From mauricio at open-bio.org  Fri Feb  5 10:48:30 2010
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Fri, 05 Feb 2010 09:48:30 -0600
Subject: [Biojava-l] Fwd: Changes to NCBI BLAST and E-utilities.
Message-ID: <4B6C3DCE.2070808@open-bio.org>

Forwarding to the proper lists...

-------- Original Message --------
Subject: [O|B|F Helpdesk #889] Changes to NCBI BLAST and E-utilities.
Date: Fri, 5 Feb 2010 10:08:51 -0500
From: mcginnis via RT <support at helpdesk.open-bio.org>
Reply-To: support at helpdesk.open-bio.org
To: chris at bioteam.net, heikki at sanbi.ac.za, hlapp at gmx.net, 
jason at bioperl.org,        mauricio at open-bio.org


Fri Feb 05 10:08:51 2010: Request 889 was acted upon.
Transaction: Ticket created by mcginnis at ncbi.nlm.nih.gov
        Queue: support at open-bio.org
      Subject: Changes to NCBI BLAST and E-utilities.
        Owner: Nobody
   Requestors: mcginnis at ncbi.nlm.nih.gov
       Status: new
  Ticket <URL: https://helpdesk.open-bio.org/rt/Ticket/Display.html?id=889 >


Dear Colleague:

There are two changes I'd like to make you aware of.

As you may or may not have noticed, we have been working on a new C++ 
version of the BLAST binaries. In the coming months we will be moving 
the C++ binaries into prominence and (slowly) phasing out the C toolkit 
binaries.

There are many changes not least of which is a move to individual 
binaries for each program (blastn, blastp, etc).  We are not sure how 
many of your users use BioPerl with the BLAST binaries, my understanding 
is that many use BioPerl to to remote BLAST. However, there isa change 
to the BLAST results in Text and presumably HTML. This could have an 
effect on any parsers which scrape these formats and do not use XML. For 
obvious reason, we want to support only the XML format for parsing, but 
we thought we should give you heads up on this.
blast 2.2.22

Query: 3307 ------------------------------------------------------------ 
3307

Sbjct: 390  GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP 449

blast 2.2.22+

Query        ------------------------------------------------------------

Sbjct  390 
GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP  449

A single line of gaps lacks the Query numbering in the blast+ output. 
The C version of blast has numbering in this case. Sample alignment 
shown below. According to users the blast+ output without the numbering 
breaks bioperl parsers. Wehave heard forma few but I think they may be 
older parsers?
The second issue is a policy concerning E-utilities. This was announced 
on the utilities-announce at ncbi.nlm.nih.gov mail-list but you may not 
have seen it.

As part of an ongoing effort to ensure efficient access to the Entrez 
Utilities (E-utilities) by all users, NCBI has decided to change the 
usage policy for the E-utilities effective June 1, 2010. Effective on 
June 1, 2010, all E-utility requests, either using standard URLs or 
SOAP, must contain non-null values for both the &tool and &email 
parameters. Any E-utility request made after June 1, 2010 that does not 
contain values for both parameters will return an error explaining that 
these parameters must be included in E-utility requests.

The value of the &tool parameter should be a URI-safe string that is the 
name of the software package, script or web page producing the E-utility 
request.

The value of the &email parameter should be a valid e-mail address for 
the appropriate contact person or group responsible for maintaining the 
tool producing the E-utility request.

NCBI uses these parameters to contact users whose use of the E-utilities 
violates the standard usage policies described 
athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. 
These usage policies are designed to prevent excessive requests from a 
small group of users from reducing or eliminating the wider community's 
access to the E-utilities. NCBI will attempt to contact a user at the 
e-mail address provided in the &email parameter prior to blocking access 
to the E-utilities.

NCBI realizes that this policy change will require many of our users to 
change their code. Based on past experience, we anticipate that most of 
our users should be able to make the necessary changes before the June 
1, 2010 deadline. If you have any concerns about making these changes by 
that date, or if you have any questions about these policies, please 
contact eutilities at ncbi.nlm.nih.gov.

Thank you for your understanding and cooperation in helping us continue 
to deliver a reliable and efficient web service.

I think you already adhere to this policy but should a user's script not 
meet these requirements, than the script will fail and requests will be 
turned away with an error message.

Scott D. McGinnis M.A.
NCBI/NLM/NIH
45 Center Drive, MSC 6511
Bldg 45, Room 4AN.44C
Bethesda, MD 20892
mcginnis at ncbi.nlm.nih.gov














From charles at imbusch.net  Mon Feb  8 11:25:23 2010
From: charles at imbusch.net (Charles Imbusch)
Date: Mon, 08 Feb 2010 17:25:23 +0100
Subject: [Biojava-l] .sff support
Message-ID: <4B703AF3.4000300@imbusch.net>

Hello,

I have been wondering whether Biojava is able to
handle sff files coming from 454 sequencing runs.

I found something here:
http://lists.open-bio.org/pipermail/biojava-dev/2009-July/003907.html

Does somebody know about the current status on Biojava and sff files?


Thanks in advance,
  Charles

From paolo.pavan at gmail.com  Mon Feb  8 16:24:49 2010
From: paolo.pavan at gmail.com (Paolo Pavan)
Date: Mon, 8 Feb 2010 22:24:49 +0100
Subject: [Biojava-l] .sff support
In-Reply-To: <4B703AF3.4000300@imbusch.net>
References: <4B703AF3.4000300@imbusch.net>
Message-ID: <56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>

Unfortunately, after spending some time on it, I didn't anything, sorry.
There is just a post more I sent to Andreas Prlic without enclose the list
by mistake, in which I report a few info more, coming from my reading on
BioPerl's way to manage contigs and assembly informations.
Nothing more.

Paolo


2010/2/8 Charles Imbusch <charles at imbusch.net>

> Hello,
>
> I have been wondering whether Biojava is able to
> handle sff files coming from 454 sequencing runs.
>
> I found something here:
> http://lists.open-bio.org/pipermail/biojava-dev/2009-July/003907.html
>
> Does somebody know about the current status on Biojava and sff files?
>
>
> Thanks in advance,
>  Charles
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From biopython at maubp.freeserve.co.uk  Mon Feb  8 19:59:37 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 9 Feb 2010 00:59:37 +0000
Subject: [Biojava-l] .sff support
In-Reply-To: <56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
References: <4B703AF3.4000300@imbusch.net>
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
Message-ID: <320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>

> 2010/2/8 Charles Imbusch <charles at imbusch.net>
>> Hello,
>>
>> I have been wondering whether Biojava is able to
>> handle sff files coming from 454 sequencing runs.
>>
>> I found something here:
>> http://lists.open-bio.org/pipermail/biojava-dev/2009-July/003907.html
>>
>> Does somebody know about the current status on Biojava and sff files?
>>
>>
>> Thanks in advance,
>>  Charles

On Mon, Feb 8, 2010 at 9:24 PM, Paolo Pavan <paolo.pavan at gmail.com> wrote:
>
> Unfortunately, after spending some time on it, I didn't anything, sorry.
> There is just a post more I sent to Andreas Prlic without enclose the list
> by mistake, in which I report a few info more, coming from my reading on
> BioPerl's way to manage contigs and assembly informations.
> Nothing more.
>
> Paolo

Hi,

I've CC'd the common OpenBio mailing list as this is probably of
interest beyond just BioJava.

Based on code from Jose Blanca (author of sff_extract), I
implemented support for the SFF (Roche 454) sequencing reads
for Biopython last year on a branch that I hope to merge into our
next release, currently here:

http://github.com/peterjc/biopython/tree/sff-seqio

In addition to the Roche Manuals (which may not be that easy to
get a copy of), the SFF format is described on this NCBI webpage:

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=formats#sff

I'm happy to answer questions on how the file format works
(including the undocumented index block which I had to reverse
engineer).

Peter

P.S. Just to clarify (from the old BioJava thread), the SFF file just
holds the raw reads - it is an input file for doing an assembly or
mapping.

From holland at eaglegenomics.com  Tue Feb  9 02:34:32 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 9 Feb 2010 20:34:32 +1300
Subject: [Biojava-l] Hibernate Exception and suggestion for change in
	BioSqlSchema
In-Reply-To: <4B710CED.5060404@gmail.com>
References: <4B710CED.5060404@gmail.com>
Message-ID: <9BB14CC0-4A89-4DC8-8928-C8475108B54A@eaglegenomics.com>

Hi. It's possible that your original email didn't make it to the list because it is HTML format, and the list only accepts plain text.

However, in answer to your two questions:

  1. The code that does the resolution of references might be better if it looks up existing IDs rather than using author, title, location to identify existing records. I would suggest modifying it to a three-step process - test ID, then if no match then test author/title/location, then if still no match create a new reference. Could someone do that? (I'm unable to do anything until late March).

  2. I think that's a bug (compound locations with null features) but not sure why. Could be that the process of constructing a CompoundRichLocation is somehow losing the feature reference from the original SimpleRichLocation. Again I can't investigate until March - can someone else take a look at the code? (A good starting point would be to look at how a CompoundRichLocation decides to select the feature from the SimpleRichLocations it is made up from).

cheers,
Richard

On 9 Feb 2010, at 20:21, Deepak Sheoran wrote:

> 
> Hi Richard
> 
> Below is the email which I sent to Biojava-1 mailing list but it never get posted on the mailing list server neither do i got any response, so please have a look on this email and tell what can be the solution of the problem described in the message.
> 
> 
> Thanks
> Deepak Sheoran
> -------- Original Message --------
> Subject:	Hibernate Exception and suggestion for change in BioSqlSchema
> Date:	Wed, 03 Feb 2010 08:07:35 -0600
> From:	Deepak Sheoran <sheoran143 at gmail.com>
> To:	biojava-l at lists.open-bio.org
> 
> Hi guys,
> 
> A couple of days back I was having some problem with hibernate exception but that exception got resolved and the reference to that email is:  http://old.nabble.com/Hibernate-Exception-when-persisting-some-richsequence-object-to-biosql-schema-to27299245.html
> On Richard  suggestion in above link  I am able to resolve some of  issues but then, I got stuck in to some other error with hibernate and then decided to investigate the matter and below are some facts and information which I found and I guess it is going to affect all of us.
> 	? The "Reference" table in bioSql schema have unique constraint on "dbxref_id" column (CONSTRAINT reference_dbxref_id_key UNIQUE (dbxref_id)). Which mean only one entry in reference table can use on dbxref_id.
> This Works wells but in cases when you have little variation in value of following column "location", "title", "authors" and all these variation refers to same PUBMED_ID. Then we can't persist or create a richsequence object .
>  Now when you tie RichObjectFactory to a  active hibernate session then the class  "BioSqlRichObjectBuilder" have method called "buildObject(Class clazz, List paramsList) " which is responsible  for looking up details of object in the database and if it find one then it will return that object, else it will try to persist the new object into the database.
> But problem is with below part of that method:
> ?..LineNumber: 114
> else if (SimpleDocRef.class.isAssignableFrom(clazz))
>  {                queryType = "DocRef";
>                 // convert List constructor to String representation for query
>                 ourParamsList.set(0, DocRefAuthor.Tools.generateAuthorString((List)ourParamsList.get(0), true));
>                 if (ourParamsList.size()<3) {
>                         queryText = "from DocRef as cr where cr.authors = ? and cr.location = ? and cr.title is null";
>                 } else {
>                         queryText = "from DocRef as cr where cr.authors = ? and cr.location = ? and cr.title = ?";
>                 }       
>  }
> ..LineNubmer: 123
> Now when hibernate search the database, it won't find any other record in "reference" table because those two record are different in string comparison, so it will return a new object back to "GenbankFormat" to following piece of code
> ?.LineNumber: 447
> else {
>                                         try {
>                                             CrossRef cr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{dbname, raccession, new Integer(0)});
>                                             RankedCrossRef rcr = new SimpleRankedCrossRef(cr, ++rcrossrefCount);
>                                             rlistener.getCurrentFeature().addRankedCrossRef(rcr);
>                                         } catch (ChangeVetoException e) {
>                                             throw new ParseException(e+", accession:"+accession);
>                                         }
>                                     }
>                     ?..LineNumber:455
> Then we will add that object to rlistener. And move to next part of genbank record and then biojava search for a new crossref in database and it will try to persist the old one it get a hibernate exception regarding violation of  "unique constraint on dbxref_id" column.
>  
> The only way to get these record in database is:
> 		? The very easy solution and the way I did it for testing my theory is Change the bioSql schema so that it can allow many to one on relation between "reference" and "dbxref" table.  Which even make sense because one paper can have many different variation of naming, and this change allow us to store that info too. But this is something BioSql people have decide and I don't know how to approach them.
> 		? Second solution is slightly difficult to implement, is to change the way  "BioSqlRichObjectBuilder.buildObject(Class clazz,List paramsList)"  make decision about weather a particular DocRef already exist in database or not. I am mean testing all possible string variations of authors, location, title of the docRef which we are searching. Which does have many complications and may slow down process of creating a richsequence object when link RichObjectFactory with a active hibernate session.
>  
> Example:Below is a sample of what i have in my local biosql schema which has modification suggested by me. (dbxref_id column have Pubmed_id , I replaced the local dbxref_id which was present on this table in my database with pubmed_id stored in "dbxref" table, for easy reference with outside world in this email)
> Reference_id
> Dbxref_id         
> Location
> Title
> Authors
> crc
> 216
> 18554304
> FEMS Microbiol. Ecol. 66 (3THEMATIC ISSUE: GUT MICROBIOLOGY), 528-536 (2008)
> Isolation of lactate-utilizing butyrate-producing bacteria from human feces and in vivo administration of Anaerostipes caccae strain L2 and galacto-oligosaccharides in a rat model
> Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y., Nomoto,K., Ito,M. and Sawada,H.
> 9E940E01F4BE3CD0
> 230
> 18554304
> FEMS Microbiol. Ecol. 66 (3), 528-536 (2008)
> Isolation of lactate-utilizing butyrate-producing bacteria from human feces and in vivo administration of Anaerostipes caccae strain L2 and galacto-oligosaccharides in a rat model
> Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y., Nomoto,K., Ito,M. and Sawada,H.
> D3BC0C17F3F786C9
> 415
> 16790744
> Infect. Immun. 74 (7), 3715-3726 (2006)
> Intrastrain Heterogeneity of the mgpB Gene in Mycoplasma genitalium Is Extensive In Vitro and In Vivo and Suggests that Variation Is Generated via Recombination with Repetitive Chromosomal Sequences
> Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and Totten,P.A.
> 60AEDFA0CEEACC38
> 969
> 16790744
> Infect. Immun. 74 (7), 3715-3726 (2006)
> Intrastrain heterogeneity of the mgpB gene in mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences
> Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and Totten,P.A.
> 4B1232999F6E8130
> 929
> 8688087
> Science 273 (5278), 1058-1073 (1996)
> Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
> Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D., Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A., Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J.-F., Adams,M.D., Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G., Merrick,J.M., Glodek,A., Scott,J.L., Geoghagen,N.S.M., Weidman,J.F., Fuhrmann,J.L., Presley,E.A., Nguyen,D., Utterback,T.R., Kelley,J.M., Peterson,J.D., Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A., Roberts,K.M., Kaine,B.P., Borodovsky,M., Klenk,H.-P., Fraser,C.M., Smith,H.O., Woese,C.R. and Venter,J.C.
> 3E79B40DD2AAA2B7
> 932
> 8688087
> Science 273 (5278), 1058-1073 (1996)
> Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
> Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D., Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A., Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J., Adams,M.D., Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G., Merrick,J.M., Glodek,A., Scott,J.D., Geoghagen,N.S., Weidman,J.F., Fuhrmann,J.L., Nguyen,D.T., Utterback,T., Kelley,J.M., Peterson,J.D., Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A., Roberts,K.M., Kaine,B.B., Borodovsky,M., Klenk,H.P., Fraser,C.M., Smith,H.O., Woese,C.R. and Venter,J.C.
> 094EB3384F8D6DE8
> 1426
> 10684935
> Nucleic Acids Res. 28 (6), 1397-1406 (2000)
> Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
> Read,T.D., Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F., White,O., Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T., Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S.L., Eisen,J. and Fraser,C.M.
> 357648D8FD8C6C8A
> 1481
> 10684935
> Nucleic Acids Res. 28 (6), 1397-1406 (2000)
> Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
> Read,T., Brunham,R., Shen,C., Gill,S., Heidelberg,J., White,O., Hickey,E., Peterson,J., Utterback,T., Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S., Eisen,J. and Fraser,C.
> 115411EB2DEE5654
> 1497
> 14689165
> Arch. Microbiol. 181 (2), 144-154 (2004)
> The effect of FITA mutations on the symbiotic properties of Sinorhizobium fredii varies in a chromosomal-background-dependent manner
> Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J., Bellogin,R., del Rosario Espuny,M., Temprano,F., Romero,F., Krishnan,H.B., Pueppke,S.G. and Ruiz-Sainz,J.E.
> 4D5D376EECCD186B
> 1501
> 14689165
> Arch. Microbiol. 181 (2), 144-154 (2004)
> The effect of FITA mutations on the symbiotic properties of Sinorhizobium fredii varies in a chromosomal-background-dependent manner
> Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J., Bellogin,R., Del Rosario Espuny,M., Temprano,F., Romero,F., Krishnan,H.B., Pueppke,S.G. and Ruiz-Sainz,J.E.
> 4D57954EECDED66B
> 1556
> 18060065
> PLoS ONE 2 (12), E1271 (2007)
> Analysis of the Neurotoxin Complex Genes in Clostridium botulinum A1-A4 and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located within Plasmids
> Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,A.C., Bruce,D.C., Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and Brettin,T.S.
> 698688FB6DB95247
> 1559
> 18060065
> PLoS ONE 2 (12), E1271 (2007)
> Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids
> Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,C.A., Bruce,D.C., Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and Brettin,T.S.
> E25E1BA99DB18F3D
>  
> 	? The second kind of error which I got was : org.hibernate.PropertyValueException: not-null property references a null or transient value: Location.feature
> 		? Which means in richsequence object some feature have location object which have its feature set to null.
> 		? My Observation:
> 			? Usually occur when you try to persist a richsequence object to database, and occur to those features which have CompoundRichLocation usually "joins" and "complement" in cds region of a genbank record
> 			? After catching the hibernate exception I went through all the features and either biojava or hibernate  changed the object type of a CompoundRichLocation  to SimpleRichLocation and set the feature variable to null.
> 			? Below is the screen shot of one of my tests
> 				? Settings before trying to persits the richsequence object to database
>  
> <Mail Attachment.png>
> 		?  
> 		? After trying to persits the richsequence object to database and got in hibernate exception catch
>  
> 		? <Mail Attachment.png>
>  
> 		? So my question is why is this happening and how to stop or how to get these record into database, I have no clue why is this happening.
> 		? Some extra information to make things more clear to you guys.
> 			? Below are some Locus line from genbank record for which I know the error of location, I mean the cds region causing error, and array index in richsequence.feature arrayList object.
> 				? LOCUS       AE001439             1643831 bp    DNA     circular BCT 19-JAN-2006
> 					? richSequence.feature Index : 2540 and line number in the genbank record : 22115
> 				? LOCUS       CP001189             3887492 bp    DNA     circular BCT 16-OCT-2008
> 					? richSequence.feature Index : 127 and line number in the genbank record : 2137
> 				? LOCUS       CP001292              328635 bp    DNA     circular BCT 17-DEC-2008
> 					? richSequence.feature Index : 389 and line number in the genbank record : 3632
> 				? LOCUS       AM279694              238517 bp    DNA     linear   BCT 23-OCT-2008
> 					? richSequence.feature Index : 47 and line number in the genbank record : 4841
> 				? LOCUS       CR931663               18517 bp    DNA     linear   BCT 18-SEP-2008
> 					? richSequence.feature Index : 45 and line number in the genbank record : 442
> 		? The complete exception msg :
> org.hibernate.PropertyValueException: not-null property references a null or transient value: Location.feature
>         at org.hibernate.engine.Nullability.checkNullability(Nullability.java:72)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:290)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
>         at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>         at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
>         at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
>         at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
>         at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
>         at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
>         at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>         at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)
>         at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
>         at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
>         at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>         at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
>         at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
>         at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>         at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
>         at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
>         at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
>         at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
>         at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
>         at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>         at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)
>         at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
>         at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
>         at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>         at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
>         at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
>         at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
>         at org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
>         at org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:27)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>         at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)
>         at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)
>         at trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:78)
>  
>  

--
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 anjolou at hotmail.com  Tue Feb  9 10:17:57 2010
From: anjolou at hotmail.com (Louise Ott)
Date: Tue, 9 Feb 2010 16:17:57 +0100
Subject: [Biojava-l] Displaying a simple alignment blastoutput-like
Message-ID: <BAY110-W2594AD362E3D0C31580D54B3500@phx.gbl>


Hi all !
I read and followed all the advices i found on the net and in this mailing list and i came to this :

public class OtherAlignmentPanel extends TranslatedSequencePanel {
    public otherAlignmentPanel(Alignment ali) {        this.setSequence((SymbolList) ali);        this.setBackground(Color.white);        this.setPreferredSize(new Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 15));
        MultiLineRenderer multi = new MultiLineRenderer();        AlignmentRenderer render1 = new AlignmentRenderer();        AlignmentRenderer render2 = new AlignmentRenderer();        AlignmentRenderer render3 = new AlignmentRenderer();        SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
        render1.setLabel(ali.getLabels().get(0));        render1.setRenderer(symbol);
        multi.addRenderer(render1);
        render2.setLabel(ali.getLabels().get(1));        render2.setRenderer(symbol);
        multi.addRenderer(render2);
        render3.setLabel(ali.getLabels().get(2));        render3.setRenderer(symbol);
        multi.addRenderer(render3);
        this.setRenderer(multi);    }
}

I created the panel in a frame like this :
        Sequence seq1;        seq1 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), "query");
        Sequence seq2;        seq2 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), "hit");
        Sequence seq3;        seq3 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), "midline");
        Map<String, Sequence> list = new HashMap();        list.put("query", seq1);        list.put("middle", seq2);        list.put("hit", seq3);
        SimpleAlignment ali = new SimpleAlignment((Map) list);        OtherAlignmentPanel pane = new otherAlignmentPanel(ali);	this.add(pane);



My problems :- First, it just shows nothing ! I am totally lost, it has been 3 days i am just trying to display this simple alignment but it doesn't work !!- I really would like the lines to be wrapped like in the blast output, so i tryied with the SequencePanelWrapper, but it doesn't work either...
Is there any simple solution ??What did i do wrong in my code ?


Have a nice day and thanks !
Louise
 		 	   		  
_________________________________________________________________
D?couvrez Windows 7 en 7 secondes?!
http://clk.atdmt.com/FRM/go/181574577/direct/01/

From jolyon.holdstock at ogt.co.uk  Tue Feb  9 10:40:54 2010
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Tue, 9 Feb 2010 15:40:54 -0000
Subject: [Biojava-l] Displaying a simple alignment
	blastoutput-like[Scanned]
References: <BAY110-W2594AD362E3D0C31580D54B3500@phx.gbl>
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>

Does nothing become visible, if so how are you calling the panels/frame to display?

Can you post all your code?

-----Original Message-----
From: Louise Ott [mailto:anjolou at hotmail.com] 
Sent: 09 February 2010 15:18
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Displaying a simple alignment blastoutput-like[Scanned]


Hi all !
I read and followed all the advices i found on the net and in this mailing list and i came to this :

public class OtherAlignmentPanel extends TranslatedSequencePanel {
    public otherAlignmentPanel(Alignment ali) {        this.setSequence((SymbolList) ali);        this.setBackground(Color.white);        this.setPreferredSize(new Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 15));
        MultiLineRenderer multi = new MultiLineRenderer();        AlignmentRenderer render1 = new AlignmentRenderer();        AlignmentRenderer render2 = new AlignmentRenderer();        AlignmentRenderer render3 = new AlignmentRenderer();        SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
        render1.setLabel(ali.getLabels().get(0));        render1.setRenderer(symbol);
        multi.addRenderer(render1);
        render2.setLabel(ali.getLabels().get(1));        render2.setRenderer(symbol);
        multi.addRenderer(render2);
        render3.setLabel(ali.getLabels().get(2));        render3.setRenderer(symbol);
        multi.addRenderer(render3);
        this.setRenderer(multi);    }
}

I created the panel in a frame like this :
        Sequence seq1;        seq1 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), "query");
        Sequence seq2;        seq2 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), "hit");
        Sequence seq3;        seq3 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), "midline");
        Map<String, Sequence> list = new HashMap();        list.put("query", seq1);        list.put("middle", seq2);        list.put("hit", seq3);
        SimpleAlignment ali = new SimpleAlignment((Map) list);        OtherAlignmentPanel pane = new otherAlignmentPanel(ali);	this.add(pane);



My problems :- First, it just shows nothing ! I am totally lost, it has been 3 days i am just trying to display this simple alignment but it doesn't work !!- I really would like the lines to be wrapped like in the blast output, so i tryied with the SequencePanelWrapper, but it doesn't work either...
Is there any simple solution ??What did i do wrong in my code ?


Have a nice day and thanks !
Louise
 		 	   		  
_________________________________________________________________
D?couvrez Windows 7 en 7 secondes !
http://clk.atdmt.com/FRM/go/181574577/direct/01/
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l











This email has been scanned by Oxford Gene Technology Security Systems.


From anjolou at hotmail.com  Tue Feb  9 11:47:47 2010
From: anjolou at hotmail.com (Louise Ott)
Date: Tue, 9 Feb 2010 17:47:47 +0100
Subject: [Biojava-l] Displaying a simple alignment
	blastoutput-like[Scanned]
In-Reply-To: <588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>
References: <BAY110-W2594AD362E3D0C31580D54B3500@phx.gbl>
	<588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>
Message-ID: <BAY110-DS2CACD0143A9BB6DAE0317B3500@phx.gbl>

Posting all the code won't help because everything is visible except the 
object of OtherAlignmentPanel.
I already tested the same code but with a SequencePanel and a 
SequencePanelWrapper added to my frame (with one sequence to display) and it 
worked fine.

So if there is a problem, I think this can be only in the code I already 
posted.

(And the code is really really big, is would be hard to read)

Sorry for my poor english, i'm french, I don't always use the good words to 
explain my problem :)

--------------------------------------------------
From: "Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent: Tuesday, February 09, 2010 4:40 PM
To: "Louise Ott" <anjolou at hotmail.com>; <biojava-l at lists.open-bio.org>
Subject: RE: [Biojava-l] Displaying a simple alignment 
blastoutput-like[Scanned]

> Does nothing become visible, if so how are you calling the panels/frame to 
> display?
>
> Can you post all your code?
>
> -----Original Message-----
> From: Louise Ott [mailto:anjolou at hotmail.com]
> Sent: 09 February 2010 15:18
> To: biojava-l at lists.open-bio.org
> Subject: [Biojava-l] Displaying a simple alignment 
> blastoutput-like[Scanned]
>
>
> Hi all !
> I read and followed all the advices i found on the net and in this mailing 
> list and i came to this :
>
> public class OtherAlignmentPanel extends TranslatedSequencePanel {
>    public otherAlignmentPanel(Alignment ali) { 
> this.setSequence((SymbolList) ali); 
> this.setBackground(Color.white);        this.setPreferredSize(new 
> Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 
> 15));
>        MultiLineRenderer multi = new MultiLineRenderer(); 
> AlignmentRenderer render1 = new AlignmentRenderer(); 
> AlignmentRenderer render2 = new AlignmentRenderer(); 
> AlignmentRenderer render3 = new AlignmentRenderer(); 
> SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
>        render1.setLabel(ali.getLabels().get(0)); 
> render1.setRenderer(symbol);
>        multi.addRenderer(render1);
>        render2.setLabel(ali.getLabels().get(1)); 
> render2.setRenderer(symbol);
>        multi.addRenderer(render2);
>        render3.setLabel(ali.getLabels().get(2)); 
> render3.setRenderer(symbol);
>        multi.addRenderer(render3);
>        this.setRenderer(multi);    }
> }
>
> I created the panel in a frame like this :
>        Sequence seq1;        seq1 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), 
> "query");
>        Sequence seq2;        seq2 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), 
> "hit");
>        Sequence seq3;        seq3 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), 
> "midline");
>        Map<String, Sequence> list = new HashMap(); 
> list.put("query", seq1);        list.put("middle", seq2); 
> list.put("hit", seq3);
>        SimpleAlignment ali = new SimpleAlignment((Map) list); 
> OtherAlignmentPanel pane = new otherAlignmentPanel(ali); this.add(pane);
>
>
>
> My problems :- First, it just shows nothing ! I am totally lost, it has 
> been 3 days i am just trying to display this simple alignment but it 
> doesn't work !!- I really would like the lines to be wrapped like in the 
> blast output, so i tryied with the SequencePanelWrapper, but it doesn't 
> work either...
> Is there any simple solution ??What did i do wrong in my code ?
>
>
> Have a nice day and thanks !
> Louise
>
> _________________________________________________________________
> D?couvrez Windows 7 en 7 secondes !
> http://clk.atdmt.com/FRM/go/181574577/direct/01/
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
>
>
>
>
>
>
>
> This email has been scanned by Oxford Gene Technology Security Systems.
>
>
>
>
>
>
>
>
>
>
>
> This email has been scanned by Oxford Gene Technology Security Systems.
> 

From anjolou at hotmail.com  Tue Feb  9 11:47:47 2010
From: anjolou at hotmail.com (Louise Ott)
Date: Tue, 9 Feb 2010 17:47:47 +0100
Subject: [Biojava-l] Displaying a simple alignment
	blastoutput-like[Scanned]
In-Reply-To: <588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>
References: <BAY110-W2594AD362E3D0C31580D54B3500@phx.gbl>
	<588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>
Message-ID: <BAY110-DS2CACD0143A9BB6DAE0317B3500@phx.gbl>

Posting all the code won't help because everything is visible except the 
object of OtherAlignmentPanel.
I already tested the same code but with a SequencePanel and a 
SequencePanelWrapper added to my frame (with one sequence to display) and it 
worked fine.

So if there is a problem, I think this can be only in the code I already 
posted.

(And the code is really really big, is would be hard to read)

Sorry for my poor english, i'm french, I don't always use the good words to 
explain my problem :)

--------------------------------------------------
From: "Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent: Tuesday, February 09, 2010 4:40 PM
To: "Louise Ott" <anjolou at hotmail.com>; <biojava-l at lists.open-bio.org>
Subject: RE: [Biojava-l] Displaying a simple alignment 
blastoutput-like[Scanned]

> Does nothing become visible, if so how are you calling the panels/frame to 
> display?
>
> Can you post all your code?
>
> -----Original Message-----
> From: Louise Ott [mailto:anjolou at hotmail.com]
> Sent: 09 February 2010 15:18
> To: biojava-l at lists.open-bio.org
> Subject: [Biojava-l] Displaying a simple alignment 
> blastoutput-like[Scanned]
>
>
> Hi all !
> I read and followed all the advices i found on the net and in this mailing 
> list and i came to this :
>
> public class OtherAlignmentPanel extends TranslatedSequencePanel {
>    public otherAlignmentPanel(Alignment ali) { 
> this.setSequence((SymbolList) ali); 
> this.setBackground(Color.white);        this.setPreferredSize(new 
> Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 
> 15));
>        MultiLineRenderer multi = new MultiLineRenderer(); 
> AlignmentRenderer render1 = new AlignmentRenderer(); 
> AlignmentRenderer render2 = new AlignmentRenderer(); 
> AlignmentRenderer render3 = new AlignmentRenderer(); 
> SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
>        render1.setLabel(ali.getLabels().get(0)); 
> render1.setRenderer(symbol);
>        multi.addRenderer(render1);
>        render2.setLabel(ali.getLabels().get(1)); 
> render2.setRenderer(symbol);
>        multi.addRenderer(render2);
>        render3.setLabel(ali.getLabels().get(2)); 
> render3.setRenderer(symbol);
>        multi.addRenderer(render3);
>        this.setRenderer(multi);    }
> }
>
> I created the panel in a frame like this :
>        Sequence seq1;        seq1 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), 
> "query");
>        Sequence seq2;        seq2 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), 
> "hit");
>        Sequence seq3;        seq3 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), 
> "midline");
>        Map<String, Sequence> list = new HashMap(); 
> list.put("query", seq1);        list.put("middle", seq2); 
> list.put("hit", seq3);
>        SimpleAlignment ali = new SimpleAlignment((Map) list); 
> OtherAlignmentPanel pane = new otherAlignmentPanel(ali); this.add(pane);
>
>
>
> My problems :- First, it just shows nothing ! I am totally lost, it has 
> been 3 days i am just trying to display this simple alignment but it 
> doesn't work !!- I really would like the lines to be wrapped like in the 
> blast output, so i tryied with the SequencePanelWrapper, but it doesn't 
> work either...
> Is there any simple solution ??What did i do wrong in my code ?
>
>
> Have a nice day and thanks !
> Louise
>
> _________________________________________________________________
> D?couvrez Windows 7 en 7 secondes !
> http://clk.atdmt.com/FRM/go/181574577/direct/01/
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
>
>
>
>
>
>
>
> This email has been scanned by Oxford Gene Technology Security Systems.
>
>
>
>
>
>
>
>
>
>
>
> This email has been scanned by Oxford Gene Technology Security Systems.
> 

From sheoran143 at gmail.com  Thu Feb 11 04:00:15 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Thu, 11 Feb 2010 03:00:15 -0600
Subject: [Biojava-l] Issues with BioSqlRichSequenceDB.java class
Message-ID: <4B73C71F.1080706@gmail.com>

Hi
This class(BiosqlRichSequence) have methods to retrieve record from a 
local instance of biosql schema but when you type in accession number 
for record it mostly show the info but in some case (Record with 
accession:M97762)  it give following error :

     Hibernate: select sequence0_.bioentry_id as bioentry1_9_, 
sequence0_1_.name as name9_, sequence0_1_.identifier as identifier9_, 
sequence0_1_.accession as accession9_, sequence0_1_.description as 
descript5_9_, sequence0_1_.version as version9_, sequence0_1_.division 
as division9_, sequence0_1_.taxon_id as taxon8_9_, 
sequence0_1_.biodatabase_id as biodatab9_9_, sequence0_.version as 
version13_, sequence0_.length as length13_, sequence0_.alphabet as 
alphabet13_, sequence0_.seq as seq13_ from biosequence sequence0_ inner 
join bioentry sequence0_1_ on 
sequence0_.bioentry_id=sequence0_1_.bioentry_id where sequence0_1_.name=?
Exception in thread "main" java.lang.RuntimeException: Error while 
trying to load by id: M97762
         at 
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:212)
         at 
com.orionbiosciences.orionGenBankLib.genBankDb.GenBankDb.GenBankDbToFileDownLoader(GenBankDb.java:355)
         at trashtesting.Main.main(Main.java:39)
Caused by: org.biojava.bio.seq.db.IllegalIDException: Id not found: M97762
         at 
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:206)
         ... 2 more
Java Result: 1

The only way to find this record in my database is to search for LOCUS 
instead of Accession number which is "BTVNS1TUBA", java doc for 
BioSqlRichSequenceDb class say the id should be Genbank Id  i can't 
understand what does that means, but when investigated the matter the 
error is in following method

public RichSequenceDB getRichSequences(Set ids, RichSequenceDB db) 
throws BioException, IllegalIDException {
         if (db==null) db = new HashRichSequenceDB();
         try {
             for (Iterator i = ids.iterator(); i.hasNext(); ) {
                 String id = (String)i.next();
                 // Build the query object
                ***************************error*******************
                  String queryText = "from Sequence where name = ?";
              ***************************error***********************
             *****************************solution**************************
                 String queryText = "from Sequence where accession = ?";
                // because name stand for Locus from gen-bank record 
which don't have any unique constraint name so its should not be good 
idea to use it for searching unique records
               // also people usually refer to a gen-bank record using 
accession number instead of LOCUS
            
*****************************solution******************************
                 Object query = this.createQuery.invoke(this.session, 
new Object[]{queryText});
                 // Set the parameters
                 query = this.setParameter.invoke(query, new 
Object[]{new Integer(0), id});
                 // Get the results
                 List result = (List)this.list.invoke(query,(Object[]) 
null);
                 // If the result doesn't just have a single entry, 
throw an exception
                 if (result.size()==0) throw new IllegalIDException("Id 
not found: "+id);
                 // Add the results to the results db.
                 for (Iterator j = result.iterator(); j.hasNext(); ) 
db.addRichSequence((RichSequence)j.next());
             }
         } catch (Exception e) {
             // Throw the exception with our nice message
             throw new RuntimeException("Error while trying to load by 
ids: "+ids,e);
         }
         return db;
     }

even ncbi says " It is better to search for the actual accession number 
rather than the locus name, because the accessions are stable and locus 
names can change."
REF: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#LocusNameB

So my suggestion is to change the query so it will look for accession 
instead of name in this method.
Also if you will try to download record from ncbi using java interface 
first with accession:M97762( as genbank_id) you can get it, but when you 
try to get using LOCUS you will get bad section  exception  around 
reference I don't know why ?


Deepak Sheoran




From holland at eaglegenomics.com  Thu Feb 11 17:18:18 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Fri, 12 Feb 2010 11:18:18 +1300
Subject: [Biojava-l] Issues with BioSqlRichSequenceDB.java class
In-Reply-To: <4B73C71F.1080706@gmail.com>
References: <4B73C71F.1080706@gmail.com>
Message-ID: <4ACB7402-D8DB-4CEF-AC70-BE228312EB37@eaglegenomics.com>

My preference would be to leave the existing method as-is, and modify the javadocs so that it is explicit that it is searching by name and not accession. This is to prevent breaking any code that may rely on this behaviour (as Genbank is not the only kind of sequence that can be stored in BioSQL, we can't guarantee that other sequence types are not using name as the unique identifier instead).

Instead, I would propose adding a second method called getRichSequencesByAccession, with the modification you suggest.

With regard to your last point about bad section errors, could you post the stack trace and the code that causes it?

cheers,
Richard

On 11 Feb 2010, at 22:00, Deepak Sheoran wrote:

> Hi
> This class(BiosqlRichSequence) have methods to retrieve record from a local instance of biosql schema but when you type in accession number for record it mostly show the info but in some case (Record with accession:M97762)  it give following error :
> 
>    Hibernate: select sequence0_.bioentry_id as bioentry1_9_, sequence0_1_.name as name9_, sequence0_1_.identifier as identifier9_, sequence0_1_.accession as accession9_, sequence0_1_.description as descript5_9_, sequence0_1_.version as version9_, sequence0_1_.division as division9_, sequence0_1_.taxon_id as taxon8_9_, sequence0_1_.biodatabase_id as biodatab9_9_, sequence0_.version as version13_, sequence0_.length as length13_, sequence0_.alphabet as alphabet13_, sequence0_.seq as seq13_ from biosequence sequence0_ inner join bioentry sequence0_1_ on sequence0_.bioentry_id=sequence0_1_.bioentry_id where sequence0_1_.name=?
> Exception in thread "main" java.lang.RuntimeException: Error while trying to load by id: M97762
>        at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:212)
>        at com.orionbiosciences.orionGenBankLib.genBankDb.GenBankDb.GenBankDbToFileDownLoader(GenBankDb.java:355)
>        at trashtesting.Main.main(Main.java:39)
> Caused by: org.biojava.bio.seq.db.IllegalIDException: Id not found: M97762
>        at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:206)
>        ... 2 more
> Java Result: 1
> 
> The only way to find this record in my database is to search for LOCUS instead of Accession number which is "BTVNS1TUBA", java doc for BioSqlRichSequenceDb class say the id should be Genbank Id  i can't understand what does that means, but when investigated the matter the error is in following method
> 
> public RichSequenceDB getRichSequences(Set ids, RichSequenceDB db) throws BioException, IllegalIDException {
>        if (db==null) db = new HashRichSequenceDB();
>        try {
>            for (Iterator i = ids.iterator(); i.hasNext(); ) {
>                String id = (String)i.next();
>                // Build the query object
>               ***************************error*******************
>                 String queryText = "from Sequence where name = ?";
>             ***************************error***********************
>            *****************************solution**************************
>                String queryText = "from Sequence where accession = ?";
>               // because name stand for Locus from gen-bank record which don't have any unique constraint name so its should not be good idea to use it for searching unique records
>              // also people usually refer to a gen-bank record using accession number instead of LOCUS
>           *****************************solution******************************
>                Object query = this.createQuery.invoke(this.session, new Object[]{queryText});
>                // Set the parameters
>                query = this.setParameter.invoke(query, new Object[]{new Integer(0), id});
>                // Get the results
>                List result = (List)this.list.invoke(query,(Object[]) null);
>                // If the result doesn't just have a single entry, throw an exception
>                if (result.size()==0) throw new IllegalIDException("Id not found: "+id);
>                // Add the results to the results db.
>                for (Iterator j = result.iterator(); j.hasNext(); ) db.addRichSequence((RichSequence)j.next());
>            }
>        } catch (Exception e) {
>            // Throw the exception with our nice message
>            throw new RuntimeException("Error while trying to load by ids: "+ids,e);
>        }
>        return db;
>    }
> 
> even ncbi says " It is better to search for the actual accession number rather than the locus name, because the accessions are stable and locus names can change."
> REF: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#LocusNameB
> 
> So my suggestion is to change the query so it will look for accession instead of name in this method.
> Also if you will try to download record from ncbi using java interface first with accession:M97762( as genbank_id) you can get it, but when you try to get using LOCUS you will get bad section  exception  around reference I don't know why ?
> 
> 
> Deepak Sheoran
> 
> 
> 
> _______________________________________________
> 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 jeedward at yahoo.com  Fri Feb 12 12:01:32 2010
From: jeedward at yahoo.com (John Edward)
Date: Fri, 12 Feb 2010 09:01:32 -0800 (PST)
Subject: [Biojava-l] Draft paper submission deadline is extended: BCBGC-10,
	Orlando, USA
Message-ID: <767436.37495.qm@web45906.mail.sp1.yahoo.com>

It
would be highly appreciated if you could share this announcement with your
colleagues, students and individuals whose research is in bioinformatics,
computational biology, genomics, data-mining, and related areas.
 
Draft
paper submission deadline is extended: BCBGC-10, Orlando, USA 
 
The 2010 International Conference on Bioinformatics,
Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA.  BCBGC is an important event in the
areas of bioinformatics, computational biology, genomics and chemoinformatics
and focuses on all areas related to the conference.
 
The conference will be held at the same time and location where several
other major international conferences will be taking place. The conference will
be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be
held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of
MULTICONF is to promote research and developmental activities in computer
science, information technology, control engineering, and related fields.
Another goal is to promote the dissemination of research to a multidisciplinary
audience and to facilitate communication among researchers, developers,
practitioners in different fields.The following
conferences are planned to be organized as part of MULTICONF-10.
 
	* International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10)
	*  International Conference on Automation, Robotics and Control Systems (ARCS-10)
	* International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10)
	* International Conference on Computer Communications and Networks (CCN-10)
	* International Conference on Enterprise Information Systems and Web Technologies (EISWT-10)
	* International Conference on High Performance Computing Systems (HPCS-10)
	* International Conference on Information Security and Privacy (ISP-10) 
	* International Conference on Image and Video Processing and Computer Vision (IVPCV-10)
	* International Conference on Software Engineering Theory and Practice (SETP-10) 
	* International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) 
 
 
MULTICONF-10 will be held at Imperial Swan Hotel
and Suites.  It is a full-service resort that puts you in the middle of
the fun! Located 1/2 block south of the famed International Drive, the hotel is
just minutes from great entertainment like Walt Disney World? Resort, Universal
Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and
on-site dining ? all situated on 10 tropically landscaped acres. Here, guests
can experience a full-service resort with discount hotel pricing in Orlando.
 
We
invite draft paper submissions. Please see the website http://www.PromoteResearch.org for
more details.
 
Sincerely
John
Edward


      

From koen.bruynseels at cropdesign.com  Sat Feb 13 12:13:54 2010
From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com)
Date: Sat, 13 Feb 2010 18:13:54 +0100
Subject: [Biojava-l] Koen Bruynseels is out of the office.
Message-ID: <OFA2B596E3.0BF6BDC5-ONC12576C9.005EA817-C12576C9.005EA817@basf-c-s.be>


I will be out of the office starting  02/13/2010 and will not return until
02/21/2010.

I will respond to your message when I return.


From charles at imbusch.net  Mon Feb 15 17:32:28 2010
From: charles at imbusch.net (Charles Imbusch)
Date: Mon, 15 Feb 2010 23:32:28 +0100
Subject: [Biojava-l] .sff support
In-Reply-To: <320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
References: <4B703AF3.4000300@imbusch.net>	
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
Message-ID: <4B79CB7C.3040008@imbusch.net>

Hi all,

I've been playing around with the sff file based on the file
format definition at NCBI.
I uploaded the output which includes the common header,
the read header and read data section for the first read
of that file.

http://home.arcor.de/cimbusch/output.txt
> I'm happy to answer questions on how the file format works
> (including the undocumented index block which I had to reverse
> engineer).
>   
Yes, I would like to know how that works.
index_magic_number:778921588 .mft
version:1.00
Couldn't find anything about ".mft" version 1.

At the moment I have two classes: sffParser and sffFile
My idea was that sffParser can hold one or multiple sff files. Each 
instance of
sffFile has a hashtable with the identifiers as keys and the 
filepointers are
stored as the values.

Now I would like to find a good representation of one single "read" 
object, which
shall be accessible with an identifier like EV5RTWS02JXUUH

At the moment I'm making use of the BigInteger class to store many 
variables
but thats probably a waste of memory.
The variables for the read object I'm thinking of:

Read Header Section:

read_header_length -> int
name_length -> int
number_of_bases -> int
clip_qual_left -> int
clip_qual_right -> int
clip_adapter_left -> int
clip_adapter_right -> int
name -> string

Read Data Section:

flowgram_values -> float[]
flow_index_per_base -> int[]
bases: -> string
quality_scores -> int[]

But I'm not very familiar with the existing data structures of BioJava, 
is there
maybe already something similar?

Cheers,
 Charles


From biopython at maubp.freeserve.co.uk  Mon Feb 22 06:35:11 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 22 Feb 2010 11:35:11 +0000
Subject: [Biojava-l] .sff support
In-Reply-To: <4B79CB7C.3040008@imbusch.net>
References: <4B703AF3.4000300@imbusch.net>
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
	<4B79CB7C.3040008@imbusch.net>
Message-ID: <320fb6e01002220335x6899a44bl68789cd4d7d772e3@mail.gmail.com>

On Mon, Feb 15, 2010 at 10:32 PM, Charles Imbusch <charles at imbusch.net> wrote:
>
> Hi all,
>
> I've been playing around with the sff file based on the file
> format definition at NCBI.
> I uploaded the output which includes the common header,
> the read header and read data section for the first read
> of that file.
>
> http://home.arcor.de/cimbusch/output.txt

Looks like you've been making excellent progress :)

Sorry for the delay in my reply, I was on leave last week (and
without internet access for most of it).

>> I'm happy to answer questions on how the file format works
>> (including the undocumented index block which I had to reverse
>> engineer).
>>
>
> Yes, I would like to know how that works.
> index_magic_number:778921588 .mft
> version:1.00
> Couldn't find anything about ".mft" version 1.

I believe ".mft" stands for "Manifest format", and Roche 454 use this
block to hold both a read index and an XML string (the manifest).
Immediately after the ".mft1.00" string are two longs which give the
lengths of the XML string and the actual index data. Then comes
the XML manifest string, followed by the actual index data (same
format as Roche's older ".srt" index only block, uses base 256).

Note the Biopython SFF code has now been merged into our trunk:
http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

> At the moment I have two classes: sffParser and sffFile
> My idea was that sffParser can hold one or multiple sff files.
> Each instance of sffFile has a hashtable with the identifiers
> as keys and the filepointers are stored as the values.

Not all SFF files will have an index, but the Roche .srt and .mft
index blocks will let you map from the ID to the offset. I take
advantage of this in Biopython for our Bio.SeqIO.index(...)
functionality with a slower fall back on scanning the file to
build the index if the index information is missing (or in an
unsupported format). The Biopython index code then uses
a Python dictionary (hash) to hold the mapping from read
name to file offset. See also:

http://github.com/biopython/biopython/blob/master/Bio/SeqIO/_index.py

> Now I would like to find a good representation of one single "read" object,
> which shall be accessible with an identifier like EV5RTWS02JXUUH

I think this is a Java question, so not my area of expertise.

Peter

From jeedward at yahoo.com  Mon Feb 22 15:37:23 2010
From: jeedward at yahoo.com (John Edward)
Date: Mon, 22 Feb 2010 12:37:23 -0800 (PST)
Subject: [Biojava-l] Call for papers: BCBGC-10, Orlando, USA, July 2010
Message-ID: <472328.10215.qm@web45916.mail.sp1.yahoo.com>

It
would be highly appreciated if you could share this announcement with your
colleagues, students and individuals whose research is in bioinformatics,
computational biology, genomics, data-mining, and related areas.
 
Call
for papers: BCBGC-10, Orlando, USA, July 2010
 
The
2010 International Conference on Bioinformatics, Computational Biology,
Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will
be held during 12-14 of July 2010 in Orlando, FL, USA.  BCBGC is an important event in the areas of
bioinformatics, computational biology, genomics and chemoinformatics and
focuses on all areas related to the conference.
 
The
conference will be held at the same time and location where several other major
international conferences will be taking place. The conference will be held as
part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during
July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to
promote research and developmental activities in computer science, information
technology, control engineering, and related fields. Another goal is to promote
the dissemination of research to a multidisciplinary audience and to facilitate
communication among researchers, developers, practitioners in different fields.
The following conferences are planned to be organized as part of MULTICONF-10.
 
?           International Conference on
Artificial Intelligence and Pattern Recognition (AIPR-10)
?            International Conference on
Automation, Robotics and Control Systems (ARCS-10)
?           International Conference on
Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10)
?           International Conference on Computer
Communications and Networks (CCN-10)
?           International Conference on
Enterprise Information Systems and Web Technologies (EISWT-10)
?           International Conference on High
Performance Computing Systems (HPCS-10)
?           International Conference on
Information Security and Privacy (ISP-10) 
?           International Conference on Image and
Video Processing and Computer Vision (IVPCV-10)
?           International Conference on Software
Engineering Theory and Practice (SETP-10) 
?           International Conference on
Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) 
 
 
MULTICONF-10
will be held at Imperial Swan Hotel and Suites.  It is a full-service resort that puts you in the middle of the fun!
Located 1/2 block south of the famed International Drive, the hotel is just
minutes from great entertainment like Walt Disney World? Resort, Universal
Studios and Sea World Orlando. Guests can enjoy free scheduled transportation
to these theme parks, as well as spacious accommodations, outdoor pools and
on-site dining ? all situated on 10 tropically landscaped acres. Here, guests
can experience a full-service resort with discount hotel pricing in Orlando.
 
We
invite draft paper submissions. Please see the website http://www.PromoteResearch.org for
more details.
 
Sincerely
John
Edward


      

From charles at imbusch.net  Thu Feb 25 05:08:38 2010
From: charles at imbusch.net (Charles Imbusch)
Date: Thu, 25 Feb 2010 11:08:38 +0100
Subject: [Biojava-l] .sff support
In-Reply-To: <320fb6e01002220335x6899a44bl68789cd4d7d772e3@mail.gmail.com>
References: <4B703AF3.4000300@imbusch.net>	
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>	
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>	
	<4B79CB7C.3040008@imbusch.net>
	<320fb6e01002220335x6899a44bl68789cd4d7d772e3@mail.gmail.com>
Message-ID: <4B864C26.3050709@imbusch.net>

Dear Peter,

thanks for your mail. I will try to make use of that index
to speed things up when I have time available.

Cheers,
  Charles


Peter schrieb:
> I believe ".mft" stands for "Manifest format", and Roche 454 use this
> block to hold both a read index and an XML string (the manifest).
> Immediately after the ".mft1.00" string are two longs which give the
> lengths of the XML string and the actual index data. Then comes
> the XML manifest string, followed by the actual index data (same
> format as Roche's older ".srt" index only block, uses base 256).
>
> Note the Biopython SFF code has now been merged into our trunk:
> http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
>   

From biopython at maubp.freeserve.co.uk  Fri Feb 26 08:33:19 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 26 Feb 2010 13:33:19 +0000
Subject: [Biojava-l] .sff support
In-Reply-To: <4B864C26.3050709@imbusch.net>
References: <4B703AF3.4000300@imbusch.net>
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
	<4B79CB7C.3040008@imbusch.net>
	<320fb6e01002220335x6899a44bl68789cd4d7d772e3@mail.gmail.com>
	<4B864C26.3050709@imbusch.net>
Message-ID: <320fb6e01002260533y148936fdg36a5c8c814deb141@mail.gmail.com>

On Thu, Feb 25, 2010 at 10:08 AM, Charles Imbusch <charles at imbusch.net> wrote:
>
> Dear Peter,
>
> thanks for your mail. I will try to make use of that index
> to speed things up when I have time available.
>
> Cheers,
> ?Charles

Hi Charles,

If found when you want random access to the reads, loading the
provided .mft or .srt index is MUCH faster than scanning the whole
file to build the index manually. So this really is worth the effort.

I hope the comments in my code are reasonably clear, but to
recap the key idea of the index block is you get chunks of data
of varying length (although typically all the same length since by
default all the Roche reads have the same read length) like this

name, null char, four character offset, terminator char of 0xFF

You divide the index block into entries for each read by
finding the 0xFF terminators. Because 0xFF (decimal 255)
is used in this way, it cannot be used to encode the offsets
which must only use 0x00 to 0xFE (decimal 0 to 254). The
offset therefore uses base 255 instead of base 256.

Note that this means that the largest offset the current
Roche index blocks can hold is 255^4, or a little under 4GB.
If you use the Roche tools to try and merge SFF files to
make an example SFF file over 4GB you get a warning
that there will be no index (and no manifest).

The index holds the reads sorted alphabetically by name.
We don't take advantage of this in Biopython since I use
a Python dictionary (like a Perl hash) to store the offsets.

In case you missed them, I'd like to draw your attention
to the SFF files I am using in the Biopython unit tests:
http://github.com/biopython/biopython/tree/master/Tests/Roche/

Regards,

Peter


From sheoran143 at gmail.com  Wed Feb  3 09:07:44 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Wed, 03 Feb 2010 14:07:44 -0000
Subject: [Biojava-l] Hibernate Exception and suggestion for change in
	BioSqlSchema
Message-ID: <4B698327.3080203@gmail.com>



      Hi guys,

      A couple of days back I was having some problem with hibernate
      exception but that exception got resolved and the reference to
      that email is:
      http://old.nabble.com/Hibernate-Exception-when-persisting-some-richsequence-object-to-biosql-schema-to27299245.html

      On Richard suggestion in above link I am able to resolve some of
      issues but then, I got stuck in to some other error with hibernate
      and then decided to investigate the matter and below are some
      facts and information which I found and I guess it is going to
      affect all of us.

   1. The "Reference" table in bioSql schema have unique constraint on
      "dbxref_id" column (CONSTRAINT reference_dbxref_id_key UNIQUE
      (dbxref_id)). Which mean only one entry in reference table can use
      on dbxref_id.

      This Works wells but in cases when you have little variation in
      value of following column "location", "title", "authors" and all
      these variation refers to same PUBMED_ID. Then we can't persist or
      create a richsequence object .

        Now when you tie RichObjectFactory to a active hibernate session
      then the class "BioSqlRichObjectBuilder" have method called
      "buildObject(Class clazz, List paramsList) " which is responsible
      for looking up details of object in the database and if it find
      one then it will return that object, else it will try to persist
      the new object into the database.

      But problem is with below part of that method:

      .....LineNumber: 114

      else if (SimpleDocRef.class.isAssignableFrom(clazz))

      {         queryType = "DocRef";

               // convert List constructor to String representation for
      query

               ourParamsList.set(0,
      DocRefAuthor.Tools.generateAuthorString((List)ourParamsList.get(0), true));

               if (ourParamsList.size()<3) {

               queryText = "from DocRef as cr where cr.authors = ? and
      cr.location = ? and cr.title is null";

               } else {

               queryText = "from DocRef as cr where cr.authors = ? and
      cr.location = ? and cr.title = ?";

               }

      }

      ..LineNubmer: 123

      Now when hibernate search the database, it won't find any other
      record in "reference" table because those two record are different
      in string comparison, so it will return a new object back to
      "GenbankFormat" to following piece of code

      ....LineNumber: 447

      else {

      try {

      CrossRef cr =
      (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new
      Object[]{dbname, raccession, new Integer(0)});

      RankedCrossRef rcr = new SimpleRankedCrossRef(cr, ++rcrossrefCount);

      rlistener.getCurrentFeature().addRankedCrossRef(rcr);

      } catch (ChangeVetoException e) {

      throw new ParseException(e+", accession:"+accession);

      }

      }

      .....LineNumber:455

      Then we will add that object to rlistener. And move to next part
      of genbank record and then biojava search for a new crossref in
      database and it will try to persist the old one it get a hibernate
      exception regarding violation of "unique constraint on dbxref_id"
      column.

      The only way to get these record in database is:

          * The very easy solution and the way I did it for testing my
            theory is Change the bioSql schema so that it can allow many
            to one on relation between "reference" and "dbxref" table.
            Which even make sense because one paper can have many
            different variation of naming, and this change allow us to
            store that info too. But this is something BioSql people
            have decide and I don't know how to approach them.
          * Second solution is slightly difficult to implement, is to
            change the way "BioSqlRichObjectBuilder.buildObject(Class
            clazz,List paramsList)" make decision about weather a
            particular DocRef already exist in database or not. I am
            mean testing all possible string variations of authors,
            location, title of the docRef which we are searching. Which
            does have many complications and may slow down process of
            creating a richsequence object when link RichObjectFactory
            with a active hibernate session.

      Example:Below is a sample of what i have in my local biosql schema
      which has modification suggested by me. (dbxref_id column have
      Pubmed_id , I replaced the local dbxref_id which was present on
      this table in my database with pubmed_id stored in "dbxref" table,
      for easy reference with outside world)

      Reference_id

      	

      Dbxref_id

      	

      Location

      	

      Title

      	

      Authors

      	

      crc

      216

      	

      18554304

      	

      FEMS Microbiol. Ecol. 66 (3THEMATIC ISSUE: GUT MICROBIOLOGY),
      528-536 (2008)

      	

      Isolation of lactate-utilizing butyrate-producing bacteria from
      human feces and in vivo administration of Anaerostipes caccae
      strain L2 and galacto-oligosaccharides in a rat model

      	

      Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y.,
      Nomoto,K., Ito,M. and Sawada,H.

      	

      9E940E01F4BE3CD0

      230

      	

      18554304

      	

      FEMS Microbiol. Ecol. 66 (3), 528-536 (2008)

      	

      Isolation of lactate-utilizing butyrate-producing bacteria from
      human feces and in vivo administration of Anaerostipes caccae
      strain L2 and galacto-oligosaccharides in a rat model

      	

      Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y.,
      Nomoto,K., Ito,M. and Sawada,H.

      	

      D3BC0C17F3F786C9

      415

      	

      16790744

      	

      Infect. Immun. 74 (7), 3715-3726 (2006)

      	

      Intrastrain Heterogeneity of the mgpB Gene in Mycoplasma
      genitalium Is Extensive In Vitro and In Vivo and Suggests that
      Variation Is Generated via Recombination with Repetitive
      Chromosomal Sequences

      	

      Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and
      Totten,P.A.

      	

      60AEDFA0CEEACC38

      969

      	

      16790744

      	

      Infect. Immun. 74 (7), 3715-3726 (2006)

      	

      Intrastrain heterogeneity of the mgpB gene in mycoplasma
      genitalium is extensive in vitro and in vivo and suggests that
      variation is generated via recombination with repetitive
      chromosomal sequences

      	

      Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and
      Totten,P.A.

      	

      4B1232999F6E8130

      929

      	

      8688087

      	

      Science 273 (5278), 1058-1073 (1996)

      	

      Complete genome sequence of the methanogenic archaeon,
      Methanococcus jannaschii

      	

      Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D.,
      Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A.,
      Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J.-F.,
      Adams,M.D., Reich,C.I., Overbeek,R., Kirkness,E.F.,
      Weinstock,K.G., Merrick,J.M., Glodek,A., Scott,J.L.,
      Geoghagen,N.S.M., Weidman,J.F., Fuhrmann,J.L., Presley,E.A.,
      Nguyen,D., Utterback,T.R., Kelley,J.M., Peterson,J.D., Sadow,P.W.,
      Hanna,M.C., Cotton,M.D., Hurst,M.A., Roberts,K.M., Kaine,B.P.,
      Borodovsky,M., Klenk,H.-P., Fraser,C.M., Smith,H.O., Woese,C.R.
      and Venter,J.C.

      	

      3E79B40DD2AAA2B7

      932

      	

      8688087

      	

      Science 273 (5278), 1058-1073 (1996)

      	

      Complete genome sequence of the methanogenic archaeon,
      Methanococcus jannaschii

      	

      Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D.,
      Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A.,
      Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J., Adams,M.D.,
      Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G.,
      Merrick,J.M., Glodek,A., Scott,J.D., Geoghagen,N.S., Weidman,J.F.,
      Fuhrmann,J.L., Nguyen,D.T., Utterback,T., Kelley,J.M.,
      Peterson,J.D., Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A.,
      Roberts,K.M., Kaine,B.B., Borodovsky,M., Klenk,H.P., Fraser,C.M.,
      Smith,H.O., Woese,C.R. and Venter,J.C.

      	

      094EB3384F8D6DE8

      1426

      	

      10684935

      	

      Nucleic Acids Res. 28 (6), 1397-1406 (2000)

      	

      Genome sequences of Chlamydia trachomatis MoPn and Chlamydia
      pneumoniae AR39

      	

      Read,T.D., Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F.,
      White,O., Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T.,
      Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B.,
      Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J.,
      McClarty,G., Salzberg,S.L., Eisen,J. and Fraser,C.M.

      	

      357648D8FD8C6C8A

      1481

      	

      10684935

      	

      Nucleic Acids Res. 28 (6), 1397-1406 (2000)

      	

      Genome sequences of Chlamydia trachomatis MoPn and Chlamydia
      pneumoniae AR39

      	

      Read,T., Brunham,R., Shen,C., Gill,S., Heidelberg,J., White,O.,
      Hickey,E., Peterson,J., Utterback,T., Berry,K., Bass,S.,
      Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R.,
      Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G.,
      Salzberg,S., Eisen,J. and Fraser,C.

      	

      115411EB2DEE5654

      1497

      	

      14689165

      	

      Arch. Microbiol. 181 (2), 144-154 (2004)

      	

      The effect of FITA mutations on the symbiotic properties of
      Sinorhizobium fredii varies in a chromosomal-background-dependent
      manner

      	

      Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J.,
      Bellogin,R., del Rosario Espuny,M., Temprano,F., Romero,F.,
      Krishnan,H.B., Pueppke,S.G. and Ruiz-Sainz,J.E.

      	

      4D5D376EECCD186B

      1501

      	

      14689165

      	

      Arch. Microbiol. 181 (2), 144-154 (2004)

      	

      The effect of FITA mutations on the symbiotic properties of
      Sinorhizobium fredii varies in a chromosomal-background-dependent
      manner

      	

      Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J.,
      Bellogin,R., Del Rosario Espuny,M., Temprano,F., Romero,F.,
      Krishnan,H.B., Pueppke,S.G. and Ruiz-Sainz,J.E.

      	

      4D57954EECDED66B

      1556

      	

      18060065

      	

      PLoS ONE 2 (12), E1271 (2007)

      	

      Analysis of the Neurotoxin Complex Genes in Clostridium botulinum
      A1-A4 and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located
      within Plasmids

      	

      Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,A.C.,
      Bruce,D.C., Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and
      Brettin,T.S.

      	

      698688FB6DB95247

      1559

      	

      18060065

      	

      PLoS ONE 2 (12), E1271 (2007)

      	

      Analysis of the neurotoxin complex genes in Clostridium botulinum
      A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located
      within plasmids

      	

      Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,C.A.,
      Bruce,D.C., Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and
      Brettin,T.S.

      	

      E25E1BA99DB18F3D

   2. The second kind of error which I got was :*
      org.hibernate.PropertyValueException: not-null property references
      a null or transient value: Location.feature*

          * Which means in richsequence object some feature have
            location object which have its feature set to null.
          * My Observation:
                o Usually occur when you try to persist a richsequence
                  object to database, and occur to those features which
                  have *CompoundRichLocation *usually "joins" and
                  "complement" in cds region of a genbank record
                o After catching the hibernate exception I went through
                  all the features and either biojava or hibernate
                  changed the object type of a CompoundRichLocation to
                  SimpleRichLocation and set the feature variable to null.
                o Below is the screen shot of one of my tests
                      + Settings before trying to persits the
                        richsequence object to database

          *
          * After trying to persits the richsequence object to database
            and got in hibernate exception catch

          *

          * So my question is why is this happening and how to stop or
            how to get these record into database, I have no clue why is
            this happening.
          * Some extra information to make things more clear to you guys.
                o Below are some Locus line from genbank record for
                  which I know the error of location, I mean the cds
                  region causing error, and array index in
                  richsequence.feature arrayList object.
                     1. LOCUS AE001439 1643831 bp DNA circular BCT
                        19-JAN-2006
                            + richSequence.feature Index : 2540 and line
                              number in the genbank record : 22115
                     2. LOCUS CP001189 3887492 bp DNA circular BCT
                        16-OCT-2008
                            + richSequence.feature Index : 127 and line
                              number in the genbank record : 2137
                     3. LOCUS CP001292 328635 bp DNA circular BCT
                        17-DEC-2008
                            + richSequence.feature Index : 389 and line
                              number in the genbank record : 3632
                     4. LOCUS AM279694 238517 bp DNA linear BCT 23-OCT-2008
                            + richSequence.feature Index : 47 and line
                              number in the genbank record : 4841
                     5. LOCUS CR931663 18517 bp DNA linear BCT 18-SEP-2008
                            + richSequence.feature Index : 45 and line
                              number in the genbank record : 442
          * The complete exception msg :

      org.hibernate.PropertyValueException: not-null property references
      a null or transient value: Location.feature

      at
      org.hibernate.engine.Nullability.checkNullability(Nullability.java:72)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:290)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)

      at
      org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)

      at
      org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)

      at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)

      at
      org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)

      at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)

      at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)

      at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)

      at
      org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)

      at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)

      at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)

      at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)

      at org.hibernate.engine.Cascade.cascade(Cascade.java:130)

      at
      org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)

      at
      org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)

      at
      org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)

      at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)

      at
      org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)

      at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)

      at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)

      at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)

      at
      org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)

      at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)

      at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)

      at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)

      at org.hibernate.engine.Cascade.cascade(Cascade.java:130)

      at
      org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)

      at
      org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)

      at
      org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)

      at
      org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:27)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)

      at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)

      at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)

      at
      trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:78)

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From charles at imbusch.net  Fri Feb 12 09:08:57 2010
From: charles at imbusch.net (Charles Imbusch)
Date: Fri, 12 Feb 2010 14:08:57 -0000
Subject: [Biojava-l] .sff support
In-Reply-To: <320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
References: <4B703AF3.4000300@imbusch.net>	
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
Message-ID: <4B7560F3.5080208@imbusch.net>

Hi all,

I've been playing around with the sff file based on the file
format definition at NCBI.
I attached the output which includes the common header,
the read header and read data section for the first read
of that file.
> I'm happy to answer questions on how the file format works
> (including the undocumented index block which I had to reverse
> engineer).
>   
Yes, I would like to know how that works.
index_magic_number:778921588 .mft
version:1.00
Couldn't find anything about ".mft" version 1.

At the moment I have two classes: sffParser and sffFile
My idea was that sffParser can hold one or multiple sff files. Each 
instance of
sffFile has a hashtable with the identifiers as keys and the 
filepointers are
stored as the values.

Now I would like to find a good representation of one single "read" 
object, which
shall be accessible with an identifier like EV5RTWS02JXUUH

At the moment I'm making use of the BigInteger class to store many variables
but thats probably a waste of memory.
The variables for the read object I'm thinking of:

Read Header Section:

read_header_length -> int
name_length -> int
number_of_bases -> int
clip_qual_left -> int
clip_qual_right -> int
clip_adapter_left -> int
clip_adapter_right -> int
name -> string

Read Data Section:

flowgram_values -> float[]
flow_index_per_base -> int[]
bases: -> string
quality_scores -> int[]

But I'm not very familiar with the existing data structures of BioJava, 
is there
maybe already something similar existing? Please comment.

Cheers,
  Charles

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From mauricio at open-bio.org  Fri Feb  5 15:48:30 2010
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Fri, 05 Feb 2010 09:48:30 -0600
Subject: [Biojava-l] Fwd: Changes to NCBI BLAST and E-utilities.
Message-ID: <4B6C3DCE.2070808@open-bio.org>

Forwarding to the proper lists...

-------- Original Message --------
Subject: [O|B|F Helpdesk #889] Changes to NCBI BLAST and E-utilities.
Date: Fri, 5 Feb 2010 10:08:51 -0500
From: mcginnis via RT <support at helpdesk.open-bio.org>
Reply-To: support at helpdesk.open-bio.org
To: chris at bioteam.net, heikki at sanbi.ac.za, hlapp at gmx.net, 
jason at bioperl.org,        mauricio at open-bio.org


Fri Feb 05 10:08:51 2010: Request 889 was acted upon.
Transaction: Ticket created by mcginnis at ncbi.nlm.nih.gov
        Queue: support at open-bio.org
      Subject: Changes to NCBI BLAST and E-utilities.
        Owner: Nobody
   Requestors: mcginnis at ncbi.nlm.nih.gov
       Status: new
  Ticket <URL: https://helpdesk.open-bio.org/rt/Ticket/Display.html?id=889 >


Dear Colleague:

There are two changes I'd like to make you aware of.

As you may or may not have noticed, we have been working on a new C++ 
version of the BLAST binaries. In the coming months we will be moving 
the C++ binaries into prominence and (slowly) phasing out the C toolkit 
binaries.

There are many changes not least of which is a move to individual 
binaries for each program (blastn, blastp, etc).  We are not sure how 
many of your users use BioPerl with the BLAST binaries, my understanding 
is that many use BioPerl to to remote BLAST. However, there isa change 
to the BLAST results in Text and presumably HTML. This could have an 
effect on any parsers which scrape these formats and do not use XML. For 
obvious reason, we want to support only the XML format for parsing, but 
we thought we should give you heads up on this.
blast 2.2.22

Query: 3307 ------------------------------------------------------------ 
3307

Sbjct: 390  GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP 449

blast 2.2.22+

Query        ------------------------------------------------------------

Sbjct  390 
GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP  449

A single line of gaps lacks the Query numbering in the blast+ output. 
The C version of blast has numbering in this case. Sample alignment 
shown below. According to users the blast+ output without the numbering 
breaks bioperl parsers. Wehave heard forma few but I think they may be 
older parsers?
The second issue is a policy concerning E-utilities. This was announced 
on the utilities-announce at ncbi.nlm.nih.gov mail-list but you may not 
have seen it.

As part of an ongoing effort to ensure efficient access to the Entrez 
Utilities (E-utilities) by all users, NCBI has decided to change the 
usage policy for the E-utilities effective June 1, 2010. Effective on 
June 1, 2010, all E-utility requests, either using standard URLs or 
SOAP, must contain non-null values for both the &tool and &email 
parameters. Any E-utility request made after June 1, 2010 that does not 
contain values for both parameters will return an error explaining that 
these parameters must be included in E-utility requests.

The value of the &tool parameter should be a URI-safe string that is the 
name of the software package, script or web page producing the E-utility 
request.

The value of the &email parameter should be a valid e-mail address for 
the appropriate contact person or group responsible for maintaining the 
tool producing the E-utility request.

NCBI uses these parameters to contact users whose use of the E-utilities 
violates the standard usage policies described 
athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. 
These usage policies are designed to prevent excessive requests from a 
small group of users from reducing or eliminating the wider community's 
access to the E-utilities. NCBI will attempt to contact a user at the 
e-mail address provided in the &email parameter prior to blocking access 
to the E-utilities.

NCBI realizes that this policy change will require many of our users to 
change their code. Based on past experience, we anticipate that most of 
our users should be able to make the necessary changes before the June 
1, 2010 deadline. If you have any concerns about making these changes by 
that date, or if you have any questions about these policies, please 
contact eutilities at ncbi.nlm.nih.gov.

Thank you for your understanding and cooperation in helping us continue 
to deliver a reliable and efficient web service.

I think you already adhere to this policy but should a user's script not 
meet these requirements, than the script will fail and requests will be 
turned away with an error message.

Scott D. McGinnis M.A.
NCBI/NLM/NIH
45 Center Drive, MSC 6511
Bldg 45, Room 4AN.44C
Bethesda, MD 20892
mcginnis at ncbi.nlm.nih.gov















From charles at imbusch.net  Mon Feb  8 16:25:23 2010
From: charles at imbusch.net (Charles Imbusch)
Date: Mon, 08 Feb 2010 17:25:23 +0100
Subject: [Biojava-l] .sff support
Message-ID: <4B703AF3.4000300@imbusch.net>

Hello,

I have been wondering whether Biojava is able to
handle sff files coming from 454 sequencing runs.

I found something here:
http://lists.open-bio.org/pipermail/biojava-dev/2009-July/003907.html

Does somebody know about the current status on Biojava and sff files?


Thanks in advance,
  Charles


From paolo.pavan at gmail.com  Mon Feb  8 21:24:49 2010
From: paolo.pavan at gmail.com (Paolo Pavan)
Date: Mon, 8 Feb 2010 22:24:49 +0100
Subject: [Biojava-l] .sff support
In-Reply-To: <4B703AF3.4000300@imbusch.net>
References: <4B703AF3.4000300@imbusch.net>
Message-ID: <56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>

Unfortunately, after spending some time on it, I didn't anything, sorry.
There is just a post more I sent to Andreas Prlic without enclose the list
by mistake, in which I report a few info more, coming from my reading on
BioPerl's way to manage contigs and assembly informations.
Nothing more.

Paolo


2010/2/8 Charles Imbusch <charles at imbusch.net>

> Hello,
>
> I have been wondering whether Biojava is able to
> handle sff files coming from 454 sequencing runs.
>
> I found something here:
> http://lists.open-bio.org/pipermail/biojava-dev/2009-July/003907.html
>
> Does somebody know about the current status on Biojava and sff files?
>
>
> Thanks in advance,
>  Charles
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From biopython at maubp.freeserve.co.uk  Tue Feb  9 00:59:37 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 9 Feb 2010 00:59:37 +0000
Subject: [Biojava-l] .sff support
In-Reply-To: <56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
References: <4B703AF3.4000300@imbusch.net>
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
Message-ID: <320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>

> 2010/2/8 Charles Imbusch <charles at imbusch.net>
>> Hello,
>>
>> I have been wondering whether Biojava is able to
>> handle sff files coming from 454 sequencing runs.
>>
>> I found something here:
>> http://lists.open-bio.org/pipermail/biojava-dev/2009-July/003907.html
>>
>> Does somebody know about the current status on Biojava and sff files?
>>
>>
>> Thanks in advance,
>>  Charles

On Mon, Feb 8, 2010 at 9:24 PM, Paolo Pavan <paolo.pavan at gmail.com> wrote:
>
> Unfortunately, after spending some time on it, I didn't anything, sorry.
> There is just a post more I sent to Andreas Prlic without enclose the list
> by mistake, in which I report a few info more, coming from my reading on
> BioPerl's way to manage contigs and assembly informations.
> Nothing more.
>
> Paolo

Hi,

I've CC'd the common OpenBio mailing list as this is probably of
interest beyond just BioJava.

Based on code from Jose Blanca (author of sff_extract), I
implemented support for the SFF (Roche 454) sequencing reads
for Biopython last year on a branch that I hope to merge into our
next release, currently here:

http://github.com/peterjc/biopython/tree/sff-seqio

In addition to the Roche Manuals (which may not be that easy to
get a copy of), the SFF format is described on this NCBI webpage:

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=formats#sff

I'm happy to answer questions on how the file format works
(including the undocumented index block which I had to reverse
engineer).

Peter

P.S. Just to clarify (from the old BioJava thread), the SFF file just
holds the raw reads - it is an input file for doing an assembly or
mapping.


From holland at eaglegenomics.com  Tue Feb  9 07:34:32 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 9 Feb 2010 20:34:32 +1300
Subject: [Biojava-l] Hibernate Exception and suggestion for change in
	BioSqlSchema
In-Reply-To: <4B710CED.5060404@gmail.com>
References: <4B710CED.5060404@gmail.com>
Message-ID: <9BB14CC0-4A89-4DC8-8928-C8475108B54A@eaglegenomics.com>

Hi. It's possible that your original email didn't make it to the list because it is HTML format, and the list only accepts plain text.

However, in answer to your two questions:

  1. The code that does the resolution of references might be better if it looks up existing IDs rather than using author, title, location to identify existing records. I would suggest modifying it to a three-step process - test ID, then if no match then test author/title/location, then if still no match create a new reference. Could someone do that? (I'm unable to do anything until late March).

  2. I think that's a bug (compound locations with null features) but not sure why. Could be that the process of constructing a CompoundRichLocation is somehow losing the feature reference from the original SimpleRichLocation. Again I can't investigate until March - can someone else take a look at the code? (A good starting point would be to look at how a CompoundRichLocation decides to select the feature from the SimpleRichLocations it is made up from).

cheers,
Richard

On 9 Feb 2010, at 20:21, Deepak Sheoran wrote:

> 
> Hi Richard
> 
> Below is the email which I sent to Biojava-1 mailing list but it never get posted on the mailing list server neither do i got any response, so please have a look on this email and tell what can be the solution of the problem described in the message.
> 
> 
> Thanks
> Deepak Sheoran
> -------- Original Message --------
> Subject:	Hibernate Exception and suggestion for change in BioSqlSchema
> Date:	Wed, 03 Feb 2010 08:07:35 -0600
> From:	Deepak Sheoran <sheoran143 at gmail.com>
> To:	biojava-l at lists.open-bio.org
> 
> Hi guys,
> 
> A couple of days back I was having some problem with hibernate exception but that exception got resolved and the reference to that email is:  http://old.nabble.com/Hibernate-Exception-when-persisting-some-richsequence-object-to-biosql-schema-to27299245.html
> On Richard  suggestion in above link  I am able to resolve some of  issues but then, I got stuck in to some other error with hibernate and then decided to investigate the matter and below are some facts and information which I found and I guess it is going to affect all of us.
> 	? The "Reference" table in bioSql schema have unique constraint on "dbxref_id" column (CONSTRAINT reference_dbxref_id_key UNIQUE (dbxref_id)). Which mean only one entry in reference table can use on dbxref_id.
> This Works wells but in cases when you have little variation in value of following column "location", "title", "authors" and all these variation refers to same PUBMED_ID. Then we can't persist or create a richsequence object .
>  Now when you tie RichObjectFactory to a  active hibernate session then the class  "BioSqlRichObjectBuilder" have method called "buildObject(Class clazz, List paramsList) " which is responsible  for looking up details of object in the database and if it find one then it will return that object, else it will try to persist the new object into the database.
> But problem is with below part of that method:
> ?..LineNumber: 114
> else if (SimpleDocRef.class.isAssignableFrom(clazz))
>  {                queryType = "DocRef";
>                 // convert List constructor to String representation for query
>                 ourParamsList.set(0, DocRefAuthor.Tools.generateAuthorString((List)ourParamsList.get(0), true));
>                 if (ourParamsList.size()<3) {
>                         queryText = "from DocRef as cr where cr.authors = ? and cr.location = ? and cr.title is null";
>                 } else {
>                         queryText = "from DocRef as cr where cr.authors = ? and cr.location = ? and cr.title = ?";
>                 }       
>  }
> ..LineNubmer: 123
> Now when hibernate search the database, it won't find any other record in "reference" table because those two record are different in string comparison, so it will return a new object back to "GenbankFormat" to following piece of code
> ?.LineNumber: 447
> else {
>                                         try {
>                                             CrossRef cr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new Object[]{dbname, raccession, new Integer(0)});
>                                             RankedCrossRef rcr = new SimpleRankedCrossRef(cr, ++rcrossrefCount);
>                                             rlistener.getCurrentFeature().addRankedCrossRef(rcr);
>                                         } catch (ChangeVetoException e) {
>                                             throw new ParseException(e+", accession:"+accession);
>                                         }
>                                     }
>                     ?..LineNumber:455
> Then we will add that object to rlistener. And move to next part of genbank record and then biojava search for a new crossref in database and it will try to persist the old one it get a hibernate exception regarding violation of  "unique constraint on dbxref_id" column.
>  
> The only way to get these record in database is:
> 		? The very easy solution and the way I did it for testing my theory is Change the bioSql schema so that it can allow many to one on relation between "reference" and "dbxref" table.  Which even make sense because one paper can have many different variation of naming, and this change allow us to store that info too. But this is something BioSql people have decide and I don't know how to approach them.
> 		? Second solution is slightly difficult to implement, is to change the way  "BioSqlRichObjectBuilder.buildObject(Class clazz,List paramsList)"  make decision about weather a particular DocRef already exist in database or not. I am mean testing all possible string variations of authors, location, title of the docRef which we are searching. Which does have many complications and may slow down process of creating a richsequence object when link RichObjectFactory with a active hibernate session.
>  
> Example:Below is a sample of what i have in my local biosql schema which has modification suggested by me. (dbxref_id column have Pubmed_id , I replaced the local dbxref_id which was present on this table in my database with pubmed_id stored in "dbxref" table, for easy reference with outside world in this email)
> Reference_id
> Dbxref_id         
> Location
> Title
> Authors
> crc
> 216
> 18554304
> FEMS Microbiol. Ecol. 66 (3THEMATIC ISSUE: GUT MICROBIOLOGY), 528-536 (2008)
> Isolation of lactate-utilizing butyrate-producing bacteria from human feces and in vivo administration of Anaerostipes caccae strain L2 and galacto-oligosaccharides in a rat model
> Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y., Nomoto,K., Ito,M. and Sawada,H.
> 9E940E01F4BE3CD0
> 230
> 18554304
> FEMS Microbiol. Ecol. 66 (3), 528-536 (2008)
> Isolation of lactate-utilizing butyrate-producing bacteria from human feces and in vivo administration of Anaerostipes caccae strain L2 and galacto-oligosaccharides in a rat model
> Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y., Nomoto,K., Ito,M. and Sawada,H.
> D3BC0C17F3F786C9
> 415
> 16790744
> Infect. Immun. 74 (7), 3715-3726 (2006)
> Intrastrain Heterogeneity of the mgpB Gene in Mycoplasma genitalium Is Extensive In Vitro and In Vivo and Suggests that Variation Is Generated via Recombination with Repetitive Chromosomal Sequences
> Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and Totten,P.A.
> 60AEDFA0CEEACC38
> 969
> 16790744
> Infect. Immun. 74 (7), 3715-3726 (2006)
> Intrastrain heterogeneity of the mgpB gene in mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences
> Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and Totten,P.A.
> 4B1232999F6E8130
> 929
> 8688087
> Science 273 (5278), 1058-1073 (1996)
> Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
> Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D., Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A., Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J.-F., Adams,M.D., Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G., Merrick,J.M., Glodek,A., Scott,J.L., Geoghagen,N.S.M., Weidman,J.F., Fuhrmann,J.L., Presley,E.A., Nguyen,D., Utterback,T.R., Kelley,J.M., Peterson,J.D., Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A., Roberts,K.M., Kaine,B.P., Borodovsky,M., Klenk,H.-P., Fraser,C.M., Smith,H.O., Woese,C.R. and Venter,J.C.
> 3E79B40DD2AAA2B7
> 932
> 8688087
> Science 273 (5278), 1058-1073 (1996)
> Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
> Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D., Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A., Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J., Adams,M.D., Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G., Merrick,J.M., Glodek,A., Scott,J.D., Geoghagen,N.S., Weidman,J.F., Fuhrmann,J.L., Nguyen,D.T., Utterback,T., Kelley,J.M., Peterson,J.D., Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A., Roberts,K.M., Kaine,B.B., Borodovsky,M., Klenk,H.P., Fraser,C.M., Smith,H.O., Woese,C.R. and Venter,J.C.
> 094EB3384F8D6DE8
> 1426
> 10684935
> Nucleic Acids Res. 28 (6), 1397-1406 (2000)
> Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
> Read,T.D., Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F., White,O., Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T., Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S.L., Eisen,J. and Fraser,C.M.
> 357648D8FD8C6C8A
> 1481
> 10684935
> Nucleic Acids Res. 28 (6), 1397-1406 (2000)
> Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
> Read,T., Brunham,R., Shen,C., Gill,S., Heidelberg,J., White,O., Hickey,E., Peterson,J., Utterback,T., Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S., Eisen,J. and Fraser,C.
> 115411EB2DEE5654
> 1497
> 14689165
> Arch. Microbiol. 181 (2), 144-154 (2004)
> The effect of FITA mutations on the symbiotic properties of Sinorhizobium fredii varies in a chromosomal-background-dependent manner
> Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J., Bellogin,R., del Rosario Espuny,M., Temprano,F., Romero,F., Krishnan,H.B., Pueppke,S.G. and Ruiz-Sainz,J.E.
> 4D5D376EECCD186B
> 1501
> 14689165
> Arch. Microbiol. 181 (2), 144-154 (2004)
> The effect of FITA mutations on the symbiotic properties of Sinorhizobium fredii varies in a chromosomal-background-dependent manner
> Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J., Bellogin,R., Del Rosario Espuny,M., Temprano,F., Romero,F., Krishnan,H.B., Pueppke,S.G. and Ruiz-Sainz,J.E.
> 4D57954EECDED66B
> 1556
> 18060065
> PLoS ONE 2 (12), E1271 (2007)
> Analysis of the Neurotoxin Complex Genes in Clostridium botulinum A1-A4 and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located within Plasmids
> Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,A.C., Bruce,D.C., Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and Brettin,T.S.
> 698688FB6DB95247
> 1559
> 18060065
> PLoS ONE 2 (12), E1271 (2007)
> Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids
> Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,C.A., Bruce,D.C., Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and Brettin,T.S.
> E25E1BA99DB18F3D
>  
> 	? The second kind of error which I got was : org.hibernate.PropertyValueException: not-null property references a null or transient value: Location.feature
> 		? Which means in richsequence object some feature have location object which have its feature set to null.
> 		? My Observation:
> 			? Usually occur when you try to persist a richsequence object to database, and occur to those features which have CompoundRichLocation usually "joins" and "complement" in cds region of a genbank record
> 			? After catching the hibernate exception I went through all the features and either biojava or hibernate  changed the object type of a CompoundRichLocation  to SimpleRichLocation and set the feature variable to null.
> 			? Below is the screen shot of one of my tests
> 				? Settings before trying to persits the richsequence object to database
>  
> <Mail Attachment.png>
> 		?  
> 		? After trying to persits the richsequence object to database and got in hibernate exception catch
>  
> 		? <Mail Attachment.png>
>  
> 		? So my question is why is this happening and how to stop or how to get these record into database, I have no clue why is this happening.
> 		? Some extra information to make things more clear to you guys.
> 			? Below are some Locus line from genbank record for which I know the error of location, I mean the cds region causing error, and array index in richsequence.feature arrayList object.
> 				? LOCUS       AE001439             1643831 bp    DNA     circular BCT 19-JAN-2006
> 					? richSequence.feature Index : 2540 and line number in the genbank record : 22115
> 				? LOCUS       CP001189             3887492 bp    DNA     circular BCT 16-OCT-2008
> 					? richSequence.feature Index : 127 and line number in the genbank record : 2137
> 				? LOCUS       CP001292              328635 bp    DNA     circular BCT 17-DEC-2008
> 					? richSequence.feature Index : 389 and line number in the genbank record : 3632
> 				? LOCUS       AM279694              238517 bp    DNA     linear   BCT 23-OCT-2008
> 					? richSequence.feature Index : 47 and line number in the genbank record : 4841
> 				? LOCUS       CR931663               18517 bp    DNA     linear   BCT 18-SEP-2008
> 					? richSequence.feature Index : 45 and line number in the genbank record : 442
> 		? The complete exception msg :
> org.hibernate.PropertyValueException: not-null property references a null or transient value: Location.feature
>         at org.hibernate.engine.Nullability.checkNullability(Nullability.java:72)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:290)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
>         at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>         at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
>         at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
>         at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
>         at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
>         at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
>         at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>         at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)
>         at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
>         at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
>         at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>         at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
>         at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
>         at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>         at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
>         at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
>         at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
>         at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
>         at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
>         at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>         at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)
>         at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
>         at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
>         at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
>         at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
>         at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)
>         at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
>         at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
>         at org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
>         at org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:27)
>         at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>         at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)
>         at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)
>         at trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:78)
>  
>  

--
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 anjolou at hotmail.com  Tue Feb  9 15:17:57 2010
From: anjolou at hotmail.com (Louise Ott)
Date: Tue, 9 Feb 2010 16:17:57 +0100
Subject: [Biojava-l] Displaying a simple alignment blastoutput-like
Message-ID: <BAY110-W2594AD362E3D0C31580D54B3500@phx.gbl>


Hi all !
I read and followed all the advices i found on the net and in this mailing list and i came to this :

public class OtherAlignmentPanel extends TranslatedSequencePanel {
    public otherAlignmentPanel(Alignment ali) {        this.setSequence((SymbolList) ali);        this.setBackground(Color.white);        this.setPreferredSize(new Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 15));
        MultiLineRenderer multi = new MultiLineRenderer();        AlignmentRenderer render1 = new AlignmentRenderer();        AlignmentRenderer render2 = new AlignmentRenderer();        AlignmentRenderer render3 = new AlignmentRenderer();        SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
        render1.setLabel(ali.getLabels().get(0));        render1.setRenderer(symbol);
        multi.addRenderer(render1);
        render2.setLabel(ali.getLabels().get(1));        render2.setRenderer(symbol);
        multi.addRenderer(render2);
        render3.setLabel(ali.getLabels().get(2));        render3.setRenderer(symbol);
        multi.addRenderer(render3);
        this.setRenderer(multi);    }
}

I created the panel in a frame like this :
        Sequence seq1;        seq1 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), "query");
        Sequence seq2;        seq2 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), "hit");
        Sequence seq3;        seq3 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), "midline");
        Map<String, Sequence> list = new HashMap();        list.put("query", seq1);        list.put("middle", seq2);        list.put("hit", seq3);
        SimpleAlignment ali = new SimpleAlignment((Map) list);        OtherAlignmentPanel pane = new otherAlignmentPanel(ali);	this.add(pane);



My problems :- First, it just shows nothing ! I am totally lost, it has been 3 days i am just trying to display this simple alignment but it doesn't work !!- I really would like the lines to be wrapped like in the blast output, so i tryied with the SequencePanelWrapper, but it doesn't work either...
Is there any simple solution ??What did i do wrong in my code ?


Have a nice day and thanks !
Louise
 		 	   		  
_________________________________________________________________
D?couvrez Windows 7 en 7 secondes?!
http://clk.atdmt.com/FRM/go/181574577/direct/01/


From jolyon.holdstock at ogt.co.uk  Tue Feb  9 15:40:54 2010
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Tue, 9 Feb 2010 15:40:54 -0000
Subject: [Biojava-l] Displaying a simple alignment
	blastoutput-like[Scanned]
References: <BAY110-W2594AD362E3D0C31580D54B3500@phx.gbl>
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>

Does nothing become visible, if so how are you calling the panels/frame to display?

Can you post all your code?

-----Original Message-----
From: Louise Ott [mailto:anjolou at hotmail.com] 
Sent: 09 February 2010 15:18
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Displaying a simple alignment blastoutput-like[Scanned]


Hi all !
I read and followed all the advices i found on the net and in this mailing list and i came to this :

public class OtherAlignmentPanel extends TranslatedSequencePanel {
    public otherAlignmentPanel(Alignment ali) {        this.setSequence((SymbolList) ali);        this.setBackground(Color.white);        this.setPreferredSize(new Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 15));
        MultiLineRenderer multi = new MultiLineRenderer();        AlignmentRenderer render1 = new AlignmentRenderer();        AlignmentRenderer render2 = new AlignmentRenderer();        AlignmentRenderer render3 = new AlignmentRenderer();        SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
        render1.setLabel(ali.getLabels().get(0));        render1.setRenderer(symbol);
        multi.addRenderer(render1);
        render2.setLabel(ali.getLabels().get(1));        render2.setRenderer(symbol);
        multi.addRenderer(render2);
        render3.setLabel(ali.getLabels().get(2));        render3.setRenderer(symbol);
        multi.addRenderer(render3);
        this.setRenderer(multi);    }
}

I created the panel in a frame like this :
        Sequence seq1;        seq1 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), "query");
        Sequence seq2;        seq2 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), "hit");
        Sequence seq3;        seq3 = ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), "midline");
        Map<String, Sequence> list = new HashMap();        list.put("query", seq1);        list.put("middle", seq2);        list.put("hit", seq3);
        SimpleAlignment ali = new SimpleAlignment((Map) list);        OtherAlignmentPanel pane = new otherAlignmentPanel(ali);	this.add(pane);



My problems :- First, it just shows nothing ! I am totally lost, it has been 3 days i am just trying to display this simple alignment but it doesn't work !!- I really would like the lines to be wrapped like in the blast output, so i tryied with the SequencePanelWrapper, but it doesn't work either...
Is there any simple solution ??What did i do wrong in my code ?


Have a nice day and thanks !
Louise
 		 	   		  
_________________________________________________________________
D?couvrez Windows 7 en 7 secondes !
http://clk.atdmt.com/FRM/go/181574577/direct/01/
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l











This email has been scanned by Oxford Gene Technology Security Systems.



From anjolou at hotmail.com  Tue Feb  9 16:47:47 2010
From: anjolou at hotmail.com (Louise Ott)
Date: Tue, 9 Feb 2010 17:47:47 +0100
Subject: [Biojava-l] Displaying a simple alignment
	blastoutput-like[Scanned]
In-Reply-To: <588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>
References: <BAY110-W2594AD362E3D0C31580D54B3500@phx.gbl>
	<588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>
Message-ID: <BAY110-DS2CACD0143A9BB6DAE0317B3500@phx.gbl>

Posting all the code won't help because everything is visible except the 
object of OtherAlignmentPanel.
I already tested the same code but with a SequencePanel and a 
SequencePanelWrapper added to my frame (with one sequence to display) and it 
worked fine.

So if there is a problem, I think this can be only in the code I already 
posted.

(And the code is really really big, is would be hard to read)

Sorry for my poor english, i'm french, I don't always use the good words to 
explain my problem :)

--------------------------------------------------
From: "Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent: Tuesday, February 09, 2010 4:40 PM
To: "Louise Ott" <anjolou at hotmail.com>; <biojava-l at lists.open-bio.org>
Subject: RE: [Biojava-l] Displaying a simple alignment 
blastoutput-like[Scanned]

> Does nothing become visible, if so how are you calling the panels/frame to 
> display?
>
> Can you post all your code?
>
> -----Original Message-----
> From: Louise Ott [mailto:anjolou at hotmail.com]
> Sent: 09 February 2010 15:18
> To: biojava-l at lists.open-bio.org
> Subject: [Biojava-l] Displaying a simple alignment 
> blastoutput-like[Scanned]
>
>
> Hi all !
> I read and followed all the advices i found on the net and in this mailing 
> list and i came to this :
>
> public class OtherAlignmentPanel extends TranslatedSequencePanel {
>    public otherAlignmentPanel(Alignment ali) { 
> this.setSequence((SymbolList) ali); 
> this.setBackground(Color.white);        this.setPreferredSize(new 
> Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 
> 15));
>        MultiLineRenderer multi = new MultiLineRenderer(); 
> AlignmentRenderer render1 = new AlignmentRenderer(); 
> AlignmentRenderer render2 = new AlignmentRenderer(); 
> AlignmentRenderer render3 = new AlignmentRenderer(); 
> SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
>        render1.setLabel(ali.getLabels().get(0)); 
> render1.setRenderer(symbol);
>        multi.addRenderer(render1);
>        render2.setLabel(ali.getLabels().get(1)); 
> render2.setRenderer(symbol);
>        multi.addRenderer(render2);
>        render3.setLabel(ali.getLabels().get(2)); 
> render3.setRenderer(symbol);
>        multi.addRenderer(render3);
>        this.setRenderer(multi);    }
> }
>
> I created the panel in a frame like this :
>        Sequence seq1;        seq1 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), 
> "query");
>        Sequence seq2;        seq2 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), 
> "hit");
>        Sequence seq3;        seq3 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), 
> "midline");
>        Map<String, Sequence> list = new HashMap(); 
> list.put("query", seq1);        list.put("middle", seq2); 
> list.put("hit", seq3);
>        SimpleAlignment ali = new SimpleAlignment((Map) list); 
> OtherAlignmentPanel pane = new otherAlignmentPanel(ali); this.add(pane);
>
>
>
> My problems :- First, it just shows nothing ! I am totally lost, it has 
> been 3 days i am just trying to display this simple alignment but it 
> doesn't work !!- I really would like the lines to be wrapped like in the 
> blast output, so i tryied with the SequencePanelWrapper, but it doesn't 
> work either...
> Is there any simple solution ??What did i do wrong in my code ?
>
>
> Have a nice day and thanks !
> Louise
>
> _________________________________________________________________
> D?couvrez Windows 7 en 7 secondes !
> http://clk.atdmt.com/FRM/go/181574577/direct/01/
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
>
>
>
>
>
>
>
> This email has been scanned by Oxford Gene Technology Security Systems.
>
>
>
>
>
>
>
>
>
>
>
> This email has been scanned by Oxford Gene Technology Security Systems.
> 


From anjolou at hotmail.com  Tue Feb  9 16:47:47 2010
From: anjolou at hotmail.com (Louise Ott)
Date: Tue, 9 Feb 2010 17:47:47 +0100
Subject: [Biojava-l] Displaying a simple alignment
	blastoutput-like[Scanned]
In-Reply-To: <588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>
References: <BAY110-W2594AD362E3D0C31580D54B3500@phx.gbl>
	<588D0DD225D05746B5D8CAE1BE971F3F02D2D448@EUCLID.internal.ogtip.com>
Message-ID: <BAY110-DS2CACD0143A9BB6DAE0317B3500@phx.gbl>

Posting all the code won't help because everything is visible except the 
object of OtherAlignmentPanel.
I already tested the same code but with a SequencePanel and a 
SequencePanelWrapper added to my frame (with one sequence to display) and it 
worked fine.

So if there is a problem, I think this can be only in the code I already 
posted.

(And the code is really really big, is would be hard to read)

Sorry for my poor english, i'm french, I don't always use the good words to 
explain my problem :)

--------------------------------------------------
From: "Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent: Tuesday, February 09, 2010 4:40 PM
To: "Louise Ott" <anjolou at hotmail.com>; <biojava-l at lists.open-bio.org>
Subject: RE: [Biojava-l] Displaying a simple alignment 
blastoutput-like[Scanned]

> Does nothing become visible, if so how are you calling the panels/frame to 
> display?
>
> Can you post all your code?
>
> -----Original Message-----
> From: Louise Ott [mailto:anjolou at hotmail.com]
> Sent: 09 February 2010 15:18
> To: biojava-l at lists.open-bio.org
> Subject: [Biojava-l] Displaying a simple alignment 
> blastoutput-like[Scanned]
>
>
> Hi all !
> I read and followed all the advices i found on the net and in this mailing 
> list and i came to this :
>
> public class OtherAlignmentPanel extends TranslatedSequencePanel {
>    public otherAlignmentPanel(Alignment ali) { 
> this.setSequence((SymbolList) ali); 
> this.setBackground(Color.white);        this.setPreferredSize(new 
> Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 
> 15));
>        MultiLineRenderer multi = new MultiLineRenderer(); 
> AlignmentRenderer render1 = new AlignmentRenderer(); 
> AlignmentRenderer render2 = new AlignmentRenderer(); 
> AlignmentRenderer render3 = new AlignmentRenderer(); 
> SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
>        render1.setLabel(ali.getLabels().get(0)); 
> render1.setRenderer(symbol);
>        multi.addRenderer(render1);
>        render2.setLabel(ali.getLabels().get(1)); 
> render2.setRenderer(symbol);
>        multi.addRenderer(render2);
>        render3.setLabel(ali.getLabels().get(2)); 
> render3.setRenderer(symbol);
>        multi.addRenderer(render3);
>        this.setRenderer(multi);    }
> }
>
> I created the panel in a frame like this :
>        Sequence seq1;        seq1 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), 
> "query");
>        Sequence seq2;        seq2 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), 
> "hit");
>        Sequence seq3;        seq3 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), 
> "midline");
>        Map<String, Sequence> list = new HashMap(); 
> list.put("query", seq1);        list.put("middle", seq2); 
> list.put("hit", seq3);
>        SimpleAlignment ali = new SimpleAlignment((Map) list); 
> OtherAlignmentPanel pane = new otherAlignmentPanel(ali); this.add(pane);
>
>
>
> My problems :- First, it just shows nothing ! I am totally lost, it has 
> been 3 days i am just trying to display this simple alignment but it 
> doesn't work !!- I really would like the lines to be wrapped like in the 
> blast output, so i tryied with the SequencePanelWrapper, but it doesn't 
> work either...
> Is there any simple solution ??What did i do wrong in my code ?
>
>
> Have a nice day and thanks !
> Louise
>
> _________________________________________________________________
> D?couvrez Windows 7 en 7 secondes !
> http://clk.atdmt.com/FRM/go/181574577/direct/01/
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
>
>
>
>
>
>
>
> This email has been scanned by Oxford Gene Technology Security Systems.
>
>
>
>
>
>
>
>
>
>
>
> This email has been scanned by Oxford Gene Technology Security Systems.
> 


From sheoran143 at gmail.com  Thu Feb 11 09:00:15 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Thu, 11 Feb 2010 03:00:15 -0600
Subject: [Biojava-l] Issues with BioSqlRichSequenceDB.java class
Message-ID: <4B73C71F.1080706@gmail.com>

Hi
This class(BiosqlRichSequence) have methods to retrieve record from a 
local instance of biosql schema but when you type in accession number 
for record it mostly show the info but in some case (Record with 
accession:M97762)  it give following error :

     Hibernate: select sequence0_.bioentry_id as bioentry1_9_, 
sequence0_1_.name as name9_, sequence0_1_.identifier as identifier9_, 
sequence0_1_.accession as accession9_, sequence0_1_.description as 
descript5_9_, sequence0_1_.version as version9_, sequence0_1_.division 
as division9_, sequence0_1_.taxon_id as taxon8_9_, 
sequence0_1_.biodatabase_id as biodatab9_9_, sequence0_.version as 
version13_, sequence0_.length as length13_, sequence0_.alphabet as 
alphabet13_, sequence0_.seq as seq13_ from biosequence sequence0_ inner 
join bioentry sequence0_1_ on 
sequence0_.bioentry_id=sequence0_1_.bioentry_id where sequence0_1_.name=?
Exception in thread "main" java.lang.RuntimeException: Error while 
trying to load by id: M97762
         at 
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:212)
         at 
com.orionbiosciences.orionGenBankLib.genBankDb.GenBankDb.GenBankDbToFileDownLoader(GenBankDb.java:355)
         at trashtesting.Main.main(Main.java:39)
Caused by: org.biojava.bio.seq.db.IllegalIDException: Id not found: M97762
         at 
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:206)
         ... 2 more
Java Result: 1

The only way to find this record in my database is to search for LOCUS 
instead of Accession number which is "BTVNS1TUBA", java doc for 
BioSqlRichSequenceDb class say the id should be Genbank Id  i can't 
understand what does that means, but when investigated the matter the 
error is in following method

public RichSequenceDB getRichSequences(Set ids, RichSequenceDB db) 
throws BioException, IllegalIDException {
         if (db==null) db = new HashRichSequenceDB();
         try {
             for (Iterator i = ids.iterator(); i.hasNext(); ) {
                 String id = (String)i.next();
                 // Build the query object
                ***************************error*******************
                  String queryText = "from Sequence where name = ?";
              ***************************error***********************
             *****************************solution**************************
                 String queryText = "from Sequence where accession = ?";
                // because name stand for Locus from gen-bank record 
which don't have any unique constraint name so its should not be good 
idea to use it for searching unique records
               // also people usually refer to a gen-bank record using 
accession number instead of LOCUS
            
*****************************solution******************************
                 Object query = this.createQuery.invoke(this.session, 
new Object[]{queryText});
                 // Set the parameters
                 query = this.setParameter.invoke(query, new 
Object[]{new Integer(0), id});
                 // Get the results
                 List result = (List)this.list.invoke(query,(Object[]) 
null);
                 // If the result doesn't just have a single entry, 
throw an exception
                 if (result.size()==0) throw new IllegalIDException("Id 
not found: "+id);
                 // Add the results to the results db.
                 for (Iterator j = result.iterator(); j.hasNext(); ) 
db.addRichSequence((RichSequence)j.next());
             }
         } catch (Exception e) {
             // Throw the exception with our nice message
             throw new RuntimeException("Error while trying to load by 
ids: "+ids,e);
         }
         return db;
     }

even ncbi says " It is better to search for the actual accession number 
rather than the locus name, because the accessions are stable and locus 
names can change."
REF: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#LocusNameB

So my suggestion is to change the query so it will look for accession 
instead of name in this method.
Also if you will try to download record from ncbi using java interface 
first with accession:M97762( as genbank_id) you can get it, but when you 
try to get using LOCUS you will get bad section  exception  around 
reference I don't know why ?


Deepak Sheoran





From holland at eaglegenomics.com  Thu Feb 11 22:18:18 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Fri, 12 Feb 2010 11:18:18 +1300
Subject: [Biojava-l] Issues with BioSqlRichSequenceDB.java class
In-Reply-To: <4B73C71F.1080706@gmail.com>
References: <4B73C71F.1080706@gmail.com>
Message-ID: <4ACB7402-D8DB-4CEF-AC70-BE228312EB37@eaglegenomics.com>

My preference would be to leave the existing method as-is, and modify the javadocs so that it is explicit that it is searching by name and not accession. This is to prevent breaking any code that may rely on this behaviour (as Genbank is not the only kind of sequence that can be stored in BioSQL, we can't guarantee that other sequence types are not using name as the unique identifier instead).

Instead, I would propose adding a second method called getRichSequencesByAccession, with the modification you suggest.

With regard to your last point about bad section errors, could you post the stack trace and the code that causes it?

cheers,
Richard

On 11 Feb 2010, at 22:00, Deepak Sheoran wrote:

> Hi
> This class(BiosqlRichSequence) have methods to retrieve record from a local instance of biosql schema but when you type in accession number for record it mostly show the info but in some case (Record with accession:M97762)  it give following error :
> 
>    Hibernate: select sequence0_.bioentry_id as bioentry1_9_, sequence0_1_.name as name9_, sequence0_1_.identifier as identifier9_, sequence0_1_.accession as accession9_, sequence0_1_.description as descript5_9_, sequence0_1_.version as version9_, sequence0_1_.division as division9_, sequence0_1_.taxon_id as taxon8_9_, sequence0_1_.biodatabase_id as biodatab9_9_, sequence0_.version as version13_, sequence0_.length as length13_, sequence0_.alphabet as alphabet13_, sequence0_.seq as seq13_ from biosequence sequence0_ inner join bioentry sequence0_1_ on sequence0_.bioentry_id=sequence0_1_.bioentry_id where sequence0_1_.name=?
> Exception in thread "main" java.lang.RuntimeException: Error while trying to load by id: M97762
>        at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:212)
>        at com.orionbiosciences.orionGenBankLib.genBankDb.GenBankDb.GenBankDbToFileDownLoader(GenBankDb.java:355)
>        at trashtesting.Main.main(Main.java:39)
> Caused by: org.biojava.bio.seq.db.IllegalIDException: Id not found: M97762
>        at org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:206)
>        ... 2 more
> Java Result: 1
> 
> The only way to find this record in my database is to search for LOCUS instead of Accession number which is "BTVNS1TUBA", java doc for BioSqlRichSequenceDb class say the id should be Genbank Id  i can't understand what does that means, but when investigated the matter the error is in following method
> 
> public RichSequenceDB getRichSequences(Set ids, RichSequenceDB db) throws BioException, IllegalIDException {
>        if (db==null) db = new HashRichSequenceDB();
>        try {
>            for (Iterator i = ids.iterator(); i.hasNext(); ) {
>                String id = (String)i.next();
>                // Build the query object
>               ***************************error*******************
>                 String queryText = "from Sequence where name = ?";
>             ***************************error***********************
>            *****************************solution**************************
>                String queryText = "from Sequence where accession = ?";
>               // because name stand for Locus from gen-bank record which don't have any unique constraint name so its should not be good idea to use it for searching unique records
>              // also people usually refer to a gen-bank record using accession number instead of LOCUS
>           *****************************solution******************************
>                Object query = this.createQuery.invoke(this.session, new Object[]{queryText});
>                // Set the parameters
>                query = this.setParameter.invoke(query, new Object[]{new Integer(0), id});
>                // Get the results
>                List result = (List)this.list.invoke(query,(Object[]) null);
>                // If the result doesn't just have a single entry, throw an exception
>                if (result.size()==0) throw new IllegalIDException("Id not found: "+id);
>                // Add the results to the results db.
>                for (Iterator j = result.iterator(); j.hasNext(); ) db.addRichSequence((RichSequence)j.next());
>            }
>        } catch (Exception e) {
>            // Throw the exception with our nice message
>            throw new RuntimeException("Error while trying to load by ids: "+ids,e);
>        }
>        return db;
>    }
> 
> even ncbi says " It is better to search for the actual accession number rather than the locus name, because the accessions are stable and locus names can change."
> REF: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#LocusNameB
> 
> So my suggestion is to change the query so it will look for accession instead of name in this method.
> Also if you will try to download record from ncbi using java interface first with accession:M97762( as genbank_id) you can get it, but when you try to get using LOCUS you will get bad section  exception  around reference I don't know why ?
> 
> 
> Deepak Sheoran
> 
> 
> 
> _______________________________________________
> 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 jeedward at yahoo.com  Fri Feb 12 17:01:32 2010
From: jeedward at yahoo.com (John Edward)
Date: Fri, 12 Feb 2010 09:01:32 -0800 (PST)
Subject: [Biojava-l] Draft paper submission deadline is extended: BCBGC-10,
	Orlando, USA
Message-ID: <767436.37495.qm@web45906.mail.sp1.yahoo.com>

It
would be highly appreciated if you could share this announcement with your
colleagues, students and individuals whose research is in bioinformatics,
computational biology, genomics, data-mining, and related areas.
 
Draft
paper submission deadline is extended: BCBGC-10, Orlando, USA 
 
The 2010 International Conference on Bioinformatics,
Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA.  BCBGC is an important event in the
areas of bioinformatics, computational biology, genomics and chemoinformatics
and focuses on all areas related to the conference.
 
The conference will be held at the same time and location where several
other major international conferences will be taking place. The conference will
be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be
held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of
MULTICONF is to promote research and developmental activities in computer
science, information technology, control engineering, and related fields.
Another goal is to promote the dissemination of research to a multidisciplinary
audience and to facilitate communication among researchers, developers,
practitioners in different fields.The following
conferences are planned to be organized as part of MULTICONF-10.
 
	* International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10)
	*  International Conference on Automation, Robotics and Control Systems (ARCS-10)
	* International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10)
	* International Conference on Computer Communications and Networks (CCN-10)
	* International Conference on Enterprise Information Systems and Web Technologies (EISWT-10)
	* International Conference on High Performance Computing Systems (HPCS-10)
	* International Conference on Information Security and Privacy (ISP-10) 
	* International Conference on Image and Video Processing and Computer Vision (IVPCV-10)
	* International Conference on Software Engineering Theory and Practice (SETP-10) 
	* International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) 
 
 
MULTICONF-10 will be held at Imperial Swan Hotel
and Suites.  It is a full-service resort that puts you in the middle of
the fun! Located 1/2 block south of the famed International Drive, the hotel is
just minutes from great entertainment like Walt Disney World? Resort, Universal
Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and
on-site dining ? all situated on 10 tropically landscaped acres. Here, guests
can experience a full-service resort with discount hotel pricing in Orlando.
 
We
invite draft paper submissions. Please see the website http://www.PromoteResearch.org for
more details.
 
Sincerely
John
Edward


      


From koen.bruynseels at cropdesign.com  Sat Feb 13 17:13:54 2010
From: koen.bruynseels at cropdesign.com (koen.bruynseels at cropdesign.com)
Date: Sat, 13 Feb 2010 18:13:54 +0100
Subject: [Biojava-l] Koen Bruynseels is out of the office.
Message-ID: <OFA2B596E3.0BF6BDC5-ONC12576C9.005EA817-C12576C9.005EA817@basf-c-s.be>


I will be out of the office starting  02/13/2010 and will not return until
02/21/2010.

I will respond to your message when I return.



From charles at imbusch.net  Mon Feb 15 22:32:28 2010
From: charles at imbusch.net (Charles Imbusch)
Date: Mon, 15 Feb 2010 23:32:28 +0100
Subject: [Biojava-l] .sff support
In-Reply-To: <320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
References: <4B703AF3.4000300@imbusch.net>	
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
Message-ID: <4B79CB7C.3040008@imbusch.net>

Hi all,

I've been playing around with the sff file based on the file
format definition at NCBI.
I uploaded the output which includes the common header,
the read header and read data section for the first read
of that file.

http://home.arcor.de/cimbusch/output.txt
> I'm happy to answer questions on how the file format works
> (including the undocumented index block which I had to reverse
> engineer).
>   
Yes, I would like to know how that works.
index_magic_number:778921588 .mft
version:1.00
Couldn't find anything about ".mft" version 1.

At the moment I have two classes: sffParser and sffFile
My idea was that sffParser can hold one or multiple sff files. Each 
instance of
sffFile has a hashtable with the identifiers as keys and the 
filepointers are
stored as the values.

Now I would like to find a good representation of one single "read" 
object, which
shall be accessible with an identifier like EV5RTWS02JXUUH

At the moment I'm making use of the BigInteger class to store many 
variables
but thats probably a waste of memory.
The variables for the read object I'm thinking of:

Read Header Section:

read_header_length -> int
name_length -> int
number_of_bases -> int
clip_qual_left -> int
clip_qual_right -> int
clip_adapter_left -> int
clip_adapter_right -> int
name -> string

Read Data Section:

flowgram_values -> float[]
flow_index_per_base -> int[]
bases: -> string
quality_scores -> int[]

But I'm not very familiar with the existing data structures of BioJava, 
is there
maybe already something similar?

Cheers,
 Charles



From biopython at maubp.freeserve.co.uk  Mon Feb 22 11:35:11 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 22 Feb 2010 11:35:11 +0000
Subject: [Biojava-l] .sff support
In-Reply-To: <4B79CB7C.3040008@imbusch.net>
References: <4B703AF3.4000300@imbusch.net>
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
	<4B79CB7C.3040008@imbusch.net>
Message-ID: <320fb6e01002220335x6899a44bl68789cd4d7d772e3@mail.gmail.com>

On Mon, Feb 15, 2010 at 10:32 PM, Charles Imbusch <charles at imbusch.net> wrote:
>
> Hi all,
>
> I've been playing around with the sff file based on the file
> format definition at NCBI.
> I uploaded the output which includes the common header,
> the read header and read data section for the first read
> of that file.
>
> http://home.arcor.de/cimbusch/output.txt

Looks like you've been making excellent progress :)

Sorry for the delay in my reply, I was on leave last week (and
without internet access for most of it).

>> I'm happy to answer questions on how the file format works
>> (including the undocumented index block which I had to reverse
>> engineer).
>>
>
> Yes, I would like to know how that works.
> index_magic_number:778921588 .mft
> version:1.00
> Couldn't find anything about ".mft" version 1.

I believe ".mft" stands for "Manifest format", and Roche 454 use this
block to hold both a read index and an XML string (the manifest).
Immediately after the ".mft1.00" string are two longs which give the
lengths of the XML string and the actual index data. Then comes
the XML manifest string, followed by the actual index data (same
format as Roche's older ".srt" index only block, uses base 256).

Note the Biopython SFF code has now been merged into our trunk:
http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

> At the moment I have two classes: sffParser and sffFile
> My idea was that sffParser can hold one or multiple sff files.
> Each instance of sffFile has a hashtable with the identifiers
> as keys and the filepointers are stored as the values.

Not all SFF files will have an index, but the Roche .srt and .mft
index blocks will let you map from the ID to the offset. I take
advantage of this in Biopython for our Bio.SeqIO.index(...)
functionality with a slower fall back on scanning the file to
build the index if the index information is missing (or in an
unsupported format). The Biopython index code then uses
a Python dictionary (hash) to hold the mapping from read
name to file offset. See also:

http://github.com/biopython/biopython/blob/master/Bio/SeqIO/_index.py

> Now I would like to find a good representation of one single "read" object,
> which shall be accessible with an identifier like EV5RTWS02JXUUH

I think this is a Java question, so not my area of expertise.

Peter


From jeedward at yahoo.com  Mon Feb 22 20:37:23 2010
From: jeedward at yahoo.com (John Edward)
Date: Mon, 22 Feb 2010 12:37:23 -0800 (PST)
Subject: [Biojava-l] Call for papers: BCBGC-10, Orlando, USA, July 2010
Message-ID: <472328.10215.qm@web45916.mail.sp1.yahoo.com>

It
would be highly appreciated if you could share this announcement with your
colleagues, students and individuals whose research is in bioinformatics,
computational biology, genomics, data-mining, and related areas.
 
Call
for papers: BCBGC-10, Orlando, USA, July 2010
 
The
2010 International Conference on Bioinformatics, Computational Biology,
Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will
be held during 12-14 of July 2010 in Orlando, FL, USA.  BCBGC is an important event in the areas of
bioinformatics, computational biology, genomics and chemoinformatics and
focuses on all areas related to the conference.
 
The
conference will be held at the same time and location where several other major
international conferences will be taking place. The conference will be held as
part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during
July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to
promote research and developmental activities in computer science, information
technology, control engineering, and related fields. Another goal is to promote
the dissemination of research to a multidisciplinary audience and to facilitate
communication among researchers, developers, practitioners in different fields.
The following conferences are planned to be organized as part of MULTICONF-10.
 
?           International Conference on
Artificial Intelligence and Pattern Recognition (AIPR-10)
?            International Conference on
Automation, Robotics and Control Systems (ARCS-10)
?           International Conference on
Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10)
?           International Conference on Computer
Communications and Networks (CCN-10)
?           International Conference on
Enterprise Information Systems and Web Technologies (EISWT-10)
?           International Conference on High
Performance Computing Systems (HPCS-10)
?           International Conference on
Information Security and Privacy (ISP-10) 
?           International Conference on Image and
Video Processing and Computer Vision (IVPCV-10)
?           International Conference on Software
Engineering Theory and Practice (SETP-10) 
?           International Conference on
Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) 
 
 
MULTICONF-10
will be held at Imperial Swan Hotel and Suites.  It is a full-service resort that puts you in the middle of the fun!
Located 1/2 block south of the famed International Drive, the hotel is just
minutes from great entertainment like Walt Disney World? Resort, Universal
Studios and Sea World Orlando. Guests can enjoy free scheduled transportation
to these theme parks, as well as spacious accommodations, outdoor pools and
on-site dining ? all situated on 10 tropically landscaped acres. Here, guests
can experience a full-service resort with discount hotel pricing in Orlando.
 
We
invite draft paper submissions. Please see the website http://www.PromoteResearch.org for
more details.
 
Sincerely
John
Edward


      


From charles at imbusch.net  Thu Feb 25 10:08:38 2010
From: charles at imbusch.net (Charles Imbusch)
Date: Thu, 25 Feb 2010 11:08:38 +0100
Subject: [Biojava-l] .sff support
In-Reply-To: <320fb6e01002220335x6899a44bl68789cd4d7d772e3@mail.gmail.com>
References: <4B703AF3.4000300@imbusch.net>	
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>	
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>	
	<4B79CB7C.3040008@imbusch.net>
	<320fb6e01002220335x6899a44bl68789cd4d7d772e3@mail.gmail.com>
Message-ID: <4B864C26.3050709@imbusch.net>

Dear Peter,

thanks for your mail. I will try to make use of that index
to speed things up when I have time available.

Cheers,
  Charles


Peter schrieb:
> I believe ".mft" stands for "Manifest format", and Roche 454 use this
> block to hold both a read index and an XML string (the manifest).
> Immediately after the ".mft1.00" string are two longs which give the
> lengths of the XML string and the actual index data. Then comes
> the XML manifest string, followed by the actual index data (same
> format as Roche's older ".srt" index only block, uses base 256).
>
> Note the Biopython SFF code has now been merged into our trunk:
> http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
>   


From biopython at maubp.freeserve.co.uk  Fri Feb 26 13:33:19 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 26 Feb 2010 13:33:19 +0000
Subject: [Biojava-l] .sff support
In-Reply-To: <4B864C26.3050709@imbusch.net>
References: <4B703AF3.4000300@imbusch.net>
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
	<4B79CB7C.3040008@imbusch.net>
	<320fb6e01002220335x6899a44bl68789cd4d7d772e3@mail.gmail.com>
	<4B864C26.3050709@imbusch.net>
Message-ID: <320fb6e01002260533y148936fdg36a5c8c814deb141@mail.gmail.com>

On Thu, Feb 25, 2010 at 10:08 AM, Charles Imbusch <charles at imbusch.net> wrote:
>
> Dear Peter,
>
> thanks for your mail. I will try to make use of that index
> to speed things up when I have time available.
>
> Cheers,
> ?Charles

Hi Charles,

If found when you want random access to the reads, loading the
provided .mft or .srt index is MUCH faster than scanning the whole
file to build the index manually. So this really is worth the effort.

I hope the comments in my code are reasonably clear, but to
recap the key idea of the index block is you get chunks of data
of varying length (although typically all the same length since by
default all the Roche reads have the same read length) like this

name, null char, four character offset, terminator char of 0xFF

You divide the index block into entries for each read by
finding the 0xFF terminators. Because 0xFF (decimal 255)
is used in this way, it cannot be used to encode the offsets
which must only use 0x00 to 0xFE (decimal 0 to 254). The
offset therefore uses base 255 instead of base 256.

Note that this means that the largest offset the current
Roche index blocks can hold is 255^4, or a little under 4GB.
If you use the Roche tools to try and merge SFF files to
make an example SFF file over 4GB you get a warning
that there will be no index (and no manifest).

The index holds the reads sorted alphabetically by name.
We don't take advantage of this in Biopython since I use
a Python dictionary (like a Perl hash) to store the offsets.

In case you missed them, I'd like to draw your attention
to the SFF files I am using in the Biopython unit tests:
http://github.com/biopython/biopython/tree/master/Tests/Roche/

Regards,

Peter



From sheoran143 at gmail.com  Wed Feb  3 14:07:44 2010
From: sheoran143 at gmail.com (Deepak Sheoran)
Date: Wed, 03 Feb 2010 14:07:44 -0000
Subject: [Biojava-l] Hibernate Exception and suggestion for change in
	BioSqlSchema
Message-ID: <4B698327.3080203@gmail.com>



      Hi guys,

      A couple of days back I was having some problem with hibernate
      exception but that exception got resolved and the reference to
      that email is:
      http://old.nabble.com/Hibernate-Exception-when-persisting-some-richsequence-object-to-biosql-schema-to27299245.html

      On Richard suggestion in above link I am able to resolve some of
      issues but then, I got stuck in to some other error with hibernate
      and then decided to investigate the matter and below are some
      facts and information which I found and I guess it is going to
      affect all of us.

   1. The "Reference" table in bioSql schema have unique constraint on
      "dbxref_id" column (CONSTRAINT reference_dbxref_id_key UNIQUE
      (dbxref_id)). Which mean only one entry in reference table can use
      on dbxref_id.

      This Works wells but in cases when you have little variation in
      value of following column "location", "title", "authors" and all
      these variation refers to same PUBMED_ID. Then we can't persist or
      create a richsequence object .

        Now when you tie RichObjectFactory to a active hibernate session
      then the class "BioSqlRichObjectBuilder" have method called
      "buildObject(Class clazz, List paramsList) " which is responsible
      for looking up details of object in the database and if it find
      one then it will return that object, else it will try to persist
      the new object into the database.

      But problem is with below part of that method:

      .....LineNumber: 114

      else if (SimpleDocRef.class.isAssignableFrom(clazz))

      {         queryType = "DocRef";

               // convert List constructor to String representation for
      query

               ourParamsList.set(0,
      DocRefAuthor.Tools.generateAuthorString((List)ourParamsList.get(0), true));

               if (ourParamsList.size()<3) {

               queryText = "from DocRef as cr where cr.authors = ? and
      cr.location = ? and cr.title is null";

               } else {

               queryText = "from DocRef as cr where cr.authors = ? and
      cr.location = ? and cr.title = ?";

               }

      }

      ..LineNubmer: 123

      Now when hibernate search the database, it won't find any other
      record in "reference" table because those two record are different
      in string comparison, so it will return a new object back to
      "GenbankFormat" to following piece of code

      ....LineNumber: 447

      else {

      try {

      CrossRef cr =
      (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new
      Object[]{dbname, raccession, new Integer(0)});

      RankedCrossRef rcr = new SimpleRankedCrossRef(cr, ++rcrossrefCount);

      rlistener.getCurrentFeature().addRankedCrossRef(rcr);

      } catch (ChangeVetoException e) {

      throw new ParseException(e+", accession:"+accession);

      }

      }

      .....LineNumber:455

      Then we will add that object to rlistener. And move to next part
      of genbank record and then biojava search for a new crossref in
      database and it will try to persist the old one it get a hibernate
      exception regarding violation of "unique constraint on dbxref_id"
      column.

      The only way to get these record in database is:

          * The very easy solution and the way I did it for testing my
            theory is Change the bioSql schema so that it can allow many
            to one on relation between "reference" and "dbxref" table.
            Which even make sense because one paper can have many
            different variation of naming, and this change allow us to
            store that info too. But this is something BioSql people
            have decide and I don't know how to approach them.
          * Second solution is slightly difficult to implement, is to
            change the way "BioSqlRichObjectBuilder.buildObject(Class
            clazz,List paramsList)" make decision about weather a
            particular DocRef already exist in database or not. I am
            mean testing all possible string variations of authors,
            location, title of the docRef which we are searching. Which
            does have many complications and may slow down process of
            creating a richsequence object when link RichObjectFactory
            with a active hibernate session.

      Example:Below is a sample of what i have in my local biosql schema
      which has modification suggested by me. (dbxref_id column have
      Pubmed_id , I replaced the local dbxref_id which was present on
      this table in my database with pubmed_id stored in "dbxref" table,
      for easy reference with outside world)

      Reference_id

      	

      Dbxref_id

      	

      Location

      	

      Title

      	

      Authors

      	

      crc

      216

      	

      18554304

      	

      FEMS Microbiol. Ecol. 66 (3THEMATIC ISSUE: GUT MICROBIOLOGY),
      528-536 (2008)

      	

      Isolation of lactate-utilizing butyrate-producing bacteria from
      human feces and in vivo administration of Anaerostipes caccae
      strain L2 and galacto-oligosaccharides in a rat model

      	

      Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y.,
      Nomoto,K., Ito,M. and Sawada,H.

      	

      9E940E01F4BE3CD0

      230

      	

      18554304

      	

      FEMS Microbiol. Ecol. 66 (3), 528-536 (2008)

      	

      Isolation of lactate-utilizing butyrate-producing bacteria from
      human feces and in vivo administration of Anaerostipes caccae
      strain L2 and galacto-oligosaccharides in a rat model

      	

      Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y.,
      Nomoto,K., Ito,M. and Sawada,H.

      	

      D3BC0C17F3F786C9

      415

      	

      16790744

      	

      Infect. Immun. 74 (7), 3715-3726 (2006)

      	

      Intrastrain Heterogeneity of the mgpB Gene in Mycoplasma
      genitalium Is Extensive In Vitro and In Vivo and Suggests that
      Variation Is Generated via Recombination with Repetitive
      Chromosomal Sequences

      	

      Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and
      Totten,P.A.

      	

      60AEDFA0CEEACC38

      969

      	

      16790744

      	

      Infect. Immun. 74 (7), 3715-3726 (2006)

      	

      Intrastrain heterogeneity of the mgpB gene in mycoplasma
      genitalium is extensive in vitro and in vivo and suggests that
      variation is generated via recombination with repetitive
      chromosomal sequences

      	

      Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and
      Totten,P.A.

      	

      4B1232999F6E8130

      929

      	

      8688087

      	

      Science 273 (5278), 1058-1073 (1996)

      	

      Complete genome sequence of the methanogenic archaeon,
      Methanococcus jannaschii

      	

      Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D.,
      Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A.,
      Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J.-F.,
      Adams,M.D., Reich,C.I., Overbeek,R., Kirkness,E.F.,
      Weinstock,K.G., Merrick,J.M., Glodek,A., Scott,J.L.,
      Geoghagen,N.S.M., Weidman,J.F., Fuhrmann,J.L., Presley,E.A.,
      Nguyen,D., Utterback,T.R., Kelley,J.M., Peterson,J.D., Sadow,P.W.,
      Hanna,M.C., Cotton,M.D., Hurst,M.A., Roberts,K.M., Kaine,B.P.,
      Borodovsky,M., Klenk,H.-P., Fraser,C.M., Smith,H.O., Woese,C.R.
      and Venter,J.C.

      	

      3E79B40DD2AAA2B7

      932

      	

      8688087

      	

      Science 273 (5278), 1058-1073 (1996)

      	

      Complete genome sequence of the methanogenic archaeon,
      Methanococcus jannaschii

      	

      Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D.,
      Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A.,
      Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J., Adams,M.D.,
      Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G.,
      Merrick,J.M., Glodek,A., Scott,J.D., Geoghagen,N.S., Weidman,J.F.,
      Fuhrmann,J.L., Nguyen,D.T., Utterback,T., Kelley,J.M.,
      Peterson,J.D., Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A.,
      Roberts,K.M., Kaine,B.B., Borodovsky,M., Klenk,H.P., Fraser,C.M.,
      Smith,H.O., Woese,C.R. and Venter,J.C.

      	

      094EB3384F8D6DE8

      1426

      	

      10684935

      	

      Nucleic Acids Res. 28 (6), 1397-1406 (2000)

      	

      Genome sequences of Chlamydia trachomatis MoPn and Chlamydia
      pneumoniae AR39

      	

      Read,T.D., Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F.,
      White,O., Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T.,
      Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B.,
      Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J.,
      McClarty,G., Salzberg,S.L., Eisen,J. and Fraser,C.M.

      	

      357648D8FD8C6C8A

      1481

      	

      10684935

      	

      Nucleic Acids Res. 28 (6), 1397-1406 (2000)

      	

      Genome sequences of Chlamydia trachomatis MoPn and Chlamydia
      pneumoniae AR39

      	

      Read,T., Brunham,R., Shen,C., Gill,S., Heidelberg,J., White,O.,
      Hickey,E., Peterson,J., Utterback,T., Berry,K., Bass,S.,
      Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R.,
      Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G.,
      Salzberg,S., Eisen,J. and Fraser,C.

      	

      115411EB2DEE5654

      1497

      	

      14689165

      	

      Arch. Microbiol. 181 (2), 144-154 (2004)

      	

      The effect of FITA mutations on the symbiotic properties of
      Sinorhizobium fredii varies in a chromosomal-background-dependent
      manner

      	

      Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J.,
      Bellogin,R., del Rosario Espuny,M., Temprano,F., Romero,F.,
      Krishnan,H.B., Pueppke,S.G. and Ruiz-Sainz,J.E.

      	

      4D5D376EECCD186B

      1501

      	

      14689165

      	

      Arch. Microbiol. 181 (2), 144-154 (2004)

      	

      The effect of FITA mutations on the symbiotic properties of
      Sinorhizobium fredii varies in a chromosomal-background-dependent
      manner

      	

      Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J.,
      Bellogin,R., Del Rosario Espuny,M., Temprano,F., Romero,F.,
      Krishnan,H.B., Pueppke,S.G. and Ruiz-Sainz,J.E.

      	

      4D57954EECDED66B

      1556

      	

      18060065

      	

      PLoS ONE 2 (12), E1271 (2007)

      	

      Analysis of the Neurotoxin Complex Genes in Clostridium botulinum
      A1-A4 and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located
      within Plasmids

      	

      Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,A.C.,
      Bruce,D.C., Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and
      Brettin,T.S.

      	

      698688FB6DB95247

      1559

      	

      18060065

      	

      PLoS ONE 2 (12), E1271 (2007)

      	

      Analysis of the neurotoxin complex genes in Clostridium botulinum
      A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located
      within plasmids

      	

      Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,C.A.,
      Bruce,D.C., Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and
      Brettin,T.S.

      	

      E25E1BA99DB18F3D

   2. The second kind of error which I got was :*
      org.hibernate.PropertyValueException: not-null property references
      a null or transient value: Location.feature*

          * Which means in richsequence object some feature have
            location object which have its feature set to null.
          * My Observation:
                o Usually occur when you try to persist a richsequence
                  object to database, and occur to those features which
                  have *CompoundRichLocation *usually "joins" and
                  "complement" in cds region of a genbank record
                o After catching the hibernate exception I went through
                  all the features and either biojava or hibernate
                  changed the object type of a CompoundRichLocation to
                  SimpleRichLocation and set the feature variable to null.
                o Below is the screen shot of one of my tests
                      + Settings before trying to persits the
                        richsequence object to database

          *
          * After trying to persits the richsequence object to database
            and got in hibernate exception catch

          *

          * So my question is why is this happening and how to stop or
            how to get these record into database, I have no clue why is
            this happening.
          * Some extra information to make things more clear to you guys.
                o Below are some Locus line from genbank record for
                  which I know the error of location, I mean the cds
                  region causing error, and array index in
                  richsequence.feature arrayList object.
                     1. LOCUS AE001439 1643831 bp DNA circular BCT
                        19-JAN-2006
                            + richSequence.feature Index : 2540 and line
                              number in the genbank record : 22115
                     2. LOCUS CP001189 3887492 bp DNA circular BCT
                        16-OCT-2008
                            + richSequence.feature Index : 127 and line
                              number in the genbank record : 2137
                     3. LOCUS CP001292 328635 bp DNA circular BCT
                        17-DEC-2008
                            + richSequence.feature Index : 389 and line
                              number in the genbank record : 3632
                     4. LOCUS AM279694 238517 bp DNA linear BCT 23-OCT-2008
                            + richSequence.feature Index : 47 and line
                              number in the genbank record : 4841
                     5. LOCUS CR931663 18517 bp DNA linear BCT 18-SEP-2008
                            + richSequence.feature Index : 45 and line
                              number in the genbank record : 442
          * The complete exception msg :

      org.hibernate.PropertyValueException: not-null property references
      a null or transient value: Location.feature

      at
      org.hibernate.engine.Nullability.checkNullability(Nullability.java:72)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:290)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)

      at
      org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)

      at
      org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)

      at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)

      at
      org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)

      at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)

      at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)

      at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)

      at
      org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)

      at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)

      at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)

      at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)

      at org.hibernate.engine.Cascade.cascade(Cascade.java:130)

      at
      org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)

      at
      org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)

      at
      org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)

      at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)

      at
      org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)

      at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)

      at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)

      at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)

      at
      org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)

      at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)

      at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)

      at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)

      at org.hibernate.engine.Cascade.cascade(Cascade.java:130)

      at
      org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)

      at
      org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)

      at
      org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)

      at
      org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)

      at
      org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:27)

      at
      org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)

      at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)

      at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)

      at
      trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:78)

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From charles at imbusch.net  Fri Feb 12 14:08:57 2010
From: charles at imbusch.net (Charles Imbusch)
Date: Fri, 12 Feb 2010 14:08:57 -0000
Subject: [Biojava-l] .sff support
In-Reply-To: <320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
References: <4B703AF3.4000300@imbusch.net>	
	<56be91b61002081324t3423359dm917b283c6a1f2474@mail.gmail.com>
	<320fb6e01002081659u793228d1g17abb4f8e0100837@mail.gmail.com>
Message-ID: <4B7560F3.5080208@imbusch.net>

Hi all,

I've been playing around with the sff file based on the file
format definition at NCBI.
I attached the output which includes the common header,
the read header and read data section for the first read
of that file.
> I'm happy to answer questions on how the file format works
> (including the undocumented index block which I had to reverse
> engineer).
>   
Yes, I would like to know how that works.
index_magic_number:778921588 .mft
version:1.00
Couldn't find anything about ".mft" version 1.

At the moment I have two classes: sffParser and sffFile
My idea was that sffParser can hold one or multiple sff files. Each 
instance of
sffFile has a hashtable with the identifiers as keys and the 
filepointers are
stored as the values.

Now I would like to find a good representation of one single "read" 
object, which
shall be accessible with an identifier like EV5RTWS02JXUUH

At the moment I'm making use of the BigInteger class to store many variables
but thats probably a waste of memory.
The variables for the read object I'm thinking of:

Read Header Section:

read_header_length -> int
name_length -> int
number_of_bases -> int
clip_qual_left -> int
clip_qual_right -> int
clip_adapter_left -> int
clip_adapter_right -> int
name -> string

Read Data Section:

flowgram_values -> float[]
flow_index_per_base -> int[]
bases: -> string
quality_scores -> int[]

But I'm not very familiar with the existing data structures of BioJava, 
is there
maybe already something similar existing? Please comment.

Cheers,
  Charles

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