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parse(String, int, int, Hashtable<String, Integer>)
- Static method in class baobab.trace.
SubTrace
parse(String, int, int)
- Static method in class baobab.trace.
SubTrace
parse(String, int, int, Hashtable<String, Integer>)
- Static method in class baobab.trace.
Trace
parse(String, int, int)
- Static method in class baobab.trace.
Trace
parseBitList(byte[], int, int, int)
- Static method in class baobab.trace.
SubTrace
parseBitList(byte[], int, int)
- Static method in class baobab.trace.
Trace
PerfectReversalConstraint
- Class in
baobab.bio.permutation
PerfectReversalConstraint(SignedPermutationBPGraph, boolean, int)
- Constructor for class baobab.bio.permutation.
PerfectReversalConstraint
performReversals
- Class in
baobab.exec.permutation
Performs reversals in the origin signed permutation (or genome).
performReversals()
- Constructor for class baobab.exec.permutation.
performReversals
PermutationBPGraph
- Interface in
baobab.bio.permutation
The PermutationBPGraph interface represents a general permutation pair and its breakpoint graph
PermutationBPGraphFormatter
- Class in
baobab.bio.permutation
The PermutationBPGraphFormatter class gives a text representation of a breakpoint graph
PermutationBPGraphIntervalFilter
- Class in
baobab.bio.permutation
The PermutationBPGraphIntervalFilter class searchs special kinds of intervals which are common to the origin and target permutations
PermutationBPGraphIntervalFilter(PermutationBPGraph)
- Constructor for class baobab.bio.permutation.
PermutationBPGraphIntervalFilter
PermutationCounter
- Class in
baobab.bio.permutation.counter
PermutationCounter(int[], long)
- Constructor for class baobab.bio.permutation.counter.
PermutationCounter
Constructs a PermutationCounter
PermutationCounterCoder
- Class in
baobab.bio.permutation.counter
The TraceCoder class codifies a trace as a bidimensional array of bytes.
PermutationCounterCoder(int)
- Constructor for class baobab.bio.permutation.counter.
PermutationCounterCoder
Constructs a TraceCoder
PermutationCounterComparator
- Class in
baobab.bio.permutation.counter
The TraceComparator class represents a comparator of traces.
PermutationCounterComparator()
- Constructor for class baobab.bio.permutation.counter.
PermutationCounterComparator
PermutationException
- Exception in
baobab.bio.permutation
The PermutationException class represents an exception when dealing with permutations
PermutationException(String)
- Constructor for exception baobab.bio.permutation.
PermutationException
PermutationException(String, Throwable)
- Constructor for exception baobab.bio.permutation.
PermutationException
PermutationUtil
- Class in
baobab.bio.permutation
The PermutationUtil class contains utility methods which deal with permutations as arrays of int
PermutationUtil()
- Constructor for class baobab.bio.permutation.
PermutationUtil
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