net.maizegenetics.analysis.rna

Class RNADeMultiPlexSeqToDBPlugin

AbstractPlugin

net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class RNADeMultiPlexSeqToDBPlugin
extends AbstractPlugin

Constructor Detail

RNADeMultiPlexSeqToDBPlugin

public RNADeMultiPlexSeqToDBPlugin()

RNADeMultiPlexSeqToDBPlugin

public RNADeMultiPlexSeqToDBPlugin(java.awt.Frame parentFrame)

RNADeMultiPlexSeqToDBPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

setTagLenException

public static void setTagLenException()

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 FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.

Returns:

org.jetbrains.dokka.NodeRenderContent@2585bbf5: Input Directory

inputDirectory

public RNADeMultiPlexSeqToDBPlugin inputDirectory(java.lang.String value)

Set Input Directory. Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.

Parameters:

value - Input Directory

Returns:

org.jetbrains.dokka.NodeRenderContent@27fe63ee: this plugin

keyFile

public java.lang.String keyFile()

Key file listing barcodes distinguishing the samples

Returns:

org.jetbrains.dokka.NodeRenderContent@7a567d23: Key File

keyFile

public RNADeMultiPlexSeqToDBPlugin keyFile(java.lang.String value)

Set Key File. Key file listing barcodes distinguishing the samples

Parameters:

value - Key File

Returns:

org.jetbrains.dokka.NodeRenderContent@4afd479d: this plugin

minimumKmerLength

public java.lang.Integer minimumKmerLength()

Minimum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@422f0724: Minimum Tag Length

minimumKmerLength

public RNADeMultiPlexSeqToDBPlugin minimumKmerLength(java.lang.Integer value)

Set Minimum Tag Length. Minimum Tag Length

Parameters:

value - Minimum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@169aed9c: this plugin

minKmerCount

public java.lang.Integer minKmerCount()

Minimum tag count

Returns:

org.jetbrains.dokka.NodeRenderContent@5f6c2509: Min Tag Count

minKmerCount

public RNADeMultiPlexSeqToDBPlugin minKmerCount(java.lang.Integer value)

Set Min Tag Count. Minimum tag count

Parameters:

value - Min Tag Count

Returns:

org.jetbrains.dokka.NodeRenderContent@7f0d50d6: this plugin

outputDatabaseFile

public java.lang.String outputDatabaseFile()

Output Database File

Returns:

org.jetbrains.dokka.NodeRenderContent@45a16e34: Output Database File

outputDatabaseFile

public RNADeMultiPlexSeqToDBPlugin outputDatabaseFile(java.lang.String value)

Set Output Database File. Output Database File

Parameters:

value - Output Database File

Returns:

org.jetbrains.dokka.NodeRenderContent@4168d11: this plugin

minimumQualityScore

public java.lang.Integer minimumQualityScore()

Minimum quality score within the barcode and read length to be accepted

Returns:

org.jetbrains.dokka.NodeRenderContent@3aecb4f7: Minimum quality score

minimumQualityScore

public RNADeMultiPlexSeqToDBPlugin minimumQualityScore(java.lang.Integer value)

Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted

Parameters:

value - Minimum quality score

Returns:

org.jetbrains.dokka.NodeRenderContent@2f72d89c: this plugin