main

Class BasicGenotypeValues

java.lang.Object

main.BasicGenotypeValues

All Implemented Interfaces:

GenotypeValues

public final class BasicGenotypeValues
extends java.lang.Object
implements GenotypeValues

Class BasicGenotypeValues stores values for each possible genotype for each sample at each marker.

Instances of class BasicGenotypeValues are thread-safe.

Constructor Summary

Constructors

Constructor and Description
BasicGenotypeValues(Markers markers, Samples samples) Constructs a new BasicGenotypeValues instance with initial value 0 for each possible genotype for each sample at each marker.

Method Summary

Modifier and Type	Method and Description
void	add(int sample, double[] values) Adds the specified genotype values to the stored genotype values for the specified sample.
void	add(int marker, int sample, int genotype, double value) Adds the specified genotype value to the stored genotype value.
Marker	marker(int marker) Returns the specified marker.
Markers	markers() Returns the list of markers.
int	nMarkers() Returns the number of markers.
int	nSamples() Returns the number of samples.
Samples	samples() Returns the list of samples.
java.lang.String	toString() Returns a string representation of this.
float	value(int marker, int sample, int genotype) Returns the specified genotype value.

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicGenotypeValues

public BasicGenotypeValues(Markers markers,
                           Samples samples)

Constructs a new BasicGenotypeValues instance with initial value 0 for each possible genotype for each sample at each marker.

Parameters:

markers - a list of markers

samples - a list of samples

Throws:

java.lang.NullPointerException - if markers == null || samples == null

Method Detail

value

public float value(int marker,
                   int sample,
                   int genotype)

Description copied from interface: GenotypeValues

Returns the specified genotype value.

Specified by:

value in interface GenotypeValues

Parameters:

marker - a marker index

sample - a sample index

genotype - a genotype index

Returns:

the specified genotype value

add

public void add(int sample,
                double[] values)

Description copied from interface: GenotypeValues

Adds the specified genotype values to the stored genotype values for the specified sample. This method is equivalent to

 for (m=0; m<this.nMarkers(); ++m) {
     offset = this.markers().sumGenotypes(m);
     for (gt=0; gt<this.marker(m).nGenotypes(); ++gt) {
         this.add(marker, sample, gt, values[offset + gt])
     }
 }
 

Specified by:

add in interface GenotypeValues

Parameters:

sample - a sample index

values - an array of length this.markers.sumGenotypes() containing the genotype values to be added.

add

public void add(int marker,
                int sample,
                int genotype,
                double value)

Description copied from interface: GenotypeValues

Adds the specified genotype value to the stored genotype value.

Specified by:

add in interface GenotypeValues

Parameters:

marker - a marker index

sample - a sample index

genotype - a genotype index

value - the value to be added

samples

public Samples samples()

Description copied from interface: GenotypeValues

Returns the list of samples.

Specified by:

samples in interface GenotypeValues

Returns:

the list of samples

nSamples

public int nSamples()

Description copied from interface: GenotypeValues

Returns the number of samples.

Specified by:

nSamples in interface GenotypeValues

Returns:

the number of samples

marker

public Marker marker(int marker)

Description copied from interface: GenotypeValues

Returns the specified marker.

Specified by:

marker in interface GenotypeValues

Parameters:

marker - a marker index

Returns:

the specified marker

markers

public Markers markers()

Description copied from interface: GenotypeValues

Returns the list of markers.

Specified by:

markers in interface GenotypeValues

Returns:

the list of markers

nMarkers

public int nMarkers()

Description copied from interface: GenotypeValues

Returns the number of markers.

Specified by:

nMarkers in interface GenotypeValues

Returns:

the number of markers

toString

public java.lang.String toString()

Description copied from interface: GenotypeValues

Returns a string representation of this. The exact details of the representation are unspecified and subject to change.

Specified by:

toString in interface GenotypeValues

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this