Documentation

Captures a complete alignment

Constructors

Fields

vhTarget :: (Int, Int): part of target sequence (start counting at 1)
vhQuery :: (Int, Int): which part of the CM/stk do we align to
vhCM :: ByteString: the CM for this alignment
vhStrand :: Strand: should be either + or -
vhScore :: Double: bit score
vhEvalue :: Double: number of hits we expect to find with score or higher for targetSequence length
vhPvalue :: Double: ?
vhGC :: Int: ?
vhScaffold :: ByteString: scaffold, chromosome, ... (the name of the sequence, not the sequence data!)
vhWuss :: ByteString: fancy secondary structure annotation using wuss notation
vhConsensus :: ByteString: query consensus (upper: highly, lower: weak/no)
vhScoring :: ByteString: represents where positive and negative scores come from
vhSequence :: ByteString: the target sequence which aligns to the model
vhAnnotation :: [ByteString]: any annotations that could be associated (# lines)

Instances

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