net.maizegenetics.pangenome.hapCalling

Class ScoreRangesByInclusionCountsPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class ScoreRangesByInclusionCountsPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Created by zrm22 on 10/11/17. This plugin will take in any number of inclusion file and will score each reference range by counting how many taxa hit this ref range at least once

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
ScoreRangesByInclusionCountsPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	filterRefRanges() Name of ref range filter file
ScoreRangesByInclusionCountsPlugin	filterRefRanges(String value) Set Filter Ref Range File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	inclusionFilenameDir() The name of the file containing read inclusion and exclusion counts for hapids.
ScoreRangesByInclusionCountsPlugin	inclusionFilenameDir(String value) Set Inclusion File Dir.
String	outputFileName() Name of output file
ScoreRangesByInclusionCountsPlugin	outputFileName(String value) Set Output File.
String	pluginDescription()
String	pluginUserManualURL()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

ScoreRangesByInclusionCountsPlugin

public ScoreRangesByInclusionCountsPlugin(Frame parentFrame,
                                          boolean isInteractive)

Method Detail

processData

public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

pluginDescription

public String pluginDescription()

Specified by:

pluginDescription in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginDescription in class net.maizegenetics.plugindef.AbstractPlugin

pluginUserManualURL

public String pluginUserManualURL()

Specified by:

pluginUserManualURL in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginUserManualURL in class net.maizegenetics.plugindef.AbstractPlugin

inclusionFilenameDir

public String inclusionFilenameDir()

The name of the file containing read inclusion and exclusion counts for hapids.

Returns:

Inclusion File Dir

inclusionFilenameDir

public ScoreRangesByInclusionCountsPlugin inclusionFilenameDir(String value)

Set Inclusion File Dir. The name of the file containing read inclusion and exclusion counts for hapids.

Parameters:

value - Inclusion File Dir

Returns:

this plugin

outputFileName

public String outputFileName()

Name of output file

Returns:

Output File

outputFileName

public ScoreRangesByInclusionCountsPlugin outputFileName(String value)

Set Output File. Name of output file

Parameters:

value - Output File

Returns:

this plugin

filterRefRanges

public String filterRefRanges()

Name of ref range filter file

Returns:

Filter Ref Range File

filterRefRanges

public ScoreRangesByInclusionCountsPlugin filterRefRanges(String value)

Set Filter Ref Range File. Name of ref range filter file

Parameters:

value - Filter Ref Range File

Returns:

this plugin