A B C D E F G H I J K L M N O P R S T U W

G

getBreakpoints() - Method in class baobab.bio.permutation.Cycle
Gets the breakpoint list of this cycle
getCanonizedString() - Method in class baobab.bio.permutation.PermutationFormatter
Generates a one-line string representation of a permutation
getComplexFirstReversals - Class in baobab.exec.permutation
 
getComplexFirstReversals() - Constructor for class baobab.exec.permutation.getComplexFirstReversals
 
getComponent() - Method in class baobab.bio.permutation.SignedCycle
Gets the component to which this cycle belongs
getContainerReversalsStartingAfter(int, Point) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the reversals starting after a specific position (inclusive) which contain a given point
getContainerReversalsStartingAfter(int, Point) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the reversals starting after a specific position (inclusive) which contain a given point
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
getCycleSplittingReversalsBetweenIntervals(int[], int[]) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the list of cycle splitting reversals of this permutation which start within the first given interval and end within the second given interval
getCycleSplittingReversalsBetweenIntervalsAsArraysOfInt(int[], int[]) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the list of cycle splitting reversals of this permutation which start within the first given interval and end within the second given interval
getCycleSplittingReversalsStartingAt(int) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the list of cycle splitting reversals starting exactly at a specific position
getCycleSplittingReversalsWithinIntervals(Vector<int[]>) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the list of proper reversals of this permutation within the given intervals
getCycleSplittingReversalsWithinIntervalsAsArraysOfInt(Vector<int[]>) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the list of proper reversals of this permutation within the given intervals
getData() - Method in class baobab.bio.permutation.ComplexSignedPermutation
 
getData() - Method in class baobab.bio.permutation.SignedPermutation
 
getData() - Method in class baobab.bio.permutation.UnsignedPermutation
 
getDebugElementData() - Method in class baobab.trace.Trace
 
getElements(int, int) - Method in class baobab.trace.Trace
Decode the trace as a Vector of elements (represented as arrays of bytes)
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
getFirstOrientedReversals - Class in baobab.exec.permutation
 
getFirstOrientedReversals() - Constructor for class baobab.exec.permutation.getFirstOrientedReversals
 
getFirstShortestReversalStartingAfter(int) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the first shortest reversal starting after a specific position (inclusive)
getFirstShortestReversalStartingAfter(int) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the first shortest reversal starting after a specific position (inclusive)
getFormatter() - Method in interface baobab.bio.permutation.Permutation
 
getFormatter() - Method in class baobab.bio.permutation.SignedPermutation
 
getFormatter() - Method in class baobab.bio.permutation.UnsignedPermutation
 
getHelp(char[], char[]) - Static method in class baobab.exec.ExecUtil
 
getHighlightedString(int, int) - Method in class baobab.bio.permutation.PermutationFormatter
Generates a two-lines string representation of a permutation
getHighlightedString(boolean, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
 
getHighlightedString(int, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
Generates a two-lines string representation of a permutation
getHighlightedString(boolean, int, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
 
getHurdleCuttingReversals() - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the list of hurdle cutting reversals
getHurdleCuttingReversalsBetweenIntervals(int[], int[]) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the list of hurdle cutting reversals of this permutation which start within the first given interval and end within the second given interval
getHurdleCuttingReversalsStartingAt(int) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the list of hurdle cutting reversals starting exactly at a specific position
getHurdleCuttingReversalsWithinIntervals(Vector) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the list of hurdle cutting reversals of this permutation within the given intervals
getHurdleMergingReversals() - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the list of hurdle merging reversals
getHurdleMergingReversalsBetweenIntervals(int[], int[]) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the list of hurdle merging reversals of this permutation which start within the first given interval and end within the second given interval
getHurdleMergingReversalsStartingAt(int) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the list of hurdle merging reversals starting exactly at a specific position
getHurdleMergingReversalsWithinIntervals(Vector) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the list of hurdle merging reversals of this permutation within the given intervals
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 (... represents an adjacency)
getIndexedCycledString(boolean) - Method in class baobab.bio.permutation.PermutationFormatter
 
getIndexedHighlightedCycledString(int, int) - Method in class baobab.bio.permutation.PermutationFormatter
Generates a five-lines string representation of a permutation (... represents an adjacency)
getIndexedHighlightedCycledString(boolean, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
 
getIndexedHighlightedCycledString(int, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
Generates a five-lines string representation of a permutation (... represents an adjacency)
getIndexedHighlightedCycledString(boolean, int, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
 
getIndexedHighlightedString(int, int) - Method in class baobab.bio.permutation.PermutationFormatter
Generates a three-lines string representation of a permutation
getIndexedHighlightedString(boolean, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
 
getIndexedHighlightedString(int, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
Generates a three-lines string representation of a permutation
getIndexedHighlightedString(boolean, int, int, int) - Method in class baobab.bio.permutation.PermutationFormatter
 
getIndexedString() - Method in class baobab.bio.permutation.PermutationFormatter
Generates a two-lines string representation of a permutation
getIndexedString(boolean) - Method in class baobab.bio.permutation.PermutationFormatter
 
getIntToNamesMap() - Method in class baobab.bio.permutation.SignedPermutation
 
getLastLongestReversalStartingAfter(int) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the last longest reversal starting after a specific position (inclusive)
getLastLongestReversalStartingAfter(int) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the last longest reversal starting after a specific position (inclusive)
getLongestCycleSplittingReversalStartingAt(int) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the longest cycle splitting reversal starting exactly at a specific position
getLongestHurdleCuttingReversalStartingAt(int) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the longest hurdle cutting reversal starting at a specific position
getLongestHurdleMergingReversalStartingAt(int) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the longest hurdle merging reversal starting at a specific position
getLongestNameLength() - Method in interface baobab.bio.permutation.Permutation
 
getLongestNameLength() - Method in class baobab.bio.permutation.SignedPermutation
 
getLongestNameLength() - Method in class baobab.bio.permutation.UnsignedPermutation
 
getLongestReversalStartingAt(int) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the longest reversal starting exactly at a specific position
getLongestReversalStartingAt(int) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the longest reversal starting exactly at a specific position
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
 
getMiddlePoint() - Method in class baobab.bio.permutation.TranspositionBlock
Gets the middle point of this block
getMiddlePosition() - Method in class baobab.bio.permutation.TranspositionBlock
Gets the middle point of this block
getMinimalReversalDistance() - Method in class baobab.bio.permutation.SignedPermutation
Gets the minimal reversal distance of this permutation (considering only the number of cycles property)
getNameOf(int) - Method in interface baobab.bio.permutation.Permutation
Gets the value of the element located at a specified position of the permutation
getNameOf(int) - Method in class baobab.bio.permutation.SignedPermutation
Gets the value of the element located at a specified position of the permutation
getNameOf(int) - Method in class baobab.bio.permutation.UnsignedPermutation
Gets the value of the element located at a specified position of the permutation
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
getNumberOfCycles() - Method in interface baobab.bio.permutation.Permutation
 
getNumberOfHurdles() - Method in class baobab.bio.permutation.ComplexSignedPermutation
Gets the number of hurdles of the permutation
getNumberOfOccurrences() - Method in class baobab.trace.Trace
Gets the number of occurrences of this trace
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
 
getReversalsStartingAt(int) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the reversals starting exactly at a specific position
getReversalsStartingAt(int) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the reversals starting exactly at a specific position
getReversalType() - Method in class baobab.bio.permutation.SignedReversalBlock
Gets the type of the reversal represented by this block
getShortestContainerReversalStartingAfter(int, Point) - Method in class baobab.bio.permutation.ComplexSignedPermutationReversalFilter
Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point
getShortestContainerReversalStartingAfter(int, Point) - Method in class baobab.bio.permutation.SignedPermutationReversalFilter
Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point
getSimpleMappedString() - Method in class baobab.bio.permutation.PermutationFormatter
Generates a one-line string representation of a permutation with its (mapped) values
getSolutionsByHeight() - Method in class baobab.trace.TraceSortedSet
 
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
getTracesByHeight() - Method in class baobab.trace.TraceSortedSet
 
getTracesByWidth() - Method in class baobab.trace.TraceSortedSet
 
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

A B C D E F G H I J K L M N O P R S T U W