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C

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
 
canBeRelaxed() - Method in class baobab.bio.permutation.PerfectReversalConstraint
 
canBeRelaxed() - Method in class baobab.bio.permutation.ReversalConstraint
 
canBeRelaxed() - Method in class baobab.bio.permutation.StrataReversalConstraint
 
canBeRelaxed() - Method in class baobab.bio.permutation.TerminusSymmetryReversalConstraint
 
canCollapse() - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Tests whether this permutation can be collapsed
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)
canonizePermutations - Class in baobab.exec.permutation
 
canonizePermutations() - Constructor for class baobab.exec.permutation.canonizePermutations
 
cardinality() - Method in class baobab.util.BitList
 
clear(boolean) - Method in class baobab.trace.TraceSortedSet
Removes all elements in this set
clear() - Method in class baobab.util.CompressibleSortedSet
Removes all elements in this set
clear(boolean) - Method in class baobab.util.CompressibleSortedSet
Removes all elements in this set
clear(boolean) - Method in class baobab.util.FreezableCompressibleSortedSet
Removes all elements in this set
clone() - Method in class baobab.bio.permutation.ComplexSignedPermutationBPGraph
 
clone() - Method in class baobab.bio.permutation.SignedPermutationBPGraph
 
clone() - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
 
clone() - Method in class baobab.util.BitList
 
close() - Method in class baobab.applogic.AppLogicUtil
 
close() - Method in class baobab.applogic.strata.StrataAppLogicUtil
 
close(boolean) - Method in class baobab.applogic.trace.benchmark.BenchmarkTraceAppLogicUtil
 
close(boolean) - Method in class baobab.applogic.trace.TraceAppLogicUtil
 
closeColinearBlock(ColinearBlock) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
closeTraceInFile() - Method in class baobab.applogic.trace.TraceAppLogicUtil
 
code(PermutationCounter, byte[][], int, int) - Method in class baobab.bio.permutation.counter.PermutationCounterCoder
 
code(Vector<PermutationCounter>) - Method in class baobab.bio.permutation.counter.PermutationCounterCoder
 
code(SubTrace) - Method in class baobab.trace.SubTraceCoder
 
code(SubTrace, byte[][], int, int, int, int) - Method in class baobab.trace.SubTraceCoder
 
code(Vector<Trace>) - Method in class baobab.trace.SubTraceCoder
 
code(Trace) - Method in class baobab.trace.TraceCoder
 
code(Trace, byte[][], int, int) - Method in class baobab.trace.TraceCoder
 
code(Vector<Trace>) - Method in class baobab.trace.TraceCoder
 
code(Vector<T>) - Method in interface baobab.util.Coder
Codes a vector of objects as a bidimensional array of bytes.
Coder<T> - Interface in baobab.util
The Coder interface represents a coder of an object as a bidimensional array of bytes
codeTraces(int, int, int, int, int, int) - Method in class baobab.applogic.trace.TraceAppLogicUtil
 
codeTraces - Class in baobab.exec.trace
 
codeTraces() - Constructor for class baobab.exec.trace.codeTraces
 
ColinearBlock - Class in baobab.bio.permutation.colinearity
 
ColinearBlock(int) - Constructor for class baobab.bio.permutation.colinearity.ColinearBlock
 
ColinearPermutation - Class in baobab.bio.permutation.colinearity
 
ColinearPermutation(String, String) - Constructor for class baobab.bio.permutation.colinearity.ColinearPermutation
 
collapse(int[], boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Collapses a permutation (eliminating the adjacencies)
collapse(boolean) - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Collapses this permutation (eliminating adjacencies)
collapseBk(int[], boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Collapses a permutation (eliminating the adjacencies)
collapsePermutation - Class in baobab.exec.permutation
Collapses a permutation breakpoint graph, eliminating its adjacencies.
collapsePermutation() - Constructor for class baobab.exec.permutation.collapsePermutation
 
compare(Object, Object) - Method in class baobab.bio.permutation.BPGraphBlockComparator
Compares two blocks
compare(BPGraphReversalBlock, BPGraphReversalBlock) - Method in class baobab.bio.permutation.BPGraphReversalBlockComparator
Compares two blocks
compare(PermutationCounter, PermutationCounter) - Method in class baobab.bio.permutation.counter.PermutationCounterComparator
 
compare(Trace, Trace) - Method in class baobab.trace.SubTraceComparator
 
compare(Trace, Trace) - Method in class baobab.trace.TraceComparator
 
compare(Trace, Trace) - Method in class baobab.trace.TraceJoinerComparator
 
compareBitLists(BitList, BitList) - Static method in class baobab.util.BitList
 
compareTo(Object) - Method in class baobab.bio.permutation.BPGraphPoint
Compares this point to another point
compareTo(Object) - Method in class baobab.bio.permutation.BPGraphReversalBlock
Compares this block to another block
compareTo(Object) - Method in class baobab.bio.permutation.BPGraphTranspositionBlock
Compares this block to another block
compareTo(Object) - Method in class baobab.bio.permutation.colinearity.LinkPermutationToColinearBlock
 
compareTo(ReversalConstraint) - Method in class baobab.bio.permutation.ReversalConstraint
 
compareTo(Object) - Method in class baobab.bio.permutation.strata.Strata
 
compareTo(Object) - Method in class baobab.util.BitList
 
compareTo(byte[], byte[]) - Static method in class baobab.util.Bytes
Compares two byte arrays as specified by Comparable.
ComplexSignedPermutationBPGraph - Class in baobab.bio.permutation
The ComplexSignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the ComplexSignedPermutationBPGraph class deals with hurdles)
ComplexSignedPermutationBPGraph(SignedPermutationBPGraph) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a complex signed permutation over a simple signed permutation
ComplexSignedPermutationBPGraph(int[]) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new linear permutation (assumes the identity permutation as target)
ComplexSignedPermutationBPGraph(int[], double[]) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new linear permutation (assumes the identity permutation as target)
ComplexSignedPermutationBPGraph(int[], boolean) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new permutation (assumes the identity permutation as target)
ComplexSignedPermutationBPGraph(int[], boolean, double[]) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new permutation (assumes the identity permutation as target)
ComplexSignedPermutationBPGraph(int[], int[]) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new linear permutation
ComplexSignedPermutationBPGraph(int[], int[], double[]) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new linear permutation
ComplexSignedPermutationBPGraph(int[], int[], boolean) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new permutation
ComplexSignedPermutationBPGraph(int[], int[], boolean, double[]) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new permutation
ComplexSignedPermutationBPGraph(Vector<String>, Vector<String>, boolean, Vector<Double>) - Constructor for class baobab.bio.permutation.ComplexSignedPermutationBPGraph
Creates a new permutation
ComplexSignedPermutationBPGraphReversalFilter - Class in baobab.bio.permutation
The ComplexSignedPermutationBPGraphReversalFilter filters valid reversal blocks for a ComplexSignedPermutationBPGraph
compressBytes(byte[]) - Static method in class baobab.util.Util
 
compressBytes(byte[], byte[]) - Static method in class baobab.util.Util
 
CompressibleSortedSet<T> - Class in baobab.util
The CompressibleSortedSet class represents a sorted set of codable objects.
CompressibleSortedSet(Comparator<T>, Coder<T>, int, int, int, double) - Constructor for class baobab.util.CompressibleSortedSet
CompressibleSortedSet constructor
CompressibleSortedSet(Coder<T>, int, int, int) - Constructor for class baobab.util.CompressibleSortedSet
CompressibleSortedSet constructor
CompressibleSortedSet(Comparator<T>, Coder<T>) - Constructor for class baobab.util.CompressibleSortedSet
CompressibleSortedSet constructor
CompressibleSortedSet(Coder<T>) - Constructor for class baobab.util.CompressibleSortedSet
CompressibleSortedSet constructor
compressString(String) - Static method in class baobab.util.Util
 
computeSolutionsByStrata - Class in baobab.exec.strata
 
computeSolutionsByStrata() - Constructor for class baobab.exec.strata.computeSolutionsByStrata
 
computeSolutionsOfTraces - Class in baobab.exec.trace
 
computeSolutionsOfTraces() - Constructor for class baobab.exec.trace.computeSolutionsOfTraces
 
computeTracesByReversal - Class in baobab.exec.trace
 
computeTracesByReversal() - Constructor for class baobab.exec.trace.computeTracesByReversal
 
computeTracesByReversalForNonCanonizedPermutations - Class in baobab.exec.trace
 
computeTracesByReversalForNonCanonizedPermutations() - Constructor for class baobab.exec.trace.computeTracesByReversalForNonCanonizedPermutations
 
condense(byte[]) - Static method in class baobab.util.ByteSetUtil
 
condense(int[]) - Static method in class baobab.util.ByteSetUtil
 
confirmPosition(int, ColinearBlock) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
contains(Strata) - Method in class baobab.bio.permutation.strata.StrataSortedSet
 
containsUnorientedComponent(int[], boolean) - Static method in class baobab.bio.permutation.PermutationUtil
Tests whether the permutation contains an unoriented component (hurdle)
containsUnorientedComponent() - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Tests whether this permutation contains an unoriented component (hurdle)
containsValue(String) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
countAllSortingSequences(SignedPermutationBPGraph, int) - Method in class baobab.applogic.AppLogicUtil
 
countAllSortingSequences - Class in baobab.exec.permutation
 
countAllSortingSequences() - Constructor for class baobab.exec.permutation.countAllSortingSequences
 
createRandomSignedPermutation(int) - Static method in class baobab.bio.permutation.RandomPermutationBPGraph
 
createRandomSignedPermutation(int, int, Vector<int[]>, Long) - Static method in class baobab.bio.permutation.RandomPermutationBPGraph
 
createRandomSignedPermutation(int, int, boolean, Vector<int[]>, Long) - Static method in class baobab.bio.permutation.RandomPermutationBPGraph
 
createRandomSignedPermutation2(int) - Static method in class baobab.bio.permutation.RandomPermutationBPGraph
 
createRandomStratifiedSignedPermutation(int, int, boolean, Vector<int[]>, int[], boolean, long) - Static method in class baobab.bio.permutation.RandomPermutationBPGraph
 
createRandomStratifiedSignedPermutation(int, int, boolean, Vector<int[]>, Vector<Integer>, boolean, long) - Static method in class baobab.bio.permutation.RandomPermutationBPGraph
 
currentFullTimeStamp() - Static method in class baobab.util.Util
 
currentSimpleTimeStamp() - Static method in class baobab.util.Util
 
currentTimeStamp() - Static method in class baobab.util.Util
 

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