[Biojava-l] Error loading ontology terms

Hello, we have a problem with the connection to a BioSQL Database. When we start our application for the very first time and try to connect to the Database, it throws an SQLException "Connection is closed." After that, when we simply repeat the process, everything works fine and one can store S

[Biojava-l] "error loading ontology terms"

day and now the database-update works fine. Greetings, Felix -- Felix Dreher Max-Planck-Institute for Infection Biology Campus Charité Mitte Department of Immunology Mailing address: Schumannstraße 21/22 Visitors: Virchowweg 12 10117 Berlin Germany Tel.: +49 (0)30 28460-254 / -494 Mobile: +49

[Biojava-l] Problem with downloading Genbank-sequence

SecurityUtil.execute(SecurityUtil.java:282) org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:165) java.security.AccessController.doPrivileged(Native Method) com.sun.web.ui.util.UploadFilter.doFilter(UploadFilter.java:179) Any help would be appreciated! Thank you, Fel

Re: [Biojava-l] Problem with downloading Genbank-sequence

list that does?) What happens if you put a line like: WalkerFactory.getInstance().addTypeWithParent (FeatureFilter.OnlyChildren.class); somewhere in your code? I'd expect this to fail, too, but hopefully it with give a more informative exception. Thomas. On 30 N

Re: [Biojava-l] Problem with downloading Genbank-sequence

n the Server-Configuration-file is not 'globally enough' to affect all custom ClassLoader-calls. Maybe someone has experienced something similar or knows something about this specific Server? Thanks, Felix -- Felix Dreher Max-Planck-Institute for Infection Biology Campus Charit

Re: [Biojava-l] Problem with downloading Genbank-sequence

e jar-file again and deleting and re-adding it in StudioCreator. Greetings, Felix Felix Dreher wrote: Hi, the problem is the security-policy of the container I use for my web-application. In this case it's the 'Sun Java System Application Server Platform Edition 8.1'. As T

[Biojava-l] BioSQL cvs versions

f the corresponding class: /BioSQLSequenceDB.java/1.70/Fri Jun 10 07:48:11 2005// Further I use the latest cvs-version of the BioSQL-script 'biosqldb-pg.sql' (it's from June 2005). Are there any suggestions how this could be solved? Thank you, Felix -- Felix Dreher Max-Planc

Re: [Biojava-l] BioSQL cvs versions

ch Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Felix Dreher <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/20/2006 10:45 PM To: biojava-l@

[Biojava-l] BioJavaX-Hibernate: Namespace problem

ttacagattaca","test")); db.addRichSequence(seq); tx.commit(); The Namespace and the sequence are actually being saved in the database, but the sequence is saved in the default namespace 'lcl' and not in the new namespace 'mRNA'. Can someone tell me what I&#

[Biojava-l] Problem: BioSQL-cvs and/or RichSequence-Annotation

.id.AbstractPostInsertGenerator.getGenerated(AbstractPostInsertGenerator.java:42) ... 20 more Thanks in advance! Greetings, Felix -- Felix Dreher Max-Planck-Institute for Infection Biology Campus Charité Mitte Department of Immunology Mailing address: Schumannstraße 21/22 Visi

Re: [Biojava-l] Problem: BioSQL-cvs and/or RichSequence-Annotation

i-pattern'. > >RichSequence seq = >(SimpleRichSequence)RichSequence.Tools.enrich(DNATools.createDNASequence("gattacagattaca","urn:local:seq")); > >As an aside there is no need to cast the return of enrich if you are >assining it to a RichSequence pointe

[Biojava-l] BioSQLRichSequenceDB: initialisation error

uenceDB, a "NoSuchMethodException" is thrown at this line. I searched for the getMethod- method and in fact it is not present in org.hibernate.Criteria. So does anyone know if this is an error in the BioJava-class or in the Hibernate-class? Greetings, Felix -- Felix Dreher Max-Planck-Institute f

[Biojava-l] BioJavaX docbook minor corrections

change its version to 99 be.setVersion(99); --> can't use the method setVersion(int) --> but e.g. setDescription("XYZ"); Regards, Felix -- Felix Dreher Max-Planck-Institute for Infection Biology Campus Charité Mitte Department of Immunology Mailing address: Schumannstra

[Biojava-l] Problem: Hibernate - RichSequence Annotation

nate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:58) at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:195) ... 57 more Any suggestions would be highly appreciated! Regards, Felix -- Felix Dreher Max-Planck-Institute for Infection Biology Campus Charité Mitte

Re: [Biojava-l] Problem: Hibernate - RichSequence Annotation

r database from previous testing that may need cleaning out (although if the hibernate mapping is correct this is not likely). - Mark Felix Dreher <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 03/09/2006 02:08 AM To: biojava-l@biojava.org cc: (bcc: Mark Schre