net.maizegenetics.phenotype

Class CorePhenotype

net.maizegenetics.phenotype.CorePhenotype

All Implemented Interfaces:

Phenotype, TableReport

public class CorePhenotype
implements Phenotype

Field Detail

myAttributeList

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> myAttributeList

myAttributeTypeList

protected java.util.List<net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE> myAttributeTypeList

myAttributeTypeMap

protected com.google.common.collect.Multimap<net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE,java.lang.Integer> myAttributeTypeMap

myAttributeNameMap

protected java.util.HashMap<java.lang.String,java.lang.Integer> myAttributeNameMap

numberOfAttributes

protected int numberOfAttributes

numberOfObservations

protected int numberOfObservations

name

protected java.lang.String name

myTaxaAttribute

protected TaxaAttribute myTaxaAttribute

Constructor Detail

CorePhenotype

public CorePhenotype(java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> attributes,
                     java.util.List<net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE> types,
                     java.lang.String name)

Method Detail

getTableColumnNames

public java.lang.Object[] getTableColumnNames()

getTableTitle

public java.lang.String getTableTitle()

getColumnCount

public int getColumnCount()

getRowCount

public long getRowCount()

getElementCount

public long getElementCount()

getRow

public java.lang.Object[] getRow(long row)

getValueAt

public java.lang.Object getValueAt(long row,
                                   int col)

value

public java.lang.Object value(int obs,
                              int attrnum)

isMissing

public boolean isMissing(int obs,
                         int attrnum)

attribute

public PhenotypeAttribute attribute(int attrnum)

indexOfAttribute

public int indexOfAttribute(PhenotypeAttribute attribute)

attributeListCopy

public java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> attributeListCopy()

attributeListOfType

public java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> attributeListOfType(net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE type)

attributeStream

public java.util.stream.Stream<net.maizegenetics.phenotype.PhenotypeAttribute> attributeStream()

dataAttributeStream

public java.util.stream.Stream<net.maizegenetics.phenotype.NumericAttribute> dataAttributeStream()

covariateAttributeStream

public java.util.stream.Stream<net.maizegenetics.phenotype.NumericAttribute> covariateAttributeStream()

factorAttributeStream

public java.util.stream.Stream<net.maizegenetics.phenotype.CategoricalAttribute> factorAttributeStream()

typeListCopy

public java.util.List<net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE> typeListCopy()

taxa

public TaxaList taxa()

numberOfAttributes

public int numberOfAttributes()

numberOfAttributesOfType

public int numberOfAttributesOfType(net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE type)

attributeIndicesOfType

public kotlin.Array[] attributeIndicesOfType(net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE type)

attributeType

public net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE attributeType(int attrnum)

numberOfObservations

public int numberOfObservations()

attributeName

public java.lang.String attributeName(int attrnum)

name

public java.lang.String name()

hasTaxaAttribute

public boolean hasTaxaAttribute()

taxaAttribute

public TaxaAttribute taxaAttribute()

attributeIndexForName

public int attributeIndexForName(java.lang.String name)

areTaxaReplicated

public boolean areTaxaReplicated()

asCorePhenotype

public Phenotype asCorePhenotype()

areAttributeAndTypeListsCompatible

public static boolean areAttributeAndTypeListsCompatible(java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> attributes,
                                                         java.util.List<net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE> types)