net.maizegenetics.analysis.gbs.v2

Class SNPQualityProfilerPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class SNPQualityProfilerPlugin
extends AbstractPlugin

Scores all discovered SNPs for various coverage, depth, and genotypic statistics for a given set of taxa (samples). For each subset of taxa, there are expectations for segregation that can be used to determine whether the SNP is behaving appropriately.

Constructor Detail

SNPQualityProfilerPlugin

public SNPQualityProfilerPlugin()

SNPQualityProfilerPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

runPlugin

public TagData runPlugin(DataSet input)

Convenience method to run plugin with one return object.

taxaFile

public java.lang.String taxaFile()

Name of taxa list input file in taxa list format

Returns:

org.jetbrains.dokka.NodeRenderContent@38979d4: Taxa List File

taxaFile

public SNPQualityProfilerPlugin taxaFile(java.lang.String value)

Set Taxa List File. Name of taxa list input file in taxa list format

Parameters:

value - Taxa List File

Returns:

org.jetbrains.dokka.NodeRenderContent@68eecd94: this plugin

dBFile

public java.lang.String dBFile()

Name of output file (e.g. GBSv2.db)

Returns:

org.jetbrains.dokka.NodeRenderContent@45f4e5a2: GBS DB File

dBFile

public SNPQualityProfilerPlugin dBFile(java.lang.String value)

Set GBS DB File. Name of output file (e.g. GBSv2.db)

Parameters:

value - GBS DB File

Returns:

org.jetbrains.dokka.NodeRenderContent@533ad70: this plugin

statFile

public java.lang.String statFile()

Name of output file (e.g. GBSv2.db)

Returns:

org.jetbrains.dokka.NodeRenderContent@4dbc23db: GBS DB File

statFile

public SNPQualityProfilerPlugin statFile(java.lang.String value)

Set GBS DB File. Name of output file (e.g. GBSv2.db)

Parameters:

value - GBS DB File

Returns:

org.jetbrains.dokka.NodeRenderContent@53a0c595: this plugin

taxaListName

public java.lang.String taxaListName()

Name of taxa set for database

Returns:

org.jetbrains.dokka.NodeRenderContent@311bf3b6: Name for taxa set in DB

taxaListName

public SNPQualityProfilerPlugin taxaListName(java.lang.String value)

Set Name for taxa set in DB. Name of taxa set for database

Parameters:

value - Name for taxa set in DB

Returns:

org.jetbrains.dokka.NodeRenderContent@295b90c8: this plugin

deleteOldData

public java.lang.Boolean deleteOldData()

Delete exisiting SNP Quality data from DB

Returns:

org.jetbrains.dokka.NodeRenderContent@555dcc3: deleteOldData

deleteOldData

public SNPQualityProfilerPlugin deleteOldData(java.lang.Boolean value)

Set Delete old data flag. True indicates we want the db tables cleared

Parameters:

value - true/false - whether to delete data

Returns:

org.jetbrains.dokka.NodeRenderContent@500c3d91: this plugin