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+library(KEGGgraph)

+library(graph)

+library(Rgraphviz)

+

+## If edges of a node is not explicitly specified in a directed graph (i.e. the node "D" in the graph object 'test' in the following example),

+## its incoming edges will be interpreted as reciprocal edges ( hence inEdges(test)[["B"]]==c("A","D") )

+test.nodes <- LETTERS[1:4];

+test.edges <- list(A=c("B","C"), B=c("C","D"), C=c("A","D"));

+test <- new("graphNEL", nodes=test.nodes, edgeL=test.edges, edgemode="directed");

+stopifnot(is.null(adj(test, "D")[[1]]))

+stopifnot(inEdges(test)[["B"]]==c("A","D"))

+

+## so if we don't want the side effect above, we have to specify the edges of a no-out-edge node to c() or NULL

+test.edges2 <- list(A=c("B","C"), B=c("C","D"), C=c("A","D"), D=NULL);

+test2 <- new("graphNEL", nodes=test.nodes, edgeL=test.edges2, edgemode="directed");

+inEdges(test2)

+stopifnot(adj(test2, "C")[["C"]] == adj(test, "C")[["C"]])

+stopifnot(length(adj(test2,"D")[["D"]]) == 0)

+stopifnot(inEdges(test2)[["B"]]=="A")

+

+## DO NOT RUN -- it leads to segfault

+# plot(test)

+## test2 without problem

+plot(test2)

+

+## question: a bug or intended so?

+

+##----------------------------------------##

+## all edges set to NULL -- disabled!

+##----------------------------------------##

+test.edge3 <- list(A=NULL, B=NULL, C=NULL, D=NULL)

+tryres <- try(test3 <- new("graphNEL", nodes=test.nodes, edgeL=test.edge3, edgemode="directed"))

+

+test.edge4 <- list(A=list(),  B=NULL, C=NULL, D=NULL)

+test4 <- new("graphNEL", nodes=test.nodes, edgeL=test.edge4, edgemode="directed")

+adj(test4, "A")

+inEdges(test4)

+

+test.edge5 <- list(A=c("B","C"),  B=c("A","C"), C=character(0), D=character(0))

+test5 <- new("graphNEL", nodes=test.nodes, edgeL=test.edge5, edgemode="directed")

+adj(test5, "B")

+inEdges(test5)

+

+##----------------------------------------##

+## edges must be unique, otherwise an implicit bug will apper

+##----------------------------------------##

+test.edge6 <- list(A=c("B","B","C"), B=c("A","C"),C=character(0), D=c("A"))

+test6 <- new("graphNEL", nodes=test.nodes, edgeL=test.edge6, edgemode="directed")

+tryerr <- try(randomSubGraph(test6))

+

+##----------------------------------------##

+## test known well-formed graph

+##----------------------------------------##

+#allpackages <- .packages(all=TRUE)

+#if("keggorthology" %in% allpackages) {

+#  library(keggorthology)

+#  data(KOgraph)

+#  randomSubGraph(KOgraph)

+#}