Uses of Class
baobab.bio.permutation.SignedBPGraphReversalBlock

Packages that use SignedBPGraphReversalBlock
baobab.bio.permutation   
 

Uses of SignedBPGraphReversalBlock in baobab.bio.permutation
 

Methods in baobab.bio.permutation that return SignedBPGraphReversalBlock
 SignedBPGraphReversalBlock ComplexSignedPermutationBPGraphReversalFilter.getFirstShortestReversalStartingAfter(int position)
          Gets the first shortest reversal starting after a specific position (inclusive)
 SignedBPGraphReversalBlock SignedPermutationBPGraphReversalFilter.getFirstShortestReversalStartingAfter(int position)
          Gets the first shortest reversal starting after a specific position (inclusive)
 SignedBPGraphReversalBlock ComplexSignedPermutationBPGraphReversalFilter.getLastLongestReversalStartingAfter(int position)
          Gets the last longest reversal starting after a specific position (inclusive)
 SignedBPGraphReversalBlock SignedPermutationBPGraphReversalFilter.getLastLongestReversalStartingAfter(int position)
          Gets the last longest reversal starting after a specific position (inclusive)
 SignedBPGraphReversalBlock SignedPermutationBPGraphReversalFilter.getLongestCycleSplittingReversalStartingAt(int position)
          Gets the longest cycle splitting reversal starting exactly at a specific position
 SignedBPGraphReversalBlock ComplexSignedPermutationBPGraphReversalFilter.getLongestHurdleCuttingReversalStartingAt(int position)
          Gets the longest hurdle cutting reversal starting at a specific position
 SignedBPGraphReversalBlock ComplexSignedPermutationBPGraphReversalFilter.getLongestHurdleMergingReversalStartingAt(int position)
          Gets the longest hurdle merging reversal starting at a specific position
 SignedBPGraphReversalBlock ComplexSignedPermutationBPGraphReversalFilter.getLongestReversalStartingAt(int position)
          Gets the longest reversal starting exactly at a specific position
 SignedBPGraphReversalBlock SignedPermutationBPGraphReversalFilter.getLongestReversalStartingAt(int position)
          Gets the longest reversal starting exactly at a specific position
 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
 

Methods in baobab.bio.permutation that return types with arguments of type SignedBPGraphReversalBlock
 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<SignedBPGraphReversalBlock> SignedPermutationBPGraphReversalFilter.getCycleSplittingReversals()
          Gets the list of cycle splitting reversals of this permutation
 java.util.TreeSet<SignedBPGraphReversalBlock> SignedPermutationBPGraphReversalFilter.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.TreeSet<SignedBPGraphReversalBlock> SignedPermutationBPGraphReversalFilter.getCycleSplittingReversalsStartingAt(int position)
          Gets the list of cycle splitting reversals starting exactly at a specific position
 java.util.TreeSet<SignedBPGraphReversalBlock> SignedPermutationBPGraphReversalFilter.getCycleSplittingReversalsWithinIntervals(java.util.Vector<int[]> intervals)
          Gets the list of proper reversals of this permutation within the given intervals
 java.util.TreeSet<SignedBPGraphReversalBlock> ComplexSignedPermutationBPGraphReversalFilter.getHurdleCuttingReversals()
          Gets the list of hurdle cutting reversals
 java.util.TreeSet<SignedBPGraphReversalBlock> ComplexSignedPermutationBPGraphReversalFilter.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> ComplexSignedPermutationBPGraphReversalFilter.getHurdleCuttingReversalsStartingAt(int position)
          Gets the list of hurdle cutting reversals starting exactly at a specific position
 java.util.TreeSet<SignedBPGraphReversalBlock> ComplexSignedPermutationBPGraphReversalFilter.getHurdleCuttingReversalsWithinIntervals(java.util.Vector intervals)
          Gets the list of hurdle cutting reversals of this permutation within the given intervals
 java.util.TreeSet<SignedBPGraphReversalBlock> ComplexSignedPermutationBPGraphReversalFilter.getHurdleMergingReversalsWithinIntervals(java.util.Vector intervals)
          Gets the list of hurdle merging reversals of this permutation within the given intervals
 java.util.TreeSet<SignedBPGraphReversalBlock> ComplexSignedPermutationBPGraphReversalFilter.getReversalsStartingAt(int position)
          Gets the reversals starting exactly at a specific position
 java.util.TreeSet<SignedBPGraphReversalBlock> SignedPermutationBPGraphReversalFilter.getReversalsStartingAt(int position)
          Gets the reversals starting exactly at a specific position