From ozborn at uab.edu  Thu Jun  5 12:20:23 2008
From: ozborn at uab.edu (John David Osborne)
Date: Thu, 5 Jun 2008 11:20:23 -0500
Subject: [Biojava-dev] BlastEcho, midline and other blast data
Message-ID: <C46D7C77.1C89%ozborn@uab.edu>

Hello,

Can anybody offer me any pointers on getting additional information such
as
the midline from the blast parser? I?m using the BlastEcho example code
from
biojava in anger which works nicely, but I would also like to get the
midline or the match consensus sequence for hits from the parser.

Digging into the code, I?m not sure what I need to do to get this info.
Do I
just need to modify BlastLikeDataSetCollection.dtd. It already has
MatchConsensus defined though (see below) but I don?t know how to pull
it
out.

 -John
<!-- A MatchConsensus element represents the consensus information
     present in a pairwise alignment produced by Blast-like programs
     (i.e. the middle line of the alignment).
-->

<!ELEMENT biojava:MatchConsensus (#PCDATA)>
<!ATTLIST biojava:MatchConsensus
                     xml:space       (default|preserve) #IMPLIED >



From markjschreiber at gmail.com  Thu Jun  5 22:37:14 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 6 Jun 2008 10:37:14 +0800
Subject: [Biojava-dev] BlastEcho, midline and other blast data
In-Reply-To: <C46D7C77.1C89%ozborn@uab.edu>
References: <C46D7C77.1C89%ozborn@uab.edu>
Message-ID: <93b45ca50806051937r59c3779ah31a302917c27ea8d@mail.gmail.com>

Hi -

This has come up before but a long time ago (and I can't remember the
solution). I think it is something like the parser does emit the
midline but nothing listens for it by default.  Try searching the mail
archives

You may need to extend one of the parsers or listeners for this.

- Mark

On Fri, Jun 6, 2008 at 12:20 AM, John David Osborne <ozborn at uab.edu> wrote:
> Hello,
>
> Can anybody offer me any pointers on getting additional information such
> as
> the midline from the blast parser? I?m using the BlastEcho example code
> from
> biojava in anger which works nicely, but I would also like to get the
> midline or the match consensus sequence for hits from the parser.
>
> Digging into the code, I?m not sure what I need to do to get this info.
> Do I
> just need to modify BlastLikeDataSetCollection.dtd. It already has
> MatchConsensus defined though (see below) but I don?t know how to pull
> it
> out.
>
>  -John
> <!-- A MatchConsensus element represents the consensus information
>     present in a pairwise alignment produced by Blast-like programs
>     (i.e. the middle line of the alignment).
> -->
>
> <!ELEMENT biojava:MatchConsensus (#PCDATA)>
> <!ATTLIST biojava:MatchConsensus
>                     xml:space       (default|preserve) #IMPLIED >
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From bugzilla-daemon at portal.open-bio.org  Fri Jun  6 02:54:03 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 6 Jun 2008 02:54:03 -0400
Subject: [Biojava-dev] [Bug 2510] New: Error when trying to retrieve a
	sequence assigned to a feature from BioSQL using Hibernate
Message-ID: <bug-2510-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2510

           Summary: Error when trying to retrieve a sequence assigned to a
                    feature from BioSQL using Hibernate
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: DB / BioSQL
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: andreas.draeger at uni-tuebingen.de


Hibernate throws an exception, which occurs inside setter of
org.biojavax.bio.seq.SimpleRichFeature.locationSet when trying to execute the
following piece of code:

Transaction tx = session.beginTransaction();
Query q1 = session.createQuery(
  "from Feature as f " +
  "inner join fetch f.noteSet as n " +
  "where n.value=:val and f.typeTerm.name=:term");
q1.setString("val","TRNF");
q1.setString("term","gene"); 
List<SimpleRichFeature> li = q1.list();
for (Iterator<SimpleRichFeature> i = li.iterator(); i.hasNext(); ){
  SimpleRichFeature f = i.next();
  System.out.println(f.getSequence().seqString());
}
tx.commit();
session.close();

==================

The exception reads:


Exception in thread "main" org.hibernate.PropertyAccessException: Exception
occurred inside setter of org.biojavax.bio.seq.SimpleRichFeature.locationSet
   at
org.hibernate.property.BasicPropertyAccessor$BasicSetter.set(BasicPropertyAccessor.java:65)
   at
org.hibernate.tuple.entity.AbstractEntityTuplizer.setPropertyValues(AbstractEntityTuplizer.java:337)
   at
org.hibernate.tuple.entity.PojoEntityTuplizer.setPropertyValues(PojoEntityTuplizer.java:200)
   at
org.hibernate.persister.entity.AbstractEntityPersister.setPropertyValues(AbstractEntityPersister.java:3571)
   at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:133)
   at
org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:854)
   at org.hibernate.loader.Loader.doQuery(Loader.java:729)
   at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
   at org.hibernate.loader.Loader.loadCollection(Loader.java:1994)
   at
org.hibernate.loader.collection.CollectionLoader.initialize(CollectionLoader.java:36)
   at
org.hibernate.persister.collection.AbstractCollectionPersister.initialize(AbstractCollectionPersister.java:565)
   at
org.hibernate.event.def.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:63)
   at
org.hibernate.impl.SessionImpl.initializeCollection(SessionImpl.java:1716)
   at
org.hibernate.collection.AbstractPersistentCollection.forceInitialization(AbstractPersistentCollection.java:454)
   at
org.hibernate.engine.StatefulPersistenceContext.initializeNonLazyCollections(StatefulPersistenceContext.java:844)
   at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:241)
   at org.hibernate.loader.Loader.loadEntity(Loader.java:1860)
   at
org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48)
   at
org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42)
   at
org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3049)
   at
org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:399)
   at
org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:375)
   at
org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:139)
   at
org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:98)
   at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878)
   at org.hibernate.impl.SessionImpl.immediateLoad(SessionImpl.java:836)
   at
org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:66)
   at
org.hibernate.proxy.AbstractLazyInitializer.getImplementation(AbstractLazyInitializer.java:111)
   at
org.hibernate.proxy.pojo.cglib.CGLIBLazyInitializer.invoke(CGLIBLazyInitializer.java:150)
   at
org.biojavax.bio.seq.ThinRichSequence$$EnhancerByCGLIB$$e3c3c7ff.seqString(<generated>)
   at meinVersuch.TestAbfragen.main(TestAbfragen.java:59)
Caused by: java.lang.reflect.InvocationTargetException
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
   at java.lang.reflect.Method.invoke(Unknown Source)
   at
org.hibernate.property.BasicPropertyAccessor$BasicSetter.set(BasicPropertyAccessor.java:42)
   ... 30 more
Caused by: java.lang.RuntimeException: Error while trying to call new class
org.biojavax.ontology.SimpleComparableOntology(class java.lang.String)
   at
org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:166)
   at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:105)
   at
org.biojavax.RichObjectFactory.getDefaultOntology(RichObjectFactory.java:221)
   at
org.biojavax.bio.seq.CompoundRichLocation.getJoinTerm(CompoundRichLocation.java:61)
   at
org.biojavax.bio.seq.CompoundRichLocation.<init>(CompoundRichLocation.java:90)
   at
org.biojavax.bio.seq.SimpleRichLocation.union(SimpleRichLocation.java:494)
   at org.biojavax.bio.seq.RichLocation$Tools.merge(RichLocation.java:363)
   at
org.biojavax.bio.seq.SimpleRichFeature.setLocationSet(SimpleRichFeature.java:181)
   ... 35 more
Caused by: java.lang.reflect.InvocationTargetException
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
   at java.lang.reflect.Method.invoke(Unknown Source)
   at
org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:133)
   ... 42 more
Caused by: org.hibernate.HibernateException: A collection with
cascade="all-delete-orphan" was no longer referenced by the owning entity
instance: Feature.locationSet
   at
org.hibernate.engine.Collections.processDereferencedCollection(Collections.java:96)
   at
org.hibernate.engine.Collections.processUnreachableCollection(Collections.java:39)
   at
org.hibernate.event.def.AbstractFlushingEventListener.flushCollections(AbstractFlushingEventListener.java:218)
   at
org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:77)
   at
org.hibernate.event.def.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:35)
   at org.hibernate.impl.SessionImpl.autoFlushIfRequired(SessionImpl.java:969)
   at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1114)
   at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
   at
org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:811)
   ... 47 more


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From Ekta.Jain at icr.ac.uk  Fri Jun  6 06:40:28 2008
From: Ekta.Jain at icr.ac.uk (Ekta Jain)
Date: Fri, 06 Jun 2008 11:40:28 +0100
Subject: [Biojava-dev] Re Uniprot Format
Message-ID: <s849223d.068@groupwise.icr.ac.uk>

Hello there,
there seems to be a bug in the UniprotFormat. It gives me an error at
line 614. In the Uniprot text data file, when i remove the records
(where my parser gets stuck) It all works okay.

How can this be fixed?

Ekta

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

From ap3 at sanger.ac.uk  Fri Jun  6 08:00:57 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Fri, 6 Jun 2008 13:00:57 +0100
Subject: [Biojava-dev] Re Uniprot Format
In-Reply-To: <s849223d.068@groupwise.icr.ac.uk>
References: <s849223d.068@groupwise.icr.ac.uk>
Message-ID: <EBA56187-CCC9-4EAC-8B25-FD25C4E048B1@sanger.ac.uk>

Hi Ekta,

We need more info in order to help. Can you provide the file you want  
to parse, the code you use for parsing, and also the exception trace?

Andreas



On 6 Jun 2008, at 11:40, Ekta Jain wrote:

> Hello there,
> there seems to be a bug in the UniprotFormat. It gives me an error at
> line 614. In the Uniprot text data file, when i remove the records
> (where my parser gets stuck) It all works okay.
>
> How can this be fixed?
>
> Ekta
>
> The Institute of Cancer Research: Royal Cancer Hospital, a  
> charitable Company Limited by Guarantee, Registered in England  
> under Company No. 534147 with its Registered Office at 123 Old  
> Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee  
> only.  If the message is received by anyone other than the  
> addressee, please return the message to the sender by replying to  
> it and then delete the message from your computer and network.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




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

From ap3 at sanger.ac.uk  Sat Jun  7 06:35:05 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Sat, 7 Jun 2008 11:35:05 +0100
Subject: [Biojava-dev] Re Uniprot Format
In-Reply-To: <s849446a.073@groupwise.icr.ac.uk>
References: <s849446a.073@groupwise.icr.ac.uk>
Message-ID: <9E93F7AF-456A-4CC1-A085-7005D9B93E94@sanger.ac.uk>

Hi Ekta,

You can parse through the whole file if you  add a try - catch around  
seq.nextRichSequence() (see below).

Still there were in fact a few records that caused problems to the  
parser. I committed a quick catch for these to SVN.

the main 2 problems were:
* some DOI reference lines contain extra ; characters, which are  
confusing to the parser For the moment such lines are ignored.
* some locations contain a ? character in front of them, added a  
catch for these to the UniProtLocationParser...

Andreas


while (seqs.hasNext()) {
	RichSequence seq = null;
	try {
		seq = seqs.nextRichSequence();
	} catch (Exception e){
		e.printStackTrace();	
		continue;
	}
	//your code here		
}





> Hi Andreas,
>
> The file im trying to parse is uniprot_sprot_human.dat.gz available  
> from
> ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/ 
> knowledgebase/taxonomic_divisions/
>
>
> Sorry its too big to attach. I have attached my entire code (the one
> that is doing the parsing).
>
> The error message is :
>
> Exception in thread "main" java.lang.NoSuchMethodError:
> org.biojava.bio.seq.io.ParseException.newMessage(Ljava/lang/ 
> Class;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/ 
> lang/String;)Ljava/lang/String;
> 	at
> org.biojavax.bio.seq.io.UniProtFormat.readRichSequence 
> (UniProtFormat.java:614)
> 	at
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence 
> (RichStreamReader.java:110)
> 	at fileReader.ParseUniprot.UniprotFromFile(ParseUniprot.java:62)
> 	at fileReader.WriteToFile.main(WriteToFile.java:50)
>
>
> The code gets stuck after the uniprotID '5HT2B_HUMAN'  and gives the
> above exception.
>
> Thanks a ton, appreciate the help.
>
> Ekta
>
>>>> Andreas Prlic <ap3 at sanger.ac.uk> 06/06/08 1:00 PM >>>
> Hi Ekta,
>
> We need more info in order to help. Can you provide the file you want
> to parse, the code you use for parsing, and also the exception trace?
>
> Andreas
>
>
>
> On 6 Jun 2008, at 11:40, Ekta Jain wrote:
>
>> Hello there,
>> there seems to be a bug in the UniprotFormat. It gives me an error at
>> line 614. In the Uniprot text data file, when i remove the records
>> (where my parser gets stuck) It all works okay.
>>
>> How can this be fixed?
>>
>> Ekta
>>
>> The Institute of Cancer Research: Royal Cancer Hospital, a
>> charitable Company Limited by Guarantee, Registered in England
>> under Company No. 534147 with its Registered Office at 123 Old
>> Brompton Road, London SW7 3RP.
>>
>> This e-mail message is confidential and for use by the addressee
>> only.  If the message is received by anyone other than the
>> addressee, please return the message to the sender by replying to
>> it and then delete the message from your computer and network.
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> ---------------------------------------------------------------------- 
> -
>
> Andreas Prlic      Wellcome Trust Sanger Institute
>                                Hinxton, Cambridge CB10 1SA, UK
>                                +44 (0) 1223 49 6891
>
> ---------------------------------------------------------------------- 
> -
>
>
>
>
> -- 
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
>
> The Institute of Cancer Research: Royal Cancer Hospital, a  
> charitable Company Limited by Guarantee, Registered in England  
> under Company No. 534147 with its Registered Office at 123 Old  
> Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee  
> only.  If the message is received by anyone other than the  
> addressee, please return the message to the sender by replying to  
> it and then delete the message from your computer and  
> network.<ParseUniprot.java>

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------




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

From bugzilla-daemon at portal.open-bio.org  Wed Jun 18 11:07:19 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 18 Jun 2008 11:07:19 -0400
Subject: [Biojava-dev] [Bug 2521] New: DNATools.toProtein(SymbolList, int,
	int) ignores the ints
Message-ID: <bug-2521-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2521

           Summary: DNATools.toProtein(SymbolList, int, int) ignores the
                    ints
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: thpar at psb.ugent.be


org.biojava.bio.seq.DNATools.toProtein(final SymbolList syms, int start, int
end)

seems to ignore the boundaries (line 519)

This is because it copies the SymbolList to a temporary 'symz' and then uses
the input var 'syms' anyway.


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From dicknetherlands at gmail.com  Thu Jun 19 08:10:15 2008
From: dicknetherlands at gmail.com (Richard Holland)
Date: Thu, 19 Jun 2008 13:10:15 +0100
Subject: [Biojava-dev] BioJava 3 work begins
Message-ID: <a0d826f40806190510l3bb7e719w75f3cb9e4508929a@mail.gmail.com>

Hello all. We are about to start coding the first bits of the new
BioJava 3 modules.

We would like to document code in parallel to writing it, and also to
write code based on use-cases rather than what we just think might be
useful. We already have a design document based on the discussions
late last year and included in that is a plan for how the internals
will work, but now we need some use-cases so that code can be written
to solve real-life problems first rather than just theoretical ones.

Please add any use-cases you can think of to the following Wiki page.
Doesn't matter if they're simple (e.g. read a file in a given format)
or really complex (e.g. serve up a bunch of Genbank files to a
web-based query interface). All will be considered and we as a team
will do our best to include as many as we can, aiming to solve all of
them if possible.

http://biojava.org/w/index.php?title=BioJava_3_Use_Cases&action=edit

cheers,
Richard

From simpleyrx at 163.com  Thu Jun 19 11:17:12 2008
From: simpleyrx at 163.com (simpleyrx at 163.com)
Date: Thu, 19 Jun 2008 23:17:12 +0800 (CST)
Subject: [Biojava-dev] Fw:Re: Dose profile-profile alignment algoritm exist
 in BioJava package ?
Message-ID: <8944613.11901213888632524.JavaMail.coremail@bj163app60.163.com>




---------- ???????????? ----------
????????""Richard Holland" <holland at ebi.ac.uk>" 
??????????2008-06-15 01:05:27
????????simpleyrx at 163.com
?????? Re: Dose profile-profile alignment algoritm exist in BioJava package ?
Since 28/03/2008 I no longer work at the EBI or on the BioMart project. I am also currently taking a break from the BioJava project.

If your query relates to BioMart, please contact

From simpleyrx at 163.com  Thu Jun 19 11:17:12 2008
From: simpleyrx at 163.com (simpleyrx at 163.com)
Date: Thu, 19 Jun 2008 23:17:12 +0800 (CST)
Subject: [Biojava-dev] Fw:Re: Dose profile-profile alignment algoritm exist
 in BioJava package ?
Message-ID: <8944613.11901213888632524.JavaMail.coremail@bj163app60.163.com>




---------- ???????????? ----------
????????""Richard Holland" <holland at ebi.ac.uk>" 
??????????2008-06-15 01:05:27
????????simpleyrx at 163.com
?????? Re: Dose profile-profile alignment algoritm exist in BioJava package ?
Since 28/03/2008 I no longer work at the EBI or on the BioMart project. I am also currently taking a break from the BioJava project.

If your query relates to BioMart, please contact

From markjschreiber at gmail.com  Thu Jun 19 21:40:49 2008
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 20 Jun 2008 09:40:49 +0800
Subject: [Biojava-dev] BioJava 3 work begins
In-Reply-To: <a0d826f40806190510l3bb7e719w75f3cb9e4508929a@mail.gmail.com>
References: <a0d826f40806190510l3bb7e719w75f3cb9e4508929a@mail.gmail.com>
Message-ID: <93b45ca50806191840y14ca932cx64f688b1649f6212@mail.gmail.com>

Can I follow this up by saying that all use cases _must_ be
accompanied by a why.  It is very important to understand what the
rationale for the use case is as this will determine how we program
it.

For example. "A binding to BioSQL" is not a use case.  The use case
would be: "I want to upload a subset of Genbank to a relational
database so that I can add my own de-novo gene predictions and then
search the results in a relational manner".

We would then analyse this use case and figure out a good way to do
it. During this analysis we would probably identify that we need a
binding from BJ3 to BioSQL. As a general rule you should never specify
the technology in the use case. Rather analysis of the requirements of
the usecase suggests the best technology.

I will put up a template for what should be in a use case tonight
(Singapore time) that people can use.  It would also be great if
people who suggest cases can provide contact details as frequently
there has to be lots of iterative discussion to pin down the details.

- Mark

On 6/19/08, Richard Holland <dicknetherlands at gmail.com> wrote:
> Hello all. We are about to start coding the first bits of the new
> BioJava 3 modules.
>
> We would like to document code in parallel to writing it, and also to
> write code based on use-cases rather than what we just think might be
> useful. We already have a design document based on the discussions
> late last year and included in that is a plan for how the internals
> will work, but now we need some use-cases so that code can be written
> to solve real-life problems first rather than just theoretical ones.
>
> Please add any use-cases you can think of to the following Wiki page.
> Doesn't matter if they're simple (e.g. read a file in a given format)
> or really complex (e.g. serve up a bunch of Genbank files to a
> web-based query interface). All will be considered and we as a team
> will do our best to include as many as we can, aiming to solve all of
> them if possible.
>
> http://biojava.org/w/index.php?title=BioJava_3_Use_Cases&action=edit
>
> cheers,
> Richard
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From bugzilla-daemon at portal.open-bio.org  Sat Jun 21 01:37:44 2008
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sat, 21 Jun 2008 01:37:44 -0400
Subject: [Biojava-dev] [Bug 2521] DNATools.toProtein(SymbolList, int,
	int) ignores the ints
In-Reply-To: <bug-2521-485@http.bugzilla.open-bio.org/>
Message-ID: <200806210537.m5L5biA2004847@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2521


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from mark.schreiber at novartis.com  2008-06-21 01:37 EST -------
Now fixed in head of SVN


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From s.camiolo at uniss.it  Mon Jun 23 06:19:27 2008
From: s.camiolo at uniss.it (Salvo Camiolo)
Date: Mon, 23 Jun 2008 12:19:27 +0200
Subject: [Biojava-dev] Installation Problems
Message-ID: <485F78AF.2020709@uniss.it>

Hi,
I am experiencing some problem with the biojava installation. I use a 
linux machine with  PcLinuxOs distro. I downloaded the file biojava.jar 
from the following website

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

and I have put it in the folder /home/salvo. I then entered that folder 
and typed the following command:

export 
CLASSPATH=/home/salvo/biojava.jar:/home/salvo/bytecode.jar:/home/salvo/commons-cli.jar:/home/salvo/commons-collections-2.1.jar:/home/salvo/commons-dbcp-1.1.jar:/home/salvo/commons-pool-1.1.jar:. 


I need biojava in order to use CAI software by Carbone et al. I 
downloaded the java files for this software and had to compile it. The 
CAI website advice to use javac which I don't have. I used jikes instead 
and got the following error message:

Found 1 system error:

*** Semantic Error: You need to modify your classpath, sourcepath, 
bootclasspath, and/or extdirs setup. Jikes could not find package 
"java.lang" in:
               /home/salvo/biojava.jar
               /home/salvo/bytecode.jar
               /home/salvo/commons-cli.jar
               /home/salvo/commons-collections-2.1.jar
               /home/salvo/commons-dbcp-1.1.jar
               /home/salvo/commons-pool-1.1.jar
               .
               .

If I use the gcj compiler I get several errors, all related to the class 
`org::biojava::bio::seq.


What's can be the problem in your opinion?
Thank you very much in helping me
kind regards
Salvo C.

From dicknetherlands at gmail.com  Mon Jun 23 07:04:46 2008
From: dicknetherlands at gmail.com (Richard Holland)
Date: Mon, 23 Jun 2008 12:04:46 +0100
Subject: [Biojava-dev] Installation Problems
In-Reply-To: <485F78AF.2020709@uniss.it>
References: <485F78AF.2020709@uniss.it>
Message-ID: <a0d826f40806230404lf5643d9v5fe5cbe256a6486b@mail.gmail.com>

Jikes needs to have all the standard Java libraries on the classpath
as well as your downloaded BioJava+commons libraries. Read the Jikes
documentation for help with that if you're unsure.

We can't help with the errors you got from GCJ unless you can post
them to the list so that we can see what they are!

cheers,
Richard

2008/6/23 Salvo Camiolo <s.camiolo at uniss.it>:
> Hi,
> I am experiencing some problem with the biojava installation. I use a linux
> machine with  PcLinuxOs distro. I downloaded the file biojava.jar from the
> following website
>
> http://biojava.org/wiki/BioJava:Download
>
> and I have put it in the folder /home/salvo. I then entered that folder and
> typed the following command:
>
> export
> CLASSPATH=/home/salvo/biojava.jar:/home/salvo/bytecode.jar:/home/salvo/commons-cli.jar:/home/salvo/commons-collections-2.1.jar:/home/salvo/commons-dbcp-1.1.jar:/home/salvo/commons-pool-1.1.jar:.
>
> I need biojava in order to use CAI software by Carbone et al. I downloaded
> the java files for this software and had to compile it. The CAI website
> advice to use javac which I don't have. I used jikes instead and got the
> following error message:
>
> Found 1 system error:
>
> *** Semantic Error: You need to modify your classpath, sourcepath,
> bootclasspath, and/or extdirs setup. Jikes could not find package
> "java.lang" in:
>              /home/salvo/biojava.jar
>              /home/salvo/bytecode.jar
>              /home/salvo/commons-cli.jar
>              /home/salvo/commons-collections-2.1.jar
>              /home/salvo/commons-dbcp-1.1.jar
>              /home/salvo/commons-pool-1.1.jar
>              .
>              .
>
> If I use the gcj compiler I get several errors, all related to the class
> `org::biojava::bio::seq.
>
>
> What's can be the problem in your opinion?
> Thank you very much in helping me
> kind regards
> Salvo C.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From cbaribault at bellsouth.net  Wed Jun 11 22:11:59 2008
From: cbaribault at bellsouth.net (cbaribault at bellsouth.net)
Date: Thu, 12 Jun 2008 02:11:59 -0000
Subject: [Biojava-dev] tbl2gff?
Message-ID: <061220080206.13462.485084B9000C35630000349622230682329B0A02D2089B9A019C04040A0DBF9B049A0E0D079D0E0D0C@att.net>

Greetings again,

Is there any tool for converting a .tbl file to .gff format?

Regards,
Carl
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From cbaribault at bellsouth.net  Wed Jun 11 22:16:48 2008
From: cbaribault at bellsouth.net (cbaribault at bellsouth.net)
Date: Thu, 12 Jun 2008 02:16:48 -0000
Subject: [Biojava-dev] biojavax src?
Message-ID: <061220080206.12993.485084AE000E1EFF000032C122230682329B0A02D2089B9A019C04040A0DBF9B049A0E0D079D0E0D0C@att.net>

Greetings,

I'd like to know if the full source code is available for biojavax.  I could not find in my download...

http://www.biojava.org/download/bj16/all/biojava-1.6-all.jar

Please forgive my error, if any.


Regards,
Carl
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