Uses of Interface
baobab.bio.permutation.Permutation

Packages that use Permutation
baobab.bio.permutation   
 

Uses of Permutation in baobab.bio.permutation
 

Classes in baobab.bio.permutation that implement Permutation
 class ComplexSignedPermutation
          The ComplexSignedPermutation class represents a signed permutation (the ComplexSignedPermutation class deals with hurdles)
 class SignedPermutation
          The SignedPermutation class represents a signed permutation (the SignedPermutation class does not deal with hurdles)
 class UnsignedPermutation
          The UnsignedPermutation class represents an unsigned permutation
 

Methods in baobab.bio.permutation that return Permutation
 Permutation SignedPermutation.getPermutation()
          Gets this permutation
 Permutation UnsignedPermutation.getPermutation()
          Gets this permutation
 Permutation PermutationFormatter.getPermutation()
           
 

Methods in baobab.bio.permutation with parameters of type Permutation
static int[] PermutationToTrace.arrayOfBytesToReversal(Permutation permutation, byte[] element)
           
static int[] PermutationToTrace.bitTraceElementToReversal(Permutation permutation, baobab.util.BitList element)
          Generates a reversal from a trace element
static int[] PermutationToTrace.byteTraceElementToReversal(Permutation permutation, byte[] element)
          Generates a reversal from a trace element
static baobab.util.BitList PermutationToTrace.reversalToBitTraceElement(Permutation permutation, int start, int end)
          Generates a TraceElement from a reversal
static byte[] PermutationToTrace.reversalToByteTraceElement(Permutation permutation, int start, int end)
          Generates a TraceElement from a reversal
static byte[] PermutationToTrace.reversalToUnsignedArrayOfBytes(Permutation permutation, int start, int end)
           
 

Constructors in baobab.bio.permutation with parameters of type Permutation
ReversalBlock(Permutation permutation, int start, int end)
          Creates a new block
ReversalBlock(Permutation permutation, Point start, Point end)
          Creates a new block
TranspositionBlock(Permutation permutation, int start, int middle, int end)
          Creates a new block
TranspositionBlock(Permutation permutation, Point start, Point middle, Point end)
          Creates a new block