net.maizegenetics.pangenome.hapCalling

Class FilterFastqUsingBAMPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin

All Implemented Interfaces:

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

public class FilterFastqUsingBAMPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Created by zrm22 on 9/13/17.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
FilterFastqUsingBAMPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	bamFile() File Name of the bam file
FilterFastqUsingBAMPlugin	bamFile(String value) Set Bam File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	output() File Name of the filtered read output
FilterFastqUsingBAMPlugin	output(String value) Set Output File.
String	pluginUserManualURL()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	reads() File Name of the read fastq
FilterFastqUsingBAMPlugin	reads(String value) Set Read File.
String	reference() File Name of the reference fasta
FilterFastqUsingBAMPlugin	reference(String value) Set Ref File.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, 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

FilterFastqUsingBAMPlugin

public FilterFastqUsingBAMPlugin(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

pluginUserManualURL

public String pluginUserManualURL()

Specified by:

pluginUserManualURL in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginUserManualURL in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

reference

public String reference()

File Name of the reference fasta

Returns:

Ref File

reference

public FilterFastqUsingBAMPlugin reference(String value)

Set Ref File. File Name of the reference fasta

Parameters:

value - Ref File

Returns:

this plugin

reads

public String reads()

File Name of the read fastq

Returns:

Read File

reads

public FilterFastqUsingBAMPlugin reads(String value)

Set Read File. File Name of the read fastq

Parameters:

value - Read File

Returns:

this plugin

bamFile

public String bamFile()

File Name of the bam file

Returns:

Bam File

bamFile

public FilterFastqUsingBAMPlugin bamFile(String value)

Set Bam File. File Name of the bam file

Parameters:

value - Bam File

Returns:

this plugin

output

public String output()

File Name of the filtered read output

Returns:

Output File

output

public FilterFastqUsingBAMPlugin output(String value)

Set Output File. File Name of the filtered read output

Parameters:

value - Output File

Returns:

this plugin