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Packages that use BPGraphPoint | |
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baobab.bio.permutation |
Uses of BPGraphPoint in baobab.bio.permutation |
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Methods in baobab.bio.permutation that return BPGraphPoint | |
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BPGraphPoint |
BPGraphCyclePartition.firstPoint()
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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()
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Methods in baobab.bio.permutation that return types with arguments of type BPGraphPoint | |
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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 | |
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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 | |
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BPGraphReversalBlock(PermutationBPGraph permutation,
BPGraphPoint start,
BPGraphPoint end)
Creates a new block |
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BPGraphTranspositionBlock(PermutationBPGraph permutation,
BPGraphPoint start,
BPGraphPoint middle,
BPGraphPoint end)
Creates a new block |
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SignedBPGraphReversalBlock(SignedPermutationBPGraph permutation,
BPGraphPoint start,
BPGraphPoint end)
Creates a new block |
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