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java.lang.Objectbaobab.bio.permutation.SignedPermutationBPGraphReversalFilter
public class SignedPermutationBPGraphReversalFilter
The SignedPermutationBPGraphReversalFilter filters valid reversal blocks for a SignedPermutationBPGraph
Method Summary | |
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java.util.TreeSet |
getContainerReversalsStartingAfter(int position,
BPGraphPoint point)
Gets the reversals starting after a specific position (inclusive) which contain a given point |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getCycleSplittingReversals()
Gets the list of cycle splitting reversals of this permutation |
java.util.Vector<int[]> |
getCycleSplittingReversalsAsArraysOfInt()
Gets the list of cycle splitting reversals of this permutation |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getCycleSplittingReversalsBetweenIntervals(int[] interval1,
int[] interval2)
Gets the list of cycle splitting reversals of this permutation which start within the first given interval and end within the second given interval |
java.util.Vector<int[]> |
getCycleSplittingReversalsBetweenIntervalsAsArraysOfInt(int[] interval1,
int[] interval2)
Gets the list of cycle splitting reversals of this permutation which start within the first given interval and end within the second given interval |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getCycleSplittingReversalsStartingAt(int position)
Gets the list of cycle splitting reversals starting exactly at a specific position |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getCycleSplittingReversalsWithinIntervals(java.util.Vector<int[]> intervals)
Gets the list of proper reversals of this permutation within the given intervals |
java.util.Vector<int[]> |
getCycleSplittingReversalsWithinIntervalsAsArraysOfInt(java.util.Vector<int[]> intervals)
Gets the list of proper reversals of this permutation within the given intervals |
SignedBPGraphReversalBlock |
getFirstShortestReversalStartingAfter(int position)
Gets the first shortest reversal starting after a specific position (inclusive) |
SignedBPGraphReversalBlock |
getLastLongestReversalStartingAfter(int position)
Gets the last longest reversal starting after a specific position (inclusive) |
SignedBPGraphReversalBlock |
getLongestCycleSplittingReversalStartingAt(int position)
Gets the longest cycle splitting reversal starting exactly at a specific position |
SignedBPGraphReversalBlock |
getLongestReversalStartingAt(int position)
Gets the longest reversal starting exactly at a specific position |
SignedPermutationBPGraph |
getPermutation()
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java.util.TreeSet<SignedBPGraphReversalBlock> |
getReversalsStartingAt(int position)
Gets the reversals starting exactly at a specific position |
SignedBPGraphReversalBlock |
getShortestContainerReversalStartingAfter(int position,
BPGraphPoint point)
Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public SignedPermutationBPGraph getPermutation()
public java.util.TreeSet<SignedBPGraphReversalBlock> getReversalsStartingAt(int position)
position
- a given position
public java.util.TreeSet getContainerReversalsStartingAfter(int position, BPGraphPoint point)
position
- a given positionpoint
- a given point
public SignedBPGraphReversalBlock getLongestReversalStartingAt(int position)
position
- a given position
public SignedBPGraphReversalBlock getLastLongestReversalStartingAfter(int position)
position
- a given position
public SignedBPGraphReversalBlock getFirstShortestReversalStartingAfter(int position)
public SignedBPGraphReversalBlock getShortestContainerReversalStartingAfter(int position, BPGraphPoint point)
position
- a given positionpoint
- a given point
public java.util.TreeSet<SignedBPGraphReversalBlock> getCycleSplittingReversalsStartingAt(int position)
position
- a given position
public SignedBPGraphReversalBlock getLongestCycleSplittingReversalStartingAt(int position)
position
- a given position
public java.util.TreeSet<SignedBPGraphReversalBlock> getCycleSplittingReversalsBetweenIntervals(int[] interval1, int[] interval2)
interval1
- (length=2, start and end positions of the first interval)interval2
- (length=2, start and end positions of the second interval)
public java.util.Vector<int[]> getCycleSplittingReversalsBetweenIntervalsAsArraysOfInt(int[] interval1, int[] interval2)
interval1
- (length=2, start and end positions of the first interval)interval2
- (length=2, start and end positions of the second interval)
public java.util.TreeSet<SignedBPGraphReversalBlock> getCycleSplittingReversalsWithinIntervals(java.util.Vector<int[]> intervals)
intervals
- a Vector of int[] (length=2, start and end positions of an interval)
public java.util.TreeSet<SignedBPGraphReversalBlock> getCycleSplittingReversals()
public java.util.Vector<int[]> getCycleSplittingReversalsAsArraysOfInt()
public java.util.Vector<int[]> getCycleSplittingReversalsWithinIntervalsAsArraysOfInt(java.util.Vector<int[]> intervals)
intervals
- a Vector of int[] (length=2, start and end positions of an interval)
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