Safe Haskell | Safe-Inferred |
---|---|
Language | Haskell2010 |
Synopsis
- newtype EditDistance e1 e2 = EditDistance (e1 -> e2 -> Bool)
- data GlobalAlignment a e1 e2 = GlobalAlignment (Scoring e1 e2) a
- data LocalAlignment a e1 e2 = LocalAlignment (Scoring e1 e2) a
- data SemiglobalAlignment a e1 e2 = SemiglobalAlignment (Scoring e1 e2) a
- substitute :: (Alignable m, Alignable m') => (IxValue m -> IxValue m' -> Int) -> m -> m' -> Index m -> Index m' -> Int
- substituteED :: EditDistance e1 e2 -> e1 -> e2 -> Int
- defStop :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> Index m -> Index m' -> Bool
- localStop :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> Index m -> Index m' -> Bool
- move :: (Alignable m, Alignable m', IsGap g) => g -> Move m m'
- moveSimple :: (Alignable m, Alignable m', IsGap g) => g -> Move m m'
- moveAffine :: (Alignable m, Alignable m', IsGap g) => g -> Move m m'
- defDiag :: (Alignable m, Alignable m') => (IxValue m -> IxValue m' -> Int) -> Matrix m m' -> m -> m' -> Index m -> Index m' -> Bool
- defStart :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> (Index m, Index m')
- localStart :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> (Index m, Index m')
- semiStart :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> (Index m, Index m')
- fillInnerMatrix :: (IsGap g, Ix ix, Ix ix', Enum ix, Enum ix') => g -> STUArray s (ix, ix', EditOp) Int -> Bool -> (ix -> ix' -> Int) -> ix -> ix' -> ST s ()
Documentation
newtype EditDistance e1 e2 Source #
EditDistance (e1 -> e2 -> Bool) |
data GlobalAlignment a e1 e2 Source #
GlobalAlignment (Scoring e1 e2) a |
Instances
IsGap g => SequenceAlignment (GlobalAlignment g) Source # | |
Defined in Bio.Chain.Alignment.Algorithms semi :: GlobalAlignment g e1 e2 -> Bool Source # cond :: (Alignable m, Alignable m') => GlobalAlignment g (IxValue m) (IxValue m') -> Conditions m m' Source # traceStart :: (Alignable m, Alignable m') => GlobalAlignment g (IxValue m) (IxValue m') -> Matrix m m' -> m -> m' -> (Index m, Index m') Source # scoreMatrix :: (Alignable m, Alignable m') => GlobalAlignment g (IxValue m) (IxValue m') -> m -> m' -> Matrix m m' Source # |
data LocalAlignment a e1 e2 Source #
LocalAlignment (Scoring e1 e2) a |
Instances
IsGap g => SequenceAlignment (LocalAlignment g) Source # | |
Defined in Bio.Chain.Alignment.Algorithms semi :: LocalAlignment g e1 e2 -> Bool Source # cond :: (Alignable m, Alignable m') => LocalAlignment g (IxValue m) (IxValue m') -> Conditions m m' Source # traceStart :: (Alignable m, Alignable m') => LocalAlignment g (IxValue m) (IxValue m') -> Matrix m m' -> m -> m' -> (Index m, Index m') Source # scoreMatrix :: (Alignable m, Alignable m') => LocalAlignment g (IxValue m) (IxValue m') -> m -> m' -> Matrix m m' Source # |
data SemiglobalAlignment a e1 e2 Source #
SemiglobalAlignment (Scoring e1 e2) a |
Instances
IsGap g => SequenceAlignment (SemiglobalAlignment g) Source # | |
Defined in Bio.Chain.Alignment.Algorithms semi :: SemiglobalAlignment g e1 e2 -> Bool Source # cond :: (Alignable m, Alignable m') => SemiglobalAlignment g (IxValue m) (IxValue m') -> Conditions m m' Source # traceStart :: (Alignable m, Alignable m') => SemiglobalAlignment g (IxValue m) (IxValue m') -> Matrix m m' -> m -> m' -> (Index m, Index m') Source # scoreMatrix :: (Alignable m, Alignable m') => SemiglobalAlignment g (IxValue m) (IxValue m') -> m -> m' -> Matrix m m' Source # |
substitute :: (Alignable m, Alignable m') => (IxValue m -> IxValue m' -> Int) -> m -> m' -> Index m -> Index m' -> Int Source #
Lift simple substitution function to a ChainLike collection
substituteED :: EditDistance e1 e2 -> e1 -> e2 -> Int Source #
Simple substitution function for edit distance
defStop :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> Index m -> Index m' -> Bool Source #
Default traceback stop condition.
localStop :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> Index m -> Index m' -> Bool Source #
Traceback stop condition for the local alignment.
moveAffine :: (Alignable m, Alignable m', IsGap g) => g -> Move m m' Source #
Move function for affine alignment traceback. Implements a "Manhattan grid".
See here: http://www.csbio.unc.edu/mcmillan/Comp555S16/Lecture14.html
or file doc/Affine_Alignment.pdf
in the repository.
defDiag :: (Alignable m, Alignable m') => (IxValue m -> IxValue m' -> Int) -> Matrix m m' -> m -> m' -> Index m -> Index m' -> Bool Source #
Default condition of moving diagonally in traceback.
defStart :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> (Index m, Index m') Source #
Default start condition for traceback.
localStart :: (Alignable m, Alignable m') => Matrix m m' -> m -> m' -> (Index m, Index m') Source #
Default start condition for traceback in local alignment.