[Bioc-devel] adding a validity method to a class

[Paul Shannon]

Combining suggestions from Hervé and Steve Lianoglou, my confusion is cleared up.  The custom validity function has to be defined before it is named in the class definition.

This works:

   myValidity = function (object) cat ('hello from myValidity')
   setClass ("A", representation(blob="raw") , validity=myValidity)
   a <- new ("A")
   print (validObject(a))

I expected the reference to the method to be resolved dynamically when validObject was first called.  Not so.

Thanks to everyone who helped on this.

 - Paul



On Mar 31, 2011, at 12:08 PM, Hervé Pagès wrote:

> Hi Paul,
> 
> On 03/31/2011 10:42 AM, Paul Shannon wrote:
>> I have defined a rather lengthy validity function for CytoscapeWindowClass.
>> 
>> In my testing, I create incomplete or broken instances of the class.
>> 
>> I get the results I want when I call the validity function like this, for example:
>> 
>>   >  RCytoscape:::validCytoscapeWindow (cw.broken)
>>    You must provide an 'edgeType' edge attribute, which will be mapped to Cytoscape's 'interaction' edge attribute.
>>    [1] FALSE
>> 
>> But when, following the example in the graphNEL source code, I try to assign this function to the 'validity' slot of the class, the function is not found.
>> 
>> The class definition:
>> 
>>   setClass ("CytoscapeWindowClass",
>>             representation = representation (title="character",
>>                                              window.id='character',
>>                                              graph="graph"),
>>             contains='CytoscapeConnectionClass',
>>             prototype = prototype (title="R graph",
>>                                   graph=new ("graphNEL", edgemode='directed'),
>>                                    uri="http://localhost:9000"),
>>             validity=function(obj) validCytoscapeWindow (obj)
>>             #validity=function(obj) RCytoscape:::validCytoscapeWindow (obj)   # I also tried this
>>             )
>> 
>> Calling 'validObject (cw)' should invoke 'validCytoscapeWindow' but does not.
> 
>                        ^^
> Are you calling validObject() on 'cw' or on 'cw.broken'?
> 
> It should work:
> 
>  setClass("A", representation(blob="raw"),
>                validity=function(object) cat("Hi!\n"))
> 
> Then:
> 
>  > a <- new("A")
>  > validObject(a)
>  Hi!
>  [1] TRUE
> 
> Cheers,
> H.
> 
>> 
>> Can anyone explain what I am doing wrong?
>> 
>> Thanks!
>> 
>>  - Paul
>> 
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> -- 
> < Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319