R/Generics.R

In jotsetung/ensembldb: Utilities to create and use Ensembl-based annotation databases

##***********************************************************************
##
##     Generic methods
##
##***********************************************************************
## A
setGeneric("activeFilter", function(x, ...) standardGeneric("activeFilter"))
setGeneric("addFilter", function(x, ...) standardGeneric("addFilter"))

## B
setGeneric("buildQuery", function(x, ...)
    standardGeneric("buildQuery"))

## C
setGeneric("cleanColumns", function(x, columns, ...)
    starndardGeneric("cleanColumns"))

## D
setGeneric("dbSeqlevelsStyle", function(x, ...)
    standardGeneric("dbSeqlevelsStyle"))
setGeneric("dropFilter", function(x, ...) standardGeneric("dropFilter"))

## E
setGeneric("ensemblVersion", function(x)
    standardGeneric("ensemblVersion"))
setGeneric("ensDbColumn", function(object, ...)
    standardGeneric("ensDbColumn"))
setGeneric("ensDbQuery", function(object, ...)
    standardGeneric("ensDbQuery"))

## F
## if (!isGeneric("filter"))
##     setGeneric("filter", function(x, ...)
##                standardGeneric("filter"))
setGeneric("formatSeqnamesForQuery", function(x, sn, ...)
    standardGeneric("formatSeqnamesForQuery"))
setGeneric("formatSeqnamesFromQuery", function(x, sn, ...)
    standardGeneric("formatSeqnamesFromQuery"))

## G
setGeneric("getGeneRegionTrackForGviz", function(x, ...)
    standardGeneric("getGeneRegionTrackForGviz"))
setGeneric("getGenomeFaFile", function(x, ...)
    standardGeneric("getGenomeFaFile"))
setGeneric("getGenomeTwoBitFile", function(x, ...)
    standardGeneric("getGenomeTwoBitFile"))
setGeneric("getMetadataValue", function(x, name)
    standardGeneric("getMetadataValue"))
setGeneric("getProperty", function(x, name=NULL, ...)
    standardGeneric("getProperty"))
setGeneric("getWhat", function(x, ...)
    standardGeneric("getWhat"))

## H
setGeneric("hasProteinData", function(x)
    standardGeneric("hasProteinData"))

## L
setGeneric("lengthOf", function(x, ...)
    standardGeneric("lengthOf"))
setGeneric("listColumns", function(x, ...)
    standardGeneric("listColumns"))
setGeneric("listGenebiotypes", function(x, ...)
    standardGeneric("listGenebiotypes"))
setGeneric("listTables", function(x, ...)
    standardGeneric("listTables"))
setGeneric("listTxbiotypes", function(x, ...)
    standardGeneric("listTxbiotypes"))
setGeneric("listUniprotDbs", function(object, ...)
    standardGeneric("listUniprotDbs"))
setGeneric("listUniprotMappingTypes", function(object, ...)
    standardGeneric("listUniprotMappingTypes"))

## O
setGeneric("orderResultsInR", function(x)
    standardGeneric("orderResultsInR"))
setGeneric("orderResultsInR<-", function(x, value)
    standardGeneric("orderResultsInR<-"))

## P
setGeneric("print", function(x, ...)
    standardGeneric("print"))
setGeneric("properties", function(x, ...)
    standardGeneric("properties"))

## R
setGeneric("requireTable", function(x, db, ...)
    standardGeneric("requireTable"))
setGeneric("returnFilterColumns", function(x)
    standardGeneric("returnFilterColumns"))
setGeneric("returnFilterColumns<-", function(x, value)
    standardGeneric("returnFilterColumns<-"))

## S
setGeneric("seqinfo", function(x)
    standardGeneric("seqinfo"))
setGeneric("setProperty", function(x, value=NULL, ...)
    standardGeneric("setProperty"))
## setGeneric("show", function(object, ...)
##     standardGeneric("show"))
setGeneric("supportedSeqlevelsStyles", function(x)
    standardGeneric("supportedSeqlevelsStyles"))

## T
setGeneric("tablesByDegree", function(x, ...)
    standardGeneric("tablesByDegree"))
setGeneric("tablesForColumns", function(x, attributes, ...)
    standardGeneric("tablesForColumns"))
setGeneric("toSAF", function(x, ...)
    standardGeneric("toSAF"))
## setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
##                                          with.utr5_len=FALSE,
##                                          with.utr3_len=FALSE, ...)
##     standardGeneric("transcriptLengths"))

## U
setGeneric("updateEnsDb", function(x, ...)
    standardGeneric("updateEnsDb"))
setGeneric("useMySQL", function(x, host = "localhost", port = 3306, user, pass)
    standardGeneric("useMySQL"))