baobab.bio.permutation
Class PermutationBPGraphIntervalFilter

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

public class PermutationBPGraphIntervalFilter
extends java.lang.Object

The PermutationBPGraphIntervalFilter class searchs special kinds of intervals which are common to the origin and target permutations

Author:
Marilia D. V. Braga

Constructor Summary
PermutationBPGraphIntervalFilter(PermutationBPGraph permutation)
           
 
Method Summary
 java.util.TreeSet<BitList> getCommonIntervals()
           
 java.util.TreeSet<BitList> getCommonIntervals(boolean monoorientedIntervals)
           
 BitList getCoorientedInterval(int acceptedNumberOfInsertions, java.lang.String[] intervalAsListOfNames)
           
 BitList getInterval(int acceptedNumberOfInsertions, java.lang.String[] intervalAsListOfNames)
           
 java.util.TreeSet<BitList> getMonoorientedCommonIntervals()
           
 PermutationBPGraph getPermutation()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PermutationBPGraphIntervalFilter

public PermutationBPGraphIntervalFilter(PermutationBPGraph permutation)
Method Detail

getPermutation

public PermutationBPGraph getPermutation()

getCommonIntervals

public java.util.TreeSet<BitList> getCommonIntervals(boolean monoorientedIntervals)

getCommonIntervals

public java.util.TreeSet<BitList> getCommonIntervals()

getMonoorientedCommonIntervals

public java.util.TreeSet<BitList> getMonoorientedCommonIntervals()

getInterval

public BitList getInterval(int acceptedNumberOfInsertions,
                           java.lang.String[] intervalAsListOfNames)

getCoorientedInterval

public BitList getCoorientedInterval(int acceptedNumberOfInsertions,
                                     java.lang.String[] intervalAsListOfNames)