Could do. On 11 Mar 2010, at 11:14, [email protected] wrote:
> > Could a subclass of the RichObjectFactory exist in the BioSQL module. If you > want your RichObjects backed by BioSQL you use the [BioSQL]RichObjectFactory > from the BioSQL package??? > > - Mark > > > [email protected] wrote on 03/10/2010 09:31:43 PM: > > > The problem is that the RichObjectFactory is generic, but the > > connectToBioSQL method is BioSQL specific. What really needs to > > happen is abstract out the connectToBioSQL method _only_ to a more > > specific class in the biosql module, and use (if necessary create) > > setters on RichObjectFactory for it to use. > > > > > > On 10 Mar 2010, at 04:10, Deepak Sheoran wrote: > > > > > Hi Andreas > > > I guess it should go in "org.biojavax.bio.db.biosql" package, it > > make sense to put this class their. > > > > > > Deepak Sheoran > > > > > > On 3/9/2010 11:28 AM, Andreas Prlic wrote: > > >> Hi Deepak, > > >> > > >> thanks for spotting this. This factory method should clearly be > > moved to the biosql module and not be part of the core. Anybody who > > has a deeper knowledge of the biosql code: Where is the best place > > in the biosql module to move this to? > > >> > > >> A work around the compile problem would be to use reflection to > > mask the calls to the methods in the other module, but it feels likea > > hack... > > >> > > >> Andreas > > >> > > >> On Mon, Mar 8, 2010 at 1:11 PM, Deepak Sheoran <[email protected] < > > mailto:[email protected]>> wrote: > > >> > > >> Hi > > >> I was making a local version of current maven project on my > > >> machine so that i can fix some reference related bugs in biojava. > > >> But when I build the local version and tried to use it. I got an > > >> error on method > > >> RichObjectFactory.connectToBioSql(Object session) of current > > >> version of bio-java live. when I had a look on it I saw a comment > > >> on it > > >> > > >> "// commenting out for the moment, since it prevents core from > > >> compiling. > > >> // TODO: move to BioSql module" > > >> > > >> then I uncommitted the code and add these import statements to > > >> RichObjectFactory.java and the problem is fixed : > > >> > > >> import org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver; > > >> import org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder; > > >> import org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler; > > >> > > >> After this I tried compiling bioSql module it went successfully > > >> and also when I compiled Core module it went successfully too.I > > >> don't if this is the only reason then please uncomment these line > > >> in main svn version since i don't how to do it. > > >> > > >> Thanks > > >> Deepak Sheoran > > >> > > >> > > >> _______________________________________________ > > >> Biojava-l mailing list - [email protected] > > >> <mailto:[email protected]> > > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > >> > > >> > > > > > > _______________________________________________ > > > Biojava-l mailing list - [email protected] > > > 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: [email protected] > > http://www.eaglegenomics.com/ > > > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure under > applicable law. If the reader of this message is not the intended recipient, > or the employee or agent responsible for delivery of the message to the > intended recipient, you are hereby notified that any dissemination, > distribution or copying of this communication is strictly prohibited. If you > have received this communication in error, please notify the sender > immediately by e-mail and delete the material from any computer. Thank you. -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
