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ignore(int)
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
incrementCurrentPos()
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
incrementDebugNumberOfElements()
- Method in class baobab.trace.
Trace
incrementOccurrences(long)
- Method in class baobab.bio.permutation.counter.
PermutationCounter
Increments the number of occurrences this permutation
incrementOccurrences(long)
- Method in class baobab.trace.
Trace
Increments the number of this trace
indexOf(String)
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
INT_TO_BYTES
- Static variable in class baobab.util.
Bytes
intersects(BitList)
- Method in class baobab.util.
BitList
IntervalUtil
- Class in
baobab.bio.permutation
The IntervalUtil class contains utility methods which deal with intervals of permutations
IntervalUtil()
- Constructor for class baobab.bio.permutation.
IntervalUtil
intsToBitList(int[], int)
- Static method in class baobab.util.
ByteSetUtil
intToFormattedString(int, int)
- Static method in class baobab.util.
Util
intToUnsignedFormattedString(int, int)
- Static method in class baobab.util.
Util
intValue()
- Method in class baobab.util.
BitList
isActive()
- Method in class baobab.bio.permutation.
BPGraphCycle
Tests whether this cycle is active (analyzed)
isAdjacency()
- Method in class baobab.bio.permutation.
BPGraphPoint
Tests whether this point is an adjacency
isAdjacency()
- Method in class baobab.bio.permutation.
BPGraphReversalBlock
Tests whether this block is an adjacency
isAdjacency()
- Method in class baobab.bio.permutation.
SignedBPGraphComponent
Tests whether this component is an adjacency
isAdjacency()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Tests whether this permutation is sorted
isAdjacency()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Tests whether this permutation is sorted
isAnalyzed()
- Method in class baobab.bio.permutation.
BPGraphPoint
Tests whether this point is already analyzed (belongs to an active cycle)
isComplete()
- Method in class baobab.bio.permutation.strata.
Strata
isCycleBreakingReversal(int, int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Tests whether a reversal is safe (the permutation obtained after performing such a reversal has a smaller reversal distance than this permutation)
isEmpty()
- Method in class baobab.bio.permutation.
BPGraphCyclePartition
Tests whether this cycle partition is empty
isEmpty()
- Method in class baobab.bio.permutation.counter.
PermutationCounter
isEmpty()
- Method in class baobab.bio.permutation.strata.
Strata
isEmpty()
- Method in class baobab.bio.permutation.strata.
StrataSortedSet
isEmpty()
- Method in class baobab.trace.
Trace
isEmpty()
- Method in class baobab.util.
CompressibleSortedSet
Tests whether this set is empty
isEmpty()
- Method in interface baobab.util.
Joinable
Tests whether this joinable object is empty
isFortress()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
Tests whether this permutation is a fortress
isHurdle()
- Method in class baobab.bio.permutation.
SignedBPGraphComponent
Tests whether this component is a hurdle
isLinear()
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Tests whether the breakpoint graph corresponds to a linear or a circular permutation
isLinear()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Tests whether the permutation is linear or circular
isLinear()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Tests whether the permutation is linear or circular
isMaxHurdle()
- Method in class baobab.bio.permutation.
SignedBPGraphComponent
Tests whether this component is the maximum hurdle
isNeighborOf(BPGraphPoint)
- Method in class baobab.bio.permutation.
BPGraphPoint
Tests whether this point is a neighbor of a given point in the breakpoint graph
isOriented()
- Method in class baobab.bio.permutation.
SignedBPGraphCycle
Tests whether this block is oriented
isPositionRelated()
- Method in class baobab.bio.permutation.
PerfectReversalConstraint
isPositionRelated()
- Method in class baobab.bio.permutation.
ReversalConstraint
isPositionRelated()
- Method in class baobab.bio.permutation.
StrataReversalConstraint
isPositionRelated()
- Method in class baobab.bio.permutation.
TerminusSymmetryReversalConstraint
isResolved()
- Method in class baobab.util.
CompressibleSortedSet
Tests whether this set is resolved (does not have pending insertions/removals).
isReversed(int)
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
isReversed()
- Method in class baobab.bio.permutation.colinearity.
LinkPermutationToColinearBlock
isRevertedAt(int)
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the value of the element located at a specified position of the permutation breakpoint graph
isRevertedAt(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the value of the element located at a specified position of the permutation
isRevertedAt(int)
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the value of the element located at a specified position of the permutation
isSorted()
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Tests whether the breakpoint graph represents a sorted permutation
isSorted()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Tests whether this permutation is sorted
isSorted()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Tests whether this permutation is sorted
isSuperHurdle()
- Method in class baobab.bio.permutation.
SignedBPGraphComponent
Tests whether this component is a super hurdle
isUnprocessed(int)
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
isValidPermutation(int[], boolean)
- Static method in class baobab.bio.permutation.
PermutationUtil
Tests whether the permutation is valid
iterator()
- Method in class baobab.util.
CompressibleSortedSet
Gets a ascending iterator of this set.
iterator()
- Method in class baobab.util.
FreezableCompressibleSortedSet
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