Functions for creating and searching a registry of file types.

Description

Functions for creating and searching a registry of file types based on file extension.

Usage

  registerFileType(type, package, regex)
  findTypeRegistry(fnames)
  makeFileType(fnames, ..., regex=findTypeRegistry(fnames))

Arguments

Details

• registerFileType The registerFileType function adds entries to the file type register created at load time. The point of the register is for discovery of file type (class) by file extension. These are List-type classes (e.g., BamFileList) that occupy the fileList slot of a GenomicFiles class.

  Each List class entry in the register is associated with (1) a regular expression that identifies the file extension, (2) a class and (3) the package where the class is defined. At load time the register is populated with classes known to GenomicFiles. New classes / file types can be added to the register with registerFileType by providing these three pieces of information.

• findTypeRegistry Searches the registry for a match to the extension of fname. Internal use only.

• makeFileType Performs a look-up in the file registry based on the supplied regular expression; returns an object of the associated class. Internal use only.

Value

registerFileType: NULL

findTypeRegistry: The regular expression associated with the file.

makeFileType: A List-type object defined in the registry.

Examples

## At load time the registry is populated with file types
## known to GenomicFiles.
sapply(as.list(.fileTypeRegistry), "[", "type")

## Add a new class to the file register.
## Not run: registerFileType(NewClassList, NewPackage, ".NewExtension$")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(GenomicFiles)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicFiles/registry-utils.Rd_%03d_medium.png", width=480, height=480)
> ### Name: registry-utils
> ### Title: Functions for creating and searching a registry of file types.
> ### Aliases: registry-utils registerFileType findTypeRegistry makeFileType
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> ## At load time the registry is populated with file types
> ## known to GenomicFiles.
> sapply(as.list(.fileTypeRegistry), "[", "type")
$`\.bw$.type`
[1] "BigWigFileList"

$`\.fa$.type`
[1] "FaFileList"

$`\.fasta$.type`
[1] "FaFileList"

$`\.bam$.type`
[1] "BamFileList"

> 
> ## Add a new class to the file register.
> ## Not run: registerFileType(NewClassList, NewPackage, ".NewExtension$")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>