Bio.Chain.Alignment

Documentation

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-0.1.1.0-3rQhVKBzPLX755B7k29wYO" 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 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

Eq AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

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

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

Show AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

showsPrec :: Int -> AffineGap -> ShowS

show :: AffineGap -> String

showList :: [AffineGap] -> ShowS

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

NFData AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

rnf :: AffineGap -> ()

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 AffineGap

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: AffineGap -> Int

insertCostExtend :: AffineGap -> Int

deleteCostOpen :: AffineGap -> Int

deleteCostExtend :: AffineGap -> Int

isAffine :: AffineGap -> Bool

type Rep AffineGap

Defined in Bio.Chain.Alignment.Type

type Rep AffineGap = D1 (MetaData "AffineGap" "Bio.Chain.Alignment.Type" "cobot-0.1.1.0-3rQhVKBzPLX755B7k29wYO" 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.

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

(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

(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

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

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

Defined in Bio.Chain.Alignment.Type

Methods

rnf :: 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-0.1.1.0-3rQhVKBzPLX755B7k29wYO" 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))))

newtype EditDistance e1 e2

Alignnment methods

Constructors

EditDistance (e1 -> e2 -> Bool)

data GlobalAlignment a e1 e2

Constructors

GlobalAlignment (Scoring e1 e2) a

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'

data LocalAlignment a e1 e2

Constructors

LocalAlignment (Scoring e1 e2) a

Instances

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'

data SemiglobalAlignment a e1 e2

Constructors

SemiglobalAlignment (Scoring e1 e2) a

Instances

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'

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 AffineGap2

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: AffineGap2 -> Int

insertCostExtend :: AffineGap2 -> Int

deleteCostOpen :: AffineGap2 -> Int

deleteCostExtend :: AffineGap2 -> Int

isAffine :: AffineGap2 -> Bool

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 SimpleGap2

Defined in Bio.Chain.Alignment.Type

Methods

insertCostOpen :: SimpleGap2 -> Int

insertCostExtend :: SimpleGap2 -> Int

deleteCostOpen :: SimpleGap2 -> Int

deleteCostExtend :: SimpleGap2 -> Int

isAffine :: SimpleGap2 -> 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

align :: forall algo m m'. (SequenceAlignment algo, Alignable m, Alignable m') => algo (IxValue m) (IxValue m') -> m -> m' -> AlignmentResult m m'

Align chains using specifed algorithm

viewAlignment :: forall m m'. (Alignable m, Alignable m', Symbol (IxValue m), Symbol (IxValue m')) => AlignmentResult m m' -> (String, String)

View alignment results as simple strings with gaps

prettyAlignmment

Arguments

:: (Alignable m, Alignable m', Symbol (IxValue m), Symbol (IxValue m'))

=> AlignmentResult m m'

Result of alignment to format

-> Int

Desired width of one alignment row

-> String

Format alignment result as pretty columns of symbols.

Example with width equal to 20:

 0 --------------------  0

 0 TTTTTTTTTTTTTTTTTTTT 19

 0 --GCCTGAATGGTGTGGTGT 17
     || |||||| |||| |||
20 TTGC-TGAATG-TGTG-TGT 36

18 TCGGCGGAGGGACCCAGCTA 37
    || |||||||||||||||
37 -CG-CGGAGGGACCCAGCT- 53

38 AAAAAAAAAA 47

53 ---------- 53

similarityGen :: forall algo m m'. (SequenceAlignment algo, Alignable m, Alignable m') => algo (IxValue m) (IxValue m') -> (IxValue m -> IxValue m' -> Bool) -> m -> m' -> R

Calculate similarity and difference between two sequences, aligning them first using given algorithm.

differenceGen :: forall algo m m'. (SequenceAlignment algo, Alignable m, Alignable m') => algo (IxValue m) (IxValue m') -> (IxValue m -> IxValue m' -> Bool) -> m -> m' -> R

similarity :: forall algo m m'. (SequenceAlignment algo, Alignable m, Alignable m', IxValue m ~ IxValue m', Eq (IxValue m), Eq (IxValue m')) => algo (IxValue m) (IxValue m') -> m -> m' -> R

difference :: forall algo m m'. (SequenceAlignment algo, Alignable m, Alignable m', IxValue m ~ IxValue m', Eq (IxValue m), Eq (IxValue m')) => algo (IxValue m) (IxValue m') -> m -> m' -> R