From susy at ysbl.york.ac.uk  Mon Apr  2 09:04:26 2007
From: susy at ysbl.york.ac.uk (Susy Griffiths)
Date: Mon, 02 Apr 2007 14:04:26 +0100
Subject: [Biojava-l] Calculate mass and pI for a protein containing
	ambiguity symbols
Message-ID: <4610FF5A.6060307@ysbl.york.ac.uk>

Hi,
how can I avoid the IllegalSymbolException to calculate the mass and pI 
of a protein using BioJava, when the sequence contains 'X' or 'B'  or 'Z'?
The Expasy comput pI /Mw tool does this, see 
http://us.expasy.org/tools/pi_tool-doc.html
"In addition to the standard one-letter-codes for the 20 amino acids, 
the characters B, Z and X are accepted:

      B   Asx   Aspartic acid or Asparagine   
      Z   Glx   Glutamine or Glutamic acid
      X   Xaa   Any amino acid

The mass values used for these residues are mean values of the 
corresponding masses, and B, Z and X are presumed to have pK values of 
0, i.e. a pI of 5.52."

Would I need to edit the ResidueProperties.xml file to provide average 
mass entries for X, B & Z ?

thanks, Susy

-- 
*********************************************************
Dr S.L. Griffiths
YSBL
Department of Chemistry
University of York
Heslington
York
YO10 5YW
UK

http://www.pims-lims.org/
email: susy at ysbl.york.ac.uk
Tel. +44 (0)1904 328270
Fax +44 (0)1904 328266
*********************************************************


From markjschreiber at gmail.com  Mon Apr  2 10:38:48 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Mon, 2 Apr 2007 22:38:48 +0800
Subject: [Biojava-l] Calculate mass and pI for a protein containing
	ambiguity symbols
In-Reply-To: <4610FF5A.6060307@ysbl.york.ac.uk>
References: <4610FF5A.6060307@ysbl.york.ac.uk>
Message-ID: <93b45ca50704020738k3f5498axc7a4ca3741ac3330@mail.gmail.com>

Hi Susy -

This issue was raised recently on (I think) the biojava-dev list. The
problem is that the MassCalc doesn't deal well (at all) with ambiguity
codes.

I think Bruce Waldon suggested a fix. Bruce, do you intend to commit
it or should I post a request for enhancement on bugzilla? I think it
should be relatively simple to fix.

As a work around you could calculate the average values (although this
is not terribly practical).

- Mark

On 4/2/07, Susy Griffiths <susy at ysbl.york.ac.uk> wrote:
> Hi,
> how can I avoid the IllegalSymbolException to calculate the mass and pI
> of a protein using BioJava, when the sequence contains 'X' or 'B'  or 'Z'?
> The Expasy comput pI /Mw tool does this, see
> http://us.expasy.org/tools/pi_tool-doc.html
> "In addition to the standard one-letter-codes for the 20 amino acids,
> the characters B, Z and X are accepted:
>
>       B   Asx   Aspartic acid or Asparagine
>       Z   Glx   Glutamine or Glutamic acid
>       X   Xaa   Any amino acid
>
> The mass values used for these residues are mean values of the
> corresponding masses, and B, Z and X are presumed to have pK values of
> 0, i.e. a pI of 5.52."
>
> Would I need to edit the ResidueProperties.xml file to provide average
> mass entries for X, B & Z ?
>
> thanks, Susy
>
> --
> *********************************************************
> Dr S.L. Griffiths
> YSBL
> Department of Chemistry
> University of York
> Heslington
> York
> YO10 5YW
> UK
>
> http://www.pims-lims.org/
> email: susy at ysbl.york.ac.uk
> Tel. +44 (0)1904 328270
> Fax +44 (0)1904 328266
> *********************************************************
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From gwaldon at geneinfinity.org  Mon Apr  2 13:12:18 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Mon, 02 Apr 2007 10:12:18 -0700
Subject: [Biojava-l] Calculate mass and pI for a protein
	containingambiguity symbols
Message-ID: <20070402171218.4295.qmail@mmm1924.dulles19-verio.com>

Hi Susy,

As I am reading your mail, a fix is already implemented in the cvs for molecular weight calculation of polypeptides containing ambiguity symbols. I haven't done anything for pKs but I can get a look at this. Give me a few days.

George (not Bruce!)


-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Susy Griffiths
Sent: Monday, April 02, 2007 6:04 AM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Calculate mass and pI for a protein containingambiguity symbols

Hi,
how can I avoid the IllegalSymbolException to calculate the mass and pI 
of a protein using BioJava, when the sequence contains 'X' or 'B'  or 'Z'?
The Expasy comput pI /Mw tool does this, see 
http://us.expasy.org/tools/pi_tool-doc.html
"In addition to the standard one-letter-codes for the 20 amino acids, 
the characters B, Z and X are accepted:

      B   Asx   Aspartic acid or Asparagine   
      Z   Glx   Glutamine or Glutamic acid
      X   Xaa   Any amino acid

The mass values used for these residues are mean values of the 
corresponding masses, and B, Z and X are presumed to have pK values of 
0, i.e. a pI of 5.52."

Would I need to edit the ResidueProperties.xml file to provide average 
mass entries for X, B & Z ?

thanks, Susy

-- 
*********************************************************
Dr S.L. Griffiths
YSBL
Department of Chemistry
University of York
Heslington
York
YO10 5YW
UK

http://www.pims-lims.org/
email: susy at ysbl.york.ac.uk
Tel. +44 (0)1904 328270
Fax +44 (0)1904 328266
*********************************************************

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

From russ at kepler-eng.com  Wed Apr 11 15:22:33 2007
From: russ at kepler-eng.com (Russ Kepler)
Date: Wed, 11 Apr 2007 13:22:33 -0600
Subject: [Biojava-l] Question on FlexibleAlignment
Message-ID: <200704111322.33268.russ@kepler-eng.com>

I've re-encountered something that has always puzzled me - I'm building a 
FlexibleAlignment with a bunch of SimpleAlignmentElements composed of 
SimpleGappedSequences.  The SimpleAlignmentElement wants a RangeLocation, but 
insists that the max()-min()+1 be sequence.length().  But the 
sequence.length() includes any gap placed at the start of the sequence, so 
necessarily you include any offseting gap to make the alignment.  This means 
that FlexibleAlignment.getLabelsAt(1) will always return the list of all the 
SimpleAlignmentElements.  It seems that either the getLabelsAt() should 
exclude the elements that don't have sequence at the position (yet) or the 
SimpleAlignmentElement shouldn't be using the length of the sequence in 
testing the RangeLocation.

Any comments?  I hope this makes sense to someone...

From ehaugen at u.washington.edu  Thu Apr 12 19:58:41 2007
From: ehaugen at u.washington.edu (Eric Haugen)
Date: Thu, 12 Apr 2007 16:58:41 -0700 (Pacific Daylight Time)
Subject: [Biojava-l] Question on FlexibleAlignment
In-Reply-To: <200704111322.33268.russ@kepler-eng.com>
References: <200704111322.33268.russ@kepler-eng.com>
Message-ID: <Pine.WNT.4.64.0704121625140.1336@THING.genome_center.genome.washington.edu>


The idea behind the UnequalLengthAlignment interface implemented by FlexibleAlignment is that you don't need to have terminal gaps in any sequence, you can just set the location's min to be the position in the alignment where the sequence's first symbol aligns.

But I haven't tried using it in that way, so I don't know how well it actually works...

-- 
Eric Haugen
Software Engineer
University of Washington Genome Center


On Wed, 11 Apr 2007, Russ Kepler wrote:

> I've re-encountered something that has always puzzled me - I'm building a
> FlexibleAlignment with a bunch of SimpleAlignmentElements composed of
> SimpleGappedSequences.  The SimpleAlignmentElement wants a RangeLocation, but
> insists that the max()-min()+1 be sequence.length().  But the
> sequence.length() includes any gap placed at the start of the sequence, so
> necessarily you include any offseting gap to make the alignment.  This means
> that FlexibleAlignment.getLabelsAt(1) will always return the list of all the
> SimpleAlignmentElements.  It seems that either the getLabelsAt() should
> exclude the elements that don't have sequence at the position (yet) or the
> SimpleAlignmentElement shouldn't be using the length of the sequence in
> testing the RangeLocation.
>
> Any comments?  I hope this makes sense to someone...
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From gwaldon at geneinfinity.org  Wed Apr 18 11:48:03 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Wed, 18 Apr 2007 08:48:03 -0700
Subject: [Biojava-l] Biojava MassCalc
Message-ID: <20070418154803.19939.qmail@mmm1924.dulles19-verio.com>

Dear Marc,

The difference is Havg = 1.00794 (see cvs). You calculated the mass MH+ (M plus one ionization H+), which - I guess - is used for mass spectrometry analysis.

Regards,
George

-----Original Message-----
From: Marc Savitsky [mailto:marc at strubi.ox.ac.uk] 
Sent: Wednesday, April 18, 2007 5:41 AM
To: george waldon
Subject: Re: Biojava MassCalc

Hi George,

I had some time to look at the MassCalc.getMolecularWeight(protein) 
method, and it does to job with regard to ambiguous symbols.

Are you aware that it doesn't return the same value as getMass() for 
sequences without ambiguous codes?
My test case examines the sequence

AASLIKPCAYEKQGLIDHAIGSYKVLHDKISESYYKVISRRLERYGIVLDLNGVKEIVKDVVVLHDMGKAGEYYQNQFDDNC
NPLKSNPLKSRFSFIYHELGSALFFYNDYEPINVEKAEEVRSLLTLAVINHLNAIRGISDYLLNRFPDNFDEEMIKLSKYGSILLE
NLRGIISKSLKVRDYSFTDYHDMLYAFSKKSDKYLKLYNLFLAPIMLGDNLDSSLVRNNGSKTRFVGILEGELNGGSTLCCCC

but getMass returns a value of 
28633.94392000000152620486915111541748046875 whereas getMolecularWeight 
returns 28632.9359800000020186416804790496826171875.

regards
Marc Savitsky

From bertrand.beckert at gmail.com  Fri Apr 20 04:38:33 2007
From: bertrand.beckert at gmail.com (bertrand beckert)
Date: Fri, 20 Apr 2007 10:38:33 +0200
Subject: [Biojava-l] Biojavax and hibernate problems
Message-ID: <500217090704200138x4c2f39d9wa80cc39fdf475ca5@mail.gmail.com>

Dear all,

I am newbie  to java and biojavax... I have installed the BioSQL database
and I have tried to connect to this base an put some data... In oder to do
this I have installed Biojavax, and also hibernate (and the different .jar
required). So I have tried to put some data but it didn't work... here is my
code and the error in the output.

Could you help me please. Thanks

---------

package fr.ustrasbg.ibmc.bbeckert;

import org.biojavax.bio.seq.io.RichSequenceBuilderFactory;
import org.biojavax.bio.seq.io.RichSequenceFormat;
import org.biojavax.bio.seq.io.RichStreamReader;
import org.biojavax.bio.seq.io.GenbankFormat;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.seq.RichFeature;
import org.biojavax.bio.db.RichSequenceDB;
import org.biojavax.bio.db.biosql.BioSQLRichSequenceDB;
import org.biojavax.RichObjectFactory;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.db.IllegalIDException;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.Transaction;
import org.hibernate.HibernateException;
import org.hibernate.cfg.Configuration;

import java.io.File;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.Iterator;

public class HibernatLoadingData {

    public RichSequence gbkRichSeq (File f) {
        [....]
       return sequence;
    }

public static void loadingData (RichSequence gbkSeq){

        SessionFactory sessionFactory = new
Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();
        RichObjectFactory.connectToBioSQL(session);
        RichSequenceDB db = new BioSQLRichSequenceDB(session);

        Transaction t=null;
        try{
            t = session.beginTransaction();
            //test to kown is the database is active->true
            System.out.println(t.isActive());
            db.addRichSequence(gbkSeq);            //it should work...
            t.commit();
        } catch (HibernateException e) {
            e.printStackTrace();
            if (t != null && t.isActive())
                t.rollback();
        } catch (BioException e) {
                e.printStackTrace();
            }
            session.close();
        }

public static void main(String[] args) {

        File f = new
File("/home/bertrand/IdeaProjects/ncRNAs/data/test.gbk");
        HibernatLoadingData hl= new HibernatLoadingData();
        RichSequence sequence=hl.gbkRichSeq(f);
        loadingData(sequence);
  }
}


output:
             RichSequence gbkRichSeq:

sequence name:CAK20891 AC:CAK20891
Division:BCT
length:688
Protein start:1 end:688 Strand:POSITIVE
MSKDFLLEIGLEEMPAQYVTSSVAQLEKRVSDWLNENQITFEKIKTYSTPRRLTVLVEAM
AEEQANRVEEAKGPAKKIALDDEGNWSKAALGFARSQKVEPADLTFREIKGVEYIYIKKE
VIGEKTTALLPSLEKVVTSMTFPVSMHWGSNDLRYIRPIKWLIAMFGEEIIPFEITGVST
SNTSRGHRFLGKTATIKQPSDYPNALLEQFVVVNAEERKQAIVEQLRELESMENWQIKED
EDLLEEVTNLVEYPTVLAGNFEKEYLELPEEVLITTMKEHQRYFPVFSKDEELLPHFVTV
RNGNHENLDTVARGNEKVLRARLSDADFFYQEDLKITIDEAVAKLQNIVFHEKLGTLTEK
MKRVQKVALMLADYLDWQEEDKQDIIRLTNIYKFDLVTNIVGEFPELQGLMGEKYALLQG
EKPAIAIAIREHYLPSSAEGALPQTDLGSIIAIADKLETLVGFFCVNIVPTGSADPFGLR
RSAFGAMRIIQANGWDIPVLELLSRIVDMERAEGAVELPSDDVKKEVQTFLKNRLRVVLQ
NHHIRHDIIDAVIGGDPNTIPQLVDRAQILNKHVESDWFRPTVEALTRVMNISKKHEGNV
EVDPSLFENKYEQALFDEIEKLKYDYANLTIVDRLRAFAALRTTIDDYFDNTLVMSENIE
LKNNRLALLFELASFIKEFAQMDEINVK
(log4j.properties)
10:14:06,582  INFO Environment:509 - Hibernate 3.2.3
10:14:06,589  INFO Environment:542 - hibernate.properties not found
10:14:06,596  INFO Environment:676 - Bytecode provider name : cglib
10:14:06,600  INFO Environment:593 - using JDK 1.4 java.sql.Timestamphandling
10:14:06,685  INFO Configuration:1426 - configuring from resource:
/hibernate.cfg.xml
10:14:06,686  INFO Configuration:1403 - Configuration resource:
/hibernate.cfg.xml
10:14:06,783  INFO Configuration:553 - Reading mappings from resource :
Namespace.hbm.xml
10:14:06,966  INFO HbmBinder:300 - Mapping class: Namespace -> biodatabase
[...]
Exception in thread "main" java.lang.RuntimeException: Error while trying to
save RichSequence with id: CAK20891
    at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB._addRichSequence(
BioSQLRichSequenceDB.java:300)
    at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.addRichSequence(
BioSQLRichSequenceDB.java:277)
    at fr.ustrasbg.ibmc.bbeckert.HibernatLoadingData.loadingData(
HibernatLoadingData.java:101)
    at fr.ustrasbg.ibmc.bbeckert.HibernatLoadingData.main(
HibernatLoadingData.java:140)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(
NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(
DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:585)
    at com.intellij.rt.execution.application.AppMain.main(AppMain.java:90)
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(
NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(
DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:585)
    at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB._addRichSequence(
BioSQLRichSequenceDB.java:297)
    ... 8 more
Caused by: org.hibernate.TransientObjectException: object references an
unsaved transient instance - save the transient instance before flushing:
Term
    at org.hibernate.engine.ForeignKeys.getEntityIdentifierIfNotUnsaved(
ForeignKeys.java:219)
    at org.hibernate.collection.AbstractPersistentCollection.getOrphans(
AbstractPersistentCollection.java:889)
    at org.hibernate.collection.PersistentSet.getOrphans(PersistentSet.java
:90)
    at org.hibernate.engine.CollectionEntry.getOrphans(CollectionEntry.java
:350)
    at org.hibernate.engine.Cascade.deleteOrphans(Cascade.java:340)
    at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java
:324)
    at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(
AbstractSaveEventListener.java:456)
    at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
AbstractSaveEventListener.java:334)
    at org.hibernate.event.def.AbstractSaveEventListener.performSave(
AbstractSaveEventListener.java:181)
    at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
(AbstractSaveEventListener.java:107)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
(DefaultSaveOrUpdateEventListener.java:187)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(
DefaultSaveOrUpdateEventListener.java:172)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
(DefaultSaveOrUpdateEventListener.java:94)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
DefaultSaveOrUpdateEventListener.java:70)
    at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
    at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
    at org.hibernate.engine.CascadingAction$1.cascade(CascadingAction.java
:218)
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave(
AbstractSaveEventListener.java:431)
    at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
AbstractSaveEventListener.java:265)
    at org.hibernate.event.def.AbstractSaveEventListener.performSave(
AbstractSaveEventListener.java:181)
    at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
(AbstractSaveEventListener.java:107)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
(DefaultSaveOrUpdateEventListener.java:187)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(
DefaultSaveOrUpdateEventListener.java:172)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
(DefaultSaveOrUpdateEventListener.java:94)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
DefaultSaveOrUpdateEventListener.java:70)
    at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
    at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
    at org.hibernate.engine.CascadingAction$1.cascade(CascadingAction.java
:218)
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave(
AbstractSaveEventListener.java:431)
    at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
AbstractSaveEventListener.java:265)
    at org.hibernate.event.def.AbstractSaveEventListener.performSave(
AbstractSaveEventListener.java:181)
    at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
(AbstractSaveEventListener.java:107)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
(DefaultSaveOrUpdateEventListener.java:187)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(
DefaultSaveOrUpdateEventListener.java:172)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
(DefaultSaveOrUpdateEventListener.java:94)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
DefaultSaveOrUpdateEventListener.java:70)
    at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
    at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
    at org.hibernate.engine.CascadingAction$1.cascade(CascadingAction.java
:218)
    at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java
:296)
    at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
    at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
    at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
    at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
    at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(
AbstractSaveEventListener.java:456)
    at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
AbstractSaveEventListener.java:334)
    at org.hibernate.event.def.AbstractSaveEventListener.performSave(
AbstractSaveEventListener.java:181)
    at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
(AbstractSaveEventListener.java:107)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
(DefaultSaveOrUpdateEventListener.java:187)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(
DefaultSaveOrUpdateEventListener.java:172)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
(DefaultSaveOrUpdateEventListener.java:94)
    at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
DefaultSaveOrUpdateEventListener.java:70)
    at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
    at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
    ... 13 more
-- 
Bertrand BECKERT
PhD student
IBMC - UPR 9002 du CNRS - ARN
15, rue Rene Descartes
F-67084 STRASBOURG Cedex

b.beckert at ibmc.u-strasbg.fr
bertrand.beckert at gmail.com

From zagato.gekko at gmail.com  Fri Apr 20 12:43:25 2007
From: zagato.gekko at gmail.com (Zagato)
Date: Fri, 20 Apr 2007 11:43:25 -0500
Subject: [Biojava-l] Biojavax and hibernate problems
In-Reply-To: <500217090704200138x4c2f39d9wa80cc39fdf475ca5@mail.gmail.com>
References: <500217090704200138x4c2f39d9wa80cc39fdf475ca5@mail.gmail.com>
Message-ID: <98028b00704200943v620d6df5j1fea96e4c85e5f13@mail.gmail.com>

Hello.... i wonder if a more simple procedure works or not....

Try don't using a RichSequenceDB, commenting:
           // RichSequenceDB db = new BioSQLRichSequenceDB(session);

And try using...

            t = session.beginTransaction();
            session.saveOrUpdate( "Sequence", gbkSeq );
            t.commit();

This is without using a RichSequenceDB object, but using a RichSequence
directly....

I used this for load a set of sequences in my postgres BioSQL database and
works for me.... Bye :D !!!!

Alan Jairo Acosta
Cali - Colombia

On 4/20/07, bertrand beckert <bertrand.beckert at gmail.com> wrote:
>
> Dear all,
>
> I am newbie  to java and biojavax... I have installed the BioSQL database
> and I have tried to connect to this base an put some data... In oder to do
> this I have installed Biojavax, and also hibernate (and the different .jar
> required). So I have tried to put some data but it didn't work... here is
> my
> code and the error in the output.
>
> Could you help me please. Thanks
>
> ---------
>
> package fr.ustrasbg.ibmc.bbeckert;
>
> import org.biojavax.bio.seq.io.RichSequenceBuilderFactory;
> import org.biojavax.bio.seq.io.RichSequenceFormat;
> import org.biojavax.bio.seq.io.RichStreamReader;
> import org.biojavax.bio.seq.io.GenbankFormat;
> import org.biojavax.bio.seq.RichSequence;
> import org.biojavax.bio.seq.RichFeature;
> import org.biojavax.bio.db.RichSequenceDB;
> import org.biojavax.bio.db.biosql.BioSQLRichSequenceDB;
> import org.biojavax.RichObjectFactory;
> import org.biojava.bio.BioException;
> import org.biojava.bio.seq.db.IllegalIDException;
> import org.hibernate.Session;
> import org.hibernate.SessionFactory;
> import org.hibernate.Transaction;
> import org.hibernate.HibernateException;
> import org.hibernate.cfg.Configuration;
>
> import java.io.File;
> import java.io.BufferedReader;
> import java.io.FileReader;
> import java.io.IOException;
> import java.util.Iterator;
>
> public class HibernatLoadingData {
>
>     public RichSequence gbkRichSeq (File f) {
>         [....]
>        return sequence;
>     }
>
> public static void loadingData (RichSequence gbkSeq){
>
>         SessionFactory sessionFactory = new
> Configuration().configure().buildSessionFactory();
>         Session session = sessionFactory.openSession();
>         RichObjectFactory.connectToBioSQL(session);
>         RichSequenceDB db = new BioSQLRichSequenceDB(session);
>
>         Transaction t=null;
>         try{
>             t = session.beginTransaction();
>             //test to kown is the database is active->true
>             System.out.println(t.isActive());
>             db.addRichSequence(gbkSeq);            //it should work...
>             t.commit();
>         } catch (HibernateException e) {
>             e.printStackTrace();
>             if (t != null && t.isActive())
>                 t.rollback();
>         } catch (BioException e) {
>                 e.printStackTrace();
>             }
>             session.close();
>         }
>
> public static void main(String[] args) {
>
>         File f = new
> File("/home/bertrand/IdeaProjects/ncRNAs/data/test.gbk");
>         HibernatLoadingData hl= new HibernatLoadingData();
>         RichSequence sequence=hl.gbkRichSeq(f);
>         loadingData(sequence);
>   }
> }
>
>
> output:
>              RichSequence gbkRichSeq:
>
> sequence name:CAK20891 AC:CAK20891
> Division:BCT
> length:688
> Protein start:1 end:688 Strand:POSITIVE
> MSKDFLLEIGLEEMPAQYVTSSVAQLEKRVSDWLNENQITFEKIKTYSTPRRLTVLVEAM
> AEEQANRVEEAKGPAKKIALDDEGNWSKAALGFARSQKVEPADLTFREIKGVEYIYIKKE
> VIGEKTTALLPSLEKVVTSMTFPVSMHWGSNDLRYIRPIKWLIAMFGEEIIPFEITGVST
> SNTSRGHRFLGKTATIKQPSDYPNALLEQFVVVNAEERKQAIVEQLRELESMENWQIKED
> EDLLEEVTNLVEYPTVLAGNFEKEYLELPEEVLITTMKEHQRYFPVFSKDEELLPHFVTV
> RNGNHENLDTVARGNEKVLRARLSDADFFYQEDLKITIDEAVAKLQNIVFHEKLGTLTEK
> MKRVQKVALMLADYLDWQEEDKQDIIRLTNIYKFDLVTNIVGEFPELQGLMGEKYALLQG
> EKPAIAIAIREHYLPSSAEGALPQTDLGSIIAIADKLETLVGFFCVNIVPTGSADPFGLR
> RSAFGAMRIIQANGWDIPVLELLSRIVDMERAEGAVELPSDDVKKEVQTFLKNRLRVVLQ
> NHHIRHDIIDAVIGGDPNTIPQLVDRAQILNKHVESDWFRPTVEALTRVMNISKKHEGNV
> EVDPSLFENKYEQALFDEIEKLKYDYANLTIVDRLRAFAALRTTIDDYFDNTLVMSENIE
> LKNNRLALLFELASFIKEFAQMDEINVK
> (log4j.properties)
> 10:14:06,582  INFO Environment:509 - Hibernate 3.2.3
> 10:14:06,589  INFO Environment:542 - hibernate.properties not found
> 10:14:06,596  INFO Environment:676 - Bytecode provider name : cglib
> 10:14:06,600  INFO Environment:593 - using JDK 1.4
> java.sql.Timestamphandling
> 10:14:06,685  INFO Configuration:1426 - configuring from resource:
> /hibernate.cfg.xml
> 10:14:06,686  INFO Configuration:1403 - Configuration resource:
> /hibernate.cfg.xml
> 10:14:06,783  INFO Configuration:553 - Reading mappings from resource :
> Namespace.hbm.xml
> 10:14:06,966  INFO HbmBinder:300 - Mapping class: Namespace -> biodatabase
> [...]
> Exception in thread "main" java.lang.RuntimeException: Error while trying
> to
> save RichSequence with id: CAK20891
>     at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB._addRichSequence(
> BioSQLRichSequenceDB.java:300)
>     at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.addRichSequence(
> BioSQLRichSequenceDB.java:277)
>     at fr.ustrasbg.ibmc.bbeckert.HibernatLoadingData.loadingData(
> HibernatLoadingData.java:101)
>     at fr.ustrasbg.ibmc.bbeckert.HibernatLoadingData.main(
> HibernatLoadingData.java:140)
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at sun.reflect.NativeMethodAccessorImpl.invoke(
> NativeMethodAccessorImpl.java:39)
>     at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:25)
>     at java.lang.reflect.Method.invoke(Method.java:585)
>     at com.intellij.rt.execution.application.AppMain.main(AppMain.java:90)
> Caused by: java.lang.reflect.InvocationTargetException
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at sun.reflect.NativeMethodAccessorImpl.invoke(
> NativeMethodAccessorImpl.java:39)
>     at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:25)
>     at java.lang.reflect.Method.invoke(Method.java:585)
>     at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB._addRichSequence(
> BioSQLRichSequenceDB.java:297)
>     ... 8 more
> Caused by: org.hibernate.TransientObjectException: object references an
> unsaved transient instance - save the transient instance before flushing:
> Term
>     at org.hibernate.engine.ForeignKeys.getEntityIdentifierIfNotUnsaved(
> ForeignKeys.java:219)
>     at org.hibernate.collection.AbstractPersistentCollection.getOrphans(
> AbstractPersistentCollection.java:889)
>     at org.hibernate.collection.PersistentSet.getOrphans(
> PersistentSet.java
> :90)
>     at org.hibernate.engine.CollectionEntry.getOrphans(
> CollectionEntry.java
> :350)
>     at org.hibernate.engine.Cascade.deleteOrphans(Cascade.java:340)
>     at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java
> :324)
>     at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
>     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
>     at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>     at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
>     at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(
> AbstractSaveEventListener.java:456)
>     at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
> AbstractSaveEventListener.java:334)
>     at org.hibernate.event.def.AbstractSaveEventListener.performSave(
> AbstractSaveEventListener.java:181)
>     at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
> (AbstractSaveEventListener.java:107)
>     at
>
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
> (DefaultSaveOrUpdateEventListener.java:187)
>     at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient
> (
> DefaultSaveOrUpdateEventListener.java:172)
>     at
>
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
> (DefaultSaveOrUpdateEventListener.java:94)
>     at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
> DefaultSaveOrUpdateEventListener.java:70)
>     at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java
> :507)
>     at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
>     at org.hibernate.engine.CascadingAction$1.cascade(CascadingAction.java
> :218)
>     at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
>     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
>     at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>     at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
>     at org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave
> (
> AbstractSaveEventListener.java:431)
>     at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
> AbstractSaveEventListener.java:265)
>     at org.hibernate.event.def.AbstractSaveEventListener.performSave(
> AbstractSaveEventListener.java:181)
>     at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
> (AbstractSaveEventListener.java:107)
>     at
>
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
> (DefaultSaveOrUpdateEventListener.java:187)
>     at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient
> (
> DefaultSaveOrUpdateEventListener.java:172)
>     at
>
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
> (DefaultSaveOrUpdateEventListener.java:94)
>     at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
> DefaultSaveOrUpdateEventListener.java:70)
>     at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java
> :507)
>     at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
>     at org.hibernate.engine.CascadingAction$1.cascade(CascadingAction.java
> :218)
>     at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
>     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
>     at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>     at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
>     at org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave
> (
> AbstractSaveEventListener.java:431)
>     at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
> AbstractSaveEventListener.java:265)
>     at org.hibernate.event.def.AbstractSaveEventListener.performSave(
> AbstractSaveEventListener.java:181)
>     at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
> (AbstractSaveEventListener.java:107)
>     at
>
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
> (DefaultSaveOrUpdateEventListener.java:187)
>     at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient
> (
> DefaultSaveOrUpdateEventListener.java:172)
>     at
>
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
> (DefaultSaveOrUpdateEventListener.java:94)
>     at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
> DefaultSaveOrUpdateEventListener.java:70)
>     at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java
> :507)
>     at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
>     at org.hibernate.engine.CascadingAction$1.cascade(CascadingAction.java
> :218)
>     at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
>     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
>     at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>     at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java
> :296)
>     at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
>     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
>     at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>     at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
>     at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(
> AbstractSaveEventListener.java:456)
>     at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
> AbstractSaveEventListener.java:334)
>     at org.hibernate.event.def.AbstractSaveEventListener.performSave(
> AbstractSaveEventListener.java:181)
>     at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
> (AbstractSaveEventListener.java:107)
>     at
>
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
> (DefaultSaveOrUpdateEventListener.java:187)
>     at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient
> (
> DefaultSaveOrUpdateEventListener.java:172)
>     at
>
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
> (DefaultSaveOrUpdateEventListener.java:94)
>     at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
> DefaultSaveOrUpdateEventListener.java:70)
>     at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java
> :507)
>     at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
>     ... 13 more
> --
> Bertrand BECKERT
> PhD student
> IBMC - UPR 9002 du CNRS - ARN
> 15, rue Rene Descartes
> F-67084 STRASBOURG Cedex
>
> b.beckert at ibmc.u-strasbg.fr
> bertrand.beckert at gmail.com
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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

From zagato.gekko at gmail.com  Tue Apr 24 10:41:40 2007
From: zagato.gekko at gmail.com (Zagato)
Date: Tue, 24 Apr 2007 09:41:40 -0500
Subject: [Biojava-l] Biojavax and hibernate problems
In-Reply-To: <500217090704230052w2bd845deu3f9df632d1aec2cb@mail.gmail.com>
References: <500217090704200138x4c2f39d9wa80cc39fdf475ca5@mail.gmail.com>
	<98028b00704200943v620d6df5j1fea96e4c85e5f13@mail.gmail.com>
	<500217090704230052w2bd845deu3f9df632d1aec2cb@mail.gmail.com>
Message-ID: <98028b00704240741m2801eccdxf53db3d2360dbbfb@mail.gmail.com>

Hello....

May be using RichStreamReader doesn't complete right the asocciate
information for the sequence, like references and annotations, i don't
know... why don't you try using org.biojavax.bio.seq.RichSequence.IOTools,
they implements a lots of good tools for reading sequences....

May be something like this:

String path = "/home/bertrand/IdeaProjects/ncRNAs/data/test.gbk";
BufferedReader br = new BufferedReader( new FileReader(path) );
RichSequenceIterator rsi =
org.biojavax.bio.seq.RichSequence.IOTools.readGenbankDNA( br, new
SimpleNamespace("sequence") );
// or readGenbankRNA if you have an ARN sequence: go to:
http://www.biojava.org/docs/api15b/org/biojavax/bio/seq/RichSequence.IOTools.html
while( rsi.hasNext() )
{
    RichSequence sequence = rsi.nextRichSequence();
    System.out.println( "Sequence identifier: "+sequence.getIdentifier() );
    try{
        tx.begin();
        session.saveOrUpdate( "Sequence", sequence );
        tx.commit();
    } catch(HibernateException ex){
        tx.rollback();
        ex.printStackTrace();
    }
}

i don't remember if this automaticaly saves the BioEntry for the Sequence, i
think yes, because the foreign key in the DB, in any case yo can retrive the
BioEntry genereted by IOTools from RichSequenceIterator using:
org.biojavax.bio.BioEntry bioentry = rsi.nextBioEntry();
// System.out.println( "Bioentry name: "+bioentry.getName() );

I hope this helps to you, and I'm recommend to you, read
http://www.biojava.org/wiki/BioJava:BioJavaXDocs ....

Bye...

Alan Jairo Acosta
Cali - Colombia

On 4/23/07, bertrand beckert <bertrand.beckert at gmail.com> wrote:
>
> Ok? I have tried what you said and it work for a simple exemple...
> Before I have tried to read my genbank file without using SessionFactory
> and it work well, it gave me the sequence and the anotation. But when I use
> SessionFactory and still using first RichStreamReader and then a
> RichSequence sequence as befotre it don't work anymore... I don't
> understand. Here is my code:
>
> public class LoadingData {
>
>      public static void addInDataBase() {
>        SessionFactory hibernateFactory = new
> Configuration().configure().buildSessionFactory();
>        Session session = hibernateFactory.openSession ();
>        RichObjectFactory.connectToBioSQL(session);
>        Transaction tx=session.beginTransaction();
>         try {
>             File f = new
> File("/home/bertrand/IdeaProjects/ncRNAs/data/test.gbk");
>             BufferedReader br = new BufferedReader(new FileReader(f));
>             RichSequenceFormat format = new GenbankFormat();
>             RichStreamReader seqsIn= new RichStreamReader(br,format,
> format.guessSymbolTokenization (f), RichSequenceBuilderFactory.FACTORY,new
> SimpleNamespace("sequence"));
>             RichSequence sequence = seqsIn.nextRichSequence();
>             tx.begin();
>             session.saveOrUpdate( "Sequence", sequence );
>             tx.commit();
>         } catch(HibernateException ex){
>              tx.rollback();
>             ex.printStackTrace();
>              System.out.println("Transaction error.");
>         }catch (IOException e) {
>         e.printStackTrace();
>         System.out.println("No file\n");
>         }catch (BioException e){
>         e.printStackTrace();
>         System.out.println("bioexeception\n");
>         } finally {
>            session.close();
>         }
>      }
>
>       public static void main(String[] args) {
>           addInDataBase();
>           }
>       }
>
> the error message:
>
> /usr/local/share/jdk1.5.0_03/bin/java - Didea.launcher.port=7533 -
> Didea.launcher.bin.path=/usr/local/share/idea-4192/bin -
> Dfile.encoding=UTF-8 -classpath
> /usr/local/share/jdk1.5.0_03/jre/lib/jce.jar:/usr/local/share/jdk1.5.0_03/jre/lib/javaws.jar:/usr/local/share/jdk1.5.0_03/jre/lib/jsse.jar:/usr/local/share/jdk1.5.0_03/jre/lib/deploy.jar:/usr/local/share/jdk1.5.0_03/jre/lib/charsets.jar:/usr/local/share/jdk1.5.0_03/jre/lib/plugin.jar:/usr/local/share/jdk1.5.0_03/jre/lib/rt.jar:/usr/local/share/jdk1.5.0_03/jre/lib/ext/sunjce_provider.jar:/usr/local/share/jdk1.5.0_03/jre/lib/ext/sunpkcs11.jar:/usr/local/share/jdk1.5.0_03/jre/lib/ext/dnsns.jar:/usr/local/share/jdk1.5.0_03/jre/lib/ext/localedata.jar:/home/bertrand/IdeaProjects/ncRNAs/build:/home/bertrand/IdeaProjects/ncRNAs/lib/mysql-
>
> connector-java-3.0.11-stable-bin.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/biojava-1.5-beta2.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/bytecode.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/commons-cli.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/hibernate3.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/log4j-1.2.11.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/asm.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/cglib-2.1.3.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/dom4j-1.6.1.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/jta.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/commons-logging-1.0.4.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/asm-attrs.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/ehcache-1.2.3.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/commons-collections-2.1.1.jar:/home/bertrand/IdeaProjects/ncRNAs/lib/antlr-2.7.5.jar:/usr/local/share/idea-4192/lib/idea_rt.jar
> com.intellij.rt.execution.application.AppMain
> fr.ustrasbg.ibmc.bbeckert.LoadingData
> 09:42:29,423  INFO Environment:509 - Hibernate 3.2.3
> 09:42:29,432  INFO Environment:542 - hibernate.properties not found
> 09:42:29,436  INFO Environment:676 - Bytecode provider name : cglib
> 09:42:29,449  INFO Environment:593 - using JDK 1.4 java.sql.Timestamphandling
> 09:42:29,656  INFO Configuration:1426 - configuring from resource:
> /hibernate.cfg.xml
> [...]
> 9:42:31,473  INFO SettingsFactory:250 - Optimize cache for minimal puts:
> disabled
> 09:42:31,474  INFO SettingsFactory:259 - Structured second-level cache
> entries: disabled
> 09:42:31,478  INFO SettingsFactory:286 - Statistics: disabled
> 09:42:31,478  INFO SettingsFactory:290 - Deleted entity synthetic
> identifier rollback: disabled
> 09:42:31,478  INFO SettingsFactory:305 - Default entity-mode: pojo
> 09:42:31,479  INFO SettingsFactory:309 - Named query checking : enabled
> 09:42:31,504  INFO SessionFactoryImpl:161 - building session factory
> 09:42:32,064  INFO SessionFactoryObjectFactory:82 - Not binding factory to
> JNDI, no JNDI name configured
> 09:42:32,467 DEBUG SQL:401 - select ontology0_.ontology_id as
> ontology1_3_, ontology0_.name as name3_, ontology0_.definition as
> definition3_ from ontology ontology0_ where ontology0_.name=?
> 09:42:32,550 DEBUG SQL:401 - insert into ontology (name, definition)
> values (?, ?)
> 09:42:32,682 DEBUG SQL:401 - insert into term (name, identifier,
> definition, is_obsolete, ontology_id) values (?, ?, ?, ?, ?)
> 09:42:32,686 DEBUG SQL:401 - insert into term (name, identifier,
> definition, is_obsolete, ontology_id) values (?, ?, ?, ?, ?)
> 09:42:32,751 DEBUG SQL:401 - insert into term (name, identifier,
> definition, is_obsolete, ontology_id) values (?, ?, ?, ?, ?)
> 09:42:32,755 DEBUG SQL:401 - insert into term (name, identifier,
> definition, is_obsolete, ontology_id) values (?, ?, ?, ?, ?)
> 09:42:32,758 DEBUG SQL:401 - insert into term (name, identifier,
> definition, is_obsolete, ontology_id) values (?, ?, ?, ?, ?)
> 09:42:32,768 DEBUG SQL:401 - select crossref0_.dbxref_id as dbxref1_16_,
> crossref0_.dbname as dbname16_, crossref0_.accession as accession16_,
> crossref0_.version as version16_ from dbxref crossref0_ where
> crossref0_.dbname=? and crossref0_.accession=? and crossref0_.version=?
> 09:42:32,771 DEBUG SQL:401 - insert into dbxref (dbname, accession,
> version) values (?, ?, ?)
> 09:42:32,785 DEBUG SQL:401 - select docref0_.reference_id as
> reference1_18_, docref0_.title as title18_, docref0_.authors as authors18_,
> docref0_.location as location18_, docref0_.crc as crc18_, docref0_.dbxref_id
> as dbxref6_18_ from reference docref0_ where docref0_.authors=? and
> docref0_.location=? and docref0_.title=?
> org.biojava.bio.BioException: Could not read sequence
>     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> RichStreamReader.java:113)
>     at fr.ustrasbg.ibmc.bbeckert.LoadingData.addInDataBase(
> LoadingData.java :41)
>     at fr.ustrasbg.ibmc.bbeckert.LoadingData.main(LoadingData.java:61)
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at sun.reflect.NativeMethodAccessorImpl.invoke(
> NativeMethodAccessorImpl.java :39)
>     at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:25)
>     at java.lang.reflect.Method.invoke(Method.java:585)
>     at com.intellij.rt.execution.application.AppMain.main( AppMain.java
> :90)
> Caused by: java.lang.RuntimeException: Error while trying to call new
> class org.biojavax.SimpleDocRef(class java.lang.String,class
> java.lang.String,class java.lang.String)
>     at org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject (
> BioSQLRichObjectBuilder.java:166)
>     at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java
> :105)
>     at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> GenbankFormat.java:396)
>     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence (
> RichStreamReader.java:110)
>     ... 7 more
> Caused by: java.lang.NoSuchMethodException: org.biojavax.SimpleDocRef
> .<init>(java.lang.String, java.lang.String, java.lang.String)
> bioexeception
>     at java.lang.Class.getConstructor0 (Class.java:2647)
>
>     at java.lang.Class.getConstructor(Class.java:1629)
>     at org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(
> BioSQLRichObjectBuilder.java:147)
>     ... 10 more
>
> Process finished with exit code 0
>
>
> 2007/4/20, Zagato <zagato.gekko at gmail.com>:
> >
> > Hello.... i wonder if a more simple procedure works or not....
> >
> > Try don't using a RichSequenceDB, commenting:
> >            // RichSequenceDB db = new BioSQLRichSequenceDB(session);
> >
> > And try using...
> >
> >             t = session.beginTransaction();
> >             session.saveOrUpdate( "Sequence", gbkSeq );
> >             t.commit();
> >
> > This is without using a RichSequenceDB object, but using a RichSequence
> > directly....
> >
> > I used this for load a set of sequences in my postgres BioSQL database
> > and works for me.... Bye :D !!!!
> >
> > Alan Jairo Acosta
> > Cali - Colombia
> >
> > On 4/20/07, bertrand beckert <bertrand.beckert at gmail.com> wrote:
> >
> > >  Dear all,
> > >
> > > I am newbie  to java and biojavax... I have installed the BioSQL
> > > database
> > > and I have tried to connect to this base an put some data... In oder
> > > to do
> > > this I have installed Biojavax, and also hibernate (and the different
> > > .jar
> > > required). So I have tried to put some data but it didn't work... here
> > > is my
> > > code and the error in the output.
> > >
> > > Could you help me please. Thanks
> > >
> > > ---------
> > >
> > > package fr.ustrasbg.ibmc.bbeckert;
> > >
> > > import org.biojavax.bio.seq.io.RichSequenceBuilderFactory;
> > > import org.biojavax.bio.seq.io.RichSequenceFormat;
> > > import org.biojavax.bio.seq.io.RichStreamReader;
> > > import org.biojavax.bio.seq.io.GenbankFormat;
> > > import org.biojavax.bio.seq.RichSequence;
> > > import org.biojavax.bio.seq.RichFeature;
> > > import org.biojavax.bio.db.RichSequenceDB;
> > > import org.biojavax.bio.db.biosql.BioSQLRichSequenceDB;
> > > import org.biojavax.RichObjectFactory ;
> > > import org.biojava.bio.BioException;
> > > import org.biojava.bio.seq.db.IllegalIDException;
> > > import org.hibernate.Session;
> > > import org.hibernate.SessionFactory;
> > > import org.hibernate.Transaction;
> > > import org.hibernate.HibernateException ;
> > > import org.hibernate.cfg.Configuration;
> > >
> > > import java.io.File;
> > > import java.io.BufferedReader;
> > > import java.io.FileReader;
> > > import java.io.IOException;
> > > import java.util.Iterator;
> > >
> > > public class HibernatLoadingData {
> > >
> > >     public RichSequence gbkRichSeq (File f) {
> > >         [....]
> > >        return sequence;
> > >     }
> > >
> > > public static void loadingData (RichSequence gbkSeq){
> > >
> > >         SessionFactory sessionFactory = new
> > > Configuration().configure().buildSessionFactory();
> > >         Session session = sessionFactory.openSession();
> > >         RichObjectFactory.connectToBioSQL(session);
> > >         RichSequenceDB db = new BioSQLRichSequenceDB(session);
> > >
> > >         Transaction t=null;
> > >         try{
> > >             t = session.beginTransaction();
> > >             //test to kown is the database is active->true
> > >             System.out.println(t.isActive());
> > >              db.addRichSequence(gbkSeq);            //it should
> > > work...
> > >             t.commit();
> > >         } catch (HibernateException e) {
> > >             e.printStackTrace();
> > >             if (t != null && t.isActive())
> > >                 t.rollback();
> > >         } catch (BioException e) {
> > >                 e.printStackTrace();
> > >             }
> > >             session.close();
> > >         }
> > >
> > > public static void main(String[] args) {
> > >
> > >         File f = new
> > > File("/home/bertrand/IdeaProjects/ncRNAs/data/test.gbk");
> > >         HibernatLoadingData hl= new HibernatLoadingData();
> > >         RichSequence sequence=hl.gbkRichSeq(f);
> > >         loadingData(sequence);
> > >   }
> > > }
> > >
> > >
> > > output:
> > >              RichSequence gbkRichSeq:
> > >
> > > sequence name:CAK20891 AC:CAK20891
> > > Division:BCT
> > > length:688
> > > Protein start:1 end:688 Strand:POSITIVE
> > > MSKDFLLEIGLEEMPAQYVTSSVAQLEKRVSDWLNENQITFEKIKTYSTPRRLTVLVEAM
> > > AEEQANRVEEAKGPAKKIALDDEGNWSKAALGFARSQKVEPADLTFREIKGVEYIYIKKE
> > > VIGEKTTALLPSLEKVVTSMTFPVSMHWGSNDLRYIRPIKWLIAMFGEEIIPFEITGVST
> > > SNTSRGHRFLGKTATIKQPSDYPNALLEQFVVVNAEERKQAIVEQLRELESMENWQIKED
> > > EDLLEEVTNLVEYPTVLAGNFEKEYLELPEEVLITTMKEHQRYFPVFSKDEELLPHFVTV
> > > RNGNHENLDTVARGNEKVLRARLSDADFFYQEDLKITIDEAVAKLQNIVFHEKLGTLTEK
> > > MKRVQKVALMLADYLDWQEEDKQDIIRLTNIYKFDLVTNIVGEFPELQGLMGEKYALLQG
> > > EKPAIAIAIREHYLPSSAEGALPQTDLGSIIAIADKLETLVGFFCVNIVPTGSADPFGLR
> > > RSAFGAMRIIQANGWDIPVLELLSRIVDMERAEGAVELPSDDVKKEVQTFLKNRLRVVLQ
> > > NHHIRHDIIDAVIGGDPNTIPQLVDRAQILNKHVESDWFRPTVEALTRVMNISKKHEGNV
> > > EVDPSLFENKYEQALFDEIEKLKYDYANLTIVDRLRAFAALRTTIDDYFDNTLVMSENIE
> > > LKNNRLALLFELASFIKEFAQMDEINVK
> > > (log4j.properties)
> > > 10:14:06,582  INFO Environment:509 - Hibernate 3.2.3
> > > 10:14:06,589  INFO Environment:542 - hibernate.properties not found
> > > 10:14:06,596  INFO Environment:676 - Bytecode provider name : cglib
> > > 10:14:06,600  INFO Environment:593 - using JDK 1.4
> > > java.sql.Timestamphandling
> > > 10:14:06,685  INFO Configuration:1426 - configuring from resource:
> > > /hibernate.cfg.xml
> > > 10:14:06,686  INFO Configuration:1403 - Configuration resource:
> > > /hibernate.cfg.xml
> > > 10:14:06,783  INFO Configuration:553 - Reading mappings from resource
> > > :
> > > Namespace.hbm.xml
> > > 10:14:06,966  INFO HbmBinder:300 - Mapping class: Namespace ->
> > > biodatabase
> > > [...]
> > > Exception in thread "main" java.lang.RuntimeException: Error while
> > > trying to
> > > save RichSequence with id: CAK20891
> > >     at
> > > org.biojavax.bio.db.biosql.BioSQLRichSequenceDB._addRichSequence(
> > > BioSQLRichSequenceDB.java:300)
> > >     at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.addRichSequence
> > > (
> > > BioSQLRichSequenceDB.java:277)
> > >     at fr.ustrasbg.ibmc.bbeckert.HibernatLoadingData.loadingData(
> > > HibernatLoadingData.java:101)
> > >     at fr.ustrasbg.ibmc.bbeckert.HibernatLoadingData.main(
> > > HibernatLoadingData.java:140)
> > >     at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
> > >     at sun.reflect.NativeMethodAccessorImpl.invoke(
> > > NativeMethodAccessorImpl.java:39)
> > >     at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> > > DelegatingMethodAccessorImpl.java:25)
> > >     at java.lang.reflect.Method.invoke (Method.java:585)
> > >     at com.intellij.rt.execution.application.AppMain.main(AppMain.java
> > > :90)
> > > Caused by: java.lang.reflect.InvocationTargetException
> > >     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > >     at sun.reflect.NativeMethodAccessorImpl.invoke(
> > > NativeMethodAccessorImpl.java:39)
> > >     at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> > > DelegatingMethodAccessorImpl.java:25)
> > >     at java.lang.reflect.Method.invoke (Method.java:585)
> > >     at
> > > org.biojavax.bio.db.biosql.BioSQLRichSequenceDB._addRichSequence(
> > > BioSQLRichSequenceDB.java:297)
> > >     ... 8 more
> > > Caused by: org.hibernate.TransientObjectException: object references
> > > an
> > > unsaved transient instance - save the transient instance before
> > > flushing:
> > > Term
> > >     at
> > > org.hibernate.engine.ForeignKeys.getEntityIdentifierIfNotUnsaved(
> > > ForeignKeys.java:219)
> > >     at
> > > org.hibernate.collection.AbstractPersistentCollection.getOrphans (
> > > AbstractPersistentCollection.java:889)
> > >     at org.hibernate.collection.PersistentSet.getOrphans(
> > > PersistentSet.java
> > > :90)
> > >     at org.hibernate.engine.CollectionEntry.getOrphans(
> > > CollectionEntry.java
> > > :350)
> > >     at org.hibernate.engine.Cascade.deleteOrphans(Cascade.java:340)
> > >     at org.hibernate.engine.Cascade.cascadeCollectionElements(
> > > Cascade.java
> > > :324)
> > >     at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
> > >     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java
> > > :219)
> > >     at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
> > >     at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
> > >     at
> > > org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(
> > > AbstractSaveEventListener.java:456)
> > >     at
> > >
> > > org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate
> > > (
> > > AbstractSaveEventListener.java :334)
> > >     at org.hibernate.event.def.AbstractSaveEventListener.performSave(
> > > AbstractSaveEventListener.java:181)
> > >     at
> > > org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
> > > (AbstractSaveEventListener.java :107)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
> > > (DefaultSaveOrUpdateEventListener.java:187)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(
> > > DefaultSaveOrUpdateEventListener.java:172)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
> > > (DefaultSaveOrUpdateEventListener.java:94)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
> > > DefaultSaveOrUpdateEventListener.java:70)
> > >     at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(
> > > SessionImpl.java:507)
> > >     at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java
> > > :499)
> > >     at org.hibernate.engine.CascadingAction$1.cascade (
> > > CascadingAction.java
> > > :218)
> > >     at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
> > >     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java
> > > :216)
> > >     at org.hibernate.engine.Cascade.cascadeProperty (Cascade.java:169)
> > >     at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
> > >     at
> > > org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave(
> > > AbstractSaveEventListener.java:431)
> > >     at
> > >
> > > org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
> > > AbstractSaveEventListener.java:265)
> > >     at org.hibernate.event.def.AbstractSaveEventListener.performSave(
> > > AbstractSaveEventListener.java:181)
> > >     at
> > > org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
> > > (AbstractSaveEventListener.java:107)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
> > > (DefaultSaveOrUpdateEventListener.java:187)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(
> > > DefaultSaveOrUpdateEventListener.java:172)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
> > > (DefaultSaveOrUpdateEventListener.java:94)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
> > > DefaultSaveOrUpdateEventListener.java:70)
> > >     at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(
> > > SessionImpl.java:507)
> > >     at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java
> > > :499)
> > >     at org.hibernate.engine.CascadingAction$1.cascade (
> > > CascadingAction.java
> > > :218)
> > >     at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
> > >     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java
> > > :216)
> > >     at org.hibernate.engine.Cascade.cascadeProperty (Cascade.java:169)
> > >     at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
> > >     at
> > > org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave(
> > > AbstractSaveEventListener.java:431)
> > >     at
> > >
> > > org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(
> > > AbstractSaveEventListener.java:265)
> > >     at org.hibernate.event.def.AbstractSaveEventListener.performSave(
> > > AbstractSaveEventListener.java:181)
> > >     at
> > > org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
> > > (AbstractSaveEventListener.java:107)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
> > > (DefaultSaveOrUpdateEventListener.java:187)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(
> > > DefaultSaveOrUpdateEventListener.java:172)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
> > > (DefaultSaveOrUpdateEventListener.java:94)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
> > > DefaultSaveOrUpdateEventListener.java:70)
> > >     at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(
> > > SessionImpl.java:507)
> > >     at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java
> > > :499)
> > >     at org.hibernate.engine.CascadingAction$1.cascade (
> > > CascadingAction.java
> > > :218)
> > >     at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
> > >     at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java
> > > :216)
> > >     at org.hibernate.engine.Cascade.cascadeProperty (Cascade.java:169)
> > >     at org.hibernate.engine.Cascade.cascadeCollectionElements(
> > > Cascade.java
> > > :296)
> > >     at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java
> > > :242)
> > >     at org.hibernate.engine.Cascade.cascadeAssociation (Cascade.java
> > > :219)
> > >     at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
> > >     at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
> > >     at
> > > org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave (
> > > AbstractSaveEventListener.java:456)
> > >     at
> > >
> > > org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate
> > > (
> > > AbstractSaveEventListener.java:334)
> > >     at org.hibernate.event.def.AbstractSaveEventListener.performSave (
> > > AbstractSaveEventListener.java:181)
> > >     at
> > > org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId
> > > (AbstractSaveEventListener.java:107)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId
> > > (DefaultSaveOrUpdateEventListener.java:187)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient
> > > (
> > > DefaultSaveOrUpdateEventListener.java:172)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate
> > > (DefaultSaveOrUpdateEventListener.java:94)
> > >     at
> > >
> > > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate
> > > (
> > > DefaultSaveOrUpdateEventListener.java:70)
> > >     at org.hibernate.impl.SessionImpl.fireSaveOrUpdate (
> > > SessionImpl.java:507)
> > >     at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java
> > > :499)
> > >     ... 13 more
> > > --
> > > Bertrand BECKERT
> > > PhD student
> > > IBMC - UPR 9002 du CNRS - ARN
> > > 15, rue Rene Descartes
> > > F-67084 STRASBOURG Cedex
> > >
> > > b.beckert at ibmc.u-strasbg.fr
> > > bertrand.beckert at gmail.com
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >
> >
> >
> >
> > --
> > Farewell.
> > http://www.youtube.com/zagatogekko
> > ruby << __EOF__
> >   puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
> > __EOF__
>
>
>
>
> --
> Bertrand BECKERT
> PhD student
> IBMC - UPR 9002 du CNRS - ARN
> 15, rue Rene Descartes
> F-67084 STRASBOURG Cedex
>
> b.beckert at ibmc.u-strasbg.fr
> bertrand.beckert at gmail.com
>



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

From koeberle at mpiib-berlin.mpg.de  Mon Apr 30 10:47:32 2007
From: koeberle at mpiib-berlin.mpg.de (=?ISO-8859-15?Q?Christian_K=F6berle?=)
Date: Mon, 30 Apr 2007 16:47:32 +0200
Subject: [Biojava-l] Ensembl Transcript ID
Message-ID: <46360184.1020002@mpiib-berlin.mpg.de>

Is it possible to download a Sequence-Object to a Ensembl Transcript ID?

-- 
Christian K?berle

Max Planck Institute for Infection Biology
Department of Immunology

Campus Charit? Mitte
Charit?platz 1

10117 Berlin

Tel: +49 30 28 460 562