baobab.bio.permutation
Class ComplexSignedPermutationBPGraphReversalFilter

java.lang.Object
  extended by baobab.bio.permutation.SignedPermutationBPGraphReversalFilter
      extended by baobab.bio.permutation.ComplexSignedPermutationBPGraphReversalFilter

public class ComplexSignedPermutationBPGraphReversalFilter
extends SignedPermutationBPGraphReversalFilter

The ComplexSignedPermutationBPGraphReversalFilter filters valid reversal blocks for a ComplexSignedPermutationBPGraph

Author:
Marilia D. V. Braga

Method Summary
 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 baobab.bio.permutation.SignedPermutationBPGraphReversalFilter
getCycleSplittingReversals, getCycleSplittingReversalsAsArraysOfInt, getCycleSplittingReversalsBetweenIntervals, getCycleSplittingReversalsBetweenIntervalsAsArraysOfInt, getCycleSplittingReversalsStartingAt, getCycleSplittingReversalsWithinIntervals, getCycleSplittingReversalsWithinIntervalsAsArraysOfInt, getLongestCycleSplittingReversalStartingAt, getPermutation
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

getReversalsStartingAt

public java.util.TreeSet<SignedBPGraphReversalBlock> getReversalsStartingAt(int position)
Gets the reversals starting exactly at a specific position

Overrides:
getReversalsStartingAt in class SignedPermutationBPGraphReversalFilter
Parameters:
position - a given position
Returns:
a collection containing the reversals

getContainerReversalsStartingAfter

public java.util.TreeSet<SignedBPGraphReversalBlock> getContainerReversalsStartingAfter(int position,
                                                                                        BPGraphPoint point)
Gets the reversals starting after a specific position (inclusive) which contain a given point

Overrides:
getContainerReversalsStartingAfter in class SignedPermutationBPGraphReversalFilter
Parameters:
position - a given position
point - a given point
Returns:
a collection with the reversals

getLongestReversalStartingAt

public SignedBPGraphReversalBlock getLongestReversalStartingAt(int position)
Gets the longest reversal starting exactly at a specific position

Overrides:
getLongestReversalStartingAt in class SignedPermutationBPGraphReversalFilter
Parameters:
position - a given position
Returns:
a reversal block

getLastLongestReversalStartingAfter

public SignedBPGraphReversalBlock getLastLongestReversalStartingAfter(int position)
Gets the last longest reversal starting after a specific position (inclusive)

Overrides:
getLastLongestReversalStartingAfter in class SignedPermutationBPGraphReversalFilter
Parameters:
position - a given position
Returns:
a reversal block

getFirstShortestReversalStartingAfter

public SignedBPGraphReversalBlock getFirstShortestReversalStartingAfter(int position)
Gets the first shortest reversal starting after a specific position (inclusive)

Overrides:
getFirstShortestReversalStartingAfter in class SignedPermutationBPGraphReversalFilter
Returns:
a reversal block

getShortestContainerReversalStartingAfter

public SignedBPGraphReversalBlock getShortestContainerReversalStartingAfter(int position,
                                                                            BPGraphPoint point)
Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point

Overrides:
getShortestContainerReversalStartingAfter in class SignedPermutationBPGraphReversalFilter
Parameters:
position - a given position
point - a given point
Returns:
a reversal block

getHurdleCuttingReversalsStartingAt

public java.util.TreeSet<SignedBPGraphReversalBlock> getHurdleCuttingReversalsStartingAt(int position)
Gets the list of hurdle cutting reversals starting exactly at a specific position

Parameters:
position - a given position
Returns:
a Collection with the list of reversal blocks

getHurdleCuttingReversalsWithinIntervals

public java.util.TreeSet<SignedBPGraphReversalBlock> getHurdleCuttingReversalsWithinIntervals(java.util.Vector intervals)
Gets the list of hurdle cutting reversals of this permutation within the given intervals

Parameters:
intervals - a Vector of int[] (length=2, start and end positions of an interval)
Returns:
a Collection with the blocks representing the hurdle cutting reversals

getHurdleCuttingReversalsBetweenIntervals

public 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

Parameters:
interval1 - (length=2, start and end positions of the first interval)
interval2 - (length=2, start and end positions of the second interval)
Returns:
a Collection with the blocks representing the hurdle cutting reversals

getHurdleCuttingReversals

public java.util.TreeSet<SignedBPGraphReversalBlock> getHurdleCuttingReversals()
Gets the list of hurdle cutting reversals

Returns:
a Collection with the list of reversal blocks

getLongestHurdleCuttingReversalStartingAt

public SignedBPGraphReversalBlock getLongestHurdleCuttingReversalStartingAt(int position)
Gets the longest hurdle cutting reversal starting at a specific position

Parameters:
position - a given position
Returns:
a reversal block

getHurdleMergingReversals

public java.util.TreeSet getHurdleMergingReversals()
Gets the list of hurdle merging reversals

Returns:
a Collection with the list of reversal blocks

getHurdleMergingReversalsStartingAt

public java.util.TreeSet getHurdleMergingReversalsStartingAt(int position)
Gets the list of hurdle merging reversals starting exactly at a specific position

Parameters:
position - a given position
Returns:
a Collection with the list of reversal blocks

getHurdleMergingReversalsWithinIntervals

public java.util.TreeSet<SignedBPGraphReversalBlock> getHurdleMergingReversalsWithinIntervals(java.util.Vector intervals)
Gets the list of hurdle merging reversals of this permutation within the given intervals

Parameters:
intervals - a Vector of int[] (length=2, start and end positions of an interval)
Returns:
a Collection with the blocks representing the hurdle merging reversals

getHurdleMergingReversalsBetweenIntervals

public 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

Parameters:
interval1 - (length=2, start and end positions of the first interval)
interval2 - (length=2, start and end positions of the second interval)
Returns:
a Collection with the blocks representing the hurdle merging reversals

getLongestHurdleMergingReversalStartingAt

public SignedBPGraphReversalBlock getLongestHurdleMergingReversalStartingAt(int position)
Gets the longest hurdle merging reversal starting at a specific position

Parameters:
position - a given position
Returns:
a reversal block