Documentation

Captures a complete alignment

Constructors

Fields

vhTargetStart :: !Int: part of target sequence (start counting at 1)
vhTargetStop :: !Int
vhModelStart :: !Int: which part of the CM/stk do we align to
vhModelStop :: !Int: which part of the CM/stk do we align to
vhModel :: !ModelIdentification: the CM for this alignment
vhStrand :: !Strand: should be either + or -
vhBitScore :: !BitScore: bit score
vhEvalue :: !Double: number of hits we expect to find with score or higher for targetSequence length
vhPvalue :: !Double: ?
vhGCpercent :: !Int: ?
vhTarget :: !Scaffold: 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