alun.genio
Class AffectionStatusLocus

java.lang.Object
  alun.genio.LinkageLocus
      alun.genio.AffectionStatusLocus

public class AffectionStatusLocus
extends LinkageLocus

This class represents a locus as specified in the linkage affectation status format.

Field Summary

java.lang.String[]	comment An array holding the comment strings for each linkage liability class.
double[][]	liab The two dimentional array containing the liability data.
java.lang.String	line2comment The string of comment from the second line of input.
java.lang.String	line3comment The string of comment from the third line of input.

Fields inherited from class alun.genio.LinkageLocus

AFFECTION_STATUS, BINARY_FACTORS, freq, line1comment, NUMBERED_ALLELES, QUANTITATIVE_VARIABLE, type

Constructor Summary

AffectionStatusLocus(AffectionStatusLocus a)

AffectionStatusLocus(LinkageFormatter b)
Creates a new locus with data read from the given input formatter.

Method Summary

double[][]	getLiabilities() Returns the two dimentional array containing the liability data.
LinkagePhenotype	readPhenotype(LinkageFormatter f) Reads the data for a phenotype at this locus from the given input formatter.
java.lang.String	toString() Returns a string representing the parameters of this locus in the same format at in the linkage .par file.

Methods inherited from class alun.genio.LinkageLocus

alleleFrequencies, firstComment, locName, nAlleles, setAlleleFrequencies

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

liab

public double[][] liab

The two dimentional array containing the liability data. These will typically be penetrance probabilities.

comment

public java.lang.String[] comment

An array holding the comment strings for each linkage liability class.

line2comment

public java.lang.String line2comment

The string of comment from the second line of input.

line3comment

public java.lang.String line3comment

The string of comment from the third line of input.

Constructor Detail

AffectionStatusLocus

public AffectionStatusLocus(LinkageFormatter b)
                     throws java.io.IOException

Creates a new locus with data read from the given input formatter.

Throws:

java.io.IOException

AffectionStatusLocus

public AffectionStatusLocus(AffectionStatusLocus a)

Method Detail

readPhenotype

public LinkagePhenotype readPhenotype(LinkageFormatter f)

Reads the data for a phenotype at this locus from the given input formatter.

Specified by:

readPhenotype in class LinkageLocus

getLiabilities

public double[][] getLiabilities()

Returns the two dimentional array containing the liability data.

toString

public java.lang.String toString()

Returns a string representing the parameters of this locus in the same format at in the linkage .par file.

Overrides:

toString in class java.lang.Object