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C

calculateSignedReversalDistance(int[]) - Static method in class baobab.bio.permutation.PermutationUtil
Calculates the reversal distance between a given signed permutation and the identity
calculateSignedReversalDistance(int[], boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Calculates the reversal distance between a given signed permutation and the identity
calculateSignedReversalDistance(int[], int[]) - Static method in class baobab.bio.permutation.PermutationUtil
Calculates the reversal distance between the given origin and target signed permutations
calculateSignedReversalDistance(int[], int[], boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Calculates the reversal distance between the given origin and target signed permutations
clone() - Method in class baobab.bio.permutation.ComplexSignedPermutation
 
clone() - Method in class baobab.bio.permutation.SignedPermutation
 
clone() - Method in class baobab.bio.permutation.UnsignedPermutation
 
compareTo(Object) - Method in class baobab.bio.permutation.Point
Compares this point to another point
ComplexSignedPermutation - Class in baobab.bio.permutation
The ComplexSignedPermutation class represents a signed permutation (the ComplexSignedPermutation class deals with hurdles)
ComplexSignedPermutation(int[]) - Constructor for class baobab.bio.permutation.ComplexSignedPermutation
Creates a new linear permutation (assumes the identity permutation as target)
ComplexSignedPermutation(int[], boolean) - Constructor for class baobab.bio.permutation.ComplexSignedPermutation
Creates a new permutation (assumes the identity permutation as target)
ComplexSignedPermutation(int[], int[]) - Constructor for class baobab.bio.permutation.ComplexSignedPermutation
Creates a new linear permutation
ComplexSignedPermutation(int[], int[], boolean) - Constructor for class baobab.bio.permutation.ComplexSignedPermutation
Creates a new permutation
ComplexSignedPermutationReversalFilter - Class in baobab.bio.permutation
The ComplexSignedPermutationReversalFilter filters valid reversal blocks for a ComplexSignedPermutation
containsUnorientedComponent(int[], boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Tests whether the permutation contains an unoriented component (hurdle)
createRandomSignedPermutation(int, int, long) - Static method in class baobab.bio.permutation.RandomPermutation
 
Cycle - Class in baobab.bio.permutation
The Cycle class represents a cycle of points of the breakpoint graph of a permutation
CyclePartition - Class in baobab.bio.permutation
The CyclePartition class represents a partition of a cycle of the breakpoint graph of a permutation Each cycle for a signed permutation has two partitions.

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