import(methods)
importFrom(utils, download.file, installed.packages, read.table)

importMethodsFrom(DBI, dbCommit, dbConnect,
                  dbDisconnect, dbExistsTable, dbGetQuery,
                  dbReadTable, dbWriteTable)

importFrom(RSQLite, SQLite, sqliteCopyDatabase, SQLITE_RO)
importMethodsFrom(RSQLite, dbBeginTransaction, dbGetPreparedQuery)

import(IRanges)

importFrom(GenomicRanges, GRanges)
importMethodsFrom(GenomicRanges, seqlengths, seqnames, strand)

importFrom(Biostrings, DNAStringSet, extractTranscripts)
importMethodsFrom(Biostrings, "masks<-")

importFrom(biomaRt, getBM, listAttributes, listDatasets, listMarts,
           useDataset, useMart)

importFrom(rtracklayer, browserSession, genome, "genome<-", ucscTableQuery,
           tableNames, getTable)

importFrom(RCurl, getURL)

exportClasses(GenomicFeatures, TranscriptDb)

export(
  transcripts_deprecated,
  exons_deprecated,
  introns_deprecated,
  extractTranscriptsFromGenome,
  makeTranscriptDb,
  supportedUCSCtables,
  makeTranscriptDbFromUCSC,
  makeTranscriptDbFromBiomart,
  saveFeatures,
  loadFeatures,
  as.list,
  transcripts,
  exons,
  cds,
  transcriptsByOverlaps,
  exonsByOverlaps,
  cdsByOverlaps,
  id2name,
  transcriptsBy,
  exonsBy,
  cdsBy,
  intronsByTranscript,
  fiveUTRsByTranscript,
  threeUTRsByTranscript
)

exportMethods(
  seqnames,
  seqlengths,
  show,
  as.list
)
