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S

scoreReversal(int, int[]) - Method in class baobab.bio.permutation.PerfectReversalConstraint
 
searchElement(T) - Method in class baobab.util.CompressibleSortedSet
Search an element in this set (WARNING: frequent use of this method can cause a high overhead because usually it forces an internal partial decompression)
set(int) - Method in class baobab.util.BitList
 
setComplete() - Method in class baobab.bio.permutation.strata.Strata
 
setConstraintScore(int[]) - Method in class baobab.trace.SubTrace
 
setCurrentPos(int) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
setDebugElementData(int[]) - Method in class baobab.trace.Trace
 
setDescriptor(Hashtable<String, String[]>, Hashtable<String, TreeSet<String>>) - Method in class baobab.bio.permutation.SignedPermutationBPGraph
 
setReadAsReversed(boolean) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
setSolutionsByHeight(long[]) - Method in class baobab.trace.TraceSortedSet
 
setSuperHurdle() - Method in class baobab.bio.permutation.SignedBPGraphComponent
Sets this component as super hurdle
setTracesByHeight(int[]) - Method in class baobab.trace.TraceSortedSet
 
setTracesByWidth(int[]) - Method in class baobab.trace.TraceSortedSet
 
SignedBPGraphComponent - Class in baobab.bio.permutation
The SignedBPGraphComponent class represents a component of signed cycles of the breakpoint graph of a signed permutation pair
SignedBPGraphCycle - Class in baobab.bio.permutation
The SignedBPGraphCycle class represents a cycle of points of a the breakpoint graph of a signed permutation pair
SignedBPGraphReversalBlock - Class in baobab.bio.permutation
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
SignedBPGraphReversalBlock(SignedPermutationBPGraph, BPGraphPoint, BPGraphPoint) - Constructor for class baobab.bio.permutation.SignedBPGraphReversalBlock
Creates a new block
SignedBPGraphReversalBlock(SignedPermutationBPGraph, int, int) - Constructor for class baobab.bio.permutation.SignedBPGraphReversalBlock
Creates a new block
SignedPermutationBPGraph - Class in baobab.bio.permutation
The SignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the SignedPermutationBPGraph class does not deal with hurdles)
SignedPermutationBPGraph(int[]) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new linear permutation (assumes the identity permutation as target)
SignedPermutationBPGraph(int[], double[]) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new linear permutation (assumes the identity permutation as target)
SignedPermutationBPGraph(int[], boolean, double[]) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new permutation (assumes the identity permutation as target)
SignedPermutationBPGraph(int[], boolean) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new permutation (assumes the identity permutation as target)
SignedPermutationBPGraph(int[], int[]) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new linear permutation
SignedPermutationBPGraph(int[], int[], boolean) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new permutation
SignedPermutationBPGraph(int[], int[], boolean, double[]) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new permutation
SignedPermutationBPGraph(Vector<String>, Vector<String>, boolean) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new permutation
SignedPermutationBPGraph(Vector<String>, Vector<String>, boolean, Vector<Double>) - Constructor for class baobab.bio.permutation.SignedPermutationBPGraph
Creates a new permutation
SignedPermutationBPGraphReversalFilter - Class in baobab.bio.permutation
The SignedPermutationBPGraphReversalFilter filters valid reversal blocks for a SignedPermutationBPGraph
size() - Method in class baobab.bio.permutation.BPGraphCycle
Gets the number of points in this cycle
size() - Method in class baobab.bio.permutation.BPGraphCyclePartition
Gets the size (number of points) of this partition
size() - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
size() - Method in interface baobab.bio.permutation.PermutationBPGraph
Gets the size (or the number of values) of the breakpoint graph
size() - Method in class baobab.bio.permutation.SignedPermutationBPGraph
Gets the size (or the number of values) of the permutation
size() - Method in class baobab.bio.permutation.strata.Strata
 
size() - Method in class baobab.bio.permutation.strata.StrataSortedSet
 
size() - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
Gets the size (or the number of elements) of the permutation
size() - Method in class baobab.util.BitList
 
sort - Class in baobab.exec.permutation
Sorts the origin permutation (or genome) into the target permutation (or genome) applying the optimal number of reversals.
sort() - Constructor for class baobab.exec.permutation.sort
 
sortBytes(byte[]) - Static method in class baobab.util.ByteSetUtil
 
sortIntegers(int[]) - Static method in class baobab.util.ByteSetUtil
 
sortWeightedSignedPermutation - Class in baobab.exec.permutation
 
sortWeightedSignedPermutation() - Constructor for class baobab.exec.permutation.sortWeightedSignedPermutation
 
span(String, int) - Static method in class baobab.util.Util
 
split(PermutationCounter) - Method in class baobab.bio.permutation.counter.PermutationCounter
 
split(Trace) - Method in class baobab.trace.Trace
 
split(T) - Method in interface baobab.util.Joinable
Split the object joinable from this object
SPLIT_CYCLE - Static variable in class baobab.bio.permutation.SignedBPGraphReversalBlock
 
start(String, boolean, ColinearBlock) - Method in class baobab.bio.permutation.colinearity.ColinearPermutation
 
Strata - Class in baobab.bio.permutation.strata
 
Strata(int) - Constructor for class baobab.bio.permutation.strata.Strata
 
Strata(int, int) - Constructor for class baobab.bio.permutation.strata.Strata
 
Strata(Strata) - Constructor for class baobab.bio.permutation.strata.Strata
 
StrataAppLogicUtil - Class in baobab.applogic.strata
 
StrataAppLogicUtil(String, String, String) - Constructor for class baobab.applogic.strata.StrataAppLogicUtil
 
StrataReversalConstraint - Class in baobab.bio.permutation
 
StrataReversalConstraint(int[], int) - Constructor for class baobab.bio.permutation.StrataReversalConstraint
 
StrataSortedSet - Class in baobab.bio.permutation.strata
The StrataSortedSet class represents a set of valid strata partitions for a permutation
StrataSortedSet(int) - Constructor for class baobab.bio.permutation.strata.StrataSortedSet
 
subSeq - Class in baobab.exec.bio
 
subSeq() - Constructor for class baobab.exec.bio.subSeq
 
SubTrace - Class in baobab.trace
The SubTrace class represents a subset of a trace
SubTrace(int[], int) - Constructor for class baobab.trace.SubTrace
Constructs a SubTrace
SubTrace(SubTrace) - Constructor for class baobab.trace.SubTrace
Constructs a SubTrace, as a clone of a given SubTrace
SubTraceCoder - Class in baobab.trace
The SubTraceCoder class codifies a subtrace as a bidimensional array of bytes.
SubTraceComparator - Class in baobab.trace
The SubTraceComparator class represents a comparator of subtraces
SubTraceComparator(int, int, int) - Constructor for class baobab.trace.SubTraceComparator
 
SubTraceSortedSet - Class in baobab.trace
The SubTraceSortedSet class represents a sorted set of subtraces (all subtraces have the same number of elements).
SubTraceSortedSet(String, int, int, int, int, int, double, int) - Constructor for class baobab.trace.SubTraceSortedSet
 
suffix(int) - Method in class baobab.bio.permutation.strata.Strata
 
SYMMETRIC_REVERSAL - Static variable in class baobab.bio.permutation.TerminusSymmetryReversalConstraint
 

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