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M

main(String[]) - Static method in class baobab.exec.bio.subSeq
 
main(String[]) - Static method in class baobab.exec.permutation.analyzeSignedPermutation
 
main(String[]) - Static method in class baobab.exec.permutation.analyzeSignedPermutationIntervals
 
main(String[]) - Static method in class baobab.exec.permutation.analyzeUnsignedPermutation
 
main(String[]) - Static method in class baobab.exec.permutation.calculateReversalDistance
 
main(String[]) - Static method in class baobab.exec.permutation.canonizePermutations
 
main(String[]) - Static method in class baobab.exec.permutation.colinearity.findColinearBlocks
 
main(String[]) - Static method in class baobab.exec.permutation.colinearity.findStrictColinearBlocks
 
main(String[]) - Static method in class baobab.exec.permutation.collapsePermutation
 
main(String[]) - Static method in class baobab.exec.permutation.countAllSortingSequences
 
main(String[]) - Static method in class baobab.exec.permutation.decomposeSignedPermutation
 
main(String[]) - Static method in class baobab.exec.permutation.evaluateRandomPermutations
 
main(String[]) - Static method in class baobab.exec.permutation.findMaxMinStrataSolution
 
main(String[]) - Static method in class baobab.exec.permutation.findStrataSolution
 
main(String[]) - Static method in class baobab.exec.permutation.findStrataSolutions
 
main(String[]) - Static method in class baobab.exec.permutation.generateAllPermutations
 
main(String[]) - Static method in class baobab.exec.permutation.getComplexFirstReversals
 
main(String[]) - Static method in class baobab.exec.permutation.getComplexFirstReversalsStartingAt
 
main(String[]) - Static method in class baobab.exec.permutation.getFirstOrientedReversals
 
main(String[]) - Static method in class baobab.exec.permutation.getFirstOrientedReversalsStartingAt
 
main(String[]) - Static method in class baobab.exec.permutation.listBreakpoints
 
main(String[]) - Static method in class baobab.exec.permutation.listBreakpointsByName
 
main(String[]) - Static method in class baobab.exec.permutation.locateCoorientedIntervals
 
main(String[]) - Static method in class baobab.exec.permutation.mapPermutation
 
main(String[]) - Static method in class baobab.exec.permutation.performReversals
 
main(String[]) - Static method in class baobab.exec.permutation.randomPermutations
 
main(String[]) - Static method in class baobab.exec.permutation.randomStrataPermutations
 
main(String[]) - Static method in class baobab.exec.permutation.sort
 
main(String[]) - Static method in class baobab.exec.permutation.sortWeightedSignedPermutation
 
main(String[]) - Static method in class baobab.exec.strata.computeSolutionsByStrata
 
main(String[]) - Static method in class baobab.exec.strata.locateStrata
 
main(String[]) - Static method in class baobab.exec.trace.analyzeTraces
 
main(String[]) - Static method in class baobab.exec.trace.analyzeTracesForRandomPermutations
 
main(String[]) - Static method in class baobab.exec.trace.benchmark.analyzeTracesBenchmark0
 
main(String[]) - Static method in class baobab.exec.trace.benchmark.analyzeTracesBenchmark1
 
main(String[]) - Static method in class baobab.exec.trace.benchmark.analyzeTracesBenchmark2
 
main(String[]) - Static method in class baobab.exec.trace.codeTraces
 
main(String[]) - Static method in class baobab.exec.trace.computeSolutionsOfTraces
 
main(String[]) - Static method in class baobab.exec.trace.computeTracesByReversal
 
main(String[]) - Static method in class baobab.exec.trace.computeTracesByReversalForNonCanonizedPermutations
 
main(String[]) - Static method in class baobab.exec.trace.decodeTraces
 
main(String[]) - Static method in class baobab.exec.trace.diffTraces
 
main(String[]) - Static method in class baobab.exec.trace.enumerateStrataTraces
 
main(String[]) - Static method in class baobab.exec.trace.enumerateTraces
 
main(String[]) - Static method in class baobab.exec.trace.enumerateTracesByStrata
 
main(String[]) - Static method in class baobab.exec.trace.enumerateTracesByStrataForRandomPermutations
 
main(String[]) - Static method in class baobab.exec.trace.enumerateTracesByStrataForRandomStratifiedPermutations
 
main(String[]) - Static method in class baobab.exec.trace.enumerateTracesByStrataForTrulyRandomStratifiedPermutations
 
mapPermutation(int[], int[]) - Static method in class baobab.bio.permutation.PermutationUtil
Maps the origin permutation, respecting a direct map between the target and the identity permutation
mapPermutation - Class in baobab.exec.permutation
mapPermutation: maps the origin permutation, respecting a map between the target and the identity permutation
mapPermutation() - Constructor for class baobab.exec.permutation.mapPermutation
 
MAX_PRIORITY - Static variable in class baobab.bio.permutation.ReversalConstraint
 
MAX_SCORE_NON_PERFECT_REVERSAL - Static variable in class baobab.bio.permutation.PerfectReversalConstraint
 
MAXIMUM_NUMBER_OF_ELEMENTS_BY_COMPRESSIBLE_BLOCK - Static variable in class baobab.util.CompressibleSortedSet
The default value for the maximum number of elements by compressible block
MAXIMUM_NUMBER_OF_UNCOMPRESSED_BLOCKS_FOR_AUTOMATIC_COMPRESSION - Static variable in class baobab.util.CompressibleSortedSet
The default value for the maximum number uncompressed blocks
MAXIMUM_PENDING_INSERTION_DELETION_LIST_FOR_COMPRESSED_BLOCK - Static variable in class baobab.util.CompressibleSortedSet
The default value for the maximum number of uncompressed elements in the pending (insertion / deletion) lists of each compressed block
MIN_SIMILARITY - Static variable in class baobab.exec.trace.computeTracesByReversal
 
MIN_SIMILARITY - Static variable in class baobab.exec.trace.computeTracesByReversalForNonCanonizedPermutations
 

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