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Packages that use SignedBPGraphReversalBlock | |
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baobab.bio.permutation |
Uses of SignedBPGraphReversalBlock in baobab.bio.permutation |
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Methods in baobab.bio.permutation that return SignedBPGraphReversalBlock | |
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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 | |
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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 |
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