[MOBY-l] moby namespace

[Carol Lushbough]

I was wondering if anyone can tell how to set the <moby:MOBY 
xmlns:moby="http://www.biomoby.org/moby">
name space through a Java method.  For example, when I execute 
client.getInput().toXML(), Im getting

<Parameter articleName='dnamatrix'><Value>IUB</Value></Parameter>

and I think I should get:

<moby:Parameter 
moby:articleName="ktuple"><moby:Value>1</moby:Value></moby:Parameter>

Thanks for your help!

Carol

--------------------------------------------------------------------------------------------------

If you need more information:

I create a client:

            Central worker = new 
CentralImpl(BioMobyDataTypeParser.MOBY_CENTRAL_ENDPOINT,
                                             
BioMobyDataTypeParser.MOBY_CENTRAL_NAMESPACE);

            MobyService templateService = new MobyService(serviceName);
            MobyService[] validServices = 
worker.findService(templateService);

            MobyRequest client = new MobyRequest(worker);
            MobyService s = validServices[0];
            client.setService(s);

Then I set the primary and secondary parameters: (Note; I'm just showing 
the secondary parameter calls and partial output)

          MobyDataSecondaryInstance[] tempSecondaryData = new 
MobyDataSecondaryInstance[allParameters.size()];
          for each parameter {
                  ...
               MobySecondaryData p1 = new MobySecondaryData(paramName);
               tempSecondaryData[count] = new 
MobyDataSecondaryInstance(p1, paramValue);   
              count++;
          }
       
          client.setSecondaryInput(tempSecondaryData);

          // print the XML representation of the input
           System.out.println("Client input:"+client.getInput().toXML());

The output is:

 <moby:mobyContent>
    <moby:mobyData queryID="1">  <Parameter 
articleName='gapdist'><Value>4</Value></Parameter>
  <Parameter articleName='dnamatrix'><Value>IUB</Value></Parameter>
  <Parameter articleName='matrix'><Value>GONNET</Value></Parameter>
  <Parameter articleName='outorder'><Value>aligned</Value></Parameter>
  <Parameter articleName='type'><Value>protein</Value></Parameter>
  <Parameter articleName='ktuple'><Value>1</Value></Parameter>
  <Parameter articleName='score'><Value>percent</Value></Parameter>
  <Parameter articleName='endgaps'><Value>FALSE</Value></Parameter>
  <Parameter articleName='gapext'><Value>0.2</Value></Parameter>
  <Parameter articleName='window'><Value>5</Value></Parameter>
  <Parameter articleName='gapopen'><Value>10.0</Value></Parameter>

Instead of:
<moby:Parameter moby:articleName="ktuple">
        <moby:Value>1</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="score">
        <moby:Value>percent</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="gapdist">
        <moby:Value>4</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="gapopen">
        <moby:Value>10.0</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="type">
        <moby:Value>protein</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="matrix">
        <moby:Value>GONNET</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="endgaps">
        <moby:Value>FALSE</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="gapext">
        <moby:Value>0.2</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="outorder">
        <moby:Value>aligned</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="dnamatrix">
        <moby:Value>IUB</moby:Value>
      </moby:Parameter>
      <moby:Parameter moby:articleName="window">

-- 
Carol Lushbough
Assistant Professor of Computer Science
University of South Dakota
Vermillion, SD 57069
(605) 677-6138