MultipleAlignment/NAMESPACE at devel · Bioconductor/MultipleAlignment · GitHub

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import(methods)
importFrom(stats, setNames)

import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(Seqinfo)
import(Biostrings)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###

exportClasses(
    MultipleAlignment,
    DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics NOT defined in this package
###

exportMethods(
    ## Methods for generics defined in the base package:
    dim, nrow, ncol,
    rownames,
    nchar,
    as.character, as.matrix,

    ## Methods for generics defined in the methods package:
    coerce, show,

    ## Generics defined in the IRanges package:
    maskedratio,

    ## Generics defined in the Biostrings package:
    seqtype, alphabetFrequency,
    consensusMatrix, consensusString,
    maskMotif, unmasked
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###

export(
    ## MultipleAlignment-class.R:
    DNAMultipleAlignment,
    RNAMultipleAlignment,
    AAMultipleAlignment,

    ## MultipleAlignment-IO.R:
    readDNAMultipleAlignment,
    readRNAMultipleAlignment,
    readAAMultipleAlignment,
    write.phylip
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in this package, and corresponding methods
###

export(
    ## MultipleAlignment-class.R:
    rowmask, "rowmask<-",
    colmask, "colmask<-",
    maskGaps,
    maskednrow, maskedncol, maskeddim,
    detail,

    ## MultipleAlignment-utils.R:
    consensusViews
)

### Same list as above.
exportMethods(
    rowmask, "rowmask<-",
    colmask, "colmask<-",
    maskGaps,
    maskednrow, maskedncol, maskeddim,
    detail,
    consensusViews
)