fr.orsay.lri.varna.models.treealign
Class ExampleDistance3.SequenceAlignResult

java.lang.Object
  extended by fr.orsay.lri.varna.models.treealign.ExampleDistance3.SequenceAlignResult
Enclosing class:
ExampleDistance3

public class ExampleDistance3.SequenceAlignResult
extends Object


Field Summary
private  int[][] alignment
           
private  double distance
           
 
Constructor Summary
ExampleDistance3.SequenceAlignResult()
           
 
Method Summary
 int[][] getAlignment()
          The result array is a matrix of height 2 and width at most length(sequence A) + length(sequence B).
 double getDistance()
           
 void setAlignment(int[][] alignment)
           
 void setDistance(double distance)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

distance

private double distance

alignment

private int[][] alignment
Constructor Detail

ExampleDistance3.SequenceAlignResult

public ExampleDistance3.SequenceAlignResult()
Method Detail

getDistance

public double getDistance()

setDistance

public void setDistance(double distance)

getAlignment

public int[][] getAlignment()
The result array is a matrix of height 2 and width at most length(sequence A) + length(sequence B). with result[0] is the alignment for A and result[1] the alignment for B. The alignment consists int the indexes of the original bases positions, with -1 when there is no match.


setAlignment

public void setAlignment(int[][] alignment)