSPSLLAL
//




From ericgibert at yahoo.fr  Fri Mar 16 21:42:38 2007
From: ericgibert at yahoo.fr (Eric Gibert)
Date: Sat, 17 Mar 2007 09:42:38 +0800
Subject: [Biojava-l] BioJava 1.5 versus BioJava 2
Message-ID: <015201c76835$8e85b070$3e00a8c0@Gecko>

Dear all,

 

I am using BioJava 1.4 and I think to upgrade to 1.5. But I would like to
benefit of the new Java language improvement (<structure> and "foreach a la
Java"). My understanding is that Biojava 1.5 uses the List type (with the
Iterator). On the other hand, I read about another project called Biojava 2
which takes the approach to implement <Sequence> and other features of Java
5.0.

 

But it looks like Biojava 2 is still new and does not offer the rich
environment of Biojava 1.x

 

Any comments?

 

Eric Gibert

http://www.asia-dragonfly.net <http://www.asia-dragonfly.net/>  &
http://www.africa-dragonfly.net <http://www.africa-dragonfly.net/> 

 


From markjschreiber at gmail.com  Sat Mar 17 01:48:10 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sat, 17 Mar 2007 13:48:10 +0800
Subject: [Biojava-l] BioJava 1.5 versus BioJava 2
In-Reply-To: <015201c76835$8e85b070$3e00a8c0@Gecko>
References: <015201c76835$8e85b070$3e00a8c0@Gecko>
Message-ID: <93b45ca50703162248m30a0319bi1ee8e70b9eaa7521@mail.gmail.com>

Hi -

BioJava2 is more of a concept than an actual usable API. I'm not sure
if the development of this project is even active right now.

BioJava 1.5 will be the next generation of biojava. It doesn't use
features of JDK1.5 like generics, foreach, and unboxing but later
versions will. However, this doesn't mean you can't use them with the
API. For example there is no reason why you cannot make a
List<Sequence> and iterate over it with a foreach statement. It's just
that BioJava 1.5 doesn't do that internally yet.

- Mark

On 3/17/07, Eric Gibert <ericgibert at yahoo.fr> wrote:
> Dear all,
>
>
>
> I am using BioJava 1.4 and I think to upgrade to 1.5. But I would like to
> benefit of the new Java language improvement (<structure> and "foreach a la
> Java"). My understanding is that Biojava 1.5 uses the List type (with the
> Iterator). On the other hand, I read about another project called Biojava 2
> which takes the approach to implement <Sequence> and other features of Java
> 5.0.
>
>
>
> But it looks like Biojava 2 is still new and does not offer the rich
> environment of Biojava 1.x
>
>
>
> Any comments?
>
>
>
> Eric Gibert
>
> http://www.asia-dragonfly.net <http://www.asia-dragonfly.net/>  &
> http://www.africa-dragonfly.net <http://www.africa-dragonfly.net/>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From hlapp at gmx.net  Sat Mar 17 16:15:01 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 17 Mar 2007 16:15:01 -0400
Subject: [Biojava-l] Phyloinformatics Summer of Code
Message-ID: <AADE6C0C-66AE-4C04-BC77-1E728765706F@gmx.net>

(Apologies if you receive multiple copies of this. The message is  
being posted to multiple channels.)

(Note that leading developers from both Biojava and BioPerl are  
amongst the mentors.)

Phyloinformatics Summer of Code 2007

A collaborative Phyloinformatics Group, sponsored by the National  
Evolutionary Synthesis Center (NESCent: http://www.nescent.org/), is  
working to develop user-interfaces, improve software interoperability  
and support data exchange standards in evolutionary bioinformatics.   
The specific projects are diverse in nature and range from the  
development of AJAX components for web-based bioinformatics  
applications, managing workflows using approaches from functional and  
logic programming, and developing data exchange standards for  
phylogenetic substitution models.

The Phyloinformatics group will be sponsoring student collaborators  
through the Google Summer of Code program (http://code.google.com/ 
soc), which provides undergraduate, masters and PhD students with a  
unique opportunity (over three summer months) to obtain hands-on  
experience writing and extending open-source software under the  
mentorship of experienced developers from around the world.  We are  
particularly targeting students interested in both evolutionary  
biology and software development.  Students will have one or more  
dedicated mentors with expertise in phylogenetic methods and open- 
source software development.  Our project proposals are flexible and  
can be adjusted in scope to match the skills of students with less  
programming proficiency. If the program sounds interesting to you but  
you are unsure whether you have the necessary skills, please email  
the mentors at phylosoc {at} nescent {dot} org.  We will work with  
those who are genuinely interested to find a project that fits your  
interest and skills.  Students will receive a stipend from Google and  
will be invited to participate in future collaborative events such as  
the NESCent Phyloinformatics Hackathons (http://www.nescent.org/wg/ 
phyloinformatics).

TO APPLY:
Students must apply on-line at the Google Summer of Code website  
(http://code.google.com/soc). The application period for students is  
now open and ends on Saturday, March 24, 2007 (one week from now).

The Phyloinformatics Summer of Code project and ideas page is at the  
following URL:
http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2007

The above page also contains links to the GSoC program rules,  
eligibility requirements, and stipend payment mechanism. We encourage  
all interested students to email any questions, or self-proposed  
project ideas, to phylosoc {at} nescent {dot} org. This will reach  
all prospective mentors.

Eligibility requirements for students:
http://code.google.com/support/bin/answer.py?answer=60279&topic=10730

Stipend for students:
http://code.google.com/support/bin/answer.py?answer=60322&topic=10731

Please disseminate this announcement to appropriate students at your  
institution.

Hilmar Lapp
Assistant Director for Informatics
NESCent




From ericgibert at yahoo.fr  Mon Mar 19 09:46:49 2007
From: ericgibert at yahoo.fr (Eric Gibert)
Date: Mon, 19 Mar 2007 21:46:49 +0800
Subject: [Biojava-l] BioJava 1.5 versus BioJava 2
In-Reply-To: <45FE5436.7000807@ebi.ac.uk>
References: <015201c76835$8e85b070$3e00a8c0@Gecko> <45FE5436.7000807@ebi.ac.uk>
Message-ID: <002901c76a2d$0ec96260$3e00a8c0@Gecko>

Thank you Richard and Mark for your answers.

So my next move is to install Hibernate and move to BJ1.5.

Eric

-----Original Message-----
From: Richard Holland [mailto:holland at ebi.ac.uk] 
Sent: Monday, March 19, 2007 5:13 PM
To: Eric Gibert
Cc: biojava-l at lists.open-bio.org
Subject: Re: [Biojava-l] BioJava 1.5 versus BioJava 2

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

BJ2 is developed by a different group of developers than BJ1.5. As far
as I know, BJ2 never got further than a framework of ideas with one or
two proof-of-concept interface implementations. It is not currently
under active development that I am aware of.

BJ1.5 still uses Java 1.4 language features, as you correctly identify.
We have discussed moving to Java 1.5 for the BJ1.6 release and will make
a decision/announcement when the time comes. One of the reasons for the
delayed conversion is that up until recently many users' systems do not
have Java 1.5 environments available (older Macs, Compaq/DEC Alphas, etc.).

cheers,
Richard

Eric Gibert wrote:
> Dear all,
> 
>  
> 
> I am using BioJava 1.4 and I think to upgrade to 1.5. But I would like to
> benefit of the new Java language improvement (<structure> and "foreach a
la
> Java"). My understanding is that Biojava 1.5 uses the List type (with the
> Iterator). On the other hand, I read about another project called Biojava
2
> which takes the approach to implement <Sequence> and other features of
Java
> 5.0.
> 
>  
> 
> But it looks like Biojava 2 is still new and does not offer the rich
> environment of Biojava 1.x
> 
>  
> 
> Any comments?
> 
>  
> 
> Eric Gibert
> 
> http://www.asia-dragonfly.net <http://www.asia-dragonfly.net/>  &
> http://www.africa-dragonfly.net <http://www.africa-dragonfly.net/> 
> 
>  
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFF/lQ14C5LeMEKA/QRAoH2AJ9Vs22ArHtlx+fDTRS9tU0PtRLztACeLnxj
lCsOBXw/oHGrEqf+Gzd0RQo=
=GOvY
-----END PGP SIGNATURE-----



	

	
		
___________________________________________________________________________ 
Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire.
http://fr.mail.yahoo.com

From Joseph.Bedell at sial.com  Mon Mar 19 11:00:58 2007
From: Joseph.Bedell at sial.com (Joseph Bedell)
Date: Mon, 19 Mar 2007 10:00:58 -0500
Subject: [Biojava-l] Joseph Bedell is out of the office.
Message-ID: <OF601BE2CC.AFED0DF8-ON862572A3.00527C8E-862572A3.00527C8E@sial.com>


I will be out of the office starting  03/19/2007 and will not return until
03/26/2007.

I will respond to your message when I return.


From mark.schreiber at novartis.com  Tue Mar 20 22:55:48 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 21 Mar 2007 10:55:48 +0800
Subject: [Biojava-l] State of the nation
Message-ID: <OFF853F626.20A43EB4-ON482572A5.000FDF3F-482572A5.001018BA@ah.novartis.com>

Hi -

Recently several of the current and former core developers of the biojava 
project happened to be in Cambridge at the same time and had some 
discussions about the directions and immediate future of the project. A 
summary of the discussion has been posted on the biojava website at 
http://biojava.org/wiki/BioJava:CambridgeDiscussion

Please take a look and feel free to add your comments to the page.

- Mark


From gwaldon at geneinfinity.org  Wed Mar 21 14:38:03 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Wed, 21 Mar 2007 11:38:03 -0700
Subject: [Biojava-l] Uniprot files
Message-ID: <200703211838.l2LIc4rM063269@mmm1924.dulles19-verio.com>

Sorry for the late response. I have also noticed the problem with uniprot files recently. I am going to file a bug report. In the future, you can submit bugs yourself on bugzilla at http://bugzilla.open-bio.org/.

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 Sofia Burvall
Sent: Friday, March 16, 2007 9:31 AM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Uniprot files

Hi!

I have just started to get to know biojava. I have written a small  
program that reads a file with the help of the biojavax method

  	RichSequence.IOTools.readFile(filen,ns );

and then tries to write the file as UniProt using

	RichSequence.IOTools.writeUniProt(System.out, seqit, ns);

This works nicely when I read a fasta file. But when I try to read a  
Uniprot file I get this error message:

org.biojava.bio.BioException: Could not read sequence
	at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence 
(RichStreamReader.java:113)
	at org.biojavax.bio.seq.io.RichStreamReader.nextSequence 
(RichStreamReader.java:92)
	at org.biojavax.bio.seq.io.RichStreamWriter.writeStream 
(RichStreamWriter.java:66)
	at org.biojavax.bio.seq.RichSequence$IOTools.writeUniProt 
(RichSequence.java:1426)
	at bc_biojava.GeneralReader.main(GeneralReader.java:81)
Caused by: org.biojava.bio.seq.io.ParseException: Bad date line  
found: 01-JAN-1990 (Rel. 13, Created)
	at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence 
(UniProtFormat.java:349)
	at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence 
(RichStreamReader.java:110)
	... 4 more


  When I try other uniprot files i get the same error. It complains  
about "Bad date line..".
What can be the reason for this? Is it the wrong file format?


Cheers
/Sofia

***
Here is the UniProt flat file:
***
ID   FOSB_MOUSE     STANDARD;      PRT;   338 AA.
AC   P13346;
DT   01-JAN-1990 (Rel. 13, Created)
DT   01-JAN-1990 (Rel. 13, Last sequence update)
DT   15-JUN-2002 (Rel. 41, Last annotation update)
DE   Protein fosB.
GN   FOSB.
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
OX   NCBI_Taxid=10090;
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=89251612; PubMed=2498083;
RA   Zerial M., Toschi L., Ryseck R.-P., Schuermann M., Mueller R.,
RA   Bravo R.;
RT   "The product of a novel growth factor activated gene, fos B,  
interacts
RT   with JUN proteins enhancing their DNA binding activity.";
RL   EMBO J. 8:805-813(1989).
RN   [2]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=92158623; PubMed=1741260;
RA   Lazo P.S., Dorfman K., Noguchi T., Mattei M.-G., Bravo R.;
RT   "Structure and mapping of the fosB gene. FosB downregulates the
RT   activity of the fosB promoter.";
RL   Nucleic Acids Res. 20:343-350(1992).
CC   -!- FUNCTION: FOSB INTERACTS WITH JUN PROTEINS ENHANCING THEIR DNA
CC       BINDING ACTIVITY.
CC   -!- SUBUNIT: HETERODIMER (BY SIMILARITY).
CC   -!- SUBCELLULAR LOCATION: NUCLEAR.
CC   -!- INDUCTION: BY GROWTH FACTORS.
CC   -!- SIMILARITY: BELONGS TO THE BZIP FAMILY. FOS SUBFAMILY.
CC    
------------------------------------------------------------------------ 
--
CC   This Swiss-Prot entry is copyright. It is produced through a  
collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL  
outstation -
CC   the European Bioinformatics Institute.  There are no   
restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is   
in  no  way
CC   modified and this statement is not removed.  Usage  by  and for  
commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/ 
announce/
CC   or send an email to license at isb-sib.ch).
CC    
------------------------------------------------------------------------ 
--
DR   EMBL; X14897; CAA33026.1; -.
DR   EMBL; AF093624; AAD13196.1; -.
DR   PIR; S04108; TVMSFB.
DR   PIR; S35477; S35477.
DR   HSSP; P01100; 1FOS.
DR   TRANSFAC; T00291; -.
DR   MGD; MGI:95575; Fosb.
DR   InterPro; IPR000837; Leuzip_Fos.
DR   InterPro; IPR004827; TF_bZIP.
DR   Pfam; PF00170; bZIP; 1.
DR   PRINTS; PR00042; LEUZIPPRFOS.
DR   SMART; SM00338; BRLZ; 1.
DR   PROSITE; PS00036; BZIP_BASIC; 1.
KW   Nuclear protein; DNA-binding.
FT   DNA_BIND    161    179       BASIC MOTIF.
FT   DOMAIN      183    211       LEUCINE-ZIPPER.
SQ   SEQUENCE   338 AA;  35976 MW;  E9D031A4BEAE48EC CRC64;
      MFQAFPGDYD SGSRCSSSPS AESQYLSSVD SFGSPPTAAA SQECAGLGEM PGSFVPTVTA
      ITTSQDLQWL VQPTLISSMA QSQGQPLASQ PPAVDPYDMP GTSYSTPGLS AYSTGGASGS
      GGPSTSTTTS GPVSARPARA RPRRPREETL TPEEEEKRRV RRERNKLAAA KCRNRRRELT
      DRLQAETDQL EEEKAELESE IAELQKEKER LEFVLVAHKP GCKIPYEEGP GPGPLAEVRD
      LPGSTSAKED GFGWLLPPPP PPPLPFQSSR DAPPNLTASL FTHSEVQVLG DPFPVVSPSY
      TSSFVLTCPE VSAFAGAQRT SGSEQPSDPL NSPSLLAL
//



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

From phidias51 at gmail.com  Thu Mar 22 22:53:50 2007
From: phidias51 at gmail.com (Mark Fortner)
Date: Thu, 22 Mar 2007 18:53:50 -0800
Subject: [Biojava-l] State of the nation
In-Reply-To: <OF843F5735.CE3A6394-ON482572A7.000CCD40-482572A7.000D7417@ah.novartis.com>
References: <OF843F5735.CE3A6394-ON482572A7.000CCD40-482572A7.000D7417@ah.novartis.com>
Message-ID: <6e1d61f50703221953y1ea5a8e0j99e8b806782351e7@mail.gmail.com>

Mark
As you point out, the build server changes (and potentially the bug tracking
system) would require the participation of the open bio folks to make these
changes to their server.  It might be a good idea to begin engaging them
now.  They may have some other ideas as well.

There are complete software development management systems like Source Forge
that could be setup.  When I worked at a previous company we had our own
internal SourceForge instance that gave us forums, a wiki, subversion, bug
tracking, etc. Atlassian offers a similar product suite.  Such an
all-encompassing solution might suit OpenBio more than a series of piecemeal
solutions.

Mark

On 3/22/07, mark.schreiber at novartis.com <mark.schreiber at novartis.com> wrote:
>
>
>
>
>
> *"Mark Fortner" <phidias51 at gmail.com>*
>
> 03/21/2007 01:22 PM
>
>         To:        "mark.schreiber at novartis.com" <
> mark.schreiber at novartis.com>
>         cc:
>         Subject:        Re: [Biojava-l] State of the nation
>
>
> Hi Mark,
> I started to edit the wiki, but then thought it might be better to discuss
> a few things first.
>
> (1) There are some new javadoc tags that can make some of this easier to
> do.  {@inheritDoc} for example can be used to inherit the documentation from
> an interface or superclass, thus saving some typing.
>
> Yes, we use these a lot in biojavax but it could be added as a
> recomendation in the wiki.
>
> (2) Unit tests will definitely make it easier to handle regression tests,
> but it might be better to simply add additional test methods to existing
> unit tests (currently located in the tests directory).  This directory
> mirrors the source packages and is fairly easy to maintain.  We can add a
> comment in the test method to indicate that it's in response to a particular
> bug fix.
>
> You could name the method testBug12345. It's a matter of style I suppose.
> Having it all together reduces redundancy. Having regression tests
> seperately makes it easier to find the appropriate regression test
> especially if it involves more than one object.
>
> (3) Regardless of the method used to build BioJava it would be useful to
> continuously build and test the project.  There are tools to do this for
> both Maven and Ant.  In addition to simply telling us that the build is
> broken, there are code coverage plugins that can tell us if the unit tests
> accurately cover the code they purport to test.  You can also generate
> documentation, HTML-browsable code (java2html), and UML diagrams (through
> UMLJGraph or doxygen) in an automated fashion.   Here's a partial plugin
> list to give you some ideas: *http://maven.apache.org/plugins/index.html*<http://maven.apache.org/plugins/index.html>
>
> I agree. I'm not much of a build expert and only an ant hacker. What we
> really need is some volunteers to help set this sort of thing up. If you
> know how to do it and have the time it would be excellent.
>
> (4) If you've reported bugs for any of the Apache projects, you may have
> noticed that they switched to JIRA.  This is a wonderful tool created by a
> company in Sydney called Atlassian.  The tool can provide users with a
> roadmap of what changes are due in which releases, you can create RSS feeds
> for different reports.  The reports are completely customizable.  If you use
> the Eclipse Mylar plugin, then tasks that are assigned to you in JIRA appear
> in Mylar.  You can also add JIRA issue numbers to code checkins in
> subversion or CVS.  When JIRA indexes the code, you it then provides you
> with a list of all classes that were modified in response to a particular
> bug.  There are numerous other features described here: *
> http://www.atlassian.com/software/jira/*<http://www.atlassian.com/software/jira/>and the software is available free of charge for open source project! s.
> *http://www.atlassian.com/software/jira/pricing.jsp*<http://www.atlassian.com/software/jira/pricing.jsp>
>
> Again, I don't have much experience. I use bugzilla because open-bio set
> it up for us. We could probably request other things if you know what you
> want.
>
> Go ahead and add some suggestions on either the wiki or the mailing list.
> Hopefully some prodding will provoke the slumbering biojava community into
> action : )
>
> - Mark
>
> Hope this helps,
>
> Mark Fortner
>
>
> On 3/20/07, *mark.schreiber at novartis.com* <mark.schreiber at novartis.com> <*
> mark.schreiber at novartis.com* <mark.schreiber at novartis.com>> wrote:
> Hi -
>
> Recently several of the current and former core developers of the biojava
> project happened to be in Cambridge at the same time and had some
> discussions about the directions and immediate future of the project. A
> summary of the discussion has been posted on the biojava website at*
> **http://biojava.org/wiki/BioJava:CambridgeDiscussion*<http://biojava.org/wiki/BioJava:CambridgeDiscussion>
>
> Please take a look and feel free to add your comments to the page.
>
> - Mark
>
> _______________________________________________
> Biojava-l mailing list  -  *Biojava-l at lists.open-bio.org*<Biojava-l at lists.open-bio.org>
> *
> **http://lists.open-bio.org/mailman/listinfo/biojava-l*<http://lists.open-bio.org/mailman/listinfo/biojava-l>
>
>
>

From e.willighagen at science.ru.nl  Fri Mar 23 13:50:54 2007
From: e.willighagen at science.ru.nl (Egon Willighagen)
Date: Fri, 23 Mar 2007 18:50:54 +0100
Subject: [Biojava-l] State of the nation
In-Reply-To: <6e1d61f50703221953y1ea5a8e0j99e8b806782351e7@mail.gmail.com>
References: <OF843F5735.CE3A6394-ON482572A7.000CCD40-482572A7.000D7417@ah.novartis.com>
	<6e1d61f50703221953y1ea5a8e0j99e8b806782351e7@mail.gmail.com>
Message-ID: <200703231850.54872.e.willighagen@science.ru.nl>

On Friday 23 March 2007, Mark Fortner wrote:
> > We can add a
> > comment in the test method to indicate that it's in response to a
> > particular bug fix.
> >
> > You could name the method testBug12345. It's a matter of style I suppose.
> > Having it all together reduces redundancy. Having regression tests
> > seperately makes it easier to find the appropriate regression test
> > especially if it involves more than one object.

I can very much recommend this, as we have good experiences with this in the 
CDK [1]. We actually tag Junit test methods, as well as the class in which 
the bug was found until it is closed. By using a simple JavaDoc Taglet, we 
link to our bug track system (e.g. [2]), so that users can always see in the 
JavaDoc if there are relevant open bug for a certain pieace of code.

Additionally, we have a nightly build service which checks about open bugs for 
which no tests are available, and a few administrative things [3].

BTW, we use the tag @cdk.bug, but that just what we have chosen it to be.

Egon

1.http://cdk.sf.net/
2.http://66.102.9.104/search?q=cache:UBsZ1moOpLwJ:cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/smiles/SmilesParser.html+cdk+SMILESParser&hl=nl&client=firefox-a&strip=1
3.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/bugs.html

(ad. 2: Yeah, it seems 'Nightly' is down, so you get the Google cache :)

-- 
e.willighagen at science.ru.nl
Cologne University Bioinformatics Center (CUBIC)
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6

From Sofia.Burvall at hgen.slu.se  Mon Mar 26 08:11:13 2007
From: Sofia.Burvall at hgen.slu.se (Sofia Burvall)
Date: Mon, 26 Mar 2007 14:11:13 +0200
Subject: [Biojava-l] biojava/biojavax
In-Reply-To: <6e1d61f50703221953y1ea5a8e0j99e8b806782351e7@mail.gmail.com>
References: <OF843F5735.CE3A6394-ON482572A7.000CCD40-482572A7.000D7417@ah.novartis.com>
	<6e1d61f50703221953y1ea5a8e0j99e8b806782351e7@mail.gmail.com>
Message-ID: <C7DE1774-5DCD-475E-9221-0AFF5011B9EE@hgen.slu.se>

Hi,

I'm currently updating some code that require biojava. I am  
interested in having as many sequence formats as possible supported  
and I want it to be stable. I was wondering if there are any  
differences between biojava and biojavax in those aspects?

Thank you
/Sofia

From kjaanson at gmail.com  Mon Mar 26 14:41:50 2007
From: kjaanson at gmail.com (Kaur Jaanson)
Date: Mon, 26 Mar 2007 21:41:50 +0300
Subject: [Biojava-l] RichSequence.IOTools
Message-ID: <4f6282d40703261141y249381efl7d5da6317e3c49b9@mail.gmail.com>

Hi.

I tried to save Sequence with RichSequence.IOTools.writeGenbank. It saved
the sequence data but not the features I just added. I was not so sure how
to use the Namespace so I used null as its value. The
SeqIOTools.writeGenbank saved features nicely.

-- 
Kaur Jaanson

From zagato.gekko at gmail.com  Mon Mar 26 17:03:08 2007
From: zagato.gekko at gmail.com (Zagato)
Date: Mon, 26 Mar 2007 16:03:08 -0500
Subject: [Biojava-l] RichSequence.IOTools
In-Reply-To: <4f6282d40703261141y249381efl7d5da6317e3c49b9@mail.gmail.com>
References: <4f6282d40703261141y249381efl7d5da6317e3c49b9@mail.gmail.com>
Message-ID: <98028b00703261403j682cca9bpcf08e70710f538d3@mail.gmail.com>

Hello, ?are you using the CVS version of BioJava?, in old days use the
lastest version from CVS solved me a problem with features.

For Namespace can you start using some like:

SimpleNamespace bacterianamespace = new SimpleNamespace("Bacterias");
or
Namespace dflNS = RichObjectFactory.getDefaultNamespace();

I'm really not an expert but i think that Namespace represents a real
Namespace in a BioSQL database, it's like a group of genes, or genomes, etc.

I Hope this helps you a few.. Bye..

Alan Jairo Acosta
Cali - Colombia

On 3/26/07, Kaur Jaanson <kjaanson at gmail.com> wrote:
>
> Hi.
>
> I tried to save Sequence with RichSequence.IOTools.writeGenbank. It saved
> the sequence data but not the features I just added. I was not so sure how
> to use the Namespace so I used null as its value. The
> SeqIOTools.writeGenbank saved features nicely.
>
> --
> Kaur Jaanson
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
Farewell.
http://www.youtube.com/zagatogekko
ruby << __EOF__
  puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
__EOF__


From markjschreiber at gmail.com  Mon Mar 26 21:08:44 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 27 Mar 2007 09:08:44 +0800
Subject: [Biojava-l] biojava/biojavax
In-Reply-To: <C7DE1774-5DCD-475E-9221-0AFF5011B9EE@hgen.slu.se>
References: <OF843F5735.CE3A6394-ON482572A7.000CCD40-482572A7.000D7417@ah.novartis.com>
	<6e1d61f50703221953y1ea5a8e0j99e8b806782351e7@mail.gmail.com>
	<C7DE1774-5DCD-475E-9221-0AFF5011B9EE@hgen.slu.se>
Message-ID: <93b45ca50703261808s643c185ctc18cf6d9802b9bf8@mail.gmail.com>

Hi -

On the whole biojavax supports more formats and has a more detailed
object model. The parsers are generally more reliable but sometimes a
little strict about modifications to a format.

We are currently trying to do some stress testing of format reading.
In the most current CVS release I have added more informative
exception statements that make it easier to debug parsing issues.

- Mark

On 3/26/07, Sofia Burvall <Sofia.Burvall at hgen.slu.se> wrote:
> Hi,
>
> I'm currently updating some code that require biojava. I am
> interested in having as many sequence formats as possible supported
> and I want it to be stable. I was wondering if there are any
> differences between biojava and biojavax in those aspects?
>
> Thank you
> /Sofia
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From markjschreiber at gmail.com  Mon Mar 26 21:09:56 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 27 Mar 2007 09:09:56 +0800
Subject: [Biojava-l] RichSequence.IOTools
In-Reply-To: <98028b00703261403j682cca9bpcf08e70710f538d3@mail.gmail.com>
References: <4f6282d40703261141y249381efl7d5da6317e3c49b9@mail.gmail.com>
	<98028b00703261403j682cca9bpcf08e70710f538d3@mail.gmail.com>
Message-ID: <93b45ca50703261809p55f2bfdeu46d1f66993b9634b@mail.gmail.com>

You can also use null for namespace and you will get the default value.

- Mark

On 3/27/07, Zagato <zagato.gekko at gmail.com> wrote:
> Hello, ?are you using the CVS version of BioJava?, in old days use the
> lastest version from CVS solved me a problem with features.
>
> For Namespace can you start using some like:
>
> SimpleNamespace bacterianamespace = new SimpleNamespace("Bacterias");
> or
> Namespace dflNS = RichObjectFactory.getDefaultNamespace();
>
> I'm really not an expert but i think that Namespace represents a real
> Namespace in a BioSQL database, it's like a group of genes, or genomes, etc.
>
> I Hope this helps you a few.. Bye..
>
> Alan Jairo Acosta
> Cali - Colombia
>
> On 3/26/07, Kaur Jaanson <kjaanson at gmail.com> wrote:
> >
> > Hi.
> >
> > I tried to save Sequence with RichSequence.IOTools.writeGenbank. It saved
> > the sequence data but not the features I just added. I was not so sure how
> > to use the Namespace so I used null as its value. The
> > SeqIOTools.writeGenbank saved features nicely.
> >
> > --
> > Kaur Jaanson
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> Farewell.
> http://www.youtube.com/zagatogekko
> ruby << __EOF__
>   puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
> __EOF__
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From kjaanson at gmail.com  Wed Mar 28 18:50:28 2007
From: kjaanson at gmail.com (Kaur Jaanson)
Date: Thu, 29 Mar 2007 01:50:28 +0300
Subject: [Biojava-l] RichSequence.IOTools
In-Reply-To: <4608DE49.9060203@ebi.ac.uk>
References: <4f6282d40703261141y249381efl7d5da6317e3c49b9@mail.gmail.com>
	<4608DE49.9060203@ebi.ac.uk>
Message-ID: <4f6282d40703281550l289b77a4k9163bc8fc896c070@mail.gmail.com>

I used example from the cookbook to add the feature and created Sequence
with DNATools.createDNASequence(..). I wanted to get the reverse complement
strand, find regions with regexp, and mark them as features.

Code used for creating reverse strand Sequence object:

SymbolList rat_rev_list = DNATools.reverseComplement(rat_gene);
Sequence rat_rev = DNATools.createDNASequence(rat_rev_list.seqString(),
"rat_gene");


Code used for creating feature:

StrandedFeature.Template feat_temp = new StrandedFeature.Template();

// fill in the template
feat_temp.annotation = Annotation.EMPTY_ANNOTATION;
feat_temp.location = new RangeLocation(matcher.start(), matcher.end() - 1);
feat_temp.source = "myself_mapped";
feat_temp.strand = StrandedFeature.POSITIVE;
feat_temp.type = key;

try {
    Feature feat = rat_rev.createFeature(feat_temp);
} catch (Exception ex) {
    ex.printStackTrace();
    return;
}


Thanks for clearing up namespace for me :).. got to look into it more.

Hopefully you can give me some leads for working with RichSequence &
RichFeature :)


Kaur Jaanson