Uses of Interface
baobab.bio.permutation.PermutationBPGraph

Packages that use PermutationBPGraph
baobab.bio.permutation   
 

Uses of PermutationBPGraph in baobab.bio.permutation
 

Classes in baobab.bio.permutation that implement PermutationBPGraph
 class ComplexSignedPermutationBPGraph
          The ComplexSignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the ComplexSignedPermutationBPGraph class deals with hurdles)
 class SignedPermutationBPGraph
          The SignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the SignedPermutationBPGraph class does not deal with hurdles)
 class UnsignedPermutationBPGraph
          The UnsignedPermutationBPGraph class represents an unsigned permutation pair and its breakpoint graph
 class WeightedSignedPermutationBPGraph
          The WeightedSignedPermutationBPGraph class represents a weighted signed permutation pair and its breakpoint graph (the WeightedSignedPermutationBPGraph class does not deal with hurdles)
 

Methods in baobab.bio.permutation that return PermutationBPGraph
 PermutationBPGraph PermutationBPGraphIntervalFilter.getPermutation()
           
 PermutationBPGraph PermutationBPGraphFormatter.getPermutation()
           
 PermutationBPGraph SignedPermutationBPGraph.getPermutationBPGraph()
          Gets this permutation
 PermutationBPGraph UnsignedPermutationBPGraph.getPermutationBPGraph()
          Gets this permutation
 

Methods in baobab.bio.permutation with parameters of type PermutationBPGraph
static BitList IntervalUtil.boundariesToList(PermutationBPGraph permutation, int start, int end)
          Generates a BitList from an interval
static int[] IntervalUtil.boundariesToSortedList(PermutationBPGraph permutation, int start, int end)
          Generates a TraceElement from a reversal
static int[] IntervalUtil.boundariesToUnsortedList(PermutationBPGraph permutation, int start, int end)
           
static int[] IntervalUtil.listToBoundaries(PermutationBPGraph permutation, BitList segment)
          Generates a reversal from a trace element
static int[] IntervalUtil.listToBoundaries(PermutationBPGraph permutation, int[] segment)
           
 

Constructors in baobab.bio.permutation with parameters of type PermutationBPGraph
BPGraphReversalBlock(PermutationBPGraph permutation, BPGraphPoint start, BPGraphPoint end)
          Creates a new block
BPGraphReversalBlock(PermutationBPGraph permutation, int start, int end)
          Creates a new block
BPGraphTranspositionBlock(PermutationBPGraph permutation, BPGraphPoint start, BPGraphPoint middle, BPGraphPoint end)
          Creates a new block
BPGraphTranspositionBlock(PermutationBPGraph permutation, int start, int middle, int end)
          Creates a new block
PermutationBPGraphIntervalFilter(PermutationBPGraph permutation)