Uses of Package
baobab.bio.permutation

Packages that use baobab.bio.permutation
baobab.applogic   
baobab.applogic.strata   
baobab.applogic.trace   
baobab.applogic.trace.benchmark   
baobab.bio.permutation   
 

Classes in baobab.bio.permutation used by baobab.applogic
SignedPermutationBPGraph
          The SignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the SignedPermutationBPGraph class does not deal with hurdles)
 

Classes in baobab.bio.permutation used by baobab.applogic.strata
SignedPermutationBPGraph
          The SignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the SignedPermutationBPGraph class does not deal with hurdles)
 

Classes in baobab.bio.permutation used by baobab.applogic.trace
ComplexSignedPermutationBPGraph
          The ComplexSignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the ComplexSignedPermutationBPGraph class deals with hurdles)
PerfectReversalConstraint
           
SignedPermutationBPGraph
          The SignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the SignedPermutationBPGraph class does not deal with hurdles)
StrataReversalConstraint
           
TerminusSymmetryReversalConstraint
           
 

Classes in baobab.bio.permutation used by baobab.applogic.trace.benchmark
PerfectReversalConstraint
           
SignedPermutationBPGraph
          The SignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the SignedPermutationBPGraph class does not deal with hurdles)
StrataReversalConstraint
           
TerminusSymmetryReversalConstraint
           
 

Classes in baobab.bio.permutation used by baobab.bio.permutation
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
ComplexSignedPermutationBPGraph
          The ComplexSignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the ComplexSignedPermutationBPGraph class deals with hurdles)
PermutationBPGraph
          The PermutationBPGraph interface represents a general permutation pair and its breakpoint graph
PermutationBPGraphFormatter
          The PermutationBPGraphFormatter class gives a text representation of a breakpoint graph
PermutationException
          The PermutationException class represents an exception when dealing with permutations
ReversalConstraint
           
SignedBPGraphComponent
          The SignedBPGraphComponent class represents a component of signed cycles of 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
UnsignedPermutationBPGraph
          The UnsignedPermutationBPGraph class represents an unsigned permutation pair and its breakpoint graph