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B

baobab.applogic - package baobab.applogic
 
baobab.applogic.strata - package baobab.applogic.strata
 
baobab.applogic.trace - package baobab.applogic.trace
 
baobab.applogic.trace.benchmark - package baobab.applogic.trace.benchmark
 
baobab.bio.permutation - package baobab.bio.permutation
 
baobab.bio.permutation.colinearity - package baobab.bio.permutation.colinearity
 
baobab.bio.permutation.counter - package baobab.bio.permutation.counter
 
baobab.bio.permutation.strata - package baobab.bio.permutation.strata
 
baobab.bio.util - package baobab.bio.util
 
baobab.exec - package baobab.exec
 
baobab.exec.bio - package baobab.exec.bio
 
baobab.exec.permutation - package baobab.exec.permutation
 
baobab.exec.permutation.colinearity - package baobab.exec.permutation.colinearity
 
baobab.exec.strata - package baobab.exec.strata
 
baobab.exec.trace - package baobab.exec.trace
 
baobab.exec.trace.benchmark - package baobab.exec.trace.benchmark
 
baobab.trace - package baobab.trace
 
baobab.util - package baobab.util
 
BenchmarkTraceAppLogicUtil - Class in baobab.applogic.trace.benchmark
 
BenchmarkTraceAppLogicUtil(String, String, String, boolean, String[], Hashtable<String, TreeSet<String>>, boolean) - Constructor for class baobab.applogic.trace.benchmark.BenchmarkTraceAppLogicUtil
 
BenchmarkTraceAppLogicUtil(String, String, String, boolean) - Constructor for class baobab.applogic.trace.benchmark.BenchmarkTraceAppLogicUtil
 
BenchmarkTraceAppLogicUtil(String, String, String) - Constructor for class baobab.applogic.trace.benchmark.BenchmarkTraceAppLogicUtil
 
BitList - Class in baobab.util
 
BitList(byte[]) - Constructor for class baobab.util.BitList
 
BitList(byte[], int, int) - Constructor for class baobab.util.BitList
 
BitList(int) - Constructor for class baobab.util.BitList
 
BitList(int, boolean) - Constructor for class baobab.util.BitList
 
bitListToBytes(BitList) - Static method in class baobab.util.ByteSetUtil
 
bitListToInts(BitList) - Static method in class baobab.util.ByteSetUtil
 
BLOCK_SPLIT_BALANCE - Static variable in class baobab.util.CompressibleSortedSet
 
boundariesToList(PermutationBPGraph, int, int) - Static method in class baobab.bio.permutation.IntervalUtil
Generates a BitList from an interval
boundariesToSortedList(PermutationBPGraph, int, int) - Static method in class baobab.bio.permutation.IntervalUtil
Generates a TraceElement from a reversal
boundariesToUnsortedList(PermutationBPGraph, int, int) - Static method in class baobab.bio.permutation.IntervalUtil
 
BPGraphBlockComparator - Class in baobab.bio.permutation
The BPGraphBlockComparator class represents a comparator of two elementary blocks of a signed permutation breakpoint graph
BPGraphBlockComparator() - Constructor for class baobab.bio.permutation.BPGraphBlockComparator
 
BPGraphCycle - Class in baobab.bio.permutation
The BPGraphCycle class represents a cycle of points of a permutation breakpoint graph
BPGraphCyclePartition - Class in baobab.bio.permutation
The BPGraphCyclePartition class represents a partition of a cycle of a breakpoint graph
BPGraphPoint - Class in baobab.bio.permutation
The BPGraphPoint class represents a point between two values of a permutation (and dark edges in the corresponding breakpoint graph)
BPGraphReversalBlock - Class in baobab.bio.permutation
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
BPGraphReversalBlock(PermutationBPGraph, BPGraphPoint, BPGraphPoint) - Constructor for class baobab.bio.permutation.BPGraphReversalBlock
Creates a new block
BPGraphReversalBlock(PermutationBPGraph, int, int) - Constructor for class baobab.bio.permutation.BPGraphReversalBlock
Creates a new block
BPGraphReversalBlockComparator - Class in baobab.bio.permutation
The BPGraphReversalBlockComparator class represents a comparator of two elementary blocks of a signed permutation
BPGraphReversalBlockComparator() - Constructor for class baobab.bio.permutation.BPGraphReversalBlockComparator
 
BPGraphTranspositionBlock - Class in baobab.bio.permutation
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
BPGraphTranspositionBlock(PermutationBPGraph, BPGraphPoint, BPGraphPoint, BPGraphPoint) - Constructor for class baobab.bio.permutation.BPGraphTranspositionBlock
Creates a new block
BPGraphTranspositionBlock(PermutationBPGraph, int, int, int) - Constructor for class baobab.bio.permutation.BPGraphTranspositionBlock
Creates a new block
Bytes - Class in baobab.util
Static methods for managing byte arrays (all methods follow Big Endian order where most significant bits are in front).
ByteSetUtil - Class in baobab.util
 
ByteSetUtil() - Constructor for class baobab.util.ByteSetUtil
 
bytesToBitList(byte[], int) - Static method in class baobab.util.ByteSetUtil
 

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