import(methods)
import(fdrtool)
import(MeSH.db)
import(MeSH.AOR.db)
import(MeSH.PCR.db)
import(MeSHDbi)
import(MeSH.Hsa.eg.db)
import(MeSH.Aca.eg.db)
import(MeSH.Bsu.168.eg.db)
import(MeSH.Syn.eg.db)
import(cummeRbund)
import(org.Hs.eg.db)
import(Category)
import(S4Vectors)

importFrom(RSQLite, dbGetQuery)
importFrom(stats, p.adjust)
importFrom(utils, data, download.file, read.delim, setTxtProgressBar, txtProgressBar)
importFrom(BiocGenerics, annotation, "annotation<-")

exportClasses(MeSHHyperGParams, MeSHHyperGResult)

exportMethods(## Results
              "meshHyperGTest",
              "meshIds",
              "meshCategory",
              "meshAnnotation",
              "meshDatabase",
              "show",
              "summary",
              "save.pdf",

              ## Params
              "initialize",
              "geneIds",
              "universeGeneIds",
              "universeGeneIds<-",
              "annotation",
              "annotation<-",
              category,
              "category<-",
              database,
              "database<-",
              "pvalueCutoff",
              "pvalueCutoff<-",
              "pAdjust",
              "pAdjust<-",
              "makeValidParams")
