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java.lang.Objectbaobab.bio.permutation.SignedPermutationBPGraphReversalFilter
baobab.bio.permutation.ComplexSignedPermutationBPGraphReversalFilter
public class ComplexSignedPermutationBPGraphReversalFilter
The ComplexSignedPermutationBPGraphReversalFilter filters valid reversal blocks for a ComplexSignedPermutationBPGraph
Method Summary | |
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java.util.TreeSet<SignedBPGraphReversalBlock> |
getContainerReversalsStartingAfter(int position,
BPGraphPoint point)
Gets the reversals starting after a specific position (inclusive) which contain a given point |
SignedBPGraphReversalBlock |
getFirstShortestReversalStartingAfter(int position)
Gets the first shortest reversal starting after a specific position (inclusive) |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getHurdleCuttingReversals()
Gets the list of hurdle cutting reversals |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getHurdleCuttingReversalsBetweenIntervals(int[] interval1,
int[] interval2)
Gets the list of hurdle cutting reversals of this permutation which start within the first given interval and end within the second given interval |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getHurdleCuttingReversalsStartingAt(int position)
Gets the list of hurdle cutting reversals starting exactly at a specific position |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getHurdleCuttingReversalsWithinIntervals(java.util.Vector intervals)
Gets the list of hurdle cutting reversals of this permutation within the given intervals |
java.util.TreeSet |
getHurdleMergingReversals()
Gets the list of hurdle merging reversals |
java.util.TreeSet |
getHurdleMergingReversalsBetweenIntervals(int[] interval1,
int[] interval2)
Gets the list of hurdle merging reversals of this permutation which start within the first given interval and end within the second given interval |
java.util.TreeSet |
getHurdleMergingReversalsStartingAt(int position)
Gets the list of hurdle merging reversals starting exactly at a specific position |
java.util.TreeSet<SignedBPGraphReversalBlock> |
getHurdleMergingReversalsWithinIntervals(java.util.Vector intervals)
Gets the list of hurdle merging reversals of this permutation within the given intervals |
SignedBPGraphReversalBlock |
getLastLongestReversalStartingAfter(int position)
Gets the last longest reversal starting after a specific position (inclusive) |
SignedBPGraphReversalBlock |
getLongestHurdleCuttingReversalStartingAt(int position)
Gets the longest hurdle cutting reversal starting at a specific position |
SignedBPGraphReversalBlock |
getLongestHurdleMergingReversalStartingAt(int position)
Gets the longest hurdle merging reversal starting at a specific position |
SignedBPGraphReversalBlock |
getLongestReversalStartingAt(int position)
Gets the longest reversal starting exactly at a specific position |
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 java.util.TreeSet<SignedBPGraphReversalBlock> getReversalsStartingAt(int position)
getReversalsStartingAt
in class SignedPermutationBPGraphReversalFilter
position
- a given position
public java.util.TreeSet<SignedBPGraphReversalBlock> getContainerReversalsStartingAfter(int position, BPGraphPoint point)
getContainerReversalsStartingAfter
in class SignedPermutationBPGraphReversalFilter
position
- a given positionpoint
- a given point
public SignedBPGraphReversalBlock getLongestReversalStartingAt(int position)
getLongestReversalStartingAt
in class SignedPermutationBPGraphReversalFilter
position
- a given position
public SignedBPGraphReversalBlock getLastLongestReversalStartingAfter(int position)
getLastLongestReversalStartingAfter
in class SignedPermutationBPGraphReversalFilter
position
- a given position
public SignedBPGraphReversalBlock getFirstShortestReversalStartingAfter(int position)
getFirstShortestReversalStartingAfter
in class SignedPermutationBPGraphReversalFilter
public SignedBPGraphReversalBlock getShortestContainerReversalStartingAfter(int position, BPGraphPoint point)
getShortestContainerReversalStartingAfter
in class SignedPermutationBPGraphReversalFilter
position
- a given positionpoint
- a given point
public java.util.TreeSet<SignedBPGraphReversalBlock> getHurdleCuttingReversalsStartingAt(int position)
position
- a given position
public java.util.TreeSet<SignedBPGraphReversalBlock> getHurdleCuttingReversalsWithinIntervals(java.util.Vector intervals)
intervals
- a Vector of int[] (length=2, start and end positions of an interval)
public java.util.TreeSet<SignedBPGraphReversalBlock> getHurdleCuttingReversalsBetweenIntervals(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> getHurdleCuttingReversals()
public SignedBPGraphReversalBlock getLongestHurdleCuttingReversalStartingAt(int position)
position
- a given position
public java.util.TreeSet getHurdleMergingReversals()
public java.util.TreeSet getHurdleMergingReversalsStartingAt(int position)
position
- a given position
public java.util.TreeSet<SignedBPGraphReversalBlock> getHurdleMergingReversalsWithinIntervals(java.util.Vector intervals)
intervals
- a Vector of int[] (length=2, start and end positions of an interval)
public java.util.TreeSet getHurdleMergingReversalsBetweenIntervals(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 SignedBPGraphReversalBlock getLongestHurdleMergingReversalStartingAt(int position)
position
- a given position
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