net.maizegenetics.analysis.rna

Class RNADeMultiplexProductionPlugin

AbstractPlugin

net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class RNADeMultiplexProductionPlugin
extends AbstractPlugin

Field Detail

readEndCutSiteRemnantLength

protected static int readEndCutSiteRemnantLength

Constructor Detail

RNADeMultiplexProductionPlugin

public RNADeMultiplexProductionPlugin()

RNADeMultiplexProductionPlugin

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

Method Detail

postProcessParameters

public void postProcessParameters()

processData

public DataSet processData(DataSet input)

setTagLenException

public void setTagLenException()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

main

public static void main(java.lang.String[] args)

runPlugin

public java.lang.String runPlugin(DataSet input)

Convenience method to run plugin with one return object.

inputDir

public java.lang.String inputDir()

Input directory containing fastq AND/OR qseq files.

Returns:

org.jetbrains.dokka.NodeRenderContent@42e76d37: Input Directory

inputDir

public RNADeMultiplexProductionPlugin inputDir(java.lang.String value)

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

Parameters:

value - Input Directory

Returns:

org.jetbrains.dokka.NodeRenderContent@6971bdd7: this plugin

keyFile

public java.lang.String keyFile()

Key file listing barcodes distinguishing the samples

Returns:

org.jetbrains.dokka.NodeRenderContent@71806d3b: Key File

keyFile

public RNADeMultiplexProductionPlugin keyFile(java.lang.String value)

Set Key File. Key file listing barcodes distinguishing the samples

Parameters:

value - Key File

Returns:

org.jetbrains.dokka.NodeRenderContent@1824f08e: this plugin

inputDB

public java.lang.String inputDB()

Input Database file if using SQLite

Returns:

org.jetbrains.dokka.NodeRenderContent@6153a868: Input GBS Database

inputDB

public RNADeMultiplexProductionPlugin inputDB(java.lang.String value)

Set Input GBS Database. Input Database file if using SQLite

Parameters:

value - Input GBS Database

Returns:

org.jetbrains.dokka.NodeRenderContent@5a82e90: this plugin

matchingType

public net.maizegenetics.analysis.rna.FindMatchByWordHash.MatchType matchingType()

Approach used for matching the reads to the contigs

Returns:

org.jetbrains.dokka.NodeRenderContent@773362ab: Matching approach

matchingType

public RNADeMultiplexProductionPlugin matchingType(net.maizegenetics.analysis.rna.FindMatchByWordHash.MatchType value)

Set Matching approach. Approach used for matching the reads to the contigs

Parameters:

value - Matching approach

Returns:

org.jetbrains.dokka.NodeRenderContent@48ac5c43: this plugin

wordSizeMatching

public java.lang.Integer wordSizeMatching()

Word size used to find matches with reference sequences

Returns:

org.jetbrains.dokka.NodeRenderContent@34c0bdd6: Word size used by match

wordSizeMatching

public RNADeMultiplexProductionPlugin wordSizeMatching(java.lang.Integer value)

Set Word size used by match. Word size used to find matches with reference sequences

Parameters:

value - Word size used by match

Returns:

org.jetbrains.dokka.NodeRenderContent@70d8d970: this plugin

maxWordRepeats

public java.lang.Integer maxWordRepeats()

Maximum repetitiveness of the word

Returns:

org.jetbrains.dokka.NodeRenderContent@1c92cbfa: Maximum repeats of word

maxWordRepeats

public RNADeMultiplexProductionPlugin maxWordRepeats(java.lang.Integer value)

Set Maximum repeats of word. Maximum repetitiveness of the word

Parameters:

value - Maximum repeats of word

Returns:

org.jetbrains.dokka.NodeRenderContent@3676c26f: this plugin

searchReverseComplement

public java.lang.Boolean searchReverseComplement()

Search of the reverse complements of the reference sequences

Returns:

org.jetbrains.dokka.NodeRenderContent@7e9f77a: Search reverse complement

searchReverseComplement

public RNADeMultiplexProductionPlugin searchReverseComplement(java.lang.Boolean value)

Set Search reverse complement. Search of the reverse complements of the reference sequences

Parameters:

value - Search reverse complement

Returns:

org.jetbrains.dokka.NodeRenderContent@314cbdae: this plugin

batchSize

public java.lang.Integer batchSize()

Number of flow cells being processed simultaneously

Returns:

org.jetbrains.dokka.NodeRenderContent@3b0b7d66: Batch size of fastq files

batchSize

public RNADeMultiplexProductionPlugin batchSize(java.lang.Integer value)

Set Batch size of fastq files. Number of flow cells being processed simultaneously

Parameters:

value - Batch size of fastq files

Returns:

org.jetbrains.dokka.NodeRenderContent@3b6ea5d2: this plugin

minQualScore

public java.lang.Integer minQualScore()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@7374d7e2: Minimum quality score

minQualScore

public RNADeMultiplexProductionPlugin minQualScore(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@2701b5ef: this plugin