baobab.bio.permutation
Class PerfectReversalConstraint

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

public class PerfectReversalConstraint
extends java.lang.Object


Field Summary
static int MAX_SCORE_NON_PERFECT_REVERSAL
           
 
Constructor Summary
PerfectReversalConstraint(SignedPermutationBPGraph permutation, boolean progressiveDetection, int maxNonPerfectReversalScore)
           
 
Method Summary
 boolean canBeRelaxed()
           
 java.lang.String getDescription()
           
 java.util.TreeSet<BitList> getIntervals()
           
 int getMaxNonPerfectReversalScore()
           
 java.util.Vector<int[]> getNextReversals()
           
 java.lang.String getScoreDescription()
           
 boolean isPositionRelated()
           
 void refreshIntervals()
           
 int scoreReversal(int permutationSize, int[] element)
           
 boolean testReversal(int start, int end)
           
 void update(SignedPermutationBPGraph permutation)
           
 void updateIntervals(int permutationSize, int[] element)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

MAX_SCORE_NON_PERFECT_REVERSAL

public static final int MAX_SCORE_NON_PERFECT_REVERSAL
See Also:
Constant Field Values
Constructor Detail

PerfectReversalConstraint

public PerfectReversalConstraint(SignedPermutationBPGraph permutation,
                                 boolean progressiveDetection,
                                 int maxNonPerfectReversalScore)
Method Detail

update

public void update(SignedPermutationBPGraph permutation)

refreshIntervals

public void refreshIntervals()

getIntervals

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

getMaxNonPerfectReversalScore

public int getMaxNonPerfectReversalScore()

canBeRelaxed

public boolean canBeRelaxed()

isPositionRelated

public boolean isPositionRelated()

testReversal

public boolean testReversal(int start,
                            int end)

scoreReversal

public int scoreReversal(int permutationSize,
                         int[] element)

updateIntervals

public void updateIntervals(int permutationSize,
                            int[] element)

getNextReversals

public java.util.Vector<int[]> getNextReversals()

getDescription

public java.lang.String getDescription()

getScoreDescription

public java.lang.String getScoreDescription()