Package baobab.exec.permutation

Class Summary
analyzeSignedPermutation Builds the breakpoint graph between two signed permutations (or genomes) and prints its properties (number of points, cycles, components and the reversal distance)
analyzeSignedPermutationIntervals  
analyzeUnsignedPermutation Builds the breakpoint graph between two unsigned permutations
calculateReversalDistance  
canonizePermutations  
collapsePermutation Collapses a permutation breakpoint graph, eliminating its adjacencies.
countAllSortingSequences  
decomposeSignedPermutation Decomposes the breakpoint graph, generating a new breakpoint graph for each big component (non adjacency).
evaluateRandomPermutations  
findMaxMinStrataSolution  
findStrataSolution  
findStrataSolutions  
generateAllPermutations  
getComplexFirstReversals Gets the list of reversals that could be part of an optimal solution when sorting this permutation by reversals.
getComplexFirstReversalsStartingAt  
getFirstOrientedReversals Gets the list of reversals that could be part of an optimal solution when sorting this permutation by reversals.
getFirstOrientedReversalsStartingAt  
listBreakpoints  
listBreakpointsByName  
locateCoorientedIntervals  
mapPermutation mapPermutation: maps the origin permutation, respecting a map between the target and the identity permutation
performReversals Performs reversals in the origin signed permutation (or genome).
randomPermutations Generates one (or more) "random" permutations.
randomStrataPermutations  
sort Sorts the origin permutation (or genome) into the target permutation (or genome) applying the optimal number of reversals.
sortWeightedSignedPermutation