[Biojava-l] need help for SimpleSequenceBuilder class

[Bruce Ling]

Hi, Greg,

Thanks a lot.  I got your code working and it really solves the need to
parse the genbank format protein files.

For the overal biojava source code, when I tried to compile everything under
IDE Jbuilder 5. I have a couple of problems and I think I might know where
the problem is:

When the demos and biojava-live/src both in the path for compiling, there is
a lot of compiling errors.  If only put biojava-live/src in the path there
should be no problems.  When I am testing your code, what I did, is that I
only put the seq/your code in the path, then it seems fine.

It seems that there some problem with the code management in the demos
directory. Problem especially under demos the biocorba part.  Whoevers are
the authors of the code under demos, please check in all your code in and
make sure your code will compile with the rest of the code on the site not
just the code in your computer.

Thanks again to Greg to help me on this.


Thanks.

Bruce Ling, Ph.D.
Director, Bioinformatics
Tularik, Inc -- http://www.tularik.com
Email: bruce@tularik.com
Phone: 650-825-7143
fax: 1-435-804-4009

> -----Original Message-----
> From: Cox, Greg [mailto:gcox@netgenics.com]
> Sent: Tuesday, July 24, 2001 6:20 AM
> To: 'xling@tularik.com'
> Subject: RE: [Biojava-l] need help for SimpleSequenceBuilder class
>
>
> I don't think that this is related to BioJava.  I searched the source for
> CORBA and SeqDBImpl, neither showed up.  I also checked the associated JAR
> files, xerces, bytecode, and jakarta-regexp.  SeqDBImpl isn't in those
> either.  You can send a message to the list, someone there might
> know what's
> going on, but it's not something I can replicate.  I've attached the test
> file.  I work from the command line, so here's how to run it in dos:
>
> copy it to [some dir]\seq\TesRefSeqPrt
> set
> classpath=.;c:\biojava\biojava-live\ant-build\biojava.jar;c:\bioja
> va\biojava
> -live\xerces.jar
> 	// Set the paths to biojava.jar and xerces.jar appropriately.  You
> shouldn't need more than this
> cd [some dir]
> javac seq\TestRefSeqPrt
> java seq.TestRefSeqPrt c:\sequences\testData.refSeq
>
> The problem that you had was that the genbank formatter assumed it would
> parse DNA seqences.  Therefore, any feature was a stranded feature.
> However, when we try to use it on a protein strand, stranded
> features don't
> apply.  That's the error you were seeing.  ProteinRefSeqProcessor creates
> sets the source to RefSeq:Protein, which then gets keyed off of to create
> the right kind of feature.  Probably more detail than you wanted.
>  Oh well.
>
> Greg
>
> > -----Original Message-----
> > From: Bruce Ling [mailto:xling@tularik.com]
> > Sent: Monday, July 23, 2001 6:48 PM
> > To: Cox, Greg
> > Subject: RE: [Biojava-l] need help for SimpleSequenceBuilder class
> >
> >
> > Hi,
> >
> > thanks for the quick reply. I am using jbuilder 5 as my IDE.
> >
> > I am putting your biojava.jar into my path and several other
> > biojava needed
> > libraries as well.
> >
> > Then I put the biojava live/src in my source path.
> >
> > When I did the build, I got the following errors:
> >
> > SeqDBImpl class not found in CorbaDBServer class
> > _SeqDB_tie class not found there as well.
> >
> > I have checked the biojava API and I cannot find those two class docs.
> >
> > Can you help me with that?
> >
> > Without build, I cannot test your code.  BTW, what is the
> > magic you did to
> > get it working?
> >
> >
> > Thanks.
> >
> > Bruce Ling, Ph.D.
> > Director, Bioinformatics
> > Tularik, Inc -- http://www.tularik.com
> > Email: bruce@tularik.com
> > Phone: 650-825-7143
> > fax: 1-435-804-4009
>
>