###
### NAMESPACE
###

importFrom("XML",
           "getNodeSet", "xmlGetAttr", "xmlNamespace",
           "xmlParseDoc", "xmlRoot", "xmlParent")
importFrom("igraph",
           "E", "V", "all_simple_paths",
           "get.edge.ids", "graph_from_data_frame",
           "neighbors", "subgraph", "set_graph_attr",
           "as_graphnel", "as_ids", "edge_attr",
           "graph_attr", "vertex_attr")
importFrom("KEGGREST", "keggGet",  "keggList")
importFrom("graphics", "legend", "polygon")
importFrom("utils", "head")
importFrom("AnnotationDbi", "select")                # Annotate KEGG genes
importFrom("org.Hs.eg.db", "org.Hs.eg.db")           # Annotate KEGG genes
importFrom("DescTools", "DrawEllipse")
importFrom("Rgraphviz", "agopen", "edgeNames")


#exportMethods("plot")

## Functions that perform steps in the process to build the final
## igraph object from WikiPAthways GPML files.
export("collectEdges", "collectNodes", "collectGroups",
       "collectAnchors", "collectLabels", "collectShapes")

## Functions that perform steps in the process to build the final
## igraph object from KEGG KGML files.
export("collectEntries", "collectRelations", "collectReactions")

## graph and cycle functions
export("GPMLtoIgraph", "nodeLegend", "edgeLegend")
export("findCycles", "interpretCycle", "cycleSubgraph")

export("as.graphNEL")
export("KGMLtoIgraph")
## objects for primary plotting routines
#exportClasses("Cycle")


