PFAM-class {AnnBuilder}R Documentation

Class "PFAM" a sub-class of pubRepo to handle data from http://www.sanger.ac.uk/Software/Pfam/

Description

This class is a sub-class of pubRepo that is implemented specifically to parse the data ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz

Objects from the Class

Objects can be created by calls of the form new("PFAM", ...). A constructor (PFAM) is available and should be used to instatiate objects of PFAM

Slots

srcUrl:
Object of class "character", from class "pubRepo" a character string for the surce url where data will be downloaded/processed
fromWeb:
Object of class "logical" for inficating whether the source file should be accessed through the web or locally

Extends

Class "pubRepo", directly.

Methods

parseData
signature(object = "PFAM"): A method to parse a source file using a specified parser

Author(s)

Ting-Yuan Liu

References

ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz

See Also

pubRepo-class

Examples

## Not run: 
## create PFAM class
pfamObj <- PFAM(srcUrl="ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz",
                fromWeb=TRUE)
tableList <- parseData(pfamObj)
## End(Not run)

[Package AnnBuilder version 1.20.0 Index]