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getBreakpoints()
- Method in class baobab.bio.permutation.
Cycle
Gets the breakpoint list of this cycle
getComponent()
- Method in class baobab.bio.permutation.
SignedCycle
Gets the component to which this cycle belongs
getCoveredUnorientedComponents()
- Method in class baobab.bio.permutation.
SignedComponent
Gets all unoriented components directly covered by this component
getCovererUnorientedComponent()
- Method in class baobab.bio.permutation.
SignedComponent
Gets the direct coverer unoriented component of this component
getCycle()
- Method in class baobab.bio.permutation.
CyclePartition
Gets the cycle of this partition
getCycle()
- Method in class baobab.bio.permutation.
Point
Gets the cycle to which this points belongs
getCyclePartition()
- Method in class baobab.bio.permutation.
Point
Gets the cycle partition to which this point belongs
getCycleSplittingReversals()
- Method in class baobab.bio.permutation.
SignedPermutationReversalFilter
Gets the list of cycle splitting reversals of this permutation
getCycleSplittingReversalsAsArraysOfInt()
- Method in class baobab.bio.permutation.
SignedPermutationReversalFilter
Gets the list of cycle splitting reversals of this permutation
getData()
- Method in class baobab.bio.permutation.
ComplexSignedPermutation
getData()
- Method in class baobab.bio.permutation.
SignedPermutation
getData()
- Method in class baobab.bio.permutation.
UnsignedPermutation
getEndPoint()
- Method in class baobab.bio.permutation.
Cycle
Gets the end point of this cycle in the permutation
getEndPoint()
- Method in class baobab.bio.permutation.
ReversalBlock
Gets the end point of this block in the permutation
getEndPoint()
- Method in class baobab.bio.permutation.
SignedComponent
Gets the end point of this component in the permutation
getEndPoint()
- Method in class baobab.bio.permutation.
SignedCycle
Gets the end point of this cycle in the permutation
getEndPoint()
- Method in class baobab.bio.permutation.
SignedPermutation
Gets the end point of the permutation
getEndPoint()
- Method in class baobab.bio.permutation.
UnsignedPermutation
Gets the end point of the permutation
getEndPointIndex()
- Method in class baobab.bio.permutation.
SignedPermutation
getEndPosition()
- Method in class baobab.bio.permutation.
ReversalBlock
Gets the end position of this block in the permutation
getFormatter()
- Method in interface baobab.bio.permutation.
Permutation
getFormatter()
- Method in class baobab.bio.permutation.
SignedPermutation
getFormatter()
- Method in class baobab.bio.permutation.
UnsignedPermutation
getHighlightedString(int, int)
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a two-lines string representation of a permutation
getHighlightedString(int, int, int)
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a two-lines string representation of a permutation
getHurdleCuttingReversals()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationReversalFilter
Gets the list of hurdle cutting reversals
getHurdleCuttingReversalsAsArraysOfInt()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationReversalFilter
Gets the list of hurdle cutting reversals
getHurdleMergingReversals()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationReversalFilter
Gets the list of hurdle merging reversals
getHurdleMergingReversalsAsArraysOfInt()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationReversalFilter
Gets the list of hurdle merging reversals
getId()
- Method in class baobab.bio.permutation.
CyclePartition
Gets the id of this partition
getIdentityPermutation(int)
- Static method in class baobab.bio.permutation.
PermutationUtil
Generates the identity permutation of a given size
getIndexedCycledString()
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a four-lines string representation of a permutation.
getIndexedHighlightedCycledString(int, int)
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a five-lines string representation of a permutation.
getIndexedHighlightedCycledString(int, int, int)
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a five-lines string representation of a permutation.
getIndexedHighlightedString(int, int)
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a three-lines string representation of a permutation
getIndexedHighlightedString(int, int, int)
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a three-lines string representation of a permutation
getIndexedString()
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a two-lines string representation of a permutation
getMappedPositions()
- Method in class baobab.bio.permutation.
SignedPermutation
getMappedValueOf(int)
- Method in interface baobab.bio.permutation.
Permutation
Gets the value of the mapped element located at a specified position of the permutation
getMappedValueOf(int)
- Method in class baobab.bio.permutation.
SignedPermutation
Gets the value of the mapped element located at a specified position of the permutation
getMappedValueOf(int)
- Method in class baobab.bio.permutation.
UnsignedPermutation
Gets the value of the mapped element located at a specified position of the permutation
getMappedValues()
- Method in class baobab.bio.permutation.
SignedPermutation
getMinimalReversalDistance()
- Method in class baobab.bio.permutation.
SignedPermutation
Gets the minimal reversal distance of this permutation (considering only the number of cycles property)
getNeighbors()
- Method in class baobab.bio.permutation.
Point
Gets the neighbors of this point in the permutation
getNextPoint()
- Method in class baobab.bio.permutation.
Point
getNumber()
- Method in class baobab.bio.permutation.
Cycle
Gets the cycle number (each cycle of a permutation is identified by a number)
getNumberOfCycles()
- Method in interface baobab.bio.permutation.
Permutation
getNumberOfHurdles()
- Method in class baobab.bio.permutation.
ComplexSignedPermutation
Gets the number of hurdles of the permutation
getNumberOfSuperHurdles()
- Method in class baobab.bio.permutation.
ComplexSignedPermutation
Gets the number of super hurdles of the permutation
getPartition(int)
- Method in class baobab.bio.permutation.
Cycle
Gets a partition of this cycle, given its id
getPartition(int)
- Method in class baobab.bio.permutation.
SignedCycle
Gets a partition of this cycle, given its id
getPermutation()
- Method in class baobab.bio.permutation.
PermutationFormatter
getPermutation()
- Method in class baobab.bio.permutation.
SignedPermutation
Gets this permutation
getPermutation()
- Method in class baobab.bio.permutation.
SignedPermutationReversalFilter
getPermutation()
- Method in class baobab.bio.permutation.
UnsignedPermutation
Gets this permutation
getPointAt(int)
- Method in interface baobab.bio.permutation.
Permutation
Gets a point at a specific position of the permutation
getPointAt(int)
- Method in class baobab.bio.permutation.
SignedPermutation
Gets a point at a specific position of the permutation
getPointAt(int)
- Method in class baobab.bio.permutation.
UnsignedPermutation
Gets a point at a specific position of the permutation
getPoints()
- Method in class baobab.bio.permutation.
Cycle
Gets the points of this cycle sorted in ascendant order
getPoints()
- Method in class baobab.bio.permutation.
CyclePartition
Gets the list of points of this cycle partition
getPointsAsCycle()
- Method in class baobab.bio.permutation.
Cycle
Gets the points of this cycle ordered as a cycle
getPosition()
- Method in class baobab.bio.permutation.
Point
Gets the position of this point in the permutation
getPositionOf(int)
- Method in interface baobab.bio.permutation.
Permutation
Gets the position where a specified element of the permutation is located
getPositionOf(int)
- Method in class baobab.bio.permutation.
SignedPermutation
Gets the position where a specified element of the permutation is located
getPositionOf(int)
- Method in class baobab.bio.permutation.
UnsignedPermutation
Gets the position where a specified element of the permutation is located
getPositionOfMapped(int)
- Method in interface baobab.bio.permutation.
Permutation
Gets the position where a specified mapped element of the permutation is located
getPositionOfMapped(int)
- Method in class baobab.bio.permutation.
SignedPermutation
Gets the position where a specified mapped element of the permutation is located
getPositionOfMapped(int)
- Method in class baobab.bio.permutation.
UnsignedPermutation
Gets the position where a specified mapped element of the permutation is located
getPreviousPoint()
- Method in class baobab.bio.permutation.
Point
getReversalDistance()
- Method in class baobab.bio.permutation.
ComplexSignedPermutation
getReversalDistance()
- Method in class baobab.bio.permutation.
SignedPermutation
Gets the reversal distance of this permutation
getReversalFilter()
- Method in class baobab.bio.permutation.
ComplexSignedPermutation
getReversalFilter()
- Method in class baobab.bio.permutation.
SignedPermutation
getReversalType()
- Method in class baobab.bio.permutation.
SignedReversalBlock
Gets the type of the reversal represented by this block
getSimpleMappedString()
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a one-line string representation of a permutation with its (mapped) values
getStartPoint()
- Method in class baobab.bio.permutation.
Cycle
Gets the start point of this cycle in the permutation
getStartPoint()
- Method in class baobab.bio.permutation.
ReversalBlock
Gets the start point of this block in the permutation
getStartPoint()
- Method in class baobab.bio.permutation.
SignedComponent
Gets the start point of this component in the permutation
getStartPoint()
- Method in class baobab.bio.permutation.
SignedCycle
Gets the start point of this cycle in the permutation
getStartPoint()
- Method in class baobab.bio.permutation.
SignedPermutation
Gets the start point of the permutation
getStartPoint()
- Method in class baobab.bio.permutation.
UnsignedPermutation
Gets the start point of the permutation
getStartPosition()
- Method in class baobab.bio.permutation.
ReversalBlock
Gets the start position of this block in the permutation
getString()
- Method in class baobab.bio.permutation.
PermutationFormatter
Generates a one-line string representation of a permutation
getValueOf(int)
- Method in interface baobab.bio.permutation.
Permutation
Gets the value of the element located at a specified position of the permutation
getValueOf(int)
- Method in class baobab.bio.permutation.
SignedPermutation
Gets the value of the element located at a specified position of the permutation
getValueOf(int)
- Method in class baobab.bio.permutation.
UnsignedPermutation
Gets the value of the element located at a specified position of the permutation
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