com.hfg.bio.phylogeny

Class UncorrectedModel

java.lang.Object

com.hfg.bio.phylogeny.UncorrectedModel

All Implemented Interfaces:

DistanceMatrixModel

public class UncorrectedModel
extends Object
implements DistanceMatrixModel

Distance matrix calculation method that is simply the fraction of mismatches.

 distance = mismatches / aligned_length
 

If both sequences contain a gap at a given position, it is not counted towards the alignment length.

Constructor Summary

Constructors

Constructor and Description
UncorrectedModel()

Method Summary

Modifier and Type	Method and Description
float	calculateDistance(BioSequence inSeq1, BioSequence inSeq2) Calculates the distance score for a pair of sequences.
String	name() Returns the model name as required by the DistanceMatrixModel interface.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

UncorrectedModel

public UncorrectedModel()

Method Detail

name

public String name()

Returns the model name as required by the DistanceMatrixModel interface.

Specified by:

name in interface DistanceMatrixModel

calculateDistance

public float calculateDistance(BioSequence inSeq1,
                               BioSequence inSeq2)

Calculates the distance score for a pair of sequences. The sequences must be aligned to be the same length. If both sequences contain a gap at a given position, it is not counted towards the alignment length.

Specified by:

calculateDistance in interface DistanceMatrixModel