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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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