PhenotypeBuilder

net.maizegenetics.phenotype.PhenotypeBuilder

```
public class PhenotypeBuilder
```

- Constructor Detail
  - PhenotypeBuilder
```
public PhenotypeBuilder()
```
- Method Detail
  - fromFile
```
public PhenotypeBuilder fromFile(java.lang.String filename)
```
    Parameters:
    
    filename - the name of a file containing phenotype data to be imported
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@49e47e19: a PhenotypeBuilder that will import a file
  - fromPhenotype
```
public PhenotypeBuilder fromPhenotype(Phenotype base)
```
    Parameters:
    
    base - the Phenotype from which to create a new Phenotype
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@a8f81ca: a PhenotypeBuilder Multiple phenotypes can be added to a list using this method.
  - fromPhenotypeList
```
public PhenotypeBuilder fromPhenotypeList(java.util.List<net.maizegenetics.phenotype.Phenotype> phenotypes)
```
    Parameters:
    
    phenotypes - a List of Phenotypes
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@5e6fdde3: a Phenotype builder that will act on all Phenotypes in the list A union join returns a Phenotype containing any taxon present in at least one of the Phenotypes to be joined. An intersect join returns a Phenotype containing only taxa present in all of the Phenotypes to be joined.
  - fromAttributeList
```
public PhenotypeBuilder fromAttributeList(java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> attributes,
                                          java.util.List<net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE> types)
```
    Parameters:
    
    attributes - a list of attributes
    
    types - a list of types matching the attribute list
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@4872f6a4: a PhenotypeBuilder that will build using these lists The attribute and type lists must be the same size and the types must be compatible with the attributes
  - unionJoin
```
public PhenotypeBuilder unionJoin()
```
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@228c5d05: a PhenotypeBuilder that will perform a union join of Phenotypes added using one or more of the from methods. A union join returns a Phenotype containing Taxa that are in any of the source Phenotypes.
  - intersectJoin
```
public PhenotypeBuilder intersectJoin()
```
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@54fb194f: a PhenotypeBuilder that will perform an intersect join of Phenotypes added using one or more of the from methods. An intersect join returns a Phenotype containing only Taxa that are in all of the source Phenotypes.
  - concatenate
```
public PhenotypeBuilder concatenate()
```
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@74db56f6: a builder that will concatenate phenotypes
  - assignName
```
public PhenotypeBuilder assignName(java.lang.String name)
```
  - keepTaxa
```
public PhenotypeBuilder keepTaxa(java.util.List<net.maizegenetics.taxa.Taxon> taxaToKeep)
```
    Parameters:
    
    taxaToKeep - a list of taxa to be kept from the base Phenotype
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@2bc3591f: a PhenotypeBuilder that will return a FilterPhenotype with taxa in the taxaToKeep list Only taxa that are in both taxaToKeep and the base Phenotype will be included in the Phenotype that is built.
  - removeTaxa
```
public PhenotypeBuilder removeTaxa(java.util.List<net.maizegenetics.taxa.Taxon> taxaToRemove)
```
    Parameters:
    
    taxaToRemove - a list of taxa to removed from the base Phenotype
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@6b674d17: a PhenotypeBuilder that will return a Phenotype with taxa from the supplied list excluded Any taxa in taxaToRemove but not in the base Phenotype will be ignored.
  - keepAttributes
```
public PhenotypeBuilder keepAttributes(java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> attributesToKeep)
```
    Parameters:
    
    attributesToKeep - a list of the attributes to be kept
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@67da0055: a PhenotypeBuilder that will return a new Phenotype with only the attributes in the supplied list Only attributes in both attributesToKeep and the base Phenotype will be included in the Phenotype that is built. The order of the attributes in the new Phenotype will match that in attributesToKeep.
  - keepAttributes
```
public PhenotypeBuilder keepAttributes(kotlin.Array[] indexOfAttributes)
```
    Parameters:
    
    indexOfAttributes - the column numbers of the attributes in the base Phenotype to be included in the newly built Phenotype
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@499886be: a PhenotypeBuilder that will build a Phenotype with the specified attributes
  - changeAttributeType
```
public PhenotypeBuilder changeAttributeType(java.util.Map<net.maizegenetics.phenotype.PhenotypeAttribute,net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE> changeMap)
```
    Parameters:
    
    changeMap - a Map of PhenotypeAttribute to ATTRIBUTE_TYPE for PhenotypeAttributes that should be assigned new types
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@78a22533: a PhenotypeBuilder that will build a phenotype with the changed attribute type
  - typesOfRetainedAttributes
```
public PhenotypeBuilder typesOfRetainedAttributes(java.util.List<net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE> attributeTypes)
```
    Parameters:
    
    attributeTypes - a list of attribute types for the attributes to be built
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@297cd0c5: a PhenotypeBuilder that will build a Phenotype that will have this list of types The order of types must be the same as the order of attributes as supplied by the keepAttributes methods if used or in the base Phenotype if the attribute list is not changed.
  - pivotOn
```
public PhenotypeBuilder pivotOn(java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> factors)
```
    Parameters:
    
    factors - a list of attributes on which to pivot the table. These must be CategoricalAttributes.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@1e13b517: a PhenotypeBuilder that will create a pivoted Phenotype. Pivoting is equivalent to using the separateOn() method followed by a union join.
  - separateOn
```
public PhenotypeBuilder separateOn(java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> factors)
```
    Parameters:
    
    factors - a list of attributes used to create separate Phenotypes. These must be CategoricalAttributes.
    
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@13336d1d: a PhenotypeBuilder that will create a separate Phenotype for each distinct level of the combined factors.
  - removeMissingObservations
```
public PhenotypeBuilder removeMissingObservations()
```
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@7ad149f5: a PhenotypeBuilder that will create a Phenotype with no missing values for any attribute by removing observations that have any missing values.
  - build
```
public java.util.List<net.maizegenetics.phenotype.Phenotype> build()
```
    Returns:
    
    org.jetbrains.dokka.NodeRenderContent@35645492: a list of new Phenotypes built with the supplied parameters

Class PhenotypeBuilder

Constructor Detail

PhenotypeBuilder

Method Detail

fromFile

fromPhenotype

fromPhenotypeList

fromAttributeList

unionJoin

intersectJoin

concatenate

assignName

keepTaxa

removeTaxa

keepAttributes

keepAttributes

changeAttributeType

typesOfRetainedAttributes

pivotOn

separateOn

removeMissingObservations

build