net.maizegenetics.analysis.gbs

Class ProductionPipeline

AbstractPlugin

net.maizegenetics.analysis.gbs.ProductionPipeline

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class ProductionPipeline
extends AbstractPlugin

Constructor Detail

ProductionPipeline

public ProductionPipeline(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()

inputDirectory

public java.lang.String inputDirectory()

Input directory containing subdirectories with fastq AND/OR qseq files

Returns:

org.jetbrains.dokka.NodeRenderContent@297c584e: Input Directory

inputDirectory

public ProductionPipeline inputDirectory(java.lang.String value)

Set Input Directory. Input directory containing subdirectories with fastq AND/OR qseq files

Parameters:

value - Input Directory

Returns:

org.jetbrains.dokka.NodeRenderContent@44feb7d7: this plugin

enzyme

public java.lang.String enzyme()

Enzyme used to create the GBS library

Returns:

org.jetbrains.dokka.NodeRenderContent@5f9de6f0: Enzyme

enzyme

public ProductionPipeline enzyme(java.lang.String value)

Set Enzyme. Enzyme used to create the GBS library

Parameters:

value - Enzyme

Returns:

org.jetbrains.dokka.NodeRenderContent@2d03775d: this plugin

productionTOPM

public java.lang.String productionTOPM()

Physical map file containing tags and corresponding variants (production TOPM)

Returns:

org.jetbrains.dokka.NodeRenderContent@6676f49b: Production T O P M

productionTOPM

public ProductionPipeline productionTOPM(java.lang.String value)

Set Production T O P M. Physical map file containing tags and corresponding variants (production TOPM)

Parameters:

value - Production T O P M

Returns:

org.jetbrains.dokka.NodeRenderContent@5707b78d: this plugin

outputGenotypeFile

public java.lang.String outputGenotypeFile()

Output (target) HDF5 genotypes file to add new genotypes to (new file created if it doesn't exist)

Returns:

org.jetbrains.dokka.NodeRenderContent@671d71fb: Output Genotype File

outputGenotypeFile

public ProductionPipeline outputGenotypeFile(java.lang.String value)

Set Output Genotype File. Output (target) HDF5 genotypes file to add new genotypes to (new file created if it doesn't exist)

Parameters:

value - Output Genotype File

Returns:

org.jetbrains.dokka.NodeRenderContent@51124bda: this plugin

archiveDirectory

public java.lang.String archiveDirectory()

Archive directory where to move processed files

Returns:

org.jetbrains.dokka.NodeRenderContent@11bf4f: Archive Directory

archiveDirectory

public ProductionPipeline archiveDirectory(java.lang.String value)

Set Archive Directory. Archive directory where to move processed files

Parameters:

value - Archive Directory

Returns:

org.jetbrains.dokka.NodeRenderContent@6ac0cb1f: this plugin