Uses of Class
baobab.bio.permutation.SignedReversalBlock

Packages that use SignedReversalBlock
baobab.bio.permutation   
 

Uses of SignedReversalBlock in baobab.bio.permutation
 

Methods in baobab.bio.permutation that return SignedReversalBlock
 SignedReversalBlock SignedPermutationReversalFilter.getFirstShortestReversalStartingAfter(int position)
          Gets the first shortest reversal starting after a specific position (inclusive)
 SignedReversalBlock ComplexSignedPermutationReversalFilter.getFirstShortestReversalStartingAfter(int position)
          Gets the first shortest reversal starting after a specific position (inclusive)
 SignedReversalBlock SignedPermutationReversalFilter.getLastLongestReversalStartingAfter(int position)
          Gets the last longest reversal starting after a specific position (inclusive)
 SignedReversalBlock ComplexSignedPermutationReversalFilter.getLastLongestReversalStartingAfter(int position)
          Gets the last longest reversal starting after a specific position (inclusive)
 SignedReversalBlock SignedPermutationReversalFilter.getLongestCycleSplittingReversalStartingAt(int position)
          Gets the longest cycle splitting reversal starting exactly at a specific position
 SignedReversalBlock ComplexSignedPermutationReversalFilter.getLongestHurdleCuttingReversalStartingAt(int position)
          Gets the longest hurdle cutting reversal starting at a specific position
 SignedReversalBlock ComplexSignedPermutationReversalFilter.getLongestHurdleMergingReversalStartingAt(int position)
          Gets the longest hurdle merging reversal starting at a specific position
 SignedReversalBlock SignedPermutationReversalFilter.getLongestReversalStartingAt(int position)
          Gets the longest reversal starting exactly at a specific position
 SignedReversalBlock ComplexSignedPermutationReversalFilter.getLongestReversalStartingAt(int position)
          Gets the longest reversal starting exactly at a specific position
 SignedReversalBlock SignedPermutationReversalFilter.getShortestContainerReversalStartingAfter(int position, Point point)
          Gets the shortest reversal block starting after a specific position (inclusive) that contains a given point
 SignedReversalBlock ComplexSignedPermutationReversalFilter.getShortestContainerReversalStartingAfter(int position, Point 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 SignedReversalBlock
 java.util.TreeSet<SignedReversalBlock> ComplexSignedPermutationReversalFilter.getContainerReversalsStartingAfter(int position, Point point)
          Gets the reversals starting after a specific position (inclusive) which contain a given point
 java.util.TreeSet<SignedReversalBlock> SignedPermutationReversalFilter.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<SignedReversalBlock> SignedPermutationReversalFilter.getCycleSplittingReversalsStartingAt(int position)
          Gets the list of cycle splitting reversals starting exactly at a specific position
 java.util.TreeSet<SignedReversalBlock> SignedPermutationReversalFilter.getCycleSplittingReversalsWithinIntervals(java.util.Vector<int[]> intervals)
          Gets the list of proper reversals of this permutation within the given intervals
 java.util.TreeSet<SignedReversalBlock> ComplexSignedPermutationReversalFilter.getHurdleCuttingReversals()
          Gets the list of hurdle cutting reversals
 java.util.TreeSet<SignedReversalBlock> ComplexSignedPermutationReversalFilter.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> ComplexSignedPermutationReversalFilter.getHurdleCuttingReversalsStartingAt(int position)
          Gets the list of hurdle cutting reversals starting exactly at a specific position
 java.util.TreeSet<SignedReversalBlock> ComplexSignedPermutationReversalFilter.getHurdleCuttingReversalsWithinIntervals(java.util.Vector intervals)
          Gets the list of hurdle cutting reversals of this permutation within the given intervals
 java.util.TreeSet<SignedReversalBlock> SignedPermutationReversalFilter.getReversalsStartingAt(int position)
          Gets the reversals starting exactly at a specific position
 java.util.TreeSet<SignedReversalBlock> ComplexSignedPermutationReversalFilter.getReversalsStartingAt(int position)
          Gets the reversals starting exactly at a specific position