TASSELpy.net.maizegenetics.trait package¶

Submodules¶

TASSELpy.net.maizegenetics.trait.AbstractPhenotype module¶

class TASSELpy.net.maizegenetics.trait.AbstractPhenotype.AbstractPhenotype(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getColumnCount`(*args)	Gets the number of columns
`getData`(*args)	Gets data from the phenotype
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getElementCount`(*args)	Gets the total number of elements in the dataset
`getNumberOfTaxa`(*args)	Gets the number of taxa or rows in this data set
`getNumberOfTraits`(*args)	Gets the number of traits or columns in this data set
`getRow`(*args)	Returns specified row
`getRowCount`(*args)	Gets the number of rows
`getTableColumnNames`(*args)	Gets the names of the columns
`getTableTitle`(*args)	Gets the title of the table
`getTaxa`(*args)	Get the taxa in this data set in order by row number
`getTaxon`(*args)	Gets a taxon
`getTrait`(*args)	Gets a trait
`getTraits`(*args)	Gets the traits or columns of this dataset, in order by column number
`getValueAt`(*args)	Returns value at given row and column
`hashCode`(*args)	Returns a hash code vlaue for the object
`setData`(*args)	Sets the double value for this trait and taxon
`toDict`()	Outputs the table as a dictionary
`toString`(*args)	Returns a string representation of the object
`whichTaxon`(*args)	Gets the index of a taxon
`whichTrait`(*args)	Gets the index of a trait
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

TASSELpy.net.maizegenetics.trait.CombinePhenotype module¶

class TASSELpy.net.maizegenetics.trait.CombinePhenotype.CombinePhenotype(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.trait.AbstractPhenotype.AbstractPhenotype

Class used for combining multiple phenotypes that may have different taxa among them

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getColumnCount`(*args)	Gets the number of columns
`getData`(*args)	Gets data from the phenotype
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getElementCount`(*args)	Gets the total number of elements in the dataset
`getInstance`(*args)	Gets an instance of CombinePhenotype, allowing combining of more than
`getNumberOfTaxa`(*args)	Gets the number of taxa or rows in this data set
`getNumberOfTraits`(*args)	Gets the number of traits or columns in this data set
`getRow`(*args)	Returns specified row
`getRowCount`(*args)	Gets the number of rows
`getTableColumnNames`(*args)	Gets the names of the columns
`getTableTitle`(*args)	Gets the title of the table
`getTaxa`(*args)	Get the taxa in this data set in order by row number
`getTaxon`(*args)	Gets a taxon
`getTrait`(*args)	Gets a trait
`getTraits`(*args)	Gets the traits or columns of this dataset, in order by column number
`getValueAt`(*args)	Returns value at given row and column
`hashCode`(*args)	Returns a hash code vlaue for the object
`setData`(*args)	Sets a particular data value
`simpleCopy`(*args)	Makes a copy of the CombinePhenotype as a SimplePhenotype
`toDict`()	Outputs the table as a dictionary
`toString`(*args)	Returns a string representation of the object
`whichTaxon`(*args)	Gets the index of a taxon
`whichTrait`(*args)	Gets the index of a trait
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

static getInstance(*args)[source]¶

Gets an instance of CombinePhenotype, allowing combining of more than one phenotype

Signature:	getInstance (Phenotype phenotype1, Phenotype phenotype2, boolean isUnion)
Signature:	getInstance (Phenotype[] phenotypes, boolean isUnion)
Parameters:	phenotype1 (Phenotype) – The first phenotype phenotype2 (Phenotype) – The second phenotype isUnion (boolean) – Whether to take the union of the taxa. If false, takes the intersection phenotypes (Phenotype[]) – List of Phenotype objects to combine

setData(*args)[source]¶

Sets a particular data value

Signature:	setData (Taxon taxon, Trait trait, double value)
Signature:	setData (int taxon, int trait, double value)
Parameters:	taxon (int) – A Taxon instance trait (int) – A Trait instance value (double) – The value to set

simpleCopy(*args)[source]¶

Makes a copy of the CombinePhenotype as a SimplePhenotype

Signature:	simpleCopy ()
Returns:	A SimplePhenotype copy of the object
Return type:	SimplePhenotype

TASSELpy.net.maizegenetics.trait.FilterPhenotype module¶

class TASSELpy.net.maizegenetics.trait.FilterPhenotype.FilterPhenotype(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.trait.AbstractPhenotype.AbstractPhenotype

Class used to filter through phenotypes

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getColumnCount`(*args)	Gets the number of columns
`getData`(*args)	Gets data from the phenotype
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getElementCount`(*args)	Gets the total number of elements in the dataset
`getInstance`(*args)	Gets an instance of the filtered phenotype
`getInstanceRemoveIDs`(*args)	Gets a FilterPhenotype after removing certain taxa
`getNumberOfTaxa`(*args)	Gets the number of taxa or rows in this data set
`getNumberOfTraits`(*args)	Gets the number of traits or columns in this data set
`getRow`(*args)	Returns specified row
`getRowCount`(*args)	Gets the number of rows
`getTableColumnNames`(*args)	Gets the names of the columns
`getTableTitle`(*args)	Gets the title of the table
`getTaxa`(*args)	Get the taxa in this data set in order by row number
`getTaxon`(*args)	Gets a taxon
`getTrait`(*args)	Gets a trait
`getTraits`(*args)	Gets the traits or columns of this dataset, in order by column number
`getValueAt`(*args)	Returns value at given row and column
`hashCode`(*args)	Returns a hash code vlaue for the object
`setData`(*args)	Sets a particular datum
`simpleCopy`(*args)	Makes a copy of the FilterPhenotype object, returning a SimplePhenotype
`toDict`()	Outputs the table as a dictionary
`toString`(*args)	Returns a string representation of the object
`whichTaxon`(*args)	Gets the index of a taxon
`whichTrait`(*args)	Gets the index of a trait
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

static getInstance(*args)[source]¶

Gets an instance of the filtered phenotype

The indices for taxa and traits must be valid indexes in the original phenotype. That is, only taxa and traits in the original phenotype can be used. This function is not appropriate for union joins

Signatures:

static FilterPhenotype getInstance(Phenotype phenotype, int[] taxa, int[] traits) static FilterPhenotype getInstance(Phenotype phenotype, TaxaList taxa,

List<Trait> traits)

Arguments:

static FilterPhenotype getInstance(Phenotype phenotype, int[] taxa, int[] traits)

phenotype – the input Phenotype taxa – an index of taxa to include in the filtered subset. If null,

all taxa will be included

traits – an index of traits to include in the filtered subset. If null,: all traits will be included

static FilterPhenotype getInstance(Phenotype phenotype, TaxaList taxa,

List<Trait> traits)

phenotype – the input Phenotype taxa – the taxa to be included in the output FIlterPhenotype traits – the traits to be included in the output FilterPhenotype

Returns:

A new FilterPhenotype

static getInstanceRemoveIDs(*args)[source]¶

Gets a FilterPhenotype after removing certain taxa

Signature:	getInstanceRemoveIDs (Phenotype phenotype, TaxaList taxa)
Parameters:	phenotype (Phenotype) – the input Phenotype taxa (TaxaList) – the taxa to be excluded in the output FilterPhenotype
Returns:	A FilterPhenotype without excluded IDs
Return type:	FilterPhenotype

setData(*args)[source]¶

Sets a particular datum

Signature:	setData (int taxon, int trait, double value)
Signature:	setData (Taxon taxon, Trait trait, double value)
Parameters:	taxon (Taxon) – taxon trait (Trait) – trait value (double) – value

simpleCopy(*args)[source]¶

Makes a copy of the FilterPhenotype object, returning a SimplePhenotype

Signature:	simpleCopy ()
Returns:	A SimplePhenotype
Return type:	SimplePhenotype

TASSELpy.net.maizegenetics.trait.MarkerPhenotype module¶

class TASSELpy.net.maizegenetics.trait.MarkerPhenotype.MarkerPhenotype(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.util.TableReport.TableReport

Class combining a GenotypeTable and a Phenotype. Enters into quantitative genetics models

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getAlignment`(*args)	Gets the alignment
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getColumnCount`(*args)	Gets the number of columns
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getElementCount`(*args)	Gets the total number of elements in the dataset
`getInstance`(*args)	Gets an instance of a MarkerPhenotype class
`getPhenotype`(*args)	Gets the phenotype
`getRow`(*args)	Returns specified row
`getRowCount`(*args)	Gets the number of rows
`getTableColumnNames`(*args)	Gets the names of the columns
`getTableTitle`(*args)	Gets the title of the table
`getValueAt`(*args)	Returns value at given row and column
`hashCode`(*args)	Returns a hash code vlaue for the object
`toDict`()	Outputs the table as a dictionary
`toString`(*args)	Returns a string representation of the object
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

getAlignment(*args)[source]¶

Gets the alignment

Signature:	getAlignment ()
Returns:	The alignment
Return type:	GenotypeTable

static getInstance(*args)[source]¶

Gets an instance of a MarkerPhenotype class

Signature:	getInstance (GenotypeTable aa, Phenotype ca, boolean union)
Signature:	getInstance (MarkerPhenotype aac, TaxaList group)
Parameters:	aa (GenotypeTable) – the GenotypeTable containing the markers ca (Phenotype) – The phenotype object containing 1 or more phenotype aac (MarkerPhenotype) – An existing MarkerPhenotype object to use group (TaxaList) – TaxaList containing the taxa to keep

getPhenotype(*args)[source]¶

Gets the phenotype

Signature:	getPhenotype ()
Returns:	The Phenotype
Return type:	Phenotype

class TASSELpy.net.maizegenetics.trait.MarkerPhenotype.metaMarkerPhenotype[source]¶: Bases: object

TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter module¶

class TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter.MarkerPhenotypeAdapter(*args, **kwargs)[source]¶

Bases: TASSELpy.java.lang.Object.Object

Class used to easily access information on MarkerPhenotype objects

Methods

`areTraitFactorsConsistent`(*args)	Returns true if traits all have the same factors or no factors
`castTo`(pyType)	Casts this object to another java/python type
`checkFactorCovariateEnvironments`(*args)	Factor columns should either have no phenotype factors, or the ones they have should match at least one data column.
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getCovariateName`(*args)	Gets the name of a covariate
`getCovariateValues`(*args)	Gets the values of a covariate
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getFactorName`(*args)	Gets a factor name
`getFactorValues`(*args)	Gets the factor values for a factor
`getLocusName`(*args)	Gets the name of a locus
`getLocusPosition`(*args)	Gets the position of a locus
`getMarkerChromosome`(*args)	Gets the chromosome of a marker
`getMarkerChromosomePosition`(*args)	Gets the position of a marker on the chromosome
`getMarkerName`(*args)	Gets a marker name
`getMarkerValue`(*args)	Gets the value of a marker over the taxa
`getMissingCovariates`(*args)	Gets a boolean array indicating whether covariate values are missing
`getMissingFactors`(*args)	Gets the missing factors for a phenotype
`getMissingMarkers`(*args)	Gets a boolean array indicating which taxa have a marker missing
`getMissingPhenotypes`(*args)	Gets array of booleans indicating which taxa have missing phenotypes
`getNumberOfBlocks`(*args)	Gets the number of blocks for a phenotype
`getNumberOfCovariates`(*args)	Gets the number of covariates
`getNumberOfFactors`(*args)	Gets the number of factors
`getNumberOfMarkers`(*args)	Gets the number of markers
`getNumberOfPhenotypes`(*args)	Gets the number of Phenotypes
`getNumberOfRows`(*args)	Gets the number of rows for a phenotype
`getPhenotypeName`(*args)	Gets the name of a phenotype
`getPhenotypeValues`(*args)	Gets the values for a Phenotype
`getTaxa`(*args)	Gets the taxa that are present for a phenotype
`hasMarkerNames`(*args)	Gets whether there are marker names present
`hashCode`(*args)	Returns a hash code vlaue for the object
`isMarkerDiscrete`(*args)	Returns whether a given marker is discrete
`toString`(*args)	Returns a string representation of the object
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

Instantiates a MarkerPhenotypeAdapter object

Signature:	MarkerPhenotypeAdapter (Phenotype aPhenotype)
Signature:	MarkerPhenotypeAdapter (MarkerPhenotype aMarkerPhenotype)
Parameters:	aPhenotype (Phenotype) – A Phenotype object, if there is no set of markers aMarkerPhenotype (MarkerPhenotype) – A MarkerPhenotype object

areTraitFactorsConsistent(*args)[source]¶

Returns true if traits all have the same factors or no factors

Signature:	areTraitFactorsConsistent ()
Returns:	true if all traits have the same factors or no factors
Return type:	boolean

checkFactorCovariateEnvironments(*args)[source]¶

Factor columns should either have no phenotype factors, or the ones they have should match at least one data column.

Signature:	checkFactorCovariateEnvironments ()
Returns:	A message giving consistency information
Return type:	String

getCovariateName(*args)[source]¶

Gets the name of a covariate

Signature:	getCovariateName (int i)
Parameters:	i (int) – The index of a covariate
Returns:	The name of the covariate
Return type:	String

getCovariateValues(*args)[source]¶

Gets the values of a covariate

Signature:	getCovariateValues (int phenotype, int covariate)
Parameters:	phenotype (int) – The index of a phenotype covariate (int) – The index of a covariate
Returns:	The values of the covariate
Return type:	double[]

getFactorName(*args)[source]¶

Gets a factor name

Signature:	getFactorName (int i)
Parameters:	i (int) – The index of a factor
Returns:	The name of the factor
Return type:	String

getFactorValues(*args)[source]¶

Gets the factor values for a factor

Signature:	getFactorValues (int phenotype, int factor)
Parameters:	phenotype (int) – The index of a phenotype factor (int) – The index of a factor
Returns:	The names of the values for the factor
Return type:	String[]

getLocusName(*args)[source]¶

Gets the name of a locus

Signature:	getLocusName (int marker)
Parameters:	marker (int) – The index of a marker
Returns:	The name of the locus
Return type:	String

getLocusPosition(*args)[source]¶

Gets the position of a locus

Signature:	getLocusPosition (int marker)
Parameters:	marker (int) – The index of a marker
Returns:	The position of the locus
Return type:	int

getMarkerChromosome(*args)[source]¶

Gets the chromosome of a marker

Signature:	getMarkerChromosome (int marker)
Parameters:	marker (int) – The index of a marker
Returns:	The chromosome of the marker
Return type:	String

getMarkerChromosomePosition(*args)[source]¶

Gets the position of a marker on the chromosome

Signature:	getMarkerChromosomePosition (int marker)
Parameters:	marker (int) – The index of a marker
Returns:	The position of the marker on a chromosome
Return type:	double

getMarkerName(*args)[source]¶

Gets a marker name

Signature:	getMarkerName (int i)
Parameters:	i (int) – The index of a marker
Returns:	The name of the marker
Return type:	String

getMarkerValue(*args)[source]¶

Gets the value of a marker over the taxa

Signature:	getMarkerValue (int phenotype, int marker)
Parameters:	phenotype (int) – The index of a phenotype marker (int) – The index of a marker
Returns:	The value of a marker over the taxa
Return type:	Object[]

getMissingCovariates(*args)[source]¶

Gets a boolean array indicating whether covariate values are missing

Signature:	getMissingCovariates (int phenotype, int covariate)
Parameters:	phenotype (int) – The index of a phenotype covariate (int) – The index of a covariate
Returns:	Boolean array indicating whether covariate values are missing
Return type:	boolean[]

getMissingFactors(*args)[source]¶

Gets the missing factors for a phenotype

Signature:	getMissingFactors (int phenotype, int factor)
Parameters:	phenotype (int) – The index of a phenotype factor (int) – The index of a factor
Returns:	Boolean array indicating factor values are missing for a taxon
Return type:	boolean[]

getMissingMarkers(*args)[source]¶

Gets a boolean array indicating which taxa have a marker missing

Signature:	getMissingMarkers (int phenotype, int marker)
Parameters:	phenotype (int) – The index of a phenotype marker (int) – The index of a marker
Returns:	Boolean array indicating which taxa have a marker missing
Return type:	boolean[]

getMissingPhenotypes(*args)[source]¶

Gets array of booleans indicating which taxa have missing phenotypes

Signature:	getMissingPhenotypes (int phenotype)
Parameters:	phenotype (int) – The index of a phenotype
Returns:	Array of booleans indicating which taxa have missing phenotypes
Return type:	boolean[]

getNumberOfBlocks(*args)[source]¶

Gets the number of blocks for a phenotype

Signatures:

int getNumberOfBlocks(int phenotype)

Argument:

phenotype – The index of a phenotype

Returns:

The number of blocks

getNumberOfCovariates(*args)[source]¶

Gets the number of covariates

Signature:	getNumberOfCovariates ()
Returns:	The number of covariates
Return type:	int

getNumberOfFactors(*args)[source]¶

Gets the number of factors

Signature:	getNumberOfFactors ()
Returns:	The number of factors
Return type:	int

getNumberOfMarkers(*args)[source]¶

Gets the number of markers

Signature:	getNumberOfMarkers ()
Returns:	The number of markers
Return type:	int

getNumberOfPhenotypes(*args)[source]¶

Gets the number of Phenotypes

Signature:	getNumberOfPhenotypes ()
Returns:	The number of Phenotypes
Return type:	int

getNumberOfRows(*args)[source]¶

Gets the number of rows for a phenotype

Signatures:

int getNumberOfRows(int phenotype)

Argument:

phenotype – The index of a phenotype

Returns:

The number of rows

getPhenotypeName(*args)[source]¶

Gets the name of a phenotype

Signature:	getPhenotypeName (int i)
Parameters:	i (int) – The index of a phenotype
Returns:	The name of the phenotype
Return type:	String

getPhenotypeValues(*args)[source]¶

Gets the values for a Phenotype

Signature:	getPhenotypeValues (int i)
Parameters:	i (int) – The index of a Phenotype
Returns:	The values for a Phenotype
Return type:	double[]

getTaxa(*args)[source]¶

Gets the taxa that are present for a phenotype

Signature:	getTaxa (int phenotype)
Parameters:	phenotype (int) – The index of a Phenotype
Returns:	The taxa that are present for a Phenotype
Return type:	Taxon[]

hasMarkerNames(*args)[source]¶

Gets whether there are marker names present

Signature:	hasMarkerNames ()
Returns:	Whether marker names are present
Return type:	boolean

isMarkerDiscrete(*args)[source]¶

Returns whether a given marker is discrete

Signature:	isMarkerDiscrete (int i)
Parameters:	i (int) – The index of a marker
Returns:	Whether the given marker is discrete
Return type:	boolean

TASSELpy.net.maizegenetics.trait.Phenotype module¶

class TASSELpy.net.maizegenetics.trait.Phenotype.Phenotype(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.util.TableReport.TableReport

A collection of data for a set of Taxa. Each taxon is expected to appear only once in the data. Data is represented as a two dimensional table of doubles, with taxa as rows and traits as columns.

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getColumnCount`(*args)	Gets the number of columns
`getData`(*args)	Gets data from the phenotype
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getElementCount`(*args)	Gets the total number of elements in the dataset
`getNumberOfTaxa`(*args)	Gets the number of taxa or rows in this data set
`getNumberOfTraits`(*args)	Gets the number of traits or columns in this data set
`getRow`(*args)	Returns specified row
`getRowCount`(*args)	Gets the number of rows
`getTableColumnNames`(*args)	Gets the names of the columns
`getTableTitle`(*args)	Gets the title of the table
`getTaxa`(*args)	Get the taxa in this data set in order by row number
`getTaxon`(*args)	Gets a taxon
`getTrait`(*args)	Gets a trait
`getTraits`(*args)	Gets the traits or columns of this dataset, in order by column number
`getValueAt`(*args)	Returns value at given row and column
`hashCode`(*args)	Returns a hash code vlaue for the object
`setData`(*args)	Sets the double value for this trait and taxon
`toDict`()	Outputs the table as a dictionary
`toString`(*args)	Returns a string representation of the object
`whichTaxon`(*args)	Gets the index of a taxon
`whichTrait`(*args)	Gets the index of a trait
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

getData(*args)[source]¶

Gets data from the phenotype

Signature:	getData (int taxon, int trait)
Signature:	getData (Taxon taxon, Trait trait)
Signature:	getData ()
Parameters:	taxon (Taxon) – an integer i, representing the ith row in the data set trait (Trait) – an integer j, representing the jth column in the data set
Returns:	The data stored for the given trait and taxon
Return type:	double

getNumberOfTaxa(*args)[source]¶

Gets the number of taxa or rows in this data set

Signature:	getNumberOfTaxa ()
Returns:	The number of taxa or rows in this data set
Return type:	int

getNumberOfTraits(*args)[source]¶

Gets the number of traits or columns in this data set

Signature:	getNumberOfTraits ()
Returns:	The number of traits or columns in this data set
Return type:	int

getTaxa(*args)[source]¶

Get the taxa in this data set in order by row number

Signature:	getTaxa ()
Returns:	The taxa in this data set in order by row number
Return type:	TaxaList

getTaxon(*args)[source]¶

Gets a taxon

Signature:	getTaxon (int taxon)
Parameters:	taxon (int) – An integer j, representing the jth row in the data set
Returns:	The Taxon for this row
Return type:	Taxon

getTrait(*args)[source]¶

Gets a trait

Signature:	getTrait (int trait)
Parameters:	trait (int) – An integer j, representing the jth column in the data set
Returns:	The Trait for this column
Return type:	Trait

getTraits(*args)[source]¶

Gets the traits or columns of this dataset, in order by column number

Signatures:

List<Trait> getTraits()

Returns:

The traits or columns of this dataset, in order by column number

setData(*args)[source]¶

Sets the double value for this trait and taxon

Signature:	setData (int taxon, int trait, double value)
Parameters:	taxon (int) – An integer i, representing the ith row in the data set trait (int) – An ineger j, representing the jth column in the data set value (double) – The data to be stored for the ith taxon, jth trait

whichTaxon(*args)[source]¶

Gets the index of a taxon

Signature:	whichTaxon (Taxon taxon)
Parameters:	taxon (Taxon) – taxon
Returns:	The index of the taxon, representing the row in which the data for this taxon is stored
Return type:	int

whichTrait(*args)[source]¶

Gets the index of a trait

Signature:	whichTrait (Trait trait)
Parameters:	trait (Trait) – trait
Returns:	The index of the trait, representing the column in which the data for this trait is stored
Return type:	int

TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils module¶

class TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils.ReadPhenotypeUtils(*args, **kwargs)[source]¶

Bases: TASSELpy.java.lang.Object.Object

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`doubleFromCharacterTrait`(*args)	Converts a character trait to doubles
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`hashCode`(*args)	Returns a hash code vlaue for the object
`makeCharacterTrait`(*args)	Makes a character trait
`readGenericFile`(*args)	Reads input file with TASSEL v3 annotations or with no input directive
`readNumericalAlignment`(*args)	Reads Phenotype from a file in TASSEL v2 numerical format
`readPolymorphismAlignment`(*args)	Reads the polymorphism data from a TASSEL v2 polymorphism format file
`toString`(*args)	Returns a string representation of the object
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

static doubleFromCharacterTrait(*args)[source]¶

Converts a character trait to doubles

Signature:	doubleFromCharacterTrait (Trait trait, String[] textdata)
Parameters:	trait (Trait) – trait textdata (String[]) – the current data
Returns:	The new trait
Return type:	double[]

static makeCharacterTrait(*args)[source]¶

Makes a character trait

Signatures:

static Trait makeCharacterTrait(String[] original, double[] tonumber,: String name, String type)

Arguments:

original – the original class or discrete data tonumber – a double array, the same length as the original data, which

will hold the class indices

name – the trait name type – the trait type

Returns:

The new trait

static readGenericFile(*args)[source]¶

Reads input file with TASSEL v3 annotations or with no input directive

Signatures:

static Phenotype readGenericFile(String inputFile) throws IOException

Arguments:

inputFile – the input file with TASSEL v3 annotations or with no input directives

Returns:

a Phenotype

static readNumericalAlignment(*args)[source]¶

Reads Phenotype from a file in TASSEL v2 numerical format

Signatures:

static Phenotype readNumericalAlignment(String inputFile) throws IOException

Arguments:

inputFile – the input file in TASSEL v2 numerical format

Returns:

a Phenotype

static readPolymorphismAlignment(*args)[source]¶

Reads the polymorphism data from a TASSEL v2 polymorphism format file

Signatures:

static Phenotype readPolymorphismAlignment(String inputFile) throws IOException

Arguments:

inputFile – The input file in TASSEL v2 polymorphism format

Returns:

a Phenotype

TASSELpy.net.maizegenetics.trait.SimplePhenotype module¶

class TASSELpy.net.maizegenetics.trait.SimplePhenotype.SimplePhenotype(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.trait.AbstractPhenotype.AbstractPhenotype

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getColumnCount`(*args)	Gets the number of columns
`getData`(*args)	Gets data from the phenotype
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getElementCount`(*args)	Gets the total number of elements in the dataset
`getNumberOfTaxa`(*args)	Gets the number of taxa or rows in this data set
`getNumberOfTraits`(*args)	Gets the number of traits or columns in this data set
`getRow`(*args)	Returns specified row
`getRowCount`(*args)	Gets the number of rows
`getTableColumnNames`(*args)	Gets the names of the columns
`getTableTitle`(*args)	Gets the title of the table
`getTaxa`(*args)	Get the taxa in this data set in order by row number
`getTaxon`(*args)	Gets a taxon
`getTrait`(*args)	Gets a trait
`getTraits`(*args)	Gets the traits or columns of this dataset, in order by column number
`getValueAt`(*args)	Returns value at given row and column
`hashCode`(*args)	Returns a hash code vlaue for the object
`setData`(*args)	Sets the double value for this trait and taxon
`toDict`()	Outputs the table as a dictionary
`toString`(*args)	Returns a string representation of the object
`whichTaxon`(*args)	Gets the index of a taxon
`whichTrait`(*args)	Gets the index of a trait
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

Instantiates a SimplePhenotype object

Signatures:

SimplePhenotype(TaxaList taxa, List<Trait> traits, DoubleMatrix2D data) SimplePhenotype(TaxaList taxa, List<Trait> traits, double[][] data) SimplePhenotype(TaxaList taxa, List<Trait> traits)

TASSELpy.net.maizegenetics.trait.Trait module¶

class TASSELpy.net.maizegenetics.trait.Trait.Trait(*args, **kwargs)[source]¶

Bases: TASSELpy.java.lang.Comparable.Comparable

Data descriptor that contains information about a trait, factor, covariate, or other item for which data may be stored. It may contain information about the experimental unit on which data was collected (factors). It may contain information about how the data is to be used in an analysis. Data values will be stored as doubles. In the case of discrete variables, the value stored will be 0, 1, ... indicating the variable level. For discrete variables, labels or names corresponding to each variable level would be stored as well.

Methods

`addFactor`(*args)	Adds a new factor and its value or changes the value of an existing factor.
`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`compareTo`(*args)	Compares this object with the specified object for order.
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getFactorNames`(*args)	Gets the names for the factors for this trait.
`getFactorValue`(*args)	Gets a factor value
`getInstance`(*args)	Gets a copy of an existing trait
`getLevelLabel`(*args)	Gets the name of a level
`getLevelLabels`(*args)	Gets the level labels
`getName`(*args)	Gets the name by which the trait is identified
`getNumberOfFactors`(*args)	Gets the number of factors for this trait
`getNumberOfLevels`(*args)	Gets the number of levels
`getNumberOfProperties`(*args)	Gets the number of entries in the property map
`getProperties`(*args)	The entry set for this trait’s property map
`getProperty`(*args)	Gets the value of this property, null if property does not exist
`getPropertyNames`(*args)	Gets all the property names for this trait
`getType`(*args)	Gets the type of this trait
`hasLevels`(*args)	Returns whether the trait has levels
`hashCode`(*args)	Returns a hash code vlaue for the object
`isDiscrete`(*args)	Gets whether this trait is discrete
`setLevelLabels`(*args)	Sets the level labels
`setProperty`(*args)	Adds a property or sets a new value for an existing property
`setType`(*args)	Sets the type of this trait
`toString`(*args)	Returns a string representation of the object
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

Constructor for Trait

Signature:	Trait (String name, boolean isDiscrete, String type)
Parameters:	name (String) – this trait isDicrete – true if this trait is discrete, false if it is continuous type (String) – the trait type; data, covariate, factor, marker, or exclude properties – a property map, which can be null

addFactor(*args)[source]¶

Adds a new factor and its value or changes the value of an existing factor. A factor might be an environment or a rep number

Signature:	addFactor (String name, String value)
Parameters:	name (String) – this factor’s name value (String) – the factor’s value for this trait

getFactorNames(*args)[source]¶

Gets the names for the factors for this trait. Returns null if there are no factors

Signatures:

ArrayList<String> getFactorNames()

Returns:

Names for the factors for this trait. Returns null if there are no factors

getFactorValue(*args)[source]¶

Gets a factor value

Signature:	getFactorValue (String factorName)
Returns:	The value of this factor or null if the factor does not exist
Return type:	String

static getInstance(*args)[source]¶

Gets a copy of an existing trait

Signature:	getInstance (Trait trait)
Parameters:	trait (Trait) – the trait to be copied
Returns:	A copy of the trait
Return type:	Trait

getLevelLabel(*args)[source]¶

Gets the name of a level

Signature:	getLevelLabel (int level)
Parameters:	level (int) – the level number (0,1,...)
Returns:	The name of this level
Return type:	String

getLevelLabels(*args)[source]¶

Gets the level labels

Signature:	getLevelLabels ()
Returns:	For a discrete trait, the names of the levels or values this trait can take
Return type:	String[]

getName(*args)[source]¶

Gets the name by which the trait is identified

Signature:	getName ()
Returns:	Name by which the trait is identified
Return type:	String

getNumberOfFactors(*args)[source]¶

Gets the number of factors for this trait

Signature:	getNumberOfFactors ()
Returns:	The number of factors for this trait
Return type:	int

getNumberOfLevels(*args)[source]¶

Gets the number of levels

Signature:	getNumberOfLevels ()
Returns:	The number of levels
Return type:	int

getNumberOfProperties(*args)[source]¶

Gets the number of entries in the property map

Signature:	getNumberOfProperties ()
Returns:	The number of entries in the property map
Return type:	int

getProperties(*args)[source]¶

The entry set for this trait’s property map

Signatures:

Set<Entry<String, Object>> getProperties()

Returns:

The entry Set for this trait’s property map

getProperty(*args)[source]¶

Gets the value of this property, null if property does not exist

Signature:	getProperty (String propertyName)
Parameters:	propertyName (String) – The name of a property for this trait
Returns:	The value of this property null if the property does not exist
Return type:	Object

getPropertyNames(*args)[source]¶

Gets all the property names for this trait

Signatures:

Set<String> getPropertyNames()

Returns:

All the property names for this trait

getType(*args)[source]¶

Gets the type of this trait

Signature:	getType ()
Returns:	The type of this trait: data, covariate, factor, marker, or exclude
Return type:	String

hasLevels(*args)[source]¶

Returns whether the trait has levels

Signature:	hasLevels ()
Returns:	true if the trait has levels
Return type:	boolean

isDiscrete(*args)[source]¶

Gets whether this trait is discrete

Signature:	isDiscrete ()
Returns:	true if this trait is discrete, false if it is continuous
Return type:	boolean

setLevelLabels(*args)[source]¶

Sets the level labels

Signatures:

void setLevelLabels(String[] levelLabels)

Arguments:

levelLabels – for a discrete trait, the names of the levels or values this trait: can take

setProperty(*args)[source]¶

Adds a property or sets a new value for an existing property

Signature:	setProperty (String propertyName, Object value)
Parameters:	propertyName (String) – a name value (Object) – The value for this property

setType(*args)[source]¶

Sets the type of this trait

Signature:	setType (String type)
Parameters:	type (String) – The type of this trait: data covariate, factor, marker, or exclude

class TASSELpy.net.maizegenetics.trait.Trait.metaTrait[source]¶: Bases: object

TASSELpy.net.maizegenetics.trait package¶

Submodules¶

TASSELpy.net.maizegenetics.trait.AbstractPhenotype module¶

TASSELpy.net.maizegenetics.trait.CombinePhenotype module¶

TASSELpy.net.maizegenetics.trait.FilterPhenotype module¶

TASSELpy.net.maizegenetics.trait.MarkerPhenotype module¶

TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter module¶

TASSELpy.net.maizegenetics.trait.Phenotype module¶

TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils module¶

TASSELpy.net.maizegenetics.trait.SimplePhenotype module¶

TASSELpy.net.maizegenetics.trait.Trait module¶

Module contents¶

Table Of Contents

This Page

Navigation

TASSELpy.net.maizegenetics.trait package¶

Submodules¶

TASSELpy.net.maizegenetics.trait.AbstractPhenotype module¶

TASSELpy.net.maizegenetics.trait.CombinePhenotype module¶

TASSELpy.net.maizegenetics.trait.FilterPhenotype module¶

TASSELpy.net.maizegenetics.trait.MarkerPhenotype module¶

TASSELpy.net.maizegenetics.trait.MarkerPhenotypeAdapter module¶

TASSELpy.net.maizegenetics.trait.Phenotype module¶

TASSELpy.net.maizegenetics.trait.ReadPhenotypeUtils module¶

TASSELpy.net.maizegenetics.trait.SimplePhenotype module¶

TASSELpy.net.maizegenetics.trait.Trait module¶

Module contents¶

Table Of Contents

This Page

Quick search

Navigation