main

Class SampleGenotypeValues

java.lang.Object

main.SampleGenotypeValues

public class SampleGenotypeValues
extends java.lang.Object

Class SampleGenotypeValues stores a value for each possible genotype at each marker for one sample.

Class SampleGenotypeValues is thread-safe.

Constructor Summary

Constructors

Constructor and Description
SampleGenotypeValues(Markers markers, Samples samples, int sampleIndex) Constructs a SampleGenotypeValues instance for the specified markers and sample with initial value 0 for each possible genotype at each marker.

Method Summary

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

SampleGenotypeValues

public SampleGenotypeValues(Markers markers,
                            Samples samples,
                            int sampleIndex)

Constructs a SampleGenotypeValues instance for the specified markers and sample with initial value 0 for each possible genotype at each marker.

Parameters:

markers - the list of markers

samples - the list of samples

sampleIndex - a sample index

Throws:

java.lang.IllegalArgumentException - if sampleIndex < 0 || sampleIndex >= sampes.nSamples()

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

Method Detail

value

public float value(int marker,
                   int genotype)

Returns the specified genotype value.

Parameters:

marker - a marker index

genotype - a genotype index

Returns:

the specified genotype value

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

java.lang.IndexOutOfBoundsException - if genotype < 0 || genotype >= this.marker(marker).nGenotypes()

add

public void add(double[] values)

Adds the specified genotype values to this. This method is equivalent to

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

Parameters:

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

Throws:

java.lang.IllegalArgumentException - if values.length != this.markers().sumGenotypes()

java.lang.NullPointerException - if values == null

add

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

Adds the specified genotype value to this.

Parameters:

marker - a marker index

genotype - a genotype index

value - the value to be added

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

java.lang.IndexOutOfBoundsException - if genotype < 0 || genotype >= this.marker(marker).nGenotypes()

markers

public Markers markers()

Returns the list of markers.

Returns:

the list of markers

samples

public Samples samples()

Returns the list of samples.

Returns:

the list of samples

sampleIndex

public int sampleIndex()

Returns the sample index.

Returns:

the sample index

marker

public Marker marker(int marker)

Returns the specified marker.

Parameters:

marker - a marker index

Returns:

the specified marker

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

nMarkers

public int nMarkers()

Returns the number of markers.

Returns:

the number of markers

toString

public java.lang.String toString()

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

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this