net.maizegenetics.phenotype

Interface Phenotype

All Superinterfaces:

TableReport

All Known Implementing Classes:

CorePhenotype, FilterPhenotype

public Phenotype
extends TableReport

Phenotype represents phenotype data as a two dimensional matrix. Rows are observations. Columns are attributes.

Method Detail

value

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

Parameters:

obs - an observation number

attrnum - the index or column number of the attribute

Returns:

org.jetbrains.dokka.NodeRenderContent@3658828f: the attribute value for the observation

isMissing

boolean isMissing(int obs,
                  int attrnum)

Parameters:

obs - an observation number

attrnum - the index or column number of the attribute

Returns:

org.jetbrains.dokka.NodeRenderContent@bf415a: true if the phenotype value of attrnum is missing for obs

attribute

PhenotypeAttribute attribute(int attrnum)

Parameters:

attrnum - the index or column number of the attribute

Returns:

org.jetbrains.dokka.NodeRenderContent@653d546e: the PhenotypeAttribute

indexOfAttribute

int indexOfAttribute(PhenotypeAttribute attribute)

Parameters:

attribute - a PhenotypeAttribute

Returns:

org.jetbrains.dokka.NodeRenderContent@7d4ea103: the index of attribute in this Phenotype, -1 if the attribute is not contained in this Phenotype

numberOfAttributes

int numberOfAttributes()

Returns:

org.jetbrains.dokka.NodeRenderContent@ff018df: the number of attributes or columns in the Phenotype

numberOfObservations

int numberOfObservations()

Returns:

org.jetbrains.dokka.NodeRenderContent@753f2dea: the number of observations or rows in this phenotype

taxa

TaxaList taxa()

Returns:

org.jetbrains.dokka.NodeRenderContent@7aae8907: the unique set of taxa in this Phenotype. Each taxon will be in the TaxaList only once though there may be more than one observation of the taxon in the Phenotype.

numberOfAttributesOfType

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

Parameters:

type - an attribute type

Returns:

org.jetbrains.dokka.NodeRenderContent@72e069e8: the number of attributes of this type

attributeIndicesOfType

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

Parameters:

type - an attribute type

Returns:

org.jetbrains.dokka.NodeRenderContent@7dd9a18b: an array of the indices of all the attributes of this type

attributeType

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

Parameters:

attrnum - the index or column number of an attribute

Returns:

org.jetbrains.dokka.NodeRenderContent@718593a7: the type of the attribute

attributeName

java.lang.String attributeName(int attrnum)

Parameters:

attrnum - the index or column number of the attribute

Returns:

org.jetbrains.dokka.NodeRenderContent@7fedda21: the name of the attribute

name

java.lang.String name()

Returns:

org.jetbrains.dokka.NodeRenderContent@eb3531d: the name of this Phenotype

hasTaxaAttribute

boolean hasTaxaAttribute()

Returns:

org.jetbrains.dokka.NodeRenderContent@3e566eb9: true, if this Phenotype type has one and only one TaxaAttribute

taxaAttribute

TaxaAttribute taxaAttribute()

Returns:

org.jetbrains.dokka.NodeRenderContent@6393ca7f: this Phenotype's TaxaAttribute, which is the Taxa represented by the observations in this Phenotype

attributeListCopy

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

Returns:

org.jetbrains.dokka.NodeRenderContent@72be28fe: a shallow copy of the attribute list for this Phenotype

attributeListOfType

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

Parameters:

type - an attribute type

Returns:

org.jetbrains.dokka.NodeRenderContent@6681b60f: a List of all attributes of the requested type

attributeStream

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

Returns:

org.jetbrains.dokka.NodeRenderContent@6baf3fc0: a sequential Stream of all PhenotypeAttributes

dataAttributeStream

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

Returns:

org.jetbrains.dokka.NodeRenderContent@1692c0f8: a sequential Stream of all data type PhenotypeAttributes as NumericAttributes

covariateAttributeStream

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

Returns:

org.jetbrains.dokka.NodeRenderContent@15e8f30c: a sequential Stream of all covariate type PhenotypeAttributes as NumericAttributes

factorAttributeStream

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

Returns:

org.jetbrains.dokka.NodeRenderContent@7eb20e70: a sequential Stream of all factor type PhenotypeAttributes as CategoricalAttributes

typeListCopy

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

Returns:

org.jetbrains.dokka.NodeRenderContent@6cf16f59: a shallow copy of the attribute type list for this Phenotype

attributeIndexForName

int attributeIndexForName(java.lang.String name)

Parameters:

name - the name of an attribute

Returns:

org.jetbrains.dokka.NodeRenderContent@6c64f73f: the index of the attribute with this name, -1 if there is no attribute with this name

areTaxaReplicated

boolean areTaxaReplicated()

Returns:

org.jetbrains.dokka.NodeRenderContent@3e46192c: true, if the number of observations is greater than the number of unique taxa, false otherwise

asCorePhenotype

Phenotype asCorePhenotype()

Returns:

org.jetbrains.dokka.NodeRenderContent@5069511a: this Phenotype as a CorePhenotype.

CorePhenotype may be more efficient in some cases than FilterPhenotype, though the difference will probably be small. For very large filtered data sets consider converting to CorePhenotype. The operation performed on a CorePhenotype will return the same Phenotype.