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R

RandomPermutation - Class in baobab.bio.permutation
 
RandomPermutation() - Constructor for class baobab.bio.permutation.RandomPermutation
 
randomPermutations - Class in baobab.exec.permutation
 
randomPermutations() - Constructor for class baobab.exec.permutation.randomPermutations
 
readParameters(String[]) - Static method in class baobab.exec.ExecUtil
 
ReversalBlock - Class in baobab.bio.permutation
The ReversalBlock class represents an elementary block of a permutation, given by its start and end points, which can be used as the breakpoints of a reversal
ReversalBlock(Permutation, Point, Point) - Constructor for class baobab.bio.permutation.ReversalBlock
Creates a new block
ReversalBlock(Permutation, int, int) - Constructor for class baobab.bio.permutation.ReversalBlock
Creates a new block
ReversalBlockComparator - Class in baobab.bio.permutation
The BlockComparator class represents a comparator of two elementary blocks of a signed permutation
ReversalBlockComparator() - Constructor for class baobab.bio.permutation.ReversalBlockComparator
 
reversalToBitTraceElement(Permutation, int, int) - Static method in class baobab.bio.permutation.PermutationToTrace
Generates a TraceElement from a reversal
reversalToByteTraceElement(Permutation, int, int) - Static method in class baobab.bio.permutation.PermutationToTrace
Generates a TraceElement from a reversal
reversalToCanonizedString(int, int) - Method in class baobab.bio.permutation.PermutationFormatter
 
reversalToUnsignedArrayOfBytes(Permutation, int, int) - Static method in class baobab.bio.permutation.PermutationToTrace
 
revert(ReversalBlock) - Method in class baobab.bio.permutation.ComplexSignedPermutation
Reverts the specified block of the permutation
revert(Point, Point) - Method in class baobab.bio.permutation.ComplexSignedPermutation
Reverts the permutation between the specified points
revert(int, int) - Method in class baobab.bio.permutation.ComplexSignedPermutation
Reverts the permutation between the specified positions
revert(ReversalBlock) - Method in class baobab.bio.permutation.SignedPermutation
Reverts the specified block of the permutation
revert(Point, Point) - Method in class baobab.bio.permutation.SignedPermutation
Reverts the permutation between the specified points
revert(int, int) - Method in class baobab.bio.permutation.SignedPermutation
Reverts the permutation between the specified positions
revert(ReversalBlock) - Method in class baobab.bio.permutation.UnsignedPermutation
Reverts the specified block of the permutation
revert(Point, Point) - Method in class baobab.bio.permutation.UnsignedPermutation
Reverts the permutation between the specified points
revert(int, int) - Method in class baobab.bio.permutation.UnsignedPermutation
Reverts the permutation between the specified positions
revertSigned(int[], int, int, boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Make a new permutation, by reverting the permutation between the specified positions
revertSigned(int[], int[], int, int, boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Make a new permutation, by reverting the permutation between the specified positions
revertToNewPermutation(Point, Point) - Method in class baobab.bio.permutation.ComplexSignedPermutation
Make a new permutation, by reverting the permutation between the specified positions
revertToNewPermutation(Point, Point) - Method in class baobab.bio.permutation.SignedPermutation
Make a new permutation, by reverting the permutation between the specified positions
revertToNewPermutation(int, int) - Method in class baobab.bio.permutation.SignedPermutation
Make a new permutation, by reverting the permutation between the specified positions
revertToNewPermutation(Point, Point) - Method in class baobab.bio.permutation.UnsignedPermutation
Make a new permutation, by reverting the permutation between the specified positions
revertUnsigned(int[], int, int, boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Make a new permutation, by reverting the permutation between the specified positions

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