net.maizegenetics.analysis.data

Class GenosToABHPlugin

AbstractPlugin

net.maizegenetics.analysis.data.GenosToABHPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class GenosToABHPlugin
extends AbstractPlugin

Plugin to convert genotypes to parental comparisons and store them in an output file. The user can get outputs as A/H/B, 0/1/2, or 0/0.5/1 for a genotype matching parent A's genotype, heterozygous, or parent B's genotype respectively. If the genotype is neither A or B or a het combination of A/B (B/A) then it is coded as "NA".

Constructor Detail

GenosToABHPlugin

public GenosToABHPlugin()

GenosToABHPlugin

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

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

The main method. Plugin to convert genotypes to parental comparisons and store them in an output file. The user can get outputs as A/H/B, 0/1/2, or 0/0.5/1 for a genotype matching parent A's genotype, heterozygous, or parent B's genotype respectively. If the genotype is neither A or B or a het combination of A/B (B/A) then it is coded as "NA".

Parameters:

input - input

Returns:

org.jetbrains.dokka.NodeRenderContent@3e6c1b9c: resulting data set or null.

createParentalByteGenos

public void createParentalByteGenos(GenotypeTable genos,
                                    kotlin.Array[] parentAGenos,
                                    kotlin.Array[] parentBGenos,
                                    kotlin.Array[] hets)

getParentalGenotype

public byte getParentalGenotype(GenotypeTable genos,
                                java.util.ArrayList<java.lang.Integer> parentIndices,
                                int site)

getToolTipText

public java.lang.String getToolTipText()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

runPlugin

public GenotypeTable runPlugin(DataSet input)

Convenience method to run plugin with one return object.

outfile

public java.lang.String outfile()

Output genotype file with ABH encoding

Returns:

org.jetbrains.dokka.NodeRenderContent@7bc49647: Output file

outfile

public GenosToABHPlugin outfile(java.lang.String value)

Set Output file. Output genotype file with ABH encoding

Parameters:

value - Output file

Returns:

org.jetbrains.dokka.NodeRenderContent@50509930: this plugin

parentA

public java.lang.String parentA()

The full name of parent to be encoded as A

Returns:

org.jetbrains.dokka.NodeRenderContent@273091e8: Parent A

parentA

public GenosToABHPlugin parentA(java.lang.String value)

Set Parent A. The full name of parent to be encoded as A

Parameters:

value - Parent A

Returns:

org.jetbrains.dokka.NodeRenderContent@79dece69: this plugin

parentB

public java.lang.String parentB()

The full name of parent to be encoded as B

Returns:

org.jetbrains.dokka.NodeRenderContent@26f709bb: Parent B

parentB

public GenosToABHPlugin parentB(java.lang.String value)

Set Parent B. The full name of parent to be encoded as B

Parameters:

value - Parent B

Returns:

org.jetbrains.dokka.NodeRenderContent@72ba9d4c: this plugin

outputFormat

public net.maizegenetics.analysis.data.GenosToABHPlugin.OUTPUT_CHECK outputFormat()

The output format enum

Returns:

org.jetbrains.dokka.NodeRenderContent@5126fd22: Output Format

outputFormat

public GenosToABHPlugin outputFormat(net.maizegenetics.analysis.data.GenosToABHPlugin.OUTPUT_CHECK value)

Set Output Format. The output format enum

Parameters:

value - Output Format

Returns:

org.jetbrains.dokka.NodeRenderContent@5e84dce9: this plugin

getCitation

public java.lang.String getCitation()

pluginUserManualURL

public java.lang.String pluginUserManualURL()