Uses of Class
baobab.bio.permutation.BPGraphPoint

Packages that use BPGraphPoint
baobab.bio.permutation   
 

Uses of BPGraphPoint in baobab.bio.permutation
 

Methods in baobab.bio.permutation that return BPGraphPoint
 BPGraphPoint BPGraphCyclePartition.firstPoint()
           
 BPGraphPoint BPGraphReversalBlock.getEndPoint()
          Gets the end point of this block in the permutation
 BPGraphPoint SignedBPGraphComponent.getFirstPoint()
          Gets the start point of this component in the permutation
 BPGraphPoint SignedBPGraphCycle.getFirstPoint()
          Gets the start point of this cycle in the permutation
 BPGraphPoint SignedPermutationBPGraph.getFirstPoint()
          Gets the first point of the permutation
 BPGraphPoint UnsignedPermutationBPGraph.getFirstPoint()
          Gets the start point of the permutation
 BPGraphPoint PermutationBPGraph.getFirstPoint()
          Gets the first point of the permutation breakpoint graph
 BPGraphPoint BPGraphCycle.getFirstPoint()
          Gets the first point of this cycle in the breakpoint graph
 BPGraphPoint SignedBPGraphComponent.getLastPoint()
          Gets the end point of this component in the permutation
 BPGraphPoint SignedBPGraphCycle.getLastPoint()
          Gets the end point of this cycle in the permutation
 BPGraphPoint SignedPermutationBPGraph.getLastPoint()
          Gets the last point of the permutation
 BPGraphPoint UnsignedPermutationBPGraph.getLastPoint()
          Gets the end point of the permutation
 BPGraphPoint PermutationBPGraph.getLastPoint()
          Gets the last point of the permutation breakpoint graph
 BPGraphPoint BPGraphCycle.getLastPoint()
          Gets the last point of this cycle in the breakpoint graph
 BPGraphPoint BPGraphTranspositionBlock.getMiddlePoint()
          Gets the middle point of this block
 BPGraphPoint[] BPGraphPoint.getNeighbors()
          Gets the neighbors of this point in the breakpoint graph
 BPGraphPoint BPGraphPoint.getNextPoint()
          Gets the point that follows this point in the breakpoint graph
 BPGraphPoint SignedPermutationBPGraph.getPointAt(int pos)
          Gets a point at a specific position of the permutation
 BPGraphPoint UnsignedPermutationBPGraph.getPointAt(int pos)
          Gets a point at a specific position of the permutation
 BPGraphPoint PermutationBPGraph.getPointAt(int pos)
          Gets a point at a specific position of the permutation breakpoint graph
 BPGraphPoint SignedPermutationBPGraph.getPointBetweenMapped(int value1, int value2)
          Gets a point between two values of the permutation
 BPGraphPoint BPGraphPoint.getPreviousPoint()
          Gets the point that precedes this point in the breakpoint graph
 BPGraphPoint BPGraphReversalBlock.getStartPoint()
          Gets the start point of this block in the permutation
 BPGraphPoint BPGraphCyclePartition.lastPoint()
           
 

Methods in baobab.bio.permutation that return types with arguments of type BPGraphPoint
 java.util.SortedSet<BPGraphPoint> BPGraphCycle.getBreakpoints()
          Gets the breakpoint list of this cycle
 java.util.SortedSet<BPGraphPoint> BPGraphCyclePartition.getPoints()
          Gets the list of points of this cycle partition
 java.util.SortedSet<BPGraphPoint> BPGraphCycle.getPoints()
          Gets the points of this cycle sorted in ascendant order
 

Methods in baobab.bio.permutation with parameters of type BPGraphPoint
 java.util.TreeSet<SignedBPGraphReversalBlock> ComplexSignedPermutationBPGraphReversalFilter.getContainerReversalsStartingAfter(int position, BPGraphPoint point)
          Gets the reversals starting after a specific position (inclusive) which contain a given point
 java.util.TreeSet SignedPermutationBPGraphReversalFilter.getContainerReversalsStartingAfter(int position, BPGraphPoint point)
          Gets the reversals starting after a specific position (inclusive) which contain a given point
 SignedBPGraphReversalBlock ComplexSignedPermutationBPGraphReversalFilter.getShortestContainerReversalStartingAfter(int position, BPGraphPoint point)
          Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point
 SignedBPGraphReversalBlock SignedPermutationBPGraphReversalFilter.getShortestContainerReversalStartingAfter(int position, BPGraphPoint point)
          Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point
 boolean BPGraphPoint.isNeighborOf(BPGraphPoint point)
          Tests whether this point is a neighbor of a given point in the breakpoint graph
 SignedPermutationBPGraph ComplexSignedPermutationBPGraph.revert(BPGraphPoint start, BPGraphPoint end)
          Reverts the permutation between the specified points
 SignedPermutationBPGraph SignedPermutationBPGraph.revert(BPGraphPoint start, BPGraphPoint end)
          Reverts the permutation between the specified points
 UnsignedPermutationBPGraph UnsignedPermutationBPGraph.revert(BPGraphPoint start, BPGraphPoint end)
          Reverts the permutation between the specified points
 SignedPermutationBPGraph ComplexSignedPermutationBPGraph.revertToNewPermutation(BPGraphPoint start, BPGraphPoint end)
          Make a new permutation, by reverting the permutation between the specified positions
 SignedPermutationBPGraph SignedPermutationBPGraph.revertToNewPermutation(BPGraphPoint start, BPGraphPoint end)
          Make a new permutation, by reverting the permutation between the specified positions
 UnsignedPermutationBPGraph UnsignedPermutationBPGraph.revertToNewPermutation(BPGraphPoint start, BPGraphPoint end)
          Make a new permutation, by reverting the permutation between the specified positions
 UnsignedPermutationBPGraph UnsignedPermutationBPGraph.transposeToNewPermutation(BPGraphPoint start, BPGraphPoint middle, BPGraphPoint end)
          Make a new permutation, by transposing the permutation between the specified positions
 

Constructors in baobab.bio.permutation with parameters of type BPGraphPoint
BPGraphReversalBlock(PermutationBPGraph permutation, BPGraphPoint start, BPGraphPoint end)
          Creates a new block
BPGraphTranspositionBlock(PermutationBPGraph permutation, BPGraphPoint start, BPGraphPoint middle, BPGraphPoint end)
          Creates a new block
SignedBPGraphReversalBlock(SignedPermutationBPGraph permutation, BPGraphPoint start, BPGraphPoint end)
          Creates a new block