Package baobab.bio.permutation

Interface Summary
Permutation The Permutation interface represents a general permutation
 

Class Summary
BlockComparator The BlockComparator class represents a comparator of two elementary blocks of a signed permutation
ComplexSignedPermutation The ComplexSignedPermutation class represents a signed permutation (the ComplexSignedPermutation class deals with hurdles)
ComplexSignedPermutationReversalFilter The ComplexSignedPermutationReversalFilter filters valid reversal blocks for a ComplexSignedPermutation
Cycle The Cycle class represents a cycle of points of a permutation
CyclePartition The CyclePartition class represents a partition of a cycle of a permutation
PermutationFormatter The PermutationFormatter class transforms a permutation to formatted strings
PermutationToTrace The PermutationToTrace class contains utility methods which convert permutation elements to trace elements and vice-versa
PermutationUtil The PermutationUtil class contains utility methods which deal with permutations as arrays of int
Point The Point class represents a point between two values of a permutation
RandomPermutation  
ReversalBlock 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
ReversalBlockComparator The BlockComparator class represents a comparator of two elementary blocks of a signed permutation
SignedComponent The SignedComponent class represents a component of signed cycles of a signed permutation
SignedCycle The SignedCycle class represents a cycle of points of a signed permutation
SignedPermutation The SignedPermutation class represents a signed permutation (the SignedPermutation class does not deal with hurdles)
SignedPermutationReversalFilter The SignedPermutationReversalFilter filters valid reversal blocks for a SignedPermutation
SignedReversalBlock The SignedReversalBlock 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
TranspositionBlock The TranspositionBlock 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
UnsignedPermutation The UnsignedPermutation class represents an unsigned permutation
 

Exception Summary
PermutationException The PermutationException class represents an exception on permutation dealing