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

Paul Shannon pshannon at systemsbiology.org
Thu Mar 31 19:42:02 CEST 2011

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",
            prototype = prototype (title="R graph",
                                  graph=new ("graphNEL", edgemode='directed'),
            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?


 - Paul

More information about the Bioc-devel mailing list