NAMESPACE

import(methods)
importFrom(utils, download.file, packageDescription, read.table, browseURL,
                  as.person, capture.output, str)
importFrom(stats, setNames)
importFrom(tools, file_ext, file_path_sans_ext)

importFrom(httr, GET, content)
importFrom(rjson, fromJSON)
importMethodsFrom(DBI, dbConnect, dbDisconnect,
                       dbExecute, dbGetQuery,
                       dbReadTable, dbWriteTable)
importFrom(RSQLite, SQLite)

import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(UCSC.utils)
import(GenomeInfoDb)
import(AnnotationDbi)
import(GenomicRanges)
import(GenomicFeatures)

importFrom(Biobase, createPackage)
importClassesFrom(BiocIO, BiocFile, CompressedFile)
importFrom(BiocIO, import, FileForFormat)

## rtracklayer only used in R/makeFeatureDbFromUCSC.R
importFrom(rtracklayer, browserSession, trackNames, ucscTables,
                        ucscTableQuery, getTable, ucscSchema)
importFrom(biomaRt, getBM, listAttributes, listDatasets, listFilters,
                    listMarts, useDataset, useEnsembl, useEnsemblGenomes)

export(
  ## makeTxDb.R:
  makeTxDb,

  ## makeTxDbFromUCSC.R:
  supportedUCSCtables,
  browseUCSCtrack,
  makeTxDbFromUCSC,

  ## makeTxDbFromBiomart.R:
  getChromInfoFromBiomart,
  makeTxDbFromBiomart,

  ## makeTxDbFromEnsembl.R:
  makeTxDbFromEnsembl,

  ## makeTxDbFromGRanges.R:
  makeTxDbFromGRanges,

  ## makeTxDbFromGFF.R:
  makeTxDbFromGFF,

  ## makeFeatureDbFromUCSC.R:
  supportedUCSCFeatureDbTracks,
  supportedUCSCFeatureDbTables,
  UCSCFeatureDbTableSchema,
  makeFeatureDbFromUCSC,

  ## makeTxDbPackage.R:
  makePackageName,
  makeTxDbPackage,
  makeTxDbPackageFromUCSC,
  makeTxDbPackageFromBiomart,
  makeFDbPackageFromUCSC,
  supportedMiRBaseBuildValues
)