From adionne at warnex.ca  Tue Jun  1 12:10:04 2004
From: adionne at warnex.ca (Alexandre Dionne Laporte)
Date: Tue Jun  1 12:13:11 2004
Subject: [Biojava-l] Biojava uses which BioSQL shema version ?
Message-ID: <AC2F1EEFE1C8C648BE52A1B0BE76BCC612D1E6@hermes.warnex.ca>


Hi and thanks for for the reply,

I have reloaded the biosql-db schema to mysql and I have inserted one sequence form a Genbank format with the 'load_seqdatabase.pl' perl script.

When I try to fetch this entry for the first time with Biojava1.4pre1 I get this error :

---------------------------------------------------------------------------------
*** Importing a core ontology -- hope this is okay
*** Importing terms
org.biojava.bio.BioException: Error accessing ontologies
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:238)
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:193)
        at ca.warnex.sab.util.helpers.biosqlTest.main(biosqlTest.java:49)
Caused by: java.sql.SQLException: General error,  message from server: "Table 'bioseqdb.term_relationship_term' doesn't exist"
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:2236)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1741)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1588)
        at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:205)
        at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:205)
        at org.biojava.bio.seq.db.biosql.OntologySQL.persistTriple(OntologySQL.java:616)
        at org.biojava.bio.seq.db.biosql.OntologySQL.processTerm(OntologySQL.java:262)
        at org.biojava.bio.seq.db.biosql.OntologySQL.processTerm(OntologySQL.java:251)
        at org.biojava.bio.seq.db.biosql.OntologySQL.addCore(OntologySQL.java:218)
        at org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java:396)
        at org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL(OntologySQL.java:71)
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:236)
        ... 2 more
--------------------------------------------------------------------------------

which added a row with '__core_ontology' in the table 'ontology';

When I try to fetch the entry for a second time, I get:

------------------------------------------------------------------------------------------
Exception in thread "main" org.biojava.bio.BioError: Invalid term id 4
        at org.biojava.bio.seq.db.biosql.OntologySQL.termForID(OntologySQL.java:691)
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.getOntologyTerm(BioSQLSequenceDB.java:951)
        at org.biojava.bio.seq.db.biosql.FeaturesSQL.retrieveFeatures(FeaturesSQL.java:155)
        at org.biojava.bio.seq.db.biosql.BioSQLAllFeatures.getFeatures(BioSQLAllFeatures.java:145)
        at org.biojava.bio.seq.db.biosql.BioSQLAllFeatures.features(BioSQLAllFeatures.java:73)
        at org.biojava.bio.seq.db.biosql.BioSQLSequence.features(BioSQLSequence.java:237)
        at ca.warnex.sab.util.helpers.biosqlTest.main(biosqlTest.java:62)
------------------------------------------------------------------------------------------

The fourth Ontology row is the one with '__core_ontology' in its name.

Any Ideas???
Are you sure the biosql-db schema (biosqldb-mysql.sql v. 1.38) is the wright one to use ?

Alexandre D.L.


-----Original Message-----
From:	Simon Foote [mailto:simon.foote@nrc-cnrc.gc.ca]
Sent:	Tue 6/1/2004 9:05 AM
To:	Alexandre Dionne Laporte
Cc:	biojava-l@biojava.org
Subject:	Re: [Biojava-l] Biojava uses which BioSQL shema version ?
Hi Alexandre,

That version of biosql schema should work fine with the biojava snapshot 
you have.
To load a Genbank file into the database, the following code should do 
the trick with the various variables set and error handling code added:

BioSQLSequenceDB bsd = new BioSQLSequenceDB(driver, url, user, password, 
biodatabase, create);
BufferedReader br = new BufferedReader(new FileReader(inFile));
SequenceIterator si = SeqIOTools.readGenbank(br);
Sequence seq = (Sequence) si.nextSequence();
bsd.addBioEntry(seq);

To write it in Genbank format you can use the getSequence() and 
appropriate writeSequence() method for the format you want.

Cheers,
Simon

Alexandre Dionne Laporte wrote:

>Hi,
>
>First of all, here are the softwares I use:
>
>1) Biojava snapshot 'biojava-20040528'
>2) latest biosql shema : biosqldb-mysql.sql v. 1.38
>3) Some of Bioperl 1.4 and bioperl-db projects
>
>
>I would like to store entries from a Genbank file from the NCBI to the
>BioSQL schema using biojava. That I can do with the 'load_seqdatabase.pl'
>script found in bioperl-db without any problem. 
>
>In a same way, I would like to retreive sequences with the Biojava package
>and dump it in Genbank file format, as I can do with 'bioentry2flat.pl'
>script.
>
>My question is : Which version of biosqldb should I use with the biojava
>snapshot ?
>
>Thanks,
>
>Alexandre D.L.
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l@biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>  
>

-- 
Bioinformatics Programmer
Pathogen Genomics
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote@nrc-cnrc.gc.ca





From gwu at molbio.mgh.harvard.edu  Wed Jun  2 11:21:59 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Wed Jun  2 11:23:07 2004
Subject: [Biojava-l] Genbank ASN.1 or XML parser
Message-ID: <AAEKLJJMIGMKFDEIPJFEMEDHCLAA.gwu@molbio.mgh.harvard.edu>

Hi everyone,

I just tried out the APIs for parsing Genbank format files. Though it works
well, I still wonder if there are APIs for parsing Genbank files in ASN.1 or
XML formats because the Genbank format was designed for human being and the
ASN.1 and XML formats should be more reliable for data exchange.

Gang Wu

From gwu at molbio.mgh.harvard.edu  Wed Jun  2 18:42:48 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Wed Jun  2 18:43:56 2004
Subject: [Biojava-l] BioSQL exception
Message-ID: <AAEKLJJMIGMKFDEIPJFEAEDMCLAA.gwu@molbio.mgh.harvard.edu>

When I tested the biosql.UploadFlat under the demos folder, got the
following exception. Seems the code can not find MySQL driver. Can anyone
tell me what I should do or where I can find related docs? Thanks.

===================================================
C:\java -cp
%CLASSPATH%;C:\development\src\lib\biojava-1.4pre1.jar -Djdbc.drivers=C:\dev
elopment\src\lib\mysql-connector-java-3.0.11-stable-bin.jar
biosql.UploadFlat jdbc:mysql://localhost root rootPass genbank genbank
C:/development/genome/arabidopsis_thaliana/IV.fcgi
Opening database: genbank
org.biojava.bio.BioException: Error getting datasource
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:
191)
        at biosql.UploadFlat.main(UploadFlat.java:31)
Caused by: java.sql.SQLException: No suitable driver
        at java.sql.DriverManager.getDriver(Unknown Source)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:
188)
        ... 1 more
==================================================
Gang

From mark.schreiber at group.novartis.com  Wed Jun  2 20:59:09 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Wed Jun  2 21:02:26 2004
Subject: [Biojava-l] Genbank ASN.1 or XML parser
Message-ID: <OFDB284D31.518FDB92-ON48256EA8.000505AE-48256EA8.00056AA9@EU.novartis.net>

Hello -

At the moment there are no parsers for XEMBL, GenBankXML or ASN.1, They 
could both be easily made if someone had that time. GenBankXML could 
easily draw on a SAX or DOM parser to pass events to the BioJava 
SequenceBuilders (using some kind of adapter). ASN.1 would need a more 
custom parser but because it is highly structured that shouldn't be too 
hard.

Any volunteers?

- Mark





"Gang Wu" <gwu@molbio.mgh.harvard.edu>
Sent by: biojava-l-bounces@portal.open-bio.org
06/02/2004 11:21 PM
Please respond to gwu

 
        To:     "Bio-Java" <biojava-l@biojava.org>
        cc: 
        Subject:        [Biojava-l] Genbank ASN.1 or XML parser


Hi everyone,

I just tried out the APIs for parsing Genbank format files. Though it 
works
well, I still wonder if there are APIs for parsing Genbank files in ASN.1 
or
XML formats because the Genbank format was designed for human being and 
the
ASN.1 and XML formats should be more reliable for data exchange.

Gang Wu

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



From Mark.Hoebeke at jouy.inra.fr  Thu Jun  3 05:39:12 2004
From: Mark.Hoebeke at jouy.inra.fr (Hoebeke Mark)
Date: Thu Jun  3 05:42:21 2004
Subject: [Biojava-l] Exporting accessions to Genbank files
Message-ID: <1086255552.2334.62.camel@hurd>

Hi all,

In the context of importing/exporting genbank files into/from a database
I stumbled across an oddity :
 - when building a Sequence instance from a genbank file
(SeqIOTools.readGenbank()), the accession is available through the
"ACCESSION" property of its Annotation
 - when exporting a Sequence instance into a genbank file
(SeqIOTools.writeGenBank()), after having intialized the accession
through the "ACCESSION" property, no ACCESSION line is generated.

Wading through the code (stable 1.3 or 1.4pre1) I noticed the following
comment in  GenBankFormat.java :
(...)
 * Added GenBank header	info to	the sequence annotation. The ACCESSION
header
 * tag is not included.	Stored in sequence.getName().
(...)

which I interpreted as "the ACCESSION property is not written to the
file".

To solve my problem I has to resort to the ugly line below :

	annot.setProperty(GenbankProcessor.PROPERTY_GENBANK_ACCESSIONS,acces);

I'm sure there must be a better way. If anyone has a pointer related to
this issue, I'll gladly adopt a cleaner way of coding this.

Thanks 

Mark

-- 
--------------------------Mark.Hoebeke@jouy.inra.fr----------------------
Unit? Statistique & G?nome                                      Unit? MIG
+33 (0)1 60 87 38 03                   T?l.          +33 (0)1 34 65 28 85
+33 (0)1 60 87 38 09                   Fax.          +33 (0)1 34 65 29 01
Tour Evry 2, 523 pl. des Terrasses              INRA - Domaine de Vilvert
F - 91000 Evry                              F - 78352 Jouy-en-Josas CEDEX


From birney at ebi.ac.uk  Thu Jun  3 12:41:25 2004
From: birney at ebi.ac.uk (Ewan Birney)
Date: Thu Jun  3 12:44:43 2004
Subject: [Biojava-l] Genome Informatics meeting.
Message-ID: <Pine.LNX.4.44.0406031739530.27588-100000@pigeon.ebi.ac.uk>


The third Genome Informatics meeting is being held in September at Hinxton
from 22nd-26th September (Hinxton is just outside Cambridge in the UK, and
is where the EBI and Sanger are). This is a meeting focused on large
scale, genome-wide data manipulation and analysis, and I think is a great
forum for people to discuss the aspects of bioinformatics which don't
other wise get alot of air time at other conferences (eg, large scale 
pipelines, or image analysis).


For more information, go to:

http://meetings.cshl.org/2004/2004infouk.htm


Abstracts are due by June 30th which is pretty soon, but it is pretty easy 
to put together an abstract for this (2 or so paragraphs). The meeting is 
run in "cold spring harbor" manner; ie, all the talks are drawn from open
abstract submission.


If people have any queries about the meeting, just drop me a line.




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


From gwu at molbio.mgh.harvard.edu  Thu Jun  3 12:52:52 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Thu Jun  3 12:53:57 2004
Subject: [Biojava-l] Genbank ASN.1 or XML parser
In-Reply-To: <OFDB284D31.518FDB92-ON48256EA8.000505AE-48256EA8.00056AA9@EU.novartis.net>
Message-ID: <AAEKLJJMIGMKFDEIPJFEAEDPCLAA.gwu@molbio.mgh.harvard.edu>

Hi,

I would be glad to write the parser. Since I am pretty new to BioJava
project, can anybody give me a guide on how to start? Thanks.

- Gang


-----Original Message-----
From: mark.schreiber@group.novartis.com
[mailto:mark.schreiber@group.novartis.com]
Sent: Wednesday, June 02, 2004 8:59 PM
To: gwu@molbio.mgh.harvard.edu
Cc: Bio-Java; biojava-l-bounces@portal.open-bio.org
Subject: Re: [Biojava-l] Genbank ASN.1 or XML parser


Hello -

At the moment there are no parsers for XEMBL, GenBankXML or ASN.1, They
could both be easily made if someone had that time. GenBankXML could
easily draw on a SAX or DOM parser to pass events to the BioJava
SequenceBuilders (using some kind of adapter). ASN.1 would need a more
custom parser but because it is highly structured that shouldn't be too
hard.

Any volunteers?

- Mark





"Gang Wu" <gwu@molbio.mgh.harvard.edu>
Sent by: biojava-l-bounces@portal.open-bio.org
06/02/2004 11:21 PM
Please respond to gwu


        To:     "Bio-Java" <biojava-l@biojava.org>
        cc:
        Subject:        [Biojava-l] Genbank ASN.1 or XML parser


Hi everyone,

I just tried out the APIs for parsing Genbank format files. Though it
works
well, I still wonder if there are APIs for parsing Genbank files in ASN.1
or
XML formats because the Genbank format was designed for human being and
the
ASN.1 and XML formats should be more reliable for data exchange.

Gang Wu

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




From mark.schreiber at group.novartis.com  Thu Jun  3 21:48:49 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Thu Jun  3 21:52:02 2004
Subject: [Biojava-l] Genbank ASN.1 or XML parser
Message-ID: <OF673CD307.B438F39A-ON48256EA9.0008EDE9-48256EA9.0009F6C1@EU.novartis.net>

Hi -

The general pattern of input in Biojava is:

BufferedReader -> SequenceFormat -> SeqIOListener -> SequenceIterator.

A specific example would be:

BufferedReader -> FastaFormat -> SequenceBuilderFactory -> 
SequenceIterator


The format object is responsible for parsing the input and generating 
events that the SequenceBuilderFactory listens for and uses to build one 
or more Sequence objects. The SequenceFormat implementation usually draws 
on a SymbolTokenization object which determines how characters are mapped 
to biojava Symbols (eg a is mapped to adenosine).


Basically you make a parser that emits callback events to a registered 
SeqIOListener. If the listener is a SequenceBuilderFactory it generates 
Sequence objects base on those events. It is very similar to the SAX API 
for XML parsing.

Hope this helps,

Mark







"Gang Wu" <gwu@molbio.mgh.harvard.edu>
06/04/2004 12:52 AM
Please respond to gwu

 
        To:     Mark Schreiber/GP/Novartis@PH
        cc:     "Bio-Java" <biojava-l@biojava.org>, 
<biojava-l-bounces@portal.open-bio.org>
        Subject:        RE: [Biojava-l] Genbank ASN.1 or XML parser


Hi,

I would be glad to write the parser. Since I am pretty new to BioJava
project, can anybody give me a guide on how to start? Thanks.

- Gang


-----Original Message-----
From: mark.schreiber@group.novartis.com
[mailto:mark.schreiber@group.novartis.com]
Sent: Wednesday, June 02, 2004 8:59 PM
To: gwu@molbio.mgh.harvard.edu
Cc: Bio-Java; biojava-l-bounces@portal.open-bio.org
Subject: Re: [Biojava-l] Genbank ASN.1 or XML parser


Hello -

At the moment there are no parsers for XEMBL, GenBankXML or ASN.1, They
could both be easily made if someone had that time. GenBankXML could
easily draw on a SAX or DOM parser to pass events to the BioJava
SequenceBuilders (using some kind of adapter). ASN.1 would need a more
custom parser but because it is highly structured that shouldn't be too
hard.

Any volunteers?

- Mark





"Gang Wu" <gwu@molbio.mgh.harvard.edu>
Sent by: biojava-l-bounces@portal.open-bio.org
06/02/2004 11:21 PM
Please respond to gwu


        To:     "Bio-Java" <biojava-l@biojava.org>
        cc:
        Subject:        [Biojava-l] Genbank ASN.1 or XML parser


Hi everyone,

I just tried out the APIs for parsing Genbank format files. Though it
works
well, I still wonder if there are APIs for parsing Genbank files in ASN.1
or
XML formats because the Genbank format was designed for human being and
the
ASN.1 and XML formats should be more reliable for data exchange.

Gang Wu

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







From mark.schreiber at group.novartis.com  Mon Jun  7 00:00:19 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Mon Jun  7 00:03:26 2004
Subject: [Biojava-l] Heat map gradients
Message-ID: <OF3BB80C5B.84C130F6-ON48256EAC.00159DF9-48256EAC.001600CF@EU.novartis.net>

Hi -

Slightly off topic but,

I am making an application that will display a heat map based on the value 
of a variable. I'm wondering if anyone has some sample code for generating 
a color on a gradient between color a and color b (red and green are 
traditional but something generic would be nice) based on the value of the 
variable?

I guess this is the sort of thing you use for microarray displays/ 
correlations etc. Cellular automata in this case but it should be useful 
to others in the list.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

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

phone +65 6722 2973
fax  +65 6722 2910

From dmb at mrc-dunn.cam.ac.uk  Mon Jun  7 05:25:37 2004
From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser)
Date: Mon Jun  7 05:11:52 2004
Subject: [Biojava-l] Heat map gradients 
Message-ID: <Pine.LNX.4.21.0406071024260.1893-100000@mail.mrc-dunn.cam.ac.uk>



A friend of mine in human computer interaction warns against such scales
(I found out when I asked him this exact same question). He prefers a
discrete scale of say 7 colors, which are clearly labeled with their
bounds. This is because we are not very good at judging the significance
of subtle color gradients, and the colors used and the context given can
all play a part in informing our decision. We can more clearly understand
a discrete color 'scale'.

Just one of those things I guess...

Dan.


On Mon, 7 Jun 2004 mark.schreiber@group.novartis.com wrote:

>Hi -
>
>Slightly off topic but,
>
>I am making an application that will display a heat map based on the value 
>of a variable. I'm wondering if anyone has some sample code for generating 
>a color on a gradient between color a and color b (red and green are 
>traditional but something generic would be nice) based on the value of the 
>variable?
>
>I guess this is the sort of thing you use for microarray displays/ 
>correlations etc. Cellular automata in this case but it should be useful 
>to others in the list.
>
>- Mark
>
>Mark Schreiber
>Principal Scientist (Bioinformatics)
>
>Novartis Institute for Tropical Diseases (NITD)
>10 Biopolis Road
>#05-01 Chromos
>Singapore 138670
>www.nitd.novartis.com
>
>phone +65 6722 2973
>fax  +65 6722 2910
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l@biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>

From dmb at mrc-dunn.cam.ac.uk  Mon Jun  7 05:26:11 2004
From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser)
Date: Mon Jun  7 05:12:16 2004
Subject: [Biojava-l] Heat map gradients
In-Reply-To: <OF3BB80C5B.84C130F6-ON48256EAC.00159DF9-48256EAC.001600CF@EU.novartis.net>
Message-ID: <Pine.LNX.4.21.0406071025460.1893-100000@mail.mrc-dunn.cam.ac.uk>


p.s. is their anything like 'matrix2png' for biojava?



On Mon, 7 Jun 2004 mark.schreiber@group.novartis.com wrote:

>Hi -
>
>Slightly off topic but,
>
>I am making an application that will display a heat map based on the value 
>of a variable. I'm wondering if anyone has some sample code for generating 
>a color on a gradient between color a and color b (red and green are 
>traditional but something generic would be nice) based on the value of the 
>variable?
>
>I guess this is the sort of thing you use for microarray displays/ 
>correlations etc. Cellular automata in this case but it should be useful 
>to others in the list.
>
>- Mark
>
>Mark Schreiber
>Principal Scientist (Bioinformatics)
>
>Novartis Institute for Tropical Diseases (NITD)
>10 Biopolis Road
>#05-01 Chromos
>Singapore 138670
>www.nitd.novartis.com
>
>phone +65 6722 2973
>fax  +65 6722 2910
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l@biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>

From thomas at derkholm.net  Mon Jun  7 06:14:35 2004
From: thomas at derkholm.net (Thomas Down)
Date: Mon Jun  7 06:04:51 2004
Subject: [Biojava-l] Heat map gradients
In-Reply-To: <OF3BB80C5B.84C130F6-ON48256EAC.00159DF9-48256EAC.001600CF@EU.novartis.net>
References: <OF3BB80C5B.84C130F6-ON48256EAC.00159DF9-48256EAC.001600CF@EU.novartis.net>
Message-ID: <20040607101435.GA13979@calette.derkholm.net>

On Mon, Jun 07, 2004 at 12:00:19PM +0800, mark.schreiber@group.novartis.com wrote:
> Hi -
> 
> Slightly off topic but,
> 
> I am making an application that will display a heat map based on the value 
> of a variable. I'm wondering if anyone has some sample code for generating 
> a color on a gradient between color a and color b (red and green are 
> traditional but something generic would be nice) based on the value of the 
> variable?
> 
> I guess this is the sort of thing you use for microarray displays/ 
> correlations etc. Cellular automata in this case but it should be useful 
> to others in the list.


This is pretty straightforward in Java, for instance:

      public Color mixColor(Color from, Color to, double amount) {
	  float x = (float) amount;
	  float y = (float) (1.0 - amount);

	  return new Color((int) (y * from.getRed() + x * to.getRed()),
			   (int) (y * from.getGreen() + x * to.getGreen()),
			   (int) (y * from.getBlue() + x * to.getBlue()));
      }

This is nice for 'fluffy' viewing of new data, but for serious
analysis I'd agree with Dan's point about using a discrete scale
instead.

      Thomas.
From MCCon012 at mc.duke.edu  Mon Jun  7 08:20:49 2004
From: MCCon012 at mc.duke.edu (Patrick McConnell)
Date: Mon Jun  7 08:23:57 2004
Subject: [Biojava-l] Heat map gradients
Message-ID: <OF62B39024.B6779280-ON85256EAC.004399D4-85256EAC.0043D388@banquo.mc.duke.edu
	>





One of the problems is that we do not perceive gradient changes in a linear
fashion.

-Patrick McConnell
Duke Bioinformatics Shared Resource
Duke Comprehensive Cancer Center
patrick.mcconnell@duke.edu


                                                                                                                                                
                      Dan Bolser                                                                                                                
                      <dmb@mrc-dunn.cam.ac.uk>          To:       mark.schreiber@group.novartis.com                                             
                      Sent by:                          cc:       biojava-l@open-bio.org                                                        
                      biojava-l-bounces@portal.o        Subject:  Re: [Biojava-l] Heat map gradients                                            
                      pen-bio.org                                                                                                               
                                                                                                                                                
                                                                                                                                                
                      06/07/2004 05:25 AM                                                                                                       
                                                                                                                                                
                                                                                                                                                






A friend of mine in human computer interaction warns against such scales
(I found out when I asked him this exact same question). He prefers a
discrete scale of say 7 colors, which are clearly labeled with their
bounds. This is because we are not very good at judging the significance
of subtle color gradients, and the colors used and the context given can
all play a part in informing our decision. We can more clearly understand
a discrete color 'scale'.

Just one of those things I guess...

Dan.


On Mon, 7 Jun 2004 mark.schreiber@group.novartis.com wrote:

>Hi -
>
>Slightly off topic but,
>
>I am making an application that will display a heat map based on the value

>of a variable. I'm wondering if anyone has some sample code for generating

>a color on a gradient between color a and color b (red and green are
>traditional but something generic would be nice) based on the value of the

>variable?
>
>I guess this is the sort of thing you use for microarray displays/
>correlations etc. Cellular automata in this case but it should be useful
>to others in the list.
>
>- Mark
>
>Mark Schreiber
>Principal Scientist (Bioinformatics)
>
>Novartis Institute for Tropical Diseases (NITD)
>10 Biopolis Road
>#05-01 Chromos
>Singapore 138670
>www.nitd.novartis.com
>
>phone +65 6722 2973
>fax  +65 6722 2910
>
>_______________________________________________
>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 gwu at molbio.mgh.harvard.edu  Mon Jun  7 14:26:34 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Mon Jun  7 14:31:43 2004
Subject: [Biojava-l] BioJava, BioSQL versions
In-Reply-To: <OF62B39024.B6779280-ON85256EAC.004399D4-85256EAC.0043D388@banquo.mc.duke.edu>
Message-ID: <AAEKLJJMIGMKFDEIPJFEIEEECLAA.gwu@molbio.mgh.harvard.edu>


Can anybody tell me what versions of BioJava work with what versions of
BioSQL?

Thanks

Gang

From Clemens_Steegborn at gmx.de  Mon Jun  7 17:28:13 2004
From: Clemens_Steegborn at gmx.de (Clemens Steegborn)
Date: Mon Jun  7 17:31:15 2004
Subject: [Biojava-l] reading sequence files
Message-ID: <21257.1086643693@www29.gmx.net>


Hi,

I have problems to extract sequence data from files (Genbank or EMBL) using
BioJava 1.3; I can get sequence names or annotations, but when I try to get
the sequence itself, I get a null pointer exception! Can anybody help?
Thanks ..

Clemens

-- 
-------------------------------
Clemens Steegborn, Ph.D.
Dept. Biochemistry
Cornell Medical School
1300 York Avenue
New York, NY 10021

"Sie haben neue Mails!" - Die GMX Toolbar informiert Sie beim Surfen!
Jetzt aktivieren unter http://www.gmx.net/info

From mark.schreiber at group.novartis.com  Mon Jun  7 21:25:24 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Mon Jun  7 21:28:33 2004
Subject: [Biojava-l] reading sequence files
Message-ID: <OFD0446F4F.C371476F-ON48256EAD.0007A50F-48256EAD.0007D213@EU.novartis.net>

Hi -

Could you post your code and an example GenBank or EMBL accession as well 
so we can get an idea of what might be going wrong? Alternatively you 
might want to look at http://www.biojava.org/docs/bj_in_anger/  for some 
examples of sequence I/O

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

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

phone +65 6722 2973
fax  +65 6722 2910





"Clemens Steegborn" <Clemens_Steegborn@gmx.de>
Sent by: biojava-l-bounces@portal.open-bio.org
06/08/2004 05:28 AM

 
        To:     biojava-l@biojava.org
        cc: 
        Subject:        [Biojava-l] reading sequence files



Hi,

I have problems to extract sequence data from files (Genbank or EMBL) 
using
BioJava 1.3; I can get sequence names or annotations, but when I try to 
get
the sequence itself, I get a null pointer exception! Can anybody help?
Thanks ..

Clemens

-- 
-------------------------------
Clemens Steegborn, Ph.D.
Dept. Biochemistry
Cornell Medical School
1300 York Avenue
New York, NY 10021

"Sie haben neue Mails!" - Die GMX Toolbar informiert Sie beim Surfen!
Jetzt aktivieren unter http://www.gmx.net/info

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



From mark.schreiber at group.novartis.com  Mon Jun  7 21:27:12 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Mon Jun  7 21:30:36 2004
Subject: [Biojava-l] BioJava, BioSQL versions
Message-ID: <OF64B5C4E2.D4D7C852-ON48256EAD.0007D94A-48256EAD.0007FC44@EU.novartis.net>

My understanding is that biojava 1.3.x is not compatable with the more 
recent versions of biosql. To use the current biosql I reccommend getting 
one of the nightly snapshots or the pre release version of biojava 1.4

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

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

phone +65 6722 2973
fax  +65 6722 2910





"Gang Wu" <gwu@molbio.mgh.harvard.edu>
Sent by: biojava-l-bounces@portal.open-bio.org
06/08/2004 02:26 AM
Please respond to gwu

 
        To:     <biojava-l@open-bio.org>
        cc: 
        Subject:        [Biojava-l] BioJava, BioSQL versions



Can anybody tell me what versions of BioJava work with what versions of
BioSQL?

Thanks

Gang

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



From gwu at molbio.mgh.harvard.edu  Tue Jun  8 17:26:52 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Tue Jun  8 17:31:56 2004
Subject: [Biojava-l] BioJava, BioSQL versions
In-Reply-To: <OF64B5C4E2.D4D7C852-ON48256EAD.0007D94A-48256EAD.0007FC44@EU.novartis.net>
Message-ID: <AAEKLJJMIGMKFDEIPJFEEEEJCLAA.gwu@molbio.mgh.harvard.edu>

Dear All,

I am using the latest nightly built Biojava(biojava-20040608.jar) and BioSQL
v1.38 for MySQL. When I tried the following code:
=================================================================
    public static void main (String [] args) throws Exception {
       BioSQLSequenceDB bdb = new BioSQLSequenceDB(
            "com.mysql.jdbc.Driver",
            "jdbc:mysql://mysql_server_ip/biosqldb",
            "root",
            "password","biosqldb", true);
    }
=================================================================

I got the following exceptions:
============================================================================
=============
*** Importing a core ontology -- hope this is okay
*** Importing terms
Exception in thread "main" org.biojava.bio.BioException: Error accessing
ontologies
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:
238)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:
164)
        at biosql.MyTest.main(MyTest.java:13)
Caused by: java.sql.SQLException: Base table or view not found,  message
from server: "Table 'biosqldb.term_relationship_term' doesn't exist"
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1905)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1109)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1203)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:2090)
        at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1680)
        at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1527)
        at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating
PreparedStatement.java:233)
        at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating
PreparedStatement.java:233)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTriple(OntologySQL.java:616
)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.processTerm(OntologySQL.java:262)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.processTerm(OntologySQL.java:251)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.addCore(OntologySQL.java:218)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java:396)
        at
org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL(OntologySQL.java:71
)
        at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:
236)
        ... 2 more
============================================================================
================
I guess the message means it can find the MySQL driver and the database, but
the Java APIs does not match the BioSQL schema.
Does the "Table 'biosqldb.term_relationship_term' doesn't exist" mean I'm
using a wrong version of BioSQL? Anybody has any idea about it? Help is
needed and deeply  appreciated.

Gang


-----Original Message-----
From: mark.schreiber@group.novartis.com
[mailto:mark.schreiber@group.novartis.com]
Sent: Monday, June 07, 2004 9:27 PM
To: gwu@molbio.mgh.harvard.edu
Cc: biojava-l@open-bio.org; biojava-l-bounces@portal.open-bio.org
Subject: Re: [Biojava-l] BioJava, BioSQL versions


My understanding is that biojava 1.3.x is not compatable with the more
recent versions of biosql. To use the current biosql I reccommend getting
one of the nightly snapshots or the pre release version of biojava 1.4

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

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

phone +65 6722 2973
fax  +65 6722 2910





"Gang Wu" <gwu@molbio.mgh.harvard.edu>
Sent by: biojava-l-bounces@portal.open-bio.org
06/08/2004 02:26 AM
Please respond to gwu


        To:     <biojava-l@open-bio.org>
        cc:
        Subject:        [Biojava-l] BioJava, BioSQL versions



Can anybody tell me what versions of BioJava work with what versions of
BioSQL?

Thanks

Gang

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




From len at reeltwo.com  Wed Jun  9 17:26:54 2004
From: len at reeltwo.com (Len Trigg)
Date: Wed Jun  9 17:30:09 2004
Subject: [Biojava-l] BioJava, BioSQL versions
In-Reply-To: <AAEKLJJMIGMKFDEIPJFEEEEJCLAA.gwu@molbio.mgh.harvard.edu>
References: <OF64B5C4E2.D4D7C852-ON48256EAD.0007D94A-48256EAD.0007FC44@EU.novartis.net>
	<AAEKLJJMIGMKFDEIPJFEEEEJCLAA.gwu@molbio.mgh.harvard.edu>
Message-ID: <hb1xkoe82p.wl%len@reeltwo.com>

"Gang Wu" <gwu@molbio.mgh.harvard.edu> wrote:
> I got the following exceptions:
> Exception in thread "main" org.biojava.bio.BioException: Error accessing
> ontologies
> Caused by: java.sql.SQLException: Base table or view not found,  message
> from server: "Table 'biosqldb.term_relationship_term' doesn't exist"

The BioJava Ontologies require an extra table in the schema, which
isn't part of the official BioSQL (this should *really* be resolved,
guys). A bit of searching on the archives will reveal more (I don't
recall the details myself).

It should also be possible to postpone creation of the core ontology
until it's actually needed, since many applications don't use it at
all (I've never used them).


Cheers,
Len.
From gwu at molbio.mgh.harvard.edu  Fri Jun 11 13:28:33 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Fri Jun 11 13:33:32 2004
Subject: [Biojava-l] BioJava, BioSQL versions
In-Reply-To: <hb1xkoe82p.wl%len@reeltwo.com>
Message-ID: <AAEKLJJMIGMKFDEIPJFEMEENCLAA.gwu@molbio.mgh.harvard.edu>

Hi,

Just searched the archive and found the extra table term_relationship_term
as following. And then the demo code works. Should some lines be added in
the BioJava package document? There is no way for new BioJava developers to
use it witout explaining what's missing in the BioSQL schema. Thanks for the
helps from all of you.

==================================================================
CREATE TABLE term_relationship_term (
    term_relationship_id INTEGER NOT NULL,
    term_id INTEGER NOT NULL,
        PRIMARY KEY ( term_relationship_id, term_id ),
        UNIQUE ( term_relationship_id ),
        UNIQUE ( term_id ) );
==================================================================

Thanks,
Gang


-----Original Message-----
From: Len Trigg [mailto:len@reeltwo.com]
Sent: Wednesday, June 09, 2004 5:27 PM
To: gwu@molbio.mgh.harvard.edu
Cc: mark.schreiber@group.novartis.com; biojava-l@open-bio.org
Subject: Re: [Biojava-l] BioJava, BioSQL versions


"Gang Wu" <gwu@molbio.mgh.harvard.edu> wrote:
> I got the following exceptions:
> Exception in thread "main" org.biojava.bio.BioException: Error accessing
> ontologies
> Caused by: java.sql.SQLException: Base table or view not found,  message
> from server: "Table 'biosqldb.term_relationship_term' doesn't exist"

The BioJava Ontologies require an extra table in the schema, which
isn't part of the official BioSQL (this should *really* be resolved,
guys). A bit of searching on the archives will reveal more (I don't
recall the details myself).

It should also be possible to postpone creation of the core ontology
until it's actually needed, since many applications don't use it at
all (I've never used them).


Cheers,
Len.

From thorsten at photono-software.de  Sat Jun 12 15:52:53 2004
From: thorsten at photono-software.de (Thorsten)
Date: Sat Jun 12 15:54:25 2004
Subject: [Biojava-l] Symbol to Token?
Message-ID: <19639836501.20040612215253@photono-software.de>

Hello,

I simply want to have the textual one letter code of a Protein Symbol.
How can I do this?

Example
Symbol ala = ProteinTools.ala();
//Now I want to print out the one letter code of Alanin:

The desired result should be "A".
Any solutions?

-Th

P.S.:
I need it for  calculating the hydrophobicity of a lot of sequences using a
hydrophobicty scale.

From thorsten at photono-software.de  Sat Jun 12 18:31:29 2004
From: thorsten at photono-software.de (Thorsten)
Date: Sat Jun 12 18:33:01 2004
Subject: [Biojava-l] Symbol to Token?
In-Reply-To: <19639836501.20040612215253@photono-software.de>
References: <19639836501.20040612215253@photono-software.de>
Message-ID: <1049352184.20040613003129@photono-software.de>

ok, I've found it:

SymbolTokenization tok =  ProteinTools.getAlphabet().getTokenization("token");
String str = tok.tokenizeSymbol(sym);

btw:
converting the BioJava-Sequence to a simple string and working with the native
Java String is much faster...

-Th
                

T> Hello,

T> I simply want to have the textual one letter code of a Protein Symbol.
T> How can I do this?

T> Example
T> Symbol ala = ProteinTools.ala();
T> //Now I want to print out the one letter code of Alanin:

T> The desired result should be "A".
T> Any solutions?

T> -Th

T> P.S.:
T> I need it for  calculating the hydrophobicity of a lot of sequences using a
T> hydrophobicty scale.

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





From mark.schreiber at group.novartis.com  Sun Jun 13 21:00:16 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Sun Jun 13 21:03:10 2004
Subject: [Biojava-l] Symbol to Token?
Message-ID: <OFB983FFCC.9519CB2B-ON48256EB3.00057F0B-48256EB3.000584CD@EU.novartis.net>

Faster than what?





Thorsten <thorsten@photono-software.de>
Sent by: biojava-l-bounces@portal.open-bio.org
06/13/2004 06:31 AM
Please respond to Thorsten Schmidt

 
        To:     biojava-l@biojava.org
        cc: 
        Subject:        Re: [Biojava-l] Symbol to Token?


ok, I've found it:

SymbolTokenization tok = 
ProteinTools.getAlphabet().getTokenization("token");
String str = tok.tokenizeSymbol(sym);

btw:
converting the BioJava-Sequence to a simple string and working with the 
native
Java String is much faster...

-Th
 

T> Hello,

T> I simply want to have the textual one letter code of a Protein Symbol.
T> How can I do this?

T> Example
T> Symbol ala = ProteinTools.ala();
T> //Now I want to print out the one letter code of Alanin:

T> The desired result should be "A".
T> Any solutions?

T> -Th

T> P.S.:
T> I need it for  calculating the hydrophobicity of a lot of sequences 
using a
T> hydrophobicty scale.

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





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



From gwu at molbio.mgh.harvard.edu  Mon Jun 14 15:35:37 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Mon Jun 14 15:38:26 2004
Subject: [Biojava-l] BioSQL successes, failures and questions
In-Reply-To: <OFB983FFCC.9519CB2B-ON48256EB3.00057F0B-48256EB3.000584CD@EU.novartis.net>
Message-ID: <AAEKLJJMIGMKFDEIPJFEGEFCCLAA.gwu@molbio.mgh.harvard.edu>

Hi everyone,
I finally can make BioSQL 1.38(MySQL) work with
BioJava(biojava-20040608.jar). Hope my frustrating learning experience can
help other new developers a little bit. I deeply appreciate it if any
experienced developers can answer my new questions.

Before you can start, you have to create a database and user later you are
going to use to connect to the database. Please refer MySQL mannual if you
don't know how to do it.

  1. Run the standard BioSQL 1.38 schema to create an empty sequence
database. I changed the unique key term.name(UNIQUE `name`
(`name`,`ontology_id`)) to key (KEY `name` (`name`,`ontology_id`)) since
later when I tried to upload sequences I got duplicate value exceptions. Any
suggestions on this?

  2. Run the "term_relationship_term" table creation schema. Without this
table, the BioJava package will throw exceptions. See ATTACHMENT 1 at the
end of this message.

  3. Create the "biodatabase" entry. Say you are uploading Genbank files,
you need create an entry in biodatabase table with value of "genbank" for
the "name" column.

  4. If you are trying to upload flat files such as Genbank files, try
ATTACHMENT 2, derived from the demo code UploadFlat.java. If the new
BioSQLSequenceDB() line does not work, try another constructor with
"dbDriver" parameter. I put all required jar files in the
JDK_ROOT/jre/lib/ext so JVM can load them automatically. BioJava needs very
much RAM. I suggest put the Xmx???m to be 10 times big as the Genbank file.
Say you have a Genbank file of 40 MB, use "java -Xmx400m
your_file_full_path".

I just uploaded the 5 Genbank genome files of Arabidopsis thaliana and it
works pretty well. Though digging information from the tables needs a lot
joins(especially with term table), it's still much much easier than writing
your own code. So far, I'm happy with it.


Questions:

1. How can I quickly pull certain pieces of sequence  from the biosequence
table? I tried to join the seqfeature, seqfeature_qualifier_value, location,
biosequence, term tables to retrieve all gene sequences. It turned out to be
not doable because the substring function is extremely slow when applying on
the 'seq' column. The following SQL takes about 20 seconds on a dual Xeon
2.6G Dell PowerEdge 2650 server and the required time varies when the gene
locations are different.

SELECT t1.seqfeature_id,t1.bioentry_id,t2.start_pos, t2.end_pos, t2.strand,
t4.value locus_tag,
substring(t6.seq, t2.start_pos,t2.end_pos) seq
FROM `seqfeature` t1 inner join location t2 on
t1.seqfeature_id=t2.seqfeature_id
inner join term t3 on t1.type_term_id=t3.term_id
inner join seqfeature_qualifier_value t4 on
t1.seqfeature_id=t4.seqfeature_id
inner join term t5 on t4.term_id=t5.term_id
inner join biosequence t6 on t1.bioentry_id=t6.bioentry_id
where t3.name='gene' and t5.name='locus_tag'
limit 2


=========================================
ATTACHMENT 1
=========================================
CREATE TABLE `term_relationship_term` (
  `term_relationship_id` int(11) NOT NULL default '0',
  `term_id` int(11) NOT NULL default '0',
  PRIMARY KEY  (`term_relationship_id`,`term_id`),
  UNIQUE KEY `term_relationship_id` (`term_relationship_id`),
  UNIQUE KEY `term_id` (`term_id`)
) TYPE=InnoDB;
========================================

=========================================
ATTACHMENT 2
=========================================
import java.io.*;

import org.biojava.bio.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.db.biosql.*;
import org.biojava.bio.taxa.*;

public class UploadFlat {
    public static void main(String [] args) {
        try {
            String dbDriver="com.mysql.jdbc.Driver";
            String dbURL =
"jdbc:mysql://mysql_server_ip_address_or_domain_name/biosql_database_name";
            String dbUser = "database_user";
            String dbPass = "password";
            String bioDB = "biodatabase.name";
            String format = "genbank"; //you can change this or input from
command line

            System.setProperty("jdbc.drivers", "com.mysql.jdbc.Driver");
            SequenceDB seqDB = new BioSQLSequenceDB(
            dbURL,
            dbUser,
            dbPass,
            bioDB,
            false
            );

            SequenceFormat sFormat;
            SequenceBuilderFactory sbFact;
            Alphabet alpha;

            if ("embl".equalsIgnoreCase(format)) {
                sFormat = new EmblLikeFormat();
                sbFact = new
EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY);
                alpha = DNATools.getDNA();
            } else if ("swissprot".equalsIgnoreCase(format)) {
                sFormat = new EmblLikeFormat();
                sbFact = new SwissprotProcessor.Factory(
                SimpleSequenceBuilder.FACTORY
                );
                alpha = ProteinTools.getAlphabet();
            } else if ("fasta".equalsIgnoreCase(format)) {
                sFormat = new FastaFormat();
                sbFact = new
FastaDescriptionLineParser.Factory(SimpleSequenceBuilder.FACTORY);
                alpha = DNATools.getDNA();
            } else if ("fasta-protein".equalsIgnoreCase(format)) {
                sFormat = new FastaFormat();
                sbFact = new
FastaDescriptionLineParser.Factory(SimpleSequenceBuilder.FACTORY);
                alpha = ProteinTools.getAlphabet();
            } else if ("genbank".equalsIgnoreCase(format)) {
                sFormat = new GenbankFormat();
                sbFact = new
GenbankProcessor.Factory(SimpleSequenceBuilder.FACTORY);
                alpha = DNATools.getDNA();
            }else {
                System.err.println("Unknown format: " + format);
                return;
            }

            SymbolTokenization rParser = alpha.getTokenization("token");

                File swissProtFile = new File(args[0]);
                BufferedReader sReader = new BufferedReader(new
InputStreamReader(new FileInputStream(swissProtFile)));
                SequenceIterator seqI =
                new	StreamReader(sReader, sFormat, rParser,	sbFact);

                while(seqI.hasNext()) {
                    try {
                        System.out.print(".");
                        Sequence seq = seqI.nextSequence();
                        seqDB.addSequence(seq);
                    } catch (Throwable t) {
                        t.printStackTrace(System.out);
                    }
                }
        }
        catch (Throwable t) {
            t.printStackTrace();
            System.exit(1);
        }
    }
}
=========================================

From Clemens_Steegborn at gmx.de  Tue Jun 15 17:04:23 2004
From: Clemens_Steegborn at gmx.de (Clemens Steegborn)
Date: Tue Jun 15 17:07:19 2004
Subject: [Biojava-l] reading sequence files
References: <OFD0446F4F.C371476F-ON48256EAD.0007A50F-48256EAD.0007D213@EU.novartis.net>
Message-ID: <5769.1087333463@www37.gmx.net>


Hi,

I used the bj_in_anger code when I had the sequence I/O problems; and
I found the reason: I used JDK 1.3; worked fine when I switched to 1.4;
Sorry, mea culpa

Clemens

> Hi -
> 
> Could you post your code and an example GenBank or EMBL accession as well 
> so we can get an idea of what might be going wrong? Alternatively you 
> might want to look at http://www.biojava.org/docs/bj_in_anger/  for some 
> examples of sequence I/O
> 
> - Mark
> 
> Mark Schreiber
> Principal Scientist (Bioinformatics)
> 
> Novartis Institute for Tropical Diseases (NITD)
> 10 Biopolis Road
> #05-01 Chromos
> Singapore 138670
> www.nitd.novartis.com
> 
> phone +65 6722 2973
> fax  +65 6722 2910
> 
> 
> 
> 
> 
> "Clemens Steegborn" <Clemens_Steegborn@gmx.de>
> Sent by: biojava-l-bounces@portal.open-bio.org
> 06/08/2004 05:28 AM
> 
>  
>         To:     biojava-l@biojava.org
>         cc: 
>         Subject:        [Biojava-l] reading sequence files
> 
> 
> 
> Hi,
> 
> I have problems to extract sequence data from files (Genbank or EMBL) 
> using
> BioJava 1.3; I can get sequence names or annotations, but when I try to 
> get
> the sequence itself, I get a null pointer exception! Can anybody help?
> Thanks ..
> 
> Clemens
> 
> -- 
> -------------------------------
> Clemens Steegborn, Ph.D.
> Dept. Biochemistry
> Cornell Medical School
> 1300 York Avenue
> New York, NY 10021
> 
> "Sie haben neue Mails!" - Die GMX Toolbar informiert Sie beim Surfen!
> Jetzt aktivieren unter http://www.gmx.net/info
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
> 
> 

-- 
-------------------------------
Clemens Steegborn, Ph.D.
Dept. Biochemistry
Cornell Medical School
1300 York Avenue
New York, NY 10021

"Sie haben neue Mails!" - Die GMX Toolbar informiert Sie beim Surfen!
Jetzt aktivieren unter http://www.gmx.net/info

From matthew_pocock at yahoo.co.uk  Wed Jun 16 07:05:13 2004
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Wed Jun 16 07:08:11 2004
Subject: [Biojava-l] biojava article
Message-ID: <40D02969.1050908@yahoo.co.uk>

from the "blowing our own trumpet" department:

Take a look at java.sun.com today - there's an article about BioJava and 
os and genomics.

Matthew
From Russell.Smithies at agresearch.co.nz  Mon Jun 21 17:34:09 2004
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon Jun 21 17:36:55 2004
Subject: [Biojava-l] Java VM performance.
Message-ID: <D5DBA313349A4B458528BE63B387F36C0BEE40@imail.agresearch.co.nz>

I just read an interesting article that re-ran the benchmark tests for
Java vs. C++. 
http://www.sys-con.com/story/?storyid=45250
According to the author, Keith Lea, "..no one should ever run the client
JVM when given the choice" and "..the Server VM is much faster than the
Client VM,".

Some simple editing of jvm.cfg will cause the server VM to be run for
all applications, unless they are run with the -client argument.

Performance rating (bigger is better)
                     G++ 3.3.1             Java 1.4.2 
               Intel 386 Intel 686  Server JVM    Client JVM 
Ackermann            73%      114%        129%          N/A* 
Fibonacci            88%      101%        132%          88% 
Hash2                79%       77%        168%         115% 
Hash                194%      193%        402%          36% 
Heapsort            101%      104%         94%          99% 
Matrix              157%      155%        111%          54% 
Method call          89%      105%        871%          54% 
Nested loop         165%      138%         89%          64% 
Object creation      62%       65%        241%         215% 
Random no. gen.     145%      204%        102%          54% 
Sieve                97%       98%        107%          97% 
String concatenation 99%      137%         94%          82% 
Sumcol              101%      108%        138%          72% 
Word count           88%       91%        128%          99% 

*The Client JVM could not run the Ackermann test 
  without producing a StackOverflowError.




Russell Smithies

Bioinformatics Software Developer
AgResearch Invermay
Private Bag 50034
Puddle Alley
Mosgiel
New Zealand
Tel: +64 3 489 9171
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 xjw2101 at columbia.edu  Mon Jun 28 16:44:30 2004
From: xjw2101 at columbia.edu (xjw2101@columbia.edu)
Date: Mon Jun 28 16:46:52 2004
Subject: [Biojava-l] DistributionLogo help
Message-ID: <1088455470.40e0832e544cc@cubmail.cc.columbia.edu>



I am trying to use DistributionLogo class to represent a PSSM for a 
transcription factor. I can generate DistributionLogos for each 
position but can't merge them together to form a nice looking 
single logo to be displayed on a panel. Basically,I don't know how 
to control the color or the size. can someone show me how this 
class works or give me some sample code of how this class works? 

Thanks,
Xuegong

From td2 at sanger.ac.uk  Tue Jun 29 09:40:33 2004
From: td2 at sanger.ac.uk (Thomas Down)
Date: Tue Jun 29 09:42:56 2004
Subject: [Biojava-l] DistributionLogo help
In-Reply-To: <1088455470.40e0832e544cc@cubmail.cc.columbia.edu>
References: <1088455470.40e0832e544cc@cubmail.cc.columbia.edu>
Message-ID: <E54892A6-C9D1-11D8-937E-000A95C8B056@sanger.ac.uk>


On 28 Jun 2004, at 21:44, xjw2101@columbia.edu wrote:

>
>
> I am trying to use DistributionLogo class to represent a PSSM for a
> transcription factor. I can generate DistributionLogos for each
> position but can't merge them together to form a nice looking
> single logo to be displayed on a panel. Basically,I don't know how
> to control the color or the size. can someone show me how this
> class works or give me some sample code of how this class works?

Hi Xuegong,

I generally use the following code, which creates a row of 
DistributionLogo objects, for displaying a BioJava WeightMatrix (i.e. 
PSSM) objects.  Can this be adapted to do what you want?

        Thomas.



import java.awt.*;

import javax.swing.*;

import org.biojava.bio.*;
import org.biojava.bio.dist.Distribution;
import org.biojava.bio.dp.WeightMatrix;
import org.biojava.bio.gui.*;

public class WMPanel extends JPanel {
     private WeightMatrix wm;
     private DistributionLogo[] logos;

     public WMPanel(WeightMatrix wm) {
         super();
         this.wm = wm;
         setBackground(Color.white);

         RenderingHints hints = new 
RenderingHints(RenderingHints.KEY_ANTIALIASING, 
RenderingHints.VALUE_ANTIALIAS_ON);

         try {
             setLayout(new GridLayout(1, wm.columns()));
             logos = new DistributionLogo[wm.columns()];
             for (int pos = 0; pos < wm.columns(); ++pos) {
                 Distribution dist = wm.getColumn(pos);
                 DistributionLogo dl = new DistributionLogo();
                 dl.setRenderingHints(hints);
                 dl.setBackground(Color.white);
                 dl.setOpaque(true);
                 dl.setDistribution(dist);
                 dl.setPreferredSize(new Dimension(40, 50));
                 dl.setLogoPainter(new TextLogoPainter());
                 dl.setStyle(new DNAStyle());
                 add(dl);
                 logos[pos] = dl;
             }
         } catch (BioException ex) {
             throw new BioError(ex);
         }
     }

     public static void wmViewer(WeightMatrix wm, String message)
     {
         WMPanel wmv = new WMPanel(wm);
         JFrame frame = new JFrame("Weight matrix viewer" + ((message == 
null) ? "" : (" (" + message + ")")));
         frame.getContentPane().add(wmv);
         frame.pack();
         frame.setVisible(true);
     }
}

From xjw2101 at columbia.edu  Tue Jun 29 10:49:07 2004
From: xjw2101 at columbia.edu (xjw2101@columbia.edu)
Date: Tue Jun 29 10:51:28 2004
Subject: [Biojava-l] DistributionLogo help
Message-ID: <1088520547.40e18163a3944@cubmail.cc.columbia.edu>

Thomas,
Seems the version is different from mine. In my version  
DistributionLogo is extension of Component and there are no 
setRenderingHints(hints) or setPreferedSize() methods.


Xuegong


--- Thomas Down <td2@sanger.ac.uk> wrote:
> 
> On 28 Jun 2004, at 21:44, xjw2101@columbia.edu
> wrote:
> 
> >
> >
> > I am trying to use DistributionLogo class to
> represent a PSSM for a
> > transcription factor. I can generate
> DistributionLogos for each
> > position but can't merge them together to form a
> nice looking
> > single logo to be displayed on a panel.
> Basically,I don't know how
> > to control the color or the size. can someone show
> me how this
> > class works or give me some sample code of how
> this class works?
> 
> Hi Xuegong,
> 
> I generally use the following code, which creates a
> row of 
> DistributionLogo objects, for displaying a BioJava
> WeightMatrix (i.e. 
> PSSM) objects.  Can this be adapted to do what you
> want?
> 
>         Thomas.
> 
> 
> 
> import java.awt.*;
> 
> import javax.swing.*;
> 
> import org.biojava.bio.*;
> import org.biojava.bio.dist.Distribution;
> import org.biojava.bio.dp.WeightMatrix;
> import org.biojava.bio.gui.*;
> 
> public class WMPanel extends JPanel {
>      private WeightMatrix wm;
>      private DistributionLogo[] logos;
> 
>      public WMPanel(WeightMatrix wm) {
>          super();
>          this.wm = wm;
>          setBackground(Color.white);
> 
>          RenderingHints hints = new 
> RenderingHints(RenderingHints.KEY_ANTIALIASING, 
> RenderingHints.VALUE_ANTIALIAS_ON);
> 
>          try {
>              setLayout(new GridLayout(1,
> wm.columns()));
>              logos = new
> DistributionLogo[wm.columns()];
>              for (int pos = 0; pos < wm.columns();
> ++pos) {
>                  Distribution dist =
> wm.getColumn(pos);
>                  DistributionLogo dl = new
> DistributionLogo();
>                  dl.setRenderingHints(hints);
>                  dl.setBackground(Color.white);
>                  dl.setOpaque(true);
>                  dl.setDistribution(dist);
>                  dl.setPreferredSize(new
> Dimension(40, 50));
>                  dl.setLogoPainter(new
> TextLogoPainter());
>                  dl.setStyle(new DNAStyle());
>                  add(dl);
>                  logos[pos] = dl;
>              }
>          } catch (BioException ex) {
>              throw new BioError(ex);
>          }
>      }
> 
>      public static void wmViewer(WeightMatrix wm,
> String message)
>      {
>          WMPanel wmv = new WMPanel(wm);
>          JFrame frame = new JFrame("Weight matrix
> viewer" + ((message == 
> null) ? "" : (" (" + message + ")")));
>          frame.getContentPane().add(wmv);
>          frame.pack();
>          frame.setVisible(true);
>      }
> }
> 
> 


From td2 at sanger.ac.uk  Tue Jun 29 11:03:13 2004
From: td2 at sanger.ac.uk (Thomas Down)
Date: Tue Jun 29 11:05:35 2004
Subject: [Biojava-l] DistributionLogo help
In-Reply-To: <1088520547.40e18163a3944@cubmail.cc.columbia.edu>
References: <1088520547.40e18163a3944@cubmail.cc.columbia.edu>
Message-ID: <71B1D264-C9DD-11D8-937E-000A95C8B056@sanger.ac.uk>


On 29 Jun 2004, at 15:49, xjw2101@columbia.edu wrote:

> Thomas,
> Seems the version is different from mine. In my version
> DistributionLogo is extension of Component and there are no
> setRenderingHints(hints) or setPreferedSize() methods.

Hmmm, do you know what version of BioJava you're using?  Those methods 
have been there since at least 1.3.0.

I'd suggest upgrading to either a 1.3.x release or (probably a better 
idea) 1.4pre1.

(Obviously, there's no problem removing the call to setRenderingHints, 
I just included that because the logos look a bit prettier with 
anti-aliasing turned on).

       Thomas.

From project4.bioinformatics at erasmusmc.nl  Tue Jun 29 11:32:38 2004
From: project4.bioinformatics at erasmusmc.nl (Selmar Leeuwenburgh)
Date: Tue Jun 29 11:32:40 2004
Subject: [Biojava-l] java.lang.NoClassDefFoundError error
Message-ID: <OPEMJHBKHFFAMPBFOGMGMEBLCAAA.project4.bioinformatics@erasmusmc.nl>

Hi,

I have a question. I know there are some messages of this subject in the
list, but I can't find the right answer.

Do someone know why I get java.lang.NoClassDefFoundError error? I get the
same error on my Linux computer with mandrake.


the command:

C:\>c:\j2sdk1.4.2_04\bin\java c:\bio-java\demos\seq\TestEmbl
C:\bio-java\demos\s
eq\AL121903.embl
Exception in thread "main" java.lang.NoClassDefFoundError:
c:\bio-java\demos\seq
\TestEmbl

the content of the ext directory:

 Directory of C:\j2sdk1.4.2_04\jre\lib\ext

29/08/2004  16:24    <DIR>          .
29/08/2004  16:24    <DIR>          ..
29/08/2004  16:11         2,385,919 biojava-1.30-jdk14.jar
29/08/2004  16:24            60,044 bytecode-0.91.jar
22/02/2004  23:18             8,896 dnsns.jar
29/08/2004  16:23            29,871 jakarta-regexp.jar
22/02/2004  23:21            53,247 ldapsec.jar
22/02/2004  23:50           769,335 localedata.jar
29/08/2004  15:58           111,374 sunjce_provider.jar
29/08/2004  16:24         1,783,457 xerces.jar
               8 File(s)      5,202,143 bytes
               2 Dir(s)  10,133,127,168 bytes free

My env variable are

C:\bio-java\demos\seq>set
ALLUSERSPROFILE=C:\Documents and Settings\All Users
APPDATA=C:\Documents and Settings\Selmar\Application Data
CLASSPATH=C:\j2sdk1.4.2_04\jre\lib\ext\biojava-1.30-jdk14.jar;C:\j2sdk1.4.2_
04\j
re\lib\ext\xerces.jar;C:\j2sdk1.4.2_04\jre\lib\ext\bytecode-0.91.jar;C:\j2sd
k1.4
.2_04\jre\lib\ext\jakarta-regexp.jar;
CommonProgramFiles=C:\Program Files\Common Files
COMPUTERNAME=SELMAR
ComSpec=C:\WINDOWS\system32\cmd.exe
HOMEDRIVE=C:
HOMEPATH=\
LOGONSERVER=\\SELMAR
NUMBER_OF_PROCESSORS=2
OS=Windows_NT
Path=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program
Files\Co
mmon Files\Adaptec
Shared\System;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls
\ENGLISH;C:\Program Files\UltraEdit;C:\Sun\AppServer\bin
PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH
PROCESSOR_ARCHITECTURE=x86
PROCESSOR_IDENTIFIER=x86 Family 15 Model 2 Stepping 9, GenuineIntel
PROCESSOR_LEVEL=15
PROCESSOR_REVISION=0209
ProgramFiles=C:\Program Files
PROMPT=$P$G
SystemDrive=C:
SystemRoot=C:\WINDOWS
TEMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
TMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
ULTRAMON_LANGDIR=C:\Program Files\UltraMon\Resources\en
USERDOMAIN=SELMAR
USERNAME=Selmar
USERPROFILE=C:\Documents and Settings\Selmar
windir=C:\WINDOWS


From gwu at molbio.mgh.harvard.edu  Tue Jun 29 11:48:23 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Tue Jun 29 11:50:44 2004
Subject: [Biojava-l] java.lang.NoClassDefFoundError error
In-Reply-To: <OPEMJHBKHFFAMPBFOGMGMEBLCAAA.project4.bioinformatics@erasmusmc.nl>
Message-ID: <AAEKLJJMIGMKFDEIPJFEOEHDCLAA.gwu@molbio.mgh.harvard.edu>

Give C:\>c:\j2sdk1.4.2_04\jre\bin\java a try. I got the similar problem,
which seems the "java" you called did not include the jar files under
C:\>c:\j2sdk1.4.2_04\jre\lib\ext properly, any hint?

Gang


-----Original Message-----
From: biojava-l-bounces@portal.open-bio.org
[mailto:biojava-l-bounces@portal.open-bio.org]On Behalf Of Selmar
Leeuwenburgh
Sent: Sunday, August 29, 2004 11:30 AM
To: biojava-l@biojava.org
Subject: [Biojava-l] java.lang.NoClassDefFoundError error


Hi,

I have a question. I know there are some messages of this subject in the
list, but I can't find the right answer.

Do someone know why I get java.lang.NoClassDefFoundError error? I get the
same error on my Linux computer with mandrake.


the command:

C:\>c:\j2sdk1.4.2_04\bin\java c:\bio-java\demos\seq\TestEmbl
C:\bio-java\demos\s
eq\AL121903.embl
Exception in thread "main" java.lang.NoClassDefFoundError:
c:\bio-java\demos\seq
\TestEmbl

the content of the ext directory:

 Directory of C:\j2sdk1.4.2_04\jre\lib\ext

29/08/2004  16:24    <DIR>          .
29/08/2004  16:24    <DIR>          ..
29/08/2004  16:11         2,385,919 biojava-1.30-jdk14.jar
29/08/2004  16:24            60,044 bytecode-0.91.jar
22/02/2004  23:18             8,896 dnsns.jar
29/08/2004  16:23            29,871 jakarta-regexp.jar
22/02/2004  23:21            53,247 ldapsec.jar
22/02/2004  23:50           769,335 localedata.jar
29/08/2004  15:58           111,374 sunjce_provider.jar
29/08/2004  16:24         1,783,457 xerces.jar
               8 File(s)      5,202,143 bytes
               2 Dir(s)  10,133,127,168 bytes free

My env variable are

C:\bio-java\demos\seq>set
ALLUSERSPROFILE=C:\Documents and Settings\All Users
APPDATA=C:\Documents and Settings\Selmar\Application Data
CLASSPATH=C:\j2sdk1.4.2_04\jre\lib\ext\biojava-1.30-jdk14.jar;C:\j2sdk1.4.2_
04\j
re\lib\ext\xerces.jar;C:\j2sdk1.4.2_04\jre\lib\ext\bytecode-0.91.jar;C:\j2sd
k1.4
.2_04\jre\lib\ext\jakarta-regexp.jar;
CommonProgramFiles=C:\Program Files\Common Files
COMPUTERNAME=SELMAR
ComSpec=C:\WINDOWS\system32\cmd.exe
HOMEDRIVE=C:
HOMEPATH=\
LOGONSERVER=\\SELMAR
NUMBER_OF_PROCESSORS=2
OS=Windows_NT
Path=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program
Files\Co
mmon Files\Adaptec
Shared\System;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls
\ENGLISH;C:\Program Files\UltraEdit;C:\Sun\AppServer\bin
PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH
PROCESSOR_ARCHITECTURE=x86
PROCESSOR_IDENTIFIER=x86 Family 15 Model 2 Stepping 9, GenuineIntel
PROCESSOR_LEVEL=15
PROCESSOR_REVISION=0209
ProgramFiles=C:\Program Files
PROMPT=$P$G
SystemDrive=C:
SystemRoot=C:\WINDOWS
TEMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
TMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
ULTRAMON_LANGDIR=C:\Program Files\UltraMon\Resources\en
USERDOMAIN=SELMAR
USERNAME=Selmar
USERPROFILE=C:\Documents and Settings\Selmar
windir=C:\WINDOWS


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

From gwu at molbio.mgh.harvard.edu  Tue Jun 29 12:03:32 2004
From: gwu at molbio.mgh.harvard.edu (Gang Wu)
Date: Tue Jun 29 12:05:52 2004
Subject: [Biojava-l] java.lang.NoClassDefFoundError error
In-Reply-To: <OPEMJHBKHFFAMPBFOGMGMEBLCAAA.project4.bioinformatics@erasmusmc.nl>
Message-ID: <AAEKLJJMIGMKFDEIPJFEKEHECLAA.gwu@molbio.mgh.harvard.edu>

Another problem is you have to include "c:\bio-java\demos" in your CLASSPATH
and call the TestEmbl as "seq.TestEmbl" because the class package started
from "c:\bio-java\demos\seq". So the command line should be like:

c:\j2sdk1.4.2_04\jre\bin\java -cp CLASSPATH;c:\bio-java\demos seq.TestEmbl
C:\bio-java\demos\seq\AL121903.embl

gang

-----Original Message-----
From: biojava-l-bounces@portal.open-bio.org
[mailto:biojava-l-bounces@portal.open-bio.org]On Behalf Of Selmar
Leeuwenburgh
Sent: Sunday, August 29, 2004 11:30 AM
To: biojava-l@biojava.org
Subject: [Biojava-l] java.lang.NoClassDefFoundError error


Hi,

I have a question. I know there are some messages of this subject in the
list, but I can't find the right answer.

Do someone know why I get java.lang.NoClassDefFoundError error? I get the
same error on my Linux computer with mandrake.


the command:

C:\>c:\j2sdk1.4.2_04\bin\java c:\bio-java\demos\seq\TestEmbl
C:\bio-java\demos\s
eq\AL121903.embl
Exception in thread "main" java.lang.NoClassDefFoundError:
c:\bio-java\demos\seq
\TestEmbl

the content of the ext directory:

 Directory of C:\j2sdk1.4.2_04\jre\lib\ext

29/08/2004  16:24    <DIR>          .
29/08/2004  16:24    <DIR>          ..
29/08/2004  16:11         2,385,919 biojava-1.30-jdk14.jar
29/08/2004  16:24            60,044 bytecode-0.91.jar
22/02/2004  23:18             8,896 dnsns.jar
29/08/2004  16:23            29,871 jakarta-regexp.jar
22/02/2004  23:21            53,247 ldapsec.jar
22/02/2004  23:50           769,335 localedata.jar
29/08/2004  15:58           111,374 sunjce_provider.jar
29/08/2004  16:24         1,783,457 xerces.jar
               8 File(s)      5,202,143 bytes
               2 Dir(s)  10,133,127,168 bytes free

My env variable are

C:\bio-java\demos\seq>set
ALLUSERSPROFILE=C:\Documents and Settings\All Users
APPDATA=C:\Documents and Settings\Selmar\Application Data
CLASSPATH=C:\j2sdk1.4.2_04\jre\lib\ext\biojava-1.30-jdk14.jar;C:\j2sdk1.4.2_
04\j
re\lib\ext\xerces.jar;C:\j2sdk1.4.2_04\jre\lib\ext\bytecode-0.91.jar;C:\j2sd
k1.4
.2_04\jre\lib\ext\jakarta-regexp.jar;
CommonProgramFiles=C:\Program Files\Common Files
COMPUTERNAME=SELMAR
ComSpec=C:\WINDOWS\system32\cmd.exe
HOMEDRIVE=C:
HOMEPATH=\
LOGONSERVER=\\SELMAR
NUMBER_OF_PROCESSORS=2
OS=Windows_NT
Path=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program
Files\Co
mmon Files\Adaptec
Shared\System;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls
\ENGLISH;C:\Program Files\UltraEdit;C:\Sun\AppServer\bin
PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH
PROCESSOR_ARCHITECTURE=x86
PROCESSOR_IDENTIFIER=x86 Family 15 Model 2 Stepping 9, GenuineIntel
PROCESSOR_LEVEL=15
PROCESSOR_REVISION=0209
ProgramFiles=C:\Program Files
PROMPT=$P$G
SystemDrive=C:
SystemRoot=C:\WINDOWS
TEMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
TMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
ULTRAMON_LANGDIR=C:\Program Files\UltraMon\Resources\en
USERDOMAIN=SELMAR
USERNAME=Selmar
USERPROFILE=C:\Documents and Settings\Selmar
windir=C:\WINDOWS


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

From fpepin at cs.mcgill.ca  Tue Jun 29 12:35:11 2004
From: fpepin at cs.mcgill.ca (Francois Pepin)
Date: Tue Jun 29 12:39:18 2004
Subject: [Biojava-l] java.lang.NoClassDefFoundError error
In-Reply-To: <OPEMJHBKHFFAMPBFOGMGMEBLCAAA.project4.bioinformatics@erasmusmc.nl>
References: <OPEMJHBKHFFAMPBFOGMGMEBLCAAA.project4.bioinformatics@erasmusmc.nl>
Message-ID: <1088526911.10990.27.camel@ybrig.MCB.McGill.CA>

Good old classpath error would be my guess.

try:

cd bio-java\demos
c:\j2sdk1.4.2_04\bin\java -cp . seq/TestEmbl

this should give you the following error (output is from linux):

[francois@bern demos]$ java -cp . seq/TestEmbl
Exception in thread "main" java.lang.NoClassDefFoundError:
org/biojava/bio/symbol/Alphabet

This means that you don't have the biojava.jar mounted. In my case, I
can do it with:
[francois@bern demos]$ java -cp ~/cvs/bias/biojava.jar:. seq/TestEmbl
seq/AL121903.embl
>HSDJ155G6 has 191 features 
[rest of normal output follows]

java classpath is a bit tricky at the beginning but you get used to it.
You can also use a IDE that takes care of everything for you.

Francois

On Sun, 2004-08-29 at 11:29, Selmar Leeuwenburgh wrote:
> Hi,
> 
> I have a question. I know there are some messages of this subject in the
> list, but I can't find the right answer.
> 
> Do someone know why I get java.lang.NoClassDefFoundError error? I get the
> same error on my Linux computer with mandrake.
> 
> 
> the command:
> 
> C:\>c:\j2sdk1.4.2_04\bin\java c:\bio-java\demos\seq\TestEmbl
> C:\bio-java\demos\s
> eq\AL121903.embl
> Exception in thread "main" java.lang.NoClassDefFoundError:
> c:\bio-java\demos\seq
> \TestEmbl
> 
> the content of the ext directory:
> 
>  Directory of C:\j2sdk1.4.2_04\jre\lib\ext
> 
> 29/08/2004  16:24    <DIR>          .
> 29/08/2004  16:24    <DIR>          ..
> 29/08/2004  16:11         2,385,919 biojava-1.30-jdk14.jar
> 29/08/2004  16:24            60,044 bytecode-0.91.jar
> 22/02/2004  23:18             8,896 dnsns.jar
> 29/08/2004  16:23            29,871 jakarta-regexp.jar
> 22/02/2004  23:21            53,247 ldapsec.jar
> 22/02/2004  23:50           769,335 localedata.jar
> 29/08/2004  15:58           111,374 sunjce_provider.jar
> 29/08/2004  16:24         1,783,457 xerces.jar
>                8 File(s)      5,202,143 bytes
>                2 Dir(s)  10,133,127,168 bytes free
> 
> My env variable are
> 
> C:\bio-java\demos\seq>set
> ALLUSERSPROFILE=C:\Documents and Settings\All Users
> APPDATA=C:\Documents and Settings\Selmar\Application Data
> CLASSPATH=C:\j2sdk1.4.2_04\jre\lib\ext\biojava-1.30-jdk14.jar;C:\j2sdk1.4.2_
> 04\j
> re\lib\ext\xerces.jar;C:\j2sdk1.4.2_04\jre\lib\ext\bytecode-0.91.jar;C:\j2sd
> k1.4
> .2_04\jre\lib\ext\jakarta-regexp.jar;
> CommonProgramFiles=C:\Program Files\Common Files
> COMPUTERNAME=SELMAR
> ComSpec=C:\WINDOWS\system32\cmd.exe
> HOMEDRIVE=C:
> HOMEPATH=\
> LOGONSERVER=\\SELMAR
> NUMBER_OF_PROCESSORS=2
> OS=Windows_NT
> Path=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program
> Files\Co
> mmon Files\Adaptec
> Shared\System;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls
> \ENGLISH;C:\Program Files\UltraEdit;C:\Sun\AppServer\bin
> PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH
> PROCESSOR_ARCHITECTURE=x86
> PROCESSOR_IDENTIFIER=x86 Family 15 Model 2 Stepping 9, GenuineIntel
> PROCESSOR_LEVEL=15
> PROCESSOR_REVISION=0209
> ProgramFiles=C:\Program Files
> PROMPT=$P$G
> SystemDrive=C:
> SystemRoot=C:\WINDOWS
> TEMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
> TMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
> ULTRAMON_LANGDIR=C:\Program Files\UltraMon\Resources\en
> USERDOMAIN=SELMAR
> USERNAME=Selmar
> USERPROFILE=C:\Documents and Settings\Selmar
> windir=C:\WINDOWS
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l

From xjw2101 at columbia.edu  Tue Jun 29 14:09:00 2004
From: xjw2101 at columbia.edu (xjw2101@columbia.edu)
Date: Tue Jun 29 14:11:27 2004
Subject: [Biojava-l] DistributionLogo help
Message-ID: <1088532540.40e1b03c7bee0@cubmail.cc.columbia.edu>

Thomas,
Thanks, that I found out later it's my mistake that I use Component 
object to represent the logo. Seems to work now but there still is 
a problem-- the height of the logos displayed seems to be only 1/2 
of the space I provided to them on the panel. Change the dimension 
of the logo dosen't help. Any thoughts?

Xuegong


>On 29 Jun 2004, at 15:49, xjw2101@columbia.edu wrote:

> Thomas,
> Seems the version is different from mine. In my version
> DistributionLogo is extension of Component and there are no
> setRenderingHints(hints) or setPreferedSize() methods.

>Hmmm, do you know what version of BioJava you're using?  Those 
>methods 
>have been there since at least 1.3.0.

>I'd suggest upgrading to either a 1.3.x release or (probably a 
>better 
>idea) 1.4pre1.

>(Obviously, there's no problem removing the call to 
>setRenderingHints, 
>I just included that because the logos look a bit prettier with 
>anti-aliasing turned on).

>       Thomas.
From project4.bioinformatics at erasmusmc.nl  Wed Jun 30 07:43:10 2004
From: project4.bioinformatics at erasmusmc.nl (Selmar Leeuwenburgh)
Date: Wed Jun 30 07:43:13 2004
Subject: [Biojava-l] java.lang.NoClassDefFoundError error
In-Reply-To: <1088526911.10990.27.camel@ybrig.MCB.McGill.CA>
Message-ID: <OPEMJHBKHFFAMPBFOGMGGEBNCAAA.project4.bioinformatics@erasmusmc.nl>

thank you al for help.

finally is work as follows:

export
CLASSPATH=/usr/java/j2sdk1.4.2_04/jre/lib/ext/biojava-1.30-jdk14.jar:/usr/ja
va/j2sdk1.4.2_04/jre/lib/ext/bytecode-0.91.jar:/usr/java/j2sdk1.4.2_04/jre/l
ib/ext/jakarta-regexp.jar:/usr/java/j2sdk1.4.2_04/jre/lib/ext/xerces.jar:/us
r/bio-java/demos

java seq.TestEmbl /bio-java/demos/seq/AL121903.embl

and on windows: properties of this computer > advanced > environment
variables en dan systemvariable CLASSPATH
C:\j2sdk1.4.2_04\jre\lib\ext\biojava-1.30-jdk14.jar;C:\j2sdk1.4.2_04\jre\lib
\ext\xerces.jar;C:\j2sdk1.4.2_04\jre\lib\ext\bytecode-0.91.jar;C:\j2sdk1.4.2
_04\jre\lib\ext\jakarta-regexp.jar;c:\bio-java\demos;

java seq.TestEmbl C:\bio-java\demos\seq\AL121903.embl zo run ik het nu

kind regards,

Selmar.

-----Original Message-----
From: Francois Pepin [mailto:fpepin@cs.mcgill.ca]
Sent: 29 June 2004 18:35
To: Selmar Leeuwenburgh
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] java.lang.NoClassDefFoundError error


Good old classpath error would be my guess.

try:

cd bio-java\demos
c:\j2sdk1.4.2_04\bin\java -cp . seq/TestEmbl

this should give you the following error (output is from linux):

[francois@bern demos]$ java -cp . seq/TestEmbl
Exception in thread "main" java.lang.NoClassDefFoundError:
org/biojava/bio/symbol/Alphabet

This means that you don't have the biojava.jar mounted. In my case, I
can do it with:
[francois@bern demos]$ java -cp ~/cvs/bias/biojava.jar:. seq/TestEmbl
seq/AL121903.embl
>HSDJ155G6 has 191 features
[rest of normal output follows]

java classpath is a bit tricky at the beginning but you get used to it.
You can also use a IDE that takes care of everything for you.

Francois

On Sun, 2004-08-29 at 11:29, Selmar Leeuwenburgh wrote:
> Hi,
>
> I have a question. I know there are some messages of this subject in the
> list, but I can't find the right answer.
>
> Do someone know why I get java.lang.NoClassDefFoundError error? I get the
> same error on my Linux computer with mandrake.
>
>
> the command:
>
> C:\>c:\j2sdk1.4.2_04\bin\java c:\bio-java\demos\seq\TestEmbl
> C:\bio-java\demos\s
> eq\AL121903.embl
> Exception in thread "main" java.lang.NoClassDefFoundError:
> c:\bio-java\demos\seq
> \TestEmbl
>
> the content of the ext directory:
>
>  Directory of C:\j2sdk1.4.2_04\jre\lib\ext
>
> 29/08/2004  16:24    <DIR>          .
> 29/08/2004  16:24    <DIR>          ..
> 29/08/2004  16:11         2,385,919 biojava-1.30-jdk14.jar
> 29/08/2004  16:24            60,044 bytecode-0.91.jar
> 22/02/2004  23:18             8,896 dnsns.jar
> 29/08/2004  16:23            29,871 jakarta-regexp.jar
> 22/02/2004  23:21            53,247 ldapsec.jar
> 22/02/2004  23:50           769,335 localedata.jar
> 29/08/2004  15:58           111,374 sunjce_provider.jar
> 29/08/2004  16:24         1,783,457 xerces.jar
>                8 File(s)      5,202,143 bytes
>                2 Dir(s)  10,133,127,168 bytes free
>
> My env variable are
>
> C:\bio-java\demos\seq>set
> ALLUSERSPROFILE=C:\Documents and Settings\All Users
> APPDATA=C:\Documents and Settings\Selmar\Application Data
>
CLASSPATH=C:\j2sdk1.4.2_04\jre\lib\ext\biojava-1.30-jdk14.jar;C:\j2sdk1.4.2_
> 04\j
>
re\lib\ext\xerces.jar;C:\j2sdk1.4.2_04\jre\lib\ext\bytecode-0.91.jar;C:\j2sd
> k1.4
> .2_04\jre\lib\ext\jakarta-regexp.jar;
> CommonProgramFiles=C:\Program Files\Common Files
> COMPUTERNAME=SELMAR
> ComSpec=C:\WINDOWS\system32\cmd.exe
> HOMEDRIVE=C:
> HOMEPATH=\
> LOGONSERVER=\\SELMAR
> NUMBER_OF_PROCESSORS=2
> OS=Windows_NT
> Path=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program
> Files\Co
> mmon Files\Adaptec
> Shared\System;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls
> \ENGLISH;C:\Program Files\UltraEdit;C:\Sun\AppServer\bin
> PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH
> PROCESSOR_ARCHITECTURE=x86
> PROCESSOR_IDENTIFIER=x86 Family 15 Model 2 Stepping 9, GenuineIntel
> PROCESSOR_LEVEL=15
> PROCESSOR_REVISION=0209
> ProgramFiles=C:\Program Files
> PROMPT=$P$G
> SystemDrive=C:
> SystemRoot=C:\WINDOWS
> TEMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
> TMP=C:\DOCUME~1\Selmar\LOCALS~1\Temp
> ULTRAMON_LANGDIR=C:\Program Files\UltraMon\Resources\en
> USERDOMAIN=SELMAR
> USERNAME=Selmar
> USERPROFILE=C:\Documents and Settings\Selmar
> windir=C:\WINDOWS
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l