[MOBY-l] Re: [MOBY-dev] moby data and parameters

[Benjamin Good]

Hi Stephen,

 You have an example of a collection of two GenericSequence objects 
(which could be either DNA or AA) in the Parser java file I sent you.  
So, yep, its a collection.

Here is the (already java Stringified!) example.

String xmlString2 = "<?xml version='1.0' encoding='UTF-8'?><moby:MOBY 
xmlns:moby='http://www.biomoby.org/moby' 
xmlns='http://www.biomoby.org/moby'><moby:mobyContent 
moby:authority='mips.gsf.de'>"+
       " <moby:mobyData moby:queryID='1'>"+
           " <moby:Collection moby:articleName=''>"+
            "<moby:Simple>"+
              "     <moby:GenericSequence namespace='AGI_LocusCode' 
id='At2g42410'>"+
               "    <CrossReference>"+
                "     <Object namespace='Global_Keyword' id='superman'/>"+
                 "  </CrossReference>"+
                  " <moby:Integer namespace='' id='' 
articleName='Length'>214</moby:Integer> "+
                  " <moby:String namespace='' id='' 
articleName='Description'>putative SUPERMAN-like C2H2 zinc finger 
transcription factor</moby:String> "+
                   "<moby:String namespace='' id='' 
articleName='SequenceString'>MKRTHLASFSNRDKTQEEEGEDGNGDNRVIMNHYKNYEAGLIPWPPKNYTCSFCRREFRSAQALGGHMNVHRRDRAKLRQIPSWLFEPHHHTPIANPNPNFSSSSSSSTTTAHLEPSLTNQRSKTTPFPSARFDLLDSTTSYGGLMMDREKNKSNVCSREIKKSAIDACHSVRCEISRGDLMNKKDDQVMGLELGMSLRNPNQVLDLELRLGYL</moby:String>"+
                  " </moby:GenericSequence></moby:Simple>"+
               " <moby:Simple>"+
                "   <moby:GenericSequence namespace='AGI_LocusCode' 
id='At3g23130'>"+
                 "  <CrossReference>"+
                  "   <Object namespace='Global_Keyword_________' 
id='superman'/>"+
                  " </CrossReference>"+
                   "<moby:Integer namespace='' id='' 
articleName='Length'>1777</moby:Integer> "+
                   "<moby:String namespace='' id='' 
articleName='Description'>superman protein</moby:String> "+
                   "<moby:String namespace='' id='' 
articleName='SequenceString'>MERSNSIELRNSFYGRARTSPWSYGDYDNCQQDHDYLLGFSWPPRSYTCSFCKREFRSAQALGGHMNVHRRDRARLRLQQSPSSSSTPSPPYPNPNYSYSTMANSPPPHHSPLTLFPTLSPPSSPRYRAGLIRSLSPKSKHTPENACKTKKSSLLVEAGEATRFTSKDACKILRNDEIISLELEIGLINESEQDLDLELRLGFA</moby:String>"+
                   "</moby:GenericSequence></moby:Simple>"+
            "</moby:Collection>"+
        "</moby:mobyData>"+
                "</moby:mobyContent></moby:MOBY>";   

 For the return datatype, I think you might actually want to define the 
"parameters" as children (ie has/hasa) of your 
Chinook-service-list-datatype and then send back a collection of these 
datatypes.

Maybe send a proposed example of this new datatype?

-Ben

Stephen Montgomery wrote:

> hi -
>
> does anyone have an example of a xml input where more than one dna 
> sequence is coming down the wire.  is this a collection?
>
> also, for a registered return data type we want to attach some 
> parameters (corresponding to the application that is going to be 
> run).  is there a java example out there of doing this?
>
> all the best,
>
> stephen
>
> ps  ben and i had an awesome crash coding session yesterday.  set-up 
> the plan, built the supports, now we just need to execute the vision.  
> rock on.
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