From holland at eaglegenomics.com  Mon Jan  4 05:57:54 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 4 Jan 2010 10:57:54 +0000
Subject: [Biojava-l] BioJava 2010 Hackathon
Message-ID: <E304F7F2-09B7-4C46-92F9-F9CA6E68C5EC@eaglegenomics.com>

Hi all,

For those attending the 2010 BioJava hackathon at the Wellcome Trust Genome Campus, near Cambridge, all details can be found on this wiki:

  http://biojava.org/wiki/BioJava:Hackathon2010

If your name is not listed on the wiki but you are planning on attending, please let us know by Jan 12th latest. Due to security arrangements at the campus it is not possible to just turn up on the day.

Subjects for the hackathon are open for discussion on the wiki.

Looking forward to seeing you all there!

cheers,
Richard

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From andylu0320 at gmail.com  Sat Jan  9 21:36:29 2010
From: andylu0320 at gmail.com (Andy Lu)
Date: Sat, 9 Jan 2010 21:36:29 -0500
Subject: [Biojava-l] Jmol help
Message-ID: <4a1a3f7d1001091836q1e084357v156a6dae902ba21f@mail.gmail.com>

Hi, does anyone know how to add menu listener in JMol through JMol script?

I tried using this:

        viewer.evalString ("set debugScript;");
        viewer.evalString ("set ScriptCallback spacefill ;");

But is there a way to make the above to an "if" statement? Like if I click
the "ball and stick" option in the menu, then something happens?

Thanks!

From andreas at sdsc.edu  Sun Jan 10 07:20:28 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 10 Jan 2010 04:20:28 -0800
Subject: [Biojava-l] Jmol help
In-Reply-To: <4a1a3f7d1001091836q1e084357v156a6dae902ba21f@mail.gmail.com>
References: <4a1a3f7d1001091836q1e084357v156a6dae902ba21f@mail.gmail.com>
Message-ID: <59a41c431001100420n58c786efv4c014984978d695a@mail.gmail.com>

Hi Andy,

Not sure what you mean - you mean you want you want to create a menu
in a frame, which also contains a Jmol panel? Probably the easiest
solution is to create a JMenu with JMenuItems, add actionListeners to
them and these can trigger a script in Jmol.

Have a look at this tutorial
http://java.sun.com/docs/books/tutorial/uiswing/components/menu.html

Andreas


On Sat, Jan 9, 2010 at 6:36 PM, Andy Lu <andylu0320 at gmail.com> wrote:
> Hi, does anyone know how to add menu listener in JMol through JMol script?
>
> I tried using this:
>
> ? ? ? ?viewer.evalString ("set debugScript;");
> ? ? ? ?viewer.evalString ("set ScriptCallback spacefill ;");
>
> But is there a way to make the above to an "if" statement? Like if I click
> the "ball and stick" option in the menu, then something happens?
>
> Thanks!
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From chris at compbio.dundee.ac.uk  Mon Jan 11 09:34:21 2010
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Mon, 11 Jan 2010 14:34:21 +0000
Subject: [Biojava-l] Error parsing ipi.HUMAN.fasta file
In-Reply-To: <E29CC4D7-00B5-4666-AD0B-C1DE762F8787@eaglegenomics.com>
References: <4B2BA575.5010007@compbio.dundee.ac.uk>
	<991F3D0D-0702-4EB7-9718-676986A1415E@eaglegenomics.com>
	<4B4B16A6.7030406@compbio.dundee.ac.uk>
	<E29CC4D7-00B5-4666-AD0B-C1DE762F8787@eaglegenomics.com>
Message-ID: <4B4B36ED.9060105@compbio.dundee.ac.uk>

[ posting back to biojava-l as omitted the address previously ]

Ah, right. It wasn't clear on the wiki whether those were included or 
not with the 'all' package.

It compiles fine now (with one warning) and through trial and error a 
buffer value of 2000 works with ipi.HUMAN.fasta as well as mouse and 
chicken.

Thanks very much for your help.

Chris

On 11/01/10 12:31, Richard Holland wrote:
> Hello. You need to make sure the support libraries are also on your classpath:
>
> http://www.biojava.org/wiki/BioJava:Download#Support_libraries
>
> cheers,
> Richard
>
> On 11 Jan 2010, at 12:16, Chris Cole wrote:
>
>> Thanks for the reply, Richard.
>>
>> Just getting back to this problem. I've upped the buffer to 1000 bytes, but I can't get it to compile with ant. I get a whole slew of compile errors, there seems to be something missing, but I don't know how to solve it. Output from ant build follows:
>>
>> caterpillar: ~/Downloads/biojava-1.7/src>  ant -f ../build.xml
>> Buildfile: ../build.xml
>>
>> init:
>>      [echo] Building biojava-1.7
>>      [echo] Java Home:                       /usr/java/jdk1.6.0_17/jre
>>      [echo] JUnit present:                   ${junit.present}
>>      [echo] JUnit supported by Ant:          ${junit.support}
>>      [echo] HSQLDB driver present:           ${sqlDriver.hsqldb}
>>      [echo] XSLT support:                    true
>>
>> prepare:
>>
>> prepare-biojava:
>>
>> compile-biojava:
>>     [javac] Compiling 1462 source files to /opt/Downloads/biojava-1.7/ant-build/classes/biojava
>>     [javac] /opt/Downloads/biojava-1.7/src/org/biojava/bio/dp/twohead/DPCompiler.java:55: package org.biojava.utils.bytecode does not exist
>>     [javac] import org.biojava.utils.bytecode.ByteCode;
>>     [javac]                                  ^
>>     [javac] /opt/Downloads/biojava-1.7/src/org/biojava/bio/dp/twohead/DPCompiler.java:56: package org.biojava.utils.bytecode does not exist
>>     [javac] import org.biojava.utils.bytecode.CodeClass;
>>     [javac]                                  ^
>>     [javac] /opt/Downloads/biojava-1.7/src/org/biojava/bio/dp/twohead/DPCompiler.java:57: package org.biojava.utils.bytecode does not exist
>>     [javac] import org.biojava.utils.bytecode.CodeException;
>>     [javac]                                  ^
>> ...etc.
>>
>> I downloaded the biojava-1.7-all.jar, originally and I can't what else I need?
>>
>> I'm also trying to do this from within Eclipse, so any Eclipse-specific pointers would be much appreciated.
>> Cheers,
>>
>> Chris
>>
>> On 18/12/09 16:58, Richard Holland wrote:
>>> The FASTA parser has a buffer which it uses to read ahead to the next
>>> complete line then back up before it actually parses it on the second
>>> pass (in order to allow it to do things like hasNext()). The
>>> exception shows that the size of that buffer is being exceeded,
>>> causing it to fail to back up again afterwards.
>>>
>>> There's two cures - one is to rewrite the FASTA parser to buffer
>>> things in a different way. The other is to open up
>>> org/biojavax/bio/seq/io/FastaFormat.java in a text editor, search for
>>> the line where it sets the buffer (somewhere around line 202
>>> according to the exception, in the readRichSequence() method - the
>>> command to look for is 'mark'), and increase the buffer size to
>>> something suitably large enough (it's currently set at 500 bytes).
>>> Then recompile BioJava and it should work.
>>>
>>> cheers, Richard
>>>
>>> On 18 Dec 2009, at 15:53, Chris Cole wrote:
>>>
>>>> I'm wanting to parse a fasta file obtained from IPI using the code
>>>> at the bottom of this message, but I get the following error:
>>>>
>>>> org.biojava.bio.BioException: Could not read sequence at
>>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>>>>
>>>>
>> at test.readFasta(test.java:39)
>>>> at test.main(test.java:18) Caused by: java.io.IOException: Mark
>>>> invalid at java.io.BufferedReader.reset(BufferedReader.java:485) at
>>>> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:202)
>>>>
>>>>
>> at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>>>> ... 2 more
>>>>
>>>> Looking at the Fasta file itself and doing some tests, it seems to
>>>> fail consistently at one or two entries /preceding/ an entry with a
>>>> very long description line e.g.:
>>>>> IPI:IPI00021421.4|SWISS-PROT:Q9UMR5-1|TREMBL:B0S868|ENSEMBL:ENSP00000382748;ENSP00000382749;ENSP00000382750;ENSP00000387679;ENSP00000388341;ENSP00000388618;ENSP00000389930;ENSP00000392885;ENSP00000393009;ENSP00000395242;ENSP00000395562;ENSP00000397025;ENSP00000399879;ENSP00000403820;ENSP00000406496;ENSP00000406566;ENSP00000408703;ENSP00000411007;ENSP00000411625;ENSP00000412827|REFSEQ:NP_005146|VEGA:OTTHUMP00000014775;OTTHUMP00000014776;OTTHUMP00000014778;OTTHUMP00000175028;OTTHUMP00000175029;OTTHUMP00000175030;OTTHUMP00000193135;OTTHUMP00000193136;OTTHUMP00000193138;OTTHUMP00000193964;OTTHUMP00000193965;OTTHUMP00000193967;OTTHUMP00000194391;OTTHUMP00000194392;OTTHUMP00000194394
>>>>> Tax_Id=9606 Gene_Symbol=PPT2 Isoform 1 of Lysosomal thioesterase
>>>>> PPT2
>>>> MLGLWGQRLPAAWVLLLLPFLPLLLLAAPAPHRASYKPVIVVHGLFDSSYSFRHLLEYIN
>>>> ETHPGTVVTVLDLFDGRESLRPLWEQVQGFREAVVPIMAKAPQGVHLICYSQGGLVCRAL
>>>> LSVMDDHNVDSFISLSSPQMGQYGDTDYLKWLFPTSMRSNLYRICYSPWGQEFSICNYWH
>>>> DPHHDDLYLNASSFLALINGERDHPNATVWRKNFLRVGHLVLIGGPDDGVITPWQSSFFG
>>>> FYDANETVLEMEEQLVYLRDSFGLKTLLARGAIVRCPMAGISHTAWHSNRTLYETCIEPW LS
>>>>
>>>> Deleting the large entries allows the code to continue until it
>>>> reaches another long description line.
>>>>
>>>> It also seems to be a feature of large Fasta files as reading the
>>>> above sequence alone or as part of a small file is fine.
>>>>
>>>> Is this a known problem or am I doing something wrong? BTW I'm
>>>> using biojava 1.7 and Java 1.6.0_17. Any help would be most
>>>> appreciated. Cheers.
>>>>
>>>> code: import java.io.*;
>>>>
>>>> import org.biojava.bio.*; import org.biojavax.*; import
>>>> org.biojavax.bio.seq.*;
>>>>
>>>> public class test { private static PrintStream o = System.out;
>>>>
>>>> public static void main(String[] args) { // TODO Auto-generated
>>>> method stub readFasta(args[0]); }  public static void
>>>> readFasta(String filename) { try { o.println("Reading file: " +
>>>> filename); //prepare a BufferedReader for file io BufferedReader br
>>>> = new BufferedReader(new FileReader(filename));
>>>>
>>>> // read Fasta file as BioJava RichSequence object Namespace ns =
>>>> RichObjectFactory.getDefaultNamespace(); RichSequenceIterator iter
>>>> = RichSequence.IOTools.readFastaProtein(br,ns);
>>>>
>>>> int numProteins = 0; while(iter.hasNext()) { ++numProteins;
>>>>
>>>> // Retrieve sequence and description data RichSequence seq =
>>>> iter.nextRichSequence(); String ipi =
>>>> seq.getName().substring(4,15); o.println(ipi);  } o.println("Found
>>>> " + numProteins + " in Fasta file"); } catch (FileNotFoundException
>>>> ex) { //can't find file specified by args[0] ex.printStackTrace();
>>>> } catch (BioException ex) { //error parsing requested format
>>>> ex.printStackTrace(); } }
>>>>
>>>> }
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>


-- 
Dr Chris Cole
Senior Bioinformatics Research Officer
School of Life Sciences Research
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096

From andreas at sdsc.edu  Mon Jan 18 11:37:48 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 18 Jan 2010 08:37:48 -0800
Subject: [Biojava-l] BioJava Hackathon - Day 1
Message-ID: <59a41c431001180837m4f9e4117j36a3dccd555b635@mail.gmail.com>

Hi,

Today is the first day of the BioJava Hackathon. We are 8 BioJava
developers meeting  here at the Genome Campus in Hinxton to hack on
the latest code-base. If you want to stay in touch which what is going
on, I am going to blog every day at:
http://openbioinformatics.blogspot.com . Andy Yates is tweeting at
http://twitter.com/search?q=%23biojava

Other ways of staying in touch with us are via Skype or Google Chat.
Send me your skype username or google account if you want to talk to
us directly.

Andreas

From gwaldon at geneinfinity.org  Mon Jan 18 14:17:08 2010
From: gwaldon at geneinfinity.org (George Waldon)
Date: Mon, 18 Jan 2010 14:17:08 -0500
Subject: [Biojava-l] BioJava Hackathon - Day 1
Message-ID: <20100118191708.68936.qmail@mxw1102.verio-web.com>

Hi Andreas,

Thanks for the link. It is quite nice to get news from the hackathon this way.

Quick question on my side. I understand that there is a need for having a bridge between sequence objects and strings, especially for beginners, but how does this becomes a critical issue to the point of saying "Sequences should be Strings as far as possible"? . 

- George





On Mon, Jan 18, 2010 at 8:37 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi,
>
> Today is the first day of the BioJava Hackathon. We are 8 BioJava
> developers meeting  here at the Genome Campus in Hinxton to hack on
> the latest code-base. If you want to stay in touch which what is going
> on, I am going to blog every day at:
> http://openbioinformatics.blogspot.com . Andy Yates is tweeting at
> http://twitter.com/search?q=%23biojava
>
> Other ways of staying in touch with us are via Skype or Google Chat.
> Send me your skype username or google account if you want to talk to
> us directly.
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From holland at eaglegenomics.com  Mon Jan 18 16:12:14 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 18 Jan 2010 21:12:14 +0000
Subject: [Biojava-l] BioJava Hackathon - Day 1
In-Reply-To: <20100118191708.68936.qmail@mxw1102.verio-web.com>
References: <20100118191708.68936.qmail@mxw1102.verio-web.com>
Message-ID: <95988839-75A3-4087-8071-5A19BEECDD04@eaglegenomics.com>

I'll be there tomorrow to explain in person to those who are there, but for now here's a brief summary:

Files are made of strings, as are streams. Therefore to grab the sequence as a string out of a file or stream is trivial and cheap. As long as the code doesn't need to do anything that can't be done at the string level, there's no need for it to be converted into a SymbolList equivalent. Therefore any code that doesn't need to convert it should be able to accept and work with a plain string, and be much faster/efficient/cheaper.

Code that does need to have more than just a string should be able to convert that string into a SymboLlist equivalent on demand, which can be backed by strings, files, nio, whatever. 

By making the new SymbolList implement the CharSequence interface, and making methods that only need strings require CharSequence parameters and not Strings, you can pass either type to those string-only methods (because String implements CharSequence), therefore if you've parsed the thing already into a SymbolList, you can keep that representation, drop the original, and still be able to use the string-only methods.

Also by making the new SymbolList implement the standard List interface from Collections, it can be used in nice Java shortcuts such as the new foreach loops, and standard iterators can be used (instead of the current SymbolListIterator method). Collections API can also be used then to do things like subsets or reverses.

...hope it all makes sense!


On 18 Jan 2010, at 19:17, George Waldon wrote:

> Hi Andreas,
> 
> Thanks for the link. It is quite nice to get news from the hackathon this way.
> 
> Quick question on my side. I understand that there is a need for having a bridge between sequence objects and strings, especially for beginners, but how does this becomes a critical issue to the point of saying "Sequences should be Strings as far as possible"? . 
> 
> - George
> 
> 
> 
> 
> 
> On Mon, Jan 18, 2010 at 8:37 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi,
>> 
>> Today is the first day of the BioJava Hackathon. We are 8 BioJava
>> developers meeting  here at the Genome Campus in Hinxton to hack on
>> the latest code-base. If you want to stay in touch which what is going
>> on, I am going to blog every day at:
>> http://openbioinformatics.blogspot.com . Andy Yates is tweeting at
>> http://twitter.com/search?q=%23biojava
>> 
>> Other ways of staying in touch with us are via Skype or Google Chat.
>> Send me your skype username or google account if you want to talk to
>> us directly.
>> 
>> Andreas
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From jw12 at sanger.ac.uk  Tue Jan 19 05:41:12 2010
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Tue, 19 Jan 2010 10:41:12 +0000
Subject: [Biojava-l] DAS Workshop Registrations now Open (workshop date 7-9
	April 2010)
Message-ID: <9EDF4E46-15F8-434E-B557-2DE5906C4182@sanger.ac.uk>

If you don't know about DAS and wish to know how to distribute your  
latest biological annotation to the world then the upcoming DAS  
workshop maybe for you.
If you know about DAS and are maybe a DAS client developer then the  
upcoming DAS workshop is for you (as you will need to know about the  
upcoming DAS 1.6 Specification and how it may affect your software).

For information on the workshop and registration please go to:

http://www.ebi.ac.uk/training/handson/DAS_070410.html



Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk








-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From andreas at sdsc.edu  Fri Jan 22 13:03:46 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 22 Jan 2010 10:03:46 -0800
Subject: [Biojava-l] BioJava hackathon - Last Day
Message-ID: <59a41c431001221003g428e6826oa5cf9f74f3435964@mail.gmail.com>

Today was the last day of the BioJava Hackathon. It has been an
exciting week and we made progress along several lines, which I will
talk about in a moment. Special thanks go to Jonathan Warren for
organizing the meeting room at the Sanger Institute. Also thanks to
our hackers without who this hackathon would not have been possible.
In particular thanks to Scooter Willis, Jules Jacobsen, Andy Yates,
Jonathan Warren, Christoph Gille, Matias Piipari for participating
during the week and to our special guests who joined us for a day,
Richard Holland and Jim Procter.

All the code that has been written is available through the new
modules labeled with the biojava3 name. Most work was related to the
new sequence and protein structure modules:

Sequence modules

There have been a lot of discussions about the current way sequences
are represented over the last years. As such the "sequence guys" among
the developers were working on coming up with a new design which is
providing a biological meaningful (think central dogma) representation
of sequences. What is still missing are file parsers using the new
modules. The first fasta parser is about to be committed by Scooter as
I am writing this. There is still more work required before the code
will be ready for the next release. Still this is the beginning of a
new data representation which should make the code base ready for the
next couple of years.

Structure modules

The protein structure modules are the BioJava3-part which is closest
to be released. During this week we added the CE algorithm for protein
structure alignment, implemented core interfaces for a generic Model
View Control wrapping of various 3D visualization tools, we added
better support for chemically modified residues (like MSE) and natural
ones like Selenocysteine. They are treated now as amino acids. We also
re-factored the code base to have the structure data model clearly
separated from the new graphical user interfaces. This gui module now
provides a nice way for calculating and visualizing protein structure
alignments.

Next BioJava release (3.0)

There is still more work required to push the new sequence module to a
state where it can be released. We also did not write any
documentation this week, so that will have to be added later on. We
will try to bring up the modules to a state where they can be released
over the next weeks. Once a module is release ready a detailed summary
of the new features will be posted to the mailing list. In any case
there will be a BioJava 3.0 release in time for the ISMB/BOSC
conference as we have been doing during the last years.

From sheoran143 at gmail.com  Sun Jan 24 16:20:03 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Sun, 24 Jan 2010 15:20:03 -0600
Subject: [Biojava-l] Hibernate Exception when persisting some richsequence
 object to biosql schema
Message-ID: <4B5CB983.6000207@gmail.com>

Hi,
I was trying to load the bct(bacteria) nucleotide genbank record from 
NCBI to my own instance of biosql and I got an hibernate exception(see 
it at the end of email):
The record which i tried to load is : LOCUS       AL596172              
248050 bp    DNA     linear   BCT 16-APR-2005
I don't why I am getting this error because I am not doing any 
manipulation to richSequence object I am simply reading it from file and 
trying to load it to database.The part of program which is responsible 
for loading the sequence is below:

while (seqs.hasNext()) {
                try {
                     richSequence = seqs.nextRichSequence();
                    // hibernate work begins
                    // start a transaction session
                    tx = session.beginTransaction();
                    // if got exception go to proper exception catch
                    session.save("Sequence", richSequence);
                    tx.commit();
                    successFullRecord++;  // one more record 
successfully added to database
                    session.clear();    // clear out the resources
                    session.flush();   // force memory cache to go to 
hardisk
                    RichObjectFactory.clearLRUCache(); // clear out LRU 
cache
                    System.out.println("Changes committed.  Records 
added: " + successFullRecord);
                    richSequence = null;  // clear out the memory 
references to richsequence
                } catch (HibernateException he) {
                    hibernateException++; // update the error count
                    he.printStackTrace();
                    richSequence = null; // reset the newRichSequence
                    tx.rollback();   // undo the changes before the 
error occured
                    session.clear(); // clear out the session
                    session.flush(); // force the session cache to hard disk
                    RichObjectFactory.clearLRUCache(); // clear out the 
LRU cache
                } catch (BioException ex) {
                    bioJavaException++;  // update the biojavaException 
error count
                    RichObjectFactory.clearLRUCache();
                    session.clear();
                    session.flush();
                    RichObjectFactory.clearLRUCache();
                    richSequence = null;
                } catch (Exception ex) {
                    otherException++; // update the otherError count
                    richSequence = null;
                    tx.rollback();  // rollBack the changes
                    //TODO make this to logger
                    System.out.println("Got general exception: " + 
ex.getLocalizedMessage());
                    ex.printStackTrace();
                    session.clear();
                    session.flush();
                    RichObjectFactory.clearLRUCache();
                    richSequence = null;
                }
            }

Please help I am really stuck on this issue.
Thanks
Deepak Sheoran
sheoran143 at gmail.com



_*Exception:*_
Jan 24, 2010 2:59:21 PM org.hibernate.jdbc.BatchingBatcher doExecuteBatch
SEVERE: Exception executing batch:
org.hibernate.StaleStateException: Batch update returned unexpected row 
count from update [1]; actual row count: 0; expected: 1
       at 
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61) 

       at 
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46) 

       at 
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
       at 
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
       at 
org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
       at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247) 

       at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660) 

       at 
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
       at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
       at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
       at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
       at 
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298) 

       at 
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27) 

       at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
       at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
       at 
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
       at 
trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)
Jan 24, 2010 2:59:21 PM 
org.hibernate.event.def.AbstractFlushingEventListener performExecutions
SEVERE: Could not synchronize database state with session
org.hibernate.StaleStateException: Batch update returned unexpected row 
count from update [1]; actual row count: 0; expected: 1
       at 
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61) 

       at 
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46) 

       at 
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
       at 
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
       at 
org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
       at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247) 

       at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660) 

       at 
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
       at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
       at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
       at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
       at 
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298) 

       at 
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27) 

       at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
       at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
       at 
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
       at 
trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)

From holland at eaglegenomics.com  Mon Jan 25 04:18:58 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 25 Jan 2010 09:18:58 +0000
Subject: [Biojava-l] Hibernate Exception when persisting some
	richsequence object to biosql schema
In-Reply-To: <4B5CB983.6000207@gmail.com>
References: <4B5CB983.6000207@gmail.com>
Message-ID: <496E6E99-CACB-4C51-97CF-A5680471193C@eaglegenomics.com>

This happens in one of two situations:

 1. Something else is modifying the database at the same time, e.g. if you are running the same piece of code in parallel.

 2. The Hibernate session has become inconsistent with the database (possibly due to partial or incomplete removal of cached objects because references to them remain elsewhere).

In your code, you're doing a lot of session.clear() and session.flush() and RichObjectFactory.clearLRUCache() calls - are these really necessary? Also your code is creating the RichSequence objects outside of the transaction - this can cause problems too.

There's some template code on Biojava.org which you can use as a shortcut to what you're trying to do:

http://www.biojava.org/wiki/BioJava:BioJavaXDocs#BioEntryDB_and_RichSequenceDB_convenience_wrappers

cheers,
Richard

On 24 Jan 2010, at 21:20, Deepak Sheoran wrote:

> org.hibernate.StaleStateException: Batch update returned unexpected row count from update [1]; actual row count: 0; expected: 1

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From sheoran143 at gmail.com  Mon Jan 25 21:02:20 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Mon, 25 Jan 2010 20:02:20 -0600
Subject: [Biojava-l] Hibernate Exception when persisting some
 richsequence object to biosql schema
In-Reply-To: <616a29411001242351x6ed40febq7442c73c81f9bbb1@mail.gmail.com>
References: <4B5CB983.6000207@gmail.com>	
	<616a29411001242249u1287a34elc874e18c23afea@mail.gmail.com>	
	<4B5D414A.3000608@gmail.com>
	<616a29411001242351x6ed40febq7442c73c81f9bbb1@mail.gmail.com>
Message-ID: <4B5E4D2C.3020407@gmail.com>

simon rayner wrote:
> it sounds like there is something up with those sequences.  are they 
> longer than some limit.  if you grep the locus line of these 
> sequences, what are the lengths?
The average length for each record which are getting hibernate exception 
is around 14715 lines, which is kind of huge but I am able to get the 
things working by the suggestion of Richard. i.e is create richSequence 
after you start a transaction. I don't if this was only the issue, 
because i am able to load the record which are causing the hibernate 
exception by creating them after I start a transaction. I don't know 
what will be the statistics once I will change my program and run it on 
my complete data set.


Thanks
Deepak Sheoran
>
> On Mon, Jan 25, 2010 at 1:59 AM, Deepak Sheoran <sheoran143 at gmail.com 
> <mailto:sheoran143 at gmail.com>> wrote:
>
>     simon rayner wrote:
>
>         do you get the error with this sequence only, or with any
>         sequence you try to load?
>
>     I get these error with around 2000 record out of 50000 record
>     which i am able to load successfully. The record number which i
>     sent you is one of the 2000 record with me waiting to enter my
>     database, I can send the accession of all those record if you need
>     them.
>
>     Thanks for helping me out
>     Deepak Sheoran
>
>
>         On Sun, Jan 24, 2010 at 4:20 PM, Deepak Sheoran
>         <sheoran143 at gmail.com <mailto:sheoran143 at gmail.com>
>         <mailto:sheoran143 at gmail.com <mailto:sheoran143 at gmail.com>>>
>         wrote:
>
>            Hi,
>            I was trying to load the bct(bacteria) nucleotide genbank
>         record
>            from NCBI to my own instance of biosql and I got an hibernate
>            exception(see it at the end of email):
>            The record which i tried to load is : LOCUS       AL596172
>                         248050 bp    DNA     linear   BCT 16-APR-2005
>            I don't why I am getting this error because I am not doing any
>            manipulation to richSequence object I am simply reading it from
>            file and trying to load it to database.The part of program
>         which
>            is responsible for loading the sequence is below:
>
>            while (seqs.hasNext()) {
>                          try {
>                               richSequence = seqs.nextRichSequence();
>                              // hibernate work begins
>                              // start a transaction session
>                              tx = session.beginTransaction();
>                              // if got exception go to proper
>         exception catch
>                              session.save("Sequence", richSequence);
>                              tx.commit();
>                              successFullRecord++;  // one more record
>            successfully added to database
>                              session.clear();    // clear out the
>         resources
>                              session.flush();   // force memory cache
>         to go
>            to hardisk
>                              RichObjectFactory.clearLRUCache(); //
>         clear out
>            LRU cache
>                              System.out.println("Changes committed.
>          Records
>            added: " + successFullRecord);
>                              richSequence = null;  // clear out the memory
>            references to richsequence
>                          } catch (HibernateException he) {
>                              hibernateException++; // update the error
>         count
>                              he.printStackTrace();
>                              richSequence = null; // reset the
>         newRichSequence
>                              tx.rollback();   // undo the changes
>         before the
>            error occured
>                              session.clear(); // clear out the session
>                              session.flush(); // force the session
>         cache to
>            hard disk
>                              RichObjectFactory.clearLRUCache(); //
>         clear out
>            the LRU cache
>                          } catch (BioException ex) {
>                              bioJavaException++;  // update the
>            biojavaException error count
>                              RichObjectFactory.clearLRUCache();
>                              session.clear();
>                              session.flush();
>                              RichObjectFactory.clearLRUCache();
>                              richSequence = null;
>                          } catch (Exception ex) {
>                              otherException++; // update the
>         otherError count
>                              richSequence = null;
>                              tx.rollback();  // rollBack the changes
>                              //TODO make this to logger
>                              System.out.println("Got general
>         exception: " +
>            ex.getLocalizedMessage());
>                              ex.printStackTrace();
>                              session.clear();
>                              session.flush();
>                              RichObjectFactory.clearLRUCache();
>                              richSequence = null;
>                          }
>                      }
>
>            Please help I am really stuck on this issue.
>            Thanks
>            Deepak Sheoran
>            sheoran143 at gmail.com <mailto:sheoran143 at gmail.com>
>         <mailto:sheoran143 at gmail.com <mailto:sheoran143 at gmail.com>>
>
>
>
>
>            _*Exception:*_
>            Jan 24, 2010 2:59:21 PM org.hibernate.jdbc.BatchingBatcher
>            doExecuteBatch
>            SEVERE: Exception executing batch:
>            org.hibernate.StaleStateException: Batch update returned
>            unexpected row count from update [1]; actual row count: 0;
>         expected: 1
>                 at
>          
>          org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
>
>                 at
>          
>          org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
>
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
>                 at
>          
>          org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247)
>
>                 at
>          
>          org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660)
>
>                 at
>          
>          org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
>                 at
>         org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
>                 at
>          
>          org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
>                 at
>          
>          org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
>                 at
>          
>          org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
>
>                 at
>          
>          org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
>
>                 at
>         org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
>                 at
>          
>          org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
>                 at
>          
>          org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
>                 at
>          
>          trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)
>            Jan 24, 2010 2:59:21 PM
>            org.hibernate.event.def.AbstractFlushingEventListener
>            performExecutions
>            SEVERE: Could not synchronize database state with session
>            org.hibernate.StaleStateException: Batch update returned
>            unexpected row count from update [1]; actual row count: 0;
>         expected: 1
>                 at
>          
>          org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
>
>                 at
>          
>          org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
>
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
>                 at
>          
>          org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247)
>
>                 at
>          
>          org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660)
>
>                 at
>          
>          org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
>                 at
>         org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
>                 at
>          
>          org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
>                 at
>          
>          org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
>                 at
>          
>          org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
>
>                 at
>          
>          org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
>
>                 at
>         org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
>                 at
>          
>          org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
>                 at
>          
>          org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
>                 at
>          
>          trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)
>            _______________________________________________
>            Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>         <mailto:Biojava-l at lists.open-bio.org>
>            <mailto:Biojava-l at lists.open-bio.org
>         <mailto:Biojava-l at lists.open-bio.org>>
>
>            http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
>         -- 
>         Simon Rayner
>
>         State Key Laboratory of Virology
>         Wuhan Institute of Virology
>         Chinese Academy of Sciences
>         Wuhan, Hubei 430071
>         P.R.China
>
>         +86 (27) 87199895 (office)
>         +86 15972923715 (cell)
>
>
>
>
>
> -- 
> Simon Rayner
>
> State Key Laboratory of Virology
> Wuhan Institute of Virology
> Chinese Academy of Sciences
> Wuhan, Hubei 430071
> P.R.China
>
> +86 (27) 87199895 (office)
> +86 15972923715 (cell)
>


From sheoran143 at gmail.com  Mon Jan 25 21:23:29 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Mon, 25 Jan 2010 20:23:29 -0600
Subject: [Biojava-l] Hibernate Exception when persisting some
 richsequence object to biosql schema
In-Reply-To: <496E6E99-CACB-4C51-97CF-A5680471193C@eaglegenomics.com>
References: <4B5CB983.6000207@gmail.com>
	<496E6E99-CACB-4C51-97CF-A5680471193C@eaglegenomics.com>
Message-ID: <4B5E5221.3060200@gmail.com>

Richard Holland wrote:
> This happens in one of two situations:
>
>  1. Something else is modifying the database at the same time, e.g. if you are running the same piece of code in parallel.
>   
Ans: No, My program is the only thing which is working with the database 
instance on which I am performing load operation and my program is 
single thread based, i.e. it will create one richsequence and then 
persist it to database and then move to next one.
>  2. The Hibernate session has become inconsistent with the database (possibly due to partial or incomplete removal of cached objects because references to them remain elsewhere).
>   
Ans: I am not referencing  cached objects any where else. The only 
operation I do with rich sequence is to create one and then load it to 
database and if it went successfully in to database, then forget about 
it and create new, on failure clean everything and start with next 
sequence. I don't know if RichSequenceFactory is doing something 
internally as far as referencing is concerned. ?
> In your code, you're doing a lot of session.clear() and session.flush() and RichObjectFactory.clearLRUCache() calls - are these really necessary? Also your code is creating the RichSequence objects outside of the transaction - this can cause problems too.
>
>   
The only reason for doing session.clear() and session.flush()  and 
clearLRUCache() was i don't need the richSequenceObject any time later 
because my program sole purpose is load sequence into database from 
genbank file. Also when I was trying to do this I found after loading 
certain number of records to database if you don't clear session or 
clear LRU cache things will get really slow and seems to be freezing.
    http://www.biojava.org/pipermail/biojava-l/2008-May/006283.html
    http://www.mail-archive.com/biojava-l at lists.open-bio.org/msg01379.html
As you suggested I tried creating richSequence object after starting a 
transaction and its working for the records which are getting hibernate 
exception, but I will only say its working once I test it on my complete 
dataset which will take another 20 hours.

Thanks
Deepak Sheoran, BSc (Senior year)
North Dakota State University

> There's some template code on Biojava.org which you can use as a shortcut to what you're trying to do:
>
> http://www.biojava.org/wiki/BioJava:BioJavaXDocs#BioEntryDB_and_RichSequenceDB_convenience_wrappers
>
> cheers,
> Richard
>
> On 24 Jan 2010, at 21:20, Deepak Sheoran wrote:
>
>   
>> org.hibernate.StaleStateException: Batch update returned unexpected row count from update [1]; actual row count: 0; expected: 1
>>     
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>   


From holland at eaglegenomics.com  Thu Jan 28 16:11:01 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 28 Jan 2010 21:11:01 +0000
Subject: [Biojava-l] Error In Fetching Data from STRING EMBL File
In-Reply-To: <326ea8620912180900l23efefads4fdc4693f11cb61c@mail.gmail.com>
References: <326ea8620912180900l23efefads4fdc4693f11cb61c@mail.gmail.com>
Message-ID: <AA8BFCED-8960-40A7-9A72-F6FD987BCC4E@eaglegenomics.com>

A full stack trace would be very helpful.

PS. I am going away so won't be able to answer, but if you post the stack trace to the list someone there can help.

On 18 Dec 2009, at 17:00, jitesh dundas wrote:

> Dear Sir/Madam,
> 
> I am trying to fetch data from EMBL STRING Database (http://string.embl.de/)
> for a list of protein interactors. The file is attached with this email.
> 
> On executing the code, it gives me a "version number" error.  The same code
> is working fine when I fetch data from NCBI databases. Thus, I am trying to
> know what is going wrong here.
> 
> I request your reply. Please let me know if you need anything else from my
> side.
> 
> Regards,
> Jitesh Dundas
> <ImportGet.jsp>_______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From jbdundas at gmail.com  Thu Jan 28 17:21:10 2010
From: jbdundas at gmail.com (jitesh dundas)
Date: Fri, 29 Jan 2010 03:51:10 +0530
Subject: [Biojava-l] Error In Fetching Data from STRING EMBL File
In-Reply-To: <AA8BFCED-8960-40A7-9A72-F6FD987BCC4E@eaglegenomics.com>
References: <326ea8620912180900l23efefads4fdc4693f11cb61c@mail.gmail.com>
	<AA8BFCED-8960-40A7-9A72-F6FD987BCC4E@eaglegenomics.com>
Message-ID: <326ea8621001281421p5a2d617am1beb114f326764fa@mail.gmail.com>

Dear Sir,

I solved the problem.

Thank you everyone for your help.

Thank you Richard Sir, you are very helpful.

I am trying to implement biojava in my system. I might need help in
the same soon.

Thanks everyone for your help.Appreciate it.

Regards,
Jitesh Dundas

On 1/29/10, Richard Holland <holland at eaglegenomics.com> wrote:
> A full stack trace would be very helpful.
>
> PS. I am going away so won't be able to answer, but if you post the stack
> trace to the list someone there can help.
>
> On 18 Dec 2009, at 17:00, jitesh dundas wrote:
>
>> Dear Sir/Madam,
>>
>> I am trying to fetch data from EMBL STRING Database
>> (http://string.embl.de/)
>> for a list of protein interactors. The file is attached with this email.
>>
>> On executing the code, it gives me a "version number" error.  The same
>> code
>> is working fine when I fetch data from NCBI databases. Thus, I am trying
>> to
>> know what is going wrong here.
>>
>> I request your reply. Please let me know if you need anything else from my
>> side.
>>
>> Regards,
>> Jitesh Dundas
>> <ImportGet.jsp>_______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>

From holland at eaglegenomics.com  Mon Jan  4 10:57:54 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 4 Jan 2010 10:57:54 +0000
Subject: [Biojava-l] BioJava 2010 Hackathon
Message-ID: <E304F7F2-09B7-4C46-92F9-F9CA6E68C5EC@eaglegenomics.com>

Hi all,

For those attending the 2010 BioJava hackathon at the Wellcome Trust Genome Campus, near Cambridge, all details can be found on this wiki:

  http://biojava.org/wiki/BioJava:Hackathon2010

If your name is not listed on the wiki but you are planning on attending, please let us know by Jan 12th latest. Due to security arrangements at the campus it is not possible to just turn up on the day.

Subjects for the hackathon are open for discussion on the wiki.

Looking forward to seeing you all there!

cheers,
Richard

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From andylu0320 at gmail.com  Sun Jan 10 02:36:29 2010
From: andylu0320 at gmail.com (Andy Lu)
Date: Sat, 9 Jan 2010 21:36:29 -0500
Subject: [Biojava-l] Jmol help
Message-ID: <4a1a3f7d1001091836q1e084357v156a6dae902ba21f@mail.gmail.com>

Hi, does anyone know how to add menu listener in JMol through JMol script?

I tried using this:

        viewer.evalString ("set debugScript;");
        viewer.evalString ("set ScriptCallback spacefill ;");

But is there a way to make the above to an "if" statement? Like if I click
the "ball and stick" option in the menu, then something happens?

Thanks!


From andreas at sdsc.edu  Sun Jan 10 12:20:28 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 10 Jan 2010 04:20:28 -0800
Subject: [Biojava-l] Jmol help
In-Reply-To: <4a1a3f7d1001091836q1e084357v156a6dae902ba21f@mail.gmail.com>
References: <4a1a3f7d1001091836q1e084357v156a6dae902ba21f@mail.gmail.com>
Message-ID: <59a41c431001100420n58c786efv4c014984978d695a@mail.gmail.com>

Hi Andy,

Not sure what you mean - you mean you want you want to create a menu
in a frame, which also contains a Jmol panel? Probably the easiest
solution is to create a JMenu with JMenuItems, add actionListeners to
them and these can trigger a script in Jmol.

Have a look at this tutorial
http://java.sun.com/docs/books/tutorial/uiswing/components/menu.html

Andreas


On Sat, Jan 9, 2010 at 6:36 PM, Andy Lu <andylu0320 at gmail.com> wrote:
> Hi, does anyone know how to add menu listener in JMol through JMol script?
>
> I tried using this:
>
> ? ? ? ?viewer.evalString ("set debugScript;");
> ? ? ? ?viewer.evalString ("set ScriptCallback spacefill ;");
>
> But is there a way to make the above to an "if" statement? Like if I click
> the "ball and stick" option in the menu, then something happens?
>
> Thanks!
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From chris at compbio.dundee.ac.uk  Mon Jan 11 14:34:21 2010
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Mon, 11 Jan 2010 14:34:21 +0000
Subject: [Biojava-l] Error parsing ipi.HUMAN.fasta file
In-Reply-To: <E29CC4D7-00B5-4666-AD0B-C1DE762F8787@eaglegenomics.com>
References: <4B2BA575.5010007@compbio.dundee.ac.uk>
	<991F3D0D-0702-4EB7-9718-676986A1415E@eaglegenomics.com>
	<4B4B16A6.7030406@compbio.dundee.ac.uk>
	<E29CC4D7-00B5-4666-AD0B-C1DE762F8787@eaglegenomics.com>
Message-ID: <4B4B36ED.9060105@compbio.dundee.ac.uk>

[ posting back to biojava-l as omitted the address previously ]

Ah, right. It wasn't clear on the wiki whether those were included or 
not with the 'all' package.

It compiles fine now (with one warning) and through trial and error a 
buffer value of 2000 works with ipi.HUMAN.fasta as well as mouse and 
chicken.

Thanks very much for your help.

Chris

On 11/01/10 12:31, Richard Holland wrote:
> Hello. You need to make sure the support libraries are also on your classpath:
>
> http://www.biojava.org/wiki/BioJava:Download#Support_libraries
>
> cheers,
> Richard
>
> On 11 Jan 2010, at 12:16, Chris Cole wrote:
>
>> Thanks for the reply, Richard.
>>
>> Just getting back to this problem. I've upped the buffer to 1000 bytes, but I can't get it to compile with ant. I get a whole slew of compile errors, there seems to be something missing, but I don't know how to solve it. Output from ant build follows:
>>
>> caterpillar: ~/Downloads/biojava-1.7/src>  ant -f ../build.xml
>> Buildfile: ../build.xml
>>
>> init:
>>      [echo] Building biojava-1.7
>>      [echo] Java Home:                       /usr/java/jdk1.6.0_17/jre
>>      [echo] JUnit present:                   ${junit.present}
>>      [echo] JUnit supported by Ant:          ${junit.support}
>>      [echo] HSQLDB driver present:           ${sqlDriver.hsqldb}
>>      [echo] XSLT support:                    true
>>
>> prepare:
>>
>> prepare-biojava:
>>
>> compile-biojava:
>>     [javac] Compiling 1462 source files to /opt/Downloads/biojava-1.7/ant-build/classes/biojava
>>     [javac] /opt/Downloads/biojava-1.7/src/org/biojava/bio/dp/twohead/DPCompiler.java:55: package org.biojava.utils.bytecode does not exist
>>     [javac] import org.biojava.utils.bytecode.ByteCode;
>>     [javac]                                  ^
>>     [javac] /opt/Downloads/biojava-1.7/src/org/biojava/bio/dp/twohead/DPCompiler.java:56: package org.biojava.utils.bytecode does not exist
>>     [javac] import org.biojava.utils.bytecode.CodeClass;
>>     [javac]                                  ^
>>     [javac] /opt/Downloads/biojava-1.7/src/org/biojava/bio/dp/twohead/DPCompiler.java:57: package org.biojava.utils.bytecode does not exist
>>     [javac] import org.biojava.utils.bytecode.CodeException;
>>     [javac]                                  ^
>> ...etc.
>>
>> I downloaded the biojava-1.7-all.jar, originally and I can't what else I need?
>>
>> I'm also trying to do this from within Eclipse, so any Eclipse-specific pointers would be much appreciated.
>> Cheers,
>>
>> Chris
>>
>> On 18/12/09 16:58, Richard Holland wrote:
>>> The FASTA parser has a buffer which it uses to read ahead to the next
>>> complete line then back up before it actually parses it on the second
>>> pass (in order to allow it to do things like hasNext()). The
>>> exception shows that the size of that buffer is being exceeded,
>>> causing it to fail to back up again afterwards.
>>>
>>> There's two cures - one is to rewrite the FASTA parser to buffer
>>> things in a different way. The other is to open up
>>> org/biojavax/bio/seq/io/FastaFormat.java in a text editor, search for
>>> the line where it sets the buffer (somewhere around line 202
>>> according to the exception, in the readRichSequence() method - the
>>> command to look for is 'mark'), and increase the buffer size to
>>> something suitably large enough (it's currently set at 500 bytes).
>>> Then recompile BioJava and it should work.
>>>
>>> cheers, Richard
>>>
>>> On 18 Dec 2009, at 15:53, Chris Cole wrote:
>>>
>>>> I'm wanting to parse a fasta file obtained from IPI using the code
>>>> at the bottom of this message, but I get the following error:
>>>>
>>>> org.biojava.bio.BioException: Could not read sequence at
>>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>>>>
>>>>
>> at test.readFasta(test.java:39)
>>>> at test.main(test.java:18) Caused by: java.io.IOException: Mark
>>>> invalid at java.io.BufferedReader.reset(BufferedReader.java:485) at
>>>> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:202)
>>>>
>>>>
>> at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>>>> ... 2 more
>>>>
>>>> Looking at the Fasta file itself and doing some tests, it seems to
>>>> fail consistently at one or two entries /preceding/ an entry with a
>>>> very long description line e.g.:
>>>>> IPI:IPI00021421.4|SWISS-PROT:Q9UMR5-1|TREMBL:B0S868|ENSEMBL:ENSP00000382748;ENSP00000382749;ENSP00000382750;ENSP00000387679;ENSP00000388341;ENSP00000388618;ENSP00000389930;ENSP00000392885;ENSP00000393009;ENSP00000395242;ENSP00000395562;ENSP00000397025;ENSP00000399879;ENSP00000403820;ENSP00000406496;ENSP00000406566;ENSP00000408703;ENSP00000411007;ENSP00000411625;ENSP00000412827|REFSEQ:NP_005146|VEGA:OTTHUMP00000014775;OTTHUMP00000014776;OTTHUMP00000014778;OTTHUMP00000175028;OTTHUMP00000175029;OTTHUMP00000175030;OTTHUMP00000193135;OTTHUMP00000193136;OTTHUMP00000193138;OTTHUMP00000193964;OTTHUMP00000193965;OTTHUMP00000193967;OTTHUMP00000194391;OTTHUMP00000194392;OTTHUMP00000194394
>>>>> Tax_Id=9606 Gene_Symbol=PPT2 Isoform 1 of Lysosomal thioesterase
>>>>> PPT2
>>>> MLGLWGQRLPAAWVLLLLPFLPLLLLAAPAPHRASYKPVIVVHGLFDSSYSFRHLLEYIN
>>>> ETHPGTVVTVLDLFDGRESLRPLWEQVQGFREAVVPIMAKAPQGVHLICYSQGGLVCRAL
>>>> LSVMDDHNVDSFISLSSPQMGQYGDTDYLKWLFPTSMRSNLYRICYSPWGQEFSICNYWH
>>>> DPHHDDLYLNASSFLALINGERDHPNATVWRKNFLRVGHLVLIGGPDDGVITPWQSSFFG
>>>> FYDANETVLEMEEQLVYLRDSFGLKTLLARGAIVRCPMAGISHTAWHSNRTLYETCIEPW LS
>>>>
>>>> Deleting the large entries allows the code to continue until it
>>>> reaches another long description line.
>>>>
>>>> It also seems to be a feature of large Fasta files as reading the
>>>> above sequence alone or as part of a small file is fine.
>>>>
>>>> Is this a known problem or am I doing something wrong? BTW I'm
>>>> using biojava 1.7 and Java 1.6.0_17. Any help would be most
>>>> appreciated. Cheers.
>>>>
>>>> code: import java.io.*;
>>>>
>>>> import org.biojava.bio.*; import org.biojavax.*; import
>>>> org.biojavax.bio.seq.*;
>>>>
>>>> public class test { private static PrintStream o = System.out;
>>>>
>>>> public static void main(String[] args) { // TODO Auto-generated
>>>> method stub readFasta(args[0]); }  public static void
>>>> readFasta(String filename) { try { o.println("Reading file: " +
>>>> filename); //prepare a BufferedReader for file io BufferedReader br
>>>> = new BufferedReader(new FileReader(filename));
>>>>
>>>> // read Fasta file as BioJava RichSequence object Namespace ns =
>>>> RichObjectFactory.getDefaultNamespace(); RichSequenceIterator iter
>>>> = RichSequence.IOTools.readFastaProtein(br,ns);
>>>>
>>>> int numProteins = 0; while(iter.hasNext()) { ++numProteins;
>>>>
>>>> // Retrieve sequence and description data RichSequence seq =
>>>> iter.nextRichSequence(); String ipi =
>>>> seq.getName().substring(4,15); o.println(ipi);  } o.println("Found
>>>> " + numProteins + " in Fasta file"); } catch (FileNotFoundException
>>>> ex) { //can't find file specified by args[0] ex.printStackTrace();
>>>> } catch (BioException ex) { //error parsing requested format
>>>> ex.printStackTrace(); } }
>>>>
>>>> }
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>


-- 
Dr Chris Cole
Senior Bioinformatics Research Officer
School of Life Sciences Research
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096


From andreas at sdsc.edu  Mon Jan 18 16:37:48 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 18 Jan 2010 08:37:48 -0800
Subject: [Biojava-l] BioJava Hackathon - Day 1
Message-ID: <59a41c431001180837m4f9e4117j36a3dccd555b635@mail.gmail.com>

Hi,

Today is the first day of the BioJava Hackathon. We are 8 BioJava
developers meeting  here at the Genome Campus in Hinxton to hack on
the latest code-base. If you want to stay in touch which what is going
on, I am going to blog every day at:
http://openbioinformatics.blogspot.com . Andy Yates is tweeting at
http://twitter.com/search?q=%23biojava

Other ways of staying in touch with us are via Skype or Google Chat.
Send me your skype username or google account if you want to talk to
us directly.

Andreas


From gwaldon at geneinfinity.org  Mon Jan 18 19:17:08 2010
From: gwaldon at geneinfinity.org (George Waldon)
Date: Mon, 18 Jan 2010 14:17:08 -0500
Subject: [Biojava-l] BioJava Hackathon - Day 1
Message-ID: <20100118191708.68936.qmail@mxw1102.verio-web.com>

Hi Andreas,

Thanks for the link. It is quite nice to get news from the hackathon this way.

Quick question on my side. I understand that there is a need for having a bridge between sequence objects and strings, especially for beginners, but how does this becomes a critical issue to the point of saying "Sequences should be Strings as far as possible"? . 

- George





On Mon, Jan 18, 2010 at 8:37 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi,
>
> Today is the first day of the BioJava Hackathon. We are 8 BioJava
> developers meeting  here at the Genome Campus in Hinxton to hack on
> the latest code-base. If you want to stay in touch which what is going
> on, I am going to blog every day at:
> http://openbioinformatics.blogspot.com . Andy Yates is tweeting at
> http://twitter.com/search?q=%23biojava
>
> Other ways of staying in touch with us are via Skype or Google Chat.
> Send me your skype username or google account if you want to talk to
> us directly.
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From holland at eaglegenomics.com  Mon Jan 18 21:12:14 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 18 Jan 2010 21:12:14 +0000
Subject: [Biojava-l] BioJava Hackathon - Day 1
In-Reply-To: <20100118191708.68936.qmail@mxw1102.verio-web.com>
References: <20100118191708.68936.qmail@mxw1102.verio-web.com>
Message-ID: <95988839-75A3-4087-8071-5A19BEECDD04@eaglegenomics.com>

I'll be there tomorrow to explain in person to those who are there, but for now here's a brief summary:

Files are made of strings, as are streams. Therefore to grab the sequence as a string out of a file or stream is trivial and cheap. As long as the code doesn't need to do anything that can't be done at the string level, there's no need for it to be converted into a SymbolList equivalent. Therefore any code that doesn't need to convert it should be able to accept and work with a plain string, and be much faster/efficient/cheaper.

Code that does need to have more than just a string should be able to convert that string into a SymboLlist equivalent on demand, which can be backed by strings, files, nio, whatever. 

By making the new SymbolList implement the CharSequence interface, and making methods that only need strings require CharSequence parameters and not Strings, you can pass either type to those string-only methods (because String implements CharSequence), therefore if you've parsed the thing already into a SymbolList, you can keep that representation, drop the original, and still be able to use the string-only methods.

Also by making the new SymbolList implement the standard List interface from Collections, it can be used in nice Java shortcuts such as the new foreach loops, and standard iterators can be used (instead of the current SymbolListIterator method). Collections API can also be used then to do things like subsets or reverses.

...hope it all makes sense!


On 18 Jan 2010, at 19:17, George Waldon wrote:

> Hi Andreas,
> 
> Thanks for the link. It is quite nice to get news from the hackathon this way.
> 
> Quick question on my side. I understand that there is a need for having a bridge between sequence objects and strings, especially for beginners, but how does this becomes a critical issue to the point of saying "Sequences should be Strings as far as possible"? . 
> 
> - George
> 
> 
> 
> 
> 
> On Mon, Jan 18, 2010 at 8:37 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi,
>> 
>> Today is the first day of the BioJava Hackathon. We are 8 BioJava
>> developers meeting  here at the Genome Campus in Hinxton to hack on
>> the latest code-base. If you want to stay in touch which what is going
>> on, I am going to blog every day at:
>> http://openbioinformatics.blogspot.com . Andy Yates is tweeting at
>> http://twitter.com/search?q=%23biojava
>> 
>> Other ways of staying in touch with us are via Skype or Google Chat.
>> Send me your skype username or google account if you want to talk to
>> us directly.
>> 
>> Andreas
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From jw12 at sanger.ac.uk  Tue Jan 19 10:41:12 2010
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Tue, 19 Jan 2010 10:41:12 +0000
Subject: [Biojava-l] DAS Workshop Registrations now Open (workshop date 7-9
	April 2010)
Message-ID: <9EDF4E46-15F8-434E-B557-2DE5906C4182@sanger.ac.uk>

If you don't know about DAS and wish to know how to distribute your  
latest biological annotation to the world then the upcoming DAS  
workshop maybe for you.
If you know about DAS and are maybe a DAS client developer then the  
upcoming DAS workshop is for you (as you will need to know about the  
upcoming DAS 1.6 Specification and how it may affect your software).

For information on the workshop and registration please go to:

http://www.ebi.ac.uk/training/handson/DAS_070410.html



Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk








-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From andreas at sdsc.edu  Fri Jan 22 18:03:46 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 22 Jan 2010 10:03:46 -0800
Subject: [Biojava-l] BioJava hackathon - Last Day
Message-ID: <59a41c431001221003g428e6826oa5cf9f74f3435964@mail.gmail.com>

Today was the last day of the BioJava Hackathon. It has been an
exciting week and we made progress along several lines, which I will
talk about in a moment. Special thanks go to Jonathan Warren for
organizing the meeting room at the Sanger Institute. Also thanks to
our hackers without who this hackathon would not have been possible.
In particular thanks to Scooter Willis, Jules Jacobsen, Andy Yates,
Jonathan Warren, Christoph Gille, Matias Piipari for participating
during the week and to our special guests who joined us for a day,
Richard Holland and Jim Procter.

All the code that has been written is available through the new
modules labeled with the biojava3 name. Most work was related to the
new sequence and protein structure modules:

Sequence modules

There have been a lot of discussions about the current way sequences
are represented over the last years. As such the "sequence guys" among
the developers were working on coming up with a new design which is
providing a biological meaningful (think central dogma) representation
of sequences. What is still missing are file parsers using the new
modules. The first fasta parser is about to be committed by Scooter as
I am writing this. There is still more work required before the code
will be ready for the next release. Still this is the beginning of a
new data representation which should make the code base ready for the
next couple of years.

Structure modules

The protein structure modules are the BioJava3-part which is closest
to be released. During this week we added the CE algorithm for protein
structure alignment, implemented core interfaces for a generic Model
View Control wrapping of various 3D visualization tools, we added
better support for chemically modified residues (like MSE) and natural
ones like Selenocysteine. They are treated now as amino acids. We also
re-factored the code base to have the structure data model clearly
separated from the new graphical user interfaces. This gui module now
provides a nice way for calculating and visualizing protein structure
alignments.

Next BioJava release (3.0)

There is still more work required to push the new sequence module to a
state where it can be released. We also did not write any
documentation this week, so that will have to be added later on. We
will try to bring up the modules to a state where they can be released
over the next weeks. Once a module is release ready a detailed summary
of the new features will be posted to the mailing list. In any case
there will be a BioJava 3.0 release in time for the ISMB/BOSC
conference as we have been doing during the last years.


From sheoran143 at gmail.com  Sun Jan 24 21:20:03 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Sun, 24 Jan 2010 15:20:03 -0600
Subject: [Biojava-l] Hibernate Exception when persisting some richsequence
 object to biosql schema
Message-ID: <4B5CB983.6000207@gmail.com>

Hi,
I was trying to load the bct(bacteria) nucleotide genbank record from 
NCBI to my own instance of biosql and I got an hibernate exception(see 
it at the end of email):
The record which i tried to load is : LOCUS       AL596172              
248050 bp    DNA     linear   BCT 16-APR-2005
I don't why I am getting this error because I am not doing any 
manipulation to richSequence object I am simply reading it from file and 
trying to load it to database.The part of program which is responsible 
for loading the sequence is below:

while (seqs.hasNext()) {
                try {
                     richSequence = seqs.nextRichSequence();
                    // hibernate work begins
                    // start a transaction session
                    tx = session.beginTransaction();
                    // if got exception go to proper exception catch
                    session.save("Sequence", richSequence);
                    tx.commit();
                    successFullRecord++;  // one more record 
successfully added to database
                    session.clear();    // clear out the resources
                    session.flush();   // force memory cache to go to 
hardisk
                    RichObjectFactory.clearLRUCache(); // clear out LRU 
cache
                    System.out.println("Changes committed.  Records 
added: " + successFullRecord);
                    richSequence = null;  // clear out the memory 
references to richsequence
                } catch (HibernateException he) {
                    hibernateException++; // update the error count
                    he.printStackTrace();
                    richSequence = null; // reset the newRichSequence
                    tx.rollback();   // undo the changes before the 
error occured
                    session.clear(); // clear out the session
                    session.flush(); // force the session cache to hard disk
                    RichObjectFactory.clearLRUCache(); // clear out the 
LRU cache
                } catch (BioException ex) {
                    bioJavaException++;  // update the biojavaException 
error count
                    RichObjectFactory.clearLRUCache();
                    session.clear();
                    session.flush();
                    RichObjectFactory.clearLRUCache();
                    richSequence = null;
                } catch (Exception ex) {
                    otherException++; // update the otherError count
                    richSequence = null;
                    tx.rollback();  // rollBack the changes
                    //TODO make this to logger
                    System.out.println("Got general exception: " + 
ex.getLocalizedMessage());
                    ex.printStackTrace();
                    session.clear();
                    session.flush();
                    RichObjectFactory.clearLRUCache();
                    richSequence = null;
                }
            }

Please help I am really stuck on this issue.
Thanks
Deepak Sheoran
sheoran143 at gmail.com



_*Exception:*_
Jan 24, 2010 2:59:21 PM org.hibernate.jdbc.BatchingBatcher doExecuteBatch
SEVERE: Exception executing batch:
org.hibernate.StaleStateException: Batch update returned unexpected row 
count from update [1]; actual row count: 0; expected: 1
       at 
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61) 

       at 
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46) 

       at 
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
       at 
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
       at 
org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
       at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247) 

       at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660) 

       at 
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
       at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
       at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
       at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
       at 
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298) 

       at 
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27) 

       at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
       at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
       at 
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
       at 
trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)
Jan 24, 2010 2:59:21 PM 
org.hibernate.event.def.AbstractFlushingEventListener performExecutions
SEVERE: Could not synchronize database state with session
org.hibernate.StaleStateException: Batch update returned unexpected row 
count from update [1]; actual row count: 0; expected: 1
       at 
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61) 

       at 
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46) 

       at 
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
       at 
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
       at 
org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
       at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247) 

       at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660) 

       at 
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
       at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
       at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
       at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
       at 
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298) 

       at 
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27) 

       at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
       at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
       at 
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
       at 
trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)


From holland at eaglegenomics.com  Mon Jan 25 09:18:58 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 25 Jan 2010 09:18:58 +0000
Subject: [Biojava-l] Hibernate Exception when persisting some
	richsequence object to biosql schema
In-Reply-To: <4B5CB983.6000207@gmail.com>
References: <4B5CB983.6000207@gmail.com>
Message-ID: <496E6E99-CACB-4C51-97CF-A5680471193C@eaglegenomics.com>

This happens in one of two situations:

 1. Something else is modifying the database at the same time, e.g. if you are running the same piece of code in parallel.

 2. The Hibernate session has become inconsistent with the database (possibly due to partial or incomplete removal of cached objects because references to them remain elsewhere).

In your code, you're doing a lot of session.clear() and session.flush() and RichObjectFactory.clearLRUCache() calls - are these really necessary? Also your code is creating the RichSequence objects outside of the transaction - this can cause problems too.

There's some template code on Biojava.org which you can use as a shortcut to what you're trying to do:

http://www.biojava.org/wiki/BioJava:BioJavaXDocs#BioEntryDB_and_RichSequenceDB_convenience_wrappers

cheers,
Richard

On 24 Jan 2010, at 21:20, Deepak Sheoran wrote:

> org.hibernate.StaleStateException: Batch update returned unexpected row count from update [1]; actual row count: 0; expected: 1

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From sheoran143 at gmail.com  Tue Jan 26 02:02:20 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Mon, 25 Jan 2010 20:02:20 -0600
Subject: [Biojava-l] Hibernate Exception when persisting some
 richsequence object to biosql schema
In-Reply-To: <616a29411001242351x6ed40febq7442c73c81f9bbb1@mail.gmail.com>
References: <4B5CB983.6000207@gmail.com>	
	<616a29411001242249u1287a34elc874e18c23afea@mail.gmail.com>	
	<4B5D414A.3000608@gmail.com>
	<616a29411001242351x6ed40febq7442c73c81f9bbb1@mail.gmail.com>
Message-ID: <4B5E4D2C.3020407@gmail.com>

simon rayner wrote:
> it sounds like there is something up with those sequences.  are they 
> longer than some limit.  if you grep the locus line of these 
> sequences, what are the lengths?
The average length for each record which are getting hibernate exception 
is around 14715 lines, which is kind of huge but I am able to get the 
things working by the suggestion of Richard. i.e is create richSequence 
after you start a transaction. I don't if this was only the issue, 
because i am able to load the record which are causing the hibernate 
exception by creating them after I start a transaction. I don't know 
what will be the statistics once I will change my program and run it on 
my complete data set.


Thanks
Deepak Sheoran
>
> On Mon, Jan 25, 2010 at 1:59 AM, Deepak Sheoran <sheoran143 at gmail.com 
> <mailto:sheoran143 at gmail.com>> wrote:
>
>     simon rayner wrote:
>
>         do you get the error with this sequence only, or with any
>         sequence you try to load?
>
>     I get these error with around 2000 record out of 50000 record
>     which i am able to load successfully. The record number which i
>     sent you is one of the 2000 record with me waiting to enter my
>     database, I can send the accession of all those record if you need
>     them.
>
>     Thanks for helping me out
>     Deepak Sheoran
>
>
>         On Sun, Jan 24, 2010 at 4:20 PM, Deepak Sheoran
>         <sheoran143 at gmail.com <mailto:sheoran143 at gmail.com>
>         <mailto:sheoran143 at gmail.com <mailto:sheoran143 at gmail.com>>>
>         wrote:
>
>            Hi,
>            I was trying to load the bct(bacteria) nucleotide genbank
>         record
>            from NCBI to my own instance of biosql and I got an hibernate
>            exception(see it at the end of email):
>            The record which i tried to load is : LOCUS       AL596172
>                         248050 bp    DNA     linear   BCT 16-APR-2005
>            I don't why I am getting this error because I am not doing any
>            manipulation to richSequence object I am simply reading it from
>            file and trying to load it to database.The part of program
>         which
>            is responsible for loading the sequence is below:
>
>            while (seqs.hasNext()) {
>                          try {
>                               richSequence = seqs.nextRichSequence();
>                              // hibernate work begins
>                              // start a transaction session
>                              tx = session.beginTransaction();
>                              // if got exception go to proper
>         exception catch
>                              session.save("Sequence", richSequence);
>                              tx.commit();
>                              successFullRecord++;  // one more record
>            successfully added to database
>                              session.clear();    // clear out the
>         resources
>                              session.flush();   // force memory cache
>         to go
>            to hardisk
>                              RichObjectFactory.clearLRUCache(); //
>         clear out
>            LRU cache
>                              System.out.println("Changes committed.
>          Records
>            added: " + successFullRecord);
>                              richSequence = null;  // clear out the memory
>            references to richsequence
>                          } catch (HibernateException he) {
>                              hibernateException++; // update the error
>         count
>                              he.printStackTrace();
>                              richSequence = null; // reset the
>         newRichSequence
>                              tx.rollback();   // undo the changes
>         before the
>            error occured
>                              session.clear(); // clear out the session
>                              session.flush(); // force the session
>         cache to
>            hard disk
>                              RichObjectFactory.clearLRUCache(); //
>         clear out
>            the LRU cache
>                          } catch (BioException ex) {
>                              bioJavaException++;  // update the
>            biojavaException error count
>                              RichObjectFactory.clearLRUCache();
>                              session.clear();
>                              session.flush();
>                              RichObjectFactory.clearLRUCache();
>                              richSequence = null;
>                          } catch (Exception ex) {
>                              otherException++; // update the
>         otherError count
>                              richSequence = null;
>                              tx.rollback();  // rollBack the changes
>                              //TODO make this to logger
>                              System.out.println("Got general
>         exception: " +
>            ex.getLocalizedMessage());
>                              ex.printStackTrace();
>                              session.clear();
>                              session.flush();
>                              RichObjectFactory.clearLRUCache();
>                              richSequence = null;
>                          }
>                      }
>
>            Please help I am really stuck on this issue.
>            Thanks
>            Deepak Sheoran
>            sheoran143 at gmail.com <mailto:sheoran143 at gmail.com>
>         <mailto:sheoran143 at gmail.com <mailto:sheoran143 at gmail.com>>
>
>
>
>
>            _*Exception:*_
>            Jan 24, 2010 2:59:21 PM org.hibernate.jdbc.BatchingBatcher
>            doExecuteBatch
>            SEVERE: Exception executing batch:
>            org.hibernate.StaleStateException: Batch update returned
>            unexpected row count from update [1]; actual row count: 0;
>         expected: 1
>                 at
>          
>          org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
>
>                 at
>          
>          org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
>
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
>                 at
>          
>          org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247)
>
>                 at
>          
>          org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660)
>
>                 at
>          
>          org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
>                 at
>         org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
>                 at
>          
>          org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
>                 at
>          
>          org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
>                 at
>          
>          org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
>
>                 at
>          
>          org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
>
>                 at
>         org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
>                 at
>          
>          org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
>                 at
>          
>          org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
>                 at
>          
>          trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)
>            Jan 24, 2010 2:59:21 PM
>            org.hibernate.event.def.AbstractFlushingEventListener
>            performExecutions
>            SEVERE: Could not synchronize database state with session
>            org.hibernate.StaleStateException: Batch update returned
>            unexpected row count from update [1]; actual row count: 0;
>         expected: 1
>                 at
>          
>          org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
>
>                 at
>          
>          org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
>
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
>                 at
>          
>          org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
>                 at
>          
>          org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247)
>
>                 at
>          
>          org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660)
>
>                 at
>          
>          org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
>                 at
>         org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
>                 at
>          
>          org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
>                 at
>          
>          org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
>                 at
>          
>          org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
>
>                 at
>          
>          org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
>
>                 at
>         org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
>                 at
>          
>          org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
>                 at
>          
>          org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
>                 at
>          
>          trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)
>            _______________________________________________
>            Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>         <mailto:Biojava-l at lists.open-bio.org>
>            <mailto:Biojava-l at lists.open-bio.org
>         <mailto:Biojava-l at lists.open-bio.org>>
>
>            http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
>         -- 
>         Simon Rayner
>
>         State Key Laboratory of Virology
>         Wuhan Institute of Virology
>         Chinese Academy of Sciences
>         Wuhan, Hubei 430071
>         P.R.China
>
>         +86 (27) 87199895 (office)
>         +86 15972923715 (cell)
>
>
>
>
>
> -- 
> Simon Rayner
>
> State Key Laboratory of Virology
> Wuhan Institute of Virology
> Chinese Academy of Sciences
> Wuhan, Hubei 430071
> P.R.China
>
> +86 (27) 87199895 (office)
> +86 15972923715 (cell)
>



From sheoran143 at gmail.com  Tue Jan 26 02:23:29 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Mon, 25 Jan 2010 20:23:29 -0600
Subject: [Biojava-l] Hibernate Exception when persisting some
 richsequence object to biosql schema
In-Reply-To: <496E6E99-CACB-4C51-97CF-A5680471193C@eaglegenomics.com>
References: <4B5CB983.6000207@gmail.com>
	<496E6E99-CACB-4C51-97CF-A5680471193C@eaglegenomics.com>
Message-ID: <4B5E5221.3060200@gmail.com>

Richard Holland wrote:
> This happens in one of two situations:
>
>  1. Something else is modifying the database at the same time, e.g. if you are running the same piece of code in parallel.
>   
Ans: No, My program is the only thing which is working with the database 
instance on which I am performing load operation and my program is 
single thread based, i.e. it will create one richsequence and then 
persist it to database and then move to next one.
>  2. The Hibernate session has become inconsistent with the database (possibly due to partial or incomplete removal of cached objects because references to them remain elsewhere).
>   
Ans: I am not referencing  cached objects any where else. The only 
operation I do with rich sequence is to create one and then load it to 
database and if it went successfully in to database, then forget about 
it and create new, on failure clean everything and start with next 
sequence. I don't know if RichSequenceFactory is doing something 
internally as far as referencing is concerned. ?
> In your code, you're doing a lot of session.clear() and session.flush() and RichObjectFactory.clearLRUCache() calls - are these really necessary? Also your code is creating the RichSequence objects outside of the transaction - this can cause problems too.
>
>   
The only reason for doing session.clear() and session.flush()  and 
clearLRUCache() was i don't need the richSequenceObject any time later 
because my program sole purpose is load sequence into database from 
genbank file. Also when I was trying to do this I found after loading 
certain number of records to database if you don't clear session or 
clear LRU cache things will get really slow and seems to be freezing.
    http://www.biojava.org/pipermail/biojava-l/2008-May/006283.html
    http://www.mail-archive.com/biojava-l at lists.open-bio.org/msg01379.html
As you suggested I tried creating richSequence object after starting a 
transaction and its working for the records which are getting hibernate 
exception, but I will only say its working once I test it on my complete 
dataset which will take another 20 hours.

Thanks
Deepak Sheoran, BSc (Senior year)
North Dakota State University

> There's some template code on Biojava.org which you can use as a shortcut to what you're trying to do:
>
> http://www.biojava.org/wiki/BioJava:BioJavaXDocs#BioEntryDB_and_RichSequenceDB_convenience_wrappers
>
> cheers,
> Richard
>
> On 24 Jan 2010, at 21:20, Deepak Sheoran wrote:
>
>   
>> org.hibernate.StaleStateException: Batch update returned unexpected row count from update [1]; actual row count: 0; expected: 1
>>     
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>   



From holland at eaglegenomics.com  Thu Jan 28 21:11:01 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Thu, 28 Jan 2010 21:11:01 +0000
Subject: [Biojava-l] Error In Fetching Data from STRING EMBL File
In-Reply-To: <326ea8620912180900l23efefads4fdc4693f11cb61c@mail.gmail.com>
References: <326ea8620912180900l23efefads4fdc4693f11cb61c@mail.gmail.com>
Message-ID: <AA8BFCED-8960-40A7-9A72-F6FD987BCC4E@eaglegenomics.com>

A full stack trace would be very helpful.

PS. I am going away so won't be able to answer, but if you post the stack trace to the list someone there can help.

On 18 Dec 2009, at 17:00, jitesh dundas wrote:

> Dear Sir/Madam,
> 
> I am trying to fetch data from EMBL STRING Database (http://string.embl.de/)
> for a list of protein interactors. The file is attached with this email.
> 
> On executing the code, it gives me a "version number" error.  The same code
> is working fine when I fetch data from NCBI databases. Thus, I am trying to
> know what is going wrong here.
> 
> I request your reply. Please let me know if you need anything else from my
> side.
> 
> Regards,
> Jitesh Dundas
> <ImportGet.jsp>_______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From jbdundas at gmail.com  Thu Jan 28 22:21:10 2010
From: jbdundas at gmail.com (jitesh dundas)
Date: Fri, 29 Jan 2010 03:51:10 +0530
Subject: [Biojava-l] Error In Fetching Data from STRING EMBL File
In-Reply-To: <AA8BFCED-8960-40A7-9A72-F6FD987BCC4E@eaglegenomics.com>
References: <326ea8620912180900l23efefads4fdc4693f11cb61c@mail.gmail.com>
	<AA8BFCED-8960-40A7-9A72-F6FD987BCC4E@eaglegenomics.com>
Message-ID: <326ea8621001281421p5a2d617am1beb114f326764fa@mail.gmail.com>

Dear Sir,

I solved the problem.

Thank you everyone for your help.

Thank you Richard Sir, you are very helpful.

I am trying to implement biojava in my system. I might need help in
the same soon.

Thanks everyone for your help.Appreciate it.

Regards,
Jitesh Dundas

On 1/29/10, Richard Holland <holland at eaglegenomics.com> wrote:
> A full stack trace would be very helpful.
>
> PS. I am going away so won't be able to answer, but if you post the stack
> trace to the list someone there can help.
>
> On 18 Dec 2009, at 17:00, jitesh dundas wrote:
>
>> Dear Sir/Madam,
>>
>> I am trying to fetch data from EMBL STRING Database
>> (http://string.embl.de/)
>> for a list of protein interactors. The file is attached with this email.
>>
>> On executing the code, it gives me a "version number" error.  The same
>> code
>> is working fine when I fetch data from NCBI databases. Thus, I am trying
>> to
>> know what is going wrong here.
>>
>> I request your reply. Please let me know if you need anything else from my
>> side.
>>
>> Regards,
>> Jitesh Dundas
>> <ImportGet.jsp>_______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>