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Hierarchy For All Packages
Package Hierarchies:
baobab.applogic
,
baobab.applogic.strata
,
baobab.applogic.trace
,
baobab.applogic.trace.benchmark
,
baobab.bio.permutation
,
baobab.bio.permutation.colinearity
,
baobab.bio.permutation.counter
,
baobab.bio.permutation.strata
,
baobab.bio.util
,
baobab.exec
,
baobab.exec.bio
,
baobab.exec.permutation
,
baobab.exec.permutation.colinearity
,
baobab.exec.strata
,
baobab.exec.trace
,
baobab.exec.trace.benchmark
,
baobab.trace
,
baobab.util
Class Hierarchy
java.lang.Object
baobab.exec.permutation.
analyzeSignedPermutation
baobab.exec.permutation.
analyzeSignedPermutationIntervals
baobab.exec.trace.
analyzeTraces
baobab.exec.trace.benchmark.
analyzeTracesBenchmark0
baobab.exec.trace.benchmark.
analyzeTracesBenchmark1
baobab.exec.trace.benchmark.
analyzeTracesBenchmark2
baobab.exec.trace.
analyzeTracesForRandomPermutations
baobab.exec.permutation.
analyzeUnsignedPermutation
baobab.applogic.
AppLogicUtil
baobab.applogic.trace.benchmark.
BenchmarkTraceAppLogicUtil
baobab.applogic.strata.
StrataAppLogicUtil
baobab.applogic.trace.
TraceAppLogicUtil
baobab.util.
BitList
(implements java.lang.Comparable<T>)
baobab.bio.permutation.
BPGraphBlockComparator
(implements java.util.Comparator<T>)
baobab.bio.permutation.
BPGraphCycle
baobab.bio.permutation.
SignedBPGraphCycle
baobab.bio.permutation.
BPGraphCyclePartition
baobab.bio.permutation.
BPGraphPoint
(implements java.lang.Comparable<T>)
baobab.bio.permutation.
BPGraphReversalBlock
(implements java.lang.Comparable<T>)
baobab.bio.permutation.
BPGraphTranspositionBlock
baobab.bio.permutation.
SignedBPGraphReversalBlock
baobab.bio.permutation.
BPGraphReversalBlockComparator
(implements java.util.Comparator<T>)
baobab.util.
Bytes
baobab.util.
ByteSetUtil
baobab.exec.permutation.
calculateReversalDistance
baobab.exec.permutation.
canonizePermutations
baobab.exec.trace.
codeTraces
baobab.bio.permutation.colinearity.
ColinearBlock
baobab.bio.permutation.colinearity.
ColinearPermutation
baobab.exec.permutation.
collapsePermutation
baobab.util.
CompressibleSortedSet
<T>
baobab.util.
FreezableCompressibleSortedSet
<T>
baobab.trace.
TraceSortedSet
baobab.trace.
SubTraceSortedSet
baobab.exec.strata.
computeSolutionsByStrata
baobab.exec.trace.
computeSolutionsOfTraces
baobab.exec.trace.
computeTracesByReversal
baobab.exec.trace.
computeTracesByReversalForNonCanonizedPermutations
baobab.exec.permutation.
countAllSortingSequences
baobab.exec.trace.
decodeTraces
baobab.exec.permutation.
decomposeSignedPermutation
baobab.exec.trace.
diffTraces
baobab.exec.trace.
enumerateStrataTraces
baobab.exec.trace.
enumerateTraces
baobab.exec.trace.
enumerateTracesByStrata
baobab.exec.trace.
enumerateTracesByStrataForRandomPermutations
baobab.exec.trace.
enumerateTracesByStrataForRandomStratifiedPermutations
baobab.exec.trace.
enumerateTracesByStrataForTrulyRandomStratifiedPermutations
baobab.exec.permutation.
evaluateRandomPermutations
baobab.exec.
ExecUtil
baobab.bio.util.
FastaUtil
baobab.exec.permutation.colinearity.
findColinearBlocks
baobab.exec.permutation.
findMaxMinStrataSolution
baobab.exec.permutation.
findStrataSolution
baobab.exec.permutation.
findStrataSolutions
baobab.exec.permutation.colinearity.
findStrictColinearBlocks
baobab.exec.permutation.
generateAllPermutations
baobab.exec.permutation.
getComplexFirstReversals
baobab.exec.permutation.
getComplexFirstReversalsStartingAt
baobab.exec.permutation.
getFirstOrientedReversals
baobab.exec.permutation.
getFirstOrientedReversalsStartingAt
baobab.bio.permutation.
IntervalUtil
baobab.bio.permutation.colinearity.
LinkPermutationToColinearBlock
(implements java.lang.Comparable<T>)
baobab.exec.permutation.
listBreakpoints
baobab.exec.permutation.
listBreakpointsByName
baobab.exec.permutation.
locateCoorientedIntervals
baobab.exec.strata.
locateStrata
baobab.exec.permutation.
mapPermutation
baobab.bio.permutation.
PerfectReversalConstraint
baobab.exec.permutation.
performReversals
baobab.bio.permutation.
PermutationBPGraphFormatter
baobab.bio.permutation.
PermutationBPGraphIntervalFilter
baobab.bio.permutation.counter.
PermutationCounter
(implements baobab.util.
Joinable
<T>)
baobab.bio.permutation.counter.
PermutationCounterCoder
(implements baobab.util.
Coder
<T>)
baobab.bio.permutation.counter.
PermutationCounterComparator
(implements java.util.Comparator<T>)
baobab.bio.permutation.
PermutationUtil
baobab.bio.permutation.
RandomPermutationBPGraph
baobab.exec.permutation.
randomPermutations
baobab.exec.permutation.
randomStrataPermutations
baobab.bio.permutation.
ReversalConstraint
(implements java.lang.Comparable<T>)
baobab.bio.permutation.
SignedBPGraphComponent
baobab.bio.permutation.
SignedPermutationBPGraph
(implements baobab.bio.permutation.
PermutationBPGraph
)
baobab.bio.permutation.
ComplexSignedPermutationBPGraph
baobab.bio.permutation.
WeightedSignedPermutationBPGraph
baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
baobab.bio.permutation.
WeightedSignedPermutationBPGraphReversalFilter
baobab.exec.permutation.
sort
baobab.exec.permutation.
sortWeightedSignedPermutation
baobab.bio.permutation.strata.
Strata
(implements java.lang.Comparable<T>)
baobab.bio.permutation.
StrataReversalConstraint
baobab.bio.permutation.strata.
StrataSortedSet
baobab.exec.bio.
subSeq
baobab.bio.permutation.
TerminusSymmetryReversalConstraint
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
baobab.bio.permutation.
PermutationException
baobab.trace.
Trace
(implements baobab.util.
Joinable
<T>)
baobab.trace.
DecomposedTrace
baobab.trace.
SubTrace
baobab.trace.
TraceCoder
(implements baobab.util.
Coder
<T>)
baobab.trace.
SubTraceCoder
baobab.trace.
TraceComparator
(implements java.util.Comparator<T>)
baobab.trace.
SubTraceComparator
baobab.trace.
TraceJoinerComparator
(implements java.util.Comparator<T>)
baobab.trace.
TraceWidth
baobab.bio.permutation.
UnsignedPermutationBPGraph
(implements baobab.bio.permutation.
PermutationBPGraph
)
baobab.util.
Util
Interface Hierarchy
baobab.util.
Coder
<T>
baobab.util.
Joinable
<T>
baobab.bio.permutation.
PermutationBPGraph
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