From pulse at mx.plaxo.com  Tue Sep  2 14:48:47 2008
From: pulse at mx.plaxo.com (kirankumarvoona)
Date: Tue, 02 Sep 2008 11:48:47 -0700
Subject: [Biojava-dev] kirankumarvoona added you as a business connection on
	Plaxo
Message-ID: <2cb4b2fe2e66260d83b56fcf049ee6e7@xpertmailer.com>



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From klerissonpaixao at gmail.com  Sun Sep  7 22:38:37 2008
From: klerissonpaixao at gmail.com (=?ISO-8859-1?Q?Kl=E9risson_Paix=E3o?=)
Date: Mon, 8 Sep 2008 00:38:37 -0200
Subject: [Biojava-dev] Integer aligner
In-Reply-To: <9e364a990809071929h3208c4cdyb0d5bf9390faea41@mail.gmail.com>
References: <9e364a990809071929h3208c4cdyb0d5bf9390faea41@mail.gmail.com>
Message-ID: <9e364a990809071938x1350b162q30577f71db7fa83f@mail.gmail.com>

Hey everyone!I really need to align integers. My alphabet won't be DNA, nor
RNA, neither Protein. It must be integers, numbers.
How can I do it using biojava?
Thanks a lot!
Klerisson

From holland at eaglegenomics.com  Mon Sep  8 03:58:44 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 8 Sep 2008 08:58:44 +0100
Subject: [Biojava-dev] Integer aligner
In-Reply-To: <9e364a990809071938x1350b162q30577f71db7fa83f@mail.gmail.com>
References: <9e364a990809071929h3208c4cdyb0d5bf9390faea41@mail.gmail.com>
	<9e364a990809071938x1350b162q30577f71db7fa83f@mail.gmail.com>
Message-ID: <a0d826f40809080058m29949959o2d0c256ebd36cf92@mail.gmail.com>

Hello.

Take a look at: http://www.biojava.org/wiki/BioJava:CookBook:DP:PairWise2

Then, you can develop your own file to feed into SubstitutionMatrix to
inform the algorithm as to how to match up the symbols in the alphabet you
are using. Use that file in combination with an instance of your own Integer
alphabet, and you should find the rest of it works fine.

cheers,
Richard

PS. The substition matrix file format should follow the format of the files
at ftp://ftp.ncbi.nlm.nih.gov/blast/matrices

2008/9/8 Kl?risson Paix?o <klerissonpaixao at gmail.com>

> Hey everyone!I really need to align integers. My alphabet won't be DNA, nor
> RNA, neither Protein. It must be integers, numbers.
> How can I do it using biojava?
> Thanks a lot!
> Klerisson
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From markjschreiber at gmail.com  Mon Sep  8 04:03:49 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 8 Sep 2008 16:03:49 +0800
Subject: [Biojava-dev] bytecode.jar download
Message-ID: <93b45ca50809080103q20406cc1y6a8d3a54cd5300c4@mail.gmail.com>

Hi -

There appears to be no way that one can download the supporting libraries
from the biojava download page. In particular the bytecode.jar is essential.
The current download page contains the biojava.jar but not any of the
others.

- Mark

From andreas at sdsc.edu  Tue Sep  9 01:15:52 2008
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 8 Sep 2008 22:15:52 -0700
Subject: [Biojava-dev] bytecode.jar download
In-Reply-To: <93b45ca50809080103q20406cc1y6a8d3a54cd5300c4@mail.gmail.com>
References: <93b45ca50809080103q20406cc1y6a8d3a54cd5300c4@mail.gmail.com>
Message-ID: <59a41c430809082215v1ce131dnfffbdf8c2b13743f@mail.gmail.com>

Hi Mark,

I updated the download page and all supporting jar files can be
downloaded individually now.

Andreas


On Mon, Sep 8, 2008 at 1:03 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> Hi -
>
> There appears to be no way that one can download the supporting libraries
> from the biojava download page. In particular the bytecode.jar is essential.
> The current download page contains the biojava.jar but not any of the
> others.
>
> - Mark
> _______________________________________________
> 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  Wed Sep 10 04:45:29 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 04:45:29 -0400
Subject: [Biojava-dev] [Bug 2582] New: SimpleRichLocation.contains() method
Message-ID: <bug-2582-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2582

           Summary: SimpleRichLocation.contains() method
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: avellozo at gmail.com


The next program should return true, but it returns false.
public class Test
{
    public static void main(String[] args) {
        RichLocation loc1 = new SimpleRichLocation(new SimplePosition(1), new
SimplePosition(10), 0);
        RichLocation loc2 = new SimpleRichLocation(new SimplePosition(2), new
SimplePosition(4), 0);
        RichLocation loc3 = new SimpleRichLocation(new SimplePosition(6), new
SimplePosition(8), 0);
        ArrayList a = new ArrayList();
        a.add(loc2);
        a.add(loc3);
        CompoundRichLocation loc4 = new CompoundRichLocation(a);
        System.out.println(loc1.contains(loc4));
    }
}


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From zainul_irfandhy at yahoo.com.sg  Wed Sep 10 05:27:57 2008
From: zainul_irfandhy at yahoo.com.sg (Zainul Irfandhy Franciscus)
Date: Wed, 10 Sep 2008 21:27:57 +1200
Subject: [Biojava-dev] Participating in biojava
In-Reply-To: <mailman.0.1221038117.30536.biojava-dev@lists.open-bio.org>
References: <mailman.0.1221038117.30536.biojava-dev@lists.open-bio.org>
Message-ID: <48C7931D.3010102@yahoo.com.sg>

Dear Members,

I came across BioJava while I was browsing Google's Summer of code. I am 
interested to contribute as a developer in Bio Java. If this project 
still needs a volunteer do let me know.

Warm Regards,
Zainul Franciscus

From holland at eaglegenomics.com  Wed Sep 10 05:56:31 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 10 Sep 2008 10:56:31 +0100
Subject: [Biojava-dev] Participating in biojava
In-Reply-To: <48C7931D.3010102@yahoo.com.sg>
References: <mailman.0.1221038117.30536.biojava-dev@lists.open-bio.org>
	<48C7931D.3010102@yahoo.com.sg>
Message-ID: <a0d826f40809100256y4256fc38md1584f5bc13b74aa@mail.gmail.com>

Hi,

Thanks for your offer of help!

Right at the moment we're making some plans for future development. As
soon as work begins on implementing those plans, we'll post a message
to this list outlining our requirements, and people will be able to
volunteer to complete various sections of code.

In the meantime, the existing code needs some maintenance work! We
have a bugzilla website up at http://bugzilla.open-bio.org/ where you
can browse through existing bug reports and maybe have a go at fixing
some of them.

cheers,
Richard

2008/9/10 Zainul Irfandhy Franciscus <zainul_irfandhy at yahoo.com.sg>:
> Dear Members,
>
> I came across BioJava while I was browsing Google's Summer of code. I am
> interested to contribute as a developer in Bio Java. If this project still
> needs a volunteer do let me know.
>
> Warm Regards,
> Zainul Franciscus
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 06:19:04 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 06:19:04 -0400
Subject: [Biojava-dev] [Bug 2582] SimpleRichLocation.contains() method
In-Reply-To: <bug-2582-485@http.bugzilla.open-bio.org/>
Message-ID: <200809101019.m8AAJ4Ym001627@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2582


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2008-09-10 06:19 EST -------
Fixed in subversion and introduced new test for it based on code in bug report.


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 07:03:44 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 07:03:44 -0400
Subject: [Biojava-dev] [Bug 2582] SimpleRichLocation.contains() method
In-Reply-To: <bug-2582-485@http.bugzilla.open-bio.org/>
Message-ID: <200809101103.m8AB3ijO003935@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2582


avellozo at gmail.com changed:

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




------- Comment #2 from avellozo at gmail.com  2008-09-10 07:03 EST -------
The next program should return true, but it returns false.
public class Test
{
        public static void main(String[] args) {
                RichLocation loc1a = new SimpleRichLocation(new
SimplePosition(2), new SimplePosition(4), 0);
                RichLocation loc1b = new SimpleRichLocation(new
SimplePosition(6), new SimplePosition(8), 0);
                RichLocation loc2a = new SimpleRichLocation(new
SimplePosition(2), new SimplePosition(4), 0);
                RichLocation loc2b = new SimpleRichLocation(new
SimplePosition(6), new SimplePosition(8), 0);
                ArrayList a = new ArrayList();
                a.add(loc2a);
                a.add(loc2b);
                CompoundRichLocation loc2 = new CompoundRichLocation(a);
                a.clear();
                a.add(loc1a);
                a.add(loc1b);
                CompoundRichLocation loc1 = new CompoundRichLocation(a);
                System.out.println(loc1.contains(loc2));
        }
}


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 07:53:36 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 07:53:36 -0400
Subject: [Biojava-dev] [Bug 2582] SimpleRichLocation.contains() method
In-Reply-To: <bug-2582-485@http.bugzilla.open-bio.org/>
Message-ID: <200809101153.m8ABrae2006544@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2582


holland at ebi.ac.uk changed:

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




------- Comment #3 from holland at ebi.ac.uk  2008-09-10 07:53 EST -------
Added code to handle compound-contains-compound, and added test for it as well.


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 10:02:17 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 10:02:17 -0400
Subject: [Biojava-dev] [Bug 2584] New: Parsing blast result only returns
	hits from first query sequence
Message-ID: <bug-2584-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584

           Summary: Parsing blast result only returns hits from first query
                    sequence
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: dtoomey at rcsi.ie


Hi

When parsing a blast result containing multiple query sequences I have found
that only the hits from the first query are returned in the array list. The
source code is taken directly from the cookbook. If the first query hits are
deleted from the file then the second query sequence hits are returned. So it
does not appear to be something specific to the result for that sequence that
prevents it from being parsed correctly.
I am using biojava 1.6 and blast 2.2.18. I have tried it with blast 2.2.14 and
2.2.16 and I get the same problem


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 10:12:35 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 10:12:35 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809101412.m8AECZuI023357@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584





------- Comment #1 from tbanks at agr.gc.ca  2008-09-10 10:12 EST -------
This issue affects parsing text format BLAST reports.  I've a fix for this bug
but haven't submitted to the group yet.  I'll try to get the changes to someone
with commit privileges within the next day or two.


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From jwalway at hotmail.com  Wed Sep 10 12:07:25 2008
From: jwalway at hotmail.com (John Alway)
Date: Wed, 10 Sep 2008 11:07:25 -0500
Subject: [Biojava-dev] Removing Myself From List
Message-ID: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>

Hello guys.    I've been lurking on the list for a while now, but would like to shut off the emails to my account.  For some reason I can't log on to change settings.    My email address is not recognized by the server, even though I get Bugzilla-daemon emails from the list regularly.       Any idea what I can do?

Thanks,
...John Always


From jwalway at hotmail.com  Wed Sep 10 12:49:50 2008
From: jwalway at hotmail.com (John Alway)
Date: Wed, 10 Sep 2008 11:49:50 -0500
Subject: [Biojava-dev] Removing Myself From List
In-Reply-To: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
Message-ID: <BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>

Thanks Russ,

I was able to logon there.   Perhaps there are multiple logon account types.

...John

--------------------------------------------------
From: "Russ Kepler" <russ at kepler-eng.com>
Sent: Wednesday, September 10, 2008 11:40 AM
To: "John Alway" <jwalway at hotmail.com>
Subject: Re: [Biojava-dev] Removing Myself From List

> On Wednesday 10 September 2008 10:07:25 you wrote:
>> Hello guys.    I've been lurking on the list for a while now, but would
>> like to shut off the emails to my account.  For some reason I can't log 
>> on
>> to change settings.    My email address is not recognized by the server,
>> even though I get Bugzilla-daemon emails from the list regularly. 
>> Any
>> idea what I can do?
>
> There's a "list-unsubscribe" link in the header:
>
> List-Unsubscribe: 
> <http://lists.open-bio.org/mailman/listinfo/biojava-dev>,
> <mailto:biojava-dev-request at lists.open-bio.org?subject=unsubscribe>
>
> -- Russ
> 

From russ at kepler-eng.com  Wed Sep 10 15:31:34 2008
From: russ at kepler-eng.com (Russ Kepler)
Date: Wed, 10 Sep 2008 13:31:34 -0600
Subject: [Biojava-dev] Removing Myself From List
In-Reply-To: <BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
Message-ID: <200809101331.34336.russ@kepler-eng.com>

On Wednesday 10 September 2008 10:49:50 John Alway wrote:

> I was able to logon there.   Perhaps there are multiple logon account
> types.

What happens when you send "unsubscribe" as the subject in a message to 
biojava-dev-request at lists.open-bio.org ?



From bugzilla-daemon at portal.open-bio.org  Thu Sep 11 17:28:07 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 11 Sep 2008 17:28:07 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809112128.m8BLS78T002586@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584





------- Comment #2 from tbanks at agr.gc.ca  2008-09-11 17:28 EST -------
Created an attachment (id=995)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=995&action=view)
Text file containing patches to 4 class files

This text file contains the patches for four biojava classes;
BlastLikeSAXParser.java, BlastLikeVersionSupport.java, BlastSAXParser.java and
HitSectionSAXParser.java.  The patches were created using Eclipse 3.4 and were
generated against biojava-live revision 4840.


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From bugzilla-daemon at portal.open-bio.org  Thu Sep 11 17:50:22 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 11 Sep 2008 17:50:22 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809112150.m8BLoMS6003856@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584





------- Comment #3 from tbanks at agr.gc.ca  2008-09-11 17:50 EST -------
I can email the class files to someone with commit privileges as an alternative
to applying the patches if that works better.  I also have some basic test
cases and supporting files that can be added to the project.


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From bugzilla-daemon at portal.open-bio.org  Fri Sep 12 01:26:47 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 12 Sep 2008 01:26:47 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809120526.m8C5QlQj025962@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584


andreas at sdsc.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #4 from andreas at sdsc.edu  2008-09-12 01:26 EST -------
I will add your patch as well as the test files to svn if you send them to me.

Thanks,
Andreas


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From zainul_irfandhy at yahoo.com.sg  Sat Sep 13 07:43:42 2008
From: zainul_irfandhy at yahoo.com.sg (Zainul Franciscus)
Date: Sat, 13 Sep 2008 23:43:42 +1200
Subject: [Biojava-dev] Unit test error
In-Reply-To: <200809101331.34336.russ@kepler-eng.com>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
	<200809101331.34336.russ@kepler-eng.com>
Message-ID: <1221306222.6534.5.camel@sleeper-laptop>

An embedded and charset-unspecified text was scrubbed...
Name: not available
URL: <http://lists.open-bio.org/pipermail/biojava-dev/attachments/20080913/e0070d90/attachment.pl>

From ayates at ebi.ac.uk  Sat Sep 13 09:14:53 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Sat, 13 Sep 2008 14:14:53 +0100
Subject: [Biojava-dev] Unit test error
In-Reply-To: <1221306222.6534.5.camel@sleeper-laptop>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
	<200809101331.34336.russ@kepler-eng.com>
	<1221306222.6534.5.camel@sleeper-laptop>
Message-ID: <5D6E1A8F-FF61-451E-9CCE-A5F51129BED8@ebi.ac.uk>

Hi Zainul,

This isn't an issue specific to running Biojava tests on Linux  
(Biojava developers work on a variety of platforms including Windows,  
Linux & Mac). The real problem here is framework is unable to find the  
AlphabetManager.xml file on your classpath. From the root of the  
biojava source tree it is located in:

resources/org/biojava/bio/symbol/AlphabetManager.xml

Try adding the resources directory to your Eclipse build path & try  
again.

Regards,

Andy

On 13 Sep 2008, at 12:43, Zainul Franciscus wrote:

> Dear All,
>
> I got this exception when I ran the unit test for :
> org 
> .biojavax 
> .ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver. Here  
> is my environment specification:
>
> IDE: Eclipse 3.2
> JRE: java-1.5.0-gcj-1.5.0.0
> OS: Ubuntu 8.04 (Hardy Heron)
>
> Does any one ever run Biojava in Linux environment ? I suspect that  
> this
> error is because of the JRE. Has anyone been successful in running
> biojava in ubuntu before ? If yes may I know your eclipse JRE  
> setting ?
>
> Thank you.
>
> Regards,
> Zainul Franciscus
>
>
> Stack trace:
>
> org.biojava.bio.BioError: Unable to initialize DNATools
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at
> org 
> .biojavax 
> .ga 
> .functions 
> .SimpleCrossOverFunctionTest 
> .testPerformCrossOver(SimpleCrossOverFunctionTest.java:56)
>   at java.lang.reflect.Method.invoke(libgcj.so.81)
>   at junit.framework.TestCase.runTest(TestCase.java:168)
>   at junit.framework.TestCase.runBare(TestCase.java:134)
>   at junit.framework.TestResult$1.protect(TestResult.java:110)
>   at junit.framework.TestResult.runProtected(TestResult.java:128)
>   at junit.framework.TestResult.run(TestResult.java:113)
>   at junit.framework.TestCase.run(TestCase.java:124)
>   at junit.framework.TestSuite.runTest(TestSuite.java:232)
>   at junit.framework.TestSuite.run(TestSuite.java:227)
>   at
> org 
> .junit 
> .internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:38)
>   at
> org 
> .eclipse 
> .jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
>   at
> org 
> .eclipse 
> .jdt 
> .internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
>   at
> org 
> .eclipse 
> .jdt 
> .internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java: 
> 196)
> Caused by: org.biojava.bio.BioError: Couldn't locate
> AlphabetManager.xml.  This probably means that your biojava.jar file  
> is
> corrupt or incorrectly built.
>   at
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java: 
> 150)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:79)
>   ...18 more
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From dicknetherlands at gmail.com  Sat Sep 13 09:23:29 2008
From: dicknetherlands at gmail.com (Richard Holland)
Date: Sat, 13 Sep 2008 14:23:29 +0100
Subject: [Biojava-dev] Unit test error
In-Reply-To: <1221306222.6534.5.camel@sleeper-laptop>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
	<200809101331.34336.russ@kepler-eng.com>
	<1221306222.6534.5.camel@sleeper-laptop>
Message-ID: <a0d826f40809130623yef0cf13o97196f8b185a73d6@mail.gmail.com>

Looks like not all the biojava JAR files (bytecode.jar, etc.) are on
your classpath when you run the test. This message appears about
halfway through your stacktrace:

Caused by: org.biojava.bio.BioError: Couldn't locate
AlphabetManager.xml.  This probably means that your biojava.jar file is
corrupt or incorrectly built.
  at


cheers,
Richard

2008/9/13 Zainul Franciscus <zainul_irfandhy at yahoo.com.sg>:
> Dear All,
>
> I got this exception when I ran the unit test for :
> org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver. Here is my environment specification:
>
> IDE: Eclipse 3.2
> JRE: java-1.5.0-gcj-1.5.0.0
> OS: Ubuntu 8.04 (Hardy Heron)
>
> Does any one ever run Biojava in Linux environment ? I suspect that this
> error is because of the JRE. Has anyone been successful in running
> biojava in ubuntu before ? If yes may I know your eclipse JRE setting ?
>
> Thank you.
>
> Regards,
> Zainul Franciscus
>
>
> Stack trace:
>
> org.biojava.bio.BioError: Unable to initialize DNATools
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at
> org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver(SimpleCrossOverFunctionTest.java:56)
>   at java.lang.reflect.Method.invoke(libgcj.so.81)
>   at junit.framework.TestCase.runTest(TestCase.java:168)
>   at junit.framework.TestCase.runBare(TestCase.java:134)
>   at junit.framework.TestResult$1.protect(TestResult.java:110)
>   at junit.framework.TestResult.runProtected(TestResult.java:128)
>   at junit.framework.TestResult.run(TestResult.java:113)
>   at junit.framework.TestCase.run(TestCase.java:124)
>   at junit.framework.TestSuite.runTest(TestSuite.java:232)
>   at junit.framework.TestSuite.run(TestSuite.java:227)
>   at
> org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
>   at
> org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:38)
>   at
> org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)
> Caused by: org.biojava.bio.BioError: Couldn't locate
> AlphabetManager.xml.  This probably means that your biojava.jar file is
> corrupt or incorrectly built.
>   at
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:150)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:79)
>   ...18 more
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From andreas at sdsc.edu  Sat Sep 13 12:13:42 2008
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 13 Sep 2008 09:13:42 -0700
Subject: [Biojava-dev] Unit test error
In-Reply-To: <1221306222.6534.5.camel@sleeper-laptop>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
	<200809101331.34336.russ@kepler-eng.com>
	<1221306222.6534.5.camel@sleeper-laptop>
Message-ID: <59a41c430809130913h4dbf719r81b38254977ae79d@mail.gmail.com>

Hi Zainul,

you need to make sure that the resources folder is  part of your
project build path.

Andreas


On Sat, Sep 13, 2008 at 4:43 AM, Zainul Franciscus
<zainul_irfandhy at yahoo.com.sg> wrote:
> Dear All,
>
> I got this exception when I ran the unit test for :
> org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver. Here is my environment specification:
>
> IDE: Eclipse 3.2
> JRE: java-1.5.0-gcj-1.5.0.0
> OS: Ubuntu 8.04 (Hardy Heron)
>
> Does any one ever run Biojava in Linux environment ? I suspect that this
> error is because of the JRE. Has anyone been successful in running
> biojava in ubuntu before ? If yes may I know your eclipse JRE setting ?
>
> Thank you.
>
> Regards,
> Zainul Franciscus
>
>
> Stack trace:
>
> org.biojava.bio.BioError: Unable to initialize DNATools
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at
> org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver(SimpleCrossOverFunctionTest.java:56)
>   at java.lang.reflect.Method.invoke(libgcj.so.81)
>   at junit.framework.TestCase.runTest(TestCase.java:168)
>   at junit.framework.TestCase.runBare(TestCase.java:134)
>   at junit.framework.TestResult$1.protect(TestResult.java:110)
>   at junit.framework.TestResult.runProtected(TestResult.java:128)
>   at junit.framework.TestResult.run(TestResult.java:113)
>   at junit.framework.TestCase.run(TestCase.java:124)
>   at junit.framework.TestSuite.runTest(TestSuite.java:232)
>   at junit.framework.TestSuite.run(TestSuite.java:227)
>   at
> org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
>   at
> org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:38)
>   at
> org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)
> Caused by: org.biojava.bio.BioError: Couldn't locate
> AlphabetManager.xml.  This probably means that your biojava.jar file is
> corrupt or incorrectly built.
>   at
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:150)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:79)
>   ...18 more
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From steffen_moeller at gmx.de  Sun Sep 14 08:01:56 2008
From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=)
Date: Sun, 14 Sep 2008 14:01:56 +0200
Subject: [Biojava-dev] bytecode tests don't work, copyleft statement?
Message-ID: <48CCFD34.5040507@gmx.de>

Dear bytecode developers,

I just updated the Debian package of bytecode and ran into a few issues.

The tests (ant runtests, called by ant dist) don't work for two reasons. 
The first I have patched, which is that the directory is named "test", 
not "tests". The second failure is the request of a method named 
"SimpleCodeMethod", which does not seem to exist any longer.

The build process (ant dist) then complains about missing directories 
"demos" and "resources", which I have then created as empty directories. 
It is not something that was lost in the cvs->svn transition, is it?

Lastly, the source seems devoid of any license information. Please add 
such a copyright file and the license should then be stated in every 
source file. From what I saw, it lists only the authors today.

Best regards,

Steffen

--- bytecode-0.92.svn.20080914.orig/build.xml   2008-09-14 
13:40:49.000000000 +0200
+++ bytecode-0.92.svn.20080914/build.xml        2008-09-14 
13:47:25.000000000 +0200
@@ -65,7 +65,7 @@
     <property name="readme" value="./README" />
     <property name="license" value="./LICENSE" />
     <property name="src.dir" value="./src" />
-    <property name="tests.dir" value="./tests" />
+    <property name="tests.dir" value="./test" />
     <property name="demos.dir" value="./demos" />
     <property name="reports.dir" value="./reports" />
     <property name="manifest.dir" value="./manifest" />


From bugzilla-daemon at portal.open-bio.org  Mon Sep 15 01:41:45 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 15 Sep 2008 01:41:45 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809150541.m8F5fjYv012701@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584


andreas at sdsc.edu changed:

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




------- Comment #5 from andreas at sdsc.edu  2008-09-15 01:41 EST -------
added patch and unit tests submitted by Travis to svn.


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From bugzilla-daemon at portal.open-bio.org  Mon Sep 15 07:36:52 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 15 Sep 2008 07:36:52 -0400
Subject: [Biojava-dev] [Bug 2587] New: Problems with adding miRNA to sequence
Message-ID: <bug-2587-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2587

           Summary: Problems with adding miRNA to sequence
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: DB / BioSQL
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gabrielle_doan at gmx.net


There is a problem if you want to insert new features (miRNA from
http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl ) into an existing
ing BioSQL
database which contains chromosomes 1-22, X, Y and MT downloaded from
ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/.
with following code: 

   private void makeAFeature(String id, String chr, int startpos,            
int endpos, Strand strand, float score, String gene)
            throws ChangeVetoExceptionIllegalSymbolException     {
        RichSequence rs = chromosomes.get(chr);
        if (rs == null) {
            rs = db.SearchForSequence(chr);
            chromosomes.put(chr, rs);
        }
        RichFeature feat = RichFeature.Tools.makeEmptyFeature();
        feat.setName(id);               
        RichLocation rl = new SimpleRichLocation(new                
        SimplePosition(startpos),new SimplePosition(endpos),                
1,strand);
        feat.setLocation(rl);
        try {                               
        feat.setTypeTerm(RichObjectFactory.getDefaultOntology()
                .getOrCreateTerm("miRNA"));
            feat.setType(feat.getTypeTerm().getName());
        } catch (InvalidTermException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        feat.getAnnotation().setProperty("score",                    
Float.valueOf(score));
        feat.getAnnotation().setProperty("gene", gene);
        feat.setParent(rs);
        rs.getFeatureSet().add(feat);
    }


The information for chromosome 3-22, X, Y and MT are inserted successfully.
But when you try to deal with chromosome 1 and 2 in the same way you get
following message:

org.hibernate.exception.DataException: could not insert: [Feature]
    at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77)
    at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
    at
org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:40)
    at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2163)
    at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2643)
    at
org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:51)
    at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279)
    at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:298)
    at
org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
    at
org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:107)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
    at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
    at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
    at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)
    at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at
org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:131)
    at
org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:122)
    at
org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:65)
    at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26)
    at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
    at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
    at
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
    at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254)
    at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220)
    at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57)
Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of
range value adjusted for column 'rank' at row 1
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2973)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
    at
com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1129)
    at
com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:681)
    at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1368)
    at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1283)
    at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1268)
    at
org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:73)
    at
org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:33)
    ... 32 more


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From bugzilla-daemon at portal.open-bio.org  Thu Sep 18 19:42:08 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 18 Sep 2008 19:42:08 -0400
Subject: [Biojava-dev] [Bug 2590] New: I am getting errors when trying to
	get Sequences from Features (read in from a Genbank file)
	that have location in the form of " join(location, location,
	... location) "
Message-ID: <bug-2590-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2590

           Summary: I am getting errors when trying to get Sequences from
                    Features (read in from a Genbank file) that have
                    location in the form of " join(location,location, ...
                    location) "
           Product: BioJava
           Version: live (CVS source)
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: symbol
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: tritt at wisc.edu
                CC: tritt at wisc.edu


I get the following Exception when I try writing to Fasta format a sequence
that was read in Genbank format using
org.biojava.bio.seq.io.SeqIOTools.readGenbank(BufferedReader). To write to the
Fasta file, I use org.biojava.bio.seq.io.SeqIOTools.writeFasta(OutputStream ,
Sequence). Features are pulled from the Genbank file and then their sequence is
converted to a SimpleSequence using the constructor
org.biojava.bio.seq.impl.SimpleSequence.SimpleSequence(Feature.getSymbols(),
null, <geneName>, null). 

I have encountered this problem multiple times, and it seems it only happens
when feature locations in Genbank files are in the form "
join(location,location, ... location) ". 



Exception in thread "main" java.lang.ClassCastException:
org.biojava.bio.symbol.AbstractSymbolList$SubList cannot be cast to org
.biojava.bio.symbol.Symbol
        at
org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:144)
        at
org.biojava.bio.seq.projection.ProjectedFeature.getSymbols(ProjectedFeature.java:104)
        at OrthologSeqExtracter.main(OrthologSeqExtracter.java:174)

Below is the class file that exposes this bug. The first argument is ortholog
data in tab-delimited format. The next 8 arguments are 8 genomes in Genbank
format. The 10th and final argument is the output directory. The exception is
by statements between lines 140-155 (note: these are not the same line numbers
given in the printed stack trace from above)

import java.util.HashMap;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Scanner;
import java.util.regex.Pattern;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.PrintStream;

import org.biojava.bio.BioException;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.SequenceTools;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.seq.impl.ViewSequence;
import org.biojava.bio.seq.io.SeqIOTools;

public class OrthologSeqExtracter {

        private static String USAGE = 
                "Usage: OrthologSeqExtracter <orthologs> <MG1655> <EDL_933>
<LT2> <CT18> " +
                                                        "<RIMD> <CFT073>
<UTI89> <EcoHS> <DNA outDir>";
        private static final int MG1655 = 0;
        private static final int EDL933 = 1;
        private static final int LT2 = 2;
        private static final int CT18 = 3;
        private static final int RIMD = 4;
        private static final int CFT073 = 5;
        private static final int UTI89 = 6;
        private static final int HS = 7;
        public static void main(String[] args) {
                String dnaDir = args[args.length-1];
                BufferedReader[] br = new BufferedReader[8];
                FileReader orthologs = null;
                for (int i = 0; i < br.length; i++)
                        br[i] = null;
                try {
                        orthologs = new FileReader(args[0]);
                        for (int i = 0; i < br.length; i++)
                                br[i] = new BufferedReader(new
FileReader(args[i+1]));
                } catch (FileNotFoundException ex){
                        ex.printStackTrace();
                        System.exit(-1);
                }
                SequenceIterator[] seqIt = new SequenceIterator[8];
                HashMap<String,Feature>[] features = new HashMap[8];
                for (int i = 0; i < features.length; i++){
                        features[i] = new HashMap<String,Feature>();
                }
                for (int i = 0; i < br.length; i++)
                        seqIt[i] = SeqIOTools.readGenbank(br[i]);
                for (int i = 0; i < seqIt.length; i++){
                        ViewSequence seq = null;
                        try {
                                seq =
SequenceTools.view(seqIt[i].nextSequence());
                                seqIt[i] = null;
                                br[i] = null;
                        } catch (NoSuchElementException ex) {
                                ex.printStackTrace();
                                System.exit(-1);
                        } catch (BioException ex) {
                                ex.printStackTrace();
                                System.exit(-1);
                        }
                        Iterator<Feature> featIt = seq.features();
                        while (featIt.hasNext()){
                                Feature tmp = featIt.next();
                                if (tmp.getType().equals("CDS")){       
                                        String asapID =
tmp.getAnnotation().getProperty("db_xref").toString();
                                        int index = asapID.indexOf("ASAP:") +
5;
                                        asapID =
asapID.substring(index,index+11);
                                        features[i].put(asapID, tmp);
                                }
                        }
                }
                Scanner in = new Scanner(orthologs);
                in.nextLine();
                int geneNum = 1;
                File dir = new File(dnaDir);
                dir.mkdir();
                while (in.hasNext()){
                        Scanner lineIn = new Scanner(in.nextLine());
                        lineIn.useDelimiter(Pattern.compile("\t"));
                        PrintStream dnaOut = null;
                        String mg1655 = lineIn.next();
                        lineIn.next();
                        lineIn.next();
                        String geneName = lineIn.next();
                        String edl_933 = null;
                        String lt2 = null;
                        String ct18 = null;
                        String rimd = null;
                        String cft073 = null;
                        String uti89 = null;
                        String hs = null;
                        try{
                                if (lineIn.hasNext()) 
                                        edl_933 = lineIn.next();
                                else 
                                        edl_933 = "";
                                if (lineIn.hasNext())
                                        lt2 = lineIn.next();
                                else 
                                        lt2 = "";
                                if (lineIn.hasNext())
                                        ct18 = lineIn.next();
                                else
                                        ct18 = "";
                                if (lineIn.hasNext())
                                        rimd = lineIn.next();
                                else
                                        rimd = "";
                                if (lineIn.hasNext())
                                        cft073 = lineIn.next();
                                else
                                        cft073 = "";
                                if (lineIn.hasNext())
                                        uti89 = lineIn.next();
                                else
                                        uti89 = "";
                                if (lineIn.hasNext())
                                        hs = lineIn.next();
                                else
                                        hs = "";
                        } catch (NoSuchElementException ex){
                                System.err.println("Stopped at " + geneName
                                        + " " + edl_933 + " " + lt2 + " " +
ct18 
                                        + " " + rimd + " " + cft073 + " " +
uti89 + " " + hs);
                                ex.printStackTrace();
                                System.exit(-1);
                        }                       
                        try {
                                File dnaFile = new File(dir,
"gene"+geneNum+"_"+geneName+".na");
                                dnaFile.createNewFile();
                                dnaOut = new PrintStream(dnaFile);
/* The bug occurs here. The Exception is thrown from the calls to
SeqIOTools.writeFasta(OutputStream,Sequence) */
                                if (features[MG1655].containsKey(mg1655))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[MG1655].get(mg1655).getSymbols() , null,
"MG1655_"+geneName+"_"+mg1655, null) );
                                if (features[EDL933].containsKey(edl_933))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[EDL933].get(edl_933).getSymbols() , null,
"EDL_933_"+geneName+"_"+edl_933, null));
                                if (features[LT2].containsKey(lt2))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[LT2].get(lt2).getSymbols() , null,
"LT2_"+geneName+"_"+lt2, null));
                                if (features[CT18].containsKey(ct18))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[CT18].get(ct18).getSymbols() , null,
"CT18_"+geneName+"_"+ct18, null));
                                if (features[RIMD].containsKey(rimd))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[RIMD].get(rimd).getSymbols() , null,
"RIMD_"+geneName+"_"+rimd, null));
                                if (features[CFT073].containsKey(cft073))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[CFT073].get(cft073).getSymbols() , null,
"CFT073_"+geneName+"_"+cft073, null));
                                if (features[UTI89].containsKey(uti89))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[UTI89].get(uti89).getSymbols() , null,
"UTI89_"+geneName+"_"+uti89, null));
                                if (features[HS].containsKey(hs))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[HS].get(hs).getSymbols() , null,
"HS_"+geneName+"_"+hs, null));      
                                dnaOut.close(); 
                        } catch (FileNotFoundException ex){
                                System.out.println(geneName);
                                ex.printStackTrace();
                                System.exit(-1);
                        } catch (IOException ex){
                                System.out.println(geneName);
                                ex.printStackTrace();
                                System.exit(-1);
                        }       
                        geneNum++;
                }
        }
}


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From ambi1999 at googlemail.com  Fri Sep 12 10:52:31 2008
From: ambi1999 at googlemail.com (ambi ambi)
Date: Fri, 12 Sep 2008 15:52:31 +0100
Subject: [Biojava-dev] Online courses and certifications in Bioinformatics,
	Biostatistics, Biotech in Engligh language
Message-ID: <164db5a80809120752q441f844ey8644b3fcdc0fb11f@mail.gmail.com>

Hi,


Subject: Online courses and certifications in Bioinformatics, Biostatistics,
Biotech in Engligh language

Does anyone know about online courses  (preferably free, offered by some
university) in Bioinformatics, Biostatistics or Biotech in English language?
Also are there any recognised certifications in those fields (like Sun Java
cerrification exam for java)?

Regards,
Ambi.

From Russell.Smithies at agresearch.co.nz  Mon Sep 22 16:46:28 2008
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 23 Sep 2008 08:46:28 +1200
Subject: [Biojava-dev] Online courses and certifications in
	Bioinformatics, Biostatistics, Biotech in Engligh language
In-Reply-To: <164db5a80809120752q441f844ey8644b3fcdc0fb11f@mail.gmail.com>
References: <164db5a80809120752q441f844ey8644b3fcdc0fb11f@mail.gmail.com>
Message-ID: <D5DBA313349A4B458528BE63B387F36C078936CD@imail.agresearch.co.nz>

The S-Star course is quite good:
http://www.s-star.org/



Russell 



> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
> bounces at lists.open-bio.org] On Behalf Of ambi ambi
> Sent: Saturday, 13 September 2008 2:53 a.m.
> To: biojava-dev at lists.open-bio.org
> Subject: [Biojava-dev] Online courses and certifications in
> Bioinformatics,Biostatistics, Biotech in Engligh language
> 
> Hi,
> 
> 
> Subject: Online courses and certifications in Bioinformatics,
Biostatistics,
> Biotech in Engligh language
> 
> Does anyone know about online courses  (preferably free, offered by
some
> university) in Bioinformatics, Biostatistics or Biotech in English
language?
> Also are there any recognised certifications in those fields (like Sun
Java
> cerrification exam for java)?
> 
> Regards,
> Ambi.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
=======================================================================
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=======================================================================


From TSN at atp.dk  Mon Sep 22 17:29:46 2008
From: TSN at atp.dk (TSN at atp.dk)
Date: Mon, 22 Sep 2008 23:29:46 +0200
Subject: [Biojava-dev] =?iso-8859-1?q?Tom_Stevns__tr=E6ffes_ikke=2E?=
Message-ID: <OFC2B78CC4.3300DAD5-ONC12574CC.007614EC-C12574CC.007614EC@atp.dk>



Jeg er ikke p? kontoret fra  22-09-2008 og vender ikke tilbage f?r
23-09-2008.

Jeg besvarer din besked, n?r jeg vender tilbage. Vedr?rende
Dokument-h?ndtering relaterede fejl henvises i  perioden til Jette Wandel
(JWH) og Claus Nordahl (YCN)

From simpleyrx at 163.com  Thu Sep 25 10:58:49 2008
From: simpleyrx at 163.com (simpleyrx)
Date: Thu, 25 Sep 2008 22:58:49 +0800 (CST)
Subject: [Biojava-dev] what is the meaning of all-vs-all classification ?
Message-ID: <9150597.435241222354729087.JavaMail.coremail@bj163app59.163.com>

  
 
Dear experts,
 
  
         I have read a SVM paper. In the paper it is say a classification scheme all-vs-all. I do not know the meaning all-vs-all. Could some one explain the all-vs-all classification scheme ? 
 
 
 

--
                                        Student


From simpleyrx at 163.com  Thu Sep 25 10:58:49 2008
From: simpleyrx at 163.com (simpleyrx)
Date: Thu, 25 Sep 2008 22:58:49 +0800 (CST)
Subject: [Biojava-dev] what is the meaning of all-vs-all classification ?
Message-ID: <9150597.435241222354729087.JavaMail.coremail@bj163app59.163.com>

  
 
Dear experts,
 
  
         I have read a SVM paper. In the paper it is say a classification scheme all-vs-all. I do not know the meaning all-vs-all. Could some one explain the all-vs-all classification scheme ? 
 
 
 

--
                                        Student


From holland at eaglegenomics.com  Thu Sep 25 12:15:22 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 25 Sep 2008 17:15:22 +0100
Subject: [Biojava-dev] what is the meaning of all-vs-all classification ?
In-Reply-To: <9150597.435241222354729087.JavaMail.coremail@bj163app59.163.com>
References: <9150597.435241222354729087.JavaMail.coremail@bj163app59.163.com>
Message-ID: <a0d826f40809250915l2ded341fpd88649dfd7fbec5c@mail.gmail.com>

This book on Google Books explains it. Page 272, last paragraph.
(All-vs-all is also known as all-against-all).

http://books.google.com/books?id=PbOHlfGfNCIC&printsec=frontcover#PPA272,M1

2008/9/25 simpleyrx <simpleyrx at 163.com>:
>
>
> Dear experts,
>
>
>         I have read a SVM paper. In the paper it is say a classification scheme all-vs-all. I do not know the meaning all-vs-all. Could some one explain the all-vs-all classification scheme ?
>
>
>
>
> --
>                                        Student
>
>
> _______________________________________________
> 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
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/

From pulse at mx.plaxo.com  Tue Sep  2 18:48:47 2008
From: pulse at mx.plaxo.com (kirankumarvoona)
Date: Tue, 02 Sep 2008 11:48:47 -0700
Subject: [Biojava-dev] kirankumarvoona added you as a business connection on
	Plaxo
Message-ID: <2cb4b2fe2e66260d83b56fcf049ee6e7@xpertmailer.com>



kirankumarvoona wants to add you as a business connection on
Plaxo.

To accept this connection request, go to:
http://pulse.plaxo.com/pulse/invite?i=41360486&k=570498213&l=en&src=email&et=1&est=business&etv=nnic1a&el=en

Thanks!
The Plaxo team

More than 20 million people use Plaxo to keep in touch with the
people they care about. 

Don't want to receive emails from Plaxo any more? Go to:
http://www.plaxo.com/stop?src=email&et=1&est=business&etv=nnic1a&el=en




From klerissonpaixao at gmail.com  Mon Sep  8 02:38:37 2008
From: klerissonpaixao at gmail.com (=?ISO-8859-1?Q?Kl=E9risson_Paix=E3o?=)
Date: Mon, 8 Sep 2008 00:38:37 -0200
Subject: [Biojava-dev] Integer aligner
In-Reply-To: <9e364a990809071929h3208c4cdyb0d5bf9390faea41@mail.gmail.com>
References: <9e364a990809071929h3208c4cdyb0d5bf9390faea41@mail.gmail.com>
Message-ID: <9e364a990809071938x1350b162q30577f71db7fa83f@mail.gmail.com>

Hey everyone!I really need to align integers. My alphabet won't be DNA, nor
RNA, neither Protein. It must be integers, numbers.
How can I do it using biojava?
Thanks a lot!
Klerisson


From holland at eaglegenomics.com  Mon Sep  8 07:58:44 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 8 Sep 2008 08:58:44 +0100
Subject: [Biojava-dev] Integer aligner
In-Reply-To: <9e364a990809071938x1350b162q30577f71db7fa83f@mail.gmail.com>
References: <9e364a990809071929h3208c4cdyb0d5bf9390faea41@mail.gmail.com>
	<9e364a990809071938x1350b162q30577f71db7fa83f@mail.gmail.com>
Message-ID: <a0d826f40809080058m29949959o2d0c256ebd36cf92@mail.gmail.com>

Hello.

Take a look at: http://www.biojava.org/wiki/BioJava:CookBook:DP:PairWise2

Then, you can develop your own file to feed into SubstitutionMatrix to
inform the algorithm as to how to match up the symbols in the alphabet you
are using. Use that file in combination with an instance of your own Integer
alphabet, and you should find the rest of it works fine.

cheers,
Richard

PS. The substition matrix file format should follow the format of the files
at ftp://ftp.ncbi.nlm.nih.gov/blast/matrices

2008/9/8 Kl?risson Paix?o <klerissonpaixao at gmail.com>

> Hey everyone!I really need to align integers. My alphabet won't be DNA, nor
> RNA, neither Protein. It must be integers, numbers.
> How can I do it using biojava?
> Thanks a lot!
> Klerisson
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From markjschreiber at gmail.com  Mon Sep  8 08:03:49 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 8 Sep 2008 16:03:49 +0800
Subject: [Biojava-dev] bytecode.jar download
Message-ID: <93b45ca50809080103q20406cc1y6a8d3a54cd5300c4@mail.gmail.com>

Hi -

There appears to be no way that one can download the supporting libraries
from the biojava download page. In particular the bytecode.jar is essential.
The current download page contains the biojava.jar but not any of the
others.

- Mark


From andreas at sdsc.edu  Tue Sep  9 05:15:52 2008
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 8 Sep 2008 22:15:52 -0700
Subject: [Biojava-dev] bytecode.jar download
In-Reply-To: <93b45ca50809080103q20406cc1y6a8d3a54cd5300c4@mail.gmail.com>
References: <93b45ca50809080103q20406cc1y6a8d3a54cd5300c4@mail.gmail.com>
Message-ID: <59a41c430809082215v1ce131dnfffbdf8c2b13743f@mail.gmail.com>

Hi Mark,

I updated the download page and all supporting jar files can be
downloaded individually now.

Andreas


On Mon, Sep 8, 2008 at 1:03 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> Hi -
>
> There appears to be no way that one can download the supporting libraries
> from the biojava download page. In particular the bytecode.jar is essential.
> The current download page contains the biojava.jar but not any of the
> others.
>
> - Mark
> _______________________________________________
> 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  Wed Sep 10 08:45:29 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 04:45:29 -0400
Subject: [Biojava-dev] [Bug 2582] New: SimpleRichLocation.contains() method
Message-ID: <bug-2582-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2582

           Summary: SimpleRichLocation.contains() method
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: avellozo at gmail.com


The next program should return true, but it returns false.
public class Test
{
    public static void main(String[] args) {
        RichLocation loc1 = new SimpleRichLocation(new SimplePosition(1), new
SimplePosition(10), 0);
        RichLocation loc2 = new SimpleRichLocation(new SimplePosition(2), new
SimplePosition(4), 0);
        RichLocation loc3 = new SimpleRichLocation(new SimplePosition(6), new
SimplePosition(8), 0);
        ArrayList a = new ArrayList();
        a.add(loc2);
        a.add(loc3);
        CompoundRichLocation loc4 = new CompoundRichLocation(a);
        System.out.println(loc1.contains(loc4));
    }
}


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From zainul_irfandhy at yahoo.com.sg  Wed Sep 10 09:27:57 2008
From: zainul_irfandhy at yahoo.com.sg (Zainul Irfandhy Franciscus)
Date: Wed, 10 Sep 2008 21:27:57 +1200
Subject: [Biojava-dev] Participating in biojava
In-Reply-To: <mailman.0.1221038117.30536.biojava-dev@lists.open-bio.org>
References: <mailman.0.1221038117.30536.biojava-dev@lists.open-bio.org>
Message-ID: <48C7931D.3010102@yahoo.com.sg>

Dear Members,

I came across BioJava while I was browsing Google's Summer of code. I am 
interested to contribute as a developer in Bio Java. If this project 
still needs a volunteer do let me know.

Warm Regards,
Zainul Franciscus


From holland at eaglegenomics.com  Wed Sep 10 09:56:31 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 10 Sep 2008 10:56:31 +0100
Subject: [Biojava-dev] Participating in biojava
In-Reply-To: <48C7931D.3010102@yahoo.com.sg>
References: <mailman.0.1221038117.30536.biojava-dev@lists.open-bio.org>
	<48C7931D.3010102@yahoo.com.sg>
Message-ID: <a0d826f40809100256y4256fc38md1584f5bc13b74aa@mail.gmail.com>

Hi,

Thanks for your offer of help!

Right at the moment we're making some plans for future development. As
soon as work begins on implementing those plans, we'll post a message
to this list outlining our requirements, and people will be able to
volunteer to complete various sections of code.

In the meantime, the existing code needs some maintenance work! We
have a bugzilla website up at http://bugzilla.open-bio.org/ where you
can browse through existing bug reports and maybe have a go at fixing
some of them.

cheers,
Richard

2008/9/10 Zainul Irfandhy Franciscus <zainul_irfandhy at yahoo.com.sg>:
> Dear Members,
>
> I came across BioJava while I was browsing Google's Summer of code. I am
> interested to contribute as a developer in Bio Java. If this project still
> needs a volunteer do let me know.
>
> Warm Regards,
> Zainul Franciscus
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 10:19:04 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 06:19:04 -0400
Subject: [Biojava-dev] [Bug 2582] SimpleRichLocation.contains() method
In-Reply-To: <bug-2582-485@http.bugzilla.open-bio.org/>
Message-ID: <200809101019.m8AAJ4Ym001627@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2582


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2008-09-10 06:19 EST -------
Fixed in subversion and introduced new test for it based on code in bug report.


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 11:03:44 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 07:03:44 -0400
Subject: [Biojava-dev] [Bug 2582] SimpleRichLocation.contains() method
In-Reply-To: <bug-2582-485@http.bugzilla.open-bio.org/>
Message-ID: <200809101103.m8AB3ijO003935@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2582


avellozo at gmail.com changed:

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




------- Comment #2 from avellozo at gmail.com  2008-09-10 07:03 EST -------
The next program should return true, but it returns false.
public class Test
{
        public static void main(String[] args) {
                RichLocation loc1a = new SimpleRichLocation(new
SimplePosition(2), new SimplePosition(4), 0);
                RichLocation loc1b = new SimpleRichLocation(new
SimplePosition(6), new SimplePosition(8), 0);
                RichLocation loc2a = new SimpleRichLocation(new
SimplePosition(2), new SimplePosition(4), 0);
                RichLocation loc2b = new SimpleRichLocation(new
SimplePosition(6), new SimplePosition(8), 0);
                ArrayList a = new ArrayList();
                a.add(loc2a);
                a.add(loc2b);
                CompoundRichLocation loc2 = new CompoundRichLocation(a);
                a.clear();
                a.add(loc1a);
                a.add(loc1b);
                CompoundRichLocation loc1 = new CompoundRichLocation(a);
                System.out.println(loc1.contains(loc2));
        }
}


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 11:53:36 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 07:53:36 -0400
Subject: [Biojava-dev] [Bug 2582] SimpleRichLocation.contains() method
In-Reply-To: <bug-2582-485@http.bugzilla.open-bio.org/>
Message-ID: <200809101153.m8ABrae2006544@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2582


holland at ebi.ac.uk changed:

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




------- Comment #3 from holland at ebi.ac.uk  2008-09-10 07:53 EST -------
Added code to handle compound-contains-compound, and added test for it as well.


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 14:02:17 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 10:02:17 -0400
Subject: [Biojava-dev] [Bug 2584] New: Parsing blast result only returns
	hits from first query sequence
Message-ID: <bug-2584-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584

           Summary: Parsing blast result only returns hits from first query
                    sequence
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: dtoomey at rcsi.ie


Hi

When parsing a blast result containing multiple query sequences I have found
that only the hits from the first query are returned in the array list. The
source code is taken directly from the cookbook. If the first query hits are
deleted from the file then the second query sequence hits are returned. So it
does not appear to be something specific to the result for that sequence that
prevents it from being parsed correctly.
I am using biojava 1.6 and blast 2.2.18. I have tried it with blast 2.2.14 and
2.2.16 and I get the same problem


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 10 14:12:35 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 10 Sep 2008 10:12:35 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809101412.m8AECZuI023357@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584





------- Comment #1 from tbanks at agr.gc.ca  2008-09-10 10:12 EST -------
This issue affects parsing text format BLAST reports.  I've a fix for this bug
but haven't submitted to the group yet.  I'll try to get the changes to someone
with commit privileges within the next day or two.


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From jwalway at hotmail.com  Wed Sep 10 16:07:25 2008
From: jwalway at hotmail.com (John Alway)
Date: Wed, 10 Sep 2008 11:07:25 -0500
Subject: [Biojava-dev] Removing Myself From List
Message-ID: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>

Hello guys.    I've been lurking on the list for a while now, but would like to shut off the emails to my account.  For some reason I can't log on to change settings.    My email address is not recognized by the server, even though I get Bugzilla-daemon emails from the list regularly.       Any idea what I can do?

Thanks,
...John Always



From jwalway at hotmail.com  Wed Sep 10 16:49:50 2008
From: jwalway at hotmail.com (John Alway)
Date: Wed, 10 Sep 2008 11:49:50 -0500
Subject: [Biojava-dev] Removing Myself From List
In-Reply-To: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
Message-ID: <BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>

Thanks Russ,

I was able to logon there.   Perhaps there are multiple logon account types.

...John

--------------------------------------------------
From: "Russ Kepler" <russ at kepler-eng.com>
Sent: Wednesday, September 10, 2008 11:40 AM
To: "John Alway" <jwalway at hotmail.com>
Subject: Re: [Biojava-dev] Removing Myself From List

> On Wednesday 10 September 2008 10:07:25 you wrote:
>> Hello guys.    I've been lurking on the list for a while now, but would
>> like to shut off the emails to my account.  For some reason I can't log 
>> on
>> to change settings.    My email address is not recognized by the server,
>> even though I get Bugzilla-daemon emails from the list regularly. 
>> Any
>> idea what I can do?
>
> There's a "list-unsubscribe" link in the header:
>
> List-Unsubscribe: 
> <http://lists.open-bio.org/mailman/listinfo/biojava-dev>,
> <mailto:biojava-dev-request at lists.open-bio.org?subject=unsubscribe>
>
> -- Russ
> 


From russ at kepler-eng.com  Wed Sep 10 19:31:34 2008
From: russ at kepler-eng.com (Russ Kepler)
Date: Wed, 10 Sep 2008 13:31:34 -0600
Subject: [Biojava-dev] Removing Myself From List
In-Reply-To: <BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
Message-ID: <200809101331.34336.russ@kepler-eng.com>

On Wednesday 10 September 2008 10:49:50 John Alway wrote:

> I was able to logon there.   Perhaps there are multiple logon account
> types.

What happens when you send "unsubscribe" as the subject in a message to 
biojava-dev-request at lists.open-bio.org ?




From bugzilla-daemon at portal.open-bio.org  Thu Sep 11 21:28:07 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 11 Sep 2008 17:28:07 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809112128.m8BLS78T002586@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584





------- Comment #2 from tbanks at agr.gc.ca  2008-09-11 17:28 EST -------
Created an attachment (id=995)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=995&action=view)
Text file containing patches to 4 class files

This text file contains the patches for four biojava classes;
BlastLikeSAXParser.java, BlastLikeVersionSupport.java, BlastSAXParser.java and
HitSectionSAXParser.java.  The patches were created using Eclipse 3.4 and were
generated against biojava-live revision 4840.


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From bugzilla-daemon at portal.open-bio.org  Thu Sep 11 21:50:22 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 11 Sep 2008 17:50:22 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809112150.m8BLoMS6003856@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584





------- Comment #3 from tbanks at agr.gc.ca  2008-09-11 17:50 EST -------
I can email the class files to someone with commit privileges as an alternative
to applying the patches if that works better.  I also have some basic test
cases and supporting files that can be added to the project.


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From bugzilla-daemon at portal.open-bio.org  Fri Sep 12 05:26:47 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 12 Sep 2008 01:26:47 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809120526.m8C5QlQj025962@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584


andreas at sdsc.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #4 from andreas at sdsc.edu  2008-09-12 01:26 EST -------
I will add your patch as well as the test files to svn if you send them to me.

Thanks,
Andreas


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From zainul_irfandhy at yahoo.com.sg  Sat Sep 13 11:43:42 2008
From: zainul_irfandhy at yahoo.com.sg (Zainul Franciscus)
Date: Sat, 13 Sep 2008 23:43:42 +1200
Subject: [Biojava-dev] Unit test error
In-Reply-To: <200809101331.34336.russ@kepler-eng.com>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
	<200809101331.34336.russ@kepler-eng.com>
Message-ID: <1221306222.6534.5.camel@sleeper-laptop>

An embedded and charset-unspecified text was scrubbed...
Name: not available
URL: <http://lists.open-bio.org/pipermail/biojava-dev/attachments/20080913/e0070d90/attachment.ksh>

From ayates at ebi.ac.uk  Sat Sep 13 13:14:53 2008
From: ayates at ebi.ac.uk (Andy Yates)
Date: Sat, 13 Sep 2008 14:14:53 +0100
Subject: [Biojava-dev] Unit test error
In-Reply-To: <1221306222.6534.5.camel@sleeper-laptop>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
	<200809101331.34336.russ@kepler-eng.com>
	<1221306222.6534.5.camel@sleeper-laptop>
Message-ID: <5D6E1A8F-FF61-451E-9CCE-A5F51129BED8@ebi.ac.uk>

Hi Zainul,

This isn't an issue specific to running Biojava tests on Linux  
(Biojava developers work on a variety of platforms including Windows,  
Linux & Mac). The real problem here is framework is unable to find the  
AlphabetManager.xml file on your classpath. From the root of the  
biojava source tree it is located in:

resources/org/biojava/bio/symbol/AlphabetManager.xml

Try adding the resources directory to your Eclipse build path & try  
again.

Regards,

Andy

On 13 Sep 2008, at 12:43, Zainul Franciscus wrote:

> Dear All,
>
> I got this exception when I ran the unit test for :
> org 
> .biojavax 
> .ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver. Here  
> is my environment specification:
>
> IDE: Eclipse 3.2
> JRE: java-1.5.0-gcj-1.5.0.0
> OS: Ubuntu 8.04 (Hardy Heron)
>
> Does any one ever run Biojava in Linux environment ? I suspect that  
> this
> error is because of the JRE. Has anyone been successful in running
> biojava in ubuntu before ? If yes may I know your eclipse JRE  
> setting ?
>
> Thank you.
>
> Regards,
> Zainul Franciscus
>
>
> Stack trace:
>
> org.biojava.bio.BioError: Unable to initialize DNATools
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at
> org 
> .biojavax 
> .ga 
> .functions 
> .SimpleCrossOverFunctionTest 
> .testPerformCrossOver(SimpleCrossOverFunctionTest.java:56)
>   at java.lang.reflect.Method.invoke(libgcj.so.81)
>   at junit.framework.TestCase.runTest(TestCase.java:168)
>   at junit.framework.TestCase.runBare(TestCase.java:134)
>   at junit.framework.TestResult$1.protect(TestResult.java:110)
>   at junit.framework.TestResult.runProtected(TestResult.java:128)
>   at junit.framework.TestResult.run(TestResult.java:113)
>   at junit.framework.TestCase.run(TestCase.java:124)
>   at junit.framework.TestSuite.runTest(TestSuite.java:232)
>   at junit.framework.TestSuite.run(TestSuite.java:227)
>   at
> org 
> .junit 
> .internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:38)
>   at
> org 
> .eclipse 
> .jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
>   at
> org 
> .eclipse 
> .jdt 
> .internal 
> .junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
>   at
> org 
> .eclipse 
> .jdt 
> .internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
>   at
> org 
> .eclipse 
> .jdt 
> .internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java: 
> 196)
> Caused by: org.biojava.bio.BioError: Couldn't locate
> AlphabetManager.xml.  This probably means that your biojava.jar file  
> is
> corrupt or incorrectly built.
>   at
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java: 
> 150)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:79)
>   ...18 more
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From dicknetherlands at gmail.com  Sat Sep 13 13:23:29 2008
From: dicknetherlands at gmail.com (Richard Holland)
Date: Sat, 13 Sep 2008 14:23:29 +0100
Subject: [Biojava-dev] Unit test error
In-Reply-To: <1221306222.6534.5.camel@sleeper-laptop>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
	<200809101331.34336.russ@kepler-eng.com>
	<1221306222.6534.5.camel@sleeper-laptop>
Message-ID: <a0d826f40809130623yef0cf13o97196f8b185a73d6@mail.gmail.com>

Looks like not all the biojava JAR files (bytecode.jar, etc.) are on
your classpath when you run the test. This message appears about
halfway through your stacktrace:

Caused by: org.biojava.bio.BioError: Couldn't locate
AlphabetManager.xml.  This probably means that your biojava.jar file is
corrupt or incorrectly built.
  at


cheers,
Richard

2008/9/13 Zainul Franciscus <zainul_irfandhy at yahoo.com.sg>:
> Dear All,
>
> I got this exception when I ran the unit test for :
> org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver. Here is my environment specification:
>
> IDE: Eclipse 3.2
> JRE: java-1.5.0-gcj-1.5.0.0
> OS: Ubuntu 8.04 (Hardy Heron)
>
> Does any one ever run Biojava in Linux environment ? I suspect that this
> error is because of the JRE. Has anyone been successful in running
> biojava in ubuntu before ? If yes may I know your eclipse JRE setting ?
>
> Thank you.
>
> Regards,
> Zainul Franciscus
>
>
> Stack trace:
>
> org.biojava.bio.BioError: Unable to initialize DNATools
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at
> org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver(SimpleCrossOverFunctionTest.java:56)
>   at java.lang.reflect.Method.invoke(libgcj.so.81)
>   at junit.framework.TestCase.runTest(TestCase.java:168)
>   at junit.framework.TestCase.runBare(TestCase.java:134)
>   at junit.framework.TestResult$1.protect(TestResult.java:110)
>   at junit.framework.TestResult.runProtected(TestResult.java:128)
>   at junit.framework.TestResult.run(TestResult.java:113)
>   at junit.framework.TestCase.run(TestCase.java:124)
>   at junit.framework.TestSuite.runTest(TestSuite.java:232)
>   at junit.framework.TestSuite.run(TestSuite.java:227)
>   at
> org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
>   at
> org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:38)
>   at
> org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)
> Caused by: org.biojava.bio.BioError: Couldn't locate
> AlphabetManager.xml.  This probably means that your biojava.jar file is
> corrupt or incorrectly built.
>   at
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:150)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:79)
>   ...18 more
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Richard Holland, BSc
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/


From andreas at sdsc.edu  Sat Sep 13 16:13:42 2008
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 13 Sep 2008 09:13:42 -0700
Subject: [Biojava-dev] Unit test error
In-Reply-To: <1221306222.6534.5.camel@sleeper-laptop>
References: <BAY119-DS647420AFE148F7DBDA94AB0570@phx.gbl>
	<200809101040.16925.russ@kepler-eng.com>
	<BAY119-DS10E3E65A1196610A8EC80AB0570@phx.gbl>
	<200809101331.34336.russ@kepler-eng.com>
	<1221306222.6534.5.camel@sleeper-laptop>
Message-ID: <59a41c430809130913h4dbf719r81b38254977ae79d@mail.gmail.com>

Hi Zainul,

you need to make sure that the resources folder is  part of your
project build path.

Andreas


On Sat, Sep 13, 2008 at 4:43 AM, Zainul Franciscus
<zainul_irfandhy at yahoo.com.sg> wrote:
> Dear All,
>
> I got this exception when I ran the unit test for :
> org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver. Here is my environment specification:
>
> IDE: Eclipse 3.2
> JRE: java-1.5.0-gcj-1.5.0.0
> OS: Ubuntu 8.04 (Hardy Heron)
>
> Does any one ever run Biojava in Linux environment ? I suspect that this
> error is because of the JRE. Has anyone been successful in running
> biojava in ubuntu before ? If yes may I know your eclipse JRE setting ?
>
> Thank you.
>
> Regards,
> Zainul Franciscus
>
>
> Stack trace:
>
> org.biojava.bio.BioError: Unable to initialize DNATools
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at
> org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver(SimpleCrossOverFunctionTest.java:56)
>   at java.lang.reflect.Method.invoke(libgcj.so.81)
>   at junit.framework.TestCase.runTest(TestCase.java:168)
>   at junit.framework.TestCase.runBare(TestCase.java:134)
>   at junit.framework.TestResult$1.protect(TestResult.java:110)
>   at junit.framework.TestResult.runProtected(TestResult.java:128)
>   at junit.framework.TestResult.run(TestResult.java:113)
>   at junit.framework.TestCase.run(TestCase.java:124)
>   at junit.framework.TestSuite.runTest(TestSuite.java:232)
>   at junit.framework.TestSuite.run(TestSuite.java:227)
>   at
> org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
>   at
> org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:38)
>   at
> org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
>   at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)
> Caused by: org.biojava.bio.BioError: Couldn't locate
> AlphabetManager.xml.  This probably means that your biojava.jar file is
> corrupt or incorrectly built.
>   at
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:150)
>   at java.lang.Class.initializeClass(libgcj.so.81)
>   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:79)
>   ...18 more
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From steffen_moeller at gmx.de  Sun Sep 14 12:01:56 2008
From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=)
Date: Sun, 14 Sep 2008 14:01:56 +0200
Subject: [Biojava-dev] bytecode tests don't work, copyleft statement?
Message-ID: <48CCFD34.5040507@gmx.de>

Dear bytecode developers,

I just updated the Debian package of bytecode and ran into a few issues.

The tests (ant runtests, called by ant dist) don't work for two reasons. 
The first I have patched, which is that the directory is named "test", 
not "tests". The second failure is the request of a method named 
"SimpleCodeMethod", which does not seem to exist any longer.

The build process (ant dist) then complains about missing directories 
"demos" and "resources", which I have then created as empty directories. 
It is not something that was lost in the cvs->svn transition, is it?

Lastly, the source seems devoid of any license information. Please add 
such a copyright file and the license should then be stated in every 
source file. From what I saw, it lists only the authors today.

Best regards,

Steffen

--- bytecode-0.92.svn.20080914.orig/build.xml   2008-09-14 
13:40:49.000000000 +0200
+++ bytecode-0.92.svn.20080914/build.xml        2008-09-14 
13:47:25.000000000 +0200
@@ -65,7 +65,7 @@
     <property name="readme" value="./README" />
     <property name="license" value="./LICENSE" />
     <property name="src.dir" value="./src" />
-    <property name="tests.dir" value="./tests" />
+    <property name="tests.dir" value="./test" />
     <property name="demos.dir" value="./demos" />
     <property name="reports.dir" value="./reports" />
     <property name="manifest.dir" value="./manifest" />



From bugzilla-daemon at portal.open-bio.org  Mon Sep 15 05:41:45 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 15 Sep 2008 01:41:45 -0400
Subject: [Biojava-dev] [Bug 2584] Parsing blast result only returns hits
	from first query sequence
In-Reply-To: <bug-2584-485@http.bugzilla.open-bio.org/>
Message-ID: <200809150541.m8F5fjYv012701@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2584


andreas at sdsc.edu changed:

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




------- Comment #5 from andreas at sdsc.edu  2008-09-15 01:41 EST -------
added patch and unit tests submitted by Travis to svn.


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Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
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From bugzilla-daemon at portal.open-bio.org  Mon Sep 15 11:36:52 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 15 Sep 2008 07:36:52 -0400
Subject: [Biojava-dev] [Bug 2587] New: Problems with adding miRNA to sequence
Message-ID: <bug-2587-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2587

           Summary: Problems with adding miRNA to sequence
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: DB / BioSQL
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gabrielle_doan at gmx.net


There is a problem if you want to insert new features (miRNA from
http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl ) into an existing
ing BioSQL
database which contains chromosomes 1-22, X, Y and MT downloaded from
ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/.
with following code: 

   private void makeAFeature(String id, String chr, int startpos,            
int endpos, Strand strand, float score, String gene)
            throws ChangeVetoExceptionIllegalSymbolException     {
        RichSequence rs = chromosomes.get(chr);
        if (rs == null) {
            rs = db.SearchForSequence(chr);
            chromosomes.put(chr, rs);
        }
        RichFeature feat = RichFeature.Tools.makeEmptyFeature();
        feat.setName(id);               
        RichLocation rl = new SimpleRichLocation(new                
        SimplePosition(startpos),new SimplePosition(endpos),                
1,strand);
        feat.setLocation(rl);
        try {                               
        feat.setTypeTerm(RichObjectFactory.getDefaultOntology()
                .getOrCreateTerm("miRNA"));
            feat.setType(feat.getTypeTerm().getName());
        } catch (InvalidTermException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        feat.getAnnotation().setProperty("score",                    
Float.valueOf(score));
        feat.getAnnotation().setProperty("gene", gene);
        feat.setParent(rs);
        rs.getFeatureSet().add(feat);
    }


The information for chromosome 3-22, X, Y and MT are inserted successfully.
But when you try to deal with chromosome 1 and 2 in the same way you get
following message:

org.hibernate.exception.DataException: could not insert: [Feature]
    at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77)
    at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
    at
org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:40)
    at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2163)
    at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2643)
    at
org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:51)
    at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279)
    at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:298)
    at
org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
    at
org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:107)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
    at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
    at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
    at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)
    at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at
org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:131)
    at
org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:122)
    at
org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:65)
    at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26)
    at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
    at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
    at
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
    at org.viewer.db.HBioSQLDB.updateSequence(HBioSQLDB.java:254)
    at org.viewer.io.MakeMiRNA.splitLine(MakeMiRNA.java:220)
    at org.viewer.io.MakeMiRNA.main(MakeMiRNA.java:57)
Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Out of
range value adjusted for column 'rank' at row 1
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2973)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
    at
com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1129)
    at
com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:681)
    at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1368)
    at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1283)
    at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1268)
    at
org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:73)
    at
org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:33)
    ... 32 more


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From bugzilla-daemon at portal.open-bio.org  Thu Sep 18 23:42:08 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 18 Sep 2008 19:42:08 -0400
Subject: [Biojava-dev] [Bug 2590] New: I am getting errors when trying to
	get Sequences from Features (read in from a Genbank file)
	that have location in the form of " join(location, location,
	... location) "
Message-ID: <bug-2590-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2590

           Summary: I am getting errors when trying to get Sequences from
                    Features (read in from a Genbank file) that have
                    location in the form of " join(location,location, ...
                    location) "
           Product: BioJava
           Version: live (CVS source)
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: symbol
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: tritt at wisc.edu
                CC: tritt at wisc.edu


I get the following Exception when I try writing to Fasta format a sequence
that was read in Genbank format using
org.biojava.bio.seq.io.SeqIOTools.readGenbank(BufferedReader). To write to the
Fasta file, I use org.biojava.bio.seq.io.SeqIOTools.writeFasta(OutputStream ,
Sequence). Features are pulled from the Genbank file and then their sequence is
converted to a SimpleSequence using the constructor
org.biojava.bio.seq.impl.SimpleSequence.SimpleSequence(Feature.getSymbols(),
null, <geneName>, null). 

I have encountered this problem multiple times, and it seems it only happens
when feature locations in Genbank files are in the form "
join(location,location, ... location) ". 



Exception in thread "main" java.lang.ClassCastException:
org.biojava.bio.symbol.AbstractSymbolList$SubList cannot be cast to org
.biojava.bio.symbol.Symbol
        at
org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:144)
        at
org.biojava.bio.seq.projection.ProjectedFeature.getSymbols(ProjectedFeature.java:104)
        at OrthologSeqExtracter.main(OrthologSeqExtracter.java:174)

Below is the class file that exposes this bug. The first argument is ortholog
data in tab-delimited format. The next 8 arguments are 8 genomes in Genbank
format. The 10th and final argument is the output directory. The exception is
by statements between lines 140-155 (note: these are not the same line numbers
given in the printed stack trace from above)

import java.util.HashMap;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Scanner;
import java.util.regex.Pattern;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.PrintStream;

import org.biojava.bio.BioException;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.SequenceTools;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.seq.impl.ViewSequence;
import org.biojava.bio.seq.io.SeqIOTools;

public class OrthologSeqExtracter {

        private static String USAGE = 
                "Usage: OrthologSeqExtracter <orthologs> <MG1655> <EDL_933>
<LT2> <CT18> " +
                                                        "<RIMD> <CFT073>
<UTI89> <EcoHS> <DNA outDir>";
        private static final int MG1655 = 0;
        private static final int EDL933 = 1;
        private static final int LT2 = 2;
        private static final int CT18 = 3;
        private static final int RIMD = 4;
        private static final int CFT073 = 5;
        private static final int UTI89 = 6;
        private static final int HS = 7;
        public static void main(String[] args) {
                String dnaDir = args[args.length-1];
                BufferedReader[] br = new BufferedReader[8];
                FileReader orthologs = null;
                for (int i = 0; i < br.length; i++)
                        br[i] = null;
                try {
                        orthologs = new FileReader(args[0]);
                        for (int i = 0; i < br.length; i++)
                                br[i] = new BufferedReader(new
FileReader(args[i+1]));
                } catch (FileNotFoundException ex){
                        ex.printStackTrace();
                        System.exit(-1);
                }
                SequenceIterator[] seqIt = new SequenceIterator[8];
                HashMap<String,Feature>[] features = new HashMap[8];
                for (int i = 0; i < features.length; i++){
                        features[i] = new HashMap<String,Feature>();
                }
                for (int i = 0; i < br.length; i++)
                        seqIt[i] = SeqIOTools.readGenbank(br[i]);
                for (int i = 0; i < seqIt.length; i++){
                        ViewSequence seq = null;
                        try {
                                seq =
SequenceTools.view(seqIt[i].nextSequence());
                                seqIt[i] = null;
                                br[i] = null;
                        } catch (NoSuchElementException ex) {
                                ex.printStackTrace();
                                System.exit(-1);
                        } catch (BioException ex) {
                                ex.printStackTrace();
                                System.exit(-1);
                        }
                        Iterator<Feature> featIt = seq.features();
                        while (featIt.hasNext()){
                                Feature tmp = featIt.next();
                                if (tmp.getType().equals("CDS")){       
                                        String asapID =
tmp.getAnnotation().getProperty("db_xref").toString();
                                        int index = asapID.indexOf("ASAP:") +
5;
                                        asapID =
asapID.substring(index,index+11);
                                        features[i].put(asapID, tmp);
                                }
                        }
                }
                Scanner in = new Scanner(orthologs);
                in.nextLine();
                int geneNum = 1;
                File dir = new File(dnaDir);
                dir.mkdir();
                while (in.hasNext()){
                        Scanner lineIn = new Scanner(in.nextLine());
                        lineIn.useDelimiter(Pattern.compile("\t"));
                        PrintStream dnaOut = null;
                        String mg1655 = lineIn.next();
                        lineIn.next();
                        lineIn.next();
                        String geneName = lineIn.next();
                        String edl_933 = null;
                        String lt2 = null;
                        String ct18 = null;
                        String rimd = null;
                        String cft073 = null;
                        String uti89 = null;
                        String hs = null;
                        try{
                                if (lineIn.hasNext()) 
                                        edl_933 = lineIn.next();
                                else 
                                        edl_933 = "";
                                if (lineIn.hasNext())
                                        lt2 = lineIn.next();
                                else 
                                        lt2 = "";
                                if (lineIn.hasNext())
                                        ct18 = lineIn.next();
                                else
                                        ct18 = "";
                                if (lineIn.hasNext())
                                        rimd = lineIn.next();
                                else
                                        rimd = "";
                                if (lineIn.hasNext())
                                        cft073 = lineIn.next();
                                else
                                        cft073 = "";
                                if (lineIn.hasNext())
                                        uti89 = lineIn.next();
                                else
                                        uti89 = "";
                                if (lineIn.hasNext())
                                        hs = lineIn.next();
                                else
                                        hs = "";
                        } catch (NoSuchElementException ex){
                                System.err.println("Stopped at " + geneName
                                        + " " + edl_933 + " " + lt2 + " " +
ct18 
                                        + " " + rimd + " " + cft073 + " " +
uti89 + " " + hs);
                                ex.printStackTrace();
                                System.exit(-1);
                        }                       
                        try {
                                File dnaFile = new File(dir,
"gene"+geneNum+"_"+geneName+".na");
                                dnaFile.createNewFile();
                                dnaOut = new PrintStream(dnaFile);
/* The bug occurs here. The Exception is thrown from the calls to
SeqIOTools.writeFasta(OutputStream,Sequence) */
                                if (features[MG1655].containsKey(mg1655))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[MG1655].get(mg1655).getSymbols() , null,
"MG1655_"+geneName+"_"+mg1655, null) );
                                if (features[EDL933].containsKey(edl_933))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[EDL933].get(edl_933).getSymbols() , null,
"EDL_933_"+geneName+"_"+edl_933, null));
                                if (features[LT2].containsKey(lt2))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[LT2].get(lt2).getSymbols() , null,
"LT2_"+geneName+"_"+lt2, null));
                                if (features[CT18].containsKey(ct18))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[CT18].get(ct18).getSymbols() , null,
"CT18_"+geneName+"_"+ct18, null));
                                if (features[RIMD].containsKey(rimd))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[RIMD].get(rimd).getSymbols() , null,
"RIMD_"+geneName+"_"+rimd, null));
                                if (features[CFT073].containsKey(cft073))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[CFT073].get(cft073).getSymbols() , null,
"CFT073_"+geneName+"_"+cft073, null));
                                if (features[UTI89].containsKey(uti89))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[UTI89].get(uti89).getSymbols() , null,
"UTI89_"+geneName+"_"+uti89, null));
                                if (features[HS].containsKey(hs))
                                        SeqIOTools.writeFasta(dnaOut, new
SimpleSequence( features[HS].get(hs).getSymbols() , null,
"HS_"+geneName+"_"+hs, null));      
                                dnaOut.close(); 
                        } catch (FileNotFoundException ex){
                                System.out.println(geneName);
                                ex.printStackTrace();
                                System.exit(-1);
                        } catch (IOException ex){
                                System.out.println(geneName);
                                ex.printStackTrace();
                                System.exit(-1);
                        }       
                        geneNum++;
                }
        }
}


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From ambi1999 at googlemail.com  Fri Sep 12 14:52:31 2008
From: ambi1999 at googlemail.com (ambi ambi)
Date: Fri, 12 Sep 2008 15:52:31 +0100
Subject: [Biojava-dev] Online courses and certifications in Bioinformatics,
	Biostatistics, Biotech in Engligh language
Message-ID: <164db5a80809120752q441f844ey8644b3fcdc0fb11f@mail.gmail.com>

Hi,


Subject: Online courses and certifications in Bioinformatics, Biostatistics,
Biotech in Engligh language

Does anyone know about online courses  (preferably free, offered by some
university) in Bioinformatics, Biostatistics or Biotech in English language?
Also are there any recognised certifications in those fields (like Sun Java
cerrification exam for java)?

Regards,
Ambi.


From Russell.Smithies at agresearch.co.nz  Mon Sep 22 20:46:28 2008
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 23 Sep 2008 08:46:28 +1200
Subject: [Biojava-dev] Online courses and certifications in
	Bioinformatics, Biostatistics, Biotech in Engligh language
In-Reply-To: <164db5a80809120752q441f844ey8644b3fcdc0fb11f@mail.gmail.com>
References: <164db5a80809120752q441f844ey8644b3fcdc0fb11f@mail.gmail.com>
Message-ID: <D5DBA313349A4B458528BE63B387F36C078936CD@imail.agresearch.co.nz>

The S-Star course is quite good:
http://www.s-star.org/



Russell 



> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
> bounces at lists.open-bio.org] On Behalf Of ambi ambi
> Sent: Saturday, 13 September 2008 2:53 a.m.
> To: biojava-dev at lists.open-bio.org
> Subject: [Biojava-dev] Online courses and certifications in
> Bioinformatics,Biostatistics, Biotech in Engligh language
> 
> Hi,
> 
> 
> Subject: Online courses and certifications in Bioinformatics,
Biostatistics,
> Biotech in Engligh language
> 
> Does anyone know about online courses  (preferably free, offered by
some
> university) in Bioinformatics, Biostatistics or Biotech in English
language?
> Also are there any recognised certifications in those fields (like Sun
Java
> cerrification exam for java)?
> 
> Regards,
> Ambi.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
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From TSN at atp.dk  Mon Sep 22 21:29:46 2008
From: TSN at atp.dk (TSN at atp.dk)
Date: Mon, 22 Sep 2008 23:29:46 +0200
Subject: [Biojava-dev] =?iso-8859-1?q?Tom_Stevns__tr=E6ffes_ikke=2E?=
Message-ID: <OFC2B78CC4.3300DAD5-ONC12574CC.007614EC-C12574CC.007614EC@atp.dk>



Jeg er ikke p? kontoret fra  22-09-2008 og vender ikke tilbage f?r
23-09-2008.

Jeg besvarer din besked, n?r jeg vender tilbage. Vedr?rende
Dokument-h?ndtering relaterede fejl henvises i  perioden til Jette Wandel
(JWH) og Claus Nordahl (YCN)


From simpleyrx at 163.com  Thu Sep 25 14:58:49 2008
From: simpleyrx at 163.com (simpleyrx)
Date: Thu, 25 Sep 2008 22:58:49 +0800 (CST)
Subject: [Biojava-dev] what is the meaning of all-vs-all classification ?
Message-ID: <9150597.435241222354729087.JavaMail.coremail@bj163app59.163.com>

  
 
Dear experts,
 
  
         I have read a SVM paper. In the paper it is say a classification scheme all-vs-all. I do not know the meaning all-vs-all. Could some one explain the all-vs-all classification scheme ? 
 
 
 

--
                                        Student



From simpleyrx at 163.com  Thu Sep 25 14:58:49 2008
From: simpleyrx at 163.com (simpleyrx)
Date: Thu, 25 Sep 2008 22:58:49 +0800 (CST)
Subject: [Biojava-dev] what is the meaning of all-vs-all classification ?
Message-ID: <9150597.435241222354729087.JavaMail.coremail@bj163app59.163.com>

  
 
Dear experts,
 
  
         I have read a SVM paper. In the paper it is say a classification scheme all-vs-all. I do not know the meaning all-vs-all. Could some one explain the all-vs-all classification scheme ? 
 
 
 

--
                                        Student



From holland at eaglegenomics.com  Thu Sep 25 16:15:22 2008
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 25 Sep 2008 17:15:22 +0100
Subject: [Biojava-dev] what is the meaning of all-vs-all classification ?
In-Reply-To: <9150597.435241222354729087.JavaMail.coremail@bj163app59.163.com>
References: <9150597.435241222354729087.JavaMail.coremail@bj163app59.163.com>
Message-ID: <a0d826f40809250915l2ded341fpd88649dfd7fbec5c@mail.gmail.com>

This book on Google Books explains it. Page 272, last paragraph.
(All-vs-all is also known as all-against-all).

http://books.google.com/books?id=PbOHlfGfNCIC&printsec=frontcover#PPA272,M1

2008/9/25 simpleyrx <simpleyrx at 163.com>:
>
>
> Dear experts,
>
>
>         I have read a SVM paper. In the paper it is say a classification scheme all-vs-all. I do not know the meaning all-vs-all. Could some one explain the all-vs-all classification scheme ?
>
>
>
>
> --
>                                        Student
>
>
> _______________________________________________
> 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
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/