Package baobab.bio.permutation

Interface Summary
PermutationBPGraph The PermutationBPGraph interface represents a general permutation pair and its breakpoint graph
 

Class Summary
BPGraphBlockComparator The BPGraphBlockComparator class represents a comparator of two elementary blocks of a signed permutation breakpoint graph
BPGraphCycle The BPGraphCycle class represents a cycle of points of a permutation breakpoint graph
BPGraphCyclePartition The BPGraphCyclePartition class represents a partition of a cycle of a breakpoint graph
BPGraphPoint The BPGraphPoint class represents a point between two values of a permutation (and dark edges in the corresponding breakpoint graph)
BPGraphReversalBlock The BPGraphReversalBlock 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
BPGraphReversalBlockComparator The BPGraphReversalBlockComparator class represents a comparator of two elementary blocks of a signed permutation
BPGraphTranspositionBlock The BPGraphTranspositionBlock class represents an elementary block of a permutation, given by its start, middle and end points, which can be used as the breakpoints of a transposition
ComplexSignedPermutationBPGraph The ComplexSignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the ComplexSignedPermutationBPGraph class deals with hurdles)
ComplexSignedPermutationBPGraphReversalFilter The ComplexSignedPermutationBPGraphReversalFilter filters valid reversal blocks for a ComplexSignedPermutationBPGraph
IntervalUtil The IntervalUtil class contains utility methods which deal with intervals of permutations
PerfectReversalConstraint  
PermutationBPGraphFormatter The PermutationBPGraphFormatter class gives a text representation of a breakpoint graph
PermutationBPGraphIntervalFilter The PermutationBPGraphIntervalFilter class searchs special kinds of intervals which are common to the origin and target permutations
PermutationUtil The PermutationUtil class contains utility methods which deal with permutations as arrays of int
RandomPermutationBPGraph  
ReversalConstraint  
SignedBPGraphComponent The SignedBPGraphComponent class represents a component of signed cycles of the breakpoint graph of a signed permutation pair
SignedBPGraphCycle The SignedBPGraphCycle class represents a cycle of points of a the breakpoint graph of a signed permutation pair
SignedBPGraphReversalBlock The SignedBPGraphReversalBlock class represents an elementary block of a signed permutation, given by its start and end points, which can be used as the breakpoints of a signed reversal
SignedPermutationBPGraph The SignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the SignedPermutationBPGraph class does not deal with hurdles)
SignedPermutationBPGraphReversalFilter The SignedPermutationBPGraphReversalFilter filters valid reversal blocks for a SignedPermutationBPGraph
StrataReversalConstraint  
TerminusSymmetryReversalConstraint  
UnsignedPermutationBPGraph The UnsignedPermutationBPGraph class represents an unsigned permutation pair and its breakpoint graph
WeightedSignedPermutationBPGraph The WeightedSignedPermutationBPGraph class represents a weighted signed permutation pair and its breakpoint graph (the WeightedSignedPermutationBPGraph class does not deal with hurdles)
WeightedSignedPermutationBPGraphReversalFilter The WeightedSignedPermutationBPGraphReversalFilter filters valid reversal blocks for a WeightedSignedPermutationBPGraph
 

Exception Summary
PermutationException The PermutationException class represents an exception when dealing with permutations