GenericSeq-class: Class "GenericSeq"

In lgatto/sequences: Generic and Biological Sequences

Class "GenericSeq"

Description

This virtual class defines a generic sequence object composed by an identifier, a sequence and an alphabet that defines the letters of the sequence. A set of accessor methods and setters are described below.

Objects from the Class

A virtual Class: No objects may be created from it.

Slots

id:

Object of class "character" that identifies the sequence instance.

alphabet:

Object of class "character" that defines all the letters that a valid sequence can be made of.

sequence:

Object of class "character" storing the actual sequence string of the sequence instance.

Methods

alphabet

signature(object = "GenericSeq"): retrieves the alphabet of valid sequence letters, returned as characher.

id

signature(object = "GenericSeq"): retrieves the identifier of the sequence instance.

id<-

signature(object = "GenericSeq", value = "character"): sets the identifier of the sequence instance to value.

length

signature(x = "GenericSeq"): returns the length the sequence instance, i.e. the number of characters of the sequence string.

print

signature(x = "GenericSeq"): prints the sequence of the instance.

rev

signature(x = "GenericSeq"): return the reverse of the sequence string of the sequence instance.

seq

signature(... = "GenericSeq"): returns the sequence character string of the instance.

seq<-

signature(object = "GenericSeq", value = "character"): changes the sequence string of the sequence instance to value. The new string must be compatbile with the sequence instance alphabet.

show

signature(object = "GenericSeq"): displays the object content.

[

signature(x = "GenSeq"): Subsets the sequence of x and returns the correspong subsetted object of same class as x.

Author(s)

Laurent Gatto

See Also

See DnaSeq and RnaSeq classes for examples of subclasses and readFasta on how to create instances.

Examples

showClass("GenericSeq")

lgatto/sequences documentation built on Dec. 2, 2024, 1:57 a.m.