[kepler-dev] RE: ClustalW_SDSC.java

[Xiaowen Xin]

Hi Zhengang,

Some of the files I mean in src/org/sdm/spa/ are:

bioservice.xml, bio.xml, DDBJ_DDBJ.xml, DDBJ_GetEntry.xml, and DDBJ.xml.

I don't believe any of these files are used anywhere.

bioservice.xml still references the edu.ncsu package name, so it can't be
used right now even if something references it.

Do you see these files being used?  If they're not used, could you please
remove them?

As for spa.xml, I agree that it should not be in the same category as
PIW.xml.  PIW.xml is in workflows/, while spa.xml is in configs/.

I didn't put spa.xml in src/ because I felt that src/ is for java files.
spa.xml determines the treeview on the left-hand side of the Ptolemy
modelling environment.  So if anything, I felt that it is a configuration
file.

What do you think?

Xiaowen

On Fri, 16 Apr 2004, Zhengang Cheng wrote:

> Hi, Ilkay, Xiaowen,
>
> Sorry for my indifference to you previous request. I were working on the
> server side services.
>
> Xiaowen, those XML files that originally at org.sdm.spa are required for SPA
> to run in Ptolemy.
> It seems that You has moved them to configs/ptolemy/configs/spa.
>
> Actually I prefer for those files to sit at org.sdm.spa.configs if possible.
> Those files are part of program, not in the same categorgy as PIW.xml. I
> think they should be under src, if possible.
>
> Zhengang
>
> ----- Original Message -----
> From: "Ilkay Altintas" <altintas at sdsc.edu>
> To: "Zhengang Cheng" <zcheng at eos.ncsu.edu>
> Cc: "Xiaowen Xin" <xin2 at llnl.gov>
> Sent: Friday, April 16, 2004 12:53 PM
> Subject: RE: [kepler-dev] RE: ClustalW_SDSC.java
>
>
> > Hi Zhengang,
> >
> > I hate to ask you this again, but would you mind checking the
> > other files that were migrated from edu.ncsu directory?
> >
> > Especially the .xml files there seem out of place/unused.
> >
> > Thanks so much,
> > Ilkay
> >
> > -----Original Message-----
> > From: Zhengang Cheng [mailto:zcheng at eos.ncsu.edu]
> > Sent: Friday, April 16, 2004 9:52 AM
> > To: Ilkay Altintas
> > Cc: Xiaowen Xin
> > Subject: Re: [kepler-dev] RE: ClustalW_SDSC.java
> >
> >
> > Specifically the ClustalW use ClustalW_SDSC to do the work. ClustalW is
> the
> > actual local actor.
> >
> > Zhengang
> > ----- Original Message -----
> > From: "Ilkay Altintas" <altintas at sdsc.edu>
> > To: "Xiaowen Xin" <xin2 at llnl.gov>
> > Cc: <kepler-dev at ecoinformatics.org>
> > Sent: Thursday, April 15, 2004 8:07 PM
> > Subject: [kepler-dev] RE: ClustalW_SDSC.java
> >
> >
> > > Xiaowen,
> > >
> > > I have started cleaning the possibbly unnecessary files in
> > > the spa directory one by one as I haven't heard anything
> > > about that process being done. I didn't think ClustalW_SDSC.java
> > > was being referenced in another file. Anyways, I have put it
> > > back.
> > >
> > > Zhengang: Could you please check if the files that Xiaowen
> > > asked in her email
> > >
> >
> (http://www.ecoinformatics.org/pipermail/kepler-dev/2004-April/000338.html)
> > > are redundant and clean the unnecessary files? That directory
> > > is quite messy now.
> > >
> > > Ilkay
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: Xiaowen Xin [mailto:xin2 at llnl.gov]
> > > Sent: Thursday, April 15, 2004 11:39 AM
> > > To: altintas at sdsc.edu
> > > Cc: kepler-dev at ecoinformatics.org
> > > Subject: ClustalW_SDSC.java
> > >
> > >
> > > Hi Ilkay,
> > >
> > > In the Kepler sources, are you able to do "ant clean", followed by "ant
> > > install" successfully?
> > >
> > > It looks like kepler/src/org/sdm/spa/ClustalW.java still references
> > > ClustalW_SDSC.java, which isn't in the repository any more.
> > >
> > > Thanks,
> > > Xiaowen
> > >
> > > _______________________________________________
> > > kepler-dev mailing list
> > > kepler-dev at ecoinformatics.org
> > > http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
> > >
> >
> >
>
>