All Classes
analyzeSignedPermutation
analyzeSignedPermutationIntervals
analyzeTraces
analyzeTracesBenchmark0
analyzeTracesBenchmark1
analyzeTracesBenchmark2
analyzeTracesForRandomPermutations
analyzeUnsignedPermutation
AppLogicUtil
BenchmarkTraceAppLogicUtil
BitList
BPGraphBlockComparator
BPGraphCycle
BPGraphCyclePartition
BPGraphPoint
BPGraphReversalBlock
BPGraphReversalBlockComparator
BPGraphTranspositionBlock
Bytes
ByteSetUtil
calculateReversalDistance
canonizePermutations
Coder
codeTraces
ColinearBlock
ColinearPermutation
collapsePermutation
ComplexSignedPermutationBPGraph
ComplexSignedPermutationBPGraphReversalFilter
CompressibleSortedSet
computeSolutionsByStrata
computeSolutionsOfTraces
computeTracesByReversal
computeTracesByReversalForNonCanonizedPermutations
countAllSortingSequences
decodeTraces
DecomposedTrace
decomposeSignedPermutation
diffTraces
enumerateStrataTraces
enumerateTraces
enumerateTracesByStrata
enumerateTracesByStrataForRandomPermutations
enumerateTracesByStrataForRandomStratifiedPermutations
enumerateTracesByStrataForTrulyRandomStratifiedPermutations
evaluateRandomPermutations
ExecUtil
FastaUtil
findColinearBlocks
findMaxMinStrataSolution
findStrataSolution
findStrataSolutions
findStrictColinearBlocks
FreezableCompressibleSortedSet
generateAllPermutations
getComplexFirstReversals
getComplexFirstReversalsStartingAt
getFirstOrientedReversals
getFirstOrientedReversalsStartingAt
IntervalUtil
Joinable
LinkPermutationToColinearBlock
listBreakpoints
listBreakpointsByName
locateCoorientedIntervals
locateStrata
mapPermutation
PerfectReversalConstraint
performReversals
PermutationBPGraph
PermutationBPGraphFormatter
PermutationBPGraphIntervalFilter
PermutationCounter
PermutationCounterCoder
PermutationCounterComparator
PermutationException
PermutationUtil
RandomPermutationBPGraph
randomPermutations
randomStrataPermutations
ReversalConstraint
SignedBPGraphComponent
SignedBPGraphCycle
SignedBPGraphReversalBlock
SignedPermutationBPGraph
SignedPermutationBPGraphReversalFilter
sort
sortWeightedSignedPermutation
Strata
StrataAppLogicUtil
StrataReversalConstraint
StrataSortedSet
subSeq
SubTrace
SubTraceCoder
SubTraceComparator
SubTraceSortedSet
TerminusSymmetryReversalConstraint
Trace
TraceAppLogicUtil
TraceCoder
TraceComparator
TraceJoinerComparator
TraceSortedSet
TraceWidth
UnsignedPermutationBPGraph
Util
WeightedSignedPermutationBPGraph
WeightedSignedPermutationBPGraphReversalFilter