TASSELpy.net.maizegenetics.taxa.distance package

Submodules

TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix module

class TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.DistanceMatrix(*args, **kwargs)

Bases: TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix, TASSELpy.net.maizegenetics.util.TableReport.TableReport

Storage for pairwise distance matrices

Methods

absoluteDistance(*args)	Compute absolute distance to second distance matrix
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.
getClonedDistances(*args)	Returns the distances as a 2-dimensional array of doubles.
getClosestIndex(*args)	Gets the index of the taxon closest to a given taxon
getColumnCount(*args)	Gets the number of columns
getColumnName(*args)	Gets a column name
getDblArray(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
getDistance(*args)	Returns the distance calculated for two taxa with the indices
getDistances(*args)	Returns the distances as a 2-dimensional array of doubles (in the actual array used
getElementCount(*args)	Gets the total number of elements in the dataset
getRow(*args)	Returns specified row
getRowCount(*args)	Gets the number of rows
getSize(*args)	Returns the number of rows and columns that the distance matrix has
getTableColumnNames(*args)	Gets the names of the columns
getTableTitle(*args)	Gets the title of the table
getTaxaList(*args)	Return TaxaList of this matrix
getTaxon(*args)	Gets a Taxon
getValueAt(*args)	Returns value at given row and column
hashCode(*args)	Returns a hash code vlaue for the object
isSymmetric(*args)	Test whether this matrix is a symmetrix distance matrix
meanDistance(*args)	Returns the mean pairwise distnace of this matrix
numberOfTaxa(*args)	Gets the number of taxa
squaredDistance(*args)	Compute squared distance to second distance matrix
toDict()	Outputs the table as a dictionary
toString(*args)	Get string representation of alignment as a string
whichIdNumber(*args)	Gets the id number of a taxon
wrap_existing_array(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)

Constructs DistanceMatrix

Signature:

DistanceMatrix ()

Signature:

DistanceMatrix (double[][] distance, TaxaList taxaList)

Signature:

DistanceMatrix (DistanceMatrix dm)

Signature:

DistanceMatrix (DistanceMatrix dm, TaxaList subset)

Parameters:

• distance (double[][]) – distances between taxa
• taxaList (TaxaList) – The taxa in the matrix
• dm (DistanceMatrix) – DistanceMatrix to clone
• subset (TaxaList) – The taxa that you want in the resulting matrix

absoluteDistance(*args)

Compute absolute distance to second distance matrix

Signature:absoluteDistance (DistanceMatrix mat) Parameters:mat (DistanceMatrix) – Second DistanceMatrix Returns:Absolute distance to second distance matrix Return type:double

getClosestIndex(*args)

Gets the index of the taxon closest to a given taxon

Signature:

getClosestIndex (int fromIndex, int[] exclusion)

Parameters:

• fromIndex (int) – the index of the thing (taxa, sequence) from which we want to find the closest (excluding self)
• exclusion (int[]) – Indexes of things that should not be considered, may be null

Returns:

The index of the member closest to the specified

Return type:

int

getColumnName(*args)

Gets a column name

Signature:getColumnName (int col) Parameters:col (int) – Index of the column Returns:Name of the column Return type:String

getDistances(*args)

Returns the distances as a 2-dimensional array of doubles (in the actual array used to store the distances)

Signatures:

final double[][] getDistances()

Returns:

A clone of the array used to store distances

getTaxon(*args)

Gets a Taxon

Signature:getTaxon (int i) Parameters:i (int) – The index of the taxon Returns:The taxon at index i Return type:Taxon

numberOfTaxa(*args)

Gets the number of taxa

Signature:numberOfTaxa () Returns:The number of taxa Return type:int

squaredDistance(*args)

Compute squared distance to second distance matrix

Signature:

squaredDistance (DistanceMatrix mat, boolean weighted)

Parameters:

• mat (DistanceMatrix) – Second DistanceMatrix
• weighted (boolean) – Whether to weight with Fitch margoliash weights

Returns:

Squared distance to second distance matrix

Return type:

double

whichIdNumber(*args)

Gets the id number of a taxon

Signature:

whichIdNumber (String name)

Signature:

whichIdNumber (Taxon id)

Parameters:

• name (String) – The name of the taxon as a string
• id (Taxon) – The taxon as a Taxon

Returns:

The id number of the taxon

Return type:

int

class TASSELpy.net.maizegenetics.taxa.distance.DistanceMatrix.metaDistanceMatrix

Bases: object

TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix module

class TASSELpy.net.maizegenetics.taxa.distance.TaxaListMatrix.TaxaListMatrix(*args, **kwargs)

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

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.
getClonedDistances(*args)	Returns the distances as a 2-dimensional array of doubles.
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.
getDistance(*args)	Returns the distance calculated for two taxa with the indices
getElementCount(*args)	Gets the total number of elements in the dataset
getRow(*args)	Returns specified row
getRowCount(*args)	Gets the number of rows
getSize(*args)	Returns the number of rows and columns that the distance matrix has
getTableColumnNames(*args)	Gets the names of the columns
getTableTitle(*args)	Gets the title of the table
getTaxaList(*args)	Return TaxaList of this matrix
getValueAt(*args)	Returns value at given row and column
hashCode(*args)	Returns a hash code vlaue for the object
isSymmetric(*args)	Test whether this matrix is a symmetrix distance matrix
meanDistance(*args)	Returns the mean pairwise distnace of this matrix
toDict()	Outputs the table as a dictionary
toString(*args)	Get string representation of alignment as a string
wrap_existing_array(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)

getClonedDistances(*args)

Returns the distances as a 2-dimensional array of doubles. Matrix is cloned first so it can be altered freely

Signature:getClonedDistances () Returns:matrix as 2-d array of doubles Return type:double[][]

getDistance(*args)

Returns the distance calculated for two taxa with the indices row and col

Signature:

getDistance (int row, int col)

Parameters:

• row (int) – row
• col (int) – col

Returns:

Distance for the two taxa at the specified indices

Return type:

double

getSize(*args)

Returns the number of rows and columns that the distance matrix has

Signature:getSize () Returns:Number of rows and columns in the distance matrix Return type:int

getTaxaList(*args)

Return TaxaList of this matrix

Signature:getTaxaList () Returns:TaxaList of this matrix Return type:TaxaList

isSymmetric(*args)

Test whether this matrix is a symmetrix distance matrix

Signature:isSymmetric () Returns:Whether this matrix is a symmetric distance matrix Return type:boolean

meanDistance(*args)

Returns the mean pairwise distnace of this matrix

Signature:meanDistance () Returns:Mean pairwise distance of this matrix Return type:double

toString(*args)

Get string representation of alignment as a string

Signature:toString () Returns:Representation of alignment as a string Return type:String

Module contents