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generateAllPermutations(int)
- Static method in class baobab.bio.permutation.
PermutationUtil
generateAllPermutations(int, int, boolean)
- Static method in class baobab.bio.permutation.
PermutationUtil
generateAllPermutations
- Class in
baobab.exec.permutation
generateAllPermutations()
- Constructor for class baobab.exec.permutation.
generateAllPermutations
get(int)
- Method in class baobab.util.
BitList
get(int, int)
- Method in class baobab.util.
BitList
get(int, int, boolean)
- Method in class baobab.util.
BitList
getAverageWeightOfInterval(int, int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the average weight of an interval of the permutation
getAverageWeightOfInterval(int, int)
- Method in class baobab.bio.permutation.
WeightedSignedPermutationBPGraph
getBlock()
- Method in class baobab.bio.permutation.colinearity.
LinkPermutationToColinearBlock
getBreakpoints()
- Method in class baobab.bio.permutation.
BPGraphCycle
Gets the breakpoint list of this cycle
getBytes(int, int)
- Method in class baobab.trace.
SubTrace
Produces a string representation of a trace
getBytes(int, int)
- Method in class baobab.trace.
Trace
Produces a string representation of a trace
getBytes()
- Method in class baobab.util.
BitList
getBytes(byte[], int)
- Method in class baobab.util.
BitList
getCanonizedString()
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a one-line string representation of a permutation
getCodedArrayLength()
- Method in class baobab.bio.permutation.counter.
PermutationCounterCoder
getCodedArrayLength()
- Method in class baobab.trace.
SubTraceCoder
getCodedArrayLength()
- Method in class baobab.trace.
TraceCoder
getCodedArrayLength()
- Method in interface baobab.util.
Coder
getColinearBlocks()
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
getCommonIntervals(boolean)
- Method in class baobab.bio.permutation.
PermutationBPGraphIntervalFilter
getCommonIntervals()
- Method in class baobab.bio.permutation.
PermutationBPGraphIntervalFilter
getComplexFirstReversals
- Class in
baobab.exec.permutation
Gets the list of reversals that could be part of an optimal solution when sorting this permutation by reversals.
getComplexFirstReversals()
- Constructor for class baobab.exec.permutation.
getComplexFirstReversals
getComplexFirstReversalsStartingAt
- Class in
baobab.exec.permutation
getComplexFirstReversalsStartingAt()
- Constructor for class baobab.exec.permutation.
getComplexFirstReversalsStartingAt
getComponent()
- Method in class baobab.bio.permutation.
SignedBPGraphCycle
Gets the component to which this cycle belongs
getConstraintScore()
- Method in class baobab.trace.
SubTrace
getContainerReversalsStartingAfter(int, BPGraphPoint)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the reversals starting after a specific position (inclusive) which contain a given point
getContainerReversalsStartingAfter(int, BPGraphPoint)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the reversals starting after a specific position (inclusive) which contain a given point
getCoorientedInterval(int, String[])
- Method in class baobab.bio.permutation.
PermutationBPGraphIntervalFilter
getCoveredUnorientedComponents()
- Method in class baobab.bio.permutation.
SignedBPGraphComponent
Gets all unoriented components directly covered by this component
getCovererUnorientedComponent()
- Method in class baobab.bio.permutation.
SignedBPGraphComponent
Gets the direct coverer unoriented component of this component
getCurrentPos()
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
getCycle()
- Method in class baobab.bio.permutation.
BPGraphCyclePartition
Gets the cycle of this partition
getCycle()
- Method in class baobab.bio.permutation.
BPGraphPoint
Gets the cycle to which this points belongs
getCyclePartition()
- Method in class baobab.bio.permutation.
BPGraphPoint
Gets the cycle partition to which this point belongs
getCycleSplittingReversals()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the list of cycle splitting reversals of this permutation
getCycleSplittingReversalsAsArraysOfInt()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the list of cycle splitting reversals of this permutation
getCycleSplittingReversalsBetweenIntervals(int[], int[])
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
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.
SignedPermutationBPGraphReversalFilter
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.
SignedPermutationBPGraphReversalFilter
Gets the list of cycle splitting reversals starting exactly at a specific position
getCycleSplittingReversalsWithinIntervals(Vector<int[]>)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the list of proper reversals of this permutation within the given intervals
getCycleSplittingReversalsWithinIntervalsAsArraysOfInt(Vector<int[]>)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the list of proper reversals of this permutation within the given intervals
getData()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
getData()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getData()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
getDebugElementData()
- Method in class baobab.trace.
Trace
getDescription()
- Method in class baobab.bio.permutation.
PerfectReversalConstraint
getDescription()
- Method in class baobab.bio.permutation.
ReversalConstraint
getDescription()
- Method in class baobab.bio.permutation.
StrataReversalConstraint
getDescription()
- Method in class baobab.bio.permutation.
TerminusSymmetryReversalConstraint
getElements(int, int)
- Method in class baobab.trace.
SubTrace
Decode the trace as a Vector of elements (represented as arrays of ints)
getElements(int, int)
- Method in class baobab.trace.
Trace
Decode the trace as a Vector of elements (represented as arrays of ints)
getElementsAsBitLists(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.
BPGraphReversalBlock
Gets the end point of this block in the permutation
getEndPosition()
- Method in class baobab.bio.permutation.
BPGraphReversalBlock
Gets the end position of this block in the permutation
getExpectedNumberOfPartitions()
- Method in class baobab.bio.permutation.strata.
Strata
getFirstOrientedReversals
- Class in
baobab.exec.permutation
Gets the list of reversals that could be part of an optimal solution when sorting this permutation by reversals.
getFirstOrientedReversals()
- Constructor for class baobab.exec.permutation.
getFirstOrientedReversals
getFirstOrientedReversalsStartingAt
- Class in
baobab.exec.permutation
getFirstOrientedReversalsStartingAt()
- Constructor for class baobab.exec.permutation.
getFirstOrientedReversalsStartingAt
getFirstPoint()
- Method in class baobab.bio.permutation.
BPGraphCycle
Gets the first point of this cycle in the breakpoint graph
getFirstPoint()
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the first point of the permutation breakpoint graph
getFirstPoint()
- Method in class baobab.bio.permutation.
SignedBPGraphComponent
Gets the start point of this component in the permutation
getFirstPoint()
- Method in class baobab.bio.permutation.
SignedBPGraphCycle
Gets the start point of this cycle in the permutation
getFirstPoint()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the first point of the permutation
getFirstPoint()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the start point of the permutation
getFirstShortestReversalStartingAfter(int)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the first shortest reversal starting after a specific position (inclusive)
getFirstShortestReversalStartingAfter(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the first shortest reversal starting after a specific position (inclusive)
getFormatter()
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets this breakpoint graph formatter
getFormatter()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getFormatter()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
getGroupedPermutation(int)
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
getHeaviestLongestReversal()
- Method in class baobab.bio.permutation.
WeightedSignedPermutationBPGraphReversalFilter
Gets the heaviest reversal
getHeightOf(BitList, int, int)
- Method in class baobab.trace.
Trace
getHelp(char[], char[])
- Static method in class baobab.exec.
ExecUtil
getHighlightedString(int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a two-lines string representation of a permutation
getHighlightedString(boolean, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getHighlightedString(int, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a two-lines string representation of a permutation
getHighlightedString(boolean, int, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getHurdleCuttingReversals()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the list of hurdle cutting reversals
getHurdleCuttingReversalsBetweenIntervals(int[], int[])
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
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.
ComplexSignedPermutationBPGraphReversalFilter
Gets the list of hurdle cutting reversals starting exactly at a specific position
getHurdleCuttingReversalsWithinIntervals(Vector)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the list of hurdle cutting reversals of this permutation within the given intervals
getHurdleMergingReversals()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the list of hurdle merging reversals
getHurdleMergingReversalsBetweenIntervals(int[], int[])
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
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.
ComplexSignedPermutationBPGraphReversalFilter
Gets the list of hurdle merging reversals starting exactly at a specific position
getHurdleMergingReversalsWithinIntervals(Vector)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the list of hurdle merging reversals of this permutation within the given intervals
getId()
- Method in class baobab.bio.permutation.
BPGraphCyclePartition
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.
PermutationBPGraphFormatter
Generates a four-lines string representation of a permutation (
...
represents an adjacency)
getIndexedCycledString(boolean)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getIndexedHighlightedCycledString(int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a five-lines string representation of a permutation (
...
represents an adjacency)
getIndexedHighlightedCycledString(boolean, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getIndexedHighlightedCycledString(int, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a five-lines string representation of a permutation (
...
represents an adjacency)
getIndexedHighlightedCycledString(boolean, int, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getIndexedHighlightedString(int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a three-lines string representation of a permutation
getIndexedHighlightedString(boolean, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getIndexedHighlightedString(int, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a three-lines string representation of a permutation
getIndexedHighlightedString(boolean, int, int, int)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getIndexedString()
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a two-lines string representation of a permutation
getIndexedString(boolean)
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getInterval(int, String[])
- Method in class baobab.bio.permutation.
PermutationBPGraphIntervalFilter
getIntervals()
- Method in class baobab.bio.permutation.
PerfectReversalConstraint
getIntToNamesMap()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getLastLongestReversalStartingAfter(int)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the last longest reversal starting after a specific position (inclusive)
getLastLongestReversalStartingAfter(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the last longest reversal starting after a specific position (inclusive)
getLastPoint()
- Method in class baobab.bio.permutation.
BPGraphCycle
Gets the last point of this cycle in the breakpoint graph
getLastPoint()
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the last point of the permutation breakpoint graph
getLastPoint()
- Method in class baobab.bio.permutation.
SignedBPGraphComponent
Gets the end point of this component in the permutation
getLastPoint()
- Method in class baobab.bio.permutation.
SignedBPGraphCycle
Gets the end point of this cycle in the permutation
getLastPoint()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the last point of the permutation
getLastPoint()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the end point of the permutation
getLastPointIndex()
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the index of the last point of the permutation breakpoint graph
getLastPointIndex()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the position of the last point of the permutation
getLastPointIndex()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
getLinksToPermutations()
- Method in class baobab.bio.permutation.colinearity.
ColinearBlock
getLongestCycleSplittingReversalStartingAt(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the longest cycle splitting reversal starting exactly at a specific position
getLongestHurdleCuttingReversalStartingAt(int)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the longest hurdle cutting reversal starting at a specific position
getLongestHurdleMergingReversalStartingAt(int)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the longest hurdle merging reversal starting at a specific position
getLongestNameLength()
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the longest length of a value name in the breakpoint graph
getLongestNameLength()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getLongestNameLength()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
getLongestReversalStartingAt(int)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the longest reversal starting exactly at a specific position
getLongestReversalStartingAt(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the longest reversal starting exactly at a specific position
getMappedPositions()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getMappedValueAt(int)
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the value of the mapped element located at a specified position of the permutation breakpoint graph
getMappedValueAt(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the value of the mapped element located at a specified position of the permutation
getMappedValueAt(int)
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the value of the mapped element located at a specified position of the permutation
getMappedValues()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getMappedValuesAroundPosition(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the two values around a position of the permutation
getMaxExternalReversalScore()
- Method in class baobab.bio.permutation.
TerminusSymmetryReversalConstraint
getMaxNonPerfectReversalScore()
- Method in class baobab.bio.permutation.
PerfectReversalConstraint
getMaxNonSymmetricReversalScore()
- Method in class baobab.bio.permutation.
TerminusSymmetryReversalConstraint
getMiddleOfInterval(int, int, double[])
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the middle position of an interval of the permutation
getMiddlePoint()
- Method in class baobab.bio.permutation.
BPGraphTranspositionBlock
Gets the middle point of this block
getMiddlePosition()
- Method in class baobab.bio.permutation.
BPGraphTranspositionBlock
Gets the middle point of this block
getMinimalReversalDistance()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the minimal reversal distance of this permutation (considering only the number of cycles property)
getMinimumTraceWithHeight(int)
- Method in class baobab.trace.
TraceSortedSet
getMonoorientedCommonIntervals()
- Method in class baobab.bio.permutation.
PermutationBPGraphIntervalFilter
getName()
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
getNameAt(int)
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the value of the element located at a specified position of the permutation breakpoint graph
getNameAt(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the name of the element located at a specified position of the permutation
getNameAt(int)
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the value of the element located at a specified position of the permutation
getNameOf(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the name of the element represented by the given value of the permutation
getNamesToIntMap()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getNeighbors()
- Method in class baobab.bio.permutation.
BPGraphPoint
Gets the neighbors of this point in the breakpoint graph
getNextPoint()
- Method in class baobab.bio.permutation.
BPGraphPoint
Gets the point that follows this point in the breakpoint graph
getNextReversals()
- Method in class baobab.bio.permutation.
PerfectReversalConstraint
getNextReversals()
- Method in class baobab.bio.permutation.
ReversalConstraint
getNextReversals(SignedPermutationBPGraph)
- Method in class baobab.bio.permutation.
StrataReversalConstraint
getNextReversals()
- Method in class baobab.bio.permutation.
TerminusSymmetryReversalConstraint
getNotCollapsed()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getNumber()
- Method in class baobab.bio.permutation.
BPGraphCycle
Gets the cycle number
getNumber()
- Method in class baobab.bio.permutation.colinearity.
ColinearBlock
getNumberOfAdjacencies()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
Gets the number of adjacencies of the permutation
getNumberOfComponents()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
Gets the number of components of the permutation
getNumberOfCycles()
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the number of cycles of the permutation breakpoint graph
getNumberOfHurdles()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
Gets the number of hurdles of the permutation
getNumberOfOccurrences()
- Method in class baobab.bio.permutation.counter.
PermutationCounter
Gets the number of occurrences of this trace
getNumberOfOccurrences()
- Method in class baobab.trace.
Trace
Gets the number of occurrences of this trace
getNumberOfOrientedComponents()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
Gets the number of oriented components of the permutation
getNumberOfPartitions()
- Method in class baobab.bio.permutation.strata.
Strata
getNumberOfSuperHurdles()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
Gets the number of super hurdles of the permutation
getNumberOfUnorientedComponents()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
Gets the number of non-oriented components of the permutation
getPartition(int)
- Method in class baobab.bio.permutation.
BPGraphCycle
Gets a partition of this cycle, given its id
getPartition(int)
- Method in class baobab.bio.permutation.
SignedBPGraphCycle
Gets a partition of this cycle, given its id
getPermutation()
- Method in class baobab.bio.permutation.colinearity.
LinkPermutationToColinearBlock
getPermutation()
- Method in class baobab.bio.permutation.counter.
PermutationCounter
getPermutation()
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
getPermutation()
- Method in class baobab.bio.permutation.
PermutationBPGraphIntervalFilter
getPermutation()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
getPermutationAsString()
- Method in class baobab.bio.permutation.counter.
PermutationCounter
Produces a string representation of a permutation counter
getPermutationBPGraph()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets this permutation
getPermutationBPGraph()
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets this permutation
getPointAt(int)
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets a point at a specific position of the permutation breakpoint graph
getPointAt(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets a point at a specific position of the permutation
getPointAt(int)
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets a point at a specific position of the permutation
getPointBetweenMapped(int, int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets a point between two values of the permutation
getPoints()
- Method in class baobab.bio.permutation.
BPGraphCycle
Gets the points of this cycle sorted in ascendant order
getPoints()
- Method in class baobab.bio.permutation.
BPGraphCyclePartition
Gets the list of points of this cycle partition
getPointsAsCycle()
- Method in class baobab.bio.permutation.
BPGraphCycle
Gets the points of this cycle ordered as a cycle
getPosition()
- Method in class baobab.bio.permutation.
BPGraphPoint
Gets the position of this point in the permutation
getPositionOf(int)
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the position where a specified element of the permutation is located
getPositionOf(String)
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the position of the element identified by the given name
getPositionOf(String)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the position of the element identified by the given name
getPositionOf(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the position where a specified element of the permutation is located
getPositionOf(String)
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the position of the element identified by the given name
getPositionOf(int)
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the position where a specified element of the permutation is located
getPositionOfMapped(int)
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the position where a specified mapped element of the permutation breakpoint graph is located
getPositionOfMapped(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the position where a specified mapped element of the permutation is located
getPositionOfMapped(int)
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the position where a specified mapped element of the permutation is located
getPositions()
- Method in class baobab.bio.permutation.strata.
Strata
getPreviousPoint()
- Method in class baobab.bio.permutation.
BPGraphPoint
Gets the point that precedes this point in the breakpoint graph
getPriority()
- Method in class baobab.bio.permutation.
ReversalConstraint
getRepresentativeElementsAsBitLists(int, int)
- Method in class baobab.trace.
SubTrace
Decode the trace as a Vector of elements (represented as arrays of BitList)
getReversalDistance()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
getReversalDistance()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the reversal distance of this permutation
getReversalFilter()
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraph
getReversalFilter()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the reversal filter of this permutation
getReversalFilter()
- Method in class baobab.bio.permutation.
WeightedSignedPermutationBPGraph
getReversalsStartingAt(int)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the reversals starting exactly at a specific position
getReversalsStartingAt(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the reversals starting exactly at a specific position
getReversalType()
- Method in class baobab.bio.permutation.
SignedBPGraphReversalBlock
Gets the type of the reversal represented by this block
getScoreDescription()
- Method in class baobab.bio.permutation.
PerfectReversalConstraint
getScoreDescription()
- Method in class baobab.bio.permutation.
ReversalConstraint
getScoreDescription()
- Method in class baobab.bio.permutation.
StrataReversalConstraint
getScoreDescription()
- Method in class baobab.bio.permutation.
TerminusSymmetryReversalConstraint
getShortestContainerReversalStartingAfter(int, BPGraphPoint)
- Method in class baobab.bio.permutation.
ComplexSignedPermutationBPGraphReversalFilter
Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point
getShortestContainerReversalStartingAfter(int, BPGraphPoint)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraphReversalFilter
Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point
getSignedDescription(String, boolean)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getSignedDescriptor()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getSimpleMappedString()
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
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.
BPGraphReversalBlock
Gets the start point of this block in the permutation
getStartPosition()
- Method in class baobab.bio.permutation.
BPGraphReversalBlock
Gets the start position of this block in the permutation
getStrataPositions()
- Method in class baobab.bio.permutation.
StrataReversalConstraint
getString()
- Method in class baobab.bio.permutation.
PermutationBPGraphFormatter
Generates a one-line string representation of a permutation
getSubstring(InputStream, int, int)
- Static method in class baobab.bio.util.
FastaUtil
getSubstring(String, int, int)
- Static method in class baobab.bio.util.
FastaUtil
getSubstring(InputStreamReader, int, int)
- Static method in class baobab.bio.util.
FastaUtil
getSymmetryRate()
- Method in class baobab.bio.permutation.
TerminusSymmetryReversalConstraint
getTotalWeight()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the total weight (the sum of the weights of all values) of this permutation
getTracesByHeight()
- Method in class baobab.trace.
TraceSortedSet
getTracesByWidth()
- Method in class baobab.trace.
TraceSortedSet
getUnsignedDescription(String)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getUnsignedDescriptor()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
getValue(int)
- Method in class baobab.bio.permutation.colinearity.
ColinearPermutation
getValueAt(int)
- Method in interface baobab.bio.permutation.
PermutationBPGraph
Gets the value of the element located at a specified position of the permutation breakpoint graph
getValueAt(int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the value of the element located at a specified position of the permutation
getValueAt(int)
- Method in class baobab.bio.permutation.
UnsignedPermutationBPGraph
Gets the value of the element located at a specified position of the permutation
getValues()
- Method in class baobab.bio.permutation.strata.
StrataSortedSet
getWeightMap()
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the weights of the values of this permutation (map[i] is the weight of the value mapped to the integer i)
getWeightOf(String)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the weight of the value identified by the given name
getWeightOf(String)
- Method in class baobab.bio.permutation.
WeightedSignedPermutationBPGraph
getWeightOfInterval(int, int)
- Method in class baobab.bio.permutation.
SignedPermutationBPGraph
Gets the total weight of an interval of the permutation
gzipFile(String)
- Static method in class baobab.util.
Util
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