A B C D E F G H I J K L M N O P Q R S T U V W

P

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
 

A B C D E F G H I J K L M N O P Q R S T U V W