net.maizegenetics.pangenome.api

Class BuildGraphFromPathsPlugin

net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin

public class BuildGraphFromPathsPlugin

Constructor Detail

BuildGraphFromPathsPlugin

public BuildGraphFromPathsPlugin(@Nullable
                                 java.awt.Frame parentFrame,
                                 boolean isInteractive)

BuildGraphFromPathsPlugin

public BuildGraphFromPathsPlugin()

Method Detail

getMyPathMethod

public net.maizegenetics.plugindef.PluginParameter<java.lang.String> getMyPathMethod()

setMyPathMethod

public void setMyPathMethod(net.maizegenetics.plugindef.PluginParameter<java.lang.String> p)

getMyTaxaList

public net.maizegenetics.plugindef.PluginParameter<net.maizegenetics.taxa.TaxaList> getMyTaxaList()

setMyTaxaList

public void setMyTaxaList(net.maizegenetics.plugindef.PluginParameter<net.maizegenetics.taxa.TaxaList> p)

getMyLogger

@NotNull
public NonExistentClass getMyLogger()

processData

@NotNull
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                net.maizegenetics.plugindef.DataSet input)

build

@NotNull
public HaplotypeGraph build()

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

pathMethod

@NotNull
public java.lang.String pathMethod()

Gametes from this path method will be added to the HaplotypeGraph.

Returns:

Path Method

pathMethod

@NotNull
public BuildGraphFromPathsPlugin pathMethod(@NotNull
                                                     java.lang.String value)

Set Path Method. Gametes from this path method will be added to the HaplotypeGraph.

Parameters:

value - Path Method

Returns:

this plugin

pathTaxaList

@Nullable
public net.maizegenetics.taxa.TaxaList pathTaxaList()

Only gametes from these taxa will be added to the graph. If null, then all gametes will be added for the path method.

Returns:

Path Taxa List

pathTaxaList

@NotNull
public BuildGraphFromPathsPlugin pathTaxaList(@NotNull
                                                       net.maizegenetics.taxa.TaxaList value)

Set Path Taxa List. Only gametes from these taxa will be added to the graph. If null, then all gametes will be added for the path method.

Parameters:

value - Path Taxa List

Returns:

this plugin