net.maizegenetics.analysis.data

Class SortGenotypeFilePlugin

AbstractPlugin

net.maizegenetics.analysis.data.SortGenotypeFilePlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class SortGenotypeFilePlugin
extends AbstractPlugin

Created by jgw87 on 6/5/14. This plugin takes a Hapmap or VCF genotype file and sorts it according to TASSEL's conventions which rely on the position, locus (chromosome), strand, and SNP name (to facilitate searching).

Constructor Detail

SortGenotypeFilePlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

pluginDescription

public java.lang.String pluginDescription()

postProcessParameters

protected void postProcessParameters()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

inputFile

public java.lang.String inputFile()

Input file

Returns:

org.jetbrains.dokka.NodeRenderContent@73e5cc60: Input file

inputFile

public SortGenotypeFilePlugin inputFile(java.lang.String value)

Set Input file. Input file

Parameters:

value - Input file

Returns:

org.jetbrains.dokka.NodeRenderContent@47fed40a: this plugin

outputFile

public java.lang.String outputFile()

Output file

Returns:

org.jetbrains.dokka.NodeRenderContent@26557aae: Output file

outputFile

public SortGenotypeFilePlugin outputFile(java.lang.String value)

Set Output file. Output file

Parameters:

value - Output file

Returns:

org.jetbrains.dokka.NodeRenderContent@65dbe6c1: this plugin

fileType

public net.maizegenetics.analysis.data.SortGenotypeFilePlugin.SupportedFileTypes fileType()

Input/output file type (if not obvious from file name)

Returns:

org.jetbrains.dokka.NodeRenderContent@3800a0d6: File type

fileType

public SortGenotypeFilePlugin fileType(net.maizegenetics.analysis.data.SortGenotypeFilePlugin.SupportedFileTypes value)

Set File type. Input/output file type (if not obvious from file name)

Parameters:

value - File type

Returns:

org.jetbrains.dokka.NodeRenderContent@9ef7d58: this plugin