net.maizegenetics.analysis.gbs.v2

Class GetTagTaxaDistFromDBPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class GetTagTaxaDistFromDBPlugin
extends AbstractPlugin

This plugin takes a GBSv2 database as input, queries for the tags and their taxa distribution, and creates a tab-delimited file of tag and taxa-distribution. IT can be used for verifying data in the db. The user may supply a file with tab-delimited columns specifying on which tags to present data. The input "tag" file must have at least 1 column named "TAGS" (any case - Tags/TAGS/tags). Other data in the file will be ignored. Output: A tab-delimited file where the first column is the tag, and subsequent columns indicate taxa found in the db. The values in the "taxa" columns are the number of occurranes of that tag for that taxa.

Constructor Detail

GetTagTaxaDistFromDBPlugin

public GetTagTaxaDistFromDBPlugin()

GetTagTaxaDistFromDBPlugin

public GetTagTaxaDistFromDBPlugin(java.awt.Frame parentFrame)

GetTagTaxaDistFromDBPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

main

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

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

inputDB

public java.lang.String inputDB()

Input database file with tags and taxa distribution

Returns:

org.jetbrains.dokka.NodeRenderContent@12aeac90: Input DB

inputDB

public GetTagTaxaDistFromDBPlugin 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@4472133c: this plugin

outputFile

public java.lang.String outputFile()

Output tab-delimited file showing tag sequences found in DB.

Returns:

org.jetbrains.dokka.NodeRenderContent@47e92804: Output File

outputFile

public GetTagTaxaDistFromDBPlugin outputFile(java.lang.String value)

Set Output File. This is tab delimited file with a list of tag sequences found in the database (either a single tag if the user is checking for a particular tag's presence, or a list of all tags found in the db (if no user tag specified).

Parameters:

value - Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@777f1dca: this plugin

tagFile

public java.lang.String tagFile()

Input file with list of tags to process. Any number of tab-delimited columns, but must have 1 called Tags.

Returns:

org.jetbrains.dokka.NodeRenderContent@1052e599: Tag File

tagFile

public GetTagTaxaDistFromDBPlugin tagFile(java.lang.String value)

Set Tag File. Input file with list of tags to process. Any number of tab-delimited columns, but must have 1 called Tags.

Parameters:

value - Tag File

Returns:

org.jetbrains.dokka.NodeRenderContent@44edff5c: this plugin