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Subject: [Biojava-dev] =?iso-8859-1?q?Get_v=ECagra_for_a_great_price=2E?=
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From rahul at genebrew.com Sat Oct 2 21:41:44 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Sat Oct 2 21:40:18 2004
Subject: [Biojava-dev] Alignment algorithms
Message-ID: <415F58D8.8090404@genebrew.com>
While reading through "Biological Sequence Analysis", I am finding it
useful to reimplement some standard alignment algorithms in Java.
Looking through the current Biojava package, I see that alignment is
limited to HMM based methods. Would there be any interest in patches
that add some standard alignment algorithms to the Biojava package? The
ones I had in mind were Smith-Waterman (with substitution matrices),
ClustalW and TCoffee. Along those lines, what would the appropriate
package to use for such classes? And where should the substitution
matrices go?
Thanks,
Rahul
From smh1008 at cam.ac.uk Sun Oct 3 08:22:51 2004
From: smh1008 at cam.ac.uk (Dr D.S-M. Huen)
Date: Sun Oct 3 08:22:16 2004
Subject: [Biojava-dev] BlastXML parser fixes
Message-ID:
I've put in some fixes and a jUnit test for the BlastXMLParserFacade class
that fix an earlier breakage from SAX changes.
Could someone using Windows please sync with CVS and check by typing:-
ant -Dtest.subtree=org/biojava/bio/program/sax/blastxml runtests
that it is working on that platform too. I have checked Linux and MacOSX.
Regards,
David Huen
From smh1008 at cam.ac.uk Sun Oct 3 08:26:07 2004
From: smh1008 at cam.ac.uk (Dr D.S-M. Huen)
Date: Sun Oct 3 08:25:30 2004
Subject: [Biojava-dev] Nightly jUnit tests
Message-ID:
Are the nightly jUnit tests still being run?
While writing another jUnit test, I came across a test that could not
possibly pass (I know, I made a change that should have broken it G&P weeks
ago). Anyway, that test is fixed too now.
Regards,
David
From thomas at derkholm.net Sun Oct 3 08:36:51 2004
From: thomas at derkholm.net (Thomas Down)
Date: Sun Oct 3 08:36:12 2004
Subject: [Biojava-dev] Nightly jUnit tests
In-Reply-To:
References:
Message-ID: <20041003123651.GA26972@kalinda.derkholm.net>
On Sun, Oct 03, 2004 at 01:26:07PM +0100, Dr D.S-M. Huen wrote:
> Are the nightly jUnit tests still being run?
Hi David,
They got disabled whenI was moving house, and I never quite got
round to reinstating the cron job that ran the builds. I'm just
testing everythng out at the moment, builds should restart properly
tommorow morning.
Thomas.
From autobuilder at derkholm.net Sun Oct 3 09:34:10 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sun Oct 3 09:04:50 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1096810450885.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041003
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.java
* biojava-live/tests/files/org/biojava/bio/program/sax/blastxml/input.xml
* biojava-live/tests/org/biojava/bio/program/sax/blastxml/BlastXMLTest.java
* biojava-live/tests/org/biojava/bio/search/MaxMismatchPatternTest.java
* biojava-live/tests/org/biojava/bio/search/MaxMissmatchPatternTest.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From m.fortner at sbcglobal.net Sun Oct 3 10:36:57 2004
From: m.fortner at sbcglobal.net (Mark A Fortner)
Date: Sun Oct 3 10:36:18 2004
Subject: [Biojava-dev] Alignment algorithms
In-Reply-To: <415F58D8.8090404@genebrew.com>
Message-ID: <20041003143657.1705.qmail@web80012.mail.yahoo.com>
I seem to recall that the neobio API already has both
the Smith-Waterman, and Needleman-Wunsch algorithms
implemented. (http://neobio.sf.net)
As for ClustalW, I've seen several wrapper
implementations but no implementation in Java.
Hope this helps,
Mark Fortner
Mgr. Bioinformatics Software Dev
Lexicon Genetics
--- Rahul Karnik wrote:
> While reading through "Biological Sequence
> Analysis", I am finding it
> useful to reimplement some standard alignment
> algorithms in Java.
> Looking through the current Biojava package, I see
> that alignment is
> limited to HMM based methods. Would there be any
> interest in patches
> that add some standard alignment algorithms to the
> Biojava package? The
> ones I had in mind were Smith-Waterman (with
> substitution matrices),
> ClustalW and TCoffee. Along those lines, what would
> the appropriate
> package to use for such classes? And where should
> the substitution
> matrices go?
>
> Thanks,
> Rahul
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev
>
From elinorgrove_sz at datacomm.de Sun Oct 3 13:41:31 2004
From: elinorgrove_sz at datacomm.de (Elinor I. Grove)
Date: Sun Oct 3 13:29:59 2004
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Date: Sun Oct 3 14:09:02 2004
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From lily at surfy.net Sun Oct 3 14:15:38 2004
From: lily at surfy.net (bill)
Date: Sun Oct 3 14:39:51 2004
Subject: [Biojava-dev] =?windows-1251?b?0uX17W/rb+Po6CAyMeNvIOLl6mEgMTg6?=
=?windows-1251?q?33=3A21?=
Message-ID: <200410031839.i93IdJKr020949@portal.open-bio.org>
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???????????? ? ???????? " ???????? ?????", ??? ???????? ??????? ???? ????????????
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?? ??????????:
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From mark.schreiber at group.novartis.com Sun Oct 3 21:34:05 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Sun Oct 3 21:33:31 2004
Subject: [Biojava-dev] Alignment algorithms
Message-ID:
Hi -
I did some work on implementing SW and NW in biojava. It works pretty
well. The only sticking point you will have is the substitution matrices.
Some give scores for ambiguities which you need to be careful of.
Ambiguities in Biojava are not atomic symbols but the substitution
matrices treat them as if they are. It may actually be more realistic to
just average the vaules of whatever the ambiguity is composed of.
Hopefully I can dig up the old code which I can submit as a basis. No
promises. I suffered a HDD failure recently so it may have shuffled off
this mortal coil.
- Mark
Rahul Karnik
Sent by: biojava-dev-bounces@portal.open-bio.org
10/03/2004 09:41 AM
To: biojava-dev@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-dev] Alignment algorithms
While reading through "Biological Sequence Analysis", I am finding it
useful to reimplement some standard alignment algorithms in Java.
Looking through the current Biojava package, I see that alignment is
limited to HMM based methods. Would there be any interest in patches
that add some standard alignment algorithms to the Biojava package? The
ones I had in mind were Smith-Waterman (with substitution matrices),
ClustalW and TCoffee. Along those lines, what would the appropriate
package to use for such classes? And where should the substitution
matrices go?
Thanks,
Rahul
_______________________________________________
biojava-dev mailing list
biojava-dev@biojava.org
http://biojava.org/mailman/listinfo/biojava-dev
From mark.schreiber at group.novartis.com Sun Oct 3 21:41:09 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Sun Oct 3 21:46:41 2004
Subject: [Biojava-dev] Alignment algorithms
Message-ID:
Nope, looks like its gone to the big Hard Drive in the Sky.
I could recode it if there is interest.
- Mark
Mark Schreiber/GP/Novartis@PH
Sent by: biojava-dev-bounces@portal.open-bio.org
10/04/2004 09:34 AM
To: Rahul Karnik
cc: biojava-dev@biojava.org, biojava-dev-bounces@portal.open-bio.org, (bcc:
Mark Schreiber/GP/Novartis)
Subject: Re: [Biojava-dev] Alignment algorithms
Hi -
I did some work on implementing SW and NW in biojava. It works pretty
well. The only sticking point you will have is the substitution matrices.
Some give scores for ambiguities which you need to be careful of.
Ambiguities in Biojava are not atomic symbols but the substitution
matrices treat them as if they are. It may actually be more realistic to
just average the vaules of whatever the ambiguity is composed of.
Hopefully I can dig up the old code which I can submit as a basis. No
promises. I suffered a HDD failure recently so it may have shuffled off
this mortal coil.
- Mark
Rahul Karnik
Sent by: biojava-dev-bounces@portal.open-bio.org
10/03/2004 09:41 AM
To: biojava-dev@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-dev] Alignment algorithms
While reading through "Biological Sequence Analysis", I am finding it
useful to reimplement some standard alignment algorithms in Java.
Looking through the current Biojava package, I see that alignment is
limited to HMM based methods. Would there be any interest in patches
that add some standard alignment algorithms to the Biojava package? The
ones I had in mind were Smith-Waterman (with substitution matrices),
ClustalW and TCoffee. Along those lines, what would the appropriate
package to use for such classes? And where should the substitution
matrices go?
Thanks,
Rahul
_______________________________________________
biojava-dev mailing list
biojava-dev@biojava.org
http://biojava.org/mailman/listinfo/biojava-dev
_______________________________________________
biojava-dev mailing list
biojava-dev@biojava.org
http://biojava.org/mailman/listinfo/biojava-dev
From rahul at genebrew.com Sun Oct 3 22:05:05 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Sun Oct 3 22:03:26 2004
Subject: [Biojava-dev] Alignment algorithms
In-Reply-To:
References:
Message-ID: <4160AFD1.8090800@genebrew.com>
mark.schreiber@group.novartis.com wrote:
> Nope, looks like its gone to the big Hard Drive in the Sky.
>
> I could recode it if there is interest.
I should have something ready in a couple of weeks. It's a good way to
get used to BioJava.
Thanks,
Rahul
From mark.schreiber at group.novartis.com Sun Oct 3 22:10:02 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Sun Oct 3 22:09:30 2004
Subject: [Biojava-dev] Alignment algorithms
Message-ID:
As a word of advice, you will find it much easier to define some
interfaces at the start such as SubstitutionTable, DPMatrix, DPAlgorithm.
If you do this you can swap any substitution scoring system like Pam450
Blosum62 etc into any DPAlgorithm (NW or SW) while using any
implementation of a DPMatrix (eg a basic one or a memory optimized sparse
matrix).
I could hopefully commit some basic Interfaces soon which could be
developed to.
- Mark
Rahul Karnik
10/04/2004 10:05 AM
To: Mark Schreiber/GP/Novartis@PH
cc: biojava-dev@biojava.org, biojava-dev-bounces@portal.open-bio.org
Subject: Re: [Biojava-dev] Alignment algorithms
mark.schreiber@group.novartis.com wrote:
> Nope, looks like its gone to the big Hard Drive in the Sky.
>
> I could recode it if there is interest.
I should have something ready in a couple of weeks. It's a good way to
get used to BioJava.
Thanks,
Rahul
From autobuilder at derkholm.net Mon Oct 4 00:10:53 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sun Oct 3 23:41:23 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1096863053686.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041004
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/program/sax/blastxml/BlastXMLParserFacade.java
* biojava-live/tests/files/org/biojava/bio/program/sax/blastxml/input.xml
* biojava-live/tests/org/biojava/bio/program/sax/blastxml/BlastXMLTest.java
* biojava-live/tests/org/biojava/bio/search/MaxMismatchPatternTest.java
* biojava-live/tests/org/biojava/bio/search/MaxMissmatchPatternTest.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
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Date: Mon Oct 4 04:48:32 2004
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From autobuilder at derkholm.net Tue Oct 5 00:10:51 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Mon Oct 4 23:41:06 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1096949451423.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041005
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From ivan.howell_wo at acroni.si Tue Oct 5 01:38:39 2004
From: ivan.howell_wo at acroni.si (Ivan Howell)
Date: Tue Oct 5 01:29:02 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
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From len at reeltwo.com Tue Oct 5 17:10:37 2004
From: len at reeltwo.com (Len Trigg)
Date: Tue Oct 5 17:10:23 2004
Subject: [Biojava-dev] Re: HSQLDB support...
In-Reply-To: <01686134-1509-11D9-A1FE-000A959EB4C4@gnf.org>
References:
<01686134-1509-11D9-A1FE-000A959EB4C4@gnf.org>
Message-ID:
Hilmar Lapp wrote:
> A year later, but I finally managed to add them to the repository.
>
> Would you test them as I don't have an HSQLDB running? Also, would you
> be willing to maintain them? I'm trying to catch up with the changes
> driven by Biojava at the end of last year (which led to issues this
> year again), and so I have already added the term_relationship_term
> table and foreign key constraints.
I'm sure either me or someone else among the BioJava people will be
happy to maintain it -- it's used in the BioJava unit tests. (I
haven't had the opportunity to do much BioJava work recently.)
There was an updated version of the schema posted to the BioJava
mailing list a month or so ago, but I haven't looked at it in detail.
Cheers,
Len.
>
> (I'm also adding this to the other RDBMS's versions and will commit
> when I tested them.)
>
> -hilmar
>
> On Tuesday, October 21, 2003, at 07:58 PM, Len Trigg wrote:
>
> > Hilmar Lapp wrote:
> > > Sounds reasonable to me. Also, would be consistent with the other 2
> > > supported platforms.
> >
> > This reminds me, I ported the BioSQL schema to support HSQLDB, and
> > added the neccessary support to BioJava's BioSQL binding. We use
> > HSQLDB in our BioSQL unit tests, and I have seen references to other
> > people making use of it. I have attached the appropriate schema files,
> > if you wish include them as part of the BioSQL project (in which case
> > BioSQL CVS can become the canonical location).
> >
> >
> > Cheers,
> > Len.
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp email: lapp at gnf.org
> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
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From: su at seznam.cz (mogens)
Date: Tue Oct 5 19:43:31 2004
Subject: [Biojava-dev] =?windows-1251?b?ze7i4P8g6u7r6+Xq9uj/?=
Message-ID: <200410052343.i95NhPKr020602@portal.open-bio.org>
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Date: Tue Oct 5 20:06:11 2004
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From autobuilder at derkholm.net Wed Oct 6 00:10:57 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Tue Oct 5 23:41:03 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1097035857684.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041006
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From j.schroedertv at cps.co.uk Wed Oct 6 01:09:05 2004
From: j.schroedertv at cps.co.uk (Janis Schroeder)
Date: Wed Oct 6 01:08:36 2004
Subject: [Biojava-dev] We sell regalis for an affordable price
Message-ID: <5ba101c4ab62$5bbe3f35$3dd3d857@fianzasmonterrey.com.mx>
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From mark.schreiber at group.novartis.com Wed Oct 6 01:21:45 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Wed Oct 6 01:21:06 2004
Subject: [Biojava-dev] Problem downloading nightly build
Message-ID:
Hello -
I don't seem to be able to download files from the nightly build. I have
tried with both IE and Konqueror. Is anyone else having these problems?
- Mark
Mark Schreiber
Principal Scientist (Bioinformatics)
Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
phone +65 6722 2973
fax +65 6722 2910
From rahul at genebrew.com Wed Oct 6 01:29:45 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Wed Oct 6 01:27:25 2004
Subject: [Biojava-dev] Problem downloading nightly build
In-Reply-To:
References:
Message-ID: <1097040585.5557.3.camel@porsche.genebrew.com>
On Wed, 2004-10-06 at 13:21 +0800, mark.schreiber@group.novartis.com
wrote:
> Hello -
>
> I don't seem to be able to download files from the nightly build. I have
> tried with both IE and Konqueror. Is anyone else having these problems?
Try:
http://calette.derkholm.net/autobuild/
The link in the emails is wrong.
Thanks,
Rahul
From mark.schreiber at group.novartis.com Wed Oct 6 01:37:40 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Wed Oct 6 01:37:04 2004
Subject: [Biojava-dev] Problem downloading nightly build
Message-ID:
I'm getting to that site but the download still doesn't work?? Eventually
it times out with a SERVER_RESPONSE_RESET message.
Rahul Karnik
10/06/2004 01:29 PM
To: Mark Schreiber/GP/Novartis@PH
cc: biojava-dev@open-bio.org, td2@sanger.ac.uk
Subject: Re: [Biojava-dev] Problem downloading nightly build
On Wed, 2004-10-06 at 13:21 +0800, mark.schreiber@group.novartis.com
wrote:
> Hello -
>
> I don't seem to be able to download files from the nightly build. I have
> tried with both IE and Konqueror. Is anyone else having these problems?
Try:
http://calette.derkholm.net/autobuild/
The link in the emails is wrong.
Thanks,
Rahul
From rahul at genebrew.com Wed Oct 6 01:45:26 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Wed Oct 6 01:43:10 2004
Subject: [Biojava-dev] Problem downloading nightly build
In-Reply-To:
References:
Message-ID: <1097041526.5557.8.camel@porsche.genebrew.com>
On Wed, 2004-10-06 at 13:37 +0800, mark.schreiber@group.novartis.com
wrote:
> I'm getting to that site but the download still doesn't work?? Eventually
> it times out with a SERVER_RESPONSE_RESET message.
Hmm, I just downloaded it successfully at about 5 KB/s. Server is quite
slow for sure. Mirrored at http://www.genebrew.com/biojava-20041006.jar.
Thanks,
Rahul
From rahul at genebrew.com Wed Oct 6 02:08:28 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Wed Oct 6 02:06:15 2004
Subject: [Biojava-dev] [TRIVIAL PATCH] fix package name in demos/ssbind
Message-ID: <1097042908.5557.14.camel@porsche.genebrew.com>
Index: demos/ssbind/CountHits.java
===================================================================
RCS
file: /home/repository/biojava/biojava-live/demos/ssbind/CountHits.java,v
retrieving revision 1.2
diff -u -r1.2 CountHits.java
--- demos/ssbind/CountHits.java 25 Oct 2002 12:15:27 -0000 1.2
+++ demos/ssbind/CountHits.java 6 Oct 2004 05:34:12 -0000
@@ -1,4 +1,4 @@
-package ssearch;
+package ssbind;
import org.biojava.bio.search.*;
Index: demos/ssbind/CountSubHits.java
===================================================================
RCS
file: /home/repository/biojava/biojava-live/demos/ssbind/CountSubHits.java,v
retrieving revision 1.2
diff -u -r1.2 CountSubHits.java
--- demos/ssbind/CountSubHits.java 25 Oct 2002 12:15:27 -0000 1.2
+++ demos/ssbind/CountSubHits.java 6 Oct 2004 05:34:12 -0000
@@ -1,4 +1,4 @@
-package ssearch;
+package ssbind;
import org.biojava.bio.search.*;
From td2 at sanger.ac.uk Wed Oct 6 06:56:42 2004
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed Oct 6 06:56:02 2004
Subject: [Biojava-dev] [TRIVIAL PATCH] fix package name in demos/ssbind
In-Reply-To: <1097042908.5557.14.camel@porsche.genebrew.com>
References: <1097042908.5557.14.camel@porsche.genebrew.com>
Message-ID: <68111071-1786-11D9-AA1C-000A95C8B056@sanger.ac.uk>
On 6 Oct 2004, at 07:08, Rahul Karnik wrote:
> Index: demos/ssbind/CountHits.java
> Index: demos/ssbind/CountSubHits.java
Applied, thanks.
Thomas.
From powersxs at cmmc.nhs.uk Wed Oct 6 09:03:45 2004
From: powersxs at cmmc.nhs.uk (Maureen Powers)
Date: Wed Oct 6 08:54:56 2004
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From hlapp at gnf.org Wed Oct 6 12:22:42 2004
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Oct 6 12:22:08 2004
Subject: [Biojava-dev] Re: HSQLDB support...
In-Reply-To:
Message-ID:
On Tuesday, October 5, 2004, at 02:10 PM, Len Trigg wrote:
> There was an updated version of the schema posted to the BioJava
> mailing list a month or so ago, but I haven't looked at it in detail.
>
Could somebody point me to the respective email in the archives, or at
least provide either of subject or author?
-hilmar
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
-------------------------------------------------------------
From len at reeltwo.com Wed Oct 6 14:30:56 2004
From: len at reeltwo.com (Len Trigg)
Date: Wed Oct 6 14:30:30 2004
Subject: [Biojava-dev] Re: HSQLDB support...
In-Reply-To:
References:
Message-ID:
At Wed, 6 Oct 2004 09:22:42 -0700,
Hilmar Lapp wrote:
>
>
> On Tuesday, October 5, 2004, at 02:10 PM, Len Trigg wrote:
>
> > There was an updated version of the schema posted to the BioJava
> > mailing list a month or so ago, but I haven't looked at it in detail.
> >
>
> Could somebody point me to the respective email in the archives, or at
> least provide either of subject or author?
http://www.biojava.org/pipermail/biojava-dev/2004-August/001950.html
I think the only additions were adding primary key statements. I can
have another look when I get to work.
Cheers,
Len.
From lfranklindb at haaland-as.no Wed Oct 6 21:11:52 2004
From: lfranklindb at haaland-as.no (Lindsey Franklin)
Date: Wed Oct 6 20:59:29 2004
Subject: [Biojava-dev] =?iso-8859-1?q?Get_v=ECagra_for_a_great_price=2E?=
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From autobuilder at derkholm.net Thu Oct 7 00:10:51 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Wed Oct 6 23:40:46 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1097122251776.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041007
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/demos/ssbind/CountHits.java
* biojava-live/demos/ssbind/CountSubHits.java
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
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Date: Thu Oct 7 02:01:34 2004
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From support.dept at sharingexperience.net Thu Oct 7 12:46:08 2004
From: support.dept at sharingexperience.net (Support Dept.)
Date: Thu Oct 7 13:53:36 2004
Subject: [Biojava-dev] One of our website users is searching for opinions
regarding: biojava-dev@biojava.org
Message-ID: <200410071646.i97Gk8KD015944@support.sharingexperience.net>
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From supp.dept at sharingexperience.net Thu Oct 7 12:46:21 2004
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From tiagojab at yahoo.com.br Thu Oct 7 15:41:28 2004
From: tiagojab at yahoo.com.br (Tiago Lopes)
Date: Thu Oct 7 15:40:44 2004
Subject: [Biojava-dev] Microarray Features
Message-ID: <20041007194128.86200.qmail@web14626.mail.yahoo.com>
Hello,
My name is Tiago Lopes, I'm from Brazil and I'm
starting my Msc. in bioinformatics dealing with
datamining, microarray and data visualization.
I have writen during my graduation project Java
classes with the most used algorithms in microarray
data analysis, that are background correction, many
normalization methods, and statistical analysis to
detect differentially expressed genes.
I'm finishing the manuscript that will be published as
an application note in the Bioinformatics Journal.
I would like to know if is interesting for the project
to put my classes in BioJava.
I think that it would increase the diversity of
classes of BioJava, because my classes can serve as
basis for softwares that deal with microarray data
analysis and data manipulation.
I wait for answer.
Tiago
_______________________________________________________
Yahoo! Acesso Gr?tis - Internet r?pida e gr?tis. Instale o discador agora! http://br.acesso.yahoo.com/
From mark.schreiber at group.novartis.com Thu Oct 7 21:46:23 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Thu Oct 7 21:45:45 2004
Subject: [Biojava-dev] Microarray Features
Message-ID:
Hello -
I think it would be great to have some of these classes. You could post
them to the list as a Tar or you could get a cvs account to commit them
and maintain them.
Thomas, who can set up CVS accounts these days?
- Mark
Tiago Lopes
Sent by: biojava-dev-bounces@portal.open-bio.org
10/07/2004 10:41 PM
To: biojava-dev@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-dev] Microarray Features
Hello,
My name is Tiago Lopes, I'm from Brazil and I'm
starting my Msc. in bioinformatics dealing with
datamining, microarray and data visualization.
I have writen during my graduation project Java
classes with the most used algorithms in microarray
data analysis, that are background correction, many
normalization methods, and statistical analysis to
detect differentially expressed genes.
I'm finishing the manuscript that will be published as
an application note in the Bioinformatics Journal.
I would like to know if is interesting for the project
to put my classes in BioJava.
I think that it would increase the diversity of
classes of BioJava, because my classes can serve as
basis for softwares that deal with microarray data
analysis and data manipulation.
I wait for answer.
Tiago
_______________________________________________________
Yahoo! Acesso Gr?tis - Internet r?pida e gr?tis. Instale o discador agora!
http://br.acesso.yahoo.com/
_______________________________________________
biojava-dev mailing list
biojava-dev@biojava.org
http://biojava.org/mailman/listinfo/biojava-dev
From autobuilder at derkholm.net Fri Oct 8 00:10:49 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Thu Oct 7 23:40:36 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1097208649988.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041008
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From dale_kgilbert_ms at jilas.dk Fri Oct 8 07:49:32 2004
From: dale_kgilbert_ms at jilas.dk (Dale K. Gilbert)
Date: Fri Oct 8 07:57:08 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
Message-ID: <21ea01c4ad2c$cf2744aa$60425c92@ih.com.br>
Hello!
We would like to offer V_I_A_G_R_A soft tabs,
These pills are just like regular V?agra but they are specially formulated
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This results in a faster more powerful effect which lasts as long as the normal.
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://zap-internet.com/st/?coupon
No thanks: http://zap-internet.com/rm.html
From SteffenBlenk at web.de Fri Oct 8 10:39:43 2004
From: SteffenBlenk at web.de (Steffen Blenk)
Date: Fri Oct 8 10:39:06 2004
Subject: [Biojava-dev] HUPO-PSI MI
Message-ID: <1526833360@web.de>
good day
i have a question: does biojava provide XML-parser for specific xml files. like HUPO-PSI MI for example. there are other common xml parsers like jdom, but perhaps it would be nice to get a special parser from biojava.
thanks a lot
steff
__________________________________________________________
Mit WEB.DE FreePhone mit hoechster Qualitaet ab 0 Ct./Min.
weltweit telefonieren! http://freephone.web.de/?mc=021201
From smh1008 at cam.ac.uk Fri Oct 8 14:29:33 2004
From: smh1008 at cam.ac.uk (Dr D.S-M. Huen)
Date: Fri Oct 8 14:28:53 2004
Subject: [Biojava-dev] Proposal for minor extension of
BlastLikeDataSetCollection DTD
Message-ID:
The current DTD does not permit the passing of a query description line
even though it permits a hit description line to be passed.
I propose to add:-
and modify the header to:-
Are there any objections?
Regards,
David Huen
From rahul at genebrew.com Fri Oct 8 22:46:24 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Fri Oct 8 22:43:18 2004
Subject: [Biojava-dev] Biojava-dev bounces
Message-ID: <41675100.9000702@genebrew.com>
I sent some patches (5 new files) to biojava-dev two days ago and it is
stuck in moderator limbo (biojava-dev-bounces) due to "suspicious
headers". Any chance someone could unblock it so I could have some
review of these changes? Also, tips on how to avoid the bounce in the
future would be much appreciated.
Thanks,
Rahul
From david.huen at ntlworld.com Sat Oct 9 04:45:24 2004
From: david.huen at ntlworld.com (David Huen)
Date: Sat Oct 9 04:44:42 2004
Subject: [Biojava-dev] Biojava-dev bounces
In-Reply-To: <41675100.9000702@genebrew.com>
References: <41675100.9000702@genebrew.com>
Message-ID: <200410090945.24906.david.huen@ntlworld.com>
On Saturday 09 Oct 2004 03:46, Rahul Karnik wrote:
> I sent some patches (5 new files) to biojava-dev two days ago and it is
> stuck in moderator limbo (biojava-dev-bounces) due to "suspicious
> headers". Any chance someone could unblock it so I could have some
> review of these changes? Also, tips on how to avoid the bounce in the
> future would be much appreciated.
>
Hi,
This behaviour is rather hard to avoid on this list - I think it rejects
enclosures and it has certainly done this to me too. OTOH, if you paste
the text directly into the message, it usually gets through.
I would unblock the email for you but i don't have moderator access.
Regards,
David Huen
From corny at ujsa.com Sat Oct 9 08:28:39 2004
From: corny at ujsa.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=)
Date: Sat Oct 9 08:38:59 2004
Subject: [Biojava-dev] =?windows-1251?b?0OXq6+Ds4Dog2MXLys7D0MDUyN8hISHU?=
=?windows-1251?b?8/Lh7uvq6CEhISDS4Ozv7u/l9+Dy/CEhISDS6PHt5e3o5SEhIQ==?=
Message-ID: <1772336655.20041009123339@>
???????????!!!????????!!! ???????????!!! ????????!!! ?????????? ?????!!!
1. ???????? (????????, ?????, ??????, ?????, ???????...).
??????????? ?????? 6?6 M&R "Chameleon" (???, ??????????????????: 3+0, 960 ??????? ??????? ? ?????).
???????? ? ??????????
????? 1 ???? 2 ????? 3 ????? 4 ?????
50 ??. 5,7 6,24 6,86 7,48
100 ??. 5,59 5,85 6,16 6,55
300 ??. 5,12 5,34 5,53 5,76
500 ??. 5,00 5,16 5,32 5,51
3000 ??. 4,74 4,84 4,50 4,65
5000 ??. 4,53 4,63 4,77 4,88
(???? ??????? ? ???????? ???????? ?? ??????? ???????? ???????.)
2. ??????????, ??????, ???????, ??????, ??????, ???? (?????? ???????? ? ???, ????????, ????? - ??????, ??????? ?/?...)
?????????????? ?????? Winnon, ??????? ????????? 30?30 ??.
???? ???????????????? ???? ????????? ????????? ??????????? ? ? ???????? ?????:
???????????. Winnon - 121.
????????? ?? ?????, ?????????, ???????, ??????, ??????????, ????, ???????, ????. ????, ????????????????.
????????.
???????? ??????? (??????, ???????, ????), ?????, ???????. ?? ????????
?? ????, ???/????: ???????? ?????, ????????, ????????, ????????, ???????????, ?????????, ???. ??????
?? ??????, ????????: ?????, ????????, ???????...
????????????? ?????????????, ???????, ?????????????, ????? -????, ?????? ?????, ????? ??? ?????? ?? ?????.
??????? ????? ???????????? ????????- ?????????? ????????? ?? ?????????.
?????????? ?????.
?????????? ??????, ???????, ?????? ???????????.
???????????? ?????????? ????????,?????????????? ???????, ??????????,???????? ??????? ????????? ???????????.
??????? ????? ?????? ?? ????????:
(095) 7-888-769
(095) 101-3527 (????????.)
8 (926)523-42-41 (?????????????)
?? ????? ??????? ????????? ???????? ???????????????.
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? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.)
???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????,
?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ????????
? ???? ??????, ?? ??????: nevajno2000@yahoo.com
?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????.
?????? ???? ???????????? 20 ????? ??????? ??????.
From smh1008 at cus.cam.ac.uk Sat Oct 9 13:16:31 2004
From: smh1008 at cus.cam.ac.uk (David Huen)
Date: Sat Oct 9 13:15:44 2004
Subject: [Biojava-dev] RE: Proposal for minor extension of
BlastLikeDataSetCollection DTD
Message-ID: <200410091816.31694.smh1008@cus.cam.ac.uk>
A correction to the last email. The element I would like to include is:-
not:-
Regards,
David
From dw_sanderson_jn at nkp.cz Sun Oct 10 14:19:42 2004
From: dw_sanderson_jn at nkp.cz (Drew W. Sanderson)
Date: Sun Oct 10 14:22:48 2004
Subject: [Biojava-dev] Purchase steroids online
Message-ID:
Hi!
The steroid dianobol a.k.a. Anabol has a very strong androgenic and anabolic
effect which manifests itself in an enormous build up of strength and muscle
mass. Dianabol is simply a mass building steroid that works quickly and reliably.
A weight gain of 2 -4 pounds per week in the first six weeks is normal.
Ordering from our online shop is private, secure and safe... and much cheaper
than other alternatives.
Go here: http://thuroebian.info/st/?wid=200014
No thanks:
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From e_connor_gi at mobilix.dk Sun Oct 10 14:50:26 2004
From: e_connor_gi at mobilix.dk (Edwina Connor)
Date: Sun Oct 10 14:50:18 2004
Subject: [Biojava-dev] We sell regalis for an affordable price
Message-ID:
Hi,
Regalis, also known as Superviagra or Cialis
- half a pill Lasts all weekend
- Has less sideeffects
- Has higher success rate
Now you can buy Regalis, for over 70% cheaper than the equivilent brand for sale in US
We ship world wide, and no prescription is required!!
Even if you're not impotent, Regalis will increase size, pleasure and power!
Try it today you wont regret!
Get it here: http://zap-internet.com/sup/
Best regards,
Jeremy Stones
No thanks: http://zap-internet.com/rm.html
From royalburnett_yh at itx.co.uk Sun Oct 10 19:59:35 2004
From: royalburnett_yh at itx.co.uk (Royal C. Burnett)
Date: Sun Oct 10 19:59:43 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
Message-ID:
Hello!
We would like to offer V_I_A_G_R_A soft tabs,
These pills are just like regular V?agra but they are specially formulated
to be soft and dissolvable under the tongue. The pill is absorbed at the
mouth and enters the bloodstream directly instead of going through the stomach.
This results in a faster more powerful effect which lasts as long as the normal.
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://zap-internet.com/st/?coupon
No thanks: http://zap-internet.com/rm.html
From autobuilder at derkholm.net Mon Oct 11 00:10:48 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sun Oct 10 23:39:53 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1097467848326.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041011
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From joshuastewart74 at yahoo.com Mon Oct 11 11:48:25 2004
From: joshuastewart74 at yahoo.com (Joshua L. Stewart)
Date: Mon Oct 11 11:48:32 2004
Subject: [Biojava-dev] OAT practice tests for students
Message-ID: <035c01c4afa9$df670120$6700a8c0@mm7>
I recommend adding a link: http://www.testprepreview.com/oat_practice.htm to your website. It has online OAT practice tests for no charge.
From mark.schreiber at group.novartis.com Mon Oct 11 15:22:58 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Mon Oct 11 15:24:47 2004
Subject: [Biojava-dev] Biojava-dev bounces
Message-ID:
Also, make sure you don't send HTML or RTF mail as these get blocked too.
Part of the anti spam approach I think.
- Mark
David Huen
Sent by: biojava-dev-bounces@portal.open-bio.org
10/09/2004 04:45 PM
Please respond to smh1008
To: biojava-dev@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: Re: [Biojava-dev] Biojava-dev bounces
On Saturday 09 Oct 2004 03:46, Rahul Karnik wrote:
> I sent some patches (5 new files) to biojava-dev two days ago and it is
> stuck in moderator limbo (biojava-dev-bounces) due to "suspicious
> headers". Any chance someone could unblock it so I could have some
> review of these changes? Also, tips on how to avoid the bounce in the
> future would be much appreciated.
>
Hi,
This behaviour is rather hard to avoid on this list - I think it rejects
enclosures and it has certainly done this to me too. OTOH, if you paste
the text directly into the message, it usually gets through.
I would unblock the email for you but i don't have moderator access.
Regards,
David Huen
_______________________________________________
biojava-dev mailing list
biojava-dev@biojava.org
http://biojava.org/mailman/listinfo/biojava-dev
From alisonacquainting at att.net Mon Oct 11 20:03:22 2004
From: alisonacquainting at att.net (Ravi Chan)
Date: Mon Oct 11 20:07:04 2004
Subject: [Biojava-dev] D0 Y0U WANT T0 P1lIEASURE YOUR PARTNER EVERY T|ME?
Message-ID:
http://XanaIx_Va|1um_Cla|1is_V||aggar_C0O000deIne.......and___mO0O00re
http://C0O0O0de1ne_Xanalx.......and___m00O0Ore
http://C000O0de|ne_Xana|x_ValIum.......and___mO000Ore
CI1CK HERE KN0W MORE http://armtelephone.biz%2e#betsey
From rahul at genebrew.com Mon Oct 11 21:12:56 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Mon Oct 11 21:10:02 2004
Subject: [Biojava-dev] ScoringMatrix interface/implementations
Message-ID: <416B2F98.50208@genebrew.com>
[Re-sending with URL instead of attachment]
As a first step in the building of a framework for sequence alignment, I
have written:
- a ScoringMatrix interface
- two simple implementations
- a matrix reader
- a junit test case and a test file
Please let me know if and how I should integrate this ScoringMatrix
design with the existing WeightMatrix used with the HMM code. Of course,
any other comments and suggestions are welcome too.
You can download the code from:
http://www.genebrew.com/biojava/scoring_matrix.tar.gz
Thanks,
Rahul
From janelle_mcMillanuj at gala.com.pl Mon Oct 11 21:57:39 2004
From: janelle_mcMillanuj at gala.com.pl (Janelle McMillan)
Date: Mon Oct 11 21:58:28 2004
Subject: [Biojava-dev] Get discount drugs without prescription
Message-ID: <6ee301c4affe$05abf06b$d6579f39@micronica.com.au>
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From halgaines_ma at sbb.ch Mon Oct 11 22:20:13 2004
From: halgaines_ma at sbb.ch (Hal Gaines)
Date: Mon Oct 11 22:21:17 2004
Subject: [Biojava-dev] =?iso-8859-1?q?Buy_cheap_V=ECagra_through_us=2E?=
Message-ID:
Hi,
We have a new offer for you. Buy cheap V?agra through our online store.
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From g_downs_wp at reedbusiness.com.au Tue Oct 12 03:15:01 2004
From: g_downs_wp at reedbusiness.com.au (Grant D. Downs)
Date: Tue Oct 12 03:17:58 2004
Subject: [Biojava-dev] We sell regalis for an affordable price
Message-ID:
Hi,
Regalis, also known as Superviagra or Cialis
- half a pill Lasts all weekend
- Has less sideeffects
- Has higher success rate
Now you can buy Regalis, for over 70% cheaper than the equivilent brand for sale in US
We ship world wide, and no prescription is required!!
Even if you're not impotent, Regalis will increase size, pleasure and power!
Try it today you wont regret!
Get it here: http://virtual-apple.com/sup/
Best regards,
Jeremy Stones
No thanks: http://virtual-apple.com/rm.html
From loweryxq at icenet.com.au Tue Oct 12 05:14:03 2004
From: loweryxq at icenet.com.au (Kelvin Lowery)
Date: Tue Oct 12 05:16:16 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
Message-ID: <8bc401c4b03b$e18574c9$387d2e1c@chuv.hospvd.ch>
Hello!
We would like to offer V_I_A_G_R_A soft tabs,
These pills are just like regular V?agra but they are specially formulated
to be soft and dissolvable under the tongue. The pill is absorbed at the
mouth and enters the bloodstream directly instead of going through the stomach.
This results in a faster more powerful effect which lasts as long as the normal.
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://virtual-apple.com/st/?coupon
No thanks: http://virtual-apple.com/rm.html
From lizzi at maroon.tc.umn.edu Tue Oct 12 06:39:28 2004
From: lizzi at maroon.tc.umn.edu (lizzi@maroon.tc.umn.edu)
Date: Tue Oct 12 09:17:14 2004
Subject: [Biojava-dev] Softiware
In-Reply-To:
References:
Message-ID:
New Q E M on http://fthy.futureplan.biz/
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Macromedia DevNet Professional - 125.00
Corel WordPerfect Family Pack 5 - 25.00
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McAfee Virusscan V 8.0 Retail - 15.00
Roxio DVD Copy - 90.00 - 65.00 - 25.00
From guo198010 at tom.com Tue Oct 12 11:09:39 2004
From: guo198010 at tom.com (guo198010@tom.com)
Date: Tue Oct 12 11:08:57 2004
Subject: [Biojava-dev] Software for Search-Engine, Mail, DNS, and more
Message-ID: <004101c4b06d$7e67c430$0201a8c0@allfaxxh>
Software for Search-Engine, Mail, DNS, and more
http://cn.1618.net
http://hk.1618.net
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ftp://1618NET:E171BB2D873546689C770BCBE415B3F6@ftp.1618.net
SORRY: this message is created by robot!
From autobuilder at derkholm.net Wed Oct 13 00:11:08 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Tue Oct 12 23:39:47 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1097640668695.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041013
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From pete at seznam.cz Wed Oct 13 04:28:50 2004
From: pete at seznam.cz (phil)
Date: Wed Oct 13 04:25:55 2004
Subject: [Biojava-dev] =?windows-1251?b?ze7i4P8g6u7r6+Xq9uj/?=
Message-ID: <200410130825.i9D8PiKr026731@portal.open-bio.org>
???????????? ??????? ??????????? ????? ? ????? ??????? ???? ??? ?? www.elitpresent.ru
From schultz_px at lindebergs.se Wed Oct 13 05:45:48 2004
From: schultz_px at lindebergs.se (Velma Schultz)
Date: Wed Oct 13 05:45:47 2004
Subject: [Biojava-dev] =?iso-8859-1?q?Buy_cheap_V=ECagra_through_us=2E?=
Message-ID:
Hi,
We have a new offer for you. Buy cheap V?agra through our online store.
- Private online ordering
- No prescription required
- World wide shipping
Order your drugs offshore and save over 70%!
Click here: http://virtual-apple.com/meds/
Best regards,
Donald Cunfingham
No thanks: http://virtual-apple.com/rm.html
From kylec_rangel_md at asseta.com.br Wed Oct 13 07:00:04 2004
From: kylec_rangel_md at asseta.com.br (Kyle C. Rangel)
Date: Wed Oct 13 07:01:59 2004
Subject: [Biojava-dev] We sell regalis for an affordable price
Message-ID: <5c5f01c4b113$d5395284$4d753651@chi.nhs.uk>
Hi,
Regalis, also known as Superviagra or Cialis
- half a pill Lasts all weekend
- Has less sideeffects
- Has higher success rate
Now you can buy Regalis, for over 70% cheaper than the equivilent brand for sale in US
We ship world wide, and no prescription is required!!
Even if you're not impotent, Regalis will increase size, pleasure and power!
Try it today you wont regret!
Get it here: http://virtual-apple.com/sup/
Best regards,
Jeremy Stones
No thanks: http://virtual-apple.com/rm.html
From virginia.reynoldsjb at harcourts.co.nz Wed Oct 13 14:04:58 2004
From: virginia.reynoldsjb at harcourts.co.nz (Virginia Reynolds)
Date: Wed Oct 13 14:06:18 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
Message-ID:
Hello!
We would like to offer V_I_A_G_R_A soft tabs,
These pills are just like regular V?agra but they are specially formulated
to be soft and dissolvable under the tongue. The pill is absorbed at the
mouth and enters the bloodstream directly instead of going through the stomach.
This results in a faster more powerful effect which lasts as long as the normal.
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://virtual-apple.com/st/?coupon
No thanks: http://virtual-apple.com/rm.html
From johannes.swartling at home.se Wed Oct 13 14:06:24 2004
From: johannes.swartling at home.se (johannes.swartling@home.se)
Date: Wed Oct 13 14:11:16 2004
Subject: [Biojava-dev] Re: Mail Delivery (failure johannes.swartling@home.se)
Message-ID: <200410131811.i9DIBEKr032133@portal.open-bio.org>
This is an automatic reply.
You can contact me at my regular address at: my first name dot my second name at polimi dot it.
From u.snyder_qa at pcc.org.uk Wed Oct 13 16:45:11 2004
From: u.snyder_qa at pcc.org.uk (Ursula Snyder)
Date: Wed Oct 13 16:49:34 2004
Subject: [Biojava-dev] Get great prices on medications
Message-ID: <6bc801c4b165$67cd92eb$b49dfab8@recordsystem.com.pl>
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From autobuilder at derkholm.net Thu Oct 14 00:11:00 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Wed Oct 13 23:39:32 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1097727061155.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041014
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From kfowler at sdsc.edu Mon Oct 4 02:19:26 2004
From: kfowler at sdsc.edu (Kevin Fowler)
Date: Thu Oct 14 09:14:23 2004
Subject: [Biojava-dev] BioSQLSequenceDB Create Behavior
Message-ID: <579B4AC4-15CD-11D9-89D9-000D93C5A5CA@sdsc.edu>
Hi,
I notice that org.biojava.bio.seq.db.biosql.BioSQLSequenceDB doesn't
set the biodatabase name on create.
for example:
db = new BioSQLSequenceDB(myDataSource,"MyName",true);
assert(db.getName()==null); // true if the DB was created, false if
it already existed.
Is this a bug or a feature?
--Kevin Fowler
void initDb(String biodatabase, boolean create)
...
PreparedStatement getID = conn.prepareStatement("select *
from biodatabase where name = ?");
getID.setString(1, biodatabase);
ResultSet rs = getID.executeQuery();
if (rs.next()) {
dbid = rs.getInt(1);
name = rs.getString(2);
rs.close();
getID.close();
conn.close();
return;
} else {
rs.close();
getID.close();
}
if (create) {
PreparedStatement createdb =
conn.prepareStatement("insert into biodatabase (name) values ( ? )");
createdb.setString(1, biodatabase);
createdb.executeUpdate();
conn.commit();
createdb.close();
dbid = getDBHelper().getInsertID(conn, "biodatabase",
"biodatabase_id");
} else {
...
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From arv_ind_ at hotmail.com Mon Oct 11 19:29:25 2004
From: arv_ind_ at hotmail.com (Arvind)
Date: Thu Oct 14 09:14:29 2004
Subject: [Biojava-dev] Biojava SearchProfile.java Problem
Message-ID:
Hi,
I am a newbie to Biojava. I obtained Biojava 1.4pre1 and compiled the source and the demos. I seem to be having some problems with the demo - especially SearchProfile.java. It seems to throw this exception:
..
..
..
Forward: -918.1011438378875
Backward: -918.1011438378877
Training whole profile
Cycle 1 completed
Score: -2754.2394913554967
Cycle 2 completed
Score: NaN
Cycle 3 completed
Score: NaN
Cycle 4 completed
Score: NaN
Cycle 5 completed
Score: NaN
Alignining sequences to the model
org.biojava.bio.seq.impl.SimpleSequence@1b3967 name: 3
java.lang.NullPointerException
at org.biojava.bio.dp.onehead.SingleDP.viterbi(Sing
at org.biojava.bio.dp.onehead.SingleDP.viterbi(Sing
at SearchProfile2.main(SearchProfile2.java:62)
Can you please help me out? I need it very badly to work.
Thanks,
Arvind
From rahul at genebrew.com Thu Oct 7 00:44:34 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Thu Oct 14 09:14:31 2004
Subject: [Biojava-dev] ScoringMatrix interface/implementations
Message-ID: <1097124274.11694.14.camel@porsche.genebrew.com>
As a first step in the building of a framework for sequence alignment, I
have attached:
- a ScoringMatrix interface
- two simple implementations
- a matrix reader
- a junit test case and a test file
Please let me know if and how I should integrate this ScoringMatrix
design with the existing WeightMatrix used with the HMM code. Of course,
any other comments and suggestions are welcome too.
Thanks,
Rahul
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# Matrix made by matblas from blosum50.iij
# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
# Blocks Database = /data/blocks_5.0/blocks.dat
# Cluster Percentage: >= 50
# Entropy = 0.4808, Expected = -0.3573
A R N D C Q E G H I L K M F P S T W Y V B Z X
A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1
R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 0 -1
N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 4 0 -1
D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 5 1 -1
C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2
Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 4 -1
E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 5 -1
G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -2 -2
H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 0 -1
I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 -3 -1
L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 -3 -1
K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 1 -1
M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 -1 -1
F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 -4 -2
P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2
S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 0
W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3
Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1
V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1
B -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 2 -1
Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 2 5 -1
X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -1 -1 -1 -1 -1
From noreply at bestlabdeals.com Thu Oct 14 12:44:58 2004
From: noreply at bestlabdeals.com (Best Lab Deals)
Date: Thu Oct 14 09:57:03 2004
Subject: [Biojava-dev] buying lab equipment can be fun
Message-ID: <200410141644.i9EGiwgQ010642@earth.planetharvest.com>
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This is to ensure that someone does not add your address to our list without your prior knowledge or consent.
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Thanks,
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From simon.foote at nrc-cnrc.gc.ca Thu Oct 14 10:21:46 2004
From: simon.foote at nrc-cnrc.gc.ca (Simon Foote)
Date: Thu Oct 14 10:21:05 2004
Subject: [Biojava-dev] BioSQLSequenceDB Create Behavior
In-Reply-To: <579B4AC4-15CD-11D9-89D9-000D93C5A5CA@sdsc.edu>
References: <579B4AC4-15CD-11D9-89D9-000D93C5A5CA@sdsc.edu>
Message-ID: <416E8B7A.6080008@nrc-cnrc.gc.ca>
Hi Kevin,
I think the thought behind that is, in order to create a new biodatabase
you have to provide a name, so it would be redundant. Unless it is
required lower down in the code somewhere, although I haven't seen a
case of this yet.
Also of note, one can't currently set the authority or version for a
biodatabase during a create or retrieve them for an existing
biodatabase. I do have the retrieve ability in my local copy, but
haven't committed it in yet.
Simon
--
Bioinformatics Programmer
Pathogen Genomics
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561 [F] 613-952-9092
simon.foote@nrc-cnrc.gc.ca
Kevin Fowler wrote:
> Hi,
>
>
> I notice that org.biojava.bio.seq.db.biosql.BioSQLSequenceDB doesn't
> set the biodatabase name on create.
>
> for example:
>
>
> db = new BioSQLSequenceDB(myDataSource,"MyName",true);
>
> assert(db.getName()==null); // true if the DB was created,
> false if it already existed.
>
>
>
> Is this a bug or a feature?
>
>
> --Kevin Fowler
>
>
>
>
> * **void* initDb(String biodatabase,* boolean* create)
>
> ...
>
> PreparedStatement getID = conn.prepareStatement(*"select * from
> biodatabase where name = ?"*);
>
> getID.setString(1, biodatabase);
>
> ResultSet rs = getID.executeQuery();
>
> * if* (rs.next()) {
>
> dbid = rs.getInt(1);
>
> name = rs.getString(2);
>
> rs.close();
>
> getID.close();
>
> conn.close();
>
> * return*;
>
> }* else* {
>
> rs.close();
>
> getID.close();
>
> }
>
>
> * if* (create) {
>
> PreparedStatement createdb = conn.prepareStatement(*"insert into
> biodatabase (name) values ( ? )"*);
>
> createdb.setString(1, biodatabase);
>
> createdb.executeUpdate();
>
> conn.commit();
>
> createdb.close();
>
>
> dbid = getDBHelper().getInsertID(conn,* "biodatabase"*,*
> "biodatabase_id"*);
>
> }* else* {
>
> ...
>
>------------------------------------------------------------------------
>
>_______________________________________________
>biojava-dev mailing list
>biojava-dev@biojava.org
>http://biojava.org/mailman/listinfo/biojava-dev
>
>
--
Bioinformatics Programmer
Pathogen Genomics
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561 [F] 613-952-9092
simon.foote@nrc-cnrc.gc.ca
From mark.schreiber at group.novartis.com Thu Oct 14 11:45:42 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Thu Oct 14 11:44:48 2004
Subject: [Biojava-dev] ScoringMatrix interface/implementations
Message-ID:
Hi Rahul -
I like this approach. The only minor problem is what to do with
ambiguities that are not found in the matrix. Currently you through an
exception which is fine although you might also want another
implementation that more gracefully averages the match values of all the
possible sub-symbols of the ambiguity.
Looking forward to seeing the rest.
Mark
Rahul Karnik
Sent by: biojava-dev-bounces@portal.open-bio.org
10/07/2004 12:44 PM
To: BioJava Dev
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-dev] ScoringMatrix interface/implementations
As a first step in the building of a framework for sequence alignment, I
have attached:
- a ScoringMatrix interface
- two simple implementations
- a matrix reader
- a junit test case and a test file
Please let me know if and how I should integrate this ScoringMatrix
design with the existing WeightMatrix used with the HMM code. Of course,
any other comments and suggestions are welcome too.
Thanks,
Rahul
_______________________________________________
biojava-dev mailing list
biojava-dev@biojava.org
http://biojava.org/mailman/listinfo/biojava-dev
[ Attachment ''SCORINGMATRIX.JAVA'' removed by Mark Schreiber ]
[ Attachment ''SIMPLESCORINGMATRIX.JAVA'' removed by Mark Schreiber ]
[ Attachment ''SYMMETRICSCORINGMATRIX.JAVA'' removed by Mark Schreiber ]
[ Attachment ''SCORINGMATRIXREADER.JAVA'' removed by Mark Schreiber ]
[ Attachment ''SCORINGMATRIXREADERTEST.JAVA'' removed by Mark Schreiber ]
[ Attachment ''BLOSUM50.MATRIX'' removed by Mark Schreiber ]
From bearvmindand at usa.com Thu Oct 14 08:04:53 2004
From: bearvmindand at usa.com (Matthew Glave)
Date: Thu Oct 14 15:09:22 2004
Subject: [Biojava-dev] Bloody Virginz
Message-ID: <9bbeaeab310$bf327bc3$e26a2ff5@usa.com>
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She didn't object to Miena.
That's why we are working so hard right now to keep the water high. Scalps, what a joke, now every trail guide would want to be decorated with the "scalps" displayed on their horse to show their "honor within the Tribe". gro.avajoib Pushing against the walls with her webbed toes, she sought to swim faster but only stirred up mud, twigs and debris that clouded the passageway. .sbk.ved.tir.avajoib He was distracted by a loud "quack-wack-wack" and "rab-rab-rab".
"Why not?"
From rahul at genebrew.com Thu Oct 14 18:58:33 2004
From: rahul at genebrew.com (Rahul Karnik)
Date: Thu Oct 14 18:53:44 2004
Subject: [Biojava-dev] ScoringMatrix interface/implementations
In-Reply-To:
References:
Message-ID: <416F0499.6060802@genebrew.com>
mark.schreiber@group.novartis.com wrote:
> I like this approach. The only minor problem is what to do with
> ambiguities that are not found in the matrix. Currently you through an
> exception which is fine although you might also want another
> implementation that more gracefully averages the match values of all the
> possible sub-symbols of the ambiguity.
Thanks for the feedback. I am going to put off the averaging for
ambiguities for now, mainly because ambiguous bases can also be added to
the ScoringMatrix. As you say, it could be yet another implementation
down the road.
Thanks,
Rahul
From autobuilder at derkholm.net Fri Oct 15 00:10:59 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Thu Oct 14 23:39:19 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1097813459887.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041015
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From rpaigeho at obt.ch Fri Oct 15 04:11:48 2004
From: rpaigeho at obt.ch (Roslyn Paige)
Date: Fri Oct 15 04:09:15 2004
Subject: [Biojava-dev] We sell regalis for an affordable price
Message-ID: <588701c4b28e$d99aa81f$aa033c13@tietoraitti.fi>
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From mari_perez_bs at solomon.com.sb Fri Oct 15 05:54:58 2004
From: mari_perez_bs at solomon.com.sb (Mari E. Perez)
Date: Fri Oct 15 05:55:04 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
Message-ID: <779501c4b29d$1a763388$802636c9@poczta.gazeta.pl>
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This results in a faster more powerful effect which lasts as long as the normal.
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
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From evangelinaheller_zw at gotanet.se Fri Oct 15 11:17:10 2004
From: evangelinaheller_zw at gotanet.se (Evangelina Heller)
Date: Fri Oct 15 11:18:38 2004
Subject: [Biojava-dev] Application is pre approved
Message-ID: <955e01c4b2ca$fbabe1ec$f3e5bfca@interflow.com.mx>
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From t.crum_aw at ebi.ac.uk Fri Oct 15 20:44:00 2004
From: t.crum_aw at ebi.ac.uk (Tyree C. Crum)
Date: Fri Oct 15 20:45:15 2004
Subject: [Biojava-dev] =?iso-8859-1?q?Buy_cheap_V=ECagra_through_us=2E?=
Message-ID: <43ee01c4b319$6f9f8ff1$c7d106be@chariot.com.au>
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From autobuilder at derkholm.net Sat Oct 16 00:11:06 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Fri Oct 15 23:39:03 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <5450181.1097899866274.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041016
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From =?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?= Sat Oct 16 00:37:18 2004
From: =?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?= (=?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?=)
Date: Sat Oct 16 00:40:32 2004
Subject: [Biojava-dev] =?iso-2022-jp?b?GyRCIXZMJD41QnohdT41Qno5LTlwGyhC?=
=?iso-2022-jp?b?GyRCIiMjMzIvMV8hIiM1Mi8xX0V5JE48fUZ+PFRCMz1QISY+WjVyGyhC?=
=?iso-2022-jp?b?GyRCJEc9UE1oJGsiI0cvNmIkTxsoQjgbJEJAaUt8MV9DeTZiJEcbKEI=?=
=?iso-2022-jp?b?GyRCSVRNVyIjN0o1JDJzSXwzKztPJE47fiQzJD0lQSVjJXMlOSEhGyhC?=
=?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?=
=?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEbKEI=?=
Message-ID: <29841313.1097901438260.JavaMail.nobody@hosyou-r01.mine.nu>
biojava-dev@biojava.org$BMM(B
$B!!(B $B!!!!7P:QJ88K!!%a%k%^%,C4EvLpBt(B
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B
$Bl9g$O$=$N;]$r(B http://gogoway.pimpdomain.com/melmaga/teishi.html$B$^$G(B
$B%a!<%k%^%,%8%s9-9p?=$79~$_$O!"$=$N;]$r(Bhttp://gogoway.pimpdomain.com/doc/honmousikomi.htm$B$^$G(B
$B%a!<%k%^%,%8%s9XFI$N?=$79~$N>l9g$O!"$=$N;]$r(Bhttp://gogoway.pimpdomain.com/melmaga/$B$^$G(B
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$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B:#$NG:$_$O!&!&!@iK|1_$G2r7h=PMh$k!*L\E*$K$b;HMQ=PMh$k!*@83h8~>e=PMh$k(B
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B>-Mh$NIT0B$O!&!&!@iK|1_Cy6b$G0B?4=PMh$k!*0B?48~>e$N:`NA$O;q6b$G=PMh$k!*(B
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B=PMh$k$NJ}K!$OM-$j$^$9!#(B
$B"!(,!N#P#R!O(,(,7J5$$O5^2sI|3+;O$7$^$7$?(,"#(B $B#22/1_!"(B $B#32/1_!"(B $B#52/#9@iK|1_<}F~Z5rM-<}F~%S%8%M%9!U7P1DeCK=w?=$79~$_=PMh$^$9!#(B
$B!!!!!!I{6H!&7s6H!&EZF|7P1D2K3hMQ7P1D$NJ}!9$KBg9%I>!*(B
$B!!!!!!!!(B
$B!!!!!!!!#3#8G/$N\$7$/$O(B http://gogoway.pimpdomain.com$B!!(B
$B!!!!!!!!!!!!2?;v$bO@$h$j>Z5r!&1=$h$j>Z5r!&>u67>Z5r$h$jJ*E*>Z5r!&:[H=41$HF1$8J*E*>Z5r$N$_$G;v$K$h$j%@%&%s%m!<%I$7$F;HMQ$7$F$$$^$9!#%a!<%k%"%I%l%9!&(B
$B!!%5!<%P!!!O2hA|$N$_$r6&M-$7;HMQ$7$F$$$^$9!#(B
*-----$B#P#R(B------------------------------------------------------------------------------------------------*
$B!!!!!!!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B $B9%$-$J;~4V$K%5%$%I%S%8%M%9(B! $B$7$+$b!V40A4:_Bp!W"v(B
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*-----$B#P#R(B------------------------------------------------------------------------------------------------*
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$B!!!!!!!!!!(B $B!!(B http://askmebiz.net/click/2/ad5.cgi
$B!z!y(B $B!2#P#R!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!y!z!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!y!z(B
$B!!(B
$B1?L?$rJQ$($k%o%s%/%j%C%/$bM-$j$^$9!#!!FCJL5.IP@J!!;D$j$o$:$+(B
*-------------------------------------------------------*
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$B!!!!!!!!!!!J(BBREW$B!"(BVodafone$BBP1~!K(B $B#1%"%W%j!o#1#5#7!A$G$9$N$G!"$*;E;v$N9g4V$N$A$g$C$H$7$?B)H4$-$K(B
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$B!z(B--$B!~(B-$B!N(BPR]-$B!z(B--$B"!(B--$B!z(B--$B!~(B--$B!z!z(B-$B!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B-$B!~(B--$B!z(B--$B"!(B--$B!z=i$a$F$NI{<}F~$OMb7n(B--$B!~(B-$B!z(B
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B
$B!!(B $B9%$-$J;~4V$K%5%$%I%S%8%M%9(B! $B$7$+$b!V40A4:_Bp!W"v$@$C$Fe$2$?$s$@$b$s(B! $BM%$7$5$,(B $B$$!A$C$Q$$(B o
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!z(B:*:$B!y(B http://www.powz.ne.nu $B!y(B:*:$B!z(B
$B!!!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B *:$B!z(B
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$B!!!!!!!!!!!!$^$?9-9pFbMF$K$h$C$F$O!!7G:\$r95$($5$;$F$$$?$@$/>l9g$b$4$6$$$^$9!#(B
$B!!!!!!!!!!!!9-9p$r?=$79~$s$G$$$?$@$$$?J}$K$O!"%a!<%k%^%,%8%s$rG[?.$5$;$F$$$?$@$-$^$9!#(B
$B!!!!!!!!!!!!$4N;>5$N>e!!$*?=$79~$_$/$@$5$$!#(B
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(Bhttp://gogoway.pimpdomain.com/doc/honmousikomi.htm
----------------------------------------------------------
$B!!!!!!!!!!!!!!!!!!!!!!(B $B%a!<%k%^%,%8%s!!9-9pC4EvLpBt!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B
$B!!!!!!!!!!!!(B
-------------------------------------------
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$B8E20(B $B@2$l(B $B@2$l(B
$B?73c(B $B@2$l$N$A;~!9F^$j(B $B@2$l(B
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$BJ!2,(B $B@2$l(B $B@2$l(B
$B
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From humph at ubi.com Sat Oct 16 16:22:42 2004
From: humph at ubi.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=)
Date: Sat Oct 16 16:38:52 2004
Subject: [Biojava-dev] =?windows-1251?b?0OXq6+Ds4Dogz/Py5fjl8fLi6P8g7+4g?=
=?windows-1251?b?xeLw7u/lLg==?=
Message-ID: <1186798459.20041016202742@>
?????. ??? ????????? ???!
???????-?????? (5?/4? ? ???????) - ?? 160 ???? ?? ????????
?????????? ? ????? "???????" 4*, ?/? ????????, 2-?? ?????????,?????????, ??????????.
????????????? ????????????: ????, ????, ????????? ? ??????.
???????.??? ????????? ???.
?????? (4?/3? ? ???????) - ?? 180 ???? ?? ????????
?????????? ? ????? "????????? ??????" 2*, ?/?, ???????? ?????????,?????????, ??????????.
????????????? ????????????: ????, ???. ?????????
?????. ?????. ????????????? ???. 9 ???? / 8 ????? ????????? ?? 305 ????.
?????????? ? ????? Pansion Akat Krystal 3*
? ????????? ????????: ?\? ?????? ??????-?????- ?????? (????), ???????-???????
?? ?/? ???????, ?????????? ? ?????, ??????? - ??????? (???????? ????),
????????????? ????????? (7 ?????????),????? ?????, ????? ?????, ??????????? ?????????.
?????. ?????. ????????????? ???. 8 ???? / 7 ????? ????????? ?? 305 ????.
?????????? ? ????? Pansion Akat Krystal 3*
? ????????? ????????: ?/? ??????-?????- ?????? , ???????-???????, ?????????? ? ?????, ??????? - ??????? (???????? ????),
????????????? ?????????, ??????????? ?????????.
??????. ????????? ????????????? ???.
?????? ???????? ? ?????. (?? 5 ????) - 520 ???? ?? ????????
?????????? ? ????? 3*, ???????????, ?????????, ?????????,??????????
????????????? ????????????: ????
???????, ??????????????? ?????????.
???????. ????? - ?? 370 ???? ?? ????????
????? 3*,???????, ???????????.
???????. ????????????? ???.
???????? ??????? ??? - ?? 369 ???? ?? ????????
????? 2*, ???????????, ??????????, ?????????, ???????? ?????????
????????????? ????????????: ????, ???. ?????????.
?????????. ???????????? ???.
?????-????-?????? - 905 ????,
???./???? : (095) 7-888-769
??????? ??? ??????????? ?????: 8-926-230-68-68
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?????????? ????????? "??????? ? ??????!"
?. "?????????????", ??. ?????????, ?. 12, ???. 6
?? ????? ??????? ????????? ???????? ???????????????.
??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????,
? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.)
???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????,
?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ????????
? ???? ??????, ?? ??????: nevajno2000@yahoo.com
?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????.
?????? ???? ???????????? 20 ????? ??????? ??????.
From autobuilder at derkholm.net Sun Oct 17 00:11:00 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sat Oct 16 23:38:50 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1097986260600.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041017
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From jeanette_dickey_sb at camfore.se Sun Oct 17 00:14:19 2004
From: jeanette_dickey_sb at camfore.se (Jeanette Dickey)
Date: Sun Oct 17 00:14:52 2004
Subject: [Biojava-dev] Application is pre approved
Message-ID: <865701c4b3ff$1e57efc8$70b82f96@bstelecom.de>
Dear Sir or Madam,
Would you REFlNANCE if you knew you'd SAVE TH0USANDS?
We'll get you lnterest as low as 1.92%.
Don't believe me? Fill out our small online questionaire and we'll show you how.
Get the house/home and/or car you always wanted, it only takes 10 seconds of your time:
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No thanks: http://www.insidefinancial.net/s5/e7.php?h8x=71r1
From allison.schaefer_ds at sissa.it Sun Oct 17 08:02:49 2004
From: allison.schaefer_ds at sissa.it (Allison Schaefer)
Date: Sun Oct 17 08:03:21 2004
Subject: [Biojava-dev] Italian Crafted Rolex from $75 to $275 - Free Shipping
Message-ID: <134b01c4b441$f2b48376$eeb03607@hus.fi>
Heya,
Do you want a rolex watch?
In our online store you can buy replicas of Rolex watches. They look
and feel exactly like the real thing.
- We have 20+ different brands in our selection
- Free shipping if you order 5 or more
- Save up to 40% compared to the cost of other replicas
- Standard Features:
- Screw-in crown
- Unidirectional turning bezel where appropriate
- All the appropriate rolex logos, on crown and dial
- Heavy weight
Visit us: http://www.toels.com/replica/rolex/
Best regards,
Hilton Jones
No thanks: http://toels.com/z.php
From hlapp at gnf.org Sun Oct 17 19:28:16 2004
From: hlapp at gnf.org (Hilmar Lapp)
Date: Sun Oct 17 19:27:22 2004
Subject: [Biojava-dev] Re: HSQLDB support...
In-Reply-To:
Message-ID: <389B9928-2094-11D9-AF76-000A959EB4C4@gnf.org>
I added the primary key constraints. Could somebody who has a
functional HSQLDB server test the DDL script to weed out any possible
typos and syntax errors?
-hilmar
On Wednesday, October 6, 2004, at 11:30 AM, Len Trigg wrote:
> At Wed, 6 Oct 2004 09:22:42 -0700,
> Hilmar Lapp wrote:
> >
> >
> > On Tuesday, October 5, 2004, at 02:10? PM, Len Trigg wrote:
> >
> > > There was an updated version of the schema posted to the BioJava
> > > mailing list a month or so ago, but I haven't looked at it in
> detail.
> > >
> >
> > Could somebody point me to the respective email in the archives, or
> at
> > least provide either of subject or author?
>
> http://www.biojava.org/pipermail/biojava-dev/2004-August/001950.html
>
> I think the only additions were adding primary key statements. I can
> have another look when I get to work.
>
> Cheers,
> Len.
>
>
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
-------------------------------------------------------------
From rhoodfi at fucam.ac.be Sun Oct 17 21:24:07 2004
From: rhoodfi at fucam.ac.be (Ronda G. Hood)
Date: Sun Oct 17 21:25:51 2004
Subject: [Biojava-dev] We sell regalis for an affordable price
Message-ID: <1eba01c4b4b1$84e794dd$89455f76@marinea.fi>
Hi,
Regalis, also known as Superviagra or Cialis
- half a pill Lasts all weekend
- Has less sideeffects
- Has higher success rate
Now you can buy Regalis, for over 70% cheaper than the equivilent brand for sale in US
We ship world wide, and no prescription is required!!
Even if you're not impotent, Regalis will increase size, pleasure and power!
Try it today you wont regret!
Get it here: http://koolrx.com/sup/
Best regards,
Jeremy Stones
No thanks: http://koolrx.com/rm.html
From autobuilder at derkholm.net Mon Oct 18 00:10:57 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sun Oct 17 23:38:35 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1098072658263.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041018
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From mmleblancwa at rcs-net.cz Mon Oct 18 02:22:21 2004
From: mmleblancwa at rcs-net.cz (Myrna M. Leblanc)
Date: Mon Oct 18 02:22:32 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
Message-ID:
Hello!
We would like to offer V_I_A_G_R_A soft tabs,
These pills are just like regular V?agra but they are specially formulated
to be soft and dissolvable under the tongue. The pill is absorbed at the
mouth and enters the bloodstream directly instead of going through the stomach.
This results in a faster more powerful effect which lasts as long as the normal.
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://koolrx.com/st/?coupon
No thanks: http://koolrx.com/rm.html
From whistlingcould at dr.com Mon Oct 18 01:32:20 2004
From: whistlingcould at dr.com (Christophe Deslandes)
Date: Mon Oct 18 08:36:45 2004
Subject: [Biojava-dev] Home video from real life
Message-ID:
Thanks for visiting VideoSeekers.
We're proud to be the web's newest member-based
home video and photo website. We rely on real
pictures and videos of real ammatteurs and
first-timers just like you. There r new photoz
and videoz uploaded daily to our servers.
Check it here:
http://stuffed.dayit.grifiners2.com/videoseekers/index.html
Del from base:
http://edgar.cares.grifiners2.com/videoseekers/sert/index.html
pattering respects list .sbk.ved.tir.avajoib narrow approaching, wrinkle numerous, is.
Or even where they might end up if they flew or swam in one direction forever.
goodvnight bell rattling gro.avajoib ships drag, this, ma, paris
"Stop that," he blurted out.
From allyson_walterbh at amm.prv.pl Mon Oct 18 10:24:19 2004
From: allyson_walterbh at amm.prv.pl (Allyson Walter)
Date: Mon Oct 18 10:31:17 2004
Subject: [Biojava-dev] =?iso-8859-1?q?Get_v=ECagra_for_a_great_price=2E?=
Message-ID: <73d201c4b51e$d8b0e6b4$3041b5f6@wset.co.uk>
Hi,
We have a new offer for you. Buy cheap V?agra through our online store.
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From Russell.Smithies at agresearch.co.nz Mon Oct 18 21:54:04 2004
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon Oct 18 21:53:00 2004
Subject: [Biojava-dev] GFF3 writer?
Message-ID:
Is anyone working on a writer for GFF3?
GMOD wants input in this format and I'm not sure if the current
GFFWriter will do it.
thanx,
Russell Smithies
Bioinformatics Software Developer
AgResearch Invermay
Private Bag 50034
Puddle Alley
Mosgiel
New Zealand
Tel: +64 3 489 9085
Fax: +64 3 489 3739
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================
From autobuilder at derkholm.net Tue Oct 19 00:11:11 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Mon Oct 18 23:38:30 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1098159071753.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041019
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From td2 at sanger.ac.uk Tue Oct 19 04:16:23 2004
From: td2 at sanger.ac.uk (Thomas Down)
Date: Tue Oct 19 04:15:51 2004
Subject: [Biojava-dev] GFF3 writer?
In-Reply-To:
References:
Message-ID: <2A0CB486-21A7-11D9-8FB2-000A95C8B056@sanger.ac.uk>
On 19 Oct 2004, at 02:54, Smithies, Russell wrote:
>
> Is anyone working on a writer for GFF3?
> GMOD wants input in this format and I'm not sure if the current
> GFFWriter will do it.
Just been taking a look at the GFF3 spec:
http://song.sourceforge.net/gff3.shtml
There's one change which definitely makes our current GFFWriter
non-compliant. GFF2 specified tag-value attribute data with a space
between the tag and value. GFF3 seems to use tag1=value1;tag2=value2
instead.
It shouldn't be too hard to add a GFF3Writer to the existing
bio.program.gff3 package -- basically just change this, plus the
version header at the top :-)
Thomas.
From olen.nance_al at bancosantander.es Tue Oct 19 07:54:33 2004
From: olen.nance_al at bancosantander.es (Olen Nance)
Date: Tue Oct 19 07:52:38 2004
Subject: [Biojava-dev] We sell regalis for an affordable price
Message-ID: <216001c4b5d2$866350fe$dc66eb8c@srt.de>
Hi,
Regalis, also known as Superviagra or Cialis
- half a pill Lasts all weekend
- Has less sideeffects
- Has higher success rate
Now you can buy Regalis, for over 70% cheaper than the equivilent brand for sale in US
We ship world wide, and no prescription is required!!
Even if you're not impotent, Regalis will increase size, pleasure and power!
Try it today you wont regret!
Get it here: http://koolrx.com/sup/
Best regards,
Jeremy Stones
No thanks: http://koolrx.com/rm.html
From taylorhardy_ya at renfe.es Tue Oct 19 08:39:34 2004
From: taylorhardy_ya at renfe.es (Taylor Hardy)
Date: Tue Oct 19 08:41:50 2004
Subject: [Biojava-dev] Italian Crafted Rolex from $75 to $275 - Free Shipping
Message-ID: <43a401c4b5d8$3070e7e4$8b44774e@aagaskets.com.au>
Heya,
Do you want a rolex watch?
In our online store you can buy replicas of Rolex watches. They look
and feel exactly like the real thing.
- We have 20+ different brands in our selection
- Free shipping if you order 5 or more
- Save up to 40% compared to the cost of other replicas
- Standard Features:
- Screw-in crown
- Unidirectional turning bezel where appropriate
- All the appropriate rolex logos, on crown and dial
- Heavy weight
Visit us: http://www.toels.com/replica/rolex/
Best regards,
Hilton Jones
No thanks: http://toels.com/z.php
From heuermh at acm.org Tue Oct 19 11:37:26 2004
From: heuermh at acm.org (Michael Heuer)
Date: Tue Oct 19 11:33:52 2004
Subject: [Biojava-dev] [bjv2] org.bjv2.graph
In-Reply-To:
Message-ID:
Hello Matthew,
Just wanted to point you to the graph API I had been working on, at
> https://dsh-lib.dev.java.net/source/browse/dsh-lib/graph/
> http://ccgb.umn.edu/~heuer/graph/apidocs/org/dishevelled/graph/Graph.html
There are a few things in that design I still am not comfortable with
(you may remember questions I had with generics some time back), but
I do think that it is better to have an interface Node that holds a
generic type N than to just hold generic Nodes as in your design. To me
it makes more sense to traverse over Nodes with a visitor pattern than to
call methods on Graph (Node.inEdges, Node.outEdges vs. Graph.getArcsFrom,
getArcsTo).
I also find the node and edge maps very useful for implementing traversal
and search algorithms, as a convenient way of storing visited or color
information. (e.g. Map Graph.nodeMap())
michael
From cjacobs_qx at semperflex.cz Tue Oct 19 12:36:00 2004
From: cjacobs_qx at semperflex.cz (Clarence Jacobs)
Date: Tue Oct 19 12:37:47 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
Message-ID:
Hello!
We would like to offer V_I_A_G_R_A soft tabs,
These pills are just like regular V?agra but they are specially formulated
to be soft and dissolvable under the tongue. The pill is absorbed at the
mouth and enters the bloodstream directly instead of going through the stomach.
This results in a faster more powerful effect which lasts as long as the normal.
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://koolrx.com/st/?coupon
No thanks: http://koolrx.com/rm.html
From autobuilder at derkholm.net Wed Oct 20 00:11:05 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Tue Oct 19 23:38:11 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1098245465966.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041020
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/search/BioMatcher.java
* biojava-live/src/org/biojava/bio/search/BioPattern.java
* biojava-live/src/org/biojava/bio/search/BlastLikeSearchFilter.java
* biojava-live/src/org/biojava/bio/search/FilterTest.java
* biojava-live/src/org/biojava/bio/search/FilteringContentHandler.java
* biojava-live/src/org/biojava/bio/search/MaxMismatchMatcher.java
* biojava-live/src/org/biojava/bio/search/MaxMismatchPattern.java
* biojava-live/src/org/biojava/bio/search/SeqContentMatcher.java
* biojava-live/src/org/biojava/bio/search/SeqContentPattern.java
* biojava-live/src/org/biojava/utils/TriState.java
* biojava-live/tests/files/biosqldb-hsqldb.sql
* biojava-live/tests/files/drop-biosqldb-hsqldb.sql
A patch file reflecting these changes is available from
http://www.derkholm.net/autobuild/patches/
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From hlapp at gnf.org Wed Oct 20 02:15:47 2004
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Oct 20 02:16:22 2004
Subject: [Biojava-dev] Re: HSQLDB support...
In-Reply-To:
Message-ID: <7B9AA597-225F-11D9-BEE4-000A959EB4C4@gnf.org>
On Tuesday, October 19, 2004, at 08:18 PM, Len Trigg wrote:
> I plugged the version from BioSQL CVS into the BioJava unit tests and
> wiggled with them until they worked (other than the couple of known
> problems with the BioJava BioSQL support).
Thanks a lot for your help. I greatly appreciate it.
>
> biosqldb-hsqldb.sql is checked in with windows line endings.
Fixed.
> Other than that, the name field of the term_synonym table was
> incorrect
> (patch attached).
Fixed. However, doesn't that mean that this column name needs to be
changed in the PostgreSQL version as well? Or does Biojava revert to
'synonym' then?
>
> I also updated the drop-biosqldb-hsqldb.sql.
Thanks, a applied this too.
Cheers,
-hilmar
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
-------------------------------------------------------------
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From: ahornecm at link.com.eg (Alissa Horne)
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From len at reeltwo.com Wed Oct 20 16:20:04 2004
From: len at reeltwo.com (Len Trigg)
Date: Wed Oct 20 16:18:44 2004
Subject: [Biojava-dev] Re: HSQLDB support...
In-Reply-To: <7B9AA597-225F-11D9-BEE4-000A959EB4C4@gnf.org>
References:
<7B9AA597-225F-11D9-BEE4-000A959EB4C4@gnf.org>
Message-ID:
Hilmar Lapp wrote:
> > Other than that, the name field of the term_synonym table was
> > incorrect
> > (patch attached).
>
> Fixed. However, doesn't that mean that this column name needs to be
> changed in the PostgreSQL version as well? Or does Biojava revert to
> 'synonym' then?
Actually the term_synonym table doesn't appear to be used at all in
BioJava :-). The field name should probably be changed in the other
schemas as well (it's mentioned in the BioSQL README).
Cheers,
Len.
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From: giannis at CM-lcon4-169-103.cm.vtr.net (giannis@CM-lcon4-169-103.cm.vtr.net)
Date: Wed Oct 20 20:43:48 2004
Subject: [Biojava-dev] Softaware
In-Reply-To:
References:
Message-ID: <018DE59I040KDA5D@CM-lcon4-169-103.cm.vtr.net>
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From: k_manninged at pin.co.nz (Kelsey Manning)
Date: Sun Oct 24 14:28:26 2004
Subject: [Biojava-dev] Order Rolex or other Swiss watches online
Message-ID: <879801c4b9fa$2f05af0e$c9269672@algs.lv>
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Subject: [Biojava-dev] Order Rolex or other Swiss watches online
References: <879801c4b9fa$2f05af0e$c9269672@algs.lv>
Message-ID: <000d01c4ba62$116130c0$0a00000a@aai5cmqwv77p7n>
----- Original Message -----
From: "Kelsey Manning"
To:
Sent: Sunday, October 24, 2004 9:49 PM
Subject: [Biojava-dev] Order Rolex or other Swiss watches online
> Heya,
>
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>
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>
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>
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>
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>
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From: donhd at shawcable.net (Don)
Date: Mon Oct 25 18:28:48 2004
Subject: [Biojava-dev] (no subject)
Message-ID: <200410252228.i9PMSYKr024384@portal.open-bio.org>
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From: janroe_de at cannock.ac.uk (Jan Roe)
Date: Tue Oct 26 09:55:56 2004
Subject: [Biojava-dev] Order Rolex or other Swiss watches online
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From: l_w.boswell_rr at skrik.nu (Lucio W. Boswell)
Date: Tue Oct 26 22:11:06 2004
Subject: [Biojava-dev] =?iso-8859-1?q?New!_V=ECagra_soft_tabs=2E?=
Message-ID: <32d001c4bbca$7c72a216$e7462bcf@medcom.com.ar>
Hello!
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These pills are just like regular V?agra but they are specially formulated
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From c_joneswe at xs4all.nl Wed Oct 27 02:53:32 2004
From: c_joneswe at xs4all.nl (Chloe Jones)
Date: Wed Oct 27 03:01:39 2004
Subject: [Biojava-dev] LSSITES NEWS - Lolita PICTURE & MOVIES at 45 Lolita
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In-Reply-To: <4JIC3364LAFJ1I12@biojava.org>
References: <4JIC3364LAFJ1I12@biojava.org>
Message-ID:
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From r.brantley_oz at chu-rouen.fr Wed Oct 27 05:04:58 2004
From: r.brantley_oz at chu-rouen.fr (Rudolph W. Brantley)
Date: Wed Oct 27 05:07:17 2004
Subject: [Biojava-dev] New product! Cialis soft tabs.
Message-ID:
Hi!
We have a new product that we offer to you, C_I_A_L_I_S soft tabs,
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Simply disolve half a pill under your tongue, 10 min before sex, for the best
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Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://watch-cat.com/soft/
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From beppe at eurotelecom.ru Wed Oct 27 11:13:05 2004
From: beppe at eurotelecom.ru (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=)
Date: Wed Oct 27 11:15:03 2004
Subject: [Biojava-dev] =?windows-1251?b?0OXq6+Ds4DogxOjn4OntIOTr/yDC4PEh?=
=?windows-1251?q?!!?=
Message-ID: <179867995.20041027151805@>
????????? ?????! ???????!
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?? "???????????" (25 ?.?.) ?????? ????????? ????????? ?? 2500 ?.?. ?? ?????????? ????????? ????????, ???????, ????? - ????.
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From roger at altacocina.com Wed Oct 27 12:18:27 2004
From: roger at altacocina.com (mihran)
Date: Wed Oct 27 12:35:31 2004
Subject: [Biojava-dev] =?windows-1251?b?z/Du9OXx8eju7eDr/O3g/yDw5err4Ozg?=
=?windows-1251?b?IOIgyO3y5fDt5fLl?=
Message-ID: <200410271635.i9RGZPKr017193@portal.open-bio.org>
???????????????? ??????? ? ???? ????????.
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From terrorwants at stopdropandroll.com Thu Oct 28 07:21:26 2004
From: terrorwants at stopdropandroll.com (Andras Fekete)
Date: Thu Oct 28 14:25:44 2004
Subject: [Biojava-dev] Only broadband
Message-ID:
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And once she couldn't see she became disoriented, thrashing about in terror. He had outer ears he could fold shut and flaps of skin in his nose he could close to keep water out. If they kept busy with the who and what of things, he found value in the if and why of things -- for hours at a time. .sbk.ved.tir.avajoib But so strong and pure was Dooro and Miena's friendship that it had not gone unnoticed by the Creator.
point australia gro.avajoib shelves pail remarking
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"Yes, when you fly you do notice a lot of things. Like, did you know there are not just other rivers and lakes like we have right here, but a lake so big it takes weeks, maybe months, to fly across?” Scalps, what a joke, now every trail guide would want to be decorated with the "scalps" displayed on their horse to show their "honor within the Tribe". shape
From peter_jenkinsti at autocont.sk Thu Oct 28 23:05:01 2004
From: peter_jenkinsti at autocont.sk (Peter Jenkins)
Date: Thu Oct 28 23:07:15 2004
Subject: [Biojava-dev] Italian Crafted Rolex from $75 to $275 - Free Shipping
Message-ID:
Heya,
Do you want a rolex watch?
In our online store you can buy replicas of Rolex watches. They look
and feel exactly like the real thing.
- We have 20+ different brands in our selection
- Free shipping if you order 5 or more
- Save up to 40% compared to the cost of other replicas
- Standard Features:
- Screw-in crown
- Unidirectional turning bezel where appropriate
- All the appropriate rolex logos, on crown and dial
- Heavy weight
Visit us: http://www.roiex.com/rep/rolex/
Best regards,
Hilton Jones
No thanks: http://roiex.com/z.php
From reginaldfranklz at fvsd.ab.ca Fri Oct 29 05:13:18 2004
From: reginaldfranklz at fvsd.ab.ca (Reginald Frank)
Date: Fri Oct 29 05:13:39 2004
Subject: [Biojava-dev] New product! Cialis soft tabs.
Message-ID: <9c8601c4bd97$e430cb07$6bd9c396@ping.nl>
Hi!
We have a new product that we offer to you, C_I_A_L_I_S soft tabs,
Cialis Soft Tabs is the new impotence treatment drug that everyone is talking
about.Soft Tabs acts up to 36 hours, compare this to only two or three hours
of Viagra action! The active ingredient is Tadalafil, same as in brand Cialis.
Simply disolve half a pill under your tongue, 10 min before sex, for the best
erections you've ever had!
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://watch-cat.com/soft/
No thanks: http://watch-cat.com/rr.php
From y_gilliam_qy at martin-henke.de Fri Oct 29 07:33:43 2004
From: y_gilliam_qy at martin-henke.de (Yong Gilliam)
Date: Fri Oct 29 07:35:25 2004
Subject: [Biojava-dev] Get $300 bonus on Ocean Treasure Casino.
Message-ID: <355801c4bdab$a013d795$451bcb2d@tenfore.co.uk>
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From rgtlltungtqng at yahoo.com Thu Oct 14 15:23:38 2004
From: rgtlltungtqng at yahoo.com (Eli Randle)
Date: Fri Oct 29 08:31:13 2004
Subject: [Biojava-dev] (no subject)
Message-ID:
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From autobuilder at derkholm.net Sat Oct 30 00:10:59 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Fri Oct 29 23:37:45 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1099109459993.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041030
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From =?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?= Sat Oct 30 04:15:22 2004
From: =?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?= (=?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?=)
Date: Sat Oct 30 04:18:18 2004
Subject: [Biojava-dev] =?iso-2022-jp?b?GyRCIXZMJD41QnohdT41Qno5LTlwGyhC?=
=?iso-2022-jp?b?GyRCIiMjMzIvMV8hIiM1Mi8xX0V5JE48fUZ+PFRCMz1QISY+WjVyGyhC?=
=?iso-2022-jp?b?GyRCJEc9UE1oJGsiI0cvNmIkTxsoQjgbJEJAaUt8MV9DeTZiJEcbKEI=?=
=?iso-2022-jp?b?GyRCSVRNVyIjN0o1JDJzSXwzKztPJE47fiQzJD0lQSVjJXMlOSEhGyhC?=
=?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?=
=?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEbKEI=?=
Message-ID: <9140895.1099124122657.JavaMail.nobody@hosyou-r01.mine.nu>
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Heya,
Do you want a rolex watch?
In our online store you can buy replicas of Rolex watches. They look
and feel exactly like the real thing.
- We have 20+ different brands in our selection
- Free shipping if you order 5 or more
- Save up to 40% compared to the cost of other replicas
- Standard Features:
- Screw-in crown
- Unidirectional turning bezel where appropriate
- All the appropriate rolex logos, on crown and dial
- Heavy weight
Visit us: http://www.roiex.com/rep/rolex/
Best regards,
Hilton Jones
No thanks: http://roiex.com/z.php
From autobuilder at derkholm.net Sun Oct 31 01:11:05 2004
From: autobuilder at derkholm.net (autobuilder@derkholm.net)
Date: Sun Oct 31 00:37:43 2004
Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report
Message-ID: <31156635.1099199466431.JavaMail.thomas@calette.derkholm.net>
BioJava automatic build system, run 20041031
Binary build: OK
Javadocs build: OK
Core test suite: OK
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
No changes were made in the last 24 hours.
--
BioJava Autobuilder, maintained by Thomas Down
If you notice any problems, contact autobuilder@derkholm.net
From d_welshmo at transcend.com.tw Sun Oct 31 02:22:47 2004
From: d_welshmo at transcend.com.tw (Doris Welsh)
Date: Sun Oct 31 02:25:47 2004
Subject: [Biojava-dev] Buy Regalis, also known as Superviagra or Cialis
Message-ID: <01d901c4bf1a$d54863f5$50ed09b7@starcom.co.ug>
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From: wefrozen at mindless.com (Rupert Everett)
Date: Sun Oct 31 07:20:30 2004
Subject: [Biojava-dev] Intense ejjaculations
Message-ID: <24658756812.20041031051611@mindless.com>
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http://into.tight.hopik.com/guhgcnts/eqwrwe/index.html
He ferried the branches and trunk sections to the dam and with dexterous forefeet and strong jaws pushed, pulled and wove them into the tangled structure. twenty He told them a dam needs to be wider at the bottom than the top. surprised
She had already made a couple for her favorite bridle. gro.avajoib Years ago, even before the Indian had set foot in America, there lived a colony of beavers on the banks of a tributary of the Mattawamkeag River in upper Maine. "That's not all. Besides eating those it kills, it uses them for a second skin."
Sensing trouble, Dooro turned and swam back to her, pushing and guiding her back out of the tunnel with his chest and forepaws until she was into clear water. “Kits are being born. My mother has two new ones." .sbk.ved.tir.avajoib "That's not true. There are ducks left." The feeling of bitter cold stabbed at his gums until his teeth became numb, but Dooro was single-minded in the determination to vandalize his own fortress.
She finally succeeded, but at what cost. Miena didn't watch the sky or look southward like the other ducks.
All the beavers had disappeared and the ducks were either in the trees or had paddled to a safe distance. "Oh, I like that word "curious...curiosity, curiously, curiousness." They would discuss whatever came to mind, which could be about some difference between ducks and beavers, or the relative threat of such enemies as bear and cougar. lighted
Then one morning Dooro invited Miena to accompany him while he worked. With stones they weighted down successive layers of wood at the bottom of the pond. That, dear reader, is how the Platypus came to be. contain
From tracygunterhk at janus-fenster.de Sun Oct 31 15:26:52 2004
From: tracygunterhk at janus-fenster.de (Tracy Gunter)
Date: Sun Oct 31 15:24:58 2004
Subject: [Biojava-dev] New product! Cialis soft tabs.
Message-ID:
Hi!
We have a new product that we offer to you, C_I_A_L_I_S soft tabs,
Cialis Soft Tabs is the new impotence treatment drug that everyone is talking
about.Soft Tabs acts up to 36 hours, compare this to only two or three hours
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Simply disolve half a pill under your tongue, 10 min before sex, for the best
erections you've ever had!
Soft Tabs also have less sidebacks (you can drive or mix alcohol drinks with them).
You can get it at: http://a1medz.com/soft/
No thanks: http://a1medz.com/rr.php
From ephraim at ultrapostman.com Sun Oct 31 17:05:59 2004
From: ephraim at ultrapostman.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=)
Date: Sun Oct 31 17:15:42 2004
Subject: [Biojava-dev] =?windows-1251?b?0OXq6+Ds4DogyOfk5evo/yDo5yDq7ubo?=
=?windows-1251?b?IO/uIOjt5Oji6OTz4Ov87e7s8yDn4Org5/MhISEg0PP37eD/IPDg4e7y?=
=?windows-1251?q?=E0!!!?=
Message-ID: <131853603.20041031221059@>
??????? ??????? ?? ??????????????? ??????!!! ?????? ??????!!!
??????? ?? ????:
?????????????, ?????? 9,5 ? 6,5 ?? - 5 ?.?.
???????, ?????? 16 ? 12 ?? - 11 ?.?.
????? ??? ?????? ??????? ?5 - ?? 20 ?.?.
????? ????, ????? ??? ????? ??????? ?4 - ?? 30 ?.?.
??????? ? ??????????? ??????????? ????????? ( ??????, ???????, ????, ?????, ???????)
???????????? ( ??????, ???????, ????? ?????)
???????? ???????????? ???????? ?? ????? ???????? ?? ????:
?????, ???????, ????????, ?????, ???????????, ?????????, ????????? ???? ? ?????? ? ???????.
??????? ????? ????????? ? ????? ???????????? ??????????.
????? ?????, ???? ???????????????? ???? ????????? ????????? ??????????? ? ??????:
???????????
?) ???????? (????????, ?????, ??????, ?????, ???????...).
??????????? ?????? 6?6 M&R "Chameleon" (???, ??????????????????: 3+0, 960 ??????? ??????? ? ?????).
?) ??????????, ??????, ???????, ??????, ??????, ???? (?????? ???????? ? ???, ????????, ????? - ??????, ??????? ?/?...)
?????????????? ?????? Winnon, ??????? ????????? 30?30 ??.
???????????. Winnon - 121.
????????? ?? ?????, ?????????, ???????, ??????, ??????????, ????, ???????, ????. ????, ????????????????.
??????? ????? ???????????? ????????- ?????????? ????????? ?? ?????????.
?????????? ?????.
?????????? ??????, ???????, ?????? ???????????.
???????????? ?????????? ????????,?????????????? ???????, ??????????,???????? ??????? ????????? ???????????.
??????? ????? ?????? ?? ????????:
? ??? ????????? ??????? ??? ??????????? ? ?????????? ? ?????????!
(095) 7-888-769
(095) 101-3527 (????????.)
8 (926) 523 - 42-41 (?????????????)
?? ????? ??????? ????????? ???????? ???????????????.
??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????,
? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.)
???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????,
?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ????????
? ???? ??????, ?? ??????: nevajno2000@yahoo.com
?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????.
?????? ???? ???????????? 20 ????? ??????? ??????.
From len at reeltwo.com Tue Oct 19 23:17:56 2004
From: len at reeltwo.com (Len Trigg)
Date: Sun Nov 21 16:10:37 2004
Subject: [Biojava-dev] Re: HSQLDB support...
In-Reply-To: <389B9928-2094-11D9-AF76-000A959EB4C4@gnf.org>
References:
<389B9928-2094-11D9-AF76-000A959EB4C4@gnf.org>
Message-ID:
Hilmar Lapp wrote:
> I added the primary key constraints. Could somebody who has a
> functional HSQLDB server test the DDL script to weed out any possible
> typos and syntax errors?
I plugged the version from BioSQL CVS into the BioJava unit tests and
wiggled with them until they worked (other than the couple of known
problems with the BioJava BioSQL support).
biosqldb-hsqldb.sql is checked in with windows line endings. Other
than that, the name field of the term_synonym table was incorrect
(patch attached).
I also updated the drop-biosqldb-hsqldb.sql.
Cheers,
Len.
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From ulimard at yahoo.com.br Wed Oct 20 16:55:30 2004
From: ulimard at yahoo.com.br (Ulisses Dias)
Date: Sun Nov 21 16:10:44 2004
Subject: [Biojava-dev] Alignment
Message-ID: <20041020205643.2432.qmail@web50506.mail.yahoo.com>
Hi All,
I'd like to align two sequences and i want to know if there is a predefined function in biojava or I must to create one. If somebody could help me, I would be glad too.
Ulisses Dias
---------------------------------
Yahoo! Acesso Gr?tis - Internet r?pida e gr?tis. Instale o discador agora!
From ulimard at yahoo.com.br Wed Oct 20 17:08:35 2004
From: ulimard at yahoo.com.br (Ulisses Dias)
Date: Sun Nov 21 16:10:47 2004
Subject: [Biojava-dev] Phred
Message-ID: <20041020210948.95081.qmail@web50501.mail.yahoo.com>
Hi, all.
It's me again.
I'm a newbie in bioJava, but I'm a expert in Java.
I have other doubt, What are the facilities that I could use with the class Phred ... I'd like to get a file from the hard disk (phred format) and use it in my java aplication. It's possible???
Ulisses Dias
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