net.maizegenetics.phenotype

Class TaxaAttribute

java.lang.Object

net.maizegenetics.phenotype.TaxaAttribute

All Implemented Interfaces:

PhenotypeAttribute

public class TaxaAttribute
extends Object
implements PhenotypeAttribute

Author:

pbradbury

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_NAME

Constructor Summary

Constructors

Constructor and Description
TaxaAttribute(List<Taxon> taxa)
TaxaAttribute(List<Taxon> taxa, String name)

Method Summary

Modifier and Type	Method and Description
Taxon[]	allTaxa()
List<Taxon>	allTaxaAsList()
Object	allValues() The return value will typically be a primitive array whose type depends on the sub class
PhenotypeAttribute	changeName(String newName)
List<Phenotype.ATTRIBUTE_TYPE>	getCompatibleTypes()
boolean	isMissing(int obs)
boolean	isTypeCompatible(Phenotype.ATTRIBUTE_TYPE type)
BitSet	missing()
String	name()
int	size()
PhenotypeAttribute	subset(int[] obs, String newName)
Taxon	taxon(int obs)
String	toString()
Object	value(int obs)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_NAME

public static final String DEFAULT_NAME

See Also:

Constant Field Values

Constructor Detail

TaxaAttribute

public TaxaAttribute(List<Taxon> taxa,
                     String name)

TaxaAttribute

public TaxaAttribute(List<Taxon> taxa)

Method Detail

allTaxa

public Taxon[] allTaxa()

allTaxaAsList

public List<Taxon> allTaxaAsList()

taxon

public Taxon taxon(int obs)

value

public Object value(int obs)

Specified by:

value in interface PhenotypeAttribute

Parameters:

obs - the observation number

Returns:

the value for this observation

allValues

public Object allValues()

Description copied from interface: PhenotypeAttribute

The return value will typically be a primitive array whose type depends on the sub class

Specified by:

allValues in interface PhenotypeAttribute

Returns:

the values of this Attribute for all observations, in order by observation number

subset

public PhenotypeAttribute subset(int[] obs,
                                 String newName)

Specified by:

subset in interface PhenotypeAttribute

Parameters:

obs - an array of observation numbers

newName - The name for the new PhenotypeAttribute

Returns:

a new PhenotypeAttribute equivalent to this one but with a subset of observations specified by obs

changeName

public PhenotypeAttribute changeName(String newName)

Specified by:

changeName in interface PhenotypeAttribute

Parameters:

newName - a new name for this PhenotypeAttribute

Returns:

a copy of this PhenotypeAttribute with newName as its name

isMissing

public boolean isMissing(int obs)

Specified by:

isMissing in interface PhenotypeAttribute

Parameters:

obs - the observation number

Returns:

if the value of the observation is missing, true, otherwise false.

missing

public BitSet missing()

Specified by:

missing in interface PhenotypeAttribute

Returns:

an array whose elements are true for each missing observation, false for observations with valid values.

name

public String name()

Specified by:

name in interface PhenotypeAttribute

Returns:

the name of this Attribute

size

public int size()

Specified by:

size in interface PhenotypeAttribute

Returns:

the number of observations in this Attribute

getCompatibleTypes

public List<Phenotype.ATTRIBUTE_TYPE> getCompatibleTypes()

Specified by:

getCompatibleTypes in interface PhenotypeAttribute

Returns:

a list of attribute types that are compatible with this attribute For instance, a CategoricalAttribute can only have a type of factor while a NumericPhenotype can have a type of data or covariate.

isTypeCompatible

public boolean isTypeCompatible(Phenotype.ATTRIBUTE_TYPE type)

Specified by:

isTypeCompatible in interface PhenotypeAttribute

Parameters:

type - an attribute type

Returns:

true if type is compatible with this attribute

toString

public String toString()

Overrides:

toString in class Object