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Class Summary | |
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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 |
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