net.maizegenetics.analysis.data

Class AddReferenceAlleleToHDF5Plugin

AbstractPlugin

net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class AddReferenceAlleleToHDF5Plugin
extends AbstractPlugin

Constructor Detail

AddReferenceAlleleToHDF5Plugin

public AddReferenceAlleleToHDF5Plugin()

AddReferenceAlleleToHDF5Plugin

public AddReferenceAlleleToHDF5Plugin(java.awt.Frame parentFrame,
                                      boolean isInteractive)

Method Detail

postProcessParameters

public void postProcessParameters()

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

inputHDF5GenotypeFile

public java.lang.String inputHDF5GenotypeFile()

Input HDF5 genotype (*.h5) file to be annotated with the reference allele

Returns:

org.jetbrains.dokka.NodeRenderContent@2ff07b79: Input HDF5 Genotype File

inputHDF5GenotypeFile

public AddReferenceAlleleToHDF5Plugin inputHDF5GenotypeFile(java.lang.String value)

Set Input HDF5 Genotype File. Input HDF5 genotype (*.h5) file to be annotated with the reference allele

Parameters:

value - Input HDF5 Genotype File

Returns:

org.jetbrains.dokka.NodeRenderContent@161079d5: this plugin

referenceGenomeFile

public java.lang.String referenceGenomeFile()

Reference genome file in fasta format

Returns:

org.jetbrains.dokka.NodeRenderContent@6925be66: Reference Genome File

referenceGenomeFile

public AddReferenceAlleleToHDF5Plugin referenceGenomeFile(java.lang.String value)

Set Reference Genome File. Reference genome file in fasta format

Parameters:

value - Reference Genome File

Returns:

org.jetbrains.dokka.NodeRenderContent@9da834a: this plugin

referenceGenomeVersion

public java.lang.String referenceGenomeVersion()

Version of the reference genome

Returns:

org.jetbrains.dokka.NodeRenderContent@255d0abb: Reference Genome Version

referenceGenomeVersion

public AddReferenceAlleleToHDF5Plugin referenceGenomeVersion(java.lang.String value)

Set Reference Genome Version. Version of the reference genome

Parameters:

value - Reference Genome Version

Returns:

org.jetbrains.dokka.NodeRenderContent@30160114: this plugin

outputHDF5GenotypeFile

public java.lang.String outputHDF5GenotypeFile()

Output HDF5 genotype file annotated with the reference allele (Default: write to same folder as input, with '*.h5' replaced '*_withRef.h5')

Returns:

org.jetbrains.dokka.NodeRenderContent@74844ffe: Output HDF5 Genotype File

outputHDF5GenotypeFile

public AddReferenceAlleleToHDF5Plugin outputHDF5GenotypeFile(java.lang.String value)

Set Output HDF5 Genotype File. Output HDF5 genotype file annotated with the reference allele (Default: write to same folder as input, with '*.h5' replaced '*_withRef.h5')

Parameters:

value - Output HDF5 Genotype File

Returns:

org.jetbrains.dokka.NodeRenderContent@291942f7: this plugin