Class Summary |
BPGraphBlockComparator |
The BPGraphBlockComparator class represents a comparator of two elementary blocks of a signed permutation breakpoint graph |
BPGraphCycle |
The BPGraphCycle class represents a cycle of points of a permutation breakpoint graph |
BPGraphCyclePartition |
The BPGraphCyclePartition class represents a partition of a cycle of a breakpoint graph |
BPGraphPoint |
The BPGraphPoint class represents a point between two values of a permutation
(and dark edges in the corresponding breakpoint graph) |
BPGraphReversalBlock |
The BPGraphReversalBlock class represents an elementary block of a permutation
given by its start and end points, which can be used as the breakpoints of a reversal |
BPGraphReversalBlockComparator |
The BPGraphReversalBlockComparator class represents a comparator of two elementary blocks of a signed permutation |
BPGraphTranspositionBlock |
The BPGraphTranspositionBlock class represents an elementary block of a permutation,
given by its start, middle and end points, which can be used as the breakpoints of a transposition |
ComplexSignedPermutationBPGraph |
The ComplexSignedPermutationBPGraph class represents a signed permutation pair
and its breakpoint graph
(the ComplexSignedPermutationBPGraph class deals with hurdles) |
ComplexSignedPermutationBPGraphReversalFilter |
The ComplexSignedPermutationBPGraphReversalFilter filters valid reversal blocks
for a ComplexSignedPermutationBPGraph |
IntervalUtil |
The IntervalUtil class contains utility methods which deal with
intervals of permutations |
PerfectReversalConstraint |
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PermutationBPGraphFormatter |
The PermutationBPGraphFormatter class gives a text representation of a
breakpoint graph |
PermutationBPGraphIntervalFilter |
The PermutationBPGraphIntervalFilter class searchs special kinds of intervals
which are common to the origin and target permutations |
PermutationUtil |
The PermutationUtil class contains utility methods which deal
with permutations as arrays of int |
RandomPermutationBPGraph |
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ReversalConstraint |
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SignedBPGraphComponent |
The SignedBPGraphComponent class represents a component of signed cycles
of the breakpoint graph of a signed permutation pair |
SignedBPGraphCycle |
The SignedBPGraphCycle class represents a cycle of points of a
the breakpoint graph of a signed permutation pair |
SignedBPGraphReversalBlock |
The SignedBPGraphReversalBlock class represents an elementary block of a signed permutation,
given by its start and end points, which can be used as the breakpoints of a signed reversal |
SignedPermutationBPGraph |
The SignedPermutationBPGraph class represents a signed permutation pair
and its breakpoint graph
(the SignedPermutationBPGraph class does not deal with hurdles) |
SignedPermutationBPGraphReversalFilter |
The SignedPermutationBPGraphReversalFilter filters valid reversal blocks
for a SignedPermutationBPGraph |
StrataReversalConstraint |
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TerminusSymmetryReversalConstraint |
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UnsignedPermutationBPGraph |
The UnsignedPermutationBPGraph class represents an unsigned permutation pair
and its breakpoint graph |
WeightedSignedPermutationBPGraph |
The WeightedSignedPermutationBPGraph class represents a weighted signed permutation pair
and its breakpoint graph
(the WeightedSignedPermutationBPGraph class does not deal with hurdles) |
WeightedSignedPermutationBPGraphReversalFilter |
The WeightedSignedPermutationBPGraphReversalFilter filters valid reversal blocks
for a WeightedSignedPermutationBPGraph |