net.maizegenetics.analysis.association

Class FastMultithreadedAssociationPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class FastMultithreadedAssociationPlugin
extends AbstractPlugin

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
FastMultithreadedAssociationPlugin()
FastMultithreadedAssociationPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
GenotypeTable.GENOTYPE_TABLE_COMPONENT	genotypeTable() If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
FastMultithreadedAssociationPlugin	genotypeTable(GenotypeTable.GENOTYPE_TABLE_COMPONENT value) Set Genotype Component.
String	getButtonName() Button name for this plugin to be used in buttons, etc.
ImageIcon	getIcon() Icon for this plugin to be used in buttons, etc.
String	getToolTipText() Tool Tip Text for this plugin
Double	maxp() The maximum p-value that will be output by the analysis.
FastMultithreadedAssociationPlugin	maxp(Double value) Set MaxPValue.
Integer	maxThreads() the maximum number of threads to be used by this plugin.
FastMultithreadedAssociationPlugin	maxThreads(Integer value) Set Max Threads.
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
String	reportFilename() The name of the file to which these results will be saved.
FastMultithreadedAssociationPlugin	reportFilename(String value) Set Output File.
TableReport	runPlugin(DataSet input) Convenience method to run plugin with one return object.
Boolean	saveAsFile() Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree.
FastMultithreadedAssociationPlugin	saveAsFile(Boolean value) Set Write to file.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

FastMultithreadedAssociationPlugin

public FastMultithreadedAssociationPlugin()

FastMultithreadedAssociationPlugin

public FastMultithreadedAssociationPlugin(Frame parentFrame,
                                          boolean isInteractive)

Method Detail

processData

public DataSet processData(DataSet input)

Description copied from interface: Plugin

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

Specified by:

processData in interface Plugin

Overrides:

processData in class AbstractPlugin

Parameters:

input - input

Returns:

resulting data set or null.

getIcon

public ImageIcon getIcon()

Description copied from interface: Plugin

Icon for this plugin to be used in buttons, etc.

Returns:

ImageIcon

getButtonName

public String getButtonName()

Description copied from interface: Plugin

Button name for this plugin to be used in buttons, etc.

Returns:

String

getToolTipText

public String getToolTipText()

Description copied from interface: Plugin

Tool Tip Text for this plugin

Returns:

String

runPlugin

public TableReport runPlugin(DataSet input)

Convenience method to run plugin with one return object.

maxp

public Double maxp()

The maximum p-value that will be output by the analysis.

Returns:

MaxPValue

maxp

public FastMultithreadedAssociationPlugin maxp(Double value)

Set MaxPValue. The maximum p-value that will be output by the analysis.

Parameters:

value - MaxPValue

Returns:

this plugin

genotypeTable

public GenotypeTable.GENOTYPE_TABLE_COMPONENT genotypeTable()

If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.

Returns:

Genotype Component

genotypeTable

public FastMultithreadedAssociationPlugin genotypeTable(GenotypeTable.GENOTYPE_TABLE_COMPONENT value)

Set Genotype Component. If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.

Parameters:

value - Genotype Component

Returns:

this plugin

saveAsFile

public Boolean saveAsFile()

Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.

Returns:

Write to file

saveAsFile

public FastMultithreadedAssociationPlugin saveAsFile(Boolean value)

Set Write to file. Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.

Parameters:

value - Write to file

Returns:

this plugin

reportFilename

public String reportFilename()

The name of the file to which these results will be saved.

Returns:

Output File

reportFilename

public FastMultithreadedAssociationPlugin reportFilename(String value)

Set Output File. The name of the file to which these results will be saved.

Parameters:

value - Output File

Returns:

this plugin

maxThreads

public Integer maxThreads()

the maximum number of threads to be used by this plugin.

Returns:

Max Threads

maxThreads

public FastMultithreadedAssociationPlugin maxThreads(Integer value)

Set Max Threads. the maximum number of threads to be used by this plugin.

Parameters:

value - Max Threads

Returns:

this plugin