NAMESPACE

import(methods)

importClassesFrom(graph, graph)

importFrom(utils,"download.file") 
importFrom(XML,
           "xmlAttrs", "xmlChildren", "xmlName",
           "xmlRoot", "xmlTreeParse", "xmlErrorCumulator")
importFrom("graphics", "par", "segments", "text")
importFrom("utils", "data")

importMethodsFrom(graph, ugraph)
importFrom(graph, "edges", "nodes<-", "nodes", "edgeData","nodeData",
           nodeDataDefaults, edgeDataDefaults,
           "nodeDataDefaults<-", "edgeDataDefaults<-",
           numEdges, numNodes, plot, subGraph, inEdges,
           addNode, ftM2graphNEL,
           "nodeRenderInfo<-", "edgeRenderInfo<-")
importFrom(RCurl, url.exists)
importFrom("Rgraphviz", "layoutGraph", "renderGraph")

## exports

export(subGraph,
       nodes, edges,
       edgeData, nodeData,
       ugraph, numEdges, numNodes, plot, subGraph,
       inEdges,
       "nodes<-")
       
exportMethods("getDisplayName",
              "getEntryID",
              "getKEGGID",
              "getKEGGgeneLink",
              "getType",
              "getName",
              "getSubtype",
              "getValue",
              "getTitle",
              "getComponent",
              "getPathwayInfo",
              "getReactions",
              "getKEGGgeneLink",
              "subtypeDisplay",
              "getSubstrate",
              "getProduct",
              "show")

export(translateKEGGID2GeneID,
       translateGeneID2KEGGID,
       translateKEGGgraph)

export(graphDensity,
       mergeGraphs,
       mergeKEGGgraphs,
       randomSubGraph,
       subKEGGgraph,
       subGraphByNodeType,
       getRgraphvizEdgeNames,
       getKEGGnodeData,
       getKEGGedgeData,
       neighborhood,
       queryKEGGsubgraph)

export(getKGMLurl,
       retrieveKGML,
       kgmlFileName2PathwayName,
       parseKGML,
       KEGGpathway2Graph,
       parseKGML2Graph,
       KEGGpathway2reactionGraph,
       parseKGML2DataFrame,
       parseKGMLexpandMaps,
       splitKEGGgroup,
       expandKEGGPathway)

export(parsePathwayInfo,
       parseEntry,
       parseRelation,
       parseReaction,
       getEntryID)

export(pvalue2asterisk,
       getNamedElement,
       isHomoList,
       plotKEGGgraph,
       KEGGgraphLegend)

exportClasses("KEGGEdge",
              "KEGGGroup",
              "KEGGNode",
              "KEGGPathwayInfo",
              "KEGGReaction",
              "KEGGEdgeSubType",
              "KEGGGraphics",
              "KEGGPathway",
              "KEGGPathwayInfo")

##export("KEGGEdgeSubtype")