Bio.Chain.Alignment.Type

Documentation

type Scoring a b = a -> b -> Int

Scoring function, returns substitution score for a couple of elements

type Scoring = Char -> Char -> Int

type SimpleGap = Int

Simple gap penalty

type SimpleGap2 = (SimpleGap, SimpleGap)

Gap penalty with different SimpleGap penalties for sequences.

First element of pair is penalty for first sequence passed to alignment algorithm, second element — penalty for second passed sequence.

data AffineGap

Affine gap penalty

Constructors

AffineGap

Fields

• gapOpen :: Int
• gapExtend :: Int

Instances

Generic AffineGap

Defined in Bio.Chain.Alignment.Type

Associated Types

type Rep AffineGap :: Type -> Type

Methods

from :: AffineGap -> Rep AffineGap x

to :: Rep AffineGap x -> AffineGap

Show AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

showsPrec :: Int -> AffineGap -> ShowS

show :: AffineGap -> String

showList :: [AffineGap] -> ShowS

IsGap AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: AffineGap -> Int

insertCostExtend :: AffineGap -> Int

deleteCostOpen :: AffineGap -> Int

deleteCostExtend :: AffineGap -> Int

isAffine :: AffineGap -> Bool

IsGap AffineGap2

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: AffineGap2 -> Int

insertCostExtend :: AffineGap2 -> Int

deleteCostOpen :: AffineGap2 -> Int

deleteCostExtend :: AffineGap2 -> Int

isAffine :: AffineGap2 -> Bool

NFData AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

rnf :: AffineGap -> ()

Eq AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

(==) :: AffineGap -> AffineGap -> Bool

(/=) :: AffineGap -> AffineGap -> Bool

type Rep AffineGap

Defined in Bio.Chain.Alignment.Type

type Rep AffineGap = D1 ('MetaData "AffineGap" "Bio.Chain.Alignment.Type" "cobot-0.1.1.8-Giff50E8qZ73qQvm66bZ3u" 'False) (C1 ('MetaCons "AffineGap" 'PrefixI 'True) (S1 ('MetaSel ('Just "gapOpen") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: S1 ('MetaSel ('Just "gapExtend") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)))

type AffineGap2 = (AffineGap, AffineGap)

Gap penalty with different AffineGap penalties for sequences.

First element of pair is penalty for first sequence passed to alignment algorithm, second element — penalty for second passed sequence.

class IsGap a where

Type class that describes possible gaps in alignments.

Minimal complete definition

insertCostOpen, insertCostExtend, deleteCostOpen, deleteCostExtend

Methods

insertCostOpen :: a -> Int

Insertions are gaps in the first argument of an alignment function.

insertCostExtend :: a -> Int

deleteCostOpen :: a -> Int

Deletions are gaps in the second argument of an alignment function.

deleteCostExtend :: a -> Int

isAffine :: a -> Bool

Instances

IsGap AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: AffineGap -> Int

insertCostExtend :: AffineGap -> Int

deleteCostOpen :: AffineGap -> Int

deleteCostExtend :: AffineGap -> Int

isAffine :: AffineGap -> Bool

IsGap AffineGap2

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: AffineGap2 -> Int

insertCostExtend :: AffineGap2 -> Int

deleteCostOpen :: AffineGap2 -> Int

deleteCostExtend :: AffineGap2 -> Int

isAffine :: AffineGap2 -> Bool

IsGap SimpleGap

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: SimpleGap -> Int

insertCostExtend :: SimpleGap -> Int

deleteCostOpen :: SimpleGap -> Int

deleteCostExtend :: SimpleGap -> Int

isAffine :: SimpleGap -> Bool

IsGap SimpleGap2

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: SimpleGap2 -> Int

insertCostExtend :: SimpleGap2 -> Int

deleteCostOpen :: SimpleGap2 -> Int

deleteCostExtend :: SimpleGap2 -> Int

isAffine :: SimpleGap2 -> Bool

data EditOp

Edit operation could be insertion, deletion or match/mismatch

Constructors

Insert

Delete

Match

Instances

Bounded EditOp

Defined in Bio.Chain.Alignment.Type

Methods

minBound :: EditOp

maxBound :: EditOp

Enum EditOp

Defined in Bio.Chain.Alignment.Type

Methods

succ :: EditOp -> EditOp

pred :: EditOp -> EditOp

toEnum :: Int -> EditOp

fromEnum :: EditOp -> Int

enumFrom :: EditOp -> [EditOp]

enumFromThen :: EditOp -> EditOp -> [EditOp]

enumFromTo :: EditOp -> EditOp -> [EditOp]

enumFromThenTo :: EditOp -> EditOp -> EditOp -> [EditOp]

Generic EditOp

Defined in Bio.Chain.Alignment.Type

Associated Types

type Rep EditOp :: Type -> Type

Methods

from :: EditOp -> Rep EditOp x

to :: Rep EditOp x -> EditOp

Ix EditOp

Defined in Bio.Chain.Alignment.Type

Methods

range :: (EditOp, EditOp) -> [EditOp]

index :: (EditOp, EditOp) -> EditOp -> Int

unsafeIndex :: (EditOp, EditOp) -> EditOp -> Int

inRange :: (EditOp, EditOp) -> EditOp -> Bool

rangeSize :: (EditOp, EditOp) -> Int

unsafeRangeSize :: (EditOp, EditOp) -> Int

Show EditOp

Defined in Bio.Chain.Alignment.Type

Methods

showsPrec :: Int -> EditOp -> ShowS

show :: EditOp -> String

showList :: [EditOp] -> ShowS

NFData EditOp

Defined in Bio.Chain.Alignment.Type

Methods

rnf :: EditOp -> ()

Eq EditOp

Defined in Bio.Chain.Alignment.Type

Methods

(==) :: EditOp -> EditOp -> Bool

(/=) :: EditOp -> EditOp -> Bool

Ord EditOp

Defined in Bio.Chain.Alignment.Type

Methods

compare :: EditOp -> EditOp -> Ordering

(<) :: EditOp -> EditOp -> Bool

(<=) :: EditOp -> EditOp -> Bool

(>) :: EditOp -> EditOp -> Bool

(>=) :: EditOp -> EditOp -> Bool

max :: EditOp -> EditOp -> EditOp

min :: EditOp -> EditOp -> EditOp

(NFData a, NFData b) => NFData (UArray (a, b, EditOp) Int)

Defined in Bio.Chain.Alignment.Type

Methods

rnf :: UArray (a, b, EditOp) Int -> ()

type Rep EditOp

Defined in Bio.Chain.Alignment.Type

type Rep EditOp = D1 ('MetaData "EditOp" "Bio.Chain.Alignment.Type" "cobot-0.1.1.8-Giff50E8qZ73qQvm66bZ3u" 'False) (C1 ('MetaCons "Insert" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "Delete" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Match" 'PrefixI 'False) (U1 :: Type -> Type)))

data Operation i j

Operation that was performed on current step of alignment

Constructors

INSERT

Fields

• getJ :: j

DELETE

Fields

• getI :: i

MATCH

Fields

• getI :: i
• getJ :: j

Instances

Generic (Operation i j)

Defined in Bio.Chain.Alignment.Type

Associated Types

type Rep (Operation i j) :: Type -> Type

Methods

from :: Operation i j -> Rep (Operation i j) x

to :: Rep (Operation i j) x -> Operation i j

(Show j, Show i) => Show (Operation i j)

Defined in Bio.Chain.Alignment.Type

Methods

showsPrec :: Int -> Operation i j -> ShowS

show :: Operation i j -> String

showList :: [Operation i j] -> ShowS

(NFData j, NFData i) => NFData (Operation i j)

Defined in Bio.Chain.Alignment.Type

Methods

rnf :: Operation i j -> ()

(Eq j, Eq i) => Eq (Operation i j)

Defined in Bio.Chain.Alignment.Type

Methods

(==) :: Operation i j -> Operation i j -> Bool

(/=) :: Operation i j -> Operation i j -> Bool

(Ord j, Ord i) => Ord (Operation i j)

Defined in Bio.Chain.Alignment.Type

Methods

compare :: Operation i j -> Operation i j -> Ordering

(<) :: Operation i j -> Operation i j -> Bool

(<=) :: Operation i j -> Operation i j -> Bool

(>) :: Operation i j -> Operation i j -> Bool

(>=) :: Operation i j -> Operation i j -> Bool

max :: Operation i j -> Operation i j -> Operation i j

min :: Operation i j -> Operation i j -> Operation i j

type Rep (Operation i j)

Defined in Bio.Chain.Alignment.Type

type Rep (Operation i j) = D1 ('MetaData "Operation" "Bio.Chain.Alignment.Type" "cobot-0.1.1.8-Giff50E8qZ73qQvm66bZ3u" 'False) (C1 ('MetaCons "INSERT" 'PrefixI 'True) (S1 ('MetaSel ('Just "getJ") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 j)) :+: (C1 ('MetaCons "DELETE" 'PrefixI 'True) (S1 ('MetaSel ('Just "getI") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 i)) :+: C1 ('MetaCons "MATCH" 'PrefixI 'True) (S1 ('MetaSel ('Just "getI") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 i) :*: S1 ('MetaSel ('Just "getJ") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 j))))

isInsert :: Operation i j -> Bool

isDelete :: Operation i j -> Bool

isMatch :: Operation i j -> Bool

type Matrix m m' = UArray (Index m, Index m', EditOp) Int

Alignment matrix type

type Stop m m' = Matrix m m' -> m -> m' -> Index m -> Index m' -> Bool

Traceback stop condition type

type Move m m'

Arguments

 = Matrix m m'

-> m

-> m'

-> Index m

-> Index m'

-> EditOp

Current matrix, used in affine alignment

-> (EditOp, Index m, Index m', Operation (Index m) (Index m'))

Next matrix, next indices, new operation

Traceback next move generator type

data Conditions m m'

A set of traceback conditions

Constructors

Conditions

Fields

• isStop :: Stop m m'

  Should we stop?

• doMove :: Move m m'

  Where to go next?

data AlignmentResult m m'

Sequence Alignment result

Constructors

AlignmentResult

Fields

• score :: Int

  Resulting score of alignment

• alignment :: [Operation (Index m) (Index m')]

  Alignment structure

• sequence1 :: m

  First chain

• sequence2 :: m'

  Second chain

Instances

Generic (AlignmentResult m m')

Defined in Bio.Chain.Alignment.Type

Associated Types

type Rep (AlignmentResult m m') :: Type -> Type

Methods

from :: AlignmentResult m m' -> Rep (AlignmentResult m m') x

to :: Rep (AlignmentResult m m') x -> AlignmentResult m m'

(NFData a, NFData b, NFData (Index a), NFData (Index b)) => NFData (AlignmentResult a b)

Defined in Bio.Chain.Alignment.Type

Methods

rnf :: AlignmentResult a b -> ()

type Rep (AlignmentResult m m')

Defined in Bio.Chain.Alignment.Type

type Rep (AlignmentResult m m') = D1 ('MetaData "AlignmentResult" "Bio.Chain.Alignment.Type" "cobot-0.1.1.8-Giff50E8qZ73qQvm66bZ3u" 'False) (C1 ('MetaCons "AlignmentResult" 'PrefixI 'True) ((S1 ('MetaSel ('Just "score") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: S1 ('MetaSel ('Just "alignment") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [Operation (Index m) (Index m')])) :*: (S1 ('MetaSel ('Just "sequence1") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 m) :*: S1 ('MetaSel ('Just "sequence2") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 m'))))

type Alignable m = (ChainLike m, Ix (Index m))

Chain, that can be used for alignment

class SequenceAlignment (a :: Type -> Type -> Type) where

Method of sequence alignment

Minimal complete definition

cond, traceStart, scoreMatrix

Methods

semi :: a e1 e2 -> Bool

Defines wheater the alignment is semiglobal or not

cond :: (Alignable m, Alignable m') => a (IxValue m) (IxValue m') -> Conditions m m'

Traceback conditions of alignment

traceStart :: (Alignable m, Alignable m') => a (IxValue m) (IxValue m') -> Matrix m m' -> m -> m' -> (Index m, Index m')

Starting position in matrix for traceback procedure

scoreMatrix :: (Alignable m, Alignable m') => a (IxValue m) (IxValue m') -> m -> m' -> Matrix m m'

Distance matrix element

Instances

IsGap g => SequenceAlignment (GlobalAlignment g)

Defined in Bio.Chain.Alignment.Algorithms

Methods

semi :: GlobalAlignment g e1 e2 -> Bool

cond :: (Alignable m, Alignable m') => GlobalAlignment g (IxValue m) (IxValue m') -> Conditions m m'

traceStart :: (Alignable m, Alignable m') => GlobalAlignment g (IxValue m) (IxValue m') -> Matrix m m' -> m -> m' -> (Index m, Index m')

scoreMatrix :: (Alignable m, Alignable m') => GlobalAlignment g (IxValue m) (IxValue m') -> m -> m' -> Matrix m m'

IsGap g => SequenceAlignment (LocalAlignment g)

Defined in Bio.Chain.Alignment.Algorithms

Methods

semi :: LocalAlignment g e1 e2 -> Bool

cond :: (Alignable m, Alignable m') => LocalAlignment g (IxValue m) (IxValue m') -> Conditions m m'

traceStart :: (Alignable m, Alignable m') => LocalAlignment g (IxValue m) (IxValue m') -> Matrix m m' -> m -> m' -> (Index m, Index m')

scoreMatrix :: (Alignable m, Alignable m') => LocalAlignment g (IxValue m) (IxValue m') -> m -> m' -> Matrix m m'

IsGap g => SequenceAlignment (SemiglobalAlignment g)

Defined in Bio.Chain.Alignment.Algorithms

Methods

semi :: SemiglobalAlignment g e1 e2 -> Bool

cond :: (Alignable m, Alignable m') => SemiglobalAlignment g (IxValue m) (IxValue m') -> Conditions m m'

traceStart :: (Alignable m, Alignable m') => SemiglobalAlignment g (IxValue m) (IxValue m') -> Matrix m m' -> m -> m' -> (Index m, Index m')

scoreMatrix :: (Alignable m, Alignable m') => SemiglobalAlignment g (IxValue m) (IxValue m') -> m -> m' -> Matrix m m'