baobab.bio.permutation
Class TerminusSymmetryReversalConstraint

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

public class TerminusSymmetryReversalConstraint
extends java.lang.Object


Field Summary
static int ASYMMETRIC_REVERSAL
           
static int EXTERNAL_REVERSAL
           
static int SYMMETRIC_REVERSAL
           
 
Constructor Summary
TerminusSymmetryReversalConstraint(double terminusSymmetryRate, int maxExternalReversalScore, int maxNonSymmetricReversalScore)
           
 
Method Summary
 boolean canBeRelaxed()
           
 java.lang.String getDescription()
           
 int getMaxExternalReversalScore()
           
 int getMaxNonSymmetricReversalScore()
           
 java.util.Vector<int[]> getNextReversals()
           
 java.lang.String getScoreDescription()
           
 double getSymmetryRate()
           
 boolean isPositionRelated()
           
 int qualifyInterval(SignedPermutationBPGraph permutation, int start, int end)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

ASYMMETRIC_REVERSAL

public static final int ASYMMETRIC_REVERSAL
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Constant Field Values

EXTERNAL_REVERSAL

public static final int EXTERNAL_REVERSAL
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Constant Field Values

SYMMETRIC_REVERSAL

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

TerminusSymmetryReversalConstraint

public TerminusSymmetryReversalConstraint(double terminusSymmetryRate,
                                          int maxExternalReversalScore,
                                          int maxNonSymmetricReversalScore)
Method Detail

getMaxNonSymmetricReversalScore

public int getMaxNonSymmetricReversalScore()

getMaxExternalReversalScore

public int getMaxExternalReversalScore()

getSymmetryRate

public double getSymmetryRate()

canBeRelaxed

public boolean canBeRelaxed()

isPositionRelated

public boolean isPositionRelated()

getNextReversals

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

getDescription

public java.lang.String getDescription()

getScoreDescription

public java.lang.String getScoreDescription()

qualifyInterval

public int qualifyInterval(SignedPermutationBPGraph permutation,
                           int start,
                           int end)