baobab.bio.permutation
Class IntervalUtil

java.lang.Object
  extended by baobab.bio.permutation.IntervalUtil

public class IntervalUtil
extends java.lang.Object

The IntervalUtil class contains utility methods which deal with intervals of permutations

Author:
Marilia D. V. Braga

Constructor Summary
IntervalUtil()
           
 
Method Summary
static BitList boundariesToList(PermutationBPGraph permutation, int start, int end)
          Generates a BitList from an interval
static int[] boundariesToSortedList(PermutationBPGraph permutation, int start, int end)
          Generates a TraceElement from a reversal
static int[] boundariesToUnsortedList(PermutationBPGraph permutation, int start, int end)
           
static int[] listToBoundaries(int[] positions, boolean isLinear, int[] segment)
           
static int[] listToBoundaries(PermutationBPGraph permutation, BitList segment)
          Generates a reversal from a trace element
static int[] listToBoundaries(PermutationBPGraph permutation, int[] segment)
           
static BitList unsortedToSortedList(int[] unsortedSegment, int permutationSize)
          Generates a BitList from an interval
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

IntervalUtil

public IntervalUtil()
Method Detail

boundariesToUnsortedList

public static int[] boundariesToUnsortedList(PermutationBPGraph permutation,
                                             int start,
                                             int end)

listToBoundaries

public static int[] listToBoundaries(int[] positions,
                                     boolean isLinear,
                                     int[] segment)

listToBoundaries

public static int[] listToBoundaries(PermutationBPGraph permutation,
                                     int[] segment)

boundariesToSortedList

public static int[] boundariesToSortedList(PermutationBPGraph permutation,
                                           int start,
                                           int end)
Generates a TraceElement from a reversal

Parameters:
permutation - the permutation
start - the start position of a reversal
end - the end position of a reversal
Returns:
the trace element generated

unsortedToSortedList

public static BitList unsortedToSortedList(int[] unsortedSegment,
                                           int permutationSize)
Generates a BitList from an interval

Parameters:
unsortedSegment - the values in the interval
permutationSize - the size of the permutation containing the interval
Returns:
a BitList representing the interval

boundariesToList

public static BitList boundariesToList(PermutationBPGraph permutation,
                                       int start,
                                       int end)
Generates a BitList from an interval

Parameters:
permutation - the permutation
start - the start position of a reversal
end - the end position of a reversal
Returns:
a BitList representing the interval

listToBoundaries

public static int[] listToBoundaries(PermutationBPGraph permutation,
                                     BitList segment)
Generates a reversal from a trace element

Parameters:
permutation - the given permutation
Returns:
a reversal as an array of int with length = 2 (position 0 = start, position 1 = end of the reversal)