net.maizegenetics.pangenome.api

Class HaplotypeGraphBuilderPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

All Implemented Interfaces:

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

public class HaplotypeGraphBuilderPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Author:

Terry Casstevens Created August 03, 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
HaplotypeGraphBuilderPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	anchorFile() File with list of anchors.
HaplotypeGraphBuilderPlugin	anchorFile(String value) Set Anchor File.
HaplotypeGraph	build()
String	configFile() Database configuration file
HaplotypeGraphBuilderPlugin	configFile(String value) Set Database Config File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
SortedSet<Integer>	hapids() List of haplotype ids to include in the graph.
HaplotypeGraphBuilderPlugin	hapids(SortedSet<Integer> value) Set Haplotype Ids.
Boolean	includeVariantContexts() Whether to include variant contexts in haplotype nodes.
HaplotypeGraphBuilderPlugin	includeVariantContexts(Boolean value) Set Include Variant Contexts.
String	method() Consensus Method
HaplotypeGraphBuilderPlugin	method(String value) Set Consensus Method.
Boolean	onlyAnchors() Whether to include only anchors (i.e.
HaplotypeGraphBuilderPlugin	onlyAnchors(Boolean value) Set Only Anchors.
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, 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

HaplotypeGraphBuilderPlugin

public HaplotypeGraphBuilderPlugin(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

build

public HaplotypeGraph build()

configFile

public String configFile()

Database configuration file

Returns:

Database Config File

configFile

public HaplotypeGraphBuilderPlugin configFile(String value)

Set Database Config File. Database configuration file

Parameters:

value - Database Config File

Returns:

this plugin

method

public String method()

Consensus Method

Returns:

Consensus Method

method

public HaplotypeGraphBuilderPlugin method(String value)

Set Consensus Method. Consensus Method

Parameters:

value - Consensus Method

Returns:

this plugin

onlyAnchors

public Boolean onlyAnchors()

Whether to include only anchors (i.e. no regions between anchors)

Returns:

Only Anchors

onlyAnchors

public HaplotypeGraphBuilderPlugin onlyAnchors(Boolean value)

Set Only Anchors. Whether to include only anchors (i.e. no regions between anchors)

Parameters:

value - Only Anchors

Returns:

this plugin

anchorFile

public String anchorFile()

File with list of anchors. All anchors in database if no file specified.

Returns:

Anchor File

anchorFile

public HaplotypeGraphBuilderPlugin anchorFile(String value)

Set Anchor File. File with list of anchors. All anchors in database if no file specified.

Parameters:

value - Anchor File

Returns:

this plugin

includeVariantContexts

public Boolean includeVariantContexts()

Whether to include variant contexts in haplotype nodes.

Returns:

Include Variant Contexts

includeVariantContexts

public HaplotypeGraphBuilderPlugin includeVariantContexts(Boolean value)

Set Include Variant Contexts. Whether to include variant contexts in haplotype nodes.

Parameters:

value - Include Variant Contexts

Returns:

this plugin

hapids

public SortedSet<Integer> hapids()

List of haplotype ids to include in the graph. If not specified, all ids are included.

Returns:

Haplotype Ids

hapids

public HaplotypeGraphBuilderPlugin hapids(SortedSet<Integer> value)

Set Haplotype Ids. List of haplotype ids to include in the graph. If not specified, all ids are included.

Parameters:

value - Haplotype Ids

Returns:

this plugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()