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T

TerminusSymmetryReversalConstraint - Class in baobab.bio.permutation
 
TerminusSymmetryReversalConstraint(double, int, int) - Constructor for class baobab.bio.permutation.TerminusSymmetryReversalConstraint
 
testReversal(int, int) - Method in class baobab.bio.permutation.PerfectReversalConstraint
 
testReversal(int, int) - Method in class baobab.bio.permutation.ReversalConstraint
 
testReversal(int, int) - Method in class baobab.bio.permutation.StrataReversalConstraint
 
toBytes(long) - Static method in class baobab.util.Bytes
Returns a 8-byte array built from a long.
toBytes(long, byte[]) - Static method in class baobab.util.Bytes
Build a 8-byte array from a long.
toBytes(long, byte[], int) - Static method in class baobab.util.Bytes
Build a 8-byte array from a long.
toBytes(int) - Static method in class baobab.util.Bytes
Returns a 4-byte array built from an int.
toBytes(int, byte[]) - Static method in class baobab.util.Bytes
Build a 4-byte array from an int.
toBytes(int, byte[], int) - Static method in class baobab.util.Bytes
Build a 4-byte array from an int.
toFullString(int) - Method in class baobab.bio.permutation.colinearity.LinkPermutationToColinearBlock
 
toInt(byte[]) - Static method in class baobab.util.Bytes
Build an int from first 4 bytes of the array.
toInt(byte[], int) - Static method in class baobab.util.Bytes
Build an int from first 4 bytes of the array.
toIntArray() - Method in class baobab.bio.permutation.BPGraphTranspositionBlock
Gets a representation of the block as an array of int, with size 3, representing its start, middle and end positions
toLong(byte[]) - Static method in class baobab.util.Bytes
Build a long from first 8 bytes of the array.
toLong(byte[], int) - Static method in class baobab.util.Bytes
Build a long from first 8 bytes of the array.
toShort(byte[]) - Static method in class baobab.util.Bytes
Build a short from first 2 bytes of the array.
toString() - Method in class baobab.bio.permutation.BPGraphCycle
 
toString() - Method in class baobab.bio.permutation.BPGraphCyclePartition
 
toString() - Method in class baobab.bio.permutation.BPGraphPoint
 
toString() - Method in class baobab.bio.permutation.BPGraphReversalBlock
 
toString(int) - Method in class baobab.bio.permutation.colinearity.LinkPermutationToColinearBlock
 
toString() - Method in class baobab.bio.permutation.ComplexSignedPermutationBPGraph
 
toString() - Method in class baobab.bio.permutation.counter.PermutationCounter
Produces a string representation of a permutation counter
toString() - Method in class baobab.bio.permutation.SignedBPGraphComponent
 
toString() - Method in class baobab.bio.permutation.SignedBPGraphCycle
 
toString() - Method in class baobab.bio.permutation.SignedBPGraphReversalBlock
 
toString() - Method in class baobab.bio.permutation.SignedPermutationBPGraph
 
toString() - Method in class baobab.bio.permutation.strata.Strata
Produces a string representation of a strata
toString() - Method in class baobab.bio.permutation.strata.StrataSortedSet
 
toString() - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
 
toString(int, int) - Method in class baobab.trace.DecomposedTrace
Produces a string representation of a trace
toString(int, int, String[], Hashtable<String, TreeSet<String>>, boolean) - Method in class baobab.trace.DecomposedTrace
Produces a string representation of a decomposed trace
toString(int, int) - Method in class baobab.trace.SubTrace
Produces a string representation of a trace
toString(int, int, String[], boolean) - Method in class baobab.trace.SubTrace
Produces a string representation of a trace
toString(int, int, String[], Hashtable<String, TreeSet<String>>, boolean) - Method in class baobab.trace.SubTrace
Produces a string representation of a trace
toString(int, int) - Method in class baobab.trace.Trace
Produces a string representation of a trace
toString(int, int, String[], boolean) - Method in class baobab.trace.Trace
Produces a string representation of a trace
toString(int, int, String[], Hashtable<String, TreeSet<String>>, boolean) - Method in class baobab.trace.Trace
Produces a string representation of a trace
toString() - Method in class baobab.trace.Trace
 
toString() - Method in class baobab.util.BitList
 
toString() - Method in class baobab.util.CompressibleSortedSet
 
toString() - Method in class baobab.util.FreezableCompressibleSortedSet
 
Trace - Class in baobab.trace
The Trace class represents a trace.
Trace(int[], int) - Constructor for class baobab.trace.Trace
Constructs a Trace
Trace(Trace) - Constructor for class baobab.trace.Trace
Constructs a Trace, as a clone of a given trace
TraceAppLogicUtil - Class in baobab.applogic.trace
 
TraceAppLogicUtil(String, String, String, boolean, String[], Hashtable<String, TreeSet<String>>, boolean) - Constructor for class baobab.applogic.trace.TraceAppLogicUtil
 
TraceAppLogicUtil(String, String, String, boolean) - Constructor for class baobab.applogic.trace.TraceAppLogicUtil
 
TraceAppLogicUtil(String, String, String) - Constructor for class baobab.applogic.trace.TraceAppLogicUtil
 
TraceCoder - Class in baobab.trace
The TraceCoder class codifies a trace as a bidimensional array of bytes.
TraceComparator - Class in baobab.trace
The TraceComparator class represents a comparator of traces.
TraceComparator(int, int, int) - Constructor for class baobab.trace.TraceComparator
 
TraceJoinerComparator - Class in baobab.trace
The TraceComparator class represents a comparator of traces.
TraceJoinerComparator(int, int, int) - Constructor for class baobab.trace.TraceJoinerComparator
 
TraceSortedSet - Class in baobab.trace
The TraceSortedSet class represents a sorted set of traces (all traces have the same number of elements).
TraceSortedSet(String, int, int, int, int, int, double) - Constructor for class baobab.trace.TraceSortedSet
 
TraceWidth - Class in baobab.trace
 
TraceWidth() - Constructor for class baobab.trace.TraceWidth
 
transpose(int[], int, int, int) - Static method in class baobab.bio.permutation.PermutationUtil
Make a new permutation, by transposing blocks at the permutation between the specified positions
transposeToNewPermutation(BPGraphPoint, BPGraphPoint, BPGraphPoint) - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
Make a new permutation, by transposing the permutation between the specified positions
transposeToNewPermutation(int, int, int) - Method in class baobab.bio.permutation.UnsignedPermutationBPGraph
Make a new permutation, by transposing the permutation between the specified positions

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