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A

add(LinkPermutationToColinearBlock) - Method in class baobab.bio.permutation.colinearity.ColinearBlock
 
addElement(int[], int, int) - Method in class baobab.trace.SubTrace
Adds a new element to this trace
addElement(int[], int, int) - Method in class baobab.trace.Trace
Adds a new element to this trace
addElement(Trace) - Method in class baobab.trace.TraceSortedSet
 
addElement(T) - Method in class baobab.util.CompressibleSortedSet
Add an element to this set (in general, additions are not processed one by one, but accumulated and then processed in batch mode, from time to time or when the set is resolved).
addElements(Vector<BitList>, int, int) - Method in class baobab.trace.DecomposedTrace
Adds a new element to this trace
addPosition(int) - Method in class baobab.bio.permutation.strata.Strata
 
addPosToIgnore(int) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
addStrata(Strata) - Method in class baobab.bio.permutation.strata.StrataSortedSet
 
addValue(String) - Method in class baobab.bio.permutation.colinearity.ColinearBlock
 
analyzeDecomposedTraces(ComplexSignedPermutationBPGraph, int, boolean, int, int, boolean, int, int, int, String, int[], int, boolean, TerminusSymmetryReversalConstraint) - Method in class baobab.applogic.trace.TraceAppLogicUtil
 
analyzeSignedPermutation - Class in baobab.exec.permutation
Builds the breakpoint graph between two signed permutations (or genomes) and prints its properties (number of points, cycles, components and the reversal distance)
analyzeSignedPermutation() - Constructor for class baobab.exec.permutation.analyzeSignedPermutation
 
analyzeSignedPermutationIntervals - Class in baobab.exec.permutation
 
analyzeSignedPermutationIntervals() - Constructor for class baobab.exec.permutation.analyzeSignedPermutationIntervals
 
analyzeTraces(SignedPermutationBPGraph, int, boolean, int, int, boolean, int, int, int, PerfectReversalConstraint, TerminusSymmetryReversalConstraint, StrataReversalConstraint) - Method in class baobab.applogic.trace.TraceAppLogicUtil
 
analyzeTraces - Class in baobab.exec.trace
Enumerates all the traces (classes of solutions) of sorting a signed permutation (or genome) into another.
analyzeTraces() - Constructor for class baobab.exec.trace.analyzeTraces
 
analyzeTracesBenchmark0(SignedPermutationBPGraph, int, boolean, int, int, boolean, int, int, int, PerfectReversalConstraint, TerminusSymmetryReversalConstraint, StrataReversalConstraint) - Method in class baobab.applogic.trace.benchmark.BenchmarkTraceAppLogicUtil
 
analyzeTracesBenchmark0 - Class in baobab.exec.trace.benchmark
Enumerates all the traces (classes of solutions) of sorting a signed permutation (or genome) into another.
analyzeTracesBenchmark0() - Constructor for class baobab.exec.trace.benchmark.analyzeTracesBenchmark0
 
analyzeTracesBenchmark1(SignedPermutationBPGraph, int, boolean, int, int, boolean, PerfectReversalConstraint, TerminusSymmetryReversalConstraint, StrataReversalConstraint) - Method in class baobab.applogic.trace.benchmark.BenchmarkTraceAppLogicUtil
 
analyzeTracesBenchmark1 - Class in baobab.exec.trace.benchmark
Enumerates all the traces (classes of solutions) of sorting a signed permutation (or genome) into another.
analyzeTracesBenchmark1() - Constructor for class baobab.exec.trace.benchmark.analyzeTracesBenchmark1
 
analyzeTracesBenchmark2(SignedPermutationBPGraph, int, boolean, int, int, boolean, PerfectReversalConstraint, TerminusSymmetryReversalConstraint, StrataReversalConstraint) - Method in class baobab.applogic.trace.benchmark.BenchmarkTraceAppLogicUtil
 
analyzeTracesBenchmark2 - Class in baobab.exec.trace.benchmark
Enumerates all the traces (classes of solutions) of sorting a signed permutation (or genome) into another.
analyzeTracesBenchmark2() - Constructor for class baobab.exec.trace.benchmark.analyzeTracesBenchmark2
 
analyzeTracesForRandomPermutations - Class in baobab.exec.trace
 
analyzeTracesForRandomPermutations() - Constructor for class baobab.exec.trace.analyzeTracesForRandomPermutations
 
analyzeUnsignedPermutation - Class in baobab.exec.permutation
Builds the breakpoint graph between two unsigned permutations
analyzeUnsignedPermutation() - Constructor for class baobab.exec.permutation.analyzeUnsignedPermutation
 
and(BitList) - Method in class baobab.util.BitList
 
append(byte[], byte[]) - Static method in class baobab.util.Bytes
Appends two bytes array into one.
AppLogicUtil - Class in baobab.applogic
 
AppLogicUtil(String, String, String, boolean) - Constructor for class baobab.applogic.AppLogicUtil
 
AppLogicUtil(String, String, String) - Constructor for class baobab.applogic.AppLogicUtil
 
applyAllReversals(SignedPermutationBPGraph, int, int, long) - Method in class baobab.applogic.AppLogicUtil
 
areEqual(byte[], byte[]) - Static method in class baobab.util.Bytes
Compares two byte arrays for equality.
ASYMMETRIC_REVERSAL - Static variable in class baobab.bio.permutation.TerminusSymmetryReversalConstraint
 
autoStart(boolean, ColinearBlock) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 

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