useDynLib(DECIPHER)

import(methods)
import(S4Vectors)
import(IRanges)
import(XVector)
import(Biostrings)
import(RSQLite)
import(DBI)
import(parallel)

export(
# interacting with a database:
Add2DB, Seqs2DB, SearchDB, DB2Seqs,
# assigning an identifier:
FormGroups, IdentifyByRank,
# lengths:
IdLengths, TerminalChar,
# grouping sequences:
DistanceMatrix, IdClusters, MODELS,
# forming consensus:
ConsensusSequence, Disambiguate, IdConsensus, TileSeqs,
# chimeras:
FindChimeras, CreateChimeras,
# microarrays:
DesignArray, Array2Matrix, NNLS, CalculateEfficiencyArray,
# primers:
Amplify, AmplifyDNA, CalculateEfficiencyPCR, DesignPrimers, DesignSignatures, DigestDNA, MeltDNA,
# probes:
CalculateEfficiencyFISH, DesignProbes,
# viewing information:
BrowseSequences, BrowseSeqs, BrowseDB,
# multiple alignment
AdjustAlignment, AlignDB, AlignProfiles, AlignSeqs, AlignTranslation, MaskAlignment, PredictHEC, StaggerAlignment
)