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 like a 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
