net.maizegenetics.analysis.gbs.v2

Class UpdateSNPPositionQualityPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class UpdateSNPPositionQualityPlugin
extends AbstractPlugin

This plugin takes as input: tab-delimited txt file with columns CHROM, POS, QUALITYSCORE dbFile: a GBSv2 database with snppositions recorded A PositionList of positions with quality scores is sent to the database where the snpposition table is updated with a qualityScore value for the specified chromosome and position.

Constructor Detail

UpdateSNPPositionQualityPlugin

public UpdateSNPPositionQualityPlugin()

UpdateSNPPositionQualityPlugin

public UpdateSNPPositionQualityPlugin(java.awt.Frame parentFrame)

UpdateSNPPositionQualityPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

getToolTipText

public java.lang.String getToolTipText()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

runPlugin

public java.lang.String runPlugin(DataSet input)

Convenience method to run plugin with one return object.

inputDB

public java.lang.String inputDB()

Input database file with tags and taxa distribution

Returns:

org.jetbrains.dokka.NodeRenderContent@13a27ff6: Input DB

inputDB

public UpdateSNPPositionQualityPlugin inputDB(java.lang.String value)

Set Input DB. Input database file with tags and taxa distribution

Parameters:

value - Input DB

Returns:

org.jetbrains.dokka.NodeRenderContent@36a71fc8: this plugin

qsFile

public java.lang.String qsFile()

Input quality score file to use for setting the qualityScore in the database's snpposition table.

Returns:

org.jetbrains.dokka.NodeRenderContent@6fbe7b3d: QualityScore File

qsFile

public UpdateSNPPositionQualityPlugin qsFile(java.lang.String value)

Set qsFile. Input quality score file used for setting the qualityScore field in the snpposition table.

Parameters:

value - Quality Score File

Returns:

org.jetbrains.dokka.NodeRenderContent@738185a7: this plugin