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R

RandomPermutationBPGraph - Class in baobab.bio.permutation
 
RandomPermutationBPGraph() - Constructor for class baobab.bio.permutation.RandomPermutationBPGraph
 
randomPermutations - Class in baobab.exec.permutation
Generates one (or more) "random" permutations.
randomPermutations() - Constructor for class baobab.exec.permutation.randomPermutations
 
randomStrataPermutations - Class in baobab.exec.permutation
 
randomStrataPermutations() - Constructor for class baobab.exec.permutation.randomStrataPermutations
 
readAsReversed() - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
readCodedTraces(int, int, int, int, int, int) - Method in class baobab.applogic.trace.TraceAppLogicUtil
 
readParameters(String[]) - Static method in class baobab.exec.ExecUtil
 
readTrace(int, int, boolean) - Method in class baobab.applogic.trace.TraceAppLogicUtil
 
readTraces(SignedPermutationBPGraph, int, boolean, int, int, int) - Method in class baobab.applogic.trace.TraceAppLogicUtil
 
refreshIntervals() - Method in class baobab.bio.permutation.PerfectReversalConstraint
 
removeElement(Trace) - Method in class baobab.trace.TraceSortedSet
 
removeElement(T) - Method in class baobab.util.CompressibleSortedSet
Remove an element from this set (in general, removals are not processed one by one, but accumulated and then processed in batch mode, from time to time or when the set is resolved).
removeFile(String) - Static method in class baobab.util.Util
 
removeFirstFrozen() - Method in class baobab.util.FreezableCompressibleSortedSet
 
removeLastFrozen() - Method in class baobab.util.FreezableCompressibleSortedSet
 
reset() - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
resetLastCreatedStrata() - Method in class baobab.bio.permutation.StrataReversalConstraint
 
resolve() - Method in class baobab.util.CompressibleSortedSet
Resolves all pending insertions/removals of this set (WARNING: this method can cause a high overhead because usually it forces several internal decompressions and recompressions).
resolvedSize() - Method in class baobab.util.CompressibleSortedSet
Gets the resolved size (number of elements) of this set.
restore() - Method in class baobab.util.FreezableCompressibleSortedSet
 
restoreNext(int, boolean) - Method in class baobab.util.FreezableCompressibleSortedSet
 
resume(int) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
ReversalConstraint - Class in baobab.bio.permutation
 
ReversalConstraint(SignedPermutationBPGraph, int) - Constructor for class baobab.bio.permutation.ReversalConstraint
 
reversalToCanonizedString(int, int) - Method in class baobab.bio.permutation.PermutationBPGraphFormatter
 
reverse(int, int) - Method in class baobab.trace.SubTrace
 
reverse(int, int) - Method in class baobab.trace.Trace
 
revert() - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
revert(BPGraphReversalBlock) - Method in class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Reverts the specified block of the permutation
revert(BPGraphPoint, BPGraphPoint) - Method in class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Reverts the permutation between the specified points
revert(int, int) - Method in class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Reverts the permutation between the specified positions
revert(BPGraphReversalBlock) - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Reverts the specified block of the permutation
revert(BPGraphPoint, BPGraphPoint) - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Reverts the permutation between the specified points
revert(int, int) - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Reverts the permutation between the specified positions
revert(BPGraphReversalBlock) - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
Reverts the specified block of the permutation
revert(BPGraphPoint, BPGraphPoint) - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
Reverts the permutation between the specified points
revert(int, int) - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
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(BPGraphPoint, BPGraphPoint) - Method in class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Make a new permutation, by reverting the permutation between the specified positions
revertToNewPermutation(BPGraphPoint, BPGraphPoint) - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Make a new permutation, by reverting the permutation between the specified positions
revertToNewPermutation(int, int) - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Make a new permutation, by reverting the permutation between the specified positions
revertToNewPermutation(BPGraphPoint, BPGraphPoint) - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
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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