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

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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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