Combining suggestions from Herv? 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, Herv? Pag?s 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
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