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calculateReversalDistance
- Class in
baobab.exec.permutation
calculateReversalDistance()
- Constructor for class baobab.exec.permutation.
calculateReversalDistance
calculateSignedReversalDistance(int[])
- Static method in class baobab.bio.permutation.
PermutationUtil
Calculates the reversal distance between a given signed permutation and the identity
calculateSignedReversalDistance(int[], boolean)
- Static method in class baobab.bio.permutation.
PermutationUtil
Calculates the reversal distance between a given signed permutation and the identity
calculateSignedReversalDistance(int[], int[])
- Static method in class baobab.bio.permutation.
PermutationUtil
Calculates the reversal distance between the given origin and target signed permutations
calculateSignedReversalDistance(int[], int[], boolean)
- Static method in class baobab.bio.permutation.
PermutationUtil
Calculates the reversal distance between the given origin and target signed permutations
calculateWidth(Trace, int, int)
- Static method in class baobab.trace.
TraceWidth
canonizePermutations(Vector<String>, Vector<String>)
- Static method in class baobab.bio.permutation.
PermutationUtil
Canonize the origin and the target permutations - eliminate insertions/deletions, replace each gene by a number between 1 and n (n is the number of common elements between the origin and the target permutations)
clone()
- Method in class baobab.bio.permutation.
ComplexSignedPermutation
clone()
- Method in class baobab.bio.permutation.
SignedPermutation
clone()
- Method in class baobab.bio.permutation.
UnsignedPermutation
clone(byte[][][])
- Static method in class baobab.trace.
TraceUtil
clone(BitList[][])
- Static method in class baobab.trace.
TraceUtil
code(Trace)
- Method in class baobab.trace.
TraceCoder
code(Trace, byte[][], int, int)
- Method in class baobab.trace.
TraceCoder
collapse(int[], boolean)
- Static method in class baobab.bio.permutation.
PermutationUtil
Collapses a permutation (eliminating the adjacencies)
compare(Object, Object)
- Method in class baobab.bio.permutation.
BlockComparator
Compares two blocks
compare(Object, Object)
- Method in class baobab.bio.permutation.
ReversalBlockComparator
Compares two blocks
compare(Trace, Trace)
- Method in class baobab.trace.
TraceComparator
compares(byte[], byte[])
- Static method in class baobab.trace.
TraceUtil
compares(byte[][], byte[][])
- Static method in class baobab.trace.
TraceUtil
compares(byte[][][], byte[][][])
- Static method in class baobab.trace.
TraceUtil
compares(BitList, BitList)
- Static method in class baobab.trace.
TraceUtil
compares(BitSet, BitSet)
- Static method in class baobab.trace.
TraceUtil
compares(BitList[], BitList[])
- Static method in class baobab.trace.
TraceUtil
compares(BitList[][], BitList[][])
- Static method in class baobab.trace.
TraceUtil
compareTo(Object)
- Method in class baobab.bio.permutation.
Point
Compares this point to another point
compareTo(Object)
- Method in class baobab.bio.permutation.
ReversalBlock
Compares this block to another block
compareTo(Object)
- Method in class baobab.bio.permutation.
TranspositionBlock
Compares this block to another block
ComplexSignedPermutation
- Class in
baobab.bio.permutation
The ComplexSignedPermutation class represents a signed permutation (the ComplexSignedPermutation class deals with hurdles)
ComplexSignedPermutation(int[])
- Constructor for class baobab.bio.permutation.
ComplexSignedPermutation
Creates a new linear permutation (assumes the identity permutation as target)
ComplexSignedPermutation(int[], boolean)
- Constructor for class baobab.bio.permutation.
ComplexSignedPermutation
Creates a new permutation (assumes the identity permutation as target)
ComplexSignedPermutation(int[], int[])
- Constructor for class baobab.bio.permutation.
ComplexSignedPermutation
Creates a new linear permutation
ComplexSignedPermutation(int[], int[], boolean)
- Constructor for class baobab.bio.permutation.
ComplexSignedPermutation
Creates a new permutation
ComplexSignedPermutationReversalFilter
- Class in
baobab.bio.permutation
The ComplexSignedPermutationReversalFilter filters valid reversal blocks for a ComplexSignedPermutation
condense(byte[])
- Static method in class baobab.trace.
TraceUtil
condense(byte[][])
- Static method in class baobab.trace.
TraceUtil
condense(byte[][][])
- Static method in class baobab.trace.
TraceUtil
containsUnorientedComponent(int[], boolean)
- Static method in class baobab.bio.permutation.
PermutationUtil
Tests whether the permutation contains an unoriented component (hurdle)
createRandomSignedPermutation(int, int, long)
- Static method in class baobab.bio.permutation.
RandomPermutation
createRandomSignedPermutation(int, int, boolean, long)
- Static method in class baobab.bio.permutation.
RandomPermutation
Cycle
- Class in
baobab.bio.permutation
The Cycle class represents a cycle of points of a permutation
CyclePartition
- Class in
baobab.bio.permutation
The CyclePartition class represents a partition of a cycle of a permutation
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