Uses of Class
baobab.bio.permutation.SignedPermutation

Packages that use SignedPermutation
baobab.bio.permutation   
 

Uses of SignedPermutation in baobab.bio.permutation
 

Subclasses of SignedPermutation in baobab.bio.permutation
 class ComplexSignedPermutation
          The ComplexSignedPermutation class represents a signed permutation (the ComplexSignedPermutation class deals with hurdles)
 

Methods in baobab.bio.permutation that return SignedPermutation
static SignedPermutation RandomPermutation.createRandomSignedPermutation(int permutationSize, int reversalDistance, boolean isLinear, long seed)
           
static SignedPermutation RandomPermutation.createRandomSignedPermutation(int permutationSize, int reversalDistance, long seed)
           
 SignedPermutation SignedPermutationReversalFilter.getPermutation()
           
 SignedPermutation ComplexSignedPermutation.revert(int start, int end)
          Reverts the permutation between the specified positions
 SignedPermutation SignedPermutation.revert(int start, int end)
          Reverts the permutation between the specified positions
 SignedPermutation ComplexSignedPermutation.revert(Point start, Point end)
          Reverts the permutation between the specified points
 SignedPermutation SignedPermutation.revert(Point start, Point end)
          Reverts the permutation between the specified points
 SignedPermutation ComplexSignedPermutation.revert(ReversalBlock block)
          Reverts the specified block of the permutation
 SignedPermutation SignedPermutation.revert(ReversalBlock block)
          Reverts the specified block of the permutation
 SignedPermutation SignedPermutation.revertToNewPermutation(int start, int end)
          Make a new permutation, by reverting the permutation between the specified positions
 SignedPermutation ComplexSignedPermutation.revertToNewPermutation(Point start, Point end)
          Make a new permutation, by reverting the permutation between the specified positions
 SignedPermutation SignedPermutation.revertToNewPermutation(Point start, Point end)
          Make a new permutation, by reverting the permutation between the specified positions
 

Methods in baobab.bio.permutation with parameters of type SignedPermutation
 boolean SignedPermutation.equals(SignedPermutation perm)
           
 

Constructors in baobab.bio.permutation with parameters of type SignedPermutation
SignedReversalBlock(SignedPermutation permutation, int start, int end)
          Creates a new block
SignedReversalBlock(SignedPermutation permutation, Point start, Point end)
          Creates a new block