import(Category)
import(graph)

importClassesFrom(methods,
                  ANY,
                  character,
                  integer,
                  logical,
                  numeric)

importMethodsFrom(AnnotationDbi,
                  Term,
                  eapply,
                  ls,
                  mget,
                  nrow,
                  revmap)

importMethodsFrom(Biobase,
                  annotation,
                  exprs,
                  featureNames)

importFrom(AnnotationDbi,
           make_eg_to_go_map)

importFrom(AnnotationForge,
           available.dbschemas)
importFrom(Biobase,
           addVigs2WinMenu,
           subListExtract)

importFrom(RBGL,
           connectedComp,
           dijkstra.sp,
           sp.between)

importFrom(annotate,
           dropECode,
           getAnnMap,
           getOntology)

importFrom(methods,
           callNextMethod,
           is,
           new)

importFrom(stats,
           cor)

importFrom(GO.db,
           GOTERM)

export(compCorrGraph, compGdist,
       enumPairs, 
       GOGraph,
       idx2dimnames, isTriad,
       makeGOGraph, notConn, oneGOGraph,
       reduce2Degreek, shortestPath, simLL,
       simLP, simUI, triadCensus,
       probeSetSummary)

exportClasses(GOHyperGResult)

exportMethods("hyperGTest",
              "pvalues",
              "description",
              "oddsRatios",
              "expectedCounts",
              "htmlReport",
              "goDag",
              "geneCounts",
              "universeCounts",
              "geneIds",
              "geneIdUniverse",
              "universeMappedCount",
              "geneMappedCount",
              "annotation",
              "testName",
              "summary")

export(termGraphs, 
       inducedTermGraph, 
       plotGOTermGraph)
