B C E F G I L M P R S T U

G

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
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.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
 
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
getHurdleMergingReversals() - 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
 
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.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
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

B C E F G I L M P R S T U