TASSELpy.net.maizegenetics.plugindef package

Submodules

TASSELpy.net.maizegenetics.plugindef.AbstractPlugin module

class TASSELpy.net.maizegenetics.plugindef.AbstractPlugin.AbstractPlugin(*args, **kwargs)

Bases: TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin

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
getCitation(*args)	Returns Citation for this plugin
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.
getInputs(*args)	Gets list of inputs
getParameter(*args)	Returns a parameter value for given parameter key
hashCode(*args)	Returns a hash code vlaue for the object
isInteractive(*args)	If interactive == true, the plugin will create dialgos and panels
performFunction(*args)	Performs the function of this plugin
pluginDescription(*args)	Returns description of the plugin
processData(*args)	For the new Generic plugin parameter design, performFunction() will automatically call this.
receiveInput(*args)	Sets up this plugin to receive input from another plugin
setParameter(*args)	Sets parameter value
setParameters(*args)	Allows self-describing Plugins to use args to set parameters specific
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)

Creates a new instance of AbstractPlugin

Signature:AbstractPlugin ()

getInputs(*args)

Gets list of inputs

Signatures:

List<Plugin> getInputs()

Returns:

List of inputs

TASSELpy.net.maizegenetics.plugindef.DataSet module

TASSELpy.net.maizegenetics.plugindef.Datum module

class TASSELpy.net.maizegenetics.plugindef.Datum.Datum(*args, **kwargs)

Bases: TASSELpy.java.lang.Object.Object

This wraps data elements used as input or output to TASSEL modules

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.
getComment(*args)	Gets the comment for the datum
getData(*args)	Gets the data
getDataType(*args)	Gets the class of the datum
getDblArray(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
getName(*args)	Gets the name of the datum
hashCode(*args)	Returns a hash code vlaue for the object
setName(*args)	Sets the name of the datum
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)

Creats a new instance of Datum

Signature:

Datum (String name, Object data, String comment)

Parameters:

• name (String) – name of this data instance
• data (Object) – data element
• comment (String) – optional comment

getComment(*args)

Gets the comment for the datum

Signature:getComment () Returns:The comment for the datum Return type:String

getData(*args)

Gets the data

Signature:getData () Returns:The data Return type:Object

getDataType(*args)

Gets the class of the datum

Signature:getDataType () Returns:The Class of the Data Return type:Class

getName(*args)

Gets the name of the datum

Signature:getName () Returns:The name of the datum Return type:String

setName(*args)

Sets the name of the datum

Signature:setName (String s) Parameters:s (String) – The name to give to the datum

TASSELpy.net.maizegenetics.plugindef.Plugin module

class TASSELpy.net.maizegenetics.plugindef.Plugin.DataSet(*args, **kwargs)

Bases: TASSELpy.java.lang.Object.Object

This is a set of Datum

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.
getCreator(*args)	Gets the creator of the dataset
getData(*args)	Gets a particular datum
getDataOfType(*args)	Gets the data of a type or list of types
getDataOfTypeWithName(*args)	Gets data of some type that has some name
getDataSet(*args)	Gets the dataset as a list
getDataWithName(*args)	Gets the data named somehow
getDblArray(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
getSize(*args)	Gets the size of the dataset
hashCode(*args)	Returns a hash code vlaue for the object
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)

Instantiates a DataSet

Signature:

DataSet (Datum theDatum, Plugin creator)

Signature:

DataSet (Datum[] list, Plugin creator)

Parameters:

• list (Datum[]) – list of data elements
• creator (Plugin) – creating plugin
• theDatum (Datum) – a single Datum

getCreator(*args)

Gets the creator of the dataset

Signature:getCreator () Returns:The creator of the dataset Return type:Plugin

getData(*args)

Gets a particular datum

Signature:getData (int i) Parameters:i (int) – The index to get Returns:The datum Return type:Datum

getDataOfType(*args)

Gets the data of a type or list of types

Signatures:

List<Datum> getDataOfType(Class theClass) List<Datum> getDataOfType(Class[] classes)

Arguments:

List<Datum> getDataOfType(Class theClass)

theClass – The class of the data to get

List<Datum> getDataOfType(Class[] classes)

classes – Classes of the data to get

Returns:

A list of the data of the type(s)

getDataOfTypeWithName(*args)

Gets data of some type that has some name

Signatures:

List<Datum> getDataOfTypeWithName(Class[] classes, String[] names)

Arguments:

classes – The array of classes of types to keep names – The list of names of the data to keep

Returns:

The list of data to keep

getDataSet(*args)

Gets the dataset as a list

Signature:getDataSet () Returns:The data set as a list Return type:List

getDataWithName(*args)

Gets the data named somehow

Signatures:

List<Datum> getDataWithName(String name) List<Datum> getDataWithName(String[] names)

Arguments:

List<Datum> getDataWithName(String name)

name – The name of the data to get

List<Datum> getDataWithName(String[] names)

names – The names of the data to get

Returns:

A list of data with the name(s)

getSize(*args)

Gets the size of the dataset

Signature:getSize () Returns:The size of the dataset Return type:int

class TASSELpy.net.maizegenetics.plugindef.Plugin.Plugin(*args, **kwargs)

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
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
getCitation(*args)	Returns Citation for this plugin
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.
getParameter(*args)	Returns a parameter value for given parameter key
hashCode(*args)	Returns a hash code vlaue for the object
isInteractive(*args)	If interactive == true, the plugin will create dialgos and panels
performFunction(*args)	Performs the function of this plugin
pluginDescription(*args)	Returns description of the plugin
processData(*args)	For the new Generic plugin parameter design, performFunction() will automatically call this.
receiveInput(*args)	Sets up this plugin to receive input from another plugin
setParameter(*args)	Sets parameter value
setParameters(*args)	Allows self-describing Plugins to use args to set parameters specific
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)

Instantiates the Plugin

getCitation(*args)

Returns Citation for this plugin

Signature:getCitation () Returns:Citation Return type:String

getParameter(*args)

Returns a parameter value for given parameter key

Signature:getParameter (Enum key) Signature:getParameter (String key) Parameters:key (String) – key Returns:value Return type:Comparable

isInteractive(*args)

If interactive == true, the plugin will create dialgos and panels to interact with the user

Signature:isInteractive () Returns:boolean for whether it’s interactive Return type:boolean

performFunction(*args)

Performs the function of this plugin

Signature:performFunction (DataSet input) Parameters:input (DataSet) – input Returns:Resulting data set or null Return type:DataSet

pluginDescription(*args)

Returns description of the plugin

Signature:pluginDescription () Returns:description Return type:String

processData(*args)

For the new Generic plugin parameter design, performFunction() will automatically call this. Therefore, coders of Plugins should override this instead of performFunction()

Signature:processData (DataSet input) Parameters:input (DataSet) – input Returns:Resulting data set or null Return type:DataSet

receiveInput(*args)

Sets up this plugin to receive input from another plugin

Signature:receiveInput (Plugin input) Parameters:input (Plugin) – input

setParameter(*args)

Sets parameter value

Signature:

setParameter (PluginParameter param, Object value)

Signature:

setParameter (String key, Comparable value)

Signature:

setParameter (String key, String value)

Parameters:

• param (PluginParameter) – parameter
• value (String) – value
• key (String) – key

Returns:

This plugin

Return type:

Plugin

setParameters(*args)

Allows self-describing Plugins to use args to set parameters specific to itself

Signature:setParameters (String[] args) Parameters:args (String[]) – arguments

class TASSELpy.net.maizegenetics.plugindef.Plugin.metaPlugin

Bases: object

TASSELpy.net.maizegenetics.plugindef.PluginParameter module

class TASSELpy.net.maizegenetics.plugindef.PluginParameter.PluginParameter(*args, **kwargs)

Bases: TASSELpy.javaObj.genericJavaObj, TASSELpy.java.lang.Object.Object

Defines the attributes of parameters to be used in the plugins

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.
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
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)

Module contents