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From td2@sanger.ac.uk  Thu Jan  2 12:54:58 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 2 Jan 2003 12:54:58 +0000
Subject: [Biojava-l] BlastLikeSAXParser and Blastall version
In-Reply-To: <3E08C0D7.5020601@bcgsc.bc.ca>
References: <3E08C0D7.5020601@bcgsc.bc.ca>
Message-ID: <20030102125458.GA331200@jabba.sanger.ac.uk>

Hi...

On Tue, Dec 24, 2002 at 12:17:27PM -0800, Rene Warren wrote:
> Hi,
> 
> I have used the BlastLikeSAXParser class and I seem to have set up 
> everything correctly.  However, it catches this exception and I find it 
> quite strange considering that I'm using an older version of blastall 
> (2000).  I also tried a blast output from blastall v 2.2.2 (current) 
> without success.  The same is observed when blastn is used.
>
> sax exception:org.xml.sax.SAXException: Program ncbi-blastp Version 
> 2.0.14 is not supported by the biojava blast-like parsing framework
> 
> Do you have any thoughts, comments or ideas regarding this?

You can try calling BlastLikeSAXParser.setModeLazy(), to indicate
that the parser should continue even if it doesn't recognize the
precise version of blast which you are using.  My experience of
this is generally good, but obviously you should double-check the
first few results to make sure everything is working.

I note from the documentation of the CVS version of biojava
that 2.2.2 (and 2.2.3) are now listed as supported versions.
If you're using an old version of BioJava which doesn't support
2.2.2, you might want to consider upgrading.

> Also, I have used the SAX XMLparser to parse a blast output in xml 
> format.  Do you guys know if NCBI is complient to the XML format, 
> because that doesn't seem to work either.

You can dump an XML representation of your blast output using
the nativeapps.BlastLike2XML script (in the demos directory).
But this XML is different from NCBI blast XML.  David Huen
has written some BioJava support for the NCBI XML format
(in very recent CVS versions, package org.biojava.bio.program.sax.blastxml).
I don't have direct experience of this myself, though.

    Thomas.

From willy.valdivia@ndsu.nodak.edu  Fri Jan  3 16:10:39 2003
From: willy.valdivia@ndsu.nodak.edu (willy.valdivia@ndsu.nodak.edu)
Date: Fri, 03 Jan 2003 10:10:39 -0600
Subject: [Biojava-l] virtual seminars
Message-ID: <1041610239.3e15b5ffa101d@webmail.ndsu.NoDak.edu>

Hello

Using the Access Grid and live video streaming technology, the monthly 
virtual seminars on genomics and bioinformatics try to promote 
discussions and generate an environment for potential collaboration 
and a dynamic exchange of ideas. Everyone is welcome to joint these 
discussions the schedule and guidelines is available at: 
http://www.ndsu.edu/virtual-genomics/seminar_schedule.htm 

Goals

1. Transcend geographical barriers and enhance interaction and 
collaboration among participants. 
2. Present another way for discussion regarding current trends and 
limitations of genomic and bioinformatic research

Topics

Computational Biology
Programmable bio-organisms
Statistical and Computational Approaches for Gene Expression Analysis 
High Throughput Computing

Willy Valdivia Granda
Plant Stress Genomics and Bioinformatics Group
North Dakota State University
PO BOX 5130
Fargo, USA
www.ndsu.edu/virtual-genomics/valdivia.htm

From hirohash@genes.nig.ac.jp  Mon Jan  6 01:48:10 2003
From: hirohash@genes.nig.ac.jp (Hiroyuki Hashimoto)
Date: Mon, 6 Jan 2003 10:48:10 +0900
Subject: [Biojava-l] help
References: <20021229053620.87433.qmail@web14202.mail.yahoo.com>
Message-ID: <007b01c2b525$aab76bc0$98c92785@TSUNAMI.local>

Hi suyee;

'log(double)' is static method.
The below example...,

int g;
int min;

g = (int)(min + Math.log((double)min));
                ^^^^^

that's OK??

Hiroyuki;

----- Original Message ----- 
From: "suyee" <leesuyee@yahoo.com>
To: <biojava-l@biojava.org>
Sent: Sunday, December 29, 2002 2:36 PM
Subject: [Biojava-l] help


> can anyone help me in this..
> 
> may i know how to use "log" in Java. 
> For example, this is the part that i need to use log algorithm: 
>  
>      g = (min + log((double)min)) ;
> 
> thanks
> 
> __________________________________________________
> Do you Yahoo!?
> Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
> http://mailplus.yahoo.com
> _______________________________________________
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> http://biojava.org/mailman/listinfo/biojava-l
> 

From jon portuondo murguiondo <jon.portuondo01@campus.upf.es>  Tue Jan  7 08:56:30 2003
From: jon portuondo murguiondo <jon.portuondo01@campus.upf.es> (jon portuondo murguiondo)
Date: Tue, 7 Jan 2003 08:56:30
Subject: [Biojava-l] PdbToXMLConverter output
Message-ID: <1041926190.8091@mail.infomail.es>

PdbToXMLConverter doesn't have main method.
For these reason, I used he program that Matthew gave me, called PDBConverter.java. This is the source of the PDBConverter.java:
 ----------------------------------------------------------------------------------------------------

 package org.biojava.bio.program; 
 import java.io.*; 
 import org.biojava.bio.program.*; 
 public class PDBConverter { 
 public static void main(String[] args) 
 throws Exception { 
 StringBuffer sbuf = new StringBuffer(); 
 BufferedReader in = new BufferedReader( 
 new FileReader( 
 new File(args[0]) ) ); 
 for( 
 String line = in.readLine(); 
 line != null; 
 line = in.readLine() 
 ) { 
 sbuf.append(line); 
 } 
 PdbToXMLConverter converter = 
 new PdbToXMLConverter(sbuf.toString()); 
 converter.convert(); 
 } 
 } 
 --------------------------------------------------------------------------------------------------

 With this program I finally get an output from
 PdbToXMLConverter, but it is really odd.
 To get it run I typed: 
 java org.biojava.bio.program.PDBConverter
 /home/jon/1FS1.pdb  
 ------------------------------------------------------------------------------------------------

 <?xml version="1.0"?> 
 no protocol: HEADER LIGASE 08-SEP-00 1FS1 TITLE
 INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE
 STRUCTURE OF TITLE 2 THE SKP1-SKP2 COMPLEX
 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN
 A/CDK2-ASSOCIATED P19; COMPND 3 CHAIN: A, C;
 COMPND 4 FRAGMENT: RESIDUES 101-153; COMPND
 5 SYNONYM: SKP2 F-BOX; COMPND 6 ENGINEERED:
 YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE:
 CYCLIN A/CDK2-ASSOCIATED P45; COMPND 9
 CHAIN: B, D; COMPND 10 FRAGMENT: RESIDUES
 1-147; COMPND 11 SYNONYM: SKP1; COMPND 12
 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2
 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3
 ORGANISM_COMMON: HUMAN; SOURCE 4
 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE
 5 EXPRESSION_SYSTEM_COMMON: BACTERIA;
 SOURCE 6 MOL_ID: 2; SOURCE 7
 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE
 ---------------------------------------------------------------------------------------------------

 This is supposed to be an structured XML, but there is no change of line and I think it's clearly a defectous output (if it isn't, tell me please). 
 
 
 Thanks for all! 

If you want to see PdbToXMLConverter.java, here it is:

----------------------------------------------------------------------------------------------------
/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.bio.program;

import org.xml.sax.ContentHandler;
import org.xml.sax.XMLReader;
import org.xml.sax.SAXException;
import java.util.*;

import org.biojava.bio.program.sax.PdbSAXParser;
import org.biojava.bio.program.xml.SimpleXMLEmitter;

/**
 * <p>
 * A class that converts Protein Data Bank (PDB) to
 * XML that will validate against the biojava:MacromolecularStructure DTD.
 * <p>
 * <b>Note this code is experimental and subject to change without notice.
 * </b>
 * <p>
 * Copyright &copy; 2000 Cambridge Antibody Technology.
 * All Rights Reserved.
 * <p>
 * Primary author -<ul>
 * <li>Simon Brocklehurst (CAT)
 * </ul>
 * Other authors  -<ul>
 * <li>Tim Dilks          (CAT)
 * <li>Colin Hardman      (CAT)
 * <li>Stuart Johnston    (CAT)
 *</ul>
 *
 * This code was first released to the biojava.org project, July 2000.
 *
 * @author Cambridge Antibody Technology (CAT)
 * @version 0.1
 * 
 * @see org.biojava.bio.program.sax.BlastLikeSAXParser
 * @see SimpleXMLEmitter
 */
public class PdbToXMLConverter {

    private String            oInput;
    private XMLReader         oParser;
    private boolean           tStrict         = true;

    /**
     * Creates a new <code>BlastToXMLConverter</code> instance.
     *
     */
    public PdbToXMLConverter(String poInput) {
        oInput = poInput;
    }

    public void convert() throws java.io.IOException,
                                 org.xml.sax.SAXException {

        //Access functionality of biojava classes through
        //standard org.xml.sax interfaces...

        /**
         * Create a SAX Parser that takes the native output
         * from blast-like bioinformatics software.
         */
        oParser = (XMLReader) new PdbSAXParser();


        /**
         * Dynamically change configuration of the parser
         * in regard of Namespace support. Here,
         * the xml.org/features/namespaces feature is simply "reset"
         * to its default value for SAX2.
         * The xml.org/features/namespaces-prefixes feature is
         * also set to true.  This is to ensure that xmlns attributes
         * are reported by the parser. These are required because we want
         * to configure the XMLEmitter to output qualified names (see below).
         */
        try {
            oParser.setFeature("http://xml.org/sax/features/namespaces",true);
            oParser.setFeature("http://xml.org/sax/features/namespace-prefixes",
                               true);

        } catch (Exception e) {
            //If an illegal conmbination of features is chosen,
            //roll back to default settings. Output a warning,
            //even though this might mess up the output...
            System.out.println("WARNING: ignoring attempt to set illegal " +
                               "combination of parser features");
        }
        /**
         * Create an XML ContentHandler. This
         * implementation of the DocumentHandler
         * interface simple outputs nicely formatted
         * XML. Passing a true value to the SimpleXMLEmitter
         * constructor instructs the ContentHandler
         * to take QNames from the SAXParser, rather
         * than LocalNames.
         */
        ContentHandler oHandler  = 
            (ContentHandler) new SimpleXMLEmitter(true);

        /**
         * Give the parser a reference to the ContentHandler
         * so that it can send SAX2 mesagges.
         */
        oParser.setContentHandler(oHandler);
        /**
         * Now make the Parser parse the output from the
         * blast-like software and emit XML as specificed
         * by the DocumentHandler.
         */
        oParser.parse(oInput);  

        System.out.println();

    }

}


From karin.lagesen@labmed.uio.no  Tue Jan  7 09:53:10 2003
From: karin.lagesen@labmed.uio.no (Karin Lagesen)
Date: Tue, 7 Jan 2003 10:53:10 +0100
Subject: [Biojava-l] locating genes in a genomic sequence
Message-ID: <20030107095309.GE3516@uracil.uio.no>

Hi!

I am trying to build a small program for finding intergenic areas.
This I am planning to do by locating all mRNA's in a genome and
outputting all the areas inbetween. Biojava seems to be able to help
with most of my tasks. However, I have a few questions. From what I
have understood I can have the genomic sequence as a SimpleSequence
with all of the genes as SimpleGene's attached via a FeatureHolder to
the genomic sequence. However, I have not figured out a smart way of
finding the location of each of the genes in the genomic sequence.
Since genomic sequences can be large, I hoped to avoid having to dump
the sequence in a string and use indexOf(gene sequence) to find the
position. Is there something I am missing here, or have I just
misunderstood all of this?

Thankyou in advance for your help. 

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen@labmed.uio.no

From jon portuondo murguiondo <jon.portuondo01@campus.upf.es>  Tue Jan  7 12:28:15 2003
From: jon portuondo murguiondo <jon.portuondo01@campus.upf.es> (jon portuondo murguiondo)
Date: Tue, 7 Jan 2003 12:28:15
Subject: [Biojava-l] Anybody works with pdb and XML?
Message-ID: <1041938895.15107@mail.infomail.es>

Hello! I am trying to convert pdb to XML. If you can help me I would be very pleased. Thank you!

From mark.schreiber@agresearch.co.nz  Tue Jan  7 20:28:37 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 8 Jan 2003 09:28:37 +1300
Subject: [Biojava-l] locating genes in a genomic sequence
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E7B4B@inbox.agresearch.co.nz>

Hi -

If you already have the SimpleGene features constructed these will
contain a Location object. However, I think you are saying how can I
find a subsequence in my Genomic sequence and locate the gene that way?

To rapidly find exact matches you can use the biojava
KnuthMorrisPrattSearch object from the org.biojava.bio.search package.
It contains a main method that demonstrates it's use. This is a very
efficient algorithm for finding exact matches.

Note: if the genome is larger than 64kb you will not be able to dump it
as a String as that is the maximum String length. You could dump it as a
char[].

- Mark


> -----Original Message-----
> From: Karin Lagesen [mailto:karin.lagesen@labmed.uio.no] 
> Sent: Tuesday, 7 January 2003 10:53 p.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] locating genes in a genomic sequence
> 
> 
> Hi!
> 
> I am trying to build a small program for finding intergenic 
> areas. This I am planning to do by locating all mRNA's in a 
> genome and outputting all the areas inbetween. Biojava seems 
> to be able to help with most of my tasks. However, I have a 
> few questions. From what I have understood I can have the 
> genomic sequence as a SimpleSequence with all of the genes as 
> SimpleGene's attached via a FeatureHolder to the genomic 
> sequence. However, I have not figured out a smart way of 
> finding the location of each of the genes in the genomic 
> sequence. Since genomic sequences can be large, I hoped to 
> avoid having to dump the sequence in a string and use 
> indexOf(gene sequence) to find the position. Is there 
> something I am missing here, or have I just misunderstood all of this?
> 
> Thankyou in advance for your help. 
> 
> Karin
> -- 
> Karin Lagesen, PhD student
> karin.lagesen@labmed.uio.no 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From russell_smithies@hotmail.com  Tue Jan  7 20:34:00 2003
From: russell_smithies@hotmail.com (Russell Smithies)
Date: Tue, 07 Jan 2003 20:34:00 +0000
Subject: [Biojava-l] JBuilder cvs?
Message-ID: <F111IW8WEo4Unho8b0y00011b83@hotmail.com>

Has anyone managed to get JBuilder 7's cvs to grab biojava-live from the 
anonymous cvs repository?
I spent a bit of time trying yesterday but was getting no-where.

These are the settings I tried:

New -> Pull project from CVS -> set up directory -> Pserver settings: server 
= cvs.open-bio.org, user = cvs -> Repository properties: path = 
/home/repository/biojava, module name = biojava-live, branch = <main>.

It seems to do something and asks for password (cvs) but doesn't d/l the 
files  :-(

If anyone's suceeded, could they please share the secret  :-)

thanx

Russell Smithies





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From mmhohman@northwestern.edu  Tue Jan  7 22:58:04 2003
From: mmhohman@northwestern.edu (Moses Hohman)
Date: Tue, 7 Jan 2003 16:58:04 -0600
Subject: [Biojava-l] locating genes in a genomic sequence
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165012E7B4B@inbox.agresearch.co.nz>
Message-ID: <7AC480AD-2293-11D7-B4A8-000393DB7722@northwestern.edu>

Small correction to this: Strings can be larger than 64kB. Prior to 
Java 1.3, if you tried to serialize (or to do anything resulting in 
serialization to) a String larger than 64kB, this would result in a 
java.io.UTFDataFormatException.

See http://java.sun.com/j2se/1.3/docs/guide/serialization/relnotes.html

The only reason I know this is I had this problem before, too ( :

Moses

On Tuesday, January 7, 2003, at 02:28  PM, Schreiber, Mark wrote:

> Hi -
>
> If you already have the SimpleGene features constructed these will
> contain a Location object. However, I think you are saying how can I
> find a subsequence in my Genomic sequence and locate the gene that way?
>
> To rapidly find exact matches you can use the biojava
> KnuthMorrisPrattSearch object from the org.biojava.bio.search package.
> It contains a main method that demonstrates it's use. This is a very
> efficient algorithm for finding exact matches.
>
> Note: if the genome is larger than 64kb you will not be able to dump it
> as a String as that is the maximum String length. You could dump it as 
> a
> char[].
>
> - Mark
>
>
>> -----Original Message-----
>> From: Karin Lagesen [mailto:karin.lagesen@labmed.uio.no]
>> Sent: Tuesday, 7 January 2003 10:53 p.m.
>> To: biojava-l@biojava.org
>> Subject: [Biojava-l] locating genes in a genomic sequence
>>
>>
>> Hi!
>>
>> I am trying to build a small program for finding intergenic
>> areas. This I am planning to do by locating all mRNA's in a
>> genome and outputting all the areas inbetween. Biojava seems
>> to be able to help with most of my tasks. However, I have a
>> few questions. From what I have understood I can have the
>> genomic sequence as a SimpleSequence with all of the genes as
>> SimpleGene's attached via a FeatureHolder to the genomic
>> sequence. However, I have not figured out a smart way of
>> finding the location of each of the genes in the genomic
>> sequence. Since genomic sequences can be large, I hoped to
>> avoid having to dump the sequence in a string and use
>> indexOf(gene sequence) to find the position. Is there
>> something I am missing here, or have I just misunderstood all of this?
>>
>> Thankyou in advance for your help.
>>
>> Karin
>> -- 
>> Karin Lagesen, PhD student
>> karin.lagesen@labmed.uio.no
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l@biojava.org
>> http://biojava.org/mailman/listinfo/biojava-l
>>
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>


From mark.schreiber@agresearch.co.nz  Wed Jan  8 01:08:14 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 8 Jan 2003 14:08:14 +1300
Subject: [Biojava-l] More tutorials
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E7BC8@inbox.agresearch.co.nz>

Hi -

More than 40 tutorials are now available on "biojava in anger"
http://bioconf.otago.ac.nz/biojava/.

New topics include locations, features and GUIs

Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
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 juguang@fugu-sg.org  Wed Jan  8 05:54:26 2003
From: juguang@fugu-sg.org (Xiao Juguang)
Date: Wed, 8 Jan 2003 13:54:26 +0800
Subject: [Biojava-l] biojava cvs
References: <AF026AF0FF4B054590228FD1F1DE5165012E7BC8@inbox.agresearch.co.nz>
Message-ID: <00c201c2b6da$6a1ff440$210aa8c0@sushibar.bii>

Hi guys,

I have dev.open-bio.org cvs account. But I am not sure which module I should checkout. Can you explain the following modules? thanks.

biodata/  
 biojava-acedb/  
 biojava-bsane/  
 biojava-corba/  
 biojava-ensembl/  
 biojava-exptl/  
 biojava-html/  
 biojava-lims/  
 biojava-live/  
 bytecode/  
 das-client/  
 das-gui/  
 dazzle/  
 egads-axis/  
 ensembl/  
 ensembl-das/  
 webservices/  
 xdas/  

Juguang.



From karin.lagesen@labmed.uio.no  Wed Jan  8 08:40:36 2003
From: karin.lagesen@labmed.uio.no (Karin Lagesen)
Date: Wed, 8 Jan 2003 09:40:36 +0100
Subject: [Biojava-l] locating genes in a genomic sequence
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165012E7B4B@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE5165012E7B4B@inbox.agresearch.co.nz>
Message-ID: <20030108084035.GG3516@uracil.uio.no>

On Wed, Jan 08, 2003 at 09:28:37AM +1300, Schreiber, Mark wrote:
> Hi -
> 
> If you already have the SimpleGene features constructed these will
> contain a Location object. However, I think you are saying how can I
> find a subsequence in my Genomic sequence and locate the gene that way?
> 
> To rapidly find exact matches you can use the biojava
> KnuthMorrisPrattSearch object from the org.biojava.bio.search package.
> It contains a main method that demonstrates it's use. This is a very
> efficient algorithm for finding exact matches.

Thankyou for your help. However, I seem to have a different version of
biojava than you, since I cannot find that class in that package (and
not in none of the others either). The biojava I am using is version
1.22 downloaded from biojava.org. I did however discover a
KnuthMorrisPrattSearch in a biojava API at
http://rosetteer.icu.ac.kr/, however, I could not figure out how to
get at the actual class....

Am I missing something again?

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen@labmed.uio.no

From kalle.naslund@genpat.uu.se  Wed Jan  8 10:03:07 2003
From: kalle.naslund@genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=)
Date: Wed, 08 Jan 2003 11:03:07 +0100
Subject: [Biojava-l] locating genes in a genomic sequence
References: <AF026AF0FF4B054590228FD1F1DE5165012E7B4B@inbox.agresearch.co.nz> <20030108084035.GG3516@uracil.uio.no>
Message-ID: <3E1BF75B.6030602@genpat.uu.se>

Karin Lagesen wrote:

>On Wed, Jan 08, 2003 at 09:28:37AM +1300, Schreiber, Mark wrote:
>  
>
>>Hi -
>>
>>If you already have the SimpleGene features constructed these will
>>contain a Location object. However, I think you are saying how can I
>>find a subsequence in my Genomic sequence and locate the gene that way?
>>
>>To rapidly find exact matches you can use the biojava
>>KnuthMorrisPrattSearch object from the org.biojava.bio.search package.
>>It contains a main method that demonstrates it's use. This is a very
>>efficient algorithm for finding exact matches.
>>    
>>
>
>Thankyou for your help. However, I seem to have a different version of
>biojava than you, since I cannot find that class in that package (and
>not in none of the others either). The biojava I am using is version
>1.22 downloaded from biojava.org. I did however discover a
>KnuthMorrisPrattSearch in a biojava API at
>http://rosetteer.icu.ac.kr/, however, I could not figure out how to
>get at the actual class....
>
>Am I missing something again?
>
>Karin
>

It seems the class you cant find, KnuthMorrisPrattSearch isnt included 
in the last
official release of Biojava. But its available in the CVS source tree.
So you will have to retrieve the biojava source from CVS, and compile 
biojava.
Instructions on how to retrieve the source code from cvs can be found at 
http://cvs.biojava.org/

In order to build biojava from source you will need to have Ant 
installed ( available
from http://jakarta.apache.org/ant/index.html ). And you build it by 
just going to the
top directory of the biojava source tree, and then run ant ( run "ant 
javadocs" to build
the javadoc documentation aswell )

Kalle



From matthew_pocock@yahoo.co.uk  Wed Jan  8 11:26:22 2003
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Wed, 8 Jan 2003 11:26:22 +0000 (GMT)
Subject: [Biojava-l] biojava cvs
In-Reply-To: <00c201c2b6da$6a1ff440$210aa8c0@sushibar.bii>
Message-ID: <20030108112622.36347.qmail@web14908.mail.yahoo.com>

Hiya,

biojava-live is the module that contains what
everybody thinks of as biojava. Everything else is
either exciting or arcane code (read, it may or may
work). bytecode contains a java bytecode generator
that looks like a macro-assembler and is used to build
new bytecode.jar files.

Matthew

 --- Xiao Juguang <juguang@fugu-sg.org> wrote: > Hi
guys,
> 
> I have dev.open-bio.org cvs account. But I am not
> sure which module I should checkout. Can you explain
> the following modules? thanks.
> 
> biodata/  
>  biojava-acedb/  
>  biojava-bsane/  
>  biojava-corba/  
>  biojava-ensembl/  
>  biojava-exptl/  
>  biojava-html/  
>  biojava-lims/  
>  biojava-live/  
>  bytecode/  
>  das-client/  
>  das-gui/  
>  dazzle/  
>  egads-axis/  
>  ensembl/  
>  ensembl-das/  
>  webservices/  
>  xdas/  
> 
> Juguang.
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

__________________________________________________
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From felipeflipp@yahoo.com.br  Wed Jan  8 18:57:01 2003
From: felipeflipp@yahoo.com.br (=?iso-8859-1?q?Felipe=20Faco?=)
Date: Wed, 8 Jan 2003 15:57:01 -0300 (ART)
Subject: [Biojava-l] (no subject)
Message-ID: <20030108185701.77386.qmail@web40505.mail.yahoo.com>

 
 

_______________________________________________________________________
Busca Yahoo!
O melhor lugar para encontrar tudo o que você procura na Internet
http://br.busca.yahoo.com/

From zren@amylin.com  Wed Jan  8 21:39:55 2003
From: zren@amylin.com (Ren, Zhen)
Date: Wed, 8 Jan 2003 13:39:55 -0800
Subject: [Biojava-l] get all symbols in an alphabet
Message-ID: <C527D913CB1168458AE19E0FECDE58DE8E9D2C@api-exch-1.amylin.com>

Hi, gang,

How do I get all symbols in an alphabet?  The Alphabet interface has a method:

Symbol getSymbol(java.util.List rl);

Can someone help me understand what symbol it really returns, a random one, the first one or what?  How do I use this?

Thanks so much.

Zhen


From russell_smithies@hotmail.com  Wed Jan  8 22:24:33 2003
From: russell_smithies@hotmail.com (Russell Smithies)
Date: Wed, 08 Jan 2003 22:24:33 +0000
Subject: [Biojava-l] anonymous cvs down?
Message-ID: <F37nzNwRC6HixqDCZx400021350@hotmail.com>

It looks like the anonymous cvs server may be down  :-(
It doesn't work using the commands from the webpage:
cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login

Can someone please try it or see what the problem is?

It seems to timeout after asking for and receiving the password (cvs).
The server seems to be running OK (it can be pinged OK) but won't login.

thanx
Russell






_________________________________________________________________
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From mark.schreiber@agresearch.co.nz  Wed Jan  8 22:26:13 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Thu, 9 Jan 2003 11:26:13 +1300
Subject: [Biojava-l] get all symbols in an alphabet
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E7CB2@inbox.agresearch.co.nz>

Hi -

If the Alphabet is a FiniteAlphabet you can get an iterator over the
Alphabet or you can use AlphabetManager to generate an AlphabetIndex
which can be used to access each Symbol.

The getSymbol method you describe generates an ambiguity symbol that
uniquely describes the set of Symbols in the list.

- Mark


> -----Original Message-----
> From: Ren, Zhen [mailto:zren@amylin.com] 
> Sent: Thursday, 9 January 2003 10:40 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] get all symbols in an alphabet
> 
> 
> Hi, gang,
> 
> How do I get all symbols in an alphabet?  The Alphabet 
> interface has a method:
> 
> Symbol getSymbol(java.util.List rl);
> 
> Can someone help me understand what symbol it really returns, 
> a random one, the first one or what?  How do I use this?
> 
> Thanks so much.
> 
> Zhen
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From jason@cgt.mc.duke.edu  Wed Jan  8 23:11:14 2003
From: jason@cgt.mc.duke.edu (Jason Stajich)
Date: Wed, 8 Jan 2003 18:11:14 -0500 (EST)
Subject: [Biojava-l] anonymous cvs down?
In-Reply-To: <F37nzNwRC6HixqDCZx400021350@hotmail.com>
References: <F37nzNwRC6HixqDCZx400021350@hotmail.com>
Message-ID: <Pine.LNX.4.50.0301081809450.994-100000@tenero.genetics.duke.edu>

Works for me testing right now - you might check your firewall settings?
Has it worked in the past?

In the future send system problems to root-l@open-bio.org please.

-jason

On Wed, 8 Jan 2003, Russell Smithies wrote:

> It looks like the anonymous cvs server may be down  :-(
> It doesn't work using the commands from the webpage:
> cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login
>
> Can someone please try it or see what the problem is?
>
> It seems to timeout after asking for and receiving the password (cvs).
> The server seems to be running OK (it can be pinged OK) but won't login.
>
> thanx
> Russell
>
>
>
>
>
>
> _________________________________________________________________
> MSN 8: advanced junk mail protection and 2 months FREE*.
> http://join.msn.com/?page=features/junkmail
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

From td2@sanger.ac.uk  Wed Jan  8 23:37:19 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 8 Jan 2003 23:37:19 +0000
Subject: [Biojava-l] get all symbols in an alphabet
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165012E7CB2@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE5165012E7CB2@inbox.agresearch.co.nz>
Message-ID: <20030108233719.GG370796@jabba.sanger.ac.uk>

On Thu, Jan 09, 2003 at 11:26:13AM +1300, Schreiber, Mark wrote:
> Hi -
> 
> If the Alphabet is a FiniteAlphabet you can get an iterator over the
> Alphabet or you can use AlphabetManager to generate an AlphabetIndex
> which can be used to access each Symbol.
> 
> The getSymbol method you describe generates an ambiguity symbol that
> uniquely describes the set of Symbols in the list.

No, you're thinking of getAmbiguity(Set symbols).

getSymbol is only really meaningful for alphabets which
represent the product of two or more other alphabets.  So
for the alphabet (DNA x DNA), it contains symbols like
(adenine thymine) and (guanine gaunine).  getSymbol(List) is
used to get hold of these composite symbols.

    Thomas.

From onlyclimb@163.com  Thu Jan  9 05:34:37 2003
From: onlyclimb@163.com (climb)
Date: Thu, 9 Jan 2003 13:34:37 +0800
Subject: [Biojava-l] (no subject)
Message-ID: <200301090533.h095XpSR009673@pw600a.bioperl.org>

Dear Biojava-l
  I tried to recompile biojava under 1.4.1 , but found many warnings. 
  Is is dangerous?
 
 
 


                                              
                     




From hirohash@genes.nig.ac.jp  Thu Jan  9 07:56:46 2003
From: hirohash@genes.nig.ac.jp (Hiroyuki Hashimoto)
Date: Thu, 9 Jan 2003 16:56:46 +0900
Subject: [Biojava-l] (no subject)
References: <200301090533.h095XpSR009673@pw600a.bioperl.org>
Message-ID: <010601c2b7b4$a867b3c0$98c92785@TSUNAMI.local>

What's kinds of warnings?
I guess "deprecation" warnings.
So, I think it may not be critical error.

Hiroyuki;

----- Original Message ----- 
From: "climb" <onlyclimb@163.com>
To: <Biojava-l@biojava.org>
Sent: Thursday, January 09, 2003 2:34 PM
Subject: [Biojava-l] (no subject)


> Dear Biojava-l
>   I tried to recompile biojava under 1.4.1 , but found many warnings. 
>   Is is dangerous?



From matthew_pocock@yahoo.co.uk  Thu Jan  9 09:56:37 2003
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Thu, 9 Jan 2003 09:56:37 +0000 (GMT)
Subject: [Biojava-l] (no subject)
In-Reply-To: <200301090533.h095XpSR009673@pw600a.bioperl.org>
Message-ID: <20030109095637.55056.qmail@web14914.mail.yahoo.com>

Hi,

If you only got warnings, everything should be OK.
What kind of warnings were they? What version of
biojava where you building (one of the releases, or
from CVS)? Did you build using ant? Did you get a new
biojava.jar at the end of it?

Java is never dangerous ;-)

Matthew

 --- climb <onlyclimb@163.com> wrote: > Dear Biojava-l
>   I tried to recompile biojava under 1.4.1 , but
> found many warnings. 
>   Is is dangerous?
>  
>  
>  
> 
> 
>                                               
>                      
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

__________________________________________________
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from News and Sport to Email and Music Charts
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From onlyclimb@163.com  Thu Jan  9 15:05:07 2003
From: onlyclimb@163.com (climb)
Date: Thu, 9 Jan 2003 23:5:7 +0800
Subject: [Biojava-l] (no subject)
Message-ID: <20030109150508.83DB61C40BEAC@sm204.163.com>

>What's kinds of warnings?            
>I guess "deprecation" warnings.
>So, I think it may not be critical error.
>
Yes. but i found 122 warnings. Why not do some thing to kill them in the release? :-)
            
             
                          Yours
                                 climb
                                 onlyclimb@163.com
                                 2003-01-09



          
             




From td2@sanger.ac.uk  Thu Jan  9 15:53:00 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 9 Jan 2003 15:53:00 +0000
Subject: [Biojava-l] (no subject)
In-Reply-To: <20030109150508.83DB61C40BEAC@sm204.163.com>
References: <20030109150508.83DB61C40BEAC@sm204.163.com>
Message-ID: <20030109155300.GI376419@jabba.sanger.ac.uk>

On Thu, Jan 09, 2003 at 11:05:07PM +0800, climb wrote:
> >What's kinds of warnings?            
> >I guess "deprecation" warnings.
> >So, I think it may not be critical error.
> >
> Yes. but i found 122 warnings. Why not do some thing to kill them in the release? :-)

Which version of BioJava are you using?

And what do these warnings say?  I've been doing all my work
on JDK1.4.1 for some time now.  By default, our ANT build script
does not display deprecation warnings, and I don't see any
warnings at compile time.  Turning them on, I see 11 deprecation
warnings, all relating to a class which uses SAX1 APIs, and doesn't
really make sense to update to SAX2 at this point (in fact, it
may be removed, but probably not this release).

In the past, there were a *lot* of warnings when building
javadocs using the 1.4.1 javadoc tool.  These have now all
been fixed in the CVS version (and therefore in the forthcoming
1.3 releases).

If you're seeing something other than these two types of warning,
then please let me know.

    Thomas.

From russell.smithies@xtra.co.nz  Thu Jan  9 19:16:52 2003
From: russell.smithies@xtra.co.nz (Russell Smithies)
Date: Fri, 10 Jan 2003 08:16:52 +1300
Subject: [Biojava-l] re: anonymous cvs down?
References: <20030109170008.14713.84901.Mailman@pw600a.bioperl.org>
Message-ID: <001401c2b813$aade25d0$0100a8c0@lexx>

Problem solved, it looks like our company may have the port may be blocked
:-)
It works fine from home but not at work.

and cvs works fine from JBuilder7

Russell



> Message: 2
> From: "Russell Smithies" <russell_smithies@hotmail.com>
> To: biojava-dev@biojava.org, biojava-l@biojava.org
> Date: Wed, 08 Jan 2003 22:24:33 +0000
> Subject: [Biojava-dev] anonymous cvs down?
>
> It looks like the anonymous cvs server may be down  :-(
> It doesn't work using the commands from the webpage:
> cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login
>
> Can someone please try it or see what the problem is?
>
> It seems to timeout after asking for and receiving the password (cvs).
> The server seems to be running OK (it can be pinged OK) but won't
> login.
>
> thanx
> Russell
>



From russell.smithies@xtra.co.nz  Thu Jan  9 19:17:51 2003
From: russell.smithies@xtra.co.nz (Russell Smithies)
Date: Fri, 10 Jan 2003 08:17:51 +1300
Subject: [Biojava-l] re: CVS down?
Message-ID: <002201c2b813$cde1c550$0100a8c0@lexx>

Problem solved, it looks like our company may have the port may be
blocked:-)
It works fine from home but not at work.

and cvs works fine from JBuilder7

Russell



> Message: 2
> From: "Russell Smithies" <russell_smithies@hotmail.com>
> To: biojava-dev@biojava.org, biojava-l@biojava.org
> Date: Wed, 08 Jan 2003 22:24:33 +0000
> Subject: [Biojava-dev] anonymous cvs down?
>
> It looks like the anonymous cvs server may be down  :-(
> It doesn't work using the commands from the webpage:
> cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login
>
> Can someone please try it or see what the problem is?
>
> It seems to timeout after asking for and receiving the password (cvs).
> The server seems to be running OK (it can be pinged OK) but won't
> login.
>
> thanx
> Russell


From zren@amylin.com  Thu Jan  9 19:52:01 2003
From: zren@amylin.com (Ren, Zhen)
Date: Thu, 9 Jan 2003 11:52:01 -0800
Subject: [Biojava-l] Sort symbols in an alphabet
Message-ID: <C527D913CB1168458AE19E0FECDE58DE0D3686@api-exch-1.amylin.com>

Hi,

Symbols in an alphabet is not sorted in any way.  How do I sort them, for instance, by name?  Thanks.

Zhen


From mark.schreiber@agresearch.co.nz  Thu Jan  9 20:39:05 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Fri, 10 Jan 2003 09:39:05 +1300
Subject: [Biojava-l] Sort symbols in an alphabet
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E7D73@inbox.agresearch.co.nz>

The following code should do it,

You could actually make the ComparableSymbol wrapper implement Symbol
and pass all the Symbol methods directly to the wrapped Symbol. I may
even submit a ComparableSymbol as a class to biojava-live if people
think they would use it.

- Mark


import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
import java.util.*;

public class SortAlphabetByName {
  public static void main(String[] args) {
    List l = new ArrayList();

    //add Symbols out of order
    l.add(new ComparableSymbol(DNATools.c()));
    l.add(new ComparableSymbol(DNATools.g()));
    l.add(new ComparableSymbol(DNATools.t()));
    l.add(new ComparableSymbol(DNATools.a()));

    //sort them
    Collections.sort(l);

    //print there names
    for (int i = 0; i < l.size(); i++) {
      ComparableSymbol cs = (ComparableSymbol)l.get(i);
      System.out.println(cs.getWrapped().getName());
    }

  }

  // a Mix in wrapper
  static class ComparableSymbol implements Comparable{
    private Symbol wrapped;

    public ComparableSymbol(Symbol wrapped){
      this.wrapped = wrapped;
    }

    public int compareTo(Object o){
      Symbol s = ((ComparableSymbol)o).getWrapped();

      return wrapped.getName().compareTo(s.getName());
    }

    public Symbol getWrapped(){
      return wrapped;
    }
  }
}
> -----Original Message-----
> From: Ren, Zhen [mailto:zren@amylin.com] 
> Sent: Friday, 10 January 2003 8:52 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Sort symbols in an alphabet
> 
> 
> Hi,
> 
> Symbols in an alphabet is not sorted in any way.  How do I 
> sort them, for instance, by name?  Thanks.
> 
> Zhen
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From zren@amylin.com  Thu Jan  9 22:10:49 2003
From: zren@amylin.com (Ren, Zhen)
Date: Thu, 9 Jan 2003 14:10:49 -0800
Subject: [Biojava-l] Sort symbols in an alphabet
Message-ID: <C527D913CB1168458AE19E0FECDE58DE0D3688@api-exch-1.amylin.com>

A copy of the symbol set in an alphabet is sorted.  What if I want to sort the original symbol set in an alphabet?  Thanks. -Zhen

-----Original Message-----
From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
Sent: Thursday, January 09, 2003 12:39 PM
To: Ren, Zhen; biojava-l@biojava.org
Subject: RE: [Biojava-l] Sort symbols in an alphabet


The following code should do it,

You could actually make the ComparableSymbol wrapper implement Symbol
and pass all the Symbol methods directly to the wrapped Symbol. I may
even submit a ComparableSymbol as a class to biojava-live if people
think they would use it.

- Mark


import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
import java.util.*;

public class SortAlphabetByName {
  public static void main(String[] args) {
    List l = new ArrayList();

    //add Symbols out of order
    l.add(new ComparableSymbol(DNATools.c()));
    l.add(new ComparableSymbol(DNATools.g()));
    l.add(new ComparableSymbol(DNATools.t()));
    l.add(new ComparableSymbol(DNATools.a()));

    //sort them
    Collections.sort(l);

    //print there names
    for (int i = 0; i < l.size(); i++) {
      ComparableSymbol cs = (ComparableSymbol)l.get(i);
      System.out.println(cs.getWrapped().getName());
    }

  }

  // a Mix in wrapper
  static class ComparableSymbol implements Comparable{
    private Symbol wrapped;

    public ComparableSymbol(Symbol wrapped){
      this.wrapped = wrapped;
    }

    public int compareTo(Object o){
      Symbol s = ((ComparableSymbol)o).getWrapped();

      return wrapped.getName().compareTo(s.getName());
    }

    public Symbol getWrapped(){
      return wrapped;
    }
  }
}
> -----Original Message-----
> From: Ren, Zhen [mailto:zren@amylin.com] 
> Sent: Friday, 10 January 2003 8:52 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Sort symbols in an alphabet
> 
> 
> Hi,
> 
> Symbols in an alphabet is not sorted in any way.  How do I 
> sort them, for instance, by name?  Thanks.
> 
> Zhen
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From mark.schreiber@agresearch.co.nz  Thu Jan  9 22:46:34 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Fri, 10 Jan 2003 11:46:34 +1300
Subject: [Biojava-l] Sort symbols in an alphabet
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E7DAE@inbox.agresearch.co.nz>

You may be able to reengineer the AlphabetIndexers so the index they
produce is based on the order of Symbols by name. Note that a Set is
never really sorted only its pointers are.

You could also make a wrapper wraps a FiniteAlphabet, implements
FiniteAlphabet, delegates all its methods to the wrapped Alphabet but
overides the iterator() method of FiniteAlphabet so that they are
returned in some desirable order. This is not really ideal as you loose
the canonical status of the Alphabet.

I'm not sure why you would want to have the actual Alphabet sorted?

> -----Original Message-----
> From: Ren, Zhen [mailto:zren@amylin.com] 
> Sent: Friday, 10 January 2003 11:11 a.m.
> To: Schreiber, Mark; biojava-l@biojava.org
> Subject: RE: [Biojava-l] Sort symbols in an alphabet
> 
> 
> A copy of the symbol set in an alphabet is sorted.  What if I 
> want to sort the original symbol set in an alphabet?  Thanks. -Zhen
> 
> -----Original Message-----
> From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> Sent: Thursday, January 09, 2003 12:39 PM
> To: Ren, Zhen; biojava-l@biojava.org
> Subject: RE: [Biojava-l] Sort symbols in an alphabet
> 
> 
> The following code should do it,
> 
> You could actually make the ComparableSymbol wrapper 
> implement Symbol and pass all the Symbol methods directly to 
> the wrapped Symbol. I may even submit a ComparableSymbol as a 
> class to biojava-live if people think they would use it.
> 
> - Mark
> 
> 
> import org.biojava.bio.seq.*;
> import org.biojava.bio.symbol.*;
> import java.util.*;
> 
> public class SortAlphabetByName {
>   public static void main(String[] args) {
>     List l = new ArrayList();
> 
>     //add Symbols out of order
>     l.add(new ComparableSymbol(DNATools.c()));
>     l.add(new ComparableSymbol(DNATools.g()));
>     l.add(new ComparableSymbol(DNATools.t()));
>     l.add(new ComparableSymbol(DNATools.a()));
> 
>     //sort them
>     Collections.sort(l);
> 
>     //print there names
>     for (int i = 0; i < l.size(); i++) {
>       ComparableSymbol cs = (ComparableSymbol)l.get(i);
>       System.out.println(cs.getWrapped().getName());
>     }
> 
>   }
> 
>   // a Mix in wrapper
>   static class ComparableSymbol implements Comparable{
>     private Symbol wrapped;
> 
>     public ComparableSymbol(Symbol wrapped){
>       this.wrapped = wrapped;
>     }
> 
>     public int compareTo(Object o){
>       Symbol s = ((ComparableSymbol)o).getWrapped();
> 
>       return wrapped.getName().compareTo(s.getName());
>     }
> 
>     public Symbol getWrapped(){
>       return wrapped;
>     }
>   }
> }
> > -----Original Message-----
> > From: Ren, Zhen [mailto:zren@amylin.com]
> > Sent: Friday, 10 January 2003 8:52 a.m.
> > To: biojava-l@biojava.org
> > Subject: [Biojava-l] Sort symbols in an alphabet
> > 
> > 
> > Hi,
> > 
> > Symbols in an alphabet is not sorted in any way.  How do I
> > sort them, for instance, by name?  Thanks.
> > 
> > Zhen
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> ==============================================================
> =========
> Attention: The information contained in this message and/or 
> attachments from AgResearch Limited is intended only for the 
> persons or entities to which it is addressed and may contain 
> confidential and/or privileged material. Any review, 
> retransmission, dissemination or other use of, or taking of 
> any action in reliance upon, this information by persons or 
> entities other than the intended recipients is prohibited by 
> AgResearch Limited. If you have received this message in 
> error, please notify the sender immediately. 
> ==============================================================
> =========
> 
=======================================================================
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 zren@amylin.com  Thu Jan  9 23:12:49 2003
From: zren@amylin.com (Ren, Zhen)
Date: Thu, 9 Jan 2003 15:12:49 -0800
Subject: [Biojava-l] Sort symbols in an alphabet
Message-ID: <C527D913CB1168458AE19E0FECDE58DE0D368A@api-exch-1.amylin.com>

I am using DP and HMM.  A distribution is an encapsulation of a probability distribution over the Symbols within an alphabet.  Set up emission probabilities like this in a HMM object:

for(int i = 0; i < symbols.length; i++)
    dist.setWeight(symbols[i], frequency[i]);

Later, a DP object is created using the HMM with the above emission probabilities:

DP dp=DPFactory.DEFAULT.createDP(myHMM);
SymbolList sequence = ProteinTools.createProtein("AGFAVENDSAQWP")
SymbolList[] array = { sequence };
double score = dp.forward(array, ScoreType.PROBABILITY);
System.out.println("score = " + score);

I expect some kind of score would be printed.  But, nothing.  Not even the string "score = ".  It seems the line is not executed.  I thought maybe the emission probability is not there at all because those probabilities may have been assigned to a copy of the original symbols.

Most likely, my understanding is completely wrong.  I just keep trying various things.  Any more tutorials on HMM and DP other than the Dice example?  It's painful to learn APIs.  Thanks.

Zhen

-----Original Message-----
From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
Sent: Thursday, January 09, 2003 2:47 PM
To: Ren, Zhen; biojava-l@biojava.org
Subject: RE: [Biojava-l] Sort symbols in an alphabet


You may be able to reengineer the AlphabetIndexers so the index they
produce is based on the order of Symbols by name. Note that a Set is
never really sorted only its pointers are.

You could also make a wrapper wraps a FiniteAlphabet, implements
FiniteAlphabet, delegates all its methods to the wrapped Alphabet but
overides the iterator() method of FiniteAlphabet so that they are
returned in some desirable order. This is not really ideal as you loose
the canonical status of the Alphabet.

I'm not sure why you would want to have the actual Alphabet sorted?

> -----Original Message-----
> From: Ren, Zhen [mailto:zren@amylin.com] 
> Sent: Friday, 10 January 2003 11:11 a.m.
> To: Schreiber, Mark; biojava-l@biojava.org
> Subject: RE: [Biojava-l] Sort symbols in an alphabet
> 
> 
> A copy of the symbol set in an alphabet is sorted.  What if I 
> want to sort the original symbol set in an alphabet?  Thanks. -Zhen
> 
> -----Original Message-----
> From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> Sent: Thursday, January 09, 2003 12:39 PM
> To: Ren, Zhen; biojava-l@biojava.org
> Subject: RE: [Biojava-l] Sort symbols in an alphabet
> 
> 
> The following code should do it,
> 
> You could actually make the ComparableSymbol wrapper 
> implement Symbol and pass all the Symbol methods directly to 
> the wrapped Symbol. I may even submit a ComparableSymbol as a 
> class to biojava-live if people think they would use it.
> 
> - Mark
> 
> 
> import org.biojava.bio.seq.*;
> import org.biojava.bio.symbol.*;
> import java.util.*;
> 
> public class SortAlphabetByName {
>   public static void main(String[] args) {
>     List l = new ArrayList();
> 
>     //add Symbols out of order
>     l.add(new ComparableSymbol(DNATools.c()));
>     l.add(new ComparableSymbol(DNATools.g()));
>     l.add(new ComparableSymbol(DNATools.t()));
>     l.add(new ComparableSymbol(DNATools.a()));
> 
>     //sort them
>     Collections.sort(l);
> 
>     //print there names
>     for (int i = 0; i < l.size(); i++) {
>       ComparableSymbol cs = (ComparableSymbol)l.get(i);
>       System.out.println(cs.getWrapped().getName());
>     }
> 
>   }
> 
>   // a Mix in wrapper
>   static class ComparableSymbol implements Comparable{
>     private Symbol wrapped;
> 
>     public ComparableSymbol(Symbol wrapped){
>       this.wrapped = wrapped;
>     }
> 
>     public int compareTo(Object o){
>       Symbol s = ((ComparableSymbol)o).getWrapped();
> 
>       return wrapped.getName().compareTo(s.getName());
>     }
> 
>     public Symbol getWrapped(){
>       return wrapped;
>     }
>   }
> }
> > -----Original Message-----
> > From: Ren, Zhen [mailto:zren@amylin.com]
> > Sent: Friday, 10 January 2003 8:52 a.m.
> > To: biojava-l@biojava.org
> > Subject: [Biojava-l] Sort symbols in an alphabet
> > 
> > 
> > Hi,
> > 
> > Symbols in an alphabet is not sorted in any way.  How do I
> > sort them, for instance, by name?  Thanks.
> > 
> > Zhen
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> ==============================================================
> =========
> Attention: The information contained in this message and/or 
> attachments from AgResearch Limited is intended only for the 
> persons or entities to which it is addressed and may contain 
> confidential and/or privileged material. Any review, 
> retransmission, dissemination or other use of, or taking of 
> any action in reliance upon, this information by persons or 
> entities other than the intended recipients is prohibited by 
> AgResearch Limited. If you have received this message in 
> error, please notify the sender immediately. 
> ==============================================================
> =========
> 
=======================================================================
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From mark.schreiber@agresearch.co.nz  Fri Jan 10 03:52:54 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Fri, 10 Jan 2003 16:52:54 +1300
Subject: [Biojava-l] Back translation
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E7E19@inbox.agresearch.co.nz>

Hi -

There was some talk a while back about adding some methods to allow the
protein alphabet to be reverse translated to a codon alphabet using one
of the translation tables.

Did anything come of this? Is the solution obvious and I'm just blind??

- Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
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to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
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From onlyclimb@163.com  Fri Jan 10 11:01:00 2003
From: onlyclimb@163.com (climb)
Date: Fri, 10 Jan 2003 19:1:0 +0800
Subject: [Biojava-l] (no subject)
Message-ID: <20030110110100.684F51CD34E30@sm212.163.com>

I am new to biojava.
How can i translate a dna with IUB character.
for example  in standard genetic code map ,
CUU CUC CUA CUG   all refers to L
so i want CUN refers to L
how can i achieve this under Symbl/Alphabit  system. 
 
 

Best regards
            
              Yours
                         climb
                         onlyclimb@163.com
                         2003-01-10

 

                                              
                     




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From: Web@yahoo.com (Web@yahoo.com)
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Subject: [Biojava-l] Happy new year!
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From td2@sanger.ac.uk  Fri Jan 10 11:58:42 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Fri, 10 Jan 2003 11:58:42 +0000
Subject: [Biojava-l] Sort symbols in an alphabet
In-Reply-To: <C527D913CB1168458AE19E0FECDE58DE0D3686@api-exch-1.amylin.com>
References: <C527D913CB1168458AE19E0FECDE58DE0D3686@api-exch-1.amylin.com>
Message-ID: <20030110115842.GC383292@jabba.sanger.ac.uk>

On Thu, Jan 09, 2003 at 11:52:01AM -0800, Ren, Zhen wrote:
> Hi,
> 
> Symbols in an alphabet is not sorted in any way. 
> How do I sort them, for instance, by name?  Thanks.

Alphabets are, by design, pretty straigforward sets of symbol
objects.  If you want to print them out in some specific order,
how about:

   FiniteAlphabet fa = ...
   List faSymbols = new ArrayList();
   for (Iterator i = fa.iterator(); i.hasNext(); ) {
       faSymbols.add(i.next());
   }
   Collections.sort(
       faSymbols,
       new Comparator() {
           public int compare(Object o1, Object o2) {
               Symbol s1 = (Symbol) o1;
               Symbol s2 = (Symbol) o2;
               return s1.getName().compareTo(s2.getName());
           }
       }
   );


Thomas.

From zren@amylin.com  Fri Jan 10 15:54:16 2003
From: zren@amylin.com (Ren, Zhen)
Date: Fri, 10 Jan 2003 07:54:16 -0800
Subject: [Biojava-l] DP forward algorithm
Message-ID: <C527D913CB1168458AE19E0FECDE58DE0D368B@api-exch-1.amylin.com>

Hi, there,

The three main DP operations are Forwards, Backwards and Viterbi. Forwards and Backwards calculate the probability of the sequences having been made in any way by the model. Viterbi finds the most supported way that the sequence could have been made.

I have seen the Dice example that demonstrates how to use Viterbi algorithm.  And I guess it would be the similar way to use Forward algorithm.  However, it's not like what I thought.  Can someone give me a direction how to use the Forward algorithm in DP class?  Is any tutorial regarding DP and HMM available?  More documentations about DP and HMM classes in BioJava other than Javadocs are also very helpful.

Thank you.

Zhen


From MCCon012@mc.duke.edu  Fri Jan 10 21:11:38 2003
From: MCCon012@mc.duke.edu (Patrick McConnell)
Date: Fri, 10 Jan 2003 16:11:38 -0500
Subject: [Biojava-l] library for running blast and formatdb
Message-ID: <OF56AD66CD.D144F87D-ON85256CAA.0073AA15-85256CAA.00749AD9@notes.duke.edu>

In the past, there have been quite a few requests on how to run blast from
a Java program.  I have developed some classes for running NCBI blastall
and formatdb.  All of the parameters for the respective programs are
implemented, and everything is reasonably well documented.  Also useful is
an option to run blast without input and output files, utilizing standard
input and output.

In the process, I developed some useful and flexible base classes for
formatting parameters and running programs.  Parameters are automatically
converted to an argument array via reflection and reading of standard out
and standard error in separate threads is handled automatically.

Check it out if you are interested:
http://www.dbsr.duke.edu/software/blast/default.htm .  The full source,
javadocs, and binary class files are available.  Also, if this seems
appropriate for BioJava, I have no problem donating it to the cause.  I
think that at least the base classes, or some modification of them, would
be useful to others.

Please email me with suggestions/comments,

-Patrick McConnell
Duke Bioinformatics Shared Resource
mccon012@mc.duke.edu



From Wiepert.Mathieu@mayo.edu  Fri Jan 10 21:37:27 2003
From: Wiepert.Mathieu@mayo.edu (Wiepert, Mathieu)
Date: Fri, 10 Jan 2003 15:37:27 -0600
Subject: [Biojava-l] library for running blast and formatdb
Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C1D7@excsrv32.mayo.edu>

I would love to see this placed in the biojava core...  Might switch me back from bioperl ;-)

-Mat


> -----Original Message-----
> From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> Sent: Friday, January 10, 2003 3:12 PM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] library for running blast and formatdb
> 
> 
> 
> In the past, there have been quite a few requests on how to 
> run blast from
> a Java program.  I have developed some classes for running 
> NCBI blastall
> and formatdb.  All of the parameters for the respective programs are
> implemented, and everything is reasonably well documented.  
> Also useful is
> an option to run blast without input and output files, 
> utilizing standard
> input and output.
> 
> In the process, I developed some useful and flexible base classes for
> formatting parameters and running programs.  Parameters are 
> automatically
> converted to an argument array via reflection and reading of 
> standard out
> and standard error in separate threads is handled automatically.
> 
> Check it out if you are interested:
> http://www.dbsr.duke.edu/software/blast/default.htm .  The 
> full source,
> javadocs, and binary class files are available.  Also, if this seems
> appropriate for BioJava, I have no problem donating it to the 
> cause.  I
> think that at least the base classes, or some modification of 
> them, would
> be useful to others.
> 
> Please email me with suggestions/comments,
> 
> -Patrick McConnell
> Duke Bioinformatics Shared Resource
> mccon012@mc.duke.edu
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 

From heuermh@acm.org  Fri Jan 10 22:18:52 2003
From: heuermh@acm.org (Michael L. Heuer)
Date: Fri, 10 Jan 2003 17:18:52 -0500 (EST)
Subject: [Biojava-l] library for running blast and formatdb
In-Reply-To: <OF56AD66CD.D144F87D-ON85256CAA.0073AA15-85256CAA.00749AD9@notes.duke.edu>
Message-ID: <Pine.GSO.4.44.0301101658590.18655-100000@shell3.shore.net>

On Fri, 10 Jan 2003, Patrick McConnell wrote:

> In the process, I developed some useful and flexible base classes for
> formatting parameters and running programs.  Parameters are automatically
> converted to an argument array via reflection and reading of standard out
> and standard error in separate threads is handled automatically.

The base classes are nice, but I prefer the design of

> http://jakarta.apache.org/commons/cli

a lot better for handling parameters.

I suppose it's a matter of another external dependency vs. reinvented
utility code in biojava . . .  Would it make sense to merge the better
qualities of the two?

I also have a few simple classes for oneoff scripts with command line &
logging facade support that I use all the time, see

> http://www.shore.net/~heuermh/oneoff.tar.gz

but they don't have any extra support for external programs.

   michael

>
> Check it out if you are interested:
> http://www.dbsr.duke.edu/software/blast/default.htm .  The full source,
> javadocs, and binary class files are available.  Also, if this seems
> appropriate for BioJava, I have no problem donating it to the cause.  I
> think that at least the base classes, or some modification of them, would
> be useful to others.
>
> Please email me with suggestions/comments,
>
> -Patrick McConnell
> Duke Bioinformatics Shared Resource
> mccon012@mc.duke.edu
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>



From onlyclimb@163.com  Sat Jan 11 05:46:56 2003
From: onlyclimb@163.com (climb)
Date: Sat, 11 Jan 2003 13:46:56 +0800
Subject: [Biojava-l] (no subject)
Message-ID: <200301110546.h0B5kASR032074@pw600a.bioperl.org>

>RNATools has methods to translate DNA. Take a look at http://bioconf.otago.ac.nz/biojava/. I have put a number of example >scripts here that do what you want.
> 
Thanks very much
But i am confused why not make 
RNATools.translate(SymbolList syms) 
into 
RNATools.translate(SymbolList sysms, TranslationTable table)

i think most program deal with translation will consider the ability to change translationtable, and the RNATools class as far as i know is for convenient usage, so if no ability to change table, the situation of  RNATools.translate(  SymbolList syms) is awkward, maybe it can only used for demos.

             
                          Yours
                                 climb
                                 onlyclimb@163.com

                                 2003-01-11
newbie





          
             




From simon.brocklehurst@cambridgeantibody.com  Sat Jan 11 12:34:29 2003
From: simon.brocklehurst@cambridgeantibody.com (Simon Brocklehurst)
Date: Sat, 11 Jan 2003 12:34:29 +0000
Subject: [Biojava-l] Anybody works with pdb and XML?
References: <1041938895.15107@mail.infomail.es>
Message-ID: <3E200F55.9070901@cambridgeantibody.com>


jon portuondo murguiondo wrote:
> Hello! I am trying to convert pdb to XML. If you can help me I would be very pleased.

Hi Jon,

If you are still having difficulties, please feel free to e-mail me or 
the biojava list with a description of what precisely you are trying to 
do.  I'll see if we can help.

Simon
-- 
Dr Simon M. Brocklehurst, Ph.D.
Director of Informatics & Robotics

Cambridge Antibody Technology
Milstein Building
Granta Park
Cambridge
CB1 6GH
UK

Telephone: + 44 (0) 1763 263233
Facsimile + 44 (0) 1763 263413
Email: mailto:simon.brocklehurst@cambridgeantibody.com
http://www.cambridgeantibody.com

Cambridge Antibody Technology Limited *
Registered Office: The Science Park, Melbourn, Cambridgeshire,
SG8 6JJ, UK. Registered in England and Wales number 2451177
(* Cambridge Antibody Technology Limited is a member of the
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If you are not the intended recipient please inform the sender
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From leesuyee@yahoo.com  Sun Jan 12 12:01:16 2003
From: leesuyee@yahoo.com (suyee)
Date: Sun, 12 Jan 2003 04:01:16 -0800 (PST)
Subject: [Biojava-l] clustalw-C to Java
Message-ID: <20030112120116.21761.qmail@web14202.mail.yahoo.com>

can anybody teach me how to convert this (in C) into Java.
this is taken from ClustalW1.8.1

typedef struct node {		/* phylogenetic tree structure */
        struct node *left;
        struct node *right;
        struct node *parent;
        float dist;
        sint  leaf;
        int order;
        char name[64];
} stree, *treeptr;

thanks

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From russell_smithies@hotmail.com  Sun Jan 12 20:27:37 2003
From: russell_smithies@hotmail.com (Russell Smithies)
Date: Sun, 12 Jan 2003 20:27:37 +0000
Subject: [Biojava-l] RE: clustalw-C to Java
Message-ID: <F145YwstFDvz4uqqtBq0000fd8c@hotmail.com>

I guess lots of people will answer this so I hope I get it right :-)
This isn't the exact answer but I hope it helps.

structs in C can be thought of class objects in Java (done the hard way)
so your tree node becomes:

class Stree implements Comparable{
   Stree left = null;
   Stree right = null;
   Stree parent = null;
   float dist;
   short leaf;
   int order;
   char[] name;
}

//then a few constructors as required

Stree(){
}

Stree(Stree l, Stree r, Stree p, float d, short l, int o, char[] n){
   left = l;
   right = r;
   parent = p;
   dist = d;
   leaf = l;
   order = o;
   name = n; // might need to clone it??
}

//and accessors and modifiers (getters and setters) as required

Stree getLeft(Stree st){
   return st.left;
}

float setDist(float d){
   dist = d;
}

//and implement Comparable somehow
public int compareTo( Object o ){
    int retVal;
    Stree n = (Stree) o;

   retVal = dist - n.dist;
    // something like this???
    if ( retVal == 0 )
        if ( this == n )
            retVal = 0;
        else
            retVal = -1;
    return retVal;
}




>Message: 1
>Date: Sun, 12 Jan 2003 04:01:16 -0800 (PST)
>From: suyee <leesuyee@yahoo.com>
>To: biojava <biojava-l@biojava.org>
>Subject: [Biojava-l] clustalw-C to Java
>
>can anybody teach me how to convert this (in C) into Java.
>this is taken from ClustalW1.8.1
>
>typedef struct node { /* phylogenetic tree structure */
>         struct node *left;
>         struct node *right;
>         struct node *parent;
>         float dist;
>         sint  leaf;
>         int order;
>         char name[64];
>} stree, *treeptr;
>
>thanks
>


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From francois.pepin@mail.mcgill.ca  Sun Jan 12 21:24:39 2003
From: francois.pepin@mail.mcgill.ca (Francois Pepin)
Date: Sun, 12 Jan 2003 16:24:39 -0500
Subject: [Biojava-l] RE: clustalw-C to Java
In-Reply-To: <F145YwstFDvz4uqqtBq0000fd8c@hotmail.com>
Message-ID: <000801c2ba81$04057810$e0abfea9@hermes>

I'd suggest a slight modification:

use String instead of char[].

It's the usual way to handle strings and you don't have to worry about
references and making a copy of the array, because Strings are immutable
(they never change so no need to make another copy).

François

-----Original Message-----
From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]
On Behalf Of Russell Smithies
Sent: 12 janvier, 2003 15:28
To: biojava-l@biojava.org
Subject: [Biojava-l] RE: clustalw-C to Java


I guess lots of people will answer this so I hope I get it right :-)
This isn't the exact answer but I hope it helps.

structs in C can be thought of class objects in Java (done the hard way)
so your tree node becomes:

class Stree implements Comparable{
   Stree left = null;
   Stree right = null;
   Stree parent = null;
   float dist;
   short leaf;
   int order;
   char[] name;
}

//then a few constructors as required

Stree(){
}

Stree(Stree l, Stree r, Stree p, float d, short l, int o, char[] n){
   left = l;
   right = r;
   parent = p;
   dist = d;
   leaf = l;
   order = o;
   name = n; // might need to clone it??
}

//and accessors and modifiers (getters and setters) as required

Stree getLeft(Stree st){
   return st.left;
}

float setDist(float d){
   dist = d;
}

//and implement Comparable somehow
public int compareTo( Object o ){
    int retVal;
    Stree n = (Stree) o;

   retVal = dist - n.dist;
    // something like this???
    if ( retVal == 0 )
        if ( this == n )
            retVal = 0;
        else
            retVal = -1;
    return retVal;
}




>Message: 1
>Date: Sun, 12 Jan 2003 04:01:16 -0800 (PST)
>From: suyee <leesuyee@yahoo.com>
>To: biojava <biojava-l@biojava.org>
>Subject: [Biojava-l] clustalw-C to Java
>
>can anybody teach me how to convert this (in C) into Java. this is 
>taken from ClustalW1.8.1
>
>typedef struct node { /* phylogenetic tree structure */
>         struct node *left;
>         struct node *right;
>         struct node *parent;
>         float dist;
>         sint  leaf;
>         int order;
>         char name[64];
>} stree, *treeptr;
>
>thanks
>


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From francois.pepin@mail.mcgill.ca  Sun Jan 12 21:25:06 2003
From: francois.pepin@mail.mcgill.ca (Francois Pepin)
Date: Sun, 12 Jan 2003 16:25:06 -0500
Subject: [Biojava-l] RE: clustalw-C to Java
In-Reply-To: <F145YwstFDvz4uqqtBq0000fd8c@hotmail.com>
Message-ID: <000901c2ba81$175af660$e0abfea9@hermes>

I'd suggest a slight modification:

use String instead of char[].

It's the usual way to handle strings and you don't have to worry about
references and making a copy of the array, because Strings are immutable
(they never change so no need to make another copy).

François

-----Original Message-----
From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]
On Behalf Of Russell Smithies
Sent: 12 janvier, 2003 15:28
To: biojava-l@biojava.org
Subject: [Biojava-l] RE: clustalw-C to Java


I guess lots of people will answer this so I hope I get it right :-)
This isn't the exact answer but I hope it helps.

structs in C can be thought of class objects in Java (done the hard way)
so your tree node becomes:

class Stree implements Comparable{
   Stree left = null;
   Stree right = null;
   Stree parent = null;
   float dist;
   short leaf;
   int order;
   char[] name;
}

//then a few constructors as required

Stree(){
}

Stree(Stree l, Stree r, Stree p, float d, short l, int o, char[] n){
   left = l;
   right = r;
   parent = p;
   dist = d;
   leaf = l;
   order = o;
   name = n; // might need to clone it??
}

//and accessors and modifiers (getters and setters) as required

Stree getLeft(Stree st){
   return st.left;
}

float setDist(float d){
   dist = d;
}

//and implement Comparable somehow
public int compareTo( Object o ){
    int retVal;
    Stree n = (Stree) o;

   retVal = dist - n.dist;
    // something like this???
    if ( retVal == 0 )
        if ( this == n )
            retVal = 0;
        else
            retVal = -1;
    return retVal;
}




>Message: 1
>Date: Sun, 12 Jan 2003 04:01:16 -0800 (PST)
>From: suyee <leesuyee@yahoo.com>
>To: biojava <biojava-l@biojava.org>
>Subject: [Biojava-l] clustalw-C to Java
>
>can anybody teach me how to convert this (in C) into Java. this is 
>taken from ClustalW1.8.1
>
>typedef struct node { /* phylogenetic tree structure */
>         struct node *left;
>         struct node *right;
>         struct node *parent;
>         float dist;
>         sint  leaf;
>         int order;
>         char name[64];
>} stree, *treeptr;
>
>thanks
>


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From matthew_pocock@yahoo.co.uk  Mon Jan 13 11:16:57 2003
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Mon, 13 Jan 2003 11:16:57 +0000 (GMT)
Subject: [Biojava-l] DP forward algorithm
In-Reply-To: <C527D913CB1168458AE19E0FECDE58DE0D368B@api-exch-1.amylin.com>
Message-ID: <20030113111657.79725.qmail@web14907.mail.yahoo.com>

Hi Zhen,

For both the forwards and backwards algorithms, you
can call them in the same way as viterbi. This will
just give you back the score. You can also call them
with an explicit dynamic programming matrix. In this
case, you get the matrix back with all the values
filled in. Both Forward and Backward give you the
probability that the sequence was generated in some
way (any way) by the model. If you look in the
matricies for forwards & backwards, the cells give the
probability that the model made all of the sequence up
to and including that position (and ending in that
state). For the forwards algorithm the probabilities
are for all the sequence from the beginning to there,
and for backwards it's all the sequence from the end
back to there.

Matthew

 --- "Ren, Zhen" <zren@amylin.com> wrote: 
> Hi, there,
> 
> The three main DP operations are Forwards, Backwards
> and Viterbi. Forwards and Backwards calculate the
> probability of the sequences having been made in any
> way by the model. Viterbi finds the most supported
> way that the sequence could have been made.
> 
> I have seen the Dice example that demonstrates how
> to use Viterbi algorithm.  And I guess it would be
> the similar way to use Forward algorithm.  However,
> it's not like what I thought.  Can someone give me a
> direction how to use the Forward algorithm in DP
> class?  Is any tutorial regarding DP and HMM
> available?  More documentations about DP and HMM
> classes in BioJava other than Javadocs are also very
> helpful.
> 
> Thank you.
> 
> Zhen
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

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From matthew_pocock@yahoo.co.uk  Mon Jan 13 12:00:01 2003
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Mon, 13 Jan 2003 12:00:01 +0000 (GMT)
Subject: [Biojava-l] RE: clustalw-C to Java
In-Reply-To: <000901c2ba81$175af660$e0abfea9@hermes>
Message-ID: <20030113120001.63983.qmail@web14902.mail.yahoo.com>

Also, if you make all the fields public, you can use
it like a struct rather than a bean:

public class Stree {
    public Stree left = null;
    public Stree right = null;
    public Stree parent = null;
    public float dist;
    public short leaf;
    public int order;
    public String name;
}

Now you can say:

Stree tree = ...;
tree.dist = 30.3;
tree.name = "George";

double d = tree.dist;

Matthew


 --- Francois Pepin <francois.pepin@mail.mcgill.ca>
wrote: > I'd suggest a slight modification:
> 
> use String instead of char[].
> 
> It's the usual way to handle strings and you don't
> have to worry about
> references and making a copy of the array, because
> Strings are immutable
> (they never change so no need to make another copy).
> 
> François
> 
> -----Original Message-----
> From: biojava-l-admin@biojava.org
> [mailto:biojava-l-admin@biojava.org]
> On Behalf Of Russell Smithies
> Sent: 12 janvier, 2003 15:28
> To: biojava-l@biojava.org
> Subject: [Biojava-l] RE: clustalw-C to Java
> 
> 
> I guess lots of people will answer this so I hope I
> get it right :-)
> This isn't the exact answer but I hope it helps.
> 
> structs in C can be thought of class objects in Java
> (done the hard way)
> so your tree node becomes:
> 
> class Stree implements Comparable{
>    Stree left = null;
>    Stree right = null;
>    Stree parent = null;
>    float dist;
>    short leaf;
>    int order;
>    char[] name;
> }
> 
> //then a few constructors as required
> 
> Stree(){
> }
> 
> Stree(Stree l, Stree r, Stree p, float d, short l,
> int o, char[] n){
>    left = l;
>    right = r;
>    parent = p;
>    dist = d;
>    leaf = l;
>    order = o;
>    name = n; // might need to clone it??
> }
> 
> //and accessors and modifiers (getters and setters)
> as required
> 
> Stree getLeft(Stree st){
>    return st.left;
> }
> 
> float setDist(float d){
>    dist = d;
> }
> 
> //and implement Comparable somehow
> public int compareTo( Object o ){
>     int retVal;
>     Stree n = (Stree) o;
> 
>    retVal = dist - n.dist;
>     // something like this???
>     if ( retVal == 0 )
>         if ( this == n )
>             retVal = 0;
>         else
>             retVal = -1;
>     return retVal;
> }
> 
> 
> 
> 
> >Message: 1
> >Date: Sun, 12 Jan 2003 04:01:16 -0800 (PST)
> >From: suyee <leesuyee@yahoo.com>
> >To: biojava <biojava-l@biojava.org>
> >Subject: [Biojava-l] clustalw-C to Java
> >
> >can anybody teach me how to convert this (in C)
> into Java. this is 
> >taken from ClustalW1.8.1
> >
> >typedef struct node { /* phylogenetic tree
> structure */
> >         struct node *left;
> >         struct node *right;
> >         struct node *parent;
> >         float dist;
> >         sint  leaf;
> >         int order;
> >         char name[64];
> >} stree, *treeptr;
> >
> >thanks
> >
> 
> 
>
_________________________________________________________________
> The new MSN 8 is here: Try it free* for 2 months 
> http://join.msn.com/?page=dept/dialup
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

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From ecerami@yahoo.com  Mon Jan 13 12:52:14 2003
From: ecerami@yahoo.com (Ethan Cerami)
Date: Mon, 13 Jan 2003 04:52:14 -0800 (PST)
Subject: [Biojava-l] Rendering Questions
Message-ID: <20030113125214.64473.qmail@web13305.mail.yahoo.com>

Hi Everyone,

I am new to BioJava, and had a few questions regarding
rendering of features.  First off, I started with the
feature rendering code from BioJava in Anger (thanks
for doing this -- these cookbook recipes are
enormously helpful.)

Right now, I am just modifying the code to display
exons.  The complete code is below.  And, I am using
the following jar file:  biojava-20020823.jar.

Here are my questions:

1.  I am using the ZiggyFeatureRenderer, and I had
expected to see boxes separated by ziggy lines,
therefore indicating exons and introns.  But, I don't
see any ziggy lines, just boxes.  What am I doing
wrong?

2.  I want to be able to render the same features
without having its actual sequence.  How do I do this?

Any help would be most appreciated.

Ethan Cerami

Code follows below:
----------------------------------------

import java.awt.*;
import java.awt.event.*;

import javax.swing.*;

import org.biojava.bio.*;
import org.biojava.bio.gui.sequence.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.genomic.Exon;
import org.biojava.bio.symbol.*;

public class FeatureView extends JFrame {
	private Sequence seq;
	private JPanel jPanel = new JPanel();

	private MultiLineRenderer mlr = new
MultiLineRenderer();
	private ZiggyFeatureRenderer featr = new
ZiggyFeatureRenderer();
	private SequenceRenderer seqR = new
SymbolSequenceRenderer();
	private RulerRenderer ruler = new RulerRenderer();

	private SequencePanel seqPanel = new SequencePanel();
	//the proxy between featr and seqPanel
	private FeatureBlockSequenceRenderer fbr = new
FeatureBlockSequenceRenderer();

	public FeatureView() {
		try {
			seq = DNATools.createDNASequence(
					"atcgcgcatgcgcgcgcgcgcgcgctttatagcgatagagatata",
					"dna 1");

			// create multiple exons
			for (int i=10; i<=30; i+=10) {
				Exon.Template exon = new Exon.Template();
				exon.annotation = Annotation.EMPTY_ANNOTATION;
				exon.location = new RangeLocation(i, i+5);
				exon.strand = StrandedFeature.POSITIVE;
				seq.createFeature(exon);
			}
			//setup GUI
			init();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	public static void main(String[] args) {
		FeatureView featureView = new FeatureView();
		featureView.pack();
		featureView.show();
	}

	/**
	 * initialize GUI components
	 */
	private void init() throws Exception {
		this.setTitle("FeatureView");
		this.getContentPane().add(jPanel,
BorderLayout.CENTER);
		jPanel.add(seqPanel, null);

		//Register the FeatureRenderer with the
FeatureBlockSequenceRenderer
		fbr.setFeatureRenderer(featr);

		//add Renderers to the MultiLineRenderer
		mlr.addRenderer(fbr);
		mlr.addRenderer(seqR);
		mlr.addRenderer(ruler);

		//set the MultiLineRenderer as the SequencePanels
renderer
		seqPanel.setRenderer(mlr);

		//set the Sequence to Render
		seqPanel.setSequence(seq);

		//display the whole Sequence
		seqPanel.setRange(new RangeLocation(1,
seq.length()));
	}

	/**
	 * Overridden so program terminates when window
closes
	 */
	protected void processWindowEvent(WindowEvent we) {
		if (we.getID() == WindowEvent.WINDOW_CLOSING) {
			System.exit(0);
		} else {
			super.processWindowEvent(we);
		}
	}
}




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From td2@sanger.ac.uk  Mon Jan 13 13:29:33 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Mon, 13 Jan 2003 13:29:33 +0000
Subject: [Biojava-l] Rendering Questions
In-Reply-To: <20030113125214.64473.qmail@web13305.mail.yahoo.com>
References: <20030113125214.64473.qmail@web13305.mail.yahoo.com>
Message-ID: <20030113132933.GD402604@jabba.sanger.ac.uk>

On Mon, Jan 13, 2003 at 04:52:14AM -0800, Ethan Cerami wrote:
>
> Right now, I am just modifying the code to display
> exons.  The complete code is below.  And, I am using
> the following jar file:  biojava-20020823.jar.

If you're using that snapshot, you might want to update
to the latest and greatest code from http://cvs.open-bio.org/

> Here are my questions:
> 
> 1.  I am using the ZiggyFeatureRenderer, and I had
> expected to see boxes separated by ziggy lines,
> therefore indicating exons and introns.  But, I don't
> see any ziggy lines, just boxes.  What am I doing
> wrong?

ZiggyFeatureRenderer can't magically work out how to
group your exons together.  What it actually does it
render features with non-contiguous locations in the
`tented exons' style.

Try:

    StrandedFeature.Template temp = new StrandedFeature.Template();
    temp.type = "transcript";
    temp.source = "just_testing";
    temp.location = LocationTools.union(
        new RangeLocation(10, 20),
        new RangeLocation(50, 60)
    );
    temp.annotation = Annotation.EMPTY_ANNOTATION;
    temp.strand = StrandedFeature.POSITIVE

> 2.  I want to be able to render the same features
> without having its actual sequence.  How do I do this?

Do you just want to remove the sequence line from the
display?  In this case, just remove the line:

   mlr.addRenderer(seqR);

If you want to draw some boxes on the screen without
knowing the sequence *at all*, I've found some code like
this works well:

    SymbolList dummySL = new DummySymbolList(
        DNATools.getDNA(),
        1000
    );
    Sequence dummySeq = new SimpleSequence(
        dummySL,
        "foo",
        "bar",
        Annotation.EMPTY_ANNOTATION
    );
    // construct features on dummySeq

Hope this helps,

     Thomas.


> Any help would be most appreciated.
> 
> Ethan Cerami
> 
> Code follows below:
> ----------------------------------------
> 
> import java.awt.*;
> import java.awt.event.*;
> 
> import javax.swing.*;
> 
> import org.biojava.bio.*;
> import org.biojava.bio.gui.sequence.*;
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.genomic.Exon;
> import org.biojava.bio.symbol.*;
> 
> public class FeatureView extends JFrame {
> 	private Sequence seq;
> 	private JPanel jPanel = new JPanel();
> 
> 	private MultiLineRenderer mlr = new
> MultiLineRenderer();
> 	private ZiggyFeatureRenderer featr = new
> ZiggyFeatureRenderer();
> 	private SequenceRenderer seqR = new
> SymbolSequenceRenderer();
> 	private RulerRenderer ruler = new RulerRenderer();
> 
> 	private SequencePanel seqPanel = new SequencePanel();
> 	//the proxy between featr and seqPanel
> 	private FeatureBlockSequenceRenderer fbr = new
> FeatureBlockSequenceRenderer();
> 
> 	public FeatureView() {
> 		try {
> 			seq = DNATools.createDNASequence(
> 					"atcgcgcatgcgcgcgcgcgcgcgctttatagcgatagagatata",
> 					"dna 1");
> 
> 			// create multiple exons
> 			for (int i=10; i<=30; i+=10) {
> 				Exon.Template exon = new Exon.Template();
> 				exon.annotation = Annotation.EMPTY_ANNOTATION;
> 				exon.location = new RangeLocation(i, i+5);
> 				exon.strand = StrandedFeature.POSITIVE;
> 				seq.createFeature(exon);
> 			}
> 			//setup GUI
> 			init();
> 		} catch (Exception e) {
> 			e.printStackTrace();
> 		}
> 	}
> 
> 	public static void main(String[] args) {
> 		FeatureView featureView = new FeatureView();
> 		featureView.pack();
> 		featureView.show();
> 	}
> 
> 	/**
> 	 * initialize GUI components
> 	 */
> 	private void init() throws Exception {
> 		this.setTitle("FeatureView");
> 		this.getContentPane().add(jPanel,
> BorderLayout.CENTER);
> 		jPanel.add(seqPanel, null);
> 
> 		//Register the FeatureRenderer with the
> FeatureBlockSequenceRenderer
> 		fbr.setFeatureRenderer(featr);
> 
> 		//add Renderers to the MultiLineRenderer
> 		mlr.addRenderer(fbr);
> 		mlr.addRenderer(seqR);
> 		mlr.addRenderer(ruler);
> 
> 		//set the MultiLineRenderer as the SequencePanels
> renderer
> 		seqPanel.setRenderer(mlr);
> 
> 		//set the Sequence to Render
> 		seqPanel.setSequence(seq);
> 
> 		//display the whole Sequence
> 		seqPanel.setRange(new RangeLocation(1,
> seq.length()));
> 	}
> 
> 	/**
> 	 * Overridden so program terminates when window
> closes
> 	 */
> 	protected void processWindowEvent(WindowEvent we) {
> 		if (we.getID() == WindowEvent.WINDOW_CLOSING) {
> 			System.exit(0);
> 		} else {
> 			super.processWindowEvent(we);
> 		}
> 	}
> }
> 
> 
> 
> 
> __________________________________________________
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From MCCon012@mc.duke.edu  Mon Jan 13 15:14:37 2003
From: MCCon012@mc.duke.edu (Patrick McConnell)
Date: Mon, 13 Jan 2003 10:14:37 -0500
Subject: [Biojava-l] library for running blast and formatdb
Message-ID: <OF2677E3BD.B804EF08-ON85256CAD.005257EB-85256CAD.0053EB29@notes.duke.edu>


>I suppose it's a matter of another external dependency vs. reinvented
>utility code in biojava . . .  Would it make sense to merge the better
>qualities of the two?

The CLI project looks like it is quite flexible and robust.  But, with
this, it is somewhat complex.  This is in contrast to the simplicity of
creating parameters via reflection.  I think that these two methods could
be effectively combined so that we gain the simplicty of reflection with
the flexibility of CLI.  The base parameters class can use CLI to build its
parameters.  As an option, it can build CLI options via reflection for
simplicity.  When users extend the base class, they can utilize the
flexibility of CLI if they need it, otherwise they can use reflection for a
quick and dirty parameter parsing.  The base class could even extend the
Options class, so we are really working with a hybrid of the two.  What
does everyone think?

-Patrick






"Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on 01/10/2003
05:18:52 PM

Sent by:    Michael Heuer <heuermh@shell3.shore.net>


To:    Patrick McConnell <MCCon012@mc.duke.edu>
cc:    biojava-l@biojava.org

Subject:    Re: [Biojava-l] library for running blast and formatdb


On Fri, 10 Jan 2003, Patrick McConnell wrote:

> In the process, I developed some useful and flexible base classes for
> formatting parameters and running programs.  Parameters are automatically
> converted to an argument array via reflection and reading of standard out
> and standard error in separate threads is handled automatically.

The base classes are nice, but I prefer the design of

> http://jakarta.apache.org/commons/cli

a lot better for handling parameters.

I suppose it's a matter of another external dependency vs. reinvented
utility code in biojava . . .  Would it make sense to merge the better
qualities of the two?

I also have a few simple classes for oneoff scripts with command line &
logging facade support that I use all the time, see

> http://www.shore.net/~heuermh/oneoff.tar.gz

but they don't have any extra support for external programs.

   michael

>
> Check it out if you are interested:
> http://www.dbsr.duke.edu/software/blast/default.htm .  The full source,
> javadocs, and binary class files are available.  Also, if this seems
> appropriate for BioJava, I have no problem donating it to the cause.  I
> think that at least the base classes, or some modification of them, would
> be useful to others.
>
> Please email me with suggestions/comments,
>
> -Patrick McConnell
> Duke Bioinformatics Shared Resource
> mccon012@mc.duke.edu
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>








From mark.schreiber@agresearch.co.nz  Mon Jan 13 20:08:08 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 14 Jan 2003 09:08:08 +1300
Subject: [Biojava-l] library for running blast and formatdb
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E7FB1@inbox.agresearch.co.nz>

One thing sorely missing from BioJava is the ability to launch and
capture the results of common bioinformatics programs. I know Java isn't
the best at this but it's not that bad. It's also needed if you want to
develop pipeline type applications.

Would it be possible to get some kind of over-arching interface based
API so that services can be made available with similar interfaces.

Possibly a Service or Program interface a Paramater list or map, some
kind of result stream?

Just my $0.02

- Mark

> -----Original Message-----
> From: Patrick McConnell [mailto:MCCon012@mc.duke.edu] 
> Sent: Tuesday, 14 January 2003 4:15 a.m.
> To: biojava-l@biojava.org
> Subject: Re: [Biojava-l] library for running blast and formatdb
> 
> 
> 
> 
> >I suppose it's a matter of another external dependency vs. 
> reinvented 
> >utility code in biojava . . .  Would it make sense to merge 
> the better 
> >qualities of the two?
> 
> The CLI project looks like it is quite flexible and robust.  
> But, with this, it is somewhat complex.  This is in contrast 
> to the simplicity of creating parameters via reflection.  I 
> think that these two methods could be effectively combined so 
> that we gain the simplicty of reflection with the flexibility 
> of CLI.  The base parameters class can use CLI to build its 
> parameters.  As an option, it can build CLI options via 
> reflection for simplicity.  When users extend the base class, 
> they can utilize the flexibility of CLI if they need it, 
> otherwise they can use reflection for a quick and dirty 
> parameter parsing.  The base class could even extend the 
> Options class, so we are really working with a hybrid of the 
> two.  What does everyone think?
> 
> -Patrick
> 
> 
> 
> 
> 
> 
> "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on 
> 01/10/2003 05:18:52 PM
> 
> Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> 
> 
> To:    Patrick McConnell <MCCon012@mc.duke.edu>
> cc:    biojava-l@biojava.org
> 
> Subject:    Re: [Biojava-l] library for running blast and formatdb
> 
> 
> On Fri, 10 Jan 2003, Patrick McConnell wrote:
> 
> > In the process, I developed some useful and flexible base 
> classes for 
> > formatting parameters and running programs.  Parameters are 
> > automatically converted to an argument array via reflection and 
> > reading of standard out and standard error in separate threads is 
> > handled automatically.
> 
> The base classes are nice, but I prefer the design of
> 
> > http://jakarta.apache.org/commons/cli
> 
> a lot better for handling parameters.
> 
> I suppose it's a matter of another external dependency vs. 
> reinvented utility code in biojava . . .  Would it make sense 
> to merge the better qualities of the two?
> 
> I also have a few simple classes for oneoff scripts with 
> command line & logging facade support that I use all the time, see
> 
> > http://www.shore.net/~heuermh/oneoff.tar.gz
> 
> but they don't have any extra support for external programs.
> 
>    michael
> 
> >
> > Check it out if you are interested: 
> > http://www.dbsr.duke.edu/software/blast/default.htm .  The full 
> > source, javadocs, and binary class files are available.  
> Also, if this 
> > seems appropriate for BioJava, I have no problem donating it to the 
> > cause.  I think that at least the base classes, or some 
> modification 
> > of them, would be useful to others.
> >
> > Please email me with suggestions/comments,
> >
> > -Patrick McConnell
> > Duke Bioinformatics Shared Resource
> > mccon012@mc.duke.edu
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> >
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
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
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sender immediately.
=======================================================================


From Wiepert.Mathieu@mayo.edu  Mon Jan 13 20:19:55 2003
From: Wiepert.Mathieu@mayo.edu (Wiepert, Mathieu)
Date: Mon, 13 Jan 2003 14:19:55 -0600
Subject: [Biojava-l] library for running blast and formatdb
Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C201@excsrv32.mayo.edu>

It would be good if a command could be described somehow (XML file?), and the interface could query that to find commands, limits, parameter acceptable values, location of programs maybe?  Short of the commands being self-describing, and you knew where they all were, that might not be so bad?  Simple website wrappers could then be written around them, common look and feel for all commands, etc...  I'd swear I had seen something like this somewhere, generically implemented (thought it was for unix commands on a machine).  Something like this would allow new programs and scripts to plug in rather easily.  Hmmm, I have strayed off topic, sorry.

-Mat

> -----Original Message-----
> From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> Sent: Monday, January 13, 2003 2:08 PM
> To: Patrick McConnell
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] library for running blast and formatdb
> 
> 
> One thing sorely missing from BioJava is the ability to launch and
> capture the results of common bioinformatics programs. I know 
> Java isn't
> the best at this but it's not that bad. It's also needed if 
> you want to
> develop pipeline type applications.
> 
> Would it be possible to get some kind of over-arching interface based
> API so that services can be made available with similar interfaces.
> 
> Possibly a Service or Program interface a Paramater list or map, some
> kind of result stream?
> 
> Just my $0.02
> 
> - Mark
> 
> > -----Original Message-----
> > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu] 
> > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > To: biojava-l@biojava.org
> > Subject: Re: [Biojava-l] library for running blast and formatdb
> > 
> > 
> > 
> > 
> > >I suppose it's a matter of another external dependency vs. 
> > reinvented 
> > >utility code in biojava . . .  Would it make sense to merge 
> > the better 
> > >qualities of the two?
> > 
> > The CLI project looks like it is quite flexible and robust.  
> > But, with this, it is somewhat complex.  This is in contrast 
> > to the simplicity of creating parameters via reflection.  I 
> > think that these two methods could be effectively combined so 
> > that we gain the simplicty of reflection with the flexibility 
> > of CLI.  The base parameters class can use CLI to build its 
> > parameters.  As an option, it can build CLI options via 
> > reflection for simplicity.  When users extend the base class, 
> > they can utilize the flexibility of CLI if they need it, 
> > otherwise they can use reflection for a quick and dirty 
> > parameter parsing.  The base class could even extend the 
> > Options class, so we are really working with a hybrid of the 
> > two.  What does everyone think?
> > 
> > -Patrick
> > 
> > 
> > 
> > 
> > 
> > 
> > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on 
> > 01/10/2003 05:18:52 PM
> > 
> > Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> > 
> > 
> > To:    Patrick McConnell <MCCon012@mc.duke.edu>
> > cc:    biojava-l@biojava.org
> > 
> > Subject:    Re: [Biojava-l] library for running blast and formatdb
> > 
> > 
> > On Fri, 10 Jan 2003, Patrick McConnell wrote:
> > 
> > > In the process, I developed some useful and flexible base 
> > classes for 
> > > formatting parameters and running programs.  Parameters are 
> > > automatically converted to an argument array via reflection and 
> > > reading of standard out and standard error in separate threads is 
> > > handled automatically.
> > 
> > The base classes are nice, but I prefer the design of
> > 
> > > http://jakarta.apache.org/commons/cli
> > 
> > a lot better for handling parameters.
> > 
> > I suppose it's a matter of another external dependency vs. 
> > reinvented utility code in biojava . . .  Would it make sense 
> > to merge the better qualities of the two?
> > 
> > I also have a few simple classes for oneoff scripts with 
> > command line & logging facade support that I use all the time, see
> > 
> > > http://www.shore.net/~heuermh/oneoff.tar.gz
> > 
> > but they don't have any extra support for external programs.
> > 
> >    michael
> > 
> > >
> > > Check it out if you are interested: 
> > > http://www.dbsr.duke.edu/software/blast/default.htm .  The full 
> > > source, javadocs, and binary class files are available.  
> > Also, if this 
> > > seems appropriate for BioJava, I have no problem donating 
> it to the 
> > > cause.  I think that at least the base classes, or some 
> > modification 
> > > of them, would be useful to others.
> > >
> > > Please email me with suggestions/comments,
> > >
> > > -Patrick McConnell
> > > Duke Bioinformatics Shared Resource
> > > mccon012@mc.duke.edu
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> ==============================================================
> =========
> Attention: The information contained in this message and/or 
> attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or 
> privileged
> material. Any review, retransmission, dissemination or other 
> use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by 
> AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> ==============================================================
> =========
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 

From mark.schreiber@agresearch.co.nz  Mon Jan 13 20:40:02 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 14 Jan 2003 09:40:02 +1300
Subject: [Biojava-l] library for running blast and formatdb
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E7FC9@inbox.agresearch.co.nz>

I notice there is a Object call AppBeanRunner that appears to make an
object from an XML file then instantiate it. Is it intended for the type
of activity below or something else?

- Mark

> -----Original Message-----
> From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu] 
> Sent: Tuesday, 14 January 2003 9:20 a.m.
> To: 'biojava-l@biojava.org'
> Subject: RE: [Biojava-l] library for running blast and formatdb
> 
> 
> It would be good if a command could be described somehow (XML 
> file?), and the interface could query that to find commands, 
> limits, parameter acceptable values, location of programs 
> maybe?  Short of the commands being self-describing, and you 
> knew where they all were, that might not be so bad?  Simple 
> website wrappers could then be written around them, common 
> look and feel for all commands, etc...  I'd swear I had seen 
> something like this somewhere, generically implemented 
> (thought it was for unix commands on a machine).  Something 
> like this would allow new programs and scripts to plug in 
> rather easily.  Hmmm, I have strayed off topic, sorry.
> 
> -Mat
> 
> > -----Original Message-----
> > From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> > Sent: Monday, January 13, 2003 2:08 PM
> > To: Patrick McConnell
> > Cc: biojava-l@biojava.org
> > Subject: RE: [Biojava-l] library for running blast and formatdb
> > 
> > 
> > One thing sorely missing from BioJava is the ability to launch and 
> > capture the results of common bioinformatics programs. I know Java 
> > isn't the best at this but it's not that bad. It's also needed if
> > you want to
> > develop pipeline type applications.
> > 
> > Would it be possible to get some kind of over-arching 
> interface based 
> > API so that services can be made available with similar interfaces.
> > 
> > Possibly a Service or Program interface a Paramater list or 
> map, some 
> > kind of result stream?
> > 
> > Just my $0.02
> > 
> > - Mark
> > 
> > > -----Original Message-----
> > > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> > > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > > To: biojava-l@biojava.org
> > > Subject: Re: [Biojava-l] library for running blast and formatdb
> > > 
> > > 
> > > 
> > > 
> > > >I suppose it's a matter of another external dependency vs.
> > > reinvented
> > > >utility code in biojava . . .  Would it make sense to merge
> > > the better
> > > >qualities of the two?
> > > 
> > > The CLI project looks like it is quite flexible and robust.
> > > But, with this, it is somewhat complex.  This is in contrast 
> > > to the simplicity of creating parameters via reflection.  I 
> > > think that these two methods could be effectively combined so 
> > > that we gain the simplicty of reflection with the flexibility 
> > > of CLI.  The base parameters class can use CLI to build its 
> > > parameters.  As an option, it can build CLI options via 
> > > reflection for simplicity.  When users extend the base class, 
> > > they can utilize the flexibility of CLI if they need it, 
> > > otherwise they can use reflection for a quick and dirty 
> > > parameter parsing.  The base class could even extend the 
> > > Options class, so we are really working with a hybrid of the 
> > > two.  What does everyone think?
> > > 
> > > -Patrick
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
> > > 01/10/2003 05:18:52 PM
> > > 
> > > Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> > > 
> > > 
> > > To:    Patrick McConnell <MCCon012@mc.duke.edu>
> > > cc:    biojava-l@biojava.org
> > > 
> > > Subject:    Re: [Biojava-l] library for running blast and formatdb
> > > 
> > > 
> > > On Fri, 10 Jan 2003, Patrick McConnell wrote:
> > > 
> > > > In the process, I developed some useful and flexible base
> > > classes for
> > > > formatting parameters and running programs.  Parameters are
> > > > automatically converted to an argument array via reflection and 
> > > > reading of standard out and standard error in separate 
> threads is 
> > > > handled automatically.
> > > 
> > > The base classes are nice, but I prefer the design of
> > > 
> > > > http://jakarta.apache.org/commons/cli
> > > 
> > > a lot better for handling parameters.
> > > 
> > > I suppose it's a matter of another external dependency vs.
> > > reinvented utility code in biojava . . .  Would it make sense 
> > > to merge the better qualities of the two?
> > > 
> > > I also have a few simple classes for oneoff scripts with
> > > command line & logging facade support that I use all the time, see
> > > 
> > > > http://www.shore.net/~heuermh/oneoff.tar.gz
> > > 
> > > but they don't have any extra support for external programs.
> > > 
> > >    michael
> > > 
> > > >
> > > > Check it out if you are interested:
> > > > http://www.dbsr.duke.edu/software/blast/default.htm .  The full 
> > > > source, javadocs, and binary class files are available.  
> > > Also, if this
> > > > seems appropriate for BioJava, I have no problem donating
> > it to the
> > > > cause.  I think that at least the base classes, or some
> > > modification
> > > > of them, would be useful to others.
> > > >
> > > > Please email me with suggestions/comments,
> > > >
> > > > -Patrick McConnell
> > > > Duke Bioinformatics Shared Resource
> > > > mccon012@mc.duke.edu
> > > >
> > > >
> > > > _______________________________________________
> > > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > > http://biojava.org/mailman/listinfo/biojava-l
> > > >
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l
> > > 
> > ==============================================================
> > =========
> > Attention: The information contained in this message and/or
> > attachments
> > from AgResearch Limited is intended only for the persons or entities
> > to which it is addressed and may contain confidential and/or 
> > privileged
> > material. Any review, retransmission, dissemination or other 
> > use of, or
> > taking of any action in reliance upon, this information by 
> persons or
> > entities other than the intended recipients is prohibited by 
> > AgResearch
> > Limited. If you have received this message in error, please 
> notify the
> > sender immediately.
> > ==============================================================
> > =========
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From gilmanb@genome.wi.mit.edu  Mon Jan 13 20:38:01 2003
From: gilmanb@genome.wi.mit.edu (Brian Gilman)
Date: Mon, 13 Jan 2003 15:38:01 -0500
Subject: [Biojava-l] library for running blast and formatdb
In-Reply-To: <2F41CC6C9777D311ACBD009027B108EA0541C201@excsrv32.mayo.edu>
Message-ID: <BA488DD9.7894%gilmanb@genome.wi.mit.edu>

On 1/13/03 3:19 PM, "Wiepert, Mathieu" <Wiepert.Mathieu@mayo.edu> wrote:

This functionality exists in the OmniGene Analysis Engine! (OAE). I could
help you get up and running if you are interested.

                                -B

> It would be good if a command could be described somehow (XML file?), and the
> interface could query that to find commands, limits, parameter acceptable
> values, location of programs maybe?  Short of the commands being
> self-describing, and you knew where they all were, that might not be so bad?
> Simple website wrappers could then be written around them, common look and
> feel for all commands, etc...  I'd swear I had seen something like this
> somewhere, generically implemented (thought it was for unix commands on a
> machine).  Something like this would allow new programs and scripts to plug in
> rather easily.  Hmmm, I have strayed off topic, sorry.
> 
> -Mat
> 
>> -----Original Message-----
>> From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
>> Sent: Monday, January 13, 2003 2:08 PM
>> To: Patrick McConnell
>> Cc: biojava-l@biojava.org
>> Subject: RE: [Biojava-l] library for running blast and formatdb
>> 
>> 
>> One thing sorely missing from BioJava is the ability to launch and
>> capture the results of common bioinformatics programs. I know
>> Java isn't
>> the best at this but it's not that bad. It's also needed if
>> you want to
>> develop pipeline type applications.
>> 
>> Would it be possible to get some kind of over-arching interface based
>> API so that services can be made available with similar interfaces.
>> 
>> Possibly a Service or Program interface a Paramater list or map, some
>> kind of result stream?
>> 
>> Just my $0.02
>> 
>> - Mark
>> 
>>> -----Original Message-----
>>> From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
>>> Sent: Tuesday, 14 January 2003 4:15 a.m.
>>> To: biojava-l@biojava.org
>>> Subject: Re: [Biojava-l] library for running blast and formatdb
>>> 
>>> 
>>> 
>>> 
>>>> I suppose it's a matter of another external dependency vs.
>>> reinvented 
>>>> utility code in biojava . . .  Would it make sense to merge
>>> the better 
>>>> qualities of the two?
>>> 
>>> The CLI project looks like it is quite flexible and robust.
>>> But, with this, it is somewhat complex.  This is in contrast
>>> to the simplicity of creating parameters via reflection.  I
>>> think that these two methods could be effectively combined so
>>> that we gain the simplicty of reflection with the flexibility
>>> of CLI.  The base parameters class can use CLI to build its
>>> parameters.  As an option, it can build CLI options via
>>> reflection for simplicity.  When users extend the base class,
>>> they can utilize the flexibility of CLI if they need it,
>>> otherwise they can use reflection for a quick and dirty
>>> parameter parsing.  The base class could even extend the
>>> Options class, so we are really working with a hybrid of the
>>> two.  What does everyone think?
>>> 
>>> -Patrick
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
>>> 01/10/2003 05:18:52 PM
>>> 
>>> Sent by:    Michael Heuer <heuermh@shell3.shore.net>
>>> 
>>> 
>>> To:    Patrick McConnell <MCCon012@mc.duke.edu>
>>> cc:    biojava-l@biojava.org
>>> 
>>> Subject:    Re: [Biojava-l] library for running blast and formatdb
>>> 
>>> 
>>> On Fri, 10 Jan 2003, Patrick McConnell wrote:
>>> 
>>>> In the process, I developed some useful and flexible base
>>> classes for 
>>>> formatting parameters and running programs.  Parameters are
>>>> automatically converted to an argument array via reflection and
>>>> reading of standard out and standard error in separate threads is
>>>> handled automatically.
>>> 
>>> The base classes are nice, but I prefer the design of
>>> 
>>>> http://jakarta.apache.org/commons/cli
>>> 
>>> a lot better for handling parameters.
>>> 
>>> I suppose it's a matter of another external dependency vs.
>>> reinvented utility code in biojava . . .  Would it make sense
>>> to merge the better qualities of the two?
>>> 
>>> I also have a few simple classes for oneoff scripts with
>>> command line & logging facade support that I use all the time, see
>>> 
>>>> http://www.shore.net/~heuermh/oneoff.tar.gz
>>> 
>>> but they don't have any extra support for external programs.
>>> 
>>>    michael
>>> 
>>>> 
>>>> Check it out if you are interested:
>>>> http://www.dbsr.duke.edu/software/blast/default.htm .  The full
>>>> source, javadocs, and binary class files are available.
>>> Also, if this 
>>>> seems appropriate for BioJava, I have no problem donating
>> it to the 
>>>> cause.  I think that at least the base classes, or some
>>> modification 
>>>> of them, would be useful to others.
>>>> 
>>>> Please email me with suggestions/comments,
>>>> 
>>>> -Patrick McConnell
>>>> Duke Bioinformatics Shared Resource
>>>> mccon012@mc.duke.edu
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l@biojava.org
>>>> http://biojava.org/mailman/listinfo/biojava-l
>>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l@biojava.org
>>> http://biojava.org/mailman/listinfo/biojava-l
>>> 
>> ==============================================================
>> =========
>> Attention: The information contained in this message and/or
>> attachments
>> from AgResearch Limited is intended only for the persons or entities
>> to which it is addressed and may contain confidential and/or
>> privileged
>> material. Any review, retransmission, dissemination or other
>> use of, or
>> taking of any action in reliance upon, this information by persons or
>> entities other than the intended recipients is prohibited by
>> AgResearch
>> Limited. If you have received this message in error, please notify the
>> sender immediately.
>> ==============================================================
>> =========
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l@biojava.org
>> http://biojava.org/mailman/listinfo/biojava-l
>> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 

-- 
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902


From td2@sanger.ac.uk  Mon Jan 13 23:31:36 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Mon, 13 Jan 2003 23:31:36 +0000
Subject: [Biojava-l] BioJava 1.3pre1
Message-ID: <20030113233136.GC406225@jabba.sanger.ac.uk>

We've had a number of requests recently for a more recent
snapshot of the biojava-live code, so I've just put together
a biojava-1.3pre1 release.  Get source, binaries, and javadocs
from:

    http://www.biojava.org/download/

This isn't absolutely set in stone yet, but should give
a reasonable indication of what the forthcoming 1.3 series
is going to look like.  All testing and comments welcome!

One thing to note about the *binary* release:  I've compiled
this using Sun JDK 1.4.1.  There may be compatibility problems
with Java 1.3 runtime envionments in some cases, so if you're
using Java 1.3 and think you've found a bug, please try downloading
the source and recompiling.  I've released jdk1.4 binaries this
time as an experiment.  If there are violent objections, we can
always do back to jdk1.3.1 for compiling binary releases, or
perhaps provide both.  Please let me know if you have any thoughts
on this, or if it causes you trouble.

      Thomas.



From francois.pepin@mail.mcgill.ca  Tue Jan 14 01:00:03 2003
From: francois.pepin@mail.mcgill.ca (Francois Pepin)
Date: Mon, 13 Jan 2003 20:00:03 -0500
Subject: [Biojava-l] library for running blast and formatdb
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165012E7FB1@inbox.agresearch.co.nz>
Message-ID: <000201c2bb68$492e5000$e0abfea9@hermes>

I have some code for the running part of it (as java is pretty finicky
about running external apps) on almost any OS.

It's pretty simple (you have to send it the string to be run), but it's
pretty robust and can capture the outputs properly for later use.

If people think that it would be useful to have something of the kind
String goes in, Stream goes out, I'll be happy to set it up so that it's
flexible and releasable.

Then if someone wants to do something fancy with it, it'll be all ready
to go.

Francois

-----Original Message-----
From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]
On Behalf Of Schreiber, Mark
Sent: 13 janvier, 2003 15:08
To: Patrick McConnell
Cc: biojava-l@biojava.org
Subject: RE: [Biojava-l] library for running blast and formatdb


One thing sorely missing from BioJava is the ability to launch and
capture the results of common bioinformatics programs. I know Java isn't
the best at this but it's not that bad. It's also needed if you want to
develop pipeline type applications.

Would it be possible to get some kind of over-arching interface based
API so that services can be made available with similar interfaces.

Possibly a Service or Program interface a Paramater list or map, some
kind of result stream?

Just my $0.02

- Mark

> -----Original Message-----
> From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> Sent: Tuesday, 14 January 2003 4:15 a.m.
> To: biojava-l@biojava.org
> Subject: Re: [Biojava-l] library for running blast and formatdb
> 
> 
> 
> 
> >I suppose it's a matter of another external dependency vs.
> reinvented
> >utility code in biojava . . .  Would it make sense to merge
> the better
> >qualities of the two?
> 
> The CLI project looks like it is quite flexible and robust.
> But, with this, it is somewhat complex.  This is in contrast 
> to the simplicity of creating parameters via reflection.  I 
> think that these two methods could be effectively combined so 
> that we gain the simplicty of reflection with the flexibility 
> of CLI.  The base parameters class can use CLI to build its 
> parameters.  As an option, it can build CLI options via 
> reflection for simplicity.  When users extend the base class, 
> they can utilize the flexibility of CLI if they need it, 
> otherwise they can use reflection for a quick and dirty 
> parameter parsing.  The base class could even extend the 
> Options class, so we are really working with a hybrid of the 
> two.  What does everyone think?
> 
> -Patrick
> 
> 
> 
> 
> 
> 
> "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
> 01/10/2003 05:18:52 PM
> 
> Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> 
> 
> To:    Patrick McConnell <MCCon012@mc.duke.edu>
> cc:    biojava-l@biojava.org
> 
> Subject:    Re: [Biojava-l] library for running blast and formatdb
> 
> 
> On Fri, 10 Jan 2003, Patrick McConnell wrote:
> 
> > In the process, I developed some useful and flexible base
> classes for
> > formatting parameters and running programs.  Parameters are
> > automatically converted to an argument array via reflection and 
> > reading of standard out and standard error in separate threads is 
> > handled automatically.
> 
> The base classes are nice, but I prefer the design of
> 
> > http://jakarta.apache.org/commons/cli
> 
> a lot better for handling parameters.
> 
> I suppose it's a matter of another external dependency vs.
> reinvented utility code in biojava . . .  Would it make sense 
> to merge the better qualities of the two?
> 
> I also have a few simple classes for oneoff scripts with
> command line & logging facade support that I use all the time, see
> 
> > http://www.shore.net/~heuermh/oneoff.tar.gz
> 
> but they don't have any extra support for external programs.
> 
>    michael
> 
> >
> > Check it out if you are interested:
> > http://www.dbsr.duke.edu/software/blast/default.htm .  The full 
> > source, javadocs, and binary class files are available.  
> Also, if this
> > seems appropriate for BioJava, I have no problem donating it to the
> > cause.  I think that at least the base classes, or some 
> modification
> > of them, would be useful to others.
> >
> > Please email me with suggestions/comments,
> >
> > -Patrick McConnell
> > Duke Bioinformatics Shared Resource
> > mccon012@mc.duke.edu
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
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which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
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From mark.schreiber@agresearch.co.nz  Tue Jan 14 01:07:37 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 14 Jan 2003 14:07:37 +1300
Subject: [Biojava-l] library for running blast and formatdb
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E8047@inbox.agresearch.co.nz>

Wouldn't be a bad place to start anyway.

- Mark


> -----Original Message-----
> From: Francois Pepin [mailto:francois.pepin@mail.mcgill.ca] 
> Sent: Tuesday, 14 January 2003 2:00 p.m.
> To: Schreiber, Mark; 'Patrick McConnell'
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] library for running blast and formatdb
> 
> 
> I have some code for the running part of it (as java is 
> pretty finicky about running external apps) on almost any OS.
> 
> It's pretty simple (you have to send it the string to be 
> run), but it's pretty robust and can capture the outputs 
> properly for later use.
> 
> If people think that it would be useful to have something of 
> the kind String goes in, Stream goes out, I'll be happy to 
> set it up so that it's flexible and releasable.
> 
> Then if someone wants to do something fancy with it, it'll be 
> all ready to go.
> 
> Francois
> 
> -----Original Message-----
> From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]
> On Behalf Of Schreiber, Mark
> Sent: 13 janvier, 2003 15:08
> To: Patrick McConnell
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] library for running blast and formatdb
> 
> 
> One thing sorely missing from BioJava is the ability to 
> launch and capture the results of common bioinformatics 
> programs. I know Java isn't the best at this but it's not 
> that bad. It's also needed if you want to develop pipeline 
> type applications.
> 
> Would it be possible to get some kind of over-arching 
> interface based API so that services can be made available 
> with similar interfaces.
> 
> Possibly a Service or Program interface a Paramater list or 
> map, some kind of result stream?
> 
> Just my $0.02
> 
> - Mark
> 
> > -----Original Message-----
> > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > To: biojava-l@biojava.org
> > Subject: Re: [Biojava-l] library for running blast and formatdb
> > 
> > 
> > 
> > 
> > >I suppose it's a matter of another external dependency vs.
> > reinvented
> > >utility code in biojava . . .  Would it make sense to merge
> > the better
> > >qualities of the two?
> > 
> > The CLI project looks like it is quite flexible and robust. 
> But, with 
> > this, it is somewhat complex.  This is in contrast to the 
> simplicity 
> > of creating parameters via reflection.  I think that these 
> two methods 
> > could be effectively combined so that we gain the simplicty of 
> > reflection with the flexibility of CLI.  The base 
> parameters class can 
> > use CLI to build its parameters.  As an option, it can build CLI 
> > options via reflection for simplicity.  When users extend the base 
> > class, they can utilize the flexibility of CLI if they need it,
> > otherwise they can use reflection for a quick and dirty 
> > parameter parsing.  The base class could even extend the 
> > Options class, so we are really working with a hybrid of the 
> > two.  What does everyone think?
> > 
> > -Patrick
> > 
> > 
> > 
> > 
> > 
> > 
> > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on 
> 01/10/2003 
> > 05:18:52 PM
> > 
> > Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> > 
> > 
> > To:    Patrick McConnell <MCCon012@mc.duke.edu>
> > cc:    biojava-l@biojava.org
> > 
> > Subject:    Re: [Biojava-l] library for running blast and formatdb
> > 
> > 
> > On Fri, 10 Jan 2003, Patrick McConnell wrote:
> > 
> > > In the process, I developed some useful and flexible base
> > classes for
> > > formatting parameters and running programs.  Parameters are 
> > > automatically converted to an argument array via reflection and 
> > > reading of standard out and standard error in separate threads is 
> > > handled automatically.
> > 
> > The base classes are nice, but I prefer the design of
> > 
> > > http://jakarta.apache.org/commons/cli
> > 
> > a lot better for handling parameters.
> > 
> > I suppose it's a matter of another external dependency vs. 
> reinvented 
> > utility code in biojava . . .  Would it make sense to merge 
> the better 
> > qualities of the two?
> > 
> > I also have a few simple classes for oneoff scripts with 
> command line 
> > & logging facade support that I use all the time, see
> > 
> > > http://www.shore.net/~heuermh/oneoff.tar.gz
> > 
> > but they don't have any extra support for external programs.
> > 
> >    michael
> > 
> > >
> > > Check it out if you are interested: 
> > > http://www.dbsr.duke.edu/software/blast/default.htm .  The full 
> > > source, javadocs, and binary class files are available.
> > Also, if this
> > > seems appropriate for BioJava, I have no problem donating 
> it to the 
> > > cause.  I think that at least the base classes, or some
> > modification
> > > of them, would be useful to others.
> > >
> > > Please email me with suggestions/comments,
> > >
> > > -Patrick McConnell
> > > Duke Bioinformatics Shared Resource
> > > mccon012@mc.duke.edu
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> ==============================================================
> =========
> Attention: The information contained in this message and/or 
> attachments from AgResearch Limited is intended only for the 
> persons or entities to which it is addressed and may contain 
> confidential and/or privileged material. Any review, 
> retransmission, dissemination or other use of, or taking of 
> any action in reliance upon, this information by persons or 
> entities other than the intended recipients is prohibited by 
> AgResearch Limited. If you have received this message in 
> error, please notify the sender immediately. 
> ==============================================================
> =========
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
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=======================================================================


From gilmanb@genome.wi.mit.edu  Tue Jan 14 01:10:21 2003
From: gilmanb@genome.wi.mit.edu (Brian Gilman)
Date: Mon, 13 Jan 2003 20:10:21 -0500
Subject: [Biojava-l] BioJava 1.3pre1
In-Reply-To: <20030113233136.GC406225@jabba.sanger.ac.uk>
Message-ID: <BA48CDAD.1C258%gilmanb@genome.wi.mit.edu>

On 1/13/03 6:31 PM, "Thomas Down" <td2@sanger.ac.uk> wrote:

Hey Thomas,

    Do you have a doc that describes the functionality in this release??
Something like a feature matrix would be nice to see.

                            Best,

                                    -B

> We've had a number of requests recently for a more recent
> snapshot of the biojava-live code, so I've just put together
> a biojava-1.3pre1 release.  Get source, binaries, and javadocs
> from:
> 
>   http://www.biojava.org/download/
> 
> This isn't absolutely set in stone yet, but should give
> a reasonable indication of what the forthcoming 1.3 series
> is going to look like.  All testing and comments welcome!
> 
> One thing to note about the *binary* release:  I've compiled
> this using Sun JDK 1.4.1.  There may be compatibility problems
> with Java 1.3 runtime envionments in some cases, so if you're
> using Java 1.3 and think you've found a bug, please try downloading
> the source and recompiling.  I've released jdk1.4 binaries this
> time as an experiment.  If there are violent objections, we can
> always do back to jdk1.3.1 for compiling binary releases, or
> perhaps provide both.  Please let me know if you have any thoughts
> on this, or if it causes you trouble.
> 
>     Thomas.
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 

-- 
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902



From mark.schreiber@agresearch.co.nz  Tue Jan 14 03:44:27 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 14 Jan 2003 16:44:27 +1300
Subject: [Biojava-l] Rendering hints and GUI's
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E8083@inbox.agresearch.co.nz>

Hi -

I would like to be able to add RenderingHints to the various renderers
in BioJava. How can I intercept the Graphics object that is passed to
the Renderers paint(Graphics g, SequencePanel sp) method?

I could overide the method to use the RenderingHints before passing the
arguments to super but that seems a bit overkill. Is there another way?

- Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
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 td2@sanger.ac.uk  Tue Jan 14 09:42:07 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Tue, 14 Jan 2003 09:42:07 +0000
Subject: [Biojava-l] BioJava 1.3pre1
In-Reply-To: <BA48CDAD.1C258%gilmanb@genome.wi.mit.edu>
References: <20030113233136.GC406225@jabba.sanger.ac.uk> <BA48CDAD.1C258%gilmanb@genome.wi.mit.edu>
Message-ID: <20030114094207.GB409088@jabba.sanger.ac.uk>

On Mon, Jan 13, 2003 at 08:10:21PM -0500, Brian Gilman wrote:
> On 1/13/03 6:31 PM, "Thomas Down" <td2@sanger.ac.uk> wrote:
> 
> Hey Thomas,
> 
>     Do you have a doc that describes the functionality in this release??
> Something like a feature matrix would be nice to see.

Now, there's a question!  This release has largely been
many, many, incremental improvements over 1.2.  But you're
right, it's time to start putting together the improvements
list ready for the 1.30-final release.  Here's a start,
all additions and corrections welcomed:

  - Many, many, additions to the FeatureFilter language
    and its associated support code, allowing more
    sophisticated querying, and better optimization of
    these queries at the back end.

  - FeatureFilters can now be applied to SequenceDBs as well
    as Sequences, allowing feature-centric querying of entire
    databases (biojava-ensembl now takes advantage of this).

  - Sequences can publish metadata about their annotations.

  - Memory-optimized SymbolList implementations
  
  - Improvements to the handler code for building object
    models from search results (Keith?).  BlastXML support.

  - Core properties of Features may now be mutable.
 
  - BioSQL adaptors rewritten for better scalability and
    strictly correct implementation of the ChangeEvent framework.

  - Updates to sequence-file parsers, and support for GAME 1.2

  - OBDA-compliant support for indexed flatfiles.

  - BioFetch.

  - Hashtable-based fast search libraries, similar to the
    SSAHA algorithm (requires J2SE 1.4 or better).

  - Many bugs fixed!

I know I've missed some important bits here, so let's get
it updated before the release.

    Thomas.

From td2@sanger.ac.uk  Tue Jan 14 09:56:26 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Tue, 14 Jan 2003 09:56:26 +0000
Subject: [Biojava-l] library for running blast and formatdb
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165012E7FC9@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE5165012E7FC9@inbox.agresearch.co.nz>
Message-ID: <20030114095626.GA409306@jabba.sanger.ac.uk>

On Tue, Jan 14, 2003 at 09:40:02AM +1300, Schreiber, Mark wrote:
> I notice there is a Object call AppBeanRunner that appears to make an
> object from an XML file then instantiate it. Is it intended for the type
> of activity below or something else?

Possibly.  The AppBean stuff is very simple, rather generic:

   <bean jclass="org.example.Foo">
     <string name="hello" value="Boo!" />
     <boolean name="isTesting" value="true" />
     <bean name="bar" jclass="org.example.Bar">
       <int name="prop1" value="42" />
       <set name="messages">
         <string value="Hello" />
         <string value="Goodbye" />
       </set>
     </bean>
   </bean>

It's something I wrote a *long* time ago, and use as a quick'n'dirty
way of configuring some of my applications.  The two you might have
come across are the Eponine trainer and Dazzle DAS server.  As I say,
it's quite old, and I'm not that happy about the format (although
I've not seen anything similar which handles collections so nicely).

I don't think I'd really advise it for new projects unless you either
like it, or need something that works very quickly.  SOAP-ENC probably
makes more sense these days.

    Thomas.


From Markus.Roth@tg.fh-giessen.de  Mon Jan 13 09:36:02 2003
From: Markus.Roth@tg.fh-giessen.de (Markus Roth)
Date: Mon, 13 Jan 2003 10:36:02 +0100
Subject: [Biojava-l] BlastLikeAlignment with BlastLikeSearchBuilder
Message-ID: <200212201445.34534.markus.roth@tg.fh-giessen.de>

hi there,
I've been trying to create SeqSimilaritySearchResults from SAX
with the BlastLikeSearchBuilder. Is there any possibility to get
the MatchConsensus from the Alignment ?
or is there nothing about the Consensus in the SeqSimilaritySearchHit 
(SeqSimilaritySearchSubHit) ?
I found something like this in  Blast2HTMLHandler --> BlastLikeAlignment,
how can I get this with the SeqSimilarityAdapter ?

regards
Max


From kdj@sanger.ac.uk  Tue Jan 14 10:58:09 2003
From: kdj@sanger.ac.uk (Keith James)
Date: 14 Jan 2003 10:58:09 +0000
Subject: [Biojava-l] BioJava 1.3pre1
In-Reply-To: <20030114094207.GB409088@jabba.sanger.ac.uk>
References: <20030113233136.GC406225@jabba.sanger.ac.uk>
 <BA48CDAD.1C258%gilmanb@genome.wi.mit.edu>
 <20030114094207.GB409088@jabba.sanger.ac.uk>
Message-ID: <sc4n0m4knge.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>

>>>>> "Thomas" == Thomas Down <td2@sanger.ac.uk> writes:
  
    Thomas>   - Improvements to the handler code for building object
    Thomas> models from search results (Keith?).  BlastXML support.

Mostly fixes in the search result arena, I think (aside from now using
StAX).

Also

   - KMP and regex searching of SymbolLists.

   - RestrictionEnzyme features with support for managing REBASE
     flatfiles.

cheers,

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -


From kdj@sanger.ac.uk  Tue Jan 14 11:46:08 2003
From: kdj@sanger.ac.uk (Keith James)
Date: 14 Jan 2003 11:46:08 +0000
Subject: [Biojava-l] BlastLikeAlignment with BlastLikeSearchBuilder
In-Reply-To: <200212201445.34534.markus.roth@tg.fh-giessen.de>
References: <200212201445.34534.markus.roth@tg.fh-giessen.de>
Message-ID: <sc4fzrwkl8f.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>

>>>>> "Max" == Markus Roth <Markus.Roth@tg.fh-giessen.de> writes:

    Max> hi there, I've been trying to create
    Max> SeqSimilaritySearchResults from SAX with the
    Max> BlastLikeSearchBuilder. Is there any possibility to get the
    Max> MatchConsensus from the Alignment ?  or is there nothing
    Max> about the Consensus in the SeqSimilaritySearchHit
    Max> (SeqSimilaritySearchSubHit) ?  I found something like this in
    Max> Blast2HTMLHandler --> BlastLikeAlignment, how can I get this
    Max> with the SeqSimilarityAdapter ?

    Max> regards Max

Hi,

The short answer is that the only alignment information retained by a
SeqSimilaritySearchSubHit is the Alignment object itself.

The long answer is that there are two main parts to the blast/fasta
handling code; the parser, which passes on absolutely all the
information in the blast reports as SAX events and the handlers, which
interpret some (or all) of the events. Not all handlers will use all
the events and the current BlastLikeSearchBuilder ignores the
MatchConsensus data, mainly because the SeqSimilaritySearch object
model is quite restricted. The Blast2HTMLHandler uses all the SAX
events, which is why you can see the MatchConsensus in its output.

This is something which could be changed if there is the
demand. Perhaps the SeqSimilaritySearch interfaces could be richer?
Does anyone on the mailing list have opinions on this?

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -


From olivier.jeffroy@wanadoo.fr  Tue Jan 14 13:25:13 2003
From: olivier.jeffroy@wanadoo.fr (Olivier JEFFROY)
Date: Tue, 14 Jan 2003 14:25:13 +0100 (MET)
Subject: [Biojava-l] Problem to translate RNA into DNA with 'N' ambuguity
Message-ID: <3E075B3200A2993F@mel-rta8.wanadoo.fr> (added by postmaster@wanadoo.fr)

Hye everyone,

I'm new using Biojava and I have a little problem to solve. I have DNA sequences which come from sequencing. in these sequences, I have N (ambiguity on a,t,g,c nucleotids). I'd like to know I could resolve my problem.

I hope someone could answer me

Best regards
Olivier



From MCCon012@mc.duke.edu  Tue Jan 14 13:32:36 2003
From: MCCon012@mc.duke.edu (Patrick McConnell)
Date: Tue, 14 Jan 2003 08:32:36 -0500
Subject: [Biojava-l] library for running blast and formatdb
Message-ID: <OF6B02261D.0899962E-ON85256CAE.00490662-85256CAE.004A93F3@notes.duke.edu>

What I have written provides two essential base classes: Program and
Parameters.  The Program class provides the functionality for launching a
program and capturing output.  I should also put in hooks for handling the
input and output as streams as an alternative to capturing it in memory.
The Parameters class builds command arguments based on the fields of the
extending class using reflection.  It provides some flexibility for
determining what the flags and delimitters look like.  There has been
discussion to change the implementation somewhat to use jakarta's CLI
library, and I think a hybrid of the two would be appropriate.

I have written Program and Parameters implementations for NCBI's blastall
and formatdb programs.  Now, after chatting with Jason Stajich here at
Duke, I am working on a flexible queueing system for Programs.  This code
isn't complete yet, though.

So, if everyone likes this framework for launching programs, I'd be glad to
donate it to BioJava.  If people don't like it, I'll change it based on
suggestions.  Whomever is interested, please check out:
http://www.dbsr.duke.edu/software/blast . My code is fully documented, and
I have added a couple examples that demonstrate the ease of launching
blast.

As to the XML description of program parameters, I think that is a good
idea, and can be a factory method in my Parameters class.  The method takes
in the XML somehow (File or Stream or whatever) and returns a Parameters
object.  But, I know that some people would prefer to handle the Parameters
internally with code instead of externally in a File.  So, we should not
limit ourselves to a single approach.

Thanks!

-Patrick





"Schreiber, Mark" <mark.schreiber@agresearch.co.nz>@biojava.org on
01/13/2003 03:08:08 PM

Sent by:    biojava-l-admin@biojava.org


To:    "Patrick McConnell" <MCCon012@mc.duke.edu>
cc:    <biojava-l@biojava.org>

Subject:    RE: [Biojava-l] library for running blast and formatdb

One thing sorely missing from BioJava is the ability to launch and
capture the results of common bioinformatics programs. I know Java isn't
the best at this but it's not that bad. It's also needed if you want to
develop pipeline type applications.

Would it be possible to get some kind of over-arching interface based
API so that services can be made available with similar interfaces.

Possibly a Service or Program interface a Paramater list or map, some
kind of result stream?

Just my $0.02

- Mark

> -----Original Message-----
> From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> Sent: Tuesday, 14 January 2003 4:15 a.m.
> To: biojava-l@biojava.org
> Subject: Re: [Biojava-l] library for running blast and formatdb
>
>
>
>
> >I suppose it's a matter of another external dependency vs.
> reinvented
> >utility code in biojava . . .  Would it make sense to merge
> the better
> >qualities of the two?
>
> The CLI project looks like it is quite flexible and robust.
> But, with this, it is somewhat complex.  This is in contrast
> to the simplicity of creating parameters via reflection.  I
> think that these two methods could be effectively combined so
> that we gain the simplicty of reflection with the flexibility
> of CLI.  The base parameters class can use CLI to build its
> parameters.  As an option, it can build CLI options via
> reflection for simplicity.  When users extend the base class,
> they can utilize the flexibility of CLI if they need it,
> otherwise they can use reflection for a quick and dirty
> parameter parsing.  The base class could even extend the
> Options class, so we are really working with a hybrid of the
> two.  What does everyone think?
>
> -Patrick
>
>
>
>
>
>
> "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
> 01/10/2003 05:18:52 PM
>
> Sent by:    Michael Heuer <heuermh@shell3.shore.net>
>
>
> To:    Patrick McConnell <MCCon012@mc.duke.edu>
> cc:    biojava-l@biojava.org
>
> Subject:    Re: [Biojava-l] library for running blast and formatdb
>
>
> On Fri, 10 Jan 2003, Patrick McConnell wrote:
>
> > In the process, I developed some useful and flexible base
> classes for
> > formatting parameters and running programs.  Parameters are
> > automatically converted to an argument array via reflection and
> > reading of standard out and standard error in separate threads is
> > handled automatically.
>
> The base classes are nice, but I prefer the design of
>
> > http://jakarta.apache.org/commons/cli
>
> a lot better for handling parameters.
>
> I suppose it's a matter of another external dependency vs.
> reinvented utility code in biojava . . .  Would it make sense
> to merge the better qualities of the two?
>
> I also have a few simple classes for oneoff scripts with
> command line & logging facade support that I use all the time, see
>
> > http://www.shore.net/~heuermh/oneoff.tar.gz
>
> but they don't have any extra support for external programs.
>
>    michael
>
> >
> > Check it out if you are interested:
> > http://www.dbsr.duke.edu/software/blast/default.htm .  The full
> > source, javadocs, and binary class files are available.
> Also, if this
> > seems appropriate for BioJava, I have no problem donating it to the
> > cause.  I think that at least the base classes, or some
> modification
> > of them, would be useful to others.
> >
> > Please email me with suggestions/comments,
> >
> > -Patrick McConnell
> > Duke Bioinformatics Shared Resource
> > mccon012@mc.duke.edu
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
>
>
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
=======================================================================
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
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From ecerami@yahoo.com  Tue Jan 14 13:50:52 2003
From: ecerami@yahoo.com (Ethan Cerami)
Date: Tue, 14 Jan 2003 05:50:52 -0800 (PST)
Subject: [Biojava-l] Sequence Range Question
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165012E7FC9@inbox.agresearch.co.nz>
Message-ID: <20030114135052.4035.qmail@web13305.mail.yahoo.com>

Ok, based on the feedback I got yesterday, I have made
much progress :-)  Right now, I am trying to create a
bare bones gene viewer that can render gene features
via a SequencePanel object.  For example, the code
below renders the Adam2 gene on chromosome 8.

Adam2 is located at:  Chromosome 8:  38997645 -
39047541 bp.  To render it, I have a 1MB dummy
sequence that starts at 1.  How do I create a dummy
sequence that starts at 38995000 so that I can show
the correct location?  Is there some way to create a
virtual offset?

Sample code is below.  Thanks again for any help!

Ethan 

import java.awt.*;
import java.awt.event.*;

import javax.swing.*;

import org.biojava.bio.*;
import org.biojava.bio.gui.sequence.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.seq.genomic.Gene;
import org.biojava.bio.symbol.*;
import org.biojava.utils.ChangeVetoException;

/**
 * Simple Gene Browser
 */
public class FeatureView extends JFrame {
	private final static int WINDOW = 1000000;  //  1
Million BP
	private Sequence sequence;
	private JPanel panel = new JPanel ();
	private MultiLineRenderer mlr = new MultiLineRenderer
();
	private RectangularBeadRenderer featr = new
RectangularBeadRenderer ();
	private RulerRenderer ruler = new RulerRenderer ();
	private SequencePanel seqPanel = new SequencePanel
();
	private FeatureBlockSequenceRenderer fbr =
			new FeatureBlockSequenceRenderer ();

	/**
	 * Constructor
	 */
	public FeatureView () throws Exception {
		sequence = createSequence ();
		addGenes (sequence);
		createGUI ();
	}

	/**
	 * Creates a Dummy Sequence
	 */
	private Sequence createSequence () {
		SymbolList dummyList = new DummySymbolList
(DNATools.getDNA (),
				WINDOW);
		Sequence sequence = new SimpleSequence (dummyList,
"ensembl", "ensembl",
				Annotation.EMPTY_ANNOTATION);
		return sequence;
	}

	/**
	 * Creates Multiple Genes
	 */
	private void addGenes (Sequence sequence)
			throws BioException, ChangeVetoException {
		//  Add Adam2 Gene
		//  Location:  Chromosome 8:  38997645 - 39047541 bp
		//  int adam2_start = 38997645;  this doesn't work
b/c
		//								 it's out of range
		int adam2_start = 20000;
		int adam2_length = 49896;
		Gene.Template gene = new Gene.Template ();
		gene.type = "gene";
		gene.source = "ensembl";
		gene.location = new RangeLocation (adam2_start,
adam2_start
				+ adam2_length);
		gene.annotation = Annotation.EMPTY_ANNOTATION;
		gene.strand = StrandedFeature.POSITIVE;
		sequence.createFeature (gene);

	}

	/**
	 * Create the User Interface
	 */
	private void createGUI () throws Exception {
		this.setTitle ("Gene Viewer");
		Container contentPane = this.getContentPane ();
		contentPane.add (panel, BorderLayout.CENTER);
		panel.add (seqPanel);

		// Register the FeatureRenderer with the
FeatureBlockSequenceRenderer
		fbr.setFeatureRenderer (featr);

		// Add Renderers to the MultiLineRenderer
		mlr.addRenderer (fbr);
		mlr.addRenderer (ruler);
		seqPanel.setRenderer (mlr);

		// Set the Sequence to Render
		seqPanel.setSequence (sequence);
		seqPanel.setRange (new RangeLocation (1, WINDOW));
		seqPanel.setScale (.0007);
	}

	/**
	 * Overridden so program terminates when window
closes
	 */
	protected void processWindowEvent (WindowEvent we) {
		if (we.getID () == WindowEvent.WINDOW_CLOSING) {
			System.exit (0);
		} else {
			super.processWindowEvent (we);
		}
	}

	/**
	 * Main Method
	 */
	public static void main (String[] args) throws
Exception {
		FeatureView featureView = new FeatureView ();
		featureView.pack ();
		featureView.show ();
	}

}



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From td2@sanger.ac.uk  Tue Jan 14 14:06:44 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Tue, 14 Jan 2003 14:06:44 +0000
Subject: [Biojava-l] Problem to translate RNA into DNA with 'N' ambuguity
In-Reply-To: <3E075B3200A2993F@mel-rta8.wanadoo.fr>
References: <3E075B3200A2993F@mel-rta8.wanadoo.fr>
Message-ID: <20030114140644.GA410454@jabba.sanger.ac.uk>

On Tue, Jan 14, 2003 at 02:25:13PM +0100, Olivier JEFFROY wrote:
> Hye everyone,
> 
> I'm new using Biojava and I have a little problem to solve. I have DNA sequences which come from sequencing. in these sequences, I have N (ambiguity on a,t,g,c nucleotids). I'd like to know I could resolve my problem.

Could you explain your problem in more detail?  In general, BioJava
has good support for ambiguous symbols, in any Alphabet.  Internally,
all possible ambiguities can be represented.

What do you mean by `translate'?  In biology, that normally
refers specifically to the RNA -> protein data conversion.

In BioJava, when you apply any kind of translation table to
an ambiguity symbol, it will translate all possible matching
symbols, then return an ambiguity symbol over all the possible
translations.  So if you convert the DNA 'n' [a,c,g,t] to RNA,
you'll get [a,c,g,u], which will also be printed as 'n' if you
write it to a file.  Similarly, if you translate the sequence
"agn" to protein, you'll get back the ambiguity symbol
[serine,argenine], since these are the two possible matching
amino acids.  But if you translate "ggn", you'll just get
back the (non-ambiguous) symbol for glycine, since that's
the only possible tranlation.

If you *are* talking about translating sequences containing
ambiguity symbols to protein, there was a problem in BioJava 1.2x
is you tried to print the resulting protein sequence, since only
a few protein ambiguities have standard single-letter
representations.  Those that don't gave an error when you tried
to print them.  BioJava 1.3 contains a workaround for this -- any
`unknown' ambiguity symbol is printed as a more general alternative
which does have a defined character.  So in a protein sequence, most
ambiguity symbols will just become "X".

Does this help?

    Thomas.

From gilmanb@genome.wi.mit.edu  Tue Jan 14 14:48:27 2003
From: gilmanb@genome.wi.mit.edu (Brian Gilman)
Date: Tue, 14 Jan 2003 09:48:27 -0500
Subject: [Biojava-l] library for running blast and formatdb
In-Reply-To: <20030114095626.GA409306@jabba.sanger.ac.uk>
Message-ID: <BA498D6B.1C68F%gilmanb@genome.wi.mit.edu>

On 1/14/03 4:56 AM, "Thomas Down" <td2@sanger.ac.uk> wrote:
Hey Guys,

    This has been written a million times before! It exists as a very nice
package on the jakarta apache web site in the "commons" called Digester.
Take a look.

                                Best,

                                    -B

> On Tue, Jan 14, 2003 at 09:40:02AM +1300, Schreiber, Mark wrote:
>> I notice there is a Object call AppBeanRunner that appears to make an
>> object from an XML file then instantiate it. Is it intended for the type
>> of activity below or something else?
> 
> Possibly.  The AppBean stuff is very simple, rather generic:
> 
>  <bean jclass="org.example.Foo">
>    <string name="hello" value="Boo!" />
>    <boolean name="isTesting" value="true" />
>    <bean name="bar" jclass="org.example.Bar">
>      <int name="prop1" value="42" />
>      <set name="messages">
>        <string value="Hello" />
>        <string value="Goodbye" />
>      </set>
>    </bean>
>  </bean>
> 
> It's something I wrote a *long* time ago, and use as a quick'n'dirty
> way of configuring some of my applications.  The two you might have
> come across are the Eponine trainer and Dazzle DAS server.  As I say,
> it's quite old, and I'm not that happy about the format (although
> I've not seen anything similar which handles collections so nicely).
> 
> I don't think I'd really advise it for new projects unless you either
> like it, or need something that works very quickly.  SOAP-ENC probably
> makes more sense these days.
> 
>   Thomas.
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 

-- 
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902



From heuermh@acm.org  Tue Jan 14 16:20:28 2003
From: heuermh@acm.org (Michael L. Heuer)
Date: Tue, 14 Jan 2003 11:20:28 -0500 (EST)
Subject: [Biojava-l] library for running blast and formatdb
In-Reply-To: <OF6B02261D.0899962E-ON85256CAE.00490662-85256CAE.004A93F3@notes.duke.edu>
Message-ID: <Pine.GSO.4.44.0301141114080.3632-100000@shell3.shore.net>

Other designs to consider

Configurable/Configuration

> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configurable.html
> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configuration.html

Parameterizable/Parameters

> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Parameterizable.html
> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Parameters.html


I find the Apache Avalon project to be completely full of good ideas
and full of completely unusable implementation.

   michael


On Tue, 14 Jan 2003, Patrick McConnell wrote:

>
> What I have written provides two essential base classes: Program and
> Parameters.  The Program class provides the functionality for launching a
> program and capturing output.  I should also put in hooks for handling the
> input and output as streams as an alternative to capturing it in memory.
> The Parameters class builds command arguments based on the fields of the
> extending class using reflection.  It provides some flexibility for
> determining what the flags and delimitters look like.  There has been
> discussion to change the implementation somewhat to use jakarta's CLI
> library, and I think a hybrid of the two would be appropriate.
>
> I have written Program and Parameters implementations for NCBI's blastall
> and formatdb programs.  Now, after chatting with Jason Stajich here at
> Duke, I am working on a flexible queueing system for Programs.  This code
> isn't complete yet, though.
>
> So, if everyone likes this framework for launching programs, I'd be glad to
> donate it to BioJava.  If people don't like it, I'll change it based on
> suggestions.  Whomever is interested, please check out:
> http://www.dbsr.duke.edu/software/blast . My code is fully documented, and
> I have added a couple examples that demonstrate the ease of launching
> blast.
>
> As to the XML description of program parameters, I think that is a good
> idea, and can be a factory method in my Parameters class.  The method takes
> in the XML somehow (File or Stream or whatever) and returns a Parameters
> object.  But, I know that some people would prefer to handle the Parameters
> internally with code instead of externally in a File.  So, we should not
> limit ourselves to a single approach.
>
> Thanks!
>
> -Patrick
>
>
>
>
>
> "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>@biojava.org on
> 01/13/2003 03:08:08 PM
>
> Sent by:    biojava-l-admin@biojava.org
>
>
> To:    "Patrick McConnell" <MCCon012@mc.duke.edu>
> cc:    <biojava-l@biojava.org>
>
> Subject:    RE: [Biojava-l] library for running blast and formatdb
>
> One thing sorely missing from BioJava is the ability to launch and
> capture the results of common bioinformatics programs. I know Java isn't
> the best at this but it's not that bad. It's also needed if you want to
> develop pipeline type applications.
>
> Would it be possible to get some kind of over-arching interface based
> API so that services can be made available with similar interfaces.
>
> Possibly a Service or Program interface a Paramater list or map, some
> kind of result stream?
>
> Just my $0.02
>
> - Mark
>
> > -----Original Message-----
> > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > To: biojava-l@biojava.org
> > Subject: Re: [Biojava-l] library for running blast and formatdb
> >
> >
> >
> >
> > >I suppose it's a matter of another external dependency vs.
> > reinvented
> > >utility code in biojava . . .  Would it make sense to merge
> > the better
> > >qualities of the two?
> >
> > The CLI project looks like it is quite flexible and robust.
> > But, with this, it is somewhat complex.  This is in contrast
> > to the simplicity of creating parameters via reflection.  I
> > think that these two methods could be effectively combined so
> > that we gain the simplicty of reflection with the flexibility
> > of CLI.  The base parameters class can use CLI to build its
> > parameters.  As an option, it can build CLI options via
> > reflection for simplicity.  When users extend the base class,
> > they can utilize the flexibility of CLI if they need it,
> > otherwise they can use reflection for a quick and dirty
> > parameter parsing.  The base class could even extend the
> > Options class, so we are really working with a hybrid of the
> > two.  What does everyone think?
> >
> > -Patrick
> >
> >
> >
> >
> >
> >
> > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
> > 01/10/2003 05:18:52 PM
> >
> > Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> >
> >
> > To:    Patrick McConnell <MCCon012@mc.duke.edu>
> > cc:    biojava-l@biojava.org
> >
> > Subject:    Re: [Biojava-l] library for running blast and formatdb
> >
> >
> > On Fri, 10 Jan 2003, Patrick McConnell wrote:
> >
> > > In the process, I developed some useful and flexible base
> > classes for
> > > formatting parameters and running programs.  Parameters are
> > > automatically converted to an argument array via reflection and
> > > reading of standard out and standard error in separate threads is
> > > handled automatically.
> >
> > The base classes are nice, but I prefer the design of
> >
> > > http://jakarta.apache.org/commons/cli
> >
> > a lot better for handling parameters.
> >
> > I suppose it's a matter of another external dependency vs.
> > reinvented utility code in biojava . . .  Would it make sense
> > to merge the better qualities of the two?
> >
> > I also have a few simple classes for oneoff scripts with
> > command line & logging facade support that I use all the time, see
> >
> > > http://www.shore.net/~heuermh/oneoff.tar.gz
> >
> > but they don't have any extra support for external programs.
> >
> >    michael
> >
> > >
> > > Check it out if you are interested:
> > > http://www.dbsr.duke.edu/software/blast/default.htm .  The full
> > > source, javadocs, and binary class files are available.
> > Also, if this
> > > seems appropriate for BioJava, I have no problem donating it to the
> > > cause.  I think that at least the base classes, or some
> > modification
> > > of them, would be useful to others.
> > >
> > > Please email me with suggestions/comments,
> > >
> > > -Patrick McConnell
> > > Duke Bioinformatics Shared Resource
> > > mccon012@mc.duke.edu
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>


From heuermh@acm.org  Tue Jan 14 16:38:55 2003
From: heuermh@acm.org (Michael L. Heuer)
Date: Tue, 14 Jan 2003 11:38:55 -0500 (EST)
Subject: [Biojava-l] library for running blast and formatdb
In-Reply-To: <Pine.GSO.4.44.0301141114080.3632-100000@shell3.shore.net>
Message-ID: <Pine.GSO.4.44.0301141137510.3632-100000@shell3.shore.net>

On Tue, 14 Jan 2003, Michael L. Heuer wrote:

>
> Other designs to consider
>
> Configurable/Configuration
>
> > http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configurable.html
> > http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configuration.html
>
> Parameterizable/Parameters
>
> > http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Parameterizable.html
> > http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Parameters.html

sorry, bad links.

should be

http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/parameters/Parameterizable.java
http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/parameters/Parameters.java

got caught by cut n' paste.

   michael

>
>
> I find the Apache Avalon project to be completely full of good ideas
> and full of completely unusable implementation.
>
>    michael
>
>
> On Tue, 14 Jan 2003, Patrick McConnell wrote:
>
> >
> > What I have written provides two essential base classes: Program and
> > Parameters.  The Program class provides the functionality for launching a
> > program and capturing output.  I should also put in hooks for handling the
> > input and output as streams as an alternative to capturing it in memory.
> > The Parameters class builds command arguments based on the fields of the
> > extending class using reflection.  It provides some flexibility for
> > determining what the flags and delimitters look like.  There has been
> > discussion to change the implementation somewhat to use jakarta's CLI
> > library, and I think a hybrid of the two would be appropriate.
> >
> > I have written Program and Parameters implementations for NCBI's blastall
> > and formatdb programs.  Now, after chatting with Jason Stajich here at
> > Duke, I am working on a flexible queueing system for Programs.  This code
> > isn't complete yet, though.
> >
> > So, if everyone likes this framework for launching programs, I'd be glad to
> > donate it to BioJava.  If people don't like it, I'll change it based on
> > suggestions.  Whomever is interested, please check out:
> > http://www.dbsr.duke.edu/software/blast . My code is fully documented, and
> > I have added a couple examples that demonstrate the ease of launching
> > blast.
> >
> > As to the XML description of program parameters, I think that is a good
> > idea, and can be a factory method in my Parameters class.  The method takes
> > in the XML somehow (File or Stream or whatever) and returns a Parameters
> > object.  But, I know that some people would prefer to handle the Parameters
> > internally with code instead of externally in a File.  So, we should not
> > limit ourselves to a single approach.
> >
> > Thanks!
> >
> > -Patrick
> >
> >
> >
> >
> >
> > "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>@biojava.org on
> > 01/13/2003 03:08:08 PM
> >
> > Sent by:    biojava-l-admin@biojava.org
> >
> >
> > To:    "Patrick McConnell" <MCCon012@mc.duke.edu>
> > cc:    <biojava-l@biojava.org>
> >
> > Subject:    RE: [Biojava-l] library for running blast and formatdb
> >
> > One thing sorely missing from BioJava is the ability to launch and
> > capture the results of common bioinformatics programs. I know Java isn't
> > the best at this but it's not that bad. It's also needed if you want to
> > develop pipeline type applications.
> >
> > Would it be possible to get some kind of over-arching interface based
> > API so that services can be made available with similar interfaces.
> >
> > Possibly a Service or Program interface a Paramater list or map, some
> > kind of result stream?
> >
> > Just my $0.02
> >
> > - Mark
> >
> > > -----Original Message-----
> > > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> > > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > > To: biojava-l@biojava.org
> > > Subject: Re: [Biojava-l] library for running blast and formatdb
> > >
> > >
> > >
> > >
> > > >I suppose it's a matter of another external dependency vs.
> > > reinvented
> > > >utility code in biojava . . .  Would it make sense to merge
> > > the better
> > > >qualities of the two?
> > >
> > > The CLI project looks like it is quite flexible and robust.
> > > But, with this, it is somewhat complex.  This is in contrast
> > > to the simplicity of creating parameters via reflection.  I
> > > think that these two methods could be effectively combined so
> > > that we gain the simplicty of reflection with the flexibility
> > > of CLI.  The base parameters class can use CLI to build its
> > > parameters.  As an option, it can build CLI options via
> > > reflection for simplicity.  When users extend the base class,
> > > they can utilize the flexibility of CLI if they need it,
> > > otherwise they can use reflection for a quick and dirty
> > > parameter parsing.  The base class could even extend the
> > > Options class, so we are really working with a hybrid of the
> > > two.  What does everyone think?
> > >
> > > -Patrick
> > >
> > >
> > >
> > >
> > >
> > >
> > > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
> > > 01/10/2003 05:18:52 PM
> > >
> > > Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> > >
> > >
> > > To:    Patrick McConnell <MCCon012@mc.duke.edu>
> > > cc:    biojava-l@biojava.org
> > >
> > > Subject:    Re: [Biojava-l] library for running blast and formatdb
> > >
> > >
> > > On Fri, 10 Jan 2003, Patrick McConnell wrote:
> > >
> > > > In the process, I developed some useful and flexible base
> > > classes for
> > > > formatting parameters and running programs.  Parameters are
> > > > automatically converted to an argument array via reflection and
> > > > reading of standard out and standard error in separate threads is
> > > > handled automatically.
> > >
> > > The base classes are nice, but I prefer the design of
> > >
> > > > http://jakarta.apache.org/commons/cli
> > >
> > > a lot better for handling parameters.
> > >
> > > I suppose it's a matter of another external dependency vs.
> > > reinvented utility code in biojava . . .  Would it make sense
> > > to merge the better qualities of the two?
> > >
> > > I also have a few simple classes for oneoff scripts with
> > > command line & logging facade support that I use all the time, see
> > >
> > > > http://www.shore.net/~heuermh/oneoff.tar.gz
> > >
> > > but they don't have any extra support for external programs.
> > >
> > >    michael
> > >
> > > >
> > > > Check it out if you are interested:
> > > > http://www.dbsr.duke.edu/software/blast/default.htm .  The full
> > > > source, javadocs, and binary class files are available.
> > > Also, if this
> > > > seems appropriate for BioJava, I have no problem donating it to the
> > > > cause.  I think that at least the base classes, or some
> > > modification
> > > > of them, would be useful to others.
> > > >
> > > > Please email me with suggestions/comments,
> > > >
> > > > -Patrick McConnell
> > > > Duke Bioinformatics Shared Resource
> > > > mccon012@mc.duke.edu
> > > >
> > > >
> > > > _______________________________________________
> > > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > > http://biojava.org/mailman/listinfo/biojava-l
> > > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> > =======================================================================
> > Attention: The information contained in this message and/or attachments
> > from AgResearch Limited is intended only for the persons or entities
> > to which it is addressed and may contain confidential and/or privileged
> > material. Any review, retransmission, dissemination or other use of, or
> > taking of any action in reliance upon, this information by persons or
> > entities other than the intended recipients is prohibited by AgResearch
> > Limited. If you have received this message in error, please notify the
> > sender immediately.
> > =======================================================================
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
> >
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>


From heuermh@acm.org  Tue Jan 14 16:59:01 2003
From: heuermh@acm.org (Michael L. Heuer)
Date: Tue, 14 Jan 2003 11:59:01 -0500 (EST)
Subject: [Biojava-l] library for running blast and formatdb
In-Reply-To: <Pine.GSO.4.44.0301141137510.3632-100000@shell3.shore.net>
Message-ID: <Pine.GSO.4.44.0301141154030.3632-100000@shell3.shore.net>

Last one, I promise.

There's also

Commons Configuration project

> http://jakarta.apache.org/commons/sandbox/configuration/index.html

   michael


On Tue, 14 Jan 2003, Michael L. Heuer wrote:

>
> On Tue, 14 Jan 2003, Michael L. Heuer wrote:
>
> >
> > Other designs to consider
> >
> > Configurable/Configuration
> >
> > > http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configurable.html
> > > http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Configuration.html
> >
> > Parameterizable/Parameters
> >
> > > http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Parameterizable.html
> > > http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/configuration/Parameters.html
>
> sorry, bad links.
>
> should be
>
> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/parameters/Parameterizable.java
> http://jakarta.apache.org/avalon/api/org/apache/avalon/framework/parameters/Parameters.java
>
> got caught by cut n' paste.
>
>    michael
>
> >
> >
> > I find the Apache Avalon project to be completely full of good ideas
> > and full of completely unusable implementation.
> >
> >    michael
> >
> >
> > On Tue, 14 Jan 2003, Patrick McConnell wrote:
> >
> > >
> > > What I have written provides two essential base classes: Program and
> > > Parameters.  The Program class provides the functionality for launching a
> > > program and capturing output.  I should also put in hooks for handling the
> > > input and output as streams as an alternative to capturing it in memory.
> > > The Parameters class builds command arguments based on the fields of the
> > > extending class using reflection.  It provides some flexibility for
> > > determining what the flags and delimitters look like.  There has been
> > > discussion to change the implementation somewhat to use jakarta's CLI
> > > library, and I think a hybrid of the two would be appropriate.
> > >
> > > I have written Program and Parameters implementations for NCBI's blastall
> > > and formatdb programs.  Now, after chatting with Jason Stajich here at
> > > Duke, I am working on a flexible queueing system for Programs.  This code
> > > isn't complete yet, though.
> > >
> > > So, if everyone likes this framework for launching programs, I'd be glad to
> > > donate it to BioJava.  If people don't like it, I'll change it based on
> > > suggestions.  Whomever is interested, please check out:
> > > http://www.dbsr.duke.edu/software/blast . My code is fully documented, and
> > > I have added a couple examples that demonstrate the ease of launching
> > > blast.
> > >
> > > As to the XML description of program parameters, I think that is a good
> > > idea, and can be a factory method in my Parameters class.  The method takes
> > > in the XML somehow (File or Stream or whatever) and returns a Parameters
> > > object.  But, I know that some people would prefer to handle the Parameters
> > > internally with code instead of externally in a File.  So, we should not
> > > limit ourselves to a single approach.
> > >
> > > Thanks!
> > >
> > > -Patrick
> > >
> > >
> > >
> > >
> > >
> > > "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>@biojava.org on
> > > 01/13/2003 03:08:08 PM
> > >
> > > Sent by:    biojava-l-admin@biojava.org
> > >
> > >
> > > To:    "Patrick McConnell" <MCCon012@mc.duke.edu>
> > > cc:    <biojava-l@biojava.org>
> > >
> > > Subject:    RE: [Biojava-l] library for running blast and formatdb
> > >
> > > One thing sorely missing from BioJava is the ability to launch and
> > > capture the results of common bioinformatics programs. I know Java isn't
> > > the best at this but it's not that bad. It's also needed if you want to
> > > develop pipeline type applications.
> > >
> > > Would it be possible to get some kind of over-arching interface based
> > > API so that services can be made available with similar interfaces.
> > >
> > > Possibly a Service or Program interface a Paramater list or map, some
> > > kind of result stream?
> > >
> > > Just my $0.02
> > >
> > > - Mark
> > >
> > > > -----Original Message-----
> > > > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> > > > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > > > To: biojava-l@biojava.org
> > > > Subject: Re: [Biojava-l] library for running blast and formatdb
> > > >
> > > >
> > > >
> > > >
> > > > >I suppose it's a matter of another external dependency vs.
> > > > reinvented
> > > > >utility code in biojava . . .  Would it make sense to merge
> > > > the better
> > > > >qualities of the two?
> > > >
> > > > The CLI project looks like it is quite flexible and robust.
> > > > But, with this, it is somewhat complex.  This is in contrast
> > > > to the simplicity of creating parameters via reflection.  I
> > > > think that these two methods could be effectively combined so
> > > > that we gain the simplicty of reflection with the flexibility
> > > > of CLI.  The base parameters class can use CLI to build its
> > > > parameters.  As an option, it can build CLI options via
> > > > reflection for simplicity.  When users extend the base class,
> > > > they can utilize the flexibility of CLI if they need it,
> > > > otherwise they can use reflection for a quick and dirty
> > > > parameter parsing.  The base class could even extend the
> > > > Options class, so we are really working with a hybrid of the
> > > > two.  What does everyone think?
> > > >
> > > > -Patrick
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
> > > > 01/10/2003 05:18:52 PM
> > > >
> > > > Sent by:    Michael Heuer <heuermh@shell3.shore.net>
> > > >
> > > >
> > > > To:    Patrick McConnell <MCCon012@mc.duke.edu>
> > > > cc:    biojava-l@biojava.org
> > > >
> > > > Subject:    Re: [Biojava-l] library for running blast and formatdb
> > > >
> > > >
> > > > On Fri, 10 Jan 2003, Patrick McConnell wrote:
> > > >
> > > > > In the process, I developed some useful and flexible base
> > > > classes for
> > > > > formatting parameters and running programs.  Parameters are
> > > > > automatically converted to an argument array via reflection and
> > > > > reading of standard out and standard error in separate threads is
> > > > > handled automatically.
> > > >
> > > > The base classes are nice, but I prefer the design of
> > > >
> > > > > http://jakarta.apache.org/commons/cli
> > > >
> > > > a lot better for handling parameters.
> > > >
> > > > I suppose it's a matter of another external dependency vs.
> > > > reinvented utility code in biojava . . .  Would it make sense
> > > > to merge the better qualities of the two?
> > > >
> > > > I also have a few simple classes for oneoff scripts with
> > > > command line & logging facade support that I use all the time, see
> > > >
> > > > > http://www.shore.net/~heuermh/oneoff.tar.gz
> > > >
> > > > but they don't have any extra support for external programs.
> > > >
> > > >    michael
> > > >
> > > > >
> > > > > Check it out if you are interested:
> > > > > http://www.dbsr.duke.edu/software/blast/default.htm .  The full
> > > > > source, javadocs, and binary class files are available.
> > > > Also, if this
> > > > > seems appropriate for BioJava, I have no problem donating it to the
> > > > > cause.  I think that at least the base classes, or some
> > > > modification
> > > > > of them, would be useful to others.
> > > > >
> > > > > Please email me with suggestions/comments,
> > > > >
> > > > > -Patrick McConnell
> > > > > Duke Bioinformatics Shared Resource
> > > > > mccon012@mc.duke.edu
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > > > http://biojava.org/mailman/listinfo/biojava-l
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > > http://biojava.org/mailman/listinfo/biojava-l
> > > >
> > > =======================================================================
> > > Attention: The information contained in this message and/or attachments
> > > from AgResearch Limited is intended only for the persons or entities
> > > to which it is addressed and may contain confidential and/or privileged
> > > material. Any review, retransmission, dissemination or other use of, or
> > > taking of any action in reliance upon, this information by persons or
> > > entities other than the intended recipients is prohibited by AgResearch
> > > Limited. If you have received this message in error, please notify the
> > > sender immediately.
> > > =======================================================================
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>


From MCCon012@mc.duke.edu  Tue Jan 14 19:28:57 2003
From: MCCon012@mc.duke.edu (Patrick McConnell)
Date: Tue, 14 Jan 2003 14:28:57 -0500
Subject: [Biojava-l] library for running blast and formatdb]
Message-ID: <OF68546921.EE599A78-ON85256CAE.00680AC7-85256CAE.006B33E2@notes.duke.edu>

Thanks for all of the comments/suggestions.  There appear to be alot of
libraries out there that deal with parameterization, configuration,
launching external programs, etc.  And, they all appear to do it somewhat
differently.

I have completed more work on my lilbrary for launching applications.  It
uses Program and Parameters objects like I described before, and I have
added a Queue interface and ProgramQueue implementation that performs basic
queuing functions.  I have also implemented an NCBIBlastQueue class and
have successfully tested it as a web service.  Finally, I have also
implemented a QueueQueue class that exposes the Queue interface and runs
jobs through a list of Queues.  Thus, one could link queues together.  I
have not tested this part.

Forwarded below is another stab at the problem that EBI has made.  After
just glancing at the docs, it looks pretty good.  And, the developer on the
project (Martin Senger) appears dedicated to moving his code to BioPerl and
BioJava.  So, that sounds good to me.  Martin: please take a look at my
implementation and see if there is anything that you like : - )

I am sure it is not the cleanest of implementations, and I am open to
suggestions/comments.  If BioJava decides to adopt something different for
it's program infrastructure, then feel free to take anything from my code.

See more docs/examples at: http://www.dbsr.duke.edu/software/blast

-Patrick


---------------------- Forwarded by Patrick McConnell/CanCtr/mc/Duke on
01/14/2003 01:58 PM ---------------------------


Martin Senger <senger@ebi.ac.uk> on 01/14/2003 09:35:04 AM

To:    Patrick McConnell <MCCon012@mc.duke.edu>
cc:    Tom Oinn <tmo@ebi.ac.uk>, Alan Robinson <alan@ebi.ac.uk>

Subject:    RE: [Biojava-l] library for running blast and formatdb]

Hi Patrick,
   [ I am not (always) on the BioJava mailing-list, but I have got your
email from my colleque Tom Oinn. If you feel appropriate you may forward
this answer to the mailing list. Or wouold you, Tom? Thanks.]

   I have written a Java-based project (but not purely, it uses also Perl
launchers) dealing with starting/running/controlling extrenal processes
(such the EMBOSS). It has advantages and disadvanatges.

   Advantages are:
      - It's around for about five years now and it's quite stable.
      - The interface (functionality ) is based on an approved standard
(OMG). This includes both the methods for calling the external processes
and the XML DTD for describing command-line programs in (very) details. It
also includes generators to create such XML files from proprietary
metadata of some known packages (GCG, EMBOSS).

   Disadvantages are:
      - It uses CORBA - not everybody is happy with it. A slight remedy
is that I have created additional interface used as a WebService which may
be used instead of CORBA (even though the current implementation still
uses CORBA under the hood).
      - It has dependency on some general Java classes which I wrote
myself and useing them in all my projects. These tools are openly
available but it makes life more difficult if I wish to put the code into
BioJava.

   My current plans which I hope to finish during this year BioHackaton
(end of February) are:
   - To make another Java implementation without dependencies on CORBA
(but using roughly the same API). To do the same for Perl. Both these
implementations will behave the same (will have the same interface)
regardless if the extrenal process is:
   - a local program,
   - a remote program accessible via a CORBA server, or
   - a remote accessible via a WebSewrvice.
   I hope that the results will be accepted as contributions both to
BioPerl and BioJava (therefore I want to finalize it during the
BioHackaton where all key developers of BioJava and BioPerl will be
present)

   The relevant URLs are:
   http://industry.ebi.ac.uk/applab   (CORBA implementation)
   http://industry.ebi.ac.uk/soaplab  (Web Service implementation)
   http://industry.ebi.ac.uk/~senger/tools (general Java tools,
      particularly class embl.ebi.tools.Executor is interesting for this
      thread).

   Regards,
   Martin

>
>
> -------- Original Message --------
> Subject: RE: [Biojava-l] library for running blast and formatdb
> Date: Tue, 14 Jan 2003 08:32:36 -0500
> From: "Patrick McConnell" <MCCon012@mc.duke.edu>
> To: <biojava-l@biojava.org>
>
>
> What I have written provides two essential base classes: Program and
> Parameters.  The Program class provides the functionality for launching a
> program and capturing output.  I should also put in hooks for handling
the
> input and output as streams as an alternative to capturing it in memory.
> The Parameters class builds command arguments based on the fields of the
> extending class using reflection.  It provides some flexibility for
> determining what the flags and delimitters look like.  There has been
> discussion to change the implementation somewhat to use jakarta's CLI
> library, and I think a hybrid of the two would be appropriate.
>
> I have written Program and Parameters implementations for NCBI's blastall
> and formatdb programs.  Now, after chatting with Jason Stajich here at
> Duke, I am working on a flexible queueing system for Programs.  This code
> isn't complete yet, though.
>
> So, if everyone likes this framework for launching programs, I'd be glad
to
> donate it to BioJava.  If people don't like it, I'll change it based on
> suggestions.  Whomever is interested, please check out:
> http://www.dbsr.duke.edu/software/blast . My code is fully documented,
and
> I have added a couple examples that demonstrate the ease of launching
> blast.
>
> As to the XML description of program parameters, I think that is a good
> idea, and can be a factory method in my Parameters class.  The method
takes
> in the XML somehow (File or Stream or whatever) and returns a Parameters
> object.  But, I know that some people would prefer to handle the
Parameters
> internally with code instead of externally in a File.  So, we should not
> limit ourselves to a single approach.
>
> Thanks!
>
> -Patrick
>
>
>
>
>
> "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>@biojava.org on
> 01/13/2003 03:08:08 PM
>
> Sent by:    biojava-l-admin@biojava.org
>
>
> To:    "Patrick McConnell" <MCCon012@mc.duke.edu>
> cc:    <biojava-l@biojava.org>
>
> Subject:    RE: [Biojava-l] library for running blast and formatdb
>
> One thing sorely missing from BioJava is the ability to launch and
> capture the results of common bioinformatics programs. I know Java isn't
> the best at this but it's not that bad. It's also needed if you want to
> develop pipeline type applications.
>
> Would it be possible to get some kind of over-arching interface based
> API so that services can be made available with similar interfaces.
>
> Possibly a Service or Program interface a Paramater list or map, some
> kind of result stream?
>
> Just my $0.02
>
> - Mark
>
>  > -----Original Message-----
>  > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
>  > Sent: Tuesday, 14 January 2003 4:15 a.m.
>  > To: biojava-l@biojava.org
>  > Subject: Re: [Biojava-l] library for running blast and formatdb
>  >
>  >
>  >
>  >
>  > >I suppose it's a matter of another external dependency vs.
>  > reinvented
>  > >utility code in biojava . . .  Would it make sense to merge
>  > the better
>  > >qualities of the two?
>  >
>  > The CLI project looks like it is quite flexible and robust.
>  > But, with this, it is somewhat complex.  This is in contrast
>  > to the simplicity of creating parameters via reflection.  I
>  > think that these two methods could be effectively combined so
>  > that we gain the simplicty of reflection with the flexibility
>  > of CLI.  The base parameters class can use CLI to build its
>  > parameters.  As an option, it can build CLI options via
>  > reflection for simplicity.  When users extend the base class,
>  > they can utilize the flexibility of CLI if they need it,
>  > otherwise they can use reflection for a quick and dirty
>  > parameter parsing.  The base class could even extend the
>  > Options class, so we are really working with a hybrid of the
>  > two.  What does everyone think?
>  >
>  > -Patrick
>  >
>  >
>  >
>  >
>  >
>  >
>  > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
>  > 01/10/2003 05:18:52 PM
>  >
>  > Sent by:    Michael Heuer <heuermh@shell3.shore.net>
>  >
>  >
>  > To:    Patrick McConnell <MCCon012@mc.duke.edu>
>  > cc:    biojava-l@biojava.org
>  >
>  > Subject:    Re: [Biojava-l] library for running blast and formatdb
>  >
>  >
>  > On Fri, 10 Jan 2003, Patrick McConnell wrote:
>  >
>  > > In the process, I developed some useful and flexible base
>  > classes for
>  > > formatting parameters and running programs.  Parameters are
>  > > automatically converted to an argument array via reflection and
>  > > reading of standard out and standard error in separate threads is
>  > > handled automatically.
>  >
>  > The base classes are nice, but I prefer the design of
>  >
>  > > http://jakarta.apache.org/commons/cli
>  >
>  > a lot better for handling parameters.
>  >
>  > I suppose it's a matter of another external dependency vs.
>  > reinvented utility code in biojava . . .  Would it make sense
>  > to merge the better qualities of the two?
>  >
>  > I also have a few simple classes for oneoff scripts with
>  > command line & logging facade support that I use all the time, see
>  >
>  > > http://www.shore.net/~heuermh/oneoff.tar.gz
>  >
>  > but they don't have any extra support for external programs.
>  >
>  >    michael
>  >
>  > >
>  > > Check it out if you are interested:
>  > > http://www.dbsr.duke.edu/software/blast/default.htm .  The full
>  > > source, javadocs, and binary class files are available.
>  > Also, if this
>  > > seems appropriate for BioJava, I have no problem donating it to the
>  > > cause.  I think that at least the base classes, or some
>  > modification
>  > > of them, would be useful to others.
>  > >
>  > > Please email me with suggestions/comments,
>  > >
>  > > -Patrick McConnell
>  > > Duke Bioinformatics Shared Resource
>  > > mccon012@mc.duke.edu
>  > >
>  > >
>  > > _______________________________________________
>  > > Biojava-l mailing list  -  Biojava-l@biojava.org
>  > > http://biojava.org/mailman/listinfo/biojava-l
>  > >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  > _______________________________________________
>  > Biojava-l mailing list  -  Biojava-l@biojava.org
>  > http://biojava.org/mailman/listinfo/biojava-l
>  >
> =======================================================================
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> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
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--
Martin Senger

EMBL Outstation - Hinxton                Senger@EBI.ac.uk
European Bioinformatics Institute        Phone: (+44) 1223 494636
Wellcome Trust Genome Campus             (Switchboard:     494444)
Hinxton                                  Fax  : (+44) 1223 494468
Cambridge CB10 1SD
United Kingdom                           http://industry.ebi.ac.uk/~senger







From mark.schreiber@agresearch.co.nz  Tue Jan 14 20:01:45 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 15 Jan 2003 09:01:45 +1300
Subject: [Biojava-l] BioJava 1.3pre1
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E80B9@inbox.agresearch.co.nz>

Also,

There has been major work done on the Annotation API
ABI, RefSeq and Unigene parsing
Serialization seems pretty stable now
Rework of the Phred package to make the Phred Alphabet more sensible and
Phred Sequence much more elegant.
Circular Sequence coordinates/ locations are much better handeled now
and even work!

And ....
Believe it or not the Javadocs are a lot better.

- Mark

> -----Original Message-----
> From: Keith James [mailto:kdj@sanger.ac.uk] 
> Sent: Tuesday, 14 January 2003 11:58 p.m.
> To: Thomas Down; biojava-l@biojava.org
> Subject: Re: [Biojava-l] BioJava 1.3pre1
> 
> 
> >>>>> "Thomas" == Thomas Down <td2@sanger.ac.uk> writes:
>   
>     Thomas>   - Improvements to the handler code for building object
>     Thomas> models from search results (Keith?).  BlastXML support.
> 
> Mostly fixes in the search result arena, I think (aside from 
> now using StAX).
> 
> Also
> 
>    - KMP and regex searching of SymbolLists.
> 
>    - RestrictionEnzyme features with support for managing REBASE
>      flatfiles.
> 
> cheers,
> 
> Keith
> 
> -- 
> 
> - Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
> - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
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From mark.schreiber@agresearch.co.nz  Tue Jan 14 20:14:11 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 15 Jan 2003 09:14:11 +1300
Subject: [Biojava-l] Sequence Range Question
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E80C4@inbox.agresearch.co.nz>

Hi -

In this case, rather than using the SequencePanel you would use a
TranslatedSequencePanel which allows you to translate (offset) the
coordinates to display the bit you want.

- Mark


> -----Original Message-----
> From: Ethan Cerami [mailto:ecerami@yahoo.com] 
> Sent: Wednesday, 15 January 2003 2:51 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Sequence Range Question
> 
> 
> Ok, based on the feedback I got yesterday, I have made
> much progress :-)  Right now, I am trying to create a
> bare bones gene viewer that can render gene features
> via a SequencePanel object.  For example, the code
> below renders the Adam2 gene on chromosome 8.
> 
> Adam2 is located at:  Chromosome 8:  38997645 -
> 39047541 bp.  To render it, I have a 1MB dummy
> sequence that starts at 1.  How do I create a dummy
> sequence that starts at 38995000 so that I can show
> the correct location?  Is there some way to create a
> virtual offset?
> 
> Sample code is below.  Thanks again for any help!
> 
> Ethan 
> 
> import java.awt.*;
> import java.awt.event.*;
> 
> import javax.swing.*;
> 
> import org.biojava.bio.*;
> import org.biojava.bio.gui.sequence.*;
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.impl.SimpleSequence;
> import org.biojava.bio.seq.genomic.Gene;
> import org.biojava.bio.symbol.*;
> import org.biojava.utils.ChangeVetoException;
> 
> /**
>  * Simple Gene Browser
>  */
> public class FeatureView extends JFrame {
> 	private final static int WINDOW = 1000000;  //  1
> Million BP
> 	private Sequence sequence;
> 	private JPanel panel = new JPanel ();
> 	private MultiLineRenderer mlr = new MultiLineRenderer
> ();
> 	private RectangularBeadRenderer featr = new 
> RectangularBeadRenderer ();
> 	private RulerRenderer ruler = new RulerRenderer ();
> 	private SequencePanel seqPanel = new SequencePanel
> ();
> 	private FeatureBlockSequenceRenderer fbr =
> 			new FeatureBlockSequenceRenderer ();
> 
> 	/**
> 	 * Constructor
> 	 */
> 	public FeatureView () throws Exception {
> 		sequence = createSequence ();
> 		addGenes (sequence);
> 		createGUI ();
> 	}
> 
> 	/**
> 	 * Creates a Dummy Sequence
> 	 */
> 	private Sequence createSequence () {
> 		SymbolList dummyList = new DummySymbolList
> (DNATools.getDNA (),
> 				WINDOW);
> 		Sequence sequence = new SimpleSequence (dummyList,
> "ensembl", "ensembl",
> 				Annotation.EMPTY_ANNOTATION);
> 		return sequence;
> 	}
> 
> 	/**
> 	 * Creates Multiple Genes
> 	 */
> 	private void addGenes (Sequence sequence)
> 			throws BioException, ChangeVetoException {
> 		//  Add Adam2 Gene
> 		//  Location:  Chromosome 8:  38997645 - 39047541 bp
> 		//  int adam2_start = 38997645;  this doesn't work
> b/c
> 		//						
> 		 it's out of range
> 		int adam2_start = 20000;
> 		int adam2_length = 49896;
> 		Gene.Template gene = new Gene.Template ();
> 		gene.type = "gene";
> 		gene.source = "ensembl";
> 		gene.location = new RangeLocation (adam2_start,
> adam2_start
> 				+ adam2_length);
> 		gene.annotation = Annotation.EMPTY_ANNOTATION;
> 		gene.strand = StrandedFeature.POSITIVE;
> 		sequence.createFeature (gene);
> 
> 	}
> 
> 	/**
> 	 * Create the User Interface
> 	 */
> 	private void createGUI () throws Exception {
> 		this.setTitle ("Gene Viewer");
> 		Container contentPane = this.getContentPane ();
> 		contentPane.add (panel, BorderLayout.CENTER);
> 		panel.add (seqPanel);
> 
> 		// Register the FeatureRenderer with the 
> FeatureBlockSequenceRenderer
> 		fbr.setFeatureRenderer (featr);
> 
> 		// Add Renderers to the MultiLineRenderer
> 		mlr.addRenderer (fbr);
> 		mlr.addRenderer (ruler);
> 		seqPanel.setRenderer (mlr);
> 
> 		// Set the Sequence to Render
> 		seqPanel.setSequence (sequence);
> 		seqPanel.setRange (new RangeLocation (1, WINDOW));
> 		seqPanel.setScale (.0007);
> 	}
> 
> 	/**
> 	 * Overridden so program terminates when window
> closes
> 	 */
> 	protected void processWindowEvent (WindowEvent we) {
> 		if (we.getID () == WindowEvent.WINDOW_CLOSING) {
> 			System.exit (0);
> 		} else {
> 			super.processWindowEvent (we);
> 		}
> 	}
> 
> 	/**
> 	 * Main Method
> 	 */
> 	public static void main (String[] args) throws
> Exception {
> 		FeatureView featureView = new FeatureView ();
> 		featureView.pack ();
> 		featureView.show ();
> 	}
> 
> }
> 
> 
> 
> __________________________________________________
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> Yahoo! Mail Plus - Powerful. Affordable. Sign up now. 
> http://mailplus.yahoo.com 
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> 
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From tmo@ebi.ac.uk  Tue Jan 14 20:46:29 2003
From: tmo@ebi.ac.uk (Tom Oinn)
Date: Tue, 14 Jan 2003 20:46:29 +0000
Subject: [Biojava-l] library for running blast and formatdb]
References: <OF68546921.EE599A78-ON85256CAE.00680AC7-85256CAE.006B33E2@notes.duke.edu>
Message-ID: <3E247725.3040208@ebi.ac.uk>


Patrick McConnell wrote:

> Forwarded below is another stab at the problem that EBI has made.  After
> just glancing at the docs, it looks pretty good.  And, the developer on the
> project (Martin Senger) appears dedicated to moving his code to BioPerl and
> BioJava.  So, that sounds good to me.  Martin: please take a look at my
> implementation and see if there is anything that you like : - )

Following up from that, I have code in my interface builder that talks 
to Martin's soaplab system, anyone curious could take a look at 
http://www.ebi.ac.uk/collab/mygrid/service1/talisman and click on the 
'emboss tutorial workflow' demo application. Soaplab has turned out to 
be remarkably easy to use, generally about five or six lines of code on 
the client side (admittedly Talisman's soaplab client code is longer, 
see 
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/talisman/talisman1.4/src/org/embl/ebi/escience/talisman/action/CallSoapLab.java?rev=1.5&content-type=text/vnd.viewcvs-markup) 
, obviously we're pushing it pretty heavily as part of this MyGrid 
project. It's maybe worth pointing out that although we're using Soaplab 
to access the EMBOSS toolset, it can (and is) accessing other systems.

Ciao!

Tom


From sediga@av8.net  Tue Jan 14 22:19:01 2003
From: sediga@av8.net (Art Sedighi)
Date: Tue, 14 Jan 2003 17:19:01 -0500
Subject: [Biojava-l] Looking to help out
Message-ID: <004801c2bc1a$f16058b0$0b01a8c0@cheetar>

Hi all,
I am very interested in helping out with some open source projects that are
going on in order to get more experience in this field.  Anyone needs any
help?

Thanks
Art
sediga@av8.net



From mark.schreiber@agresearch.co.nz  Tue Jan 14 22:29:34 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Wed, 15 Jan 2003 11:29:34 +1300
Subject: [Biojava-l] Looking to help out
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E810C@inbox.agresearch.co.nz>

Hi -

Help is always welcome, perhaps if you outline what you are experienced
at and what you would like to do with biojava.

Regards

- Mark

> -----Original Message-----
> From: Art Sedighi [mailto:sediga@av8.net] 
> Sent: Wednesday, 15 January 2003 11:19 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Looking to help out
> 
> 
> Hi all,
> I am very interested in helping out with some open source 
> projects that are going on in order to get more experience in 
> this field.  Anyone needs any help?
> 
> Thanks
> Art
> sediga@av8.net
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
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From sediga@av8.net  Tue Jan 14 22:59:24 2003
From: sediga@av8.net (Art Sedighi)
Date: Tue, 14 Jan 2003 17:59:24 -0500
Subject: [Biojava-l] Looking to help out
References: <AF026AF0FF4B054590228FD1F1DE5165012E810C@inbox.agresearch.co.nz>
Message-ID: <005101c2bc20$95b1fb80$0b01a8c0@cheetar>

Hi Mark, et. al.
I have a strong background in Software Engineering which mostly includes
software architecture, design, and implementation.  I can go pretty much
anything, but GUI stuff...

I hope this helps...

Thanks
Art
----- Original Message -----
From: "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>
To: "Art Sedighi" <sediga@av8.net>; <biojava-l@biojava.org>
Sent: Tuesday, January 14, 2003 5:29 PM
Subject: RE: [Biojava-l] Looking to help out


Hi -

Help is always welcome, perhaps if you outline what you are experienced
at and what you would like to do with biojava.

Regards

- Mark

> -----Original Message-----
> From: Art Sedighi [mailto:sediga@av8.net]
> Sent: Wednesday, 15 January 2003 11:19 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Looking to help out
>
>
> Hi all,
> I am very interested in helping out with some open source
> projects that are going on in order to get more experience in
> this field.  Anyone needs any help?
>
> Thanks
> Art
> sediga@av8.net
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
=======================================================================
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From support@biotaq.com  Thu Jan 16 02:17:26 2003
From: support@biotaq.com (support@biotaq.com)
Date: Wed, 15 Jan 2003 21:17:26 -0500
Subject: [Biojava-l] SRI's Antibody World Summit
Message-ID: <002cf2617021013VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net>

Antibody World Summit to be Attended by Global Pharma & Biotech Industries
in San Diego, CA Feb 24-28, 2003

Jan. 15, San Diego, CA. The world antibody community will convene in San
Diego, CA on from February 24-28, 2003 to attend a series of four related
antibody meetings in what promises to be the most comprehensive industry
information, business development and networking extravaganza ever offered
on this topic, announces Strategic Research Institute.

The meeting schedule is as follows:

Antibody Discovery & Pre-Clinical Drug Development, February 24-26

Antibody Clinical Development & Marketing, February 24-26

Trends in Antibody Deal-Making & Financing, February 27-28

Macromolecule Production & Economics, February 27-28

Detailed agenda and speaker list available at
http://www.srinstitute.com/abworldsummit


FEATURES:

The Summit features over 100 speakers, dozens of exhibits, and will draw
over 600+ attendees all focused on every aspect of the field.

Research advances, emerging therapeutics, new technologies, antibody
marketing, clinical cost optimization, production economics, large scale
manufacturing, partnering and financing topics, intellectual property and
the latest in the clinical pipeline are some of the Summit highlights.

VENUE:
The Summit will take place at the Wyndham U.S. Grant in San Diego, CA.
Socializing and networking events are scheduled throughout the week.

REGISTRATION:
To register, call 1-888-666-8514, 646-336-7030, or online at
http://www.srinstitute.com/abworldsummit.  Mention Priority Code DEM002388
when registering.

SPONSORSHIP & EXHIBITION OPPORTUNITIES:
To register for the exposition or explore sponsorship opportunities to
best suit your goals, please contact Mark Alexay at
malexay@srinstitute.com or 212.967.0095 x251. Lead sponsors for the
meeting are Amersham Biosciences and Bioforesight Strategies.

CONTACT:
Ed Drilon
Strategic Research Institute
333 Seventh Avenue
New York, NY  10001
Tel: 646-336-7030
Email: edrilon@srinstitute.com
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From matthew_pocock@yahoo.co.uk  Thu Jan 16 16:10:12 2003
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Thu, 16 Jan 2003 16:10:12 +0000
Subject: [Biojava-l] Rendering hints and GUI's
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE5165012E8083@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE5165012E8083@inbox.agresearch.co.nz>
Message-ID: <3E26D964.7080104@yahoo.co.uk>

You could write a thin renderer impl that passes all methods through to 
a delegate except the drawing method, where it first sets rendering 
hints. I guess that functionality should realy be in the component that 
requests the rendering though (i.e. SequencePanel).

Matthew

Schreiber, Mark wrote:
> Hi -
> 
> I would like to be able to add RenderingHints to the various renderers
> in BioJava. How can I intercept the Graphics object that is passed to
> the Renderers paint(Graphics g, SequencePanel sp) method?
> 
> I could overide the method to use the RenderingHints before passing the
> arguments to super but that seems a bit overkill. Is there another way?
> 
> - Mark
> 
> 
> Mark Schreiber PhD
> Bioinformatics
> AgResearch Invermay
> PO Box 50034
> Mosgiel
> New Zealand
>  
> PH:   +64 3 489 9175
> 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
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> 


-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk


From mark.schreiber@agresearch.co.nz  Thu Jan 16 21:03:52 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Fri, 17 Jan 2003 10:03:52 +1300
Subject: [Biojava-l] Rendering hints and GUI's
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E8376@inbox.agresearch.co.nz>

Hi -

I have added set and get rendering hints methods to SequencePanel,
SequencePoster and DistributionLogo. TranslatedSequencePanel already has
them.

Anti-aliasing for ever!!

- Mark


> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
> Sent: Friday, 17 January 2003 5:10 a.m.
> To: Schreiber, Mark
> Cc: biojava-l@biojava.org
> Subject: Re: [Biojava-l] Rendering hints and GUI's
> 
> 
> You could write a thin renderer impl that passes all methods 
> through to 
> a delegate except the drawing method, where it first sets rendering 
> hints. I guess that functionality should realy be in the 
> component that 
> requests the rendering though (i.e. SequencePanel).
> 
> Matthew
> 
> Schreiber, Mark wrote:
> > Hi -
> > 
> > I would like to be able to add RenderingHints to the 
> various renderers 
> > in BioJava. How can I intercept the Graphics object that is 
> passed to 
> > the Renderers paint(Graphics g, SequencePanel sp) method?
> > 
> > I could overide the method to use the RenderingHints before passing 
> > the arguments to super but that seems a bit overkill. Is 
> there another 
> > way?
> > 
> > - Mark
> > 
> > 
> > Mark Schreiber PhD
> > Bioinformatics
> > AgResearch Invermay
> > PO Box 50034
> > Mosgiel
> > New Zealand
> >  
> > PH:   +64 3 489 9175
> > 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 
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> > entities other than the intended recipients is prohibited 
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> > Limited. If you have received this message in error, please 
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> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> 
> 
> -- 
> BioJava Consulting LTD - Support and training for BioJava 
> http://www.biojava.co.uk
> 
> 
> _______________________________________________
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From sales@mbfax.com  Fri Jan 17 00:41:27 2003
From: sales@mbfax.com (sales@mbfax.com)
Date: Thu, 16 Jan 2003 19:41:27 -0500
Subject: [Biojava-l] Own your Hong Kong Fax Line
Message-ID: <200301170041.h0H0fRSQ027263@pw600a.bioperl.org>

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From leesuyee@yahoo.com  Fri Jan 17 01:28:04 2003
From: leesuyee@yahoo.com (suyee)
Date: Thu, 16 Jan 2003 17:28:04 -0800 (PST)
Subject: [Biojava-l] scoring matrices
Message-ID: <20030117012804.89345.qmail@web14208.mail.yahoo.com>

  can anyone tell me why the scoring matrices used in ClustalW
is PAM 350 and Blosum 30 not Pam250 or Blosum 62 which are more
popular then PAM 350 and Blosum 30. And anyone know where i can
read more on Fast & Slow Pairwise alignment on ClustalW.

  thanks

suyee

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From russell_smithies@hotmail.com  Fri Jan 17 03:16:18 2003
From: russell_smithies@hotmail.com (Russell Smithies)
Date: Fri, 17 Jan 2003 03:16:18 +0000
Subject: [Biojava-l] reading pdb format or using tagvalue?
Message-ID: <F1231JeKi0K41uSBoYX0000b857@hotmail.com>

Hi,
Has anyone got an example of how to use Matthew's new 
biojava\bio\program\tagvalue package?

I wantto read 'tags' off .pdb files and get the property (atom x,y,z coords) 
back and to do many(everything Brookhaven/RCSB has maybe?) files so 
converting to xml first is probably a bit time/resource-consuming.

Maybe creating new Annotations is the better way to do it?
Or can I trick SeqIOTools.readEmbl() to do it?

Any ideas?

thanx
Russell




_________________________________________________________________
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From matthew_pocock@yahoo.co.uk  Fri Jan 17 11:56:40 2003
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Fri, 17 Jan 2003 11:56:40 +0000
Subject: [Biojava-l] Re: [Biojava-dev] reading pdb format or using tagvalue?
In-Reply-To: <F1231JeKi0K41uSBoYX0000b857@hotmail.com>
References: <F1231JeKi0K41uSBoYX0000b857@hotmail.com>
Message-ID: <3E27EF78.504@yahoo.co.uk>

Hi Russell,

The tag-value stuff assumes that each line can be broken into a single 
tag with a value. Things like pdb don't look quite like this (multiple 
types of values on some lines), but I recently added some handlers to 
fool the system. You will need the 1.3 snapshot, and a Java 1.4 or 
higher vm.

Start off by creating a LineSplitParser instance. You will then have to 
configure it to match PDB. For example, each record seems to have a 6 
char tag, so you need to call lsp.setSplitOffset(6). Also, every line is 
a new piece of data (unlike embl where multiple lines with the same tag 
are part of the same entry), so you need to call 
lsp.setMergeSameTag(false). Continue in this vein untill you think you 
have something that should process the skeleton of the file.

Then, look at the demo code under demos-1.4/unigene/ParseUnigene.java 
for a simple skeleton for hooking your customized parser to some debug 
output. Once this is done, you should be able to see what kind of job 
it's made of the pdb entries.

Now comes the fun bit. The values so far will be single strings for the 
entire bit of the line that's not a tag. This is next to useless. You 
realy need to tokenize each line. You do this using a combination of 
TagDelegator and RegexFieldFinder. Let's call the instance of 
TagDelegator td. Now, for example, call td.setListener("HEADER", 
headerHandler). You can make headerHandler an instance of 
RegexFieldFinder, configure it with a regex to match the name and date 
and ID, and name them sanely. Don't forget to pass in your debug 
listener as the delegate for headerHandler - that way the events will 
get dumped out. For entries like AUTHOR that are lists, you can 
associate a listener that splits the output up. Use ChangeTable, 
RegexSplitter and ValueChanger to describe the process.

Sorry, this has got too long already. See how far you can get on your 
own and then pester me. It's not that hard to write these things once 
you're up to speed, but there's a steep learning curve.

Matthew

Russell Smithies wrote:
> 
> Hi,
> Has anyone got an example of how to use Matthew's new 
> biojava\bio\program\tagvalue package?
> 
> I wantto read 'tags' off .pdb files and get the property (atom x,y,z 
> coords) back and to do many(everything Brookhaven/RCSB has maybe?) files 
> so converting to xml first is probably a bit time/resource-consuming.
> 
> Maybe creating new Annotations is the better way to do it?
> Or can I trick SeqIOTools.readEmbl() to do it?
> 
> Any ideas?
> 
> thanx
> Russell
> 
> 
> 
> 
> _________________________________________________________________
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> http://join.msn.com/?page=features/virus
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> 


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From cmason@cmason.com  Fri Jan 17 19:34:51 2003
From: cmason@cmason.com (Christopher Mason)
Date: Fri, 17 Jan 2003 12:34:51 -0700
Subject: [Biojava-l] What could be improved in biojava GUI code?
Message-ID: <2147483647.1042806891@[10.0.1.3]>

I was hoping I could generate a bit of discussion about what, if any, 
improvements could be made to the GUI bits of biojava.  In particular, are 
there any features which you might find useful, or any technical or 
architectural problems you face when using that code?  What are you using 
it for?  What would you use it for, but can't because it's too difficult, 
too confusing, not supported, etc?

Although trained as one, I don't work daily as a biologist, so it's often 
hard for me to envision how people use biological software.  I have some 
ideas that I'll present next week, but before then I wanted to hear what 
others thought.  Now, I'm not implying there's anything wrong with the 
biojava code; I'm just interested in helping make it better.  I'm hoping to 
generate a kind of wish-list that I can help implement.  I notice that on 
the wiki there is a wish-list for biojava 2, but there's no mention of GUI 
code.

Thanks,

-c

[ Christopher Mason    <cmason@cmason.com>   http://www.cmason.com/ ]


From support@biotaq.com  Tue Jan 21 01:29:25 2003
From: support@biotaq.com (support@biotaq.com)
Date: Mon, 20 Jan 2003 20:29:25 -0500
Subject: [Biojava-l] IBC Life Sciences Presents Protein Discovery & Engineering
Message-ID: <0007c2629011513VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net>

IBC Life Sciences Presents
Protein Discovery & Engineering

When: March 24-27, 2003
Where: San Francisco, CA, USA

Learn more and register!
http://www.LifeSciencesInfo.com/protein?source=2845btq

IBC's Protein Discovery & Engineering event will bring together the
technologies and tools enabling research in these 2 critical areas for a
4-day, 2-conference
forum featuring:

Protein Discovery Technologies: Directed Evolution
Monday - Tuesday, March 24 - 25, 2003
Take a look at phage, yeast, ribosome and other technologies that enable
the engineering and discovery of proteins, and implement evolutionary
algorithms of
mutation and selection to obtain new functional features.

     Evolving enzymes and functional peptides
     Protein-protein interactions
     Construction of libraries from new scaffolds
     Expression and folding of proteins from combinatorial libraries

Engineered Protein Expression: The Latest Tools
Wednesday - Thursday, March 26 - 27, 2003
Learn about the latest innovative advances occurring in protein expression
for discovery purposes -- engineered expression hosts, the expression of
multiple
members of protein families, structural protein elements, membrane and
signaling proteins as well as post-translational modifications and
associated purification
techniques.

     in vivo expression
     in vitro protein expression
     Expressing membrane associated proteins
     Expression systems and applications

This combined event unites renowned scientists and researchers from
disciplines including display technologies, molecular biology, cell
biology, biochemistry,
chemistry, target validation, protein engineering, protein expression,
chemical engineering, drug discovery and proteomics. Join these industry
leaders as they share
their discoveries and new research initiatives at this 4-day combined
event. Register Today!

To review the complete program and to register online, please visit

IBC's Protein Discovery & Engineering Web site at:

http://www.lifesciencesinfo.com/protein?source=2845btq-reg

Phone: (508) 616-5550 * Fax: (508) 616-5522 * E-Mail: inq@ibcusa.com

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From mark.schreiber@agresearch.co.nz  Tue Jan 21 03:49:51 2003
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 21 Jan 2003 16:49:51 +1300
Subject: [Biojava-l] getCodon methods
Message-ID: <AF026AF0FF4B054590228FD1F1DE5165012E873F@inbox.agresearch.co.nz>

Hi -

As the CrossProduct codon Alphabets are frequently used I have added
static convenience methods to DNATools and RNATools called
getCodonAlphabet()

- Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
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 matthew_pocock@yahoo.co.uk  Tue Jan 21 13:27:48 2003
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Tue, 21 Jan 2003 13:27:48 +0000
Subject: [Biojava-l] web service problems
Message-ID: <3E2D4AD4.5060304@yahoo.co.uk>

Hi,

I'm having some problems with biojava in a web service I wrote. I'm 
using biojava.jar and bj-ensembl.jar along with my own jsp and servlets. 
It used to work (before xmas), but now I get an exception: 
"NoSuchFieldError: naturalOrder". This is a field in Location (in 
biojava.jar), and the calling code is EnsemblTranscript (in 
bj-ensembl.jar). I can build both jars from scratch using ant, so javac 
thinks the field exists. I can javap the Location interface (using the 
biojava.jar in the deployed .war) and naturalOrder appears, so it realy 
should be available.

I've tried deploying in tomcat (v 4.0.6 & 4.1.18, LE and full versions) 
and in JBoss (v3). They all give the same exception. Has anybody seen 
symptoms like this before?

Thanks,

Matthew

-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk


From heuermh@acm.org  Tue Jan 21 14:52:33 2003
From: heuermh@acm.org (Michael L. Heuer)
Date: Tue, 21 Jan 2003 09:52:33 -0500 (EST)
Subject: [Biojava-l] web service problems
In-Reply-To: <3E2D4AD4.5060304@yahoo.co.uk>
Message-ID: <Pine.GSO.4.44.0301210950430.19307-100000@shell3.shore.net>

Just grasping at straws here, but is it possible that classes
from biojava.jar and bj-ensembl.jar are being loaded by different
classloaders within the servlet engines?  Maybe try building a single .war
file from both projects.

   michael

On Tue, 21 Jan 2003, Matthew Pocock wrote:

> Hi,
>
> I'm having some problems with biojava in a web service I wrote. I'm
> using biojava.jar and bj-ensembl.jar along with my own jsp and servlets.
> It used to work (before xmas), but now I get an exception:
> "NoSuchFieldError: naturalOrder". This is a field in Location (in
> biojava.jar), and the calling code is EnsemblTranscript (in
> bj-ensembl.jar). I can build both jars from scratch using ant, so javac
> thinks the field exists. I can javap the Location interface (using the
> biojava.jar in the deployed .war) and naturalOrder appears, so it realy
> should be available.
>
> I've tried deploying in tomcat (v 4.0.6 & 4.1.18, LE and full versions)
> and in JBoss (v3). They all give the same exception. Has anybody seen
> symptoms like this before?
>
> Thanks,
>
> Matthew
>
> --
> BioJava Consulting LTD - Support and training for BioJava
> http://www.biojava.co.uk
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>


From p.lord@russet.org.uk  Tue Jan 21 16:15:33 2003
From: p.lord@russet.org.uk (Phillip Lord)
Date: 21 Jan 2003 16:15:33 +0000
Subject: [Biojava-l] web service problems
In-Reply-To: <Pine.GSO.4.44.0301210950430.19307-100000@shell3.shore.net>
References: <Pine.GSO.4.44.0301210950430.19307-100000@shell3.shore.net>
Message-ID: <vf4r82xyvu.fsf@rpc71.cs.man.ac.uk>

>>>>> "Michael" == Michael L Heuer <heuermh@acm.org> writes:

  Michael> Just grasping at straws here, but is it possible that
  Michael> classes from biojava.jar and bj-ensembl.jar are being
  Michael> loaded by different classloaders within the servlet
  Michael> engines?  Maybe try building a single .war file from both
  Michael> projects.  


I'm not sure this would do this. You might get a ClassNotFound.


  michael On Tue, 21 Jan 2003, Matthew
  Michael> Pocock wrote:
  >> Hi, I'm having some problems with biojava in a web service I
  >> wrote. I'm using biojava.jar and bj-ensembl.jar along with my own
  >> jsp and servlets.  It used to work (before xmas), but now I get
  >> an exception: "NoSuchFieldError: naturalOrder". This is a field
  >> in Location (in biojava.jar), and the calling code is
  >> EnsemblTranscript (in bj-ensembl.jar). I

You may have two copies of the Location source around, and are
compiling against one, and running against the other. You've tried
javap'ing things, but you might also want to try introspecting over
the class object that's giving the error. 

Also try deleting Location from the jar file. If you are lucky, and
nothing else calls if first, make sure that the system crashes with
the expected ClassNotFound. 

Other possibilities are corrupt classes, although javap should pick
this up. Are you building with jikes? 

I hate this sort of problem. 

Phil

From simon.foote@nrc.ca  Tue Jan 21 17:10:15 2003
From: simon.foote@nrc.ca (Simon Foote)
Date: Tue, 21 Jan 2003 12:10:15 -0500
Subject: [Biojava-l] Parsing Blast Results
Message-ID: <3E2D7EF7.5040906@nrc.ca>

Is there an easy way to get the QueryID from the blast result one is 
parsing.  There's no getQueryID method in SeqSimilaritySearchResult, so 
I'm guessing its hidden somewhere else if it exists.

Thanks,
Simon Foote


-- 
Bioinformatics Programmer
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092


From td2@sanger.ac.uk  Wed Jan 22 13:32:51 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 22 Jan 2003 13:32:51 +0000
Subject: [Biojava-l] web service problems
In-Reply-To: <3E2D4AD4.5060304@yahoo.co.uk>
References: <3E2D4AD4.5060304@yahoo.co.uk>
Message-ID: <20030122133251.GH455490@jabba.sanger.ac.uk>

On Tue, Jan 21, 2003 at 01:27:48PM +0000, Matthew Pocock wrote:
> Hi,
> 
> I'm having some problems with biojava in a web service I wrote. I'm 
> using biojava.jar and bj-ensembl.jar along with my own jsp and servlets. 
> It used to work (before xmas), but now I get an exception: 
> "NoSuchFieldError: naturalOrder". This is a field in Location (in 
> biojava.jar), and the calling code is EnsemblTranscript (in 
> bj-ensembl.jar). I can build both jars from scratch using ant, so javac 
> thinks the field exists. I can javap the Location interface (using the 
> biojava.jar in the deployed .war) and naturalOrder appears, so it realy 
> should be available.

I've just experienced this very same probelm, also using
biojava-ensembl, from a simple command-line script, so there's
definitely no container-specific classloading issues.  I was
able to fix it by doing a clean build of biojava-ensembl.

Any chance of version skew in your case?

   Thomas.

From matthew_pocock@yahoo.co.uk  Wed Jan 22 15:23:29 2003
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Wed, 22 Jan 2003 15:23:29 +0000
Subject: [Biojava-l] web service problems
In-Reply-To: <20030122133251.GH455490@jabba.sanger.ac.uk>
References: <3E2D4AD4.5060304@yahoo.co.uk> <20030122133251.GH455490@jabba.sanger.ac.uk>
Message-ID: <3E2EB771.7060607@yahoo.co.uk>

Thanks for all the sudgestions. I got this working in the end. The bug 
appeared in JBoss as well as various tomcats. It was fixed by doing a 
totaly clean rebuild of biojava-live followed by a totaly clean rebuild 
of biojava-ensembl. I blame the pixies. The only thing I can think is 
that some files may have had debugging (-g) information, and others may 
not have. Weird.

Matthew

Thomas Down wrote:
> On Tue, Jan 21, 2003 at 01:27:48PM +0000, Matthew Pocock wrote:
> 
>>Hi,
>>
>>I'm having some problems with biojava in a web service I wrote. I'm 
>>using biojava.jar and bj-ensembl.jar along with my own jsp and servlets. 
>>It used to work (before xmas), but now I get an exception: 
>>"NoSuchFieldError: naturalOrder". This is a field in Location (in 
>>biojava.jar), and the calling code is EnsemblTranscript (in 
>>bj-ensembl.jar). I can build both jars from scratch using ant, so javac 
>>thinks the field exists. I can javap the Location interface (using the 
>>biojava.jar in the deployed .war) and naturalOrder appears, so it realy 
>>should be available.
> 
> 
> I've just experienced this very same probelm, also using
> biojava-ensembl, from a simple command-line script, so there's
> definitely no container-specific classloading issues.  I was
> able to fix it by doing a clean build of biojava-ensembl.
> 
> Any chance of version skew in your case?
> 
>    Thomas.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 


-- 
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http://www.biojava.co.uk


From td2@sanger.ac.uk  Wed Jan 22 15:50:22 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 22 Jan 2003 15:50:22 +0000
Subject: [Biojava-l] web service problems
In-Reply-To: <3E2EB771.7060607@yahoo.co.uk>
References: <3E2D4AD4.5060304@yahoo.co.uk> <20030122133251.GH455490@jabba.sanger.ac.uk> <3E2EB771.7060607@yahoo.co.uk>
Message-ID: <20030122155022.GJ455490@jabba.sanger.ac.uk>

On Wed, Jan 22, 2003 at 03:23:29PM +0000, Matthew Pocock wrote:
> Thanks for all the sudgestions. I got this working in the end. The bug 
> appeared in JBoss as well as various tomcats. It was fixed by doing a 
> totaly clean rebuild of biojava-live followed by a totaly clean rebuild 
> of biojava-ensembl. I blame the pixies. The only thing I can think is 
> that some files may have had debugging (-g) information, and others may 
> not have. Weird.

Actually, I semi-understand it now.  I think it's related to a change
I made before christmas whereby I changed LocationComparator
from being a static nested class of Location (which forced it to
be public) to a normal, package-private class.  The resulting
error message is *very* odd though...  I was thrown off by the
idea that it was something which only occurred in webapps.

     Thomas.

From support@biotaq.com  Thu Jan 23 01:30:48 2003
From: support@biotaq.com (support@biotaq.com)
Date: Wed, 22 Jan 2003 20:30:48 -0500
Subject: [Biojava-l] IBC Life Sciences 2003 Conference Collection
Message-ID: <0042c4830011713VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net>

IBC Life Sciences 2003 Conference Collection

Information on the Knowledge You Need,
Answers to the Challenges You Face
Preview the Lineup Today

Westborough, MA, January 23, 2003 -- From North America to Europe, IBC
Life Sciences continues to supply the life science industry with
specialized information through quality learning and networking events
organized into three primary market sectors: Drug Discovery,
Biopharmaceutical Production and Microtechnology. Read below for a select
listing of conferences and see why we are recognized around the globe for
quality, service and value.

DRUG DISCOVERY SERIES
Global events highlighting technological advancements and applications in
niche areas of the drug discovery pipeline. Topics include genomics,
proteomics, target validation, high-throughput screening, assay
development, bioinformatics, ADME toxicology and more.

Applications of RNA Interface
February 10-11, 2003, San Diego, CA
http://www.lifesciencesinfo.com/RNAi?source=btq-rnai

Genomic & Proteomic Technological Advances in Cancer Research
February 10-12, 2003, Bethesda, MD
http://www.lifesciencesinfo.com/2808?source=btq-2808

BioTechniques(R) Live!
March 5, 2003, Boston, MA
http://www.biotechniqueslive.com/?source=btq-btlive

Pharmacology for Drug Discovery & Development
March 17-18, 2003, Boston, MA
http://www.lifesciencesinfo.com/2840?source=btq-2840

ScreenTech(R) World Summit
March 23-27, 2003, San Diego, CA
http://www.lifesciencesinfo.com/screentech?source=btq-stech
Four Events - One Venue
· HTS & Assay Technologies · Protein Kinases & Phosphatases · Protease
Inhibitors
·In Silico & Experimental Target Validation

Protein Discovery & Engineering
March 24-27, 2003, San Francisco, CA
http://www.lifesciencesinfo.com/protein?source=btq-protein
Four Days - Two Conferences
Protein Discovery Technologies: Directed Evolution
Engineered Protein Expression: The Latest Tools

Drug Discovery Technology European Congress
March 31-April 3, 2003, Stuttgart, Germany
http://www.drugdisc.com/europe?source=btq-ddtuk

Drug Discovery Technology&trade; World Congress
August 10-15, 2003, Boston, MA
http://www.drugdisc.com/us?source=btq-ddtus

BIOPHARMACEUTICAL PRODUCTION SERIES
Global conferences and courses covering the latest information on
technologies, economics and regulatory strategies that facilitate the
production of biopharmaceuticals. Subjects include upstream through
downstream process design, development and scale-up; process validation;
viral clearance; process optimization; project planning; drug development,
formulation and stability.

Process Validation for Biologicals
March 3-4, 2003, La Jolla, CA
http://www.lifesciencesinfo.com/process?source=btq-process

Antibody Partnering & Collaboration
March 3-4, 2003, La Jolla, CA
http://www.lifesciencesinfo.com/2837?source=btq-2837

Antibody Production & Downstream Processing
March 5-7, 2003, La Jolla, CA
http://www.lifesciencesinfo.com/antibodyprod?source=btq-antiprod

TIDES 2003: Oligonucleotide and Peptide(R) Technologies Conference
April 28-May 1, 2003, Las Vegas, NV
http://www.lifesciencesinfo.com/tides?source=btq-tides

Recombinant Antibodies
May 13-14, 2003, Munich, Germany
http://www.ibc-lifesci.com/antibodies?source=btq-antibod

MICROTECHNOLOGY SERIES
Global events providing first-hand information on the latest emerging
technology and applications. This series meets the informational needs of
industry and academia by presenting the latest innovations and
applications, as well as evaluation of emerging technologies. Subjects
include microarray technologies, bioMEMs and microfluidics, informatics,
molecular diagnostics and more.

InfoTechPharma 2003
February 10-13, 2003, London, UK
http://www.infotechpharma.com/?source=btq-infotech

BioMEMs & Microfluidics
April 30-May 2, 2003, San Diego, CA
http://www.lifesciencesinfo.com/2881?source=btq-2881

EuroBiochips 2003
May 20-23, 2003, London, UK
http://www.eurobiochips.com/?source=btq-eurobio

Chips to Hits(R)
October 27-31, 2003, Boston, MA
http://www.chipstohits.com/?source=btq-chips

For more information on these conferences or to register, visit the
conference-specific Web site listed above, call (508) 616-5550, e-mail
reg@ibcusa.com or visit our main Web site at
www.LifeSciencesInfo.com?source=btq-lsi

ABOUT IBC LIFE SCIENCES

The worldwide leader in scientific, technical and business conferences and
courses in the drug discovery arena. During the past year, IBC has
experienced substantial growth and emerged as the premier information
provider to the market. IBC Life Sciences actively researches the
advancements, technologies and trends impacting and driving the race for
new drugs and therapies. No other organization can make claim to the
breadth and quality that IBC Life Sciences delivers in each event.


********************************************************
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To edit or change your interest category selections or unsubscribe,
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****


From simon.foote@nrc.ca  Thu Jan 23 20:38:45 2003
From: simon.foote@nrc.ca (Simon Foote)
Date: Thu, 23 Jan 2003 15:38:45 -0500
Subject: [Biojava-l] CVS compiling
Message-ID: <3E3052D5.1060501@nrc.ca>

I've tried compiling a fresh checkout of biojava-live after my cvs 
update compiling failed and it also failed.
There appears to be errors in numerous programs. The majority are 
relating to Sequence, see below for example:

    [javac] Found 48 semantic errors compiling 
"/usr/local/src/OpenBio/biojava-live-new/ant-build/src/main/org/biojava/bio/seq/ragbag/RagbagCachedSequence.java":

    [javac]    154.   private Sequence instantiateSequence()
    [javac]                   ^------^
    [javac] *** Error: The type "org/biojava/bio/symbol/Sequence" has 
default access and is not accessible here.


Anyone else experiencing similar problems.

Simon

-- 
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092



From td2@sanger.ac.uk  Thu Jan 23 21:40:24 2003
From: td2@sanger.ac.uk (Thomas Down)
Date: Thu, 23 Jan 2003 21:40:24 +0000
Subject: [Biojava-l] CVS compiling
In-Reply-To: <3E3052D5.1060501@nrc.ca>
References: <3E3052D5.1060501@nrc.ca>
Message-ID: <20030123214024.GB471477@jabba.sanger.ac.uk>

On Thu, Jan 23, 2003 at 03:38:45PM -0500, Simon Foote wrote:
> I've tried compiling a fresh checkout of biojava-live after my cvs 
> update compiling failed and it also failed.
> There appears to be errors in numerous programs. The majority are 
> relating to Sequence, see below for example:
> 
>    [javac] Found 48 semantic errors compiling 
> "/usr/local/src/OpenBio/biojava-live-new/ant-build/src/main/org/biojava/bio/seq/ragbag/RagbagCachedSequence.java":
> 
>    [javac]    154.   private Sequence instantiateSequence()
>    [javac]                   ^------^
>    [javac] *** Error: The type "org/biojava/bio/symbol/Sequence" has 
> default access and is not accessible here.

Do you have anything on your CLASSPATH?  If so, try removing
it then doing an `ant clean`.

I've just tried compiling, without any trouble.  There is not
now (and has never been) a class org.biojava.bio.symbol.Sequence
of *any* accessability, so I'm not sure where the compiler is
getting that idea...

     Thomas.


From yshigemo@genes.nig.ac.jp  Fri Jan 24 05:13:00 2003
From: yshigemo@genes.nig.ac.jp (Yasumasa Shigemoto)
Date: Fri, 24 Jan 2003 14:13:00 +0900
Subject: [Biojava-l] Circular Location
Message-ID: <3E30CB5B.A77AF4DF@genes.nig.ac.jp>

Hi

I use the CircularLocation and LocationTools as follows,
but it seems to return the wrong response.

import org.biojava.bio.symbol.*;

public class CircularTest {
        public static void main(String[] args) {
                try {
                        Location[] locs = new Location[10];
                        locs[0] = LocationTools.makeCircularLocation(18,24,20);
                        locs[1] = LocationTools.makeCircularLocation(18,24,20);
                        locs[2] = LocationTools.makeCircularLocation(2,8,20);
                        locs[3] = LocationTools.makeCircularLocation(4,10,20);
                        locs[4] = LocationTools.makeCircularLocation(18,23,20);
                        System.out.println(LocationTools.areEqual(locs[0], locs[1]));
                        System.out.println(LocationTools.contains(locs[0], locs[1]));
                        System.out.println(LocationTools.overlaps(locs[0], locs[2]));
                        System.out.println(LocationTools.overlaps(locs[2], locs[3]));
                        System.out.println(LocationTools.overlaps(locs[0], locs[4]));
                } catch (Exception ex) {
                        ex.printStackTrace();
                }
        }
}

> java CircularTest
true
true
false
true
false

I think the whole of result is 'true'.

Environment
biojava-1.3pre1.jar, j2sdk1.4.0

Any help would be most appreciated.

Yasumasa Shigemoto


From mark.schreiber at agresearch.co.nz  Mon Jan 27 13:07:31 2003
From: mark.schreiber at agresearch.co.nz (Schreiber, Mark)
Date: Sun Jan 26 18:59:10 2003
Subject: [Biojava-l] Biojava in the news
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650135B664@inbox.agresearch.co.nz>

Hi All,

Just noticed a little snippit about biojava in the latest issue of the
scientist http://www.the-scientist.com/yr2003/jan/labcon_030127.html
(free registration required to view the article)

Hmm, that logo looks to be derived from a very familiar piece of code
;-)

- Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
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
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=======================================================================

From mark.schreiber at agresearch.co.nz  Mon Jan 27 13:14:34 2003
From: mark.schreiber at agresearch.co.nz (Schreiber, Mark)
Date: Sun Jan 26 19:06:23 2003
Subject: [Biojava-l] Circular Location
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650135B669@inbox.agresearch.co.nz>

Oops, this looks like a bug. Thanks for spotting it!!

I'll try to fix it in the next day or so.

- Mark


> -----Original Message-----
> From: Yasumasa Shigemoto [mailto:yshigemo@genes.nig.ac.jp] 
> Sent: Friday, 24 January 2003 6:13 p.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Circular Location
> 
> 
> Hi
> 
> I use the CircularLocation and LocationTools as follows,
> but it seems to return the wrong response.
> 
> import org.biojava.bio.symbol.*;
> 
> public class CircularTest {
>         public static void main(String[] args) {
>                 try {
>                         Location[] locs = new Location[10];
>                         locs[0] = 
> LocationTools.makeCircularLocation(18,24,20);
>                         locs[1] = 
> LocationTools.makeCircularLocation(18,24,20);
>                         locs[2] = 
> LocationTools.makeCircularLocation(2,8,20);
>                         locs[3] = 
> LocationTools.makeCircularLocation(4,10,20);
>                         locs[4] = 
> LocationTools.makeCircularLocation(18,23,20);
>                         
> System.out.println(LocationTools.areEqual(locs[0], locs[1]));
>                         
> System.out.println(LocationTools.contains(locs[0], locs[1]));
>                         
> System.out.println(LocationTools.overlaps(locs[0], locs[2]));
>                         
> System.out.println(LocationTools.overlaps(locs[2], locs[3]));
>                         
> System.out.println(LocationTools.overlaps(locs[0], locs[4]));
>                 } catch (Exception ex) {
>                         ex.printStackTrace();
>                 }
>         }
> }
> 
> > java CircularTest
> true
> true
> false
> true
> false
> 
> I think the whole of result is 'true'.
> 
> Environment
> biojava-1.3pre1.jar, j2sdk1.4.0
> 
> Any help would be most appreciated.
> 
> Yasumasa Shigemoto
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
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From matthew_pocock at yahoo.co.uk  Mon Jan 27 12:48:46 2003
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Mon Jan 27 07:57:50 2003
Subject: [Biojava-l] Biojava in the news
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE51650135B664@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE51650135B664@inbox.agresearch.co.nz>
Message-ID: <3E352AAE.40306@yahoo.co.uk>

Cool! Did I realy say that? Let's get that 1.3 release out ASAP (since 
it was meant to be out in December ;) ). Anybody who hasn't yet should 
pick up the 1.3pre1 from http://www.biojava.org/download/binaries/ and 
give it a test-drive.

Matthew

Schreiber, Mark wrote:
> Hi All,
> 
> Just noticed a little snippit about biojava in the latest issue of the
> scientist http://www.the-scientist.com/yr2003/jan/labcon_030127.html
> (free registration required to view the article)
> 
> Hmm, that logo looks to be derived from a very familiar piece of code
> ;-)
> 
> - Mark
> 
> 
> Mark Schreiber PhD
> Bioinformatics
> AgResearch Invermay
> PO Box 50034
> Mosgiel
> New Zealand
>  
> PH:   +64 3 489 9175
> 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.
> =======================================================================
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 


-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk

From staatsb at mail.nih.gov  Mon Jan 27 12:19:08 2003
From: staatsb at mail.nih.gov (staatsb)
Date: Mon Jan 27 12:10:59 2003
Subject: [Biojava-l] BLAST Parser in Anger!
Message-ID: <71B26E3B-321B-11D7-AE6C-000393B2A794@mail.nih.gov>

I was successful in getting the BLAST parser to work outlined by the 
"BioJava in Anger" doc by changing the version number too 2.0.11 (thank 
you Mark Schreiber X2).  However, a few of the APIs dont seem to 
function i.e.  getSequenceID() is not recognized, but I dont think 
thats due to the version change.  Also, I have noticed many API calls 
to certain BLAST file features missing i.e. getQueryID, getGaps, 
getQuerySequence, getSubjectSequence, and more.  Are these really 
missing or does the programmer (me) need to define them from the APIs 
existing  structure?  Has anyone else been able to obtain these 
features with the missing APIs?  Can anyone offer any advise, 
suggestions, explanations, etc, to these issues?

Thanks

Brian Staats
Bioinformatics Programmer Analyst
NIH/NCI/Core Genotyping Facility
staatsb@mail.nih.gov

From stein.aerts at esat.kuleuven.ac.be  Mon Jan 27 18:40:29 2003
From: stein.aerts at esat.kuleuven.ac.be (Stein Aerts)
Date: Mon Jan 27 12:32:03 2003
Subject: [Biojava-l] GUI for cis-regulatory analysis 
Message-ID: <3E356F0D.9030108@esat.kuleuven.ac.be>


We have built a Java GUI on top of BioJava for cis-regulatory sequence 
analysis, especially in higher eukaryotes. It is linked with Ensembl for 
the retrieval of genes and intergenic sequences and with several 
algorithms for comparative genomics and motif detection (using SOAP web 
services).

The description of the program, the jar file, Java Web Start version, 
tutorial, manual, etc. can be found here: 
http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php.
Currently the classes cannot be used directly from the API, and I have 
no good Javadocs at present. If people would find it useful, I could 
consider cleaning up my code for this purpose.

Thank you BioJava!

Best regards & all comments are appreciated,

Stein Aerts.

-- 
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI


From mark.schreiber at agresearch.co.nz  Tue Jan 28 09:24:05 2003
From: mark.schreiber at agresearch.co.nz (Schreiber, Mark)
Date: Mon Jan 27 15:15:55 2003
Subject: [Biojava-l] BLAST Parser in Anger!
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650135B76E@inbox.agresearch.co.nz>

Hi -

There are some deficiencies in the blast parsing API. I know that there
is some reluctance to add new methods to the interface as things will
break, however blast parsing is a core task and it would be v good if we
could make this more functional. One way to get around the interface
thing is to simlply extend it and then make all the classes we have now
implement the extended interface.

Another way is to simply break the interface before bj1.3 is released
and make it stable from there on.

Can we please, please sort this out before bj1.3 is released? Perhaps
the development team could get together over a beer at the hackathon and
nut this one out. It really can't be that hard can it?

Hear endeth the sermon.

- Mark

> -----Original Message-----
> From: staatsb [mailto:staatsb@mail.nih.gov] 
> Sent: Tuesday, 28 January 2003 6:19 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] BLAST Parser in Anger!
> 
> 
> I was successful in getting the BLAST parser to work outlined by the 
> "BioJava in Anger" doc by changing the version number too 
> 2.0.11 (thank 
> you Mark Schreiber X2).  However, a few of the APIs dont seem to 
> function i.e.  getSequenceID() is not recognized, but I dont think 
> thats due to the version change.  Also, I have noticed many API calls 
> to certain BLAST file features missing i.e. getQueryID, getGaps, 
> getQuerySequence, getSubjectSequence, and more.  Are these really 
> missing or does the programmer (me) need to define them from the APIs 
> existing  structure?  Has anyone else been able to obtain these 
> features with the missing APIs?  Can anyone offer any advise, 
> suggestions, explanations, etc, to these issues?
> 
> Thanks
> 
> Brian Staats
> Bioinformatics Programmer Analyst
> NIH/NCI/Core Genotyping Facility
> staatsb@mail.nih.gov
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================

From mark.schreiber at agresearch.co.nz  Tue Jan 28 11:48:48 2003
From: mark.schreiber at agresearch.co.nz (Schreiber, Mark)
Date: Mon Jan 27 17:40:40 2003
Subject: [Biojava-l] Circular Location
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650135B7E8@inbox.agresearch.co.nz>

Hi -

I have committed a fix to CVS for this, please feel free to test it. The
circular stuff is, logically speaking, really weird with many odd
concepts so the more testing the better.

- Mark


> -----Original Message-----
> From: Yasumasa Shigemoto [mailto:yshigemo@genes.nig.ac.jp] 
> Sent: Friday, 24 January 2003 6:13 p.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Circular Location
> 
> 
> Hi
> 
> I use the CircularLocation and LocationTools as follows,
> but it seems to return the wrong response.
> 
> import org.biojava.bio.symbol.*;
> 
> public class CircularTest {
>         public static void main(String[] args) {
>                 try {
>                         Location[] locs = new Location[10];
>                         locs[0] = 
> LocationTools.makeCircularLocation(18,24,20);
>                         locs[1] = 
> LocationTools.makeCircularLocation(18,24,20);
>                         locs[2] = 
> LocationTools.makeCircularLocation(2,8,20);
>                         locs[3] = 
> LocationTools.makeCircularLocation(4,10,20);
>                         locs[4] = 
> LocationTools.makeCircularLocation(18,23,20);
>                         
> System.out.println(LocationTools.areEqual(locs[0], locs[1]));
>                         
> System.out.println(LocationTools.contains(locs[0], locs[1]));
>                         
> System.out.println(LocationTools.overlaps(locs[0], locs[2]));
>                         
> System.out.println(LocationTools.overlaps(locs[2], locs[3]));
>                         
> System.out.println(LocationTools.overlaps(locs[0], locs[4]));
>                 } catch (Exception ex) {
>                         ex.printStackTrace();
>                 }
>         }
> }
> 
> > java CircularTest
> true
> true
> false
> true
> false
> 
> I think the whole of result is 'true'.
> 
> Environment
> biojava-1.3pre1.jar, j2sdk1.4.0
> 
> Any help would be most appreciated.
> 
> Yasumasa Shigemoto
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================

From matthew_pocock at yahoo.co.uk  Tue Jan 28 09:59:45 2003
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Tue Jan 28 05:09:37 2003
Subject: [Biojava-l] BLAST Parser in Anger!
In-Reply-To: <AF026AF0FF4B054590228FD1F1DE51650135B76E@inbox.agresearch.co.nz>
References: <AF026AF0FF4B054590228FD1F1DE51650135B76E@inbox.agresearch.co.nz>
Message-ID: <3E365491.6070208@yahoo.co.uk>

Please, let's get it right b4 1.3 goes live - I know we're meant to be 
only making small changes now, but blast parsing is so important that 
it's worth doing properly.

Mark, do you have a list of methods you want added/removed/renamed, or 
are the problems more deep-seated than that?

Matthew

Schreiber, Mark wrote:
> Hi -
> 
> There are some deficiencies in the blast parsing API. I know that there
> is some reluctance to add new methods to the interface as things will
> break, however blast parsing is a core task and it would be v good if we
> could make this more functional. One way to get around the interface
> thing is to simlply extend it and then make all the classes we have now
> implement the extended interface.
> 
> Another way is to simply break the interface before bj1.3 is released
> and make it stable from there on.
> 
> Can we please, please sort this out before bj1.3 is released? Perhaps
> the development team could get together over a beer at the hackathon and
> nut this one out. It really can't be that hard can it?
> 
> Hear endeth the sermon.
> 
> - Mark
> 
> 
>>-----Original Message-----
>>From: staatsb [mailto:staatsb@mail.nih.gov] 
>>Sent: Tuesday, 28 January 2003 6:19 a.m.
>>To: biojava-l@biojava.org
>>Subject: [Biojava-l] BLAST Parser in Anger!
>>
>>
>>I was successful in getting the BLAST parser to work outlined by the 
>>"BioJava in Anger" doc by changing the version number too 
>>2.0.11 (thank 
>>you Mark Schreiber X2).  However, a few of the APIs dont seem to 
>>function i.e.  getSequenceID() is not recognized, but I dont think 
>>thats due to the version change.  Also, I have noticed many API calls 
>>to certain BLAST file features missing i.e. getQueryID, getGaps, 
>>getQuerySequence, getSubjectSequence, and more.  Are these really 
>>missing or does the programmer (me) need to define them from the APIs 
>>existing  structure?  Has anyone else been able to obtain these 
>>features with the missing APIs?  Can anyone offer any advise, 
>>suggestions, explanations, etc, to these issues?
>>
>>Thanks
>>
>>Brian Staats
>>Bioinformatics Programmer Analyst
>>NIH/NCI/Core Genotyping Facility
>>staatsb@mail.nih.gov
>>
>>_______________________________________________
>>Biojava-l mailing list  -  Biojava-l@biojava.org 
>>http://biojava.org/mailman/listinfo/biojava-l
>>
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 


-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk

From cullepm3_registrations at hotmail.com  Tue Jan 28 11:03:59 2003
From: cullepm3_registrations at hotmail.com (cullepm3 registrations)
Date: Tue Jan 28 05:55:37 2003
Subject: [Biojava-l] 
 Does EnsemblGenericSeqFeatureSource limit the size of the POST request?
Message-ID: <F70p8ARf3sllNY30kkZ0000012a@hotmail.com>

Do either of the classes AbstractGenericSeqFeatureSource or 
EnsemblGenericSeqFeatureSource limit the size of the POST request?

We are using the Ensembl Web Application and Dazzle (with the above classes) 
to display our annotations.  We modified the Ensembl Perl classes to 
generate feature tracks for the entire chromosome (rather than images 
limited to 2Mbs).  This worked with ensemble 4_28 but does not seem to work 
since upgrading to 9_30.

Requests to the DAS server time-out.  Through testing, I have determined 
that the problem is independent of the number of features being returned.

I supsect the problem is related to the size of the POST request.  When 
requesting features from chromosome 1, the Ensembl Perl code builds a das 
request with over 2500 segments.  Can the ensembl-das classes above handle 
this?

If there is a more appropriate list for this question, please refer me to 
it.

Thanks
Patrick

_________________________________________________________________
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From mark.schreiber at agresearch.co.nz  Wed Jan 29 11:11:56 2003
From: mark.schreiber at agresearch.co.nz (Schreiber, Mark)
Date: Tue Jan 28 17:03:40 2003
Subject: [Biojava-l] BLAST Parser in Anger!
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650135B983@inbox.agresearch.co.nz>

Hi -

I don't think the problems are deepseated. Actually the BlastParsing API
is really good. Basically if we can add appropriate accessor methods for
all the info available in the BlastLikeDataCollection.dtd then the API
will pretty much do everything you could want.

The other option would be to write a SAX parser for the new NCBI blast
dtd. This might be a bit of a major overhaul but it could be a nice
standardization.

I think it would be worth delaying 1.3 till we get this fully
functional.

- Mark


> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
> Sent: Tuesday, 28 January 2003 11:00 p.m.
> To: Schreiber, Mark
> Cc: staatsb; biojava-l@biojava.org; biojava-dev@biojava.org
> Subject: Re: [Biojava-l] BLAST Parser in Anger!
> 
> 
> Please, let's get it right b4 1.3 goes live - I know we're 
> meant to be 
> only making small changes now, but blast parsing is so important that 
> it's worth doing properly.
> 
> Mark, do you have a list of methods you want 
> added/removed/renamed, or 
> are the problems more deep-seated than that?
> 
> Matthew
> 
> Schreiber, Mark wrote:
> > Hi -
> > 
> > There are some deficiencies in the blast parsing API. I know that 
> > there is some reluctance to add new methods to the 
> interface as things 
> > will break, however blast parsing is a core task and it would be v 
> > good if we could make this more functional. One way to get 
> around the 
> > interface thing is to simlply extend it and then make all 
> the classes 
> > we have now implement the extended interface.
> > 
> > Another way is to simply break the interface before bj1.3 
> is released 
> > and make it stable from there on.
> > 
> > Can we please, please sort this out before bj1.3 is 
> released? Perhaps 
> > the development team could get together over a beer at the 
> hackathon 
> > and nut this one out. It really can't be that hard can it?
> > 
> > Hear endeth the sermon.
> > 
> > - Mark
> > 
> > 
> >>-----Original Message-----
> >>From: staatsb [mailto:staatsb@mail.nih.gov]
> >>Sent: Tuesday, 28 January 2003 6:19 a.m.
> >>To: biojava-l@biojava.org
> >>Subject: [Biojava-l] BLAST Parser in Anger!
> >>
> >>
> >>I was successful in getting the BLAST parser to work outlined by the
> >>"BioJava in Anger" doc by changing the version number too 
> >>2.0.11 (thank 
> >>you Mark Schreiber X2).  However, a few of the APIs dont seem to 
> >>function i.e.  getSequenceID() is not recognized, but I dont think 
> >>thats due to the version change.  Also, I have noticed many 
> API calls 
> >>to certain BLAST file features missing i.e. getQueryID, getGaps, 
> >>getQuerySequence, getSubjectSequence, and more.  Are these really 
> >>missing or does the programmer (me) need to define them 
> from the APIs 
> >>existing  structure?  Has anyone else been able to obtain these 
> >>features with the missing APIs?  Can anyone offer any advise, 
> >>suggestions, explanations, etc, to these issues?
> >>
> >>Thanks
> >>
> >>Brian Staats
> >>Bioinformatics Programmer Analyst
> >>NIH/NCI/Core Genotyping Facility
> >>staatsb@mail.nih.gov
> >>
> >>_______________________________________________
> >>Biojava-l mailing list  -  Biojava-l@biojava.org
> >>http://biojava.org/mailman/listinfo/biojava-l
> >>
> > 
> > 
> ======================================================================
> > =
> > Attention: The information contained in this message and/or 
> attachments
> > from AgResearch Limited is intended only for the persons or entities
> > to which it is addressed and may contain confidential 
> and/or privileged
> > material. Any review, retransmission, dissemination or 
> other use of, or
> > taking of any action in reliance upon, this information by 
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> by AgResearch
> > Limited. If you have received this message in error, please 
> notify the
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> > http://biojava.org/mailman/listinfo/biojava-l
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> -- 
> BioJava Consulting LTD - Support and training for BioJava 
> http://www.biojava.co.uk
> 
> 
=======================================================================
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
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From support at biotaq.com  Tue Jan 28 23:32:08 2003
From: support at biotaq.com (support@biotaq.com)
Date: Tue Jan 28 23:30:19 2003
Subject: [Biojava-l] IBC LIFE SCIENCES 10TH ANNUAL ANTIBODY PRODUCTION &
	DOWNSTREAM PROCESSING EVENT
Message-ID: <002580832041d13VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net>

KEITH WEBBER, Ph.D., OF CBER, FDA TO PRESENT AT
IBC LIFE SCIENCES 10TH ANNUAL
ANTIBODY PRODUCTION & DOWNSTREAM PROCESSING EVENT

IBC's Antibody Production & Downstream Processing is celebrating 10 years
of providing superior content and networking to the Biopharmaceutical
industry. It has announced that Keith Webber, of CBER and FDA will present
the Keynote Address at this meeting to be held on March 5-7, 2003 at the
Hilton La Jolla Torrey Pines in La Jolla, CA.  Co-Located with Process
Validation for Biologicals and Antibody Partnering & Collaboration both
held March 3-4, 2003, this 10 year celebration will provide the top notch
presenters a venue to discuss the essentials for producing therapeutic
antibodies and learn how to maximize production efficiency. The meeting is
expected to surpass its previous year's attendance of over 500 attendees
and over 40 exhibit booths.

Keith Webber, Director, Division of Monoclonal Antibodies, Office of
Therapeutic Research and Review, CBER, FDA will present the Keynote
Address on FDA Regulation of Biologics Produced in Bioengineered Plants.
Dr. Webber is Chair of the FDA/USDA Interagency Working Group that has
recently published a draft Guidance for Industry on drugs, biologics, and
medical devices derived from bioengineered plants for use in humans and
animals.

The content of the meeting focuses primarily on the most relevant aspects
of antibody manufacturing. Some of the highlights will include:
·	Thomas Harnett revealing the design considerations for start-up and
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Processing in La Jolla, March 5-7, 2003, visit
http://www.lifesciencesinfo.com/antibodyprod
Or call 508-616-5550, X1004
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From stein.aerts at esat.kuleuven.ac.be  Wed Jan 29 09:57:10 2003
From: stein.aerts at esat.kuleuven.ac.be (Stein Aerts)
Date: Wed Jan 29 03:51:40 2003
Subject: [Biojava-l] Ensembl gene parsing
Message-ID: <3E379766.9020405@esat.kuleuven.ac.be>

Hi,

When currently parsing an exported sequence of an Ensembl mouse gene 
(using the Export Data function at www.ensembl.org) there appear to be 3 
problems:
I tried to attach an example of an exported sequence of the Igf1 gene 
but then the message was bounced because of a suspicious header...

1. Some of the exon locations start with .0:
I think this is a bug of the EMBL formatting at Ensembl?

FT   exon            .0:44020..44364
FT                   /exon_id="ENSMUSE00000233709"
FT                   /start_phase=0
FT                   /end_phase=0



2. The first annotation of a CDS feature is written on the next line 
after CDS. This is not found by the EMBL parser.
I think that is is also a bug at Ensembl?

FT   CDS             
FT                   /gene="ENSMUSG00000020053"



3. Some of the lines cannot be parsed, for example the parser writes to 
System.out: "This line could not be parsed: exon            2001..2159"
This one I don't understand, I cannot see a problem for these features?

FT   exon            2001..2159
FT                   /exon_id="ENSMUSE00000248454"
FT                   /start_phase=0
FT                   /end_phase=0



Thank you in advance!

Stein.

-- 
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI


From birney at ebi.ac.uk  Wed Jan 29 09:08:22 2003
From: birney at ebi.ac.uk (Ewan Birney)
Date: Wed Jan 29 04:00:02 2003
Subject: [Biojava-l] Ensembl gene parsing
In-Reply-To: <3E379766.9020405@esat.kuleuven.ac.be>
Message-ID: <Pine.LNX.4.44.0301290906140.3870-100000@pigeon.ebi.ac.uk>

On Wed, 29 Jan 2003, Stein Aerts wrote:

> Hi,
> 
> When currently parsing an exported sequence of an Ensembl mouse gene 
> (using the Export Data function at www.ensembl.org) there appear to be 3 
> problems:
> I tried to attach an example of an exported sequence of the Igf1 gene 
> but then the message was bounced because of a suspicious header...
> 
> 1. Some of the exon locations start with .0:
> I think this is a bug of the EMBL formatting at Ensembl?

Yes, this is pretty certainly a fault our end, and I think I know where 
this is.

> 
> FT   exon            .0:44020..44364
> FT                   /exon_id="ENSMUSE00000233709"
> FT                   /start_phase=0
> FT                   /end_phase=0
> 
> 
> 
> 2. The first annotation of a CDS feature is written on the next line 
> after CDS. This is not found by the EMBL parser.
> I think that is is also a bug at Ensembl?
> 

This is probably a line-length issue. I wonder what the right thing to do 
here is... Hmmm

> FT   CDS             
> FT                   /gene="ENSMUSG00000020053"
> 
> 
> 
> 3. Some of the lines cannot be parsed, for example the parser writes to 
> System.out: "This line could not be parsed: exon            2001..2159"
> This one I don't understand, I cannot see a problem for these features?
> 
> FT   exon            2001..2159
> FT                   /exon_id="ENSMUSE00000248454"
> FT                   /start_phase=0
> FT                   /end_phase=0
> 
> 
> 
> Thank you in advance!
> 

Stein - have you tried Mart inside Ensembl? For most people, this is far 
easier way to get bulk downloads of stuff in very-easy-to-parse-format.


http://www.ensembl.org/Homo_sapiens/martview


choose feature list and/or gene structure when you get to output.



The Ensembl bugs should be fixed of course... ;)



> Stein.
> 
> -- 
> Stein Aerts BioI@SISTA
> K.U.Leuven ESAT-SCD Belgium
> http://www.esat.kuleuven.ac.be/~dna/BioI
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------

From saerts at mailserv.esat.kuleuven.ac.be  Wed Jan 29 10:35:11 2003
From: saerts at mailserv.esat.kuleuven.ac.be (saerts)
Date: Wed Jan 29 04:26:49 2003
Subject: [Biojava-l] Ensembl gene parsing
Message-ID: <1043832911.3e37a04fe220e@webmail.kuleuven.ac.be>

Hi Ewan,
I know of Mart (and I like it) but it is not suited for automated sequence
retrieval using gene_stable_id's (a SOAP web service for the export data
function would be nice). Anyway, the Mart output would have currently the same
faults I guess. Do you reckon that the fixing of the Ensembl bugs is a short
term matter?
No ideas on the cause of the 3rd problem? I would probably have to print the
stack trace in the source code instead of the message "could not be parsed" when
parsing errors occur.

Thx,
Stein.

PS it is very annoying that my mails are always bounced because of a 'suspicious
header'; am I doing something wrong?


Ewan Birney wrote:

On Wed, 29 Jan 2003, Stein Aerts wrote:

  

Hi,

When currently parsing an exported sequence of an Ensembl mouse gene 
(using the Export Data function at www.ensembl.org) there appear to be 3 
problems:
I tried to attach an example of an exported sequence of the Igf1 gene 
but then the message was bounced because of a suspicious header...

1. Some of the exon locations start with .0:
I think this is a bug of the EMBL formatting at Ensembl?
    


Yes, this is pretty certainly a fault our end, and I think I know where 
this is.

  

FT   exon            .0:44020..44364
FT                   /exon_id="ENSMUSE00000233709"
FT                   /start_phase=0
FT                   /end_phase=0



2. The first annotation of a CDS feature is written on the next line 
after CDS. This is not found by the EMBL parser.
I think that is is also a bug at Ensembl?

    


This is probably a line-length issue. I wonder what the right thing to do 
here is... Hmmm

  

FT   CDS             
FT                   /gene="ENSMUSG00000020053"



3. Some of the lines cannot be parsed, for example the parser writes to 
System.out: "This line could not be parsed: exon            2001..2159"
This one I don't understand, I cannot see a problem for these features?

FT   exon            2001..2159
FT                   /exon_id="ENSMUSE00000248454"
FT                   /start_phase=0
FT                   /end_phase=0



Thank you in advance!

    


Stein - have you tried Mart inside Ensembl? For most people, this is far 
easier way to get bulk downloads of stuff in very-easy-to-parse-format.


http://www.ensembl.org/Homo_sapiens/martview


choose feature list and/or gene structure when you get to output.



The Ensembl bugs should be fixed of course... ;)



  

Stein.

-- 
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI


_______________________________________________
Biojava-l mailing list  -  Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l

    


-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------

_______________________________________________
Biojava-l mailing list  -  Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l

  


-- 
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI



-- 
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI


From birney at ebi.ac.uk  Wed Jan 29 09:58:18 2003
From: birney at ebi.ac.uk (Ewan Birney)
Date: Wed Jan 29 04:50:03 2003
Subject: [Biojava-l] Ensembl gene parsing
In-Reply-To: <3E379E69.5030300@esat.kuleuven.ac.be>
Message-ID: <Pine.LNX.4.44.0301290953260.3870-100000@pigeon.ebi.ac.uk>

On Wed, 29 Jan 2003, Stein Aerts wrote:

> Hi Ewan,
> I know of Mart (and I like it) but it is not suited for automated 
> sequence retrieval using gene_stable_id's (a SOAP web service for the 
> export data function would be nice). Anyway, the Mart output would have 
> currently the same faults I guess. Do you reckon that the fixing of the 
> Ensembl bugs is a short term matter?


(a) we know that people want to script against Mart and are working 
towards this - Arek might be able to fill you in (over to Arek)


(b) Scripting against the core is best done probably with a specific
ensembl script (perl) that doesn't bounce through genbank format - tell us
what you want and I suspect Arne or Graham can whip up a (perl) script
quickly


(c) If you don't like Perl ( ... this is the biojava mailing list...) then 
there is a pretty complete and stable Java binding to Ensembl - it doesn't 
use BioJava - it is more just a vanilla Java binding to Ensembl. Craig 
melsopp is the lead on that. The web page is

http://www.ensembl.org/java/


(d) Almost certainly, parsing GenBank/EMBL format is one of the worst ways 
to get information out of Ensembl - there is lots of stuff inside Ensembl 
which we can't dump due to format and/or space issues; we don't consider 
it to be a primary route of information...


... it doesn't change the fact there are bugs on our side ;) and we will 
fix those.


k

From td2 at sanger.ac.uk  Wed Jan 29 11:56:21 2003
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed Jan 29 06:48:25 2003
Subject: [Biojava-l] Ensembl gene parsing
In-Reply-To: <Pine.LNX.4.44.0301290953260.3870-100000@pigeon.ebi.ac.uk>
References: <3E379E69.5030300@esat.kuleuven.ac.be>
	<Pine.LNX.4.44.0301290953260.3870-100000@pigeon.ebi.ac.uk>
Message-ID: <20030129115621.GB505610@jabba.sanger.ac.uk>

On Wed, Jan 29, 2003 at 09:58:18AM +0000, Ewan Birney wrote:
> 
> (c) If you don't like Perl ( ... this is the biojava mailing list...) then 
> there is a pretty complete and stable Java binding to Ensembl - it doesn't 
> use BioJava - it is more just a vanilla Java binding to Ensembl. Craig 
> melsopp is the lead on that. The web page is
> 
> http://www.ensembl.org/java/

(d) There's also a completely different BioJava-based mechanism
for accessing Ensembl databases:

   http://biojava.org/pipermail/biojava-l/2002-December/003418.html

Unlike ensj, this is 100% read-only.  It does give you access
without an additional API, though, and as far as I know it's the
only thing which supports multiple versions of the Ensembl database
schema off a single codebase.

     Thomas.
From td2 at sanger.ac.uk  Wed Jan 29 12:48:15 2003
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed Jan 29 07:39:47 2003
Subject: [Biojava-l] Ensembl gene parsing
In-Reply-To: <3E37CC0A.4040501@esat.kuleuven.ac.be>
References: <3E379E69.5030300@esat.kuleuven.ac.be>
	<Pine.LNX.4.44.0301290953260.3870-100000@pigeon.ebi.ac.uk>
	<20030129115621.GB505610@jabba.sanger.ac.uk>
	<3E37CC0A.4040501@esat.kuleuven.ac.be>
Message-ID: <20030129124814.GC505610@jabba.sanger.ac.uk>

On Wed, Jan 29, 2003 at 01:41:46PM +0100, Stein Aerts wrote:
> 
> The BioJava-Ensembl should be ideal. However, retrieving a gene with 
> flanking sequence based on gene_stable_id using the code below takes a 
> million years.
> 
>        Ensembl ens = new Ensembl(
>              org.ensembl.db.sql.SQLDatabaseAdaptor.connectSQL(dbURL, 
> dbUser, dbPass, dbSchemaVersion)
>        );
>        SequenceDB chromos = ens.getChromosomes();
>        FeatureHolder transHolder = chromos.filter(
>              new FeatureFilter.ByAnnotation("ensembl.gene", 
> "ENSG00000167779")
>        );

Try "ensembl.gene_id" instead (or better still, the convenience
constant Ensembl.TRANSCRIPT_GENEID).  That said, it should be
able to prove by schema comparison that no features have
the ensembl.gene property, and return the empty set instantly
rather than trawling the database.  I'll check up on this later.

> The output gives:
> 
> Querying:  where contig_id = '592075'
> Querying:  where contig_id = '162233'
> Querying:  where contig_id = '162238'
> Querying:  where contig_id = '162241'

Are you sure you're using an up-to-date version?  That debugging
output looks old.

     Thomas.
From matthew_pocock at yahoo.co.uk  Wed Jan 29 12:43:14 2003
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Wed Jan 29 07:56:34 2003
Subject: [Biojava-l] Ensembl gene parsing
In-Reply-To: <Pine.LNX.4.44.0301290953260.3870-100000@pigeon.ebi.ac.uk>
References: <Pine.LNX.4.44.0301290953260.3870-100000@pigeon.ebi.ac.uk>
Message-ID: <3E37CC62.1050103@yahoo.co.uk>

Ewan Birney wrote:
> (c) If you don't like Perl ( ... this is the biojava mailing list...) then 
> there is a pretty complete and stable Java binding to Ensembl - it doesn't 
> use BioJava - it is more just a vanilla Java binding to Ensembl. Craig 
> melsopp is the lead on that. The web page is
> 
> http://www.ensembl.org/java/


And also the biojava-ensembl may do what you want 
(http://biojava.org/download/biojava-ensembl/) - it's the code that 
backs the ensembl DAS server. To make this work, you need a JDBC url to 
point it at. I think ensembl provides a public sql server.

Matthew

From stabenau at ebi.ac.uk  Wed Jan 29 13:17:24 2003
From: stabenau at ebi.ac.uk (Arne Stabenau)
Date: Wed Jan 29 08:00:31 2003
Subject: [Biojava-l] Ensembl gene parsing
References: <3E379E69.5030300@esat.kuleuven.ac.be>
	<Pine.LNX.4.44.0301290953260.3870-100000@pigeon.ebi.ac.uk>
	<20030129115621.GB505610@jabba.sanger.ac.uk>
	<3E37CC0A.4040501@esat.kuleuven.ac.be>
Message-ID: <3E37D464.3010202@ebi.ac.uk>

Hi Stein,

The EMBL export function on the current website used to work when we 
released the site. For some reason the mistakes you spotted got 
introduced. We tested the new release website which will come out next 
monday and it doesnt seem to have the problem (yet). So I would like to 
take the easy route for us and wait for the next release. We will 
however be careful not to reinvent the bug on that one.

If there is any pressing reason for a fix earlier than that, please let 
us know. Please consider to use ensj for what you want to do, its as 
fast as the perl code for most of the stuff it does. It just doesnt give 
you biojava objects.

Arne


Stein Aerts wrote:

>
> The BioJava-Ensembl should be ideal. However, retrieving a gene with 
> flanking sequence based on gene_stable_id using the code below takes a 
> million years.
>
>         Ensembl ens = new Ensembl(
>               org.ensembl.db.sql.SQLDatabaseAdaptor.connectSQL(dbURL, 
> dbUser, dbPass, dbSchemaVersion)
>         );
>         SequenceDB chromos = ens.getChromosomes();
>         FeatureHolder transHolder = chromos.filter(
>               new FeatureFilter.ByAnnotation("ensembl.gene", 
> "ENSG00000167779")
>         );
>
> The output gives:
>
> Querying:  where contig_id = '592075'
> Querying:  where contig_id = '162233'
> Querying:  where contig_id = '162238'
> Querying:  where contig_id = '162241'
> etc.
>
> So that is not very efficient.
>
> Would there an alternative here that is similar to the export data 
> function (based on any feature: gene, contig, clone, cDNA, peptide...) 
> which runs via HTTP and is very very fast.

If you want to see fast, construct URLs for the Mart and extract the 
data you want from the result ...

>
>     
> Stein.
>
>
> Thomas Down wrote:
>
>>On Wed, Jan 29, 2003 at 09:58:18AM +0000, Ewan Birney wrote:
>>  
>>
>>>(c) If you don't like Perl ( ... this is the biojava mailing list...) then 
>>>there is a pretty complete and stable Java binding to Ensembl - it doesn't 
>>>use BioJava - it is more just a vanilla Java binding to Ensembl. Craig 
>>>melsopp is the lead on that. The web page is
>>>
>>>http://www.ensembl.org/java/
>>>    
>>>
>>
>>(d) There's also a completely different BioJava-based mechanism
>>for accessing Ensembl databases:
>>
>>   http://biojava.org/pipermail/biojava-l/2002-December/003418.html
>>
>>Unlike ensj, this is 100% read-only.  It does give you access
>>without an additional API, though, and as far as I know it's the
>>only thing which supports multiple versions of the Ensembl database
>>schema off a single codebase.
>>
>>     Thomas.
>>
>>  
>>
>
>-- 
>Stein Aerts BioI@SISTA
>K.U.Leuven ESAT-SCD Belgium
>http://www.esat.kuleuven.ac.be/~dna/BioI
>
>

-- 
------------------------------------------------
Arne Stabenau         Phone: +44 (0) 1223 494413
<stabenau@ebi.ac.uk>  Fax:   +44 (0) 1223 494468

EMBL-EBI
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD UK
------------------------------------------------



From stein.aerts at esat.kuleuven.ac.be  Wed Jan 29 15:56:03 2003
From: stein.aerts at esat.kuleuven.ac.be (Stein Aerts)
Date: Wed Jan 29 09:51:46 2003
Subject: [Biojava-l] Ensembl gene parsing
References: <3E379E69.5030300@esat.kuleuven.ac.be>
	<Pine.LNX.4.44.0301290953260.3870-100000@pigeon.ebi.ac.uk>
	<20030129115621.GB505610@jabba.sanger.ac.uk>
	<3E37CC0A.4040501@esat.kuleuven.ac.be> <3E37D464.3010202@ebi.ac.uk>
	<3E37DE11.9020503@esat.kuleuven.ac.be> <3E37EB6C.4060608@ebi.ac.uk>
Message-ID: <3E37EB83.2060106@esat.kuleuven.ac.be>


I'm not at all dependent on EMBL files. I only need a sequence with some 
annotation and some features. Any format that is parsable with BioJava 
would do. What alternatives are currently at hand?

Stein.




Arne Stabenau wrote:

>
>
> Stein Aerts wrote:
>
>>
>> OK, then we will wait until monday.
>> I am indeed considering to use ensj. Would it be possible to inform 
>> me on how to construct a EMBL formatted flat file of a gene (with 
>> some features of choice) using ensj? I couldn't find that in the 
>> documentation.
>
>
> Ensj does not support EMBL flat file dumps and I seriously consider 
> not to do it in the future for EnsEMBL. Its not well documented format 
> and very complicated occasionally. Is there a reason why you depend so 
> much on EMBL files?
> I would rather provide alternatives.
>
> Arne
>
>
>
>>
>> Regards and thanks a lot,
>> Stein.
>>
>> Arne Stabenau wrote:
>>
>>> Hi Stein,
>>>
>>> The EMBL export function on the current website used to work when we 
>>> released the site. For some reason the mistakes you spotted got 
>>> introduced. We tested the new release website which will come out 
>>> next monday and it doesnt seem to have the problem (yet). So I would 
>>> like to take the easy route for us and wait for the next release. We 
>>> will however be careful not to reinvent the bug on that one.
>>>
>>> If there is any pressing reason for a fix earlier than that, please 
>>> let us know. Please consider to use ensj for what you want to do, 
>>> its as fast as the perl code for most of the stuff it does. It just 
>>> doesnt give you biojava objects.
>>>
>>> Arne
>>>
>>>
>>> Stein Aerts wrote:
>>>
>>>>
>>>> The BioJava-Ensembl should be ideal. However, retrieving a gene 
>>>> with flanking sequence based on gene_stable_id using the code below 
>>>> takes a million years.
>>>>
>>>>         Ensembl ens = new Ensembl(
>>>>               
>>>> org.ensembl.db.sql.SQLDatabaseAdaptor.connectSQL(dbURL, dbUser, 
>>>> dbPass, dbSchemaVersion)
>>>>         );
>>>>         SequenceDB chromos = ens.getChromosomes();
>>>>         FeatureHolder transHolder = chromos.filter(
>>>>               new FeatureFilter.ByAnnotation("ensembl.gene", 
>>>> "ENSG00000167779")
>>>>         );
>>>>
>>>> The output gives:
>>>>
>>>> Querying:  where contig_id = '592075'
>>>> Querying:  where contig_id = '162233'
>>>> Querying:  where contig_id = '162238'
>>>> Querying:  where contig_id = '162241'
>>>> etc.
>>>>
>>>> So that is not very efficient.
>>>>
>>>> Would there an alternative here that is similar to the export data 
>>>> function (based on any feature: gene, contig, clone, cDNA, 
>>>> peptide...) which runs via HTTP and is very very fast.
>>>
>>>
>>>
>>>
>>> If you want to see fast, construct URLs for the Mart and extract the 
>>> data you want from the result ...
>>>
>>>>
>>>>     Stein.
>>>>
>>>>
>>>> Thomas Down wrote:
>>>>
>>>>> On Wed, Jan 29, 2003 at 09:58:18AM +0000, Ewan Birney wrote:
>>>>>  
>>>>>
>>>>>> (c) If you don't like Perl ( ... this is the biojava mailing 
>>>>>> list...) then there is a pretty complete and stable Java binding 
>>>>>> to Ensembl - it doesn't use BioJava - it is more just a vanilla 
>>>>>> Java binding to Ensembl. Craig melsopp is the lead on that. The 
>>>>>> web page is
>>>>>>
>>>>>> http://www.ensembl.org/java/
>>>>>>   
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> (d) There's also a completely different BioJava-based mechanism
>>>>> for accessing Ensembl databases:
>>>>>
>>>>>   http://biojava.org/pipermail/biojava-l/2002-December/003418.html
>>>>>
>>>>> Unlike ensj, this is 100% read-only.  It does give you access
>>>>> without an additional API, though, and as far as I know it's the
>>>>> only thing which supports multiple versions of the Ensembl database
>>>>> schema off a single codebase.
>>>>>
>>>>>     Thomas.
>>>>>
>>>>>  
>>>>>
>>>>
>>>> -- 
>>>> Stein Aerts BioI@SISTA
>>>> K.U.Leuven ESAT-SCD Belgium
>>>> http://www.esat.kuleuven.ac.be/~dna/BioI
>>>>
>>>>
>>>
>>
>

-- 
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI



From saerts at mailserv.esat.kuleuven.ac.be  Tue Jan 28 17:27:25 2003
From: saerts at mailserv.esat.kuleuven.ac.be (saerts)
Date: Thu Jan 30 10:46:55 2003
Subject: [Biojava-l] EMBL parsing problems
Message-ID: <1043771245.3e36af6df04ab@webmail.kuleuven.ac.be>

Hi,

When currently parsing an exported sequence of an Ensembl mouse gene (using the
Export Data function at www.ensembl.org) there appear to be 3 problems:
(I have attached the exported sequence with gene features for Igf1)

1. Some of the exon locations start with .0:
I think this is a bug of the EMBL formatting at Ensembl?

2. The first annotation of a CDS feature is written on the next line after CDS.
This is not found by the EMBL parser.
I think that is is also a bug at Ensembl?

3. Some of the lines cannot be parsed, for example the parser writes to
System.out: "This line could not be parsed: exon            2001..2159"
This one I don't understand, I cannot see a problem for these features?

Thank you in advance!

Stein.


#########
#output when parsing the attached .embl file
################
>From must be less than To: exon            .0:44020..44591
>From must be less than To: exon            .0:44020..44364
>From must be less than To: exon            .0:44020..44364
This line could not be parsed: exon            complement(.0:13156..13348)
>From must be less than To: exon            .0:46248..46337
This line could not be parsed: exon            complement(245..653)
This line could not be parsed: exon            2001..2159
This line could not be parsed: exon            2003..2159
This line could not be parsed: exon            2003..2159
This line could not be parsed: exon            2003..2159
This line could not be parsed: exon            50907..51088
This line could not be parsed: exon            50907..51088
This line could not be parsed: exon            50907..51088
This line could not be parsed: exon            50907..51088
This line could not be parsed: exon            52586..52637
This line could not be parsed: exon            52586..52637
This line could not be parsed: exon            68128..69089
This line could not be parsed: exon            68128..69089
This line could not be parsed: exon            68128..69254
This line could not be parsed: exon            68132..69089
-------------- next part --------------
z'??mj?Zr?????+???t??z???j.???nT?????X?j????
??l????(?{^5??[???
?
??Z???i?^R??*^?f??????!???????}5???k?x?~???-???z??
From stein.aerts at esat.kuleuven.ac.be  Tue Jan 28 17:00:47 2003
From: stein.aerts at esat.kuleuven.ac.be (Stein Aerts)
Date: Thu Jan 30 10:49:23 2003
Subject: [Biojava-l] EMBL parsing problems
Message-ID: <3E36A92F.7040600@esat.kuleuven.ac.be>

Hi,

When currently parsing an exported sequence of an Ensembl mouse gene 
(using the Export Data function at www.ensembl.org) there appear to be 3 
problems:
(I have attached the exported sequence with gene features for Igf1)

1. Some of the exon locations start with .0:
I think this is a bug of the EMBL formatting at Ensembl?

2. The first annotation of a CDS feature is written on the next line 
after CDS. This is not found by the EMBL parser.
I think that is is also a bug at Ensembl?

3. Some of the lines cannot be parsed, for example the parser writes to 
System.out: "This line could not be parsed: exon            2001..2159"
This one I don't understand, I cannot see a problem for these features?

Thank you in advance!

Stein.


#########
#output when parsing the attached .embl file
################
 From must be less than To: exon            .0:44020..44591
 From must be less than To: exon            .0:44020..44364
 From must be less than To: exon            .0:44020..44364
This line could not be parsed: exon            complement(.0:13156..13348)
 From must be less than To: exon            .0:46248..46337
This line could not be parsed: exon            complement(245..653)
This line could not be parsed: exon            2001..2159
This line could not be parsed: exon            2003..2159
This line could not be parsed: exon            2003..2159
This line could not be parsed: exon            2003..2159
This line could not be parsed: exon            50907..51088
This line could not be parsed: exon            50907..51088
This line could not be parsed: exon            50907..51088
This line could not be parsed: exon            50907..51088
This line could not be parsed: exon            52586..52637
This line could not be parsed: exon            52586..52637
This line could not be parsed: exon            68128..69089
This line could not be parsed: exon            68128..69089
This line could not be parsed: exon            68128..69254
This line could not be parsed: exon            68132..69089

-- 
Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI

-------------- next part --------------
ID   ENSMUSG00000020053 and 2000bp 5'/3' flanking  ENSEMBL; DNA; ; 71254 BP.
XX
AC   Chromosome 10 88047681 to 88118934;
XX
SV   NO_SV_NUMBER
XX
DE   Reannotated sequence via Ensembl
XX
KW   HTG.
XX
OS   Mus musculus (House mouse)
OC   Eukaryota; Metazoa; Chordata; Vertebrata; Mammalia; Eutheria; Rodentia;
OC   Sciurognath; Muridae; Murinae; Mus.
XX
CC   This sequence was reannotated via the Ensembl system. Please visit the
CC   Ensembl web site, http://www.ensembl.org/ for more information.
XX
CC   All feature locations are relative to the first (5') base of the sequence
CC   in this file.  The sequence presented is always the forward strand of the
CC   assembly. Features that lie outside of the sequence contained in this file
CC   have clonal location coordinates in the format: <clone
CC   accession>.<version>:<start>..<end>
XX
CC   The /gene indicates a unique id for a gene, /cds a unique id for a
CC   translation and a /exon a unique id for an exon. These ids are maintained
CC   wherever possible between versions.
XX
CC   All the exons and transcripts in Ensembl are confirmed by similarity to
CC   either protein or cDNA sequences.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..71254
FT                   /classification="musculus, Mus, Murinae, Muridae,
FT                   Sciurognath, Rodentia, Eutheria, Mammalia, Vertebrata,
FT                   Chordata, Metazoa, Eukaryota"
FT                   /organism="House mouse"
FT   CDS             
FT                   /gene="ENSMUSESTG00000001479"
FT                   /cds="ENSMUSESTP00000001483"
FT                   /transcript="ENSMUSESTT00000001483"
FT                   /db_xref="SPTREMBL:O88703"
FT                   /db_xref="EMBL:AJ225122"
FT                   /db_xref="protein_id:CAA12406"
FT                   /db_xref="MarkerSymbol:Hcn2"
FT                   /db_xref="RefSeq:NM_008226"
FT                   /db_xref="LocusLink:15166"
FT                   /translation=""
FT   CDS             
FT                   /gene="ENSMUSG00000020053"
FT                   /cds="ENSMUSP00000020244"
FT                   /transcript="ENSMUST00000020244"
FT                   /db_xref="SWISSPROT:IGFA_MOUSE"
FT                   /db_xref="EMBL:X04480"
FT                   /db_xref="protein_id:CAA28168"
FT                   /db_xref="MarkerSymbol:Igf1"
FT                   /db_xref="SWISSPROT:IGFB_MOUSE"
FT                   /db_xref="EMBL:X04482"
FT                   /db_xref="protein_id:CAA28170"
FT                   /db_xref="RefSeq:NM_010512"
FT                   /db_xref="LocusLink:16000"
FT                   /translation=""
FT   CDS             
FT                   /gene="ENSMUSESTG00000001293"
FT                   /cds="ENSMUSESTP00000001241"
FT                   /transcript="ENSMUSESTT00000001241"
FT                   /translation=""
FT   CDS             
FT                   /gene="ENSMUSESTG00000001737"
FT                   /cds="ENSMUSESTP00000002001"
FT                   /transcript="ENSMUSESTT00000002001"
FT                   /db_xref="SPTREMBL:Q9D9J9"
FT                   /db_xref="EMBL:AK006825"
FT                   /db_xref="protein_id:BAB24758"
FT                   /db_xref="MarkerSymbol:1700057K13Rik"
FT                   /translation=""
FT   CDS             
FT                   /gene="ENSMUSESTG00000013317"
FT                   /cds="ENSMUSESTP00000013016"
FT                   /transcript="ENSMUSESTT00000013016"
FT                   /db_xref="RefSeq:NM_013528"
FT                   /db_xref="LocusLink:14583"
FT                   /db_xref="SWISSPROT:GFA1_MOUSE"
FT                   /db_xref="EMBL:U00932"
FT                   /db_xref="protein_id:AAC27348"
FT                   /db_xref="MarkerSymbol:Gfpt1"
FT                   /translation=""
FT   exon            .0:44020..44364
FT                   /exon_id="ENSMUSE00000233709"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            .0:44020..44364
FT                   /exon_id="ENSMUSE00000304540"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            complement(.0:13156..13348)
FT                   /exon_id="ENSMUSE00000228995"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            .0:44020..44591
FT                   /exon_id="ENSMUSE00000101271"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            .0:46248..46337
FT                   /exon_id="ENSMUSE00000101369"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            complement(245..653)
FT                   /exon_id="ENSMUSE00000229152"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            2001..2159
FT                   /exon_id="ENSMUSE00000248454"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            2003..2159
FT                   /exon_id="ENSMUSE00000102117"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            2003..2159
FT                   /exon_id="ENSMUSE00000154915"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            2003..2159
FT                   /exon_id="ENSMUSE00000100129"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            50907..51088
FT                   /exon_id="ENSMUSE00000102735"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            50907..51088
FT                   /exon_id="ENSMUSE00000297513"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            50907..51088
FT                   /exon_id="ENSMUSE00000100134"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            50907..51088
FT                   /exon_id="ENSMUSE00000236186"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            52586..52637
FT                   /exon_id="ENSMUSE00000224203"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            52586..52637
FT                   /exon_id="ENSMUSE00000248442"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            68128..69089
FT                   /exon_id="ENSMUSE00000100227"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            68128..69089
FT                   /exon_id="ENSMUSE00000324611"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            68128..69254
FT                   /exon_id="ENSMUSE00000248438"
FT                   /start_phase=0
FT                   /end_phase=0
FT   exon            68132..69089
FT                   /exon_id="ENSMUSE00000228555"
FT                   /start_phase=0
FT                   /end_phase=0
XX
SQ   Sequence 71254 BP; 21337 A; 14824 C; 14160 G; 20350 T; 583 other;
     ctctgagtct cactctccaa acaagtgggg attgaatgaa tttgcctcaa ctgtgagatt        60
     caaaaaaaaa aaaaaaagaa aaaagaaaag aaaagaaaaa agaaaaagaa aacctccttt       120
     aaaaattata gcttccagta tatctccgtt acccctttta tagggtggct cacctcatac       180
     tctactggtg actctttcca caatattgaa agcatatgtc tctgaaaggg gtgaagtcgc       240
     tcaccttagg ggccttcctg gaagaaagta cacgctggtt ccacaagcag caaccctgaa       300
     aagtgggacg tcaccacagt gtctgactgc ttcttagaat gaagagcgac tggagtccca       360
     ggaatgctga ctttggcagg ggtgccattt ggctactaac catcggctag cttgtgccaa       420
     acaagggttc cttggtagat tttgttataa agttgataac agggatccgt gagtgcttcc       480
     cagagaataa gtcagagtgg ctgctgctca agaaaaggct cttgcaggtt ttaagcccag       540
     tgtcctgcat ttaaaaaacg tctctcagtc tgatagtgag ctagaagaga ggaccctggc       600
     gtaaaagatt acatttacgt cctgttgaag tttgggagat gattgttaaa ctccctgacc       660
     tgctgccagc ctcccttttc ctgcttgtca ctctccccta aggcaggaag agaaatgaga       720
     aaccctcttc cccaaggcag ccataaaact tgaacatttg cttctgacct cccatgactt       780
     ccagtagagg agctggccag agagaagtct gctgcctgcc ctgtctgatg gcaggccact       840
     ggcccctccc cccagagggg tcctaaatct tatacccagg atttatgaat gcttcacaaa       900
     ggggcataga agaatcagga gaagcaagac acactgggtt ttccacctca gtctaccggt       960
     cattaaatga taattctgcc cactgtccac gcccccattg aacaacaaca tatgggaaag      1020
     tttacccctg ttatggaggc ttcttttttt cttttttttt tcctgaaggc tctcacctca      1080
     cataaacctt taattaaata aagacatcat gactttcatc agcctgcact atgttatgga      1140
     ggtacagact atgaccttca tggtgtgtaa ggagagggaa tcacaccttc ctttcacaat      1200
     gcttttgtga gacaattgca ttcctaaatc ttgcatgatt ttcctgtttt gagactgctt      1260
     gtttggtttt ccacctgtgg ttgtgttagc tgctaatatt cgcaggtaag atttctccgc      1320
     ctcgtccccc acctctgctc tccctgcctc ccttcctttc tctctctctc tctctctgga      1380
     aggctataat aatagatttt tttaatactg ttctggccag tataaaatct tcttaatcta      1440
     tggacagaga atgatgccct ggttaattta atattcaaag caataataaa tataatgaat      1500
     atatgtacca tctggaaatg gtcaggtttt agattattta agttgaaaca gtttgaatgt      1560
     aaagctgagc acaatttaat atttgataat ttagatgttt tatatcagac tggcatgggg      1620
     atcccacccc acacacacac ataaacacat cccaccacaa gcacacacat atacgcgcac      1680
     acactaaaat aactgcatct tttgtcaccc aataaatgtt tgtagccctt ttaccctact      1740
     tattaataat aggaactcat aaaagctcca ggagaacctc tgaagaccca gtagcaaagg      1800
     gactaaccac agtttgtctg atgtcaagat gggctcaggc caggtccctc gggggccctt      1860
     catgccacac tgctcttcta ggacagagcg tttgaatgaa tgatgagaag gagtaccaag      1920
     tgcgagtcaa cacatcgctg ccccatcctt tcaggaccca gaaggatacc tgaacctcct      1980
     ttttattttc cccctccgac agataaagat acacatcatg tcgtcttcac acctcttcta      2040
     cctggcgctc tgcttgctca ccttcaccag ctccaccaca gctggaccag agaccctttg      2100
     cggggctgag ctggtggatg ctcttcagtt cgtgtgtgga ccgaggggct tttacttcag      2160
     tgagtagctc tcccatcccc tctcccaacc ctcttctccc tgctacaatg attcagaagt      2220
     agatggtttc ctggatttat aaccacaggg attggtcgaa taactgagtg actgcctatg      2280
     gctaacagcc accctccacc ccccaacccc catatccatc accttaatgt atgcataaca      2340
     cttcagtggg gcattggcag gtttgggaga tttagggtcg aattttcttc cttaagagtt      2400
     tgcctttaac tgcttcctct ggggcccgct tccagaattt atggtcaacc cccactctcc      2460
     tgttcctccc aatgaagaaa tgagacagca taaccctaaa gtattgcaga ttttgttctt      2520
     agacatttgg gcacatatag aaacatccag agggcgtaca ggactactgt gggtgttctg      2580
     aaatttaaag caaaatggta aggatcttgc accccgaact catgtgaact taagaaatga      2640
     attaaatgga gaacaaagta gatgtctcca tgcaacacaa agccagcatg agtggacaaa      2700
     aggtgatcat tgccaagaga tgtttgtaag tacataagct ttctaactgt gaactatggc      2760
     gtcattatca atatgccctc tatgcagact gactttaata ctttcttttc ttccttttgt      2820
     cattatgtcc ctttgatgta gtccttccct gggtattata tccatctaga aaggagtctt      2880
     tgaaaacttc agcaccacat atcttttaaa agtaggtctc agacaatcag agagtcagca      2940
     gtccatggga aggagacaga ggaatcaatg tctgtaaata agtcaatggc caccaagggg      3000
     agtgatcact tgaaaaaaaa aatctacctc ataggtatcc atctcacaga atattacaat      3060
     gcagtgaaaa actgaaagac agatgtgaac tctgtacatt tctttggaag tgcaaagagt      3120
     tcttggaacc tgggcgtgag tcatttgcca gggctcctgt cactcaagtg gagacaaatc      3180
     acctcagtga acccccacac ccacccccaa gctcaggctc ctgagatgat tcacactctt      3240
     gaagtctcgc ttgtcttctt gccaaatgcc agcctctctt gaggcaggtg atagtggctg      3300
     tggcttgtgt ggtattgtgt gtgtgtgtgt gtgtgcgtgt gcgtgtgcgt gtgcgtgtgc      3360
     gtgtgcgtgt gcgtgtgtgt gtgtgtgtgt gtgtaagaag gaggcaaaag tttattcata      3420
     taagtttgaa actacgaaag gaactaccaa ggagactggt aatgtgtatt taccatggtt      3480
     ttggcaaaat aaaataaaaa agacaacttg gcagaatagc gtcagagacg gacatgcttt      3540
     cggctgtttg aatgggaaat tttccacttt gtgctccctg ccagtccttt atttgaataa      3600
     attcacttac tcttctggca atagaacagt tccatccagt tctctggtgt aggagaaatg      3660
     aatgagttca ttaggtgggt gacttttttt ttaataccag acttgtttca cctttaagaa      3720
     catactatat caagtgaaat gagacatgaa cacaactgca caacgaattg agagcattct      3780
     ataactcgct gtaatcgagc catgttttct ctttggaaga cataagtcat tcttatctcc      3840
     agttcccaag gactttgtct cctcttggca gggcacttgt gtaagggcct tctgggtagt      3900
     ggcaggttga actgtaacac ccaccctgat gtactccagg aattccatgc acgggacatg      3960
     agtatgcttg tgctgtttac atcagataac gaaaactgag acgagaaata acaactcagc      4020
     tgtagataac tgggcaatac ttacatgtgt ttgcacagac acttgagcgt tgagcactga      4080
     caacggaaac cagttttaat gggctggaaa ggtttttgca tttgatcacc aggaggatca      4140
     aatttcaata cgtgtgttta agttgtgttt taataactta aagggaaaag aattcatacg      4200
     gtcacttgat acttttagca gggttctgga tttcaaaaca gtggctgtat gaaacacgtg      4260
     ctgttgtgaa ttctgccatt aagagtgttt ttttttaaat cacatcccac catatacatg      4320
     acttaaacta aatcccaagc cctgtttggt tccttaaatg tgaaggtatt cttgatagct      4380
     ttctgatcaa ctccacaatc ctctctacac gagaagagcc gatcctttta aattgcttta      4440
     gtttacttca aaacactggg ggcagggagg ggaagcattt tgtgtgtgtg tgtgtgtgtg      4500
     tgtgtggtag cacaagatat aaatgagaaa ccgggagatg actgagagac tgaccttgcc      4560
     tttgaagtac tcagaggtta gaaaaagagt gtatatcata tgctgtaagg gaaaacaacc      4620
     ttgggaaaag aagtgcaatt ctttaagctc tccctgaatc ttccccatca ctcatgacat      4680
     gtctttgcca ggctctgccc tctaggtgaa ctcctcaaag gctgtagcta tttatctttg      4740
     aagatcagtg tcaagttcaa tgtttgagtg atacagtagc tgctggtatc tatccattgg      4800
     aactggcaag attgaatcca agtaaactga atagaactgt ttttgtgggg ctctcccagg      4860
     aagaaccacc aaggattagg atcgccaaac actttacaac atacttctcg cctccctcgt      4920
     gcctacctag ttatttgatg aaactgctta gctttctttg cagaatgcag tgtaggtata      4980
     tcaccaggaa cttagaagct gtcctttggc catctctaag ctacactcat ggtctgtttc      5040
     cttccagagc caattattct tacaggcatt aactgttgtc aacaaatttt attgagtttc      5100
     cttttcatcc cctaagattt actgtgtggg ggaaagtcag cactaagcat ttacagtcct      5160
     cgaagcacct tttaaaggag agtacccttt gcatgtctgt acccgcagtt gacatttact      5220
     agattttgct cttatttaca aagttttatt gagcccatac ctttttattt taagctggtt      5280
     caacttcaat ttggaagtat atatttctct ccatggtgga aggcagggtc tgatcttgga      5340
     ttgatattta aacatcataa agaaatttgc ctctatattt atttatttat ttatggataa      5400
     tacaaactat ttaacaaaga ggggttctaa aatcctatta aaactgttct gagtatgttt      5460
     tttttttgtt tgtttgcttt gtttgtttgt tttgctaata cttgctttgt gtaggttgac      5520
     ccaattttgc aaatgagctc acaatcccag tctatcctaa gttctgtgga agcagacaca      5580
     acctccagga tgatcagttg tgagtctccc tccagcataa gtagagcagt tgatccaaaa      5640
     ttaatgtggc ttccccagac attttacaaa atgaaggagc caatgacgag ctaattatgg      5700
     gttcttcccc atgtaccata gagagagggc atgtcaatca gatggatgct cttttggttc      5760
     tgtgaggagg gcagcgccat tgtggagatg aaagcttact agcagagatt agctggtttg      5820
     ctggaaccca cacagaggac agacgtcccg ttataacttt gttttgtctg aagcacacca      5880
     gtgggtaaaa caaagtgaaa gaagtgacgc ttgccgcagg tataattttg gacagttatg      5940
     gcaagaaacc atttttaaca tgctctttgg gaacttctgg agtttttctc ctttgaggta      6000
     gttaagaagt tgacagacaa ccaaccatct tgaatggttt caattaagaa cgaccagaag      6060
     aaagagaggt tctggggtcc ttttcagttt taagagtcta taaacagtcc cttaaataaa      6120
     ctgtatgtgc tttacctcag gcagtctggg gaaagcgaga agtaaatcaa ttaaaaaaga      6180
     aagttggata ccctttcagc taccccagat tcatggcttt tgtaaaacat ccctccaatg      6240
     catgcttatt aggaacagat ctgaataaac cgatgacatt cttcatgtgt taaagcatac      6300
     tgtttttaaa gggtttaagt gaaactttgc aattagcttt cgttattatt gattgcacaa      6360
     accttccgag gctttggtta ttattataaa ctcggacttc ttcctttgat atgcagagct      6420
     cagaaaacta cctccagacc tgtcaatcat tatttatagg actttggcag gcatttaaac      6480
     ttcctgagct gaaatgccct tgtctataaa acaaggggat tttgttaaag caaatgacct      6540
     ttaactttaa cagacttgac atctaggttg caagcaacaa gcattcatgc tattggagaa      6600
     gggagaaccc tggacttaac tagtgcctga ggaccattta acttctttta tcttcttgac      6660
     atcatttcag ttggtcccca aaggtagcca atccgctcac ttcaagaaat aagagccagc      6720
     tgctttgctt tatttcagtt tgaacttcag tcctccaagg acagaacaga aattcagacc      6780
     tgaccacaaa gtccgaggtc ataaacctaa gcttgtcatt tctctttgtt atcaaagatg      6840
     attggatgat actcatcttt caaacacttt cacactgctt tgacatgggt ggtggtggtg      6900
     gtggggcaat gagtaaattt gttcattatc tcagaagaga attttatgaa tccacctcaa      6960
     tcctttgggc atcctattag atacagcctg tctagtgaaa gaagaacaac acagtttaaa      7020
     aaggcaccca tccacccacc actcacttag ggctagtgtg gactttgagc tccatccatc      7080
     tgcatttcct tgcacagcac ccctatggga attccaggca tgcatttgtg tgagttctgg      7140
     tacaagttag gggcatggtc cctgcctatg gaaaaacaat tctctttgaa attgatacat      7200
     ctggaattga ccttataacc ttgccctcat tagcacacag agctaatagg ccacagatat      7260
     tgtttgttta aaaggacact gggcttttat cttgaccctc caatgctcgc tactaccttt      7320
     taaaatatac ccaaggggac ttgtgtgagg gactaagaaa aatggaagtt tctgtgtgaa      7380
     attagaaaaa aactttcaag tttatgacat gttaatattc attatgactg tcttctcctg      7440
     gatcaatgac ctataaacag gagaatgaca ggttcaagac caagactgtg gcctcttttg      7500
     aaaagaatcc agagttgagc cttagctctg caaacttact cagtgggaga ccttgaaact      7560
     atgcggtgcc tcaatttctt catctgtaaa atgggacctg ccttacggtg ttgatattgg      7620
     ggttgaatga acagagagtt ttgaacatgt tagtttagag tggtgcctgg cacatcacac      7680
     catcctaatt agctagccca tctatttact ctcatctgag cctcagttgc agaatctgcc      7740
     ataaaaggtt caatatctga aaagtccact tagttattga ctcactattt tttctgcttg      7800
     gggcagaaac aattcattgt tgagacaatc aatagtagta acaattgtgt gcatagcatc      7860
     agtataaatg atgagaaggg tgatctgctt gtctccctgc tctgtcttta tcaccacttt      7920
     gacagataga gatggtttac tgtattagac gaacaagaaa tgtaaaggca tgggctggga      7980
     agatgctcag caggtcacac ttgtcccaca aatgtgaaga tgtaaagcca gatgcggtgg      8040
     tggtgcaagt ctgcaattgt agtgctccaa taaagagacg tgggaggtat tcataggaga      8100
     accttagagg cttgcaatcc agctagtctg acatacacag tgatgagaga ccctgcctca      8160
     tacaaggtgg gagttaggaa cttacatcca tggatggcat ccccacgtat gtgatggcat      8220
     tcaggcttgc actcagatac agaacagata caccacatac atgctcatgt acacacaaag      8280
     tgagatgaga ggtgcggaga ttttgaaact tgatgggtca aaaagccaag tccacagttt      8340
     cttgtctcca tgaaatactc tcattttgtc acttgtatta ttcagaagtc cacagttttg      8400
     tagcctaggg aaatgctccc taaaccctag tcaacccctg aaaaaatata gagcaagacc      8460
     cctggtatga agcagttggt tttcaacatt ctcttgaaat gaggccctta gggggtgggg      8520
     agaggtatat ctatgtaatg aacttgcatt tttacctctg agaccattga gaaaatacta      8580
     agaaaatttc aacagagtaa agaagaaaag tttcctttga tgagagatag ctgctgtaca      8640
     agacattgcc taggactccc ccagtcacta cacacaccct ttcctgtgag atccaagatg      8700
     ccctctgttc tggggatcct cacccatcat tcacaggttt catattcttc ttcctctacc      8760
     agaaaacctc aaaggtttag cttcttgcag catttagttt ggaaggcttg cttcttctca      8820
     aagaattgcc gggaggctat ttagttggaa cacatgcttc taggggggta ccaggaaagt      8880
     gttgccaaag gtgataaagg accagatggg agcccgatca aagtgggagt ggccggtggg      8940
     ttgtaacaca agatttccat ctgtgcgatg tgtatttcaa ccatgggatg agaagacctt      9000
     acatcatcaa ttgcaggtag acatttaaga ccccaaaggg aaattgagtg tcacatagct      9060
     tgactgttct tccaaatacc ttgtccagat acaatgtgcc atgccagcat cgcttaggta      9120
     ctccgtcaga accagtccca tctctgtggg cttctaaaca atacaagtga gcaaatgagt      9180
     gtacttcatg gagacaagaa gctgtgggct tggcttttgg acccataaag ttccagaagc      9240
     cttccttttt atttcaaaac ccacagccca gatccagaca cactgagaat aggcacaagg      9300
     tctctcccaa ggagattccc cattgtcctc acttacagac cacagaggct ttgatccttc      9360
     ctctagctag atgtccttga caaccacggt ggcaaattac cctgtttgct ctgggctgtt      9420
     tgtctggcat agttcccacc cagcaccttt ccacaaaact tcataagctc ttctatccca      9480
     aagaattatt ttggttgcct ggaaagttca aacctcccat gaactgtcag actggggaga      9540
     cgacatctcg gaggaggagt tgtgtttgtc tttatctata tgtgagatcg tgtttcaaac      9600
     acagcaaaga gctgttagtt gacatgcaat tccctaactg tagcaagttg tatgcctatt      9660
     taatgcattg tttagtctca cattggctag agccatttaa agaagcactt ggcaagctct      9720
     aggtttgcat tcttggcata actgcccctt ttagttttcc actgaaccct ggataccaag      9780
     aaaaaccctt cacttgcttt acgtctggtg tactgcttga tgcaattcac cagaccctct      9840
     gcgagtggtc ccctctgtat tcgtccgaag gtaattaatg gctttgcaat atttgatctg      9900
     cagaagcagg gacacaaagg gaaattgtgc aacccagaag agaccacaca gccttttaaa      9960
     attaaaacct tttgctttaa atgttcttca ggcattctgc aggagtagaa atttccattt     10020
     caagagaaaa aataaagtca tgctgaaatg cccaggaaga tacttaagaa cctgataatt     10080
     ggtcagatgt acacacctct atctcccttt taaagctacc tgattgttaa aaggaaggaa     10140
     catcgagtgc tcctacaagc ttagaaactt ttggaaaata atcttcccaa cactaaaaca     10200
     gaaacctaga gagaagttat gtgttcaagg tcacatagct aattagtggc agtaggagac     10260
     gtgtggattc tgttctctaa tcccagtgca gcctgcctct gcttagcatg attaatcatg     10320
     cctgtgtgaa attacctggt aacttcaaat gagtgggaac aggggaaggg ggggctcaag     10380
     tcaagttcct gcaaacgagc agagcagtcc cccagggaac cgtgcattct aataagcgca     10440
     cctgagagtt gacaatttgc tcccttgtgg cagaaattaa agtcatctgc ctgcctgtag     10500
     atatggaata caatgccttc agatgtgctt tgggcattga aatctactta tggtataatt     10560
     tagactaata ttgtatatta tgttcttctg gtcctctgac tactctctcc aaactcaact     10620
     tcagtagaac tcctttggaa tgacaaagct gtgtgttcct ggaaactctg aaacagtctc     10680
     ttgaattgga agatctgccg cccccccccc ccccgagaga tttctctgtc tcatgccaaa     10740
     aaaaaaaaaa tttatacctg atattttttt cagactctta agcagatact ctgtgaatct     10800
     ctagtggttt ccttctttgt gccttttatg gggtagacaa gaaaggctgt ctgaggagaa     10860
     gtgtggttaa gctaaagttt ggttacactt cgtaagaact gtcaggcaat cctgtgtttc     10920
     tgggaagata gcactacctc tgtgccattt accctggtga aatggctctt tcatcagaaa     10980
     caagcaattt agaaagactg ttgggagcca agcccatgga gccaacttct gattatccaa     11040
     tgaaactggg ggaaaggagc atgagcgtta gaactgtgga ttaaactcat gtgtggactc     11100
     cgcagaatgt ttctctcatt cttcctccat gcccatttat gaaaccaggt aacatgttct     11160
     gaaatcatat tcattcttag acagcccctc cttttcctga cagtgctact agcaataggg     11220
     gtttcagctg caggaatatt gatgtctggg gtctggtaaa ttctactgaa aggagattcc     11280
     tgtccagtat aggttcagag cagtatgttt ggctcctgcc aatgccagga gtcccatcct     11340
     cccattgtaa taaacacaga tattgcctaa tatattttgg ggtgctaaat caccccctcc     11400
     aattcagaac tactggacta ggaaagtgtc tagaagagaa ataactaaca aagtggaaca     11460
     aaatcaggca taaaattaaa gataacacac cacctaggaa gccttcctaa atgaagggat     11520
     tatggtctca ggccttggtc gctgattcca ggagttgata acccattgcc tgggtcaagc     11580
     aatgagaaga gtcaatggag ctagaaaaac ttttctatgg aaatacacag ctctttctag     11640
     aagctatgtg aaaaagcttc agcaggcttt cctttctgcc ttgcagctat agaacccact     11700
     cacctgcttt tggtaagagc ggttaggaca aaaagaaatg gtctactaca aatctgtagg     11760
     ccttagaagt gagcttgaga tcacctgaag ccagtataaa tgacactggc tgctggcacc     11820
     tttgtgccta tgcctgttcc tttcttagac ccataataaa taaactctct atccttcact     11880
     agtaaaaggc atagttcaaa gcaaatgacc ttccccccac cttattatgc ttttcctatc     11940
     tgagcatcat cagactcact gtctagaaag tcagcagtcg caagttgagt ttgacccata     12000
     tcacaaacag ctctgtggtc ctggggaggt cactctgatc atgagcctca cactcctcat     12060
     cataaactgg gaataaaaag attatagctc agaaatcttc tgagactcag ccatagtagg     12120
     gcttctgaaa ctcaaagagc catccacaga cacatcccta ttaacacatt gaaggagaca     12180
     ctttaccttg tgtccttact caggactgac tatttagttc agtcattcaa cctccacaac     12240
     attttctgta ataattacaa tctagaaaag ttagctcagc cacgtattct ccttgacctt     12300
     cttcattaaa agtaacggca cactgagatc ttcttctcac ctatctcctt gtctttagat     12360
     tgaccaagga ctacttactg cttagcttta gtgtcagttt ttcattttct ctttctggaa     12420
     gaagcaagaa tgagacaaag cctatcatgt taccacactg aggctgctga gagagtttat     12480
     tctctcggag gtagtcaggt agtcactgaa gcagcatgcg taggcaaaag atctgtttcc     12540
     accagtcagc tattagtgag ttctgcttcg cctcaaagca tagtgttcag cggaggggtt     12600
     ttatttctag tctgaaaagt aattttctct ctcaagttgc tcattgaaag gatgtttttg     12660
     tttcatgatt gtctgactta gatgatgatt tacaaagcag ctttttgctt acgcctgact     12720
     ttaatggaat caaaagtatg agttgtatca ccctatggac caggagcaag gtggtttttc     12780
     tctctcagag gatttccatg caaccatctc tcgagataca gatctgatgt agaaaatata     12840
     catccagggc acacagtgat gtattagcta ctgttgctgt ggatttccat cctattttat     12900
     agcttgttgg gaaaaacaga gactaaatat ccatagattt ctttttcctg atcaccacag     12960
     ttgccggcat gagacgctta ataaatccct gatttgatat tgaaaacctc actccaaaat     13020
     cgagtttatt ctgcccattc ccagaataag ccccttgact ttctgttggc tacactgtca     13080
     ttgtgtgttg agactgaaga gatgggagaa ttcagtcttc cggtctactt gaactatcag     13140
     ctctaaggtt ttcctcacca ctgaacagtc agctcaagac taaggcaaca gagacttttc     13200
     gaagccttcc agactctcat ttatatgtcc tcccaagttt gaaaacccta cctcatactc     13260
     cattcttctc tcttgtgttt cttgattcat ttacaagaag ccattgtaga ccagggaagt     13320
     gaaaccctgg catataatca gaaagacagc acagccggag ggcctttgct cagtaaacac     13380
     cacaataagg ttctatttgc caaccagaac taaagaattg aagagctatg gagaaccata     13440
     cacagccatc agatccagag aaccaagaat gagagaaaac ctggtgtgca ccaggcccta     13500
     aagtagacta ttggggaaag caaactgctc atccacatcc agtcctaaga aactcctgaa     13560
     cgagcaggca cattaagtgg aaccttaaaa actcaagtaa aatagtcctg gtgactacag     13620
     tctaagtccc caccatgaat tactaggtca cattttctgg ttagtgaaag agaacagtca     13680
     tgaaaactcc aagtgttcaa tcattctgaa aacacttctt tcgatttcta tgaaccaacc     13740
     tcattgggtt tcctttcttc tctatcagtg tgactttatt atactaaatt agcttcctaa     13800
     aacttagaag tttgatacat tggaggcttc aaagagaaag agcaaaggtg aaaagggaat     13860
     tttcctgagt cagtttaatg ttagctgctt ggctaattaa cacactttct ttcgctagct     13920
     gatataagct acccaaagca aaaggtgtat attccagtct tccatgaaga agcttaaatt     13980
     ttcctatgta ttttgagttt tctatttctt tccattcaag tctccagttg ttcataggct     14040
     tatttagttt ggcagaaggt gatggtgatt cacgaaatga aaaaatttga aggcaaagct     14100
     actgaaaatg gatctaattt cttagagtaa tttgggagcg agaaattgat aatttgtctc     14160
     ctttttttct ggtttcatca gctgccatgc tgccaaatac ttgcactgta tggatgtttg     14220
     gttattcctg aaacgcataa caaatcttag ctgcaactct atctaatatg gctgaagaat     14280
     aaaactatag ttggctctcg ggctcattgt tcttggctgg gcagcctcga tcaatggcta     14340
     ttgagtgaaa acacaagatc agatggaaac catttccagc ttgttccctc ctatggctcc     14400
     agccatttta ctgtgttcgt caagcacagc aagtgttccc aacaagtatg gctatatttt     14460
     cagcacagat gcaaatgata gtgagttcca ctctctcagc ttgggtgttg agagagtatt     14520
     ttttacgttt gggattactt ctttcctgct ggctcttacc tcccagggtg gaacagttat     14580
     ttggaggcaa tgtcttagat gctcaatgat gtagtcacat agtaggcttc ccttaagtta     14640
     gatttttttt ttgaggatcc taaagttgta ggaatgtaag actttgaaaa gtgttcatgc     14700
     cctaagtctg gttggcattc ttagacttat cataataatg cttttacatg agactgtggg     14760
     attttatctt aatacataag ctactgattg accagtaact atgcagaagt gatgtataag     14820
     ctaaagacaa agagggactt acttctagct agttcagaag ctctcacttg ctcctggaaa     14880
     ccttacagtc gctagatagg tgatgggttt caagataaat aactttgacc tcactcttac     14940
     caccacatta aaaaacaaca acaacaacaa aaaaaaaaaa ctagcaatac taaaaaatag     15000
     agaaatctat cccttcaggg atgtgattga taaatataaa aagtgtttta tatccagaaa     15060
     caacctattg ttcacattgg gtcaagtgtg tttgactagc aaatgctctt aaagatgcat     15120
     gttaatgtcg cgtggtgtat gaaggtagat ctgaaggcag gctgctcaaa acaccctagg     15180
     agcttattgg agaggcagga tcaggggctc ctagcaccct caaataatct caaatttgca     15240
     tgttaactag atcccttggg ggattgcatg ggcactgggg tcggagaaaa cttgttttag     15300
     aaaataatgt gtggcattca ttccagaaga aagaataaaa agtaggcact gctcagcttc     15360
     tactgaagcc gaacgataat gctgaggtca agcctgctta tagtttcttc caatgtagaa     15420
     ggcgaggcag tagcctctat tttctcaagt tagtggtttc tctacagagg aaatacagag     15480
     atgctctaag gataaccctg tggcctgatt ttctgtgaac tagaaattgg aattcccaat     15540
     tgctgtagct gcaattttca aacctgtcac cagggccagg aactgagctc caagacctta     15600
     agatcttgcc agtttctttc tcaagagtta cagttttcag aaataaccca gcaacagtgc     15660
     tgtgtgtata tgtgcgtgca tgtacgcata tgtgtctacg tatatacgtg catttgtaca     15720
     catatatgtc tgcttatgtg tgtatattat ataaaagtgc attaagcaag aaaatgtgtt     15780
     tcattcctat cactttgcct ccatctttat gccagccaga ttctcagatt tctattagtc     15840
     tctgctgact gtttccctca tggctcctgt tttggtttaa tagaaatgat tgggtatgat     15900
     aagaatatat ttctaccacc catcagaagg caaaggataa actttgaaac tgtgtctcaa     15960
     agtaatatcc aagtttcccc agggccattc tagaatatga caaatcccct gcttgagcat     16020
     aataatacag gaccaggcac acacacacac acacacacac acacacacac acactcacac     16080
     acacaagaca gcctcctggg gatttggtcc tatagcagag cagataaaga tgaaagcaag     16140
     ccagcttgaa cttctgtccc ttaaatgagg ctagaaagaa acaagagtgg ttttaaatca     16200
     gatagttaga agatcttgga actactcaga actaaataaa tctagtgaat gtaataatca     16260
     aatttgccac tggaacaatg ctattaagat taactaaggt gttctacctt ggaaataggt     16320
     aatggtgatc tcttttctct gtttttcagg ggaaaagaat agacaataca acttccacgt     16380
     tttcttatat gcacttttct taagctcttt gaaacttctt aaagatactt ggtctagaat     16440
     cttggtgttg ttcttagacc aaattgttac atttgatctg tttagaacca ggtgacaact     16500
     atttgcatac aatcacatca ctgactcaat attgacaaaa taatatctac agccttatct     16560
     ggaacaagca gttcacaatg aatctgaatc tccttagtcc tgcttttaaa gggtccagtt     16620
     agatacggag tcaagtatat tgtttgtctt cacggttgct agcactcttc tctcattaac     16680
     ctttacctgg ctctttgata aaaacacata gaagttaaat cacagcaacc accagtttca     16740
     ctgtagactc agccactgag tatctgcttt gtggtgaacg gagtccatgg gaaaatgaag     16800
     cctgccttga cagaagattt actcttgtgc cacaaggact ccttaaatat caatcttaca     16860
     acccaaatca taagggtata tttcctgcat tctctgattc cgtctcttga tttcaccatt     16920
     tacagaatgt gctctgcttg gccctggcct gataacaaga ggttaaaaag taagcacaac     16980
     cactacactc atggagttgg tgagcagatc tcacaagatt ccagtcgcca ctcaaaaccc     17040
     atccaactgt aacccacata catgaattgt tatatgtgtg tgtgtgtgtg tgtgtgtgtg     17100
     tgtttataaa catcaaaata tcctaaatga aagcaaaagg taacacagtc tcttggaaaa     17160
     taggctggca tactatggcg ggatctgctt tgaagcccaa gtggcatccc ttgtctgcag     17220
     ctttcagaat atgcactgtg agcccagcac acaccatagt gaccttgaag ggttgcttca     17280
     ttcatttata tagtcatctg ctgttagcac cagcccacac tgtttctgct gaagatatgc     17340
     acaatccctt tggatgcaaa atatccactt ttctctcatt caatccatca tgcatttatt     17400
     ggctctgtaa gatcacccac tcactcggct aacttccgct gactcatagg aataccacac     17460
     agactttatc ttttgcacaa cttcatagct ctccccagac ataccaaagg tacacgtcat     17520
     caagaatttg taagctatca ggctctcttt attgaaagaa gaacccaagt ctgaaatccc     17580
     aaacatttaa taaacttaga gatcatcaaa gggatgctcc ttcaacagca agtgaagaat     17640
     ttggctacag gccttgtcaa gcagaaaagg ccaggtttta gccaacttaa nnnnnnnnnn     17700
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn     17760
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn ccacgtttgt tttgcaccaa gatcgagaac     17820
     agctgttacc aattcactgg aagattccac atgtgtccct ccatccagtc ccatcaccat     17880
     tctgagcctc ctcatcactc agcaaaacta ttgcaacagc ttcctcgata ctcgctctgt     17940
     gtccaatctt gcctgactcc agccatccca cccaggagat tcatctttat aaacacagtt     18000
     ctaatcgctt tattcctttc ctaaacaact ttccagtgac catgcatggc taaataaatt     18060
     gagcccaaat tctctaattt gacagcaagg catgttaaaa gagggccact gccagacttt     18120
     gtccagttgc atttcttaat gtttccctac agcagaaccc acaaaccaac agcctgtatc     18180
     ttgtatctag tcttcataag tatttttctt ggaaaagact gtgttggttt tttttaatct     18240
     gaattatctg ccaatatctt atttatttat ttatttattt acaacccaaa tgttgcctcc     18300
     cccgaacccc cactgatttc ccctcaaaga attcctctcc tcatcccatc tccccttagc     18360
     ctctaagacc tgggataggt ctaagagggt agctccccct gcttaccacc ccacactggt     18420
     gcatgaagtc tctacaggat taggcacatc ttctcccact gagtccaaac aaggcagcac     18480
     tctgctacat atgtgccagg ggccttgaac cagcccatgt atgctctttg gttggtggct     18540
     cagtccctga gagctcccag gggtccaagt tagttgacac tgttggtctt cctgtaggat     18600
     tgtcattttt tgagggcctt caatctttcc ccctaactct tccacagggg tccccgacct     18660
     ccatccaaag tttgtctgtg ggtatctgca tctgtctcag ttggctgatg ggtagcgcct     18720
     ctcagagggc tactatacta ggcccctgtc ttcaagtgta acatagcatc attgatagtg     18780
     tgatgaattg ttacctgttc ctgaaatagg tcttaaaatg ggctagtcag ccattccttc     18840
     agtctctgct ccatctttgt ccttgcattg cttttagaca ggaccaattt ttggccaata     18900
     ttcattgaag gacaactctc ttcatcttga tacgtctttt cctttctgcc tcacctaaac     18960
     ttccattgtt ctcaactatc ttactctggc ccatttcacc tcttaatatg acttgcttca     19020
     gtccaaaagt ccctgaatca gttggcttat tgggtctaca aatgtccgca acatcttcca     19080
     acatccaacc tacatgattt attaccaggt tttgttcatg ggtttgttct ctcagatgta     19140
     actgactttg taaagtcttc tagcagatgt caactttctt ctgaaacaag aaagcattaa     19200
     tattactcta gatgctttta taatgtgttc tatttcatgt tgttgggttt ggaggttttg     19260
     gagggtgggg gttgttttgt tttgttttgg tgagtgttcc tgctttctac tatctgctta     19320
     gaaataagct tgtcaaaggt aagagcgggc cacatttaat taatttctgt aagatttccc     19380
     tagctccctg tacacagtat gctaatgttg catggaattc attacgttgc ccatttttct     19440
     ttggacccca caggctgaga gtagttgtgc attcccatgg gaatgcagta actcatttca     19500
     aatgcagtca tggctgggtt ggatgctccc tctggacttt taggcatttt caaggagaaa     19560
     gtgaggagtg atgtatcaaa agaaaactgc agagggaatt taggtaaata gaacatgaac     19620
     ctttctgttg gaagcttgct atgatctcca gattaaaaca ctatggcatg tctcacaagg     19680
     agcaactcgt ttagaaatat aggagccggt ctatctccag ggccccaact gaaagctgag     19740
     cattggccca atgctaggta aaccacaaat atcacaagaa aaatgaaaca ctaaagttct     19800
     gtctcctaga tccaaaaata cctatttcta cagttttgga gtgcctataa aacagattct     19860
     catccctgag gacctggaaa gatgggttat tcaccatcaa gattatagag tcaattttat     19920
     gttacagaaa tggattcaac ataatgattt ttgatttgaa tggtcaactg taaaatgcta     19980
     tagaaaaagc agaaagtccc tattgtaaat gtaattaaag tctgagatat ttcatgaact     20040
     actatttatt tactatagag ttagtgtcaa caagaaagct gaatgaataa agccaaagac     20100
     tgtacagtac tgttgatggg cacctatcat actatcaaaa gtatgttgta aggtctgtca     20160
     atcacgtttt aaaaactgat ccttacctgt ttattagtaa gttccaaaac ctgctattta     20220
     aaatgataca ttaaaatatt attcctttct ctccatttgc cttcagacca tattcctgaa     20280
     tttccaaatc aataccaaga attttaattt tactctcttt atacatgatc atgtaagagt     20340
     gcccactgat gtttaaatgg acgatgggtt gtattacttc tgagcactct ctgctgagat     20400
     gcctggtgag gtagaggttt gaatgtgttt cctatcctga cagaggccag agagagtatg     20460
     aggacaagct gatctaagtt agaattgttg gaaagatcac ctaggaatcc ttcttcttgt     20520
     gagcttgtta gaccagcctt tccaacataa aattaatact ttccaaatcc tacctagagt     20580
     tgtaagatcc atcagcctca cccccggctg atctccatcc cacaatacag atagggtctg     20640
     acagagagca ccgtgggcat tgataatttc tcaaagcata agaatatttt tcctgaatta     20700
     agcagagatc ctgctctaag tgactgtatg tattgacgta acatttattt cactaccaaa     20760
     aagacaacaa ttgttatata agggaactct tatagcttga agttaactct ggtcatcaca     20820
     aagagctttg aagtagcagc tttgagctgg gaagtttcag gcaattttct ccctttaaaa     20880
     cagggatctg agtatcccac ctgtctgcca agtgatatga atgacatctg tgatgttgtt     20940
     accaaattca gagactcaag gctcaccact aacttctaga tgtaatttgc ataacaagtt     21000
     ctcagaacag aaggagaatt ggactacagt acatgttgaa gcagaaagtg ggtcagccag     21060
     gctggtcttc atgcaccttt ctggagagcc ggagtgctat catttcttac ttggggtcat     21120
     gtatcatttc ttctgactgg aatgccaagg gcaaaactgg gagtcattat atcattggtc     21180
     agtcctttgc acattccacc atcccttgag tagggctaaa aggttaatta catacatctc     21240
     tcgggctaca ggaatgatca agactgtccc tggaatacag ttacttcaaa aactaggctt     21300
     ttgtttcagg gaaaaatctc ccacagagaa acatggaagg cgaaggagaa ctataaataa     21360
     gactgccatg tatgtcaatt ataaatagat ttgttccctt ttgattagaa tattaatggt     21420
     agcagaatgt ctacactcaa acagaaacaa aggaagagtc tctgacaaaa tattactaaa     21480
     tgttaacagg tttgacacct gctccttcgg gagttagttt ctctgacttt tccttaaatg     21540
     agggctttcc ttctcttttc agtttagaat tcagcatagt cttcaaattc tttgccaagt     21600
     ctccatgtac atgcagatcc ttataagcac ttataaactg tgagtaacct gaccaaggga     21660
     tgacagaaaa gggaaagtct acttctcaca cctggacact tgctagataa ggaatgagtt     21720
     ttcctttcat tctgaaggaa tgaaactcat tcccttatcc ggagggatca caactctgtc     21780
     tctatcactg gtttgccatt tccctattct ctgcttgtgt tcatgagtca tcttttccca     21840
     gtgtcagggt gagaaatggc agcttccaat ccaagctgcc tgctgagttc actctgggat     21900
     gaggacaaaa cagtagggtg cctttgtcct gcaccaggct cccctccgtg caatgcagag     21960
     acctgcatct cctctctgct aggataagag gacaggacat cttgcccaag tctacccacc     22020
     ttggcccatt aagggttttg actctagcca ccccagatgg agtattaaag gaggggcagt     22080
     tgataaaagt agctgagagg tgagggctga gacactgagc agtgatccct ctggaaaact     22140
     catatacatc tgatatggcc ccttctgatt tcactgtggg atatttttaa aatgagttta     22200
     actcatcagt tggaaattca cttcttgaca aacagtgacc accatgacaa aactgatgat     22260
     agggtattga aaagcctggc tcccaacact taaacataag ttcttagaac tcttggacag     22320
     gttgctgtgt gtgagttctg tctccaagtg gcattgctga acagctcagc tcccatcaga     22380
     aagctggtgt gctcttgtct gacccagagc cacagcaagg gaattctgct aactacactt     22440
     gctgtgcatt caaggtttga gtcagaagat ccaaacaaga ccattaccct gggggaaaaa     22500
     aaatgagccc ttcattcctc ttaaatgtca aaataccttt gggccttaga agtccagact     22560
     atcatatcta gtattttcct aatcaaaacc tagaaatggc gatgtgggtg gctggagcca     22620
     tggcctccgt cccttttcta ccctccctcc acaccccaag ccaagattct tcaggctttg     22680
     ccagatctga agtgacaaag caactcagga ccttatgtgg ccagccctca acctccctgc     22740
     caagcactac attaatggca gactgactca atgggaggtg aagacatgag tgtgtgcaca     22800
     ccaatttgtt cccagactgt taggtaaaca gaaaacagaa aacaccctct tgtcatccct     22860
     gtaagatgtc tgacctgtac ccaatagcct gactttatag ccagtgttga cctctaactt     22920
     agctggcccc ttgatgagcc atctttcacc ttcactgaat catgtatctg gctctattgg     22980
     tgaacagttt tcataattga ggatgtgagg tctttttaaa aatgattctt aaataagctg     23040
     tccgagaatg tgcttggagg cttcataaaa agagtgccaa gtcctggctt gctcacaaag     23100
     gtggaggtgg cctttagact cagtgaagtc aaacattggc acatgcccat tgaccagatg     23160
     atatgtttgt cttgttcctt tggtattgct gtcatctttc agggaaatct aggaatagca     23220
     gaaagatgag tctgcccttt tcctgctgca tgtcctcctc tctgaggata aagaagaagc     23280
     ccagccactc ttagatccta tgagtcactt ccaaaggtca ttctcaggct cggttactct     23340
     gaaggcaaat tctgttatat gcactgggag aatccttgtg ttcctctgca atccgtagct     23400
     agcagttaag gtagactgtg ggacctgcta aatggagatg ttctagagaa tgggagggag     23460
     aatctagaga tcaccgtatg gaatgtgtgg cagtagtcta catattaggg ggtttatggg     23520
     gaggagggca aaataagcca aatatataac atttacattg tagaataata aattacacat     23580
     tctgagctct cattacatgc atggcactgt cttaaacact tctgtgtgtc gttcacacac     23640
     ttcattctca gccacccgtg taaaacagga agcatcgtta taattacaag tgagtgcact     23700
     gagaaacaca gatgcacact aacacctatg agaacataaa aggctaaatg tgactgctga     23760
     tatcttcact caggcaacca aactaggccc aagctgtgca ggtgacagtc atgtcgttag     23820
     tcctttgctc tctctttcag tcctttttct gggtaacacc taaggctgag accatctatt     23880
     ctttacttac tatagtctct gatatcatta gcaagcagca gtgccttcac attccaagca     23940
     tctctttatt tgtacatgaa aaaaatcccc atatatactt acaatagagt taagtgtaca     24000
     tttaattcta aggttcatcc agccagactc aatggcctac tcctctgtat cgtcttagaa     24060
     tgtcagacaa tgtttagcac atggagacca cacaattaaa agttcctgaa ttaggctgaa     24120
     tgcccgagct tcaaagtgct tttactactg caatatgtct ttaagattat cttttgcaat     24180
     tcaaaacaag agctccacac aaataagtaa gtgtctaaga aatgctgagc cctacaggga     24240
     actctcccac tcccttaagt ctataaccta taaaaatgag tttgcaaagg cacagtatag     24300
     acattcctgg gctaccacca agtccgacca tcccaggctt agccacccat ggccataaaa     24360
     gaatgccatt gaccacaata cttctaaagg caaaactgtg tccgcaagtg gattacttgc     24420
     ctcaccaaga gctgtggggt tccaggattt tctagaaggc ttcttccatc ctaataaaag     24480
     ttctcagctt cacaacccct caacctgaac aactctgagg gagatttaaa aaaatccaat     24540
     ttaattgaaa cctctttttt tttttcacat tgaagtcaca agttttcaca gggtacgatg     24600
     tgttgccaat ctagcatttt ccaaactaac tcttccgcaa ggcacttgca gttttctttt     24660
     tcaaatttct ttgcgacata gttgtctcta agtattcttt gcactataga ctaggttctc     24720
     agtagaaaaa caaatatcaa cctttaaaca tacatttttt ttttaaatgt ttgctgctgg     24780
     ttgtctcaac tcagcaagtc agtatcaata gtaaggatgt catggagcct acgctgatct     24840
     aacagctact attccagatg tgcacatctg agtgctggta aatacgtggc tgtgtgagca     24900
     cctatcagga gcaagtgctg gtgctgaact gctgacatgg tttttgccat aggtgcttag     24960
     agctttggaa agcttcagga ccatgagaaa gggaacgagc cctgactact ggaagtatct     25020
     gattggaaga tacatagtat atttactagg cattcttttc tttccatccc aatgactggt     25080
     atatatacat gaccaaactc ctgcctcctt catctctctt tttctcctta ttaagtcctg     25140
     cggcgtgtgt tgttgtatac ccactgtggt ggaaactgac tggaattttc tgtggtgagg     25200
     gagcttcact gtaaggtgca gtttaggctc ttggttgttc cttttatctc actctgccag     25260
     aggaggcatg ttggtcccta tctagcatca gactttttgt ttccacttgt cctgtgtacc     25320
     ttggaacaat ctgagtgcat tgtccttgcc atgagaaggt ccccaattct ataagtgtca     25380
     agaaaaggta tcttggtacc ctgatctaaa acttttagga gtatgaatgt ctttaacatg     25440
     ttttgtaaac attatattta ctatgctctg taaacaaaca agaaagacga tgatgacaaa     25500
     tggtaatgct catggtcctt gttggggaaa tgttgaactg agagcagtca tctcatatcc     25560
     ttgaaggtag actttgtcta tcttcagtca gggagactaa tacacattta ctgaccaagt     25620
     caatcccagc tgggaagttc aatggtttgt ctgcatgatt tctggaaaaa tacaagctag     25680
     actaagtgtg tggacccact gataaaattc cacatagaag actttgactt cacttgatac     25740
     agctttgggg tgttttaacc ctagcttggt ttcttaccag agcctttgtg atcttacaga     25800
     acccttttct gtttgtcttt aaacattatt tagggtgact gactataata gaacaagatc     25860
     ctcccaggtt tcttttagtg ctgatttgtg actccgttta cccagaacac aaatcctaac     25920
     tctagttatc agaggcttga agagaaatga actcaatccc actcttctga cagtctacct     25980
     aaggtattat gacagtctta ttaaaattag acagaataag tcaaaagtgg atgaacagat     26040
     ggaaagatgg ctatattggc aaaaaaaagc acgtaaatat gggaaaatga agctaagagt     26100
     atcaagaaat attgactcaa tgaaccaaat aaattgtaac aaaatatata aataattgct     26160
     taaaatgaca aatgtatcct ttatctgtat tgttcatgta gagaattaga gtgtggttag     26220
     tcttagcctt caaatgaaga gcaaagagga catggataac cccctcctct agaaaaaaaa     26280
     tcaatcaata ctttatcagg actaatttag tctcagagcc aatgagagtg catctgtctc     26340
     catgtgaaac attatttagt ggcttgtttt cattcatcac aaaagttgct tgttctattg     26400
     gagcaactga ggcttttgat ctctggcatt ttctaattct ttgtcatgga aagacttcat     26460
     tccaaaaata gacgttgatt tgttctagtc cagccaatgt ggcagttgtt aaaagaatga     26520
     ataaaacaaa tgctggccag gatgtgggaa aaggggagtc ttatatactg ctgattggaa     26580
     tgtaaaccaa tctagacact gtggaagtca ggatggaggc tccccaggac tctaaaagga     26640
     gatctatcag attcagctat accacttgtg agtattcccc tgaaggacct caagtcaatg     26700
     tatcctagag atagttctac accagggctt gctgcagctt tgctcacagt acctaagtca     26760
     cagaacccaa tctacatgtt caacaacaga gactggataa agaaaatgtg ctgtgcacac     26820
     agttcgagta agttatgttc ttttccggaa acggacacaa ctgggcataa tgaagagagt     26880
     taattatgtc tcaaggacaa ataccatgtt ttctttcatt tgttgttttt acatagatac     26940
     ttcatgtata tacatatgac atgagagtag aacccaagct gtctagagga acaaaagcct     27000
     gatgaagggg aaggacaaag gtatagtgag aaatatagtc aaagaacaat ataaacttac     27060
     atgaaagtgc ctgtgtaaca tggtatcttg taccaagaat agacacaatg gaaactgaaa     27120
     acaaaattta aaaaaaaaat ctcagaatta aggagttggg aaagacctcc ctcctcataa     27180
     aacatgtctg tagagaagac agttgtttcc tctacatcct gaaagaggcc tgtgctgaaa     27240
     tatctccagg gactgggccc agaaacagct tcccagccac ccctactctg caaacagaaa     27300
     agcacatcag ggtagcatca caccagccag tgggagaatg actcagctga gttccttccc     27360
     tgaaccttcc ttgcctgcac ctgctgaggc actgaacttc cttctgtttt gtattttcct     27420
     tatttatggg ttgcttttct ctctgctgag tcatagagtc cttgagggtc actgttcttg     27480
     ctttcccatc cattttcata ttacactgca ttgggactca gtgccctaaa tatggtgggt     27540
     aaccaatggt ctggctcgat ttttaacaac tgctgttttt aaattgacta acagcttaac     27600
     tctctgagaa ggcaatcagg ttaaaagaaa ttatgtcatg ttcactgagt tggatagacc     27660
     tggggtccat taaatttttg tgtcttctgt ttttatttct ttacaagtct tttaaaagtt     27720
     tataaatttt ttaaattaaa aagaaatttt tgtcaacata catccaaatt tctttactat     27780
     ttaatccact gaaaattatt tctgacacag tagactataa ataagtattt ggagtgaact     27840
     tatgaatgaa tgaatgaatg aattaatgaa tgaatgaatg gatgctcatt gttgtccatt     27900
     tccctgggaa gtacaaaccc tgtcccagaa gtacctgttt tgtgcctcct tttgctcttt     27960
     tcatgtattg tatgtcttcc cagaatctcc atccgaattt aatagtctaa agatgtagcc     28020
     ttccagtcat ctgttccttt ctttattcaa gagatgagaa ggaagagtgt cttgggattg     28080
     tccaaacttt aataagatga aaatacaatc tctcatctat aagatttaag atacgtagtt     28140
     caatactact gaattctatg tcatgcaagg cagttctgct ccatagcatc ctcaagaatc     28200
     cagctcttga gctagtgagg cagcagataa aagtgcttgt cctgcaatcc tgatgacctg     28260
     aggtcaatcc ccagcaccca tatcccagtg gaaggagaga actgactcca caaaaaaatg     28320
     tcctcagaca tacattcaca agctgctgtg gtatatgtga acacacacac acacaccata     28380
     ataaatgagc acataataat aataataata ataataataa taataataac aaaaacaaag     28440
     tatttttata taaagaatcc agctctttct agcattcaat tttatcctcc tgtgttttat     28500
     tcttcaccaa catggccata tatgtttact gggcattcaa ctttgtaatc atgctatacc     28560
     caaaagaaag atgacagaga ggaagagaga cagagacaca gagactgaga gacagcgaga     28620
     ttgagacaca cacagaaagt ggggagggtt actggatgac ctttgaggaa gaatcccaaa     28680
     gctcttatat gatgctttca cttatattct tttgtgcaga acttgagaaa atggtcaaat     28740
     gtagctgcaa gggaggcggg ctaagaaatg tagtcatctg aagattagta gttctgttat     28800
     cacacaaaaa aggaaggata gaaaaaccat aagaataaat ctccttgggt tctttaagtt     28860
     atatgagtta ggtaaagcac ttgaggcact gtaaaatctg aggctgctct cgtgttagcc     28920
     aggtcttcac ttatatcttg tctttgggca tcatttattg agctgtgtga tttctgaact     28980
     atttccaaag ctgccaaaaa ctgaagcaaa acctctttct aaggtttctg tggaatgata     29040
     tgggacaact tggtggtgcc gagcacagac agacagagag tagatgctca gatcacattt     29100
     atcactttta tacttcagcc gatatgtaag actggcttga aatcaatctg ggcaagaaaa     29160
     tattcccgaa gttcctgaca gctgtgtttc ttgagtaatt tcacactcta tccactcacc     29220
     agatgcattt gagcaaatga gcagctgcta aagagagtgt agtgtcctca tcttcaccta     29280
     ccctttcctt cccaccttgg ttggatgcta ttgaaccagg cagaagacac caataaactt     29340
     ctcagaggtg taaaaaataa gcctggataa acaagaagaa atagcaagtc taaagatctg     29400
     acttgggtca acttggcttt agttggtagc aaagatgttg ctcttgattt ttatagatac     29460
     tgaaccacaa ataataggca atgctcatgg gtcattagga taagaatcca aagctgaaag     29520
     agggcatcac agaagaactg gcttacaagt gtcactgtat aggcaacagc tacagcacag     29580
     ccttctacta tactcagtaa acatgagtaa ataaattact tttttaatgg aaaaaaatag     29640
     tctgtggagg taacttcagt gggtaatatg tttgttgcac aaggatccag gtccctgggg     29700
     cctgtgtata aagccctgtg tgtgtcagca tgtacctata accttagccc aaggggcatg     29760
     gggtgtgact gaaacagaca atccctaaag ctcattggct agccaacctt gcttaactga     29820
     atcaatgaat ttcatgttca gagagaaact ttgcctcaaa gagaaaatgg agagccatta     29880
     aagaagattt atggtctcca cacatacatg aatacacaat cagtgcatat acaccacaca     29940
     cacacacaca cacacacaca cacacacacc acaccacacc acaccatacc atacacatac     30000
     acaacttttt aaaaaataaa tattaccatt ttagagtctc aaaaatattg aaagactcaa     30060
     tcacataagt gatcttctaa gaaaattcac cctttggacc attaaccgaa catctacaca     30120
     ttgttatttt ttgaaatcat aaattcacag aaatataaca tattgcaact agtagtaaga     30180
     ctttcagtgc tcttgttcca aatgcctccc ttctattgag gataacagca actcgggtgg     30240
     taattctact aaaatatgta ttctcccttg ctcattatct cacttctagc taagctatca     30300
     aagataggat tttagacact ttatcttcat caaaaatatt ccttctagct aaagcacaga     30360
     cacgggttaa cagtagacct tgtgggctaa ggggcttaca attctgtcca ttgcagaaag     30420
     aaccagctgg attccttgag agtttttttt tttggtttgg tttggttttt ggtttttggt     30480
     ttatttttgt tgttgttgtt gtttttaagt tcttagtctg agcctgagca acaaggggat     30540
     agatccaaac tggatctcaa atgtcttgga gatgtggcaa ctcatgacta tgtctagttt     30600
     gcacccacct tccaatccca cacaagatgg tgaagcgcct gctgcaacat gttaggagcc     30660
     ccaacaagac aagagctggc ctctctctgt gggggctgca gaaaggaagc agctgaagca     30720
     acactatcag tttccttcca gtactgagaa gaacaattgc actcctccca ggggaagcta     30780
     ttcagagttg gacagtgtgg ggtctgtcct gtgatggcaa tggaggattc ctgaataatg     30840
     gtggtgctta gtcaccacaa ttctctaaac acagactcaa agatagatgg aaagccaaga     30900
     ggtccttagg tccagttccc tgcctctatc taagccttcc aaagcagatg gtagtcatcc     30960
     cacatttaga gatctccagg gtagcaacct cttcccacag accctgttta atcaaattct     31020
     tcctgactct aaatggaaat gcattgggtg tagatagaac ctacttctct gtgtctgttc     31080
     ttcagggcat tggatgtcta gtcctcaggg gagatgaaga ttgtaacctt gcttttacct     31140
     caccacagtg attaagtcac cttgcttagc cttgtctttc taggagacct acatcttaac     31200
     ttcgctttcc atccagttaa tcataaaaaa aaaaaaactt gctggaatat ctccagcttc     31260
     tccaaatgaa tcttaaaata gagcgaaatc taagttccca ctctaattaa aagctcggga     31320
     ttgccaagtt ttgtgaaaag ataactctct aggctttcat ttcataatct tcctcatgag     31380
     cctgcctcat attacagtgt gttgtacttt cttggtcacc cagagctcac agatattttt     31440
     ctatagtgtt tgctgccaga tggaaccagt ggcttccatt ttaaatagtt ttctgtttgc     31500
     agtgactctg tactggagtc actaaagatc gctttacatt ctaaccgcta ccttcaactg     31560
     ttctgatgat ctacttccag actcaaggct atctgaaaac tattcttttc tattatttgt     31620
     catgaaggaa ggagtccaat cctgtgaagg gctggaatat cactcatttc tcccactccc     31680
     catgaacttt atttgaacat gaaaaatagt gccaatcacc cctgtccatt cacttaggca     31740
     gtggtcatct cctgagcagt aatcatgtga gcttgggttg gaataataga caaattagct     31800
     tccctatcca ttcatgagcc catctaccca tgtattaaga tgggttcatt cagcaatgac     31860
     tctctgcaga gctagtctga ctggtgtggc aaaagtcctt ggcttctgag acctcacatt     31920
     ctaatggttt gagggctaaa agagacaaag tacaagtcaa caaataaata aataggacca     31980
     tgtcgaattt tggcaaatgc cttgaaagaa tcgataggat aatagaattg agggtggaat     32040
     tgccttagat agagtggaca atagggtctt ctttgagtag gatatactga agagattaca     32100
     gcttaagaca gacctgatat tctgaaccaa tcccctctag caaacccttc tgttttcttt     32160
     gacccagaac atgtaatggg atgttaacat ttggtaacac attgttcatt ggttaattat     32220
     taacatacct cgtggattcg tttcagaact tttaatcaaa tgtgataaac agggaatttt     32280
     gagattgttc ctggaaagaa atgggagcat ggtatcatta aatgcagaac aagtgacttt     32340
     agtatcatct gatagacttc ttcatcaggg ggctttccat gagctcagga ctctcaacac     32400
     atactttcag cccatctgaa tatttttata tggaatatct tgaacaacaa atactctttt     32460
     atgagtgctg acataaagaa acatcttgga cctttaggtg tcttttaaca atataattgg     32520
     cattagggat ataaagcctg ataggcaggc aagccctggg tgtctgagaa aagattgcag     32580
     tgggagacag agcactgact acttcagttc ctctgtgagg ctgggcctgc acttctccag     32640
     tttctttgga ggatggagac ttttgaattt tttaatttcc tctctgttag aaaatccaca     32700
     gacatgtggt tatatatcat gcaaagggtg ctgactattg acatagacca gcagatttct     32760
     aaggacctgc cctttgctgt aatttgaata agtctttgct tttggatcac atgagcctct     32820
     ggatcatgat tttttagtaa cctttgaaca ttttggacca ggcaacgtgt tttgccagcc     32880
     ttcaaaggtt ttctggccat ggtggagtat ctgcttatta aggaaggctc atcaatattt     32940
     cctgtgcctg tagcaggtcc tccctaaagg cccttggaaa gtttgtaaga aatcattaaa     33000
     gaagatgaag agtatctcaa cccagagacg ccagtcatcc ctggggacac ataacagcct     33060
     tctggttgag tgaatgagac cattcccatc ttatctatcc caggaataga tctttgaaga     33120
     agatatgtga agagctccag agagtcaatg gaaagtagat acctaggaaa agtatgattg     33180
     aaaactcttg gttttttttt ttaagaggaa aatgcaaaca gggacttgaa gggagttgcc     33240
     acaccagcca cagcttctgt cccccttctc cattcaacca gttgggagct gctgccgaca     33300
     gggcactatt tggcttaaag ctatgtgaag ctccaagtaa gcctcatgag gcaggcttgg     33360
     aaactaaata aagcatcatt tgccctccac cccaatactt ctctctggag acaattgaat     33420
     caataaatcc tgggtttgca gcaagaccca tcctaggcct tgcttgagac atgttgatga     33480
     ctatggatat agcttgactg acagacagaa agttgtaatt cttcttccca tacacatgtc     33540
     ctctcgtctg acacccctag ttgactctgt aagtaatcat taatggtatg cctcttccaa     33600
     cacccctttt gttccagtcc tgaaacaagg ttttgatgat acagtcctga atgcgtgtca     33660
     taaacctact gtacttcatt ttacttctct atattactct aggagataat aaaggttgaa     33720
     ggcacagtca aaggtatagg ttttgatgga tcctgccttc tgtgccttgt tttacctgag     33780
     cagggtggtg ttgagcatgg gtgaaacacc cactgtagaa ttttgaaagc tcaaaaaaca     33840
     aatggaactc agaaaagcag tgttcagtat gagagggtgt ttctagcttt ctggtttggc     33900
     taggggactt gttaaggctc caatttccta ccctcagacc cagcgtcttg tcttcaggta     33960
     ctagctgaaa tccagaccaa cacagactgt gaaaataaaa gaacagtgaa gggggaaagg     34020
     tcaacatatg gtttttgttt catttcgttt cttcctttgg aaggttttga tggttttttt     34080
     ttttccttcc tctctgattt gcaataaaat tggttctgct accagactaa catatggata     34140
     cctttatgag gcaatcatca aaagagatat gaaaatagtc tggcatattt taaatgtttg     34200
     aaagaggtct ttctcagcac tgccattctc aatggttcct tctttccatt cttcttcctg     34260
     ggtcctatcc atatcctatt cagtgtcatt aggtgacatt attcagtgcc acacagaagc     34320
     aatggttatc aactgagaac ttgaaaatgt gaattctcag gcactaggtt agactgagtg     34380
     aaacaaagat ctgaggtatg gtccattggc ccgggttcta atagcccctc caggtgatgg     34440
     caatgcaaac ttaagtttga gaaccactat gcatgttcac tgtgcatcct gggatgttag     34500
     tcctcctgtc cactagctgc ttgagggacc gccacatatt ctgaagcttt gaggacagga     34560
     ttgagaatca aagacctggc acttgaggac aaaggaactt ccagattcat ccaccactta     34620
     agctttggct tattcaccta tacaatggga acgaaacaat tccagggaat ttttagggtt     34680
     gttaaaaggg ttaaaggaca gaaaacctgt gacaatgatt tgtactgcca gggcatttct     34740
     ggagatagtt gcacagtaag ttgactgtat gaatcgataa tgctgacgta cattatgaac     34800
     tgcaagttcc aggaggtggg gacaagaggc aggaactgtc tgtctccttt gtcctcttct     34860
     gcattcaaag caccaagtct gggtccataa tggccaatca ctgactcttt acgggatgac     34920
     atcaactaaa cttgccaagt gcttattcat gcatccatcc caagccttat gaggccactg     34980
     cctcttggga tgagccctga gaggttcact agtttactcg tgtcacacag cttgacatag     35040
     tggaaccaat gtcttcactt aagaaaagct ccatattcaa accagcttcc cacaaaatct     35100
     cactctggaa tcatcatggt gatgattaga aaagtgatct gaggtggcat ctttcaagtt     35160
     cctgctatgc cacctcagat ctctctacac cttaatttga aattgcccat agaaataagt     35220
     atgattaaca gacactagcc agaatacttg ggggtggggt ggggttgttt gtttggtagt     35280
     tattattgtg tgtggtggtg gtgatggtgg tagtgttgaa gtatgtgttg ttccaaactc     35340
     aaacccagga ccgcacacag ccaaggccag aattttattg ctatgtccaa tccttagtct     35400
     ctgatgctag gtttcttttt cctaatgccc aggtgttttc atatggcttc tctttgtgat     35460
     atatttgtgt accagctttg tcaatatggg taccaatgag catttaggaa atgcccacat     35520
     agctgacatg attttatacc tcgaagtaca tagatgacat ttctggtttt aaggtacaaa     35580
     aaagcaaaca agaaaagtgg gctgatattt gaaaagcaga aggcaaaggc aaagaaacag     35640
     ttaaatactg attgtcggtt gcttttatat gttcagagag gttaatggaa tcagaataga     35700
     gcagagtata ccccaggacc caaaataact ttcttgtgag atttaaactt tctgagattt     35760
     aaacactgaa ctgttgagtt cagcatccct gcacggcagt atccaataag attgccatag     35820
     tcactaggct catgggtgta ttgatctgtc atatccttca taatttttgc ggagaagagt     35880
     gtctagactg tagacagaat aacaaatatg gttgcctact tattttcttt acatgggaag     35940
     ttagatcgtc agcatcttat gtgccccctc cccgcccccc acccccccaa gaaggctaaa     36000
     caagagccca gttctccaga gagcacctca gctcaaaaga agcataaaaa cagcaccttt     36060
     gttatttggg aggagaaagt ctactttctt ccctggggtg gtatgttgct gtggcaactg     36120
     tgacccttga gtgcctccct agagaggaaa cctcataggt acatagtgct tttgaaaatt     36180
     gagaagcagg atttaggatt tcttgtcatc gatttcattt cccttggttt ttctcctatt     36240
     tggtaaacct ttgaatgcca aactcaagct tggttacacc ccatgttccc ttcataagaa     36300
     acagcactag taattgaaaa cagaaagtgg ttcctttatt ctaactcatg ggacgcaggt     36360
     atgtttcctg tttgggcccc accttaactt tctctttcca aacactggga gaaaatctgg     36420
     atataattat ctgcttttgt gactaaattc tttctagttc ttatggtgaa aaggcagtct     36480
     gtcatcaaaa taggactgtc ggataatatc ctttgatttg acaactccat ttccgaacat     36540
     ttactctcat agatagtaga tagtctagga acatatcttt atcaaaaaaa aaaaaaaaaa     36600
     aaaaataaaa cccctaattg ctgcattagt taaaacaata ataaaactaa aaatagccaa     36660
     aatatatagt aacacaaaaa tgaagaaact aaggatgata aatctacccg ataaaatatt     36720
     ctgcaagttt aaaattatga ctatgaagat caggtggcaa cattggaaaa tgtttgcaat     36780
     aaaacattat tttaattaga ttaaataatt aaataaattt taattaaaga aatgcagcat     36840
     catattacat tttggctatg actgtagctt tatcataatt atctacctcc gaataaaaat     36900
     gaggaaaatt tgtaaaaaca ttggtaatgc aatttgttga gatatttgag tgatgggtga     36960
     tatttcatta ttttactata acatttgaaa cccagtaggg ttggaagtga aattgtctag     37020
     gtatgtgaca gagctgaata tccccatctg aaactgagtc ttggttttat ggatgagatg     37080
     tgagcatcca atgtccaagc tatgttcttg gcaggagaag tccaaagaca tctctccccc     37140
     agggacaaaa gccacttgtt ccctttgaga actttttcta gtgcctagga gaaaacaact     37200
     taatgcaaat gcttgaataa ttgagttgag ggctcaactt aaaagacccc tcacaccccc     37260
     ttcacttata tcatgtagta tgcaagtctc attaatggtt cttactttga gagtgttccc     37320
     aggaaggtag actgattctg ctacttaata aactaagtta aaacgtactc tttgtaaatc     37380
     tcagcttcca gacatgttaa atgaatatag gcataatgcc tagcccatgt agacgctata     37440
     aagatatgca taagatgtac aaagtaatta gtaagacatg aaaagtttaa taaaagtccc     37500
     ttaaaaggaa gacactgttg gctatgtgtt gtcggaaagg ctttggtttt tcaaagaaaa     37560
     cagtgtttaa ttggattgta tctctgtctc tttataagtg tccctttggc tcacttgcta     37620
     gtggatttcc tcaaggtatt aatcttcatc tgtgttcttg tttctatgga attattgtct     37680
     atactatagt gtgtaagttg ggttagggaa ttttagactt cagataaggt agcattgcct     37740
     ccttagcaac tctggcattt gaagaaaagc agcatttcaa gttaggtaaa agtgttggag     37800
     tagtgcaact ggagatgccc cagatgacta acccagatgg gggctgtgag aggactcata     37860
     tgccaagagc cacagccaag gacaagagag ggattttggt taaaggaaga gtgttaggcc     37920
     atgcatggcc tggaaaaaga agcaaggggt gatttgtggc ctattgagca caaaggacaa     37980
     ggtttggcca aagaaggcag ggatgctgtg aagaatgtga ggaatttatg acgggtcatc     38040
     atcccactgc aagaaatgtc tgccaaagac aagtctccac caaccaagtc tcttgcattc     38100
     agtgagaaga aagagagggg cttggaccca ccaactgacc tttatctgag tctcttcttg     38160
     atccagaagc agaaaggaca aggagagttt atgttaggag agggaaggaa ttggtgaacc     38220
     ctttgaagca gatgaaagtg ttcccacgcc atccatttcc taacattctc ttctttcaaa     38280
     gtcatcttct ttctcagtga ctcaagttta cagtctaggt gtgtctgatt tgaacatgaa     38340
     gtgatgccca cagcttcaga tccttgaggc ctgggttcct agcctgtgtt gttattgaca     38400
     ggtagttgga taataaagac attagcttca tgaacagatg gatttgatga tgatgcctaa     38460
     atggactact agggagtggg gcatggtttg aggaagaagg tcactggagt ttattttgaa     38520
     gggcacatct tatctattca tctctctctt tctctccctc ccttcatctc ctcccttcct     38580
     tttctctccc ttctcctctc tctttccttc cctgttttgc catccgtcca taaggtaaaa     38640
     tccattcctt caccatgcct ttctagcatg acgctttctg ccttgaccca gaaccatgct     38700
     caaagcaact gagccagctc atcatgaact gaaaccatga gtcaaaataa ctcttccttc     38760
     ctgaagttga ttaggtagtt catcacagcc acagcaagat acctcacaca gttaagaaca     38820
     tctgaggtgt tctctgccag ttcttagcag acctactatt caaagccaaa agcttcactt     38880
     atctccgcta tccctactat acagaaatgg ctaagagacc gagaggatca cttcttctca     38940
     ttagtccatt tatagatgca gttctctcat gaaaacacat gtatttatca tggtggagcc     39000
     tatacagacc atgcccatca caggtcacta ggttttaaac tgtctttttc ttccaagatg     39060
     agaaacttta catgggattc tgaggaaaac agtcctgaag gcaggctaaa aaatggggtg     39120
     aaggctgacc tgctgcaggg ttatatagca gaagagacca ttagacccca attctgctat     39180
     aatagggaca gagtttattg tactttagta cccctgaagc ttccctaaac ctaagctaaa     39240
     gtgggcagac agaagcagtc agggaaccac aggcaccatg ccccggcatg aaatattcct     39300
     cccagctgtg tgtcacatta ggtctcacac tgcctgctct ccatgaggcc aactcagtcg     39360
     gcaactgtga attcgtttgg cgaagaattg gaaaatgact tctgaggcaa cgggctccag     39420
     ttctcagaaa ggaaattcgc agaagtgagt gaatggtcag aaggccaaaa ggccattgcc     39480
     tcagaccaag tcccagggca gagtgctggg gccgttctgg gtttaggctt gtaataaaaa     39540
     aattaaaaaa aaaatacaag tgaaaatgtg atttctctat ccaatatcac aaccccaaag     39600
     tggtttttct atgctgaatt tagtaaaata attaagagaa acagttttcc cccccttggt     39660
     ggacaattat atttgctaaa aagcgtttaa tgagttttgg aatgtaggca tgagattggt     39720
     cccagatgaa ataaagatga gaacatcttc taacttggag tcaggcaatt atttgactct     39780
     ctggcccttc ctctggccct cctctcttct ctctctctct ctctctctct ctctctcacc     39840
     tcctttgggt ggggctaggc tgggagtgta atggctcaaa gctaacagac tctatgattg     39900
     ccaaaagttc accgagaaac caatttattt gactctgact ttgttgtaat atccaaagaa     39960
     atttcttttt caaaagctaa agtgcaagag tttgaagaaa actcataagg tctcatggtt     40020
     atatttttaa aaaatcaaat gctagggaga agggataaga acagtggtag ggaaacttaa     40080
     taatgataag ttcactctta tctaaaatgc cctaaaataa tataattatt tattaatatg     40140
     tatttatagg gataatatct aatatattta tatactataa ataatccatc tggctccact     40200
     ctgtatgctt gcatggaacc ttgacaagta atagattctg gaaggcttaa gaacttctta     40260
     tatgcactta aaatcttttg aaaccataga aaaagttagt tttacaaaca gagaggaaaa     40320
     gaacaagaga gaaggagggg aagggagaga ggaaatgaga ataagagggc acttgaaaaa     40380
     cgcattaccc gacgttgtcc cctgggaaag catggcagcc tgcctagaag cccatttatg     40440
     ttatctaagt ggagatacta gaaactgtaa ctagtctttt ccaaggaaac tgcgtgtgcc     40500
     cacctcatag gaaggaaata tcacacagaa ggaccatatg ccattgacag acattatgga     40560
     acttggggag ttaaaacccc cactgagtac taggaagtta aacattctaa tcaacaatat     40620
     taatagcctt tctgcctatc acagaaaaca acttattacc ttctgcagat gaaactttgc     40680
     aaatggtaac aatagagcag tagtaaaata atagaataat agtaaaagac ccatcaaaga     40740
     tattaaaaga aagaaaaaaa cagcgctaga gaggtggttc agcagttaaa agtacttaat     40800
     gtcctggcag agcaccctcg tcgtggctca cactgtctgt aactccagtt tcaggcgctc     40860
     ccgcactcta tcctgacttc catgggctcc agccatgttt gtgtgtattt atacatgcag     40920
     gtaaagtgtt catacacata aaatacaaca aagctttcaa aaatttcagg gacgttttgc     40980
     aagcactctt ttttatacca agactcattt gcaaatccca atgtaataag aagcactcct     41040
     ctttgttaac atcttggtta gcaatatgta gttagtttct tcatgttgtc tccaacaaat     41100
     aactttctgg tgagttctct cctattctcc ttctaactta tactagaacc ctacctctag     41160
     tagcctctga agtccccaca aatattcctg gttttgtccc ttaatggagc atcagaattt     41220
     gacattttct tcattttttt tttttttttt ttttttggct aagcctaaca ctggtcttaa     41280
     ctgtccttaa attgagctga tgaaacttgc gtgtatctaa aactaatcag agaaggaact     41340
     tcagattccc ctatcagacc cttcttacct cagaatgcat tcatgcacca tatgtaaaca     41400
     ttatttagcc acaaagtggg aagcatagct cacctaacac tttgaagagt tgaggcttca     41460
     ctaagggtgc ctgatgctat cccgagttta ttttgctcat gtgaatgaat cacgaaggct     41520
     gtatttgcat ttttcaagtg aaggctgtaa ggctgagctc cagtgttgct ctcggtatac     41580
     cataccatca cctttctctc ccctggttgt gtatggctca gcactgggtg ctttagaaac     41640
     tctctccgtg atctttcaat cagagaacag cagtgttgac ataccagcat gaaaggactg     41700
     tcgcacacaa cccaactggc atctcagtgc acatcaggaa gttatttatg atgtgtaaca     41760
     cccaaactgt ctcctcctgc ccaccctcct cctttcctct ccctgcgtgt gtttcaatct     41820
     gtcattgact ctggctgcct tttcctctgc catagtgcca agagctgttc ctgctgctgc     41880
     gaaggctgtc ttccaacagt ttcctctctg gtgcaaacct ggatgcccgt ctttcagggc     41940
     ctccacctct caaggctctc ccttcagaca tgccagactt ccttggcagc tatcacctct     42000
     ttacctgcca tactgaccct gtcacaggca cctctgagaa aatgtccaga tgtgcccata     42060
     caaaaagcaa acaaacaaaa gagcaccccc ccccagaaaa aaaaaaccca gaagcctgag     42120
     tagagaagat tgacagggaa caggacccct gagaacccag ggcaagtgcc aaattgcaaa     42180
     aagaatagag aaacaataga ctctggagtg aaactaaaaa tagtgtgttt taataccccc     42240
     ctcaccctct gtgtctgatt catctctctg tggcaccaga aagagaggta ttgccctcta     42300
     atcatgaatg cttgtgtttt gactacaagg ctcctatcac agctaagagg aaccaacaat     42360
     aacagtgtat gtgaaggaga taataccaat agcaaggtta ttatctccag attggagcca     42420
     gactctctga caacttttgt ctcaatgttt cggcaagaga aaggagaagg cgggcactga     42480
     gggtcaaaaa tgtggttcct cagctccaag tctcattctt tctcttagag tttctacctc     42540
     agccaggctc aaggccaaga tagagtggtg attagcagtc tggtaatcct ggatgcctgg     42600
     tgactattca ttcccaaagc agacctggca ggaaggaatc cctagttttt gattatttaa     42660
     ggagggaact agtatctaat tcctagccta ccatgaactc agcatggcat gagcttccct     42720
     gcttgatagt ccttagtagg gataaataac accaaatggc cttcaccatc gaaacaggaa     42780
     aggcaaactt aagggtgaaa agaaaggtga gagtcacagg aaagaacagt gtctgcaagt     42840
     gtgaggctga cctctccgac cctgtgttca gcccataccc atctcatgcc ttgcaagttg     42900
     ttttgatgtg agttggctat ggaaaagcaa tggttgtaac tagtagatca cttgggatga     42960
     accaaaggca gcaataggca aagatacaca tatctggcat catgttatta gacctggctg     43020
     gaggatccaa tcaagtcagg gtggtttaca caacataaac gttagctatc ccctcaaggg     43080
     aacagttatt tatttaccta aacacagaaa gcctcgtcta tcttgaaaac ctgtttcaaa     43140
     cagactctcc tttggggagg ggtgggatgg gtgcaatcta aacaggaagt gaggaagaca     43200
     atcttgccct aatcaccatg ttaatcaaca tgacccaata atacagatag tcaatatgta     43260
     tgcagtttac tgcataccag tcattaggca aagagctact taataatttc agaatttcta     43320
     ggagatattc ttggtatagc aagtctactg atgaagatct gaatctcaga tttgatccca     43380
     tcccaacatc atacagttga gtaagaggaa aaatctaaat agactgactc caaaccctgg     43440
     gctttaacca ctcattcctc tgcttccacc attggtgtga cagacattat tggaagacct     43500
     cagattcagt catgtgttgc aaatggaata aattgcctaa ctggttaatg gtagctaact     43560
     tacgtggaga gggccataga gttgaaatag ttccaacata aaaatgacct cttggtattt     43620
     gattaccttt caccttagac attgataaac caaactgttc cctcaggaca acagttctgt     43680
     acagggaagc acttctcttg ccaaagtata attttgttgg ctatatctat ctccttcaag     43740
     ccttggaata agccccaaac tagtaaattc tgctgtcctg gcaagacgcg tttcctccag     43800
     ggcattatat caggctaaag taatacatca cattgcttcc cactctgtca gcccatttct     43860
     ctaaagagtc ttaaagcagt aatgtttctg ctttgaatct cagttgctct tgcccctaag     43920
     tattgcactt tgactctctg acctttgaaa caaagggcac gagaagagtc tccttcccat     43980
     acctgccctt gagttggggc tcgcgagaga gagagagaga gagagagaga gagagagaga     44040
     gagagagtat gtgtcaagaa agggtcagcc tcctgatgct ttatttcatt cattttagac     44100
     caagagatac ataaacattg acataattgg gtaacaagga gactttggtc tttggcatta     44160
     tggggattta gtcaatggga aaggaaggct gggtggtagg gtgggatggg gtgggtacta     44220
     tagggtcatg attcctagaa gagatgacct catccaactg agaagtagtg ggactagcaa     44280
     aaactgccaa ttaaaaatta acataggcca aaagtgaaat cgatgcctaa atctgatagg     44340
     ttgtcaggac cgtttctgac acatagttca cagaaaaaga gaacattttc tcagtgtgca     44400
     cttttacaga tgccaaaggt caggctttgg aaagatcctt ccacagacat gcaggactga     44460
     acacagctat ctagagaagg ctctgtcagg tgttatgtgt aaatacagat tttaaacctt     44520
     ctccaaataa tcctaatttg aaaaacatta acattgatta tgattcactt tattctataa     44580
     tacatgtatg taagtacaaa tgcatgttat cataaataag taatgatagg tccagcaatg     44640
     aattctcttt ctacattttt ttctaagcat acagccatgc ataccttatt aatttattta     44700
     atttaaataa gacttctata aagtctttag agaataaaat attgactctc aaagacatca     44760
     aatgttaagt gctatagatt caggaaatac caaccataca atgttttatc atagttttcc     44820
     ttacattggg aattatgaaa gatgtcagtt ttccatataa agctatcaga gtaggaaaga     44880
     ttggaaagca actttcattt atacaaatga aaattaaaat gtttccagga gttgcagctt     44940
     aaacttacag tcccagcact cagtgggttg gagctcccga gttcaaggtt aaggccagcc     45000
     tgagctatgt cacaaaacat gtctccaaga aacaaaggga ggaaggatac aaaaaaaaaa     45060
     aaaggagtga gggagaaagg gaggaagggg aagagaggag gagaggagga aggaagggaa     45120
     ggaggagtgg aaggagggag ggaagtaaga agggagggga ggaaggaggc agggagggaa     45180
     gcaaggagag aaggacggag ggagagagca aggaaggagg tgaaggagga aggacattaa     45240
     aatgctcaaa tgtagggcaa gtaacttagt tcagtggtgc attgtgtgtt cagcatgcat     45300
     agggtccaca gggtaacaaa agagatttca ctggacagct ataatattgc ttcttaacat     45360
     aattttcaaa actttcctac taatatgcaa tgcaaattga tatcaactga atttatttct     45420
     attagataag tttcttaaag accaatactg acttaagaag aattaaccta tattgtcagt     45480
     gaatctagag attagcaaaa ttaacaacaa caacaacaac aactacaaca ataataataa     45540
     taataactta cagaagaaaa caaaggttct ggctcctaca gatcctaact gtgatatttc     45600
     attgtgtaat caatcttcag ctaataaaag ttaagggcaa attgtttatt atctaacaat     45660
     atcatttata ttttctatta aacacgttac tgagacattt ctagaaactg ctcccaaacc     45720
     ccaacttgaa atttcttgct tcttcatcct gtttttaact ttaaacacta aatttaattt     45780
     gtaaaaagaa aaaaggactc tactttggta cttcttcctc ctattaataa tggttttaga     45840
     gaattgttgt atactttata acccagaaag gaataagtat gtatcttcaa aactaggtat     45900
     gctcctaatt tgaaaatgtt tacatttgac attatttaaa tattgatgca ccaaatcaat     45960
     attttttctc cttccaatga cagtttaaag agctttctca gtaatcagaa ggggaaattt     46020
     cccagggaac caaggtactg tatctcaagt ccatttccag aaactgatga gaaccacagc     46080
     tgtgtgtagg ttggtaggct tagttttact cctggttaat ggccacaact cttccctcta     46140
     gaaacaatga ccccagttaa ctctcagaag tgcacacttc tctcagagaa ggaggggagt     46200
     gagttgcttg catccatgac aaaatgtgat actcagctaa ttggtgtggt tttgatgata     46260
     ccacagttct gcccaaaacc cttgtaacta gcaagttttg ccctgaagat tcttgagtta     46320
     ctccactgac catgcattat ttaaagggaa gtgctactaa acagaggcca tctgtttaac     46380
     cattggaagt ctctctgttg gccccagttt tgacaaaaca ttatgtctcc tcagagtgga     46440
     ctcaaaaatc taggttaagt ggtggccagc ttgtctggaa agctttggtc tacatgctag     46500
     acaatctctg aaccaaaact actgacaaaa taaatatgct attatacatt ttctcctttt     46560
     ttttcttagt ttatcttttt attcactttg tatcctggtc gtggtccccc tcctcctctc     46620
     ctcaagtccc accttcacaa gtcctttctt ccattgcccc ctgcccttct cctcagagaa     46680
     agagaagccc ggtttgggta cctgcccacc ctgggacatc aagttgcagc aggaccagat     46740
     gcatcctctc acactgaggc cagacaaggt ggcccagtta gggggaggga tccaaaggct     46800
     ggcaacagag tcagagacag ccagtgctcc agttgttagg ggacccacgt gaggacccag     46860
     ctgcatgtcg actataagtt tcagtgttaa gtctttgtca gcaaattatc tgtggagtgt     46920
     tacacagtca aacaattaag cagatagaca aggttagaga ctcctcagac tgtgtcccat     46980
     tgtaaaaggc actggcccag tcacttgtct tttactattg cattggcaaa agacaataag     47040
     tagttttgag ctttctggag aactgaacga taatcaaatt tcatcttcta agtttaaaca     47100
     tatttaaagc tctttcttga agacaatgta agtgtttccc aactaggctg aataagtatc     47160
     caagattttc tatacaatct ctggcataga aaagatcaca gcaggcatct tattcccaat     47220
     ataggattct gctcctaagg tcaccaacag gtatttgtac agccatcgct tagctgcttt     47280
     ctacagtgga gacttcatta tagttcaaga aagtcttttt ttaaacttat tttttggtaa     47340
     caaattgttt aaaacatttt atgttaagac aattttattt tctgttcacc tgataattct     47400
     gattgaacca accagaataa aatatgtaac aggagtgttt aaaggcaaca acgtcacccc     47460
     tagttccacc tcattacaaa aatagtcaaa tgatcaaatg actaaaattt tctgtaattt     47520
     agatgtgatt aagatactca tttatatcaa aaaaggtgct gagaagattt gttgattgcc     47580
     tacctgataa actgtattac actagttttt ctattttagg ccacaaccgt aaatagtttt     47640
     attaaggttc ttttaaaaag actaatagga ggtggttgaa gaaaaaccaa acactttgac     47700
     ccacaactgt ggtccctcag ttgctgagag gtggctgtta aaatcaagcc tataggagac     47760
     ttcaaaggat ggattaagct ttaagcagca ataggtaaac atttgctaca ttcataaatt     47820
     ttgaataaag tacaacgagt ccattgtagt cattgtgaat tggcaaagac aaatatccct     47880
     ctagaattgt ggtagctaga atgaatataa gtggttgttg tattcctggg aaaatccaca     47940
     tgtgtatatt accactccaa tagcacttaa aaaaaaagat acagatgtta cataagacca     48000
     aagttcttaa tcgaacatta tataaaaatc ctaaagctct ctgcttcaaa ccctatcagt     48060
     gtgtggcctg gaaagcacag aggaactgca ccaaactcga agttcctctg tgagagtcag     48120
     caagctaggc actgagcacg tgggttattc tctgctgtag tgatgactac tgtccatttc     48180
     atcttctgag atggtctcgt ggctgttgag agtcacctgg aagtatcaca tggaagtgtt     48240
     tttggttatg ccaaaataat ggctggtatc ttcttctcgg agcaagcaag gatcacagaa     48300
     gtaagattag ccaagaaggg cttcaagtgg aagtcctaaa taggtcctcg aatcccccct     48360
     cctcccacct ctctccattt caaattcata agcctgagtt gtgaaaacag ttatagctga     48420
     actggccaag ttcagaagtt tctggaagaa ctcctacaac cctaatccta aacatcaaat     48480
     aactattcca taatcaacaa ctgatggagt aaaaaatcag tttcttaaga aatcaggctc     48540
     tttaagaaac atgtactaca aacaaaggac agtcattgca tgaaggtatt gttctgatag     48600
     gtacagcaaa agcaataggc ctcttctctc ttttgcccct acctgcaaag agaacccaaa     48660
     tgaatcctct agtcttaact ggttagccag ttagaaaact atgcagaagt ccttcatgga     48720
     ttacaaaagc catgtgcacc catttgtgtc tttcctctaa tttattgtcc caggaaaaga     48780
     ttattaaaga aaaaagtcag gaaaacaaaa aacattgttt acattgccca ggggaccagc     48840
     cagtttgaac tttccagggc ctgaatggca aacaaaagcc ctgagtccaa ttctatgtta     48900
     gtccttcctc caatggccag taaaagtgtt gctgagactc cactgagacc agccgcctgg     48960
     cccctcccaa agcccacaac catgaggagc ccacagggtc ggctgagggg gttgggggga     49020
     gtaagaaggg agggaggaag aaagagaaac ctttccttcc caaagagacc acaaatgaac     49080
     cctcagtaag ttactacctc cagctgccct gagaataaac cttccttgtg tgaggaagca     49140
     gcaacaaggc tcctgtgcca agcatcagga aaacatttgg gttcttagaa gacgccataa     49200
     acagttggcc tctccagcag tgaagcagcc aagctaatgt gagtgtgggc cattgccatg     49260
     gtcctgatct ccccagtgag gaagctgaaa atatagatga agactttgat tgtcaaatgc     49320
     ccattcttaa gtattgtgtc agtcagtacc tgtgtgataa taagtcttta tttaatgcca     49380
     tgccttcttg ggttgggaat taagactaag catatatcag gttactaatc gaattctcgt     49440
     ggtgtatgac tctctctctc tctctctctc tgacaaaagc ctacatggca aaggagagat     49500
     gagaagcatc cagcctccca aaggatgtaa agaagatgag aacagaccaa aatgttgtga     49560
     ccctatctac aacaacacag cttcacattt ggtgtgaatc aaatcaaatg ttatccatac     49620
     agtactgcat caacgccagt aaacgtatgg tcaaaaccaa gatcaaattg actcaatacc     49680
     tacttggcca attaaggtgt ctaactgatg tgcaaatatc aaaataggtt tgatagcctc     49740
     agtttcactg ccacttagct ctctgcctgt ccttagtcca gtagtttctt ctataggaaa     49800
     catacatgtt gctccaggct ttctggggca actaggcaag ccccttcccc actagtattg     49860
     taatcagttc tgagtttcca ggcttctgca tatgctcaat agcaacaatg ggctggttat     49920
     ttttttatag gtcatttaag accttggaaa agatcctcag gagaagcaaa ctaatatgag     49980
     gttaagatct cttctgtagc aagtgctata tattacttta tttaatacgt catttcatct     50040
     tatcctcaat tctgacaaga aatatgtcac tgcctatcac acaattcaat ggagacctcc     50100
     agagctctca ctgcttttct ggggttattc cccagaattt tctggactcc atgaagtcct     50160
     tgggcttaac agcagaaaga tcagagtttg aagcccaact ccaccaatta cttcaaactc     50220
     tgagtctcag ttatctcacc aataaaagga agatatatgt tttgacttcc aactttgctt     50280
     aaatgaaatt taatttacaa gagaaataga agataaaaga gcagctgagc tgcccaagtc     50340
     tgaaactgta ggcatttact aaagtgattg gaaagatcca gtgtcccagc accatgcatc     50400
     caagggggct cttgctcaaa aatttgagat gatgagcaac ctaaatacct tcagttgatt     50460
     attaaacagt atgcatcata ctgtaccctc ccaatattac aattgccttg tcaatttaac     50520
     aatagaacaa tatgtttgca acattttaaa aaacttggtc tatgatttta ttttaactag     50580
     aactgttaaa agcctctcaa ctaagacaat aaaaagaaag gtgataggac tgggcatagg     50640
     caggatcctg gaacacagac tgaaaacatg ggaagacttc atacaaataa agtgcatgac     50700
     aagtgaagtc ttacttcttg agtatgctta catatgggaa tctaaaagaa agtactgggt     50760
     caggcatatt ggaaatactt aaagaaaaga gtgacatgtt ggagaagtat gtagacttga     50820
     tgtgggaaga agaaaggcat cagaggatag ataaaagtct ttgaaaaata ggcagttcta     50880
     acaccagccc attctgattt gtgcagacaa gcccacaggc tatggctcca gcattcggag     50940
     ggcacctcag acaggcattg tggatgagtg ttgcttccgg agctgtgatc tgaggagact     51000
     ggagatgtac tgtgccccac tgaagcctac aaaagcagcc cgctctatcc gtgcccagcg     51060
     ccacactgac atgcccaaga ctcagaaggt acgatcgagt gggtgaaatg cagtcattct     51120
     tgaacggtct gttatatgtg atgcaggggg aggggggcaa atggaaatcc tatgtctcct     51180
     gagtgatagg tcacaaagtt ccaattctac caataagatg gcttatgggt gcacccttcc     51240
     aattactttc tactctgaat tatcttttcc actcccctgg acaatctgac acttggaagg     51300
     tggtagaaag ccaggactaa acctgtgaaa actcaaattg cccaatgagg ccggttggcc     51360
     aaataggaca gcaagtctag gctgccagaa tttggtaagg tgatatacgc taagatggag     51420
     accatgtaca agtggaatgc ctgcaccaag taactgttag acaaggatta acatcgtctg     51480
     tcataattgt atctaatatc aaaagttaca agtcctggaa ttctacaatg gtccaaatac     51540
     agactcctta gtgggaccta tttgaaattc tcagcagcaa ttataaatta aagagaaatg     51600
     cattgaaact agacatactt ggtttagctg taggaatgtt tagatgtttc tgatgatcaa     51660
     aacacaaggc atcctttgtc caagccttta ttataacgca accccaggaa gaccatctgt     51720
     gccataagaa acaggtaaaa catctgacac atgttggcta cttgatacac ttataaaatg     51780
     aatgaatgaa tgaatgaatg aatgaatata ttagagtcta agtagaatca tagtttttat     51840
     atagaaataa agagaagata aaatagaaag agaaagaaag agagaaagaa tgagagaaag     51900
     agagaaagaa aggaaagaaa gaaagagaga gagagagaga aagagagaga gacagaaaga     51960
     gggaaagaaa tagggagaga aagaaagagg gaaaggaagg acggaaggaa aggagggagg     52020
     gagggaggga gagaggaagg gaggaaggaa gaaagaaaga agtaaaagcc ctctcttagg     52080
     tgttttgagg cattttttaa aaaagtgaac acataaattc tatcattgaa actaaacaaa     52140
     cattgtgcag aaagcacaag ataagagact caaacgttca ctctgacacc tttgctgctt     52200
     cctgatccta agctaaagcc gaggctgaaa gaggaccctg gggtcttagt ggagacatca     52260
     ccccaatgag tctcctgaaa ggatttgagg ggactgttta ggacttgaga tagacaggat     52320
     acggtgggca caagagtcag aaaggatatc actgtgcaaa ttaagggaaa aggagtgttc     52380
     cttctagctg aagaggaagt gggtattaga gataaggcgc aaagctcggg cacctcggct     52440
     ctggtgcctg aggtgtagaa ccctctccag cagtaaagct agcttctgtt tcctatggag     52500
     cccaggcatt ctgggcagat tcaaagaccg tcttcagcac aggagccacc cgttctcaat     52560
     gcaattattt ttgtgatgtt tgcagtcccc gtccctatcg acaaacaaga aaacgaagct     52620
     gcaaaggaga aggaaaggtg agccaaagac acacccagaa ggggaacagg aggaggtaac     52680
     ggaggcaact cggaaaatca gaggtcccag agaaaaaaga ctgggctagg aactgtgagc     52740
     aagcaggcaa agagggacat gcgggaacag ggatgaagga cgtgcgggaa cagggatgaa     52800
     gaaggagcag acaggagccc aggaaagccg cagaggagct gaagcaaggc agtcctcact     52860
     aagctagata atgtctgtga cggaagtaag aaagtcctcc tctgggatac ggcacttaca     52920
     catgggaaga atggtacggg gaagtgtaac acctcagaaa gtgacaagtg accaggatgg     52980
     aacatcaaca acaataacaa ccattaaaaa catgccacca agaccttccc tccccttctt     53040
     aaaaatataa atcagagtaa aaaaaaaaaa aaaaaactat gcaaaacaaa gattgcatct     53100
     tcagcctgca ttccaaattt tatacaaatc ttttatagaa gaattgccca tgtcaatata     53160
     tgttcagagt taaatattaa ccataaattc gcagcaatgc tgtattgtgt cattgaagtt     53220
     cccagatttc tgtcctgaat ttcaccggtg gttctgcttc ttggtcaagt ccagggtata     53280
     ggccaaagaa catcgggtat ttacaaaaag gcctgtgagg taacttttaa aaagatcact     53340
     gaacttttat tttgtactgt ggtatcagac acaaagacat attagttcac catggctgct     53400
     ataacaccac agactaaatg gcttaaccca cagacacatt ttcccctcat agttctagag     53460
     agtggaagtc ctcactcaag gtatcagttc cttggaggtc tcctgcctgt gtccatacaa     53520
     tcttccctct gtaggtatct cagtgtctat atattgtgtt ttcattagaa tatcattaag     53580
     acgggagtgg ggttcgccct aatgacctca ttttaatttg atgaccttaa tacagactct     53640
     atttttgagg tgctaggaat tagaacctta aacatgaatt ttggggtaga ggatagcagt     53700
     taatccataa taatgaacat caaactatat tatatcattt agttctctct ctctctctct     53760
     ctctctctct ctctctctct ctctctctct ctgtcacaca cacacacaca caggcacaca     53820
     cacacacann nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn     53880
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnncg cacacacaca     53940
     cacaggcaca cacacacaca cagacacagg cacacacaga caggcacaca cacacacaca     54000
     cacaggcaca cacacatgca cacacacaca caggcacaca cacaggcaca cgcacacata     54060
     ggcacatgca cgcacacaca cacacacagg cacatgcacg cgcacacaca cacacacaca     54120
     caggcacatg cacgcacaca cacacacaca caggcacaca cacacaggca cacacacaca     54180
     cacaggcaca cacgcacaca cacacacaca ggcacacgca cacacacatg tacacagagc     54240
     tagattctga ggtctcaaat cttatgagat tcttcgttag aagactctta agctgttagt     54300
     ggtggtaaag gccttggaag cctttcaatt ctgcctcttt attttaaaga ctgggatact     54360
     gggatctgga cataggtgag atctctaatt ggtttctaag cttcttctgg gcaccaagtc     54420
     acaactatca agtgaaccga gtaaaaagag aagaagggca cagaattgga catggggatt     54480
     taatatttgt ctgccagaag acagcttgca agtgctatca agagtgctga attttctggg     54540
     gaaggtggca atcaactccc agaagaaggt gggtcttagt gacctttgca atcactacaa     54600
     gcaagattgt catggggcag aaagcaaaac ctcgagatta tctaaatttg aatccccaca     54660
     caacaagaga gtatagaaga cagaagaaat gaccctttgg ggtggtaaaa tgactgaaag     54720
     ccacaagtga gacatttcat ctacatcatc tacttcgaag acccagtata aagaagcatc     54780
     tttcggccta gtccttccag ttcctttttt ttttttccta ctccaggatt ataacttctc     54840
     cgtggctcac tgaaaatctt ggatgtcctc aatattacaa aggtgttcag agctcaagat     54900
     agggttgaag attcaattag cagtctgtgt caaaactccc aatgaaagca agtttacttc     54960
     cattatcact gcaaaaagat tatctttacc taggttatca ggagaagctg tgttttatta     55020
     agtcagaaca atttagggac agactcaggc aaaagctgtc actaatgcca ctgtagcctg     55080
     agccttcaga ctcagacagc tcttgaggaa agcacagttc aacaaaagaa ttcagaatct     55140
     atgtcctatg gaaaaaattg ggtggttgta cttaattata aacttcattc aaaggaaact     55200
     taaagtgatg ggactttcta gttaaagtaa gttctcatag ccctagactg tgtattggaa     55260
     tacatttctt tatgaagtag gttttaacca tttaaaagca atccttagta tgcctacata     55320
     tcttctctca aacatgccga caactgaatc tatctcatac tgttgtgagg atatatcaaa     55380
     agtatattta ggcatatcta tatttgtata tatatttata tatgtgtgtt tattgtacat     55440
     acacatagat tactctaaat aatgctggca cataatataa gcactattga actactagct     55500
     agtattgcca tgcttctgga tattggagca atagaaaagt ctcctgaagt agaagtgtct     55560
     catattgcca ataatgtcaa gccaacattt gacaacagtt ccagcaatgt gcatattctc     55620
     gtacatacaa cagaagagat cttagtagtc taagattact cccaacctgt agaatacctg     55680
     attctgtgac taattccaat taaaatggtt agccagctct tccacatgaa gaactgtcta     55740
     catttattta tgtcttagtc agggtttgta ttcctacaca aaacatcaag ttggggagga     55800
     aagggtttat ttagctaata cttccacatg gctgctcatc aacaaaggaa gtcagaacag     55860
     gaactcacac agggcaggaa catggaggca ggagctgatg cagaggccat ggagggtgct     55920
     gcttattggc ttgcttcccc tgccttgctc agcttgcttt ttttaataga actcaggacc     55980
     accagcccag ggatgacacc aaccacaatg ggctgggccc tccccatttt gatcactaat     56040
     tgagaaaatg ccttacaccc ggatctcatg gaggtatttc ctcaactgag actcctatct     56100
     tggtgataac tccagtttgt gtcaaggtga cacacaaaac cagccagtac aactgacccg     56160
     cttgtcaact tgacacacaa acacattaca agtaagcctc aacctttact ttctgattca     56220
     tccccaagat ctaaacaact ttaaaagtcc cacagtcttt acatattaaa atttccatcc     56280
     ttttaaaata tccagtatct ttaaaaattc aaagtcttgt tacaactcaa agtctcttaa     56340
     ctgtgggctc cattaaaata ctttcttact tcaagaggga aaaaaaaatc agggcacagt     56400
     cacaatcaaa agcaaaatca aactctaacc atccaatgtc tgcgatccac tcaccatctt     56460
     ctgggtccct ccaagggctt gtgtcacttc tccagctctg ccctttgtag cacacacctt     56520
     gtcttctagg ttccagatgc ctgtagtcca ctgctgctgt tgttcttggt ggtcatctca     56580
     cggtactggc atctctaaaa cactgctatc ttctgttgca actgggcttc actttcacaa     56640
     atagtctctc ataggctctt ttcatgttgc taggcctcaa cttctctgca tgaccccttt     56700
     cagtcctgga ccttcaactg ccactgaggc ttcaccttcg ccaatggcct ctcctggctt     56760
     ctcaccgtgc caagcatcag ctgctacccc ttcatgtttc aaagccagta ccacctgggt     56820
     gactcattca taaacaaatc tggctgccaa caagaggcac gaccatggct gcctcttgaa     56880
     cacagcttct ctgtgctctc aggaaacact tcccagaaga tttcacctta gtattgttgg     56940
     tctcttctta atcaccgcta atttcttagc tccagctaac cagcaccaat ggtcccagta     57000
     atgcaaagag ttcactttgc tttagttgtt ctggtatctt gttaatcaca gctgattctt     57060
     cagcctcagc taaccaaaac cacagaattt tcacaatcaa tatagcaatg gatctgataa     57120
     gaatctttat tcttccctct gaaatttcac aagacagccc tccatcattt gcactgttct     57180
     caacattatc ttccaagctc ctacagaaca tcccccagag ctcttaatac ccagtggttc     57240
     ttctagccca aaattccaaa gtccttccac agtcctctca aaaacatggt caggttgtca     57300
     taggaatatc tcactatgct ggtaccaatt tgccttagcc agggcttgta ttcatgcata     57360
     aaacatcccg accaaaaagc aagttaggga gggaagtgtt tatacatctt acacttccat     57420
     attgctgttc atcactaaag gaagtcagaa caagaactca cacagggcag gaacatggag     57480
     gcaggagctg atgcagaggc catggagggt gctgcttact gggttgcctc ccattgcttg     57540
     ctcagcttgc tttcttatag aacccagaat caccagccca aggatggcac tactgaccac     57600
     cagcccaggg atggcactac ctacaatggg ctgggccctc cccctttgaa cactaattga     57660
     gaagatgcct tacagttcaa tctcatggag gcacttcctc aactgaggct cctatctctg     57720
     tgataactcc agcttgtgtc aagttgacac aaaaccagcc aatatagatt atacaatgga     57780
     ctttggagaa agccatcatt ttcttctcaa caagttaaaa ccaaatgtaa tatgtgtttc     57840
     catgatggtg cctggggaaa ttttaattgt agcctgaatt ctagatctca atagttttaa     57900
     gtgaaactgt caaaataaat agaaacatgg gacatttctg agctcacaga gcttctagga     57960
     cactttggtt cctagggtag ctaatctagt gcttttcatt ggcatttgat ctttcacctg     58020
     tctctttaaa acaagccaac ttcatacagc tttgaatgtg tactgttaag ttgtaagggg     58080
     tagtaaaggg gacaaagaaa atcctccaaa gagtaattcc tcttctgcta ccatctcctg     58140
     acctccaagc aacaatggaa aggaaatagg gctttccaag gtaatgcagc cagcgagtgg     58200
     tcaagttcat aagaatccat aagggggaga gggaaggcta gtttatatcc ttgtcgggaa     58260
     gagaatcaaa cttttttgaa atatgtaata gataactcaa agttgactct tcaggcagaa     58320
     tggaattaat gtgagggctt tcgaaagcaa tgggaagatt aatgagtttt aatcaaacac     58380
     gatctcttta tttcagtttt agaacatcta ttatagactt tactgtaaat gttacctaga     58440
     gactgaaagg ccagttattg gttcccataa cccaagcaag aaaaggcccc ctgacaccag     58500
     ttaaagaaga ttcttcagga gccaccaaac atgcaacagt gaagtcagtt tctctcccag     58560
     ggcctgactg aaatcagaat tcttccctga agtccacata tttgggaacc tatctctaat     58620
     aagattttcc aacaccattg gctcttatcc agcaaccaag atatataatt tagaaaagtc     58680
     aacttgggtt tacactccag aaaacagaag tagatgtagc aaagactggg aatgagtgtg     58740
     aggtagggta gaacaaatct gtgagtttat gcctgatgct cagcacctct aagaaagttc     58800
     tcagaacatc aggccctgaa acaatgctgt atcctactgg atgagtcccc agatatttta     58860
     attctaaatg cctttggtag gacttaggaa tgtgtaattc actacaataa acagtcttgt     58920
     gagaagagaa agagtgtgtg tgtgttcaaa ggaacacaag tgtacacgta tgtatgtcta     58980
     tgatgcgtgt gcttctgtag cttttttttt ttttttgacc cagtagggtt tgtgggtaag     59040
     tgactttcca aaatcatggg taactaccag ggctctttct ttcagtggat gtaaattcct     59100
     ttgtaaacat cacttgtcat ccaccaagat ctcaagagtc ctttgtcttc tgggaaataa     59160
     agggaatgtt tttggatagg cagaaggaaa ttggtcttgt ttcatatctc ttagggaaca     59220
     aggggcttca accaattctc agctaaagta caatctatgg agctctcata tctgtgaatc     59280
     ttggtggttt cccataaaat gacattacaa cttgagacac gtggtccgca ttgaaatctt     59340
     gactccacag gttccttcca ccaacctgtc agagattagg attattgtcc atcactgccc     59400
     caggcttctg cttcctcttt cccctttcct ttaaaacatt ttaaaattat gtctatttat     59460
     tctggaggag ggcatatgcc atggagtgta tgtggtgggt ggagaacaac ctcacacagt     59520
     caattctctc cttctaccat gactttcctg aggatcaaac tcaagttgtt agactcagaa     59580
     gcaatttcct ttaccctcta agccatcttg ccaggccccc actctttctt agccataagt     59640
     cgctgatgcc ctctcctcac ttcagagcat ccctaacagt ctaagcaagc tcgcaaatat     59700
     tcttctttgt gaaaatggct ctaaagttcc cagggacaga tgaagaaatt tcattttttt     59760
     ttaaatcaac acttagactg gctgaatggc ccggacttcc aagcaagaat tcatatgcca     59820
     aaagttttta caaaattctg tgtaaagtct agaagcgttc acatggggct ttctgtctag     59880
     ccaacaccaa gaggttaagt aatcaaagac caaccagccc tgccatctgt gaaaatatga     59940
     tgggctattt tcacagctgg agataacaat gatggcagga caaaaatatt tcagataatt     60000
     aagagcaaga gtgtggcagg ttgggggttt gggaaagatc cctacccatt tgacaactgt     60060
     gctcttggaa atgggtagtg ctgatgtcac ggcaagcatg tttaaaagtt tatggaacat     60120
     tgcaaaacaa gagaaaaaac tagcgtgtaa atgatgagat atatgcatgg catcattacc     60180
     gttcttttgc cagtattggt tgtccaggtc actatcagat gctctgtttg cctctgtgaa     60240
     taatattcat gttcttcaaa agaatatgag gctaggagtt gaggtgctct gagcacaaca     60300
     aaatgattct aaatttttaa agctggatga atcacgcttg tagactgttc tgtcttggaa     60360
     aaccactgat tggcagtccc catgtttgct tttatatgtc gagggctccc atcgacctca     60420
     aatagatgca aatcacttca acctgtcact gtgttatttt gttcatccta aaagtttggg     60480
     agagtcttcc aagcttccaa aatttctctc gactcagtga gaaggaaaat tcagaacaca     60540
     gagtttgaat gttctgccca gatttgtcac acactctaag accgagtgga agagaacaat     60600
     gccctttctt actaaccctg tgaactcacc accagtccat tgaactgaca ccagaagact     60660
     tttcagagcc tcaggtctct caaggacact gtgatacaaa ttcacacaca cacacacaca     60720
     cacacacaca cacacacaca cacacacaca cacacacatt aggtcaacat tagcctaagc     60780
     cagttggaac aatggctcgg gaaaagcatg gggaagaaga acatcaaaac aggtcctcag     60840
     gtgagatgtg caaacatcag ttgcattagc agagtctggt attgcccttt tgaaatgtcg     60900
     cattgaaacc cttttagaaa ttccaaaatc aaccacctcc ggggacgata gtatggctta     60960
     gttaggctaa tttgtcacca tcaccaccat tgttgttatt tttgtcattg ttgtcattgt     61020
     tattgaattt atcacaaata aaaataccta agcaacttgt ccataaaacc taatctaaac     61080
     aaccttgaac ctgcaggatt ttgtaacatc tttccagact gttaaagaca atataaatat     61140
     tttctgcctg cttagccccc aaaaaatttc ttcagtattt tcttcttctt ttatttccct     61200
     ctagccttta aaaccattta ccaggagttt cttacatcac aggaaggtat gctggaaatc     61260
     aaatcaagtg gctatttgca gagtgagaga gttgctaaat taggctgggc taaatcagaa     61320
     aataaaggga agaagaatgc aagttccttg actcctgaga tgcctactta tttatcagac     61380
     atttatttgt tacttattca tttgttatta tgtattaaaa gagcaaagga tgaaagagct     61440
     atgggcatgc tatcccaaca tttgagggta ctctgcaaac ccaggaggta gctaatttgg     61500
     cccataatca gcagtaaaag aggtggcatt ctagcatgga aaatactctg gtagtaggaa     61560
     ctgttaaaca ctagataata agaatagcta ccagttattc aatgcttacc ctatgccact     61620
     ggctttagtg aataaccttg ccataagcct acataggaaa tgctatcatt ttccctgcta     61680
     tggagataag aaaataaact gagaaaggct aaatgtcttg tcaaaatctt gctctcattt     61740
     gtccaagtca ggatacacac ccaagatgga tcccatttgg ccaagtcagg atacacaccc     61800
     aagatggatc ccaacatgtt aaccaggctc cccactattc cattcacttc ttagttaaca     61860
     cagattgtgc cacagtcatc agcgtaagtt ctgagacagg agagggtcat tctatattgc     61920
     tttgtgaaca caacaagtgg ccatacaatg cttactgttg acctaaactc taccccattg     61980
     tttctgcaga aaatttaagt cagtataaat gagaagccac atttgctatt ggcttttgtt     62040
     tctccaacac cctgcttgag tttagggagg atacggagat aaaagaaata tgtcccccca     62100
     gcctcaggga gcttcccttt aagtggggga gataaacatg ttcaaaattt actctaaaac     62160
     atgtcagtat tcttacaaaa gtcggcacac caaggttgca cacaagccag actagaatag     62220
     cattgctaag ggccaagttc acagagtgga tctgaaccaa ctgtctctga tatggagcct     62280
     ccatgcacac aatggtagct atctccctgt gctaaataaa agtactaaag ttaaagcaac     62340
     caatcaaatg gcttggtgac atcagtgctt ttaccccaac tctttcaagt tatagaagag     62400
     gaaactgagg ccagaacaag tcagtgactg tctaaagtca cataactctt gtgaggtagg     62460
     gaatctgcga tcaaacctag acatggaagc ccatggcttc tgggaaaaca agcaagactt     62520
     gataagaata tgtacctata tcaaagaaaa tagtttagta atttgggaaa accatcaaat     62580
     agcaacaata cctgatccca agagaagaag agttagaaag gagctcgggt aggactgtct     62640
     gagattaata tcaggtgtta agggcagtgt aacaaccata gggggagtct ttaagacaac     62700
     gttggccact gaagatgtat attttctaag agtgtgtcca gtctttgtat tcccactaca     62760
     ttcagacaca gcttaggtga agagtcagcc tggaacaata gaaatgttca aaggaagaag     62820
     tcatagggat ggagaggagt aactagagat tcccatcaga ttaaaggagg aagaaagccg     62880
     tgctaggaag acagccagag gctaggcaaa ctaaaatcat gtacacacgt gtgtgtgcct     62940
     cgctcctaaa gagtcaacca tacacaatag gagtatgggt ctttcgaact atcctaacac     63000
     tcagcttggc taccaagaag gaaaggccaa ctggagtgtc ctggaatttg aacttggaat     63060
     tccttgaagt caaaagatgt caaagctggt agcaagacat ctgaatcatc ccgcacagtg     63120
     ccagtgctgt gtgttccaat cagaaaaaac aaaaacaaaa aacaacaaca acaacaaaac     63180
     ctacagcata tccttttcaa caagtgaaga gttgctgtct gtgccacctg tcaatcatcc     63240
     actgttcttt cttcttctat ttgtccttct atggagaagg tcactgctga gttagtactt     63300
     tgttctgtaa ataagatgct aatgttctat gccagacatt atttccccag cattttttat     63360
     aggatgccag gcccttcata gactatgccc tacaatactt aacttgtttg cagtgggtgg     63420
     aagatggaaa cacagtctat tgaaactatc aaggcttcct tcctgaagtt tattaaagag     63480
     tctatcatct ttcttttata tcctttcccc taggcaaacc ccgacccaaa aaaataggca     63540
     tggtgaaaaa aataagaaat aataatatcc aaggagatag ctcttgctaa ctggaagtgc     63600
     tacatttcta gatctctata aacaaccatg cgaatgtagc caagctgaca ttgtggtcag     63660
     gaaggacacc caccctgtta tcttacagtc ctctacccga gacatcatgc cttcattcat     63720
     aaaccagcag gggaggtgga cagctgatga catcatgagc taccactgtt agatctttga     63780
     gacttttgag atctttgagg tttttttttt tttctttttt cttatctctt tggagtggtg     63840
     agtagcagag taactaacag gtcacctcca gaatcagaaa gcacttccat aaatctaaac     63900
     cagaagccca gcttaactgt aataagaaat gtcaaatgat catgatgcca gtgcccatcc     63960
     tgtgtaatag tgtgggataa acaagaaagc ttaagcagaa gccatggatg acgtaaccct     64020
     tagcatgtga tggatgcttc agtgatgatt actgtcattg cttctcttga ctctaacaat     64080
     caccttagag gaatctaacg gttcctctgc ggccttaggc acgtcagtaa atcttagcaa     64140
     gcctcagtct ggaaatggag tggacacaaa taaggtcacc ttgccaaaat ggatgtgagg     64200
     agctggtgag agaattcact caaccataaa gcctcagcag gtgtcgaatg agattcttgt     64260
     gacatttgtt agtaacctct gatgaccttc actctcaaag agtctagggg taacttttca     64320
     ggggaaagtg tgagagccgt ggaagagagt aaacggcctc cgttacagat taatcccttc     64380
     cccagctcat tccttaataa gctggttagc ccttctttca aaagggttgg tttctttcat     64440
     caaccccaga gagctggaga actggcattt ttcttttaaa tcttaccttc tctggtgtca     64500
     attggaaata atatttactc actactgttt tcctttcaaa aaaatctgtc tagttgcaca     64560
     ctagaaacag tttcagctgg tttgtttgtc ttggacaagc tgctgaagtg agaaaaaaaa     64620
     agtttttgct tggctgcatg tgaaactgtt tcataaccgt tcaataagtg cattgaaggt     64680
     gggtgccagc tccgaggagc gctgctccta aaggacctcc acttgtagac tattgtcaag     64740
     ggtaaccagc ataattaaat taagacaatg agaaaagcaa cagatgcaac tgagaccaag     64800
     tccctgagtg cttttgttag tcactatcat tgtctgcaac aaagaagtca catgtgagag     64860
     actgggaagg gagccaagtg caaactagac tgcacagctg gttttaaatg ggttctctga     64920
     gcctgtgtgc ctggaagcat gctacttaga gcagtggatg aggtgggtga gcttcgatcc     64980
     accccccacc ccctcacccc accttgtcct cccgcccccg tcccccctgg aggaggctga     65040
     gtcagaccca tgggataacc actaggggac acttcggctc aaccgcaccc tgcctatctt     65100
     ctactttcag agaaaagaaa ggcccagaag ataaagatct gtaaaatggc caatcgaacc     65160
     tcatctctcc actttcagct gctgcacaac ccttgtgcgc atttaaaaag taaagtacag     65220
     aagataccta aatgtgatct ttaacaaagt tgcagctcag cttgagaatt ggagattcaa     65280
     cagatcatgg gattcctttc gctgttgcca gttcattctt gagctggtct accgtgtaca     65340
     tttcttgact cctttcttta tttctaagct agtgtgcatc ttaaatagga aagaaaatat     65400
     tcaaatccaa attagtatac ttccctatat gttggttcat ttagttagca atttagtaga     65460
     atagtgccat ccttaaaact attccaagct tttggtatga taatcagatg agcccatatg     65520
     taaagtttct aatagtttgg aaactttaat gaccccattc ttttgccaga tatcttcctt     65580
     tcatttctct attaaaaaaa tgattataag aagcagaata aggaacaaac gttcatccat     65640
     agcttagtgg gtaatgcttt gtccagcaac aaatgtgcgt tgagggaact ttataagatg     65700
     tatgctacat aaagggaagg tctcaggatt tttaactgat ggcacttcaa ggtgctctac     65760
     tcaaggcccc acttcctgtt ggcctgcttc ttttataatg gccatgaacc tgttacttta     65820
     aagagtgatg tttatataat gccacttttc ttctgttctg tccttatgat aatgaccatt     65880
     gactcacaaa gggatagttt cctttcatgt ttcatgaagg actcagaggc agaacacatg     65940
     ttccagtagt gatgatccat ttgtgtgata aaattctcca catgtctaag aggcttagtt     66000
     gataagtatt ggtttgtatt tctttggttg ggtttttttt ttaagattat ttttattttt     66060
     atgagtacac tgtagctgtc ttcagataca caccagaaga gggcatcaga tcccattaca     66120
     gatggttgtg agccaccttg tggctgctgg gaactgaact cagtggttaa gagcactgac     66180
     tgctcttaac cactgagcca tctctccagc cctcgtattt gtttgtattg gtagtattca     66240
     tcagtgttag atcctctccc tctccctaac tctctaaagt ctcttagttc caaacagcat     66300
     tgagactgag tgggtgtgca ttcccttagg taggagaaaa gtttggcagt tctgaatgcc     66360
     agtgtgagaa tgactggtct tgacagaaac atgtcccaat gataaaagct actgtgactt     66420
     atggcgtgtc attctgtacc tataactgtc tactgcatcc tcctacagaa tgccctctga     66480
     ttagagctaa agtaacctgc aacatcccaa atgagactca gagttttaac actcacaaag     66540
     ccgatgagtc tctagtctca taggacttct gttctaaaca aaattcatat tccttcagtg     66600
     acatctttat ctgttgagga aataataggg atatcaactc aaagtagttg gcattttggc     66660
     cttgggaggg ttactttctg actactgtga catgacaagg gcagggagac atctcagttg     66720
     gtggagaact taccattgaa agcatgagaa cctgagttca gaattctaag cattcctata     66780
     aagaatcggc agccaggcat tgatgctcag agagtagaga ggaaacaggc agatgccctg     66840
     agcttactct tcaatattct agttgtgttt gatgaaaaag tctgtttaaa aataaaatat     66900
     tgcagctcca caggtatagc cacatacaca tttacataca cacccacaat acacacacac     66960
     acacacacac acacacacac acacacacac acatacatga atacaaagac gacacaagaa     67020
     agagaagaaa tgaataatag catctaatgc tcatgttgat tatgcctctg gtccagaaaa     67080
     gggccttcat gaatgccaaa tccttgctct tataacctag atactattgt tccattttat     67140
     gggtgaggaa gcaagttcac atggtcgaaa ggagccgagg atagggggtt gagctcacat     67200
     caaactgttg tgatttttac ctgatttttc aatcttctgc tccaaagatg ctccatagga     67260
     ggtggggaaa aaacattatt taaagcaatg tttccttttt acaaaacagt agtataaaac     67320
     aatgtgtagc aagacaatag aggtaacccc aggatctgat gggtttggtg ttgttgggtt     67380
     ggattgagtt ggattggatt gggttgggtt gnnnnnnnnn nnnnnnnnnn nnnnnnnnnn     67440
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn     67500
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn     67560
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn     67620
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnntt     67680
     gaattattaa ctaaaaacct gaccatctgt atgtttctca aagaattcaa gactccaaac     67740
     cctccttaag ataggttggt gaggcataag atacaaaagg ctgagggcca gtgttagaat     67800
     cggctggcac agtacctaga aggaatcagt actggcatcc tacagcacaa gaaccaaggg     67860
     gaaggtggtt ataaattcta agattttgtt gtatcccatg taaagaacta caagagagca     67920
     tgaacgctag cataataaag aaataatgat tcaatacctg caaaggtatt gaaatactac     67980
     tctgttcagt catggcatat gagtatcaag ttaattatct atcacacact ggctaaaaaa     68040
     cataagggat aaatgaatcg cttaaagaca taaatggata tagaaaacca caacaactta     68100
     atggccgctt atctttctta tttgcaggaa gtacatttga agaacacaag tagaggaagt     68160
     gcaggaaaca agacctacag aatgtaggag gagcctccca cggagcagaa aatgccacat     68220
     caccgcagga tcctttgctg cttgagcaac ctgcaaaaca tcgaaacacc taccaaataa     68280
     caataataag tccaataaca ttacaaagat gggcatttcc cccaatgaaa tatacaagta     68340
     aacattccaa catcgtcttt aggagtgttt gtttaaaaag ctttgcacct tgcaaaagtg     68400
     gtcctggcgt gggtagattg ctgttggtcc tttatcaata acattctata gagaaaaaaa     68460
     atatatatat aactatatct cctagtccct gcctctaaag agccgaaaat gcatggatgt     68520
     tgtagagatc cagttgctct aagtttctct ctgaattttg gctgctgaag ccattcattt     68580
     agcaactgtg tagaggtggt ttatgaatgg ttcccttatc ttcacctctt cccacgtagc     68640
     tcaagctgct tgttttacag agtctaatca tcttgtctag ctgcattaga cacacccttt     68700
     cctaacactt gtatttgttg aatttggcct ccttaagagc aatagcaaat aagtagtcaa     68760
     gtggcctacc aagttttaac gtacctgact ccatctgtgg catttgtacc aaatataagt     68820
     tgaatgcatt tattttagac acaaagcttt attttttttg acattgtgtt tcaagaaaaa     68880
     aaatagaata acaataacta caactttgag gccaatcatt tttaggtgtg tgtttgaagc     68940
     atagaacgtc tcttaaactc tcaatggttt cttcaaatga taagttagta tgtaacctaa     69000
     gtatagcagt ttctctcttt tttatttttt tccatataga gcactatgta aagttagtat     69060
     atcaataata caggaaatat caaacagtat gtaaaactct gttgttgttg ttttttagta     69120
     caatggtgct attttgtagt ttgttatatg aaagaatcta gtcaacacag taaaaggaga     69180
     aagcaaagca aaaacaacaa acgaaagcct ggagcctaag atgacaaaac gaggaaggga     69240
     actgaaaaaa aaaatccttc ctcttgggag atgcaaaggc ctccccaatt atgccttcca     69300
     agaagaactt aagatataga gtccattaag acgcacttac ttgtcaagtc cagagaggaa     69360
     gctatggagt gggaaaagca agaggctagg gatttgggag tcctggtttc tttttaatca     69420
     ctgaagaagt aagtatttgc aacctgggtc acacaaactc accaccctgt gacctcagtc     69480
     aaatcactcc acctatcggt gcctcagttt tcctcatctg caaaatgnnn nnnnnnnnnn     69540
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn     69600
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnngtagacc ttcagatttt     69660
     tgttctgggt ttccaggagg gtgcaacatc agaacccttg aattgctagg atgcaaggaa     69720
     ttctgtaaat aacccactaa caatgtagct ccaaggatca ttcatctgtc actgggatgc     69780
     caccacaata tccaagttct tattggtgaa gctgtgcaac taattagtga caagctaagg     69840
     actcagtctc cccagcatgt cacacggcag gagacatttg atttgcagtt ttatttaact     69900
     tctgcatttg agcttatgac tataaagact agtgaaaaga agggagagag gagaaagaag     69960
     atccttgcca agtaaagggt aattaattat tattccattt atccactctc attaaagggt     70020
     aattaattat tccatgtatc cactctcatt aatccttcca gtcacttagt atctagaaat     70080
     aactctaaca ttgtcaatga gactctactc agtttgccaa acacaattct ccttccccat     70140
     agcatatgaa aaaaaggcgc tgacattctt aaattttgaa atagtatcta ttacaatcac     70200
     aggttgctgt agcagatgta gtcttgccct tgtttgtaca tgcatgtatt ttttttttaa     70260
     ttttatgaaa atgtgctagc aagaattgct acttgagggg caaaattctt ccttctcaag     70320
     cctgaggttc tccctagtgt ctgcttagaa ggaaggatcc agcttcctgg aaatgtgttg     70380
     gatgcattca actgggcatt gctaaccaaa aacatttaga aaaatgttct ctatgtatat     70440
     agcaagattg tctccctctt ttaaaaacaa aatccaatat tcacatctta ttacctacaa     70500
     ccttgattct ctattgcaag cttccttaat attcttataa aatgtattaa gaaaaacaaa     70560
     aaggacacct ttagctctcc ttccgccagg ttgcctctag aatctctggg gaaatgcaga     70620
     aggtgctgtt gagtaaagcc ctcagaagga ttggatttag gaacatcagg cacgctgtac     70680
     atcccctgat tactgtagaa atgtaaatgg aataagaggt cagctgacca tccacctgct     70740
     tccccagaag gatacaggga aaagttaggc cctcacacac cctgggtgac acttctgact     70800
     tctagttctt gttcacagtg tgtacttttt caaattggta attcccagaa aaacacatag     70860
     gtggccttct ccagatctgt gggcttcctg ccatggttgg atttggtgat tccaagtgtc     70920
     tatcacatat tttgttcact taattctatc cacagtcaga aattctttca atgaggaaag     70980
     tttaaatatg caatccttta tccaatacct aattctctcc aactgcatca taaatcaagt     71040
     aataaaaatt aattgtacta attaatcata ataatgtacc attgtacttt taaatgaatg     71100
     aacactgcaa gacaaatcta tgtaaactct gaaaagtaac tgatcattat atggtgaatc     71160
     aaaatgactc aagattgata gaaagggaca tttaaaattt tacaactcaa aattttgtag     71220
     actttgctat ggaggtaaat tgttttagtg ccta                                 71254
//
From achurbanov at yahoo.com  Thu Jan 30 14:07:22 2003
From: achurbanov at yahoo.com (Alexander Churbanov)
Date: Thu Jan 30 16:58:49 2003
Subject: [Biojava-l] Problems with SAX parsing
Message-ID: <20030130220722.20676.qmail@web14310.mail.yahoo.com>

   Hello Matthew or Thomas,

   I just use SAX BLAST parser to parse a massive of
BLAST output. Unfortunately this package does a really
poor job in a batch mode. It runs out of memory
because of the recursive self-calls which adversely
affects the heap.
   I know that you have borrowed this from another
team, but are there any ways to fix it, outherwise I
run into strange situation while parsing 18,000 Blast
runs.
   Sincerely,

   Alexander Churbanov

__________________________________________________
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From simon.brocklehurst at cambridgeantibody.com  Fri Jan 31 11:40:29 2003
From: simon.brocklehurst at cambridgeantibody.com (Simon Brocklehurst)
Date: Fri Jan 31 06:32:29 2003
Subject: [Biojava-l] Problems with SAX parsing
References: <20030130220722.20676.qmail@web14310.mail.yahoo.com>
Message-ID: <3E3A60AD.2050205@cambridgeantibody.com>



Alexander Churbanov wrote:
>    Hello Matthew or Thomas,
> 
>    I just use SAX BLAST parser to parse a massive of
> BLAST output. Unfortunately this package does a really
> poor job in a batch mode. It runs out of memory
> because of the recursive self-calls which adversely
> affects the heap.
>    I know that you have borrowed this from another
> team, but are there any ways to fix it, outherwise I
> run into strange situation while parsing 18,000 Blast
> runs.

We've heard of this before - this *may* be due to an old bug that was 
*supposed* to have been fixed in the biojava code base long ago i.e. 
something not getting popped of a stack when it should be.  Should be 
easy to fix if this bug is somehow still in the biojava code.

If could e-mail the code of the ContentHandler you are using it would be 
helpful. It would be useful to confirm that the problem you are 
experiencing is nothing to do with object creation *outside* of the SAX 
driver itself.

An obvious work around for your problem is to split the blast output 
into smaller chunks.

Simon
-- 
Dr Simon M. Brocklehurst, Ph.D.
Director of Informatics & Robotics

Cambridge Antibody Technology
Milstein Building
Granta Park
Cambridge
CB1 6GH
UK

Telephone: + 44 (0) 1763 263233
Facsimile + 44 (0) 1763 263413
Email: mailto:simon.brocklehurst@cambridgeantibody.com
http://www.cambridgeantibody.com

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From wintas2003 at netscape.net  Fri Jan 31 18:00:53 2003
From: wintas2003 at netscape.net (MR martizega@netscape.net)
Date: Fri Jan 31 11:49:19 2003
Subject: [Biojava-l] winning notification
Message-ID: <200301311649.h0VGnE7E021139@pw600a.bioperl.org>

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From support at biotaq.com  Fri Jan 31 13:06:06 2003
From: support at biotaq.com (support@biotaq.com)
Date: Fri Jan 31 12:58:12 2003
Subject: [Biojava-l] 
 CHI's PepTalk event piques the interest ofproteomics researchers 
Message-ID: <001f60606181f13VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net>

Cambridge Healthtech Institute's PepTalk event piques the interest
ofproteomics researchers

This four-day event took place January 13-16, 2003 in San Diego,
California and delivered the ideal
mix of science, discussion and networking missing from many recent
proteomic events. Over 600
protein researchers and biotech business leaders experienced the expanded
agenda at PepTalk 2003.

The first two days of PepTalk was composed of three concurrent tracks on
Protein Arrays, Protein
Informatics and Protein Expression. All three of these tracks were busy
and attendees showed their
enthusiasm by asking many questions during each session panel discussions.
Over 60% of those
participating in the track sessions stayed on to hear the latest on the
Human Proteome Project
including updates on HUPO's five initiatives.  Attendees at the two days
of the Human Proteome
Project forum were presented with true insight into the future of
proteomics and were active partici-
pants in defining the future of the Human Proteome Project.

Click here to be receive details on next year’s event:
http://www.chi-peptalk.com/info.asp

Here's what attendees were saying about the event:

"Once again CHI has produced another successful conference. I always find
that CHI has a good
balance of excellent talks and a comprehensive exhibit hall with all the
key people in attendance.
PepTalk proved to be successful for us."


Russell Wheatcroft, Technology Networks Ltd

"I would recommend my colleagues attend the next Peptalk conference.
Holding the conference
in San Diego in January is the best place and time for us. I really
enjoyed the conference
and learned a great deal."


Rick Chu, Ph.D., Aventis Pharmaceuticals, Inc.

The meeting also included great opportunities for networking including
receptions, multiple breaks as well
as the one of a kind Proteins in 3D keynote. Exhibiting companies
exhibiting were thrilled by both the volume and quality of visitors that
stopped by their booths. Many exhibitors have already reserved their booth
space for next year's event.

Read two articles about the event at

http:// www.proteomonitor.com:

ARTICLE TITLES:

Arrays, Expression, and Informatics: Proteins get PepTalk at CHI meeting

HUPO, Opening It's Umbrella, Reports Progress on Initiatives, Adds
Education

CHI is determined to deliver the latest and most exciting proteomic
science at PepTalk. We appreciate all those that participated at this
year's event.

Special thanks to all our 2003 Sponsors:

VivaScience
Invitrogen
NonLinear
Physiome Sciences
Confirmant
Accelrys
Cipheragen


PEPTALK 2004
January 12-15, 2004
San Diego, California
http://www.chi-peptalk.com
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