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U

unfreeze() - Method in class baobab.util.FreezableCompressibleSortedSet
 
unset(int) - Method in class baobab.util.BitList
 
UnsignedPermutationBPGraph - Class in baobab.bio.permutation
The UnsignedPermutationBPGraph class represents an unsigned permutation pair and its breakpoint graph
UnsignedPermutationBPGraph(int[]) - Constructor for class baobab.bio.permutation.UnsignedPermutationBPGraph
Creates a new linear permutation (assumes the identity permutation as target)
UnsignedPermutationBPGraph(int[], boolean) - Constructor for class baobab.bio.permutation.UnsignedPermutationBPGraph
Creates a new permutation (assumes the identity permutation as target)
UnsignedPermutationBPGraph(int[], int[]) - Constructor for class baobab.bio.permutation.UnsignedPermutationBPGraph
Creates a new linear permutation
UnsignedPermutationBPGraph(int[], int[], boolean) - Constructor for class baobab.bio.permutation.UnsignedPermutationBPGraph
Creates a new permutation
UnsignedPermutationBPGraph(Vector<String>, Vector<String>, boolean) - Constructor for class baobab.bio.permutation.UnsignedPermutationBPGraph
Creates a new permutation
unsortedToSortedList(int[], int) - Static method in class baobab.bio.permutation.IntervalUtil
Generates a BitList from an interval
update(SignedPermutationBPGraph) - Method in class baobab.bio.permutation.PerfectReversalConstraint
 
updateIntervals(int, int[]) - Method in class baobab.bio.permutation.PerfectReversalConstraint
 
updateLastCreatedStrata(int) - Method in class baobab.bio.permutation.StrataReversalConstraint
 
updateReversalDistance(int) - Method in class baobab.bio.permutation.StrataReversalConstraint
 
Util - Class in baobab.util
 
Util() - Constructor for class baobab.util.Util
 

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