Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
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
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
R
S
T
U
W