import(tools)
import(methods)
import(stats)
import(utils)

importClassesFrom(graph, graphNEL, renderInfo)
importMethodsFrom(graph, acc, adj, nodes, "nodes<-", edges)
importFrom(graph, reverseEdgeDirections, subGraph, addEdge, nodeRenderInfo, "nodeRenderInfo<-", edgeRenderInfo, "edgeRenderInfo<-")
importFrom(RBGL, transitive.closure, sp.between)
importFrom(annotate, lookUp, getSYMBOL)
importFrom(Rgraphviz, layoutGraph, renderGraph)


exportClasses("GeneAnswers")
exportMethods("getGeneInput", "getTestType", "getPValueT", "getGenesInCategory", "getGeneExprProfile", "getAnnLib", "getCategoryType", "getEnrichmentInfo", "setGeneInput", "setTestType", "setPValueT", "setGeneExprProfile", "setAnnLib", "setCategoryType", "setGenesInCategory", "setEnrichmentInfo")

export("categoryNet", "chartPlots", "drawTable", "geneAnnotationHeatmap", "geneAnswersBuilder", "geneAnswersChartPlots", "geneAnswersConceptNet", "geneAnswersConcepts", "geneAnswersHeatmap", "geneAnswersHomoMapping", "geneAnswersReadable", "geneAnswersSort", "geneConceptNet", "getCategoryList", "getCategoryTerms", "getConceptTable", "getDOLiteTerms", "getGOList", "getHomoGeneIDs", "getPATHList", "getPATHTerms", "getSymbols", "groupReport", "searchEntrez", "topCategory", "topCategoryGenes", "topDOLITE", "topDOLITEGenes", "topGO", "topGOGenes", "topPATH", "topPATHGenes", "topREACTOME.PATH", "topREACTOME.PATHGenes", "topcaBIO.PATH", "topcaBIO.PATHGenes", "geneAnswersConceptRelation", "getConnectedGraph", "getMultiLayerGraphIDs", "getSingleLayerGraphIDs", "getNextGOIDs", "buildNet", "getTotalGeneNumber", "getREACTOMEPATHList", "getREACTOMEPATHTerms", "getcaBIOPATHList", "getcaBIOPATHTerms", "entrez2caBIO", "caBIO2entrez", geneFunSummarize, plotGeneFunSummary, plotGraph, plotOntologyGraph, saveGeneFunSummary, simplifyGeneFunSummary)

