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

[Paul Shannon]

Hi Steve,

  validity=validCytoscapeWindow

rather than

  validity=function(obj) validCytoscapeWindow (obj)

does not work, because the function is not defined at the time the class definition is read.  By including it in a function body, the evaluation is deferred until all the source has been read.  I suspect...

Your second suggestion:

  setValidity("CytoscapeWindowClass", validCytoscapeWindow)

*does* work.  But where should such an assignment be made?  At global scope at the bottom of the class file?   That seems a little ragged!

 - Paul


On Mar 31, 2011, at 10:54 AM, Steve Lianoglou wrote:

> Hi,
> 
> On Thu, Mar 31, 2011 at 1:42 PM, Paul Shannon
> <pshannon at systemsbiology.org> 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.
>> 
>> Can anyone explain what I am doing wrong?
> 
> What if you do:
> 
> setClass(...
>   validity=validCytoscapeWindow
> )
> 
> Or define your class first w/o the `validity` argument, then set it
> after like so:
> 
> setValidity("CytoscapeWindowClass", validCytoscapeWindow)
> 
> Maybe?
> 
> -steve
> 
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact