SRUtil-class: ".SRUtil" and related classes

In Bioconductor/ShortRead: FASTQ input and manipulation

".SRUtil" and related classes

Description

These classes provide important utility functions in the ShortRead package, but may occasionally be seen by the user and are documented here for that reason.

Objects from the Class

Utility classes include:

• .SRUtil-class a virtual base class from which all utility classes are derived.

• SRError-class created when errors occur in ShortRead package code.

• SRWarn-class created when warnings occur in ShortRead package code

• SRList-class representing a list (heterogeneous collection) of objects. The S4Vectors::SimpleList class is a better choice for a list-like container.

• SRVector-class representing a vector (homogeneous collection, i.e., all elements of the same class) of objects.

Objects from these classes are not normally constructed by the user. However, constructors are available, as follows.

SRError(type, fmt, ...), SRWarn(type, fmt, ...):

type

character(1) vector describing the type of the error. type must come from a pre-defined list of types.

fmt

a sprintf-style format string for the message to be reported with the error.

...

additional arguments to be interpolated into fmt.

SRList(...)

...

elements of any type or length to be placed into the SRList. If the length of ... is 1 and the argument is a list, then the list itself is placed into SRList.

SRVector(..., vclass)

...

elements all satisfying an is relationship with vclass, to be placed in SRVector.

vclass

the class to which all elements in ... belong. If vclass is missing and length(list(...)) is greater than zero, then vclass is taken to be the class of the first argument of ....

SRVector errors:

SRVectorClassDisagreement

this error occurs when not all arguments ... satisfy an ‘is’ relationship with vclass.

Slots

SRError and SRWarn have the following slots defined:

.type:

Object of class "character" containing the type of error or warning. .type must come from a pre-defined list of types, see, e.g., ShortRead:::.SRError_types.

.message:

Object of class "character" containing a detailed message describing the error or warning.

SRList has the following slot defined:

.srlist:

Object of class "list" containing the elements in the list.

SRVector extends SRList, with the following additional slot:

vclass:

Object of class "character" naming the type of object all elements of SRVector must be.

Methods

Accessors are available for all slots, and have the same name as the slot, e.g., vclass to access the vclass slot of SRVector. Internal slots (those starting with ‘.’ also have accessors, but these are not exported e.g., ShortRead:::.type.

SRList has the following methods:

length

signature(x = "SRList"): return the (integer(1)) length of the SRList.

names

signature(x = "SRList"): return a character vector of list element names. The length of the returned vector is the same as the length of x.

names<-

signature(x = "SRList", value = "character"): assign value as names for members of x.

[

signature(x = "SRList", i = "ANY", j = "missing"): subset the list using standard R list subset paradigms.

[[

signature(x = "SRList", i = "ANY", j = "missing"): select element ‘i’ from the list, using standard R list selection paradigms.

lapply

signature(X = "SRList", FUN="ANY"): apply a function to all elements of X, with additional arguments interpreted as with lapply.

sapply

signature(X = "SRList"): apply a function to all elements of X, simplifying the result if possible. Additional arguments interpreted as with sapply.

srlist

signature(object="SRList"): coerce the SRList object to a list.

show

signature(object = "SRList"): display an informative summary of the object content, including the length of the list represented by object.

detail

signature(x = "SRList"): display a more extensive version of the object, as one might expect from printing a standard list in R.

SRVector inherits all methods from SRList, and has the following additional methods:

show

signature(object = "SRVector"): display an informative summary of the object content, e.g., the vector class (vclass) and length.

detail

signature(x = "SRVector"): display a more extensive version of the object, as one might expect from a printing a standard R list.

Author(s)

Martin Morgan

Examples

getClass(".SRUtil", where=getNamespace("ShortRead"))
ShortRead:::.SRError_types
ShortRead:::.SRWarn_types

detail(SRList(1:5, letters[1:5]))

tryCatch(SRVector(1:5, letters[1:5]),
         SRVectorClassDisagreement=function(err) {
             cat("caught:", conditionMessage(err), "\n")
         })

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.