[MOBY-dev] [moby] Re: Suggestion for newtag in Parameter(Secondary Input specification)

Paul Gordon gordonp at ucalgary.ca
Tue Feb 28 15:09:53 UTC 2006


Given that the size of the human genome exceeds the limits of a xsd:int, 
and that we often use e-values exceeding the limits of xsd:double, may I 
suggest that we mandate the equivalents to xsd:integer and xsd:decimal?  
I have built my jMOBY code using arbitrary precision numbers, but I'm 
sure we'll need to change other parts of it, and of the Perl libraries...

>I think we should choose the corresponding XML Schema types for each 
>primitive object. For instance:
>
>moby:String -> xsd:string (it would not allow XML content) or 
>xsd:anyType (any content)
>
>moby:Integer -> xsd:int [-2147483648,2147483647] or xsd:integer (*any* 
>integer)
>
>moby:Float -> xsd:double (IEEE double-precision 64-bit floating point 
>type), xsd:float (IEEE single-precision 32-bit floating point type) or 
>xsd:decimal (*any* real number with a finite number of decimal digits)
>
>moby:DateTime -> xsd:dateTime
>
>moby:Boolean -> xsd:boolean or an enumerated xsd:string 
>{'0','1','false','true'}
>
>	Best Regards,
>		José María
>
>Paul Gordon wrote:
>  
>
>>The main problem:
>>
>>If somebody specifies a float, can I legally submit a e-value cutoff 
>>like "1.0e-180" (i.e. are we going to assume bit capacity, such as 
>>2^-149 for 16-byte IEEE floating point, or are we supporting arbitrary 
>>precision)? Underflow and overflow can cause problems on many 
>>systems...  same thing for integers > 2^32...
>>
>>Actually, do we support scientific notation?  That isn't mentioned either.
>>
>>Cheers,
>>Paul
>>
>>P.S. Yes, you are right Pieter.  You could enumerate integers, or even 
>>floats for that matter: this distinction matters for a server with 
>>strong types, but not for the client.  I've been too client centric 
>>lately :-)
>>
>>    
>>
>>>On Mon, 2006-02-27 at 23:44 +0100, Pieter Neerincx wrote:
>>>
>>> 
>>>
>>>      
>>>
>>>>Hmmm I use enum for some integers as well. I think it's perfectly  
>>>>normal to say for example: enum [1,2,4,8].
>>>>   
>>>>
>>>>        
>>>>
>>>Perhaps Paul can clarify what problem he is trying to solve.  My
>>>instincts tell me that maybe he is having difficulty with casting un-
>>>typed XML blocks as either Integer or String, as appropriate... is that
>>>a correct interpretation of the problem Paul?  
>>>
>>>I think the combination of the <datatype> block and the <enum> block
>>>should be able to indicate whether the ENUM is of type String or of type
>>>Integer (or Float, or whatever).  Is that not sufficient?  Or am I
>>>misunderstanding what the root of the problem is?
>>>
>>>M
>>>
>>>
>>>
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>>>http://biomoby.org/mailman/listinfo/moby-dev
>>> 
>>>
>>>      
>>>
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>>
>>
>>    
>>
>
>  
>




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