net.maizegenetics.analysis.data

Class ThinSitesByPositionPlugin

AbstractPlugin

net.maizegenetics.analysis.data.ThinSitesByPositionPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class ThinSitesByPositionPlugin
extends AbstractPlugin

Plugin to thin out sites based on their physical position on the chromosome. Expects the user to enter a minimum distance between sites in base pair. Accepts and writes .hmp.txt, .hmp.txt.gz, .vcf, .vcf.gz and .h5 files.

Constructor Detail

ThinSitesByPositionPlugin

public ThinSitesByPositionPlugin()

ThinSitesByPositionPlugin

public ThinSitesByPositionPlugin(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()

outFile

public java.lang.String outFile()

Output genotype file

Returns:

org.jetbrains.dokka.NodeRenderContent@17662308: Output file

outfile

public ThinSitesByPositionPlugin outfile(java.lang.String value)

Set Output file. Output genotype file

Parameters:

value - Output file

Returns:

org.jetbrains.dokka.NodeRenderContent@3a07c0ed: this plugin

minDist

public java.lang.Integer minDist()

Minimum distance in bp between adjacent sites

Returns:

org.jetbrains.dokka.NodeRenderContent@5cb3d355: Minimum distance

minDist

public ThinSitesByPositionPlugin minDist(java.lang.Integer value)

Set Minimum distance. Minimum distance in bp between adjacent sites

Parameters:

value - Minimum distance

Returns:

org.jetbrains.dokka.NodeRenderContent@1843c83d: this plugin

getCitation

public java.lang.String getCitation()

runPlugin

public GenotypeTable runPlugin(DataSet input)

Convenience method to run plugin with one return object.