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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
compareTo(Object)
- Method in class baobab.bio.permutation.
ReversalBlock
Compares this block to another block
ComplexSignedPermutation
- Class in
baobab.bio.permutation
The ComplexSignedPermutation class represents a signed permutation and its breakpoint graph (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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