importFrom("graph", ftM2graphNEL)
importMethodsFrom("graph", edges, nodes, subGraph, edgeNames)
importMethodsFrom("RBGL", bfs)
importFrom(AnnotationDbi, columns, keys, keytypes, select, metadata, dbconn, dbfile)
#importFrom(AnnotationDbi, cols)
importFrom("GenomicFeatures",
           transcripts,
           exons,
           cds,
           genes,
           transcriptsBy,
           exonsBy,
           cdsBy,
           seqinfo,  ## Import this from GenomicFeatures b/c we need txdb vers.

           ## Below are methods that we are 'just wrapping' from TxDbs
           ## transcriptsByOverlaps,
           ## exonsByOverlaps,
           ## cdsByOverlaps,
           promoters,
           disjointExons,
           microRNAs,
           tRNAs,
           intronsByTranscript,
           fiveUTRsByTranscript,
           threeUTRsByTranscript,
           extractUpstreamSeqs,
           isActiveSeq ,
           "isActiveSeq<-",
           asBED, asGFF,
           distance,
           mapToTranscripts
           )
importFrom("stats", setNames)

importClassesFrom("graph", graphNEL)
exportClasses("OrganismDb")
exportMethods("columns",
              "keys",
              "keytypes",
              "select",
              "transcripts",
              "exons",
              "cds",
              "genes",
              "transcriptsBy",
              "exonsBy",
              "cdsBy",
              "dbconn",
              "dbfile",
              "metadata",
              seqinfo,
              getTxDbIfAvailable,

              ## Below are methods that we are 'just wrapping' from TxDbs
              ## transcriptsByOverlaps,
              ## exonsByOverlaps,
              ## cdsByOverlaps,
              promoters,
              disjointExons,
              microRNAs,
              tRNAs,
              intronsByTranscript,
              fiveUTRsByTranscript,
              threeUTRsByTranscript,
              extractUpstreamSeqs,
              isActiveSeq ,
              "isActiveSeq<-",
              asBED, asGFF,
              distance,
              mapToTranscripts
              )
export(getTxDbIfAvailable,  ## b/c the generic is here
       "makeOrganismPackage")



## checkUsagePackage("OrganismDbi",all=TRUE)
