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

[Hervé Pagès]

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
>
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-- 
Hervé Pagès

Program in Computational Biology
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