net.maizegenetics.pangenome.api

Class FilterGraphPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.api.FilterGraphPlugin

All Implemented Interfaces:

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

public class FilterGraphPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Author:

Terry Casstevens Created August 29, 2017

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
FilterGraphPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
HaplotypeGraph	filter(HaplotypeGraph graph)
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
Integer	minCountTaxa() Minimun number of taxa represented in reference range for reference range to remain in graph
FilterGraphPlugin	minCountTaxa(Integer value) Set Min Count Taxa.
Double	minPercentTaxa() Minimum percent of taxa represented in reference range for reference range to remain in graph.
FilterGraphPlugin	minPercentTaxa(Double value) Set Min Percent Taxa.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
List<ReferenceRange>	refRanges() Reference range list to remove from graph
FilterGraphPlugin	refRanges(List<ReferenceRange> value) Set Reference Ranges.
net.maizegenetics.taxa.TaxaList	taxaList() Optional list of taxa to include.
FilterGraphPlugin	taxaList(String value) Set Taxa List.
FilterGraphPlugin	taxaList(net.maizegenetics.taxa.TaxaList value) Set Taxa List.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

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

FilterGraphPlugin

public FilterGraphPlugin(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

filter

public HaplotypeGraph filter(HaplotypeGraph graph)

taxaList

public net.maizegenetics.taxa.TaxaList taxaList()

Optional list of taxa to include.

Returns:

Taxa List

taxaList

public FilterGraphPlugin taxaList(net.maizegenetics.taxa.TaxaList value)

Set Taxa List.

Parameters:

value - Taxa List

Returns:

this plugin

taxaList

public FilterGraphPlugin taxaList(String value)

Set Taxa List. Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.

Parameters:

value - Taxa List

Returns:

this plugin

minCountTaxa

public Integer minCountTaxa()

Minimun number of taxa represented in reference range for reference range to remain in graph

Returns:

Min Count Taxa

minCountTaxa

public FilterGraphPlugin minCountTaxa(Integer value)

Set Min Count Taxa. Minimun number of taxa represented in reference range for reference range to remain in graph

Parameters:

value - Min Count Taxa

Returns:

this plugin

minPercentTaxa

public Double minPercentTaxa()

Minimum percent of taxa represented in reference range for reference range to remain in graph.

Returns:

Min Percent Taxa

minPercentTaxa

public FilterGraphPlugin minPercentTaxa(Double value)

Set Min Percent Taxa. Minimum percent of taxa represented in reference range for reference range to remain in graph.

Parameters:

value - Min Percent Taxa

Returns:

this plugin

refRanges

public List<ReferenceRange> refRanges()

Reference range list to remove from graph

Returns:

Reference Ranges

refRanges

public FilterGraphPlugin refRanges(List<ReferenceRange> value)

Set Reference Ranges. Reference range list to remove from graph

Parameters:

value - Reference Ranges

Returns:

this plugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()