@@ -1,6 +1,6 @@

 Package: annotate

 Title: Annotation for microarrays

-Version: 1.65.0

+Version: 1.65.1

 Author: R. Gentleman

 Description: Using R enviroments for annotation.

 Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>

@@ -87,25 +87,23 @@ hasGOannote <- function(x, which="MF") {

      if(length(x) == 0 )

          return(list())

      loadNamespace("GO.db")

-     hasMF <- mget(x, envir=GO.db::GOMFPARENTS, ifnotfound=NA)

-     hasBP <- mget(x, envir=GO.db::GOBPPARENTS, ifnotfound=NA)

-     hasCC <- mget(x, envir=GO.db::GOCCPARENTS, ifnotfound=NA)

-     lenx <- length(x)

-     rval <- vector("list", length=lenx)

-     names(rval) <- x

-     rval <- vector("list", length=lenx)

-     names(rval) <- x

-     for(i in 1:lenx) {

-         if( (length(hasMF[[i]]) > 1 ) || !is.na(hasMF[[i]]) )

-             rval[[i]] <- list(Ontology="MF", Parents=hasMF[[i]])

-         else if( (length(hasMF[[i]]) > 1 ) || !is.na(hasBP[[i]]) )

-             rval[[i]] <- list(Ontology="BP", Parents=hasBP[[i]])

-         else if( (length(hasMF[[i]]) > 1 ) || !is.na(hasCC[[i]]) )

-             rval[[i]] <- list(Ontology="CC", Parents=hasCC[[i]])

-         else

-             stop(paste(x[i], "is not a member of any ontology"))

-     }

-     return(rval)

+     MF_parents <- mget(x, envir=GO.db::GOMFPARENTS, ifnotfound=NA)

+     BP_parents <- mget(x, envir=GO.db::GOBPPARENTS, ifnotfound=NA)

+     CC_parents <- mget(x, envir=GO.db::GOCCPARENTS, ifnotfound=NA)

+     lapply(setNames(seq_along(x), x),

+         function(i) {

+             xi_parents <- MF_parents[[i]]

+             if (!identical(xi_parents, NA))

+                 return(list(Ontology="MF", Parents=xi_parents))

+             xi_parents <- BP_parents[[i]]

+             if (!identical(xi_parents, NA))

+                 return(list(Ontology="BP", Parents=xi_parents))

+             xi_parents <- CC_parents[[i]]

+             if (!identical(xi_parents, NA))

+                 return(list(Ontology="CC", Parents=xi_parents))

+             stop(paste(x[[i]], "is not a member of any ontology"))

+         }

+     )

  }

  getGOChildren <- function(x) {

@@ -114,23 +112,23 @@ hasGOannote <- function(x, which="MF") {

      if(length(x) == 0 )

          return(list())

      loadNamespace("GO.db")

-     hasMF <- mget(x, envir=GO.db::GOMFCHILDREN, ifnotfound=NA)

-     hasBP <- mget(x, envir=GO.db::GOBPCHILDREN, ifnotfound=NA)

-     hasCC <- mget(x, envir=GO.db::GOCCCHILDREN, ifnotfound=NA)

-     lenx <- length(x)

-     rval <- vector("list", length=lenx)

-     names(rval) <- x

-     for(i in 1:lenx) {

-         if( (length(hasMF[[i]]) > 1 ) || !is.na(hasMF[[i]]) )

-             rval[[i]] <- list(Ontology="MF", Children=hasMF[[i]])

-         else if( (length(hasMF[[i]]) > 1 ) || !is.na(hasBP[[i]]) )

-             rval[[i]] <- list(Ontology="BP", Children=hasBP[[i]])

-         else if( (length(hasMF[[i]]) > 1 ) || !is.na(hasCC[[i]]) )

-             rval[[i]] <- list(Ontology="CC", Children=hasCC[[i]])

-         else

-             rval[[i]] <- list()

-     }

-     return(rval)

+     MF_children <- mget(x, envir=GO.db::GOMFCHILDREN, ifnotfound=NA)

+     BP_children <- mget(x, envir=GO.db::GOBPCHILDREN, ifnotfound=NA)

+     CC_children <- mget(x, envir=GO.db::GOCCCHILDREN, ifnotfound=NA)

+     lapply(setNames(seq_along(x), x),

+         function(i) {

+             xi_children <- MF_children[[i]]

+             if (!identical(xi_children, NA))

+                 return(list(Ontology="MF", Children=xi_children))

+             xi_children <- BP_children[[i]]

+             if (!identical(xi_children, NA))

+                 return(list(Ontology="BP", Children=xi_children))

+             xi_children <- CC_children[[i]]

+             if (!identical(xi_children, NA))

+                 return(list(Ontology="CC", Children=xi_children))

+             list()  # not an error (unlike for getGOParents() above)

+         }

+     )

  }

  getGOTerm <- function(x) {