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