updateObject {Biobase}R Documentation

Update an object to its current class definition

Description

These generic functions return an instance of object updated to its current class definition (or to the class definition of template, in the case of updateObjectTo).

Updating objects is primarily useful when an object has been serialized (e.g., stored to disk) for some time (e.g., months), and the class definition has in the mean time changed. Because of the changed class definition, the serialized instance is no longer valid.

updateObject requires that the class of the returned object be the same as the class of the argument object, and that the object is valid (see validObject). By default, updateObject has the following behaviors:

updateObject(ANY, ..., verbose=FALSE)

By default, updateObject uses heuristic methods to determine whether the object should be the ‘new’ S4 type (introduced in R 2.4.0), but is not. If the heuristics indicate an update is required, the updateObjectFromSlots function tries to update the object. The default method returns the original S4 object or the successfully updated object, or issues an error if an update is required but not possible. The optional named argument verbose causes a message to be printed describing the action. Arguments ... are passed to link{updateObjectFromSlots}.

updateObject(list, ..., verbose=FALSE)

Visit each element in list, applying updateObject(list[[elt]], ..., verbose=verbose).

updateObject(environment, ..., verbose=FALSE)

Visit each element in environment, applying updateObject(environment[[elt]], ..., verbose=verbose)

updateObjectTo requires that the class of the returned object be the same as the class of the template argument, and that the object is valid. Usually, updating proceeds by modifying slots in template with information from object, and returning template. Use as to coerce an object from one type to another; updateObjectTo might be useful to update a virtual superclass. By default, updateObjectTo has the following behavior:

updateObjectTo(ANY-object,ANY-template)

Attempt as(ANY-object,class(ANY-template)).

Sample methods are illustrated below.

updateObjectFromSlots(object, objclass = class(object), ..., verbose=FALSE) is a utility function that identifies the intersection of slots defined in the object instance and objclass definition. The corresponding elements in object are then updated (with updateObject(elt, ..., verbose=verbose)) and used as arguments to a call to new(class, ...), with ... replaced by slots from the original object. If this fails, updateObjectFromSlots then tries new(class) and assigns slots of object to the newly created instance.

getObjectSlots(object) extracts the slot names and contents from object. This is useful when object was created by a class definition that is no longer current, and hence the contents of object cannot be determined by accessing known slots.

Usage

updateObject(object, ..., verbose=FALSE)
updateObjectTo(object, template, ..., verbose=FALSE)
updateObjectFromSlots(object, objclass=class(object), ..., verbose=FALSE)
getObjectSlots(object)

Arguments

object

Object to be updated, or for slot information to be extracted from.

template

Instance representing a template for updating object.

objclass

Optional character string naming the class of the object to be created.

verbose

A logical, indicating whether information about the update should be reported. Use message to report this.

...

Additional arguments, for use in specific update methods.

Value

updateObject returns a valid instance of object. updateObjectTo returns a valid instance of template. updateObjectFromSlots returns an instance of class objclass. getObjectSlots returns a list of named elements, with each element corresponding to a slot in object.

Author(s)

Biocore team

See Also

Versions-class

Examples

## update object, same class
data(sample.ExpressionSet)
obj <- updateObject(sample.ExpressionSet)

setClass("UpdtA", representation(x="numeric"), contains="data.frame")
setMethod("updateObject", signature(object="UpdtA"),
          function(object, ..., verbose=FALSE) {
              if (verbose) message("updateObject object = 'A'")
              object <- callNextMethod()
              object@x <- -object@x
              object
})

a <- new("UpdtA", x=1:10)
## See steps involved
updateObject(a)

removeClass("UpdtA")
removeMethod("updateObject", "UpdtA")

[Package Biobase version 2.14.0 Index]