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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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