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I

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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