net.maizegenetics.analysis.association

Class FastMultithreadedAssociationPlugin

AbstractPlugin

net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class FastMultithreadedAssociationPlugin
extends AbstractPlugin

Constructor Detail

FastMultithreadedAssociationPlugin

public FastMultithreadedAssociationPlugin()

FastMultithreadedAssociationPlugin

public FastMultithreadedAssociationPlugin(java.awt.Frame parentFrame,
                                          boolean isInteractive)

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

runPlugin

public TableReport runPlugin(DataSet input)

Convenience method to run plugin with one return object.

maxp

public java.lang.Double maxp()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@258e15fe: MaxPValue

maxp

public FastMultithreadedAssociationPlugin maxp(java.lang.Double value)

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

Parameters:

value - MaxPValue

Returns:

org.jetbrains.dokka.NodeRenderContent@67195dbd: this plugin

genotypeTable

public net.maizegenetics.dna.snp.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:

org.jetbrains.dokka.NodeRenderContent@27c7fb13: Genotype Component

genotypeTable

public FastMultithreadedAssociationPlugin genotypeTable(net.maizegenetics.dna.snp.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:

org.jetbrains.dokka.NodeRenderContent@15fee6c9: this plugin

saveAsFile

public java.lang.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:

org.jetbrains.dokka.NodeRenderContent@408a206d: Write to file

saveAsFile

public FastMultithreadedAssociationPlugin saveAsFile(java.lang.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:

org.jetbrains.dokka.NodeRenderContent@6d536974: this plugin

reportFilename

public java.lang.String reportFilename()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@755418ae: Output File

reportFilename

public FastMultithreadedAssociationPlugin reportFilename(java.lang.String value)

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

Parameters:

value - Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@177e7063: this plugin

maxThreads

public java.lang.Integer maxThreads()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@6e6a3a9: Max Threads

maxThreads

public FastMultithreadedAssociationPlugin maxThreads(java.lang.Integer value)

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

Parameters:

value - Max Threads

Returns:

org.jetbrains.dokka.NodeRenderContent@700862c8: this plugin