jabaws questions

Hello,

I am working to add some additional msa tools to our jabaws installation. I have a question about the configuration files for my new services. What is the difference between an option and a parameter in a settings file? For example, in the ClustalParameters.xml file there are both nodes and nodes, but I’m not sure what the difference is.

Thanks,
Joni

···


Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net

Hi Joni,

The “Option” is a single value whereas the “Parameter” is a key value pair.
For example option:

No transition weighting
Disable sequence weighting
-NOWEIGHTS

Will be converted by JABAWS to the command line option: -NOWEIGHTS

While the parameter:

Transition weighting
Type of the sequence (PROTEIN or DNA)
-TRANSWEIGHT
prog_docs/clustalw.txt
0.5

Float
0
10


In the command line will look like this: -TRANSWEIGHT=0.5
if no value is specified by the user.
The actual delimiter between the parameter and the value is defined by the “prmSeparator” value, in this case it is defined like this: =

I hope that helps.

Regards,
Peter

Hi Peter,

Thanks for your quick reply!

That makes perfect sense.

Joni

···

On Mon, Nov 7, 2011 at 10:40 AM, Peter Troshin <p.v.troshin@dundee.ac.uk> wrote:

Hi Joni,

The “Option” is a single value whereas the “Parameter” is a key value pair.
For example option:

No transition weighting
Disable sequence weighting
-NOWEIGHTS

Will be converted by JABAWS to the command line option: -NOWEIGHTS

While the parameter:

Transition weighting
Type of the sequence (PROTEIN or DNA)
-TRANSWEIGHT
prog_docs/clustalw.txt
0.5

Float
0
10


In the command line will look like this: -TRANSWEIGHT=0.5
if no value is specified by the user.
The actual delimiter between the parameter and the value is defined by the “prmSeparator” value, in this case it is defined like this: =

I hope that helps.

Regards,
Peter

On 07/11/2011 18:20, Joni Fazo wrote:

Hello,

I am working to add some additional msa tools to our jabaws installation. I have a question about the configuration files for my new services. What is the difference between an option and a parameter in a settings file? For example, in the ClustalParameters.xml file there are both nodes and nodes, but I’m not sure what the difference is.

Thanks,
Joni


Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net

_______________________________________________
Jalview-discuss mailing list
[Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)


Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net