net.maizegenetics.pangenome.api

Class AddPathsToGraphPlugin

net.maizegenetics.pangenome.api.AddPathsToGraphPlugin

public class AddPathsToGraphPlugin

This class is used to add path information to an existing graph to provide more information for calculating transition probabilities for finding new paths. If the paths contain haplotypes not included in the original graph they will be added without variant info or seuences. The reason is that the plugin results will be used by path finding, which does not use either variant info or sequence.

Constructor Detail

AddPathsToGraphPlugin

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

This class is used to add path information to an existing graph to provide more information for calculating transition probabilities for finding new paths. If the paths contain haplotypes not included in the original graph they will be added without variant info or seuences. The reason is that the plugin results will be used by path finding, which does not use either variant info or sequence.

AddPathsToGraphPlugin

public AddPathsToGraphPlugin()

This class is used to add path information to an existing graph to provide more information for calculating transition probabilities for finding new paths. If the paths contain haplotypes not included in the original graph they will be added without variant info or seuences. The reason is that the plugin results will be used by path finding, which does not use either variant info or sequence.

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)

processData

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

addPathsToGraph

@NotNull
public HaplotypeGraph addPathsToGraph(@NotNull
                                               HaplotypeGraph inGraph)

getToolTipText

@NotNull
public java.lang.String getToolTipText()

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

pathMethod

@NotNull
public java.lang.String pathMethod()

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

Returns:

Path Method

pathMethod

@NotNull
public AddPathsToGraphPlugin 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

taxaList

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

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

taxaList

@NotNull
public AddPathsToGraphPlugin taxaList(@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