[Biojava-l] Re: update seqfeature

and the source doesn't change. At least that is what I suppose is happening. My question was how to handle this situation? Martina Simon Foote wrote: Hi Martina, Biojava should handle that correctly. I haven't done it by changing a feature source, but I have with changing a featu

[Biojava-l] update seqfeature

ry to update the rank unless its a unique combination? Or should I rather not mess with the BioJava and delete that entry and insert it as new to let BioJava handle the rank increase? Thanks for any advise Martina Simon Foote wrote: Hi Martina, In fact you can, as rank is the field that allows

[Biojava-l] Re: [BioSQL-l] _removeSequence

rt of that key), how can I get different ranks? Martina Hilmar Lapp wrote: The Biojava people will respond to this. Note though that Term_Relationship is for storing subject-predicate-object triples of terms, so I'm not sure why you want to use it for storing/associating annotat

[Biojava-l] Re: [BioSQL-l] _removeSequence

the identifier of the term (would that be the BioSQLfeatureId ?) and insert it in the term_relationship table? And there is no nice BioJava method for this, I have to do it "manually", like conn.prepareStatement(..) and stuff? BioJava spoiled me so!

[Biojava-l] Re: [BioSQL-l] _removeSequence

rstood the feature relationships, the graph is a tree, with only one parent for a given feature, and if that feature is deleted, all its children should get deleted too? Martina Hilmar Lapp wrote: There's one thing that I'm unsure about in Martina's original email, namely whe

[Biojava-l] Re: [BioSQL-l] _removeSequence

changes. Is that what is to be expected? Cause I still have trouble with the dublicate entry key, but that must be my code then. Thanks Martina ___ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] Re: [BioSQL-l] _removeSequence

and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. - -Original Message- From: Martina [mailto:[EMAIL PROTECTED] Sent: Monday, June 20, 2005 6:21 PM To: Richard HOL

[Biojava-l] Re: [BioSQL-l] _removeSequence

My tables are all InnoDB tables and in the biosqldb-mysql.sql (v 1.40 2004/11/04 01:49:41) which created them, it says ON DELETE CASCADE. Do I need to do anything else? Thanks, Martina Richard HOLLAND wrote: To do cascading deletes in MySQL requires the tables to have been set up using the

[Biojava-l] _removeSequence

? If so - what is the best way do delete the features of the features (and so on)? And how to empty the db completly? Martina ___ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] [BioSQL-l] hierachy of features

mplicon contains: 0 Just in case, I attached the source. I can see only 4 features in Table seqfeature - but that might not be the right table to look into? Can anybody help me with this? Thanks Martina import org.biojava.bio.BioException; import org.biojava.bio.symbol.*; import

Re: [Biojava-l] Re: [BioSQL-l] How to add a feature?

Thanks - I knew it would be quite simple, as always with BioJava (once I've figuered out how to, that is)! Martina Simon Foote wrote: Hi Martina, To add a feature to a sequence stored in a BioSQL database, all you have to do is retrieve the sequence and then add a feature to it.

Bio Java (was: Re: [Biojava-l] Re: [BioSQL-l] How to add a feature?)

se do :-) It would increase the popularity of BioJava/BioSQL, which it deserved, I would think. Martina [EMAIL PROTECTED] wrote: There must be a simpler way? BioJava In Anger is rather sparse on things like that, I could do with a lot more examples .. All donations of examples are grate

[Biojava-l] Re: [BioSQL-l] How to add a feature?

Thanks Marc, but I don't know how to make a feature persistent in Biojava. Maybe someone from the bioJava list can help me? Martina Marc Logghe wrote: Hi Martina, I don't know how it goes in BioJava but in BioPerl the flow looks like this: 1) create your feature 2) make it persist

Re: [Biojava-l] nested features

It looks like it was a database problem and had nothing to do with biojava - since MySQL 4.1.12 is running, I don't have that problem anymore. Sorry to have bothered you! Martina ___ Biojava-l mailing list - Biojava-l@biojava.org

Re: [Biojava-l] nested features

Type: Amplicon contains: 0 I am trying to upgrade to MySQL 4.1.12 (was 4.1 alpha before (maybe it was a problem there)) and it is not working right now, but I will post the results of the sql statements as soon as the db is up again. Martina Richard HOLLAND wrote: Just to get this straight, if I follow

[Biojava-l] nested features

licon contains: 0 I can't see any difference in the biosql db (MySql), but I don't know where to look exactly. If I don't delete the record, just retrieve it on different runs, the output stays the same. I'm using biojava live from last month. I would be very grateful if someo

[Biojava-l] lage data sets/filtersByAnnotation ?

access? 2. I noticed in the source that filters by annotation also existed, but commented out. Are there any plans to reactivate these? Regards, Martina ___ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] Re: [BioSQL-l] location in features

I'm using MySQL, biojava-1.4pre1, biosql,v 1.40 Richard HOLLAND wrote: Hullo Martina. I must admit I am confused. I have been using BioJava+BioSQL to load Genbank records with features with no trouble, they always come out again with no exceptions raised and none missing. I am using Oracle