net.maizegenetics.analysis.gbs.v2

Class SNPCutPosTagVerificationPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class SNPCutPosTagVerificationPlugin
extends AbstractPlugin

This class allows a user to specify a Cut or SNP position for which they would like data printed. For a Cut Position, the tags associated with that position are printed along with the number of times it appears in each taxa. For a SNP Position, each allele and the tags associated with that allele are printed along with the number of times the tag appears in each taxa. The tag is shown both as it is stored in the db, and as a forward strand. The SNP alignments are based on forward strand.

Constructor Detail

SNPCutPosTagVerificationPlugin

public SNPCutPosTagVerificationPlugin()

SNPCutPosTagVerificationPlugin

public SNPCutPosTagVerificationPlugin(java.awt.Frame parentFrame)

SNPCutPosTagVerificationPlugin

public SNPCutPosTagVerificationPlugin(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@13dfe355: Input DB

inputDB

public SNPCutPosTagVerificationPlugin 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@646edb49: this plugin

chrom

public java.lang.String chrom()

Chromosome as String

Returns:

org.jetbrains.dokka.NodeRenderContent@329846cc: Chromosome name

chrom

public SNPCutPosTagVerificationPlugin chrom(java.lang.String value)

Set outputDir path. Directory file path where output files will be writen

Parameters:

value - Directory path

Returns:

org.jetbrains.dokka.NodeRenderContent@7642ec3e: this plugin

cutOrSnpPosition

public java.lang.Integer cutOrSnpPosition()

Cut Position

Returns:

org.jetbrains.dokka.NodeRenderContent@1a6b7ce8: Cut position

cutOrSnpPosition

public SNPCutPosTagVerificationPlugin cutOrSnpPosition(java.lang.Integer value)

Set cut position.

Parameters:

value - cut position

Returns:

org.jetbrains.dokka.NodeRenderContent@8cd587f: this plugin

strand

public java.lang.Byte strand()

Strand direction

Returns:

org.jetbrains.dokka.NodeRenderContent@7813d18c: Strand direction

strand

public SNPCutPosTagVerificationPlugin strand(java.lang.Byte value)

Set strand direction.

Parameters:

value - strand direction

Returns:

org.jetbrains.dokka.NodeRenderContent@19d1e1ac: this plugin

positionType

public java.lang.String positionType()

SNP Position

Returns:

org.jetbrains.dokka.NodeRenderContent@581c4242: SNP position

positionType

public SNPCutPosTagVerificationPlugin positionType(java.lang.String value)

Set SNP position.

Parameters:

value - SNP position

Returns:

org.jetbrains.dokka.NodeRenderContent@3a70f79e: this plugin

outputFile

public java.lang.String outputFile()

output directory path

Returns:

org.jetbrains.dokka.NodeRenderContent@5c09ceed: outPutDir directory string

outputFile

public SNPCutPosTagVerificationPlugin outputFile(java.lang.String value)

Set outputDir path. Directory file path where output files will be writen

Parameters:

value - Directory path

Returns:

org.jetbrains.dokka.NodeRenderContent@4ac39841: this plugin