net.maizegenetics.analysis.rna

Class LoadRNAContigsToGBSDBPlugin

AbstractPlugin

net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class LoadRNAContigsToGBSDBPlugin
extends AbstractPlugin

Develops a discovery TBT file from a set of GBS sequence files. Keeps only good reads having a barcode and a cut site and no N's in the useful part of the sequence. Trims off the barcodes and truncates sequences that (1) have a second cut site, or (2) read into the common adapter. Originally the reference throughout was to "tag". This is being changed to "kmer" as the pipeline is a kmer alignment process.

Constructor Detail

LoadRNAContigsToGBSDBPlugin

public LoadRNAContigsToGBSDBPlugin()

LoadRNAContigsToGBSDBPlugin

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

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

runPlugin

public java.lang.String runPlugin(DataSet input)

Convenience method to run plugin with one return object.

contigFile

public java.lang.String contigFile()

Input file containing contigs in fasta format.

Returns:

org.jetbrains.dokka.NodeRenderContent@38cd762d: Input Fasta Contig File

contigFile

public LoadRNAContigsToGBSDBPlugin contigFile(java.lang.String value)

Set Input Fasta Contig File. Input file containing contigs in fasta format.

Parameters:

value - Input Fasta Contig File

Returns:

org.jetbrains.dokka.NodeRenderContent@6d49d280: this plugin

outputDB

public java.lang.String outputDB()

Output Database File

Returns:

org.jetbrains.dokka.NodeRenderContent@68017dd0: Output Database File

outputDB

public LoadRNAContigsToGBSDBPlugin outputDB(java.lang.String value)

Set Output Database File. Output Database File

Parameters:

value - Output Database File

Returns:

org.jetbrains.dokka.NodeRenderContent@77593c8: this plugin

deleteOldData

public java.lang.Boolean deleteOldData()

Delete existing SNP quality data from db tables

Returns:

org.jetbrains.dokka.NodeRenderContent@545af115: Delete Old Data

deleteOldData

public LoadRNAContigsToGBSDBPlugin deleteOldData(java.lang.Boolean value)

Set Delete Old Data. Delete existing SNP quality data from db tables

Parameters:

value - Delete Old Data

Returns:

org.jetbrains.dokka.NodeRenderContent@77a4f4cc: this plugin

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()