alun.genio
Class LinkageLocus

java.lang.Object
  alun.genio.LinkageLocus

Direct Known Subclasses:

AffectionStatusLocus, NumberedAlleleLocus, QuantitativeLocus

public abstract class LinkageLocus
extends java.lang.Object

This is the base class from which the linkage locus types are derived. Only the numbered alleles type of locus is currently properly implemented.

Field Summary

static int	AFFECTION_STATUS Represents the linakge affectation status locus type.
static int	BINARY_FACTORS Represents the linkage binary factors locus type.
double[]	freq
java.lang.String	line1comment
static int	NUMBERED_ALLELES Represents the linkage numbered alleles locus type.
static int	QUANTITATIVE_VARIABLE Represents the linkage quantiative variable locus type.
int	type The type of the locus specified.

Constructor Summary

LinkageLocus()

LinkageLocus(LinkageLocus l)

Method Summary

double[]	alleleFrequencies() Returns the allele frequencies for the locus.
java.lang.String	firstComment() Returns the comment string from the first line of input associated with this locus.
java.lang.String	locName()
int	nAlleles() Returns the number of alleles that this locus has.
abstract LinkagePhenotype	readPhenotype(LinkageFormatter f) A method to read in the data for this locus from the given input formatter.
void	setAlleleFrequencies(double[] f)

Methods inherited from class java.lang.Object

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

Field Detail

type

public int type

The type of the locus specified. This will be one of QUANTITATIVE_VARIABLE, AFFECTION_STATUS BINARY_FACTORS or NUMBERED_ALLELES.

QUANTITATIVE_VARIABLE

public static final int QUANTITATIVE_VARIABLE

Represents the linkage quantiative variable locus type.

See Also:

Constant Field Values

AFFECTION_STATUS

public static final int AFFECTION_STATUS

Represents the linakge affectation status locus type.

See Also:

Constant Field Values

BINARY_FACTORS

public static final int BINARY_FACTORS

Represents the linkage binary factors locus type.

See Also:

Constant Field Values

NUMBERED_ALLELES

public static final int NUMBERED_ALLELES

Represents the linkage numbered alleles locus type.

See Also:

Constant Field Values

freq

public double[] freq

line1comment

public java.lang.String line1comment

Constructor Detail

LinkageLocus

public LinkageLocus(LinkageLocus l)

LinkageLocus

public LinkageLocus()

Method Detail

readPhenotype

public abstract LinkagePhenotype readPhenotype(LinkageFormatter f)

A method to read in the data for this locus from the given input formatter. This is defined by the subclasses.

nAlleles

public int nAlleles()

Returns the number of alleles that this locus has.

alleleFrequencies

public double[] alleleFrequencies()

Returns the allele frequencies for the locus.

setAlleleFrequencies

public void setAlleleFrequencies(double[] f)

firstComment

public java.lang.String firstComment()

Returns the comment string from the first line of input associated with this locus.

locName

public java.lang.String locName()