Nothing
# Privates
setGeneric(".getProteins",
function(object) {
standardGeneric(".getProteins")
}
)
setGeneric(".getTaxId",
function(object,...) {
standardGeneric(".getTaxId")
}
)
setGeneric(".getTaxName",
function(object,...) {
standardGeneric(".getTaxName")
}
)
setGeneric(".getInteractions",
function(object,...) {
standardGeneric(".getInteractions")
}
)
setGeneric(".getReferenceInteractions",
function(object,...) {
standardGeneric(".getReferenceInteractions")
}
)
setGeneric(".addReferenceSpecies",
function(object,taxName,taxId,proteins,irefindex.file) {
standardGeneric(".addReferenceSpecies")
}
)
setGeneric(".removeReferenceSpecies",
function(object,species) {
standardGeneric(".removeReferenceSpecies")
}
)
setGeneric(".getAllTaxIds",
function(object) {
standardGeneric(".getAllTaxIds")
}
)
setGeneric(".getReferenceSpecies",
function(object,species,info=FALSE,detailed=FALSE) {
standardGeneric(".getReferenceSpecies")
}
)
setGeneric(".getSourceDBs",
function(object, irefindex) {
standardGeneric(".getSourceDBs")
}
)
setGeneric(".countSpecies",
function(object) {
standardGeneric(".countSpecies")
}
)
setGeneric(".getHomologs",
function(object,taxId,...) {
standardGeneric(".getHomologs")
}
)
setGeneric(".addHomologs",
function(object,taxId,homologs) {
standardGeneric(".addHomologs")
}
)
setGeneric(".removeHomologs",
function(object,species) {
standardGeneric(".removeHomologs")
}
)
# Publics
setGeneric("addReference",
function(path2ppi,taxName,taxId,proteins,irefindex, homologs) {
standardGeneric("addReference")
}
)
setGeneric("showReferences",
function(path2ppi,species=NA,returnValue=NA) {
standardGeneric("showReferences")
}
)
setGeneric("plot.Path2PPI",
function (x,type="ppi",multiple.edges=FALSE,scores=FALSE,
species.colors=c(),vertices.opacity=0.8,
use.identifiers=FALSE,protein.labels=NA,show.legend=TRUE,
vertices.coordinates=NA,return.coordinates=FALSE,
tkplot=FALSE,...) {
standardGeneric("plot.Path2PPI")
}
)
setGeneric("getHybridNetwork",
function(path2ppi, igraph=FALSE) {
standardGeneric("getHybridNetwork")
}
)
setGeneric("getPPI",
function(path2ppi, raw=FALSE, igraph=FALSE) {
standardGeneric("getPPI")
}
)
setGeneric("showInteraction",
function(path2ppi,interaction, mode="default", verbose=TRUE) {
standardGeneric("showInteraction")
}
)
setGeneric("predictPPI",
function(path2ppi,mode="both",h.thresh=1e-5,h.range=c(1e-100,1e-20),
i.thresh=0.7,consider.complexes=FALSE,max.complex.size=5,
decline.self.interaction.ref=FALSE,
decline.self.interaction.tar=TRUE,verbose=TRUE) {
standardGeneric("predictPPI")
}
)
setGeneric("removeReference",
function(path2ppi,species) {
standardGeneric("removeReference")
}
)
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