1 {- |
    2    This is a meta-module importing and re-exporting sequence-related stuff.
    3 
    4    It encompasses the "Bio.Sequence.SeqData", "Bio.Sequence.Fasta", and "Bio.Sequence.TwoBit" modules.
    5 -}
    6 
    7 module Bio.Sequence 
    8     (
    9     -- * Data structures etc ("Bio.Sequence.SeqData")
   10       Sequence(..), Offset, SeqData, Qual, QualData
   11     -- ** Accessor functions
   12     , seqlength, seqlabel, seqheader, seqdata, seqqual, (!)
   13     , appendHeader, setHeader
   14 
   15     -- ** Converting to and from String.
   16     , fromStr, toStr
   17     -- ** Nucleotide functionality.
   18     , compl, revcompl
   19     -- ** Protein sequence functionality
   20     , Amino(..), translate, fromIUPAC, toIUPAC
   21 
   22     -- * File formats
   23     -- ** The Fasta file format ("Bio.Sequence.Fasta")
   24     , readFasta, hReadFasta 
   25     , writeFasta, hWriteFasta
   26     -- ** Quality data 
   27     -- | Not part of the Fasta format, and treated separately.
   28     , readQual, writeQual, hWriteQual
   29     , readFastaQual
   30     , writeFastaQual, hWriteFastaQual
   31 
   32     -- ** The phd file format ("Bio.Sequence.Phd")
   33     -- | These contain base (nucleotide) calling information,
   34     --   and are generated by @phred@.
   35     , readPhd, hReadPhd
   36 
   37     -- ** TwoBit file format support ("Bio.Seqeunce.TwoBit")
   38     -- | Used by @BLAT@ and related tools.
   39     , decode2Bit, read2Bit, hRead2Bit 
   40     -- ,encode2Bit, write2Bit, hWrite2Bit
   41 
   42     -- * Hashing functionality ("Bio.Sequence.HashWord")
   43     -- | Packing words from sequences into integral data types 
   44     , HashF (..)
   45     , contigous, rcontig, rcpacked
   46 
   47     -- * Entropy calculations
   48     , KWords(..), entropy
   49     ) where
   50 
   51 -- basic sequence data structures
   52 import Bio.Sequence.SeqData
   53 
   54 -- file formats
   55 import Bio.Sequence.Fasta
   56 import Bio.Sequence.Phd
   57 import Bio.Sequence.TwoBit
   58 
   59 -- sequence-oriented stuff
   60 import Bio.Sequence.Entropy
   61 import Bio.Sequence.HashWord